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olegt



Posts: 1405
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.


--------------
If you are not:
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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: 11178
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: 3668
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: 316
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: 533
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: 3504
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?

--------------
"[A] book said there were 5 trillion witnesses. Who am I supposed to believe, 5 trillion witnesses or you? That shit's, like, ironclad. " -- stevestory

"Wow, you must be retarded. I said that CO2 does not trap heat. If it did then it would not cool down at night."  Joe G

  
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: 533
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: 4991
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: 3061
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: 1828
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: 3061
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: 1554
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

Frequency is just the plural of wavelength...
-JoeG

  
DiEb



Posts: 312
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: 4402
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: 2089
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 Montańez, 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: 2333
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: 2089
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 Montańez, 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: 2780
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: 2363
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.

  
Henry J



Posts: 5787
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: 316
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: 2089
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: 1039
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: 1039
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: 2089
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: 2089
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 Montańez
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: 1267
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?

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

  
Wesley R. Elsberry



Posts: 4991
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: 388
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: 252
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: 388
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: 1267
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: 1554
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: 3504
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.

--------------
"[A] book said there were 5 trillion witnesses. Who am I supposed to believe, 5 trillion witnesses or you? That shit's, like, ironclad. " -- stevestory

"Wow, you must be retarded. I said that CO2 does not trap heat. If it did then it would not cool down at night."  Joe G

  
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: 1554
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: 1036
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: 1100
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: 1267
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: 1554
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: 4003
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.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Timothy McDougald



Posts: 1036
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: 4003
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

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
The whole truth



Posts: 1554
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: 1554
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: 1036
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: 4003
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.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
fnxtr



Posts: 3504
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... :-)

--------------
"[A] book said there were 5 trillion witnesses. Who am I supposed to believe, 5 trillion witnesses or you? That shit's, like, ironclad. " -- stevestory

"Wow, you must be retarded. I said that CO2 does not trap heat. If it did then it would not cool down at night."  Joe G

  
The whole truth



Posts: 1554
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: 1267
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?

--------------
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.

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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
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
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



Posts: 638
Joined: Sep. 2006

(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



Posts: 312
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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



Posts: 1961
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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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Rocks have no biology.
              Robert Byers.

  
midwifetoad



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

Joe was much smarter when he was dead.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
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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You never step on the same tard twice—for it's not the same tard and you're not the same person.

   
DiEb



Posts: 312
Joined: May 2008

(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



Posts: 2089
Joined: April 2007

(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



Posts: 2089
Joined: April 2007

(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



Posts: 638
Joined: Sep. 2006

(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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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Henry J



Posts: 5787
Joined: Mar. 2005

(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



Posts: 4003
Joined: Mar. 2008

(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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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
sparc



Posts: 2089
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(Permalink) Posted: Dec. 19 2014,23:08   

Jeffrey Shallit has done us the great favor of reviewing the contributions to the 2014 volume of Bio-Complexity (reprinted at PT):
Quote
How many papers did Bio-Complexity manage to publish this year? A grand total of four! Why, that's 1/8th of a paper per member of the editorial team. By any measure, this is simply astounding productivity. They can be proud of how much they have added to the world's knowledge!

Looking a little deeper, we see that of these four, only one is labeled as a "research article". Two are "critical reviews" and one is a "critical focus". And of these four stellar contributions, one has 2 out of the 3 authors on the editorial team, two are written by members of the editorial team, leaving only one contribution having no one on the editorial team. And that one is written by Winston Ewert, who is a "senior researcher" at Robert J. Marks II's "evolutionary informatics lab". In other words, with all the ideas that ID supporters are brimming with, they couldn't manage to publish a single article by anyone not on the editorial team or directly associated with the editors.


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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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Joined: Sep. 2006

(Permalink) Posted: Aug. 29 2015,12:08   

Here we are, 2/3 of the way through 2015, and Biocomplexity has an outstanding -0- publications.

30 or so editors, the work of the full-time research staff of the Biologic institute.......

  
Henry J



Posts: 5787
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(Permalink) Posted: Aug. 29 2015,13:30   

I guess there were complications?

  
REC



Posts: 638
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(Permalink) Posted: Aug. 29 2015,14:25   

Quote (Henry J @ Aug. 29 2015,13:30)
I guess there were complications?

Such as the complete collapse of ID, which has left the little scientific facade they created dangling in the breeze?

  
Bob O'H



Posts: 2564
Joined: Oct. 2005

(Permalink) Posted: Aug. 31 2015,06:40   

Quote (REC @ Aug. 29 2015,12:08)
Here we are, 2/3 of the way through 2015, and Biocomplexity has an outstanding -0- publications.

30 or so editors, the work of the full-time research staff of the Biologic institute.......

But as of June they do have a new editor in chief. I'm not sure who should be more embarrassed - us for not noticing, or them for being so irrelevant that nobody noticed, not us and not UD either.

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It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
Occam's Aftershave



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(Permalink) Posted: Aug. 31 2015,08:36   

Quote (Bob O'H @ Aug. 31 2015,06:40)
Quote (REC @ Aug. 29 2015,12:08)
Here we are, 2/3 of the way through 2015, and Biocomplexity has an outstanding -0- publications.

30 or so editors, the work of the full-time research staff of the Biologic institute.......

But as of June they do have a new editor in chief. I'm not sure who should be more embarrassed - us for not noticing, or them for being so irrelevant that nobody noticed, not us and not UD either.

I wonder if Editor Marks will bring back his "Galapagos Finch" character he used to post as on UD.  That would make their phony science rag almost worth reading.  Almost.   :D

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"CO2 can't re-emit any trapped heat unless all the molecules point the right way"
"All the evidence supports Creation baraminology"
"If it required a mind, planning and design, it isn't materialistic."
"Jews and Christians are Muslims."

