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  Topic: BIO-Complexity, the shiny new ID journal< Next Oldest | Next Newest >  
olegt



Posts: 1387
Joined: Dec. 2006

(Permalink) Posted: May 13 2010,21:56   

The previous ID research journal PCID folded in 2005 after four glorious years.  (Check out this cool article by William Brookfield: In Search of a Cosmic Super-Law: The Supreme “Second law” of Devolution).

The next ID journal JOEI never saw the light of day.  We only knew that its Editor in Chief was supposed to be Gloppy.  Here is the AtBC thread.

Anyway, the shiny new ID journal is BIO-Complexity put together by Biologic Institute.  The Editorial Board involves the usual suspects (including Gloppy).  

Two papers are up: Current volume.  With comments!  The authors and the commenters happen to be members of the editorial board.  Talk about a self-sustaining journal!  

Comment sample:
   
Quote

Reader Comments

Director, The Gene Emergence Project, Department of ProtoBioCybernetics & ProtoBioSemiotics

by David L. Abel (2010-05-12)


EMAIL REPLY

Excellent paper.


--------------
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Venus Mousetrap



Posts: 201
Joined: Aug. 2007

(Permalink) Posted: May 14 2010,04:37   

Those scrunched up balls of paper on the front page look so designed.

  
Richardthughes



Posts: 10231
Joined: Jan. 2006

(Permalink) Posted: May 14 2010,08:34   



--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
OgreMkV



Posts: 3320
Joined: Oct. 2009

(Permalink) Posted: May 14 2010,08:52   

I skimmed the abstract of the 'article' by Axe.  It's just a rehash of "I can't see how it happened that way".  And with commentary from Abel, you know it's got to be... ummm... nevermind.

From what I've seen this is just a small circle jerk.  

I'd love to see the internet statistics for their website.  I'd be willing to bet that 90% of their incoming links are from websites like this.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
George



Posts: 313
Joined: Feb. 2006

(Permalink) Posted: May 14 2010,09:37   

I predict that this thread will either be very short, mirroring the output of the new journal, or will turn into a UD-thread-esque monster complete with LOLcats if the journal proves to be rich new vein of tard.  Middle ground highly unlikely.  At this point, I'd have to put my money on option one.

  
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: May 14 2010,09:41   

Certainly the incestuous little group they have there.
 I was amused by Axe's reply to Gauger's paper. i mean, why doesn't he just walk a few steps to her desk and ask her his question?  It's obviously all for the show, not the substance.

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
fnxtr



Posts: 2137
Joined: June 2006

(Permalink) Posted: May 14 2010,09:57   

Quote (sledgehammer @ May 14 2010,07:41)
Certainly the incestuous little group they have there.

Or at lease endogamous. :-)

Self-pollinating?

--------------
"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

  
SLP



Posts: 136
Joined: Dec. 2002

(Permalink) Posted: May 17 2010,17:43   

Has anyone else read any of Abel's papers and concluded, like I have, that
1. I am astonished at how such nonsense gets past peer review
2. question begging shoiuld not be considered a valid scientific endeavor?

  
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: May 17 2010,19:27   

Quote (SLP @ May 17 2010,15:43)
Has anyone else read any of Abel's papers and concluded, like I have, that
1. I am astonished at how such nonsense gets past peer review
2. question begging shoiuld not be considered a valid scientific endeavor?

Not only that, but when i read a paper  full of jargon of the author's own creation,    
Quote
“Physicodynamics cannot spontaneously traverse The Cybernetic Cut ”
using circular definitions (like CSI and IC: that which cannot be produced by natural causes) , followed by the challenge "prove me wrong! (but I get to make the rules)":  
Quote
A single exception of non trivial, unaided spontaneous optimization of formal function by truly
   natural process would falsify this null hypothesis.

I can only roll my eyes and  shrug.

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Wesley R. Elsberry



Posts: 4505
Joined: May 2002

(Permalink) Posted: May 18 2010,07:32   

Another antievolutionist who can't understand modus tollens, it looks like.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Kristine



Posts: 3046
Joined: Sep. 2006

(Permalink) Posted: May 18 2010,09:45   

Quote (olegt @ May 13 2010,21:56)

Anyway, the shiny new ID journal is BIO-Complexity put together by Biologic Institute.  The Editorial Board involves the usual suspects (including Gloppy).

All men. Women do the housework, er, copyediting. ;)

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
didymos



Posts: 1825
Joined: Mar. 2008

(Permalink) Posted: May 18 2010,09:57   

Quote (Kristine @ May 18 2010,07:45)
Quote (olegt @ May 13 2010,21:56)

Anyway, the shiny new ID journal is BIO-Complexity put together by Biologic Institute.  The Editorial Board involves the usual suspects (including Gloppy).

All men. Women do the housework, er, copyediting. ;)

That is weird.  Why is Gauger isolated like that?

--------------
I wouldn't be bothered reading about the selfish gene because it has never been identified. -- Denyse O'Leary, professional moron
Again "how much". I don't think that's a good way to be quantitative.-- gpuccio

  
Kristine



Posts: 3046
Joined: Sep. 2006

(Permalink) Posted: May 18 2010,12:23   

Quote (didymos @ May 18 2010,09:57)
Quote (Kristine @ May 18 2010,07:45)
 
Quote (olegt @ May 13 2010,21:56)

Anyway, the shiny new ID journal is BIO-Complexity put together by Biologic Institute.  The Editorial Board involves the usual suspects (including Gloppy).

All men. Women do the housework, er, copyediting. ;)

That is weird.  Why is Gauger isolated like that?

To guard against e-babies. :D

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
khan



Posts: 1483
Joined: May 2007

(Permalink) Posted: May 18 2010,12:25   

Quote (didymos @ May 18 2010,10:57)
Quote (Kristine @ May 18 2010,07:45)
Quote (olegt @ May 13 2010,21:56)

Anyway, the shiny new ID journal is BIO-Complexity put together by Biologic Institute.  The Editorial Board involves the usual suspects (including Gloppy).

All men. Women do the housework, er, copyediting. ;)

That is weird.  Why is Gauger isolated like that?

Obeying Leviticus?

--------------
"It's as if all those words, in their hurry to escape from the loony, have fallen over each other, forming scrambled heaps of meaninglessness." -damitall

That's so fucking stupid it merits a wing in the museum of stupid. -midwifetoad

  
DiEb



Posts: 238
Joined: May 2008

(Permalink) Posted: Nov. 05 2010,07:27   

Wow, congrats: this vibrant magazine is now on the market for six months! Check it out for its new thought-provoking articles... Even the The Evolutionary Informatics Lab  (www.evoinfo.org)  has an article under submission there. It hasn't been published yet - most probably the peers are to busy reading all the other papers coming in...

