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+--Forum: After the Bar Closes...
+---Topic: BIO-Complexity started by olegt


Posted by: olegt on 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 ďSecond lawĒ 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.
---------------------QUOTE-------------------


Posted by: Venus Mousetrap on May 14 2010,04:37

Those scrunched up balls of paper on the front page look so designed.
Posted by: Richardthughes on May 14 2010,08:34


Posted by: OgreMkV on 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.
Posted by: George on 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.
Posted by: sledgehammer on 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.
Posted by: fnxtr on May 14 2010,09:57

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


Or at lease endogamous. :-)

Self-pollinating?
Posted by: SLP on 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?
Posted by: sledgehammer on 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?
---------------------QUOTE-------------------


Not only that, but when i read a < paper > †full of jargon of the author's own creation, †  

---------------------QUOTE-------------------
ďPhysicodynamics cannot spontaneously traverse The Cybernetic Cut Ē
---------------------QUOTE-------------------

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.
---------------------QUOTE-------------------


I can only roll my eyes and †shrug.
Posted by: Wesley R. Elsberry on May 18 2010,07:32

Another antievolutionist who can't understand modus tollens, it looks like.
Posted by: Kristine on 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).
---------------------QUOTE-------------------


All men. Women do the housework, er, copyediting. ;)
Posted by: didymos on 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).
---------------------QUOTE-------------------


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


That is weird.  Why is Gauger isolated like that?
Posted by: Kristine on 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).
---------------------QUOTE-------------------


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


That is weird. †Why is Gauger isolated like that?
---------------------QUOTE-------------------


To guard against < e-babies >. :D
Posted by: khan on 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).
---------------------QUOTE-------------------


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


That is weird. †Why is Gauger isolated like that?
---------------------QUOTE-------------------


Obeying Leviticus?
Posted by: DiEb on 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...
Posted by: J-Dog on 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-------------------




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



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!
---------------------QUOTE-------------------



Fixed That For You!
Posted by: SLP on 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 ďSecond lawĒ 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.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


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

Talk about credential embellishment....
Posted by: SLP on 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?
Posted by: sparc on 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 MontaŮez, 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-------------------

† † †  

---------------------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
---------------------QUOTE-------------------

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 StructureĖFunction; 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 LŲnnig, 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 Universitšt MŁnchen, 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?Ū VŠcha, 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

---------------------QUOTE-------------------


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.
Posted by: Dr.GH on 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.
Posted by: sparc on Sep. 17 2011,05:51

BTW, until 2003 < Scherer has been a fellow of the DI > as well.
Posted by: Art on 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 MontaŮez, 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-------------------

† † † †  

---------------------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
---------------------QUOTE-------------------

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 StructureĖFunction; 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 LŲnnig, 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 Universitšt MŁnchen, 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?Ū VŠcha, 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

---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


It would seem as if the DI has something against Asians.
Posted by: Albatrossity2 on Sep. 18 2011,15:53

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


Perhaps Wells could help them be more inclusive by introducing Dembski et al. to the Rev. Moon...
Posted by: CeilingCat on 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.
---------------------QUOTE-------------------


So far, option one is winning big.
Posted by: Henry J on Sep. 18 2011,17:49



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


That's probably just because the DI is disoriented.
Posted by: George on 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.
---------------------QUOTE-------------------


So far, option one is winning big.
---------------------QUOTE-------------------


I can has magic 8-ball?
Posted by: sparc on 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 Ďworldí 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.
---------------------QUOTE-------------------


Posted by: Doc Bill on 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.
Posted by: Tom Ames on 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 Ďworldí 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.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


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.
Posted by: Doc Bill on 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.
Posted by: sparc on 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.
Posted by: sparc on 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 MontaŮez
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.
Posted by: Kattarina98 on April 07 2012,08:19

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


How else can they cope with the avalanche of papers submitted each day?
Posted by: Wesley R. Elsberry on 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 ďanswersĒ are surreptitiously introduced into the program via the algorithmís fitness
testing function

---------------------QUOTE-------------------



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.

---------------------QUOTE-------------------



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".
Posted by: BillB on 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 ďanswersĒ are surreptitiously introduced into the program via the algorithmís fitness
testing function

---------------------QUOTE-------------------



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.

---------------------QUOTE-------------------



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".
---------------------QUOTE-------------------


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.
Posted by: fusilier on 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 ďanswersĒ are surreptitiously introduced into the program via the algorithmís fitness
testing function

---------------------QUOTE-------------------



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.

---------------------QUOTE-------------------



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".
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


That's not what theistic evolution says.

The CSI bullshit is from creationism, not evolutionary biology.
Posted by: BillB on 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 ďanswersĒ are surreptitiously introduced into the program via the algorithmís fitness
testing function

---------------------QUOTE-------------------



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.

---------------------QUOTE-------------------



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".
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


That's not what theistic evolution says.

