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Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: April 01 2006,04:52   

Let's recap:
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(Avo: ) Well, a lot of people are not satisfied to simply decide to believe in evolution because the evidence that paleontolgoy points to is unacceptable.
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(me: )Who are those people? Specifically. Are they the ones who have seriously studied the evidence, or are they the usual gang of creationists precommitted to rejecting evolution?
Actually, I'm looking for specific names and references. It's my observation that when you try to nail down creationist rhetoric to specifics, in fact it never gets more specific ...
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(Avo: )Are you saying that I couldn't come up with a list if I were willing to spend the time on your homework assignment? Are you saying I couldn't come up with names and references of people who find problems with paleontology and other aspects of NDE?
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(me: )That's  exactly what I'm saying.
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(Avo: ) Obviously the most famous paleontologist with a problem is Gould. Not that he gave up on evolution, but he definitely saw a problem with the data.

Right. Gould. Just as I expected, someone with issues having nothing to do with yours.

I see a pattern here. You believe what you believe; facts, evidence, the fruits of millions of person-hours of research - they are made to fit your preconceptions. Some are ignored, some are "mis-remembered". Lee Spetner, "Mike Gene", Behe (and I'm guessing Dembski, Wells and the rest of the DI's propagandists?) - their word need not be questioned. And to back up their skepticism, there's this ghost army of Darwin-doubting paleontologists that exist in your mind. When pressed, and pressed, and pressed again for any specific examples, you offer up... Stephen Jay Gould!

And you're not interested in petty bickering, but you accuse me of being only interested in "tossing insults" - without being able to identify one.

'nuff said.

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Must... not... scratch... mosquito bite.

  
Jay Ray



Posts: 92
Joined: Feb. 2006

(Permalink) Posted: April 01 2006,16:04   

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...we are not having the discussion I thought we were having.


What discussion do you think we were having?  Here all this time I thought we were trying to establish the relevance of theology (or just plain god) to biology.  I've never hidden the fact that I am an atheist.  What is so different about this latest post of mine that invalidates our entire communication?

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The whole thing became meaningless since we were not in the same discussion.


I sense the cold shoulder.  Sigh.  Such is the lot of an atheist.   Anyway, have a good one. :)

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: April 01 2006,16:45   

Well you know Russell, you can twist things how you like. You ignored the part where I said I once had a list. That was some months ago. The list might not be as big as you'd like. I recall about 5 names. But when I said a lot of people, I didn't mean only actual paleontoloists.

I make a statement about how evolution skeptics react to paleontology, and suddenly I am discredited because I am not willing to look up names for you. It would no doubt take a while. Or maybe not. You ask for details on why I doubt evolution, but when I provide them I get little comment.

And I don't know why you say Gould's issues have nothing to do with mine. I haven't read his books, but I have read some excerpts.

Jay Ray,

I don't actually recall you saying you were an atheist, but that is fine with me. No cold shoulder. My husband is or was an atheist. Now he says he is an agnostic, and I'm not cold to him at all.   ;)    Furthermore, I actually respect him as a fairly spiritually advanced person. See, in my weird view of things, one's professed beliefs or lack thereof has only a little to do with one's spiritual life.  
I didn't get the sense from our discussions though, that your sum assessment of theology is that God is a figment of the imagination. I mean, in that case, what is there to say? At any rate, it caused a misunderstanding.

But I am intrigued by your hope for an afterlife. Can you elaborate?

  
Jay Ray



Posts: 92
Joined: Feb. 2006

(Permalink) Posted: April 01 2006,17:14   

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I don't actually recall you saying you were an atheist, but that is fine with me.


I guess I never came out and used that label.  I don't like labels.  Too confining.  But I have said many times I have seen no compelling evidence for an eternal, external, concious creative intelligence.  At one point, I even said I'd be tickled pink if it turned out there was one.  The gist being, I don't believe it, but hey, if it turns out there is one I'm willing to hear the guy out.

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But I am intrigued by your hope for an afterlife. Can you elaborate?


Well, let me put it as simply as I can.

At this point, I want to live indefinately.  I'm not in any way satisfied with the length of the human lifespan.  I want my personality to continue on for as long as I want it to.  That could be forever, that could be some amount less.  So I'm not so much concerned about an afterlife as I am extending the one I am living right now.

I'd settle for an afterlife of some sort, so long as its *me* doing the afterliving.  However, I'm not at all persuaded by typical theological propositions for this.  It's wishful thinking with no evidence whatsoever for their claims.  If it turns out I'm wrong and there is an afterlife where my personality lives on, I'm willing to listen to the organizers or controllers or managers of the thing.  It could be a good time.

But back down here on reality-based earth, I realize that I will die, that my body will decompose into its constituent parts, and that those parts will be taken up into later generations of life.  I suppose in a wiggly sort of way this is immortality.  But the whole that is *me* will necessarily end when my body dies.  I accept this fact.  Doesn't mean I have to like it. :)

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: April 02 2006,04:28   

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You ignored the part where I said I once had a list
Rather than be accused of "tossing insults", I'll just repeat this. I think it speaks for itself.
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But when I said a lot of people, I didn't mean only actual paleontoloists.
That's true. You said:
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Well, a lot of people are not satisfied to simply decide to believe in evolution because the evidence that paleontolgoy points to is unacceptable
So I'm challenging you to name some of them. I want to see whether there's any reason to believe any of them understand the paleontology they question.

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And I don't know why you say Gould's issues have nothing to do with mine. I haven't read his books,
Hmmm. That is  a dilemma. Hey! I've got an idea! Why don't you read one or two of them?  
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but I have read some excerpts.
Yeah. So have I. Excerpted by scrupulous scholars, like our friends at Answers in Genesis, or the Discovery Institute. Are you familiar with the term "quote-mining"?

Let's cut to the chase. Your whole issue is that the evidence - paleontological, molecular, whatever - leads serious students of the field to the conclusion that life on earth requires intelligent input, right?  There's no doubt where Gould stood on that issue, and it wasn't with you. If you want to discuss the timing and dynamics by which "random mutation and natural selection" happened, then Gould's your man.

But that's not the point, is it?

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Must... not... scratch... mosquito bite.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: April 02 2006,06:39   

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You ask for details on why I doubt evolution, but when I provide them I get little comment.
"Providing details" has to amount to more than "I once had a list of authors I haven't read who have been quote-mined by creationists" or "it seems improbable to me - and to Behe, too!" Was there something more substantive than that that I missed?

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Must... not... scratch... mosquito bite.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: April 02 2006,12:41   

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But as we know, the chances of repeating any sequence is very low, and yet is 100% guaranteed to unfold randomly. But the pattern to the throwing of dice is meaningless and incapable of accomplishing anything, so far as we can see. So I don't think the two are comparable at all. No matter how many times we run the lottery, there isn't any importance to who wins in what order. It doesn't build anything.

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I don't know about Dembski, but it is hard to see how this idea of pruning could work to create billions of highly ordered and complex systems, or IC systems in which it is very hard to see how many small steps could have each been selected as positive when it does not appear that each one could have been positive. You know the Dawkins experiment about "Methinks it is like a weasel"? There are some good arguments against it.  

I did say it wasnt a good analogy, I havent heard any decent analogy describing biological evolution. I think IC is a different argument from probability, Im not trying to argue that an entire protein or set of proteins will from form random sequences or anything like that, so I am inferring that there is some kind of path. Thinking about it perhaps the probabilistic arguments are irrelevant, if the flagellum had to evolve by entirely new proteins evolving spontaneously from hundreds of simeltaneous mutations in random sequence, that IDists would have a good argument, although I dont think any biologist is claiming that. On the other hand if it could have formed by succesive mutations, then the population size and mutation rate of E.coli mean "search space" or whatever people are calling it these days is explored fairly quickly. I will have a look through NFL again and remind myself exactly how Dembski calculates his probability.

