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



Posts: 1378
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: 10064
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: 3260
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: 312
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: 530
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: 2080
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: 530
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: 4465
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: 3037
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: 1776
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: 3037
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: 1479
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: 228
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: 4360
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: 1671
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: 1950
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: 1671
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: 2777
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: 1648
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

‘Anything is a “real possibility” in the mind of one seeking to deny the obvious.’ – William J Murray

  
Henry J



Posts: 3999
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: 312
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: 1671
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: 1000
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: 1000
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.

  
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