- Joke "Sharon" Gallien, world's dumbest YEC.

  
The whole truth



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(Permalink) Posted: Aug. 31 2015,15:31   

Quote (Bob O'H @ Aug. 31 2015,04:40)
   
Quote (REC @ Aug. 29 2015,12:08)
Here we are, 2/3 of the way through 2015, and Biocomplexity has an outstanding -0- publications.

30 or so editors, the work of the full-time research staff of the Biologic institute.......

But as of June they do have a new editor in chief. I'm not sure who should be more embarrassed - us for not noticing, or them for being so irrelevant that nobody noticed, not us and not UD either.


Hmm, there have been no publications in 'Bio-Complexity' this year, including since Marks became editor-in-chief, so what is editor-in-chief Marks chiefly editing? And what was the former editor-in-chief chiefly editing?

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

   
J-Dog



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Joined: Dec. 2006

(Permalink) Posted: Aug. 31 2015,16:13   

Quote
And what was the former editor-in-chief chiefly editing?


I'm guessing fart noises.   It's what he's qualified for.
And Barry A and Gordo are certainly qualified to put their noses to the grindstone on this for the Honor & Glory That is ID.

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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

  
Henry J



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(Permalink) Posted: Aug. 31 2015,16:30   

Maybe notpologies?

  
Leftfield



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(Permalink) Posted: Aug. 31 2015,18:53   

Quote (Henry J @ Aug. 31 2015,16:30)
Maybe notpologies?



Notractions?

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Speaking for myself, I have long been confused . . .-Denyse O'Leary

  
k.e..



Posts: 5432
Joined: May 2007

(Permalink) Posted: Aug. 31 2015,19:11   

Quote (Leftfield @ Sep. 01 2015,02:53)
Quote (Henry J @ Aug. 31 2015,16:30)
Maybe notpologies?



Notractions?

Well as a vanity publication peer review free, it's mainly missing vanity.

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"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
Dr.GH



Posts: 2333
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(Permalink) Posted: Aug. 31 2015,22:30   

Quote (k.e.. @ Aug. 31 2015,17:11)
Quote (Leftfield @ Sep. 01 2015,02:53)
Quote (Henry J @ Aug. 31 2015,16:30)
Maybe notpologies?



Notractions?

Well as a vanity publication peer review free, it's mainly missing vanity.

And publication.
???

   
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Aug. 31 2015,22:42   

Wonder how many submissions they rejected?

  
k.e..



Posts: 5432
Joined: May 2007

(Permalink) Posted: Aug. 31 2015,23:39   

Quote (Dr.GH @ Sep. 01 2015,06:30)
Quote (k.e.. @ Aug. 31 2015,17:11)
 
Quote (Leftfield @ Sep. 01 2015,02:53)
 
Quote (Henry J @ Aug. 31 2015,16:30)
Maybe notpologies?



Notractions?

Well as a vanity publication peer review free, it's mainly missing vanity.

And publication.
???

By definition one follows the other, either word is redundant.

--------------
"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
Bob O'H



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Joined: Oct. 2005

(Permalink) Posted: Sep. 01 2015,03:36   

Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Clearly they're trying to rival the Journal of Universal Rejection.

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It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Sep. 01 2015,08:00   

Quote (Bob O'H @ Sep. 01 2015,03:36)
Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Clearly they're trying to rival the Journal of Universal Rejection.

Maybe it's just that their standards are so strident that their own people can't get...

Wait... no, that doesn't help them either. nevermind.

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

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

   
KevinB



Posts: 525
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(Permalink) Posted: Sep. 01 2015,09:30   

Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

  
k.e..



Posts: 5432
Joined: May 2007

(Permalink) Posted: Sep. 01 2015,11:42   

Quote (KevinB @ Sep. 01 2015,17:30)
Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

Indeed why publish if the subject is obviously and indubitably self evident? There is undoubtedly a 100% surety that any superfluous tautologically redundant pleonasms that the ID crowd are fond of would just be sesquipedalian obscurantism. No wonder they don't publish they have nothing to say!

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"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Sep. 01 2015,12:21   

Quote (k.e.. @ Sep. 01 2015,12:42)
Quote (KevinB @ Sep. 01 2015,17:30)
Quote (Henry J @ Aug. 31 2015,22:42)
Wonder how many submissions they rejected?

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

Indeed why publish if the subject is obviously and indubitably self evident? There is undoubtedly a 100% surety that any superfluous tautologically redundant pleonasms that the ID crowd are fond of would just be sesquipedalian obscurantism. No wonder they don't publish they have nothing to say!

And they say it at great, nigh unto interminable, length.

  
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Sep. 01 2015,14:13   

Yeah, isn't it funny how the ones with the least to say use the most words?

  
rthearle



Posts: 15
Joined: May 2005

(Permalink) Posted: Nov. 11 2015,17:25   

Just checked BIO-Complexity, the Discovery Institute's peer-reviewed journal, to see if they have published anything this year (they haven't, but it is only November). I did notice though that the last paper they published last year - Reeves/Gauger/Axe on enzymes - is listed with a citation of "BIO-Complexity 2014 (4):1â’16". This struck me as rather odd since BIO-Complexity only published four papers last year in total.

A few moments of digging uncovered that BIO-Complexity is indeed publishing each article as a separate issue, even when they're just 6 pages long and published less than a week apart.

Is this normal for on-line journals? I haven't seen anything similar elsewhere. Or could it be an attempt to make their output seem greater than it is?

