* Louisiana & disclaimers (1 replies)
Wesley R. Elsberry2002-12-11 13:45:12
Evolution disclaimer supported

Quote
High school biology textbooks would include a disclaimer that evolution is only a theory under a change approved Tuesday by a committee of the state's top school board.

If the disclaimer wins final approval, it would apparently make Louisiana just the second state in the nation with such a provision. The other is Alabama, which is the model for the disclaimer backers want in Louisiana.


The article quotes Darrell White, who was one of the agitators for last year's legislation aimed at declaring Charles Darwin, noted abolitionist, to have been a racist.
* Defaulted IDist promises (7 replies)
Tom Ames2004-02-07 22:16:52
In the spirit of Rafe Gutman's catalog of IDist misrepresentations, I'd like to start a thread to catalog IDist promises of forthcoming material: books, research results, etc.

It would be useful to check up on the status of these as time goes by. Also, if a promise is made, it would nice to let the promiser know that his words have been logged over here.
* "Darwinism in Crisis" (0 replies)
Wesley R. Elsberry2002-10-24 08:58:29
Darwinism in Crisis

Quote
For well over a century now the reigning scientific view has been that the existence of life in the universe could be explained on the basis of natural processes alone. In the light of new research in science and philosophy by a group of first-rank Christian scholars, this view is no longer tenable and is being challenged around the world.

YOU ARE INVITED TO THIS RARE OPPORTUNITY TO COME AND LEARN ABOUT “INTELLIGENT DESIGN” THEORY FROM THE VERY SCHOLARS WHO HAVE STARTED THIS REVOLUTION IN THE HISTORY OF IDEAS!

Witness the news media and academic community from around southern California ask the tough questions about the “Intelligent Design” Revolution.

WHEN: Thursday evening, October 24, 2002 from 7:00 to 9:30PM

WHERE: Chase Gymnasium on the Biola University campus in La Mirada

COST: $10 per person. Tickets are available at the door only. Best seats available for early arrivals.


I plan on going, but I can't say that I was specifically requested as part of the academic community in SoCal.  I can well imagine that they may have requested press coverage, but I haven't heard anybody say that they've encouraged the skeptics to attend.

This is held just prior to the Research & Progress in Intelligent Design (RAPID) Conference at Biola.  I tried to register for this conference, but was told it is a closed event.

Notice that Biola's Christian Apologetics program, which is organizing the "Darwinism in Crisis" panel, identifies the group as "Christian scholars".  It is a refreshing break from the false claim of "top scientists" deployed in the past by the Discovery Institute.

* Wesclin, Illinois (0 replies)
Wesley R. Elsberry2003-02-15 06:17:02
Wesclin committee will investigate teaching of 'intelligent design'


Quote
Trimble, who is a teacher in the McLuer school district in St. Louis, offered his assistance in helping administrators and the committee in sorting through "intelligent design" issues. Trimble said he has taught "intelligent design" theory in several private religious schools. "It's a fascinating topic, and there's much information available, and I'd be happy to provide whatever input I can," said Trimble, who also noted that he is a graduate theology student.


I somehow doubt that Trimble's briefing will cover objections by Orr, Sober, Pennock, Van Till, and Wilkins.

Wesley
* "Icons" video as a political weapon (2 replies)
Wesley R. Elsberry2002-05-17 19:40:34
The "Coldwater Media" video of Jonathan Wells's "Icons of Evolution" premiered on 2002/05/10, and since has been reported to have aired on several television stations in Ohio.  This deployment seems to be obviously political in nature, with an aim to influence voters, who in turn would influence the Board of Education to include "intelligent design" in school science standards, or at the least officially single out evolutionary biology as "controversial" and require the teaching of "evidence against" evolution.  These two ways of stating things are pretty much synonymous for "intelligent design" advocates.

Anyone with information on specific times, locales, and dates when the "Icons" video has been aired is requested to add to
this thread in the "Intelligent Design News" forum.
* West Virginia Science Standards (4 replies)
Wesley R. Elsberry2003-01-14 12:46:09
'Intelligent design' believers, sect seek curriculum change

Quote
People who believe in “intelligent design” are trying to change the way science is taught in West Virginia’s public schools. This time, they have an unlikely ally: the Raelian sect espoused by baby-cloner Brigitte Boisselier. On Friday, the public comment period ended for four statewide education standards. The standards for reading, math and social studies slipped through fairly quietly — but not science. More than 100 people spoke out about the new science standards, the state Department of Education estimates.
* Some help with a research paper (0 replies)
CaptRuss2005-02-26 14:13:23
I'm starting a research paper for my Sociology class. The research is to understand, who becomes a Creationist, why, where you’re from etc. Your help is most appreciated.

Please give basic background:
Age, State of residence, marital status, Education Level, Religious Affiliation, Occupation.

What type of Creationist are you? Examples:

Flat Earthers - believe that the earth is flat and is covered by a solid dome or firmament. Waters above the firmament were the source of Noah's flood. This belief is based on a literal reading of the Bible, such as references to the "four corners of the earth" and the "circle of the earth." Few people hold this extreme view, but some do.

Geocentrism - accept a spherical earth but deny that the sun is the center of the solar system or that the earth moves. As with flat-earth views, the water of Noah's flood came from above a solid firmament. The basis for their belief is a literal reading of the Bible. "It is not an interpretation at all, it is what the words say." (Willis 2000) Both flat-earthers and geocentrists reflect the cosmological views of ancient Hebrews. Geocentrism is not common today, but one geocentrist (Tom Willis) was instrumental in revising the Kansas elementary school curriculum to remove references to evolution, earth history, and science methodology.

Young Earth Creationists - claim a literal interpretation of the Bible as a basis for their beliefs. They believe that the earth is 6000 to 10,000 years old, that all life was created in six literal days, that death and decay came as a result of Adam & Eve's Fall, and that geology must be interpreted in terms of Noah's Flood. However, they accept a spherical earth and heliocentric solar system.

Old-Earth Creationists - accept the evidence for an ancient earth but still believe that life was specially created by God, and they still base their beliefs on the Bible. There are a few different ways of accommodating their religion with science.

Day-age creationists - interpret each day of creation as a long period of time, even thousands or millions of years. They see a parallel between the order of events presented in Genesis 1 and the order accepted by mainstream science. Day-Age Creationism was more popular than Gap Creationism in the 19th and and early 20th centuries.

Evolutionary Creationism - differs from Theistic Evolution only in its theology, not in its science. It says that God operates not in the gaps, but that nature has no existence independent of His will. It allows interpretations consistent with both a literal Genesis and objective science, allowing, for example, that the events of creation occurred, but not in time as we know it, and that Adam was not the first biological human but the first spiritually aware one.

Theistic Evolution - says that God creates through evolution. Theistic Evolutionists vary in beliefs about how much God intervenes in the process. It accepts most or all of modern science, but it invokes God for some things outside the realm of science, such as the creation of the human soul. This position is promoted by the Pope and taught at mainline Protestant seminaries.

Materialistic Evolution - differs from Theistic Evolution in saying that God does not actively interfere with evolution. It is not necessarily atheistic, though; many Materialistic Evolutionists believe that God created evolution, for example. Materialistic evolution may be divided into methodological and philosophical materialism. Methodological materialism limits itself to describing the natural world with natural causes; it says nothing at all about the supernatural, neither affirming nor denying its existence or its role in life.

Philosophical materialism - says that the supernatural does not exist. It says that not only is evolution a natural process, but so is everything else.

Vedic Creationism
Hinduism speaks of a very ancient earth. One book influenced by Hindu belief argues that anatomically modern humans have existed for billions of years.

Finally, What brought you to believe what you believe?

Your help is most appreciated.
* Oklahoma Anti-evolution Bill Introduced (0 replies)
Michael2003-01-28 14:31:37
Rep. Bill Graves has introduced HB 1504 (or rather it will formally introduced on February 3) that will require an anti-evolution disclaimer on all textbooks.  It is the same disclaimer that the Oklahoma Textbook Committee tried to introduce in 1999 but which the Oklahoma attorney general struck down which was copied from the Alabama disclaimer.  

The text of the measure
* Minnesota Machinations (5 replies)
Wesley R. Elsberry2003-08-18 06:58:06
EDUCATION: State names 85 to panels (Pioneer Press)

Quote
Education Commissioner Cheri Pierson Yecke will ask the committee to consider an amendment that Sen. Rick Santorum, R-Pennsylvania, tried unsuccessfully to add to the federal No Child Left Behind law. It says that when controversial topics — such as biological evolution — come up in the classroom, the curriculum should help students understand other views as well.

One of the alternatives Santorum has written about is "intelligent design," which says an organism's complexity is evidence of an other-worldly designer. The amendment passed the Senate and was included in a conference committee's report, but was struck from the final version of the law.

"We're not making grand claims that No Child Left Behind requires us to do this," said Education Department spokesman Bill Walsh. "But saying that NCLB and the Senate gives us guidance, (Yecke) is recommending that the committee go this way."
* New Mexico (0 replies)
Wesley R. Elsberry2003-08-30 05:20:58
Evolution To Stay In N.M. Schools

A short AP report says that the NM State Board of Education unanimously approved new standards that include evolution.

The report doesn't discuss the campaign by ID advocates to incorporate the usual ID buzz phrases in the new standards.  One advocate sent around copies of Michael Behe's "Darwin's Black Box" and a letter to schools around New Mexico.  A full page ad appeared shortly before the vote urging people to push for ID-related changes.  ID advocates publicized a Zogby poll which, it turned out, was called "bogus" by Sandia Labs administration, who disclaimed any association with the poll.

Details are available at the New Mexicans for Science and Reason page.

Wesley
* Ohio Board of Education (25 replies)
Wesley R. Elsberry2002-10-10 19:52:48
This thread is for items relating to the Ohio Board of Education's consideration of new science standards.

An interesting press statement came out today.

Quote
October 10, 2002
Press Conference Statement of
Professor Joseph F Koonce
Chair, Dept of Biology
Case Western Reserve University
jfk7@po.cwru.edu
216-368-3561

Many claims have been made in recent months as to what Ohio scientists think about intelligent design "theory." However, until now, no data existed on this issue. My colleagues and I set about to collect the data so that the public may gain an accurate impression of what Ohio's scientists think. The results are gratifying and unequivocal.

Nine out of ten Ohio scientists from Ohio public, private (including both secular and religious) universities say that intelligent design is primarily a religious view and is simply not part of science.

We designed and conducted this survey with the Internet Public Opinion Laboratory at the University of Cincinnati.  We sent out email messages around the state to faculty in departments of astronomy, biology, chemistry, geology, physics and other natural sciences, inviting them to answer a set of questions and to give their thoughts about the evolution-intelligent design debate.  The survey ran between September 26 and October 9.

Prior to polling the scientists, the Institute for Policy Research at the University of Cincinnati included questions on the September Ohio Poll (conducted September 4 through 15, 2002) asking the general public to respond to two questions about intelligent design. Like the scientists, a clear majority of Ohio residents found intelligent design to be religious, and not a scientific view.

Next Monday and Tuesday the Ohio Board of Education will vote on whether to include intelligent design or other forms of anti-evolutionism in the new K-12 science standards.  Intelligent design advocates claim life is too complex to have developed without the intervention of a supernatural being or force, and they claim their view is scientific. Clearly Ohio's citizens are not convinced that this argument should be taught as science.

I want to make clear that I am a religious person myself. As a Roman Catholic, I do believe in God and in concurrence with teachings of the Catholic Church, I have never found these beliefs in conflict with Evolutionary Theory.  Science addresses the nature of the physical universe, not the supernatural or the eternal. Like me, 84% of my colleagues also report that they find evolutionary theory compatible with belief in God.

I wish this would lay to rest the destructive notion that science and religion are at war in America. There is no such inherent conflict. Science and religion can promote and enhance each other without having to pretend we know less than we actually do about how the world is constructed and how it functions.

Most all of Ohio's science professors (92%) thought "Ohio high school students should be tested on their understanding of the basic principles of the theory of evolution in order to graduate." When asked if such students should also be tested on their knowledge of the concept of "Intelligent Design" in order to graduate, 90% said "no." Only 2% said that intelligent design was strongly supported by scientific evidence.

The survey also explored scientists' views on antievolutionism beyond the intelligent design movement. Some critics of evolution claim evidence against the theory of evolution has caused it to fall out of favor among scientists. This is clearly not the case in Ohio where the vast majority (93%) of science professors said they were not aware of "any scientifically valid evidence or an alternate scientific theory that challenges the fundamental principles of the theory of evolution."

We are extremely pleased with the response. Nearly 500 scientists responded, a rate of 31%.  The survey had an error of plus or minus 4.5 percent. Equally pleasing was the outpouring of gratitude for providing the opportunity to express their concern with the erosion of scientific literacy in the developing K-12 standards for Ohio.
* Thanks for "The Wedge" (0 replies)
mperkel2005-12-06 16:28:39
Hi,

I'm new - just wanted to thank you for "The Wedge" article. I've added it to the evolution section of the Church of Reality.

http://www.churchofreality.org/wisdom/evolution/
* Kansas accepts IDio - The Intelligent Designer GOD (0 replies)
dougsha2005-11-09 12:50:47
OPEN EPISTLE TO KANSAS SCHOOL BOARD
November 8th, 2005
I write with joy and thanks in my heart after having read of your bold decision to promote the Church of The Intelligent Designer and its one true God IDio. Finally, our Church needs no longer cower behind a façade of science.

Now that your blessed action on IDio's behalf has rendered the Constitution, with its irritating religious establishment clause, inoperative, we can proudly proclaim in every Kansas classroom, "There is but one Intelligent Designer and His name is IDio!" We thank the taxpayers of Kansas for donating their money to proselytize for His church. May IDio mutate you all intelligently.

Finally, we see an end to the dark decades of awkward debates, of the tedious aping of scientific method, of endless self-publication to mesmerize the faithful. No more need we pay our devout 'scientists' to appear in court, only to be insulted by the IDioless forces of logic. Never again must we shrug uneasily and mumble, "Umdon'tknowbutit'snotagod," when Darwinists ask the identity of the Intelligent Designer.

GODinabox - The Church of IDio the Intelligent Designer GOD
* The Law of Evolution (24 replies)
MidnightVoice2005-08-28 10:30:58
One way to get round the current impasse in the States is to persuade the AAAS or a similar body to make an announcement at the next Annual Conference.  Some thing along the lines of  “Having passed all the required scientific analyses for over a Century, we hereby declare that evolution is no longer a theory, but has the status of a law.  

As a corollary to this, as it is now a Law, no alternate theories need be taught, and such theories should be rigorously excluded from text books at any level.  “
* Advice on fighting antievolution (3 replies)
Attila2005-07-02 05:26:30
Greeting to all and sundry,
I'm writing to you from Girona, Catalonia, Spain where our city council with no public consultation has undertaken steps to twin with Nashville, Tennessee as part of their (i.e. Nashville's) "Sister Cities" programme. When word of this got out, a number of objections were raised among them the (lack of) teaching of evolution in Tennessee schools. We are hoping to exert enough pressure so that the city council reverses itself and rejects the twinning proposal - the initiative did come from Nashville and not from us. Note that antievolution is only one of many issues in this debate but it is an important one. (see below). If I were living in Nashville and word came out that this proposal was rejected by our "twin" because of (among other things) Tennessee's approach to science teaching I would be thrilled; but this is just my opinion. I would appreciate hearing anyone's views on the matter but most particularly scientists from Tennessee and especially from Nashville.
For those interested here's a link to an article that appeared today (Saturday) in our local paper, Diari de Girona. It's in Catalan but if you have some French you ought to be able get the gist of it. If there's any strong desire for it, I can translate it into English.
Thanks for listening and thanks in advance for any advice, comments, criticisms, etc.
Jonathan Kaye
http://www.diaridegirona.es/seccion....ccion=2
* Fighting Religion with Religion (8 replies)
mperkel2005-12-06 16:37:47
Quick introduction, I am Marc Perkel, founder of the Church of Reality, a religion based on believing in everything that's real. Since we don't kno everything it is really about the pursuit of reality the way it really is. It is like a religious commitment to science. Of all the religious choices out there, I thought reality should be one of them.

One of our goals is evangelizing reality and giving religious and religious rights to Realists and Atheists. We are a 501C3 tax exempt organization. One of the things we do is to keep science sacred. Any rights that the government gives Christians, we get too.

Always looking for new ideas and suggestions. Keep up the good work.

Yours in Reality
Marc Perkel
* Post-Modern Critical Anti-Evolutionism (7 replies)
Middle St. Man2004-09-22 15:40:17
Hi to all on this board,

I'm new here and have just begun reading your site. I've heard of the YEC and AiG approaches before. But I'm curious as to what is the Post-Modernist Criticism anti-evolutionist approach? Is there a particular practitioner of such an approach to keep an eye out for? Or if you've mentioned something further on your site that I might have missed, please direct me to it.

Hopefully this is the proper section to address this topic as it likely covers socio-political aspects of antievolution.

Thanks,

Middle St
* Politicized Pseudosciences (3 replies)
lpetrich2003-10-09 15:29:29
Has anyone tried to explore why creationism has been so politicized? Politicization is not very common among pseudoscientists, even those who advocate very popular beliefs.

Astrologers, for example, are apolitical; they don't seem to want equal time for astrology in astronomy classes.

But a better comparison is with vitalism, the view that the processes of living things are due to some "vital force." It is a centuries-old view that survives as the "theoretical justification" of certain "alternative medical therapes." Aristotle had even identified three kinds of this force: the vegetable soul, the animal soul, and the rational soul.

But vitalism has suffered defeat after defeat after crushing defeat over the last few centuries, and it has become totally discredited among respectable scientists. Though there are still plenty of physiological puzzles, "vitalism of the gaps" is never thought worth considering.

Vitalists can easily make arguments parallel to creationists, like mentioning physiological processes that continue to be puzzles, the simplicity of "VitalForceDoesIt", how teenagers would be more likely to commit suicide and kill their classmates if they believe themselves to be biochemical robots rather than animated by some "vital force", etc.

Yet vitalists are apolitical, not wanting equal time for vitalism in classrooms. And creationists who appear to believe in some form of vitalism do not make an issue out of it, and coexist with apparently non-vitalist creationists like Michael Behe.


Notable politicized pseudosciences in the past have been Hanns Hörbiger's Welteislehre (Cosmic Ice Theory) and Lysenkoism.

The advocates of the Cosmic Ice Theory would apply pressure to get people to accept the theory; they were known to heckle astronomers' meetings with "Out with astronomical orthodoxy! Give us Hörbiger!". They even aligned themselves with Nazism, though the Nazi Party never officially endorsed it.

Trofim Lysenko had claimed that he could breed improved crop plants by altering their heredity; he believed that genes do not exist. He claimed impressive "results", but his experimental procedures were shoddy beyond belief -- he had no conception of a controlled experiment, and he believed that doing statistics is a waste of time. However, he got the support of Joseph Stalin himself, and mainstream geneticists were forced to recant, sent to gulags, or executed. Even the great biologist Nikolai Vavilov could not escape; he was sent to prison for allegedly being a British spy, dying there.
* )The U.S. Congress (3 replies)
Wesley R. Elsberry2003-09-01 16:29:29
Rep. Pence of Indiana:

Quote

I believe that God created the known universe, the Earth and everything in it, including man. And I also believe that someday scientists will come to see that only the theory of intelligent design provides even a remotely rationale explanation for the known universe. But until that day comes, and I have no fear of science, I believe that the more we study the science, the more the truth of faith will become apparent. I would just humbly ask as new theories of evolution find their ways into the newspapers and into the textbooks, let us demand that educators around America teach evolution not as fact, but as theory, and an interesting theory to boot. But let us also bring into the minds of all of our children all of the theories about the unknowable that some bright day in the future through science and perhaps through faith we will find the truth from whence we come.

(Source: [Congressional Record: July 11, 2002 (House)] [Page H4527])


For others wishing to examine what the U.S. congress has said, check out
the Congressional Record online.

Wesley
* Quotes & Misquotes (2 replies)
Wesley R. Elsberry2002-05-19 14:25:05
One of the staples of the antievolution movement is the deployment of "quotations".  When one examines the antievolutionary literature, one will note a relative superabundance of quoted material within it.  Closer examination will reveal that many of these supposed quotations are quoted out of context, have been edited to adjust their meaning to something in line with the argument the antievolutionist wants to make, are from "experts" of dubious reputation or from long ago, are patched together from widely separated sentences in the source, or otherwise fail to accurately reflect the intent and meaning of the author.

In this thread, I would like people to contribute examples of misquotations deployed by antievolutionists.  This should include the citation of the misquotation (who deployed the quote and where), the misquotation itself, and the original quote with sufficient context to show that the antievolutionist did indeed engage in misquotation.

I'll also encourage people to contribute such examples to my quotation database at this URL.

Additonally, people are directed to Michael Hopkins's Quotation and Misquotations FAQ at the TalkOrigins Archive.
* Origins & "Ordinary People" (6 replies)
johndcal2003-01-21 00:20:49
In the July/August 1999 issue of TOUCHSTONE, Nancy Pearcey writes, "Finally, [intelligent] design is a winner with the public because it is a scientific research program that actually makes sense to ordinary people."

Is it true? Do "ordinary people" need scientific mythology, just as children need Santa Claus? Or, does God hope that "ordinary people" will mature enough to accept known scientific facts, such as the Big Bang, Earth's age, and Darwinian biological evolution?

The existence of God and historical reality of Jesus and His deity are not dependent on Biblical inerrancy and scientific mythology (modern creationism): YEC, OEC, ID. Wouldn't it be better, in the long run, to show the compatibility of Christianity with correct science?

See Faith & Reason Ministries: Reconciling Christianity with Accepted Science, http://www.faithreason.org/
* Antievolution, antiscience (1 replies)
Tom Ames2002-12-06 19:28:27
Most of my scientist colleagues are highly skeptical of the value of addressing anti-evolutionist tactics head-on. Generally, the thinking is that the stuff is so self-evidently wrong that there is no need to waste time on it. They're right in some senses, of course. But the antievolution movements might better be seen as part of a wider attempt to reduce the influence science has on public policy and public education. It seems clear that the DI/CRSC for example are engaged in this general anti-science campaign, wherein they hope to replace science's authority with a more religiously conservative one.

What I wonder is this: is the focus on evolution and its teaching in public schools necessarily the best place to take a stand against anti-science/anti-rationality movements? In a sense, I believe that the teaching of evolution in public high schools might be a distraction. We're talking about a high school biology unit that takes up maybe a week, but probably more like a single day of classes. Given the complexity of the material, it is doubtful that it can be covered adequately in the time alotted.

And (despite our fondest wishes) it really does seem to be controversial among most people. In a sense we might be taking a stand at the most politically difficult-to-defend point (analogous maybe to defending late-term abortions in order to ensure pro-choice policies).

Might there be a compromise that allows the scientifically minded to better convey the importance of rational empiricism, while eliminating the heat caused by "forcing" a controversial topic upon unwilling local school boards? Can we better maintain the separation between church and state by focusing on issues that are more salient to the largest group of people? Or is this truly a case of a "slippery slope" whereby giving in on any point will be surrendering a bulwark against further attacks?
* Cobb County, Georgia antievolution (6 replies)
Wesley R. Elsberry2002-09-30 11:08:38
On September 26th, 2002, the Cobb County school board voted unanimously for a provision that singles out evolutionary biology as controversial and requires teachers to engage in "discussion of disputed views of academic subjects".

Cobb County policy

There will be "implementing regulations" related to this policy.  I see a high potential for mischief at the administrative level.  The policy does not stipulate that the level of "dispute" must be scientific in nature, which opens the door to any sort of "dispute", no matter how lacking in scientific merit it might be.

Here's an article on how teachers are reacting to the change:

Cobb teachers ponder new evolution rule

Wesley
* DeLay, Baylor, & Texas A&M (1 replies)
Wesley R. Elsberry2002-05-06 02:19:43
DeLay was asked where kids should go to college. The questioner apparently asked this in the context of teaching creationism.

Houston Chronicle article

William Dembski is mentioned in the above article.

Note the mode of discussion DeLay's spokesman, Jonathan Grella, uses in talking about Barry Lynn. "Guilt by association" tactics seem to come in both rightist and leftist flavors.

As a student at A&M, I have to say that I saw no evidence of a lack of conservatism on campus.  I didn't live in the dorms, so I can't speak to the reports of rampant hanky-panky.

Dallas Morning News article
* anti-religious bias lawsuit in Texas (0 replies)
VoxRat2003-02-06 08:36:50
Here's an OpEd piece from Boston Globe columnist Ellen Goodman on the latest creationist legal gambit:


http://www.boston.com/dailygl....+.shtml
* Worland, Wyoming (0 replies)
Wesley R. Elsberry2003-09-01 09:16:45
School board gives nod to creationism, abstinence-only

Quote
Also endorsed was a recommendation for teaching biology: "It shall be the policy ... when teaching Darwin's theory of evolution that it is only a theory and not a fact. Teachers shall be allowed in a neutral and objective manner to introduce all scientific theories of origin and the students may be allowed to discuss all aspects of controversy surrounding the lack of scientific evidence in support of the theory of evolution."

Board member Tom Ball, who opened the discussion on the proposed changes, said he thought the evolution recommendation should use the word "required," rather than "allowed."

Several people addressed the board including Pastor Bud Surles who said "evolution is more a product of Hollywood movies than based on real science." He also said the district should teach that "sex is safe only in a heterosexual, monogamous relationship" and that abstinence until marriage should be the message delivered by the district.

Another pastor, Mike Brush, quoted scholars he said "understand the misconception of evolution" and are more inclined to accept the "intelligent shaping of matter."

"Intelligent design is not religious-based. I would not want you to teach religion in any way, shape or form," he said.
* Recognition of ID (0 replies)
Wesley R. Elsberry2003-09-06 12:33:13
Robert Weitzel: Theory puts a serpent in the garden of education

Quote
The Wedge Strategy's focus and funding are not on the research necessary to cause a shift in the prevailing scientific paradigm. Rather, they are aimed at convincing an uninformed public that intelligent design creationism deserves equal consideration as a "scientific theory." This is the "wedge" that intelligent design creationists hope will split the authority of the First Amendment and allow the Christian creation story to substitute for science in our country's public schools.


The word is getting out, but rather slowly.
* ID seminars at "prestigious" universities (4 replies)
rafe gutman2004-02-07 16:49:12
advocates of Intelligent Design often hold seminars and conferences to present their arguments to the public.  some of these seminars are held in churches or community centers, but a sizeable number of them take place in well-respected research institutions.  this does not require the endorsement of the institution itself (or i think even their knowledge of what the event is about), as any university club can book a room on campus for their events.  however, through clever word play, IDists can give the appearance that their position is officially acknowledged.

for example, this announcement was posted on ARN, under the title, "Dembski at UC-Davis":
Quote
William Dembski
Lecture: "Detecting Design in Biological Systems"

Friday, 16 January 2004
7:30 PM
194 Chemistry Building
University of California, Davis


as is, it seems pretty innocuous, although the choice to present it in a building named after an entire field of science, and the title of his talk, leave the impression that somehow this talk is affiliated with the chemistry department of UC davis.  however, there's no overt deception here.

but who is sponsoring the talk?  not the chemistry or biology departments, but the grace valley christian center under the "faith and reason" seminar series whose express purpose is to:
Quote
The Faith and Reason series seeks to bring eminent scientists, logicians, and theologians to Davis to
speak on issues regarding the proper relationship between human reason and vital Christian faith.

The purpose of this series is to demonstrate that the Christian worldview correctly defines ultimate
reality and is consistent with all that is known about the world through the proper application of
logic and the scientific method.


although i think it would have been fairer had the poster of this event mentioned who was sponsoring it, i don't think he was trying to be deceptive.  but when an ID critic did mention who the sponsor was, they were immediately accused of trying to dismiss the talk as religiously-motivated.  look how one IDist responded:

Quote
I suppose that in your perspective there's no overlap between the 'scientific' and 'religious'. So by saying the talk has a 'religious goal', it's automatically not a scientific goal or a scientific talk, even though given in a science department of a major university.


and so now we see the strategy come full circle.  while there was no attempt by the original poster (or the sponsors of the talk) to imply that the talk was endorsed by either UC davis or its biology or chemistry departments, the net effect is that people come away with the impression that the talk is endorsed by those groups.



i'd like this thread to be a place where people can cut and paste examples like these.  so if you see a flyer or website for an ID-related event at a university, where the language implies that the university endorses ID, feel free to post it here.  i'd also like to see examples where IDists post comments like the one above, mistakenly interpreting the location of an ID event at a university for the university's endorsement of it.
* Texas & Textbooks (0 replies)
Wesley R. Elsberry2002-10-29 23:53:59
Publishers alter texts to try to make grade (Houston Chronicle, 2002/10/29)

Quote
Bowing to political pressure, publishers of social studies textbooks have changed passages dealing with events ranging from the Alamo to last year's terrorist attacks.

The publishers are hoping the changes will help their 200 textbooks gain approval next month from the State Board of Education. That approval is key to getting a piece of the $345 million market.

[...]

For example, a reference in a sixth-grade social studies book to glaciers forming the Great Lakes "millions of years ago" was changed to "in the distant past."

Robert Raborn, a member of the conservative Citizens for a Sound Economy, had complained that "millions of years ago" supported the theory of evolution and excluded theories such as intelligent design.


How can ID be excluded by a reference to millions of years, when ID advocates won't take a stand on how old the earth is?
* Phoenixville, Pennsylvania (1 replies)
Wesley R. Elsberry2002-12-25 05:54:39
Phoenixville School District Addresses Evolution Alternatives

Quote
New wording in the Phoenixville Area School District's mission statement is already accomplishing its purpose: provoking discussion of hot-button issues such as evolution alternatives.

[...]

The mission statement was altered at the urging of school board vice president, David M. Langdon.

Langdon had sought a more detailed statement, urging the teaching of "intelligent design" as an alternative to evolution.

[...]

Langdon, a software quality-control manager who earned a bachelor's degree in biochemistry at Lehigh University, is a devout Christian and said he believes the Biblical account of creation is literally true. He criticized the way evolution is taught.

"My opinion is that evolution has some problems with it that the scientific community doesn't want to talk about," Langdon said.


As John Stear points out, "Creationism is not the alternative to evolution; ignorance is."
* The "wedge" at work in Ohio (1 replies)
Wesley R. Elsberry2004-02-16 23:30:05
Situation Alert for Ohio Public Education

PDF version

Phillip Johnson's "Wedge" strategy for the "intelligent design" movement can be seen at work now in Ohio. Johnson's strategy is designed to attack evolutionary biology as the first step in making science safe for the sort of theism Johnson prefers. The bluntest expression of the "Wedge" strategy appeared in promotional material for the Discovery Institute's Center for the Renewal of Science and Culture. (See http://www.antievolution.org/features/wedge.html for the text of the "Wedge Document" and Barbara Forrest and Paul R. Gross's new book, "Creationism's Trojan Horse: The Wedge of Intelligent Design" (Oxford, 2003), for a minutely detailed critique. The Discovery Institute attempts damage control in http://www.discovery.org/csc/TopQuestions/wedgeresp.pdf) As with magicians, one needs to get past the patter and watch for the action.  It is in the actions and not the words that one can most clearly see that the dictates of the "Wedge" strategy are fully ascendant.

In 2002, the Ohio State Board of Education approved new science standards that mandated the teaching of evolution in science classes. At the urging of antievolutionists, the Ohio State Board of Education also included a statement calling for teaching how evolutionary theory was the subject of "critical analysis" by scientists.

Quote


23. Describe how scientists continue to investigate and critically analyze aspects of evolutionary theory. (The intent of this indicator does not mandate the teaching or testing of intelligent design.)

-
http://agpa.uakron.edu/k12....10.html
or http://tinyurl.com/2jqk9

This sort of language was suggested by Stephen Meyer and Jonathan Wells (both Fellows of the Discovery Institute's Center for the Renewal of Science and Culture, since renamed as the Center for Science and Culture) in a presentation before the Ohio Board of Education on March 11, 2002.  The apparently innocuous wording was deceptive, though, because rather than teach students about actual hot topics in evolutionary biology (e.g., allopatric versus sympatric speciation, punctuated equilibria in the fossil record, the evolution of sex, theories of eusociality, etc.), "Wedge" advocates took the wording as code for their own set of discredited objections to mainstream science.  While Meyer and Wells had originally sought to push for the specific inclusion of "intelligent design" in science classes, they decided instead to ask for a "compromise." The "compromise" suggested by Meyer and Wells was to "teach the controversy." See http://www.ohioroundtable.org/library/articles/ed/boardstudy.html http://www.creationists.org/20020311OSBEwells.html and http://www.ncseweb.org/resourc....002.asp.

Although the adopted standards specifically stated that "intelligent design" was not to be part of the curricula (see quoted text above), the "Wedge" advocates got what they wanted with the above language: a hole large enough to attempt to drive a big antievolutionary semi straight into science classrooms. See: http://www.sciohio.org/sbe1015.htm.

Over the past several months, the ID advocates on the Ohio Board of Education have loaded their truck. Model curricula comprised of lesson plans had to be generated to fulfill all the indicators of the science standards.  These new lesson plans were kept out of the public's reach, preventing scientists from reviewing these materials until shortly before official consideration for adoption.  (The embargo on access apparently did not extend to "Wedge" advocates; see http://www.sciohio.org/orcweb.htm.)

In particular, a lesson plan based upon indicator 23 of the science standards for Grade 10 (the "critical analysis" guideline quoted above) presented several items from Jonathan Wells's "Icons of Evolution", included "Icons" in its bibliography, included a non-existent reference in its bibliography whose citation only existed on creationist web sites, and directed students to antievolutionary web sites (including http://www.origins.org and http://www.arn.org). This attempt to insert "trash science" (as it was called by cognitive scientist Richard Hoppe in a Board of Education meeting on January 13) or "junk science" (as it was called by Sam Fulwood in a column for the Cleveland Plain Dealer on February 8) into science classrooms should be viewed as the expected outcome of the "compromise" language inserted into the standards.  This was no compromise, but rather the "Wedge" Trojan Horse in action.  Various cosmetic changes have been made to the lesson plan, but the blatantly deceptive content and many of the antievolution web resources remain. See http://www.cleveland.com/news....191.xml or http://tinyurl.com/22gvp for Fulwood's column.  See http://ecology.cwru.edu/ohioscience/L10-H23_Critical_Analysis.pdf for the lesson plan and http://ecology.cwru.edu/ohioscience/lesson_plan_critique.htm for a critique of it.

A red herring being used by "Wedge" advocates is to say that "intelligent design" is not present in the lesson plan being critiqued, therefore there is no problem. For example:

Quote


"I think it's going to be great for science. This lesson, in my opinion, has been misunderstood. I am very familiar with intelligent design and it just is not in there," said Robert Lattimer, an intelligent design proponent and a scientist who was on the standards writing team from two years ago.

-
http://www.daytondailynews.com/localne....ce.html

Although the phrase "intelligent design" may indeed be absent from the lesson plan, the content is easily recognizable, despite Lattimer's disavowal.  The content derives most notably from Jonathan Wells's "Icons of Evolution", which was hailed as a "Wedge Book" of the year 2000, and even now heads the poster-style ad on "ID Books" at http://www.discovery.org/csc/favoriteItems/IDBookAd.jpg.  "Intelligent design," having failed to develop any positive scientific research program of its own, consists entirely of often-rebutted negative argumentation against evolutionary biology, fully deserving the moniker of "trash science."  The material in the "critical analysis" lesson plan demonstrably is the content of "intelligent design" advocacy. Its role in the "Wedge" is clear (see http://www.antievolution.org/features/wedge.html, especially "Phase III: Cultural Confrontation and Renewal").

Scientists in Ohio and across the nation took notice.  For an account of the recommendations of the Ohio Academy of Sciences and the National Academy of Sciences, see http://www.fortwayne.com/mld/journalgazette/7965530.htm. More detail can be seen in the Cleveland Plain Dealer article:

Quote


The nation's most prestigious science organization added its voice Monday to criticism of model science lesson plans that the state school board is expected to vote on today.

Scientists are "rightfully concerned about attempts to introduce tenets of intelligent design into your state's science curriculum and instruction," Bruce Alberts, president of the National Academy of Sciences, said in a letter Monday to Jennifer Sheets, president of the Ohio Board of Education.

-
http://www.cleveland.com/news....720.xml
or http://tinyurl.com/2kh7u

The letter from NAS can be seen at http://ecology.cwru.edu/ohioscience/NAS_Letter.html or http://www.antievolution.org/features/nas_ohio_20040209.pdf

Despite the strong recommendations from Ohio state and national scientific organizations to reject this and other "Wedge" lesson plans, the Ohio Board of Education voted an "intent to adopt" the lesson plans, including the one on "critical analysis," at its February 13 meeting. It was a date that proved unlucky for good science education.

An editorial appeared in the Dayton Daily News offering timely advice:

Quote


Citizens who are not in a position to read all the documentation -- or interpret all the buzz words that only the fully initiated understand -- might wonder where to turn.

Best to turn to the scientists. And not just individual scientists, but the organizations that are representative of scientists and that have people who have responsibility for looking into these matters fully.

- http://www.daytondailynews.com/opinion....ol.html

The editorial calls for Ohio Governor Bob Taft to weigh in on this issue. So far, the governor has chosen to let the Board of Education move the discussion along -- and take the political heat.

The Cleveland Plain Dealer has also called upon Governor Taft to take responsibility and an active role in the process:

Quote


JEERS . . .

to Gov. Bob Taft for taking a walk on the debate over the state's proposed science education standards. He must figure enough people are arguing that they'll eventually drift to a solution. That's not leadership.

- http://www.cleveland.com/search....l?oxedi

Jeffrey McKee had an instructive opinion letter which appeared in the Columbus Dispatch on February 20:

Quote


Can scientists comprehend a simple lesson plan? According to State Board of Education member Deborah Owens-Fink, "Some of these scientists are so paranoid, they don't understand it."

The truth is that scientists understand it all too well: The proposed lesson plan on evolution is a thinly disguised attempt to promote creationism in Ohio's science classrooms. But the lesson is one of politics, not science. One need not be a scientist to connect the dots, as board members should know.

Did she really think that we would not notice the highly misleading statements on the fossil record of evolution, fraudulent claims about today's evolution of bacteria and direct references to creationist literature?

The proposed lesson plan must be replaced by an honest and serious portrayal of contemporary biology.

Owens-Fink's cavalier attitude is characteristic of certain board members who would rather play political games than ensure a quality science education for Ohio's young scholars. Along with board member Michael Cochran, the other main perpetrator of this fraud, Owens-Fink is pushing a desperation agenda instead of fostering understanding.

The "standards committee" of the State Board of Education needs a new chairperson with higher standards. Owens-Fink and Cochran should resign.

JEFFREY K. McKEE
Professor
Ohio State University

- http://www.dispatch.com/editori....05.html

The next meeting of the Board of Education and final vote on the lesson plans is scheduled for March 8-9, which does not leave much time for feedback.  The leadership in Ohio needs to hear from you. When contacting them, brevity and courtesy are virtues to keep in mind. Also, if you have scientific training or credentials, please do mention those. Please also consider putting a copy of your comments in a public forum, where they may be referred to as a resource and inform the commentary of others. A thread suitable for this purpose is located at http://tinyurl.com/3a2sy

Those who wish to make their views known to Governor Taft -- especially if you live in Ohio or know someone there -- can contact him at the following address:

Governor Bob Taft
30th Floor
77 South High Street
Columbus, OH 43215-6117

Phone 614-466-3555 or 614-644-HELP

http://governor.ohio.gov/contactinfopage.asp


Members of the State Board of Education of Ohio

Members are grouped by how they voted on the intent to adopt the model curriculum. A "for" vote does not necessarily mean that the member is sympathetic to the "Wedge" advocates; several members are likely to have voted "for" simply to move the process forward, knowing that another vote would be taken in March.


Voted AGAINST intent to adopt on February 13:

Robin C. Hovis, Millersburg (330) 674-5000
Robin.Hovis@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-5/default.asp

Cy B. Richardson, Jr., Bethel (513) 734-6700
Cyrus.Richards@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-10/

G. R. (Sam) Schloemer, Cincinnati (513) 821-4145
Sam.Schloemer@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-4/

Jennifer H. Stewart, Zanesville (740) 452-4558
Jennifer.Stewart@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-9/


ABSENT during vote on February 13:

Martha W. Wise, Avon (440) 934-4935
Martha.Wise@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-2/

Virginia E. Jacobs, Lima (419) 999-4219
Virginia.Jacobs@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-1/


Voted FOR intent to adopt on February 13:

Jennifer L. Sheets, Pomeroy, President (740) 992-2151
jennifer.Sheets@ode.state.oh.us
http://www.ode.state.oh.us/board/members/sheets/default.asp

Richard E. Baker, Hollansburg, Vice President (937) 997-2101
http://www.ode.state.oh.us/board/members/baker/

Virgil E. Brown, Jr., Shaker Heights (216) 851-3304
virgil.Brown@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-11/

Michael Cochran, Blacklick (614) 863-0045
ota@ohiotownships.org
http://www.ode.state.oh.us/board/members/district-6/

Jim Craig, Canton (330) 492-5533
Jim.Craig@ode.state.oh.us
http://www.ode.state.oh.us/board/members/district-8/

John W. Griffin, West Carrollton (937) 866-1210
http://www.ode.state.oh.us/board/members/district-3/default.asp

Stephen M. Millett, Columbus (614) 424-5335
stephen.millett@ode.state.oh.us
http://www.ode.state.oh.us/board/members/millet/default.asp

Deborah Owens Fink, Richfield (330) 972-8079
deb@uakron.edu
http://www.ode.state.oh.us/board/members/district-7/

Emerson J. Ross, Jr., Toledo (419) 537-1562
ejross@buckeye-express.com
http://www.ode.state.oh.us/board/members/ross/

Jo Ann Thatcher, McDermott (740) 858-3300
http://www.ode.state.oh.us/board/members/thatcher/

James L. Turner, Cincinnati (513) 287-3232
jturner@cinergy.com
http://www.ode.state.oh.us/board/members/turner/

Sue Westendorf, Bowling Green (419) 352-2908
Sue.Westendorf@ode.state.oh.us
http://www.ode.state.oh.us/board/members/westendorf/

Carl Wick, Centerville (937) 433-1352
Carl.Wick@ode.state.oh.us
http://www.ode.state.oh.us/board/members/wicks/default.asp

Ex Officio Members

Senator Robert Gardner, Madison (614) 644-7718
Representative Arlene Setzer, Vandalia (614) 644-8051

For further information regarding upcoming Board meetings or general information about the State Board of Education, contact

Ohio Department of Education
Board Relations
25 South Front Street, 7th Floor
Columbus, Ohio 43215-4183

Phone: (614) 466-4838 Fax: (614) 466-0599
Department Information Line: 1-877-644-6338
Catherine Clark-Eich, Executive Director
Clark-Eich@ode.state.oh.us
Clayton D. Cormany, Editor

The Ohio State Board of Education page is at
http://www.ode.state.oh.us/board/default.asp


Please copy whatever you send to Ohio representatives to the thread here.

This will make it easy for those in Ohio to reference your opinions.


Wesley

* Texas Textbook Selection (11 replies)
Wesley R. Elsberry2003-08-14 10:53:44
For decades, antievolutionists have attempted to influence the state of Texas in its selection of science textbooks (and all too often succeeded).  Texas is an attractive target for antievolutionists.  The state's constituency is largely conservative and religious, so there is an overlap with the ideological outlook of most antievolutionists.  The state of Texas is also one of the largest markets for secondary school textbooks in the USA.  Antievolutionists know that if they can influence Texas to cause textbook publishers to de-emphasize evolution or eliminate references to evolution entirely, they get the added bonus of changing the textbook content for the rest of the USA as well.  This is because publishers aren't going to offer a "science lite" version to Texas and a "real science" version to the rest of the country.  That would be an expensive proposition for publishers, and publishers are at basis simply looking to maximize their profits.  So the whole country gets "science lite" or even "pseudoscience" versions of textbooks because of the political machinations of antievolutionists in Texas.

For several decades, the names of Mel and Norma Gabler were the most familiar of antievolutionists involved in the selection process.  The Gablers would offer long critiques of candidate textbooks, suggesting rewording or deletion of any content having to do with evolutionary biology.  (Antievolution was not their exclusive focus, though; their criticisms covered a number of the political hobby-horses of the religious right.)

Now, the Discovery Institute has entered the fray in trying to influence the Texas textbook selection process.  A letter to the editor from DI fellow John G. West shows their intent nicely:

Institute supports accurate science, by John G. West

Quote
First, we believe students should be exposed to legitimate scientific (not religious) controversies over evolutionary theory. Peer-reviewed science journals are filled with articles raising issues about various aspects of neo-Darwinism, the prevailing theory of evolution taught in textbooks. In 2000, for example, an article in the journal Cell noted that there is a ''long-standing question of the sufficiency of evolutionary mechanisms observed at or below the species level ('microevolution') to account for the larger-scale patterns of morphological evolution ('macroevolution').'' Yet this ''long-standing question'' about neo-Darwinism isn't covered in most textbooks. Why not?

In addition, we favor correcting clear factual errors in textbook presentations of evolution.


In the first instance, the Discovery Institute has a vested interest in keeping its antievolutionist activities labelled as something besides " creationism".  The DI rather obviously is looking forward to taking a test case to the courts, and there is way too much precedent attached to "creationism" and "creation science".  But the religious motivation of the high-profile DI fellows is easy to find (see Brian Poindexter's excellent page, From the Horse's Mouth).  The DI fellows have also liberally borrowed antievolution arguments from the SciCre young-earth creationist (YEC) contingent. The DI also encourages the YEC contingent to join forces with them in their antievolution activities.  This sort of "front" strategy doesn't fool people when it is employed by organized crime, so there should be no expectation that organized antievolution will be able to hide its intent in that fashion, either.

The Discovery Institute has no interest in correcting factual errors in textbooks.  They wish to suppress certain well-known examples in evolutionary biology from textbooks and have taken a page from Orwell in their rhetoric on this topic.  The analysis of the targeted "factual errors" presented by DI fellow John C. "Jonathan" Wells, while lauded by West, has been shown to itself be rife with factual errors and misrepresentation (see Nic Tamzek's Icon of Obfuscation and Alan Gishlick's essay).

West's letter has elicited several critical responses.

First, Dr. Sean Carroll takes exception to the misuse of his words by John G. West of the Discovery Institute.

Quote
Editor:

John G. West of the Discovery Institute, in his guest column Friday, quoted an article in a leading biology journal as purported support for his view that alternatives to contemporary evolutionary science ought to be presented in biology textbooks. I am the author of the article he quoted (but did not properly cite) and I am writing to make it absolutely clear that West is gravely mistaken in taking the excerpted sentence out of its full context.


Oak H. DeBerg and Dr. Eugenie C. Scott also criticized West.

Please enter further information about the Texas textbook selection process in this thread.

Wesley

* Oklahoma "Academic Freedom Act"/Creationist Bill (2 replies)
Michael2006-01-10 14:41:24
HB 2107 is called the "Academic Freedom Act" and is an explicate antievolution bill.  It based on the failed Florida bill that made a lot of news a few months back and it explicately singles out evolution.

Oklahomans for Excellence in Science Education is the local pro-science group.
* Internet sites on the Kitzmiller v. Dover case (0 replies)
MidnightVoice2005-09-28 10:32:00
http://aclupa.blogspot.com/

Daily briefings

http://www.aclupa.org/legal....ial.htm

List of media reports
* Kansas & teaching evolution (7 replies)
Wesley R. Elsberry2002-10-11 15:27:57
Kansas got the national spotlight in 1999 when creationists rewrote the science standards and excised evolution from them.  Since then, some creationist board members were voted out, and evolution was restored to the science standards.  The voters of Kansas will be making choices between candidates again this year.  Will we see a cyclical pattern of change in the science standards?

Here's a news item concerning two of the candidates in Kansas and some mention of their views on evolution.

Board of ed hopefuls have similar stances (Newton Kansan, 2002/10/09)

Quote
Neither candidate distinguished himself. Even on the divisive issue of teaching evolution vs. creationism, candidates basically agreed on what policy should be. Both said they would not support the teaching of creationism as an alternative to evolution.

"I support academic freedom," Willard said. "That means giving the scientific evidence on all sides of the issue and encourage them to make up their minds. I think that is what education is about, teaching kids to inquire and come to a decision."

"I would not teach creationism as an alternative to evolution," Anstine said. "In my mind creationism is a function of my home, my wife and eight kids. It is a function of our church. We've been there for more than 40 years. I think the creation story and other parts of religion are taught by the home."
* thoughts on the Dover classroom statementThe Dover (0 replies)
"Rev Dr" Lenny Flank2005-03-30 21:07:54
The Dover School District's treatment of Intelligent Design "Theory" depends upon two things; a written statement that is read to all students during class, and the availability of the ID textbook "Of Pandas and People". I would like to examine the Board's written statement, particularly in light of the recent ruling made by various judges (particularly Judge Cooper in Cobb County, GA) concerning the very similar "disclaimer stickers" that ID supporters have forced into school biology textbooks. I conclude that many of the reasons why the textbook stickers have been consistently ruled unconstitutional, will also apply to the Dover statement.

The Dover statement says:

   "The Pennsylvania Academic Standards require students to learn about Darwin's Theory of Evolution and eventually to take a standardized test of which evolution is a part. Because Darwin's Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations. Intelligent Design is an explanation of the origin of life that differs from Darwin's view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves. With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments."(York Daily Record, January 8, 2005)

Let's look at this statement one piece at a time;

The Pennsylvania Academic Standards require students to learn about Darwin's Theory of Evolution and eventually to take a standardized test of which evolution is a part.

And now the Board will lay out its reasons for altering those standards, and adding something to the curriculum which is not required or tested by the Academic Standards . . .

"Because Darwin's Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.

Much of this has already been covered in the Cobb ruling. Just like the Cobb "disclaimer stickers", the Dover statement makes lots of noise about evolution being problematic in some way ("gaps in the theory exist for which there is no evidence"). The Cobb judge wrote, on this point, "The Sticker also has the effect of implicitly bolstering alternative religious theories of origin by suggesting that evolution is a problematic theory even in the field of science. In this regard, the Sticker states, in part, that 'evolution is a theory, not a fact, concerning the origin of living things' that should be 'approached with an open mind, studied carefully, and critically considered' . . . By denigrating evolution, the School Board appears to be endorsing the well-known prevailing alternative theory, creationism or variations thereof, even though the Sticker does not specifically reference any alternative theories."

All of this applies to the Dover statement. The statement has the effect (and, I think, the intent), solely of misleading students regarding the significance and value of evolution in the scientific community, and "denigrates" evolution in order to endorse the "alternative theory" of intelligent design.

And, despite the Board's rather transparent attempt to cover its butt by defining a "theory" in the scientific sense, the Dover statement also clearly attempts to maintain the same "evolution is a theory, not a fact" argument that already lost in Cobb County. "In this regard," says the Cobb County judge, "the Sticker states, in part, that 'evolution is a theory, not a fact, concerning the origin of living things' . . . However, the evidence in the record and the testimony from witnesses with science backgrounds, including the co- author of one of the textbooks into which the Sticker was placed and Defendants' own witness, Dr Stickel, reflect that evolution is more than a theory of origin in the context of science. To the contrary, evolution is the dominant scientific theory of origin accepted by the majority of scientists."

Note too that the Dover statement specifically and clearly singles out evolution, and ONLY evolution, as worthy of special mention as "a theory" with "gaps". The Cobb Judge found similar focus in the Cobb sticker, and cited it as a reason why the statement is unconstitutional: "[T]he message communicated to the informed, reasonable observer is that the School Board believes there is some problem peculiar to evolution. In light of the historical opposition to evolution by Christian fundamentalists and creationists in Cobb County and throughout the Nation, the informed, reasonable observer would infer the School Board's problem with evolution to be that evolution does not acknowledge a creator."

"Intelligent Design is an explanation of the origin of life that differs from Darwin's view.

Note that "Intelligent Design" is not identified as being "a theory", or even as scientific. It is just "an explanation that differs from Darwin's view" (it should be noted, though, that several Board memebrs have declared in despotions that they DO indeed consider intelligent design to be a scientific theory). I suspect this is a transparent attempt to try to avoid having to demonstrate in court that ID is a scientific theory, or has any scientific validity whatsoever. Of course, the statement that ID is just an EXPLANATION, and NOT identified as science, indicates that the Board is quite aware that it is NOT science but just religious objections to "Darwin's view", and that it is being cited in the classroom specifically and solely to bring attention to this non-scientific "explanation", for the sole and only reason of denigrating evolution in favor of an alternative. Which the Cobb judge has already ruled is illegal. Also, by citing evolution as "a theory" but NOT citing ID as "a theory", I think the board is deliberately trying to use the popular meaning of the word "theory" to attempt to case doubt on evolution and to give preference to the ID "alternative" -- evolution is just "a theory", but ID in contrast is "an explanation".

The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves.

This sentence is important, since the Thomas More Law Center has, in the press, taken to making the rather silly argument that the school is not "teaching" intelligent design, merely "mentioning" it. As a newspaper report puts it: "The attorney for the Dover Area School District said no one will be teaching intelligent design. . . The entire statement on the subject of intelligent design in next semester's ninth-grade biology class will take about a minute, said Richard Thompson, president of the Thomas More Law Center, which is representing the district. And because intelligent design -- the concept that life is too complex to have evolved through natural selection, and therefore must have been created by an intelligent designer -- is only "mentioned," Thompson said; it's not being "taught." A news release issued last month by Dover's administration states that intelligent design will not be taught. Instead, teachers are to read a prepared statement and note that students can read "Of Pandas and People," a book about the concept. The news release goes on to state that Nilsen "has directed that no teacher will teach Intelligent Design, Creationism, or present his or her, or the Board's, religious beliefs."

The district's argument that they are not "teaching" ID, only "mentioning" it, is too patently silly to waste time on. I find it laughable that they plan on actually arguing this in court, with a straight face. However, since the Dover Board is not only making "Pandas" available to students, but is actually suggesting it for students to "gain an understanding of what Intelligent Design actually involves", it is crushingly clear that the Board's combined actions and statements represent an endorsement of "Pandas" and the "alternative" it embodies. Thompson's idiotic word games aside, it is illegal for school officials to endorse a religious view. Period. And by presenting "Pandas" as an "alternative" and making it available to students during class time, Dover is endorsing the religious view given within "Pandas".

"With respect to any theory, students are encouraged to keep an open mind.

If this applies to "any theory", one wonders why the board is not making similar statements to the class advising them to "keep an open mind" about the theory of gravity, or the germ theory of disease, or relativity theory, or the quantum theory of physics. Once again, the board makes it very clear that its admonition to "keep an open mind" is intended to apply only to a particular "theory" -- evolution --- to which they are offering a religious "alternative". All of this is already covered by the Cobb ruling.

The school leaves the discussion of the Origins of Life to individual students and their families.

This part is interesting. Why on earth would the school district want to leave matters of science education to "individual students and their families"? Does the school board seriously think that parents throughout its district are scientifically literate enough to discuss scientific investigation of the origins of life with their kids? Of course, the Board's admonition to students to "ask your parents" makes perfect sense if what the Board really wants is for parents to tell their kids about their RELIGIOUS feelings concerning the origins of life. The board seem to be arbitrarily banning the teaching of a particular area of scientific research -- the origins of life --- solely because of its religious objections to it, or, as the Supreme Court put it, as "an attempt to blot out a particular theory because of its supposed conflict with the Biblical account, taken literally." (US Supreme Court, Epperson v Arkansas, 1968). Not only does the Dover School Board seem to be blotting out a particular theory for no known scientific or academic reason, but it seems to be specifically and purposefully giving its endorsement and support to the religious beliefs of parents concerning this scientific matter. Indeed, given its expressed hostility to evolution and its expressed endorsement of the "intelligent design alternative", the board seems to be giving its official blessing to the religious beleifs of just a PARTICULAR SEGMENT of those parents --- those who reject evolution on religious grounds. I would like to see the Board argue how this does not constitute an endorsement of religion . . . .

As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments."

And here, the Board makes clear what its real aim is, or rather, is not. Despite its stated "secular purpose" -- "preparing students to achieve proficiency on Standards-based assessements" -- the board makes it very clear that this is NOT its real purpose. After all, ID "theory" is not covered in any Pennsyvlania standards and does not appear on any assessement test, so it is difficult to see how making students "aware of" ID helps them pass standards assessements in any way shape or form. Indeed, by deflecting attention and classroom time AWAY from evolution (the board, after all, wants the "Pandas" book to be made available INSIDE THE CLASSROOM), the board's ID efforts DETRACT from the ability of students to achieve proficiency in the state's standards assessments -- which test students' knowledge of evolution but do not test for profiency in Intelligent Design. This, also, is covered in the Cobb decision: "While there may be an educational benefit to students spending time learning the general difference between a theory and a fact as a scientific matter, teachers have less time to teach the substance of evolution. Thus, although evolution is required to be taught in Cobb County classrooms as a technical matter, distracting tangential issues effectively dilute evolution instruction to the benefit of the anti- evolutionists who are motivated to advance their religious beliefs."

It seems that the Board's stated purpose here, to help students pass assessements, is, in the words of the Supreme Court's Aguillard decision, "a sham". The Board's actions make it clear that they have no intent at all of teaching ID to produce greater proficiency in meeting the testing standards for evolution. Indeed, the entire statement read to the class makes it obviously apparent that the Board's only intent is to denigrate evolution in favor of a religious "alternative", and to "dilute evolution instruction to the benefit of the anti-evolutionists" and their "religious beliefs".

On top of all these fatal legal factors, the Dover School Board is also hampering itself by its own actions, by doing such crushingly stupid actions as hiring a Christian law firm to argue that ID doesn't have anything to do with religion, and selecting Discovery Institute bigshots as witnesses when DI is already on record as declaring that ID "theory" shouldn't be taught in schools.

This case will be SUCH a slam dunk.


[I]
* some thoughts on cobb county (3 replies)
"Rev Dr" Lenny Flank2005-02-07 20:04:30
In going through the text of the judge's decision to ban the Cobb County, Georgia stickers, I found some points that could be potentially interesting and useful precedent in Dover, as well. OK, actually they are legal precedents that will kill ID's "teach the controversy" strategy. Completely and utterly.

The text of the judge's decision is a pdf file at:

http://www.aclu.org/Files/OpenFile.cfm?id=17310

(the PDF is a scan of the printed decision, and alas it is loaded with typos and OCR errors--I've tried to correct all of these.)

Some interesting points in the decision:

The judge has killed the "disclaimer stickers" on several different and independent lines of reasoning, any ONE of which, all by itself, would be enough to kill it on "establishment clause" grounds, and all of which, together, make it virtually impossible for the fundies to win any appeal of this case. But it is interesting that these lines of reasoning also apply to the "teach the controversy" being pushed by the intelligent design advocates in Dover.

Beginning on page 35 of the judge's decision, we find:

"There is no evidence in this ease that the School Board included the statement in the Sticker that "evolution is a theory, not a fact" to promote or advance religion. Indeed, the testimony of the School Board members and the documents in the record all indicate that the School Board relied on counsel to draft language for the sticker that would pass constitutional muster. Thus, the presence of this language does not change the Court's opinion that the Sticker survives the purpose prong of the Lemon analysis. Still, the informed, reasonable would perceive the School Board to be aligning itself with proponents of religious theories of origin."

This is important. Discovery Institute and other intelligent design creationists makes lots of noise about how their viewpoint is all "science" and has no religious aim or purpose. In the Freiler v Tangipahoa case in Louisiana, which also involved a "disclaimer sticker", the stated purpose of the law as written also claimed to be secular and without any religious aim or purpose. The law specifically stated that its purpose was to "encourage critical thinking". The judge in that case, however, concluded that the stated purpose of the law was, in his words, "a sham", and that "the primary effect of the disclaimer is to protect and maintain a particular religious viewpoint, namely belief in the Biblical version of creation. (US Circuit Court, Freiler v Tangipahoa, 1999) But in the Cobb decision, the judge expands upon and strengthens this conclusion, by pointing out that even if it is accepted that the stated purpose of the law was not just a "sham" and is really and totally true and EVEN IF IT HAS NO EXPLICIT RELIGIOUS PURPOSE, it STILL fails the Lemon test if it has the EFFECT of advancing religion.

This has application to the Dover case as well as any future case the IDers might bring (since the history of ID/creationism is nothing more than a search for some wording in the law that will pass Constitutional muster). Even if a court in Dover were to rule that the DI's "teach the controversy" policy had a secular aim and was NOT intended to be religious in nature (as the DI argues), it would STILL fail the Lemon test if a reasonable informed person would conclude that it aligned itself with "proponents of religious theories of origin". As we have seen, ID proponents speak openly at every available opportunity about their "religious theories of origin" and how ID supports them. And, as the Cobb judge ruled, that is enough right there to kill it as unconstitutional. No matter how hard they try, the ID/creationists will NEVER find a suitable legal language or wording in any proposed law that will allow them to do exactly what the Constitution says they CANNOT do --- use public school classrooms to advance their religious beliefs by pretending those religious beleifs are really "science".

In the next paragraph, we find another independent criteria for finding the stickers unconstitutional, and it too applies directly to the Dover "teach the controversy" strategy:

"The Sticker also has the effect of implicitly bolstering alternative religious theories of origin by suggesting that evolution is a problematic theory even in the field of science. In this regard, the Sticker states, in part, that "evolution is a theory, not a fact, concerning the origin of living things" that should be "approached with an open mind, studied carefully, and critically considered." This characterization of evolution might be appropriate in other contexts, such as in an elective course on theories of origin or a religious text. However, the evidence in the record and the testimony from witnesses with science backgrounds, including the co- author of one of the textbooks into which the Sticker was placed and Defendants' own witness, Dr Stickel, reflect that evolution is more than a theory of origin in the context of science. To the contrary, evolution is the dominant scientific theory of origin accepted by the majority of scientists. While evolution is subject to criticism, particularly with respect to the mechanism by which it occurred, this Sticker misleads students regarding the significance and value of evolution in the scientific community for the benefit of the religious alternatives. By denigrating evolution, the School Board appears to be endorsing the well-known prevailing alternative theory, creationism or variations thereof, even though the Sticker does not specifically reference any alternative theories."

This too is important. The judge is ruling that the simple act of implying or stating that evolution is a substandard theory or in some sort of crisis or is "problematic", is misleading about the scientific value and significance of evolution, and when such "denigration" is done for the purpose of benefiting "religious alternatives"-- EVEN IF THAT ALTERNATIVE IS NOT SPECIFICALLY REFERENCED, then it is illegal.

The sole and only POINT of "teach the controversy", of course, is to denigrate evolution as "problematic" (indeed, "teach the controversy" itself consists solely of telling students about all these putative "problems"), and mislead people about its significance and value, all to the benefit of a religious alternative. That, too, is enough right there to kill it as unconstitutional.

A few paragraphs later, we find a third independent reason for killing the disclaimer stickers that also applies directly to the "teach the controversy":

"In addition to the foregoing, the Sticker targets only evolution to be approached with an open mind, carefully studied, and critically considered without explaining why it is the only theory being isolated as such. The School Board members convincingly testified at trial that they believed all scientific theories should be critically considered, and they also stated that they singled out evolution because it was the topic causing the controversy at the time. The Court finds the School Board's explanation to be rational and does not declare the Sticker to violate the purpose prong of Lemon However, because the administration suggested alternative language that did not place the emphasis so heavily on evolution, albeit after the Board adopted the Sticker, the message communicated to the informed, reasonable observer is that the School Board believes there is some problem peculiar to evolution. In light of the historical opposition to evolution by Christian fundamentalists and creationists in Cobb County and throughout the Nation, the informed, reasonable observer would infer the School Board's problem with evolution to be that evolution does not acknowledge a creator."

This is the strongest argument against the "teach the controversy", and will probably be the one cited when it is killed in court. The sticker singles out ONLY EVOLUTION for criticism and "critical thinking", for the simple reason that evolution, and not other areas of science, are the historical targets of religious opposition. The "teach the controversy" strategy also targets evolution, and ONLY evolution, specifically. And ID rhetoric makes it crystal clear that the source of this targeted opposition to evolution is that it "does not acknowledge a creator" (or designer, or whatever else they want to call it). This, too, is enough all by itself to kill the "teach the controversy" tactic.

Further on in the decision, we find:

"Due to the manner in which the Sticker refers to evolution as a theory, the Sticker also has the effect of undermining evolution education to the benefit of those Cobb County citizens who would prefer that students maintain their religious beliefs regarding the origin of life. As Plaintiffs argue and Dr Miller, the co-author of the science textbook, testified, the use of "theory" in the Sticker plays on the colloquial or popular understanding of the term and suggests to the informed, reasonable observer that evolution is only a highly questionable "opinion" or a "hunch ". The Sticker thus has a great potential to prompt confusion among the students. While there may be an educational benefit to students spending time learning the general difference between a theory and a fact as a scientific matter, teachers have less time to teach the substance of evolution. Thus, although evolution is required to be taught in Cobb County classrooms as a technical matter, distracting tangential issues effectively dilute evolution instruction to the benefit of the anti- evolutionists who are motivated to advance their religious beliefs."

While this reasoning doesn't impact directly onto Dover and "teach the controversy", it does so indirectly. In essence, the court is ruling that the sticker's inaccurate statement about "just a theory" requires teachers to use up class time to explain why "just a theory" is inaccurate, thus "diluting evolution instruction". I think the same reasoning can be applied to all the "criticisms of evolution" that the IDers want to have taught --- NONE of these "criticisms" is accepted as valid science by anyone in the scientific community. They are all inaccurate and have no recognized place in science, and therefore requiring them to be taught would just dilute the teaching of evolution by using up class time to explain that they are inaccurate (to the benefit of the anti-evolutionists and their religious beliefs).

The final line of reasoning against the disclaimer stickers also can be applied to the "teach the controversy" argument:

"Defendants persuasively argue that the Sticker in this case does not explicitly reference any alternative theory of origin, religious or otherwise. Nor does the Sticker explicitly urge students to consider alternative theories of origin or remind them that they have the right to maintain their home teachings regarding the origin of fife. Nevertheless, the Sticker here disavows the endorsement of evolution, a scientific theory, and contains an implicit religious message advanced by Christian fundamentalists and creationists, which is discernible after one considers the historical context of the statement that evolution is a theory and not a fact. The informed, reasonable observer is deemed aware of this historical context."

In essence, what the court is saying is that even if the actual language of the law doesn't directly reference any specific alternative theory or religious viewpoint, if the "historical context" of the law indicates that it is based on particular religious wishes, then it is unconstitutional. The DI's "teach the controversy" rhetoric doesn't mention any alternative theories or religious views (all of those already having been ruled illegal to teach on church/state grounds), but the historical context of "teach the controversy" is crushingly clear to anyone -- it is just the latest in a long string of attempts by fundies in general and Discovery Institute in particular, to blot out the teaching of evolution because it conflicts with their religious views. This is especially clear after considering the previous (religious) objections to "scientific materialism" and "darwinism" that Dembski, Behe and Johnson have been writing about publicly for years. This too, all by itself, is enough to kill "teach the controversy" as unconstitutional.

So, in order to win in Dover, the "teach the controversy" advocates will have to demonstrate that (1) "teaching the controversy" does not have the EFFECT of advancing religion even if it does NOT have that explicit aim, (2) "teaching the controversy" does NOT denigrate evolution in favor of any religious view, even if that religious view is NOT explicitly stated, (3) "teaching the controversy" does NOT single out evolution specifically because of religious objections that evolution allegedly denies a creator (or "designer"), (4) "teaching the controversy" does NOT take time away from the effective teaching of evolution by forcing teachers to spend time on "criticisms" that are not recognized as scientific or substantive, *AND* that (5) "teaching the controversy" does NOT have a readily viewable historical context as religious opposition to the idea of evolution. (All of this assumes that the judge buys the DI's argument in the first place that ID is "science" and isn't about religion at all, and the judge doesn't simply conclude, as the Freiler judge did, that the DI's entire argument is just "a sham" to hide their religious goals.)

In my view, there is simply no way that the Dover advocates (or anyone else) will be able to get over all five of those hurdles. I doubt they can get over ANY of them. Yet only *one* of them is enough, all by itself, to kill the IDers.

Pardon the pun, but they haven't got a prayer.
* Towards the public understanding of science (3 replies)
rebo2005-11-14 17:20:40
The recent debates and attacks on evolution are worrying.  Not so much for scientists as I'm sure they can handle themselves just fine. What worries me is that much of the unneccessary debate is fuelled by the public's ignorance of science.

Face facts the average Joe in the street couldn't care less about Physics, Chemistry, or the Scientific Method for that matter.

Science is boring , and often taught in a boring and disinterested manner by grey faceless high school science teachers.

So what happens when passionate scammers with the gift of the gab come along and try to peddle their moral friendly science .  Well Joe Bloggs falls for it hook line and sinker.