The weasel program was meant to demonstrate cumulative selection not evolution.

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But the more we find out about biology, the more a designer hypothesis seems the less improbable of the two.
Why? I read several evolutionary biology papers a week and I think the exact opposite. I don't even think that biological systems have the 'appearence' of design. Just because Im a scientist doesn't mean Im right of course but I certainly haven't heard a designer hypothesis that explains the evidence better than current evolutionary theory.

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Maybe not active interference, but it certainly ups the likelihood of the pre-existence of consciousness.
This may be an irreconcilable philosophical difference, sufficed to say any of the laws I described would not be any more proof of this consiouness to me than if they did not exist. Having said that I am perfectly willing to accept the existence of a god, but I would still need scientific evidence of his involvement in evolution.

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So all those are nonrandom? So the ability to intelligently and purposefully turn on mutation events evolved randomly?
I had this problem over at UD, the best way to look at it is that random means that the organism does not know which mutations will increase fitness.

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It cannot be retraced I guess, but there needs to be plausible ideas for how these systems could have evolved.
Presumably you mean that we need an evolutionary path for every single system for it to be scientifically acceptable to infer that it did evolve?

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At one point I kept a list of paleontologists who tried to find some kind of saltation theory that could somehow coincide with a belief in evolution.
I would say that modern evolutionary theory certainly does not rule it out.

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As to flaws. Homology.
Why is that a flaw, have I missed something?

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I'm pretty sure I already linked to an essay by Frank Tipler about the problems with the peer review process, how it enforces orthodoxy, and resists innovation.
This may be true in some cases, but in many cases journals are so eager to publish innovative 'against the grain' work that big name journals can end up publishing bad papers.

EDIT: And no Im not referring to Strenberg or any other 'ID' paper.

  
GCT



Posts: 1001
Joined: Aug. 2005

(Permalink) Posted: April 03 2006,01:41   

Quote (avocationist @ Mar. 31 2006,11:43)
GCT,

I acquiesce to all your accusations. But I am curious. What is your gender?

I'm not sure why that would be important, but my gender is "Mike Gene."  Just messing with you.  I'm male.

Hey, thanks for playing.  I'm glad that we could come to a solution about how ID is not only not science, but also religious apologetics.

  
Seven Popes



Posts: 190
Joined: Mar. 2006

(Permalink) Posted: April 03 2006,02:48   

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You ignored the part where I said I once had a list. That was some months ago. The list might not be as big as you'd like. I recall about 5 names.

A list of 57 names:
My list

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Cave ab homine unius libri - Beware of anyone who has just one book.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: April 03 2006,03:28   

Regarding probability arguments and the evolution of systems, it is also probably worth pointing out that short random sequences being bound by a transcription factor, and random rearrangement of short protein domains resulting in novel protein interactions is a fairly common phenomenon (evolutionarily speaking). I suspect that this gives evolution a lot to play with, although I imagine there's some very good reason why it doesn't count as generating specified complexity.

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: April 04 2006,20:32   

Russell, you said:

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Now, apologies for sending what looks like a "form letter" to all our anti-evo friends, but I contend  that their arguments always founder when you demand specifics: specific quotes, specific numbers, specific data...

If you let them get away with "it's common knowledge that..." or "Darwinists always claim that...",  it never ends.

Works for Shi, works for Avo, even works for Thordaddy. (Oh, sure, Thor keeps coming back for more, but you'll notice he never follows up - he just changes the subject.)


And all this because I pointed out that a lot of people are disturbed by the problems in paleontolgoy, more perhaps than anything else. And you've gone from wanting a list of paleontologists, to just a list of said people. But I have authors here in my bookcaase that discuss problems with paleontology. What is so special about this "detail" other than avoiding the details that I have brought up to discuss - such as why do you and others here think that Miller ever really refuted anything that Behe said about the flagellum in his paper the Flagellum Unspun, and what is your reaction to the very specific details that Mike Gene brings out in the assembly and function of the flagellum? But no, you think you've got brownie points for asking me to come up with names of people who have a problem with paleontology.

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Are you familiar with the term "quote-mining"?
Yes. I am familiar with quoting out of context. A big sin in my book. So what is quote mining?
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Let's cut to the chase. Your whole issue is that the evidence - paleontological, molecular, whatever - leads serious students of the field to the conclusion that life on earth requires intelligent input, right?
Yes, or at least that current theory is inadequate to the extent that when the real facts become known (if ever) that it will be fundamentally altered.
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There's no doubt where Gould stood on that issue, and it wasn't with you.
But it doesn't matter. Unless the items are quoted out of context so that they convey a different meaning than the author intended, there is nothing wrong with noting the sheer magnitude of of admitted problems in evolution. That said authors adhere steadfastly to evolution adds to the human interest.

Jay Ray,

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At this point, I want to live indefinately. I'm not in any way satisfied with the length of the human lifespan.
It's absolutely unacceptable.
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I want my personality to continue on for as long as I want it to.
Agreed. I applaud your honesty.

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That could be forever, that could be some amount less.  So I'm not so much concerned about an afterlife as I am extending the one I am living right now.
May I suggest you become an alchemist?

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I'd settle for an afterlife of some sort, so long as its *me* doing the afterliving.
That's a bit tricky. The question is, who are you?

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However, I'm not at all persuaded by typical theological propositions for this.  It's wishful thinking with no evidence whatsoever for their claims.
Some of it  is wishful thinking, and most of what people consider the "me" of them, their personality, is an encumbrance and a barrier. But one does want one's consciousness. I think there is evidence for these things, but it is not accepted by some people. However, the evidence seems to be accumulating. We are living in interesting times.

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If it turns out I'm wrong and there is an afterlife where my personality lives on, I'm willing to listen to the organizers or controllers or managers of the thing.  It could be a good time.
But the reason I asked is that atheism doesn't usually mix with hopes for an afterlife.

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But back down here on reality-based earth, I realize that I will die, that my body will decompose into its constituent parts, and that those parts will be taken up into later generations of life.  I suppose in a wiggly sort of way this is immortality.
Notvery satisfying, is it?

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But the whole that is *me* will necessarily end when my body dies.  I accept this fact.
May be only the body dies.

Anyway, the answers to these questions has been my quest.

  
Jay Ray



Posts: 92
Joined: Feb. 2006

(Permalink) Posted: April 05 2006,01:50   

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May I suggest you become an alchemist?


I remember Newton and some of those wacky taoists became sidetracked down the red herring called alchemy.  This should come as no surprise in modern times.  Anytime we've tried to combine mysticism with science, its failed.  Gee, I wonder why that could be....

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That's a bit tricky. The question is, who are you?


I'm familiar and comfortable with the idea that this thing called "me" is an illusion.  What I am really is just a wave in the ocean we know as the universe.  Every wave eventually crashes against the shore, whereupon it takes another form.  I'm cool with that.

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But one does want one's consciousness.


I do.  How cool would it be to be a wave that rolls up onto the shore and manages to keep on going, maneuvering at will?  It won't happen, but it would be preferable.

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I think there is evidence for these things, but it is not accepted by some people. However, the evidence seems to be accumulating.


I'd be one of those that wants evidence beyond what can be provided by anecdote.  Channeling doesn't count.  Regression hypnosis doesn't count.  Near death experiences don't count.  In the end, no matter how many of these stories accumulate, they are still all just stories.  

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We are living in interesting times.


Every moment is interesting, don't you think?

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But the reason I asked is that atheism doesn't usually mix with hopes for an afterlife.