Roy

  
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Nov. 11 2015,20:26   

Re "Or could it be an attempt to make their output seem greater than it is?"

Surely not!

  
Bob O'H



Posts: 2564
Joined: Oct. 2005

(Permalink) Posted: Nov. 14 2015,05:57   

Online journals don't need to have issues, but the software they're using has that model. When a paper is published it's put online straight away rather than bundling it together with others as an issue. But the software is set up to publish papers in issues, rather than as they come, so this way they don't need to fight the system.

--------------
It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
REC



Posts: 638
Joined: Sep. 2006

(Permalink) Posted: Dec. 29 2015,18:04   

Wow....2nd 2015 publication from BioComplexity, and it is a doozy:

Axe and Gauger "tested these proposals by observing how the endpoint of simple evolutionary optimization depends on the starting point. Beginning with optimization of protein-like constructs in the Stylus computational model, we compared promiscuous and junk starting points, where design elements specific to the test function were completely absent, to a starting point that retained most elements of a good design (mutation having disrupted some). In all three cases, evolutionary optimization improved activities by a large factor."

Another round of  Axe and Gauger running experiments designed to fail, therefore design (except again, some worked, but you know, still design. Not evolution. Nope. Not ever).

Oopsy.

Much handwaving BS follows. Mostly that good 'designs' (defined by them as starting points closer to their target) perform better in a few rounds of directed evolution than more distant starting points, which they call promiscuous or junk (which are totes not-designed, cuz please they be evolutionary random 'junk'). Duh.

My favorite junky 'non-design' is a totally deranged protein* with a huge deletion which apparently fails to achieve full activity in a couple rounds of kit mutagenesis. This kit in my hands only changes a few bases per clone. No insertions more than a base. They don't try shuffling to mimic recombination. Shockingly, it didn't work!! But nearer starting points (again, called designs) do, therefore design and Jesus and all that.

*Their words: "In addition to the 36 residues that are missing in the deletion mutant, another 29 residues are unequivocally prevented from adopting the wild-type conformation because of the missing segment, meaning that the structural disruption extends to 65 residues. Because this is the minimum extent of impact to the whole structure, the images on the right show the maximum amount of wild-type structure that could remain in TEMΔ. What actually remains may be much less. In addition to the deletion, TEMΔ carries 32 amino acid substitutions (see Supplement S1 [28])"

When you read that, remember that TEM is ~280 amino acids.

eta: I'm actually most bothered by their misrepresentation of some very fine science.

eta 2: I wonder what the DI and UD say about this paper. Wonder if even they are a bit ashamed.

Edited by REC on Dec. 29 2015,22:55

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Dec. 30 2015,00:06   

Quote (REC @ Dec. 29 2015,19:04)
I wonder what the DI and UD say about this paper. Wonder if even they are a bit ashamed.

....uh...hmm.....um.....

   
rthearle



Posts: 15
Joined: May 2005

(Permalink) Posted: Dec. 30 2015,06:51   

From the Discovery Institute's latest peer-reviewed article comes a vital question:  
Quote
If we shared a digital versatile disc (DVD), is information being destroyed?
Answers on a postcard please.

  
sparc



Posts: 2089
Joined: April 2007

(Permalink) Posted: Sep. 11 2016,22:58   

Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Edited by sparc on Sep. 11 2016,22:58

--------------
"[...] 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 -

   
timothya



Posts: 280
Joined: April 2013

(Permalink) Posted: Sep. 12 2016,05:48   

Quote (sparc @ Sep. 11 2016,22:58)
Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Since when does a user guide for a piece of software qualify as a scientific paper?

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"In its majestic equality, the law forbids rich and poor alike to sleep under bridges, beg in the streets and steal loaves of bread." Anatole France

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Sep. 12 2016,06:39   

Quote (timothya @ Sep. 12 2016,06:48)
Quote (sparc @ Sep. 11 2016,22:58)
Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Since when does a user guide for a piece of software qualify as a scientific paper?

Oh, don't ask that where Gary can hear you.
Next thing you know you'll be accused of bashing 'real-science'.

  
sparc



Posts: 2089
Joined: April 2007

(Permalink) Posted: Sep. 13 2016,03:40   

Since they already run a journal by he same name this could have been an opportunity for for the ID-creationists:  
Quote
11/22/2016
DARPA-BAA-16-08
Biological Technologies Office EZ BAA
BTO
This announcement seeks revolutionary research ideas for topics not being addressed by ongoing BTO programs or other published solicitations. Of particular interest are those proposals from entities (both small and large business) that have never received Government funding, or who do not normally propose to Government solicitations.
| Bio-complexity | Bio-systems | Health | Opportunities |


--------------
"[...] 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: 2089
Joined: April 2007

(Permalink) Posted: Nov. 08 2016,12:56   

Stop the presses: According to @DougAxe            
Quote
Ground-breaking computational model may sweep away the flimsy case for dismissing Adam and Eve. http://bio-complexity.org/ojs.........2016.3 …

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract:            
Quote
Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches
Ola Hössjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.
Looking forward for part 2.


ETA: They even discuss if the first couple could have lived in the Middle East.

Edited by sparc on Nov. 08 2016,13:46

--------------
"[...] 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: 2089
Joined: April 2007

(Permalink) Posted: Nov. 08 2016,13:11   

Part 2 is actually appeared at the same time (http://bio-complexity.org/ojs.........2016.4).
I wonder why their model needs something that they call "created diversity" "for autosomal and X chromosomal DNA" "as a second source of variation"? Is there something special about the Y-chromosome?
Looking forward for the next paper which will explain how to dicipher the process of the formation of Eve from Adam's rib out of human genome data.