It amazes me the number of times otherwise intellegent and reasonable people repeat some of the pointless creationist drivel, such as "If we came from apes why are apes still here?" and "Evolution is just a theory".

Fact is You lot are doing a shite job. Sorry to say it but its the truth.  If you lot can't get some of these basic ideas across to the public well we are never gonna get rid of the likes of Dembski et al.

So rant over, what can we do about it. Well I have several thoughts.

1) Don't treat people who don't understand science like idiots. (I do this alot and its a very bad habit of mine)

2) Be passionate about what you do.

3) Any other ideas??

I thought about putting a small simple web page up explaining the history of science for the lay person/ young adult. But i'm not a great writer maybe some of you guys could help me write it a bit better.
* If creationism should be taught, so should... (4 replies)
MidnightVoice2005-08-28 10:22:40
http://www.venganza.org/

OPEN LETTER TO KANSAS SCHOOL BOARD

I am writing you with much concern after having read of your hearing to decide whether the alternative theory of Intelligent Design should be taught along with the theory of Evolution. I think we can all agree that it is important for students to hear multiple viewpoints so they can choose for themselves the theory that makes the most sense to them. I am concerned, however, that students will only hear one theory of Intelligent Design.

Let us remember that there are multiple theories of Intelligent Design. I and many others around the world are of the strong belief that the universe was created by a Flying Spaghetti Monster. It was He who created all that we see and all that we feel. We feel strongly that the overwhelming scientific evidence pointing towards evolutionary processes is nothing but a coincidence, put in place by Him.

It is for this reason that I’m writing you today, to formally request that this alternative theory be taught in your schools, along with the other two theories. In fact, I will go so far as to say, if you do not agree to do this, we will be forced to proceed with legal action. I’m sure you see where we are coming from. If the Intelligent Design theory is not based on faith, but instead another scientific theory, as is claimed, then you must also allow our theory to be taught, as it is also based on science, not on faith.

.....more

:)
* proposed antiID tactic (12 replies)
"Rev Dr" Lenny Flank2005-02-07 20:09:32
I posted this on t.o this past summer. I'm re-posting it
because I think the creationist loss in Georgia and their soon-to-be loss in Pennsylvania has increased its relevance and made it even more necessary that we begin taking the fight TO the creationists.


Over on another email list, I am having a discussion about a proposal of mine for an anti-creationist campaign that will, I think, cut away the creationist support in local school
districts and will, I think, pound the final nail into their coffin.

My proposal is this:

Most states in the US have, in the past years, either
srengthened or added in their state curriculum standards a
requirement that evolution be taught as a part of a good
science education. While some states have very strong
detailed standards and others have brief ambiguous ones,
the fact remaisn that they have decided that evolution is an
important part of biology and must be taught as part of any
good science education.

Creationist, on the other hand, have still been able to
intimidate many local schools into dropping mention of
evolution as "too controversial", and this local base of
support is the only thing holding the creationists up right
now.

So I propose we kill it.

I propose we find a state which has very strong detailed
standards requiring evolution, find a district within that state which is NOT teaching evolution (either because the local school board "doesn't believe in it" or because they "don't want to offend parents" or because the subject is "too controversial"), and then sue them on the grounds that they are not meeting the state's educational standards and are therefore, by the state's own definition, providing a sub-standard science education to its students.

Here is why I think it's a good tactic to take:

(1) we can't lose. The district has no defense to offer ----
they must meet the state standards, and they are not. Case closed.

(2) It will accomplish what we all have said for years that we want -- it will get evolution into all our schools and
textbooks, and it will make it impossible for creationists to
intimidate or pressure anyone into keeping it out.

(3) it will establish the legal precedent that evolution is
standard part of any good science education and that any
school which does not teach evolution (for whatever reason)
is not meeting its obligation to teach good science

(4) it will negate the fundie's power in local school board
elections by making those elections irrelevant to the issue -- state school standards apply to every school in the state,
and those districts MUST comply, no matter WHAT their
local school board wants to do. Even if the fundies capture
the entire local school board and they ALL vote to drop
evolution, they can't do it -- they *must* comply with the
state education standards.

(5) Winning in one district will establish the legal precedent, and force every school district in the state to comply. It will also send the message to all the other districts in other states, sicne they will all be equally vulnerable to such a lawsuit. At that point, the fundies will have a choice; they can either choose to contest us in each and every state, which will lead into a long drawn out legal fight for them which will drain their resources and disrupt their own plans, all for a fight that they cannot possibly win anyway; or they can choose to not waste their resources and to cede the field to us, giving up their influence in local districts. Either choice makes me happy. We win either way, they lose either way.

(6) such a strategy disrupts the fundies' coherent national
strategy. For too long, the fundies have been calling all the
shots, free to pick and choose fights when and where they
want, and the anti-creationist movement has just been
following behind them, reacting to what they do. It's time we stop being defensive with them and go on the attack, forcing them to react to *us*.

As I noted before, the fundies are in retreat everywhere.
The local school board is their last remaining power base.
So let's take that power base away from them.

Whaddya think?
* "The Wedge Update" (1 replies)
Wesley R. Elsberry2002-12-09 18:12:01
Hartwig's "Darwinian Resolution"

Mark Hartwig responds to the AAAS anti-ID resolution with the following:

Quote
Placed side-by-side with other public statements, the resolution and op-eds show how widespread Darwinist anxiety has become. [1] More importantly, however, they also reveal why Darwinists are losing ground: namely, because they are misleading their supporters.


How are supporters being misled?

Quote
In his op-ed for the Beacon Journal, Leshner attributed the ID movement’s success to “a sophisticated marketing campaign based on a three-pronged penetration of the scientific community, educators, and the general public.” This echoes a key theme of ID foes, which says the ID movement is succeeding by duping the public with shrewd tactics and a big-bucks marketing campaign.

Such claims are a great way to rally the troops: “Don’t worry boys, they’re just shooting blanks.” But they’re also a great way to get those troops mowed down, due to cockiness and lack of preparation.

Imagine someone repeating Leshner’s claim in a public forum. It would be a small matter to show that the balance of marketing power lies with the Darwinists. Indeed, the byline for Leshner’s piece in the Beacon-Journal notes that his organization “has 134,000 members serving 10 million scientists worldwide and publishes the weekly journal Science.”

[details of the marketing plan for the Evolution TV series skipped - WRE]

With the financial and talent resources that the Darwinist establishment has at its disposal, anyone repeating Leshner’s claim in a public forum is likely to end up looking foolish or disingenuous.


Note carefully what Hartwig does not do: he does not show that the claim in question is false, but rather engages the tu quoque fallacy.  AAAS has a lot of members and sends them information, sure, but what has that got to do with the issue of whether ID's success is due to marketing or to content?  Where is it that Leshner misleads?  It appears to me that the person looking foolish or disingenuous is likely to be the one who had to use tu quoque in order to have the semblance of a response.

Next up, Hartwig tries again on another issue:

Quote
The same is true for anyone who tries to defend the notion that there is no evidence against evolution and that ID success is a matter of deception and style rather than substance. Darwinist leaders have repeated these claims for years, arguing that dissent is unreasonable and should be banished from science classrooms. Such tactics are an easy mark for ID proponents, who have responded by publicizing scientific evidence against naturalistic evolution, by documenting the pervasiveness of egregious errors in biology textbooks’ treatment of evolution, and by doggedly insisting that debate be based on facts and reason rather than alleged motives.


And again Hartwig fails to touch the issue, which is whether ID advocacy has any content of its own.  Even Hartwig can't name any, for his list is composed entirely of negative arguments concerning evolutionary biology and meta-arguments about debating style.

Again, where is it that Leshner misled anyone?  Hartwig certainly develops no argument that such was the case.

Wesley
* More stupidity from the mind of the master (2 replies)
Tom Ames2004-02-10 16:08:27
OK, this is just too much.

Dembski is posting a blog (""Unfinished Thoughts") and for the life of me I can't tell whether he's being disingenuous or stupid.

He writes:
Quote

Koza spoke on "biologically inspired computation." He is one of the key people in the field, and every few years edits a book whose title begins with Genetic Programming . . . (he's now up to Genetic Programming IV: Routine Human-Competitive Machine Intelligence, which appeared last summer).   In example after example, he described setting up a fitness/objective function and then seeking an optimal solution for it. 

Interestingly, however, in all his examples the fitness/objective function always remained fixed. I therefore approached him after his talk and asked him whether he knew of any research in evolutionary computation that also changed/evolved the fitness/objective function in the search for an optimal solution to a computational problem. He replied no.

I found this quite interesting since the Darwinists claim that one of the things that gives added power to Darwinian evolution is the fact that environmental fitness is dynamic rather than static, changing, for instance, in response to evolving organisms (this is supposed to be a key factor in evolving irreducibly complex biochemical machines). Yet such coevolving fitness landscapes, which I don't deny occur in biology, are absent from evolutionary computation.

The Darwinist might want to interpret this difference thus: "Isn't it amazing that nature has given us a form of natural evolutionary computation which varies its fitness/objective functions and which therefore makes biological evolution that much more powerful than it is in silico? Just wait until computer scientists capture this feature of biological evolution. Just think of how much more powerful evolutionary computation will be then."

My own view is rather different. The fact that fitness/objective functions that vary over time are not employed in biologically inspired computing, especially after all these years of genetic algorithms hype, tells me that they are not the key to solving interesting engineering problems. And if they can't do it in the engineering context, there's no reason to think they can do it in biological contexts.

(emphasis added)

Is he daft? "The Darwinist" might think no such thing.

Try to transcend your parochial, sectarian worldview for a second, Bill, and think.

What makes evolutionary computing work? It solves a problem.

What happens when the fitness function is allowed to change during the course of the evolution? The problem changes.

So if I am an engineer who wants to solve a problem should I use a procedure in which the problem is allowed to vary? Uh, no.

The fact that engineers don't incorporate every phenomenon in evolutionary biology into their code says not a #### thing about the relevance of those feature to real world evolution.

Seriously, is this guy capable of stringing two thoughts together? Or is he just so infatuated with the sound of his own shrill voice that he doesn''t bother looking at the meaning of what he says?

* INTELLECTUAL CURRENTS: Intelligent Design Finds F (0 replies)
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* ACADEMICS consider "intelligent design" museum ta (0 replies)
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* KANSAS class calls intelligent design "pseudoscie (0 replies)
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* CREATIONISM proponents already in classrooms (0 replies)
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* CHAT with JW's Sophia Maines and Scott Rothschild (0 replies)
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* NORTH Kansas City students mull evolution, intell (0 replies)
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* NAS exchange on ID (0 replies)
Wesley R. Elsberry2003-11-22 00:15:12
Responses to "Intelligent Design and that Vast Right-Wing Conspiracy"

The National Association of Scholars published an opinion piece by Paul Gross on "intelligent design". Gross pulled no punches, and showed that ID displays many of the well-known signs of "crank science". This did not endear him to our friends at the Discovery Institute, who wrote several lengthy responses and one short sneer. The PDF linked above has those responses, some letters of support for Gross, and the response by Gross to cap it off. It all comes to about 45Kbytes.
* PROFESSOR of new creationism course criticized fo (0 replies)
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* Flogging the flagellum to death (0 replies)
Bebbo2003-02-18 07:37:03
Dembski has posted the same article to ARN and ISCID:

http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000620

http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000300

This links to his response to a piece by Kenneth Miller. All the same stuff we've seen before: Dembski looking for a God of the gaps in the flagellum.

--
Dene
* Phil Johnson on Boy Scouts and Evolution (0 replies)
niiicholas2003-04-14 01:38:47
Well, famed antievolutionist demagogue Phil Johnson took the opportunity to try to spread his message to the Boy Scouts.  Speaking as an Eagle Scout I find the whole thing intensly annoying, but that's another story.

From NMSR.org:

Quote

Phillip Johnson on Boy Scouts and Evolution ...

In the March 2003 issue of Touchstone magazine (Vol. 16, No. 2), leading "Intelligent Design" spokesman Phillip Jonhson writes "If it is important to the Boy Scouts that their members be and remain believers in God, then they need to make some effort to protect the
boys under their care from the predictable effects of the teaching of evolution, that 'universal acid,' to use Daniel Dennett's classic phrase, which has dissolved the religious faith of so many. Perhaps there should be a merit badge for understanding the evolution controversy, including knowledge of the truth about the Haeckel
embryo drawings, the Cambrian explosion, and the peppered moth story .... For now, the law may allow the Boy Scouts to exclude atheists and homosexuals, but is it right for them to do so? That question will trouble the Scouts continually until the culture is persuaded again that God really is our creator rather than merely a
product of the human imagination, and that he cares about what we do sufficiently to build a moral code into the bedrock of reality."

Source: http://www.touchstonemag.com/docs/issues/16.2docs/16-2pg16.html


There are a number of dumb things in this article, but it would have behooved PJ to actually do some reading on the history of the Boy Scouts before spouting off.  But this is PJ we're talking about, he's still repeating Wells' errors on the peppered moth etc...

The Boy Scouts were founded by Robert Baden-Powell.  See here for an extensive webpage on him and the history of scouting:

http://www.pinetreeweb.com/homepage.htm

Now, Robert's father was:

The Rev. Baden Powell, F.R.S.,  
Savilian Professor of Geometry,
Oxford University

...and he lived from 1796-1860.  "F.R.S." means "Fellow of the Royal Society", and yes, this means he was well aware of Darwin and his Origin of Species.  Baden-Powell senior even contributed a positive review:

Quote

Source:
http://www.pinetreeweb.com/bp-father.htmsource

Professor Baden Powell wrote on mathematics, physics, theology and philosophy and fought for the principle acknowledging scientific advances were compatible with Christian religion. Following Darwin's "Origin of Species" in 1859, he contributed one of seven essays in "Essays and Reviews," 1860. This was violently attacked, and the authors denounced as being inspired by "the Evil One himself." "There was some expectation of him becoming a Bishop, before Essays and Reviews were published" (letter from his widow to her nephew 20.8.1909)


Further down on the page we have:

Quote

Science and Religion: Baden Powell and the Anglican Debate, 1800-1860 by Pietro Corsi was published by the Cambridge University Press in 1988. The publishers describe the context of this debate and the content of Corsi's research in the Cambridge University Press online catalogue:

Science and Religion assesses the impact of social, political and intellectual change upon Anglican circles, with reference to Oxford University in the decades which followed the French Revolution and the Napoleonic wars. More particularly, the career of Baden Powell, father of the more famous founder of the Boy Scout movement, offers material for an important case-study in intellectual and political reorientation: his early militancy in right-wing Anglican movements slowly turned to a more tolerant attitude towards radical theological, philosophical and scientific trends. During the 1840s and 1850s, Baden Powell became a fearless proponent of new dialogues in transcendentalism in theology, positivism in philosophy, and pre-Darwinian evolutionary theories in biology. He was for instance the first prominent Anglican to express full support for Darwin’s Origin of Species. Analysis of his many publications, and of his interaction with such contemporaries as Richard Whately, John Henry and Francis Newman, Robert Chambers, William Benjamin Carpenter, George Henry Lewes and George Eliot, reveals hitherto unnoticed dimensions of mid-nineteenth-century British intellectual and social life.


& here is quote of what Baden Powell senior had to say about Darwin:

Quote

"Just a similar scepticism has been evinced by nearly all the first physiologists of the day, who have joined in rejecting the development theories of Lamarck and the Vestiges; and while they have strenuously maintained successive creations, have denied strenuously maintained successive creations, have denied and denounced the alleged production of organic life by Messrs. Crosse and Weekes, and stoutly maintained the impossibility of spontaneious generation, on the alleged ground of contradiction to experience. Yet it is now acknowledged under the high sanction of the name of Owen (British Association Address 1858), that 'creation' is only another name for our ignorance of the mode of production; and it has been the unanswered and unanswerable argument of another reasoner that new species must have originated either out of their inorganic elements, or out of previously organized forms; either development or spontaneous generation must be true: while a work has now appeared by a naturalist of the most acknowledged authority, Mr. Darwin's masterly volume on The Origin of Species by the law of 'natural selection,' - which now substantiates on undeniable grounds the very principle so long denounced by the first naturalist, - the origination of new species by natural causes: a work which must soon bring about an entire revolution of opinion in favour of the grand principle of the self-evolving powers of nature."

source



And Darwin wrote in a letter:

Quote

http://www.talkorigins.org/faqs/ce/3/part9.html

"Henslow [says he]... will go a very little way with us [in accepting the Darwinian theory of evolution], but brings up no real argument against going further. He also shudders at the eye! It is really curious (and perhaps is an argument in our favour) how differently different opposers view the subject... Baden Powell says he never read anything so conclusive as my statement about the eye!" (Darwin to Charles Lyell Feb. 15, 1860)


Anyway, this is Baden Powell's father, not the founder of scouts himself.  Baden Powell jr. was a military man, not a scientist, and never said much about Darwin one way or the other, although:

Quote

source

    In Chapter 6 of his book Rovering To Success, Powell addressed "irreligion" and atheism.  He clearly opposed the attacks upon religion expressed by many atheists and the divisiveness it caused.  He believed that nature showed evidence of God and that religion was essential for happiness.  He marveled, as so many religionists have, at the amazing workings of the eye.  B-P wrote, "Ask Mr. Atheist who it was who invented and made that wonderful machine?"  

    Curiously, Charles Darwin, whose observations of nature led him to embrace agnosticism, also marveled at the complexity of the eye, though came to believe its development would be explained by natural selection.  Darwin actually acknowledged B-P's father in the introduction to The Origin of the Species and wrote in a letter, (Rev.) "Baden Powell says he never read anything so conclusive as my statement about the eye!"   Indeed, Darwin's theory had been embraced and defended by the senior Baden Powell; yet, the only reference B-P made to Darwin in his writings was to use him as an example to boys that even those who did poorly in school could become successful scientists.

B-P's view of God was much more inclusive than most.  He always told the scouts that they needed to be tolerant and respectful of others' differing religious beliefs.  God, he said, is "a vast Spirit of Love that overlooks the minor differences of form and creed and denomination and which blesses every man who really tries to do his best, according to his lights, in His service."

    B-P's writings show a broad appreciation of culture and diversity and a deep desire to develop strong, moral character in the world's young men.  He staunchly maintained that chivalry and self-sacrifice were the basis of religion and this was necessary in scouting.


Heh.  Here's the Darwin quote from B-P jr:

Quote

http://old.jccc.net/~mbrownin/badenp/bp_boy.htm

"Is it not true that both Newton and Darwin, founders of the scientific method, were both regarded as blockheads by their school teachers?



Hmm, I guess other people have made my connections before:

Quote

http://www.lib.calpoly.edu/infocomp/modules/09_treat/Ic7.html

Boy Scouts
Letter to the Editor
Los Angeles Times January 18, 1998.

Re Jan. 13 letters concerning atheism and the Boy Scouts: Lord Baden-Powell, the founder of the Boy Scouts, once stated emphatically in response to the question of religion, a quotation of the philosopher Carlyle. "The religion of a man is not the creed he professes, but his life—what he acts upon and knows of life and his duty in it. A bad man who believes in a creed is no more religious than a good man who does not." Lord Baden-Powell’s father was a professor and a great friend and admirer of Charles Darwin, and at one time had been reported to the bishop of London for heretical preaching, and so he was acutely aware of the tyranny of religious zealots. I would point out that most Nazi troops in World War II were Lutherans or Roman Catholics and very probably none were atheistic Boy Scouts!

--Alex Sheppard Reseda



A discussion at a scouting forum:
http://www.scouter.com/forums/viewAllPosts.asp?userID=905&p=14
* Intelligent Design good for evolution? (4 replies)
kurt2005-09-23 14:52:22
I am a bio teacher and a huge fan of evolution.  I integrate it throughout my curriculum and am psyched to the collegeboard adopt a new design centered on evolution (which any biology class that makes sense has to be).  We discuss intelligent design and creationism and the reasons why people may choose to reject scientific discoveries.  

Having had many conversations on this awesome topic, I often wonder whether allowing students to make the choice of accepting ID might not be such a bad idea.  Of course, recognizing that there is no evidence for it whatsoever and it obviously must be taken on faith, is it wrong to let them hang on to ID?  

Although I truly enjoy discussing religion (I'm an atheist), my goal is not to convince students that god or spirits or whatever don't exist, but rather to let them see the difference between science and faith, and to allow them to accept both.  ID seems like a good compromise.  

I think the important thing is for them to see what a beautiful perspective of life's history we have discovered.  Evolution is cool, and I want them to see it.  If I make it a choice between science and religion, then I am guaranteed to lose many of them.  I could  say that what looks like its random mutations could be directed by a higher power, but we'll never know because it wil always appear random to us.  This is true and I certainly don't need to buy into that, but do I really care if they do?   They will still have a true knowledge of evolution and may find a way to reconcile it with their personal beliefs.
* Yes, we have no bananas (1 replies)
Tom Ames2003-01-10 15:02:34
For your amusement. From Grace Bible Church.

Quote
Let me give you a simple example. Anything showing complex design demonstrates that there is a designer. When you see a house, you know there was a house builder. When you see a painting, you know there was a painter. Even the atheistic evolutionist does understand this because in their quest for finding life beyond earth they using radio-telescopes trying to find some pattern in what they are picking up. They are looking for design in order to prove an intelligent designer.

What would you say if I took a can of soda and told you it was the result of billions of years of evolution. That the magnetic properties of the metal drew the metal atoms together in such a way that they formed a cylinder with a bottom, and then after millions of years a brown, sweet liquid formed inside. After more millions of years a top formed with lid that could open easily. Then after more millions of years it became colored, in this case, with red, gold and white in such a way that it read in English, "Diet Dr. Pepper" and "12 FL OZ." That sounds pretty foolish doesn't it, and even more so if I added that thousands of these soda cans evolved and then arranged themselves in rows of 3 by 2 with a plastic material forming around their tops so six of them can be carried at a time.

But consider what people believe about something like a banana. The outside is a biodegradable wrapper that changes color according to the condition of what is inside. Green is too early, Yellow is just right and Black is too late. It has a "pop top" and seems so that it can be easily opened and still protect the contents from contamination. You can eat this even if your hands are dirty - perfect for boys and men! Its shape is perfect for the human hand and mouth, and if you hold it correctly, it even bends toward you for easy consumption. Nutritionists tell us that the contents of a banana are one of the best foods for humans. It is easily digested and provides the body with energy as well as vitamins and minerals. The banana also contains seeds inside it which can grow into a banana tree and then produce more bananas. Try planting a soda can and see what grows! The banana is infinitely more complex than a can of soda and demonstrates the design of a wise creator, yet many people willingly ignore the obvious to claim it is the product of the chance mixing together of molecules in chemical reactions over millions and millions of years. It is more plausible to get the soda can by evolution than a banana - hence a good name for a banana is "The Atheist Nightmare."

* ID *is* "God of the Gaps" after all (2 replies)
niiicholas2002-12-20 21:02:53
Over at the ID network's response to the AAAS resolution:

[url=http://www.intelligentdesignnetwork.org/ResponseToAAAS.htm#Reason 6 text]Here if the internal spaces don't muck it up[/url]

...it is written:

Quote

6. The AAAS claim that a design inference is not testable is simply disingenuous. An inference of design is testable. Many scientific disciplines test for design every day, including routine testing of radio and light waves for alien intelligence by the SETI program.

   If ID is not testable and thus "non-scientific," then neither are several other disciplines currently held to be scientific. For example, in the SETI program, researchers are testing patterns in light and radio waves from outer space for non-human alien intelligence. ID and SETI both use the same design detection methodology. How could the SETI enterprise be considered scientific if its design detection methods are not scientifically valid? If design cannot be falsified, how can the AAAS consider it to be false? The AAAS claim that a design inference is not testable is refuted every day by countless design detection experts whose livelihood depends on design detection (e.g., forensic scientists, arson and crime investigators, cryptologists, archaeologists and SETI researchers).

   How does one "test" a design inference? A pattern or system that yields an inference of design must satisfy all of three criteria. If it cannot, then a design inference is not warranted (i.e., design is rejected as an explanation).

  • First, the pattern must exhibit apparent design - something that appears to be "specified." A specification is a pattern that has been configured for a purpose or that conveys some meaning or message that is independent of the significance of the individual events that make up the pattern. For example, the pattern "DESIGN" appears designed because it reflects meaning that is independent of the significance of each of the six letters that comprise it. DNA has the same characteristic.

  • Second, there must be no adequate natural explanation for the pattern. It cannot be a pattern that is required to appear by the operation of natural law. For example, a salt crystal and a river channel are regular patterns that can be explained by natural law (electromagnetism, gravity, erosion, moving water, the natural terrain). However, the precise sequence of the genetic symbols in "message bearing" DNA are not dictated by any known law.

  • Third, the pattern must be sufficiently complex that its arrangement by chance and law alone is statistically improbable. As mentioned above, the chance formation of the necessary DNA sequence for the first cell would appear to be statistically impossible.

       These general criteria are used in the analysis of patterns in all design detection sciences - archaeology, forensic sciences, cryptanalysis and the search for extraterrestrial intelligence. They are deemed adequate to test for design in those sciences. Why not in evolutionary biology? No scientific rational has been provided for accepting design detection methodologies in these other historical sciences and rejecting them in evolutionary biology.

    [italics original]


  • Point #2 looks like GOTG to me...

    There are lots of other problems here but this was particularly clear IMO.
    * Dover, PA School Board (4 replies)
    Wesley R. Elsberry2004-12-06 22:07:15
    The Dover, Pennsylvania school board has adopted a policy concerning the teaching of evolution.

    Quote

    The Science Department teachers researched and recommended to the administration the science book, Biology (Prentice Hall) as the textbook for our High School Biology class.  The Dover Area School District adopted, approved, and purchased 220 copies of the teacher-and administration-recommended book.

    The district also received as a donation 60 copies of Of Pandas and People and the book is now listed as a reference book in the curriculum.  It is not a required text, but in an effort to present a balanced curriculum the book is made available to all students who wish to review the book.

    The Biology curriculum was also updated to include the following statement:

    “Students will be made aware of gaps/problems in Darwin’s Theory and of other theories of evolution including, but not limited to Intelligent Design. The Origins of Life is not taught.”

    The Assistant Superintendent in charge of curriculum development, Mr. Baksa, in coordination with the Science department teachers, the district solicitor, and the School Board has developed the following procedural statement to use in implementing the new Biology curriculum language.  The following will be read to all students:

             “The state standards require students to learn about Darwin’s Theory of Evolution and to eventually take a standardized test of which evolution is a part.

             Because Darwin’s Theory is a theory, it is still being tested as new evidence is discovered.  The Theory is not a fact.  Gaps in the Theory exist for which there is no evidence.  A theory is defined as a well-tested explanation that unifies a broad range of observations.

             Intelligent Design is an explanation of the origin of life that differs from Darwin’s view.  The reference book, Of Pandas and People, is available for students to see if they would like to explore this view in an effort to gain an understanding of what Intelligent Design actually involves.  As is true with any theory, students are encouraged to keep an open mind.

             The school leaves the discussion of the Origins of Life up to individual students and their families.  As a standards-driven district, class instruction focuses on the standards and preparing students to be successful on standards-based assessments.”



    (Source: http://www.dover.k12.pa.us/doversd/cwp/view.asp?A=3&Q=261852 , as of 2004/11/19)
    * ON teaching intelligent design (0 replies)
    NULLNULL
    NULL
    * Why Intelligent Design Fails (0 replies)
    Wesley R. Elsberry2004-07-21 18:57:43
    Why Intelligent Design Fails

    A Scientific Critique of the New Creationism


    Edited by Matt Young and Taner Edis

    http://www2.truman.edu/~edis/books/id/

    Buy directly from Rutgers University Press on-line and get a 20 % discount and free shipping (see below)

    "This book is a readable and devastating scientific analysis of intelligent design creationism. . . .unlike ID's proponents, these authors have done the real science that deflates the claims of intelligent design. Their work deserves the respect of everyone with a say in what is taught in public school science classes." -- Barbara Forrest, co-author of Creationism's Trojan Horse: The Wedge of Intelligent Design

    "A terrific book that explores, fairly and openly, whether proponents of ID have any scientifically valid gadgets in their toolbox at all. . . .accessibly written throughout and an invaluable aid to teachers and scientists." -- Kevin Padian, Professor and Curator, University of California, Berkeley, and President, National Center for Science Education

    "'Intelligent-design theory' makes extravagant claims, but refuses to come up with even a small fraction of the evidence needed to sustain them. Why Intelligent Design Fails brings together clear and devastating arguments by true scientists, which will convince perceptive and fair-minded readers that 'intelligent design' belongs to the history of propaganda, not to the achievements of science." -- Norman Levitt, Author of Prometheus Bedeviled: Science and the Contradictions of Contemporary Culture

    Is Darwinian evolution established fact, or a dogma ready to be overtaken by the next scientific revolution? Today, a comparatively sophisticated group of Darwin-deniers have coalesced in the "intelligent-design" movement, arguing that the molecular machines in cells cannot be assembled by natural selection, and that the information in our universe cannot be generated by mindless processes. They have even claimed to detect design in complex structures by rigorous mathematical means.

    In Why Intelligent Design Fails, a team of scientists call on their expertise in physics, biology, computer science, and archaeology to examine intelligent design. They take design claims at face value, without attempting to rule out the hypothesis of a designed universe just because of its supernatural overtones. They consistently find grandiose claims with no scientific merit. The questions intelligent-design advocates raise have largely already been answered, or else mainstream scientists have been making excellent progress on them with a Darwinian, naturalistic approach.

    After an overview of intelligent design and its intellectual context, Why Intelligent Design Fails moves on to biological claims concerning common descent, and the arguments of Michael Behe. Contributors show how the notion of "irreducible complexity" does not challenge Darwinian evolution, explaining how mainstream science comfortably accounts for examples of biochemistry, bacterial flagella, and bird wings.

    Intelligent-design advocates, however, have ambitions beyond overturning Darwinian thinking in biology. So the authors examine the information-based arguments of William Dembski. They discuss thermodynamics and self-organization, the ways human design is actually identified in fields such as forensic archaeology, how real complexity theory thoroughly undermines Dembski's notions, how research in machine intelligence indicates that intelligence itself is the product of chance and necessity, and the misunderstandings of the no-free-lunch theorems propagated by Dembski. The book closes with an investigation of cosmological fine-tuning arguments said to show that the universe was designed for humans, and reflections on the place of the intelligent-design movement at the fringes of mainstream science.

    Intelligent design turns out to be a complete scientific mistake, but also a useful contrast highlighting the amazing power of Darwinian thinking and the wonder of a world filled with complexity without design.

    The chapters are authored by Taner Edis, Matt Young, Gert Korthof, David Ussery, Ian Musgrave, Alan Gishlick, Niall Shanks, Istvan Karsai, Gary Hurd, Jeffrey Shallit, Wesley Elsberry, Mark Perakh, and Victor Stenger.

    Matt Young http://www.mines.edu/~mmyoung is the author of No Sense of Obligation: Science and Religion in an Impersonal Universe http://www.1stBooks.com/bookview/5559. He is a former physicist with the National Institute of Standards and Technology and now teaches physics at the Colorado School of Mines. Taner Edis http://www2.truman.edu/~edis/ is an assistant professor of physics at Truman State University in Kirksville, Missouri, and the author of The Ghost in the Universe: God in the Light of Modern Science http://www2.truman.edu/~edis/books/ghost/.
    Buy at a 20 % discount and get free shipping from Rutgers University Press by ordering on-line!

    (See below.)

    Preface http://www2.truman.edu/~edis/books/id/preface.html

    Reviews http://www2.truman.edu/~edis/books/id/reviews/
    ISBN: 0-8135-3433-X 240 pp., illustrated with figures and tables.

    --------------------

    To reiterate online ordering information:

    Rutgers University Press (20% off!):
    http://165.230.98.36/acatalog/__1147.html

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    * God and the Explanatory Filter (0 replies)
    Wesley R. Elsberry2003-01-16 21:57:40
    God and the Explanatory Filter

    Quote
    From: rossum <rossum48@coldmail.com>
    Newsgroups: talk.origins
    Subject: God and the Explanatory Filter
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    God and the Explanatory Filter

    Dembski's Explanatory Filter (EF) is intended to distinguish regularity, chance and design.  Dembski claims that the filter does not register false positives for design, though it is susceptible to false negatives.  When we apply the EF to God we get some interesting results.

    The filter has three stages, first a check for regularity, second a check for chance and third a check for design.


    1 First Stage - Check for Regularity

    If something is due to regularity then it is the outcome of the working of the laws of the universe.  Since God is the creator of the universe it is not possible for God to be due to regularity.  I am sure that all believers would agree that God is not a product of the laws of the universe.

    2 Second Stage - Check for Chance

    For something to be due to chance the probability of it happening by chance must be greater than Dembski's Universal Probability Bound (UPB).  This is 1 in 2 ^ 500, equivalent to 1 in 10 ^ 150, or 10 ^-150.  This equates to 500 bits of information.  Evaluating the probability of God is not easy.  There are two possibilities: God is simple or God is complex.

    2.1 God is Simple

    If God is simple, then God does not contain a lot of information.  Low information corresponds to high probability, so a simple God would be more probable than the UPB.  In this case the EF would assign God to chance.  I do not think that there are many believers who would agree that the existence of God is due to chance alone.  This incorrect result might indicate a problem with the assumption that God is simple or else it might show a problem with the Explanatory Filter.

    2.2 God is Complex

    God is complex, but how complex relative to the UPB?  This question is dependent on how much information God contains. God is omniscient, knowing everything; a very large amount of information indeed. However we can put a lower limit on the information contained in God. Given that God wrote the Bible, the minimum amount of information is the amount contained in the Bible. God knows more than is in the Bible; knowing less is not possible.

    Looking at one of my Bibles, I find that it has about 30 characters per line, 56 lines in a column and two columns per page. The Old Testament contains 840 pages and the New Testament 240 pages. A total of 1080 pages.  This is 30 x 56 x 2 x 1080 = 3628800 characters. For simplicity let us take the number of possible characters as 30, 26 letters plus space and some punctuation.  Therefore by the standard probability argument the likelihood of the Bible having arisen by chance is 1 in 30 ^ 3628800. Remember that this is an upper bound, God is less probable than this because he contains more information than is in the Bible.

    Working out the numbers, 1 in 30 ^ 3628800 is a probability of 1.8 x 10 ^ -3628942.  This is less than the UPB of 10 ^ -150 with a good margin for error.  Hence the EF does not assign God to chance at this stage.

    This is a better result.  God is not due to chance, which is in agreement with the opinion of all believers.  I will proceed on the assumption that God is complex.


    3 Third Stage - Check for Design

    3.1 Look for a Specification

    The third stage starts by looking for an independent specification. God certainly has a specification, scripture.  Given that God is specified then God is again not a result of chance: the EF assigns low probability non-specified events to chance.  Again this is a good result indicating that God is indeed specified.  Had God not been specified then the EF would have indicated chance which we have already rejected in 2.1.

    3.2 Design is Detected

    At the third stage the EF says that if something is both complex and specified then it is due to design.  God is both complex, by 2.2, and specified, by 3.1.  Hence the EF says that God is due to design. Remember also that Dembski claims that the EF does not show false positives for design so this result is supposed to be reliable.  Of course the EF says nothing about the nature of the designer, it merely asserts the presence of intelligent design.


    4 Conclusions

    I think all believers would agree that God did not arise from either regularity or chance.  However by Dembski's definition of design only regularity, chance and design are allowed -- Dembski defines design as everything which is neither regularity nor chance.  With this definition of design it is inevitable that the Explanatory Filter decides that God is designed.

    Given the wider aims of the ID movement it is amusing to see that Dembski's Explanatory Filter appears to give support to the atheist argument that God was designed by humans.  I am more inclined to think that either the EF is flawed or that this is an example of a false positive for the EF.
    * Antievolutionism in Singapore (0 replies)
    budak2005-12-10 01:26:41
    Dear Pandasthumbers,

    First of all, thanks for creating this great site (along with talkorigins.org) and the lively discussions on the main board and in the forum.

    I am not a professional scientist, just an amateur who grew up immersed in creationist environments but found them hollow while becoming an evolutionist via the Wallacean route (i.e. biodiversity and biogeographical studies of the Malesian region – I keep freshwater fishes and plants from this part of the world and keep track of the region's habitats, species distribution and ecological issues on my blog at: http://budak.blogs.com/the_ann.....html).

    Recently, in Singapore (which most of you probably know through draconian social laws coupled with official enthusiasm about the life sciences), a letter to the leading newspaper sparked a short debate which continued online on my blog and another individual. The main links are here:

    http://budak.blogs.com/the_ann....nd.html

    http://noself.blogspot.com/2005....02.html

    The creationist in question hasn't made up his mind on whether he is old or young earth, but his main lines of assault are via the supposed improbability of abiogenesis as well as the supposed conclusion of forensic science that an intelligence (he disingenously separates the notion of non-human intelligence and supernatural causes to avoid the theistic accusation) can be detected in the functional complexity of life (using examples from cellular chemistry and DNA origins). His definition of science is akin to Philip Johnson's.

    With no real training in biochemistry, I can only address the logical, philosophical and deductional aspects of his arguments, which seem to me extended expositions based on incredulity, ignorance and outright hostility to materialistic science. My request here, if you could spare some time, is that you could assess the points (from both sides) and provide us some feedback and leads on their soundness. I am not intending to have the last word on the matter, as the good doctor has already proclaimed 'victory'. Neither do I seek to convert him. A clear, objective evaluation of the issues raised for the benefit of genuinely disinterested individuals reading the discussion is what I am for.

    Thanks and regards,

    Budak
    * INTELLIGENT design's long march to nowhere (0 replies)
    NULLNULL
    NULL
    * Stop codon thievery (0 replies)
    efvinson2002-05-30 08:41:26
    A very recent example of a "stop" codon being
    sometimes coopted for another use is the subject of two papers and a "perspective" (1-3) in the 24 May 2002 issue of Science. These all are reporting on the "new" amino acid "pyrrolysine", which is coded for by the (usually) stop codon UAG in a certain methanogenic archaeon's mRNA. To quote from (1):
    Quote

    The way in which pyrrolysine is encoded bears striking parallels to the encoding of the 21st amino acid, selenocysteine. Selenocysteine is found in Archaea, eubacteria and animals, including mammals . Both nonstandard amino acids are encoded by the RNA nucleotide triplets (codons) that signify a command to stop translation of mRNA into protein (UGA is the "stop codon" encoding selenocysteine). The notion that at least 22 amino acids are directly encoded by the nucleotide sequence of mRNA reflects the greater richness of the genetic code than is apparent from the standard textbook account.

    Originally, the coding problem was defined in terms of how the 20 common amino acids could be specified by four RNA nucleotides. As the triplet nature of the genetic code began to unfold in the early 1960s, it might have been tempting to speculate that some of the 64 possible codons encoded the many rare amino acids found in proteins. However, it became clear that 20 is the correct number of amino acids, and that the great majority of nonstandard amino acids are created by chemical modifications of standard amino acids after translation. In 1986 came the surprise discovery that the nonstandard amino acid selenocysteine is directly specified by the genetic code and is not created by posttranslational modification. Selenocysteine is now joined by pyrrolysine, and together these two amino acids demonstrate that the genetic code can be expanded by redefining the meaning of a stop codon.   {references omitted}




    Reference (1) goes into some depth, with references, as to how the stop signal is subverted in the case of selenocysteine, the only other non-canonical amino acid known to be specified by the code and not built by modification after translation. In the selenocysteine case, only a minority of the UGA codons are used to code the amino acid: most are still stop codons. Signals elsewhere in the mRNA determine which. It is still unknown just hoe the UAG coding pyrrolysine works, however.

    (1) Atkins JF, Gesteland R. Science 2002 May 24;296(5572):1409-10
    (2) G. Srinivasan et al., Science 296, 1459 (2002).
    (3) B. Hao et al., Science 296, 1462 (2002).
    * DI reviews Texas textbook choices (0 replies)
    niiicholas2003-07-22 19:42:58
    http://www.discovery.org/articleFiles/PDFs/TexasPrelim.pdf

    Yee ha, mostly more of the same.

    Random observations:

    1) Several typos in quotes of textbooks, presumably introduced by the DI author (aka Wells and/or a lackey)

    2) Miller-Urey: DI attempts to establish via repeated assertion that (a) a neutral prebiotic atmosphere is established and (b) that the miller-urey experiment absolutely doesn't work in such conditions.  Neither is particularly true, and if (a) is even mildly wrong then (b) is very wrong.

    2.5) I should like to find out if this paper really is trustworthy or if there is something wrong with it.  It pretty much says that a neutral atmosphere *can* produce abundant amino acids, which AFAIK has been denied by Stanley Miller and collegues.

    ===========
    F. Hanic, M. Morvova and I. Morva

    Thermochemical aspects of the conversion of the gaseous system CO2-N2-H2O into a solid mixture of amino acids. Journal of Thermal Analysis and Calorimetry. Vol.60, 2000, pp. 1111-1121. I.F.: 0,607.

    Abstract
    Conversion of the gaseous mixture CO2(g)+N2(g)+H2O(g) to a solid amino acid condensate in an electric discharge plasma has high efficiency of the energy transfer from the different plasma components
    into chemical processes. The basic activation process is activation of the N2 metastable electronic state, followed by formation of NCO* and ONñNCO free-radicals and generation of many reactive radicals. These radicals help to overcome the high activation energy of thermal dissociation of N2 to N (950 kJ=9.846 eV).

    The major product is a statistical polycondensate containing the amino acids: arginine, lysine, histidine, methionine, glycine, alanine, serine and aspartic acid. This information was obtained by
    comparing the IR spectra of the products with reference IR absorption spectra of pure components. Identification of the individual amino acids in the solid product was performed by HPLC, when samples
    were dissolved using 6MHCl applied at 100°C for 24 h. Properties of the condensate were estimated using thermogravimetric analysis. Small amounts of oxamidato complexes and oligo pyrrole structures are formed on the electrode surface giving the surface catalytic properties. The gas cleaning process has practical applicability (production of useful fertilizers, reduction of the CO2 concentration in the atmosphere) and may also contribute to explanation of the origin of life on Earth.
    ===========





    3) Peppered moths.  Same ol', same ol'.  Very selective citation of sources as usual.  Disturbingly, though, one quote from a textbook appears to have bought into the press accounts:

    ==========
    Peter H. Raven & George B. Johnson
    Biology, 6th edition (2002)

    DI says:
    The lengthy account in the text retells the classical story. Although a student who reads all the way to the end of the account learns that scientists are now reconsidering the story and that "wherever the moths rest during the day, it does not appear to be on tree bark" (p. 447), such important information should be discussed in the body of the account and not merely tacked on as an afterthought.
    ==========

    ...yet another instance of a highly garbled and second-hand version of Majerus' comments making it into respected print as the new default position.  But, cripes, except for tree bark, the only things for moths to rest on are the ground, which is right out, or leaves.  If they rest underneath branches, which seems like the most likely most common spot, this is still tree bark, and still lichened tree bark at that.  Undoubtedly some rest under leaves, but the actual expert consensus, from Kettlewell to Majerus, has not changed.  Majerus (2002) explicitly endorses Kettlewell's opinion on resting positions, "underneath the larger boughs of trees, less commonly on trunks").  And the most recent Majerus data on resting positions supports this:

    exposed trunk   - 6
    unexposed trunk - 6
    trunk/branch joint - 21
    branches        - 19

    (Notably the DI bit says that the resting position of peppered moths was only discovered in the 1980's...sigh)

    Hooper and favorable reviews thereof prominently mentioned, the skeptical reviews from the experts are not...

    3.5) The Raven & Johnson quotes including a mini-rebuttal of ID are interesting, though, they're not taking the controversy lying down...

    4) Haeckel.  Richardson's later work not mentioned, nor the complexities about when and why Haeckel put out various drawings.  The DI continues to make use of tactical ambiguity about "early" stages vs. "earliest" stages, what exactly "close resemblance" means, and obfuscation over whether or not (a) all vertebrate classes should be equally similar (a flabbergasting strawman) or whether similarity should follow the accepted phylogeny of vertebrates (the actual theory).  The latter is admirably addressed in Gishlick's review of Icons:

    http://www.ncseweb.org/icons/figure08.jpg


    The similarities in obfuscational terminology are so similar to Wells' that he almost has to be the author.

    5) DI criteria cleverly put n/a for many books on specific topics.  If the treatment of embryos in Campbell 2003 is similar to that for Campbell 1993, then Wells just totally left them out because they use photos but also discuss the differences between mammals and birds at the blastula stage.

    6) Unfortunately the DI is able to jump on several more-or-less blatant errors in the history of science (e.g., that the flat earth was a popular idea in the 1400-1500's).  They do overcorrect and try and leave the Roman Church blameless for what happened to Galileo, and implying that house arrest was the most serious threat he faced from the inquisition, which is dubious.

    7) Finally, the DI does pick the probably-best textbook (Campbell, or actually Campbell and Reese in the 6th edition) as their least-worst pick, so on the off-chance that the Texas board picks Campbell for some course or other, be prepared for DI crowing.  However, Campbell is pretty much a college biology text, and is probably a bit much for anything except A.P. Bio, so perhaps its selection is unlikely.
    * What about Russia? (1 replies)
    RussoEnt2005-04-21 04:55:36
    Hi there
    what do u think about Russia and russian entertainment web-portals?

    tnhx
    * ISCID Brainstorms needs money to get better (0 replies)
    Bebbo2002-12-21 07:25:48
    Seems that ISCID feels money is necessary to get improved constributions to the Brainstorms forum:

    http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000262

    Overthrowing materialism doesn't come cheap I guess!

    --
    Dene
    * An Inordinate Fondness for Flagella (1 replies)
    Wesley R. Elsberry2004-02-17 18:46:34
    Dembski's Response to WSJ Article on "intelligent design"

    Quote
    Design theorists have known all along about microsyringes and other supposed evolutionary precursors to irreducibly complex systems like the bacterial flagellum.


    This raises some questions. The first is whether the statement is true. I don't recall any ID theorist, and certainly not Dembski, discussing T3SS's when the topic of flagella arose prior to Larry Moran's encounter with Dembski in Toronto on March 7, 2002. If Moran's mini-lecture filled in this gap in the knowledge of "ID theorists" then much would be explained. Even Dembski appears to acknowledge the lack of discussion of T3SS's in ID argumentation in STILL SPINNING JUST FINE: A RESPONSE TO KEN MILLER, where he says this:

    Quote
    If the biological community had even an inkling of how such systems arose by naturalistic mechanisms, Miller would not -- a full six years after the publication of Darwin's Black Box by Michael Behe -- be lamely gesturing at the type three secretory system as a possible evolutionary precursor to the flagellum. It would suffice simply to provide a detailed explanation of how a system like the bacterial flagellum arose by Darwinian means. Miller's paper, despite its intimidating title ("The Flagellum Unspun") does nothing to answer that question.


    A Google search for "microsyringe" coupled with either "intelligent design" or "irreducible complexity" turns up nothing by any "ID theorist".

    If the statement that "ID theorists" have known all along about "microsyringes" and so forth is true, then the question becomes, "Why didn't they discuss those issues when discussing bacterial flagella?" For folks who love to quote Darwin to their purpose, they seem loath to demonstrate that they embrace the point by example:

    Quote
    Darwin himself would have agreed: "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question."


    Source: NO FREE LUNCH

    If "ID theorists" did know all along about "microsyringes". etc., then the obvious implication is that they weren't interested in achieving a "fair result" when they chose not to reveal this knowledge to their readers.

    My thanks to Ian Musgrave for noticing this bit of rhetoric on Dembski's part.

    Wesley
    * General Wells reviews (0 replies)
    niiicholas2003-05-05 23:01:02
    General Wells reviews:

    A PowerPoint presentation by Tony Hiatt for the 2003 HASTI (Indiana Science Teachers) Convention
    Icons of Evolution
    A Critical Review
    by Tony J. Hiatt
    HASTI 2003
    http://www.indiana.edu/~ensiweb/pap.tony.pdf
    * Vagueness and Explanatory Constraints (1 replies)
    niiicholas2003-01-19 00:48:17
    I was thinking about posting this on this ISCID thread, and then I thought, "why bother?" Besides I am too busy to start a big debate.

    Here is the thread, started by Mike Gene:

    Topic: Brainstorming Lessons
    link to thread

    I quote the end of RBH's post:

    Quote

    If Mike Gene's reference to an "attempt to squelch discussions of design until we first extract a data base of definite information (i.e., actual mechanisms, identity of design, etc.)" means that speculation or questions about the mechanisms of design and the nature, identity, and/or properties of the designing agents ought to be out of bounds, then I think it is he who draws the wrong conclusion from the account of OOL he gives in the OP. I'll give him another example to think about.

    Wegener's 1915 hypothesis of continental drift was not accepted for nearly five decades because there was no known mechanism by means of which continents could be propelled across the earth. There were suggestive data that it had occurred - e.g., geographical form matches across seas, distributions of fossils, and so on - but no mechanism, and hence no broad acceptance. It wasn't until the 1960s, when actual drift rates could be measured and a plausible mechanism for drift was offered that it became broadly accepted. (I have stood in the valley at Thingvellir, in Iceland, where the mid-Atlantic Ridge crosses the island, and have seen the lasers that measure the drift rate as the North American Plate drifts west and the Eurasian Plate drifts east. It is an eerie feeling to be there, knowing that.)

    That example suggests ID itself ought not squelch questions and speculations about mechanisms and designing agents. No matter how many entries there are in the CCF, absent testable hypotheses about how they came to be IC, it will be merely a marginally interesting list of biological oddities and a set of targets for enterprising graduate students in molecular biology.

    RBH


    I agree that it is ID that is squelching hypotheses, namely the details in origins scenarios that make them testable (strengthenable or weakenable, not always strict true/false).

    There is nothing wrong with going out on a limb and proposing hypotheses with specifity that goes beyond the data; this is how science proceeds into the unknown. This is why OOL researchers propose specific hypotheses, test them, and then revise -- e.g. RNAworld has become pretty well supported as a stage preceeding the origin of modern life, but difficulties in prebiotic syntheses of RNA are provoking studies of RNA precursors, e.g NA or PNA "worlds".

    The way science does *not* proceed is by maximizing vagueness, e.g. "a designer did something somewhere sometime for unhypothesized reasons by unhypothesized means". With ID, not even the laws of physics are considered legitimate constraints on the hypothesized IDer(s). I would argue that every successful (e.g. archaeology/forensics) or viable (e.g. SETI) "ID-detecting" discipline has hypothesized far more details regarding the IDer(s) than any hypothesis put forward by Mike Gene or anyone else in the ID movement.

    The problem with ultravague hypotheses is that they are explanatorily unconstrained; the problem with an unconstrained hypothesis is that there is no objective way to strengthen it or weaken it by consideration of further data.

    E.g., with Mike Gene's front-loading via mutational bias idea (leaving aside questions of what the actual biases are, which Art and others will have to work out), it seems to me that front-loading via evolution is approximately the most difficult and clumsy possible way to design something that I can think of. It would be like trying to type with your elbows even though you had fingers. Trying to get to, say, multicellularity through a nonspecific mutational bias would be rather like trying to convert from the Articles of Confederation to the Constitution via a bias in the replacement frequencies of various letters.

    Such a conversion could be accomplished either by intelligent or algorithmic selection of specific letters (in the case of biology we should convert this analogy to natural selection's *documented* ability to sweep specific beneficial nucleotide substitutions to fixation in the population, to avoid the usual Dawkins-METHINKS debates) -- but if these capabilities are in play, what's the point of the mutational bias? The mutations will happen slightly slower without the bias (well, assuming that the necessary mutations are those included in the bias, which seems completely unsubstantiated to me), but they will happen sooner or later and then can get selected. (In the case of an IDer, they would presumably not even bother with waiting for the mutations and just design straight-up whatever they wanted to design).

    Do these considerations have any weight in weakening Mike Gene's hypothesis? Only if you hypothesize some things about the designer, which Mike Gene does not, because his hypothesis is basically "someone frontloaded something for no specified reason" and thus considerations of efficiency, effectiveness, etc. (even though these are often invoked by Mike Gene and others in support of ID in other situations) will just be brushed aside as "we don't know anything about the IDer".

    IMO, this "unconstrainedness" of ID-movement "hypotheses" is their central weakness. This is a problem that supernatural hypotheses have, but is common to "superpowerful but unspecified aliens" "completely unspecified designer(s)", etc., as well. ("Unspecified natural processes" falls in the same boat, BTW) None of them predict or explain anything without further details. Full exhaustive detail is not necessary, but a least enough detail to make us expect some pattern in the data that we wouldn't otherwise expect, and which could be weakened by other patterns, is what it takes to get started.

    Vagueness will insulate an idea from refutation but will also doom it to the land of non-explanation.

    End of Saturday Night Sermon,
    nic


    [edit: cross-posted to II evo board:

    Vagueness and Explanatory Constraints
    http://www.iidb.org/vbb/showthread.php?s=&postid=791441#post791441

    ]

    * Flogging the flagellum to death (1 replies)
    Bebbo2003-02-18 07:45:36
    Dembski has posted the same article to ARN and ISCID:

    http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000620

    http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000300

    This links to his response to a piece by Kenneth Miller. All the same stuff we've seen before: Dembski looking for a God of the gaps in the flagellum.

    --
    Dene
    * CSICOP ID Panel (0 replies)
    Wesley R. Elsberry2002-05-31 21:33:37
    I'll be on a panel to discuss "intelligent design" at CSICOP's Fourth World Skeptics Conference, June 21, 2002, in Burbank, California.

    The panel will be moderated by Massimo Pigliucci.  Other panelists are Kenneth Miller of Brown University, William Dembski of the Discovery Institute's Center for Renewal of Science and Culture, and Paul Nelson, also of the DI CRSC.

    My abstract for my set 15-minute presentation was printed in the conference program, so it's public knowledge now.

    Quote
    Title of talk: "Beyond the 'wedge': Intelligent design, science, and culture

    Abstract: The "intelligent design" movement is primarily coordinated by the Discovery Institute's Center for Renewal of Science and Culture (DI CRSC). While the highest-profile activity of the DI CRSC so far has been its anti-evolutionary activism, its long-term goals are far more ambitious. As promulgated in the "wedge" document, early versions of the DI CRSC web site, and seen in the actions of the Fellows of the CRSC, no less than the re-definition of science itself is intended. Despite statements that ID is primarily a scientific research program, the fact is that  most of the effort of the CRSC Fellows is directed into political action. While scientific justification was one of the primary goals outlined in the "wedge" document, this area remains little-developed and apparently has been abandoned.  The current and projected activities of the DI CRSC indicate that the next 25 years will be filled with more confrontation with mainstream science.


    Links:

    CSICOP

    CSICOP Fourth World Skeptics Conference

    The DI CRSC "Wedge" document

    I would appreciate comments on things to bring up during the panel session.
    * FAITH & values (0 replies)
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    * KANSAS professor apologizes for critique (0 replies)
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    * UNIVERSITY cancels creationism "mythology' class (0 replies)
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    * Defining "Anti-evolution" (3 replies)
    Michael2002-06-01 22:24:40
    Sometime what a first might seem a simple question in the end can start lengthy philosophical debates and turn out not to be so simple after all.

    Consider Michael Behe.  His views are often classified as a variety of evolution denial.  

    There can be no doubt that he rejects the modern understanding of the process of evolution.  I believe that a convincing case has been made that he has done so due to religious motivations.  Many biologists have also taken him to task for a lack of understanding of evolutionary biology as well.  If the above is to be considered correct than Behe has a lot in common with the YEC Henry Morris whose views are clearly motivated by religious beliefs.

    But Behe differs from Morris in an important way.  Behe accepts that he shares a common ancestor with a chimp.  Thus he can be said to accept some form of evolution beyond the "microevolution" only proposed by most special creationists.  So can he be said to "accept evolution"?  Should the term "evolutionist" be restricted to those who accept most mainstream scientific ideas about evolution?

    Behe clearly thinks that God outright created "irreducibly complex" structures and thus arguably can be classified as a type of creationist.  (And "creationist" here is not merely being used for those who believe in some sort of creator like Theodosius Dobzhansky.)

    People in the context of the evolution/creation debate have not been using terms like "evolutionist" or "creationist" in the same way.  This can often result in misunderstandings or talking past each other.  It would be a good thing if some some sort of understanding of where to draw the lines in the sand.

    So who is an evolutionist?
    Who is a creationist?
    Who is an anti-evolutionist?

    One might note that this sort of arguments can considered analogous to the splitter-lumper debates in systematics.  Sometimes sensu lato or sensu stricto are added to a name of a taxon to make it clear if that taxon is being defined as a splitter would define it or as a lumper would define it.  So maybe if agreement is not readed we can say that Behe is an evolutionist s.l. but not an evolutionist s.s.  That would be a fairly ugly "solution."
    * INTELLIGENT design is a mixed-up creation Intelli (0 replies)
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    * Dembski on publishing houses (1 replies)
    Tom Morris2004-09-02 03:22:40
    Hi all,

    I found a quote recently from Dembski talking about how he published one of his books through Cambridge University Press but then changed publisher, presumably so he could avoid the problem of anyone telling him that his theories are a load of bunk.

    Anyone know where it is?

    Thanks.
    * ABRAMS at the eye of the evolution storm (0 replies)
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    * Intelligent Designer / Stupid people (4 replies)
    KingsFisher2005-10-01 12:05:29
    I'm not going to fool myself into thinking that I have more brains or a better education than most people within these forums, but I've noticed that everyone seems to be missing a rather simple fact regarding the Bible. The Old Testament was written literally thousands upon thousands of years ago. A time when people had little scientific knowledge if any. If evolution was part of God's plan, explaining it to the people of that time (Thousands and thousands of years ago) would have been pointless because it was far beyond thier ability to understand. Did the people of those times have the ability to comprehend the enormity of space or even numbers that reached into the billions? The answer is no. The Bible wasn't written to combat science, it was written to educate the people of this earth about their God. Attacking a paragraph in ancient text about creation with modern science is a rediculas waste of time. Whether evolution is proven or not won't make the Bible any less credible.
    * Meyer 2004 (3 replies)
    Wesley R. Elsberry2004-08-26 16:17:46
    From http://www.pandasthumb.org/pt-archives/000430.html :

    Quote


    Review of Meyer, Stephen C. 2004. The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington 117(2):213-239.

    by Alan Gishlick, Nick Matzke, and Wesley R. Elsberry

    [The views and statements expressed here are our own and not necessarily those of NCSE or its supporters.]

    "Intelligent design" (ID) advocate Stephen C. Meyer has produced a "review article" that folds the various lines of "intelligent design" antievolutionary argumentation into one lump.  The article is published in the journal Proceedings of the Biological Society of Washington.  We congratulate ID on finally getting an article in a peer-reviewed biology journal, a mere fifteen years after the publication of the 1989 ID textbook Of Pandas and People, a textbook aimed at inserting ID into public schools.  It is gratifying to see the ID movement finally attempt to make their case to the only scientifically relevant group, professional biologists.  This is therefore the beginning (not the end) of the review process for ID.  Perhaps one day the scientific community will be convinced that ID is worthwhile.  Only through this route -- convincing the scientific community, a route already taken by plate tectonics, endosymbiosis, and other revolutionary scientific ideas -- can ID earn a legitimate place in textbooks.

    Unfortunately, the ID movement will likely ignore the above considerations about how scientific review actually works, and instead trumpet the paper from coast to coast as proving the scientific legitimacy of ID.  Therefore, we would like to do our part in the review process by providing a preliminary evaluation of the claims made in Meyer's paper.  Given the scientific stakes, we may assume that Meyer, Program Director of the Discovery Institute.s Center for Science and Culture, the major organization promoting ID, has put forward the best case that ID has to offer.   Discouragingly, it appears that ID's best case is not very good.  We cannot review every problem with Meyer's article in this initial post, but we would like to highlight some of the most serious mistakes.  These include errors in facts and reasoning. Even more seriously, Meyer's paper omits discussion or even citation of vast amounts of directly relevant work available in the scientific literature.

    [...]

    * Evolution of Antibiotics (0 replies)
    JxD2003-01-11 08:42:29
    Quote
    Mol Biol Evol 1990 Sep;7(5):399-406
     
    Evolution of isopenicillin N synthase genes may have involved horizontal gene transfer.

    Landan G, Cohen G, Aharonowitz Y, Shuali Y, Graur D, Shiffman D.

    Interdisciplinary Program for Fostering Excellence, Tel Aviv University, Ramat Aviv, Israel.

    The isopenicillin N synthase genes from three fungal species, three Gram-positive species, and one Gram-negative bacterial species share an unusually high sequence similarity. A phylogenetic analysis was carried out to determine which type of evolutionary scenario best accounts for this similarity. The most plausible scenario is one in which a horizontal gene-transfer event, from the prokaryotes to the eukaryotes, occurred at a time close to the divergence between the Gram-positive and the Gram-negative bacteria.

    Quote
    Proc R Soc Lond B Biol Sci 1990 Sep 22;241(1302):164-9

    Sequences of isopenicillin N synthetase genes suggest horizontal gene transfer from prokaryotes to eukaryotes.

    Penalva MA, Moya A, Dopazo J, Ramon D.

    Centro de Investigaciones Biologicas del C.S.I.C., Madrid, Spain.

    Evolutionary distances between bacterial and fungal isopenicillin N synthetase (IPNS) genes have been compared to distances between the corresponding 5S rRNA genes. The presence of sequences homologous to the IPNS gene has been examined in DNAs from representative prokaryotic organisms and Ascomycotina. The results of both analyses strongly support two different events of horizontal transfer of the IPNS gene from bacteria to filamentous fungi. This is the first example of such a type of transfer from prokaryotes to eukaryotes.

    Quote
    J Mol Evol 1996 May;42(5):537-42
     
    Phylogenetic analysis of the isopenicillin-N-synthetase horizontal gene transfer.

    Buades C, Moya A.

    Departamento de Genetica, Facultad de Biologia, Universidad de Valencia, Spain.

    A phylogenetic study of the isopenicillin-N-synthetase (IPNS) gene sequence from prokaryotic and lower eukaryotic producers of beta-lactam antibiotics by means of a maximum-likelihood approach has been carried out. After performing an extensive search, rather than invoking a global molecular clock, the results obtained are best explained by a model with three rates of evolution. Grouped in decreasing order, these correspond to A. nidulans and then to the rest of the eukaryotes and prokaryotes, respectively. The estimated branching date between prokaryotic and fungal IPNS sequences (852 +/- 106 MY) strongly supports the hypothesis that the IPNS gene was horizontally transferred from bacterial beta-lactam producers to filamentous fungi.

    For more bibliography on IPNS, see: http://metallo.scripps.edu/PROMISE/IPNS.html among others.
    * KU pulls intelligent design course (0 replies)
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    * Premodern birthing mortality rates (4 replies)
    passionlessDrone2005-05-05 11:32:08
    Hello friends.  Despite how well our bodies work, the notion that they were designed by an omnipotent and benevolent entity has always struck me as ridiculous.  

    I wonder if anyone has good data on what percentage of females died during childbirth before the advent of modern sanitation.  Even today there are places where that value is grotesquely high.  

    In a common sense approach, this seems like the most obvious evidence that the human body was not designed by an entity generally thought of as God (i.e., omnipotent and benevolent).  What all powerful, loving entity would create humans that frequently died in the process of giving birth?  

    Take care.
    pd
    * ARN's moderation policies (13 replies)
    ExYECer2002-12-10 23:46:58
    Moderator 4 (aka Jack F) has decided to ban me for two weeks for posting the following message on an off topic board at ARN

    Quote

    I'll lose interest in ARN soon, but have followed some posts that I was interested in before I decided to quit. But I happened to see this post by Mike B.

    I was threatened with removal after two postings, one which asked why YXCs post was spam and one that simple said I agreed with Douglas, XYCs post should stay because it brought up interesting points for discussion on Dembski's overly repetitive arguments. I then suggested a new direction for the thread to focus of Dembski's limiting the definintion of Direct evolution and IC.

    Tell Mike B, I formally left ARN (had my membership removed) because I could ignore a lot from Jazz, but not this hair trigger threat to ban me simply because I was in agreement with another poster. In none of my posts did I call call Jazz out as a horrible moderator, then everything I post there after gets deleted.

    Mike B, know what you are talking about before you criticize another poster for being disgruntled. I did not highjack a single thread (ala DNAunion and his obsession with Julie/Wolf), nor did I make joking threats (ala CML). Or post little sidetracking quips (ala Jazz himself on
    several posts).

    RB


    Jack responded that

    Quote

    I just deleted a post from XYC. He posts a note from RB slamming the site.


    Funny how Moderator 4 seems to consider RB's response to be 'slamming the site'.
    * The Media Gets It Right on ID (0 replies)
    Moderator2005-02-02 00:58:34
    The "Intelligent Design" of a Monkey Trial: A Case of Hidden Agendas

    Quote

    To understand the significance of these "monkey trials," one must look beyond the legal decisions to the hidden agendas.  This long view is crucial, especially now with school districts in 40 states under attack by creationists and with the reelection of an evangelical president who wears his religion on his political sleeve and who believes that "God did create the world."


    Quote

    Much of the Discovery Institute¹s funds are spent maintaining a stable of authors who write creationist books for the popular press. William Dembski, whose sobriquet is "God's mathematician," is arguably the Wedge¹s leading intellectual. His book, the Design Inference, is the screed most often cited, but least read or understood, by letter-to-the-editor writers attacking evolution. But even Dembski's agenda is recoverable from the labyrinth of his text. He writes, "Indeed, intelligent design is just the Logos theology of John's Gospel restated in the idiom of information theory."
    * Do the Calculation! (6 replies)
    Wesley R. Elsberry2002-05-06 02:25:59
    I would like to announce the availability of the "Finite Improbability Calculator".

    The Finite Improbability Calculator is a tool for exploring the very small probabilities encountered in applying some of the formulas in William Dembski's "No Free Lunch" to biological phenomena. Some basic functions are implemented, such as factorial, change of base, permutation, and combination. Further, several of the formulas found in section 5.10 of "No Free Lunch" are implemented.

    I did this as an aid to my own analysis of Dembski's work, and realized that others could benefit from it as well. The routines are specifically made so that they handle very large and very small numbers without causing floating-point overflow or underflow errors.

    Comments are welcome.
    * INTELLIGENT design front quiet so far (0 replies)
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    * THE Evolution of a Darwin Show (0 replies)
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    * Church of the Flying Spaghetti Monster (1 replies)
    Chuck2006-01-23 10:06:09
    This has probably come up at this site before but I thought I'd throw it out there for anyone who hasn't discovered it yet.  The Church of the Flying Spaghetti Monster is a wonderful, humorous stab at the Intelligent Design Movement.  It's been around for awhile, and from the looks of the website, it has attracted a healthy following.  Just thought I'd share...

    http://www.venganza.org
    * CONTROVERSIAL course will not be taught at U. Kan (0 replies)
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    * Uncommon Dissent: Intellectuals Who Find Darwinism (11 replies)
    niiicholas2003-07-22 20:51:13
    Da next book:

    Quote

    NEW AS OF 22 July 2003
    <> Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing. [22July03] Table of contents, introduction, and list of contributors to edited collection by William Dembski, due out with Intercollegiate Studies Institute early spring 2004.


    http://www.designinference.com/

    Looks like some old stuff, some new.  Chances of actual biology being included: less than Dembski's UPB.

    Link to table of contents and Dembski's intro:
    http://www.designinference.com/documen....rib.pdf
    * Fighting pop-pseudoscience with pop-science (0 replies)
    nameinuse22004-12-09 17:59:07
    Hi guys,

    I'd like your comments on something I wrote during a lengthy debate at another board.  The debate arose from the Dover decision and the population of this other board is very diverse general audience.  There are a lot of ID supporters there.  There is one guy there who seems to believe in evolution but not the big bang(!)  I should mention that this other board is well, odd.  If you are offended by profanity or ... well, lets just say this board prides itself on the offensive in all its forms.  So keep in mind the target audience I was addressing.  They have a warped sense of humour (as do I which is why I love it there).  

    I'm thinking of turning what I wrote into a proper essay or pop-science piece.  I figure if ID's wide support has been due to a couple of pop-pseudoscience books, why not fight back with pop-science?

    Anyway, here it is.
    * EF/DI & "the lust for certainty" (5 replies)
    Wesley R. Elsberry2002-12-13 10:07:02
    Paul,

    I'm not sure that John is disagreeing with Kitcher.  Kitcher is talking about postulates, things that are assumed to be true for some line of inquiry.  Rarefied design as an inference, though, is something that some people assert can be concluded from particular premises.

    The problem with a postulate of the sort that Kitcher discusses, though, is that someone like Paul Nelson will come along and claim that what is being argued is theology and not science (as your 1997 NTSE talk set forth).

    If "postulating an unobserved Creator" were as generally productive as "postulating unobserved particles" has been in physics, I don't think that we would be having this sort of discussion now.  Postulating unobserved particles has led to specific hypotheses and experiments aimed at producing empirical data which would bear on whether outcomes based on the existence of those heretofore unobserved particles are actually there.  So far in ID, though, there is no similar push to test the postulate: once the unobserved Creator is postulated, no evidence concerning whether that Creator exists is sought after or solicited.