I think you misunderstand many atheists.  Atheism isn't necessarily a rejection of god or other mystical tenets.  Rather, it is disbelief in the reality of these things for lack of credible evidence.  We withhold judgement until the facts are in.  Many of us would welcome these things if they were demonstrated.  But so far, the the so-called evidence is anecdotal, vague, contradictory and entirely unpersuasive.  "Extraordinary claims require extraordinary evidence."  

Deep down, I tend to think that god doesn't exist, in just the same way that I don't believe in the invisible Sock Gnome who lives in my laundry room and steals my socks from time to time.  Or that I can make a red light turn green through an act of focused willpower.  Or that spellcasting is possible.  But I'd be fascinated if these or a million other magical things were true.  Its just that they aren't.

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But back down here on reality-based earth, I realize that I will die, that my body will decompose into its constituent parts, and that those parts will be taken up into later generations of life.  I suppose in a wiggly sort of way this is immortality.
Notvery satisfying, is it?


Nope.  Yet I'm glad I have the opportunity to experience it for at least a little while.

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May be only the body dies.

Anyway, the answers to these questions has been my quest.


The way I see it, if there is an afterlife I'll find out soon enough.  Meanwhile, I find there are plenty of amazing things going on in the sensible parts of the universe to occupy my attention.  To spend my time in distracting myself with unanswerables takes away my ability to be in the now.  It could be that there are gods and an afterlife.  I doubt it, but hey, maybe the Sock Gnome is real.  However, I see no benefit to myself or to any other life on this dazzling planet if I continually strive for that which is always out of reach of the living.  What counts is right here and now.  The afterlife will take care of itself.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: April 05 2006,03:07   

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Quote  
But back down here on reality-based earth, I realize that I will die, that my body will decompose into its constituent parts, and that those parts will be taken up into later generations of life.  I suppose in a wiggly sort of way this is immortality.

Not very satisfying, is it?

I find it quite comforting, and have done ever since I was a child and used to sit in the garden: imagining bits of myself pushing up through the grass as trees and crawling around as insects. The fact that people seek more still puzzles me, and seems to be one of the main reasons in my experience that people are religious other than tradition.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: April 05 2006,08:56   

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And all this (pointing out that creationist arguments always founder when you insist on specifics) because I pointed out that a lot of people are disturbed by the problems in paleontolgoy, more perhaps than anything else.
Why, no. You seem to have jumped to that conclusion because that happens to be the most recent request I made for you to substantiate your claims. Seems to me we've gone through a few cycles of your assertions turning out to be baseless when you really get down to the details. Starting with your claims about what Dawkins wrote.
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And you've gone from wanting a list of paleontologists, to just a list of said people.
And here I thought I was doing you a favor; I thought it was you that wanted to expand the scope from Official Paleontologists to scholars of any description who could read the paleontology literature sensibly. Hey, either way is fine with me!
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But I have authors here in my bookcaase that discuss problems with paleontology.
Do you! Who are they?
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What is so special about this "detail"
Nothing at all. That's my point. Every one of your arguments, when you get down to the details, founders.

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...avoiding the details that I have brought up to discuss - such as why do you and others here think that Miller ever really refuted anything that Behe said about the flagellum in his paper the Flagellum Unspun
What details? I believe I pointed out that Behe never made any claims beyond "seems improbable to me" that even could be refuted.
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and what is your reaction to the very specific details that Mike Gene brings out in the assembly and function of the flagellum?
I believe you will find the answer to that if you go back over this thread. But just to summarize: my reaction is "Biological systems are, indeed, complex. Really complex. Really, really complex. But no amount of documenting how really, really, really complex they are gets us any closer to 'couldn't have evolved'". Now, if there's anything that you feel "Mike Gene" wrote that actually argues "couldn't have evolved" - as opposed to "is really complex" - that I failed to address, please: point it out. I certainly don't want to pass up any opportunity to pursue these things right down to the specifics.
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But no, you think you've got brownie points for asking me to come up with names of people who have a problem with paleontology.
Hey, I can take or leave  "brownie points". But it is passing strange how much effort you've expended on explaining your not providing these references, because providing them would just be too much effort.

Here's the thing. And correct me if I'm wrong about any assumptions. When you said:
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Well, a lot of people are not satisfied to simply decide to believe in evolution because the evidence that paleontolgoy points to is unacceptable.
I assumed that you meant that "a lot of people" had concluded from an informed analysis of paleontological data that the basic idea of "evolution" was fundamentally inadequate - that the idea that species evolved from pre-existing species as a result of random genetic change and selection was incompatible with the bones and fossils.

Well, "a lot of people" turns out to be five. On a list you lost. And the only one of them you've supplied a name for is Stephen Jay Gould, whom you have only read as quote(mine)d by creationists. And his issues have nothing to do with those I assumed you were suggesting.

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Must... not... scratch... mosquito bite.

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: April 06 2006,06:44   

Chris,

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The weasel program was meant to demonstrate cumulative selection not evolution.
Yes, but without deciding the end result at the beginning, blind forces might never get there.

The whole question of search space is an interesting one, because we may not really know the factors that would help to narrow down the search. When certain evolution detractors have put forth what would appear to be the search space, the possibility of a solution to this or that problem is often quite out of reach, no matter how many e coli you have working for you. Problem is, organizing factors or emergent properties all seem to change the nature of our universe. They all seem to require some fundamental intelligence.

Why do you read several evolutionary papers per week?

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This may be an irreconcilable philosophical difference, sufficed to say any of the laws I described would not be any more proof of this consiouness to me than if they did not exist. Having said that I am perfectly willing to accept the existence of a god, but I would still need scientific evidence of his involvement in evolution.
Are you familiar with cosmic fine tuning? It's not just a few laws here and there. They say, for example, that the amount of matter in the universe is within one billionth of what it needs to be in order to have a stable universe. That is, the parameters are that narrow. Nature's Destiny by Denton does a good job of explaining a wide array of them.

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Having said that I am perfectly willing to accept the existence of a god, but I would still need scientific evidence of his involvement in evolution.
There is no way for God to be omnipotent or omniscient unless God is actually everywhere, and in everything. I think of evolution as an inside job, not one of an external being. It seems to me the evidence is fairly strong that random processes didn't cause this universe, or its laws, or its existence in the first place. What do you think of the information based arguments for ID?

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I had this problem over at UD, the best way to look at it is that random means that the organism does not know which mutations will increase fitness.
It's too bad you guys over there have different names and I am clueless what's going on. It may be that the organism turns on a mutation feature, and in a specific area of the genome, and then suddenly gets the mutation for digesting nylon. For me, that's just too good to be true but we must also account for the organism's ability to direct itself like that in the first place.

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Presumably you mean that we need an evolutionary path for every single system for it to be scientifically acceptable to infer that it did evolve?
I don't think so. Behe complains that there are none in the literature that are really any good. If we had a couple of quite good and plausible routes for some very complex systems to evolve, then the pressure would be off. It wouldn't matter that we couldn't explain each one.
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I would say that modern evolutionary theory certainly does not rule it out.
Saltation?

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(homology flaw)  Why is that a flaw, have I missed something?

I'm referring to the problem that homologous organs often do not arise from the same genes, and that during development, they are often grown from different body segments or in a different order or from a different group of cells. Animal forelimbs develop from different body segments. Homology is difficult because many or most genes control widely divergent body parts. The eye color of drosphila is controlled by a gene th also controls female sex organs. Mouse coat color and mouse size are on the same gene. Chickens are subject to a detrimental mutation in a single gene that causes a wide array of malformations, some of which are unique to birds and others which are shared by other vertebrates.

No only do homologous structures in closely related species arise from different genes, but nonhomologous structures can arise from the same gene.
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This may be true in some cases, but in many cases journals are so eager to publish innovative 'against the grain' work that big name journals can end up publishing bad papers.
I suspect that this greatly depends on just which grains are being rubbed.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: April 06 2006,06:53   

You appear to have responded to some of my points in the gay gene thread:

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Problem is, organizing factors or emergent properties all seem to change the nature of our universe. They all seem to require some fundamental intelligence.
Why?