   
J-Dog



Posts: 4365
Joined: Dec. 2006

(Permalink) Posted: Nov. 05 2010,08:36   

Quote (DiEb @ Nov. 05 2010,07:27)
Wow, congrats: this vibrant magazine is now on the market for six months! Check it out for its new thought-provoking articles... Even the The Evolutionary Informatics Lab  (www.evoinfo.org)  has an article under submission there. It hasn't been published yet - most probably the peers are to busy reading all the other papers coming in...

Quote
most probably the peers are to busy reading all the other papers coming in...


Yes... If they can squeeze the time in, what with all the bible reading they all do too.

Quote
this vibrant pungent magazine is now on the market for six months!


Fixed That For You!

--------------
Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
SLP



Posts: 136
Joined: Dec. 2002

(Permalink) Posted: Nov. 05 2010,13:51   

Quote (olegt @ May 13 2010,21:56)
The previous ID research journal PCID folded in 2005 after four glorious years.  (Check out this cool article by William Brookfield: In Search of a Cosmic Super-Law: The Supreme “Second law” of Devolution).

The next ID journal JOEI never saw the light of day.  We only knew that its Editor in Chief was supposed to be Gloppy.  Here is the AtBC thread.

Anyway, the shiny new ID journal is BIO-Complexity put together by Biologic Institute.  The Editorial Board involves the usual suspects (including Gloppy).  

Two papers are up: Current volume.  With comments!  The authors and the commenters happen to be members of the editorial board.  Talk about a self-sustaining journal!  

Comment sample:
   
Quote

Reader Comments

Director, The Gene Emergence Project, Department of ProtoBioCybernetics & ProtoBioSemiotics

by David L. Abel (2010-05-12)


EMAIL REPLY

Excellent paper.

"Director, The Gene Emergence Project, Department of ProtoBioCybernetics & ProtoBioSemiotics"

Talk about credential embellishment....

  
SLP



Posts: 136
Joined: Dec. 2002

(Permalink) Posted: Nov. 05 2010,13:58   

So, let me get this straight - this 'journal' has TWO articles in it?

And has a 'large readership' based on th esupposed fact that PDFs of these 2 articles have been downloaded 2000 times?

  
sparc



Posts: 1711
Joined: April 2007

(Permalink) Posted: Sep. 17 2011,00:21   

IMO this thread needed an update.
Since the announcement at UD on May 1st, 2010 Bio-Complexity published the six articles listed below:
Quote
Vol 2010

Research Articles

The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations
Douglas Axe

A Vivisection of the ev Computer Organism: Identifying Sources of Active Information
George Montañez, Winston Ewert, William Dembski, Robert Marks

Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness
Ann K Gauger, Stephanie Ebnet, Pamela F Fahey, Ralph Seelke

Critical Reviews

The Case Against a Darwinian Origin of Protein Folds
Douglas Axe
       
Quote
Vol 2011

Research Articles

The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
Ann K Gauger, Douglas D Axe

Critical Reviews
Can the Origin of the Genetic Code Be Explained by Direct RNA Templating?
Stephen C Meyer, Paul Nelson
Underlined are authors who happen to be members of the editorial board of Bio-Complexity which is quite impressive number-wise:    
Quote
Editor in Chief

Matti Leisola, Enzymology and Enzyme Engineering; Aalto University School of Chemical Technology, Finland

Managing Editor

Douglas Axe, Protein Structure–Function; Biologic Institute, United States

Editorial Board

David Abel, Origin of Life; The Origin-of-Life Science Foundation, United States

William Basener, Statistics and Population Modeling; Rochester Institute of Technology, United States

Michael Behe, Biochemistry and Biological Complexity; Lehigh University, United States

Walter Bradley, Origin of Life; Baylor University, United States

Stuart Burgess, Biomimetics and Biomechanics; University of Bristol, United Kingdom

Russell Carlson, Biochemistry; University of Georgia, United States

William Dembski, Mathematics and Information Theory; Discovery Institute, United States

Marcos Eberlin, Chemistry; State University of Campinas, Brazil

Charles Garner, Prebiotic Chemistry; Baylor University, United States

Loren Haarsma, Biophysics; Calvin College, United States

Peter Imming, Organic Chemistry; Martin Luther University, Germany

James Keener, Bioengineering and Mathematics; University of Utah, United States

David Keller, Biophysical Chemistry and Molecular Machines; University of New Mexico, United States

Branko Kozulic, Biochemistry; Gentius Ltd, Croatia

Wolf-Ekkehard Lönnig, Plant Genetics; Max Plank Institute for Plant Breeding Research (retired), Germany

Jed Macosko, Biophysics and Molecular Machines; Wake Forest University, United States

Robert Marks, Evolutionary Computing and Information Theory; Baylor University, United States

Scott Minnich, Bacterial Pathogenicity; University of Idaho, United States

Norman Nevin, Medical Genetics; Queen's University of Belfast (emeritus), Ireland

Edward Peltzer, Ocean Chemistry, United States

Colin Reeves, Genetic Algorithms and Information Theory; Coventry University, United Kingdom

Siegfried Scherer, Microbial Ecology; Technische Universität München, Germany

Ralph Seelke, Microbiology; University of Wisconsin-Superior, United States

David Snoke, Physics and Modeling; University of Pittsburgh, United States

Richard Sternberg, Genomics, Cladistics and Theoretical Biology; Biologic Institute, United States

Scott Turner, Physiology, Ecology and Evolution; State University of New York-Syracuse, United States

Ji?í Vácha, Pathological Physiology and Evolutionary Theory; Masaryk University (emeritus), Czech Republic

John Walton, Chemistry; University of St Andrews, United Kingdom

Jonathan Wells, Cell and Developmental Biology; Biologic Institute, United States

Copyeditor

Ann Gauger, Molecular Genetics and Molecular Biology; Biologic Institute, United States

32 editors for six articles by a total of 11 authors of which five belong to the editorial team. At the same time five members of the editorial team (underlined) and three authors (Dembski, Meyer, Nelson) are fellows of the Discovery Institute. Quite an endeavor for six articles.

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
Dr.GH



Posts: 1956
Joined: May 2002

(Permalink) Posted: Sep. 17 2011,01:17   

Weird affiliations, eg.

Jonathan Wells, Cell and Developmental Biology; Biologic Institute, United States

It is not in the realm of possibles that Wells could actually do any biology. But, then, who could expect the "Biologic Institute" to do any biology. Why aren't they just listed as Discotutes?