Edited by sparc on Nov. 08 2016,13:45

--------------
"[...] 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 -

   
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Nov. 08 2016,13:11   

History Part 1? When Mel Brooks did a history part 1, he never got around to part 2, AFAIK. So it this about as intellectual as that was?

  
JohnW



Posts: 3217
Joined: Aug. 2006

(Permalink) Posted: Nov. 08 2016,18:06   

Quote (sparc @ Nov. 08 2016,10:56)
Stop the presses: According to @DougAxe            
Quote
Ground-breaking computational model may sweep away the flimsy case for dismissing Adam and Eve. http://bio-complexity.org/ojs.........2016.3 …

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract:            
Quote
Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches
Ola Hössjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.
Looking forward for part 2.


ETA: They even discuss if the first couple could have lived in the Middle East.

ID science at its finest.

1.  If Genesis was correct, we would expect to see DNA variation with certain statistical properties in the human population
2.  But in fact we see completely different statistical properties, incompatible with the account in Genesis.
3.  Add arbitrary Poof!
4.  Look again at the DNA variation.
5.  Repeat 3 and 4 until problem solved.
6.  Therefore Jesus.

--------------
Math is just a language of reality. Its a waste of time to know it. - Robert Byers

There isn't any probability that the letter d is in the word "mathematics"...  The correct answer would be "not even 0" - JoeG

  
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Nov. 09 2016,10:11   

Isn't "single couple" an oxymoron?

  
Acartia_Bogart



Posts: 2927
Joined: Sep. 2014

(Permalink) Posted: Nov. 09 2016,12:27   

These two papers has doubled the number of papers published this year. And two of the authors are on the editorial board.

  
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Nov. 09 2016,14:46   

Do they have any authors that aren't on board?

(That's if "on board" is the right term for those who missed the boat.)

  
sparc



Posts: 2089
Joined: April 2007

(Permalink) Posted: Dec. 10 2016,09:16   

Quote (JohnW @ Nov. 08 2016,18:06)
Quote (sparc @ Nov. 08 2016,10:56)
Stop the presses: According to @DougAxe              
Quote
Ground-breaking computational model may sweep away the flimsy case for dismissing Adam and Eve. http://bio-complexity.org/ojs.........2016.3 …

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract:              
Quote
Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin Approaches
Ola Hössjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.
Looking forward for part 2.


ETA: They even discuss if the first couple could have lived in the Middle East.

ID science at its finest.

1.  If Genesis was correct, we would expect to see DNA variation with certain statistical properties in the human population
2.  But in fact we see completely different statistical properties, incompatible with the account in Genesis.
3.  Add arbitrary Poof!
4.  Look again at the DNA variation.
5.  Repeat 3 and 4 until problem solved.
6.  Therefore Jesus.

Since Bio-Complexity's readership remains limited Gauger felt the need to further outline her breathtaking findings in an interview she gave to Salvo which actually lists Science only after Society and Sex in its header.
I am afraid though, that not even their sex pages are better than their science section.
(original link: http://salvomag.com/new........lap.php)

--------------
"[...] 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 -

   
clamboy



Posts: 299
Joined: May 2006

(Permalink) Posted: Dec. 10 2016,12:16   

Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

  
Dr.GH



Posts: 2333
Joined: May 2002

(Permalink) Posted: Dec. 10 2016,12:46   

Quote (clamboy @ Dec. 10 2016,10:16)
Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

Did you see this little charmer, "Has Science Shown That We Evolved from Ape-like Creatures?" by Casey Luskin

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

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

   
clamboy



Posts: 299
Joined: May 2006

(Permalink) Posted: Dec. 10 2016,13:54   

Quote (Dr.GH @ Dec. 10 2016,12:46)
Quote (clamboy @ Dec. 10 2016,10:16)
Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

Did you see this little charmer, "Has Science Shown That We Evolved from Ape-like Creatures?" by Casey Luskin

Well, that was a waste of three minutes, thank you so bloody bloody much, Dr. GH. The entire site appears to consist of conclusions in search of any, ANY, justification.

The only benefit I've had in perusing their, um, "articles," has been the opening of my mental files in search of appropriate nouns: wingnuts...wackaloons...dingbats...spasmoids...im-BEH-ciles (a la Bugs Bunny)...cretins...dorkweasels...maroons (again, a la Bugs Bunny)...moronistic morons (a term my sister invented)...

  
Dr.GH



Posts: 2333
Joined: May 2002

(Permalink) Posted: Dec. 10 2016,21:25   

Quote (clamboy @ Dec. 10 2016,11:54)
The only benefit I've had in perusing their, um, "articles," has been the opening of my mental files in search of appropriate nouns: wingnuts...wackaloons...dingbats...spasmoids...im-BEH-ciles (a la Bugs Bunny)...cretins...dorkweasels...maroons (again, a la Bugs Bunny)...moronistic morons (a term my sister invented)...

:D  :D  :D  :D  :D  :D  :D

   
khan



Posts: 1554
Joined: May 2007

(Permalink) Posted: Dec. 11 2016,07:44   

Quote (clamboy @ Dec. 10 2016,13:16)
Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.

One of the articles I read was anti-vaccine.