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Why do you read several evolutionary papers per week?
I am a biologist, I have to read papers. In October I came back of a two week holiday to find something I had been working on for months had been published by someone else, the field moves pretty fast. My works involves the study of complex biological systems, understanding how they evolved is vital for properly analysing them. Plus after reading several arguments by creationists when I first heard this debate, I decided my knowledge of evolutionary biology was lacking. Unlike creationists, I rectify this by reading evolutionar biology papers.

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Are you familiar with cosmic fine tuning?

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There is no way for God to be omnipotent or omniscient unless God is actually everywhere, and in everything.
Fair enough, if this is true we should be able to detect it with more than arguments from ignorance.

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What do you think of the information based arguments for ID?
I find it ironic that complex specified information was originaly defines as exactly what evolution is supposed to create. Do you have anyone other than Dembski in mind, I think his is the only information based argument I have read, and as applying it to biology relies on IC, it amounts to an argument from ignorance.

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It's too bad you guys over there have different names and I am clueless what's going on.
I post under the same name, although not very often, it gets quite frustrating.

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It may be that the organism turns on a mutation feature, and in a specific area of the genome, and then suddenly gets the mutation for digesting nylon.
Does that happen? Im not to up on this, I was under the impression it was to do transposons. In any case Demski says this does not count as gsin of CSI.

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Behe complains that there are none in the literature that are really any good.
Behe also said he requires a list of every single mutation and the time at which each one occured, I dont expect to see that any time soon.

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Saltation?
Yes, it is known that mutations in regulation can produce quite different yet viable phenotpyes, which if selectable may appear as a jump in the fossil record.

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No only do homologous structures in closely related species arise from different genes, but nonhomologous structures can arise from the same gene.
Do you mean different transcription factors activate them in the developmental cycle? I don't see this as a problem I see it as a method of macroevolution.

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This may be true in some cases, but in many cases journals are so eager to publish innovative 'against the grain' work that big name journals can end up publishing bad papers.

I suspect that this greatly depends on just which grains are being rubbed.
Well the DI maintain a list of 'ID' papers published in peer reviewed journals. I asked an editor from Nature about this and he said they hadn't recieved any submissions describing new research in ID,  and several other people have said the same. The templeton foundation asked the DI for research proposals and recived none, and despite being asked many times what they would do with a research grant, Dembski at least has never come up with an answer. As an example John Davison published a paper in the journal of theoretical biology, it goes over a lot of data and describes a potential mechanism. Im really not sure what ID has that it could publish at this point.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: April 06 2006,07:54   

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When certain evolution detractors have put forth what would appear to be the search space, the possibility of a solution to this or that problem is often quite out of reach, no matter how many e coli you have working for you
Citation, please.

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It may be that the organism turns on a mutation feature, and in a specific area of the genome, and then suddenly gets the mutation for digesting nylon. For me, that's just too good to be true but we must also account for the organism's ability to direct itself like that in the first place.
I can't make much sense out of this. Can you state it more clearly? I do get the sense, though, that you're rejecting the simplest explanation - random mutation and selection. Why? What evidence is there for a "mutation feature" in this bug? And what "ability to direct itself like that in the first place" are you talking about?

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Behe complains that there are none in the literature that are really any good. If we had a couple of quite good and plausible routes for some very complex systems to evolve, then the pressure would be off. It wouldn't matter that we couldn't explain each one.
Seems like circular reasoning to me. The "very complex systems" are, by definition, the ones that are very difficult to figure out a likely route. Any system for which a plausible route is offered is defined as not one of the "very complex" ones. And any route that is offered for one of Behe's "very complex" paradigms is dismissed as Behe confuses "plausible" with "likely" with "actual".
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I'm referring to the problem that homologous organs often do not arise from the same genes, and that during development, they are often grown from different body segments or in a different order or from a different group of cells. Animal forelimbs develop from different body segments. Homology is difficult because many or most genes control widely divergent body parts. The eye color of drosphila is controlled by a gene th also controls female sex organs. Mouse coat color and mouse size are on the same gene. Chickens are subject to a detrimental mutation in a single gene that causes a wide array of malformations, some of which are unique to birds and others which are shared by other vertebrates.
Here's a passage that could really benefit from a few specifics to anchor it to reality.

"Homologous organs do not arise from the same genes". Do you envision a "one gene - one organ" hypothesis? What does this refer to?

"Animal forelimbs develop from different body segments." I suppose. What systems are you talking about, and how does that bear on evolution vs. ID?

"Homology is difficult because many or most genes control widely divergent body parts". In what way does that make homology difficult?

"The eye color of drosphila is controlled by a gene th also controls female sex organs." Again, what gene, and what bearing does that have on evolution vs. ID?

"Mouse coat color and mouse size are on the same gene." Well, that's just wrong. Color is controlled by multiple genes, and size is controlled by multiple genes. Maybe one of those genes is in both sets. Which one are you referring to? And, so what?

"Chickens are subject to a detrimental mutation in a single gene that causes a wide array of malformations, some of which are unique to birds and others which are shared by other vertebrates."
Again, what gene, and what bearing does that have on evolution vs. ID?

--------------
Must... not... scratch... mosquito bite.

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: April 06 2006,07:58   

Jay Ray,

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I remember Newton and some of those wacky taoists became sidetracked down the red herring called alchemy.  This should come as no surprise in modern times.  Anytime we've tried to combine mysticism with science, its failed.  Gee, I wonder why that could be....
Why must people think Newton was the only alchemist? He failed, as did most. Alchemy isn't the queen of science and philosophy for nothing. What do you think mysticism is? Your very sentence contains the supposition that it isn't true. Mysticism is the experience or intuition about things which are very subtle, hard to prove, hard to control, hard to repeat at will. So the question is, have they any truth or not? But if they do have some truth, then they are absolutely within the realm of science. All phenomena are within the realm of science. Alchemy may deal with what you consider mystical phenomena, but it is a matter of scientific experiment, nothing else. Alchemy involves ideas about how nature works.
The idea that science is a separate realm from mysticism or God is a false idea. And luckily, it won't be around much longer.
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I'm familiar and comfortable with the idea that this thing called "me" is an illusion.
Yeah, but all such descriptions are only approximations. Looked at another way, the thing called 'me' is the one and only endurable phenomenon. That is, "I Am."
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What I am really is just a wave in the ocean we know as the universe.  Every wave eventually crashes against the shore, whereupon it takes another form.  I'm cool with that.
This means that the form is not the true essence. The illusion of me or self is mistaking the external compilation for the true essence.

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I do.  How cool would it be to be a wave that rolls up onto the shore and manages to keep on going, maneuvering at will?  It won't happen, but it would be preferable.
Why won't it happen?
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I'd be one of those that wants evidence beyond what can be provided by anecdote.  Channeling doesn't count.  Regression hypnosis doesn't count.  Near death experiences don't count.  In the end, no matter how many of these stories accumulate, they are still all just stories.  
When one of them happens to you, it will count. I haven't paid much attention to channeling or hypnosis, but I am impressed with near death experiences.