My guess is that the more "institutes" and "laboratories"  they pretend to be with, the more they can pretend to be all sciencecy.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
sparc



Posts: 1711
Joined: April 2007

(Permalink) Posted: Sep. 17 2011,05:51   

BTW, until 2003 Scherer has been a fellow of the DI as well.

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
Art



Posts: 69
Joined: Dec. 2002

(Permalink) Posted: Sep. 18 2011,14:31   

Quote (sparc @ Sep. 17 2011,00:21)
IMO this thread needed an update.
Since the announcement at UD on May 1st, 2010 Bio-Complexity published the six articles listed below:  
Quote
Vol 2010

Research Articles

The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations
Douglas Axe

A Vivisection of the ev Computer Organism: Identifying Sources of Active Information
George Montañez, Winston Ewert, William Dembski, Robert Marks

Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness
Ann K Gauger, Stephanie Ebnet, Pamela F Fahey, Ralph Seelke

Critical Reviews

The Case Against a Darwinian Origin of Protein Folds
Douglas Axe
         
Quote
Vol 2011

Research Articles

The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
Ann K Gauger, Douglas D Axe

Critical Reviews
Can the Origin of the Genetic Code Be Explained by Direct RNA Templating?
Stephen C Meyer, Paul Nelson
Underlined are authors who happen to be members of the editorial board of Bio-Complexity which is quite impressive number-wise:      
Quote
Editor in Chief

Matti Leisola, Enzymology and Enzyme Engineering; Aalto University School of Chemical Technology, Finland

Managing Editor

Douglas Axe, Protein Structure–Function; Biologic Institute, United States

Editorial Board

David Abel, Origin of Life; The Origin-of-Life Science Foundation, United States

William Basener, Statistics and Population Modeling; Rochester Institute of Technology, United States

Michael Behe, Biochemistry and Biological Complexity; Lehigh University, United States

Walter Bradley, Origin of Life; Baylor University, United States

Stuart Burgess, Biomimetics and Biomechanics; University of Bristol, United Kingdom

Russell Carlson, Biochemistry; University of Georgia, United States

William Dembski, Mathematics and Information Theory; Discovery Institute, United States

Marcos Eberlin, Chemistry; State University of Campinas, Brazil

Charles Garner, Prebiotic Chemistry; Baylor University, United States

Loren Haarsma, Biophysics; Calvin College, United States

Peter Imming, Organic Chemistry; Martin Luther University, Germany

James Keener, Bioengineering and Mathematics; University of Utah, United States

David Keller, Biophysical Chemistry and Molecular Machines; University of New Mexico, United States

Branko Kozulic, Biochemistry; Gentius Ltd, Croatia

Wolf-Ekkehard Lönnig, Plant Genetics; Max Plank Institute for Plant Breeding Research (retired), Germany

Jed Macosko, Biophysics and Molecular Machines; Wake Forest University, United States

Robert Marks, Evolutionary Computing and Information Theory; Baylor University, United States

Scott Minnich, Bacterial Pathogenicity; University of Idaho, United States

Norman Nevin, Medical Genetics; Queen's University of Belfast (emeritus), Ireland

Edward Peltzer, Ocean Chemistry, United States

Colin Reeves, Genetic Algorithms and Information Theory; Coventry University, United Kingdom

Siegfried Scherer, Microbial Ecology; Technische Universität München, Germany

Ralph Seelke, Microbiology; University of Wisconsin-Superior, United States

David Snoke, Physics and Modeling; University of Pittsburgh, United States

Richard Sternberg, Genomics, Cladistics and Theoretical Biology; Biologic Institute, United States

Scott Turner, Physiology, Ecology and Evolution; State University of New York-Syracuse, United States

Ji?í Vácha, Pathological Physiology and Evolutionary Theory; Masaryk University (emeritus), Czech Republic

John Walton, Chemistry; University of St Andrews, United Kingdom

Jonathan Wells, Cell and Developmental Biology; Biologic Institute, United States

Copyeditor

Ann Gauger, Molecular Genetics and Molecular Biology; Biologic Institute, United States

32 editors for six articles by a total of 11 authors of which five belong to the editorial team. At the same time five members of the editorial team (underlined) and three authors (Dembski, Meyer, Nelson) are fellows of the Discovery Institute. Quite an endeavor for six articles.

It would seem as if the DI has something against Asians.

   
Albatrossity2



Posts: 2779
Joined: Mar. 2007

(Permalink) Posted: Sep. 18 2011,15:53   

Quote (Art @ Sep. 18 2011,14:31)
It would seem as if the DI has something against Asians.

Perhaps Wells could help them be more inclusive by introducing Dembski et al. to the Rev. Moon...

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
CeilingCat



Posts: 1670
Joined: Dec. 2007

(Permalink) Posted: Sep. 18 2011,16:32   

Quote (George @ May 14 2010,09:37)
I predict that this thread will either be very short, mirroring the output of the new journal, or will turn into a UD-thread-esque monster complete with LOLcats if the journal proves to be rich new vein of tard.  Middle ground highly unlikely.  At this point, I'd have to put my money on option one.

So far, option one is winning big.

--------------
Like every other academic field, philosophy of religion has its share of hacks and mediocrities.  Edward Feser

  
Henry J



Posts: 4079
Joined: Mar. 2005

(Permalink) Posted: Sep. 18 2011,17:49   

Quote
It would seem as if the DI has something against Asians.

That's probably just because the DI is disoriented.

  
George



Posts: 313
Joined: Feb. 2006

(Permalink) Posted: Sep. 19 2011,02:20   

Quote (CeilingCat @ Sep. 18 2011,16:32)
Quote (George @ May 14 2010,09:37)
I predict that this thread will either be very short, mirroring the output of the new journal, or will turn into a UD-thread-esque monster complete with LOLcats if the journal proves to be rich new vein of tard.  Middle ground highly unlikely.  At this point, I'd have to put my money on option one.

So far, option one is winning big.