    But I wonder if this is going far afield from the topic of the first post.

    Have readers of Dembski really been "thrown" by the "reliability issue"?  Is it the critics who have the "lust for certainty"?  I don't think so.

    Let's revisit some history.  Back in 1998, Dembski published his book, "The Design Inference".  Before TDI came out, though, Dembski had a short piece published in "First Things" which discussed what TDI would be about.  Here's a snippet of that article:

    Quote
    Biologists worry about attributing something to design (here identified with creation) only to have it overturned later; this widespread and legitimate concern has prevented them from using intelligent design as a valid scientific explanation.

    Though perhaps justified in the past, this worry is no longer tenable. There now exists a rigorous criterion—complexity-specification—for distinguishing intelligently caused objects from unintelligently caused ones.

    (Source: http://www.firstthings.com/ftissues/ft9810/dembski.html)


    This claim has not been explicitly retracted.  It is echoed in the pages of "No Free Lunch" (p.6, IIRC).  It sure looks like a claim concerning certainty to me.

    In that initial post, Dembski writes:

    Quote
    I argue that we are justified asserting specified complexity (and therefore design) once we have eliminated all known material mechanisms. It means that some unknown mechanism might eventually pop up and overturn a given design inference.


    This seems to me to be inconsistent with, if not contradictory to, the earlier claim.  Perhaps, though, you have a different perspective that can accommodate both the "untenable worry" claim and the later admission that Dembski's "design inferences" can be overturned with additional knowledge.

    Until such time as we get a statement from Dembski that the "untenable worry" claim is retracted, though, I think the critics are completely correct to hammer on this point.  Else we have the apparently inconsistent stance that the critics responding to the "untenable worry" claim are mistaken because application of the EF/DI is fallible, coupled with the continued use of the "untenable worry" claim whose basis is that application of the EF/DI is infallible for distinguishing intelligently caused objects.

    Quote
    This is known as having your cake and eating it. Polite society frowns on such obvious bad taste.


    Wesley
    * About the Designer (0 replies)
    m1isaak2002-12-13 22:09:48
    A premise of intelligent design is that we know nothing about the Designer.  Therefore we cannot predict qualities of design (such as optimization) based upon supposed qualities of the desiger (such as omniscience).  This is true; we cannot infer conclusions based on the unknown.  However, the IDists assert that the design of life is now established.  And we know a lot about life.  If we provisionally accept design, we can base inferences on life and begin to say things about the Designer.

    IDists seem reluctant to take this step.  Yet it is a logical -- I would say inevitable -- extension of their research.  And it is perfectly in line with their stated goal (e.g., "to see purpose in nature", from the subtitle on ISCID Forums home page).  If IDists will not undertake this line of investigation, it is up to us to do so.

    So, what are some aspects of life that could indicate qualities of the Designer?  Here are a few that come to mind:

    - Pain and suffering.  The "problem of evil" has been around for millennia.  Intelligent Design theory requires we address it.

    - Suboptimal processes.  Some designs appear jury-rigged or otherwise inefficient.

    - Profligate variety.  There is much more variety in the world than is apparently necessary.

    Since the question of suffering is the most interesting of these, my focus will be on it.

    What does suffering tell us about the Designer?  To begin, we can say that it must either be deliberate or incidental.  If incidental, it may arise either because the Designer doesn't care or can't do anything about it.  The case where an aspect of life is incidental is perhaps less interesting, since it says basically that the aspect isn't designed after all.  That could explain suboptimal processes, but for the other aspects, it seems to contradict the premise that life is designed.  The suffering and the variety that we see in life are fundamental.  They are part of the complexity that IDists claim as evidence for design in the first place.  In fact, many of the design examples that IDists use, from bomardier beetles to flagella to the immune system, either contribute to the suffering or are defenses that would be meaningless without it.

    There are still apologists who claim that suffering is not part of design.  A common claim is that suffering is the result (via the Fall of Adam) of having free will.  This claim, however, is vacuous rationalization.  Adam did not choose to redesign cobras to put poison into their fangs.  Free will does not make infants die of malaria.  No, suffering is an integral part of life, and is as much designed as life is.

    So Design Theory implies that the Designer deliberately planned for people to suffer.  What sort of Designer does that imply?

    One possibility is that the Designer is simply evil.  This hypothesis, however, is contradicted by the observation that there is a great deal of pleasure to be found in the world, too.  Thus Design Theory must reject the hypothesis of a purely evil God.  For the same reasons, however, Design Theory must reject the hypothesis of a purely good God.

    Another possibility is that there is more than one designer, and that different designers are responsible for different lifeforms and/or different aspects of life.  Multiple Designers Theory was introduced by RBH on ISCID on 28 September 2002.  (http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000172)  It explains such things as predador/prey and host/parasite arms races, intermittent interventions, and different solutions to a common problem.  It also has a venerable tradition in religions.  The designers may be dualistic, as in Zoroastrianism, or polytheistic, as in Celtic and Scandinavian tradition.

    A somewhat related hypothesis is that the Designer's character is inconstant.  This hypothesis is expressed in the article, "God Diagnosed With Bipolar Disorder" in The Onion (http://www.theonion.com/onion3716/god_diagnosed_bipolar.html).  This article is satire, but Design Theory forces us to take the idea seriously.

    It might still be argued that suffering is an unavoidable consequence of a greater good.  To some extent, this is certainly the case.  Pain, for example, often gives warning that allows us to avoid serious injury.  Still, much suffering would seem to be avoidable. Smallpox and polio have caused a great deal of suffering in the past, and yet the planet has been virtually free of them for the last few decades.  Could the designer simply not have created them in the first place?  Other more complex banes of humanity, including salmonella, onchocerciasis, and malaria, appear just as unnecessary.

    It is possible that design is as inscrutible as the designer.  As expressed by Pope:

    Quote
    All nature is but art, unknown to thee;
    All chance, direction, which thou canst not see;
    All discord, harmony not understood;
    All partial evil, universal good;
    And spite of pride, in erring reason’s spite,
    One truth is clear, Whatever is, is right.
    [Alexander Pope, Essay on Man, i, 289-294]


    This philosophy, that suffering is good for reasons we can't understand, contradicts the premise that purpose can be found in nature.  It claims that not only is the designer unknown, but so is the design.  If we accept Design Theory, we must reject this position and assume that design has implications.

    Pope's view of an inscrutible purpose to design is the only way I can see to allow anything close to a traditional designer into Design Theory.  However, in the process, it makes Design Theory useless.  It is worth noting that Pope's view is compatible with evolution, but Dembski's The Design Inference contradicts its first two lines.  Design theory is more compatible with multiple designers or an unconstant designer.
    * Intelligent Design jargon explained! (2 replies)
    niiicholas2002-12-20 01:10:56
    Intelligent Design jargon explained!
    By Casey Luskin
    http://www.ideacenter.org/idjargon.htm

    Lesse, by my count there were 3-4 terms discussed and none were significantly clarified...basically "trust me, ID is for real".
    * A Sober Sighting (0 replies)
    Wesley R. Elsberry2003-02-15 06:33:34
    Students build skills at conference

    Quote
    The keynote speaker of the event was Elliot Sober, a professor from the University of Wisconsin. Sober is a nationally recognized professor who is known for his work regarding the philosophy of biology. Sober gave a speech on scientific philosophy, titled, “Intelligent Design is untestable. What about Natural Selection?”  Sober was the only professor to give a presentation, with the rest of the presentations being put on by students.
    * Information. ID versus non-ID (4 replies)
    ExYECer2003-01-11 16:56:49
    I started a separate thread to keep the original thread about survival of the least appetizing on track per suggestion of Irving.
    Irving suggested that Noel was looking for a real demonstration but I believe the issue was

    Those who want Darwinism to be true must demonstrate that random incremental change and selection can increase information.

    And ev and others have shown that in principle mutation and natural selection are sufficient to increase information in the genome. Experiments in real life are more complicated but SELEX experiments are the next step to show that in 'real life' mutations and selection can be shown to increase information in the genome.

    Hi Noel,

    you state

           
    Quote

    Those who want Darwinism to be true must demonstrate that random incremental change and selection can increase information. Should they be able to do this, which is doubtful, it still does not follow that everyone would opt for their explanation.
    That is a very simple demonstration and various experiments and simulations have shown that this is indeed the case
    ev: Evolution of Biological Information

           
    Quote

    The ev model quantitatively addresses the question of how life gains information, a valid issue recently raised by creationists [32] (Truman, R. (1999), http://www.trueorigin.org/dawkinfo.htm) but only qualitatively addressed by biologists [33]. The mathematical form of uncertainty and entropy implies that neither can be negative, but a decrease in uncertainty or entropy can correspond to information gain, as measured here by Rsequenceand Rfrequency. The ev model shows explicitly how this information gain comes about from mutation and selection, without any other external influence, thereby completely answering the creationists
    Evolution of Biological Complexity

           
    Quote

    In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that because natural selection forces genomes to behave as a natural ``Maxwell Demon'', within a fixed environment genomic complexity is forced to increase.
    In fact as I have argued elsewhere, the fourth law of thermodynamics as proposed by Dembski is imho nothing more than a reformulation of the second law of thermodynamics for a closed system. When realizing that in open systems, entropy can decrease/information can increase and that in evolution it is the environment which infuses information into the genome through selection, and we realize that information increase is not that hard to realize.

    Source

    Others have comment on this
    Victor J. Stenger and Here

    found via this link

    Adrian L. Melott

    Common objections are that ev somehow smuggled in information and although noone really seems to have shown that there is any smuggling done, increase of information of course requires 'smuggling in information' just as selection 'smuggles in' information from the environment into the genome.
    I would be interested in any evidence that the information was pre-coded.
    * Schneider v. Strachan (0 replies)
    niiicholas2003-07-05 16:19:19
    Here's a post I wrote that I'm archiving:

    I was reading recent comments on the Schneider/Strachan discussion, and it suddenly occurred to me that the arguments of both authors are a bit beside the point.

    To wit, the mod posted,

    Quote

    Well, if you take notice, Strachan has taken Schneider to task, and it is far from clear whether Schneider has shown much of anything. [...] He's got a Ph.D. in the field and is an expert in both genetic algorithms and neural networks. He deserves to be taken seriously.


    And similarly Micah or someone at ISCID went to the trouble of putting Strachan's modified METHINKS-type simulation up on the web, here:

    http://www.iscid.org/vignere/vete.php
    http://www.iscid.org/vignere/vignere-text-evolution.php

    ...so clearly someone thinks that Schneider's paper draws a conclusion that is worth debating.

    Here is my question: isn't the central question "Can evolution increase 'information' in the genome?" or something similar?  

    It seems to me that, if this is the question that people are interested in, Schneider's simulation is pretty small potatos.  At most it was a modified 1984 computer program that showed that variation and selection for binding strength could produce strong binding, with the interesting side-conclusion that binding strength has an interesting information-theoretic property such that information measures Rfreq and Rseq ended up matching.  This information amounted to a few bits per binding site.  Schneider threw into his paper some incindiary anti-ID remarks and has similarly promoted the paper, so it has gained attention in ID circles.

    But really, is the proposition "evolution can increase 'information' in the genome?" really in any doubt at all?  I mean, Dembski himself (see Intelligent Design, for example), argues that chance alone can produce small amounts of specified information, and that selection can preserve these small amounts.  The only reason that this process can't build up to produce large amount of specified information, i.e. complex specified information (CSI), is basically irreducible complexity (IC).

    Perhaps people will cite Dembski's supposed "Law of Conservation of Information", but that is similarly said to apply only to CSI, not mere SI.  One could additionally argue that the information that increases in genomes is gathered from the environment (so no "conservation" is being violated) although I think that this is a fairly confused position: IMO information can't really be said to "exist" until it is encoded somewhere.

    Apart from Dembski's admission, we have reams of evidence in biology for the creation of new genes by duplication and modification of old genes, which I think would have to be intepreted as increases in information on any reasonable definition.  Behe similarly concedes such processes (e.g. hemoglobin), he just objects when it comes to IC.

    The only people would I can think of who've really asserted that evolution really can't increase information in the genome are Phil Johnson and creationists such as Spetner.

    So, what's the big deal?

    Cross-refs:
    An Evaluation of "Ev"
    http://www.iscid.org/boards/ubb-get_topic-f-6-t-000384.html

    Mod quote:
    http://www.iscid.org/boards/ubb-get_topic-f-18-t-000001-p-19.html
    * Leiter, Beckwith, & van Dyke (0 replies)
    Wesley R. Elsberry2004-03-19 15:13:05
    Brian Leiter reviews a book review:

    Harvard Law Review Embarrasses Itself

    This received some attention in the blogosphere:

    Remind me...

    The discussion prompted me to post the following:

    Greg berates Leiter for not taking account of William Dembski's contributions and a few citations. Leiter's comments, though, exclude Dembski, since Leiter was discussing scientists, and Dembski is not in that class of people.

    Dembski's ideas have been tried and found wanting. Greg is invited to peruse http://www.antievolution.org/people/wre/papers/eandsdembski.pdf for a long examination of the arguments made by Dembski.

    The citations Greg lists likewise show no glimmer of a positive scientific program for "intelligent design". At most, they do something toward criticism of current evolutionary biology. The paper which Greg says cites Behe and Dembski favorably simply includes them in lists of citations documenting that opinions differ.

    Greg could try to argue that I'm "uninformed" or "unread" on the topic of "intelligent design". Greg would be wrong, but he could try.

    "Intelligent design" is subset creationism. It's the same old hoary chestnuts long used past their sell-by dates by young-earth creationists, stripped of explicit references to God and the bible. (Leiter's remark about lawyers and PR agents was right on the mark, IMO.) Behe's "irreducible complexity" is the "what good is half a wing?" argument updated to "what good is half a flagellum?" Dembski's "specified complexity" is the "evolution is too improbable" argument with extra mathematical notation and propositional logic. Both are strictly negative arguments against the sufficiency of evolutionary theory to account for all the phenomena of life's history and diversity. Saying that someone else is wrong doesn't mean that one thereby has a theory.
    * Elliott Sober on ID and probability reasoning (5 replies)
    Tom Ames2003-01-03 12:24:40
    I just read a fascinating analysis of the structure of ID's probability argument [Sober, E. (2002), "Intelligent design and probability reasoning." Int. J. Phil. Rel. 52:65-80].

    In his paper, Sober argues that the ID movement relies upon a probabilistic analog of modus tollens. Modus tollens is a deductively valid argument of the form:
    If X then Y
    ~Y
    -------------
    (therefore) ~X

    The relevant probabilistic analog of this would be the argument: "if a theory X says that Y is improbable, and we observe Y, then we should conclude that the theory is probably false." (This is not deductively valid.) ID makes this into an argument against naturalistic evolution by arguing that some feature (the vertebrate eye, or "irreducible complexity" in general) is improbable under naturalistic laws, and that therefore those laws can be rejected as the sole mechanism for generating that feature.

    Sober describes why observing a low probability event does not necessarily provide evidence against the corresponding theory. One example he gives is taken from Richard Royall's wonderful book Statistical Evidence -- A Likelihood Paradigm. Suppose you are brought an urn, and you want to test the hypothesis that it contains 2% white balls. Is drawing a white ball evidence against this hypothesis? If you know that there exist two urns, one containing 2% white balls and the other containing 0.0001% white balls, drawing a white ball is actually evidence in favor of the hypothesis that the urn contains 2% white balls!

    This example highlights the need to discuss evidence in comparative terms. You observe an event (such as the existence of the vertebrate eye) that has a low probability under theory X. But it is crucial to know the probability that that event would occur under theory Y as well, if one is to distinguish between them.

    How probable is the vertebrate eye or the bacterial flagellum under ID? We do not know. Furthermore, there is a concerted attempt by the ID movement to avoid any committment that would allow such a probability to be calculated, even in principle.

    I highly recommend this paper to anyone who finds the probabilistic arguments of the ID movement as annoying as I do. Sober does an admirable job of undercutting the basis of Dembski and Behe's major claims.
    * The Multi-Design Inference (1 replies)
    lpetrich2003-01-19 01:45:45
    Taken from two postings in the thread "The Multi-Design Inference" over at the Internet Infidels.

    This is an inference that multiple designers had designed some entities; this is a natural extension of Dembski's "Design Inference". And it is an inference often made about human designers.

    This is an essential part of efforts to detect forged signatures; handwriting styles are individualized, and a close examination of a signature may reveal whether it was written with an imperfect imitation of someone else's style.

    Handwriting analysis has also been useful in archeology; by that means, it was shown that the various Mycenaean Linear B tablets had been written by several scribes, each of whom had written several tablets.

    Such stylistic analyses have been used in other fields; much of the debate about the authorship of various parts of the Bible has been based on stylistic analyses -- characteristic vocabulary, preoccupations, etc. More recently, the Unabomber was identified when someone recognized some familiar styling in the text of his manifesto.

    Applying that to the world of life, one concludes that if many features had been designed, then there had likely been more than one designer. Camera-like eyes are sometimes pointed to as examples of design, but those of vertebrates have one characteristic architecture and those of cephalopods have another. So could there have been a separate designer for each? Charles Darwin himself, in his creationist years, had concluded that Australia's distinctive fauna might suggest that "there had been two Creators at work."

    Likewise, predator-prey relationships suggest multiple designers, one for the predators and one for the prey, because predators are adapted for finding and catching prey, and prey are adapted for avoiding and resisting predators. Multiple food-chain levels suggest additional designers. Thus, in a grass-deer-wolf food chain, with deer eating grass and wolves eating deer, the grass, deer, and wolves had had separate designers.

    Host-parasite relationships are a close analogue of predator-prey relationships, with parasites being adapted to live off of their hosts and hosts being adapted to resist their parasites. Thus, in this example, the wolves can be afflicted with fleas, heartworms, and distemper viruses, adding yet another designer to the list.

    In an attempted rebuttal, Walter ReMine has claimed to have demonstrated that there had only been one designer, but I've yet to see his "proof".

    The multi-design inference must be an embarrassment for the Intelligent Design movement, because it goes against the theological predilections of many of its participants. However, I doubt that those like the Raelians would be terribly bothered by a multi-design inference.

    However, it must be conceded that single superpowerful designer can imitate several less-powerful designers. But the trouble is that such a hypothesis tends to lack falsifiability; for sufficiently powerful designers, it would be difficult to rule out hypotheses like creation with apparent age, like Philip Gosse's Omphalos hypothesis.

    Also, there is a parallel to the single-powerful-designer hypothesis in Biblical criticism.

    Among present-day scholars, the favorite hypothesis of the authorship of its first five books is the JEDP hypothesis, which posits four separate sets of authors, each with a characteristic vocabulary and preoccupations.

    The traditional hypothesis, however, is that all those five books had been written by Moses and only Moses, and its present-day defenders maintain that he had repeatedly switched stylistic gears as he wrote.
    * Discovery Institute responds to Project Steve, sor (2 replies)
    niiicholas2003-02-20 02:10:10
    [cross-posted to t.o. and AE]

    The release of this *can't* be accidental.  I don't think the DI has ever published a random "let's restate our same old arguments for no explicit reason" article like this.  But "Media Advisory on Evolution Controversies" is a particularly oblique term methinks.

    And any mention of the Stevolutionists is conspicuous by it's absence.

    Perhaps they've been getting a few skeptical calls from press people?

    http://www.discovery.org/viewDB....am=CRSC
    ===============
    Media Advisory on Evolution Controversies

    Discovery Institute
    Press Release
    February 19, 2003
    -----------------------------------------------------------------------
    Contact: Mark Edwards, 206-292-0401 x 107 medwards@discovery.org

    As you report on controversies over evolution and intelligent design, here are some facts you might find useful:


    1. There is a growing scientific controversy over Darwinian evolution.

    a) Today there are critics of Darwinian evolution within the scientific community, including biologists at mainstream American universities. In 2001, more than 100 scientists including scholars at such institutions as Yale, Princeton, MIT, and the Smithsonian signed a public statement announcing that they were "skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged." [A complete list of these scientists can be found in A Scientific Dissent from Darwinism.]

    b) Because of the scientific critics of Darwin's theory, it is misleading to present the modern controversy over Darwinian evolution as a simplistic battle between "science" and "religious fundamentalists." Accurate reporting on this issue should do justice to the complexities of the real situation, not resurrect stereotypes from the fictional movie Inherit the Wind.


    2. It is constitutional and legal for teachers to teach about the scientific controversies surrounding Darwinian evolution.

    a) The courts have frowned upon raising religious objections to evolution in science classrooms, but these legal restrictions are irrelevant to discussions of scientific controversies over evolution.

    b) According to law professor David DeWolf, co-author of the leading law review article about how to teach the evolution controversy legally, there is absolutely no constitutional problem with acquainting students with scientific criticisms of Darwin's theory currently being made by scientists. [See David DeWolf et. al., Teaching the Origins Controversy: Science, Or Religion, Or Speech? Utah Law Review (2000)].

    "Teaching a variety of scientific theories about the origins of humankind to schoolchildren might be validly done with the clear secular intent of enhancing the effectiveness of science instruction."
    - U.S. Supreme Court, Edwards vs. Aguillard Ruling (1987)


    3. The failure of biology curricula to discuss the weaknesses as well as the strengths of Darwin's theory is attracting increased criticism from educators, scientists, and the general public.

    a) According to biology professor Scott Minnich of the University of Idaho, Darwinian evolution has become "the exceptional area that you can't criticize" in science education, something he considers "a bad precedent." In his view, we need to "teach it more, and teach it critically."

    b) According to a 2001 Zogby Poll, an overwhelming majority of Americans (71%) believe that "biology teachers should teach Darwin's theory of evolution, but also the scientific evidence against it."

    c) Recent scientific reports have shown that some of the most common scientific proofs for Darwin's theory that are cited in high school and college textbooks are now widely known to be flawed, notably Haeckel's embryos and the Peppered Moth experiments [see linked NY Times' articles].


    4. Federal education policy as articulated by Congress now calls for an balanced approach when teaching about controversial scientific topics such as evolution.

    a) In the Conference Report to the landmark No Child Left Behind Act of 2001, Congress clearly advised states to provide for the balanced treatment of controversial scientific issues like evolution. According to Congress, "where topics are taught that may generate controversy (such as biological evolution), the curriculum should help students to understand the full range of scientific views that exist, why such topics may generate controversy, and how scientific discoveries can profoundly affect society." (This language originally came from Sen. Rick Santorum , R-PA, and is sometimes called The Santorum Amendment.)

    b) U.S. Senator Robert Byrd (Dem-WV) expressed the sentiments of many lawmakers when he declared that "it is important that students be exposed not only to the theory of evolution, but also to the context in which it is viewed by many in our society. If students cannot learn to debate different viewpoints and to explore a range of theories in the classroom, what hope have we for civil discourse beyond the schoolhouse doors?" [Congressional Record, June 13, 2001]

    5. Darwin himself would have likely agreed to a 'teach the controversy' approach.

    In The Origin of Species Darwin wrote: "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question."


    Conclusion
    Can teachers discuss the scientific controversy over Darwinian theory? Yes, in fact, good education demands it.

    About Discovery Institute

    Discovery Institute is non-profit, non-partisan policy and research organization on issues from transportation to technology to tax policy. In science education, it supports a "teach the controversy" approach to Darwinian evolution. Its Center for Science and Culture has more than 40 affiliated biologists, biochemists, physicists, philosophers and historians of science, and public policy and legal experts, most of whom also have positions with colleges and universities.

    -------------------------------------------------------------------------------Discovery Institute is a non-profit, non-partisan, public policy think tank headquartered in Seattle dealing with national and international affairs. The Institute is dedicated to exploring and promoting public policies that advance representative democracy, free enterprise and individual liberty. For more information visit Discovery's website at http://www.discovery.org.

    Please report any errors to webmaster@discovery.org
    ===============
    * Dembski, natural selection, & math (0 replies)
    Wesley R. Elsberry2002-09-18 03:38:03
    William Dembski has offered a very interesting piece concerning what he believes needs to be demonstrated to show that natural selection is a sufficient causal explanation for some system.  See it on the ISCID Brainstorms board.

    The basic gist is relatively straightforward, though the notation looks a bit overblown.

    Dembski starts with an analogy to demonstrating common ancestry of two lineages X and Y, whose initial states X_0 and Y_0 are actually the single common ancestor of all derived X_n and Y_n.   Dembski asserts:

    Quote
    In the best circumstance, each such X(i) and Y(j) must be explicitly exhibited and any arrows of causation connecting two organisms must produce small incremental changes that are highly probable on the basis of the Darwinian selection mechanism. The more intermediates that are missing from this picture and the more handwaving and just-so story-telling to describe the arrows of causation, the more problematic the evolutionary explanation.


    It should be noted that common ancestry is not dependent upon the mechanism of natural selection being operative at every step, or indeed at any step.  Dembski's scenario completely ignores the evidence of molecular biology in applying sequence comparisons, which is largely based upon the evidence of the X_n and Y_n extant organisms, rather than X_0, Y_0, or any intermediates, since the molecular data from long extinct organisms is generally not available for anlaysis.  Nor does natural selection eschew incorporation of "large" changes, should such change have an adaptive advantage for the bearer.  It is well-developed in the evolutionary literature that "small" changes are more likely to have an adaptive advantage than "large" changes, and thus we should expect more "small" changes to be observed in lineages undergoing selection.  But that doesn't limit natural selection to *only* using "small" changes, as Dembski seems to imply above.  These departures Dembski takes from the biological reality of inferring common ancestry of lineages suggest that Dembski's approach is problematic.

    As G.G. Simpson pointed out, intermediates are always missing, except where they are found.  Let me point out  what should count as a non-problematic example of common ancestry of two lineages, Globigerinoides trilobus and Orbulina universa.  A very good plate appears in the paper by Pearson et alia.

    Quote
    Pearson, P.N.; Shackleton, N.J.; and Hall, M.A., 1997.  Stable isotopic evidence for the sympatric divergence of _Globigerinoides_trilobus_ and _Orbulina_universa_ (planktonic foraminifera).  Journal of the Geological Society, London, v.154, p.295-302.


    Figures from this paper are reproduced on the web in this page by Don Lindsay.

    Pearson et alia adduce other evidence than what Dembski has offered in his argument.  They examine stable isotopic evidence to show that the divergence of G. trilobus into O. universa occurred sympatrically.  This also has a bearing on the sufficiency of the evolutionary account of common ancestry of these two species.  Notably, though, Pearson et alia do not invoke natural selection as the sole mechanism of change in this divergence.  The fact of the divergence is an issue separate from the underlying mechanism.

    Dembski's underlying analogy for the remainder of his argument concerning the sufficiency of evolutionary explanations for IC systems excludes relevant classes of evidence, unnecessarily invokes a particular process as needed to be demonstrated, and ignores actual biological practice in showing common ancestry of lineages.  This, to say the least, is an inauspicious beginning for the remainder of his argument.
    * Evolution's Sexy Death (0 replies)
    johndcal2004-06-09 01:50:14
    Will the theory of evolution die a sexy death?

    Or are sex and death proof of evolution?

    See
    "Death, Sex, and Evolution"
    at
    Faith & Reason Ministries
    http://www.faithreason.org/
    * ADDING ID could hurt college odds (0 replies)
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    * EVOLUTION v. intelligent design (0 replies)
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    * Optimality arguments & theological themata (1 replies)
    Wesley R. Elsberry2002-05-17 19:19:04
    In this ARN forum topic, the issue of arguing concerning optimality was raised.  The person bringing this up cited Dembski, but several of his ideas seem to stem from Paul Nelson's presentation back at the 1997 NTSE conference.

    Basically, ID advocates object to optimality arguments by biologists when these venture into the realm of contrasting natural mechanisms with supposed supernatural mechanisms.  Paul Nelson made the observation that such argumentation presupposes certain "theological themata".  Nelson also asserted that in order to argue that some state observed in nature was sub-optimal, one would have to reliably know what the absolute optimal state was, and calculate an optimality deficit figure.

    I responded to Nelson's assertion that knowledge of absolute optimality was a necessary part of a sub-optimality argument some time ago on the talk.origins newsgroup.  The response can be seen here, but the essential message is that a valid sub-optimality argument can be warranted on a strictly relative basis, with no need for absolute optimality to be known.

    I also responded to William Dembski's essay on optimality argumentation, pointing out several problems in his argumentation.  Dembski's essay is here, and my response is here.

    * WHEN it comes to creationism and evolution, I bel (0 replies)
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    * Creationist Replies (1 replies)
    jasonparker2004-09-24 09:39:31
    A creationist book…i saw it in another forum, creationists there were referancing from this source, i started to read it and the transitional fossil section is what i looked for. http://www.harunyahya.com/refuted1.php
    * INTELLIGENCE, design and Shakespeare (0 replies)
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    * DARWIN on Trial (0 replies)
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    * Banned IDists at ARN (11 replies)
    Bebbo2002-12-21 09:50:18
    Quote (dayton @ Dec. 21 2002,08:54)
    So what happened to get mturner, Genie, and Chris banned at ARN?  Did some thread that I missed go down in flames?  Does anyone know?

    I've also been wondering about Chris and Genie, but I didn't know mturner had also been banned. It looks like they've got rid of Mod 4 (aka jazzraptor). Curiouser and curiouser.

    --
    Dene
    * Creation from absolute ignorance (0 replies)
    maurice.mccarthy2003-07-24 16:18:58
    Hi to all,

    I'm a new member and an amateur philosopher.

    I think therefore thinking is. Minimally, I know that I brought it forth and it exists in that sense. I experience it's existence. To know that anything is then it must be experienced in some sense. Whether it is real or not may be another matter. I can doubt that I exist but can it be doubted that thinking exists?

    If thinking does not exist then it cannot produce knowledge of nor have any true relation to reality and, since all hypothesis is produced by thinking, then all science is dead in the water - at best it could describe but not predict. Successful prediction guarantees the genuine hold by science upon reality itself.

    Science is the application of thinking to observation. Then if thinking exists then, ultimately, knowledge and reality must coincide. Granted this is already highly contentious - we are exactly at De Anima III.5 (430a10-26), the most heavily disputed 16 lines in all Western philosophy:

    "But since in all nature one thing is the material for each kind (this is what is in potency all the particular things of that kind), but it is something else that is the causal and productive thing by which all of them are formed, as is the case with an art in relation to its material, it is necessary in the soul to that these distinct things be present; the one sort is intellect by becoming all things, the other sort by forming all things, in the way an active condition such as light does, for in a certain way light too makes the colors that are in potency be at work as colors.  This sort of intellect is separate, as well as  being without attributes and unmixed, since it is by its thinghood a being-at-work, for what acts is  always distinguished in stature above what is acted upon, as a governing source is above the material it works on. Knowledge, in its being-at-work, is the same as the thing it knows, and while knowledge in potency comes first in any one knower, in the whole of things it does not take precedence even in time. This does not mean that at one time it thinks but at another time it does not think, but separated it is just exactly what it is and this alone is deathless and everlasting (though we  have no memory, because this sort of intellect is not acted upon, while the sort that is acted upon is destructible), and without this nothing thinks."   -   On the Soul, Joe Sachs, Green Lion Press, 2001, p142-3.

    Greek - Scholastic vocabulary - Sachs

    hyle (timber) - matter - material
    dynamis - potential - potency
    energeia - actual - being-at-work
    ousia - substance - thinghood

    (This last is "a way of being that belongs to anything which has attributes but but is not an attribute of anything, which is also separate and a this (Metaphysics 1028b 38-39, 1029a 27-28)." Sachs p201.)

    The dynamis of knowledge is observation, the energeia is thinking. Traditional dispute over the passage is whether the activity is something merely human or extra-human. If thinking exists whether or not 'I' do then the answer is both.


    Assume for a moment that thinking is the permanent, deathless and everlasting being and therefore this generates all reality, simultaneously with the possibility for finite knowers to cognise that reality. How could the creation of the world possibly proceed?

    There is no dynamis, nothing, no material to be designed. It has to be creation from absolute ignorance. Thinking on its own is ignorant. The only thinghood is that of thinking itself.

    If thinking puts forth its own being into a many, who have the possibility to be knowers because there are others to be known. This many form a community around the hub of thinking. Now this next point is the most speculative that I'm putting forth here. Let a community be a relation between mutually dependent existents, i.e. one die, the community dies - the very existence of each is dependent upon the existence of the others (you'll see why soon).

    Now break the communal relation. Either the existents become separately independent or they become mutally exclusive but remain dependent (I can think of no other possiblities). The idea of separation between independent existents is better known as space and mutually exclusive dependency is necessarily a sequence or the idea of time.

    This is sure to sound too far-fetched but you may well have read last december's Scientific American with the cover story on Fotini Markopoulou. She generates space and time by placing human beings upon the nodes of a network. A network is the mathematical abstraction of community.

    Best wishes
    Maurice
    * The Blind Leading the Blind (17 replies)
    niiicholas2003-04-04 23:50:11
    As Commentary has once again indulged Berlinski's meanderings around evolutionary theory (they never appear to run out of purple ink for his prose), I am starting a thread to discuss him, accumulate links, etc., perhaps eventually have a FAQ.

    Eye-evolution specific, or general picking of nits, as there are many to pick with Berlinski and he sure loves doing it to the Darwinists...


    First, background links on Berlinski and his writings:

  • In the ID-files section of AE.
  • The Discovery Institute bio and articles list.


    Recent articles under discussion:
  • Has Darwin Met His Match? David Berlinski, Commentary, December 1, 2002
    (Berlinski on ID and evolution; full-text must be purchased, but his section on the eye is hosted by the DI under The Vexing Eye)

  • The many letters in response to Berlinski were originally online here at Commentary's website but now are not (although you can purchase them here). However, we do have:

  • The subset of responses from DI fellows
  • Some of the critics' responses online at Talk.Reason

    And then:
  • A Scientific Scandal
    (Commentary.  April 1, 2003: On the 1994 paper by Nilsson and Pelger on eye evolution, and the usage thereof.  Online at the DI with a few typos and weirdly-formatted equations)

    Older articles:
  • Keeping an Eye on Evolution
    (Berlinski reviews Dawkins Climbing Mount Improbable and comments on eye evolution at length) (also hosted by the DI)

    And the famous:
  • The Deniable Darwin
  • Denying Darwin: David Berlinski and Critics

  • * Does Science Point to God? (11 replies)
    niiicholas2003-04-08 23:41:28
    [note, the thread title is wrong as Glenn points out, it should be "Wiker".  I am officially dumb.]

    Just came across this:

    Does Science Point to God?
    The Intelligent Design Revolution
    By Benjamin D. Wiker
    Crisis Magazine

    URLs:
    Crisis link

    DI link

    * Thread of the day: Art on Silverswords (0 replies)
    niiicholas2003-01-13 23:05:54
    Hey,

    Ever see a thread/post and said "Hey!  That thread/post is so good it should be recorded for posterity"?  I have.

    Here is an example.  Art wrote a great post, with pics, over on this ARN thread:

    http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000568

    ...on how the widely divergent Silversword alliance clearly demonstrates how Jonathan Wells is wrong about RM-NS and morphological "macroevolution".

    Art's post repeated below
    =========
    Quote
    Originally posted by Geoff:
    [qb]...
    Seriously, so yours and Charlie's examples show, in my limited understanding, that at least different, apparently viable types at least, can be produced by changes in developmental genes within the species.  So, to that extent, I guess Wells is indeed wrong.

    Perhaps the next line of defense would ask for examples of really macroevolutionary morphologic changes via this route (or even mere speciation of a less impressive type).  I personally am really more interested in changes beyond the production of intraspecific types.

    But you guys did indeed answer the assertion that Wells made and that I then posed -- and I accept your answers and those of others (like Mike B) with thanks.

    Regards,

    Geoff[/qb]
    Hi Geoff,

    About your question as to possible known correlations between mutations in developmentally-important genes and macroevolutionary events, I submit the following for your consideration.  

    First, another accursed pubmed abstract (that need not be read in detail - instead, just note that some of the genes mentioned are the same as those you have agreed represent developmentally-important ones in which non-lethal mutations are known):

     
    Quote
    Proc Natl Acad Sci U S A 2001 Aug 28;98(18):10208-13

    Accelerated regulatory gene evolution in an adaptive radiation.

    Barrier M, Robichaux RH, Purugganan MD.

    Department of Genetics, Box 7614, North Carolina State University, Raleigh, NC 27695, USA.

    The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.
    Now, consider three plants from the group (pardon my taxonomical crudeness here) mentioned in this abstract:    ,
     ,
    and
     .  

    It doesn’t take much of an eye to see stupendous morphological differences, easily dramatic enough to qualify as possibly macroevolutionary in nature.  Of course, this could only be if it could be shown that these plants share a common ancestry.

    And indeed it can be so shown.  By a standard that even the staunchest YECer accepts, it can be strongly concluded that each of these (as well as other members of the Silversword alliance) share a common ancestry.  This is because, the vast morphological differences aside, they are interfertile.  As interestingly, for a number of other reasons (biological, geographic, historical, and molecular), it can be safely concluded that these vastly-different plants diverged from a common ancestor that looked something like

    .

    Reflect, now, on the abstract.  In this study, evidence for positive selection of alleles (that must have arisen via mutation - this follows from the natural history of the different genera) of developmentally-important genes - genes involved in flower structure and evolution - was described.  While it’s not a videotape, it stands as evidence of the sort that Wells claims does not exist - namely, that changes in developmentally-important genes are important in macroevolutionary progressions.

    (Keep in mind that among the dramatic morphological differences that are seen in these examples are ones that involve floral structures.  Also, while others might argue with me, I would claim here that the range of morphologies shown in this post exceeds the range seen in placental mammals - just to give readers an idea of the scope of the differences.)

    (These images, and many others, can be found at the Silverswords link given above.)
    =========

    (Hint: Hit "reply with quote" in UBBs to get access to the formatting)
    * PBS Firing Line Debate, 1997 (0 replies)
    Wesley R. Elsberry2005-02-09 10:35:54
    REVIEW OF PBS' FIRING LINE CREATION/EVOLUTION DEBATE

    John Forester provides detailed notes on the Firing Line debate.

    Quote

     This two-hour debate was presented on the Public Broadcasting System program
    Firing Line in December, 1997. The moderator was Michael Kingsley.

     For the proposition that evolutionists should acknowledge creation were:
     William F. Buckley, Jr., conservative author
     Michael Behe, professor of biochemistry
     Philip E. Johnson, professor of law
     David Berlinskey, writer on mathematics and religion.

     Against the proposition were:
     Barry Lynn, minister and attorney, director of American's United for
     Separation of Church and State.
     Eugenie Scott, anthropologist, CSICOP fellow and director of Center for
    Science Education
     Michael Ruse, professor of philosophy
     Kenneth Miller, professor in cell biology.


    Transcript of the debate

    On an antievolution site, with some graphics added.
    * Request for Elsberry and Shallit (0 replies)
    scordova2005-06-26 22:03:36
    Dear Wesley and Jeffrey,

    William Dembski has released two papers on his website.  Since you all have written critiques of his work in the past, I would be interested in any critiques of his latest work.  


    http://www.designinference.com/documen....ces.pdf

    http://www.designinference.com/documents/2005.06.Specification.pdf

    Thanks,

    Salvador Cordova
    * AMNH 2002/04/23 (2 replies)
    Wesley R. Elsberry2002-05-06 02:31:29
    I was able to attend the event due to good timing on other travel.  

    Eugenie Scott moderated.  William Dembski and Michael Behe presented on "intelligent design" and were questioned by Robert Pennock and Kenneth Miller.

    Dembski used a lot of negative argumentation in his presentation.   One of the parts which wasn't so negative included his capsule example of specified complexity as needing a long message and an independent pattern to match it.  Dembski invoked the bacterial flagellum as an example of specified complexity in biology.  He floated the claim that the only known examples of successful co-option come from human engineering.  He touted section 5.10 of his book, "No Free Lunch", as giving the probability calculations needed to find "horrendous" probabilities of getting a flagellum.  While Dembski had a section of his talk devoted to talking about "arguing from ignorance", it did not seem to me that he actually disposed of the issue.  Dembski reiterated the claim that design is a notion belonging to statistics and complexity theory.  And to top things off, Dembski even repeated his claim that there is a room at the Smithsonian devoted to artifacts known to be designed but for which no purpose is known.

    Of course, there is no such room, which can be confirmed by contacting the Smithsonian, as Jeff Shallit has done.  There was once an exhibit (1980-81) with one display case in which some artifacts were displayed.

    I have to wonder why it is that if design is properly a statistical and complexity theoretic notion, why hasn't Dembski published his "design inference" in that literature.  It would seem to be a neutral ground in which to gain some credibility for the concept.  I don't think that the statisticians really care about the evolution/creation issue, so the whole thing about the "Darwinist conspiracy" should be a non-issue in that context.

    Rob Pennock tried to get Dembski to commit to saying what sorts of things can be taught if one accepts "intelligent design" by contrasting that to what science already has resolved.  Issues like the age of the earth and whether a global flood could be taught were brought up.  But Dembski dodged making any stand on these issues, saying that his stance is that "design" is detectable.  I think this showed that Dembski is simply evasive on these points which might lose the ID movement the support of YEC fellow-travelers.  Others have opined that this showed Dembski's fortitude in refusing to grant Pennock any points.

    Miller tried to get Dembski to state when the intelligent designer had to infuse the "specified complexity" seen in various events mentioned by Dembski and other ID advocates.  Did the origin of life 3 billion years ago indicate an intervention by the intelligent designer?  Maybe, maybe not was about the extent of Dembski's reply.  For the bacterial flagellum, the Cambrian explosion, the emergence of various animal groups, "maybe, maybe not" was the sum total of Dembski's stance.  The specified complexity might have been input at the origin of the universe, and subsequent examples would have to be examined in detail.  ID could thus be compatible with some form of Deism, or an interventionist theology, but doesn't seem to have any way within it to decide between the two.

    Michael Behe gave his usual talk on "irreducible complexity", including some discussion of mousetraps.

    Ken Miller presented a four-step logical argument based upon things that Behe has said in the past.  Behe stated flatly that the second point was something he had never said, but Miller was able to pop up the full quote and citation showing that Behe had, indeed, said just that.  Miller then proceeded to show that for each of three biological systems that Behe has used in the past (the blood clotting cascade, the bacterial flagellum, and the eukaryotic cilium) that functional systems with fewer parts do exist.  Behe was caught flat-footed by Miller's citation of work from 1969 documenting that dolphins and whales lack Hagemann factor from their blood clotting cascade.  "I feel sorry for the dolphins," said Behe.  "There's no need to feel sorry for the dolphins," said Miller, "they are doing just fine."  Take away 40 proteins from the bacterial flagella, or 80% of the system, said Miller, and you still have a fully functional Type III secretory system.  Behe objected that these were not exactly the same proteins, but Miller countered that in each case they were quite similar with high sequence similarity in conserved regions.  For the eukaryotic cilium, Miller presented the case of cilia from eel sperm, that are missing several parts found in other cilia, but which are still fully functional.

    One criticism of Miller's presentation would be that Behe kept saying that Miller was not taking into account Behe's full argument.  I think that Behe would have a point here if he could just cite the places where he had retracted the claims that Miller did critique.

    Pennock made an incredibly telling point, in that neither Behe nor Dembski would reduce "irreducible complexity" to an independent and objective criterion that would not require Behe to pass judgment on whether a system was actually IC or not.  Pennock proposed that the use of knockout experiments could establish what is or is not IC.  Behe said that this would be a good place to start, but that he would reserve judgment.

    Each of the participants was asked to give a URL.

    Kenneth Miller

    Rob Pennock

    Michael Behe

    William Dembski

    Eugenie Scott
    * PROFESSOR of New Creationism Course Criticized fo (0 replies)
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    * Replacing Dembski's "specification" (0 replies)
    Wesley R. Elsberry2003-11-12 08:04:00
    Jeff Shallit and I have a topic on replacing Dembski's notion of specification in the appendix of our long paper critiquing William Dembski's ideas . (See Information Theory, Evolutionary Computation, and Dembski's "Complex Specified Information".)

    In the article, we note a number of problems with "specification" as given by Dembski. Our replacement, specified anti-information (SAI), does not have the drawbacks that we note for specification. SAI is grounded in algorithmic information theory and can be considered an application of the universal distribution. (See the original article by Kirchherr, Li, and Vitanyi.)

    Some of our colleagues reading the drafts of our long paper back in 2002 were non-plussed: why did we attempt to "rescue" the notion of specification with a replacement? The answer is that we felt that some positive statement needed to be made rather than making an entirely negative critique. Dembski's examples resonate with readers, so we felt that a non-Dembskian approach was needed to show that the examples could be dealt with in a rigorous way, but that the further conclusions about intelligent agency that Dembski urges were unsupported.

    SAI accomplishes both these goals. SAI is easy to apply to problems that can be reduced to a bit-string representation, as Dembski has done for some of his examples. SAI also warrants a far weaker implication than intelligent agency as a cause: an event with high SAI is likely caused by a simple computational process. Elsewhere in the article, we discuss the ubiquity of natural computational processes. There is no "design inference" that can be based upon SAI, just a "simple computational process inference".

    * Help with a research paper (0 replies)
    CaptRuss2005-02-26 14:16:08
    I'm starting a research paper for my Sociology class. The research is to understand, who becomes a Creationist, why, where you’re from etc. Your help is most appreciated.

    Please give basic background:
    Age, State of residence, marital status, Education Level, Religious Affiliation, Occupation.

    What type of Creationist are you? Examples:

    Flat Earthers - believe that the earth is flat and is covered by a solid dome or firmament. Waters above the firmament were the source of Noah's flood. This belief is based on a literal reading of the Bible, such as references to the "four corners of the earth" and the "circle of the earth." Few people hold this extreme view, but some do.

    Geocentrism - accept a spherical earth but deny that the sun is the center of the solar system or that the earth moves. As with flat-earth views, the water of Noah's flood came from above a solid firmament. The basis for their belief is a literal reading of the Bible. "It is not an interpretation at all, it is what the words say." (Willis 2000) Both flat-earthers and geocentrists reflect the cosmological views of ancient Hebrews. Geocentrism is not common today, but one geocentrist (Tom Willis) was instrumental in revising the Kansas elementary school curriculum to remove references to evolution, earth history, and science methodology.

    Young Earth Creationists - claim a literal interpretation of the Bible as a basis for their beliefs. They believe that the earth is 6000 to 10,000 years old, that all life was created in six literal days, that death and decay came as a result of Adam & Eve's Fall, and that geology must be interpreted in terms of Noah's Flood. However, they accept a spherical earth and heliocentric solar system.

    Old-Earth Creationists - accept the evidence for an ancient earth but still believe that life was specially created by God, and they still base their beliefs on the Bible. There are a few different ways of accommodating their religion with science.

    Day-age creationists - interpret each day of creation as a long period of time, even thousands or millions of years. They see a parallel between the order of events presented in Genesis 1 and the order accepted by mainstream science. Day-Age Creationism was more popular than Gap Creationism in the 19th and and early 20th centuries.

    Evolutionary Creationism - differs from Theistic Evolution only in its theology, not in its science. It says that God operates not in the gaps, but that nature has no existence independent of His will. It allows interpretations consistent with both a literal Genesis and objective science, allowing, for example, that the events of creation occurred, but not in time as we know it, and that Adam was not the first biological human but the first spiritually aware one.

    Theistic Evolution - says that God creates through evolution. Theistic Evolutionists vary in beliefs about how much God intervenes in the process. It accepts most or all of modern science, but it invokes God for some things outside the realm of science, such as the creation of the human soul. This position is promoted by the Pope and taught at mainline Protestant seminaries.

    Materialistic Evolution - differs from Theistic Evolution in saying that God does not actively interfere with evolution. It is not necessarily atheistic, though; many Materialistic Evolutionists believe that God created evolution, for example. Materialistic evolution may be divided into methodological and philosophical materialism. Methodological materialism limits itself to describing the natural world with natural causes; it says nothing at all about the supernatural, neither affirming nor denying its existence or its role in life.

    Philosophical materialism - says that the supernatural does not exist. It says that not only is evolution a natural process, but so is everything else.

    Vedic Creationism
    Hinduism speaks of a very ancient earth. One book influenced by Hindu belief argues that anatomically modern humans have existed for billions of years.

    Finally, What brought you to believe what you believe?

    Your help is most appreciated.
    * Top 5 reasons ID is bunk (3 replies)
    brian.holly2005-05-27 12:06:28
    Top 5 reasons intelligent design is nonsense:

    1. Reliance on ad ignoratiam arguments. This is just the old "you can't produce an eye" by chance argument, which completely ignores the fact that evolutionary biologists have traced a clear and logical
    progression in stages from having a few light sensitive cells to having a full-blown human eye, with each stage showing an adaptive advantage. Behe tries to use the same tactic with complex proteins.This is just foolishness. Evolution hasn't explained everything yet,
    but it keeps explaining more and more.

    2. Intelligent Design fails to explain. An explanation has to explain why things are one way rather than another, but ID has no theory of what we might expect the Big Designer in the sky to do. "A magic being did it," explains nothing.

    3. Intelligent Design just pushes the problem back. The most crucial thing ID should explain is, well,  intelligence, but it leaves it wholly unexplained. Evolution has an explanation for how intelligence
    arose, starting with a few neural cells and progressing in
    advantageous stages step by step to the most complex structure known in the universe, the human brain. ID says in effect, well, let's just assume the existence of something even more complex and wondrous: a
    super-intelligence.

    4. ID is incoherent. Everything depends on the mind of the Intelligent Designer, but no coherent theory of the ID's mind is possible. By hypothesis, the Designer existed before the universe, but then where did he get his ideas for designing the universe? Ideas can have two sources: they can be derived from experience or they can
    be innate. Neither explanation could explain the where the Designer's ideas came from. And if the plan for the universe just arose spontaneously in the mind of the Designer, then that is an even greater wonder than the spontaneous big bang.

    5. ID contradicts everything we know about intelligence.
    Intelligence, by its very nature, involves storage and processing of information, and this can only be done within a physical structure. To suppose that there could have been information processing before there was any physical reality is nonsense.
    * Falsehoods on the Air (2 replies)
    Wesley R. Elsberry2004-11-21 22:30:13
    The "Powerpoint" radio show from Atlanta, Georgia this evening was about evolution and "intelligent design". The guests included Barbara Forrest, Casey Luskin, David Schwimmer, and John Calvert. It was an interesting discussion, to say the least.

    I called in to make a comment, in response to an assertion by John Calvert that "intelligent design theory" was being used in science, referencing "design detection" methods in archeology and life sciences.

    My response:

    Quote


    I'm a theist who is a critic of the claims of "intelligent design" advocates. I'd like to focus on the claim made by Dr. Calvert that ID has theoretical content, and that the design detection methods of ID are being applied in science. Briefly, design detection in ID refers to the concept of "complex specified information" expounded by William Dembski. However, Dembski has never shown the full and successful application of his concept to any phenomenon whatsoever. No one else has, either. Dembski's design detection method is both incoherent and unworkable. It is of no value to science. This is detailed in the recent book, Why Intelligent Design Fails.



    I started off the way I did because Calvert was doing his best to cast this as a "theists vs. atheists" sort of issue.

    What was instructive was the response from the ID advocates, Calvert and Luskin.

    Calvert asserted that biochemists assume design in trying to "reverse engineer" biological systems, and thus are using "design detection" without giving ID the proper credit for what they are doing. This is, of course, so much flapdoodle. What biochemists assume has nothing to do with intervening disembodied designers and everything to do with evolutionary processes constrained by the environment. It also overlooks identifying exactly what process of "design detection" proposed by ID advocates has been unfairly denied credit... which is explicable on the view that there is no such process to be credited.

    Luskin simply asserted that I was wrong, and that Dembski had applied his concept of CSI, notably to the E. coli flagellum in the pages of Dembski's book, No Free Lunch. I'm not sure what to make of this, because I'm pretty sure that Casey and I discussed Dembski's failed methodology before. In any case, Dembski failed to fully apply his "generic chance elimination argument" to the E. coli flagellum. First, Dembski failed to give a specification for the flagellum. Second, Dembski failed to eliminate any evolutionary hypothesis of origin for the E. coli flagellum. The single hypothesis Dembski considered was one of random assembly, a thoroughly non-evolutionary proposition.

    It does show the advantage to being a guest on a show, since any sort of nonsense may be spouted with little threat of exposure. [...] I do appreciate that Barbara Forrest did note that Dembski's work, including No Free Lunch, has been extensively debunked.

    For those who still think Dembski's CSI has something going for it, check out this article by myself and Jeff Shallit.

    * INTELLIGENT design targeted (0 replies)
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    * Pretty much no defence of ID by AAAS & others (1 replies)
    jhigbee2005-08-05 10:36:06
    [I meant to say: No defense against ID by AAAS & others]

    Yesterday I listened to a debate between Alan Leshner of the American Association for the Advancement of Science and baptist bible beater Richard Land.

    Here are some irritating points Mr. Leshner made:

    1. "...Whether or not there is an intelligent designer is not a scientific question. Science is restricted..."

    2. "...Darwin did not decide yes or no about an intelligent designer..."

    3. "...I don't know if there were an intelligent designer or not... It doesn't matter, but science classes should be about science regardless of whether there was an intelligent designer or not."

    There was also a point made by religionist Land about how evolution is primarily a chance process.

    Note that Nick Matzke of the National Center for Science Education was also on the show for a time. The show can be found at:
    http://www.wamu.org/programs/dr/05/08/04.php

    Here are some problems with how the debate went:

    1. It seems to me that AAAS and maybe NCSE are taking the following weak no-testicular-fortitude approach to this whole issue: Pretend that science has nothing to say about the validity or usefulness of religions which oppress people, and religions which infuse a love of non-critical-non-rational-thought into their followers. Pretend that science is "restricted" and can only comment on things which are "testable."

    What comment can science make about non-testable myths? That the scientific method of peer review is the best method humans have come up with thus far to separate fact from fiction, and that because of this the comment science >can< make on non-testible myths is this: They have a much higher likelihood of >not< being factual because they are >not< testible and >not< peer reviewed and therefore have >no< basis in scientific theory or fact.

    Science is not "restricted." It simply remains science. And the "commenting" it can make on religion can be made not only via the above method, but also via anthropologic and social science methods. Anthropology allows a comparing of cultures. And then there's the issue of memes, and about how religion is a meme (and it's also a virus - as from Dawkins).

    2. If Mr. Leshner of the AAAS and maybe the NCSE doesn't know whether there was an intelligent designer or not, I guess they haven't been reading the key works of Dr. Richard Dawkins.

    3. Mr. Leshner of the AAAS also apparently hasn't read that (I believe?) Darwin did comment on intelligent design - although I would like to request the reference since I cannot remember.

    4. However simply relying on Darwin even if he didn't specifically comment on intelligent design, ignores the fact that there ARE highly prominent scientists who HAVE commented on intelligent design and about how it's bunk and about WHY it's bunk. It's not bunk merely because it's religion. It's bunk because, as Dawkins has shown, our feable brains CAN begin to comprehend scientific methods of very long term evolution which doesn't require the meddling of a more advanced alien.

    5. Also a glaring negative point about the debate between AAAS/NCSE and religionist Land is about how both the AAAS and NCSE reps said nothing about how natural selection is the opposite of chance. Random genetic mutation more often than not leads of bad effects. Natural selection chooses among prospective genetic transmitters, and that choosing is not random, nor is it chance. I was shocked that the AAAS and NCSE reps said absolutely nothing about this key point on Ms. Rehm's show.

    Anyway I really am verry sorry to see the national orgs who're supposed to be out there defending this whole point taking such a weak buttoxed approach . The reps of these orgs apparently aren't visiting their local libraries and they aren't reading the works of key prominent scientific figures like Richard Dawkins. And the reps apprently feel that the best way to "promote science" is to pretend that science has nothing to say about religion or whether there is an intelligent designer or not.

    The whole history of science and religion shows that as science progressed it's real satisfying answers about the nature of the universe and of existence were far more satisfying than the myths iron fistedly promulgated by religion. That is a key comment which should >not< be forgotten by the AAAS and the NCSE.

    If you have additional references on these topics please provide them as I am preparing letters for others on this issue, especially about whether Darwin actually said anything about intelligent design or not. But I realize that even if he did not maybe his contemporary helpers did. And regardless the science of evolution didn't stop with Darwin.

    Sincerely,

    Jonathan Higbee

    p.s. The claim that "Religious beliefs that are outside the limits of science may be true or not; science is silent on the issue" is also a lame & bogus & weak-buttoxed statement. Such statements serve as an enabling force for the demon haunted world. Science is not silent on religious beliefs. It strongly implies and states by it's grand history that it's method of truth finding superceds that of religion. That is a fact, and if science is about facts, then it should not be afraid to state this fact about it's history, and about the related bloody myth filled waste filled history of religion. Also there are prominent scientists who >are< commenting on religion - and that fact should not be ignored. And the fact that most leading scientists are not believers (as per a survey in Nature) is also a fact - a scientific fact even.
    * JUDGE to rule on schools' policy (0 replies)
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    * IDT vs. IDM (25 replies)
    deepred2004-12-14 03:00:54
    If you ask William Dembski what the theory of ID is, youll probably get some analogy with the idea of SETI. In short, an explanation of mathmatically deciphering between signs of non-intelligence and intelligence. And in the end youll get something like "If SETI is a geniune science why cant ID be?" But what is defined by ID proponents and what they actually do are two compeltely seperate things.

    If you see what Dembski and camp try to do youll notice they write books called "Intelligent Design the Bridge Between Theology and Science". And most recently what the intelligent design camp has done is brought stickers onto our highschool biology textbooks that read "Evolution is just a theory...". On the very recent article on the ARN homepage the headline reads "Evolution: Call a theory a theory". Proponents of ID ask that you only "Teach the controversy."

    If there is one thing proponents of ID -HATE-, it is to be categorized with Creationist. This has become very hypocritical, Creationist dont beleive evolution even occured as where ID'st say evolution could have occured but not by chance alone etc...and then again resort to the analogy of SETI. If this is trully so of ID proponents, then why do they say "Call the theory of evolution a theory?" And mark our highschool books with "Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully, and critically considered." If these propnents of ID are going to define ID as a perfect comparison to SETI, and a theory that doesnt denie the fact part of evolution, why are they calling -Evolution- a theory, just like any creationist? The proponents of ID when debating intelligent design are constantly attacking the idea of neo-darwinism as the explanation of evoluiton, yet what they do in the public school district and even in there own books, is consider the fact of evolution and its theory (neo darwinism) one in the samething. But why should attacking the theory (neo darwinism) of a fact (evolution), destroy the fact (evolution)? If they think this is so then they are no better than there counter part creationist.

    Critics of ID are no better in this mis-understanding, thouhg the blame can all be put on the IDst for the confusion in the first place. For example, if ID is a science in the same sense SETI is, then ID doesnt have to put forth a theory of ID like hoped for by many on this thread. For example if SETI found an intelligent signal from outerspace it wouldnt be SETI's job to understand and form a theory of the biological origins, organisms and there evolution, of the signal, in order to validate if it was made by intelligence. Theyve simply done there part in deciphering between the signs of intelligence and chance. If ID is going to keep moving forward, its proponents have to stop pretending like it needs to not just remove neo-darwinism but also evolution. They need to stop pretending like removing neo-darwinism -is- removing evolution as a whole. And if its critics are going to be correct in critizing it they must stop asking useless questions like 'what is the theory of ID?". What is the theory of SETI? Is it testable? ID shouldnt (if it is to be as Dembski defines it) seek to replace any theories of science. And it also doesnt claim to be a theory (if it is to be as Dembski defines it) of evolution. And therefore any questions of how do we test this theory is also irrelevant. Asking questions like how is ID better than Neo darwinism, is again irrelevant. They do -not-, because they -cannot- replace each other.

    This part of the intelligent design movement is maddening. Frustrating even. Ridiculous, and creates mass confusion even among its followers, or observors.
    * Avida simulation of IC evolution (12 replies)
    niiicholas2003-05-13 00:23:09
    This thread is intended to serve as a central reference for disparate net resources and discussions on this recent paper:

    Quote

    Nature 2003 May 8;423(6936):139-44
     
    The evolutionary origin of complex features.

    Lenski RE, Ofria C, Pennock RT, Adami C.

    Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA.

    A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms-computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.


    The pdf of the paper, and supplementary information, links to Avida, etc., are all freely online here:

    http://myxo.css.msu.edu/papers/nature2003/

    Links to discussions:

    ISCID: Nature refutes ID [?]

    ARN: The evolutionary origin of complex features

    IIDB: A-life and the evolution of "complex functions"

    t.o. thread 1
    t.o. thread 2


    Other related material:

    Pennock's role in the ID debate is well-known.  Lenski evidently wrote a letter on the NY Times' ID article:

    http://www.jodkowski.pl/ip/Letters003.html
    * How Evolutionists do things (42 replies)
    The Ghost of Paley2005-10-17 06:41:38
    Evolutionists only accept data that conforms to their pre-conceived amoral ontology and reject the rest. In discussions in the "After the Bar closes" thread I cited several papers under undermining the evolutionistic "Tree of Life" assumption of common ancestry. Evolutionists responded by citing other papers with different data, and based on nothing more than question-begging assumptions of the truth of their ontology, claimed this proved the "Tree of Life" conclusively. However, without these assumptions, such data is inconclusive and meaningless.  Only the a priori assumption of evolutionism over Christianity makes such such inferences possible. As a Christian I look at the same data and draw different conclusions than evolutionists.

    Intellegent design theory (IDT) provides an empirical basis to explain the data of functional genes. IDT has shown that similar structures are not the result of common ancestry, but merely the results of the designer's choice to use materials in the same way a human engineer would. In conjunction with my hypothesis that all "junk DNA" common to diverse organisms come from some of the organisms eating the others parsimoniously explains all of the data. Intellegent design theory and endosymbiotic exchange (eating) explains allof the data parsimoniously. Why do we need Darwinism to explain anything? Darwinism can now be relegated to the ashcan of the other amoral ontologies of the 19th century--Marxism and Freudianism.
    * CREATIONISM Course Canceled After Prof. Mocks Chr (0 replies)
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    * NPR documentary on ID (0 replies)
    Strider2006-01-28 09:45:52
    I just heard an announcement for an hour long broadcast on the local NPR station airing Sunday 1/29 at 11AM CT, hosted by Ray Suarez.  Tracking it down, I found this information:  Intelligent Designs on Evolution.  There are also links on this page to audio and a transcript.

    Sorry if this has already been posted.

    John
    * Orson Scott Card, ID, and Creation Science (8 replies)
    Wesley R. Elsberry2006-01-25 00:18:38
    Orson Scott Card, popular SF author (Ender's Game and sequels of particular note), wrote an essay about ID and the "Darwinist" response to it.

    http://www.ornery.org/essays/warwatch/2006-01-08-1.html

    There's a discussion forum at the same site:

    http://www.ornery.org/ubb/ultimatebb.php?ubb=forum;f=15

    I'll be copying my entries from threads there in this thread.
    * INTELLIGENT Design: Sound and Fury, Signifying No (4 replies)
    jasin2006-02-19 18:13:01
    Creationism and Intelligent Design theory are two separate things, but I guess you would not understand that since you have never actually studied either and are just asserting one man's opinions.
    * COURSE Debunking Intelligent Design Canceled (0 replies)
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    * Spiroplasma (2 replies)
    nanosoliton2003-08-04 23:36:36
    Nic writes:

    Quote

    This page on spiroplasma:
    http://www.oardc.ohio-state.edu/spiroplasma/what.htm
    ...says that sprioplasmas are related to gram-positive bacteria, and have no cell wall, have a cytoskeleton and membranes with cholesterol.  This all seems to go along fairly well with Cavalier-Smith's proposed scheme for the evolution of eukaryotes as something like:

    gram-negative --> gram-positive --> early divergence from archaeabacteria --> eukaryotes



    I doubt it. Spiroplasma seems to have evolved by regressive evolution from clostridia, so they are not a step forward.  Unlike mreb and ftsz, which have actin and tubulin analogs in eukaryotes, fib has no homologs whatsoever.
    * Phylogenetic conflicts (0 replies)
    niiicholas2003-07-08 06:26:28
    A good old thread cited by a new thread by Arm.  Some good wisdom from Myrmecos:

    http://www.arn.org/cgi-bin....907;p=1

    The new thread:
    http://www.arn.org/boards/ubb-get_topic-f-13-t-000771-p-2.html
    * NCSE Creation/Evolution archives (3 replies)
    niiicholas2003-07-06 06:46:20
    Howdy,

    The archives of the online journal Creation/Evolution are now quite substantial; however, they are just listed by issue and are not indexed anywhere AFAIK; so, I will post links to articles that I come across that seem particularly relevant to the ID debate.

    Others should add whatever they like along similar lines...

    (I started from 1988 and went backwards BTW)

    Design, Created Kinds, and Engineering
    Francis J. Arduini

    Makes several points about the differences between (human) intelligent design and design by natural processes that I've tried to make occasionally, e.g.:

    Quote
    The Process of Intelligent Design

    The "created kinds" of modern technology have indeed evolved but in a manner quite different from living organisms. Where living organisms are constrained in their development by their evolutionary histories, machines are constrained only by the level of technology available to their designers. Design selection is based upon the unique design criteria of each individual creative act. Previous designs can be used, modified, or completely abandoned. Changes over time reflect technological advances, and such advances often manifest themselves in distinct ways.

    1. The Quantum Leap. The achievement of a new technology will show up in machines with a previous design history as completely new systems or subsystems that only minimally affect the other independent systems in the machine. For example, when the technology of turbine engines became available, aeronautic engineers began designing aircraft using jet engines, while most of the other aircraft systems were unaffected. Control systems, building materials, even most of the aerodynamic design of our first jets were almost unchanged from their cylinder-propeller-driven predecessors. These other systems did change later but only with the development of other new technologies.

    — page 21 —

    The point is not that this type of mosaic evolution is unlike that of living organisms. One need only look at Archaeopteryx to see that this is actually quite like a living organism. The point is that the design of a turbine engine is so radically different from that of a cylinder engine that one cannot possibly construct a "Darwinian history" that could evolve one from the other. Unlike the fusing of two clavicles to form a wishbone or the fraying of a keeled scale to form a feather, the turbine engine is a completely original design with complex parts and subsystems that have no homologs and often no analogs in the other design.

    Innovations in design are often unrestrained by whatever designs existed prior to them. They are therefore often revolutionary changes. Innovations in living organisms, however, do not show this type of wholesale replacement of systems. The very fact that it is possible to construct plausible Darwinian histories for living organisms, while at the same time it is impossible to do the same for our own "created kinds," is a crucial point of comparison.

    2. Contagious Technology. Living systems evolving from different directions to fill the same ecological niche often develop strikingly similar adaptations. But again, constrained by their evolutionary histories, these adaptations are formed out of the parts available, and different parts are used for similar purposes. Dolphins do look remarkably like large fish and even more like icthyosaurs. But no competent zoologist would ever confuse the three. Past the most superficial level, the differences are dramatic.

    Machines, constrained only by the level of technology of their creators, need not be so dissimilar when designed for similar functions. Grumman, Northrop, and McDonnel Douglas may be designing three individual air superiority fighters, but, if the specific design criteria so dictate, they can use the identical Pratt and Whitney engines for all three aircraft. This is not convergent evolution, but it is a fact of contemporary design.

    And once turbine engines became available for aircraft, they need not be limited to the aircraft "clade." Engineers have placed turbines into boats, automobiles, motorcyles, and the M-1 main battle tank. The organic equivalent to this would be for feathers, once evolved in birds, also to appear suddenly on bats and fl, ying squirrels or for whales, dolphins, and icthyosaurs to have gills. Needless to say, we do not see this.

    An innovation in a "created kind" is contagious between "created kinds." Physical traits (systems, technologies) are not confined within specific clades by the limitations of genetic transfer through phylogenetic descent.

    — page 22 —

    3. Extrafunctional Homology. Design engineers do tend to specialize and develop their own unique design styles. A bridge designer will often use similar designs for different bridges. A common designer should be expected to use similar designs for similar functional purposes. But what about different functional purposes?

    What engineer in his or her right mind would use the same design only slightly modified to build an aircraft and a submarine? The different functions and design criteria mandate drastically different designs for these purposes. An aircraft requires a specially designed hull to hold air pressure in; a submarine requires an equally special hull to hold water pressure out. An aircraft will normally utilize internal combustion engines, even at high altitude; a submerged submarine requires electric or nuclear power. An aircraft requires airfoils for lift; a submarine requires ballast tanks for buoyancy. The list of profound differences could go on for pages.