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Every moment is interesting, don't you think?
Well, yeah, but dam*  these are interesting times!
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We withhold judgement until the facts are in.  Many of us would welcome these things if they were demonstrated.
Well, there's nothing wrong with that. I suspect it's a developmental stage. It's a way of cleansing out the bullsh*t.
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But so far, the the so-called evidence is anecdotal, vague, contradictory and entirely unpersuasive.  "Extraordinary claims require extraordinary evidence."  
What can you expect but anecdotal stories from people who have experienced the invisible (to our senses)? There is a tremendous amount of consistency in near death experiences.
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Deep down, I tend to think that god doesn't exist, in just the same way that I don't believe in the invisible Sock Gnome who lives in my laundry room and steals my socks from time to time.
No, that's the Borrowers!
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Nope.  Yet I'm glad I have the opportunity to experience it for at least a little while.
It's a terrible thing to have one's consciousness snatched away, to be part of this incredible universe and have it fade forever before your eyes. What a cruel, cruel reality we live in. But it is a bit better than the classic Christian one, where most beings are to be tormented horribly forever.
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However, I see no benefit to myself or to any other life on this dazzling planet if I continually strive for that which is always out of reach of the living.
Does anyone reach enlightenment without striving? There is great benefit to others if you strive with the right attitude. Despair and a sense of lack don't benefit, but increasing one's level of consciousness does, since all consciousness is one, and all beings partake of the collective unconscious.
The right attitude is to enjoy the ride and not be impatient about the unfolding of understanding - which I think is pretty much what you said.

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for that which is always out of reach of the living.  
Identify with that which lives, not that which dies. This is the sole doctrine of no-self, or the illusion of self.

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I find it quite comforting, and have done ever since I was a child and used to sit in the garden: imagining bits of myself pushing up through the grass as trees and crawling around as insects. The fact that people seek more still puzzles me, and seems to be one of the main reasons in my experience that people are religious other than tradition.
Comforting and beautiful it is, since this whole big shebang - the universe - is one big writhing process, but loss of consciousness, awareness, being part of it all: this doesn't bother you? I don't doubt your sincerity yet when people say this I cannot quite believe them.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: April 06 2006,08:56   

Quote (avocationist @ April 06 2006,11:44)
It may be that the organism turns on a mutation feature, and in a specific area of the genome, and then suddenly gets the mutation for digesting nylon. For me, that's just too good to be true but we must also account for the organism's ability to direct itself like that in the first place.


There is NO EVIDENCE that organisms "turn on a mutation feature" to "direct" themselves in any particular way (e.g., towards an ability to digest nylon). People have looked for that evidence. They haven't found any. (Various people, including reputable scientists, have sometimes thought they'd found such evidence, but it's never panned out.) The reasonable scientific conclusion is that it doesn't work that way!

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I'm referring to the problem that homologous organs often do not arise from the same genes, and that during development, they are often grown from different body segments or in a different order or from a different group of cells. Animal forelimbs develop from different body segments. Homology is difficult because many or most genes control widely divergent body parts.


Perhaps you mean analogous instead of homologous? By definition, homologous structures are those that can be traced to a common ancestor. A human heart and a dog heart are homologous, not because they do the same job, but because they are both derived from the same organ that existed in the last common ancestor of humans and dogs.

I admit I don't know that much developmental genetics. It wouldn't surprise me at all if there are some genes involved in human heart development that are different from some genes involved in dog heart development. However, I think a general claim that truly homologous organs "often do not arise from the same genes" is almost certainly wrong.

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No only do homologous structures in closely related species arise from different genes, but nonhomologous structures can arise from the same gene.


I agree with the latter (with the obvious proviso that entire structures do not typically arise from a single gene). I strongly doubt the former, unless you merely mean that there can be some limited discrepancies between the relevant gene sets for the two species.

If you really believe that very different gene sets can give rise to the same homologous organ in closely related species, can you please provide an example? Thanks.

  
Jay Ray



Posts: 92
Joined: Feb. 2006

(Permalink) Posted: April 06 2006,23:33   

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Why must people think Newton was the only alchemist? He failed, as did most.


I think you mean, as did all.  Also, I'm not sure who thinks Newton was the only alchemist.  Obviously alchemy has a long and dubious history.  Newton just has name recognition.  And his case is illuminating.  All that great work he did with gravity, optics and calculus--clearly he was a man of great genius--and yet he went so far astray in his declining years with his obsession of alchemy.  He may have well turned to astrology for all that came of it.   His descent into alchemy doesn't detract one iota from his other accopmlishments.  But is an important lesson in what can happen if one believes science can be applied to mysticism.  Nothing, except for a waste of a good mind.

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Alchemy isn't the queen of science and philosophy for nothing.


Erm.  This is quite a stretch.  Even before Pythagorus you had guys running around postulating atoms, inferring the general structure of the solar system and planetary orbits, estimating the circumference of the earth.  None of that had anything to do with alchemy.  People were experimenting, rubbing up against what in 2000 years would become that little thing called the scientific method.

Then Pythargorus came along shortly afterward with some excellent math.  Except he really messed things up by turning it into a mystical cult of numbers.  He and his creepy band of fellow mathemystics hoarded their incorrect bizarre extrapolations of the five perfect solids on the grounds that only a select few could handle the inherent power of the information; namely themselves.  In the ensuing centuries, this combination of mysticism and data would broaden its influence into what we know today as western monotheism.  Ptolemy's ideas about the structure of the solar system were stunted by this unfertile soil.  Earth centered universe?  (In a lot of ways, we're still living with this idea.)  And don't get me started on epicycles.

Ring a bell?  How much of humanities potential was wasted by what Pythagorus number cult set into motion?  About a thousand years went by before Kepler, struggling for most of his life with the "perfect solid" nonsense, finally figured it out once and for all.  This despite the stern objections of established authority.  He was afraid for his life.  The mystics had him by the balls.  

Somehow, Newton bought into all this, and it went absolutely nowhere.  Mysticism and knowledge are oil and water.  

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Mysticism is the experience or intuition about things which are very subtle, hard to prove, hard to control, hard to repeat at will.


I'd amend your description: it is so subtle as to be perhaps imaginary, and impossible to prove or repeat.  Nothing mystical has ever been proven.  Controlling isn't in the picture--mysticism is entirely in the mind.

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So the question is, have they any truth or not?


If you mean truth as in, "this is objective reality", then I'd have to say no.  But if you mean truth as in "perception is everything" then I suppose its true for the perceiver.  

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But if they do have some truth, then they are absolutely within the realm of science. All phenomena are within the realm of science.


Depends on the kind of "truth" we are talking about.  And sure, subjectivity can be studied as an objective phenomenon all its own.  We know this kind of science within categories of sociology and psychology.  We see subjective impressions have effects on objective reality all the time.  I proffer the stock market and advertising as prime examples.  

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Alchemy may deal with what you consider mystical phenomena, but it is a matter of scientific experiment, nothing else. Alchemy involves ideas about how nature works.


Alchemy is like Phthagorus' five perfect solids, Ptolemy's geocentricism or the fabled perpetual motion machine.  How many failed attempts does it take to come to the realization that one is on the wrong track?  Basing the study on false premises?

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The idea that science is a separate realm from mysticism or God is a false idea. And luckily, it won't be around much longer.


*sigh*  Maybe we can clone Newton.  Perhaps with all of the latest technology and accumulated data, he will be able to Uncovere that Philosophick Mercury.  And, uh, then what, exactly?

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How cool would it be to be a wave that rolls up onto the shore and manages to keep on going, maneuvering at will?  It won't happen, but it would be preferable.
Why won't it happen?


It might.  If it does, it does.  *shrug*

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When one of them happens to you, it will count. I haven't paid much attention to channeling or hypnosis, but I am impressed with near death experiences.


Once about sixteen years ago, I heard a clear male whisper two words inside my head.  It said, "watch out."  Its the only time in my 36 years that I ever heard a voice in my head.  Does that mean the voice was real?  It happened to me.

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What can you expect but anecdotal stories from people who have experienced the invisible (to our senses)? There is a tremendous amount of consistency in near death experiences.


There is also a tremendous consistancy to alien abduction stories, and going further back into the middle ages, the "little people" stories.  There are better explanations.  Anecdotes make unreliable evidence.