I can has magic 8-ball?

  
sparc



Posts: 1711
Joined: April 2007

(Permalink) Posted: Oct. 31 2011,00:12   

There's a new Axe paper in Bio_complexity:
Quote
A Stylus-Generated Artificial Genome with Analogy to Minimal Bacterial Genomes
Douglas Axe, Philip Lu, Stephanie Flatau

Abstract

The difficulty of explaining evolutionary innovation on a scale that would account for the functional diversity of life and its components continues to dog evolutionary theory. Experiments are shedding light on this, but the complexity of the subject calls for other approaches as well. In particular, computational models that capture some aspects of simple life may provide useful proving grounds for ideas about how evolution can or cannot work. The challenge is to find a model ‘world’ simple enough for rapid simulation but not so simple that the real thing of interest has been lost. That challenge is best met with a model world in which real-world problems can be solved, as otherwise the connection with real innovation would be in doubt. Stylus is a previously described model that meets this criterion by being based on one of the most powerful real-world problem-solving tools: written language. Stylus uses a genetic code to translate gene-like sequences into vector sequences that, when processed according to simple geometric rules, form patterns resembling penned strokes. These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes. In order for this possibility to be realized, we here provide a complete Stylus genome as an experimental starting point. To construct it we first wrote a concise description of the Stylus algorithm in Chinese. Using that as a proteome specification, we then constructed the Stylus genes to encode it. In this way the Stylus proteome specifies how its encoding genome is decoded, making it analogous to the gene-expression machinery of bacteria. The complete 70,701 base Stylus genome encodes 223 vector proteins with 112 distinct vector domain types, making it more compact than the smallest bacterial genome but with comparable proteomic complexity for its size.


--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
Doc Bill



Posts: 1006
Joined: April 2007

(Permalink) Posted: Nov. 02 2011,08:58   

Research to produce Chinese shadow characters, because, er, why?  Does it count if it's upside down?

Why is there air?

Tell me the Journal of Irreproducible Results is still published.

  
Tom Ames



Posts: 238
Joined: Dec. 2002

(Permalink) Posted: Nov. 02 2011,15:24   

Quote (sparc @ Oct. 30 2011,22:12)
There's a new Axe paper in Bio_complexity:  
Quote
A Stylus-Generated Artificial Genome with Analogy to Minimal Bacterial Genomes
Douglas Axe, Philip Lu, Stephanie Flatau

Abstract

The difficulty of explaining evolutionary innovation on a scale that would account for the functional diversity of life and its components continues to dog evolutionary theory. Experiments are shedding light on this, but the complexity of the subject calls for other approaches as well. In particular, computational models that capture some aspects of simple life may provide useful proving grounds for ideas about how evolution can or cannot work. The challenge is to find a model ‘world’ simple enough for rapid simulation but not so simple that the real thing of interest has been lost. That challenge is best met with a model world in which real-world problems can be solved, as otherwise the connection with real innovation would be in doubt. Stylus is a previously described model that meets this criterion by being based on one of the most powerful real-world problem-solving tools: written language. Stylus uses a genetic code to translate gene-like sequences into vector sequences that, when processed according to simple geometric rules, form patterns resembling penned strokes. These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes. In order for this possibility to be realized, we here provide a complete Stylus genome as an experimental starting point. To construct it we first wrote a concise description of the Stylus algorithm in Chinese. Using that as a proteome specification, we then constructed the Stylus genes to encode it. In this way the Stylus proteome specifies how its encoding genome is decoded, making it analogous to the gene-expression machinery of bacteria. The complete 70,701 base Stylus genome encodes 223 vector proteins with 112 distinct vector domain types, making it more compact than the smallest bacterial genome but with comparable proteomic complexity for its size.

I love how the paper's footer lists the citation as "Vol. 2011, Issue 3". As if there is other content besides this.

Each article in the "Journal of Bio-DougAxe-ity" is its own issue, of course.

--------------
-Tom Ames

  
Doc Bill



Posts: 1006
Joined: April 2007

(Permalink) Posted: Nov. 02 2011,21:45   

These people, Axe et al, are so STUPID they don't even realize how STUPID they are!

It's not even an echo chamber any more.  It's a stupid, tard-filled echo chamber inside of an insane echo chamber surrounded by an irrational echo chamber.

If they could only make this stuff into a vest they could compete in the Kevlar market.

  
sparc



Posts: 1711
Joined: April 2007

(Permalink) Posted: Nov. 05 2011,01:36   

Axe's latest paper got shredded by PZ. One of the Pharyngula comments pointed to the page of Thomas D. Schneider the inventor of EV where he demolishes Montanez, Ewert, Dembski, Marks "A Vivisection of the ev Computer Organism: Identifying Sources of Active Information" from the 2010 issue of Bio-Complexity.

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
sparc



Posts: 1711
Joined: April 2007

(Permalink) Posted: April 07 2012,05:51   

The new Ewert, Dembski, Marks article on the Steiner problem didn't change the number of authors who published in Bio-Complexity. The number increased from 11 to 13 when Axe's Stylus paper appeared in 2011. Right now it's still the same 13 authors. 5 of them belong to the Biocomplexity's editorial team of 32 (!) editors. 5 members of the editorial team and 3 authors (Dembski, Meyer, Nelson) are fellows of the Discovery Institute. The 13 authors of the now 7 papers come from only 5 Instituitions:

Biologic Institute, Seattle, Washington, USA
1. Philip Lu
2. Stephanie Flatau
3. Ann K. Gauger
4. Pamela F. Fahey
5. Douglas D. Axe*

Department of Biology and Earth Science, University of Wisconsin, Superior, Wisconsin, USA
6. Stephanie Ebnet
7. Ralph Seelke

Department of Computer Science, Baylor University, Waco, Texas, USA
8. George Montañez
9. Winston Ewert

Discovery Institute, Seattle, Washington, USA;
10. William A. Dembski
11. Stephen C. Meyer
12. Paul A. Nelson

Department of Electrical and Computer Engineering, Baylor University, Waco, Texas, USA
13. Robert J. Marks II

Marks, Ewert and Montanez seem to prefer the credentials of Baylor rather than their (and Dembski's) other affiliation the Evolutionary Informatics Lab. If they would use the later the number of institutions contributing to the journal would decrease to 4. Taking into account that the Biological Institute belongs to the DI  only 3 remain.

--------------
"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
Kattarina98



Posts: 1255
Joined: Sep. 2009

(Permalink) Posted: April 07 2012,08:19   

Quote (sparc @ April 07 2012,05:51)
... the Biocomplexity's editorial team of 32 (!) editors ...

How else can they cope with the avalanche of papers submitted each day?

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Barry Arrington is a bitch.

  
Wesley R. Elsberry



Posts: 4505
Joined: May 2002

(Permalink) Posted: April 07 2012,12:26   

It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

Quote


They claim that GAs cannot generate true novelty
and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness
testing function


They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.


There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
BillB



Posts: 359
Joined: Aug. 2009

(Permalink) Posted: April 16 2012,07:38   

Quote (Wesley R. Elsberry @ April 07 2012,18:26)
It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

Quote


They claim that GAs cannot generate true novelty
and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness
testing function


They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.