    But whales and bats are both air-breathing, warm-blooded, milk-giving mammals. Their design differences are quantitative, not qualitative. This cross clade similarity of design is completely unheard of in "created kinds," whether the design team consists of fifty engineers or only one.
    * ID and religion (0 replies)
    niiicholas2003-05-27 12:46:06
    A list o' quotes of ID advocates linking ID to apologetics:

    New Brown Bagger article/flier: The Horse's Mouth.
    http://home.kc.rr.com/bnpndxtr/IDBB.html
    * Public Understanding of Science (0 replies)
    niiicholas2003-04-09 01:23:39
    This comes up often in Ev/Cre debates, basically "where the press got it wrong".  I just discovered that there is whole journal devoted to the topic of science & the public:

    http://www.iop.org/EJ/S/1/NCA179192/DmgN0tbZFSW2tE2bP63lzA/journal/PUS

    E.g. here's an interesting article:

    Quote

    http://www.iop.org/EJ/abstract/0963-6625/4/4/002

    Newspaper coverage of maverick science: creating controversy through balancing

    James W Dearing
    Department of Communication, Michigan State University, East Lansing, MI 48824-1212, USA

    Abstract. How do journalists portray the ideas of maverick scientists to the general public? Are mavericks portrayed as credible scientific sources? Do the stories written by journalists function to merely translate maverick theories for nonscientific audiences, or do they more often transform those maverick theories into the realm of scientific controversies? This study hypothesized answers to these questions by analysing how journalists wrote about three maverick theories: (1) a 1990 earthquake prediction, (2) an alternative theory about the cause of AIDS, and (3) cold fusion. A content analysis of 393 news articles in 26 US newspapers and a mailed survey of the journalists who wrote those stories suggest that scientific theories which are believed to be credible by a minority of scientists may be lent credibility in mass media stories, even though the journalists themselves thought that the maverick scientists lacked credibility. Implications for the communication of risk through the mass media are discussed.
    * Animal Intelligent Design? (5 replies)
    lpetrich2003-01-19 02:20:58
    William Dembski apparently believes that beavers intelligently design their dams.

    However, beavers have some sort of dam-building instinct that consists of placing sticks and mud wherever they hear rushing water, such as at an underwater speaker playing that sound. This document on beaver control warns about that, and understanding that has enabled the design of a Beaver Deceiver fence around a culvert inlet.

    I find it curious that both supporters and critics of Intelligent Design theory have said so little about the question of intelligent design by species other than Homo sapiens, because there is an abundance of seeming evidence of such design, like beaver dams, spiderwebs, and so forth. And if much of that is true intelligent design, then we have an abundance of nonhuman intelligent design right under our noses, in a sometimes very literal sense!

    Animal-intelligent-design capability is part of a lot of folklore, and many pet owners seem to think that their pets have that capability. And the reputable biologist George Romanes had offered numerous seeming examples of that capability in the late 19th cy. Only to be repeatedly ridiculed later as an example of how not to do animal-behavior research.

    Much animal behavior has been found to be a combination of instinct and simple forms of learning, though the instincts involved may be very complicated, and though instinct and learning are often closely intertwined. For example, web-building spiders know how to build their webs without being taught, and the webs they build have a stereotyped, species-specific architecture, despite their complexity. There has been some simulated-spider research that implements web building with a combination of algorithms with the form of "if you feel this configuration of nearby strands, go here".

    And much animal learning would be hard to call intelligent design on the animal's part; this includes mechanisms like

    Imprinting (Konrad Lorenz became the "mother" of some geese)
    Habituation (not responding to "meaningless" stimuli)
    Latent learning (wandering around and picking up detail)
    Classical/Pavlovian conditioning
    Instrumental/operant conditioning

    There is an exception:

    Insight learning (pausing and then implementing a solution)

    This may be called a form of intelligent designing. But it has been seen in only a few species, most notably chimpanzees. So one reasonably concludes that the intelligent-design ability is rare in the animal kingdom. And the closeness to our species of the main counterexample is consistent with what one would expect from evolutionary biology -- in fact, Wolfgang Koehler had used evolutionary biology to decide on an experimental subject for his pioneering experiments.

    And what, precisely, might Koehler's chimps have been doing? An analogy with human problem-solving suggests that they were manipulating a mental model of their solution before implementing that model. Thus, a chimp who sees a lot of crates and an out-of-reach banana may imagine crates stacked on other crates to reach that banana before actually trying to stack those crates.

    So performing intelligent design may simply be manipulating a mental model of something before building it. Thus, if I wish to build a dam across a creek, I don't get seized with an uncontrollable urge to collect mud and sticks and place it where I hear rushing water. Instead, I picture in my mind that dam and imagine where best to place it and how I'd build it.

    By contrast, intelligent-design advocates generally treat intelligent design as some sort of unanalyzable fundamental principle.

    And from the occurrence of structures that appear to be produced by intelligent design, but that are not, one obtains a powerful counterargument to the "design inference".

    One counterargument is that spiders, beavers, etc. were designed with their instincts, but that does not change how the appearance of design had been produced by a non-design mechanism. The ultimate origin of those instincts is an entirely separate question.
    * Wells doesn't review NCSE review (4 replies)
    niiicholas2002-12-20 02:11:24
    This was posted on the DI website.  

    Quote

    Alan Gishlick and the NCSE: Full of Sound and Fury, Signifying Nothing New on the Icons of Evolution

    Jonathan Wells
    Discovery Institute
    December 13, 2002

    On November 22, 2002, the National Center for Science Education posted Alan D. Gishlick’s “Icons of Evolution?: Why much of what Jonathan Wells writes about evolution is wrong” on their website.

    Gishlick’s piece is a long-winded version of a review of my book, Icons of Evolution: Why much of what we teach about evolution is wrong (Regnery, 2000), that he and NCSE President Kevin Padian published in March, 2002, in The Quarterly Review of Biology. Like their review, Gishlick’s new essay is primarily an attempt to defend the icons; and like the review, Gishlick’s essay is heavily seasoned with ad hominem attacks on me. But it adds nothing substantially new to the debate.

    One point that Gishlick’s essay establishes beyond a shadow of a doubt, however, is that the icons of evolution are NOT simply textbook mistakes. In their March book review, Padian and Gishlick likened me to “kids who used to write to the letters page of Superman comics years ago” to complain about trivial typos. “Okay, kid,” they wrote, “mistakes happen, but did it really affect the story?” Apparently, Gishlick has decided that the icons of evolution are not simply mistakes that can be corrected or ignored; instead, they must be defended at all costs. Gishlick’s essay thereby reaffirms what I wrote in my response to published book reviews (including the one by him and Padian) a few months ago:

    “If Darwinists could show that my criticisms of the icons of evolution were unwarranted, or if they would stop trying lamely to defend the icons and simply replace them with better evidence, I would drop my case. But Darwinists cannot defend the icons, and they cannot afford to abandon them, so they resort to insults and smears.”

    Unfortunately for Gishlick, the cats are already out of the bag. When I lectured to biology students on a state university campus recently, their professors were incredulous when I told them that some people still defend the Miller-Urey experiment, Haeckel’s embryo drawings and the peppered myth. The NCSE’s desperate attempts to defend the indefensible are not fooling biologists in the field.

    For more information, and for my previous responses to the sorts of things Gishlick rehashes in his essay, see my postings on the Discovery Institute website, especially the following:

    “Critics Rave Over Icons of Evolution: A Response to Published Reviews” (June 12, 2002)

    “Inherit the Spin: Darwinists Answer ‘Ten Questions’ with Evasions and Falsehoods” (January 15, 2002)

    “Desperately Defending the Peppered Myth: A Response to Bruce Grant” (October 2, 2002)

    “Moth-eaten Statistics: A Reply to Kenneth R. Miller” (April 16, 2002)

    “There You Go Again: A Response to Kenneth R. Miller” (April 9, 2002)


    Funny, Bruce Grant (lots of articles linked) was originally supposed to be one of the experts who had overturned the icon, but now the foremost American expert on the peppered moth has been relegated to being a non-authority by Wells.

    Grant's most pointed comments are here:
    http://www.talkorigins.org/faqs/wells/default.htm#mothgrant

    Too bad Wells didn't take the opportunity to attempt to rebut a review that actually had the space to debunk his arguments in the detail they deserve.

    ICONS OF EVOLUTION?
    Why much of what Jonathan Wells writes about evolution is wrong
    by Alan D. Gishlick
    http://www.ncseweb.org/icons/

    * Rarified design (0 replies)
    niiicholas2002-12-21 18:45:33
    Over on this ARN thread,

    http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000536;p=2

    ...Joy & Mike Gene are missing JP's point.  As explanatory hypotheses in science, an unconstrained supernatural designer and an unconstrained natural designer (or an unconstrained designer of unspecified supernaturalness or naturalness) have the same problem: they have no empirical implications.  

    (I am speaking of "constraint" in terms of "explanatory constraint" here -- an omnipotent designer or super-technological designer would be all-powerful but would still be a "constrained" explanation if his actions followed a pattern motivated by a specific goals.  But an unconstrained ID hypothesis is essentially what is often called "rarified design")

    Note that the point is not that we have to know these things about the IDer ahead of time, the point is that we have to hypothesize something with some empirical implications so that we have some idea of what kinds of evidence would strengthen or weaken our confidence in the hypothesis.

    Otherwise nothing is getting explained at all, even hypothetically.

    The two major explanatory constraints that can begin to elevate design hypotheses to something above the "IDdidit" level are, I think:

    1) Designer methods/capabilities
    2) Designer goals

    ...although there may be others.  Notably, for human-design hypotheses we have a lot of evidence informing both #1 and #2, even for prehistoric cases.

    For SETI, the scientists involved are quite clearly hypothesizing that alien designers will be like us in certain minimal but ways, namely:

    1) Designer methods/capabilities: radio
    2) Designer goals: interstellar communication (with us or others)

    If either of these hypotheses is wrong, then even if the universe is teeming with intelligent life, we will not discover it through SETI no matter how much money and time are put in.  This is not a weakness but a strength: the status of the hypothesis can be fairly rigorously evaluated at any point.  Currently it is:

  • Positive evidence: none
  • Negative evidence: a little bit (nothing found with current restricted detection limits)

    As for the general likelihood of intelligent life in the universe, this can begin to be assessed if we constrain our "existence of intelligent life" hypothesis to something like "basically like human life and formed by the same processes we think created us".

    If, on the other hand, our "existence of intelligent life" hypothesis is "intelligent life of unknown characteristics formed by unknown processes" then we have no basis on which to procede and the hypothesis is relegated to the shrugworthy category of "undetectable invisible pixies exist".

    As for ID, I think that IDists do specify constraints #1 and/or #2 fairly regularly, it's just that they usually do it in passing (or even in a semi-hidden fashion) rather than explicitly, they tend to deny such specifications in public, and when an ID skeptic thinks they detect a specific hypothesis and raises counterevidence that weakens it, the IDist tends to deny that such a specific hypothesis was ever proposed.  Such vagueness may be helpful in debates, but it stands no chance of moving the ID ball towards the goal line of science.
  • * ICSID moderation policies (9 replies)
    ExYECer2003-01-13 23:11:18
    Now that the moderator at ISCID has removed my posting privileges at ISCID for no apparant reason, other than asking him not to attack me in public, I will be posting my response to Nelson on this forum. I hope that this forum will be less hostile to the scientific inquiry.
    * Dembski and Finessing Criticism (1 replies)
    Wesley R. Elsberry2004-04-26 06:27:54
    What does it mean to finesse a criticism? The sort of scenario I am referring to is when William Dembski alters his argument but fails to note the criticism that prompted the change entirely, as if it never existed.  The particularly insidious thing about finessing criticism is that it takes a lot of background knowledge concerning Dembski's prior arguments, present arguments, and criticism of those arguments to even detect that it has happened. The casual reader of Dembski's works will have no clue that he or she has been deprived of information concerning the argument in question.

    This thread is for collecting instances of places where Dembski has engaged in finessing criticisms. Test your knowledge of what Dembski and his critics have said, and contribute entries here. I'm especially interested in examples from Dembski's latest book, "The Design Revolution". I'll lead off with one of mine shortly for an example.
    * THE Daily Dose: Creationism on the sly (0 replies)
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    * KU professor apologizes for mythology e-mail (0 replies)
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    * KANSAS class calls intelligent design "pseudoscie (13 replies)
    Pangloss2006-02-16 01:22:12
    Nothing is more embarrassing to a Darwinian than the logic which dictates the evolution of belief in the paranormal.
    * DESIGN vs. Darwin (0 replies)
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    * EVOLUTION debate has universities tackling intell (0 replies)
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    * John G. West Jr. (2 replies)
    niiicholas2002-12-18 12:20:34
    Here is a masterful bit of propaganda from the DI's John West (he is a political scientist, literally). Particularly annoying is the "truth is established by endless repetition" tactic used by demagogues in the media, and by IDists regarding Icons of Evolution.

    http://www.nationalreview.com/comment/comment-west121702.asp

    This guy oughta read the Icons FAQs:
    http://www.talkorigins.org/faqs/wells/
    http://www.ncseweb.org/icons/
    http://www.nmsr.org/iconanti.htm

    If there was ever a bit of propaganda that deserved a refutation, it is below, so if you can't resist spending some time debunking this, CC your replies here.

    Quote

    December 17, 2002, 9:20 a.m.
    Darwin in the Classroom
    Ohio allows alternatives.

    By John G. West Jr.

    After months of debate, the Ohio State Board of Education unanimously adopted science standards on Dec. 10 that require Ohio students to know "how scientists continue to investigate and critically analyze aspects of evolutionary theory."

    Ohio thus becomes the first state to mandate that students learn not only scientific evidence that supports Darwin's theory but also scientific evidence critical of it. While the new science standards do not compel Ohio's school districts to offer a specific curriculum, Ohio students will need to know about scientific criticisms of Darwin's theory in order to pass graduation tests required for a high-school diploma.

    Ohio is not the only place where public officials are broadening the curriculum to include scientific criticisms of evolution. In September the Cobb County School District in Georgia, one of the largest suburban school districts in the nation, adopted a policy encouraging teachers to discuss "disputed views" about evolution as part of a "balanced education." And last year, Congress in the conference report to the landmark No Child Left Behind Act urged schools to inform students of "the full range of scientific views" when covering controversial scientific topics "such as biological evolution."

    After years of being marginalized, critics of Darwin's theory seem to be gaining ground. What is going on? And why now?

    Two developments have been paramount.

    First, there has been growing public recognition of the shoddy way evolution is actually taught in many schools. Thanks to the book Icons of Evolution by biologist Jonathan Wells, more people know about how biology textbooks perpetuate discredited "icons" of evolution that many biologists no longer accept as good science. Embryo drawings purporting to prove Darwin's theory of common ancestry continue to appear in many textbooks despite the embarrassing fact that they have been exposed as fakes originally concocted by 19th-century German Darwinist Ernst Haeckel. Textbooks likewise continue to showcase microevolution in peppered moths as evidence for Darwin's mechanism of natural selection even though the underlying research is now questioned by many biologists.

    When not offering students bogus science, the textbooks ignore real and often heated scientific disagreements over evolutionary theory. Few students ever learn, for example, about vigorous debates generated by the Cambrian Explosion, a huge burst in the complexity of living things more than 500 million years ago that seems to outstrip the known capacity of natural selection to produce biological change.

    Teachers who do inform students about some of Darwinism's unresolved problems often face persecution by what can only be termed the Darwinian thought police. In Washington state, a well-respected biology teacher who wanted to tell students about scientific debates over things like Haeckel's embryos and the peppered moth was ultimately driven from his school district by local Darwinists.

    Science is supposed to prize open minds and critical thinking. Yet the theory of evolution is typically presented today completely uncritically, as a dogma to be accepted rather than as a theory to be explored and questioned. Is it any wonder that policymakers and the public are growing skeptical of such a one-sided approach?

    A second development fueling recent gains by Darwin's critics has been the demise of an old stereotype.

    For years, Darwinists successfully shut down any public discussion of Darwinian evolution by stigmatizing every critic of Darwin as a Biblical literalist intent on injecting Genesis into biology class. While Darwinists still try that tactic, their charge is becoming increasingly implausible, even ludicrous. Far from being uneducated Bible-thumpers, the new critics of evolution hold doctorates in biology, biochemistry, mathematics and related disciplines from secular universities, and many of them teach or do research at American universities. They are scientists like Lehigh University biochemist Michael Behe, University of Idaho microbiologist Scott Minnich, and Baylor University philosopher and mathematician William Dembski.

    The ranks of these academic critics of Darwin are growing. During the past year, more than 150 scientists — including faculty and researchers at such institutions as Yale, Princeton, MIT, and the Smithsonian — adopted a statement expressing skepticism of neo-Darwinism's central claim that "random mutation and natural selection account for the complexity of life."

    Deprived of the stock response that all critics of Darwin must be stupid fundamentalists, some of Darwin's public defenders have taken a page from the playbook of power politics: If you can't dismiss your opponents, demonize them.

    In Ohio critics of Darwinism were compared to the Taliban, and Ohioans were warned that the effort to allow students to learn about scientific criticisms of Darwin was part of a vast conspiracy to impose nothing less than a theocracy. Happily for good science education (and free inquiry), the Ohio Board of Education saw through such overheated rhetoric. So did 52 Ohio scientists (many on the faculties of Ohio universities) who publicly urged the Ohio Board to require students to learn about scientific criticisms of Darwin's theory.

    The renewed debate over how to teach evolution is not likely to stop with Ohio.

    Under the No Child Left Behind Act, every state must enact statewide science assessments within five years. As other states prepare to fulfill this new federal mandate, one of the looming questions will be what students should learn about evolution. Will they learn only the scientific evidence that favors the theory, or will they be exposed to its scientific criticisms as well?

    Ohio has set a standard other states would do well to follow.

    — John West is a senior fellow of the Seattle-based Discovery Institute and chair of the department of political science at Seattle Pacific University.
    * TWO Ivy presidents take stand on intelligent desi (0 replies)
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    * My ISCID classification... (3 replies)
    Wesley R. Elsberry2002-12-08 00:05:34
    The ISCID moderator (John Bracht, if my sources know what they are talking about) recently posted concerning how ID critics came in 4 categories.

    Quote
    1. Open-minded skeptic: I'm interested, but not convinced.
    2. Closed-minded skeptic: Not convinced and no longer interested in being convinced. Call me only if something new develops somewhere to cause quite a commotion.
    3. Debunker: Not convinced; no longer interested in being convinced; interested only in convincing others they are wrong.
    4. Debunking Crusader: Debunking to save humanity.

    (Source: On Criticism - Four Types of Critics )


    I've asked for what category I might be classed in.  Stay tuned for the results...

    Wesley
    * Front loading and intelligent design (11 replies)
    ExYECer2003-01-12 17:36:46
    From Here

    Mike seems to have avoided addressing the real issues and instead focused on some minor issues. First of all Mike objects to me stating that his approach and Poole's approach led to the same conclusion. Mike correctly points out that I confused Poole's paper with the papers in which the link between cytosine deamination and increase hydrophobicity was made. While I thank Mike for correcting my minor error he seems to have ignored the real issue namely that he used methodological naturalism to explain the tendency of cytosine deamination to incrase hydrophobicity. In fact from the moment he defined the instance of 'front loading' his approach is indistinguishable from methodological naturalism. Neiter Mike nor others may have explained or shown how cytosine became incorporated but both work from the assumption that it was. Mike suggests that his approach allowed him to address the claim that 'an engineer would have replaced cytosine' but nothing in his approach supports this argument. All he has shown is that natural processes seem to have led to cytosome deamination and a corresponding increase in hydrophobicity. No effort was made to show that an engineer would or would not have used cytosine or would or would not have replaced cytosine. In fact Mike has made no effort to show any link between his findings and the idea of front loading. Looking back in time and then saying that it must have been front loaded because it seems to have been selected for is begging the question. Mike complains the evolutionary approach claims that it must have been chance/evolution but that is not very different from 'it must have been design'. Both are assumptions which would require some supporting evidence. The fact that cytosine deamination leads to increased hydrophobicity is no evidence of the premise that 'chance did it' nor 'an intelligent designer did it'. Mike wants to argue that different perspectives give different approaches but I'd argue that these approaches are not distinguishable from methodological naturalism. No teleology is required to explain what happened t>t_0 and no evidence of the need of teleology at t=t_0 has been provided.

    Mike does suggest that he provided a description with 'purpose' but that seems to be like painting the bulls eye around the arrow, to use a common metaphore. Mike suggests that his approach allowed him to pre-specify that deamination of cytosine increased hydrophobicity but that seems hard to imagine. The concept of evolution would also predict that if cytosine deamination were an important contributor to the increase of hydrophobicity and that if such increase would be increasing fitness that cytosine deamination events would be common.

    It has been argued that Mike's approach canm not been distinguished from methodological naturalism approach and that the findings do not help us answer the question of the presence of cytosine at instance t_0, the moment of front loading. Thus either chance/necessity or intelligent design may have been responsible for what happened at time t_0 but after time t_0 it was all methodological naturalism and not intelligent design.

    Mike suggests that since cytosine inclusion was not a frozen accident his premise may be preferable. But lets point out that Mike does not explain anything about the 'frozen design incident' thus leaving it for all practical purposes indistinguishable from a 'frozen accident'. Additionally Mike may have created a strawman of 'frozen accident' when the actual mechanisms may have been a combination of availability and selective advantages. That an engineer may exploit the same pathways that evolution may exploit also does not help us address the issue of front loading. Front loading/origins are separate from the evolution t>t_0. Mike however has not provided any evidence that the event at t=t_0 involved front loading. Mike did initially suggest that there was some problem with cytosine formation in prebiotic world which would have been a way to eliminate chance/regularity as a possibility and thus strengthening a design inference but as I have pointed out our knowledge has increased and potential and realistic pathways may have been identified.


    Mike seems to agree that from t=t0 forward evolution did play a role, so now the question is if t=t_0 requires an intelligent designer or preferably involved an intelligent designer. So far no evidence has been provided that this is the case. If Mike wants to limit his claims to just refuting Poole then his efforts may have helped towards this goal but then the issue of front loading seems irrelevant. But I would say that Mike has not shown how the engineer is in any way limited in what he/she would or would not do.

    Mike still seems to be confused when insisting that I claim that design has to be supernatural. I am pointing out that t>t_0 does not help resolving the intelligent design claim and that t=t_0 has not been addressed. You suggest that at t=t_0 some event took place without really defining the moment t=t_0, the circumstances of the event, the goals of the event. Mike merely claims that at t=t_0 there was an initial state namely cytosine was present as one of the four bases in DNA. Unless Mike wants to argue that at t=t_0 a supernatural design event took place, he has no reason to suggest that I am requiring a supernatural design.

    Mike now suggests that the existence of a 'sophisticated, universal genetic code' is positive evidence of a design event but Mike once again fails to show this to be the case. In fact no positive evidence of such a design event has been provide, merely claimed. But that sounds like a 'front loading of the gaps' explanation. Since Mike seems to agree that from this moment forward everything was fully explainable in natural terms, and no need for intelligent design was required he basically has used the data which supports common descent to argue for 'common design' without really explaining anything about this 'design'. Countless papers and hours of research have been involved in providing for and actually finding plausible pathways to explain the origins of the genetic code and none so far seem to have found any evidence of this intelligent design event, in fact what may have been a good point to place t_0 seems to have been pushed back over time from the Cambrian to the prebiotic RNA world.
    Mike wants to know what data would cause me to suspect that evolution was front loaded. This would require the following 1. Mike needs to define what the purpose or goal(s) are of the intelligent agent 2. Mike has to show that given the chaotic and unpredictable nature of the world around us, this goal can be reliably reached 3. it can be shown that natural processes without intelligent design could not have achieved the state at t=t_0 4. it can be shown that there was indeed an intelligent agent present at t=t_0.

    Mike objects to my scenarios of how cytosine may have become part of the genetic code as irrelevant but they are very relevant in understanding what happened at t=t_0. Mike does not seem to have any evidence of front loading at t=t_0 to required intelligent agent. Thus it is very relevant to show that the front loading at t=t_0 can be explained from a naturalistic perspective without the need for ID. At t>t_0 Mike and I seem to agree that it was purely natural processes at work without the need for intelligent design.

    As far as Nic's analogy, Mike may have responded but that may be far from having addressed Nic's observations. In fact I would argue that you did not even address Nic's claims.

    * ID,antievolution? (22 replies)
    nanosoliton2003-01-07 19:28:40
    I decided to join this group (among others) mostly because I suspect that there are a lot of misconceptions about intelligent design. For example, the very title of the group is called "Antievolution", and yet not only am I an IDer, but I also consider myself an evolutionist (for example, I agree with common descent as Michael
    Behe does). What intelligent design does question is the Darwinian mechanism, that it cannot adequetely explain evolution. I have been reading several ID postings on the deamination of cytosine and I wanted to discuss it in several places.

    When the DNA strand replicates, cytosine, and not thymine, pairs with the altered base. Similarly, deamination of cytosine produces uracil, which behaves like thymine. This has lead many to think that an
    intelligent designer would not have used cytosine, especially with such a high rate of deaminiation. Since one of the driving principles of intelligent design might be error correction, why use cytosine when it can easily lead to errors? The half-life for deamination at 25 degrees C is approximately 340 yr. No reactions have
    been described thus far that would produce cytosine, even in a specialized local setting, at a rate sufficient to compensate for its decomposition.

    There are three considerations that make this actually support ID rather than argue against it that I will summarize.

    One of the major points in this essay is that Hydrophobic interactions play a large role in protein folding and structure as well as alpha helix and beta sheet elongation/formation, further substantiation of this is shown from the fact that serine and not proline, which is a helix breaker, is formed after C-T transitions. So C-T transitions are used to evolve new proteins.

    This hypothesis opens the door to a testable prediction from Intelligent Design theory:

    "This hypothesis also makes a prediction that can be tested. For example, if the multicellular state was front-loaded with life's design, we would expect to find conserved, multicellular-specific proteins have crucial FLIYWVMCS residues that can explained by C-T
    transitions relative to their ancestral state."
    http://www.idthink.net/biot/deam/index.html


    We may be seeing a direction on evolution forced by intelligent design principles.
    * Who's a creationist? (1 replies)
    Wesley R. Elsberry2002-09-26 10:25:36
    Quote
    Clearing up confusion requires a careful and consistent use of terms.  In this book, "creation science" refers to young-earth, six-day special creation.  "Creationism" means belief in creation in a more general sense.  Persons who believe that the earth is billions of years old, and the simple forms of life evolved gradually to become more complex forms including humans, are "creationists" if they believe that a supernatural Creator not only initiated this process but in some meaningful sense controls it in furtherance of a purpose.  As we shall see, "evolution" (in contemporary usage) excludes not just creation-science but creationism in the broad sense.  By "Darwinism" I mean fully naturalistic evolution, involving chance mechanisms guided by natural selection.

    (Source: Phillip E. Johnson, Darwin on Trial (2nd ed.), Intervarsity Press, p.4 (footnote).)


    [Fixed typo.]

    * ID threat in Nebraska (3 replies)
    Lizard2002-05-21 20:32:31
    Now IDers are putting on a full-court press to have ID taught in Nebraska K-12 schools. They are testifying before the Nebraska BOE, and the local Rationalists are scrambling to get pro-science people to testify in favor of science.

    What the ID promoters learned in Kansas, they are applying in Ohio. What they are learning in Ohio, they're applying in Nebraska. And so on and on ID strategy evolves. It's scary how relentless they are.

    It would be extremely useful to have a comprehensive anti-ID resource for activists in Ohio, Nebraska, Washington and elsewhere to go to for information, ideas, tactics, etc. Could that be part of our website?

    My organization, KCFS, sponsored a meeting of pro-science activists from 9 or 10 states about a year ago. One great project that came out of it was an "Activists' Handbook" that is in the process of being readied for the Web. I recommend that we link to it and think of other helpful content for anti-creationist activists to include.

    My $.02.

    Liz
    * NCSE Unveils Project Steve (7 replies)
    Wesley R. Elsberry2003-02-16 15:57:13
    Evolution theory bonds scientists named Steve

    Quote
    That makes four Steves who support evolution, and there are apparently 221 other scientists who agree -- all of them named Steve.

    With tongue firmly in cheek, the Oakland-based National Center for Science Education trotted out the long list of evolution-minded Steves today at the annual convention of the American Association for the Advancement of Science in Denver.  

    The so-called Project Steve takes satirical aim at creationists who use similar lists of scientists to lend credence to their belief in a theistic model of creation, which does include a common ancestry.

    "Creationists are fond of amassing lists of Ph.D.s who deny evolution to try to give the false impression that evolution is somehow on the verge of being rejected by the scientific community," said Eugenia Scott, executive director of the Oakland-based center. "Nothing could be further from the truth."


    See the National Center for Science Education's
    Project Steve page.

    Wesley
    * WHY Intelligent Design Flunks Science And Why It (0 replies)
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    * WHY Rational Thinkers Value the Theory of Intelli (0 replies)
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    * Does God Direct Evolution? (0 replies)
    johndcal2004-06-29 01:57:44
    A 2001 Gallup poll found that 45% of Americans agree with the statement "God created human beings pretty much in their present form at one time within the last 10,000 years or so," 37% prefer a blended belief that "Human beings have developed over millions of years from less advanced forms of life, but God guided this process," and only 12% choose that "Human beings have developed over millions of years from less advanced forms of life, but God had no part in this process."

    The correct choice -- absent from above -- is, "Human beings have developed over millions of years from less advanced forms of life. These less advanced forms also evolved in a process of evolution dating back billions of years. There is no evidence that God directly intervened (did miracles) in the process, but neither does evolution disprove the existence of God, miracles, and His creation of a universe facilitating evolution."

    See "God, Order and Evolution" at Faith & Reason Ministries, http://www.faithreason.org/
    * STUDENTS join debate on intelligent design (0 replies)
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    * KU cancels intelligent design class (0 replies)
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    * Moon missions (2 replies)
    TheMissingLink2005-10-19 16:34:33
    All school boards should be this progressive, open minded, and concerned about the presentation of issues in a fair and balanced manor:

    http://sourflour.blogspot.com/2005....es.html



    ;)
    * Please drop in and leave a comment! (1 replies)
    Loki2005-10-23 01:37:34
    Hi!

    My friend and I have started a brief forum at http://iddiscussion.proboards58.com and I am hoping for some people to stop by and visit!

    There is no need to register, and leaving one post as a guest is more than enough! Just leave a post telling us your views on this issue, whether you're for or against Intelligent Design!

    Thank you,
    Loki
    * PROPOSED Religion Class in Kansas Labels Intellig (0 replies)
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    * Get help (3 replies)
    Shelama2005-06-29 04:41:17
    I am a firm believer in Intelligent Design and the Designer. While I stand in awe of Her imperfect designs, it is clear to me that She has some serious problems and issues, including Manic-Depressive Illness and Multiple Personality Disorder. The sooner the study of  Intelligent Design is introduced into the public schools, the sooner me might, just possibly, be able to get Her the help She needs.

    Furthermore, since Christianity and the Christian Bible have had such an enormous influence on Western civilization, history and culture, the Christian Bible should also be STUDIED (not "taught"), ... seriously, honestly, openly and critically as part of the public school curriculum.
    * IDEA center response to Project Steve (1 replies)
    niiicholas2003-02-27 19:45:43
    IDEA club (/center) responds to Project Steve in their page:

    Scientists and other Intellectuals that Doubt Darwinism and other Naturalistic Theories of Origins
    An incomplete and continually updated list


    I hadn't seen this page before, but Casey Luskin (and perhaps others...) compiled all the various lists of creationist scientists, DI list-signers, etc.  This is actually a useful service as we can see how many Steves there are in all the lists put together (note that the net is quite wide, being very much international and non-biology specific).

    At the end Luskin says there's 9 Steves in the list.  For your enjoyment, here they are (the list is in subsections but the numbers are cumulative as different lists are appended):

    Quote

    14. STEPHEN MEYER (Ph.D. in History & Philosophy of Science University of Cambridge), currently professor of philosophy at Whitworth College.

    43. STEPHEN FAWL, Ph.D. Chemistry, Napa Valley College

    106. Steven Austin, PhD Geology (Pennsylvania State University). See his biography.

    229. Stephen Brocott, Ph.D. Organometallic Chemistry (University of Western Australia). Listed on the Institute for Creation Research Creation Scientists Page.

    237. Stephen Taylor, Ph.D. Electrical Engineering (University of Liverpool). Listed on the Institute for Creation Research Creation Scientists Page.

    347. Stephen W. Deckard (Ed.D. Univesity of Sarasota), Assistant Professor of Education. See his bio on the Answers in Genesis website.

    349. Stephen Grocott, Industrial Chemist (Ph.D. (1981), University of Western Australia in the field of organometallic chemistry of optically active metal complexes), Adjunct Professor of Chemistry at an Australian University. Member of Royal Australian Chemical Institute and American Chemical Society. See his bio on the Answers in Genesis website.

    398. Stephen Huxley, Ph.D., Professor of Information and Decision Modeling at the University of San Francisco as seen in his involvement with the IDEA 2002 Conference at USF.

    454. Steven Gollmer, Ph.D., Associate Professor of Physics, Cedarville College


    In case you weren't counting:

    Number of (probable) YECs: 5

    Number of biologists = 0.  Organometallic chemistry is as close as they get...

    nic

    * Convergence (0 replies)
    Wesley R. Elsberry2004-12-06 13:16:18
    Over on Ed Brayton's blog, an unnamed ID advocate was trying to claim that convergence, such as that seen between placental wolves and thylacines, posed a problem for evolution. Here's my response:

    I'm not sure what the placental/marsupial wolf example is supposed to show as a criticism of evolution. Is it really unreasonable that the niche of "terrestrial cursorial quadruped predator" would be filled in two different lineages?

    It's certain that the similarities are less "uncanny" than current antievolutionists would make them. You don't have to be an anatomist to recognize that the skulls of the two have very different shapes of bones and (of course, when talking about mammals) dentition. Yet, as recently as a conference in 2002 (IIRC), we had the spectacle of an antievolutionist opining that the two were indistingishable -- and presenting two illustrations of these animals to buttress the point. The funny thing was that it was apparent right off the bat to me that the pair were actually the very SAME illustration, with one of them flipped left to right and colorized.

    A nice page with comparison of the thylacine and wolf skulls and dentition is at http://www.naturalworlds.org/thylacine/index.htm

    Note the differences in neural foramina between the two.
    * Elsberry & Shallit on Dembski (51 replies)
    Wesley R. Elsberry2003-11-12 08:26:56
    I'm starting this thread for discussion of the paper that Jeff Shallit and I wrote on Dembski's ideas. Since it is now known to the public, I expect some criticisms of our criticisms will be made.

    For example...

    In a thread on ARN, "Rock" gripes that we imply that we have a positive theory but that we don't expound upon it. Well, we do have a positive approach to examining bit strings that is expounded upon for a couple of pages in our appendix. This is apparently not clear when one is simply "skimming" our paper. I have also started a thread here for discussion of our specified anti-information (SAI) as a replacement for Dembski's notion of specification.

    "Rock" also complained that there was "nothing original" in our paper. It is certainly true that many of our criticisms had been expressed less formally and separately elsewhere in discussion on the Internet, but I'm not sure that that applies to all of the criticisms that we made. SAI is an application of the universal probability distribution, but the application itself is original with us.

    In his last sentence, "Rock" asks if our ideas bear closer examination than Dembski's on these matters. Clearly, I think so. We identified a number of problems in Dembski's approach that we feel are insurmountable. Our SAI addresses each of those problems.


    Please use this thread to bring attention to criticism made in other fora.
    * Biosonar and ID? (9 replies)
    Wesley R. Elsberry2002-12-27 00:08:00
    From an ISCID thread:

    Cornelius G. Hunter wrote:

    Quote
    I don't think we have scientific reason or evidence to believe complex systems such as echolocation or the DNA code could have evolved.


    Hmm.  I don't think that we have scientific reason or evidence to indicate that echolocation is due to anything other than evolutionary processes.

    There are several different approaches to biosonar.  The examples of bats and odontocetes are pretty sophisticated, but those of oilbirds and honey badgers are relatively simple.  Even humans can use hearing for directional cues, as several aids for the blind demonstrate.

    So I'd like to know what, specifically, puts the dolphin biosonar system (the one I'm most familiar with) outside the scope of evolutionary process.

    Wesley

    * Sympathetic magic (2 replies)
    mark isaak2002-05-06 11:04:52
    It occurred to me that ID and sympathetic magic probably share a common psychological basis.  In sympathetic magic, it is believed that there is a link between A and B because A shares properties with B.  For example, a voodoo doll shares appearance with a person, so a link is supposed to exist between them, and harming the doll is supposed to harm the person.  (There is more to it than that, but that is enough for illustration.)

    With ID, life and machines share some properties in common, such as moving parts and a certain amount of complexity.  That is enough to suggest a link between them, which leads to the idea of designers for both.

    I think I'm overanalyzing the situation.  Probably the psychology behind ID is much more basic, and I don't need to draw in sympathetic magic.  But you wanted the bullitin board tested, so I had to write something.
    * INTELLIGENT Design is not scientific theory (0 replies)
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    * BEN Bova: Arguments for intelligent design are un (0 replies)
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    * Archdeacon Paley and the Museum of Watches (0 replies)
    lpetrich2005-02-10 07:00:04
    Archdeacon Paley and the Museum of Watches

    Let's imagine that Archdeacon Paley, of watches-need-watchmakers fame, could come to our time and visit some museum of watches and clocks and other timepieces over the centuries. He'd see:

    Sundials
    Hourglasses
    Purely-mechanical clocks and watches
    Electromechanical clocks and watches
    Purely-electrical clocks and watches

    Their displays would be:
    Analog
    Digital
    /
    Mechanical
    Electrical

    Their timing would be controlled by:
    The Sun
    Falling sand
    Pendulums
    Springs
    Quartz crystals
    Oscillating atomic nuclei (in atomic clocks)

    Archdeacon Paley might scratch and scratch his head and ask who designed all these timepieces. There are two main possibilities:

    1. A single master designer who has designed every timepiece there ever was.
    2. Multiple designers of timepieces over the centuries and at each time.

    Would Archdeacon Paley try to argue (1)? And argue that all that single designer's designs are the best possible, in Panglossian fashion? Or would he recognize that it is (2) that had actually happened?

    Turning to the Earth's biota, I think that a strong case can be made that if much or most of its features was designed, then this designing would be designed evolution in (2) fashion.

    Back in his creationist days, Charles Darwin was inspired by Australia's distinct fauna to note in his diary that:
    Quote
    A Disbeliever in everything beyond his reason might exclaim "Surely two Creators must have been at work".

    And over at The Panda's Thumb, there is a nice article discussing Multiple Designers Theory, which is (2) applied to the Earth's biota.

    Also, How I decoded the human genome featured this comment from someone with a lot of experience in computer programming:
    Quote
    Kent spoke to me in nerdspeak, with geekoid locutions such as the use of "build" as a noun: "That's the most recent build of the genome. Build 31." I was used to hearing biologists talking about the elegance of DNA with what might be called reverence. By contrast Kent spoke of DNA as if it were the most convoluted, ill-documented, haphazardly maintained spaghetti code -- not God's most sublime handiwork, but some hack's kludge riddled with countless generations of side effects, and "parasites on parasites."

    "It's a massive system to reverse-engineer," he said. "DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes ... the analogy breaks down at the margins but offers useful insights." It was nearly impossible to tell the working code from cruft, Kent said. "That's why a lot of people say, 'The genome is junk.'" But that's what he found interesting: a high-quality programmer's code is always self-evident, but legacy assembler handed down from generation to generation of bricoleurs (I'm paraphrasing again) provides a real challenge for people who like puzzles.

    To sum up, it looks like (2) rather than (1) to that experienced designer.

    I think that it is a good test of the open-mindedness of IDers whether they are willing to take seriously the possibility of multiple designers. And one can ask why they present ID in opposition to evolution and natural selection. Evolution can proceed by ID (evolution by genetic engineering), and ID and natural selection can coexist as mechanisms of evolution -- they are NOT mutually exclusive, despite what some IDers seem to think.

    I have, however, seen some counterarguments offered to the multiple-designers hypothesis.

    One of them is that nearly all Earth organisms use DNA as their molecule of heredity, something that somehow implies only a single designer doing all the designing.

    If you people find it hard to keep yourselves from laughing, you have my sympathy, because that argument is almost absurdly weak. It's like Archdeacon Paley maintaining that all those clocks and watches had a single master desginer because they all measure time in the same units -- 1 day = 24 hours, 1 hour = 60 minutes, 1 minute = 60 seconds.

    I wrote "nearly all", because RNA viruses are an exception, and apparently the only one. But RNA is a close chemical relative of DNA, making that exception a weak one.

    I note in passing that it seems to me that DNA is often described as some sort of "magic molecule of life" in quasi-vitalist fashion. Though it's the nearly-universal carrier of genetic information, that appears to be its only function. What makes a living thing alive is the interaction of its various parts, not any particular substance.

    Another counterargument is that one superpowerful designer is somehow a simpler hypothesis than a multitude of less-powerful designers. In my watch-museum example, it is deciding on hypothesis (1) rather than (2) -- even though (2) is what has happened. Unless one wishes to believe that there was some superpowerful designer behind these designers' thoughts and efforts, a case of (1) having the appearance of (2).
    * ID, Creationism, Evolution... - all nonsene! (7 replies)
    DonFernando2005-09-15 13:19:28
    ID? Religious motivated pseudo-science crap. Creationism? Ludicrous. Evolution? All wrong.

    The overwhelming scientific evidence points towards Flying Spaghetti Monsterism!

    See the OPEN LETTER TO KANSAS SCHOOL BOARD
    * The Death of Irreducible Complexity (5 replies)
    RBH2005-03-27 21:01:38
    Since ARN's Moderation is twitchy and its archived threads occasionally disappear from view, I''m archiving two posts I made there on irreducible complexity.  This is the first.

    In another thread jon_e provided a link to a recent paper by Dembski revisiting irreducible complexity.  jon_e was making the point that "irreducible complexity" is alive and well in ID.  I had previously scanned the paper but had not read it carefully.  Looking again at it tonight, I see that Dembski has made a significant change in Behe's original conception of irreducible complexity, a change that eviscerates the utility of "irreducible complexity."  Rather than being alive and well, in the light of Dembski's new paper irreducible complexity is dead on arrival.

    To realize the nature of the change, it's first necessary to know what an "operational definition" is.  Very briefly, an operational definition is a description of the procedures (operations) used to measure the value of a variable.  So, for example, an operational definition of "temperature" is a description of how temperature is measured -- the apparatus used, conditions that apply, and steps performed in making the measurement.  The Methods section of research papers contain explicit or implicit operational definitions of the variables under study.

    With respect to any system, "irreducible complexity" is a variable that takes one of two values, 1 or 0 -- present or absent, true or false.  So an operational definition of irreducible complexity is a description of the steps carried out to determine whether a given system is or is not IC.  In Behe's original conception, the IC value for a system is assigned to be "1" (true) if the loss of any part/element/component prevents the system from performing the primary function that it performs when it is whole -- a 'knock-out' operation -- and "0" (false) otherwise.  So Dembski wrote in 1998, two years after DBB    
    Quote
    Central to his [Behe's] argument is his notion of irreducible complexity. A system is irreducibly complex if it consists of several interrelated parts so that removing even one part completely destroys the system’s function.
    and    
    Quote
    Also, whether a biochemical system is irreducibly complex is a fully empirical question: Individually knock out each protein constituting a biochemical system to determine whether function is lost. If so, we are dealing with an irreducibly complex system. Experiments of this sort are routine in biology.
    The operation specified for determining IC is knock out a part and see if the system still works: that's the operational definition of "irreducible complexity".

    In the recent paper referenced by jon_e, though, Dembski adds another operation to the procedure used to determine the value taken by IC:    
    Quote
    Thus, removing parts, even a single part, from the irreducible core results in complete loss of the system’s basic function. Nevertheless, to determine whether a system is irreducibly complex, it is not enough simply to identify those parts whose removal renders the basic function unrecoverable from the remaining parts. To be sure, identifying such indispensable parts is an important step for determining irreducible complexity in practice. But it is not sufficient. Additionally, we need to establish that no simpler system achieves the same basic function.  (Emphasis added)
    and    
    Quote
    To determine whether a system is irreducibly complex therefore employs two approaches: (1) An empirical analysis of the system that by removing parts (individually and in groups) and then by rearranging and adapting remaining parts determines whether the basic function can be recovered among those remaining parts. (2) A conceptual analysis of the system, and specifically of those parts whose removal renders the basic function unrecoverable, to demonstrate that no system with (substantially) fewer parts exhibits the basic function. (Emphases added)
    That last criterion is an IC killer, at least empirically.  One must show that no system that is simpler than the system under analysis can perform the function performed by the system under analysis.  (I'm leaving aside the other change, the "rearranging and adapting remaining parts" addition to the original knockout operation.  That change also raises problems for determining the value taken by IC.)

    Note carefully that it's not sufficient to show that some subsystem of the system under analysis can't perform the function; according to Dembski it is necessary to show that no simpler system can perform it, regardless of whether that simpler system resembles the system under analysis or not.

    It might be thought that I'm giving Dembski's words an uncharitable reading, but that's belied by Dembski's own example, sandwiched between the two quotations above:    
    Quote
    Consider, for instance, a three-legged stool. Suppose the stool’s basic function is to provide a seat by means of a raised platform. In that case each of the legs is indispensable for achieving this basic function (remove any leg and the basic function can’t be recovered among the remaining parts). Nevertheless, because it’s possible for a much simpler system to exhibit this basic function (for example, a solid block), the three-legged stool is not irreducibly complex.
    Please pause and think about that for a moment.  

    Now continue reading.

    On Behe's original operational definition, that three-legged stool is irreducibly complex: remove any of the four components (three legs and the seat -- Dembski forgot to mention the seat) and it can no longer function "to provide a seat by means of a raised platform", and so on the original operational definition the stool is irreducibly complex.  But under Dembski's revised operational definition, a three-legged stool is not irreducibly complex because some simpler system (that does not contain any of the parts of the original stool) can perform that same function.

    As a result, in order to show that a system is IC, intelligent design "theorists" must show not only that the system fails to perform its function when any part is removed, but they must also show that no other simpler system can perform that function.  That is, they must establish a universal negative.  And (ask your friendly neighborhood logician) it is impossible to establish a universal negative.  (Hint: black swans.)  Dembski is back in the inductive soup.  On Dembski's new operational definition, not even Behe's mousetrap is irreducibly complex!

    In my less-than-humble opinion, in revising its operational definition Dembski has thoroughly gutted the notion of irreducible complexity.

    RBH

    * FORMER Tech professor opened floodgates of creati (0 replies)
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    * Horizon on ID (2 replies)
    counterpane2006-01-25 23:09:42
    Hi, new guy here.  

    I've just noticed in my newspaper's TV listings that BBC2's Horizon programme tinight (Thursday 26th January) is covering Intelligent Design.  Should be worth watching.

    Richard C
    * Antievolutionism in Singapore (0 replies)
    budak2005-12-10 01:17:50
    Sorry, repeated post.
    * CREATIONISM, Intelligent Design Course Withdrawn (0 replies)
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    * The Intelligent Designer Speaks (1 replies)
    The Designer2006-02-09 08:53:31
    Have any of you seen this yet?

    designerspeaks.com
    * I Debate Michael Behe (1 replies)
    Kuglo2003-03-15 12:26:49
    Disbelief in the processes of mutation and natural selection as the sole cause of life is due to logical and scientific misunderstandings and misinformation.  Evolution has been and will almost certainly continure to be the scientifically accepted view of biological origins for all of time.  Further there is no scientific case for intelligent design.
    In the following exchange I debate Michael Behe, a biochemist from Lehigh University, via email.  A few very small changes have been made in the wording of a few sentences, grammar, spelling; but nothing significant to the debate in any way whatsoever.
    The conversation exposes the complete fraud that is "intelligent design".  I thank Behe for his time, and the discussion is, hopefully, due to continue at some point if he will indulge me in that.

    **********************************************
    Hi,
    My name is Clay Schentrup and I've completed the majority of my computer engineering degree at the Univsersity of Kansas. I've read quite a few excerpts of your work involving intelligent design, and in fact I've even seen Philip Johnson speak at KU a few years back. I also plan to see you speak this summer in Kansas City.

    I understand you are busy so I'll make this as brief as possible. My question relates not so much to your research or the physical structures (like flagella) but to the reasoning behind your conclusions. I'll briefly illustrate with an example. Say I flip a coin 100 times and get the sequence "THHTHTTHHHHTT..." (you get the idea). Now once I have obtained that particular sequence of tails and heads, I could calculate that the odds off getting that particular combination would be 1/2^100. Now say I jump up and shout, "My goodness..out of all possible combinations that could have occured..the odds this one would occur were only one in several trillion trillion..therefore an intelligent being must have affected the trajectories of the coins to make them land in that particular pattern. This sounds quite strange, but it seems indistinguishable from your argument; that the genetic mutations involved with potentially creating a flagellum in an organism whose ancestors didn't have one, are so improbable that an intelligent entity must have had something to do with them.

    I've been proven wrong about matters of science before, and I truly seek the best knowledge possible. But regardless of any level of detail you go into regarding these so called "irreducibly complex" systems, the fundamental premise is the same. "This event was so unlikely to have happened by chance that an intelligent being who wanted the event to happen must have caused it."

    Perhaps you can explain my apparent confusion.

    Thanks very much,
    Clay Schentrup

    **********************************************
    Hi, Clay, nice to meet you. Yours is a very good question, and goes to the heart of detecting design. It turns out that improbability is not enough to infer design, for the reason you apprehended. Any event is improbable. The exact structure of a pile of rubble is improbable, and the faces on Mt. Rushmore are improbable. So why do we feel compelled to conclude design in the latter case but not the former? The key is the notion of "specification". Not only is Mt Rushmore very improbable, but it also matches the faces of four presidents. Not only is the arrangement of the amino acids in the proteins of the flagellum improbable, but they also code for a functional machine, unlike virtually any other arrangement of amino acids. So the key is not just improbability, but improbability plus specification.

    You might enjoy reading more about this. A good book for a computer fellow like yourself would be William Dembski's The Design Inference, published a few years back by Cambridge University Press.

    Best wishes.
    Mike Behe

    **********************************************
    Prof. Behe,
    First let me say that it is an honor and a pleasure to hear from you. I know that you are a busy person. I appreciate your literary suggestions, but I am already familiar with their underlying "design inference" argument, and that is specifically the topic with which I take issue. This is why I wrote to you personally. I am very patient, so if you could reply at your leisure I would very much appreciate it. Time is no issue. But I'll understand if you can't. I'll go ahead and reply to your letter, and see what comes of it.

    > The exact structure of a pile of rubble is improbable, and
    > the faces on Mt. Rushmore are improbable. So why do we feel
    > compelled to conclude design in the latter case but not the
    > former?
    > The key is the notion of "specification". Not only is Mt.
    > Rushmore very improbable, but it also matches the faces of four
    > presidents.

    Exactly. The monument "matches" known patterns of behavior of a specific known and observed process: humans. Humans are observed, and they are known to create visual replicas of other people, animals, trees, etc. So if we weigh the probability of human creation of those monuments against the probability of erosion and other non-human processes creating them, we can deduce humans. And we know that humans are "intelligent", therefore we can additionally deduce that the monument was intelligently created.
    Flagella, on the other hand, don't match any known intelligent processes. I don't know what you mean when you say they "code for a functional machine". "Code", "functional", and "machine" all suggest intelligence to begin with, which is what you are trying to prove. I would state the matter more objectively. That particular sequence of amino acids chemically reacts forming a particular arrangement of atoms that we have dubbed a "flagellum". But how does this particular arrangement of atoms match any known intelligent process?
    And now to get back to the pile of rubble. Say you were to visit an architect's house and snoop through his computer while he was in another room. And say you turned up well diagrammed plans for an arrangement of steel and other materials that precisely matched the "pile of rubble" you saw earlier. And say he came into the room and said, "Oh that..yeah I designed and built it. I'm into abstract art." Now suddenly you would find that the pile actually _had_ been intelligently designed. Now if you found another virtually identical pile elsewhere the distinct possiblity would still exist that it had been laid down with no intelligent intent and just had happened to fall that way. But because you would then be familiar with a known "process" with a greater-than-random liklihood of causing that particular (arbitrary) arrangement, you would be better to deduce that he had something to do with it.
    I could go into analogy after analogy, but the point is glaringly obvious. "Specificity" is just "familiarity". You have cited numerous examples of cellular components that you believe to have been intelligently created. But the fact remains that you have not observed that God, or any other "process", has a greater-than-random propensity for causing these particular arrangements of DNA. In order for you to deduce that they were intelligently designed you have to show some process that is both intelligent and could has a propensity for designing such things.
    For my final analogy back to your flagellum contention: Say I drop a bag of rocks on a gym floor and then drop a basketball on them and watch it roll, because of their inconsistencies and positions to one of the thousands of places it could potentially end up, and then mark off that spot. I could make the exact same argument you made. Not only is that location improbable, but virtually all other ways those rocks could have ended up on the floor would have caused the ball to land in a location other than that one. Therefore God, or some other intelligence, altered the seemingly random way in which they fell on the floor. It's the same argument you are using, so far as I can tell.

    Thanks so much for your time,
    Clay

    **********************************************
    Hi, Clay. You're right, like everyone else I'm rather busy. To compound matters, my wife had a new baby three weeks ago, so things are pretty hectic for us these days. So I'll be able to give you just a few more comments, and then sign off.

    You are right that the "design inference" can give false negatives. I have pointed out in my book Darwin's Black Box and Bill Dembski has emphasized in The Design Inference that one can never rule out design, because intelligent agents can imitate random processes. However, the problem of false negatives is not the critical issue. The crucial issue is whether the design inference gives false positives. That is, does one ever come across something like Mount Rushmore and discover that it was the result of random processes? In your basketball example, suppose I had painted red all the rocks the basketball would bounce on, and marked with an "X" the spot on the floor where it would come to rest. If, when I dropped it, the ball did indeed hit all those marks, most people would easily conclude the ball was aimed, it wasn't bouncing randomly. The critical question is not whether a pile of rubble was designed, it's whether a system that looks very specific and functional was not designed.

    You write that ""Code", "functional", and "machine" all suggest intelligence to begin with, which is what you are trying to prove." Perhaps those words do suggest intelligence, but they are not my words. They are widely used by the entire biology community. Biologists routinely speak of "molecular machines" that are "functional" and are "coded" for by an organism's genome. If you think it is incorrect to use such language, then your argument is with the biology community as a whole, not just me.

    Best wishes.
    Mike Behe

    **********************************************
    Prof. Behe:
    Congrats on your new baby. As to this discussion I don't expect a future response, but I would at least appreciate that you read my response in its entirety at your leisure. I do believe it goes into exceptional depth about the nature of the invalidity of your contention for the inference of design.

    >..one can never rule out design, because intelligent agents can
    >imitate random processes. However, the problem of false
    >negatives is not the critical issue.

    The only point I was making by bringing up the pile of rubble (intelligent design that one wouldn't initially think was designed)is that the only difference between it and Mt. Rushmore is that we know of a phenomenon with a substantial propensity for creating visual replicas of humans--humans! Were we to find a phenomenon with a propensity for making a particular type of pile of rubble, we would then be able to do the same thing with the pile of rubble, and if we ever saw that particular type of rubble pile in the future we would certainly deduce that it had been made by our intelligent architect friend than by being randomly dropped with no care as to its placement. There is nothing inherently different between the pile of rubble and the monument. Both have an overwhealmingly low probability of being in their particular arbitrary arrangement as opposed to all others. The one and only reason we deduce that intelligence made Mount Rushmore is that we know humans to be adept and likely to create such things, and we know that humans are intelligent. On the same token, were an alien race to visit our planet in the distant future, and have no familiarity with humans they would have no valid reason to deduce that Rushmore was intelligently designed. It would just be another "random" rock formation. It's just one of a zillion different ways those rock particles could be arranged.

    > [the issue is] whether a system that looks very specific and
    > functional was not designed.

    Well for starters it would be nice to know what objective measurable property you are referring to when you say "specific". Can I analyze an object and state how "specific" it is with any sort of standard units? And if I can, and I agree that a flagellum, for example, is extremely "specific" (whatever that's supposed to mean) how is this significant to your argument? Are there any verifable observations of any intelligent phenomena which have a propensity for producing things which are highly "specific"? The only intelligent things I know of are humans. Do they tend to produce things which are "specific"? I don't know, but it really doesn't matter because we can already rule them out as the potential designers/builders of flagella, for obvious reasons.
    And then there's this term "functional". As you pointed out scientists frequently speak of cellular components in terms of performing "functions". Yes, it is handy to use these terms because flagella remind us of things like motorboat propellers and other propulsion mechanisms. But the reason I took issue with your use of the term is that you go beyond just using it out of convenience, and instead truly believe that it _is_ performing a purposeful intelligently designed function.
    In the case of flagella they whip microorganisms along through liquids. This is their "function". In the case of the water molecules a puddle in the road, they (the water molecules) perform the function of rapidly moving, bouncing around off one another and exerting minute gravitational and electromagnetic forces upon each other. Both the flagellum and the puddle of water are examples of arbitrary arrangements of molecules. But I don't hear you claiming that some intelligent entity purposefully and intelligently put those trillions upon trillions of water molecules in that specific arrangement.
    The intelligent design argument, in a nutshell is as follows:

    I. This structure (say flagellum) reminds me of something made by humans.
    II. Humans are intelligent.
    III. Humans couldn't have made this structure (obviously).
    IV. Therefore some other phenomenon with algorithmically similar behavior to humans must exist and have designed/built this structure.

    >The crucial issue is whether the design inference gives false
    >positives. That is, does one ever come across something like
    >Mount Rushmore and discover that it was the result of random
    >processes?
    Put into more clear objective terms your question is, "What is the probability that an object which can be reasonably deduced to have been intelligently created is in fact not intelligently created?" The most obvious problem here is that you are specifically talking about objects which we have already deduced _are_ intelligently designed. To deduce that something is intelligently designed in the first place you would have already shown that there is a known intelligent process which has a significantly greater liklihood for producing the given object than any known unintelligent process. In the case of Mount Rushmore the reason we deduce in the first place that it was designed by humans, an intelligent process, is that the odds humans would make a large visual replica like that is far greater than the odds of its being created by erosion. And we know this only because we are familiar with human activities and thus we know very well that humans are prone to making sculptures, especially of other humans. And no other known processes are very likely to do so. So your question is like asking, "How often do you find eggs for sale in a sports store?"
    The bigger issue though is that this has nothing to do with anything in biology. We _do_ know of an intelligent process (a human being) which has a tendency to create sculptures like Mt. Rushmore. We _don't_ know of any intelligent process with a tendency to create flagella, or any other cellular components. So you have no justification for comparing Mt. Rushmore to cellular components. The entire analogy is invalid.
    If your conclusion is that the flagellum was intelligently designed, you must have some verifiable observations of a "phenomenon X" such that:

    A) Phenomenon X has a tendency to alter DNA in such a way as to produce flagella (or any other cellular components you suspect as being intelligently designed) that is more likely than all other known processes (carcinogens, radiation, etc.)
    B) Phenomenon X is intelligent.
    C) Phenomenon X is older than any cellular components it may potentially be alleged to have produced.

    I have yet to see any observations of any such phenomenon from yourself or any other ID scientist. And if you claim that "God" was the intelligent designer behind the "flagella alleles", then you would have to additionally satisfy a third requirement:

    D) Phenomenon X has the necessary characteristics to fit the definition of "God".

    The only known phenomenon that satisfies B is a human being, but it most certainly doesn't satisfy any of the other three requirements. Simply put, DNA, flagella, the blodd clotting cascade (activator, zymogen, substrate coagulogen), etc. are not consistent with any known intelligent phenomena, period. The design inference is scientifically empty. It stands purely because of the psychological habit of anthropomorphism.

    And to thoroughly address the basketball analogy you made: In order to determine whether the basketball had landed on the X by chance, we would need two values. First the probability that the basketball _would_ land there by chance, and second the probability that the person dropping the ball would make it end up at it's destination intentionally.
    Now the former we could calculate with reasonable precision by using data like floor surface area, the ball's size, and perhaps even some trial drops. Let's say we get some value, p, around one in a million, one in a trillion..whatever reasonably low number you prefer. Now as for the liklihood that the person dropping the ball (we'll call him Ed) would have intentionally altered it's course to land at its specific destination; that would be product of two other probabilities, we'll call k and m: k = the probability that Ed would _want_ the ball to end up in that particular spot, and m = the probability that a method exists by which this could be done.
    Now most people are aware, mainly because of televised "magicians" like David Copperfield, that there is a dazzling array of techniques that various illusionists have employed to perform feats that have no immediate logical explanation. Typically though, when the explanations are revealed we are striken with how plausible they are; we simply wouldn't have thought of them on our own . And aside from all this, the extent of human technology is so vast that there would most certainly be a plausible manner by which Ed could make this happen if he so chose, which makes the theory of intentional placement at least slightly plausible. So m is greater than zero.
    As to k, the probability that Ed would _want_ the ball to end up in its particular destination, there is a drastic difference between the ball's ending up on the X compared to its ending up on any other spot. If it did not land on the X we would have no reason to suspect he had intentionally caused it to land in that particular spot. There is simply no motive, because it wouldn't impress anyone. We have no reason to suspect that Ed would have gone to some great lengths if the ball landed on any particular unmarked spot on the floor. So the odds he would have wanted it to land in any such spot would be some extremely low value, which we could essentially deem insignificant or effectively zero. And even if we considered the chance that he did want the ball to land on that particular unmarked spot, the odds that he would have chosen that spot out of all potential spots is already essentially the same as the odds that the ball would have landed in that particular spot at random, by definition.
    If the ball lands on a spot aside from the X, then k can be assumed to be extremely low. So mk is most certainly lower than the odds that the ball would end up in the destination spot purely by chance. On the other hand if the ball _did_ land on the the X, the probability that Ed had some intent for it to land there would be dramatically higher, simply because we know that this would be dramatically more impressive to the observers. And we know that people in general have a much higher tendency, in these types of situations, to do things that impress people as compared to things that don't. That is, we don't see people practicing for hours every week learning to shoot a basketball and make it pass directly through an imaginary hoop precisely 1 meter to the left of the rim, so if we were to see someone shoot a ball in that spot we wouldn't assume it was intentional.
    So were the ball to land on the X we would have to consider the probability that randomness would have landed the ball there compared to the probability, mk, that Ed would have intentionally caused it to land there by some unknown technique. Because the human brain automatically tends to search for explanations to uncommon events which seem to fit a pattern consistent with known intelligent behaviors, we would initially feel compelled to see significance in the case that the ball landed on the X. That is we would search for some explanation which dealt with intelligence. Were we to fully investigate the matter with a large body comprised of physicists, illusionists, and detectives, and find some fairly plausible mechanism by which Ed could have directed the ball to that spot, we could possibly conclude that he had indeed caused it to happen intentionally and that it was not simply random, depending on how mk compared to p. This would especially be true if we found some evidence of such a technique, such as an electromagnetic system within the floor and some magnetic material hidden within the ball.
    However if this body was to exhaustively search for such a technique and not be able to find one, we would have to conclude an extremely low value for m, and thus mk. If mk was less than p then we could conclude it was just a random event. And there's nothing impressive about that.

    Now getting back to cellular biology with our flagellum example. Were we to know of any intelligent process with a probability of wanting to make flagella genes _and_ a probability of being able to, which, when multiplied together, were greater than the liklihood of flagellum DNA having been formed by unintelligent mutative processes [*that is, the probability that unintelligent mutative processes would create flagellum DNA], then we could reasonably conclude that this intelligent process was behind it. But as I've pointed out again and again you haven't shown any such process. And that's the critical hole in the intelligent design argument.

    Sincerely,
    Clay

    **********************************************

    I very much hope to hear back.  We'll see whether the ID movement has anything more substantial in their arsenal.  Judging by this I'd wager not.

    Clay
    * Discovery Institute Caught Misquoting (2 replies)
    Wesley R. Elsberry2003-08-14 03:29:03
    Guest columnist misrepresents views

    Dr. Sean Carroll takes exception to the misuse of his words by John G. West of the Discovery Institute.

    Quote
    Editor:

    John G. West of the Discovery Institute, in his guest column Friday, quoted an article in a leading biology journal as purported support for his view that alternatives to contemporary evolutionary science ought to be presented in biology textbooks. I am the author of the article he quoted (but did not properly cite) and I am writing to make it absolutely clear that West is gravely mistaken in taking the excerpted sentence out of its full context.
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    * (probably)new creationist 'argument' (1 replies)
    aarobyl2005-02-15 05:33:35
    Hi, all,

    I've just encountered a new form of creationist attempt to refute evolution -
    the main line of it goes like :
    "vertebrate immune system ( + proteolytic system )
    is so gargantuanly efficient and precise that it wipes out any mutation, except few deliberately allowed for microevolution's sake,
    and therefore evolution in vertebrates doesn't exist"

    This claim is of course absurd. But...How to explain that to them ?
    And, more over, this is ( I believe ) none of the standard creationist objections to evolution.

    Author does't explicitelly claim that God, or the Designer did it, and only keeps proclaiming that evolution doesn't work.

    Has anyone here encountered something similar ?
    Or is this a next step in the evolution of creationism meme ?
    * ID-Velikovsky comparison (0 replies)
    niiicholas2002-12-18 13:00:29
    Here it is, I hadn't seen it before

    The Wedge: A Christian Plan to Overthrow Modern Science?
    Doubting Thomas, Feature Story, No. 6, April/May 1999. By Keith Lankford

    http://www.stephenjaygould.org/ctrl/archive/thomas_wedge.html

    Some minor inaccuracies and now a little out of date, but it features:

    - a cogent comparison of ID to the 1950's Velikovskian movement

    - a fair amount of material about Ed Larson, author of Summer of the Gods, and his conflict with the DI over his book being cited as part of the "Wedge" strategy.
    * Nelson Alonso and front loading (2 replies)
    ExYECer2003-01-12 20:28:32
    Dear Nelson.

    It seems clear to me that you are ignoring the details provided by me about possible pathways for evolution.

    If you claim that front loading explains Pecten then you accept that evolution can generate the eye as found in Pecten unless you are not talking really about front loading but intervention.

    Perhaps you can first share with us your front loading hypothesis wrt for instance Pecten and the Lobster? In fact you suggested that Pax-6 gene 'supports front loading' but if that is the case your argument seems to be that given the existence of Pax-6 at an instant t=t_0 you expect evolution to lead to the large variety of eye 'designs' as found in nature. Is that correct or are you backtracking your claims that let's say every species/family/genus/ or at whatever level was 'front loaded' independently at different instances in time/space?

    I doubt that one can make a logically consistent claim of front loading that is not contradicted by the data other than through the Pax-6 gene. But Pax-6 seems to be going back in time quite some distance, long before the family Pectinidae arose.
    To me it seems that you are not arguing for front loading but rather intervention since your objections seem to be terribly ad hoc and seem to refuse to recognize natural pathways to these structures. If that is the case then you cannot be arguing for front loading since teleological front loading is defined to be at t=t_0 the necessary information was inserted so that at a given time t1, with t1>t0, a certain feature arises in a certain family/species. Non teleological front loading would be that at a certain instance t=t_0 an initial state exists and we can trace back to such an initial state showing how the various eye 'designs' all seem to trace back to ancestral forms.


    As far as the references to Korthof et al, they are meant to help the interested reader understand many of the problems found in Denton's work.

    It seems evident to me that Nelson has not familiarized himself with the papers he quotes but rather that he is relying on second hand information which may or may not be relevant or even accurate. As I have shown, Dakin's 1908 statements are explained in more detail in 1967 and onwards where it was shown that the Pecten eye is very likely an evolutionary  continuation of the single retina eye with the addition of a reflecting layer. The transition is even better to understand from a selective evolutionary viewpoint when realizing the advantage of these changes namely the ability to see both in and outside water. Combine this with the fact that the Pecten resides in a tidal affected area and thus may be exposed to both water and air and one realizes the selective advantage of the Pecten eye. Thus we have found the answer to Dakin's uncertainties. Nelson complains that I do not provide sufficient detail how natural selection and mutation built these eyes but if Nelson were to argue for front loading he would have no choice but to accept that natural forces can lead to the Pecten eye or Nelson should drop his claims about Pecten and front loading. Surely our ignorance of certain details should not be taken as evidence for front loading. In fact although we have not yet obtained all the necessary evidence a plausible pathway has been provided. Nelson may be complaining about 'sufficient details' but the amount of detail so far already exceeds any alternative hypothesis. And since Nelson seems to want to argue front loading he also by default has to accept some time period in which evolutionary processes shaped the eye of Pecten to what it is right now.

    Nelson then raises the spectre of Spondylus, which attaches to rocks as if this forms a problem. Until Nelson can show us from the original research papers what the eye of the Spondylus looks like as compared to Pecten we have no real way to discuss this. Secondly until Nelson shows that there is actually a problem explaining the evolution of the eye in Spondylus and Pecten, we merely can speculate about what Nelson's 'argument may be'. Since Nelson seems to accept the evolutionary history of Pecten and Spondylus one may wonder why he seems to oppose that evolutionary processes led to the eye 'designs' since he does seem to accept front loading and common descent. Perhaps Nelson believes that another mechanism than evolutionary mechanisms played a role? He mentions front loading but as I have shown that merely states that at a given stage in time t=t_0 information was injected into the genome to allow Pecten and Spondylus to form their respective eyes. The fact the pectinacea were ancestral to Spondylidae surely supports the evolutionary pathway. So it is not clear to me how Nelson suggests front loading could have helped Pecten and Spondylidae. In fact, if Nelson is correct about the location of the Spondylus and its eyes (so far the data seem to be vague on either aspect) then Nelson may have to explain why a front loader would lead to a system which is now defunct namely the ability to see in air.