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Deep down, I tend to think that god doesn't exist, in just the same way that I don't believe in the invisible Sock Gnome who lives in my laundry room and steals my socks from time to time.
No, that's the Borrowers!


Gnomeless Heathen!

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There is great benefit to others if you strive with the right attitude. Despair and a sense of lack don't benefit, but increasing one's level of consciousness does, since all consciousness is one, and all beings partake of the collective unconscious.
The right attitude is to enjoy the ride and not be impatient about the unfolding of understanding - which I think is pretty much what you said.


Yup. :)  We certainly agree on this.

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Identify with that which lives, not that which dies. This is the sole doctrine of no-self, or the illusion of self.


I identify with all of it.


EDIT:  It occurs now to me that you might have been joking about the alchemy bit.  Apologies if this is so. :)

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: April 10 2006,16:23   

Russell,

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I thought it was you that wanted to expand the scope from Official Paleontologists to scholars of any description who could read the paleontology literature sensibly. Hey, either way is fine with me!
Gould was one. And I remember Goldschmidt, no doubt the same one loved by JAD. Also, Colin Patterson.

I've got some quote mines for you. D. Raup and Stanley, Principles of Paleontology, 1978,

"Unfortunately, the origins of most higher categories are shrouded in mystery; commonly new higher categories appear abruptly in the fossil record without evidence of transitional ancestral forms".

White, former president of the Linnean Society,
" Whatever ideas authorities may have on the subject, the lungfishes, like every other major group of fishes that I know, have their origins firmly based on nothing" (credentials not named)

Woodruff, Evolution, The Paleobiological View
"the record fails to contain a single example of a significant transition"

T. Huxley, Three lectures on Evolution
"if it could be shown that this fact [gaps between widely distinct groups] had always existed, the fact would be fatal to the doctrine of evolution"

Gould and Simpson,

"New species almost always appeared suddenly in the fossil record with no intermediate links to ancestors in older rocks of the same region."

Simpson,
"In spite of these examples, it remains true, as every paleontologist knows, tha most new species, genera, and families and that nearly all new categories above the level of families appear in the record suddenly and are not led up to by known gradual, completely continuous transitional sequences."

Raup, Conflicts between Darwinism and Paleontology-
"Paleontology is now looking at what it actually finds,...As is now well known most fossil species appear instantaneiously in the record, persist for some millions of years virtually unchanged, only to disappear abruptly-"

All but one or two were paleontoligists. The rest evolutionary biologists. Evolutionists all, with the possible exceptions of Patterson, who at the least went through a crisis of belief.

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But I have authors here in my bookcaase that discuss problems with paleontology.

Do you! Who are they?
W. R. Bird, Jonathan Wells,  Richard Milton, Michael Denton (Behe?) Lee Spetner, Philip Johnson.

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I believe I pointed out that Behe never made any claims beyond "seems improbable to me" that even could be refuted.
Well, if that is what you took away from his book I don't know what to say.

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and what is your reaction to the very specific details that Mike Gene brings out in the assembly and function of the flagellum?+++++++++++++++
I believe you will find the answer to that if you go back over this thread.
Well, that effort was certainly a waste of time.
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But just to summarize: my reaction is "Biological systems are, indeed, complex. Really complex. Really, really complex. But no amount of documenting how really, really, really  complex they are gets us any closer to 'couldn't have evolved'".
Really? No amount of complexity? Isn't that like saying no evidence could possibly convince you? That there is no limit to the complexity that random and undirected processes could generate?
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Now, if there's anything that you feel "Mike Gene" wrote that actually argues "couldn't have evolved" - as opposed to "is really complex" - that I failed to address, please: point it out. I certainly don't want to pass up any opportunity to pursue these things right down to the specifics.
Well, pretty much what I posted, actually. It's a 5-part essay, and I went through and found what I thought were some of the most interesting parts. You know, on another question, maybe yours, I spent at least 20 hours going through the Flagellum Unspun and Spinning Fine papers, and critiqued it. But no one really got into the nitty gritty of what's there.

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I assumed that you meant that "a lot of people" had concluded from an informed analysis of paleontological data that the basic idea of "evolution" was fundamentally inadequate - that the idea that species evolved from pre-existing species as a result of random genetic change and selection was incompatible with the bones and fossils.

Well, "a lot of people" turns out to be five. On a list you lost. And the only one of them you've supplied a name for is Stephen Jay Gould, whom you have only read as quote(mine)d by creationists. And his issues have nothing to do with those I assumed you were suggesting.
If the quotes are out of context, or misleading, then that's a problem. Simply searching the literature for those moments when evolutionsists have spoken about the problems does not constitute quote mining. I believe when I said a lot of people, at that point I was talking about all of them, from the paleontologists on down to ignorant folk like me.

If you are looking for paleontologists who have gone beyond being troubled and have abandoned belief in evolution, and have publicly said so, the list would probably be only 3 or 4 or 5.
I'm not sure what you think Gould's issues were, but I do believe he found that the fossil record does not support gradualism, and therefore he came up with punctuated equilibrium and isolation of small populations to allow him to accommodate the data.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: April 10 2006,17:42   

Geez, Avo. You're like a cartoon of quote-miner. Check out all your favorite quotes, in context, here.

As for this motley crew:
W. R. Bird, Jonathan Wells,  Richard Milton, ... Lee Spetner, Philip Johnson.

They have about as much credibility with people who actually know what they're talking about as do Ken Ham and Pat Robertson. Personally, I have zero respect for any of them. I can only guess that they've earned yours by the usual route: supporting a conclusion that you're already committed to, even if the arguments they use to support it are illogical and mutually contradictory. I know. You say potayto, I say potahto. But there's a reason these guys are not part of the ongoing dialog known as science. Can you guess what that might be?

As for Behe and Denton, I thought we decided that they were OK with the standard evolutionists' interpretation of the paleontological record. Have we changed our minds again?

Now, let's get one thing out of the way, once and for all. Your issue is the inadequacy of "random mutation/natural selection" to account for the unity and diversity of life, right? Not the kinetics by which those things occur in biological populations. Right? Go through those mined quotes - in context - and tell me how many of them have anything do do with your issues.

If your problem is "gradualism" vs. "punctuated equilibrium" that's a whole different thing. Darwin's rough approximation to the history of life was a lot closer than his creationist predecessors'. But we've learned quite a bit since then, haven't we? And we've refined our understanding. In light of what we know now about DNA, population genetics, environmental metastability, etc. etc. why would you think that a punctuated equilibrium pattern is at all inconsistent with good ol' RM/NS? Gould certainly didn't.

As for "sudden appearance" of species - remember, we're talking "sudden" on a geological time scale. Read Gould on this. (Not just the mined quotes.)

So at this point, I regard your "list" as the null set - until such time as you show your skeptics have anything to say about the inadequacy of RM/NS or the need to invoke intelligent design.

As for Behe's Irreducible Complexity scam, read the current post on Panda's Thumb about evolution of hormone-receptor complexity. If that doesn't explain what I mean by the difference between "really really complex" and "irreducibly complex", I can't help you.

--------------
Must... not... scratch... mosquito bite.

  
avocationist



Posts: 173
Joined: Feb. 2006

(Permalink) Posted: April 10 2006,19:06   

Chris,
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You appear to have responded to some of my points in the gay gene thread:
Disconcerting, wasn't it?