--------------
"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

Frequency is just the plural of wavelength...
-JoeG

  
clamboy



Posts: 299
Joined: May 2006

(Permalink) Posted: Dec. 11 2016,20:05   

Denyse O'Leary! Jonathan Wells! Casey Luskin! Hugh Ross! It's truly a "who's who" of "who's a purveyor of ignorant twaddle"!

  
sparc



Posts: 2089
Joined: April 2007

(Permalink) Posted: Feb. 13 2018,09:09   

Just opened Bio-Complexity and found the following from 2014
Quote
This document doi:10.5048/BIO-­â€C.2011.1.e1 Published: November 19, 2014

Erratum for: Gauger AK, Axe D (2011) The evolutionary accessibility of new
enzyme functions: A case study from the biotin pathway. BIO-­â€Complexity 2011(1):1-­â€
17. doi:10.5048/BIO-­â€C.2011.1

Using genes from E. coli, we previously found one instance where a single amino acid replacement in BioF that increases sequence identity with Kbl appeared to eliminate the BioF2 function in vivo. We reported this substitution to be H152N. In the course of further study, we discovered that our original plasmid that fails to confer BioF2 function actually has a second mutation in the bioF gene, this one encoding the substitution S265G. By making new plasmid constructs carrying the H152N mutation alone and the S265G mutation  alone,  we determined  that neither  of these  mutations  eliminates  BioF2 function  on its own. Function is lost only when the two are combined.

This  correction  reduces  our  previous  estimate  of  the  minimum  number  of  nucleotide  substitutions required  for  conversion  from  seven  to  six,  with  corresponding  revisions  needed  in  our  Results  and Discussion  sections.  In  particular,  most  of  the  first  three  paragraphs  under  the  subheading  Stage  2: Testing short-­â€listed  candidates  by BioF →Kbl mutation are now irrelevant, as they discuss the essential role  of  an  amino-­â€acid  residue  now  known  not  to  be  essential.  Also,  the  following  sentence  in  our
discussion (page 12) should be revised:

In fact, even the unrealistically favorable assumption that kbl duplicates carry no fitness cost leaves the conversion just beyond the limits of feasibility.

The corrected sentence should read:

Only under the unrealistically favorable assumption that kbl duplicates carry no fitness cost does the Kbl→BioF conversion fall just within the limits of feasibility.

The main point of the paper is unchanged.

Further details, including a brief discussion of the functional significance of H152 and S265, may be found in a forthcoming paper (in press): Reeves MA, Gauger AK, Axe DD (2014) Enzyme families—Shared evolutionary history or shared design? A study of the GABA-­â€aminotransferase family. BIO-­â€Complexity
2014 (4). doi:10.5048/BIO-­â€C.2014.4.

I am just wondering if the main point of the paper really remained unchanged if it now says that even their own unrealistic assumptions that were designed to let evolution look impossible would now allow for Kbl turn into BioF.

--------------
"[...] 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: 2089
Joined: April 2007

(Permalink) Posted: May 01 2018,11:46   

GĂĽnter Blechly describes a new fossil insect species Chrismooreia michaelbehei sp in Bio-Complexity which
Quote
is named in honor of Professor Michael Behe (Lehigh University) for his groundbreaking
contributions to intelligent design theory, which had great
influence on the personal views of the author [Blechly].

linky: http://bio-complexity.org/ojs.....2018.1

--------------
"[...] 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 -

   
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Mar. 28 2019,17:39   

Oh this amuses me to no end--

Which "peer-reviewed journal" published more research papers in 2018?

A) BIO-Complexity, the ID journal

-or-

B) Correlation, the Astrological Association Journal of Research in Astrology

Edited by stevestory on Mar. 28 2019,18:41

   
fnxtr



Posts: 3504
Joined: June 2006

(Permalink) Posted: Mar. 28 2019,18:18   

Quote (stevestory @ Mar. 28 2019,15:39)
Oh this amuses me to no end--

Which "peer-reviewed journal" published more research papers in 2018?

A) BIO-Complexity, the ID journal

-or-

B) Correlation, the Astrological Association Journal of Research in Astrology

Well, you know, they're both  
Quote
All original and all irrefutable science
.

--------------
"[A] book said there were 5 trillion witnesses. Who am I supposed to believe, 5 trillion witnesses or you? That shit's, like, ironclad. " -- stevestory

"Wow, you must be retarded. I said that CO2 does not trap heat. If it did then it would not cool down at night."  Joe G

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: April 23 2019,13:51   

ID is such a failed dumpster fire. The Young Earth Creationists already have six research papers out in 2019.

ID has diddly-shit. Some halfwits posting on a blog about the shroud of Turin and shit. Calling ID creationism may technically be true but it's an insult to the honest and productive creationists.  :p  :p  :p

   
DiEb



Posts: 312
Joined: May 2008

(Permalink) Posted: Oct. 22 2019,06:40   

A Single-Couple Human Origin is Possible

Ola Hössjer, Ann GaugerOla Hössjer, Ann Gauger
Quote

Abstract

The problem of inferring history from genetic data is complex and underdetermined; there are many possible scenarios that would explain the same data. It can be made more tractable by making reasonable simplifications to the model, but it is continually important to remember what has been demonstrated and what is merely a parsimonious working assumption. In this paper we have chosen to model the demographic ancestry of humanity using the simplest of assumptions, with a homogeneous population whose size can vary over time. All other assumptions such as the mutation rates were standard, and no natural selection was in operation. Using a previously published backwards simulation method and some newly developed and faster algorithms, we run our single-couple origin model of humanity and compare the results to allele frequency spectra and linkage disequilibrium statistics from current genetic data. We show that a single-couple origin of humanity as recent as 500kya is consistent with data. With only minor modifications of our parsimonious model assumptions, we suggest that a single-couple origin 100kya, or more recently, is possible.


Adam and Eve! I have not read the article yet, so I do not know whether the insertion of an apple is necessary.