    Nelson then confuses the issue of front loading and intervention even further when he states
    Quote
    If these biological features were poised to evolve into greater complexity through an intelligent agent then it wouldn't have been as difficult as a blind force tinkering with such a complex system.


    Is Nelson suggesting that evolution is guided through an intelligent agent. Then he should not be arguing for front loading but instead for intervention.

    Nelson still seems to be unwilling to deal with the available evidence which includes intermediate stages for the varieties of simple and compound eyes. Perhaps Nelson wants to argue that the details are not sufficient but that's just a matter of time for science to find all the common genes and variations that have led to the variety of eyes as found in nature. So far the evidence strongly suggests both evolutionary mechanisms and at least for many basic components a common ancestor.

    If Nelson had taken the time to look at the pictures then he would have noticed how these portray the variety of intermediate paths likely to have been taken in the evolution of the various eye forms.

    Nelson still repeats his so far unsupported assertion that
    Quote
    Again, none of this shows how blind natural forces would, nor does it even explain why, natural selection would guide the organism down the difficult road of refraction to reflection in my particular examples


    1. Could Nelson show that the road of refraction to reflection is difficult
    2. Could Nelson show that the road of refraction to reflection is even relevant for the lobster?

    Nelson confuses the situation even further by claiming that

    Quote

    However, what I would expect from a Front-Loading persepective is that every step of the way was every bit more complex then the last, however, through the help of pre-positioned elements the evolution of these eyes was directed through intelligent agency.


    So is it front loading or is it intervention? If it is front loading then we have the situation that at a certain time the information needed for evolution to play out was injected into the genome of a common ancestor and that from this common ancestor all the descendants arose with the large variety of eyes. Ignoring for the moment the grasping at straw nature of such a front loading scenario which would have to play out through an inherent chaotic and thus unpredictable system and interactions to eventually lead to the eye of the Pecten. Nelson presents no more evidence than that a some moment the basic building blocks were present that eventually would allow the Pecten or any other organism to evolve an eye design. No effort is made by Nelson to show that the eyes of the lobster are optimal for the functioning of the lobster. In fact Nelson merely argues that for the lobster eye, the eyes are perfect squares that are fine-tuned for the vision of lobster. No further information is presented to support this case. And if Nelson wants to consider fine-tuning and continue to argue for front loading then Nelson de facto has accepted the fine tuning power of evolutionary processes.



    Given the contradictory stance of Nelson on the issue of front loading I would encourage Nelson to address the following issues.

    1. Explain the hypothesis of front loading as it applies to Pecten.
    2. If Nelson accepts front loading then does Nelson accepts that natural processes are responsible for the shaping of the eyes of Pecten? In absence of such an acceptance, Nelson cannot be talking about front loading here.
    3. Can Nelson explain in detail the similarities and differences between Pecten and Spondylus and can Nelson provide us with the arguments proposed by Dakin? Do the findings apply to the whole family of Spondylus or just some particular species? After all the various species of Spondylus do seem to occupy a large variety of ecological niches
    4. Can Nelson show that the lobster eyes are perfect squares or is Nelson using stylized drawings to reach these conclusions?


    Perhaps Nelson may want to explain why the squares in the following picture are all but perfect?



    Perhaps Nelson was confused by the resulting drawings?



    Perhaps Nelson can also appreciate what perfect squares really would look like?

    * http://www.antievolutionIslamic Intelligent Design (1 replies)
    tufail2005-11-04 00:12:31
    For most people, both evolutionists and creationists, intelligent design means Christian creationism. All across Islamic Centers in US and the world and almost every Muslim web sites promote Evolution Deciet, a book published by Harun Yahya. This book is a carbon copy of Institute for Creation Research (ICR) Publications. He uses ICR's distorted "science" to reject science. Only difference is that Yahya does not support recent origin of the earth.

    Recently, A book, Creation AND/OR Evolution An Islamic Perspective, by a Muslim theist evolutionist, T.O.Shanavas was released. The author is very critical about Yahya. However, he claims that Theory of evolution has an Islamic root and, in fact, according to him, Muslims proposed theory of evolution centuries before Charles Darwin.

    This book is a challenge to those who want to teach Christian creationism or Intelligent design in science class in American public school. America being a secular country, there is a separation of church and state. Government cannot promote any purticular religion. Christian fundamentalists will be frighted and and may back off from corrupting science curriculum if Muslims in any of the states such as Kansas, Pennsylvania, etc demand Shanavas's Islamic creationism to be incuded in the science class along with Christian intelligent design.

    Shanavas is a creationist but strongly opposes the teaching of any form of creationism in public schools in America. In a news paper (The Daily Telegram) interview Shanavas states that there is no place for intelligent design in science class rooms. (http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=Post;CODE=00;f=2)[I][B]
    * Anthropic/anthropocentric principle (1 replies)
    niiicholas2003-06-12 16:54:35
    I have no strong opinions on the anthropic principle, but I figured I'd repost this little Sagan quote I posted at ARN:

    Quote
    Originally posted by LlaniteDave:
    [qb] [QUOTE]Originally posted by Another:
    [qb]
    However, in regards to complexity - we have a problem (and not just the usual problem of definition). Complexity cannot be selected for in and of itself - and evolution has no foresight to the future opportunities complexity affords.  This will be true of all life, not just life of the substrate we know. Complex life is rare not because the earth is rare, but because there is no immediate selective benefit to complexity - usually only costs.

    Complexity did not evolve with any reasonable speed on earth. It was a major transformation and an unintended result of symbiosis or predation.  That complex than bacteria only evolved once is telling. It is a silent, lonely answer to Fermi's paradox.[/qb]
    Which also poses a problem for the "fine tuning" issue.  If the universe is "fine tuned" so that life can exist, in all the universe is the earth the only beneficiary of that fine tuning?  If ID is true, doesn't that predict that life, and complex life as well, should be ubiquitous throughout the galaxy?[/qb][/QUOTE]An exceedingly good point.  I recall a clever bit of Carl Sagan:

    Quote
    Our universe is almost incompatible with life -- or at least what we understand as necessary for life: Even if every star in a hundred billion galaxies had an Earthlike planet, without heroic technological measures life could prosper in only about 10^(-37) the volume of the Universe.  For clarity, let's write it out: only 0.000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 1 of our universe is hospitable to life.  Thirty-six zeroes before the one.  The rest is cold, radiation-riddled black vacuum.
    (Pale Blue Dot, p. 34)



    It is perfectly possible to imagine universes much more hospitable to life -- most early cosmologies were exactly that.

    While I'm here, the interaction of the anthropic-principle-type design argument with the biological ID argument is *very* peculiar.  It was stated most pithily here:

    Quote
    The fact that the laws of the universe are perfect for life is evidence for a Designer. The fact that the laws of the universe can't produce life is evidence for a Designer. [23]
    "The Quixotic Message", or "No Free Hunch"
    http://www.talkdesign.org/faqs/hunch/hunch.html

    (In http://www.arn.org/boards/ubb-get_topic-f-13-t-000751.html )
    * testing... (0 replies)
    niiicholas2002-05-06 19:19:54
    testing, testing, 1 2 3...

    Wow, this looks like a spiffy software package, all the code tags are right above there...

    Quote
    Curious green ideas sleep furiously


    ...well, it's sticking all of the tags at the *end* of the line, regardless of the cursor position.

    Trying smilies:
    :0  ???  :D

    Trying a URL:
    Talkorigins webpage link test

    ...hey, that worked pretty well..


    A graphic:

    ...hmm, it stuck the code at the end of the post, I'll move it up.



    I won't even trying the Flash movie posting option...

    nic
    * AiG on scientific theory (8 replies)
    Jacor2002-11-10 15:28:27
    I just want to make the observation that if the level of scientific "thought " as presented by the person with the title of "Information Representative" of AiG is true of the actual science used by them.  I predict that within 2 generations of Creationists being able to teach their "science" as a valid alternative theory, society will be well on its way back to pre-scientific levels of health and knowledge.  This is due to the superficial level of thinking that is encouraged.

    John Verderame, in a fairly detailed non-answer to my statement on why I did not accept his generalizations as answers to my specific questions. gave this Bio.  "I have a B.S. in Biology and a Master of Theology degree from a highly respected Seminary and almost 30 years of work experience both in ministry and in the fields of biology and astronomy, so have done some studying too."

    In response to my observation that the problem with relying on the Bible to answer anything that is not currently in the "known" column in science is that it discourages the original research needed to find the answers.  His response was "prove that".  He also referred me to a list of "research" done by creationists.
    Here is what I found.

    Dr Steve Austin PhD, describes self as Creationist Geology Professor, B.S. (Geology), University of Washington, Seattle, WA, M.S. (Geology), San Jose State University, San Jose, CA, Ph.D. (Geology), Pennsylvania State University, University Park, PA.
    Only acknowledged publications are in Creationist publications, and are not on field of specialty of Geology.  No original research.

    Dr Don Batten  He is doing work that any self-respecting agriculturist does.  He might have a new hybrid, but no original research.  Does have publications in Creationist publications on mutation as evidence of divine intervention, other than "the Bible tells me so", no supporting evidence.  He makes unsupported statements about the number of nucleotides that can be changed before becoming fatal (3).  I will point out that 3 nucleotides do not make up a single gene.  His degree is in Horticulture.

    Dr John Baumgardner  (B.S, M.S., PhD (UCLA)) is a geophysicist employed at the Los Alamos National Laboratory in New Mexico. His work involves detailed computer modeling of the structure and processes of the earth's interior, as well as a variety of other fluid dynamics phenomena.  
    Only published works supporting Creationism is at 3 Creation Conferences, and are not related to his field of study.  
    Is this supposed to impress me?  Especially since his bio states that he changed majors to prove creationism is correct.  Since he has not run any tests to prove or disprove his hypothesis he can not claim that his belief is anything other than an opinion.

    Jerry Bergman  PhD Psychology  Published in Creationist publications on topic of why there is no scientific support for evolution.
    I know a master level psychologist that believes that watermelons are cucumbers left on the vine too long.  So?

    I do not see any original research here.  How does this disprove my statement?

    Dr. Verderame's response:  "(What are YOUR credentials, that you are in such a position to pass judgment?)"

    Like an idiot I actually sent them.  AAS Nursing, BS double major Chemistry and Biology

    His response: "Please don't expect any further responses.  We are not getting anywhere.

    Have a good weekend.

    John"

    Since the following are verbatim quotes from him in two earlier communications I must state that I do not have his permission to quote this, however I am quoting just to show his level of response when he can't think of anything better.
    He cited Pasteur as being the perfect "Creationist Scientist" because he developed the germ theory despite opposition by scientific thought.  In response I sent an abbreviated history of contributors to the germ theory going back to 50 AD.  He now changes his argument to:
    JV:  "What is your point?  Of course, no theory arises in isolation.  We point out that evolution has its basis in ancient Greek philosophy.  But Darwin helped to systematize and quantify the concept so that those who followed him recognize his work as a watershed.  Same with Pasteur.  
    I could not resist, so my response and his reply follows.
    He inserted responses in my answer and they are designated as "JV".

    Technically since Pasteur did not publish, and Koch provided the proof, Koch should be credited with the formulation of the theory.
    JV:  Nice try.  So 'publishing' is what distinguishes the men from the boys, eh?

    Otherwise credit would have to go to Henle in 1840. As pointed out in the section on Koch, just like evolution, the Germ Theory continues to "evolve."

    JV:  Which you have yet to demonstrate ;-)  Throw the word around all you want.  But back it up with facts.  You know those microorganisms Pasteur and Koch played with?  Make one.  Starting with nothing.  And then, if you can do it, prove to me it took no intelligence to do it.

    I could not reply to his comments as he cut communication with me.  The range of topics had grown to the proportion that there was no cohesive way to respond to all of them in each communication.  The list kept growing as Dr. Verderame added to the list each time.  I think he was planning on overwhelming me with the sheer volume of topics.

    Paul C



    ???
    * Advantages of Theft over Toil (1 replies)
    Wesley R. Elsberry2004-05-25 09:10:53
    This thread is for discussion of the paper by John Wilkins and I, "The advantages of theft over toil: the design inference and arguing from ignorance" (Biology and Philosophy 16(5) (November, 2001):711-724).

    The abstract:

    Quote

    Intelligent design theorist William Dembski has proposed an "explanatory filter" for distinguishing between events due to chance, lawful regularity or design. We show that if Dembski's filter were adopted as a scientific heuristic, some classical developments in science would not be rational, and that Dembski's assertion that the filter reliably identifies rarefied design requires ignoring the state of background knowledge. If background information changes even slightly, the filter's conclusion will vary wildly. Dembski fails to overcome Hume's objections to arguments from design.


    * Bill emulates Christ (2 replies)
    vpenguin2005-07-04 02:54:46
    Dembski posted this picture with the following message to his blog:
    "Here’s an image I found amusing that someone sent me about my lack of faith in Darwinism. I’ve always wanted an image of Darwin and me as professional wrestlers with me doing a piledriver on him."

    See:
    http://www.uncommondescent.com/index.php/archives/170

    Gee, Bill, how Christian of you.
    * BY evolution or design? (0 replies)
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    * FARIBAULT teacher holds firm on his design belief (0 replies)
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    * Peppered moths and the moon (8 replies)
    ExYECer2003-01-28 00:51:36
    http://groups.yahoo.com/group/IntelligentDesignUpdate/message/176

    Good posting on the effects of the moon phase on the recapture experiments by Kettlewel
    Quote

    To get a better idea if there is any significance in the phases of the moon for Peppered Moth experimentation, I provide the following analysis of average daily capture rates of unmarked moths from the three experiments
    correlated to moon phase:

    Code Sample

    Phase               B_53 B_55  D_55
    New_Moon         NA   0.34   1.42
    Waxing_Cresent NA   NA     0.62
    First_Quart         NA   NA     0.58
    Waxing               NA   NA     0.42
    Full_Moon           0.96   NA     0.1
    Waning               0.78   1.59     NA
    Last_Quarter      1.1   1.3     NA
    Crescent_Waning  NA   0.77     1.79
    Average_Daily      56.45   35.31     17.67



    (Figures are the average daily capture rate for the phase / average daily capture rate for the entire experiment. I have expressed the data this way so that the generally low capture rates in Dorset do not conceal
    correlations. The data for New Moon, First Quarter, Full Moon and Last Quarter are the figures for the day of the New Moon (etc) plus the day on either side. Other figures are for all days between the flanking phases.
    The one exception is the Full Moon phase for Birmingham, 1953 which includes the two days prior to the Full Moon. Raw figures and moon phase data is
    available in Appendix A.)


    The Dorset 55 data does seem to show a reasonable correlation of recapture rates and moon light with more moon light leading to lower recapture rates as the moon attracts the moths. Were the Birmingham experiments perhaps with phermone traps? Anyone knows?



    I am archiving the appendix data here

    ***********
    Appendix
    ***********

    Kettlewell's Captures of unmarked Biston Betularia in 1953 and 1955
    experiments correlated for moon phase. Some 1955 Birmingham data appears
    twice (once in each column) to assist comparisons. Data reads as
    Total(Carbonaria/Typica).

    1955 | 1955/1953
    Date| Catches | Date| Catches | Phase
    12/6 | | 12/7| 100(89/6)| Last Quarter
    13/6 | | 13/7| 29(25/4) |
    14/6 | 17(0/16) | 14/7| 56(53/2) |
    15/6 | 20(0/18) | 15/7| 24(20/2) |
    16/6 | 37(1/34) | 16/7| 15(13/2) |
    17/6 | 54(0/51) | 17/7| 22(20/2)|
    18/6 | 30(0/29) | 18/7| 19(15/2)|
    19/6 | 21(0/20) | 19/7| 6(5/1) |
    20/6 | 43(0/41) | 20/7| 11(10/1)| New Moon
    21/6 | 11(0/9) | | |
    22/6 | 10(0/9) | | |
    23/6 | ..... | | |
    24/6 | ..... | | |
    25/6 | 12(1/11) | | |
    26/6 | 8(1/6) | | |
    27/6 | 8(0/8) | 19/6 | | First Quarter
    28/6 | 15(0/15) | | |
    29/6 | 9(0/9) | | |
    30/6 | 7(1/5) | | |
    1/7 | 7(0/7) | | |
    2/7 | 7(0/7) | | |
    3/7 | ..... | 25/6| 9(8/0) |
    4/7 | ..... | 26/6|144(124/14)
    5/7 | 2 (0/2) | 27/6| 38(33/5) | Full Moon
    6/7 | | 28/6| 25(21/3) |
    7/7 | | 29/6| 57(50/6) |
    8/7 | 74(62/7) | 30/6| 40(36/3) |
    9/7 | 41(40/0) | 1/7| 64(57/7) |
    10/7 | 53(48/3) | 2/7| 58(47/7) |
    11/7 | 9(4/5) | 3/7| 69(52/8) |
    12/7 |100(89/6)| 4/7 | 52(43/7) | Last Quarter
    13/7 | 29(25/4)| 5/7 | 65(57/3) |
    14/7 | 56(53/2)| | |
    15/7 | 24(20/2)| | |
    16/7 | 15(13/2)| | |
    17/7 | 22(20/2)| | |
    18/7 | 19(15/2)| | |
    19/7 | 6(5/1) | | | New Moon
    20/7 | 11(10/1)| | |

    Kettlewell's total catches for 1953 and 1955 experiments.

    1955 | 1955/1953
    Date| Catches | Date| Catches | Phase
    12/6 | | 12/7| 101(89/7)| Last Quarter
    13/6 | | 13/7| 29(25/4) |
    14/6 | 23(4/17) | 14/7| 56(53/2) |
    15/6 | 34(2/27) | 15/7| 24(20/2) |
    16/6 | 37(1/34) | 16/7| 15(13/2) |
    17/6 | 68(7/58) | 17/7| 22(20/2)|
    18/6 | 31(0/30) | 18/7| 19(15/2)|
    19/6 | 29(2/26) | 19/7| 6(5/1) |
    20/6 | 47(1/44) | 20/7| 11(10/1)| New Moon
    21/6 | 16(1/13) | | |
    22/6 | 19(5/13) | | |
    23/6 | ..... | | |
    24/6 | ..... | | |
    25/6 | 12(1/11) | | |
    26/6 | 12(3/8) | | |
    27/6 | 8(0/8) | 19/6 | | First Quarter
    28/6 | 21(1/20) | | |
    29/6 | 14(0/14) | | |
    30/6 | 16(4/11) | | |
    1/7 | 11(2/9) | | |
    2/7 | 7(0/7) | | |
    3/7 | ..... | 25/6| 9(8/0) |
    4/7 | ..... | 26/6|149(127/15)
    5/7 | 9 (0/9) | 27/6| 40(34/5) | Full Moon
    6/7 | | 28/6| 29(23/3) |
    7/7 | | 29/6| 66(55/10)|
    8/7 | 64(62/7) | 30/6| 42(37/3) |
    9/7 | 85(73/11)| 1/7| 87(76/9) |
    10/7 | 58(51/5) | 2/7| 92(75/13)|
    11/7 | 59(50/7) | 3/7| 98(77/11)|
    12/7 |101(89/7)| 4/7 | 77(66/9) | Last Quarter
    13/7 | 29(25/4)| 5/7 | 81(73/3 |
    14/7 | 56(53/2)| | |
    15/7 | 24(20/2)| | |
    16/7 | 15(13/2)| | |
    17/7 | 22(20/2)| | |
    18/7 | 19(15/2)| | |
    19/7 | 6(5/1) | | | New Moon
    20/7 | 11(10/1)| | |


    Phases of the moon for 1953/1955

    Lun# New Moon First Quarter Full Moon Last
    Quarter
    ---- ---------------- ---------------- ---------------- ------------
    ----
    +0376 1953/05/13 05:06 1953/05/20 18:20 1953/05/28 17:03 1953/06/04
    17:36
    +0377 1953/06/11 14:55 1953/06/19 12:01 1953/06/27 03:29 1953/07/03
    22:03
    +0378 1953/07/11 02:28 1953/07/19 04:47 1953/07/26 12:21 1953/08/02
    03:16
    +0379 1953/08/09 16:10 1953/08/17 20:08 1953/08/24 20:21 1953/08/31
    10:46


    +0400 1955/04/22 13:06 1955/04/29 04:23 1955/05/06 22:14 1955/05/15
    01:42
    +0401 1955/05/21 20:59 1955/05/28 14:01 1955/06/05 14:08 1955/06/13
    12:37
    +0402 1955/06/20 04:12 1955/06/27 01:44 1955/07/05 05:28 1955/07/12
    20:31
    +0403 1955/07/19 11:34 1955/07/26 16:00 1955/08/03 19:30 1955/08/11
    02:33
    +0404 1955/08/17 19:58 1955/08/25 08:52 1955/09/02 07:59 1955/09/09
    07:59
    http://www.lunaroutreach.org/phases/phases.cgi



    [QUOTE]

    * SCIENCE and Torah: Conflict or Complement? (0 replies)
    NULLNULL
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    * ID versus evolutionary science (0 replies)
    ExYECer2002-12-27 11:39:22
    Cornelius states that

     
    Quote

    Unfortunately, evolution has always relied on #1 to establish itself as a scientific fact.
    It seems that Cornelius may be unfamiliar with the scientific evidence supporting evolution if he believes that evolution has ALWAYS relied on #1 to establish itself as a scientific fact.

    Reality will show that it is #3 and #2 which are the methods through which science has established evolution as a viable theory. I am somewhat surprised to see Cornelius make the statement and others such as    
    Quote
    To me it is clearly flawed, and it is little wonder that evolutionists dwell so much on #1. It clearly is the motivation for the theory.
    Which suggests to me that he has not really looked at the scientific evidence supporting evolution. It may be helpful if Cornelius could help us understand how he reaches conclusions like the ones above or    
    Quote
    I'm merely claiming that the scientific evidence points away from this.
    What scientific evidence points away from naturalistic pathways?

    If Cornelius really believes that God and thus ID fails if we can show that naturalistic pathways are sufficient or that natural pathways explain the preponderance of evidence then for all practical purposes we can consider ID to be refuted. ID by itself according to Cornelius' definition seems to be providing us with nothing more to understand the world around us, it merely makes claims based on a religious motivation without attempting to provide for a better explanation than that provided by scientific inquiry. And for good reasons since I do not believe that ID in this format can do much to compete with science.
    ID seems to require that we ignore the vaste amounts of data that support #2 and #3 while focusing on the strawman of #1. If Cornelius were serious about the statement that    
    Quote
    ID is using all our knowledge to identify evolution as flawed.
    then he would not have focused on making claims that evolution focuses on #1. Hundreds, thousands of papers on evolutionary mechanisms and theory would put significant doubt on the validity or even supportability of Cornelius' claims.

    Cornelius also states that
     
    Quote

    We had a good and fruitful discussion. My hunch that evolution is quite flexible vis-à-vis these phylogenetic results, if anything, were corroborated
    seems to ignore the strengths of the phylogenetic results vis-a-vis common descent and seems to focus on the fact that scientific theory can adapt to our increasing knowledge. So far the arguments seem to not really focus on scientific arguments but rather on hand waving, strawmen arguments while ignoring the vaste amounts of evidences supporting the fact of evolution.

    In a previous posting Cornelius confused my comments about nested hierarchies with correlated characteristics. Nested hierarchies are als correlated but correlated characteristics need not be hierarchical.

    Finally Cornelius wondered why I made the following statement

    [quote]
    We should be careful not to mix our faith and science, since both will suffer. -- Francis
    [quote]

    Cornelius states that:

    "This obviously does not derive from science nor the Scriptures, so I'm not sure why you say this."

    If science has to give way to our theological thinking then both science and theology will suffer. Of course science and theology can live together in their own realm but when it gets misapplied like for instance found in many YEC approaches, it becomes a destructive force to science and religion. As an ex-YEC-er I have seen much of this.

    In Christ
    F
    * "Monologues passing in the night" (0 replies)
    Wesley R. Elsberry2003-01-13 15:10:39
    Design Theory and its Critics

    Quote
    The present book, Intelligent Design Creationism and its Critics, is intended as a sourcebook of materials from both sides of the present debate. The editor, Robert T. Pennock, who is a vocal critic of ID, takes it that ID claims fail more or less on all fronts, and while giving both sides a platform, intends for the present volume to make ID's untenability (as he sees it) amply clear.


    Ratzch apparently does not distinguish an accusation of ignorance from ad hominem.

    Quote
    One individual particularly singled out is, surprisingly, Alvin Plantinga, who al-
    though an ID sympathisizer is not an ID advocate.

    Ruse:
    We know that Plantinga's agenda is Christianity. That is fair enough. But it is an agenda backed by a deliberate ignorance of work that is going on today in science. Plantinga is able to talk so confidently about science stoppers only because he has not and apparently will not look at what scientists are saying and achieving. [Ruse, p. 382]


    Ad hominem arguments are irrelevancies directed at aspects of personality.  Demonstrable ignorance of topics at issue, though, is directly relevant and is a legitimate point of argument.

    Wesley
    * Evolution education still a factor in Kansas elect (0 replies)
    NULLNULL
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    * Evolution Question #1 (3 replies)
    dougp592006-11-03 10:08:10
    From www.evolutionsucks.org

    Evolution Question Number One;

    The theory of Evolution says that all life evolved from lower life forms. In other words, we came from fish.  Which of course came from even simpler blobs of something.  

    Oddly enough though, evolutionists say that the whales (a mammal) evolved from a hoofed land animal called Mesonychids.  Textbooks describe these beasts as about the size of a hyena.  

    The Mesonychids would have of course evolved from a reptile from a fish from a simpler blob of something, you get the picture.

    Simpler to more complex life forms, that is the essence of Evolution by natural selection.  They call this; "speciation".

    So, a simple form of life in the ancient seas evolves into a fish, which evolved into a reptile,which evolved into a land animal.  

    Once it had accomplished this monumental feat, it then decided to get REALLY BIG, loose its' legs and return to the seas!  

    Oh, and do not forget that it has to move its’ nostrils to the top of the head so they become blow holes so they can breath when they surface.

    Question #1  Can you show the transitional fossils that prove ANY of this?
    Evolution Sucks
    * What should make one suspect ID? (9 replies)
    niiicholas2002-12-18 18:24:58
    Over at ARN, Mike Gene is again claiming that the question "What should make one suspect ID?" has not/cannot be sufficiently answered by ID skeptics.  The implication is basically that ID skeptics are close-minded and unable to consider the matter in a neutral, open, explorative way.

    http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000536

    But there are lots of things that would make me suspect ID.  Note that these things are not the same things that would prove it beyond a reasonable doubt, although a lot of these "evidences for suspicion" put together might fit that bill.

    MG specifically put forward the flagellum as an example, conveniently a particularly ancient system for which the kinds of evidence available for e.g. the immune system are much more difficult to come by.

    Quote

    Tell me what would cause you to suspect the flagellum as designed. Thus far, not one ID critic has shared a useful criterion.


    As JP has noted in the thread, many answers to the "suspect" question have already been provided, it's just that Mike Gene doesn't like them because design does not entail that these things exist.  That's pretty much the problem with Mike-Gene-design, it doesn't appear to entail anything in particular at all.  Even IC systems are apparently accessible to evolution under MG-ID, so if the tremendously complicated immune system is shown to have plenty of evidence of gradual natural origins, he can just shrug it off and say that ID designed something more remote, like the flagellum.

    Still, an observation does not have to be *entailed* by design in order to be an observation that would legitimately raise suspicion.  Evolution does not predict that any particular transitional fossil will be found, just that some will be found somehwere, and these legitimately raise suspicion.  Presumably even a rarified design hypothesis predicts that some kind of positive evidence will be found somewhere.

    I would suspect (not conclude) design for the flagellum if there were evidence for any of the following:

    1) A purpose other than maximizing the reproduction of the genes of the bacterium in question, that fits with some hypothesized designer.  E.g., mousetraps are designed for trapping mice that are annoying humans.  Note that in contrast, evolutionary theory predicts this for all complex "designed" systems.  Find a counterexample and you've disproved evolution.  Find a counterexample with a purpose that fits some specific designer hypothesis and you've got reason to suspect that designer hypothesis.

    2) True IC, i.e. if the parts of the flagellum really did not have any function apart from contributing to flagellar function, i.e. that any subset of flagellar parts really was "by definition nonfunctional".  This was Behe's original attempted argument, and if it had held up under the weight of evidence then he would have had something.

    3) Biologically impossible transplants of the complex "design" across phylogenetic lines.  This is seen *in spades* in human design systems.  However, in biological systems, such transplants appear to be limited in numerous ways:

    a) Basically limited to single-celled critters without protected germ-line cells
    b) Most commonly there to prokaryotes that are *known* to do all kinds of conjugation, DNA uptake, etc.
    b.5) In eukaryotes, the most impressive cases lateral transfer are the cases of symbiosis, in which the genomes of the host and symbiont are in close association for millions of years and transfers can occur bit-by-bit while maintaining function
    c) Suspicions of transplants are often confirmed by finding plasmids, insertion remnants, and evidence of other known lateral transfer mechanisms
    d) Transplants are most common between prokaryotes (a) closely related or (b) living in close proximity
    e) Apparently limited to relatively simple systems (single operon?), and the more complex the system, the more closely related must be the donor/acceptor.  The most complex system transferred that I can think of is Type III virulence systems, and (IIRC) these are all restricted to a relatively narrow group.

    As an example of the contrast seen in human designs, the following highly complex systems originated locally and were rapidly transplanted into any manner of larger devices (cars, planes, boats, etc.) without any regard for the kinds of biological, ecological, and phlyogenetic patterns described above:

    - computers
    - GPSs
    - satellite phones
    - emergency transponders

    4) It occurs to me suddenly that the pattern that all of these designed transplants follow is that they are useful *to the designer*, i.e. safety, navigation, etc.  So, even in a case where the lateral transfers were biologically possible, if the pattern of transfer fit the purposes of a hypothesized designer(s), I would suspect design.

    5) Evidence of "front-loading", e.g. if many bacteria had buried instructions for flagella, protected somehow from degradative mutations (not a tough burden for your average superadvanced designer), that were waiting to be "turned on" at some point in the future for some purpose of a hypothesized designer (this is a modified version of Behe's supercell idea)

    6) A communication-to-intelligent-beings signal encoded in the flagellar genes.  E.g., a prime number sequence apparently cleverly encoded in the essential nucleotides or amino acids of the flagellum.  I say "apparently" because just the bare fact of a prime number sequence would not constitute proof, only suspicion (which is all MG wants anyway), unlike in astronomy it is just possible that there are ways for biological mechanisms to generate primes (although it is quite a stretch from 17-year cicadas to genome sequences).

    I'm sure there's more...I won't, however, say the one that I think MG prefers, namely "it looks designed", because it's pretty clear that natural selection can produce complex "designed" adaptation when the adaptation benefits the genes of the organism.  Even Mike Gene concedes this, so IMO it appears that he is being inconsistent when he places the thus-far-unverified-in-biology ID hypothesis on the same footing as the well-verified-in-biology NS hypothesis.  Why not also include Lamarkian evolution and complexity theory on the same footing also?  I would say that each of these has at least a wee bit of positive evidence raising a little bit of suspicion, unlike ID.

    Links to other threads and CCed posts on this topic would be worthwhile.
    * The Debate (0 replies)
    Kuglo2003-03-15 12:29:44
    **********************************************
    * Are Honeybee Societies Irreducibly Complex? (1 replies)
    lpetrich2003-02-02 17:14:46
    I wish to propose an analogy that may be helpful in understanding the evolution of irreducible complexity.

    Honeybee societies.

    Honeybee hives contain a queen, as many as 10,000 workers, and some drones (male bees). The queen depends on the workers for all her needs -- food, shelter, protection, etc., while the workers depend on the queen to replenish their numbers. Queens cannot exist without workers, and workers cannot exist without queens. Thus, irreducible complexity.

    This total dependency extends to the founding of new hives. Workers do all the work of founding; they scout for hive locations and then go to whichever one attracts the most interest. And then they do all the work of construction in that location.

    Compare solitary bees, in which a female does all the tasks that honeybee queens and workers do, though with much simpler nests.

    Which makes it seem difficult to picture how honeybee societies could have been a result of evolution by natural selection, or at least that's what an entomological counterpart of Michael Behe would say.

    But fortunately, the diversity of life offers examples with a very plausible intermediate state: bumblebees. A bumblebee queen overwinters in isolation and founds a hive in the coming spring, constructing it and bringing food to her offspring in the fashion of a solitary bee. But her offspring become workers who help her with the next generations over the year.

    Thus, the evolution of honeybees can be broken up into two steps:

    1. Some of a female's daughters staying home and helping to raise that female's other offspring, thus the evolution of the queen/worker distinction.

    2. A queen recruiting some workers to help found a hive, thus giving that queen "instant" workers at that new hive. This makes it unnecessary for a queen to do anything but lay eggs all day.

    Michael Behe's work, it seems to me, focuses on the molecular equivalent of honeybees; the challenge for understanding the origin of these features is to find the molecular equivalent of bumblebees, or at least work out some plausible scenario for their occurrence. And biologist Kenneth R. Miller has attempted to do exactly that, finding plausible bumblebees for the bacterial flagellum's honeybee.

    I think that he'd have a bit more respect if he simply decided that the origin of what he discusses is a mystery. he could have been like Robert Shapiro, who has criticized various origin-of-life scenarios in detail without claiming that that means that the Earth had been "seeded" with its first organisms.
    * Evolution Before the Common Ancestor (1 replies)
    lpetrich2003-02-11 01:38:28
    Over in this Internet Infidels thread, I had posted some interesting recent research into the evolution of life before the Last Universal Common Ancestor (LUA, LCA, LUCA) of all known cellular Earth life. To summarize, both papers I'd looked at point to the earliest Earth life as being closer to prebiotic chemistry than more recent life. And the second paper points to evidence of much less complexity in the earliest life.

    The enormous volume of genetic data collected over the last few decades, including the sequencing of over 100 genomes, has made possible the reconstruction of several of the genes and proteins contained by the Last Universal Common Ancestor.

    The amino-acid content of these proteins is interesting; according to the work of Brooks DJ, Fresco JR, Lesk AM, Singh M, the LUCA's proteins were enhanced in amino acids known to be produced in prebiotic-synthesis experiments, and depleted in amino acids known to be rare or absent in such experiments. This adds support to the hypothesis that the original source of amino acids was prebiotic synthesis; the earliest organisms simply eat some Primordial Soup.

    By comparison, Brian K. Davis's work focuses on 10 proteins, and uses a different criterion for assigning amino-acid origin time; how many metabolic steps are necessary to produce some amino acid from a Krebs-Cycle predecessor. Aspartate and glutamate, for example, score very low, while lysine and arginine score very high. The low scorers are also those relatively abundant in prebiotic syntheses, which suggest that biosynthesis of them was developed as a substitute for Primordial-Soup eating (the Horowitz hypothesis).

    The "code age" of a protein he determined by finding the average score of its amino acids; he used this to work out the proteins' order of appearance.

    The oldest of these proteins was ferredoxin, a biosynthesis enzyme that contains iron-sulfur clusters and that transfers electrons (hydrogen-atom equivalents). This protein he reconstructs as having a negatively-charged tail; this can stick to positively-charged objects like mineral surfaces with their metal ions -- which is consistent with the view of Gunter Wachtershauser that life originated from iron-sulfur-associated chemical reactions on mineral surfaces, and that the Krebs Cycle dates from this time. Note that the Krebs Cycle's members are all acids -- negatively-charged ions -- meaning that they can stick to mineral surfaces.

    This suggests that the earliest life had not had well-defined cells, that it had been a sort of Haeckelian Urschleim living in the mud of hydrothermal vents.

    Not much younger than ferredoxin is a protein involved in cell division and an ATPase component that resides in cell membranes; as a consequence, nearly all the rest of Brian Davis's scenario takes place in distinct cells, including the acquisition of "difficult" amino acids like the benzene-ring and alkaline ones.

    Also after the origin of cells but before the LUCA is the origin of DNA; enzymes for synthesizing DNA nucleotides from RNA ones, copying DNA to RNA, and copying RNA to DNA date from this period. So DNA is younger than both RNA and proteins.

    However, DNA-to-DNA copying systems are much more difficult to place in this period, since those of the (eu)bacterial and the archaeo-eukaryotic lineages are very different, suggesting separate elaboration -- or even separate origin. The LUCA could have had a DNA-RNA genome, with DNA being copied to RNA and back.

    Brian Davis's paper did not address the RNA-world question, but his work suggests that an RNA world, if it had existed, had been pre-cellular.

    An interesting result is that the earliest Earth life is closer to various sorts of prebiotic chemistry than later Earth life. This poses an interesting conundrum for the hypothesis that some designer had "seeded" the Earth with some organism that became the ancestor of all its later life. Why this choice of "seed"? Why not a "seed" with a chemistry more like that of present-day organisms?

    Also interesting is the absence from the earliest life of DNA, distinct cells, and several amino acids; this indicates the absence of the enzyme systems necessary for constructing and handling them. Thus, the origin of life has to account for much less complexity than one would expect from present-day cell architecture.

    References:

    Brooks DJ, Fresco JR, Lesk AM, Singh M.
    Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.
    Mol Biol Evol  2002 Oct;19(10):1645-55
    At this PubMed entry.

    Davis BK.
    Molecular evolution before the origin of species.
    Prog Biophys Mol Biol  2002 May-Jul;79(1-3):77-133
    At this PubMed entry.
    * Clone Wars (3 replies)
    niiicholas2003-01-13 22:17:00
    Originally posted here.

    Quote

    January 13, 2003

    ID and Human Cloning

    By Paul Nesselroade

    Does the Intelligent Design (ID) movement have anything to say about current experimentation with human cloning?


    Clearly, starting points are critical in shaping how we view the appropriateness of any action. If our starting point is the belief that human life was accidental and brought about solely by the impersonal forces of natural selection and random mutation, then, any purpose or meaning for life has to be assigned by us, chiseled out of the void of meaninglessness with our own hands. Starting here, the idea of cloning new life explicitly for the enhancement of our own lives (through organ replacement, stem cell harvesting, or for reproductive purposes) can be legitimized. The human ‘cost’ associated with both fine-tuning the cloning process (animal cloning rarely results in birth and virtually all of those born have serious abnormalities and/or die early) and creating life expressly for sacrificial purposes, may be considered unfortunate, but can hardly be considered wrong.

    (bolds added)


    Strange that this ARN missive doesn't recognize the Raelian's oh-so-crucial "starting point":

    Quote

    Evidence
    Introduction

    Supporting evidence

    Welcome to the Evidence page, a subsection of the Raelian Revolution website.

    If we truly were created by people from space, then there would be traces of this creation in our history, mythology and religion, be it Judaic, Buddhist, Christian, Islamic or other. Science should confirm this and there should be UFOlogical evidence of them monitoring our progres and even visitations.

    In fact, if one takes the trouble to look, this is exactly the case and the horisontal navigation bar above provides links to such evidence including a bibliography section listing references and authors whose totally independent conclusions support the validity of the Raelian Message.

    [...]

    Supporting evidence p. 3

    EMBARRASSING QUESTIONS FOR THE EVOLUTIONISTS
    For 20 years, the Raelian vision of "scientific creationism" : a step ahead of science ?

    It is striking to note that while the Raelian theory is being confirmed by a continual series of scientific discoveries, the theory of Evolution is, on the other hand, being increasingly challenged as its old questions remain unanswered and even more embarrassing new questions are appearing.


    An anti-evolutionist system in our genes:

    Perhaps the most awkward question today for the theory of evolution is the one raised by the recently discovered p53 and since then a mutlitude of others - the DNA repair mechanism. This has been found to be common to all mammals and repairs damaged DNA. If the damage is too great to repair, it organises the cell's self-destruction.

    Therefore if any defect in the transcription of the genetic code arises, (the foundation on which evolution is based) then this repair or programmed cell death mechanism will remove such a mutation. If not, then the organism as a whole will die of cancer.

    This control system is clearly present to avoid all mutation. Thus, if this system is common to all mammals, according to the theory of Evolution, it should also be present in the common ancestors of mammals.

    If it were present in our ancestors, how were they able to diversify in order to render so many different species ? This is clearly a major contradiction which can only put a serious doubt on the theory of evolution.

    [...]



    [Bibliography]

    Here you will find other resource material  which support the messages given  to Rael by the Elohim
    - in whole or in part.

    [...]

    The Triumph of Design

    The Triumph of Design clearly and dramatically shows the gaping holes in Darwinian theory and the mounting evidence for the intelligent design of the universe. This video features Phillip Johnson, the distinguished law professor from the University of California, Berkeley whose best-selling book, Darwin On Trial, re-ignited the evolution controversy in the early 1990's. (more info)



    Evolution - Fact or Belief ?
    ( also released in French as "Enquetes & Reportages")

    More and more scientists are abandoning the Evolution Theory on the grounds that it is contrary to the basic laws of modern science. They maintain that it is a philosophy, not a science.
    This video interviews scientists from around the world to find out why they do not accept evolution as a reasonable explanation for the origin of man and the universe.


    I do agree with the ARN wedge update about one thing: your starting point is important.  For instance, if you start out by ignoring evidence contrary to your position, there is no end to the silly conclusions you will come to.
    * ID and peer-review (2 replies)
    niiicholas2003-07-02 14:31:09
    Several discussions ongoing on the topic of whether ID has any support in the peer-reviewed literature, and whether this matters.

    Cross-referencing other similar discussions:

    From March (particularly good reply by RBH):
    http://www.arn.org/cgi-bin....=000637

    ID and Peer-Review (Dembski)
    http://www.iscid.org/boards/ubb-get_topic-f-6-t-000386.html

    Tipler on Peer-Review
    http://www.iscid.org/boards/ubb-get_topic-f-6-t-000385.html

    Dembski on Peer-Review
    http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000783
    * The IDEA Club and Center (0 replies)
    Wesley R. Elsberry2004-05-29 09:57:20
    This thread is for discussion of various things related to the IDEA Club and IDEACenter.
    * CHAT Wednesday about KU and intelligent design (0 replies)
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    * EVOLUTION controversy boosts sales of niche produ (0 replies)
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    * INTELLIGENT design sparks new debate (0 replies)
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    * CLASS on Debunking Creationism Cancelled (0 replies)
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    * Evolution of Genetic Code (4 replies)
    JxD2002-12-30 21:53:03
    David Ardell has several papers he authored on this subject, linked on his website at Stanford.

    There is also The Coevolution of Genes and the Genetic Code, put up at the Santa Fe site.

    Other interesting papers:
    Shigehiko Kanaya, Yuko Yamada, Makoto Kinouchi, Yoshihiro Kudo, Toshimichi Ikemura:
    Codon Usage and tRNA Genes in Eukaryotes: Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis
    J Mol Evol 53 (2001) 4, 290-298

    Robin D. Knight, Laura F. Landweber, Michael Yarus:
    How Mitochondria Redefine the Code
    J Mol Evol 53 (2001) 4, 299-313

    Shin-ichi Yokobori, Tsutomu Suzuki, Kimitsuna Watanabe:
    Genetic Code Variations in Mitochondria: tRNA as a Major Determinant of Genetic Code Plasticity
    J Mol Evol 53 (2001) 4, 314-326
    * A Programmer Unimpressed with Biological "Design" (0 replies)
    lpetrich2003-10-24 01:25:40
    An article in http://www.salon.com , How I decoded the human genome, features this comment from someone with a long career in programming:
    Quote
    Kent spoke to me in nerdspeak, with geekoid locutions such as the use of "build" as a noun: "That's the most recent build of the genome. Build 31." I was used to hearing biologists talking about the elegance of DNA with what might be called reverence. By contrast Kent spoke of DNA as if it were the most convoluted, ill-documented, haphazardly maintained spaghetti code -- not God's most sublime handiwork, but some hack's kludge riddled with countless generations of side effects, and "parasites on parasites."

    "It's a massive system to reverse-engineer," he said. "DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes ... the analogy breaks down at the margins but offers useful insights." It was nearly impossible to tell the working code from cruft, Kent said. "That's why a lot of people say, 'The genome is junk.'" But that's what he found interesting: a high-quality programmer's code is always self-evident, but legacy assembler handed down from generation to generation of bricoleurs (I'm paraphrasing again) provides a real challenge for people who like puzzles.

    A bricoleur is a tinkerer, someone who constructs with whatever is available.
    * K-STATE, others tackling intelligent design in cl (0 replies)
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    * dembski's "EVOLUTION'S LOGIC OF CREDULITY" (18 replies)
    rafe gutman2002-12-05 17:13:26
    allen orr recently wrote a review of dembski's "no free lunch" in the boston review.  dembski wrote a response to it, and orr responded to that:

    http://bostonreview.mit.edu/BR27.5/exchange.html

    this article is currently being discussed on several intelligent design fora (such as ARN and ISCID), but considering the intense moderation/censorship of those sites, i thought i would bring the topic here for discussion.  those critics of ID who are concerned that their comments will be censored can post them here.

    here is the intro:
    Quote
    Allen Orr wrote an extended critical review (over 6000 words) of my book No Free Lunch for the Boston Review this summer (http://bostonreview.mit.edu/BR27.3/orr.html). The Boston Review subsequently contacted me and asked for a 1000 word response. I wrote a response of that length focusing on what I took to be the fundamental flaw in Orr's review (and indeed in Darwinian thinking generally, namely, conflating the realistically possible with the merely conceivable). What I didn't know (though I should have expected it) is that Orr would have the last word and that the Boston Review would give him 1000 words to reply to my response (see the exchange in the current issue at http://bostonreview.mit.edu/BR27.5/exchange.html).



    In his reply Orr takes me to task for not responding to the many particular objections he raised against my work in his original review, suggesting that this was the result of bewilderment on my part and intelligent design running out of steam and not, as was the case, for lack of space. This sort of rule-rigging by Orr and the Boston Review -- give the respondent a little space, and then let the original author crow about winning -- is to be expected. I actually find it encouraging, taking it as an indication of intelligent design's progress. Orr's review and follow-up hardly spell the death-knell for intelligent design or for my work in this area. Sooner or later (and probably sooner) Orr will find himself in a forum on intelligent design where the rules of engagement are not rigged in his favor. I look forward to his performance then.


    * CLASSROOM challenges (0 replies)
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    * BRAHMA, Buddha, Or Allah: Why Intelligent Design (0 replies)
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    * ISCID moderation (1 replies)
    Wesley R. Elsberry2002-05-16 16:52:01
    On the ARN forum, "Ex-YEC-er" made this comment:

    Quote
    As far as the Brainstorm forum is concerned, my experiences differ significantly from yours, perhaps because I tend to be critical of Dembski's arguments. When mentioning references to Wesley Elsberry my posting was removed by the moderator. "No interest in the gospel of Elsberry...". When I forwarded my response to the administrator to Dembski (I was responding to his posting), Dembski had me banned and warned me that any attempt to complain about this would likely lead to my permanent banishment from the forum.


    ARN forum thread on flagellar evolution

    This, of course, intrigues me.

    If anyone knows who "Ex-YEC-er" is, please ask him or her to get in touch with me about this.

    Also, if you have direct experience with ISCID moderation removing or editing posts based upon references to particular critics, I would like to hear from you.

    * The Truth About Fossils (1 replies)
    darkdumpty2005-02-23 10:52:29
    Secrets of The  Fossil Record

    There is a secret that all people who believe in evolution know, but that we keep secret from Cretinists, Intelligent Design advocates, and other assorted septics.

    It is this.

    We know the fossil record is perfect.

    That is, every inch of every layer of every deposit of sedimentary rock has been excavated on all continents, and under every sea and every ocean.  We have also taken apart every building made of these rocks.  This has been a spectacular feat of engineering, I mean, did you notice us replace the Himalayas?  Did you see us rip out the grand canyon and replace it with multicoloured layers of concrete?  And did you see us hide all that broken rock behind the bike shed?

    The process of fossilisation is also perfect.  Every single one of the 9 billion chickens eaten each year, regardless of what you do to it, is fossilised, and this is true of spiders, sparrows, dogs, frogs, antelopes, lions, beavers, hawks, sharks, crabs, and every other living thing on the planet, regardless of how, why, or where it dies; and regardless of what happens to the corpse.

    This process can be directly observed if you blink very, very fast while turning your head left and right quickly.  It helps if you are spinning around, say on an office chair.  Do this and you will see a slight blurring of the ground.  That is fossilisation taking place.

    We even known who are doing it and how.  It’s a function of the insect world, where ant and beetles have for millions of years been collecting each and every bit of dead living thing and returning them to their nests.  In these nests there are numerous open chambers where the ants work their magic, sorting through all the rubbish they take (and the excrement the beetles bring; “Hey what have you got there?”, “Oh, just some bird shit, it contains the remains of spiders you need to fossilise”, “Dammit!  We’ve got 15 tones of bird shit.  Cant you get us some something else?”), sorting through the proteins, and when they’ve got all the bits of an animal that died, sit there welding them together in the chamber before back filling the room, and doing it all over again from square on in another chamber, while the queen ant screams “Jesus, we need another 69,634,001 workers for this whale…boy I’m gonna be tired..

    This leads to some important conclusions about what we have found and what it means.

    Firstly, lets take the Coelacanth.  This fish is alive and well living off the coast of Africa and South America.   But the last fossil of this creature were discovered from 65,000,000 years ago (ants get to the bones by scuba diving, by the way, and for really deep areas, they ride in genetically engineered spider crabs).  Clearly this means that Every living Coelacanth around today has lived for 65,000,000 years.  Yes, they are very, very, very, very old fish.  Infact, so old that whales, sharks and sea cucumbers often go to them to benefit from their wisdom.  Other animals avoid them because they start most conversations with “when I was sprat, a long time ago..”

    Only about 30 Tyrannosaurus fossils have been found, mostly in the western part of the United States. Fossils have been found in the USA (in Montana, Texas, Utah, and Wyoming), Canada (Alberta and Saskatchewan), and east Asia (Mongolia). One T. rex footprint has been found, in an undisclosed location in New Mexico, USA, across the late cretaceous period.

    Thus we know the following.  Only 30 of these magnificent beasts ever, ever, existed but they covered vast intercontinental distances with a very efficient hoping motion.

    The Rose and Brown study of a monkey population that showed speciation over 4 million years from 700 skeletons was complete and we know that no other skeletons will be found cause we tore the ground up.  Thus we calculate that these monkey lived an average of 5714 years each.  Very impressive compared to the human maximum of 110 years.  Incidentally, the same calculation shows each Tyrannosaurus lives about 3,700,000 years each, which just shows to go how truly impressive these monsters were.

    Another fact we know from the fossil record relates directly to the hominid line.  A number of proto-humans have been found, clearly identified as such from foot, leg, hip and skull fragments.  Actually, a lot of fossils have something of this nature to them.

    What most people don’t realise is that there were no other parts.  Yep, that’s right.  Those isolated fossil sharks teeth weren’t actually attached to a shark (we would have found the complete fossil otherwise) but actually roved the ancient seas slicing up creatures and then slowly dying because they didn’t have a metabolism to support them.

    The early humans actually did just hope around on one leg, with a perfectly formed human foot, and their internal organs supported and protected 2 ribs on the left hand side and three on the right.  Their brains were almost completely unprotected and supported only by soft body parts, parts the ants really cant be bothered to extract from animal dung (though dung beetles keep bringing them more.  Poor sods.).

    Another fact we know from the fossil records is that we are completely wrong about the habitats animals lived in.  Despite the pleasiosaur and the Icthyosaur being perfectly adapted for life in the water, no fossils of these creatures have ever been found by an underwater expedition.  We therefore conclude that these creatures actually lived on dry land, obviously hunting fishes and other aquatic animals that also (unfortunately) had to manage on dry land.  Fitness being a relative thing, and all of them being reduced to flapping around, the Icthys and Plesies managed to survive long enough to produce young (who died and the ants fossilised) and to grow to great size, even reaching 50 feet in length before Queenie shouted “Kill it!, that will take a age to rebuild if the bits get lost!”

    So there you have it.  Something all evolutionists know, something we’ve kept secret.

    Boy I am gonna be in trouble when they know I’ve told people.

    But I don’t care.  Let the truth be known.
    * President Bush's bright idea (2 replies)
    jminnis2005-08-04 11:10:44
    Can it get worse? President Bush now wants ID taught in schools (NYT, Aug. 3, 2005, "Dear Old Golden Rule Days in Texas"):

    "... Mr. Bush, before he headed for Texas, voiced support for the idea that schools should teach an alternate theory of evolution known as "intelligent design" alongside the scientific version, which has been subjected to rigorous examination and testing over generations. "I think that part of education is to expose people to
    different schools of thought," he declared.
    * INTELLIGENT Design, Roman Catholicism, and the Su (0 replies)
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    * Pictures never lie (1 replies)
    thealater2006-01-30 14:55:32
    As you all know, pictures never lie. *cough*  This may be an old one, but it's priceless.

    Proof! Proof, I tell you!

    thea
    * New "Dino Museum" (1 replies)
    Sheikh Mahandi2005-05-23 09:42:09
    Creationist dinosaur museum opens in Arkansas
    Spotted this from Paul Harris, Eureka Springs, Arkansas.
    I have already mailed the Guardian to let them know, sorry this isn't the first, Kent Hovind had one running in Floriday years ago.
    * Hovind in the newspaper (21 replies)
    Wesley R. Elsberry2002-09-05 10:03:05
    Check out the Pensacola News Journal "For The Record" page.

    Search for "hovind".  The mention is in the "felony arrests" section.

    Wesley
    * Sarfati and Hitler (1 replies)
    Wesley R. Elsberry2005-01-31 20:54:11
    Re: The Holocaust and Evolution

    (A comment at http://www.theconservativevoice.com/modules....ent2132 in response to the opinion piece by AiG's Jonathan Sarfati.)

    I've long held that propagandists use whatever is convenient to advance their agenda. In Hitler's case, it is apparent that he claimed both a divine calling in his genocidal program, as well as pragmatics to influence the intelligentsia.

    In this regard, one should expect that a propagandist of whatever stripe will inappropriately utilize whatever concepts have widespread currency in the target culture. The issue is not whether a propagandist makes reference to a concept, since such a person will do or say whatever will render others more likely to give them assistance or assent. That a concept is widespread is enough to make it likely for a propagandist to usurp it to his own ends. The issue, then, is whether adherence to some conceptual framework compels a particular course of action.

    It is clear that accepting the concepts of evolutionary biology does not compel genocidal behavior. Nor does it compel fascism, communism, or robber-baron style Social Darwinism. (If it did compel behavior of some sort, only one of the options would be engaged, not some opting for A, others for B, and still others for options C through Z.)

    Antievolution advocates know they have no chance of showing compelled human behavior stemming from evolutionary biology. Instead, they concentrate upon hints and allegations that evolutionary biology was mentioned by history's villains, or was discussed by them, or even that they must have been taught the concepts and therefore influenced in some malign fashion. While antieovlutionists will readily recognize that Hitler and the Nazi leadership's use of Christian rhetoric and references in their public speeches and writings are belied by their actions, the antievolutionists seem not to recognize that Nazi invocation of recognizable scientific concepts has no more reliability as an indication of causal influence.

    While Sir Arthur Keith's views on Hitler and Darwinism are a staple of antievolutionist screeds, it is my opinion that Keith was simply mistaken in his analysis of Hitler. Even a cursory reading of Hitler's own output shows far more familiarity and reliance upon scriptural sources than any esoteric realm of scientific endeavor. The passages in Mein Kampf that are offered as evidence of Hitler's adherence to Darwinian principles are invariably weak allusions which would require nothing more than listening to overheard conversations in a cafe for buzzphrases to spice up a speech or passage, not nuanced arguments showing any depth of acquaintance with biological practice. Hitler and his band of fellow propagandists did what dissembling dictators and sycophants have always done, which was to try to bind the people to them through rhetoric. And, as dissemblers past, present, and future will show, that is done by referring to concepts that are known to the people and spinning a tale that suits their ends.

    Wesley R. Elsberry

    Further reading:

    http://www.talkorigins.org/indexcc/CA/CA006_1.html

    http://www.stcynic.com/blog....omments

    http://www.talkreason.org/articles/eandp.cfm

    http://www.antievolution.org/people/wre/evc/argresp/hitler.faq

    http://www.antievolution.org/people/wre/evc/argresp/hitler.add

    Examples of invidious comparisons by antievolutionists:

    http://www.antievolution.org/cgi-bin....f=9;t=1
    * Ben Moore Memorial Lecture (2 replies)
    Wesley R. Elsberry2003-02-19 10:52:19
    Pupils keep memory of meningitis victim alive

    Quote
    A SCHOOL has paid a special tribute to an outstanding 15-year-old pupil who died suddenly last August as a result of meningitis.

    [...]

    The school held the Ben Moore Memorial Lecture on Creation or Evolution last week which was introduced by Ben's father and given by Dr Farid Abou-Rahme.

    Mrs Otter said: "Everyone contributed something to the assembly, whether it was a reading or a song. My tutor group collected the money for the memorial."
    * Edward Max Debates Duane Gish (5 replies)
    Wesley R. Elsberry2003-01-22 06:00:48
    ICR Event Announcement Calendar (click on Jan. 24)

    You can find a mini-bio of Edward Max at this New Mexicans for Science and Reason web page.

    If you haven't seen the "Gish Gallop" in person yet, this is likely to be an excellent opportunity to experience it.

    Wesley
    * New YEC Whoopers (0 replies)
    Michael2002-10-06 13:08:15
    Answers in Genesis in Kingdom of the plants there there is no evidence progymnosperms ever existed.  Nevermind we have fossils!  This was initially pointed out in this thread.

    The Institute of Creation research made a really nasty misrepresentation by falsely citing a paper as saying the closure temperature for helium in zircons is 196 degrees below zero.  Reverse the sign and it would be much closer to what the cited paper really said.  See this thread for details.
    * Hovind/Callahan Debate Upcoming Dec-5-04 (0 replies)
    johndcal2004-11-20 18:01:55
    Genesis: History or Myth? will be the topic when well-known creationist Dr. Kent Hovind, http://www.drdino.com/ , with over 85 debates to his credit, takes on John D. Callahan, a theistic evolutionist and president of Faith & Reason Ministries, http://www.faithreason.org/ . Callahan accepted Hovind's evolution challenge in an open letter: http://www.faithreason.org/farmprov.htm .

    The Debate will happen at Faith Baptist Church, http://www.faithbaptist.org/ , 7644 Farralone Avenue, Canoga Park, CA 91304, on Sunday December 5, 2004 from 3:30 to 5p. All are welcome.
    * YEC Archaeology (2 replies)
    Wesley R. Elsberry2003-02-15 06:52:24
    Ministries say expeditions to archaeological sites support creationism

    Quote
    A San Antonio ministry that subscribes to creationism is giving home-schooled children a chance for hands-on learning at archaeological digs that it says enhances the youths' knowledge of both science and faith.

    Vision Forum is a 5-year-old evangelical Protestant ministry that provides instructional materials for Christian home-schooling parents across the country. Last year it began booking family expeditions with a Florida-based ministry, Creation Expeditions, to archaeological sites they believe support biblical claims that God created the world in six days.


    The sites discussed in the article relate to paleontology instead of archaeology.

    * geocentrism (8 replies)
    VoxRat2003-02-21 13:31:11
    Have any of you YEC trackers followed this guy, Marshall Hall? :0  Check out his website I especially like this pearl of wisdom:
    Quote
    Qualified and able Creationist/Geocentrists around the world are speaking out on the two facts that ICR (and AIG) are steadfastly resisting, viz., The Bible teaches a moving sun, not a moving earth; &: Both the heliocentricity and the geocentricity models explain all the phenomena. Thus, support of heliocentricity is a philosophical, not a scientific, choice, & not fit for Biblical Creationists.
    Point that out when our more urbane pseudointellectual anti-intellectual friends(e.g. Discovery Institute) use the same "philosophical bias" gambit.
    * Hovind/Callahan Debate Now Online! (0 replies)
    johndcal2005-02-10 20:35:49
    Don't miss the action: young Earth creationism (YEC) vs. theistic evolution. Included are the entire debate (Dec-5-04) or excerpts (MP3), photos, commentary and links (including links to Callahan's letter to Hovind and Hovind's radio response, Aug-26-04, MP3).

    See the Hovind/Callahan debate link at Faith & Reason Ministries, http://www.faithreason.org/
    * Young-Earth Arguments (5 replies)
    Wesley R. Elsberry2002-05-27 08:50:39
    This thread is for documenting the various young-earth arguments and responses to those arguments.

    I'll start off with one that is based upon ecology.

    The Population Argument

    The following quotes are selected from an online essay of mine.

    Quote
    Certain proponents of "scientific creationism" (SciCre) have put forward an argument that humans could not have evolved, simply because human population size shows that humans have only been around a few thousand years.  Those putting forward the argument tie the original population size to either two (sometimes Adam and Eve, sometimes Noah and his wife) or eight (Noah's immediate family), note a current population figure, and derive a rate of increase by use of some Biblical chronology to either creation, Noah's birth, or The Flood.  It should be noted that biblically, what should be argued is either descent from two (Adam and Eve) or from six (Noah's sons and their wives).  While some admit up front that the calculation of rate of increase yields an average value and that the actual rate of increase varies, many do not. The crux of the argument comes when they use the derived rate of increase for comparison to the deep time that evolutionary timetables give.  The numbers of humans that would be present, they say, were evolution true, would be far greater than what we observe today, and thus evolution of humans must be false. Some are precise enough to restrict their conclusion to only humans, others leave how much is disproved unspecified.  Some utilize the numbers to infer intermediate population sizes.
     
    I am going to point out some problems with the SciCre population argument.  First, the argument assumes what it is supposed to prove. Second, all such arguments yield absurd values for population sizes at historical times.  Third, the argument ignores what is known about population dynamics from other species.  Fourth, final population size is an unreliable indicator of initial population time.  I am only interested in the anti-evolutionary components of the SciCre population argument; use of the population argument in apologetics is not something I care about.  I don't think that anyone can demonstrate that real population dynamics disbar Global Flood scenarios, so if use in apologetics is all that is intended from some source, I have no real beef with it.


    Quote
    Third, the argument ignores what is known about population dynamics from other species.  Various other species can be observed to sometimes reproduce exponentially, but we observe that such populations fluctuate, stabilize, or crash.  In no case do exponentially reproducing populations "take over the world" as SciCre'ists assure us would be the case if evolution were true.  In recent times, human population growth has been exponential, but this does not mean that the human population has been growing exponentially for all its residence time.  Just as the number of E. coli present in your gut will not tell us your birthday or the time of your last use of an antibiotic, so human population size is decoupled from when Homo sapiens arose, or even when a bottleneck may have occurred.


    Quote
    In short, the SciCre population argument fails on many different criteria.  Honest creationists should eschew its use.


    -- Population Size and Time of Creation or Flood

    Interestingly, the population argument is not listed among those that "Answers in Genesis" recommends that YECs should not use.
    * Satire of YECism (1 replies)
    Wesley R. Elsberry2003-01-14 21:52:52
    Creationist Museum Acquires 5,000 Year Old T. rex Skeleton

    Quote
    TULSA, OK—In a major coup for the growing field of creation science, the perfectly preserved remains of a 5,000-year-old Tyrannosaurus Rex were delivered Monday to Tulsa's Creationist Museum of Natural History.
    * Basics of debates with YECs (2 replies)
    Alter2005-08-15 13:52:13
    Hey, I'm not clued in to all of the arguments of the YECs, is there anyone willing to give me a summary of the major "contrary" scientific evidence touted by YECs, kind of their list for the supposed "teach the controversy" thing?

    I know it's an ambitious question, thanks in advance.
    * $250,000 Evolution Challenge Accepted! (13 replies)
    johndcal2002-10-01 16:56:30
    SUN VALLEY, CA - October 1, 2002 - A long-standing offer to prove evolution has been accepted by John D. Callahan, a theistic evolutionist and president of Faith & Reason Ministries: Reconciling Christianity with Accepted Science, http://www.faithreason.org/. The offer is being made by Dr. Kent Hovind, a young-Earth creationist and leader of Creation Science Evangelism, http://www.drdino.com/.

    Callahan writes Dr. Hovind, in a widely distributed open letter: "I accept your offer to prove evolution and win $250,000. I will prove secular, scientific evolution as it is appropriately taught in our schools. As you stipulate, this includes both the large-scale evolution of the universe, from the Big Bang, and Darwinian biological evolution. I could appeal to the mountain of empirical evidence (observation and experimentation) from many areas of science, which puts evolution beyond doubt to almost all scientists. However, this would be overkill, and since evolution is so simple to prove, I will do it in this letter. You insist evolution is an unsubstantiated, immoral religion; this is incorrect."

    "First consider biological evolution. Besides innumerable transitional fossils -- dating billions of years to very primitive forms -- there are many living species (of the millions on Earth) and breeds that are obvious cousins and direct descendants of one another. An illustration is the domestic dog, which can produce a generation 30 times faster than man. From gray wolf populations the domestic dog has evolved (naturally and via human intervention) into dozens of species and hundreds of breeds (enormous gene pool) over the last 10,000 years. These are more than minor variations and indicative of macroevolution. Further, since a gray wolf has evolved into a pug dog, an ape has surely evolved into a Homo erectus and then a man."

    "As far as large-scale evolution, the cosmic background radiation confirms the Big Bang and structure of the universe. Also light travels at 186,000 miles per second. Thus when astronomers look at distance objects, they are looking back in time. This 'time travel' clearly shows the evolution of the universe, from quasars and primitive galaxies (billions of years ago) to the modern appearance of our local universe. In addition we see stars in various stages of evolution, nucleosynthesis in supernova 1987A, molecules in space, and solar systems forming from dust and gas. Not every detail is understood, such as dark matter and energy, but this in no way negates the basic age and evolution of the universe."

    "However, evolution makes no statement as to the existence of God. (For proof of His being, please see http://www.faithreason.org/.) Therefore I address your point, '1. Time, space, and matter came into existence by themselves,' by stating that God created the universe with physical and spiritual laws facilitating evolution. Moreover, God is present and working in our lives and the universe, but not as envisioned by modern creation mythology: young-Earth creationism (your conviction), old-Earth creationism, and intelligent design theory."

    "Please send my $250,000 to the address above. Thanks. If you wish more detail, from the ever-increasing mountain of empirical evidence, I would be happy to present before your review committee (or debate) provided you sponsor a public event and pay my traveling expenses (outside the Los Angeles, CA area)."

    Dr. Hovind's challenge has been a rallying cry for creationists, and he asserts few, if any, legitimate inquires have been made -- and certainly no proof. However, evolutionists contend Dr. Hovind is not open to empirical evidence and scientific method. How will Dr. Hovind respond to the Callahan letter, which claims to concisely prove evolution consistent with belief in God?
    * The Thomas-ReMine Debate Is Complete (0 replies)
    lpetrich2003-04-13 19:20:52
    I'm posting my announcement here because I don't know where a good place for it is; it's not YEC, and it's not explicitly "Intelligent Design".

    Here is one of that debate's home pages. Walter ReMine has just submitted his final contribution, the final one of the debate. The subject:

    "Comparisons of molecules (proteins, DNA) of various species provide independent and compelling support for the hypothesis of biological macro-evolution"

    It seems to me that Dave Thomas has made a much more reasonable case than Walter ReMine, who liked to wander all over the place without really explaining what his "Message Theory" was. ReMine often seemed to me to not really understand what he was talking about, and he has apparently spent a sizable amount of time working in a quote mine.
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    * CREATIONISM is based on faith; it is not a science (0 replies)
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    * KERN County school to drop 'intelligent design' cl (0 replies)
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    * ON Intelligent Design and the First Amendment (0 replies)
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    * BRITISH may teach 'Adam and Eve' theory (0 replies)
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    * DARWIN: Putting a Human Face on Evolution (0 replies)
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    * BILL takes aim at intelligent design (0 replies)
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    * DEE: The two black holes in Intelligent Design (0 replies)
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    * SC governor OK with intelligent design (0 replies)
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    * CALIF. high school sued over class discussing 'int (0 replies)
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    * WHAT Is Science? Part II: Pennsylvania 's Intellig (0 replies)
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    * PA. school board expected to rescind "intelligent (0 replies)
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    * KU'S intelligent design course is cancelled (0 replies)
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    * ID and HIV denialists (1 replies)
    bspitzer2005-07-06 16:29:30
    I've been doing a little research into HIV denialism, the popular movement spearheaded by Peter Duesberg in the late 1980's that insisted that AIDS was not caused by a virus. It seems as though a number of the people now prominent in ID were also HIV denialists.