You ask why emergent order of some kind changes the nature of the universe. I guess it all comes down to what we find. But the fine tuning that seems to be turning up just makes this universe a more and more fantastic place. It begins to take more credulity to suppose pure materialism than to suppose consciousness precedes matter, or perhaps that they operate together.
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Fair enough, if this is true we should be able to detect it with more than arguments from ignorance.
From the IDEA site: intelligent design theory is not merely a negative argument against evolution. Intelligent design begins with positive predictions based upon our observational experience of how intelligent designers operates.
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Do you have anyone other than Dembski in mind, I think his is the only information based argument I have read, and as applying it to biology relies on IC, it amounts to an argument from ignorance.
I believe the phrase CSI is his, but others have argued the same or similar points. He was not the first. At least, I don't think he was. I should dig up some. Let me think.

Here is Meyer:

"Experience teaches that information-rich systems … invariable result from intelligent causes, not naturalistic ones. Yet origin-of-life biology has artificially limited its explanatory search to the naturalistic nodes of causation … chance and necessity. Finding the best explanation, however, requires invoking causes that have the power to produce the effect in question. When it comes to information, we know of only one such cause.

"Indeed, in all cases where we know the causal origin of 'high information content,' experience has shown that intelligent design played a causal role."
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Fair enough, if this is true we should be able to detect it with more than arguments from ignorance.
We should have infinite patience for the unknown and unsolved if it relates to NDE, but we should have no patience at all for anything that ID theory has failed to answer up front. Darwin's argument for natural selection was an argument from ignorance, because he was so utterly ignorant of what he was dealing with. So a kid could make up a fairy tale, and that is positive, but if someone says the fairy tale events could not be true, why, it is an argument from ignorance, and incredulity too. And it's negative.

Meyer on the argument from ignorance accusation:

   Well, Chris, (wasn't you was it?) all scientific theories are based on inferences from evidence. If we could see everything directly, we wouldn’t need to theorize. And Darwin’s theory is in fact an inference from a number of different classes of evidence. And Darwin justified the theory not because he could make observable predictions in the laboratory – after all he was trying to reconstruct the distant past – instead he justified it because it provided a better explanation of the evidenced than the main competitor hypothesis, and that’s precisely how the theory of intelligent design is formed, framed, and justified. We argue that our theory provides a better explanation of some of the critical pieces of evidence of biology, namely the irreducibly complex molecular machines and circuits that we seen in cells and the presence of this informational software that drives everything in the cell as it’s embedded in the DNA molecule.
   ...
   ...
   Well, what you’re getting at is that our argument is an argument from ignorance, but it’s not an argument from ignorance, it’s based on the evidence that has been discovered of the complexity in the cell, the information-bearing properties in particular, but it’s also based on what we know about it takes to build informational systems. That in our experience, our repeated and uniform experience, intelligence is always involved in the production of information. So when we find information in the living system, the most natural inference to draw is that there was an intelligent source. Now that form of reasoning happens to be precisely the form of reasoning that is always used in the historical sciences, where our present knowledge of the cause and effect structure of the world guides our judgment as to what is the most likely explanation of what happened in the past.

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Does that happen? Im not to up on this, I was under the impression it was to do transposons. In any case Demski says this does not count as gsin of CSI.

I'll need to look into it more because someone else has said there's no evidence for it, and I have run into articles about it more than once, but I'll have to see if they were right. But that was my understanding. I'm not sure what you mean about doing transposons. Genetic shuffling during meiosis? It was not meant as an argument for CSI, just as something pretty impressive, hard to imagine it evolving via luck.

Try this:
http://www.eurekalert.org/pub_releases/2005-05/sri-tse051805.php
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Behe also said he requires a list of every single mutation and the time at which each one occured, I dont expect to see that any time soon.
Did he really? Because I was not aware of that, and it isn't what I recall reading.
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Yes, it is known that mutations in regulation can produce quite different yet viable phenotpyes, which if selectable may appear as a jump in the fossil record.
What is a mutation in regulation?
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Do you mean different transcription factors activate them in the developmental cycle?
I'm not sure. Wells gives the example of a gene called Distal-less that is involved in generating appendages in 5 phyla (mouse, worm, butterfly, sea urchin and spiny worm) but the structures are not homologous. He also says that gene transplant experiments show that developmental genes from mice and humans can replace their counterparts in flies.  So this indicates that genes do not control structure, but something else.
He quotes Gavin de Beer: "Because homology implies community of descent from...a common ancestor it might be thought that genetics would proovide the key to the problem of homology. This is where the worst shock of all is encountered...[because] characters controlled by identical genes are not necessarily homologous...[and] homologous structures need not be controlled by identical genes."

Says the Crevo guy: If homologies are continually found outside the expected evolutionary tree, then it can't be said that homologies provide evidence for evolution.

and
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But first, let's take note of why evolutionists don't think that convergent evolution is a problem for them. They believe that there are perfectly valid explanations other than evolution for homology. The main one they point to is environmental selective pressures which select the same mutations across two lineages. There are a number of problems with this stance:

   * If evolutionists agree that there are other possibilities for the origin of homologies than common descent, then they should also agree with us that this makes the use of homologies as evidence of common descent null and void, since homology can be just as much evidence of other mechanisms.
   * The idea that the same set of beneficial mutations can occur randomly twice is astronomically low. First of all, the chances of getting one beneficial mutation is astronomically low. The chances of finding a sequence from point A to point B with all containing beneficial or at least non-lethal configurations is astronomically low. The chances of two different organisms finding the same configuration from the same random space is even more astronomically low.

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As an example John Davison published a paper in the journal of theoretical biology, it goes over a lot of data and describes a potential mechanism. Im really not sure what ID has that it could publish at this point.
I think it is not quite the case that there have been no research proposals or papers, but it isn't a serious drawback for me. One thing is that they may come. Another is that ID is just another supposition like Darwinism, but in the real world, research will go on just the same. Same data, different spin.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: April 11 2006,01:31   

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From the IDEA site: intelligent design theory is not merely a negative argument against evolution. Intelligent design begins with positive predictions based upon our observational experience of how intelligent designers operates.
Great, what are these predictions?

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Darwin's argument for natural selection was an argument from ignorance, because he was so utterly ignorant of what he was dealing with.
If we were having this discussion in the 1800s I would not ask for the same evidence as I do now. The same way if Darwin was working today the proof he gave in Origin would not be sufficient to convince most people.

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And Darwin’s theory is in fact an inference from a number of different classes of evidence. And Darwin justified the theory not because he could make observable predictions in the laboratory – after all he was trying to reconstruct the distant past – instead he justified it because it provided a better explanation of the evidenced than the main competitor hypothesis, and that’s precisely how the theory of intelligent design is formed, framed, and justified.
I never said that ID wasn't an inference from evidence, I said it was an argument from ignorance. Do you have a link to an explanation of how it explains the evidence better than evolution that isn't some variation of: we don't know how it evolved, therefore 'it was designed' explains it better.

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Well, what you’re getting at is that our argument is an argument from ignorance, but it’s not an argument from ignorance, it’s based on the evidence that has been discovered of the complexity in the cell, the information-bearing properties in particular, but it’s also based on what we know about it takes to build informational systems.
Apologies as information theory is not my strong point, but do we have examples of infomational systems that are not either organisms or machines built by humans. There may be arguments for ID that I haven't seen, but CSI as it is currently calculated for the falgellum is an argument from ignorace so long as it is based on IC and the assumption that the only possible evolutionary pathway is all of the genes spontaneously appearing.

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We should have infinite patience for the unknown and unsolved if it relates to NDE, but we should have no patience at all for anything that ID theory has failed to answer up front.
I would have patience, except for the fact that ID advocates claim that they have produced the evidence to dismiss evolution and accept design, so I think what I ask for is not too great. If they said what they have is a hypothesis and a work in progress, then I would ask for less evidence based on the claim.

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Intelligent design begins with positive predictions based upon our observational experience of how intelligent designers operates.
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it provided a better explanation of the evidenced than the main competitor hypothesis, and that’s precisely how the theory of intelligent design is formed, framed, and justified.
Combine these two and you could make some interesting predictions, so far I haven't seen many.