   
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Oct. 22 2019,07:01   

Quote (DiEb @ Oct. 22 2019,07:40)
A Single-Couple Human Origin is Possible

Ola Hössjer, Ann GaugerOla Hössjer, Ann Gauger
Quote

Abstract

The problem of inferring history from genetic data is complex and underdetermined; there are many possible scenarios that would explain the same data. It can be made more tractable by making reasonable simplifications to the model, but it is continually important to remember what has been demonstrated and what is merely a parsimonious working assumption. In this paper we have chosen to model the demographic ancestry of humanity using the simplest of assumptions, with a homogeneous population whose size can vary over time. All other assumptions such as the mutation rates were standard, and no natural selection was in operation. Using a previously published backwards simulation method and some newly developed and faster algorithms, we run our single-couple origin model of humanity and compare the results to allele frequency spectra and linkage disequilibrium statistics from current genetic data. We show that a single-couple origin of humanity as recent as 500kya is consistent with data. With only minor modifications of our parsimonious model assumptions, we suggest that a single-couple origin 100kya, or more recently, is possible.


Adam and Eve! I have not read the article yet, so I do not know whether the insertion of an apple is necessary.

it's the end of October, and all they've managed to publish all year in their own journal is "Adam and Eve totally could have been real you guys"?

Jesus Christ Answers Research Journal has published 11 papers so far.

   
Bob O'H



Posts: 2564
Joined: Oct. 2005

(Permalink) Posted: Oct. 23 2019,09:37   

Quote (DiEb @ Oct. 22 2019,06:40)
A Single-Couple Human Origin is Possible

Ola Hössjer, Ann GaugerOla Hössjer, Ann Gauger
Quote

Abstract

The problem of inferring history from genetic data is complex and underdetermined; there are many possible scenarios that would explain the same data. It can be made more tractable by making reasonable simplifications to the model, but it is continually important to remember what has been demonstrated and what is merely a parsimonious working assumption. In this paper we have chosen to model the demographic ancestry of humanity using the simplest of assumptions, with a homogeneous population whose size can vary over time. All other assumptions such as the mutation rates were standard, and no natural selection was in operation. Using a previously published backwards simulation method and some newly developed and faster algorithms, we run our single-couple origin model of humanity and compare the results to allele frequency spectra and linkage disequilibrium statistics from current genetic data. We show that a single-couple origin of humanity as recent as 500kya is consistent with data. With only minor modifications of our parsimonious model assumptions, we suggest that a single-couple origin 100kya, or more recently, is possible.


Adam and Eve! I have not read the article yet, so I do not know whether the insertion of an apple is necessary.

They simulate these two scenarios:
Quote
Scenario 1 A single couple 100,000 generations ago (about 2mya) having zero heterozygosity (identical homozygous chromosomes), grows rapidly to a population of 10,000 people, then grows slowly and linearly to 16,000 people near the present.
Scenario 2 A single couple 25,000 generations ago (about 500kya) having primordial heterozygosity of 0.012,5 grows rapidly to a population of 16,000 people, then holds steady

So they are assuming if you live anywhere larger than a small town, most of the people you live with are imaginary.

--------------
It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Oct. 23 2019,16:53   

Quote (Bob O'H @ Oct. 23 2019,09:37)
Quote (DiEb @ Oct. 22 2019,06:40)
A Single-Couple Human Origin is Possible

Ola Hössjer, Ann GaugerOla Hössjer, Ann Gauger
 
Quote

Abstract

The problem of inferring history from genetic data is complex and underdetermined; there are many possible scenarios that would explain the same data. It can be made more tractable by making reasonable simplifications to the model, but it is continually important to remember what has been demonstrated and what is merely a parsimonious working assumption. In this paper we have chosen to model the demographic ancestry of humanity using the simplest of assumptions, with a homogeneous population whose size can vary over time. All other assumptions such as the mutation rates were standard, and no natural selection was in operation. Using a previously published backwards simulation method and some newly developed and faster algorithms, we run our single-couple origin model of humanity and compare the results to allele frequency spectra and linkage disequilibrium statistics from current genetic data. We show that a single-couple origin of humanity as recent as 500kya is consistent with data. With only minor modifications of our parsimonious model assumptions, we suggest that a single-couple origin 100kya, or more recently, is possible.


Adam and Eve! I have not read the article yet, so I do not know whether the insertion of an apple is necessary.

They simulate these two scenarios:
Quote
Scenario 1 A single couple 100,000 generations ago (about 2mya) having zero heterozygosity (identical homozygous chromosomes), grows rapidly to a population of 10,000 people, then grows slowly and linearly to 16,000 people near the present.
Scenario 2 A single couple 25,000 generations ago (about 500kya) having primordial heterozygosity of 0.012,5 grows rapidly to a population of 16,000 people, then holds steady

So they are assuming if you live anywhere larger than a small town, most of the people you live with are imaginary.

16000 vs 7.53 billion is 99.9998% error.

6000 vs 4.5 billion is 99.9999% error.

So right on message.

--------------
"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Aug. 24 2020,18:26   

Let’s check in on the fake journals!