    I was wondering if anyone out there knew more about this pattern. In particular, I'm trying to get a sense of how widespread HIV denialism was (and is) among the people who now make up the ID movement. I'm also very curious about *why* these two movements are linked. HIV denialism seems to have attracted quite a few social conservatives, and I'd like to be able to document why this was the case.

    --Brian
    * Forum Guidelines (0 replies)
    Wesley R. Elsberry2002-05-17 10:02:05
    This forum is for brief posts relating upcoming or past events having to do with "intelligent design".  Discussion should be taken to the "All About Antievolution -> Intelligent Design" forum or one of the fora under "Specifically About Intelligent Design".

    Please provide a link to online articles or announcements.  A short summary would be appropriate to describe what is linked.

    Wesley
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    * DEVOLVING Ohio (0 replies)
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    * BIG Bang vs Intelligent Design of TOPU - Series 1 (0 replies)
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    * WHITE House accused of censoring Nasa (0 replies)
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    * INTELLIGENT Design and Darwinism: Science Will Pre (0 replies)
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    * JUDGE: Stick to evolution (0 replies)
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    * DON'T expect Intelligent Design advocates to stop (0 replies)
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    * KEEPING Church and State apart (0 replies)
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    * INTELLIGENT design ruling was misguided (0 replies)
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    * WHAT we have here is a failure to communicate (0 replies)
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    * TEACHING debate over evolution necessary" (0 replies)
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    * THE Renaissance Man and Intelligent Design: A prop (0 replies)
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    * Behe's colleague makes statement (1 replies)
    Maven2005-08-29 03:24:46
    The ID debate has really heated up here in PA where we are treated to a daily dose of insanity in the local press.  Lehigh University professor Lynn Cassimeris wrote the following op-ed piece for our local paper.  

    http://www.mcall.com/news....2.story


    From The Morning Call
    Science's fast pace undercuts allure of intelligent design

    August 28, 2005

    More than 10 years ago, my Lehigh University faculty colleague Michael J. Behe
    asked me to read a chapter of a manuscript that was later published as
    ''Darwin's Black Box: The Biochemical Challenge to Evolution.'' In this book,
    Dr. Behe suggested that biochemical systems inside of cells are ''irreducibly
    complex'' and cannot have evolved without the hand of a supernatural designer.
    Over the past decade, I have had considerable time to ponder the ideas Dr. Behe
    put forward in his book, and time and again I concluded that his arguments lack
    scientific credibility and are equally offensive to religious faith.

    Dr. Behe's idea of irreducible complexity suggests that certain structures
    inside a cell are too complex to have evolved by step-by-step modifications and
    must therefore have required a designer to make them. Cells do contain seemingly
    complex biochemical structures, formed of many protein parts, but is it
    necessary to invoke a supernatural designer to explain their existence?

    Without describing the inner workings of a cell, I will use an analogy, much as
    Dr. Behe does, to illustrate how seemingly complex structures might have
    evolved. He often uses the mousetrap example to illustrate irreducible
    complexity, but mousetraps actually better illustrate the concept of evolution
    of protein complexes.

    Catching and killing a mouse is easily achieved by the modern glue trap,
    requiring nothing more than glue and a cardboard base upon which to spread the
    glue. Both glue and the cardboard support have other purposes and were only
    recently brought together to form a mousetrap. Increasing the complexity by a
    notch, peanut butter can be used to bait the glue trap, and it also has another
    use. Biologists consider evolution of large protein complexes within cells to
    have followed a similar course of evolution, taking pieces with one function and
    co-opting and combining them for another function. Evidence abounds to support
    the co-opting of one component, much like a piece of cardboard or glue, for
    different use in the cell.

    Dr. Behe uses the bacterial flagellum (a structure that enables bacteria to
    move) as another model of irreducible complexity, yet recent work has
    established that one part of the flagellum, a collection of several proteins, is
    related to a syringe-like structure that many bacteria use to inject a toxin
    into other cells. Another part of the flagellum is a protein channel through
    which ions flow. Ion channels are found in all cells, including our own. The
    bacterial flagellum is just one example of how cells take one part, combine it
    with a different part, and end up with something new.

    We still have much to learn about how our cells function and how structures and
    biochemical pathways developed over the course of billions of years. To suggest
    that we throw up our hands and ascribe everything to a supernatural designer
    does nothing to advance biology. Instead, we need to continue research to better
    understand how living cells work if we want to conquer current problems, such as
    the growing bacterial resistance to antibiotics. Progress in understanding cell
    evolution is likely to gain speed rapidly with Harvard's new initiative to fund
    research into the origin of life.

    The fast pace of scientific progress should give pause to those who would like
    to see intelligent design taught in the science classroom. The ideas and
    examples suggesting the need for a designer are likely to fall by the wayside as
    science progresses. It is not that long ago (1994) that Dr. Behe suggested that
    whale evolution could not be explained because of gaps in the fossil record.
    That argument collapsed when three fossil intermediates were discovered within
    the next year.

    Much like filling in gaps in the fossil record, new discoveries at the cellular
    level will continue to contradict intelligent design and ''irreducible
    complexity.'' Then what happens to faith built on the so-called evidence for a
    designer? Does that faith waiver when the ''evidence'' disappears? Faith should
    not require scientific evidence; looking for physical evidence of a designer
    only serves to undermine faith. Scientists are battling to keep intelligent
    design out of the science classroom because it is not science. Religious leaders
    should join the fight.

    Lynne Cassimeris, Ph.D., is a professor in the Biological Sciences Department at
    Lehigh University. She is a cell biologist studying how cells reproduce and how
    the errors in cell division associated with birth defects and cancer occur.
    Copyright © 2005, The Morning Call
    * PROFESSOR Beaten; Says Attackers Cited Creationis (1 replies)
    celtic_elk2005-12-06 10:14:57
    And, of course, the critics on the right are already trying to claim that he faked the attack, or that he somehow started the fight.  I was engaged in some rather vigorous debate over this issue on the Yahoo news forums this morning.  None of them seem to want to address the idea that fundamentalists could physically assault an intellectual who espoused a position contrary to theirs.  After all, that could never happen in thiscountry, right? *sigh*
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    * 2002/05/10: "Icons" video premiere (1 replies)
    Wesley R. Elsberry2002-05-17 11:12:21
    2002/05/10

    Jonathan Wells's "Icons of Evolution" has been produced as a film suitable for television broadcast by "Coldwater Media".  It premiered in Seattle at Seattle Pacific University.

    Origins of life film to premiere at SPU

    Not the Whole Truth, a review by Roger Downey.

    Documentation of the history of the DeHart case.  DeHart was featured in the "Icons" video.

    Please add "Icons" video related links to this thread.
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    * Another ridiculous opinion piece... (0 replies)
    FishyFred2005-10-03 04:38:28
    ... by someone who clearly doesn't know any better.

    http://www.taemag.com/issues/articleid.18771/article_detail.asp

    Can you say "taken out of context" and "misinterpretation?" Here's a one-paragraph sample.

    Quote
    Early in his testimony, Rothschild claimed that “intelligent design is not science in its infancy, it's not science at all.” Yet Miller’s own testimony contradicts this. In cross-examination, when asked by Robert Muise, the defense attorney, if during a debate between Miller and Michael Behe, an ID proponent, at the American Museum of Natural History, “you [Miller] were presenting your scientific argument against intelligent design, and Dr. Behe was presenting his scientific argument in support of intelligent design?” Miller responded: “Absolutely.”
    * 2002/05/22: Cobb County, Georgia (0 replies)
    Wesley R. Elsberry2002-05-22 12:07:18
    Creative Loafing Atlanta has an excellent front-page article on "intelligent design" and the textbook disclaimers mandated by the Cobb County school board.

    Sidebar articles cover scientists responding to "intelligent design" and the Cobb County disclaimer, where Ken Miller is featured in both of those pieces.
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    * Science Education (3 replies)
    scase2005-10-19 08:46:14
    Let me see if I understand this line of reasoning; “Rothschild asked Behe about the scientific community, which has largely denounced the idea of ID as science. The National Academy of Sciences, for instance, regards ID and its supernatural ideas as inaccurate and unfounded. Even the Lehigh University Biological Sciences faculty, where Behe is a professor, has stated that ID has “no basis in science.

    Behe argued that scientists and scientific organizations misunderstand intelligent design. Not only is ID science, Behe claimed, it is also an appropriate scientific theory to introduce to students.”

    So the leading scientific minds in the country misunderstand ID but your average 15 year old in general biology is going to figure it out?
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    * 2002/03/11: Ohio Board of Education (2 replies)
    Wesley R. Elsberry2002-05-23 22:08:15
    Jonathan Wells has a very interesting report on the debate before the Ohio Board of Education.  Wells and Stephen Meyer of the Discovery Institute's Center for Renewal of Science and Culture were matched up against Kenneth Miller and Lawrence Krauss.

    Other resources of interest in the Ohio situation:

    Ohio Citizens for Science, a group for the acceptance of the new science standards as written by the advisory team.

    Science Excellence for All Ohioans, a group advocating the inclusion of "intelligent design" in the K12 science curriculum, or at least something singling out evolutionary biology as a subject requiring "teaching the controversy".

    Substandard Education for All Ohioans, a parody site poking fun at the antievolution stance of the page just above.

    Events from Ohio, a collection of resources at the National Center for Science Education.
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    * ID in Australia (2 replies)
    jo5ef_k2005-10-20 02:28:42
    Some may be interested to know that the public TV broadcaster here in Australia - the ABC - had an piece tonight on the ID movement here in Australia and pretty much demolished it. Although the quote at the beginning from the Federal Minister for education indicating his support for "equal time" was not so encouraging.
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    * 2002/06/21: Panel on "Intelligent Design" (0 replies)
    Wesley R. Elsberry2002-05-24 14:04:09
    The Fourth World Skeptics Conference sponsored by CSICOP, June 20-23, 2002, in Burbank, California, will feature a panel on "Evolution and Intelligent Design".

    The moderator will be Massimo Pigliucci.  Panelists will include William Dembski and Paul Nelson of the Discovery Institute's Center for Renewal of Science and Culture, Kenneth Miller of Brown University, and myself (Texas A&M, if you don't know already).
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    * Indiana, the next ID hot spot? (1 replies)
    Wesley R. Elsberry2002-09-07 07:33:29
    An Indianapolis Star editorial by Andrea Neal shows that the Discovery Institute's "Center for (the Renewal of) Science and Culture"'s propaganda machine continues to bamboozle the credulous public.

    Neal buys into several falsehoods told by the DI C®SC.  First and foremost, Neal seems to think that there is some scientific content to "intelligent design" claims.  Second, Neal asserts ID represents cutting-edge science rather than warmed-over nineteenth century apologetics.  Third, Neal buys the tale that there is no religious component to the ID movement.

    The question to pose to those who think that "intelligent design" is science is to ask where the science is.  The only things cited by Neal add up to critiques of the sufficiency of current natural explanations.  There is nothing beyond assertion that ID has any role whatever in accounting for biological complexity.  I've asked some of the "scientists at top institutions" that Neal refers to for a progress report on the ID community making a positive case for ID conjectures, and in each instance have received answers that translate into an admission of "no progress" since 1997.

    The assertion that there is any "cutting edge" to the ID wedge fails the most cursory examination of the evidence.  Phillip Johnson's original ID tome, "Darwin On Trial", simply goes to show that there is hardly an antievolution chestnut that he doesn't like.  Many of the favorites of the young-earth creationist movement are happily recycled by Johnson.  The whole "irreducible complexity" edifice erected by Michael Behe is simply a more technical gloss on the ancient "what good is half a wing" canard common in YEC circles.  Behe's innovation resides in locating systems in which there is both a paucity of evidence and no expectation that further evidence bearing on the origin of the structures will be forthcoming.  That's a prerequisite for any argument from ignorance that is expected to hold up over time.  But the central part of ID argumentation can be traced to the Reverend William Paley's arguments made in 1802.  The scientific community actually did take up such arguments and examine them seriously -- and decided that they did not fit the evidence.  ID is not "cutting edge".  At best, it's "reheated leftovers".

    Neal asserts that skeptics cannot show any religious underpinnings of ID in court because ID is "a scientific possibility".  Neal is obviously ignorant of the massive paper trail left by the "scientists at top institutions" of the DI C®SC concerning the goals and motivations of the ID movement, most succinctly expressed in the famous "Wedge" document.  This will be one of the easiest tasks for skeptics to accomplish in court, not one of the hardest.

    Neal's innovation in the editorial is to characterize opposition to the ID movement as "anti-religious".  This, of course, is bunk.  Plenty of religious people are part of the community of skeptics of ID.  The panelists at the recent CSICOP Fourth World Skeptics Conference session on evolution and intelligent design included two ID advocates and two ID skeptics, all Christian believers.

    Neal ends with this:

    Quote
    Teaching intelligent design to our children is gaining strength too, as it should. Students need to know the latest research about how it all began, even if it points to an all-knowing creator.

    It would be a sad irony to let Darwin write the final chapter because we fear where science might lead us.


    Why should a set of religiously-motivated conjectures based solely upon negative argumentation and wishful thinking be taught to students as if it were "research"?  Why should students be given the mistaken impression that such conjectures represent the "latest" in scientific thinking, when in fact various components of these arguments can be traced back decades or centuries?

    But the capping irony is the construction of Neal's final sentence.  Science should lead, all right, and it is precisely because the politics of the ID movement lead it rather than the science that we should reject these premature moves to force ID into school science curricula.  Let ID prove itself in the marketplace of scientific ideas, and then it will be ready for inclusion in science education.  It is not there yet, and even ID advocates say that they are just beginning now to see glimmers of the formation of an ID research program.  The unseemly haste with which the ID advocates push for inclusion of their untested and unresearched claims into school curricula bespeaks an unscientific attitude, one more similar to a salesman trying to offload stock that is past its sell-by date.  Something smells fishy in that.
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    Glenn Branch2002-12-23 18:43:37
    Heir spends family fortune to discredit evolution theory
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    * PCID editorial policy (30 replies)
    Tom Ames2003-01-10 00:03:36
    I'm trying to figure out PCID's (the premier peer-reviewed journal of intelligent design) editorial policy.

    The claim is made that papers are first submitted to the archive. After the paper has been on the archive for three months or more, two ISCID fellows may forward it to the editorial board for publication in the journal. There does not appear to be any mechanism for independent review, revisions, etc.

    Furthermore, the average waiting time on the archive for published papers has been less than three months for all of PCID's issues (and substantially less -- 51 days -- for the most recent issue). One manuscript (Langan's "CTMU") did not appear on the archive at all.

    Permissible topics seem to be "anything that two fellows think might be interesting", e.g., Jackson's fairly mundane computer science paper in issue 1.4.

    The question I have is this: is ISCID really claiming that PCID is a rigorous peer-reviewed journal, instead of a platform for the unedited opinions of the ISCID fellows? (Of the 28 papers published, 5 are by Dembski alone, and many of the other authors are also fellows.) Does anyone have a citation where this claim is made?
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    * thoughts on Cobb County decision (0 replies)
    "Rev Dr" Lenny Flank2005-02-07 20:00:46
    In going through the text of the judge's decision to ban the Cobb County, Georgia stickers, I found some points that could be potentially interesting and useful precedent in Dover, as well. OK, actually they are legal precedents that will kill ID's "teach the controversy" strategy. Completely and utterly.

    The text of the judge's decision is a pdf file at:

    http://www.aclu.org/Files/OpenFile.cfm?id=17310

    (the PDF is a scan of the printed decision, and alas it is loaded with typos and OCR errors--I've tried to correct all of these.)

    Some interesting points in the decision:

    The judge has killed the "disclaimer stickers" on several different and independent lines of reasoning, any ONE of which, all by itself, would be enough to kill it on "establishment clause" grounds, and all of which, together, make it virtually impossible for the fundies to win any appeal of this case. But it is interesting that these lines of reasoning also apply to the "teach the controversy" being pushed by the intelligent design advocates in Dover.

    Beginning on page 35 of the judge's decision, we find:

    "There is no evidence in this ease that the School Board included the statement in the Sticker that "evolution is a theory, not a fact" to promote or advance religion. Indeed, the testimony of the School Board members and the documents in the record all indicate that the School Board relied on counsel to draft language for the sticker that would pass constitutional muster. Thus, the presence of this language does not change the Court's opinion that the Sticker survives the purpose prong of the Lemon analysis. Still, the informed, reasonable would perceive the School Board to be aligning itself with proponents of religious theories of origin."

    This is important. Discovery Institute and other intelligent design creationists makes lots of noise about how their viewpoint is all "science" and has no religious aim or purpose. In the Freiler v Tangipahoa case in Louisiana, which also involved a "disclaimer sticker", the stated purpose of the law as written also claimed to be secular and without any religious aim or purpose. The law specifically stated that its purpose was to "encourage critical thinking". The judge in that case, however, concluded that the stated purpose of the law was, in his words, "a sham", and that "the primary effect of the disclaimer is to protect and maintain a particular religious viewpoint, namely belief in the Biblical version of creation. (US Circuit Court, Freiler v Tangipahoa, 1999) But in the Cobb decision, the judge expands upon and strengthens this conclusion, by pointing out that even if it is accepted that the stated purpose of the law was not just a "sham" and is really and totally true and EVEN IF IT HAS NO EXPLICIT RELIGIOUS PURPOSE, it STILL fails the Lemon test if it has the EFFECT of advancing religion.

    This has application to the Dover case as well as any future case the IDers might bring (since the history of ID/creationism is nothing more than a search for some wording in the law that will pass Constitutional muster). Even if a court in Dover were to rule that the DI's "teach the controversy" policy had a secular aim and was NOT intended to be religious in nature (as the DI argues), it would STILL fail the Lemon test if a reasonable informed person would conclude that it aligned itself with "proponents of religious theories of origin". As we have seen, ID proponents speak openly at every available opportunity about their "religious theories of origin" and how ID supports them. And, as the Cobb judge ruled, that is enough right there to kill it as unconstitutional. No matter how hard they try, the ID/creationists will NEVER find a suitable legal language or wording in any proposed law that will allow them to do exactly what the Constitution says they CANNOT do --- use public school classrooms to advance their religious beliefs by pretending those religious beleifs are really "science".

    In the next paragraph, we find another independent criteria for finding the stickers unconstitutional, and it too applies directly to the Dover "teach the controversy" strategy:

    "The Sticker also has the effect of implicitly bolstering alternative religious theories of origin by suggesting that evolution is a problematic theory even in the field of science. In this regard, the Sticker states, in part, that "evolution is a theory, not a fact, concerning the origin of living things" that should be "approached with an open mind, studied carefully, and critically considered." This characterization of evolution might be appropriate in other contexts, such as in an elective course on theories of origin or a religious text. However, the evidence in the record and the testimony from witnesses with science backgrounds, including the co- author of one of the textbooks into which the Sticker was placed and Defendants' own witness, Dr Stickel, reflect that evolution is more than a theory of origin in the context of science. To the contrary, evolution is the dominant scientific theory of origin accepted by the majority of scientists. While evolution is subject to criticism, particularly with respect to the mechanism by which it occurred, this Sticker misleads students regarding the significance and value of evolution in the scientific community for the benefit of the religious alternatives. By denigrating evolution, the School Board appears to be endorsing the well-known prevailing alternative theory, creationism or variations thereof, even though the Sticker does not specifically reference any alternative theories."

    This too is important. The judge is ruling that the simple act of implying or stating that evolution is a substandard theory or in some sort of crisis or is "problematic", is misleading about the scientific value and significance of evolution, and when such "denigration" is done for the purpose of benefiting "religious alternatives"-- EVEN IF THAT ALTERNATIVE IS NOT SPECIFICALLY REFERENCED, then it is illegal.

    The sole and only POINT of "teach the controversy", of course, is to denigrate evolution as "problematic" (indeed, "teach the controversy" itself consists solely of telling students about all these putative "problems"), and mislead people about its significance and value, all to the benefit of a religious alternative. That, too, is enough right there to kill it as unconstitutional.

    A few paragraphs later, we find a third independent reason for killing the disclaimer stickers that also applies directly to the "teach the controversy":

    "In addition to the foregoing, the Sticker targets only evolution to be approached with an open mind, carefully studied, and critically considered without explaining why it is the only theory being isolated as such. The School Board members convincingly testified at trial that they believed all scientific theories should be critically considered, and they also stated that they singled out evolution because it was the topic causing the controversy at the time. The Court finds the School Board's explanation to be rational and does not declare the Sticker to violate the purpose prong of Lemon However, because the administration suggested alternative language that did not place the emphasis so heavily on evolution, albeit after the Board adopted the Sticker, the message communicated to the informed, reasonable observer is that the School Board believes there is some problem peculiar to evolution. In light of the historical opposition to evolution by Christian fundamentalists and creationists in Cobb County and throughout the Nation, the informed, reasonable observer would infer the School Board's problem with evolution to be that evolution does not acknowledge a creator."

    This is the strongest argument against the "teach the controversy", and will probably be the one cited when it is killed in court. The sticker singles out ONLY EVOLUTION for criticism and "critical thinking", for the simple reason that evolution, and not other areas of science, are the historical targets of religious opposition. The "teach the controversy" strategy also targets evolution, and ONLY evolution, specifically. And ID rhetoric makes it crystal clear that the source of this targeted opposition to evolution is that it "does not acknowledge a creator" (or designer, or whatever else they want to call it). This, too, is enough all by itself to kill the "teach the controversy" tactic.

    Further on in the decision, we find:

    "Due to the manner in which the Sticker refers to evolution as a theory, the Sticker also has the effect of undermining evolution education to the benefit of those Cobb County citizens who would prefer that students maintain their religious beliefs regarding the origin of life. As Plaintiffs argue and Dr Miller, the co-author of the science textbook, testified, the use of "theory" in the Sticker plays on the colloquial or popular understanding of the term and suggests to the informed, reasonable observer that evolution is only a highly questionable "opinion" or a "hunch ". The Sticker thus has a great potential to prompt confusion among the students. While there may be an educational benefit to students spending time learning the general difference between a theory and a fact as a scientific matter, teachers have less time to teach the substance of evolution. Thus, although evolution is required to be taught in Cobb County classrooms as a technical matter, distracting tangential issues effectively dilute evolution instruction to the benefit of the anti- evolutionists who are motivated to advance their religious beliefs."

    While this reasoning doesn't impact directly onto Dover and "teach the controversy", it does so indirectly. In essence, the court is ruling that the sticker's inaccurate statement about "just a theory" requires teachers to use up class time to explain why "just a theory" is inaccurate, thus "diluting evolution instruction". I think the same reasoning can be applied to all the "criticisms of evolution" that the IDers want to have taught --- NONE of these "criticisms" is accepted as valid science by anyone in the scientific community. They are all inaccurate and have no recognized place in science, and therefore requiring them to be taught would just dilute the teaching of evolution by using up class time to explain that they are inaccurate (to the benefit of the anti-evolutionists and their religious beliefs).

    The final line of reasoning against the disclaimer stickers also can be applied to the "teach the controversy" argument:

    "Defendants persuasively argue that the Sticker in this case does not explicitly reference any alternative theory of origin, religious or otherwise. Nor does the Sticker explicitly urge students to consider alternative theories of origin or remind them that they have the right to maintain their home teachings regarding the origin of fife. Nevertheless, the Sticker here disavows the endorsement of evolution, a scientific theory, and contains an implicit religious message advanced by Christian fundamentalists and creationists, which is discernible after one considers the historical context of the statement that evolution is a theory and not a fact. The informed, reasonable observer is deemed aware of this historical context."

    In essence, what the court is saying is that even if the actual language of the law doesn't directly reference any specific alternative theory or religious viewpoint, if the "historical context" of the law indicates that it is based on particular religious wishes, then it is unconstitutional. The DI's "teach the controversy" rhetoric doesn't mention any alternative theories or religious views (all of those already having been ruled illegal to teach on church/state grounds), but the historical context of "teach the controversy" is crushingly clear to anyone -- it is just the latest in a long string of attempts by fundies in general and Discovery Institute in particular, to blot out the teaching of evolution because it conflicts with their religious views. This is especially clear after considering the previous (religious) objections to "scientific materialism" and "darwinism" that Dembski, Behe and Johnson have been writing about publicly for years. This too, all by itself, is enough to kill "teach the controversy" as unconstitutional.

    So, in order to win in Dover, the "teach the controversy" advocates will have to demonstrate that (1) "teaching the controversy" does not have the EFFECT of advancing religion even if it does NOT have that explicit aim, (2) "teaching the controversy" does NOT denigrate evolution in favor of any religious view, even if that religious view is NOT explicitly stated, (3) "teaching the controversy" does NOT single out evolution specifically because of religious objections that evolution allegedly denies a creator (or "designer"), (4) "teaching the controversy" does NOT take time away from the effective teaching of evolution by forcing teachers to spend time on "criticisms" that are not recognized as scientific or substantive, *AND* that (5) "teaching the controversy" does NOT have a readily viewable historical context as religious opposition to the idea of evolution. (All of this assumes that the judge buys the DI's argument in the first place that ID is "science" and isn't about religion at all, and the judge doesn't simply conclude, as the Freiler judge did, that the DI's entire argument is just "a sham" to hide their religious goals.)

    In my view, there is simply no way that the Dover advocates (or anyone else) will be able to get over all five of those hurdles. I doubt they can get over ANY of them. Yet only *one* of them is enough, all by itself, to kill the IDers.

    Pardon the pun, but they haven't got a prayer.
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    * Sunday 12/18 Doonesbury re:Creationism/ID (0 replies)
    Sweet Hill Observatory2005-12-18 04:17:29
    Excellent Doonesbury today...so, should we allocate scarce/expensive drugs based on whether or not the patient believes in them???

    http://www.doonesbury.com/strip/dailydose/

    Peter
    Sweet Hill Observatory
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    * A natural process for creating information (0 replies)
    djmullen2006-01-26 21:23:11
    In the ID-Files section of this BBS, under the topic "Phil Johnson, Links to interviews, works, reviews, etc", niiicholas quotes Phillip Johnson as saying, "The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism."

    Professor Johnson should read a little on the subject before opening his mouth.  Darwinian evolution has a mechanism for creating genetic information that's simple enough for even a lawyer to understand if he tries hard enough.

    I was going to write this to Zardoz in the "After the bar closes/Official Uncommon Pissant Discussion Thread", but he has shown himself to be emotionally resistant to all attempts at education, so I'll post it here where it can be read by people who are emotionally capable of understanding the concept.  Professor Johnson is invited to read and comment if he's in that group.

    Abstract: Mutations create new genetic information.  Natural selection tests the new information to see if it's useful or not where "useful" is defined as improving the ability of the organism to produce more offspring capable of reproducing the new information.  If the new information is useful, natural selection leaves it in the genome, if it's not, it gets rid of it.

    Detail: Suppose you have a stretch of DNA that contains this sequence: "CAGTAGTTAC".  If the organism that contains that stretch of DNA reproduces and the DNA is copied perfectly, the offspring will have the exact same sequence of DNA and there will be no new information generated.  (In one of his books, Dembski compares this to printing a second copy of a book.  No new information is generated, the information that already exists is merely copied.)

    Now suppose that an organism with that stretch of DNA reproduces and an error is made copying the DNA.  Suppose that "CAGTAGTTAC" becomes "CATTAGTTAC".  This is new information because it's not exactly the same as the original sequence.  

    So we have new information, courtesy of mutation/copying errors, but we don't know if this new information is bad, neutral or one of the rare instances of good new information that improves on the original.  The odds are low that the new information is an improvement.  As Richard Dawkins once said, "...however many ways there may be of being alive, it is certain that there are vastly more ways of being dead!"  Similarly, there are 4^10 or 1,048,576 different ways of arranging 10 DNA base-pairs and most of them won't do anything useful, which is lethal if the organism is depending on those ten base-pairs to do something vital.

    So how do we find out if the new information is useful or harmful?  Simple, we allow the new organism to try to make a living and reproduce using the new DNA sequence.  Most of the time, the new organism does as well as its parent did because most changes in the DNA sequence change non-functioning "junk DNA" or code for amino acids that are buried deep inside a protein molecule and have no effect on how it works.  If this turns out to be the case with the new DNA sequence, then mutation has given us two different ways of making DNA that can successfully run this specific organism - the original DNA and the new mutated DNA.  This is creating new genetic information through a natural process, Dr. Johnson!  

    Before the mutation, we had one set of information that would run a successful organism, "CAGTAGTTAC".  After the mutation, we have a second set of information that will run a successful organism, "CATTAGTTAC".  This is not the same as printing another copy of an existing book, it's printing a second book that differs from the first, but which works just as well.  It's new genetic information!  Since the new information is no better than the original, organisms containing the new DNA may increase in numbers or decrease or disappear altogether.  This is the "genetic drift" you hear about.  An organism has new DNA, but it works as well as the old DNA, so nothing much happens.

    If the new DNA sequence does make a difference in how the organism functions, the odds are that it will make the organism work worse than it's parent.  Remember that there are lots more ways of being dead than alive.  In the extreme case, the organism won't function at all and it will die.  If it dies before it has a chance to reproduce and copy the new DNA, the new DNA sequence dies with it and all the other organisms carry on with the original DNA.  Mutation generated some new information and natural selection tested it, discovered that it was bad and got rid of it.  We're back to where we started.

    If the organism lives, but doesn't function as well as its parent(s), it may reproduce, but it won't reproduce as successfully as organisms with the old, original DNA and over the long run the organisms with the new DNA will be crowded out and disappear, taking their new but less effective DNA with them.  Again, the other organisms, with the original DNA, will continue to live, preserving the old DNA sequence.

    In the rare case where the new DNA works better than the original sequence, the organism will tend to reproduce better than it's parents and it will gradually spread and increase its percentage of the population until it eventually takes over and replaces the old DNA sequence with the new, improved sequence.  

    That is how new, useful information is created by the natural process of evolution:  Mutations create the new information, natural selection (which means, basically, having the new organism try to make a living with the new DNA) tests it, destroys new sequences that don't work as well as the original and preserves new sequences that work as well as or better than the original.

    Your turn, Dr. Johnson.
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    * Daniel Schwabauer's "Troubled House" (0 replies)
    Wesley R. Elsberry2003-01-10 18:05:34
    Troubled House, a play by Daniel Schwabauer

    Reviewed by Wesley R. Elsberry

    People like playing "what-if" games.  Hypotheticals appear in arguments regularly to test the boundaries of application.  Daniel Schwabauer tries his hand at a "what-if" game in his three-act play, "Troubled House" (http://www.troubledhouse.com/TH.SCRIPT.final.pdf, last accessed 2003/01/09).  It is useful to enumerate the conjunction of "what-if" conditions that this play comprises:

    What if an agnostic biology professor doubted the suffiency of evolutionary theory to account for the diversity and history of life on earth?

    What if that agnostic professor were enamored of antievolutionary literature?

    What if journalists goaded students into falsely claiming that the professor's doubts were religious in nature and that he was attempting to bring religion into the science classroom?

    What if an academic inquisition were launched to accuse the professor of blasphemy against science and decline to renew his teaching contract?

    What if those persecuting the professor had no answer whatever to classic antievolutionary chestnuts like "natural selection has never been observed and cannot be measured", "there are no clearly transitional fossils", "genetic information cannot  increase by evolutionary processes", and "evolution has no mechanism of change"?

    What if the professor's old mentor turned out to be the most clueless of dogmatic, atheistic Darwinists around?

    What if the student body were interested in "evidence against evolution" to the extent of attending hearings and starting a riot concerning the issue?

    What if the professor's moral sense leads him to repudiate a "statement of faith" in Darwinism rather than recant his doubts and hang onto his job?

    What if the professor's love interest, otherwise on the brink of marrying him, decided that she could not stand to leave her own academic position to go with him?


    This very special set of hypothetical circumstances gives rise to Schwabauer's script.  Schwabauer's script is obviously patterned as an inverse of Lawrence and Lee's "Inherit the Wind".  The allusions of "Inherit the Wind" are overt enough as an indictment of the McCarthy era, but this aspect of the original work does not seem to have been taken into account in Schwabauer's derivation.

    The result is a predictable morality play based on some of the fears common to conservative fundamentalist Christianity.  The venue is an "ivy-league university".  Journalists, represented here by students writing for the campus newspaper, are conniving manipulators who make William Randolph Hearst look like a saint.  The campus atmosphere is depicted as crushingly anti-religious.  The protagonist is a quietly stalwart agnostic, and examples of Christians whose intellectualism and cowardice dilute their faith are thrown into the mix.

    "Troubled House" as a set piece borrows much from the earlier one-act play by Schwabauer and intelligent design advocate John Calvert, "The Rule" (http://www.intelligentdesignnetwork.org/TheRule.PDF, last accessed 2003/01/09).  Act two of "Troubled House" is a re-worked version of "The Rule".  While in "The Rule", the protagonist explicitly mentions "intelligent design" and espouses easily recognizable assertions from the ID literature, "Troubled House" avoids having its protagonist even say the word "design".  All explicit mention of "intelligent design" instead comes from the inquisitors -- and I use the term advisedly, since "inquisition" is what Schwabauer prominently features on his home page for this play.

    The inquisitorial nature of the "hearing" on possible misconduct by the protagonist is premised upon a general acceptance of philosophical naturalism by the administration.  The panel consists of the humorless dean of the university (it says she is humorless right there in the dramatis personae, as if we could not tell by the dialogue Schwabauer stuffs into her mouth), an emeritus professor of life sciences (who plays the inverse role from the William Jennings Bryan character of "Inherit the Wind"), the dean of the college of religious studies (who illustrates the lapse from real religious belief that sophisticated study of religion often implies to fundamentalists), and a mathematics professor who professes to be Christian but refuses to show any sign of it to the panel.  Points of logic brought up by the protagonist are passed over, points of procedure are broken by the "prosecutor", and no one even hints that the assertions made by the protagonist concerning evolution demonstrate considerable ignorance of the available evidence and state of the science.

    The protagonist offers a number of claims during the course of the proceedings, and as mentioned above, none of them are effectively countered in the script.  He defines science as "empirically verifiable knowledge".  He asserts that evolutionary biology has offered no effective mechanism for change.  He asserts that natural selection has never been observed or measured.  He asserts the "all genetic change is a loss of information" argument.  ID advocate Jonathan Wells's arguments on four-winged fruit flies and peppered moths are treated as factual.  (Although, of course, Wells receives no credit here for those arguments.)  The 'panda's thumb' is asserted to simply be a "spur" with no pretensions to thumb-hood.  The Cambrian explosion is cited as a difficulty, and he asserts that no "clearly" transitional fossils exist.  Of course, any halfway clued-in lurker in this debate could supply the missing rebuttals to all these supposedly unanswerable ojections.  But cluelessness in the opposition is apparently just one of the hypothetical conditions in force here. Some years ago, I had the opportunity to remonstrate with a proponent of education in evolutionary biology for her over-optimistic imaginary debate with ID advocate Phillip Johnson (http://groups.google.com/groups?selm=67lv1r%24t3i%241%40news.tamu.edu&output=gplain, last accessed 2003/01/09).  It seldom comes about that participants on either side have it all their way when put to face-to-face discussion with the other side.  The incompetence of the inquisitors in Schwabauer's play takes us ever further away from anything like verisimilitude.

    The protagonist refuses to go through with an offered compromise, and thus loses his job and his love interest.  The "compromise" is for him to read a prepared statement, which is actually a statement of faith in the completeness and accuracy of Darwinian evolution.  His point is to say that truth requires anyone to say "I don't know" when it comes to evolution.  Certainly there are unknowns in evolutionary biology, but any evolutionary biologist is likely to come up with a far different list than the ones which the protagonist is urging as reasons to doubt.

    It's certainly the case that the protagonist is personally ignorant of much.  He is thrilled that a student on campus asks to borrow some of his books expressing the "doubt" he espouses toward evolution.  In the play, he is falsely accused of biblical evangelism, but his real evangelical calling is for a generalized ignorance masquerading as moral fortitude.  In the end, only lip service is paid to the concept of looking at the empirical evidence.

    I think that we can count on ID advocates pushing for student groups to perform this extended work of propaganda.  But as with most propaganda, I suspect that its value as entertainment will remain low.

    The "study questions" at http://www.troubledhouse.com/study.html are notable for their absence of examination of the claims made in the play.  Although Schwabauer claims that his site gives a brief introduction to "both sides of the controversy", I see remarkably little accurate information about evolutionary biology given there, and rather a lot of what ID advocates claim evolutionary biology is.  There are no links to sites which argue whether ID claims are valid, such as TalkDesign, TalkReason, and Antievolution.Org, or even those which take the part of mainstream science, such as The TalkOrigins Archive or the National Center for Science Education.

    Schwabauer sells manuscript copies for $6 each, and charges a $60 royalty for performances.

    Wesley

    * Phillip E. Johnson's "Darwin on Trial" (0 replies)
    Wesley R. Elsberry2002-05-07 00:58:23
    I have an extended critique of this book at this page.
    * William A. Dembski's "The Design Inference" (0 replies)
    Wesley R. Elsberry2002-05-07 00:47:12
    There are a number of critical reviews of Dembski's "The Design Inference".

    Review by Ellery Eells

    Review by Wesley R. Elsberry

    Review by Fitelson et alia

    Review by Richard Wein
    * Roughgarden's "Evolution's Rainbow" (0 replies)
    Wesley R. Elsberry2004-05-16 07:05:37
    This is based upon an interview with Roughgarden. I'm working on getting a review copy of the book. While not an ID book (yet), the general Darwin-bashing tone argues for it getting some attention here.

    Let me start this off with a quote from Charles Darwin:

    Quote

    I have been struck with the likeness of many of the half-favourable criticisms on sexual selection, with those which appeared at first on natural selection; such as, that it would explain some few details, but certainly was not applicable to the extent to which I have employed it.  My conviction of the power of sexual selection remains unshaken; but it is probable, or almost certain, that several of my conclusions will hereafter be found erroneous; this can hardly fail to be the case in the first treatment of a subject.  When naturalists have become familiar with the idea of sexual selection, it will, as I believe, be much more largely accepted; and it has already been fully and favourably received by several capable judges.

    (Descent of Man, preface)


    And now let's look at this news story that has as its focus a "challenge" to sexual selection.

    Lunch with the FT: Rainbow warrior

    Quote

    "If you have a theory that says something is wrong with so many people, then the theory is suspect," says Joan Roughgarden, looking up from her Caribbean chicken salad. "It is counter-intuitive that nature should have done such a bad job - or, if you prefer, that God should have made so many mistakes."

    The theory in question is Charles Darwin's theory of sexual selection; the "mistakes" are homosexuals, bisexuals, transsexuals - anyone who does not fit into the neat categories of heterosexual male and female.

    By challenging the great 19th-century naturalist, Roughgarden, a professor of biological sciences and geophysics at Stanford University, is making waves in academia and beyond. The implications, not only for science but also for society, could be profound. After all, you don't need to be versed in the Origin of Species to share Darwin's twin assumptions that, broadly, the purpose of sex is reproduction and that females select mates on the basis of genetic characteristics or traits.


    Being versed in Darwin studies would mean that one would know that instead of Origin of Species one should be looking at Descent of Man for Darwin's full explication of his theory of sexual selection. And when one looks there, does one find that sexual selection is founded strictly upon the two "assumptions" identified above? No, one does not.

    The first assumption, that the sole purpose of sex is reproduction,  is simply absent from Darwin's work, so far as I can determine. Someone may have advanced that notion, but until I am presented with the particular passage from Darwin that confirms it I will remain unconvinced of the veracity of the claim that it is Darwin who advanced it. To this end, I have examined etexts of both Origin of Species and Descent of Man and have satisfied myself that such a passage is not to be found within these works.

    Let's look at how Darwin framed sexual selection.

    Quote

    We are, however, here concerned only with sexual selection.  This depends on the advantage which certain individuals have over others of the same sex and species solely in respect of reproduction.  When, as in the cases above mentioned, the two sexes differ in structure in relation to different habits of life, they have no doubt been modified through natural selection, and by inheritance limited to one and the same sex.

    (Descent of Man)


    There is no dependence given here by Darwin on sex itself having the purpose of reproduction, as represented by Roughgarden. Instead, Darwin presents sexual selection as a function of differential reproductive success -- which says nothing about what the "purpose" of sex itself is.

    What of the second assumption identified by Roughgarden, that of female choice? That certainly is part of Darwin's theory of sexual selection. The problem lies not in what Roughgarden provides here, but in what she omits. Sexual selection as explicated by Darwin also concerned how the traits found in the males affected male-male interactions.

    Quote

    When the two sexes follow exactly the same habits of life, and the male has the sensory or locomotive organs more highly developed than those of the female, it may be that the perfection of these is indispensable to the male for finding the female; but in the vast majority of cases, they serve only to give one male an advantage over another, for with sufficient time, the less well-endowed males would succeed in pairing with the females; and judging from the structure of the female, they would be in all other respects equally well adapted for their ordinary habits of life.  Since in such cases the males have acquired their present structure, not from being better fitted to survive in the struggle for existence, but from having gained an advantage over other males, and from having transmitted this advantage to their male offspring alone, sexual selection must here have come into action.  It was the importance of this distinction which led me to designate this form of selection as Sexual Selection.

    (Descent of Man)


    Not only does Darwin recognize male-male interactions here, but he emphasizes the importance of these in his development of the theory of sexual selection. That seems a rather glaring oversight on Roughgarden's part.

    Consider this from the same interview with Roughgarden:

    Quote

    Her alternative paradigm, presented in Evolution's Rainbow, starts with evidence that the natural world is more sexually diverse than usually appreciated. For example, about a third of the species of tropical fish swimming over coral reefs change sex at some point during their lifetime. The conclusion, she says, is that our tendency to divide creatures into neat piles labelled "male" and "female" is mistaken.


    It's funny how Roughgarden positions herself as breaking new ground in discussing diversity of sexual habits. It becomes especially funny when one peruses both Origin of Species and Descent of Man and finds the many discussions of hermaphroditism, gender change, and parthenogenesis contained therein.

    Further on in the article on Roughgarden, we find this:

    Quote

    Roughgarden isn't suggesting an overhaul of Darwin's theory of sexual selection - she is proposing demolition and redevelopment. Her explanation is that Darwin was wrong to regard sex as solely a matter of reproduction. It also has a social role. Thus homosexual behaviour, she says, is a way of building same-sex relationships and strengthening the position of an individual within a group. Far from being an anomaly, she says it is widespread and useful.


    It would appear that strawman construction and demolition is not only useful for career-building, but also seems to be lucrative, if book royalties amount to anything. Compare the grandstanding that comes through this text to Darwin's own assessment of sexual selection quoted up at the top of this post. The comparison is not favorable to Roughgarden.

    Roughgarden's thesis of the social utility of homosexuality should properly be considered as complementary to Darwin's theory of sexual selection rather than as a supplanting alternative theory. For while Darwin did not treat characters like homosexuality directly, there is nothing within what Darwin actually wrote on the topic that would exclude  social behaviors of this sort from the general framework of sexual selection. But that, of course, would not give Roughgarden the iconoclast status that she apparently seeks.
    * ID myth: IC subsets "functionless" by themselves (2 replies)
    rafe gutman2002-09-24 13:45:26
    have you ever heard behe (or more recently dembski) imply that subsets of IC systems have no function?  i certainly have.  however, in a recent internet discussion over on ISCID, dembski clearly stated that that was false, and that ID critics were misrepresenting their opinion.  in his own words,
    Quote
    You've charged me with moving the goalposts and adjusting the definition of irreducible complexity because I require of evolutionary biologists to "connect the dots" in a causally convincing way. The dots here are functional precursors that could conceivably have evolved into the final system of interest. You state that previously I claimed that the dots couldn't exist because they wouldn't be functional. Please show me in Michael Behe's writings or my own where we deny that IC systems can be made up of subsystems that can be functional in their own right. The point is not whether subsystems can be functional on their own but whether they can exhibit the same function in the same manner as the system in question. You misrepresent our position.

    then later, when presented with quotes implying such (which will be given later):
    Quote
    I wrote, "Please show me in Michael Behe's writings or my own where we deny that IC systems can be made up of subsystems that can be functional in their own right." Both Behe and I have always defined IC with reference to the basic function of the system in question (if we've not said it explicitly -- and I have in NFL -- then a charitable reading would have granted that -- neither Behe nor I are that stupid). We therefore left open the possibility of subsystems having function in their own right. You and Yersinia charge us with a denial.

    one of the key arguments of irreducible complexity being a roadblock to evolution is the lack of "functional intermediates" for selection to act upon.  if a purportedly IC system has 20 components, and homologues to all 20 are observed in 20 separate systems, then an IDist might propose that all 20 components had to come together in one step in order for the IC system to evolve.  of course, to say this is to deny that 3, or 5, or 10 components could have a function all to their own (whether it be the IC function or something else).  i'd like this thread to serve as a place where ID critics could post quotes of behe or dembski, or any other IDist where they propagate this myth.  please indicate the source of the quote in your post.  i'll post my initial contributions below.
    * The rise and fall of adaptive mutation (1 replies)
    niiicholas2003-01-25 18:00:34
    Charlie D gives a great brief intro on why adaptive mutation ain't:

    ===========
    ARN thread:
    Topic: Directed mutation
    http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000588


    Originally posted by charlie d:
    I have no idea when that paper was written, but it lists no references later than 1995.  Thus, its enthusiasm for the "targeted mutation" phenomenon, its belief that it represents a fundamental challenge to the prevailing genetic paradigm, and its conclusion that "there is no explanation for it", is not surprising, considering that the hypothesis itself began to crumble in earnest in 1996 with the publication of this article by Prival and Cebula:
    Prival MJ, Cebula TA Adaptive mutation and slow-growing revertants of an Escherichia coli lacZ amber mutant. Genetics 1996 Dec;144(4):1337-41,
    and eroded further after this article by Patricia Foster (who was one of the original discoverers of the adaptive mutations phenomenon):
    Foster PL. Nonadaptive mutations occur on the F' episome during adaptive mutation conditions in Escherichia coli. J Bacteriol. 1997 Mar;179(5):1550-4.

    These and other findings prompted Foster herself to write the now classic review (available for free here): Foster PL. Adaptive mutation: has the unicorn landed? Genetics. 1998 Apr;148(4):1453-9,
    a virtual obituary for the "lamarckian" interpretation of the phenomenon.

    A more detailed review is this one (but subscription is required to access the actual paper): Foster PL. Mechanisms of stationary phase mutation: a decade of adaptive mutation. Annu Rev Genet. 1999;33:57-88.

    At the current state of affairs, it is very clear that mutations during "adaptive mutagenesis" are not specifically directed towards the gene(s) under selection, i.e. they are entirely darwinian (random wrt to fitness), and are often the result of generalized hypermutation mechanisms (the last important piece of the puzzle being the publication of this paper last year):  Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth JR. Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2164-9.

    For those interested in the most recent and actual history of the "targeted mutation" saga, I recommend this recent excellent review of the issue, available for free here: Rosenberg SM Evolving responsively: adaptive mutation. Nat Rev Genet 2001 Jul;2(7):504-15

    ===========

    * Denton quotes (1 replies)
    niiicholas2003-01-19 04:19:00
    Michael Denton has said a lot of things over the years.  However on the whole he appears to have moved in a wholly evolutionary direction after he kicked off "the modern ID movement" with his 1986 book Evolution: Theory in Crisis.

    E.g., here is a quote that I'd read but never had handy:

    originally posted here

    From Darwinism Defeated?, 1999:

    Quote

    In conclusion, I agree with [Phillip] Johnson that the Darwinian model is an inadequate explanation for how evolution occurred. And I think he is right to attack the exaggerated claims of certain Darwinian theorists who extend Darwinian explanations to include all aspects of human nature and behaviour. Where he does this I applaud his efforts. I also agree with him that the living organisms exhibit design. However I am not aware of any convincing arguments put forward by Johnson to show that this design necessitates special creation. I am also unaware of any serious systematic attempt by Johnson to show how the facts of biology, such as those of geographical distribution discussed above, can be accounted for more plausibly in creationist than evolutionary terms. Until he does this, academic biology will not take his antievolutionism seriously.
    In his advocacy of special creationism I believe Johnson is merely the latest in a succession of vigorous creationist advocates who have been very influential within conservative Christian circles, particularly in the United States, during the twentieth century. None of these advocates, however, has had any lasting influence among academic biologists. This is not because science is biased in favour of philosophical naturalism but because the special creationist model is not supported by the facts and is incapable of providing a more plausible explanation for the pattern of life's diversity in time and space than its evolutionary competitor. The reason why no current member of the US National Academy of Science is a special creationist is because of the facts, the same facts that in the nineteenth century convinced Darwin and Wallace and all the leading Christian biologists, including Joseph Hooker, Asa Gray, and Charles Lyell, of the reality of descent with modification


    (some typos may remain, I fixed one)

    There is no point in quote mining, so whatever anti-evolution statements one comes across from Denton are fine also.
    * Convergence (3 replies)
    niiicholas2002-12-26 02:19:56
    A post from ICSID here:

    Perhaps the reason that Hunter finds the evidence for common descent weak is that he misunderstands crucial points.

    E.g., he has repeatedly alleged, without evidence, that designed objects will produce nested hierarchies.  But it just ain't so:

    Quote

    source

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically - perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese. The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

    Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

    The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).


    He also severely misunderstands convergence.  Convergence can only produce functionally-relevant similarities, because that is all that selection can "see".  Homologies, i.e. similarities between systems that are not necessary for functional similarity between systems, are what allows paleontologists to easily distinguish between these placental wolf and marsupial "wolf" skulls that cre8tionist posted in another thread:



    I invite readers to go to The Thylacine Museum and look at the side-by-side comparison of 'wolf' skulls (with cool magnifier lense).

    The caption reads:

    Quote

    Portrayed here are side-by-side images demonstrating the anatomical differences between the skulls of the Grey wolf (Canis lupus) and the thylacine (Thylacinus cynocephalus).  In the dorsal view, note that the thylacine has a much broader forehead than the wolf, and there are differences in the design of the zygomatic arches and brain case.  Also, the rostrum (snout) of the thylacine is far narrower than that of the wolf, and the thylacine has proportionately larger eye sockets which are rather more square in shape.  In the ventral view, one can easily see the great differences in dentition that  readily distinguish the two species as being members of distinct mammal groups.  The dentition of both species will be represented in greater detail on the following page.  Also visible in the ventral view is the thylacine's maxillary palatal vacuity (the two parallel openings in the roof of the mouth).  This is a feature that the wolf and other placental mammals do not have.


    ...on the next page...

    Quote

    Here I show some diagrams which I have prepared to illustrate the extreme difference in dental anatomy which exists between the thylacine and its placental counterpart, the wolf.  The images are portrayed at life size.  Although there are also a number of notable differences in post cranial skeletal structure between the thylacine and wolf, I felt that the dentition represented one of the most striking dissimilarities.  As you can easily see in the image of the maxilla, the thylacine has 8 top incisors, whereas the wolf has only 6.  In the mandible however, the thylacine and wolf have an equal number of incisors.  Another major difference is the presence of a specialized shearing tooth, the carnassial, in the wolf.  This tooth design is a trademark of the wolf and other members of the placental mammal family Carnivora.  Also make note that unlike the wolf, the thylacine lacks large grinding surfaces on its molars.  Altogether, the wolf has a complement of 42 teeth, and the thylacine 46.


    I can't post the images here because they are copyright protected, but the differences in the tooth-numbering are dramatic.

    All commonly-sighted cases of "uncanny convergence" in biology turn out, on investigation, to be externally impressive but superficial when you get down to details.  This is notably different from the kinds of things that have happened in aircraft design, e.g. the addition of (the same) transponders, GPS units, computers, TV screens, etc., to planes of widely different models.

    This has been pointed out many times over the years, so I'm not sure why these cases still get seriously cited.

    yersinia

    PS: There is also the interesting question of:

    If the hypothesized IDer decided that there needed to be some carnivorous canine-type critters in Australia, why bother with all the genetic engineering that would be required, when a simple aboriginal boat sufficed to bring dingos to Australia only ~15,000 years ago?

    Such ID puzzles are absolutely ubiquitous in biogeography.  To me they indicate strongly that whatever creativity made these wonderful adaptations was, for some odd reason, highly constrained so that "design information" could not be transmitted across deep water barriers and instead had to be re-invented from scratch each time the adaptation was "needed" in particular locations.  Strangely, such geographical constraints did not apply to flying birds, sea mammals, and other easily-dispersed organisms.

    If you can find an ID theory that can explain this (and "the designer's actions are  mysterious" is not an explanation), I'll eat my hat.  If on the other hand you give natural selection the credit for these instances of creativity, then I guess natural selection can "design" things after all, and quite skillfully too...
    * Incongruence in phylogenetic trees (3 replies)
    niiicholas2002-12-23 23:39:22
    I think that several considerations have to be added to Hunter's post before serious discussion can be had.  

    1) "Congruence" and "noncongruence" are not either/or entities, they a matter of degree.  Given N species being analyzed, there are something like (2n-3)!/(2n-2(n-2)!;) hypothetically possible ways of arranging them into a tree (Theobald 2002), and the (dis)similarity between two trees can be rigourously quanitified.

    This equation will differ slightly depending on whether the trees are rooted vs. unrooted, binary splits only, etc.  Regardless, the number of possible trees gets very big very fast: 4 species = 15 possible trees, 8 species = 135,135 possible trees.

    You can randomly generate tree diagrams at this cool page (Phylogeny and Reconstructing Phylogenetic Trees) and get the idea very quickly what the odds are of getting the same tree twice by random chance.

    So the question is not whether two phylogenies from different data sources/research labs are congruent or incongruent, full stop, the question is how congruent or incongruent are they?  Most of the examples touted as showing "incongruence" are actually quite minor phylogenetic disagreements.  E.g., the interrelationships of different groups of bats is a pretty trivial issue in the context of vertebrates or animalia.  If the microbats grouped most closely with anthropoid apes, and the macrobats with giraffes, then we'd have a significant disagreement.  This kind of thing does not happen in multicellular organisms with protected germ line cells, rather different datasets keep returning highly congruent phylogenies.

    So, just like any scientific measurement, there will be noise in input data.  The analogy here is to radiometric dating: if two measurement dates of a moon rock return ages of 4.6 and 4.5 billion years, this is very minor disagreement relative to the result (100 million years sounds like alot but is only a 2% disagreement).  If someone were to go around saying "geological measurements disagree by 100 million years and this is evidence against an old earth" they would be wrong. Similar minor disagreements, such as Teeling et al.'s 2002 bat study,  should not be cited as evidence for Hunter's proposition "there are also plenty of character/species sets that do not produce congruent phylogenies".  A real disagreement would occur if all of these different bat species did not group together and instead were randomly associated with the outgroup taxa, but as we can see this did not occur:

    [img]http://www.pnas.org/content/vol99/issue3/images/medium/pq0224771001.gif[/[img]

    The odds of all these bat species grouping together by chance are astronomical.


    2. Scale of the study and range of dataset

    As the age-of-the-moon example points out, what is important in considering disagreement in results is not the absolute measurement, but the size of the disagreement relative to the scale of the study.  100 million years sounds like alot but is peanuts in terms of the age of the earth.  Such a disagreement would be major, however, in a radiometric dating of dinosaur bones, and a data source with a smaller error would have to be used.  

    Radiometric datasets have ranges and scales over which they are useful, due essentially to their rate of decay.  You use uranium-lead to date the age of the moon, because it has a half-life of hundreds of millions of years, but it would be ridiculous to use it for dating an archeological artifact because the answer you would get (assuming the artifact was, say, something that had been forged by remelting the ore) would be "0 +/- millions of years".  Similarly, the half-life of C-14 is only ~5,000 years, so it is excellent for archeology but for anything older than 50,000 years it is useless (a result of "50,000 years old" for a carbon date essentially means "this sample is between 50,000 and infinite years old").  In the first case, the noise is much larger than the signal, and in the second case the signal is much smaller than the noise (these are slightly different, think about it for a sec.).

    With molecular sequences the same factors must be taken into account.  I don't currently have access to Hunter's cited Balter (1997), " Morphologists learn to live with molecular upstarts", but I would note that there is apparently a contrasting commentary (Mindell 1997) on that very article from the next month of Science, entitled ""Misleading" molecules?".  Probably the basic point is that the particular mtDNA sequences being used evolve too quickly (certain mtDNA sequences are, after all, used for tracing migration patterns within the human species), such that sequence similarity is low and therefore "noise" in the form of mutational biases is larger than the signal.  Certainly comparing chickens, amphibians, and fish is a long ways from what one normally sees mtDNA used for, e.g. species within a genus.  

    (Note in passing: not all mtDNA within a mitochondrion is the same.  It's possible that the above study used a very slowly evolving mtDNA sequence and similarity between e.g. birds and fish was high, e.g. >75%.  But I doubt it.  Let's get the Balter and Mindell articles and see what they say, shall we?)

    In summary, anytime one sees a cited "incongruence" they must consider the dataset is appropriate for the scale of the analysis.  If sequence similarity is approaching randomness then mutational biases are increasingly important to consider.


    3. Actual violation of lineal descent.  This is commonly the case for single-celled prokaryotes without protected germline DNA.  If you like, the tree hypothesis has been falsified, because it is known and has been observed in the lab that they can trade DNA laterally.  But this leaves the evidence for the common descent of e.g. all animals unquestioned.  Much more can be said here because LGT is itself a nonrandom process and certainly some things are harder to LGT than others, but this is another topic.  If we saw the kinds of disagreements in animals that we have in prokaryotes, as we have no mechanism for significant LGT in animals (viral transfers is about it I think), this would be a significant problem for the common descent theory.  But we don't.  "Disagreements" that I have seen cited for multicellular critters basically fall into the above categories.

    In summary, in answer to Hunter's question,

    Quote

    My point is not to say explanatory mechanisms are out of bounds or that complicating factors should not be expected, but merely to raise the question: At what point does the use of these explanatory mechanisms become ad hoc and do we consider the Step 1 in the syllogism falsified?


    ...basically, these explanatory mechanisms are allowed when they themselves are well-supported by available data.  We can measure mtDNA rates of change and mutational biases.  We can observe and explain why LGT occurs in prokaryotes but not in mammals.  We can measure the degree of disagreement between trees and determine if the error is equivalent to 100 million years/4.6 billion years or not.

    There is a massive literature on all of this, which is why I'm surprised that Hunter thinks that biologists haven't thought about it.  The best introduction to it all is Theobald's FAQ at that talkorigins archive, referenced below. It references a lot of articles with titles like "Testing Common Descent" about the probabilities of hitting on congruent trees by chance.

    Refs:

    Theobald, Doug. 2002.  29 Evidences for Macroevolution

    Teeling, Emma C. et al. 2002 Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 3, 1431-1436.

    (bold added below)

    Quote

    Molecular phylogenies challenge the view that bats belong to the superordinal group Archonta, which also includes primates, tree shrews, and flying lemurs. Some molecular studies also challenge microbat monophyly and instead support an alliance between megabats and representative rhinolophoid microbats from the families Rhinolophidae (horseshoe bats, Old World leaf-nosed bats) and Megadermatidae (false vampire bats). Another molecular study ostensibly contradicts these results and supports traditional microbat monophyly, inclusive of representative rhinolophoids from the family Nycteridae (slit-faced bats). Resolution of the microbat paraphyly/monophyly issue is essential for reconstructing the temporal sequence and deployment of morphological character state changes associated with flight and echolocation in bats. If microbats are paraphyletic, then laryngeal echolocation either evolved more than once in different microbats or was lost in megabats after evolving in the ancestor of all living bats. To examine these issues, we used a 7.1-kb nuclear data set for nine outgroups and twenty bats, including representatives of all rhinolophoid families. Phylogenetic analyses and statistical tests rejected both Archonta and microbat monophyly. Instead, bats are in the superorder Laurasiatheria and microbats are paraphyletic. Further, the superfamily Rhinolophoidea is polyphyletic. The rhinolophoid families Rhinolophidae and Megadermatidae belong to the suborder Yinpterochiroptera along with rhinopomatids and megabats. The rhinolophoid family Nycteridae belongs to the suborder Yangochiroptera along with vespertilionoids, noctilionoids, and emballonuroids. These results resolve the apparent conflict between previous molecular studies that sampled different rhinolophoid families. An important implication of rhinolophoid polyphyly is independent evolution of key anatomical innovations associated with the nasal-emission of echolocation pulses.


    Originally posted here:

    ICSID thread

    * Chromosome evolution (0 replies)
    Art2003-03-09 09:44:49
    The discussion on ARN about chromosome evolution, and the supposed difficulties that karyotype differences pose for the evolution of, say, humans from a common ancetsor with other primates, brings to mind several similar discussions on AOL that have dealt with the same subject.  I won't begin to pretend that the following are an exhaustive list, or that they are the first or last word on the subject, but they are among the abstracts that address some specific issues.

    The first one describes a great deal of karyotpic variability in populations of rats on Mauritius, all of which most likely arose from a small ancestral population.  The ramifications vis-a-vis the possibilities of chromosome evolution are obvious.

    Quote
    Chromosoma 1979 Oct 2;75(1):51-62

    Mauritius type black rats with peculiar karyotypes derived from Robertsonian fission of small metacentrics.

    Yosida TH, Kato H, Tsuchiya K, Moriwaki K, Ochiai Y, Monty J

    All seventeen black rats collected from Mauritius Island were characterized by having many extra small acrocentric autosomes. Their basic karyotype was of Oceanian type, because of the presence of the large metacentric M1 and M2 pairs, but chromosome numbers in 13 specimens among them were 42, those of 3 specimens 43, and those of the remaining one specimen 44. Although the Oceanian type rat had 2 small acrocentric autosomes (pair no. 13), 16 Mauritius rats had 10 small acrocentrics, and the remaining one had 8 small acrocentrics. Comparative karyotype analysis between Oceanian and Mauritius type rats showed that the extra small acrocentrics found in Mauritius rats were due to Robertsonian fission of small metacentric pairs no. 14 and 18 of the original Oceanian type rat. Only one rat with 8 small acrocentrics showed the heteromorphic pair no. 18 consisting of one metacentric and two acrocentrics. The large metacentric M1 chromosome in 13 of 17 rats examined showed homologous pair, but two of them were heteromorphic by involving one metacentric M1 and two acrocentrics. In the remaining two rats M1 chromosome was not observed, but acrocentric pairs no. 4 and 7 were included. These acrocentrics were also suggested to be originated from Robertsonian fission of the large metacentric M1 chromosome. Robertsonian fission seemed to be one of the important mechanism found in karyotype evolution.


    The second abstract describes variations in the karyotypes of a primate.  Of particular note is the occurrence of heterozygotes that from matings of parents with different karyotypes - this demonstrates conclusively that, in primates, changes in chromosome morphology are not always, invariably detrimental with respect to fertility or health.

    Quote
    Am J Phys Anthropol 1999 Oct;110(2):129-42

    Complex, compound inversion/translocation polymorphism in an ape: presumptive intermediate stage in the karyotypic evolution of the agile gibbon Hylobates agilis.

    Van Tuinen P, Mootnick AR, Kingswood SC, Hale DW, Kumamoto AT

    Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
    vantuine@post.its.mcw.edu

    Karyotypic variation in five gibbon species of the subgenus Hylobates (2n = 44) was assessed in 63 animals, 23 of them wild born. Acquisition of key specimens of Hylobates agilis (agile gibbon), whose karyotype had been problematic due to unresolved structural polymorphisms, led to disclosure of a compound inversion/translocation polymorphism. A polymorphic region of chromosome 8 harboring two pericentric inversions, one nested within the other, was in turn bissected by one breakpoint of a reciprocal translocation. In double-inversion + translocation heterozygotes, the theoretical meiotic pairing configuration is a double inversion loop, with four arms of a translocation quadrivalent radiating from the loop. Electron-microscopic analysis of synaptonemal complex configurations consistently revealed translocation quadrivalents but no inversion loops. Rather, nonhomologous pairing was evident in the inverted region, a condition that should preclude crossing over and the subsequent production of duplication-deficiency gametes. This is corroborated by the existence of normal offspring of compound heterozygotes, indicating that fertility may not be reduced despite the topological complexity of this polymorphic system. The distribution of inversion and translocation morphs in these taxa suggests application of cytogenetics in identifying gibbon specimens and avoiding undesirable hybridization in captive breeding efforts.


    The last abstract makes mention of a variant chromosomal race in  Australian aphids.  As I read the abstract, it seems as if this race arose while the aphids were "cultured" - e.g., there is not much question as to the ancestry of the race, nor of the fact that such a chromosomal variation was, in this instance, not an insurmountable barrier to overall karyotpic evolution.  If others see this differently or are more familiar with these things, please feel free to comment.

    Quote
    Genetics (1996) 144, 747-756

    Microsatellite and chromosome evolution of parthenogenetic sitobion aphids in Australia.

    Sunnucks P, England PR, Taylor AC, Hales DF

    School of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.

    Abstract: Single-locus microsatellite variation correlated perfectly with chromosome number in Sitobion  miscanthi aphids. The microsatellites were highly heterozygous, with up to 10 alleles per locus in this species. Despite this considerable allelic variation, only seven different S. miscanthi genotypes were discovered in 555 individuals collected from a wide range of locations, hosts and sampling periods.  Relatedness between genotypes suggests only two successful colonizations of Australia. There was no evidence for genetic recombination in 555 S. miscanthi so the occurrence of recent sexual reproduction must be near zero. Thus diversification is by mutation and chromosomal rearrangement alone. Since the aphids showed no sexual recombination, microsatellites can mutate without meiosis. Five of seven microsatellite differences were a single repeat unit, and one larger jump is likely. The minimum numbers of changes between karyotypes corresponded roughly one-to-one with microsatellite allele changes, which suggests very rapid chromosomal evolution. A chromosomal fission occurred in a cultured line, and a previously unknown chromosomal race was detected. All 121 diverse S. near fragariae were heterozygous but revealed only one genotype. This species too must have a low rate of sexual reproduction and few colonizations of Australia.


    * Genetic Code origins (1 replies)
    theyeti2002-12-30 14:51:11
    I thought we had a thread for the evolution of the genetic code, and some of the IDists claims about it.  I guess it got lost in the server crash.  Anyway, I thought I'd start this one up anew, and post a recent paper that's relevant to the origins of the genetic code.

    Philos Trans R Soc Lond B Biol Sci 2002 Nov 29;357(1427):1625-42

    No accident: genetic codes freeze in error-correcting patterns of the standard genetic code.

    Ardell DH, Sella G.


    Quote
    The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic codes are generally coadapted with, or 'frozen' by, the protein-coding genes that they translate, and so cannot easily change by natural selection. Yet the standard code has a significantly non-random pattern that corrects common errors in the transmission of information in protein-coding genes. Because of the freezing effect and for other reasons, this pattern has been proposed not to be due to selection but rather to be incidental to other evolutionary forces or even entirely accidental. We present results from a deterministic population genetic model of code-message coevolution. We explicitly represent the freezing effect of genes on genetic codes and the perturbative effect of changes in genetic codes on genes. We incorporate characteristic patterns of mutation and translational error, namely, transition bias and positional asymmetry, respectively. Repeated selection over small successive changes produces genetic codes that are substantially, but not optimally, error correcting. In particular, our model reproduces the error-correcting patterns of the standard genetic code. Aspects of our model and results may be applicable to the general problem of adaptation to error in other natural information-processing systems.


    theyeti
    * Synthesis: Origins of Complexity (0 replies)
    niiicholas2003-02-02 06:43:20
    Originally posted over at ARN, perhaps this could serve as starting material for an overall "progressive case for the origins of complexity" FAQ, i.e. that starts with the small processes and then builds them up.

    Feel free to add relevant links, posts, etc., especially to threads that better document specific points, e.g. adaptive radiation, transitional fossils, IC, etc.

    Original thread: http://www.arn.org/cgi-bin....#000004

    =========

    Berthajane, Vivid, et al.,

    I've often thought that there should be a FAQ somewhere specifically on the evolution of complexity, since that is what is the sticking point for a lot of people.

    I don't really have the time to write a FAQ or even do more than hit-and-run post, but perhaps I can communicate how I think it might go.  Perhaps you can comment if you think all of this is old hat and would be pointless and unconvincing to you in a FAQ or if you think it would be worth reading.

    OK, here goes.

    The case for RM & NS producing complexity is cumulative.  You start from small-scale processes and then work up.

    1) "Microevolution" -- local adaptation: drug resistance, peppered moths, pesticide resistance, guppy size change, etc.  Presumably everyone accepts this.level of evolution.

    It is worth considering, for a moment, some of the implications of even this minor level of evolution:

    a) Microevolutionary forces can, in short order, take a single mutation in a single individual and spread it to fixation, so that it exists in every member of a population of millions.  All of the millions of bad mutations don't matter a bit, they rarely made it further than a generation or two.  That one-in-a-million lucky mutation is the one that natural selection picks (even if it is lost by chance the first few times, sooner or later it or an equivalent mutation will spread far enough that its success becomes guarenteed).

    Also, note that even at this minor level we have a fair bit of design-mimicking occurring.  Peppered moths, for example, don't change color in any random direction, they change color to match the color of tree bark (please refer to the Wells FAQ before critiquing the peppered moth example).  Modern militaries only got around to producing decent camoflague in the mid-1900's.