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Did he really? Because I was not aware of that, and it isn't what I recall reading.
He also said that each mutation needs a 'fitness coefficient' so we know how natural selection was able to operate on it.

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What is a mutation in regulation?
The developmental cycle is contolled by a network of transcription factors (eg the Hox genes) which control the time ordered tissue specific gene expression which creates all the different cells in the right order. Because transcription factors bind to short promoter stretches of DNA mutations not only cause loss of binding, but also binding of transcription factors to new random sequences. Random rearrangement of DNA binding domains in transcription factor proteins themselves can create novel binding properties. Changes in how this network is wired can cause significant chages in phenotype, for example a change in the expression of certain hormones may cause larger brains in humans comapred to other primates. Also, because of phenotypic plasticity and genetic assimilation, different genotypes can produce different phenotypes in response to environmental stimulation, which can be eventually translated into genotype.

Because of this we would not expect body plan development to be controlled the same way, as this is likely the main cause of change in body plans. We cannot just look at individual genes for homology, we need to look at the structure of the network as a whole.

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I think it is not quite the case that there have been no research proposals or papers, but it isn't a serious drawback for me.
Again if they are saying that this is a work in progress then it is not a problem, and some people are starting to talk that way now. It is a problem if the claim if all the data they have proves ID, and it is already enough to dismiss Darwinism, and there has been no published research. It is also relevent when complaining they are being kept out of the literature, which is what I think the original point was.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: April 11 2006,09:06   

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Here is Meyer:

"Experience teaches that information-rich systems … invariable result from intelligent causes, not naturalistic ones. Yet origin-of-life biology has artificially limited its explanatory search to the naturalistic nodes of causation … chance and necessity. Finding the best explanation, however, requires invoking causes that have the power to produce the effect in question. When it comes to information, we know of only one such cause.

"Indeed, in all cases where we know the causal origin of 'high information content,' experience has shown that intelligent design played a causal role."

These are some very strong statements. Completely wrong, in my opinion, and maybe I'll have time soon to get into it. But for the present, I'd like to point out that in 14 or so pages, we seem to have made no progrees on what was one of the central points of contention early in the thread: your argument is largely one of incredulity toward the accounts of mainstream biologists that contradict your received notions about the universe, yet you seem completely credulous toward extremely questionable assertions from second-rate philosophers and apologists like Meyer.
It's fine to be skeptical about appeals to authority and the claims of so-called experts. But when it doesn't cut both ways, it begins to look like your mind is utterly made up, and in your mind no ID proponent can ever be wrong.

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The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: April 11 2006,09:50   

This whole argument about the conservation of information, or that evolution cannot increase information is just full of sh**.

Life as nothing to do with information intrinsically, because information is only relevant to an observer. It doesn't mean anything on its own. I've never seen any biology textbook discussing information.

You have several identical replicators. A mutation occures in of them, which increases its replication rate. Therefore this mutation is selected. If the increase depends on the environment, this can lead to different types of replicators.
Wether that increases or decreases information entropy or whatever is just intellectual masturbation of pseudo-scientists like Dembski in order to fool the ignorant or the skeptic.
Needless to say that none of them has been able to point a specific evolutionnary process that should be impossible, according to their law of 'conservation of information'.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: April 11 2006,11:13   

Intelligent Design theory specifically states that the evolution of the bacterial flagellum without intelligent input is impossible because the probability that every protein would form simeltaneously as a random combination of amino acids, along with the correct expression and arrangement mechanisms in place, is less than the universal probability bound. Have you not read No Free Lunch?

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: April 11 2006,11:36   

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From the IDEA site: intelligent design theory is not merely a negative argument against evolution. Intelligent design begins with positive predictions based upon our observational experience of how intelligent designers operates.
What are these predictions besides "things are expected to look designed"? And most important, what predictions does ID make that can falsify its hypothesis? Can it predict things that cannot have been designed?
And don't you understand that the argument of comparison cannot scientific? Following such comparison, every ecosystem, snowflake, planet... must have be specifically designed. Do you think that plate tectonics was designed?
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Darwin's argument for natural selection was an argument from ignorance, because he was so utterly ignorant of what he was dealing with.

WHAT? Have you read his book?
When the current theory about the origin of species was just "poof" (like ID), do you think that a verbal model based on evidence and able to produce predictions was an argument from ignorance?
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Darwin justified the theory not because he could make observable predictions in the laboratory – after all he was trying to reconstruct the distant past – instead he justified it because it provided a better explanation of the evidenced than the main competitor hypothesis, and that’s precisely how the theory of intelligent design is formed, framed, and justified.
In which way is ID different from the old argument from Paley?
I'm sorry, CSI and IC don't constitute a theory, they don't explain why things are what they are, unless you're satisfied with "poof".
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We argue that our theory provides a better explanation of some of the critical pieces of evidence of biology, namely the irreducibly complex molecular machines and circuits that we seen in cells and the presence of this informational software that drives everything in the cell as it’s embedded in the DNA molecule.
This argument from comparison is useless, see above. And BTW, the genome is not a program. Is was not written before its execution, and the the genetic code is part of the genome (as if the programming language was part of the program).
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Genetic shuffling during meiosis? It was not meant as an argument for CSI, just as something pretty impressive, hard to imagine it evolving via luck.
Crossing-overs happen when two homologous chromosomes are close to each other. What is impressive here?
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"Because homology implies community of descent from...a common ancestor it might be thought that genetics would proovide the key to the problem of homology. This is where the worst shock of all is encountered...[because] characters controlled by identical genes are not necessarily homologous...[and] homologous structures need not be controlled by identical genes."
A gene is not a phenotype. If you change its environment, the same gene can produce very different traits. A gene alone is meaningless, this is just a random string of symbols. Nothing in the gene for insulin says 'this is gene for a 7 amino acid peptide designed for the regulation of glycemy'... nothing.
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   * If evolutionists agree that there are other possibilities for the origin of homologies than common descent, then they should also agree with us that this makes the use of homologies as evidence of common descent null and void, since homology can be just as much evidence of other mechanisms.
There is a term for homologies that are not inherited from a common ancestor. These are called 'homoplasies' and have been a parameter in phylogenetics for decades.
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   * The idea that the same set of beneficial mutations can occur randomly twice is astronomically low.
Who said that an homoplasy should be caused by the same set of mutations in two lineages? Do you think that wing developments in birds and bats are based on the same mutations?
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First of all, the chances of getting one beneficial mutation is astronomically low.

Every drug resistance, adaptation to abiotic stress... that have been observed in the lab and in the wild are the results of beneficial mutations.
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The chances of finding a sequence from point A to point B with all containing beneficial or at least non-lethal configurations is astronomically low.

This calculation is flawed because the mutations don't have to happen simultaneously or to follow a singe pathway. Anf most important mutations don't have any direction to follow. '... to point B' is just meaningless. I know you consider yourself as the product of a purpose, but I'm afraid you are not.

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: April 11 2006,11:40   

Quote (Chris Hyland @ April 11 2006,16:13)
Intelligent Design theory specifically states that the evolution of the bacterial flagellum without intelligent input is impossible because the probability that every protein would form simeltaneously as a random combination of amino acids, along with the correct expression and arrangement mechanisms in place, is less than the universal probability bound. Have you not read No Free Lunch?

I was referring to their blurry arguments regarding the conservation information, not IC.
I will edit my post to make that clear.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: April 11 2006,11:58   

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[avo:] Darwin's argument for natural selection was an argument from ignorance, because he was so utterly ignorant of what he was dealing with.
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[a dumbfounded Jeannot:] WHAT? Have you read his book?
Probably not. But she's read all the important parts, as quote-mined by creationists!

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Must... not... scratch... mosquito bite.

  
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