Correlation, The journal of astrology
Quote

Volume 32 (2) 2020
CURRENT ISSUE​

TABLE OF CONTENTS

Editorial: The Evidence Accumulates, but Proof is never possible
The Evidence List: 63 studies
Robert Currey

An Automated Matching Test: Comparing astrological charts with biographies
Vincent Godbout

Suicide and Birthtime
Peter Fraiss

Estimation of aspect orbs by the computer
Kyösti Tarvainen PhD

A Brief Introduction to Qualitative Research in Astrology
Glenn Perry

Evaluating the effect of the rounding errors in the Gauquelin data
Kyösti Tarvainen PhD and Vincent Godbout


Bio-complexity, the jounal of renamed creationism

Quote
Vol 2020

Research Articles
Active Information Requirements for Fixation on the Wright-Fisher Model of Population Genetics PDF
Daniel Andrés Díaz Pachón, Robert Marks

Generalized Active Information: Extensions to Unbounded Domains PDF
Daniel Andrés Díaz-Pachón, Robert Marks

Measuring Active Information in Biological Systems PDF
Jonathan Laine Bartlett

The Solar System: Favored for Space Travel PDF
Guillermo Gonzalez
oooo, creationists still behind the astrologers  :p  :D  :)

By how the way how is evolution doing. Let’s look up Google scholar

Quote
Biology evolution 2020
Scholar
About 2,360,000 results

[PDF] academia.edu
[BOOK] Bioinformatics
AD Baxevanis, GD Bader, DS Wishart - 2020 - books.google.com
… titles: Bioinformatics (Baxevanis) Description: Fourth edition.| Hoboken, NJ: Wiley, 2020.| Includes
bibliographical … book Microbiome Analysis in the Methods in Molecular Biology series. His research
focuses on microbial genomics, evolution, and ecology, with concentrations in …
 Cited by 929 Related articles All 15 versions


[HTML] nature.com
[HTML] SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects
AG Wrobel, DJ Benton, P Xu, C Roustan… - … & Molecular Biology, 2020 - nature.com
SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary host. Here, we
investigate the relationship of spike (S) glycoprotein from SARS-CoV-2 with the S protein of
a closely related bat virus, RaTG13. We determined cryo-EM structures for RaTG13 S and …
 Cited by 3 All 5 versions
[PDF] dal.ca


A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution
CT Jones, N Youssef, E Susko… - Systematic biology, 2020 - academic.oup.com
A central objective in biology is to link adaptive evolution in a gene to structural and/or
functional phenotypic novelties. Yet most analytic methods make inferences mainly from
either phenotypic data or genetic data alone. A small number of models have been …
 Cited by 3 Related articles All 3 versions


[BOOK] Plant Strategies and the Dynamics and Structure of Plant Communities.(MPB-26), Volume 26
D Tilman - 2020 - books.google.com
… Oster and Edward O. Wilson The Dynamics of Arthropod Predator-Prey Systems, by Michael
P. Hassell Some Adaptations of March-Nesting Blackbirds, by Gordon H. Orians Evolutionary
Biology of Parasites, by Peter W. Price

...


Edited by stevestory on Aug. 24 2020,19:48

   
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Aug. 24 2020,19:35   

Hmmm. If the solar system is somehow favored for space travel, why does it take over half a year to get to the next planet outward using chemical propellant?

And why would it still take 2 or 3 months even after somebody manages to invent working fusion rockets? (Which optimistically might occur in 1 or 2 decades.)

And also, why for both of those does the launch have to be timed for when the planets are in a relative position that only occurs about every 2 years?

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Aug. 24 2020,20:08   

Quote (Henry J @ Aug. 24 2020,20:35)
Hmmm. If the solar system is somehow favored for space travel, why does it take over half a year to get to the next planet outward using chemical propellant?

And why would it still take 2 or 3 months even after somebody manages to invent working fusion rockets? (Which optimistically might occur in 1 or 2 decades.)

And also, why for both of those does the launch have to be timed for when the planets are in a relative position that only occurs about every 2 years?

Yeah totally favored for space travel. If we had shot Deep Space 1, at 35,000 mph, to the very nearest star it would take 81,000 years to get there. How convenient. And we would have no way to slow it down once it got there. And the radiation from here to there would probably destroy it utterly.

   
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Aug. 24 2020,20:15   

Quote (Henry J @ Aug. 24 2020,20:35)
Hmmm. If the solar system is somehow favored for space travel, why does it take over half a year to get to the next planet outward using chemical propellant?

And why would it still take 2 or 3 months even after somebody manages to invent working fusion rockets? (Which optimistically might occur in 1 or 2 decades.)

And also, why for both of those does the launch have to be timed for when the planets are in a relative position that only occurs about every 2 years?

The easiest planet for us to settle on, Mars, has toxic perchlorate soil. No atmosphere. Radiation shielding such that you need to be 10 feet underground for half the day. Half the efficiency of solar panels.

Quote
@AstroKatie

“But we need a backup planet in case this one is ruined!”

There is virtually nothing we — or the Universe — could do to Earth that would make it less habitable than Mars. Global warming, nuclear winter, extinction-level asteroid... still easier to live in caves here than there.


And all the other options are worse.

   
Henry J



Posts: 5787
Joined: Mar. 2005

(Permalink) Posted: Aug. 26 2020,08:39   

Re "And all the other options are worse."

You mean aside from too cold, too hot, no air, too much "air", wrong kind of "air", radiation issues, no water, probably no usable soil, too little or too much gravity?

  
k.e..



Posts: 5432
Joined: May 2007

(Permalink) Posted: Aug. 26 2020,10:26   

Quote (Henry J @ Aug. 26 2020,16:39)
Re "And all the other options are worse."

You mean aside from too cold, too hot, no air, too much "air", wrong kind of "air", radiation issues, no water, probably no usable soil, too little or too much gravity?

look on the bright side those places might not have any easy to extract hydocarbons or guns

--------------
"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
k.e..



Posts: 5432
Joined: May 2007

(Permalink) Posted: Aug. 26 2020,10:27   

Quote (k.e.. @ Aug. 26 2020,18:26)
Quote (Henry J @ Aug. 26 2020,16:39)
Re "And all the other options are worse."