    Now think about all the other amazing instances of camoflague in the animal (and plant!;) world.

    A few examples:

    A frog in Madagascar:




    Those were fairly modest examples.

    Look for the plants in this picture, they're in plain view:

    The well-named Lithops:


    And here, which one is the ant and which one is the ant-mimicking spider?


    (hint: count legs)



    Here is a fairly decent webpage on mimicry (Kimballs pages are about the best online pseudo-bio text I've seen, decent pictures etc)

    Camoflague and prey-mimicry combined in this one:



    (Click here for an II thread discussing anglerfish evolution BTW)

    Anyhow, I went on a tangent with camoflague and mimicry.  My point: I submit that all of these cases are rather easily explained by "microevolution" of the peppered moth type (and there are many other studies of natural selection for camoflague BTW) -- indeed, many of these impressive designs are specific to species in genera or families with completely different coloration...e.g. anglerfish that live so deep that no light reaches them don't bother with camoflague.

    If this kind of thing is conceeded, then we've already allowed that microevolution has a rather substantial ability for "creativity" and acheiving very specific "designs".

    (b) Returning to the population-genetics-level processes described at the top of (a)...Now think about them happening continually (many different mutations will be under the influence of selection in any given species at any given point in time) for millions of years.  Here we add in speciation, both due to geographical separation (allopatric) and niche partitioning (sympatric).  Many species going in many different directions.  Many recent adaptive radiations of species, where very-closely related species are morphologically very different and "designed" for very different niches, could be cited.  Here are a few:

    Kimball's speciation page

    Darwin's Finches (Darwin did not even realize they were all finches for years after he collected them; they fill the niches fufilled by various birds on continents -- seed eaters, insect eaters, woodpecker, warbler, etc.):

    (this, BTW, is the most important point about Darwin's Finches, although Peter & Rosemary Grant's studies of recent natural selection are also interesting)

    The Hawaiian honeycreepers are even better examples.  These are all closely related (well, were, some were driven extinct when Europeans and their pets invaded):



    And be sure to check out Art's post on the Hawaiian Silversword Alliance (sounds like an army in an online wargame, I know...):

    Some of these Silverswords are trees, some are little herbs, and yet they are all closely related and many are even interfertile

    © If it is conceeded that RM & NS can account for the rather astounding diversity of the above groups, then we've agreed that natural evolutionary processes can account for family-level diversity.  Now, if the same processes produced orders (e.g. the various mammal groups) and classes (e.g., reptiles, amphibians, etc.), we should see some fossil evidence of this, and we do.  In the case of vertebrates, rather a lot, and a bunch of new ones in the last 10 years.  Just to review what we've got intermediates or close-offshoots for:

    fish-amphibian
    amphibian-reptile
    reptile-mammal
    dinosaur-bird
    artiodactyl-whale
    walking sirienians (manatees etc., forget what they're descended from)
    horses
    elephants
    ...and of course, humans.

    Why any of these should exist, except on the hypothesis that all modern organisms originated by modification of previous organisms by a process limited to fairly gradual changes (like RM&NS) is a useful question to consider.

    2) Turning from morphology to molecules: while the lower levels of evolution and adaptation might be explained basically by selection of point mutations, at some point new genetic information has to be created.  There is a mechanism for this, namely the combination of gene duplication (and variations on this, e.g. deletions, rearrangments, etc.) with the mutation-and-selection processes discussed back in 1a.

    Even unmodified gene duplications are often selected; e.g., some DDT resistant mosquitos have 100+ copies of a DDT-resistance gene (see Weiner, Beak of the Finch).  Plus we have genome duplications, duplication of whole segments of chromosomes, etc.  These kinds of processes give evolution a lot of material to play with, and there are numerous documented and published cases of observed or recent origins of novel genes by various combinations of the above processes.

    Lots of them are described in this origin of information thread

    And of course the same kinds of adaptive radiation patterns found in morphology can be found in molecules, and here we even have hard-and-fast evidence that directional natural selection was operating millions of years back in the unobservable past, in the form of substitution biases, e.g.:

    Quote

    Gene 2000 Dec 30;261(1):43-52
     
    Adaptive evolution of animal toxin multigene families.

    Kordis D, Gubensek F.

    Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia. dusan.kordis@ijs.si

    Animal toxins comprise a diverse array of proteins that have a variety of biochemical and pharmacological functions. A large number of animal toxins are encoded by multigene families. From studies of several toxin multigene families at the gene level the picture is emerging that most have been functionally diversified by gene duplication and adaptive evolution. The number of pharmacological activities in most toxin multigene families results from their adaptive evolution. The molecular evolution of animal toxins has been analysed in some multigene families, at both the intraspecies and interspecies levels. In most toxin multigene families, the rate of non-synonymous to synonymous substitutions (dN/dS) is higher than one. Thus natural selection has acted to diversify coding sequences and consequently the toxin functions. The selection pressure for the rapid adaptive evolution of animal toxins is the need for quick immobilization of the prey in classical predator and prey interactions. Currently available evidence for adaptive evolution in animal toxin multigene families will be considered in this review.
    And here is the tip of the iceberg (Drosophila is always the tip of the iceberg) for the molecules giving us an even better handle on just how important a force directional natural selection is on genomes:

    Quote

    Adaptive protein evolution in Drosophila.

    Nature 2002 Feb 28;415(6875):1022-4
     
    Smith NG, Eyre-Walker A.

    Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK.

    For over 30 years a central question in molecular evolution has been whether natural selection plays a substantial role in evolution at the DNA sequence level. Evidence has accumulated over the last decade that adaptive evolution does occur at the protein level, but it has remained unclear how prevalent adaptive evolution is. Here we present a simple method by which the number of adaptive substitutions can be estimated and apply it to data from Drosophila simulans and D. yakuba. We estimate that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species.
    If this is not impressive enough, think about what the population of a species of fruit fly must be (billions? trillions?).

    As for the origin of new morphology, the combination of the origins-of-genes processes described above, with recent knowledge of the genes patterning development, has made this much clearer.  E.g.:

    Quote

    Philos Trans R Soc Lond B Biol Sci 1995 Sep 29;349(1329):313-9

    Hox genes and the evolution of diverse body plans.

    Akam M.

    Wellcome/CRC Institute and Department of Genetics, Cambridge, U.K.

    Homeobox genes encode transcription factors that carry out diverse roles during development. They are widely distributed among eukaryotes, but appear to have undergone an extensive radiation in the earliest metazoa, to generate a range of homeobox subclasses now shared between diverse metazoan phyla. The Hox genes comprise one of these subfamilies, defined as much by conserved chromosomal organization and expression as by sequence characteristics. These Hox genes act as markers of position along the antero-posterior axis of the body in nematodes, arthropods, chordates, and by implication, most other triploblastic phyla. In the arthropods this role is visualized most clearly in the control of segment identity. Exactly how Hox genes control the structure of segments is not yet understood, but their differential deployment between segments provides a model for the basis of segment diversity. Within the arthropods, distantly related taxonomic groups with very different body plans (insects, crustaceans) may share the same set of Hox genes. The expression of these Hox genes provides a new character to define the homology of different body regions. Comparisons of Hox gene deployment between insects and a branchiopod crustacean suggest a novel model for the derivation of the insect body plan.

    Annu Rev Cell Dev Biol 2002;18:53-80
     
    Gene co-option in physiological and morphological evolution.

    True JR, Carroll SB.

    Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, New York 11794-5245, e-mail: jrtrue@life.bio.sunysb.edu

    Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit.
    In fact, right now we are living through the merging of developmental biology with the modern synthesis, e.g.:

    Quote

    Genetica 2001;112-113:45-58

    Toward a new synthesis: population genetics and evolutionary developmental biology.

    Johnson NA, Porter AH.

    Department of Entomology and Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst 01003, USA.

    Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.
    I have put the above articles and some others over in this thread.

    3) OK, so at this point we perhaps have reached the amount of evolution that Mike Behe accepts or at least doesn't argue about, that is: a heck of a lot.  I tend to be of the opinion that if natural evolutionary processes can produce new genes, novel morphological traits, and even body plans, we ought to expect that it's powerful enough to do just about anything that that we see in biology today.  But, some will raise IC at this point, arguing that, sure, evolution could have produced mammals, humans, wings, whales, innumerable new genes and adaptations, but that a designer still intervened to produce a certain class of system (*really* complex or rather simple-but-irreducible, depending on who you talk to...) that Behe calls IC.

    This has been discussed to death in numerous places, but suffice it to say that for the most complicated of Behe's IC systems, namely the vertebrate immune system, Behe's claims about lack of evidence for an evolutionary origin, and lack of scientific publications on the topic of the origin of the immune system, he has been decisively refuted.

    Basically:

    Read this: Evolving Immunity by Matt Inlay

    Then read: This ISCID thread where IDists were hapless in their attempt to defend Behe

    If natural processes can produce even ridiculously complex IC like this, then there is no particular reason to invoke ID to explain IC.

    4) Finally, once all of the above is accepted or considered probable, we are in a position to consider the origin of eukaryotes and prokaryotes.  In my opinion, if RM&NS processes can create something like the metazoan phyla and the immune system, there's no reason to suspect that anything else was responsible for earlier events.

    We are however getting into events that occurred on a microscopic scale 1+ billion years ago, so details are necessarily much more speculative.  All I can recommend is some of the better reading I've found on these topics:

    Maynard Smith and Szathmary, Major Transitions in Evolution, 1995.  Here is a brief review by someone.

    The short version of the above is their 1998 Origins of Life but it is pretty much pointless compared to the bigger book.

    The other good source is pretty much anything written by Cavalier-Smith (type his name in here), e.g. this series of articles:

    Quote

    J Mol Evol 2001 Oct-Nov;53(4-5):555-95
     
    Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis.

    Cavalier-Smith T.

    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom. tom.cavalier-smith@zoo.ox.ac.uk

    I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects. Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the outer surface of an 'inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later added to signal peptides, yielding a ten-acid doublet code. A primitive proto-ecology of molecular scavenging, parasitism, and predation evolved among obcells. I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells, to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup, causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code. Anticodons were recruited sequentially: GNN, CNN, INN, and *UNN. CO2 fixation, photoreduction, and lipid synthesis probably evolved in the protocell before photophosphorylation. Signal recognition particles, chaperones, compartmented proteases, and peptidoglycan arose prior to the last common ancestor of life, a complex autotrophic, anaerobic green bacterium.

    Int J Syst Evol Microbiol 2002 Jan;52(Pt 1):7-76
     
    The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

    Cavalier-Smith T.

    Department of Zoology, University of Oxford, UK. tom.cavalier-smith@zoo.ox.ac.uk

    Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein lob; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolution, not chimaeric evolution by lateral gene transfer. No symbiogenesis occurred. Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient, radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.

    Int J Syst Evol Microbiol 2002 Mar;52(Pt 2):297-354
     
    The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

    Cavalier-Smith T.

    Department of Zoology, University of Oxford, UK. tom.cavalier-smith@zoo.ox.ac.uk

    Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. [...abstract too long... (!!!;)]

    Heredity 2002 Feb;88(2):125-41
     
    Origins of the machinery of recombination and sex.

    Cavalier-Smith T.

    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. tom.cavalier-smith@zoo.ox.ac.uk

    Mutation plays the primary role in evolution that Weismann mistakenly attributed to sex. Homologous recombination, as in sex, is important for population genetics--shuffling of minor variants, but relatively insignificant for large-scale evolution. Major evolutionary innovations depend much more on illegitimate recombination, which makes novel genes by gene duplication and by gene chimaerisation--essentially mutational forces. The machinery of recombination and sex evolved in two distinct bouts of quantum evolution separated by nearly 3 Gy of stasis; I discuss their nature and causes. The dominant selective force in the evolution of recombination and sex has been selection for replicational fidelity and viability; without the recombination machinery, accurate reproduction, stasis, resistance to radical deleterious evolutionary change and preservation of evolutionary innovations would be impossible. Recombination proteins betray in their phylogeny and domain structure a key role for gene duplication and chimaerisation in their own origin. They arose about 3.8 Gy ago to enable faithful replication and segregation of the first circular DNA genomes in precellular ancestors of Gram-negative eubacteria. Then they were recruited and modified by selfish genetic parasites (viruses; transposons) to help them spread from host to host. Bacteria differ fundamentally from eukaryotes in that gene transfer between cells, whether incidental to their absorptive feeding on DNA and virus infection or directly by plasmids, involves only genomic fragments. This was radically changed by the neomuran revolution about 850 million years ago when a posibacterium evolved into the thermophilic cenancestor of eukaryotes and archaebacteria (jointly called neomurans), radically modifying or substituting its DNA-handling enzymes (those responsible for transcription as well as for replication, repair and recombination) as a coadaptive consequence of the origin of core histones to stabilise its chromosome. Substitution of glycoprotein for peptidoglycan walls in the neomuran ancestor and the evolution of an endoskeleton and endomembrane system in eukaryotes alone required the origin of nuclei, mitosis and novel cell cycle controls and enabled them to evolve cell fusion and thereby the combination of whole genomes from different cells. Meiosis evolved because of resulting selection for periodic ploidy reduction, with incidental consequences for intrapopulation genetic exchange. Little modification was needed to recombination enzymes or to the ancient bacterial catalysts of homology search by spontaneous base pairing to mediate chromosome pairing. The key innovation was the origin of meiotic cohesins delaying centromere splitting to allow two successive divisions before reversion to vegetative growth and replication, necessarily yielding two-step meiosis. Also significant was the evolution of synaptonemal complexes to stabilise bivalents and of monopolins to orient sister centromeres to one spindle pole. The primary significance of sex was not to promote evolutionary change but to limit it by facilitating ploidy cycles to balance the conflicting selective forces acting on rapidly growing phagotrophic protozoa and starved dormant cysts subject to radiation and other damage.
    Even if one disagrees with TCS on certain issues (his late-dating of the origin of eukaryotes and archaeabacteria is certainly a minority position), this gives one some vague idea (read the 200+ pages of articles to get a somewhat improved but still incomplete idea) of the kind of background knowledge level one must be at to even begin to discuss the Really Long Ago issues of evolution in an informed fashion.

    Hope that helps,

    Reposting this to AE...
    * Co-option/change of function (7 replies)
    niiicholas2002-06-11 00:44:21
    This thread is for accumulating examples of cooption/change of function from the literature, and citations of the importance of this process in the literature.

    The purpose of examining this is that Behe and Dembski both fail to give cooption the attention it absolutely deserves.  In particular the occurence of cooption disproves Behe's IC argument.

    Thanks, nic
    * Redundant complexity (0 replies)
    niiicholas2004-02-17 18:42:11
    Niall Shanks, in particular, has argued that redundancy is an answer to Behe's arguments about irreducible complexity.  Systems may evolve with multiple parts with redundant function, and then lose parts to produce and IC system.  This is essentially the common "scaffolding" argument.

    Compared to co-option and helpful-part-becomes-necessary, I think that redundancy elimination is a relatively minor player.  However, it is worth gathering examples of the phenomenon in order to further evaluate this.

    So, here is a starter example that I came across:

    Quote
    J Bacteriol. 2004 Feb;186(3):646-53.
     
    Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes.

    Frigaard NU, Li H, Milks KJ, Bryant DA.

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. mxf10@psu.edu

    Chlorosomes of the green sulfur bacterium Chlorobium tepidum comprise mostly bacteriochlorophyll c (BChl c), small amounts of BChl a, carotenoids, and quinones surrounded by a lipid-protein envelope. These structures contain 10 different protein species (CsmA, CsmB, CsmC, CsmD, CsmE, CsmF, CsmH, CsmI, CsmJ, and CsmX) but contain relatively little total protein compared to other photosynthetic antenna complexes. Except for CsmA, which has been suggested to bind BChl a, the functions of the chlorosome proteins are not known. Nine mutants in which a single csm gene was inactivated were created; these mutants included genes encoding all chlorosome proteins except CsmA. All mutants had BChl c contents similar to that of the wild-type strain and had growth rates indistinguishable from or within approximately 90% (CsmC(-) and CsmJ(-)) of those of the wild-type strain. Chlorosomes isolated from the mutants lacked only the protein whose gene had been inactivated and were generally similar to those from the wild-type strain with respect to size, shape, and BChl c, BChl a, and carotenoid contents. However, chlorosomes from the csmC mutant were about 25% shorter than those from the wild-type strain, and the BChl c absorbance maximum was blue-shifted about 8 nm, indicating that the structure of the BChl c aggregates in these chlorosomes is altered. The results of the present study establish that, except with CsmA, when the known chlorosome proteins are eliminated individually, none of them are essential for the biogenesis, light harvesting, or structural organization of BChl c and BChl a within the chlorosome. These results demonstrate that chlorosomes are remarkably robust structures that can tolerate considerable changes in protein composition.


    Articles/books by Shanks:

    Shanks, Niall (2004). God, the Devil, and Darwin.  Oxford University Press. Amazon.com

    Shanks, Niall, and Joplin, Karl (2001).  Behe, Biochemistry, and the Invisible Hand. Philo 4(1).  URL: http://www.philoonline.org/library/shanks_4_1.htm


    Shanks, Niall, and Joplin, Karl (2000).  Of Mousetraps and Men: Behe on Biochemistry. RNCSE 20 (1-2): 25-30.  Online at NCSE.

    Shanks, Niall, and Joplin, Karl (2000).  Redundant Complexity:A Critical Analysis of Intelligent Design in Biochemistry. Philosophy of Science 66 (June): 268-282.  Online at ASA.
    * Hooper's 'Of Moths and Men' and reviews thereof (8 replies)
    niiicholas2002-09-21 13:26:13
    This thread is for accumulating links on Judith Hooper's recent book Of Moths and Men.

    We might as well start with the link to the book:

    Of Moths and Men at amazon.com

    Most reviews of the book are positive, but my is not.  Mine, posted at amazon.com:

    Quote
    Hooper gets the science wrong, August 27, 2002

    Reviewer: ntamzek (see more about me) from Santa Barbara, CA United States


    The fundamental rule of science journalism should be "first, get the science right". Unfortunately, Hooper's book is marred by One Big Mistake: namely, Hooper misrepresents the state of the scientific question on Kettlewell's explanation for industrial melanism in the peppered moth, namely differential predation by birds against moth morphs more or less cryptic in polluted woodlands. Reading Hooper's book, one would think that this thesis, what I call the "Bird Predation Theory" (BPT), was on the rocks. But this just ain't so -- if we read peppered moth researcher Michael Majerus' (2002) book Moths, we find him writing on page 252,

    ========
    [E]very scientist I know who has worked on melanism in the Peppered moth in the field still regards differential predation of the morphs in different habitats as of prime importance in the case. The critics of work on this case and those who cast doubt on its validity are, without exception, persons who have, as far as I know, never bred the moth and never conducted an experiment on it. In most cases they have probably never seen a live Peppered moth in the wild. Perhaps those who have the most intimate knowledge of this moth are the scientists who have bred it, watched it and studied it, in both the laboratory and the wild. These include, among others, the late Sir Cyril Clarke, Professors Paul Brakefield, Laurence Cook, Bruce Grant, K. Mikkola, Drs Rory Howlett, Carys Jones, David Lees, John Muggleton and myself. I believe that, without exception, it is our view that the case of melanism in the Peppered moth still stands as one of the best examples of evolution, by natural selection, in action.
    ========

    Hooper, however, presents the peppered moth case as if it were falling apart, a story which of course the press reviews have uncritically repeated.

    Hooper's hero in the book is the one critic of the bird predation thesis who is actually a moth expert, Ted Sargent, although even here Sargent is actually an expert on an entirely different family of moths (the Underwings, e.g. Catocala) and has done almost no work on peppered moths. Hooper, however, gives Sargent a huge platform and gives his numerous critics, and their published rebuttals to Sargent, very short shrift. Hooper portrays Sargent as a lone rebellious American taking on the dogmatic British establishment, but of course American peppered moth researcher Bruce Grant, who supports the BPT and has done numerous studies on peppered moths specifically, is not given the same chance to make his case.

    As for Sargent's actual arguments against the bird predation thesis, both Bruce Grant and Laurence Cook wrote articles rebutting Sargent's critique, but Hooper gives Cook's article merely a brief brush-off in a paragraph, completely ignoring, for example, Cook's statistical analysis of all the previous peppered moth experiments, proving a correlation between moth fitness and morph frequency with a >99% confidence. This was a direct rebuttal to Sargent's most important argument, that the statistical support for the bird predation thesis was weak, but Hooper doesn't deal with it directly like she should if she is going to advocate an alternative view.

    Hooper does come up with a few arguments that not even the creationists have proposed -- most importantly, that Kettlewell faked his results, or almost as bad, unconsciously mislead himself. This is despite the fact that the predation and mark-release-recapture experiments have been repeated by other researchers and have in the main confirmed his results (see the articles by Cook, Grant, and the books by Majerus 1998 and 2002 for detailed reviews). The most astounding passage in Of Moths and Men occurs when Hooper spends a paragraph "squinting" at the tables in Kettlewell's paper, and she notes that Kettlewell's moth recapture numbers increase suddenly on July 1, 1953. The implication is that Kettlewell fudged things somewhere.

    But a modicum of investigation shreds Hooper's fraud hypothesis. What Hooper fails to look at seriously was that when Kettlewell released more moths, he recaptured more. Kettlewell started releasing far more moths on June 30th, and started catching far more moths on the morning of July 1st. In fact, when one does a linear regression, one discovers that "number of moths released" explains 80% of the variance in "number of moths recaptured". This is a nice strong linear relationship. Fraud is not a necessary explanation. Why didn't Hooper realize the obvious answer? Later in the book, Sargent keys off the same change in numbers, and he too mysteriously ignores the obvious explanation -- as in most of the book, Sargent's word is taken as gospel and is substituted for rigorous scientific evaluation.

    In addition to the major issues discussed above, Hooper's book is peppered with small but disturbing mistakes of logic and science; there is a particularly nasty one about genetics that shows up Hooper's amateurishness (and frankly, that of her editors and glowing reviewers) rather blatantly. I will, however, leave these as exercises for future reviewers to acknowledge or not, so that readers of the reviews may distinguish the critical thinkers from the whatever-a-science-journalist-says-must-be-true types.

    The peppered moth story is an awfully good story; but just as this doesn't make it true, it doesn't make it too good to be true either. Hooper's story, the story of a rebel (Sargent) overturning an oppressive orthodoxy is a "good story" also. As Hooper should know, the only way to tell if a "good story" is a true one is by a careful, balanced and weighted review of the evidence. The peppered moth researchers have and are doing this repeatedly, as every bit of new evidence comes in; this is their job as scientists; and their scientific conclusion is that Kettlewell's central finding, that bird predation is the agent of selection, remains firm. Hooper, however, chooses sensationalism, psychoanalysis, and a very selective review of authorities and evidence to reach her conclusion that the bird predation thesis is unsupported; this is the central flaw of her book.

    Reader beware.


    (9 of 19 people found this review helpful!;)

    * Luskin: ID vs Evolution Predictions (0 replies)
    niiicholas2003-08-14 15:45:26
    Luskin's article:
    http://www-acs.ucsd.edu/~idea/falsify.htm

    II discussion:
    http://www.iidb.org/vbb....1125552


    I'm beginning to think that Casey Luskin's a YEC.  He never declared himself in an email debate I had with him awhile ago, and now he says:

    Quote

    Indeed, many forms of "creation science" make a variety of predictions which are empirically testable. One example is that young earth creationism predicts that various observable lines of evidence will be found to show that rocks, the oceans, and the solar system are young. Regardless of whether or not such evidence is found, the theory makes scientific predictions which can be tested in the natural world, and thus qualifies the young earth hypothesis as a falsifiable and testable scientific theory.


    The basic answers to Luskin's points are listed below.  The quotes are from his last table, I've inserted 'Ev', 'ID', and ''Fact''.

    Quote

    1. Biochemical complexity
    Ev: High information content machine-like irreducibly complex structures will NOT be found.
    ID: High information content machine-like irreducibly complex structures will be found.
    'Fact': High information content machine-like irreducibly complex structures are commonly found.


    As has been discussed ad nauseum, gradual evolutionary process can, and regularly do, produce intricate systems with multiple required parts.  The most important mechanism is simply change-of-function, emphasized by Darwin and every biological authority since, and supported by numerous examples.

    The Origin of "Information" via natural causes
    http://www.antievolution.org/cgi-bin....f=9;t=6

    immune system evolution
    http://www.antievolution.org/cgi-bin....=9;t=16

    Evolution of multiple-parts-required pathways
    http://www.antievolution.org/cgi-bin....=9;t=17

    Co-option/change of function
    http://www.antievolution.org/cgi-bin....f=9;t=8

    Evolving Immunity
    http://www.talkdesign.org/faqs/Evolving_Immunity.html

    Irreducible Complexity Demystified
    http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html


    Quote

    2. Fossil Record
    Ev: Forms will appear in the fossil record as a gradual progression with transitional series.
    ID: Forms will appear in the fossil record suddenly and without any precursors.
    'Fact': Forms tend to appear in the fossil record suddenly and without any precursors.


    There are plenty of transitional fossils:
    http://www.talkorigins.org/faqs/faq-transitional.html

    'Punk Eek' is an application of Mayr's theory of allopatric speciation to paleontology, and applies only to species-species transitions, which are indeed commonly (but not always, studies of good fossil records often put the number at 50-50) absent.  Gould himself has said that for transitions between higher taxonomic levels there are plenty of transitionals.

    A classic example is the horse fossil record, where some species "microevolve" and some appear abruptly:
    http://www.talkorigins.org/faqs/horses/


    The Cambrian 'Explosion', OTOH, is probably mostly the result of the emergence of large, hard-bodied critters from their microscopic, wormlike ancestors, see:
    http://www.talkorigins.org/faqs/wells/iconob.html#cambrian-explosion

    Quote

    3. Distribution of Molecular and Morphological Characteristics

    Ev: Genes and functional parts will reflect those inherited through ancestry, and are only shared by related organisms.
    ID: Genes and functional parts will be re-used in different unrelated organisms.
    'Fact': Genes and functional parts often are not distributed in a manner predicted by ancestry, and are often found in clearly unrelated organisms.


    Luskin quote-mines a whole bunch of quotes on incongruence, but neglects to mention that the big picture is that of congruence with a high degree of statistical confidence:
    http://www.talkorigins.org/faqs....ergence

    Quote-mining with molecular phylogeny:
    http://www.talkorigins.org/faqs/wells/iconob.html#molecular-phylogeny

    The major exceptions only occur in (1) the well-accepted symbiotic theory for the origin of eukaryotes, and (2) prokaryotes, where we know **on independent evidence** that Lateral Gene Transfer is a common event.
    http://www.talkorigins.org/faqs/wells/iconob.html#root


    Quote

    4. Genetic Code
    Ev: The genetic code will NOT contain much discarded genetic baggage code or functionless "junk DNA."
    ID: The genetic code will contain much discarded genetic baggage code or functionless "junk DNA."
    'Fact': Increased knowledge of genetices has created a strong trend towards functionality for "junk-DNA"; examples of DNA of unknown function persist, but function can be expected or explained under a design pardigm.


    "Junk" DNA
    http://www.antievolution.org/cgi-bin....=9;t=35

    The basic observation supporting the 'junk DNA' inference is not pseudogenes -- these are a small fraction of noncoding DNA.  The basic observation is that closely-related critters can have widely-varying amounts of non-coding DNA with no apparent ill-effects.

    Quote

    The C-value paradox emerged from among the first applications of spectrophotometric analysis of nuclear DNA content1. The haploid DNA content of eukaryotic organisms ranges over a factor of 80,000. Some of the largest genomes are found among the lowliest of eukaryotes, such as the amoebae, and some of the smallest genomes are found among organisms with complex developmental and behavioural repertoires, such as Drosophila melanogaster.



    Charlie d explains it quite well here:
    http://www.arn.org/boards/ubb-get_topic-f-14-t-000365.html

    Quote

    Ironically, the anti-ID letter the DI complains about led me to read an article by a German biologist, apparently an ID sympathizer. Inexplicably, it was published in the prestigious, by-invitation-only Annual Review in Genetics - perhaps because it contained actual information (along with many unsupported and overextended interpretations, but that's just my opinion), and not just a pointless, self-defeating whine like Behe's letter.

    Anyway, that paper happens to cite an interesting piece of data that I was unaware of, and which significantly undermines Behe's entire argument that the attribution of lack of function to non-genic DNA is based only on a negative argument (there are many more lines of evidence, of course, but I thought this was nice, especially given the coincidence about the sources).

    The data is as follows. These guys (Muntiacus reevesi):



    and this (M. muntjak):



    are almost identical, they live in very similar environments in Southern China vs. India/South Asia/Indonesia, and just happened to be classified as differnet species because they do not interbreed. The major difference between them is that one has 46 chromosomes and the other 6/7, and one has 20% less DNA than the other, entirely ascribable to the reduction of various kind of non-genic, repetitive elements (ref here.

    Go figure: a 20% DNA content difference between practically identical vertebrates (by comparison, remember chimps and humans differ by a few % at most). Gee, I wonder why biologists tend to conclude that most non-genic DNA has no significant function. Must be all that "negative argumentation", indeed.


    Until IDists start talking about these kinds of facts they aren't even in the ballpark regarding 'junk DNA'.

    PS: Oh yeah.  Luskin accidentally switched his 'predictions' regarding junk DNA.

    PPS: The problem Luskin has with creating a "falsifiable" ID theory, when he explicitly says that he is open to a mix-n-match view, where if A is proven to be a result of evolution, he can accept that and instead assert that B, or C is a result of ID, shall be left for others to explore.

    * The Canonical Genetic Code (14 replies)
    Wesley R. Elsberry2002-05-23 08:35:09
    A popular antievolution argument often deployed by "intelligent design" advocates concerns the non-universality of the genetic code:Jonathan Wells, Paul Nelson, Stephen Meyer, Michael Behe, and Cornelius G. Hunter.

    I'm opening this thread for discussion of the canonical genetic code and its variants, and also for examination of the claims of ID advocates concerning the canonical code.

    Kenneth Miller of Brown University has a couple of essays on this topic: here and here.
    * "ID" as "Irony Deprivation" (0 replies)
    Wesley R. Elsberry2004-02-17 08:22:16
    "Accurate representation"

    This one's a treat: William Dembski complaining that someone else fails to use "accurate representation" and compounding that with a claim that he himself delivers "accurate representation".

    Dembski's reply to WSJ article `flaws in intelligent design'

    Quote

    Sharon Begley's article regarding "flaws in intelligent design" misrepresents the current state of the debate.

    [...]

    If evolutionists really had an answer to the origin of the bacterial flagellum in purely materialistic terms (i.e., invoking only material mechanisms like natural selection and random variation), they would merely need to state the answer and intelligent design would be dead in the water. The very fact that these issues are being discussed in the Wall Street Journal indicates that the debate is far from over. For an accurate representation of the current debate about microsyringes, bacterial flagella, and irreducibly complex systems generally, see my article "Irreducible Complexity Revisited" at URL=http://www.designinference.com/documents/2004.01.Irred_Compl_Revisited.pdf.]http://www.designinference.com/documen....ed.pdf.[/URL]


    We can be sure that "accurate representation" was not at the top of Dembski's agenda when he described Richard Dawkins's "weasel" program as having three steps, when two of the steps provided by Dembski do not appear anywhere in Dawkins's writings. (Further, the second time Dembski did this was in "No Free Lunch", and I had already written him in email and via an email list some months before NFL was published to inform him of the problem.)

    Similarly, "accurate representation" was not Dembski's concern when he sought to make a sweeping claim that evolutionary computation was inclusive of artificial neural systems.

    Quote


    By an evolutionary algorithm I mean any well-defined mathematical procedure that generates contingency via some chance process and then sifts it via some law-like process. The Darwinian mechanism, simulated annealing, neural nets, and genetic algorithms all fall within this broad definition of evolutionary algorithms.



    Source -- WA Dembski, "CAN EVOLUTIONARY ALGORITHMS GENERATE SPECIFIED COMPLEXITY?", presentation at the "Nature of Nature" conference, Baylor University, April, 2000.]

    I pointed out that this classification was quite erroneous at Classification of Artificial Neural Systems: Is Stochasticity a Reliable Diagnostic Character?

    NFL was published one and a half years after my critique was put on the web. That would give anyone time to fix things, right? Wrong.

    Previously, Dembski had stated that "neural nets" were instances of evolutionary algorithms; in NFL, Dembski says that "training neural nets" by evolutionary computation are instances of evolutionary algorithms. The previous claim was simply false and the new claim is based upon the fact that some people do apply evolutionary computation to the problem of training neural nets. It reduces to the claim that instances of evolutionary computation are evolutionary computation; mentioning "neural nets" at all in that context seems unlikely to do anything but lead readers to the erroneous conclusion that the original claim has not been abandoned. Such basic errors as these reduce the credibility of his claims to achieve "accurate representation".

    Wesley
    * "Junk" DNA (3 replies)
    niiicholas2003-04-30 18:28:04
    The topic of so-called "junk" DNA (or, apparently disposable noncoding DNA, more neutrally) has come up endless times in various online debates.  Often, someone will find a new article indicating a function for some bit of DNA, and declare that the "junk" hypothesis is dead and that those evil materialists were blinded by their evil materialism for ever believing it.

    The situation is of course much  more complex, so link/post articles, posts (both sides), etc. in this thread.

    nic
    * Evolutionary Algorithms and GAs (2 replies)
    RBH2003-02-27 11:52:43
    This thread is to archive material relevant to the ID argument that evolutionary algorithms in general, and genetic algorithms in particular, either cannot generate "new information" or somehow show that an intelligent designer is necessary in order for an EA to generate new information.  It will include relevant postings from other boards as well as summaries and references to the appropriate literature.

    I'll start it with a posting by Francis on ISCID's Brainstorms (a posting I was in the process of sporadically cobbling together until Francis anticipated me :))  In this posting Francis is responding to John Bracht's contention that (according to the TRIZ model of innovation), there are two sorts of inventions, routine and innovative, and that evolutionary processes can generate the former but not the latter.

    Francis wrote as follows:

    After having established that Genetic algorithms can indeed increase their hypervolume and thus cannot be in one grand swoop be excluded from being able to generate innovative/creative designs it may be interesting to explore if there may be some examples of such. Such a project however is complicated by the vague definitions of innovative/creative as used in TRIZ and thus on how to recognize creative/innovative solutions from routine design. In order to at least provide some foundation allowing us to define the various forms of design lets discuss the various forms of design.

    Gero distinguished between routine and non-routine design. Routine design involves instances in which all necessary knowledge is available or more formally
    Quote
    ...that designing activity which occurs when all the knowledge about the variables, objectives expressed in terms of those variables, constraints expressed in terms of those variables and the processes needed to find values for those variables, are all known a priori.

    Source: MASS CUSTOMISATION OF CREATIVE DESIGNS John S. Gero

    Gero points out that in addition routine design limits the available range of the variables.

    Gero identifies two forms of non-routine designing:

    Innovative designing and creative designing.
    Quote
    Innovative designing, in computational terms, can be defined as that designing activity that occurs when the constraints on the available ranges of the values for the variables are relaxed so that unexpected values become possible,

    Innovative designing produces designs that belong to the same class as their routine 'brothers' but are also 'new'.

    Creative designing:
    Quote
    in computational terms, can be defined as the designing activity that occurs when one or more new variables is introduced into the design. Processes that carry out this introduction are called "creative designing processes". Such processes do not guarantee that the artifact is judged to be creative, rather these processes have the potential to aid in the design of creative artifacts. Thus, creative designing, by introducing new variables, has the capacity to produce novel designs and as a result extends or moves the state space of potential designs.

    Lets look at the following paper

    "Automatic Creation of Human-Competitive Programs and Controllers by Means of Genetic Programming" by Koza et al.

    Abstract:
    Quote
    Genetic programming is an automatic method for creating a computer program or other complex structure to solve a problem. This paper first reviews various instances where genetic programming has previously produced human-competitive results. It then presents new human-competitive results involving the automatic synthesis of the design of both the parameter values i.e., tuning and the topology of controllers for two illustrative problems. Both genetically evolved controllers are better than controllers designed and published by experts in the field of control using the criteria established by the experts. One of these two controllers infringes on a previously issued patent. Other evolved controllers duplicate the functionality of other previously patented controllers. The results in this paper, in conjunction with previous results, reinforce the prediction that genetic programming is on the threshold of routinely producing human-competitive results and that genetic programming can potentially be used as an "invention machine" to produce patentable new inventions.

    Koza provides us with two examples in which GA's were used to file innovative design patents
    Quote
    There are at least two instances where evolutionary computation yielded an invention that was granted a patent, namely a design for a wire antenna created by a genetic algorithm and a patent for the shape of an aircraft wing created by a genetic algorithm with variable-length strings.

    Koza continues with a table of 24 examples of "results where genetic programming has produced results that are competitive with the products of human creativity and inventiveness."

    15 of these 24 examples involve previously patented inventions, 6 infringe on patents and one improves on a patent. Nine duplicate the functionality of the patent in a novel manner.

    The question remains, are these examples of routine or creative/non-routine design?

    Koza specifies twoways of running GA's

    There are two ways of determining the architecture for a program that is to be evolved using genetic programming.

    1 The human user may prespecify the architecture of the overall program as part of the preparatory steps required for launching the run of genetic programming.

    2 Architecture-altering operations may be used during the run to automatically create the architecture of the program.

    Koza continues on to apply GA to a controller problem in the following manner
    Quote
    In this paper, programs trees in the initial random generation generation consist only of result-producing branches. Automatically defined functions are introduced sparingly on subsequent generations of the run by means of the architecture-altering operations.

    The two lag plant:
    Quote
    As will be seen below, the result produced by genetic programming differs from a conventional PID controller in that the genetically evolved controller employs a second derivative processing block. As will be seen, the genetically evolved controller is 2.42 times better than the Dorf and Bishop 28 controller as measured by the criterion used by Dorf and Bishop namely, the integral of the time-weighted. absolute error . In addition, the genetically evolved controller has only 56% of the rise time in response to the reference input, has only 32% of the settling time, and is 8.97 times better in terms of suppressing the effects of a step disturbance at the plant input.

    The three lag plant:
    Quote
    As will be seen below, the controller produced by genetic programming is better than 7.2 times as effective as the textbook controller as measured by the integral of the time-weighted absolute error, has only 50% of the rise time in response to the reference input, has only 35% of the settling time, and is 92.7 dB better in terms of suppressing the effects of a step disturbance at the plant input.

    In both instances the controller included P, I and D, or proportional constants, integrators and differentiators and the genetic algorithm was allowed to vary its hyperspace by including one or more of each. Not surprisingly the program re-discovers the PID and PI topology as invented by Callender et al.

    They conclude
    Quote
    This paper has demonstrated that genetic programming can be used to automatically create both the parameter values tuning and the topology for controllers for illustrative problems involving a two-lag plant and a three-lag plant.

    Thus not only did the GA control the parameter values but also the topology allowing the GA to vary the hyperspace.

    But not only did the GA find solution but the solutions were better than the best solution provided by experts in the field of control technology.

    A propos, Kroo, one of the inventors who patented design in which GA's were used comments that "This configuration was independently "discovered" by a genetic algorithm that was asked to find a wing of fixed lift, span, and height with minimum drag. The system was allowed to build wings of many individual elements with arbitrary dihedral and optimal twist distributions. The figure below depicts front views of the population of candidate designs as the system evolves. On the right, the best individual from a given generation is shown. "

    Adrian Thompson describes in "Notes on Design Through Artificial Evolution: Opportunities and Algorithms" an experiment of the design of an electronic circuit in which it was attempted "to allow evolution to explore the design space as a type © system, with the minimum or simplifying constraints or prejudice."

    A type © system refers to a system in which neither the forward nor inverse model is tractable.
    Quote
    It is expected that the performance of a circuit will fall with rising temperature, but Figure 5 reveals that the evolved circuit's behaviour also degrades as the temperature is decreased from 340mK. This kind of behaviour had never been seen in such proposed `single electron' circuits before, and indicates that the circuit actually exploits or relies upon the thermal noise of the electrons at 340mK. This is not necessarily desirable, and perhaps by evaluating across a range of temperatures during evolution a thermally robust solution could be found [7], but we see immediately that evolution is exploring a previously inaccessible part of design space. Desirable or not, it is obvious that evolution is exploring new design space.

    Finally a paper which I believe I have already mentioned but which captures much of my argument

    JOHN GERO AND VLADIMIR KAZAKOV, "ADAPTING EVOLUTIONARY COMPUTING FOR EXPLORATION"
    Quote
    Abstract. This paper introduces a modification to genetic algorithms which provides computational support to creative designing by adaptively exploring design structure spaces. This modification is based on the re-interpretation of the GA's crossover as a random sampling of interpolations and its replacement with the random sampling of direct phenotype-phenotype interpolation and phenotype-phenotype extrapolation. Examples of the process are presented.

    And here the relevant part
    Quote
    Non-routine designing maps onto creative designing. In routine designing all the variables which specify designs are given in advance. This means that the space of possible designs is known a priori, each point in this space can be constructed and evaluated directly. What needs to be done is to search this space in order to locate an appropriate or most appropriate design. The result here is the "best" design from this space. In nonroutine designing the result is the "best" space of possible designs as well as the "best" design from this space. Processes which modify the design space of the search problem are called exploratory processes.

    Gero comments
    Quote
    One of the well-established notions related to creative designing processes is that an important means of characterising them is to determine whether they have the capacity to expand the state space of possible designs - exploration (Gero, 1994).
    And finally
    Quote
    As can be seen from the example the resulting designs are unpredictable in the sense that they are unexpected given only knowledge of the original designs and of the interpolation/extrapolation functions. In this sense the process matches well the meaning of exploration both in the technical sense used in this paper and in the natural language sense. The designs produced by the system demonstrate both the novelty and unexpectedness of what can be generated.

    It seems that John was correct in pointing out that creative design requires one to leave the hyperspace of the original and explore different design spaces. As I have shown however, GA's are very capable of doing exactly this, exploring hyperspace by varying the dimensions of the search space. As such I would argue that not only do GA's have the potential for innovative/creative solutions but have actually been shown to exactly produce such designs.
    * "Cabbages and Kings" basics (0 replies)
    niiicholas2002-05-17 02:35:38
    Howdy,

    Wes has kindly made me a moderator on this forum.  I'd like to briefly mention a few things for background's sake.  As other things come up they will be added to this thread (or the thread can be bumped if someone needs an introduction).

    First, the title of the forum.  Here is the reference (from Wes):

    Quote

    "The time has come," the Walrus said, "to speak of many things.  Of shoes and ships and sealing wax, of cabbages and kings."

    -- Lewis Carroll



    Guidelines:

    1) This is a public-viewing, but restricted posting forum.  Posting access is granted by (I think) either Wes or me, basically if we feel like the poster will contribute to the purpose of this particular forum, detailed below.

    2) The purpose of this forum is to give ID skeptics a place to gather references, citations, bits of arguments, etc., in one place, either just for reference, or for a possible future article or FAQ.  

    The idea is to do things on a thread-specific basis.  A random example thread title might be "Examples of co-option in evolution", and the person who starts the thread says something like:

    "I would like this thread to focus on well-documented examples of cooption in evolution.  The reason, of course, is that antievolutions frequently assert, without documentation, that change-of-function is a very low probability event, and use this pseudo-argument to brush off the "what about cooption?" objection to the arguments of Behe and Dembski regarding the nonevolution of functional complexity.

    The best way to rebut the IDists' assertion is simply to list the numerous examples of cooption in evolution, with references.  So, if you come across a good example, mention it and if possible cite what references you have; others may be able follow up suggestions of places to look, e.g. "I think I read an essay by Gould on this once".

    Additional things worth posting in a thread like this:

    - links to other threads discussing cooption
    - links to high-quality webpages
    - links to the Pubmed abstracts of specific papers
    - references on the topic generally, e.g. papers on the topic of the fate of gene duplications, for example.
    - images and highly relevant quotes can be posted also

    Both molecular and macro cases are welcome, part of the point of this thread is to show that the same process occurs commonly in both realms.
    "

    See how this would work?  The potential topics are endless, but hopefully when you run across something, e.g. "Hey, a new article on the evolution of blood-clotting!", you can check the forum to see if there is already a thread on blood-clotting, and add the reference there.


    3) Discussions of the above are welcome in this forum, however if very long-winded debates develop they are better put in the general ID discussion.  Also, active debates with internet IDists should be conducted in the general ID discussion (where they have a chance to fight back); I think a good policy would be to stick a link to a debate thread in the relevant thread here.  The main focus here is on "collaborative informational resource gathering/displaying" -- hopefully it will develop into a high-quality resource for ID skeptics across the net.

    Have fun,

    nic
    niiicholas@yahoo.com
    * The mousetrap argument (1 replies)
    niiicholas2002-12-13 03:35:04
    History of mousetraps:

    http://www.uh.edu/engines/epi1163.htm

    Quote

    "Build a better mousetrap, and the world will beat a path to your door," Emerson supposedly wrote. But writer Jack Hope finds what Emerson really wrote: "If a man has good corn, or wood, or boards, or pigs, to sell ... you will find a broad hard-beaten road to his house." [1] Nothing there about mousetraps. In 1889, seven years after Emerson died, someone quoted him as having said, "If a man can write a better book, preach a better sermon, or make a better mousetrap than his neighbor ..." and so on.

    Emerson meant that quality prevails in the marketplace, and that comes to light in an odd way with the history of mousetraps. We've made a vast investment of ingenuity in them. By now the Patent Office has issued over 4400 mousetrap patents. Yet only twenty or so of those patents have ever made any money.

    Today some 400 people still apply for mousetrap patents each year. That leaves me to wonder whether mousetraps really promise a fast track to inventive success, or if they're simply born of some morbid fascination with killing mice.

    Actually, the mousetrap problem was solved in 1899 by one John Mast of Lititz, Pennsylvania. Mast filed for a patent on his now-familiar snap-trap. A heavy spring-steel wire swings down and breaks the mouse's neck when he nibbles cheese on the trigger mechanism. That was only ten years after the mousetrap quotation became common currency. The inventive muse (or maybe the inventive mouse!;) keeps generating mousetrap patents, but none has yet beaten the snap-trap in the marketplace. No one has really built a better mousetrap.

    Before (and after) Mast, inventors cooked up an unending series of gadgets for mashing, cutting, and maiming mice -- for drowning them -- for catching them alive. Early in the 20th century, people tried electrocution. The problem is, an electrocuted mouse continues to fry until someone smells the mess.

    In the end, esthetics and mercy are twin factors that've strongly determined what the public will and will not use. In the 1980s, a superglue trap came out. It worked, but homeowners found themselves faced with a screaming mouse, still living, glued to a piece of sticky cardboard, dying of exhaustion. If mice have to be killed, most people can deal with a quickly broken neck. The more gruesome stuff won't sell in the long run.

    And when snap-trap makers found most people throwing the trap out with the mouse, not even trying to disengage it, they followed the public's lead and began advertising snap-traps as "disposable."

    So while the mousetrap has become an icon for inventive creativity, the public eventually stipulates what's acceptable and what is not -- in the grisly business of holding a competing species at bay.

    I'm John Lienhard, at the University of Houston, where we're interested in the way inventive minds work.

    (Theme music)

    --------------------------------------------------------------------
    1. Hope, J., A Better Mousetrap. American Heritage, October 1996, pp. 90-97.
    Here's a mousetrap for you! See the following website: http://www.lightlink.com/bbm/wmouse.html.



    Clipart

    The Conventional Snap Trap
    * Evolution of multiple-parts-required pathways (3 replies)
    niiicholas2002-12-19 00:04:03
    This is a big enough topic to deserve a thread separate from the origin of information or the origin of particular systems.

    Short version: there is lots of evidence that multiple-parts-required metabolic pathways have originated via known evolutionary processes, in human and even lab lifetimes.

    Here is a synthesis article I just came across:

    Quote

    Curr Opin Struct Biol 2002 Jun;12(3):374-82
     
    Pathway evolution, structurally speaking.

    Rison SC, Thornton JM.

    Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

    Small-molecule metabolism forms the core of the metabolic processes of all living organisms. As early as 1945, possible mechanisms for the evolution of such a complex metabolic system were considered. The problem is to explain the appearance and development of a highly regulated complex network of interacting proteins and substrates from a limited structural and functional repertoire. By permitting the co-analysis of phylogeny and metabolism, the combined exploitation of pathway and structural databases, as well as the use of multiple-sequence alignment search algorithms, sheds light on this problem. Much of the current research suggests a chemistry-driven 'patchwork' model of pathway evolution, but other mechanisms may play a role. In the future, as metabolic structure and sequence space are further explored, it should become easier to trace the finer details of pathway development and understand how complexity has evolved.



    Then of course we have:

    Quote

    Trends in Biochemical Sciences
    Volume 25, Issue 6, 1 June 2000, Pages 261-265
    Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach

    Shelley D. Copley


    The pathway for degradation of the xenobiotic pesticide pentachlorophenol in Sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. The first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. The second enzyme, a reductive dehalogenase, may have evolved from a maleylacetoacetate isomerase normally involved in degradation of tyrosine. This apparently recently assembled pathway does not function very well: pentachlorophenol hydroxylase is quite slow, and tetrachlorohydroquinone dehalogenase is subject to severe substrate inhibition.


    An important update:

    Quote

    J Bacteriol 2003 Jan;185(1):302-10
     
    A Previously Unrecognized Step in Pentachlorophenol Degradation in Sphingobium chlorophenolicum Is Catalyzed by Tetrachlorobenzoquinone Reductase (PcpD).

    Dai M, Rogers JB, Warner JR, Copley SD.

    The first step in the pentachlorophenol (PCP) degradation pathway in Sphingobium chlorophenolicum has been believed for more than a decade to be conversion of PCP to tetrachlorohydroquinone. We show here that PCP is actually converted to tetrachlorobenzoquinone, which is subsequently reduced to tetrachlorohydroquinone by PcpD, a protein that had previously been suggested to be a PCP hydroxylase reductase. pcpD is immediately downstream of pcpB, the gene encoding PCP hydroxylase (PCP monooxygenase). Expression of PcpD is induced in the presence of PCP. A mutant strain lacking functional PcpD has an impaired ability to remove PCP from the medium. In contrast, the mutant strain removes tetrachlorophenol from the medium at the same rate as does the wild-type strain. These data suggest that PcpD catalyzes a step necessary for degradation of PCP, but not for degradation of tetrachlorophenol. Based upon the known mechanisms of flavin monooxygenases such as PCP hydroxylase, hydroxylation of PCP should produce tetrachlorobenzoquinone, while hydroxylation of tetrachlorophenol should produce tetrachlorohydroquinone. Thus, we proposed and verified experimentally that PcpD is a tetrachlorobenzoquinone reductase that catalyzes the NADPH-dependent reduction of tetrachlorobenzoquinone to tetrachlorohydroquinone.

    Introduction

    Pentachlorophenol (PCP) is a widely used and highly toxic wood preservative. It was first introduced as a pesticide in 1936 (7) and is not known to be a natural product. Despite its recent introduction into the environment and its high toxicity, several strains of Sphingobium chlorophenolicum (previously Sphingomonas chlorophenolica) (24) that can mineralize PCP have been identified. The best studied of these are strains ATCC 39723 (19), RA-2 (23), and UG30 (6). It appears that S. chlorophenolicum has assembled a new metabolic pathway capable of converting this anthropogenic compound into a recognizable metabolite. Our previous studies suggest that this pathway has been assembled by patching together enzymes from at least two different metabolic pathways (8). PCP hydroxylase (PCP monooxygenase; EC 1.14.13.50) and 2,6-dichlorohydroquinone dioxygenase may have originated from enzymes that hydroxylated a naturally occurring chlorinated phenol and then cleaved the resulting hydroquinone. Tetrachlorohydroquinone (TCHQ) dehalogenase appears to have originated from a glutathione-dependent double bond isomerase such as maleylacetoacetate isomerase or maleylpyruvate isomerase (which are involved in degradation of tyrosine and benzoate, respectively) (2). If this pathway has evolved recently in response to the introduction of PCP into the environment, then it would not be expected to perform at the high level characteristic of pathways that have evolved over periods of millions or billions of years. Indeed, the PCP degradation pathway shows signs of immaturity in several respects. First, PCP hydroxylase, the first enzyme in the pathway, is very inefficient in vitro (P. M. Kiefer and S. D. Copley, unpublished data), and appears to severely limit the flux of PCP through the pathway in vivo (17). Second, TCHQ dehalogenase is profoundly inhibited by its aromatic substrate (K. Anandarajah, P. M. Kiefer, and S. D. Copley, unpublished data). Third, TCHQ dehalogenase expression is not regulated in tandem with the other known enzymes in the pathway but is apparently constitutive (21). All of these findings are consistent with the idea that the PCP degradation pathway has been patched together rather recently and has not been fine-tuned to perform as effectively as do most bacterial metabolic pathways.

    The gene encoding PCP hydroxylase (pcpB) is immediately upstream of two additional genes. pcpR encodes a regulatory protein that responds to PCP (5). pcpD, which is immediately downstream of pcpB, resembles genes for the reductase components of two-component oxygenases, some of which hydroxylate aromatic compounds. Based upon this resemblance, it has been proposed that PcpD is a reductase that facilitates the hydroxylation of PCP by PCP hydroxylase (19), and the annotation of PcpD in GenBank states that it is PCP 4-monooxygenase reductase. We suspected that this assignment was incorrect because PCP hydroxylase is a flavin monooxygenase, and such enzymes do not generally require reductases. Consequently, we undertook studies to determine whether PcpD is required for degradation of PCP. We find that transcription of pcpD is induced by PCP, as previously reported for pcpA (29) and pcpB (20). A mutant strain in which PcpD has been knocked out is able to remove PCP from the medium when it is present at low concentrations, but not when it is present at high concentrations. In contrast, the knockout strain can remove tetrachlorophenol (TCP) from the medium as well as the wild-type strain, even at high concentrations. These results suggest that PcpD may catalyze a step that is critical for degradation of PCP but not TCP and therefore must involve the chlorine at the 4 position of PCP. Based upon the expected mechanism of the hydroxylase reaction, the sequence of PcpD, and our experimental results, we propose that PcpD is a tetrachlorobenzoquinone (TCBQ) reductase required for degradation of PCP but not TCP.
    * The Origin of "Information" via natural causes (42 replies)
    niiicholas2002-05-30 00:02:55
    Hi,

    While reading this interview with Phil Johnson, leader of the ID movement:

    Berkeley’s Radical
    An Interview with Phillip E. Johnson


    ...I was struck by this section:

    Quote

    You have said there is no natural explanation for the rise of genetic information. How important is that question in the debate?

    PJ: The Wedge of Truth is all about those issues. The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism. They’ll start out talking about the peppered moth, and when that self-destructs, then they’ll say, "Oh, self-organizing systems, or the fourth law of thermodynamics," and other nonsense, which is just covering up ignorance.

    Genetic information is the issue, but it isn’t the final issue. After you make that breakthrough, then you see other ways in which the theory is questionable. Darwinists will say, "Oh, well, maybe the mechanism has some problems, but the "fact of evolution"—common ancestry—is not in question. We distinguish the fact of evolution from the mechanism of evolution."

    But that’s a bogus distinction because the "fact"—common ancestry—incorporates the mechanism. It’s just a matter of "now you see it, now you don’t." They are saying the mechanism by which a father and mother give birth to children is the same mechanism by which our "bacterial ancestors" gave birth to human beings. They say it’s all a process of natural reproduction and naturally occurring variation in the offspring.

    Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations do not create evolution in any significant sense. Instead, they make birth defects, so the whole thing is false from the get-go. There is no way you can establish that a bacterium is the parent of a complex animal. There is no mechanism to make the change, no historical or fossil evidence that such a change ever occurred, and there’s no way to duplicate the process in a lab.

    Once you get that in the debate, then we will be poised for a metaphysical and intellectual reversal that is every bit as profound as the one with Copernicus. People will say, "My gosh, we’ve been completely misled by this fundamental truth of the creation story of our culture. We can no longer understand the world that way."

    How do you change the way people regard the authority of science? Get them to think of it as a much more limited thing. Science is very reliable when scientists stick to the kinds of things that can be tested by refutable experiments, but much of what they tell us is outside that. When they have to fake the mechanisms, it becomes a very dubious philosophy. That raises the question of why so many very brilliant people were misled for so long and did such a good job of rationalizing these things.

    When the mechanism of Darwinism becomes discredited, it’s like a train that’s been turned around. You can say, "Well, that’s interesting, but the train is still in the same place. The world, Yale, Berkeley, are still there. The New York Times is still telling us what to think. So why isn’t everything different?" Well, it is different, but you can’t see it yet. The train is turned in the opposite direction. It’s going to start out very slowly, but it’s moving on the logical tracks towards something very different, and when we get there, our great-great-grand-children will see how different things are.


    Note that the "scientific key" to the whole ID argument (according to Johnson) is this: "No natural processes create genetic information."  

    This strikes me as easily and trivially refutable by numerous examples.  Anything that starts with genetic information amount X, and ends up with genetic information amount X+Y, should qualify.  The classic case would be X=information in a genome before a gene duplicates & diverges under selection, and X+Y being the information in the genome after this has occurred.

    Another less-often considered example should be (IMO) when a mutation (let's say "beneficial to at least part of the population" to avoid the obvious objection) arises in a *population*.  Here,

    X=information in the genomes of a population
    Y=information in the beneficial mutation

    I realize that "information" has no single definition in biology, one could also argue that "new information" would arise through novel combinations of alleles, etc.  For the purposes of this thread, I suggest the following working definition:

    Genetic information=functional DNA that encodes useful/beneficial proteins or regulatory sequences

    ...as this is what the IDers mean by "genetic information" (except of course when they are challenged on the topic, wherein they promptly begin the obfuscation and goal-post moving, rather like eternally elusive creationist definition of "kind").

    So, let's use this thread to accumulate examples of natural processes increasing "genetic information" in the above-described sense.  Other things that might be relevant, e.g. studies of the increase of Shannon information in selective algorithms, could also be posted, just note the form of information as relevant.

    nic

    PS: I'll start off with one of my favorite examples:

    Sdic, sperm dynein intermediate chain, a new gene which evolved over the past few million years by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome.

    Here is a brief introduction from Ian Musgrave:

    Quote

    My second favorite example is the Sdic gene, where the annexin and dynenin intermediate chain genes were duplicated in tandem, then the intervening sequences deleted to form a single new gene, (the Sperm specific dynenin intermediate chain gene Sdic). The good thing about this example is that a previously non-coding part of the sequence became the protein coding sequence, and the protein coding sequence has a non-coding role.


    Capy P. (1998 Dec 10). Evolutionary biology. A plastic genome [news; comment] Nature, 396, 522-3.

    Nurminsky DI, Nurminskaya MV, De Aguiar D, and Hartl DL. (1998 Dec 10). Selective sweep of a newly evolved sperm-specific gene in Drosophila [see comments] Nature, 396, 572-5.



    Here is the Nurminsky et al. 1998 article:

    Quote

    pubmed link

    Nature 1998 Dec 10;396(6711):572-5

    Selective sweep of a newly evolved sperm-specific gene in Drosophila.

    Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL.

    Harvard University, Department of Organismic & Evolutionary Biology, Cambridge, Massachusetts 02138, USA.

    The pattern of genetic variation across the genome of Drosophila melanogaster is consistent with the occurrence of frequent 'selective sweeps', in which new favourable mutations become incorporated into the species so quickly that linked alleles can 'hitchhike' and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any putative selective sweep. Here, however, we identify a new gene in D. melanogaster that codes for a sperm-specific axonemal dynein subunit. The gene has a new testes-specific promoter derived from a protein-coding region in a gene encoding the cell-adhesion protein annexin X (AnnX), and it contains a new protein-coding exon derived from an intron in a gene encoding a cytoplasmic dynein intermediate chain (Cdic). The new transcription unit, designated Sdic (for sperm-specific dynein intermediate chain), has been duplicated about tenfold in a tandem array. Consistent with the selective sweep of this gene, the level of genetic polymorphism near Sdic is unusually low. The discovery of this gene supports other results that point to the rapid molecular evolution of male reproductive functions.



    Since then, this article has been published:

    Quote

    Pubmed link

    Nurminsky D, Aguiar DD, Bustamante CD, Hartl DL.
    Chromosomal effects of rapid gene evolution in Drosophila melanogaster.
    Science. 2001 Jan 5;291(5501):128-30.

    Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.



    This article is a good review of the general topic of the evolution of new genes:

    Quote

    pubmed link

    Curr Opin Genet Dev 2001 Dec;11(6):673-80

    Evolution of novel genes.

    Long M.

    Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago Illinois 60637, USA. mlong@midway.uchicago.edu

    Much progress in understanding the evolution of new genes has been accomplished in the past few years. Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling, a major process for generating new genes, are better understood. The identification of young genes in invertebrates and vertebrates has revealed a significant role of adaptive evolution acting on initially rudimentary gene structures created as if by evolutionary tinkers. New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans.


    Have fun,
    nic
    * IDists distort open-mindedness with support (0 replies)
    rafe gutman2002-06-03 21:54:07
    IDists like to complain that they are being treated unfairly, that their ideas are being dismissed without being considered or discussed.  that may be a fair complaint, but when these very same IDists abuse any display of open-mindedness made by members of the scientific community, they absolve their right to complain.  i'd like this thread to be a place where ID critics can post examples of IDists confusing open-mindedness with support.

    one example of this is when IDists use book sales as an indicator of the success of ID.  considering that an individual has to first buy the book in order to read it, it doesn't necessarily mean that they will then agree with the arguments presented within.  on that note, it is interesting what IDists consider to be an endorsement of their work.  consider this one, which is printed on the dust jacket of no free lunch:
    Quote
    I disagree strongly with the position taken by William Dembski. But I do think that he argues strongly and that those of us who do not accept his conclusions should read his book and form our own opinions and counter-arguments. He should not be ignored.

    Michael Ruse, Lucyle T. Werkmeister Professor of Philosophy, Florida State University; editor of Biology and Philosophy; author of Monad to Man and many other books on Darwinism


    IDists have even tried to spin disagreement in their favor:
    Quote
    "If we're generating such strong, visceral responses, we must be doing something right." william dembski


    so even if a scientist disagrees with ID, they interpret that to mean that ID is taken seriously.

    i'd like to keep this thread open to more quotes and examples of how IDists have preyed upon the open-mindedness of scientists and perverted their comments to support ID.
    * Predictions of RM&NS (0 replies)
    niiicholas2002-09-24 04:48:34
    This thread is for accumulating links and posts on the topic of predictions made by the modern theory of evolution, i.e. the theory that processes we observe or directly infer today (especially random mutation (broadly construed to include everything from point mutations to genome duplications) and natural selection, but also the well-known sidekicks such as genetic drift, neutral evolution, etc.), were also acting in the long-distant past and produced the biodiversity of today.

    This was prompted by Jesse's excellent post at ARN on this topic, which we should quote somewhere:

    ARN post

    nic
    * Origin of new organs (1 replies)
    niiicholas2002-12-26 16:57:06
    I think I started a thread on this back in before The Great Server crash; there was a PNAS paper on yucca moth mouthparts, or something.

    Here is another case:

    Source: http://www.sciencedaily.com/releases/2002/12/021226071202.htm


    T.o. discussion: here

    Quote

    UC Riverside Study Suggests Placentas Can Evolve In 750,000 Years Or Less; Guppy-Like Fish Help Fill In The Gaps In The Evolution Of Complex Organs

    RIVERSIDE, Calif. -- Dec. 20, 2002 -- Evolutionary biologists have long been intrigued by how natural selection -- the process in nature by which the organisms best suited to their environment are the ones most likely to survive and leave descendants -- gradually creates a complex organ such as the eye, heart, or kidney.
    Now UC Riverside biologists, David Reznick and Mark Springer, along with Mariana Mateos, research associate at the University of Arizona, present in the journal Science a model system for studying the evolution of complex organs. They focus on the placenta (the organ that provides nutrients for the fetus and eliminates its waste products) in the fish genus, arguing that placentas serve as a good stand-in for complex organs whose histories have eluded evolutionary biologists.

    The dilemma posed by complex adaptation, which are organs of extreme complexity that have evolved through the action of natural selection, is that these organs demand contributions from a large number of adaptations at individual genetic loci to function properly. Darwin addressed the difficulty of complex adaptations with his treatment of the evolution of the eye. "He had to use organisms from different classes," explained Reznick, "because there isn't a living group of related organisms that have all the steps for making an eye." The organisms in Darwin's model are, however, distantly related to one another.

    Darwin proposed that complex eyes could have been formed with a succession of photosensitive organs, each a bit more complex than its predecessor and each favored by natural selection because of the advantages that the possessor received. Visualizing such a process would be easiest if steps in this sequence were preserved in closely related living organisms; but no such sequence exists for eyes because the intermediate stages have been lost through extinction.

    Reznick and his colleagues studied guppy-like fish in the genus Poeciliopsis. They report that placentas have evolved independently three times in closely related Poeciliopsis species. Other species in the genus lack placentas, and some have partial maternal provisioning via tissues that may be precursors of placentas. "Thus the fish present the full trajectory of steps involved in the evolution of this organ," said Reznick. "It allows researchers to examine what's been added, or what has changed, and eventually identify the genes associated with the evolution of each trait."

    The study by Reznick and colleagues first argues that the placenta is a complex organ, in the sense that it represents a composite of many adaptations and is controlled by many genes. "The origin of complex, novel organs plays a key role in evolution since they often define new categories of animals, such as the placenta for placental mammals," said Reznick. "They are also a source of controversy both within evolutionary biology and between evolutionary biology and the religious public. This is because their origin unfolds on a time scale considerably longer than human existence, so the process must be inferred indirectly."

    In the Science paper, the researchers show that: 1) Fish in the genus Poeciliopsis have placentas in various stages of evolution, and 2) There are clusters of closely related species that either have highly evolved placentas, placentas in intermediate stages of evolution, or no placentas at all. These provide ideal material for studying how such complexity evolves.

    The researchers then use the combination of molecular and geological data to yield estimates for how long it took the placenta to evolve in some lineages. Based on collected data, they find that the shortest time interval between a poeciliid species with a placenta and its last common ancestor without one was 750,000 years, suggesting that placentas can evolve in 750,000 years or less.

    "This result demonstrates that complex organs can evolve rapidly, on the same scale as predicted by a theoretical estimate of 400,000 years for the evolution of the eye," said Springer.

    Reznick has been collecting comparative life history data for around 15 years. For the study, he traveled around Latin America collecting the fish, going to museums to work with their collections, and then doing the appropriate dissections at UC Riverside. Several UC Riverside undergraduate students contributed to the dissections. Reznick also worked on live fish in his laboratory on campus.

    The molecular work for the study was done by Mateos over the past two years. Springer did the phylogenetic work for the study. His statistical methods helped the researchers make inferences about how traits have evolved from the combination of DNA sequence data (collected by Mateos) and the descriptions of modes of reproduction (generated by Reznick).

    The UC Riverside Department of Biology serves three main functions: undergraduate instruction, graduate education, and research in basic biology. The department conducts research and teaching in many areas of life science including cell biology, conservation biology, developmental biology, ecology, evolution, molecular biology, physiology, and population biology. The department is part of the College of Natural and Agricultural Sciences, a multi-departmental unit dedicated to instruction and basic research in the physical and life sciences, and also to 'mission-oriented' applied research in the agricultural sciences. The Biology major is a popular undergraduate major on the UC Riverside campus, with approximately 1000 students currently enrolled. Biology also provides much of the undergraduate instruction for majors in other life science departments and other science majors.


    * Hemoglobin IC? (1 replies)
    Tom Ames2003-01-23 11:58:43
    Has anyone seen claims made for the IC-ity of Hemoglobin? Seems like a natural: tetrameric structure, cooperative binding of oxygen, looks designed to change loading capacity in just the right way to deliver oxygen from lungs to tissues.
    * Antibiotic/pesticide resistance (0 replies)
    niiicholas2003-03-02 21:49:25
    Links/material on this topic that refute various common antievolutionist distortions of the topic:

    II Evo forum thread

    nic
    * Ant-fungus-parasite coevolution (0 replies)
    niiicholas2003-02-24 20:18:43
    Online here:

    Evolution and Ant Agriculture: a response to Ilíon.
    http://www.arn.org/cgi-bin....#000000

    Some of his other posts:
    Successful predictions of evolutionary theory
    http://www.arn.org/cgi-bin....=001603

    Here's da whole thing:

    ========================
    In the "Still Spinning Just Fine" thread, Ilíon brought to our attention the purportedly co-evolved ant-fungus-mold-bacterium system as a case that presents difficulties for the traditional Darwinian paradigm.  As an ant evolution researcher, I am of the opinion that the ant/fungus/mold/bacterium relationship is fascinating regardless of one's perspective, and think that the topic merits its own thread.  I also happen to think that much of what we know about the workings (and even the existence) of this complex relationship is a direct consequence of the use of Darwinian theory by biologists, and I echo Marc's sentiments that the system is a fine example of evolutionary biology in practice.