There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

So how does that work if you are a theistic evolutionist - All living things we see today are the result of evolutionary processes acting on, and from, the first life forms - but none of the specified complexity we see in life today is a result of those processes.

  
fusilier



Posts: 212
Joined: Feb. 2003

(Permalink) Posted: April 16 2012,07:54   

Quote (BillB @ April 16 2012,08:38)
Quote (Wesley R. Elsberry @ April 07 2012,18:26)
It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

 
Quote


They claim that GAs cannot generate true novelty
and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness
testing function


They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

 
Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.


There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

So how does that work if you are a theistic evolutionist - All living things we see today are the result of evolutionary processes acting on, and from, the first life forms - but none of the specified complexity we see in life today is a result of those processes.

That's not what theistic evolution says.

The CSI bullshit is from creationism, not evolutionary biology.

--------------
fusilier
James 2:24

  
BillB



Posts: 359
Joined: Aug. 2009

(Permalink) Posted: April 16 2012,09:05   

Quote (fusilier @ April 16 2012,13:54)
Quote (BillB @ April 16 2012,08:38)
Quote (Wesley R. Elsberry @ April 07 2012,18:26)
It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

 
Quote


They claim that GAs cannot generate true novelty
and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness
testing function


They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

 
Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.


There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

So how does that work if you are a theistic evolutionist - All living things we see today are the result of evolutionary processes acting on, and from, the first life forms - but none of the specified complexity we see in life today is a result of those processes.

That's not what theistic evolution says.

The CSI bullshit is from creationism, not evolutionary biology.

Yes, I know. My question was aimed at creationists.

Perhaps I should have put an 'irony' tag before my comment.

  
Kattarina98



Posts: 1255
Joined: Sep. 2009

(Permalink) Posted: July 04 2012,02:02   

Denyse informs us that BIO-Complexity proudly published a review by Matti Leisola, Ossi Pastinen, Douglas Axe: Lignin—Designed Randomness
   
Quote
Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

You didn't expect actual research, did you? It's a critical review - duh!

   
Quote
In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:    
Quote
The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

ETA: My emphasis

Edited by Kattarina98 on July 04 2012,02:03

--------------
Barry Arrington is a bitch.

  
The whole truth



Posts: 1030
Joined: Jan. 2012

(Permalink) Posted: July 04 2012,08:38   

Quote (Kattarina98 @ July 04 2012,00:02)
Denyse informs us that BIO-Complexity proudly published a review by Matti Leisola, Ossi Pastinen, Douglas Axe: Lignin—Designed Randomness
       
Quote
Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

You didn't expect actual research, did you? It's a critical review - duh!

       
Quote
In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:        
Quote
The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

ETA: My emphasis

I think we should move on to a more philosophical level ;) by considering whether the existence of IDiots is more readily explained from the "Darwinian" perspective or from the design perspective or from the 'some people are just arrogant loons that believe and promote religious bullshit pretending to be science' perspective.

We should also consider, from a more philosophical level of course ;), that the design account/perspective must somehow reconcile an allegedly perfect, omnipotent, omniscient designer-god creating bullshit believing/promoting IDiots, and that that allegedly perfect god has had at least 13 billion years to get its creation (the universe and everything in it) right and yet it's still far from perfect.

And one more thing we should consider is that the perfect, omnipotent, omniscient designer-god account/perspective must somehow reconcile the thousands of years of the failure of religious beliefs to provide any useful human knowledge, especially in comparison to the fact that reality based science (which also isn't perfect, and has been stifled by religious zealots) has produced an enormous amount of useful knowledge in far less time and continues to produce useful knowledge.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
fnxtr



Posts: 2137
Joined: June 2006

(Permalink) Posted: July 04 2012,09:39   

must not submit blue "dine on my wood" comment.
must not submit blue "dine on my wood" comment.
must not submit blue "dine on my wood" comment.

--------------
"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

  
NormOlsen



Posts: 104
Joined: Nov. 2011

(Permalink) Posted: July 04 2012,09:54   

Quote
Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective. Next, we praise Jesus for the existence of lignin and what it tells us about the poverty of the Darwinian explanation.  And finally, we speculate that the long age of Methuselah and other antediluvians listed in Genesis 5 was due to the fact that they were actually made of lignin and thus could live as long as many trees, praise be to God.


Last draft before final edit.

  
The whole truth



Posts: 1030
Joined: Jan. 2012

(Permalink) Posted: July 04 2012,10:07   



--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Timothy McDougald



Posts: 1012
Joined: Dec. 2006

(Permalink) Posted: July 04 2012,10:23   

Quote (Kattarina98 @ July 04 2012,02:02)
Denyse informs us that BIO-Complexity proudly published a review by Matti Leisola, Ossi Pastinen, Douglas Axe: Lignin—Designed Randomness
     
Quote
Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

You didn't expect actual research, did you? It's a critical review - duh!

     
Quote
In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:      
Quote
The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

ETA: My emphasis

I'm not a biochemist, but I think the answer to their riddle can be found in the abstract:
Quote
Fungi accomplish the biodegradation, and the surprising fact that it costs them energy to do so keeps the process gradual.
Bolding mine.

I expect their next paper to argue that extremophiles and the environments they live in are evidence of design because no animals evolved to live there...

Edit to add: I'm not sure why it is surprising that it takes energy to biodegrade lignin

--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Glen Davidson



Posts: 752
Joined: May 2006

(Permalink) Posted: July 04 2012,10:36   

Quote (Kattarina98 @ July 04 2012,02:02)
Denyse informs us that BIO-Complexity proudly published a review by Matti Leisola, Ossi Pastinen, Douglas Axe: Lignin—Designed Randomness
     
Quote
Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

You didn't expect actual research, did you? It's a critical review - duh!

     
Quote
In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:      
Quote
The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

ETA: My emphasis

Because with God, most things are impossible.

Lignin digestion, native radio communication between intelligent brains (why don't we have some sort of ESP?), and getting beyond the limits of evolution.

Evolution, by contrast, has no limits.  The IDiots themselves have said so over and over again, and they wouldn't be wrong.

Glen Davidson

--------------
http://tinyurl.com/mxaa3p....p

Nothing in biology makes sense except in the light of coincidence---ID philosophy

   
Kattarina98



Posts: 1255
Joined: Sep. 2009

(Permalink) Posted: July 04 2012,10:40   

Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

--------------
Barry Arrington is a bitch.