You mean aside from too cold, too hot, no air, too much "air", wrong kind of "air", radiation issues, no water, probably no usable soil, too little or too much gravity?

look on the bright side those places might not have any easy to extract hydocarbons or guns

or for that matter foreigners

--------------
"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus
"I'm busy studying scientist level science papers" Galloping Gary Gaulin

  
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Aug. 26 2020,15:26   

Quote (k.e.. @ Aug. 26 2020,10:27)
Quote (k.e.. @ Aug. 26 2020,18:26)
Quote (Henry J @ Aug. 26 2020,16:39)
Re "And all the other options are worse."

You mean aside from too cold, too hot, no air, too much "air", wrong kind of "air", radiation issues, no water, probably no usable soil, too little or too much gravity?

look on the bright side those places might not have any easy to extract hydocarbons or guns

or for that matter foreigners

I’m pretty sure whoever wasn’t on the first ship there would rapidly be “foreigners”.  The only question is if would take a whole generation, a decade, or a couple months?

--------------
"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
sparc



Posts: 2089
Joined: April 2007

(Permalink) Posted: Dec. 09 2021,07:16   

Quote (stevestory @ Aug. 24 2020,18:26)
Let’s check in on the fake journals!


Correlation, The journal of astrology
   
Quote

Volume 32 (2) 2020
CURRENT ISSUE​

TABLE OF CONTENTS

Editorial: The Evidence Accumulates, but Proof is never possible
The Evidence List: 63 studies
Robert Currey

An Automated Matching Test: Comparing astrological charts with biographies
Vincent Godbout

Suicide and Birthtime
Peter Fraiss

Estimation of aspect orbs by the computer
Kyösti Tarvainen PhD

A Brief Introduction to Qualitative Research in Astrology
Glenn Perry

Evaluating the effect of the rounding errors in the Gauquelin data
Kyösti Tarvainen PhD and Vincent Godbout


Bio-complexity, the jounal of renamed creationism

   
Quote
Vol 2020

Research Articles
Active Information Requirements for Fixation on the Wright-Fisher Model of Population Genetics PDF
Daniel Andrés Díaz Pachón, Robert Marks

Generalized Active Information: Extensions to Unbounded Domains PDF
Daniel Andrés Díaz-Pachón, Robert Marks

Measuring Active Information in Biological Systems PDF
Jonathan Laine Bartlett

The Solar System: Favored for Space Travel PDF
Guillermo Gonzalez
oooo, creationists still behind the astrologers  :p  :D  :)

By how the way how is evolution doing. Let’s look up Google scholar

 
Quote
Biology evolution 2020
Scholar
About 2,360,000 results

[PDF] academia.edu
[BOOK] Bioinformatics
AD Baxevanis, GD Bader, DS Wishart - 2020 - books.google.com
… titles: Bioinformatics (Baxevanis) Description: Fourth edition.| Hoboken, NJ: Wiley, 2020.| Includes
bibliographical … book Microbiome Analysis in the Methods in Molecular Biology series. His research
focuses on microbial genomics, evolution, and ecology, with concentrations in …
 Cited by 929 Related articles All 15 versions


[HTML] nature.com
[HTML] SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects
AG Wrobel, DJ Benton, P Xu, C Roustan… - … & Molecular Biology, 2020 - nature.com
SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary host. Here, we
investigate the relationship of spike (S) glycoprotein from SARS-CoV-2 with the S protein of
a closely related bat virus, RaTG13. We determined cryo-EM structures for RaTG13 S and …
 Cited by 3 All 5 versions
[PDF] dal.ca


A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution
CT Jones, N Youssef, E Susko… - Systematic biology, 2020 - academic.oup.com
A central objective in biology is to link adaptive evolution in a gene to structural and/or
functional phenotypic novelties. Yet most analytic methods make inferences mainly from
either phenotypic data or genetic data alone. A small number of models have been …
 Cited by 3 Related articles All 3 versions


[BOOK] Plant Strategies and the Dynamics and Structure of Plant Communities.(MPB-26), Volume 26
D Tilman - 2020 - books.google.com
… Oster and Edward O. Wilson The Dynamics of Arthropod Predator-Prey Systems, by Michael
P. Hassell Some Adaptations of March-Nesting Blackbirds, by Gordon H. Orians Evolutionary
Biology of Parasites, by Peter W. Price

...

It's this time of the year again when the comparison of fake journals is due:
 
Quote
CORRELATION
The Astrological Association Journal of Research in AstrologyVolume 34 (1) 2021

CURRENT ISSUE​

TABLE OF CONTENTS

Editorial: The Past Honoured, Mysteries Unravelled, Secrets Revealed and some Self-Reflection.

Interview with Simon Best, the first editor of Correlation

Confirmation of Ptolemy’s 5-degree rule for Koch and Equal houses by Kyösti Tarvainen

Can success with IVF treatment following astrological advice be accounted for by the Placebo Effect? by Nicola Smuts-Allsop

The New York Suicide Study – Reconsidered and Reversed by Robert Currey

Human longevity, the Gauquelin Effect and Helio-centric cycles by Graham Douglas

Guessing aspects from interviews and obituaries by Kyösti Tarvainen

Book review by Philip Graves: A Critical Introduction to Psychological Astrology with Scientific Backing Authored by Kyösti Tarvainen & Raimo Nikula.

Letter from Gerhard Mayer

 
Quote
BIO-Complexity
Research Articles
An Engineering Perspective on the Bacterial Flagellum: Part 3 – Observations
Waldean A Schulz
An Engineering Perspective on the Bacterial Flagellum: Part 2 – Analytic View
Waldean A Schulz
An Engineering Perspective on the Bacterial Flagellum: Part 1 - Constructive View
Waldean A Schulz

They've lost again but would this be the first issue to which the editors didn't contribute anything? Still, about 30 editors and a single author.

--------------
"[...] 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 -

   
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