    This is a long post, and it has the following structure:

    • 1. Short ant/fungus background.
    • 2. The role of evolutionary theory in ant/fungus research.
    • 3. Some quibbles over technical issues.
    • 4. Overview of evidence for common descent and natural selection in the ant/fungus/mold/bacteria system.

    ******
    1. Quick background.
         

    In a nutshell, there are some 200+ species of ants in the new world tropics that are obligate fungivores. These are mostly small, inconspicuous ants, but the group also includes the famous and economically important leaf-cutter ants.  These ants are involved in a largely mutualistic relationship with a fungus.  The fungus is eaten by the ants, but the fungus also depends on the ants for its propogation: a true agricultural system.  In the past 4 years, a twist has been discovered: an Escovopsis mold that is a specialized parasite of the ant fungus, and a Streptomyces bacterium that produces an antibiotic that the ants use to combat the parasitic Escovopsis.

    Links:
    The attine ants

    The discovery of the Streptomyces

    Ulrich Mueller's publications

    photo gallery of Atta leaf-cutters and gardens

    photo gallery of Acromyrmex leaf-cutters

    photo gallery of Mycocepurus, a more "primitive" attine.

    (note, the final three links are shameless self-promotion of my brand-new web site)

    2. The role of evolutionary theory in ant/fungus research.

    To say that most of what we know about fungus-growing ants and their fungi stems directly or indirectly from evolutionary research would not be an exaggeration. To say that everything we know about the Escovopsis parasite is due to evolutionary research is a simple, observational truth.

    I bring this up because Ilíon wrote:      
    Quote
    "Why are 'evolutionary biologists scratching their heads?' Aside from the obvious interesting questions, I think it's because the facts don't fit the paradigm"
    I have a hard time believing that the facts cause problems for the paradigm, because "the facts" to which Ilíon refers wouldn't even be known if it weren't for the Darwinian paradigm in the first place.  Escovopsis was re-discovered, and the details of its biology were described, as the result of research into a widely-held idea that contradicted Darwinian theory.  The following passage is from the introduction to the pioneering study:

         
    Quote
    "The longstanding assumption that ant fungal gardens are free of significant pathogenic pressure is surprising because it contradicts some fundamental theories of the evolution of parasitism... To resolve the conflict between the theoretical prediction that parasites should exist in the clonal attine fungicultural systems and the widespread yet untested belief that ants maintain their gardens free of parasites, we conducted an extensive examination of fungal parasitism of gardens of attine ants."

    Source: Currie, C.R., U.G.Mueller, and D. Malloch. 1999. The agricultural pathology of ant fungus gardens. Proc.Nat.Acad.Sci.USA. 96:7998-8002. (Download pdf)
    Briefly, evolutionary theory predicted that there should be serious parasites of this system as a consequence of prolonged asexual reproduction.  So these researchers- primarily Currie, a graduate student at the time- went chasing a Darwinian notion and discovered Escovopsis.

    But this discovery is just the tip of the iceberg.  Biologists have flocked to the attine/fungus system because the system raises so many interesting evolutionary issues, some of which may be easily resolved and others of which are real head-scratchers. Besides the discovery of the fungal parasite, here are a few other bits of knowledge that owe their existence to evolutionary theory. It is by no means an exhaustive list.  (Note: by ‘evolutionary theory', I don't mean as Ilíon insinuates that observations are merely reported in ‘Darwinspeak'. I mean that these discoveries were motivated by Darwinian research questions, or that their discovery would not have happened without knowledge of common descent or natural selection.)

    1. Ant fungi have been transmitted horizontally between ant nests, in addition to vertical transmission from parent to daughter colony. This result emerged from phylogenetic analysis (See Mueller, U.G. 2002. American Naturalist 160(supplement): s67-s98.).

    2. Attine ant species with more complex caste systems are polyandrous (See Murakami, T. et al 2000. Behav. Ecol. SocioBiol.48:276-284.)

    3. Escovopsis fungi likely had a single origin (See Currie et al 2003. Science 299:386-388.)

    4. The fungal cultivars do sometimes depart from the ant mutualism and become free-living (See Mueller, U.G. 2002. American Naturalist 160(supplement): s67-s98.).

    I don't bring up these examples as a demonstration that Darwinian evolutionary theory is ultimately the best explanation of the ant/fungus/mold/bacteria relation. Rather, I bring them up to show that Darwinian theories have been extremely fruitful in both bringing this system to light and in stimulating further research. The ability to generate questions is *extremely* important in scientific theories, and the ‘head scratching' produced by Darwinian theories is a natural consequence of their usefulness.  Head-scratching means questions, and questions mean research.  A theory that doesn't raise questions does not provide a useful substrate for science.

    It is worth noting that so far answers have been forthcoming to these questions, which I take as an indication that we are on the right track.

    It is also worth noting that little, if anything, in this system can be traced to creationist or Intelligent Design thought.  Simply put, advocates of those schools will need to provide quite a bit more detail about how, where, and when design was affected in this system before a design research program will be possible.  If you would like to see design adopted by scientists working in this system, you've got to provide an alternative that is more useful in the lab and in the field than Darwinism.  This will entail doing better than making non-committal statements about the "unknowability" of the design process of the sort that permeates I.D.ist writings.  Meanwhile, Darwinian reseach keeps suggesting and finding new players in the symbiosis.


    3. Some quibbles over technical issues.

    Some of my issues are with Ilíon, but most are with the NYTimes article that Ilíon cites.
    Ilíon wrote:
         
    Quote
    Also, note that the story says the mold seems to be related to a mold that devastates commercial mushroom farms. The mushrooms we grow have not been prohibited from sexually reproducing for the last 50 million years, so by your argument they have been able to continue evolving to resist the mold attacking them. And yet, it doesn't sound as though they do a much better job than the ants' fungus does.
    I have a minor correction to make.  The fungi have not been prohibited from sexually reproducing for 50 million years.  They have been observed to reproduce sexually in both the lab and in the field.  (See again the Mueller 2002 Am Nat paper).  This may not have been clear from the NYT article, but then, the popular media has never been known for the accuracy of its reporting. Rather, the issue is that the fungal cultivar only rarely reproduces sexually, so its rate of production of genetic novelty is lower than that of the parasite.  It still is true, however,  that within each nest the fungus garden is a clonal monoculture.

         
    Quote
    You're forgetting that the evidence indicates that all nests are using the same clonal cultivar of the mold.
    An error in the reportage of the NYTimes.  Some species of Apterostigma, one of the "lower" attines,  use a distantly-related species of fungus. But, I consider your point valid, as most species use cultivars from the same clade, and it seems clear from the phylogeny that the original domestication happened once.

         
    Quote
    In your nice little story, the ant are becoming increasingly dependent on the fungus, but the mold is increasing, reducing their yields. During this time, and during the time that the ants are 'learning' to use the bacteris to fight the mold, some of the nests will even lose their crops, which will cause some of those nests to die, but others will restart their gardens with a new batch of 'wild' fungus - thus we should find multiple cultivars of the fungus.
    I think you've taken the simplistic reporting of the NY Times a bit too seriously.  Not your fault. The inference of a single domestication event comes from phylogeny, and you've got to be careful with what you can and cannot conclude from a phylogeny.  By "single event", what the original researchers mean is that all current fungal cultivars, and their ants, trace their ancestry back to a single fungal and a single ant species.  Beyond this inference, there is simply no resolution to distinguish an actual one ant-one fungus domestication event, and a population that did it gradually with many original cultivars.  Specifically, here are three situations that will look identical in phylogenetic retrospect:

    1. A literal single origin, where one colony picks up one fungus and the rest is history. I think this is the interpretation that you object to.  Not without  reason, IMHO.

    2. Multiple origins, but all the fungal cultivars involved are closely related and share a common ancestor.  If that ancestor left no descendants that are not cultivated by ants in the present day, then the fungi will still trace back to a single node on the phylogeny as an artifact of extinction, even though there may actually have been multiple domestication events.

    3. Multiple origins, but when the ants lose their fungi they re-acquire not from the wild but from another ant nest.  There is some evidence that this is what modern attine ants do when they lose their fungus.  This way the fungus spreads laterally among colonies, and given a stochastic process of fungal lineage loss throughout the population all colonies will eventually come to cultivate a single lineage.  The other original fungal lineages, having gone extinct, will not appear in the phylogenetic analysis and the phylogeny will trace back to a single node.  

    The take-home message is that "single origin" claims can be a bit misleading.  Currently there is no way to test between these different possibilities, so for the time being we are stuck with a "single origin" only in the broad sense.

         
    Quote
    The three-way symbiosis of the ant (and apparently, we're talking about more than one species of ant but they're all using the same fungus clone), the fungus, and the bacterium has to be all in place from the beginning to be able to successfully fight the mold.
    Correction: there are multiple species of fungi, some of them specific to particular attine species.  The fungus is only clonal at the level of the colony.  They are all descended from a 50my or so old fungus, but they've had plenty of time to diversify.  Interestingly, the pattern of diversification is *very* suggestive of coevolution with the ants.  I'll get back to this point in a bit.

         
    Quote
    If the queens didn't 'know' from the beginning to take a start of the parent nest's fungus (and, BTW, don't they have a special 'chamber' in their heads in which they transport their sample?), there should be multiple cultivars.
    You aren't the first to have thought of this. Ulrich Mueller also finds this idea a bit suspect, and he has proposed that what originally happened was a fungus exploiting the ant for dispersal.  Ants of many kinds commonly pick stuff up in their infrabuccal chamber (the ‘special chamber' of which you speak), mostly stuff that they've filtered from food, and dump it out when it's full.  The symbiosis may have arisen as a result of the fungus getting picked up and dispersed by ants.  This is interesting, because it is a fungal-centered hypothesis.  Most explanations are ant-centered, and IMHO have come off as a bit weird.

    4. The evidence for common descent and natural selection in the ant/fungus/mold/bacteria system.

    One compelling reason to look for evolutionary processes as explanations for the ant/fungus/mold/bacteria relationship is that there is a great deal of evidence for common descent and for Darwinian evolution in these organisms.  Here it is, in no particular order:

    • Geography.  Attines and their cultivars are restricted to the new world tropics.  The estimated age of the symbiosis is 50 million years, which is after the break-up of Gondwana and the isolation of South America.  Given limited across-water dispersal (Attine queens are heavy and clumsy fliers, if you've seen them fly...), the agreement of date and location are supportive of common descent.  It is also relevant that the ant groups that come out as sister to the attines are also South American.  In contrast, many ant groups whose estimated ages (from phylogenies that were calibrated with fossils) are older than break-up of Gondwana are found in both the old and the new worlds. These include army/driver ants and elongate twig ants.  Does design theory have anything to say about the geographic distribution of the ant/fungus system?
    • Large scale phylogenetic congruence between ants, cultivars, and Escovopsis. This is the subject of the Jan 2003 Science article that sparked the NY Times commentary.  I strongly recommend that you read the paper:
      Ancient Tripartite Coevolution in the Attine Ant-Microbe Symbiosis
      Here is the abstract:      
      Quote
      Currie CR, et al.2003. Ancient tripartite coevolution in the attine ant-microbe symbiosis. Science 299:386-388.
      The symbiosis between fungus-growing ants and the fungi they cultivate for food has been shaped by 50 million years of coevolution. Phylogenetic analyses indicate that this long coevolutionary history includes a third symbiont lineage: specialized microfungal parasites of the ants' fungus gardens. At ancient levels, the phylogenies of the three symbionts are perfectly congruent, revealing that the ant-microbe symbiosis is the product of tripartite coevolution between the farming ants, their cultivars, and the garden parasites. At recent phylogenetic levels, coevolution has been punctuated by occasional host-switching by the parasite, thus intensifying continuous coadaptation between symbionts in a tripartite arms race.
      Two congruent phylogenies is good evidence for common descent, but three pretty much clinches it.  I suppose that it is true that congruence could also reflect an intelligent design process as well (probably one integrated with descent), but since no mechanisms exist for how or when or to what effect such design might take place they are of little immediate use to researchers.
    • Complexity and specialization of the attines correlates with phylogeny, as expected under co-evolution and common descent. The oldest lineages of Attines have the smallest nests, a single worker morphological caste, the least specialized foraging habits, and the least prevalence of Escovopsis in their nests. They also have the highest rate of fungal swapping.  The most recent lineages of attines, have enormous colonies, with a dozen or so morphologically different worker castes (the largest workers are orders of magnitude larger than the smallest workers), multiple fungus gardens, highly specialized foraging habits, and the highest prevalence of Escovopsis.  And the lineages that are of intermediate age, such as Trachymyrmex+Sericomyrmex, are somewhere in between. This pattern makes sense under common descent.
    • Present day attine colonies have some life-history features with the signature of natural selection.  Most notable, sex investment ratios.  A ton has been written on how the differing Darwinian "goals" of queens and workers in ant colonies play out in manipulations of population sex investment ratio, such that species with particular mating systems should produce different sex ratios.  Attines, with some exceptions, fall into the generally predicted pattern of monandrous species investing very heavily in females. It's a bit too complicated to explain here, but I find the evidence compelling and you can read more about it in this book:

      Social Evolution in Ants

      In the past, I've also written threads on ARN about sex ratios and evolution, here:
      Successful predictions of evolutionary theory

    ******

    There.  Now I'm done.

    Enjoy,

    Myrmecos
    ===============
    * (relatively) Unexplained things and what they mean (0 replies)
    niiicholas2003-02-17 15:41:23
    This thread is devoted to the Argument from Ignorance and what happens to various sciences if it were allowed the same free reign that IDists give the Argument from Ignorance in biology.

    E.g.:

    http://www.arn.org/cgi-bin....#000018


    Quote

    BTW, since the Steves have no serious scientific doubt that natural selection was the major mechanism behind the origin of the bacterial flagellum, have them drop me an e-mail providing some of this evidence. The evidence must be immense, given there is no serious doubt. Oddly enough, it seems to be secret evidence. SShhh.  


    Similarly, because the origin of the rings of Saturn is still unknown except for some general models and scraps of data, we should have "serious doubt" that current physical theory can account for it.

    Any schmoe in any field can go dig up something unexplained (or only generally explained, as in the cases of both the flagellum and the rings of Saturn) in any field, that is old enough or otherwise "distant" enough to make evidence hard to come by.  None of this justifies "serious doubt" in a well-established theory, especially for problems that are routinely brought up and solved within the field ("complex adaptive structure #1241" in biology, evolutionary theory has already explained a number of complex adaptive structures so what difference does one more make?).  

    On Mike Gene's logic these mysterious, highly symmetrical structures should put mainstream geology into "serious doubt":



    ...and these should put mainstream anthropology/archeology into doubt:

    The "Bahgdad Battery" -- apparently a 2200 year old battery.


    And yes, both of these puzzles have been invoked in support of radical theories like, oh I don't know, alien intervention in the history of life.

    I guess we should be teaching this "serious doubt" about mainstream science in school earth sciences and history classes also, just to be fair.

    Post your favorite mysteries here!!
    * The importance of specific hypotheses about IDer (0 replies)
    niiicholas2003-04-06 13:13:29
    Here is a good one:

    Link

    Code Sample


    Glenn <gsheldon@qwest.net> wrote in message news:<3E8F2388.80900@qwest.net>...
    > Steven J. wrote:
    > -- [snip]
    >
    > > The "design hypothesis" need not protect itself from falsification by
    > > continually incorporating _ad hoc_ hypotheses.  It has the mother of
    > > all _ad hoc_ hypotheses built into it from the beginning: the identity
    > > (by which ID propenents mean not merely the name, but the motives,
    > > methods, and abilities of the Designer) are said to be irrelevant to
    > > and inaccessible by science.
    >
    >
    > EH?? The "identity" of a designer is not necessary, nor are the
    > abilities required to be known to detect design in structures.
    > And you said yourself that mechanisms are not needed as long as there is
    > evidence of an event(s).
    > You'll have to do a little better than that, Steven.
    >
    Let me restate my position.  One recognizes "design" not by
    identifying "irreducibly complexity" or "specified complexity," but by
    recognizing similarities to things known to be designed, in structure,
    composition and methods of construction, and purpose.  To take Paley's
    famous watch example, he could tell that the watch has gears and
    springs, because he recognized them as members of known classes of
    manufactured items.  He recognized that it told time, because he
    already had the concept of telling time.  Whether he understood either
    how these gears and springs told time, or how they were manufactured,
    is another question.  At the low extreme of complexity, one recognizes
    the crudest stone tools of early hominids because they show the sorts
    of chips we recognize as the results of human manipulation.  Design is
    recognized by analogy with the work of known and observed designers.

    This applies, of course, to SETI as well -- the search for
    extraterrestrial intelligence depends crucially on the assumption that
    ETIs would design in similar ways and for similar purposes to those of
    humans.  One could, I suppose, hypothesize a Designer of radically
    different capabilities, methods, and goals; if one had a sufficiently
    detailed hypothesis, one could predict what sort of results one should
    expect of that design.  That is, one must *recognize* the
    specifications of the complexity.  IDers argue, on the one hand, that
    living things are obviously designed for their functions.  But when
    examples of seemingly bad or just eccentric design (what Designer
    would use one basic wing design for all birds, flying or nonflying,
    and another for all bats, of all sizes?) are adduced, they retort that
    we can't know the purposes of the Designer.  Well, if we can't know
    them, we can't very well marvel at how wonderfully the design
    accomplishes them, can we?

    Now, ID proponents argue that SCI can be recognized because no natural
    mechanism can produce it, and intelligence can, even if we can't be
    sure what exactly the specification is.  But even to the extent that
    currently known regularities of nature, operating alone or in
    combination in currently known ways, can't explain a phenomenon, all
    that shows is that some currently unknown mechanism (whether employed
    by an intelligent Agent, or purely nonteleological) produced it.
    Without an exhaustive knowledge of all nonteleological regularities of
    nature, and all their possible combinations, we can't rule out the
    possibility of unknown, natural, unintelligent causes.  Nor, of
    course, can we rule out intelligent causes of sorts (e.g.
    intelligences no more interested in our morals, welfare, or worship
    than we would be in that of bacteria in a petri dish) that would not
    greatly interest most ID supporters.
    >
    > > That is, they have no idea how their proposed explanation is supposed
    > > to work, or what sort of systems the Designer should be expected to
    > > design, or to refrain from designing.  They've no foggiest idea
    > > whether the Designer should give every creation identical
    > > cytochrome-c, or arrange variants in a nested hiearchy, or arrange
    > > variants in a pattern clearly NOT a nested hierarchy.  Because of
    > > this, they can't explain why anything in nature is the way it is,
    > > rather than some other imaginable way.
    >
    >
    > All I know is that I'm not taking your word for this.
    >
    *shrug*  Take the IDers' own word for it.  In Phillip Johnson's
    _Darwin on Trial_ , Behe's _Darwin's Black Box_, and quite a few other
    books, the author deals with some variant of the "panda's thumb"
    argument that the sort of design we see in living things is *not* the
    sort of design we would expect from any observed sort of intelligent
    designer.  The response is invariably that this is a theological, not
    scientific, position -- that we aren't entitled to any assumptions
    about how the Designer would work.  But if we aren't entitled to any
    assumptions about how the Designer would work, we surely can't make
    any predictions about what design will and will not look like.
    Therefore we can't tell design from the results of unknown, but
    unintelligent, causes -- or, indeed, from the results of known
    unintelligent causes (maybe the Designer crafts each snowflake
    individually and intelligently -- how would we ever know otherwise?).
    >
    > >
    > > ID theory predicts *nothing* except that there will be aspects of
    > > biological complexity and diversity not explicable by current theories
    > > -- and these gaps will be seized upon as places to stuff a "Designer
    > > of the gaps."
    > >
    > Unlike what Ho and Sanders claim "But a real synthesis should begin
    > by identifying conflicting elements in the theory, rather than in
    > accommodating contradictions as quickly as they arise."
    >
    Very unlike that, indeed.  ID does not seize on newly identified
    mechanisms with which to explain this or that aspect of design.  Its
    flaws do not include finding one purpose or technique for design, and
    using it to explain the bacterial flagellum, while seizing on a
    different sort of design for a completely different purpose to explain
    the immune system.  It does not seek mechanisms or explanations for
    anything at all, or make predictions detailed enough that it needs to
    rescue them with _ad hoc_ explanations.  Rather, it simply argues that
    this, and that, and some other thing can't be explained in perfect
    detail by current models, so "theDesignerdidit" (in some unspecified
    manner, at some unspecified time, for some unspecified purpose) is
    somehow a superior explanation.

    -- Steven J.


    ...coudla written it myself, although I didn't.

    * Mechanisms of mutation (0 replies)
    niiicholas2003-04-30 18:50:00
    A good complement to a junk DNA FAQ would be a "mechanisms of mutation" FAQ, which I don't think exists anywhere.  People seem to treat mutation as some kind of magically process and therefore get mislead into all kinds of directed mutation, etc. stuff.

    Most stuff on the web appears to be either lecture outlines or very technical "my research is"-type pages.

    But there is some good stuff.  For example:

    Mutation, Mutagens, and DNA Repair
    http://www-personal.ksu.edu/~bethmont/mutdes.html

    Quote

    Outline
    Introduction: Definitions and mutation rates
    Types of Mutations
    Origins of Spontaneous Mutation
    Mutagens
    DNA Repair Systems
    Checkpoints
    * Peppered moth resting locations (8 replies)
    niiicholas2002-09-21 13:06:12
    This thread is for accumulating

    (1) Assertions
    (2) Links to articles
    (3) Facts

    ...regarding the question "where do peppered moths rest during the day".  The importance of this topic lies in that many have argued that peppered moths don't rest where Kettlewell thought they did, and that therefore his experiments were invalid, and that therefore the entire peppered moth bird-predation-theory is without support.  Or something.

    Another avenue taken by Jonathan Wells in particular is the "this means that textbook photos of moths are fake and a fraud has been committed on students" avenue.  I suggest that we collect pictures that we can find on the web, with comments on the source (if we can find 'em), whether or not they are staged (if known), with a goal of getting a sense of whether or not textbook pictures are misleading.

    nic

    * Silverswords (0 replies)
    Art2003-01-13 22:56:59
    In the never-ending quest for "icons", I submit the following for everyone's consideration.  Comments, additional references, and more examples that combine molecular and morphological perspectives would be most appreciated.  (This is a slightly-modified version of a recent ARN post - suggestions to make it more suited for this board are invited as well.)

    First, another accursed pubmed abstract (that need not be read in detail - instead, just note that some of the genes mentioned are known to be developmentally important ones Arabidopsis and other plants):

    Quote
    Proc Natl Acad Sci U S A 2001 Aug 28;98(18):10208-13

    Accelerated regulatory gene evolution in an adaptive radiation.

    Barrier M, Robichaux RH, Purugganan MD.

    Department of Genetics, Box 7614, North Carolina State University, Raleigh, NC 27695, USA.

    The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.


    Now, consider three plants from the group (pardon my taxonomical crudeness here) mentioned in this abstract:  ,
    ,
    and
    .  

    It doesn’t take much of an eye to see stupendous morphological differences, easily dramatic enough to qualify as possibly macroevolutionary in nature.  Of course, this could only be if it could be shown that these plants share a common ancestry.

    And indeed it can be so shown.  By a standard that even the staunchest YECer accepts, it can be strongly concluded that each of these (as well as other members of the Silversword alliance) share a common ancestry.  This is because, the vast morphological differences aside, they are interfertile.  As interestingly, for a number of other reasons (biological, geographic, historical, and molecular), it can be safely concluded that these vastly-different plants diverged from a common ancestor that looked something like

    .

    Reflect, now, on the abstract.  In this study, evidence for positive selection of alleles (that must have arisen via mutation - this follows from the natural history of the different genera) of developmentally-important genes - genes involved in flower structure and evolution - was described.  While it’s not a videotape, it stands as evidence of the sort that Wells claims does not exist - namely, that changes in developmentally-important genes are important in macroevolutionary progressions.

    (Keep in mind that among the dramatic morphological differences that are seen in these examples are ones that involve floral structures.  Also, while others might argue with me, I would claim here that the range of morphologies shown in this post exceeds the range seen in placental mammals - just to give readers an idea of the scope of the differences.)
    * Origin of morphological novelty (0 replies)
    niiicholas2003-02-02 05:53:36
    Put your favorite examples here!

    Discussed on Evolving Inventions:

    Quote

    Before I attempt to answer your question, John, I would like to try and narrow down the exact, final, definitive definition of "inventive solution" in TRIZ-terms.  The best I can seem to find are terms like "non-routine" and "resolving a technical contradiction", which help a bit but are difficult to apply.

    Is there perhaps an authoritative quote you could post that would constitute the best-available definition?

    Perhaps (especially since you focused on morphological evolution in your reply) answering the following would help:

    Regarding morphology/development, would the following set of stages, if evolved through, constitute an "inventive" or "routine" solution:

    1) Start with segmented metazoan.

    2) Duplicate a segment (e.g. the corresponding Hox gene is serially duplicated).  Critter now has an extra segment somewhere in the middle (say, 5 instead of 4) and corresponding pair of legs, etc., that go with the segment.

    3) Repeat step 2 a number of times (e.g., selection for larger body size retains these duplications)

    4) Once there are a fair number of segments, mutation and selection modify one or several of the more forward pairs, e.g. to improve prey capture or food-chewing or substrate/mate clasping (large number of possibilities here, lots of arthropods have these kinds of specializations).

    Below is a slightly less abstract case (in arthropods, but dealing with the origin of a novel structure not from legs but from another structure).  Would we have a novel or routine kind of solution here?

    [QUOTE]
    Proc Natl Acad Sci U S A 2002 Apr 16;99(8):5498-502

    [which is free online I think]

    Origin of a complex key innovation in an obligate insect-plant mutualism.

    Pellmyr O, Krenn HW.

    Evolutionary key innovations give organisms access to new ecological resources and cause rapid, sometimes spectacular adaptive radiation. The well known obligate pollination mutualism between yuccas and yucca moths is a major model system for studies of coevolution, and it relies on the key innovation in the moths of complex tentacles used for pollen collecting and active pollination. These structures lack apparent homology in other insects, making them a rare example of a novel limb. We performed anatomical and behavioral studies to determine their origin and found evidence of a remarkably simple mechanism. Morphological analyses of the tentacles and adjacent mouthparts in pollinators and closely related taxa showed that the tentacle appears abruptly in female pollinating yucca moths. Several morphological synapomorphies between the galeae, which constitute the characteristic lepidopteran proboscis, and the tentacle suggest that the tentacle evolved quickly through expression of the genetic template for the galea at an apical growth bud on the first segment of the maxillary palp. Behavioral data indicate that tentacle and proboscis movements are controlled by a shared hydraulic extension mechanism, thus no new mechanism was needed for tentacle function. Known developmental paths from other insects can explain the origin of this sex-specific key innovation in a few steps.



    Other relevant articles:

    Quote

    J Exp Zool 2003 Feb 15;295B(1):1-11 Related Articles, Links  

     
    Hox genes as synchronized temporal regulators: Implications for morphological innovation.

    Crawford M.

    Department of Biological Sciences, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.

    In vertebrates, clusters of Hox genes express in a nested and hierarchical fashion to endow the embryo's segments with discrete identities. Later in development, members of the same gene family are employed again to pattern the limb, intestinal, and reproductive systems. A careful analysis of the morphologies of Hox mutant mice suggests that the genes provide qualitatively different cues during the specification of segments than they do during the development of more recently derived structures. In addition to the regulatory differences noted by others, the activity of Hox genes during specification of the vertebrate metameres in some recent deletion experiments is inconsistent with a role for them as strictly spatial determinants. On the contrary, the phenotypes observed are suggestive of a role for them as elements of a generic time-keeping mechanism. By contrast, the specification of more recent evolutionary structures appears to be more spatial and gene-specific. These differences in role and effect may suggest some simple mechanisms by which the Hox clusters operate, and rules by which gene networks can be diverted to create new structures over the course of evolution. Specific predictions and experiments are proposed. J. Exp. Zool. (Mol. Dev. Evol.) 295B:1-11, 2003. Copyright 2003 Wiley-Liss, Inc.


    Curr Biol 2002 Oct 1;12(19):1711-6
     
    Diverse adaptations of an ancestral gill: a common evolutionary origin for wings, breathing organs, and spinnerets.

    Damen WG, Saridaki T, Averof M.

    Institute for Genetics, University of Cologne, Weyertal 121, D-50931, Koln, Germany.

    Changing conditions of life impose new requirements on the morphology and physiology of an organism. One of these changes is the evolutionary transition from aquatic to terrestrial life, leading to adaptations in locomotion, breathing, reproduction, and mechanisms for food capture. We have shown previously that insects' wings most likely originated from one of the gills of ancestral aquatic arthropods during their transition to life on land. Here we investigate the fate of these ancestral gills during the evolution of another major arthropod group, the chelicerates. We examine the expression of two developmental genes, pdm/nubbin and apterous, that participate in the specification of insects' wings and are expressed in particular crustacean epipods/gills. In the horseshoe crab, a primitively aquatic chelicerate, pdm/nubbin is specifically expressed in opisthosomal appendages that give rise to respiratory organs called book gills. In spiders (terrestrial chelicerates), pdm/nubbin and apterous are expressed in successive segmental primordia that give rise to book lungs, lateral tubular tracheae, and spinnerets, novel structures that are used by spiders to breathe on land and to spin their webs. Combined with morphological and palaeontological evidence, these observations suggest that fundamentally different new organs (wings, air-breathing organs, and spinnerets) evolved from the same ancestral structure (gills) in parallel instances of terrestrialization.



    A detailed review of the origin of feathers:

    Quote

    Q Rev Biol 2002 Sep;77(3):261-95

    The evolutionary origin and diversification of feathers.

    Prum RO, Brush AH.

    Department of Ecology and Evolutionary Biology, and Natural History Museum, University of Kansas, Lawrence, Kansas 66045, USA. prum@ku.edu

    Progress on the evolutionary origin and diversification of feathers has been hampered by conceptual problems and by the lack of plesiomorphic feather fossils. Recently, both of these limitations have been overcome by the proposal of the developmental theory of the origin of feathers, and the discovery of primitive feather fossils on nonavian theropod dinosaurs. The conceptual problems of previous theories of the origin of feathers are reviewed, and the alternative developmental theory is presented and discussed. The developmental theory proposes that feathers evolved through a series of evolutionary novelties in developmental mechanisms of the follicle and feather germ. The discovery of primitive and derived fossil feathers on a diversity of coelurosaurian theropod dinosaurs documents that feathers evolved and diversified in nonavian theropods before the origin of birds and before the origin of flight. The morphologies of these primitive feathers are congruent with the predictions of the developmental theory. Alternatives to the theropod origin of feathers are critique and rejected. Hypotheses for the initial function of feathers are reviewed. The aerodynamic theory of feather origins is falsified, but many other functions remain developmentally and phylogenetically plausible. Whatever their function, feathers evolved by selection for a follicle that would grow an emergent tubular appendage. Feathers are inherently tubular structures. The homology of feathers and scales is weakly supported. Feathers are composed of a suite of evolutionary novelties that evolved by the duplication, hierarchical organization, interaction, dissociation, and differentiation of morphological modules. The unique capacity for modular subdivision of the tubular feather follicle and germ has fostered the evolution of numerous innovations that characterize feathers. The evolution of feather keratin and the molecular basis of feather development are also discussed.


    Body plans:

    Quote

    Evol Dev 2002 Nov-Dec;4(6):459-99

    Hox genes and the evolution of the arthropod body plan.

    Hughes CL, Kaufman TC.

    Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, IN 47405, USA.

    In recent years researchers have analyzed the expression patterns of the Hox genes in a multitude of arthropod species, with the hope of understanding the mechanisms at work in the evolution of the arthropod body plan. Now, with Hox expression data representing all four major groups of arthropods (chelicerates, myriapods, crustaceans, and insects), it seems appropriate to summarize the results and take stock of what has been learned. In this review we summarize the expression and functional data regarding the 10 arthropod Hox genes: labial proboscipedia, Hox3/zen, Deformed, Sex combs reduced, fushi tarazu, Antennapedia, Ultrabithorax, abdominal-A, and Abdominal-B. In addition, we discuss mechanisms of developmental evolutionary change thought to be important for the emergence of novel morphological features within the arthropods.


    [...]


    Philos Trans R Soc Lond B Biol Sci 1995 Sep 29;349(1329):313-9

    Hox genes and the evolution of diverse body plans.

    Akam M.

    Wellcome/CRC Institute and Department of Genetics, Cambridge, U.K.

    Homeobox genes encode transcription factors that carry out diverse roles during development. They are widely distributed among eukaryotes, but appear to have undergone an extensive radiation in the earliest metazoa, to generate a range of homeobox subclasses now shared between diverse metazoan phyla. The Hox genes comprise one of these subfamilies, defined as much by conserved chromosomal organization and expression as by sequence characteristics. These Hox genes act as markers of position along the antero-posterior axis of the body in nematodes, arthropods, chordates, and by implication, most other triploblastic phyla. In the arthropods this role is visualized most clearly in the control of segment identity. Exactly how Hox genes control the structure of segments is not yet understood, but their differential deployment between segments provides a model for the basis of segment diversity. Within the arthropods, distantly related taxonomic groups with very different body plans (insects, crustaceans) may share the same set of Hox genes. The expression of these Hox genes provides a new character to define the homology of different body regions. Comparisons of Hox gene deployment between insects and a branchiopod crustacean suggest a novel model for the derivation of the insect body plan.



    Quote

    Annu Rev Cell Dev Biol 2002;18:53-80
     
    Gene co-option in physiological and morphological evolution.

    True JR, Carroll SB.

    Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, New York 11794-5245, e-mail: jrtrue@life.bio.sunysb.edu

    Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit.


    In fact, right now we are living through the merging of developmental biology with the modern synthesis, e.g.:

    Quote

    Genetica 2001;112-113:45-58

    Toward a new synthesis: population genetics and evolutionary developmental biology.

    Johnson NA, Porter AH.

    Department of Entomology and Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst 01003, USA.

    Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.
    * The origins of nitrogen fixation systems (0 replies)
    niiicholas2003-12-30 17:48:38
    A references thread, here:

    http://www.iidb.org/vbb/showthread.php?s=&threadid=72089
    * Protein folding and evolution (3 replies)
    theyeti2002-12-20 01:15:32
    I decided to start this thread to collect references about protein evolution specifically as it relates to folding.  First I'll repost an essay that I posted to the ISCID forum, skipping the irrelevant parts:

    [...]

    Now for some more general stuff about protein folding and evolution.  Josh gives us a very educational post about some of the complexities of protein folding and what it means to biology.  I'm going to skip most of the stuff about the dynamics of protein folding, because I think, at least as it relates to the suboptimality argument, I've addressed that above, and also because I don't have the necessary background in physics to know that much about it.  I think Josh can appreciate that, because he notes that there's tons of stuff that we don't know.  The literature on the dynamics of protein folding is very large, but it's also difficult to read (for me anyway).  But I have reviewed some of the literature at it pertains to the evolution of protein folds, and I'll present some of that.

    First of all, it’s a misconception even among many biochemists that all proteins need to fold to be functional.  In fact, the importance of disordered proteins and those with long disordered regions is now becoming more clear.  Try searching the lit for “intrinsically disordered proteins” and you’ll come up with a number of hits.  These proteins (or certain domains) are unfolded and yet are perfectly functional, and in many cases are just as highly conserved as folded protein domains, though often of lower sequence complexity [1] (and hence, easier to evolve via random generation).  In fact, there is evidence that disordered proteins outnumber ordered proteins, but that the ordered ones represent more resolved structures in the PDB simply because (big shock) they’re easier to crystallize.  So one possible way for folded proteins to come about is by evolving from functional yet disordered proteins, and in this case there would never be a period of time when there was not a selectable function.  And of course it’s not like there are only two kinds of proteins, folded and unfolded.  There is also the intermediate molten globule state.  

    However, most protein folds are thought to evolve from other folds.  This can be seen with the arrangement of protein folds into scale free networks.  Two recent papers on this are relevant.  The first one is Proc Natl Acad Sci U S A 2002 Oct 29;99(22):14132-6, Expanding protein universe and its origin from the biological Big Bang.  I posted a number of excerpts from this paper here, so I won’t bother reproducing them.  The point however is that the scale-free network in which protein folds fit is highly indicative of a duplication / divergence process from one or a few initial folds.  The second paper, which came out about the same time, is Nature 2002 Nov 14;420(6912):218-23, The structure of the protein universe and genome evolution.  Here’s the abstract:

    Quote
    Despite the practically unlimited number of possible protein sequences, the number of basic shapes in which proteins fold seems not only to be finite, but also to be relatively small, with probably no more than 10,000 folds in existence. Moreover, the distribution of proteins among these folds is highly non-homogeneous -- some folds and superfamilies are extremely abundant, but most are rare. Protein folds and families encoded in diverse genomes show similar size distributions with notable mathematical properties, which also extend to the number of connections between domains in multidomain proteins. All these distributions follow asymptotic power laws, such as have been identified in a wide variety of biological and physical systems, and which are typically associated with scale-free networks. These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle.


    So both of these papers support the idea that an evolutionary process not only can account for the emergence of protein folds, but that the distribution of folds is a predicted consequence of evolution.

    Now finally, if you want a “beginning to end” account for protein evolution, there is this recent review article (and there are others out there):

    FEBS Lett 2002 Sep 11;527(1-3):1-4, Molecular evolution from abiotic scratch.

    I’ll see if I can reproduce what they’ve got listed as the five stages of protein evolution, though I’ll have to skip the discussion:

    1. Homopeptides of Ala and Gly encoded by (GCC)-(GGC) duplexes.
    2. Mixed peptides of two alphabet types.
    3. Chains of optimal length close the ends by interactions between two amino acid residues.
    4. The loops are joined in linear arrays and form folds (domains)
    5. Modern, multidomain proteins are formed.

    I don’t know if this model will last, or even if it can stand up to serious scrutiny right now, but it’s the kind of thing that needs to be explored in detail before we can really say anything about the likelihood of protein evolution de novo.  Keep in mind that this particular model is trying to account for the evolution of proteins from the origin of life, which is necessarily tricky because it’s difficult to learn about this just from looking at modern life.  However, once you have a functioning cell, I don’t see any problem with the ability of current theory to account for protein evolution.  

    [This last reference is at the end here for no real good reason]

    1. Proteins 2001 Jan 1;42(1):38-48, Sequence complexity of disordered protein.
    Quote
    Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins.
    * ATPase origins (5 replies)
    niiicholas2002-10-01 13:47:50
    This thread is for references to lit. on, or relevant to, the origins of F1F0 ATPase.  I just came across some and I know of some others, I will post them whenever I dig 'em up.

    Quote

    http://www.pnas.org/cgi/content/abstract/202149599v1

    Subunit rotation of ATP synthase embedded in membranes: a or ß subunit rotation relative to the c subunit ring

    Kazuaki Nishio *, Atsuko Iwamoto-Kihara *, Akitsugu Yamamoto , Yoh Wada *, and Masamitsu Futai *
    *Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Core Research for Evolutional Science and Technology (CREST) of the Japan Science and Technology Corporation, Osaka 567-0047, Japan; and Department of Physiology, Kansai Medical University, Moriguchi, Osaka 570-8506, Japan



    Edited by Paul D. Boyer, University of California, Los Angeles, CA, and approved August 15, 2002 (received for review March 13, 2002)

    ATP synthase FoF1 (3ß3ab2c10-14) couples an electrochemical proton gradient and a chemical reaction through the rotation of its subunit assembly. In this study, we engineered FoF1 to examine the rotation of the catalytic F1 ß or membrane sector Fo a subunit when the Fo c subunit ring was immobilized; a biotin-tag was introduced onto the ß or a subunit, and a His-tag onto the c subunit ring. Membrane fragments were obtained from Escherichia coli cells carrying the recombinant plasmid for the engineered FoF1 and were immobilized on a glass surface. An actin filament connected to the ß or a subunit rotated counterclockwise on the addition of ATP, and generated essentially the same torque as one connected to the c ring of FoF1 immobilized through a His-tag linked to the  or ß subunit. These results established that the c10-14 and 3ß3ab2 complexes are mechanical units of the membrane-embedded enzyme involved in rotational catalysis.


    Some have argued that the ATPase may be descended from a pyrophophatase, so this is relevant:

    Quote

    Proc. Natl. Acad. Sci. USA, 10.1073/pnas.212410399

    Pyrophosphate-producing protein dephosphorylation by HPr kinase/phosphorylase: A relic of early life?

    In most Gram-positive bacteria, serine-46-phosphorylated HPr (P-Ser-HPr) controls the expression of numerous catabolic genes (10% of their genome) by acting as catabolite corepressor. HPr kinase/phosphorylase (HprK/P), the bifunctional sensor enzyme for catabolite repression, phosphorylates HPr, a phosphocarrier protein of the sugar-transporting phosphoenolpyruvate/glycose phosphotransferase system, in the presence of ATP and fructose-1,6-bisphosphate but dephosphorylates P-Ser-HPr when phosphate prevails over ATP and fructose-1,6-bisphosphate. We demonstrate here that P-Ser-HPr dephosphorylation leads to the formation of HPr and pyrophosphate. HprK/P, which binds phosphate at the same site as the ß phosphate of ATP, probably uses the inorganic phosphate to carry out a nucleophilic attack on the phosphoryl bond in P-Ser-HPr. HprK/P is the first enzyme known to catalyze P-protein dephosphorylation via this phospho-phosphorolysis mechanism. This reaction is reversible, and at elevated pyrophosphate concentrations, HprK/P can use pyrophosphate to phosphorylate HPr. Growth of Bacillus subtilis on glucose increased intracellular pyrophosphate to concentrations (6 mM), which in in vitro tests allowed efficient pyrophosphate-dependent HPr phosphorylation. To effectively dephosphorylate P-Ser-HPr when glucose is exhausted, the pyrophosphate concentration in the cells is lowered to 1 mM. In B. subtilis, this might be achieved by YvoE. This protein exhibits pyrophosphatase activity, and its gene is organized in an operon with hprK.
    * immune system evolution (23 replies)
    rafe gutman2002-12-17 18:45:01
    i'd like to use this thread to collect references to articles and research relevant to the evolution of the immune system.  i imagine that i'll be the only one contributing to this, but others are certainly welcome.  i included several references in my posts in an ISCID thread on the topic, and i'll probably copy my posts from there to here.

    there are also some good references here.
    * Blood-clotting, evolution, and Behe (24 replies)
    niiicholas2002-05-17 22:00:37
    Hi,

    Following my own suggestion, here is a thread devoted to collection material/links/references relevant to blood-clotting and the claims IDists make about it.  As there is not yet a single webpage anywhere that has gathered all of the relevant material in a single place, this might as well be it.  Perhaps at some point it could be edited into a FAQ, or could inspired someone to write a FAQ (since much of the hard work of finding the references, IDist quotes, etc., would be done).

    Specifically relevant would be things like:

    1) blood-coagulation/clotting (or hemolyph coagulation for you invertebrates out there), especially e.g. webpages/literature that describe the basics in an easily understandable manner such that a FAQ reader could be referred there

    2) references to articles/lit. on the evolution of blood clotting

    3) Links to/quotes of antievolutionist assertions regarding blood-clotting, with commentary on problems if you are inspired

    4) Links to the various webpages already out there rebutting IDist claims.

    Awhile ago I did a search and dug up a pretty good starting reference list, I'll post that in a moment.

    nic

    * Invidious comparisons (49 replies)
    Wesley R. Elsberry2002-05-07 10:07:10
    Intelligent Design advocates often deploy very negative analogies concerning their critics.  Such analogies have included things like the former Soviet regime, McCarthyites, and Nazis.

    This thread is for documenting specific instances where ID advocates engage in political speech at the expense of their critics.

    I'll start things off with a recent example.

    Mark Hartwig: Compares Darwinists to Nazis

    Mark Hartwig has taken over the "Weekly Wedge Update".  In his column for May 5, 2002, Hartwig makes an analogy between "Darwinists" and the Nazi oppressors of Czechoslovakia.

    Quote
    The intimidation tactics, however, signal something important about Darwinists. That "something" was explained in an insightful little piece by one A.J. Obrdlik. Published in 1942, it was a study of "gallows humor" in Czechoslovakia during the Nazi occupation. In that article, Obrdlik made a very keen observation:

    Gallows humor is a reliable index of the morale of the oppressed whereas the reaction to it on the part of the oppressors tells a long story about the actual strength of the dictators: If they can afford to ignore it, they are strong; if they react wildly with anger, striking their victims with severe reprisals and punishment, they are not sure of themselves, no matter how much they display their might on the surface.

    With the growing success of the Wedge, I'm sure we're going to see a lot more of this stuff. But Darwinist tactics will become a lot less intimidating as people realize that they signify not strength but panic.


    * Dembski's "The Design Revoluion" (3 replies)
    Wesley R. Elsberry2004-02-27 22:13:56
    The Design Revolution: Answering the Toughest Questions About Intelligent Design

    William Dembski's new book is now available at bookstores (the link above will take you to the page at Barnes and Noble).

    Over on the ARN forum, Dembski called on "thoughtful critics" to let him know if he had overlooked any topics of criticism.

    The index of his book doesn't help much with this task. While Richard Wein's one positive comment about Dembski's "No Free Lunch" was that it had an excellent index, the same cannot be said of "The Design Revolution". Perhaps I haven't closely scrutinized every entry, but every one I have scrutinized is a person's name. I haven't found even one entry that relates to a concept (e.g., "argument from ignorance", "specification", "flagellum").

    Perhaps Dembski addresses certain criticisms without reference to the critic who raised the criticism. There are certainly critics of Dembski's arguments who are not listed in the index. It is difficult to compile a complete list, since it requires someone who knows that a certain critic has commented on Dembski's arguments and a bit of effort to confirm that the person is not listed in the index (Why, for example, is there an entry for "Thomas Aquinas" in the T's, and not "Aquinas, Thomas" in the A's? This necessitates checking a couple of different parts of the index.). Here are some of the critics who were passed over completely by Dembski:

    Chiprout, Eli
    Edis, Taner
    Eells, Ellery
    Fitelson, Branden
    Kitcher, Philip
    Matzke, Nick
    Perakh, Mark
    Pigliucci, Massimo
    Ratzsch, Del
    Rosenhouse, Jason
    Shallit, Jeff
    Shanks, Niall
    Stephenson, Christopher
    Tellgren, Erik
    Wein, Richard
    Young, Matt

    It could be argued that a few of these critics made their criticisms more recently than could be expected to appear in the manuscript for this book. For others, though, that excuse obviously does not hold. Why is there no mention of Eli Chiprout's criticisms of "The Design Inference", for example? (For that matter, why is there no mention of the critiques I made in my review of "The Design Inference"?)

    Other critics get an entry in the index, but very short shrift in the text. The list as I have it now is:

    Schneider, Tom
    Wolpert, David

    I'll likely be expanding this list as I become more familiar with the text. In the cases above, Schneider is only mentioned as an "offender" in claiming that evolutionary computation yields specified complexity, and Wolpert is only mentioned as one of the mathematicians who proved "No Free Lunch" theorems rather than in regard to his very sharp criticism of Dembski's deployment of NFL concepts.

    I may be adding my name to the list. Despite a fairly voluminous amount of material I've written in criticism of Dembski's arguments, Dembski has chosen to address only a part of one article that I co-authored with John Wilkins.

    * Advantages of theft over toil (0 replies)
    Wesley R. Elsberry2002-09-16 07:46:44
    William Dembski comments upon the paper John Wilkins and I wrote last year:

    Quote
    (1) Then why not withhold judgment in the Contact example and simply attribute a long sequence of prime numbers from outer space to unknown causes? The problem is that Wilkins and Elsberry's revised filter scotches all design inferences and not just the ones they don't like in biology. For the ID critic, the answer is not to revise the filter but to try to substitute a different picture of scientific rationality (e.g., Sober's likelihood approach). But that is deeply problematic itself.

    (2) With regard to false positives, to say that the design filter does not commit false positives if there is specified complexity remains true. And to say that an attribution of specified complexity may be mistaken is also true -- and not inconsistent with the latter claim. There's a difference between specified complexity as it subsists in nature and our knowledge of it. You might want to reread my post about what sort of property is specified complexity.  


    Thread on ISCID Brainstorms board

    Dembski is incorrect in his assertion in (1).  Our revised filter does not eliminate all design inferences.  We went to some trouble to distinguish two classes of design inferences, ordinary and rarefied.  Ordinary design inferences are still just as valid as they ever were under our revised filter.  But the revised filter makes it clear that the epistemic warrant for rarefied design inferences is an illusion based upon invalid analogy to ordinary design inferences.

    I find the point of (2) to be exactly what I've forwarded as a critique in the past, notably in my presentation at the "Interpreting Evolution" conference in 2001.  I have not been shy in saying before that Dembski's explanatory filter/design inference (EF/DI) is only reliable in the sense Dembski gives when one has complete knowledge, i.e., the true causal history is already known.  In that case, one has no need for Dembski's EF/DI -- it's entirely superfluous.  It is only in the case of limited knowledge that false positives become an issue, but these cases are also the only ones where Dembski's EF/DI could possibly have any utility.

    It's nice to have Dembski confirm that I was right in making that critique.
    * The Origins of Photosynthesis (8 replies)
    niiicholas2002-05-28 15:10:09
    I came across a new article on the evolution of photosynthesis; there are a number of articles on this topic, I will post them as I rediscover them, others may have come across interesting stuff also.

    Quote

    Reaction centres: the structure and evolution of biological solar power
    Peter Heathcote b, Paul K. Fyfe a and Michael R. Jones a
    Trends in Biochemical Sciences 2002, 27:79-87

    Abstract  



    Reaction centres are complexes of pigment and protein that convert the electromagnetic energy of sunlight into chemical potential energy. They are found in plants, algae and a variety of bacterial species, and vary greatly in their composition and complexity. New structural information has highlighted features that are common to the different types of reaction centre and has provided insights into some of the key differences between reaction centres from different sources. New ideas have also emerged on how contemporary reaction centres might have evolved and on the possible origin of the first chlorophyll–protein complexes to harness the power of sunlight.

    [...I'll quote the last part of the review to give a sense of where things are at...]

    Common structural blueprint

    The crystallographic information summarized in Fig. 4 highlights structural features that are common to all types of reaction centre [3,10,25] . At the heart of each complex is a core domain consisting of an arrangement of two sets of five transmembrane  helices. This protein scaffold encases six (bacterio)chlorin and two quinone cofactors that are arranged in two pseudosymmetric membrane-spanning branches. These cofactors catalyse the photochemical transmembrane electron transfer reaction that is the key to the photosynthetic process. Added to this basic structural blueprint are a variety of protein–cofactor structures, such as antenna complexes, the oxygen-evolving complex or Fe–S centres, which represent further adaptations. In particular, in the PSII reaction centre and all known Type I reaction centres, the core electron transfer domain is flanked by two homologous antenna domains, each consisting of a bundle of six membrane-spanning  helices binding antenna pigments [24], and antenna chlorophylls are also bound to the ten-helix core ( Fig. 4). These antenna domains are not present in purple bacteria such as Rhodobacter sphaeroides or green filamentous bacteria such as Chloroflexus.

    Which is the oldest reaction centre?

    The realization that all reaction centres are based on a common design has provoked much discussion over the evolutionary links between the different complexes and the nature of the ancestral reaction centre. This is a challenging topic because it is clear that chlorophyll-based photosynthesis is a very old process that appeared during the first few hundred million years of evolution [38]. One approach to this problem has been to examine which of the five distinct groups of photosynthetic bacteria represents the oldest photosynthetic lineage, through phylogenetic studies of both photosynthetic and non-photosynthetic proteins. However, such studies have produced conflicting results, with green filamentous bacteria, heliobacteria and purple bacteria all being identified as the oldest lineage in different studies [39–42] . The problem of tracing the evolutionary development of modern day photosystems is not helped by some of the variety and complexity exhibited by photosynthetic organisms, which indicates some interchange of photosynthetic components by lateral gene transfer between groups during the course of evolution [41,43] . At present, it is probably prudent to conclude that the use of this approach requires additional data and a more extensive analysis.

    Primordial reaction centre: Type I, Type II or both?

    Setting aside the question of which is the oldest photosynthetic organism, several models have been proposed to account for the development of modern day reaction centres from simpler ancestors [41]. Most recently, a new evolutionary scheme for contemporary reaction centres has been proposed that envisages the ancestral reaction centre as homodimeric, with the three-domain antenna–core–antenna organization seen in extant Type I complexes [37]. It is proposed that this ancestral reaction centre had two membrane-spanning electron transfer chains, each terminating in a loosely bound quinone that could dissociate when reduced and move into the membrane pool, and that it occupied a membrane that had already developed a fully functional anaerobic respiratory chain, in accordance with the 'respiration early' hypothesis [44]. Therefore, the ancestral reaction centre proposed had a mixed character, with the three-domain organization and (possibly) symmetric electron transfer characteristic of contemporary Type I reaction centres but a capacity to reduce the intramembrane quinone pool, as seen in contemporary Type II reaction centres [37].


    The future ... and the dim, distant past

    The increasingly detailed crystallographic information now available for the cyanobacterial Type I and Type II reaction centres is provoking renewed interest in the detailed mechanism of these elegant transducers of energy. In particular, the first crystallographic glimpses of the machinery for oxygen evolution are both intriguing and exciting, and will trigger much re-evaluation of our current understanding of a reaction that is of obvious importance to aerobes such as ourselves. It is also becoming apparent that a detailed understanding of quinone chemistry of the homodimeric reaction centres from heliobacteria and green sulfur bacteria might help to focus ideas about the nature of the ancestral reaction centre and the evolutionary route that has led to contemporary complexes.

    Finally, peering even further back in evolutionary time, an intriguing question that remains relatively unexplored concerns the origins of the ancestral reaction centre. What was the function of this (bacterio)chlorophyll-containing membrane protein before it evolved into a system capable of harnessing light energy? One suggestion is that early organisms used pigment–protein complexes to protect themselves against the ultraviolet (UV) radiation that bathed the surface of the planet before the development of the atmospheric ozone layer [45]. Such proteins might originally have operated by absorbing high-energy UV photons and dissipating the energy through internal conversion between the (bacterio)chlorophyll Soret absorbance transition and the visible-region absorbance bands, before emitting the energy as a much more benign visible or near-infrared photon [45]. Light-activated electron transfer might originally have developed as an extension to this photoprotective function, excited state energy being converted first into the energy of a charge separated state (similar to the P870+HA- state formed in the purple bacterial reaction centre) and subsequently lost as heat as the charge-separated state recombines (as occurs in purple bacterial reaction centres when forward electron transfer from HA- is blocked). Another suggestion is that photosynthetic function evolved from bacteriochlorophyll-containing proteins involved in infrared thermotaxis [46]. Whatever the truth, addressing these questions requires a journey back to an early stage in the evolution of life, and presents a fascinating challenge.


    [37] Baymann F. et al. (2001) Daddy, where did PS(I) come from?
    Biochim. Biophys. Acta, 1507:291-310. MEDLINE Cited by

    [38] Nisbet E.G. and Sleep N.H. (2001) The habitat and nature of early life.
    Nature, 409:1083-1091. Cited by

    [39] Olsen G.J. et al. (1994) The winds of (evolutionary) change: breathing new life into microbiology.
    J. Bacteriol., 176:1-6. MEDLINE Cited by

    [40] Gupta R.S. et al. (1999) Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis.
    Mol. Microbiol., 32:893-906. MEDLINE Cited by

    [41] Xiong J. et al. (1998) Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis.
    Proc. Natl. Acad. Sci. U. S. A., 95:14851-14856. Full text MEDLINE Cited by

    [42] Xiong J. et al. (2000) Molecular evidence for the early evolution of photosynthesis.
    Science, 289:1724-1730. Full text MEDLINE Cited by

    [43] Blankenship R.E. (2001) Molecular evidence for the evolution of photosynthesis.
    Trends Plant Sci., 6:4-6. Full text Cited by

    [44] Castresana J. et al. (1994) Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.
    EMBO J., 13:2516-2525. MEDLINE Cited by

    [45] Mulkidjanian A.Y. and Junge W. (1997) On the origin of photosynthesis as inferred from sequence analysis.
    Photosynth. Res., 51:27-42.

    [46] Nisbet E.G. et al. (1995) Origins of photosynthesis.
    Nature, 373:479-480.
    * Truth in Advertising (1 replies)
    VoxRat2003-01-22 17:01:31
    Doing a little idle bottom-feeding, I ran across this gem from Jonathan Wells' iconsofevolution.com website:

    "Dr. Wells's work in developmental biology poses a serious challenge to the neo-Darwinian idea that random mutations can create new body plans and organisms. "

    Anyone know of any conceivable basis for this rather bold claim?

    :0 VR
    * Phil Johnson (0 replies)
    niiicholas2002-05-29 23:30:40
    Hi,

    This would seem to be as good a place as any to collect links/references to things like Johnson's

    - works
    - reviews of his works
    - interviews
    - online talks

    ...etc.  I think there is already at least one fairly comprehensive PJ links page on the web so maybe we could just 'high-grade' particularly interesting things here.

    E.g., I started this thread because I just heard about this link:

    Berkeley’s Radical
    An Interview with Phillip E. Johnson


    Johnson bares his soul & gives quite a detailed history of his own 'evolution'.

    Quote

    You have said there is no natural explanation for the rise of genetic information. How important is that question in the debate?

    PJ: The Wedge of Truth is all about those issues. The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism. They’ll start out talking about the peppered moth, and when that self-destructs, then they’ll say, "Oh, self-organizing systems, or the fourth law of thermodynamics," and other nonsense, which is just covering up ignorance.

    Genetic information is the issue, but it isn’t the final issue. After you make that breakthrough, then you see other ways in which the theory is questionable. Darwinists will say, "Oh, well, maybe the mechanism has some problems, but the "fact of evolution"—common ancestry—is not in question. We distinguish the fact of evolution from the mechanism of evolution."

    But that’s a bogus distinction because the "fact"—common ancestry—incorporates the mechanism. It’s just a matter of "now you see it, now you don’t." They are saying the mechanism by which a father and mother give birth to children is the same mechanism by which our "bacterial ancestors" gave birth to human beings. They say it’s all a process of natural reproduction and naturally occurring variation in the offspring.

    Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations do not create evolution in any significant sense. Instead, they make birth defects, so the whole thing is false from the get-go. There is no way you can establish that a bacterium is the parent of a complex animal. There is no mechanism to make the change, no historical or fossil evidence that such a change ever occurred, and there’s no way to duplicate the process in a lab.

    Once you get that in the debate, then we will be poised for a metaphysical and intellectual reversal that is every bit as profound as the one with Copernicus. People will say, "My gosh, we’ve been completely misled by this fundamental truth of the creation story of our culture. We can no longer understand the world that way."

    How do you change the way people regard the authority of science? Get them to think of it as a much more limited thing. Science is very reliable when scientists stick to the kinds of things that can be tested by refutable experiments, but much of what they tell us is outside that. When they have to fake the mechanisms, it becomes a very dubious philosophy. That raises the question of why so many very brilliant people were misled for so long and did such a good job of rationalizing these things.

    When the mechanism of Darwinism becomes discredited, it’s like a train that’s been turned around. You can say, "Well, that’s interesting, but the train is still in the same place. The world, Yale, Berkeley, are still there. The New York Times is still telling us what to think. So why isn’t everything different?" Well, it is different, but you can’t see it yet. The train is turned in the opposite direction. It’s going to start out very slowly, but it’s moving on the logical tracks towards something very different, and when we get there, our great-great-grand-children will see how different things are.


    Not a man with small goals, PJ.

    Note also the "scientific key" to the whole ID argument (according to Johnson): "No natural processes create genetic information."  Hmm.  I think I'll start a thread.

    nic
    * The Dean Kenyon Story (2 replies)
    Tom Ames2003-06-03 02:18:36
    The Dean Kenyon Story
    How an ID perspective ruined my career

    Dean Kenyon is an interesting fellow. In 1969 he wrote a book on then-current origin-of-life theories, in which he advanced the hypothesis that primordial proteins may have arisen because of the intrinsic self-assembly properties of amino acids. The book, "Biochemical Predestination", is moderately well cited in the relevant literature during the early 70s (peaks of 13 citations in '72 and '75), but drops off quickly thereafter.

    Kenyon's publications drop off quickly too: he published NOTHING of a scientific nature after 1975.

    The recent ID propoganda piece "Unlocking the Mysteries of Life" tells the story this way: in 1975, Kenyon was faced with a dilemma. His theory of a primordial protein world, if true, would not account for how protein sequence information could have ended up in an unrelated molecule, i.e., in DNA. Kenyon realized that his theory was fatally flawed. His response to this realization? To decide that "ID did it", and to literally give up on the project. On all projects, in fact. (Although Kenyon did go on to co-author "Of Pandas and People").

    [Side note: at around this time, Thomas Cech was developing the system that would lead to the discovery of ribozymes -- molecules that could simultaneously catalyze chemical reactions and code for their own primary structure. The implications of this led to the RNA-world hypotheses for the origin of life. Cech won the Nobel Prize.]

    This story should be pointed out to the scientific wannabes (Mike Gene, are you there?) who claim that an ID perspective is useful to expand the creative direction of a research program.

    Does anyone else have anecdotal correlations between a scientist's explicit adoption of an ID stance and the drying up of his productivity? Please share!
    * David Berlinski (1 replies)
    Glenn Branch2002-12-09 18:37:52
    David Berlinski published "Has Darwin Met His Match?" in the December 2002 issue of Commentary (vol. 114, no. 5, pp. 31-41). Here Berlinski, a Senior Fellow of the Discovery Institute's Center for Science and Culture, chastizes not only "Darwinians" but "design theorists" for accepting theories that are empirically vacuous:
    Quote
    ...Darwinian theorists may be observed standing in silence. They are looking upward, apparently much occupied in assessing cracks in the ceiling. Beyond saying that that is just the way things are, what could they say? ... Design theorists may now be observed standing in companionable silence alongside Darwinian biologists. They, too, seem to be gazing upward, studying the same queer little cracks in the ceiling.

    (From p. 33.) A fascinating, if florid, article. I rushed out and bought a copy of his Black Mischief: Language, Life, Logic, Luck (second edition, Boston: Harcourt Brace Jovanovich, 1988) for purposes of comparison. If anyone wants to talk about Berlinski, here's a thread.
    * William A. Dembski (2 replies)
    Wesley R. Elsberry2002-05-07 02:24:06
    My page on William A. Dembski.  This links to his own pages and essays, and also to critical views of his ideas.

    Please use this thread for pointing out new essays, books, criticism, and news concerning William Dembski.
    * Richard von Sternberg and Antievolution (1 replies)
    Wesley R. Elsberry2005-02-06 06:59:48
    Richard von Sternberg has this to say about his own stance on antievolutionary issues:

    Quote

    Although it is irritating to have to respond to ad hominem arguments rather than arguments on the issues, I will state for the record that I do not accept the claims of young-earth creationism. Rather, I am a process structuralist.

    (Ref: Sternberg's home page)


    This is a remarkably unhelpful statement. There are lots of ways of being an antievolutionist and creationist; young-earth creationist is just one, and "process structuralism" doesn't do much in the way of refining where Sternberg's personal views lie.

    Under a linked article outlining "process structuralism", Sternberg offers some further information on his personal viewpoint.

    Quote

    I subscribe to a school of biological thought often termed “process structuralism.” Process or biological structuralism is concerned with understanding the formal, generative rules underlying organic forms, and focuses on the system architectures of organisms and their interrelationships. Structuralist analysis is generally ahistorical, systems-oriented, and non-evolutionary (not anti-evolutionary). Both creationism and neo-Darwinism are, in contrast, emphatically historicist with one positing extreme polyphyly (de novo creation of species) and the other radical monophyly (common descent). Since the structuralist perspective runs somewhat perpendicular to the origins debate, creationists and evolutionists tend to see it as inimical to their positions. The truth is structuralism has little at stake in the origins issue, leaving a person like myself free to dialogue with all parties. For this reason, I frequently discourse with ultra-Darwinians, macromutationists, self-organization theorists, complexity theorists, intelligent design advocates, theistic evolutionists, and young-earth creationists without necessarily agreeing with any of their views.

    Structuralism does, however, provide an important perspective on the origins debate. Structuralists' lack of commitment to an historical theory of biology allows them to explore the historical evidence more objectively. Moreover, because they focus on formal analysis, struturalists are far more open than neo-Darwinians to the powerful evidence for continuity within species (forms) and discontinuity between and among species. They also allow themselves to wonder about the cause of the amazing repetition of forms across the biological world rather than being forced by prior commitments to accept a major neo-Darwinian epicycle known as "convergent evolution."

    (Ref: Sternberg's page on process structuralism)


    Process structuralism is an anti-Darwinian view, though not necessarily antievolutionary. The second paragraph of Sternberg's prose briefly notes, though, that Sternberg's process structuralism is "open" to common descent being false.

    Sternberg says in the above that he has discourse with people of various viewpoints, both evolutionary and anti-evolutionary. What I am interested in, though, is what Sternberg's actions tell us rather than simply relying on Sternberg's words.

    This thread is for gathering together information on what Sternberg has done that bears upon antievolution. People have limited time and energy to spend during their lives, and how they choose to spend it tells you something about them that is far more informative than the content of what they might say about themselves. For example, I received email from someone saying that Jonathan Wells had advocated Darwinian evolution and common descent earlier in his career. I asked for some documentation or references to where I could see this advocacy for myself and my correspondent stopped corresponding. In Wells's case, his current antievolutionary advocacy is easy to find and his earlier alleged advocacy of evolutionary biology is apparently difficult or impossible to find.
    * Transport systems: evolutionary origin (2 replies)
    niiicholas2003-06-04 00:21:20
    Came across some refs on transport systems and even some discussions of evolutionary origins:

    Quote

    Biochim Biophys Acta 1999 Feb 25;1422(1):1-56

    Phylogenetic characterization of novel transport protein families revealed by genome analyses.

    Saier MH Jr, Eng BH, Fard S, Garg J, Haggerty DA, Hutchinson WJ, Jack DL, Lai EC, Liu HJ, Nusinew DP, Omar AM, Pao SS, Paulsen IT, Quan JA, Sliwinski M, Tseng TT, Wachi S, Young GB.

    Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA. msaier@ucsd.edu

    As a result of recent genome sequencing projects as well as detailed biochemical, molecular genetic and physiological experimentation on representative transport proteins, we have come to realize that all organisms possess an extensive but limited array of transport protein types that allow the uptake of nutrients and excretion of toxic substances. These proteins fall into phylogenetic families that presumably reflect their evolutionary histories. Some of these families are restricted to a single phylogenetic group of organisms and may have arisen recently in evolutionary time while others are found ubiquitously and may be ancient. In this study we conduct systematic phylogenetic analyses of 26 families of transport systems that either had not been characterized previously or were in need of updating. Among the families analyzed are some that are bacterial-specific, others that are eukaryotic-specific, and others that are ubiquitous. They can function by either a channel-type or a carrier-type mechanism, and in the latter case, they are frequently energized by coupling solute transport to the flux of an ion down its electrochemical gradient. We tabulate the currently sequenced members of the 26 families analyzed, describe the properties of these families, and present partial multiple alignments, signature sequences and phylogenetic trees for them all.



    This review of a proceedings volume mentions:

    Quote

    Review
    Transport of molecules across microbial membranes
    http://www.socgenmicrobiol.org.uk/QUA/020014.pdf
    SGM Symposium
    Volume 58

    The book ends with a stimulating chapter from Saier &Tseng on the evolutionary origins of transport systems, withseveral surprises about the likely evolutionary origin andfrequency of `genesis' of permease families, topologicalconstraints operating in membrane transporters, and mosaicand modular construction. This topic ­ how it all started, howit may have evolved and how it may evolve in future ­ is afitting terminal chapter to the symposium volume.


    Here is the full ref:

    Saier, M.H. Jr. and Tseng, T.T. 1999. Evolutionary origins of transmembrane transport systems; in Transport of Molecules Across Microbial Membranes. Symposium 58. Society for General Microbiology. Broome-Smith, J.K., Baumberg S., Stirling C.J. and Ward F.B. (eds.). Cambridge, Cambridge University Press, pp. 252-274.

    The introduction to the volume is freely available online here as a sample chapter:

    http://assets.cambridge.org/0521772702/sample/0521772702WSC00.PDF
    * Evolution of eukaryotic cilia/flagella (5 replies)
    niiicholas2002-11-28 23:11:25
    Similar to the prokaryotic flagella thread.

    Introductory material:

    http://www.wikipedia.org/wiki/Flagellum
    (don't confuse eukaryotic cilia/flagella with prokaryotic flagella)


    http://www.wikipedia.org/wiki/Evolution_of_flagella


    Here we have the interesting sideshow of Margulis' and fans' hypothesis that the cilium is derived from a spirochete.  For many critical comments on this see:

    Cavalier-Smith T. Int J Syst Evol Microbiol 2002 Mar;52(Pt 2):297-354
     
    The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.