  
The whole truth



Posts: 1030
Joined: Jan. 2012

(Permalink) Posted: July 04 2012,11:39   

Quote (Kattarina98 @ July 04 2012,08:40)
Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
midwifetoad



Posts: 3568
Joined: Mar. 2008

(Permalink) Posted: July 04 2012,12:17   

Quote (The whole truth @ July 04 2012,11:39)
Quote (Kattarina98 @ July 04 2012,08:40)
Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

--------------
”let’s not make a joke of ourselves.”

Pat Robertson

  
Timothy McDougald



Posts: 1012
Joined: Dec. 2006

(Permalink) Posted: July 04 2012,13:13   

Quote (midwifetoad @ July 04 2012,12:17)
Quote (The whole truth @ July 04 2012,11:39)
Quote (Kattarina98 @ July 04 2012,08:40)
Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

Yes

--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
midwifetoad



Posts: 3568
Joined: Mar. 2008

(Permalink) Posted: July 04 2012,14:06   

I was thinking of this peer reviewed journal.

http://www.washingtonpost.com/wp-dyn....71.html

--------------
”let’s not make a joke of ourselves.”

Pat Robertson

  
The whole truth



Posts: 1030
Joined: Jan. 2012

(Permalink) Posted: July 04 2012,14:32   

Quote (afarensis @ July 04 2012,11:13)
Quote (midwifetoad @ July 04 2012,12:17)
Quote (The whole truth @ July 04 2012,11:39)
 
Quote (Kattarina98 @ July 04 2012,08:40)
Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

Yes

Maybe I missed it but I don't see anything at the end of that link that says anything about anything eating and digesting uranium. I also didn't see anything about extremophiles that use the heat from radioactive decay in lieu of sunlight. What I saw is an article about resistance to radiation. It's interesting but I don't think it refutes what I said.

Besides, it really doesn't matter whether I put uranium or lugnuts in that sentence. What really matters is that the IDiots are playing their usual game where they look for something unrelated to whether evolution (at least in general) occurs and then they try to get people to take them seriously and play along with their ridiculous game.

I'm sure that there are plenty of things that are not digestible and that organisms can't "grow on", yet evolution obviously occurs anyway. For instance, I really don't think that a human can digest and "grow on" water hemlock plants or asteroids but I'm pretty sure that humans have evolved. Even if nothing could eat, digest, or "grow on" lignin, it wouldn't mean a thing to whether evolution occurs.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
The whole truth



Posts: 1030
Joined: Jan. 2012

(Permalink) Posted: July 04 2012,14:52   

Quote (midwifetoad @ July 04 2012,12:06)
I was thinking of this peer reviewed journal.

http://www.washingtonpost.com/wp-dyn.....71.html

That study appears to link the bacteria to using radiation in lieu of sunlight but it also appears that the bacteria are feeding on sulfur, not uranium. It's pretty cool anyway.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Timothy McDougald



Posts: 1012
Joined: Dec. 2006

(Permalink) Posted: July 04 2012,15:16   

Quote (The whole truth @ July 04 2012,14:32)
Quote (afarensis @ July 04 2012,11:13)
Quote (midwifetoad @ July 04 2012,12:17)
 
Quote (The whole truth @ July 04 2012,11:39)
 
Quote (Kattarina98 @ July 04 2012,08:40)
Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

Yes

Maybe I missed it but I don't see anything at the end of that link that says anything about anything eating and digesting uranium. I also didn't see anything about extremophiles that use the heat from radioactive decay in lieu of sunlight. What I saw is an article about resistance to radiation. It's interesting but I don't think it refutes what I said.

Besides, it really doesn't matter whether I put uranium or lugnuts in that sentence. What really matters is that the IDiots are playing their usual game where they look for something unrelated to whether evolution (at least in general) occurs and then they try to get people to take them seriously and play along with their ridiculous game.

I'm sure that there are plenty of things that are not digestible and that organisms can't "grow on", yet evolution obviously occurs anyway. For instance, I really don't think that a human can digest and "grow on" water hemlock plants or asteroids but I'm pretty sure that humans have evolved. Even if nothing could eat, digest, or "grow on" lignin, it wouldn't mean a thing to whether evolution occurs.

I wasn't trying to refute anything you said, I was responding to midwifetoad...

--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
midwifetoad



Posts: 3568
Joined: Mar. 2008

(Permalink) Posted: July 04 2012,15:17   

Feeding is associated with "burning" in animals, but what does feeding mean to an organism that turns radiant energy into complex molecules? Couldn't you say that some organisms feed on energy gradients?

Just asking.

--------------
”let’s not make a joke of ourselves.”

Pat Robertson

  
fnxtr



Posts: 2137
Joined: June 2006

(Permalink) Posted: July 04 2012,19:29   

Quote (midwifetoad @ July 04 2012,13:17)
Feeding is associated with "burning" in animals, but what does feeding mean to an organism that turns radiant energy into complex molecules? Couldn't you say that some organisms feed on energy gradients?

Just asking.

Oh hell yes. Just ask Mike Elzinga... :-)

--------------
"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

  
The whole truth



Posts: 1030
Joined: Jan. 2012

(Permalink) Posted: July 05 2012,08:42   

Quote (midwifetoad @ July 04 2012,13:17)
Feeding is associated with "burning" in animals, but what does feeding mean to an organism that turns radiant energy into complex molecules? Couldn't you say that some organisms feed on energy gradients?

Just asking.

I suppose it depends on how "feeding" is defined. In a way it could be said that all organisms "feed" on radiant energy because without radiant energy there wouldn't be any organisms. Feeding is usually thought of as something that's done through a mouth but of course there are many organisms that "feed" on various things in ways other than through a mouth.

A bunch of words could be used to describe the ways that  organisms take in the energy they need to survive, such as feed, eat, consume, absorb, drink, digest, inhale, burn, convert, synthesize, and probably more that I can't think of right now. I guess the phrase "Nature will find a way" is true.

By the way, I didn't mean to sound harsh to you or afarensis. That's the trouble with the written word. It leaves a lot to be desired when trying to convey some things.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
blipey



Posts: 2061
Joined: June 2006

(Permalink) Posted: July 05 2012,10:10   

Quote (The whole truth @ July 05 2012,08:42)
By the way, I didn't mean to sound harsh to you or afarensis. That's the trouble with the written word. It leaves a lot to be desired when trying to convey some things.

The written word has not evolved!  Evolution is false!!!

Whan that Aprill with his shoures soote
The droghte of March hath perced to the roote,
And bathed every veyne in swich licour
Of which vertu engendred is the flour;

--------------
But I get the trick question- there isn't any such thing as one molecule of water. -JoeG

And scientists rarely test theories. -Gary Gaulin

   
Kattarina98



Posts: 1255
Joined: Sep. 2009

(Permalink) Posted: July 07 2012,11:36   

Cross post from the Uncommonly Dense thread:

It's getting even weirder - now Gauger has defended Axe et al.'s paper on lignin at BioComplexity, and O'Leary has copied it onto UD. What a bunch of cowards.

Edit: http://tinyurl.com/c6p6u5a....c6p6u5a leads to UD

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Barry Arrington is a bitch.

  
The whole truth



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(Permalink) Posted: July 07 2012,13:19   

Quote (Kattarina98 @ July 07 2012,09:36)
Cross post from the Uncommonly Dense thread:

It's getting even weirder - now Gauger has defended Axe et al.'s paper on lignin at BioComplexity, and O'Leary has copied it onto UD. What a bunch of cowards.

Edit: http://tinyurl.com/c6p6u5a....c6p6u5a leads to UD

Man oh man, are those IDiots screwed up or what? Why on Earth do they think that lignin, or the digestibility of it, or anything else about it, has ANYTHING to do with whether THEIR god or ANY god exists or not?

Something I often think about is that even IF it could be shown that the universe is designed or is likely designed, it would NOT show that the universe was/is designed by the christian god or any other particular god, unless the IDiots can find and show DIRECT evidence to the christian god or some other particular god.

And of course they will never accept that a god other than the christian god is the creator/designer, so any suggestion of a different god is a non-starter with IDiots anyway. Oh sure, they're a so-called "big tent" and they pretend that they're open minded about "the Designer" or "God" or which god is the alleged creator/designer but it's abundantly clear that the only designer/god they believe in and promote is the christian god, and of course they all have their own version of the christian god.

Arguments/assertions that lignin somehow disproves evolution and proves design shows just how desperate, delusional, arrogant, and ridiculous the IDiots are. They KNOW that their beliefs are absolute bullshit and they have no faith in their own so-called faith. They constantly bring up shit that is so absurd, and so irrelevant, and so insane that it's just mind-boggling!

They spend all of their time looking for so-called "gaps" and other even more ridiculous shit and will resort to ANYTHING, no matter how asinine, desperate, or dishonest it is, to try to destroy science and to con people into swallowing their fairy tales. What a way to waste their lives.

And what's next from the IDiot god zombies? No organisms have evolved that eat black holes dipped in galactic quasar sauce with atomic sprinkles on top, therefor jesus?

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Henry J



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(Permalink) Posted: July 07 2012,23:01   

Quote
And what's next from the IDiot god zombies? No organisms have evolved that eat black holes dipped in galactic quasar sauce with atomic sprinkles on top, therefor jesus?

Don't forget the ad homonym word salad on the side.

Henry

  
DiEb



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(Permalink) Posted: Jan. 29 2014,12:19   

Has anyone read BIO-Complexity's only "research article" for 2013:  Active Information in Metabiology? It was published last month...

   
OgreMkV



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(Permalink) Posted: Jan. 29 2014,16:37   

Quote (DiEb @ Jan. 29 2014,12:19)
Has anyone read BIO-Complexity's only "research article" for 2013:  Active Information in Metabiology? It was published last month...

That's the funniest thing I've seen in a while.

I don't recall ever seeing the phrase "fascinating intellectual romp" in a peer reviewed paper before.

Of course, when one's peers are morons...

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Dr.GH



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(Permalink) Posted: Jan. 31 2014,01:06   

Quote (OgreMkV @ Jan. 29 2014,14:37)
Quote (DiEb @ Jan. 29 2014,12:19)
Has anyone read BIO-Complexity's only "research article" for 2013:  Active Information in Metabiology? It was published last month...

That's the funniest thing I've seen in a while.

I don't recall ever seeing the phrase "fascinating intellectual romp" in a peer reviewed paper before.

Of course, when one's peers are morons...

Wow. The entire abstract is a word fest.

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
sparc



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(Permalink) Posted: Feb. 12 2014,23:16   

No new articles. Still, D. Klinghoffer is celbrating Bio-Complexity's 4th birthday

[mibad--meant to reply but hit Edit instead. -Steve]

Edited by stevestory on Feb. 13 2014,11:00

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"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
k.e..



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(Permalink) Posted: Feb. 13 2014,08:10   

Tard to ass resuscitation....where's Joe?

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"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"Abbie Smith (ERV) who's got to be the most obnoxious arrogant snot I've ever seen except for when I look in a mirror" DAVE TARD
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus

  
stevestory



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(Permalink) Posted: Feb. 13 2014,10:00   

Quote (sparc @ Feb. 13 2014,00:16)
No new articles. Still, D. Klinghoffer is celbrating Bio-Complexity's 4th birthday

[mibad--meant to reply but hit Edit instead. -Steve]

Quote
Happy Darwin Day! To Celebrate, Go Review Four Years of BIO-Complexity
David Klinghoffer February 12, 2014 3:34 AM

Why not? It sure won't take long  :p

   
REC



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(Permalink) Posted: Feb. 13 2014,16:32   

Wonder what happened to the follow-up on this one:

Quote
These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes. In order for this possibility to be realized, we here provide a complete Stylus genome as an experimental starting point.


Kinda goofy, but they built a 70,000 word genome. Not a small amount of work. This was done and written up by May 2011. And then, did they try to 'evolve' it?

Guesses:
1) They did, it works, shhh....
2) DI gets into a fight: providing a fitness landscape is "smuggling information" in even though that is exactly what the environment does in evolution, crap our analogy defeats our point...shh
3) The Chinese speaker bailed
4) The bug evolved into the prolific writings of VJTorley, translated and dumped onto UD for us.

Link

Edited by REC on Feb. 13 2014,16:32

  
DiEb



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(Permalink) Posted: April 08 2014,15:13   

Winston Ewert wrote the first paper of 2014: Digital Irreducible Complexity: A Survey of Irreducible Complexity in Computer Simulations. I've just started to read it and I already have a problem with the last paragraph of his section on "Avida" (p. 3):
Quote
The parts in Avida are the individual steps in the process. If any of the steps in the process are missing, Avida will fail to calculate the EQU function. In this sense Pennock is correct, but we will discuss whether he is correct with respect to the other terms of Behe’s definition.

Isn't the EQU function the irreducibly complex system, and Avida just the environment in which it dwells?

   
Quack



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(Permalink) Posted: April 08 2014,16:25   

Quote (k.e.. @ Feb. 13 2014,08:10)
Tard to ass resuscitation....where's Joe?

Here

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The first principle is that you must not fool yourself — and you are the easiest person to fool.
                                                                                               Richard Feynman

  
midwifetoad



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(Permalink) Posted: April 08 2014,17:32   

Joe was much smarter when he was dead.

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”let’s not make a joke of ourselves.”

Pat Robertson

  
Zachriel



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(Permalink) Posted: April 08 2014,19:22   

Quote
Ewert 2014: The largest model considered here, Avida, uses approximately fifty million digital organisms [14]. The smallest model considered, Sadedin’s geometric model, uses fifty thousand digital organisms [17]. The individual components should be improbable enough that the average guessing time exceeds these numbers. We can determine this probability by taking one over the cube root of the number of digital organisms in the model. We are taking the cube root because we are assuming the minimal number of parts to be three. The actual system may have more parts, but we are interested in the level of complexity that would make it impossible to produce any system of several parts. Making this calculation gives us minimal required levels for complexity of approximately 1/368 for Avida and 1/37 for Sadedin’s model.

If you want to know the probability of calculating the random assembly of a specific sequence of three with an alphabet of 26, it is 1/(26^3) = 1/17576.

If there is a population of random sequences of 50 million, then it is virtually certain to occur. However, if the specific sequence has a length of nineteen, then the probability is 1/(26^19) = 1/7e26, which is virtually impossible in 50 million trials, or even 50 million trials a million million times.

-
xposted from uncommon thread


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Tard Acquisition and Repository Department

   
DiEb



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(Permalink) Posted: April 11 2014,06:19   

Quote (Zachriel @ April 09 2014,01:22)
Quote
Ewert 2014: The largest model considered here, Avida, uses approximately fifty million digital organisms [14]. The smallest model considered, Sadedin’s geometric model, uses fifty thousand digital organisms [17]. The individual components should be improbable enough that the average guessing time exceeds these numbers. We can determine this probability by taking one over the cube root of the number of digital organisms in the model. We are taking the cube root because we are assuming the minimal number of parts to be three. The actual system may have more parts, but we are interested in the level of complexity that would make it impossible to produce any system of several parts. Making this calculation gives us minimal required levels for complexity of approximately 1/368 for Avida and 1/37 for Sadedin’s model.

If you want to know the probability of calculating the random assembly of a specific sequence of three with an alphabet of 26, it is 1/(26^3) = 1/17576.

If there is a population of random sequences of 50 million, then it is virtually certain to occur. However, if the specific sequence has a length of nineteen, then the probability is 1/(26^19) = 1/7e26, which is virtually impossible in 50 million trials, or even 50 million trials a million million times.

-
xposted from uncommon thread

Winston Ewert started a thread on his article at Sal Cordova's Creation Evolution University: Digital Irreducible Complexity - Author Thread

   
sparc



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(Permalink) Posted: April 11 2014,07:21   

Quote (DiEb @ April 11 2014,06:19)
Quote (Zachriel @ April 09 2014,01:22)
 
Quote
Ewert 2014: The largest model considered here, Avida, uses approximately fifty million digital organisms [14]. The smallest model considered, Sadedin’s geometric model, uses fifty thousand digital organisms [17]. The individual components should be improbable enough that the average guessing time exceeds these numbers. We can determine this probability by taking one over the cube root of the number of digital organisms in the model. We are taking the cube root because we are assuming the minimal number of parts to be three. The actual system may have more parts, but we are interested in the level of complexity that would make it impossible to produce any system of several parts. Making this calculation gives us minimal required levels for complexity of approximately 1/368 for Avida and 1/37 for Sadedin’s model.

If you want to know the probability of calculating the random assembly of a specific sequence of three with an alphabet of 26, it is 1/(26^3) = 1/17576.

If there is a population of random sequences of 50 million, then it is virtually certain to occur. However, if the specific sequence has a length of nineteen, then the probability is 1/(26^19) = 1/7e26, which is virtually impossible in 50 million trials, or even 50 million trials a million million times.

-
xposted from uncommon thread

Winston Ewert started a thread on his article at Sal Cordova's Creation Evolution University: Digital Irreducible Complexity - Author Thread

Why did he chose the pages of this not-even-intelligent-design-proponent-YEC? He could have offered you some of the space available for online comments in Bio-Complexity.

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"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
sparc



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(Permalink) Posted: April 11 2014,07:33   

Here's a link to a google search for all comments ever left at Bio-Complexity: "Reader comments" site:bio-complexity.org

ETA: Judge yourself.

Edited by sparc on April 11 2014,07:34

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"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

- William Dembski -

   
REC



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(Permalink) Posted: July 10 2014,21:19   

I see Bio-Complexity has posted their 3rd! (review) article of 2014, by David Snoke. As in "Behe and Snoke." Champagne corks popping!!!!

What is odd to me is that it seemed to get 0 fanfare, from UD, DI news, ENV.... at least that I saw or can find by google.

True, the subject is genuinely embarrassing: "Systems Biology as a Research Program for Intelligent Design." Snoke went to a conference that featured Systems Biology, declares it springs from ID.

But why the silence?

Quote
..in 2001 I wrote:
A theory of design can in principle be predictive and
quantitative. For example, a computer chip manufacturer,
which takes apart a chip made by a rival
company, proceeds on the assumption that the circuits
are well designed; this does not lead them to
end their investigation, but rather, drives their study
of the chip. The good-design assumption leads to
specific predictions and applications, e.g., the prediction
that it is unlikely to find wires which take up
metal and space but serve no purpose, so that there
should be few wires which are dead ends, with the
application that studying any particular wire is likely
to be useful. A bad-design assumption (e.g. that the
chip maker made many random circuits and then
just picked out the ones that worked) would give
very different predictions.


Hmm.... so "bad design" isn't a religious statement. The ID design inference is, and has been, to good design only.

Lots of "there is no junk" and the that the language "design or function or mechanism"="Designed Functions and God's Machines."

  
midwifetoad



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(Permalink) Posted: July 12 2014,17:04   

Actually there is an evolved circuit that works better than most designed circuits and has stuff that goes nowhere.

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Pat Robertson

  
Henry J



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(Permalink) Posted: July 14 2014,10:42   

Quote (midwifetoad @ July 12 2014,16:04)
Actually there is an evolved circuit that works better than most designed circuits and has stuff that goes nowhere.

Is that from its EM field affecting other circuits, or is it a quantum effect? (Not that I'd understand the details, but anyway.)

  
midwifetoad



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(Permalink) Posted: July 15 2014,06:11   

Rather old.

http://www.genetic-programming.com/publish....96.html

http://en.m.wikipedia.org/wiki....ardware

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”let’s not make a joke of ourselves.”

Pat Robertson

  
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