The CSI bullshit is from creationism, not evolutionary biology.
---------------------QUOTE-------------------


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

Perhaps I should have put an 'irony' tag before my comment.
Posted by: Kattarina98 on July 04 2012,02:02

Denyse < informs > us that BIO-Complexity proudly published a < review > by Matti Leisola, Ossi Pastinen, Douglas Axe: LigninóDesigned 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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 innovationógrowth on ligninówith a long list of spectacular innovations thought to have evolved in a fraction of that time.
---------------------QUOTE-------------------


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


Posted by: The whole truth on 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: LigninóDesigned 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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 innovationógrowth on ligninówith a long list of spectacular innovations thought to have evolved in a fraction of that time.
---------------------QUOTE-------------------


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
---------------------QUOTE-------------------


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.
Posted by: fnxtr on 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.
Posted by: NormOlsen on 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.
---------------------QUOTE-------------------



Last draft before final edit.
Posted by: The whole truth on July 04 2012,10:07


Posted by: Timothy McDougald on 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: LigninóDesigned 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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 innovationógrowth on ligninówith a long list of spectacular innovations thought to have evolved in a fraction of that time.
---------------------QUOTE-------------------


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
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------

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
Posted by: Glen Davidson on 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: LigninóDesigned 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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 innovationógrowth on ligninówith a long list of spectacular innovations thought to have evolved in a fraction of that time.
---------------------QUOTE-------------------


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
---------------------QUOTE-------------------


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
Posted by: Kattarina98 on 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.
Posted by: The whole truth on 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.
---------------------QUOTE-------------------


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.
Posted by: midwifetoad on 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.
Posted by: Timothy McDougald on 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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


< Yes >
Posted by: midwifetoad on July 04 2012,14:06

I was thinking of this peer reviewed journal.

< http://www.washingtonpost.com/wp-dyn....71.html >
Posted by: The whole truth on 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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


< Yes >
---------------------QUOTE-------------------


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.
Posted by: The whole truth on 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 >
---------------------QUOTE-------------------


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.
Posted by: Timothy McDougald on 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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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


< Yes >
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


I wasn't trying to refute anything you said, I was responding to midwifetoad...
Posted by: midwifetoad on 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.
Posted by: fnxtr on 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.
---------------------QUOTE-------------------


Oh hell yes. Just ask Mike Elzinga... :-)
Posted by: The whole truth on 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.
---------------------QUOTE-------------------


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.
Posted by: blipey on 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.
---------------------QUOTE-------------------


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;
Posted by: Kattarina98 on 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
Posted by: The whole truth on 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
---------------------QUOTE-------------------


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?
Posted by: Henry J on 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?
---------------------QUOTE-------------------


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

Henry
Posted by: DiEb on 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...
Posted by: OgreMkV on 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...
---------------------QUOTE-------------------


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...
Posted by: Dr.GH on 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...
---------------------QUOTE-------------------


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...
---------------------QUOTE-------------------


Wow. The entire abstract is a word fest.
Posted by: sparc on 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]


Posted by: k.e.. on Feb. 13 2014,08:10

Tard to ass resuscitation....where's Joe?
Posted by: stevestory on 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-------------------




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


Why not? It sure won't take long  :p
Posted by: REC on 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.
---------------------QUOTE-------------------



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 >


Posted by: DiEb on 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 Beheís definition.
---------------------QUOTE-------------------


Isn't the EQU function the irreducibly complex system, and Avida just the environment in which it dwells?
Posted by: Quack on April 08 2014,16:25

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


< Here >
Posted by: midwifetoad on April 08 2014,17:32

Joe was much smarter when he was dead.
Posted by: Zachriel on 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, Sadedinís 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 Sadedinís model.
---------------------QUOTE-------------------


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

Posted by: DiEb on 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, Sadedinís 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 Sadedinís model.
---------------------QUOTE-------------------


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

---------------------QUOTE-------------------


Winston Ewert started a thread on his article at Sal Cordova's Creation Evolution University: < Digital Irreducible Complexity - Author Thread >
Posted by: sparc on 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, Sadedinís 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 Sadedinís model.
---------------------QUOTE-------------------


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

---------------------QUOTE-------------------


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


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 >.
Posted by: sparc on 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.


Posted by: REC on 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.
---------------------QUOTE-------------------



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."
Posted by: midwifetoad on July 12 2014,17:04

Actually there is an evolved circuit that works better than most designed circuits and has stuff that goes nowhere.
Posted by: Henry J on 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.
---------------------QUOTE-------------------


Is that from its EM field affecting other circuits, or is it a quantum effect? (Not that I'd understand the details, but anyway.)
Posted by: midwifetoad on July 15 2014,06:11

Rather old.

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

< http://en.m.wikipedia.org/wiki....ardware >
Posted by: sparc on 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.
---------------------QUOTE-------------------


Posted by: REC on 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.......
Posted by: Henry J on Aug. 29 2015,13:30

I guess there were complications?
Posted by: REC on Aug. 29 2015,14:25

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


Such as the complete collapse of ID, which has left the little scientific facade they created dangling in the breeze?
Posted by: Bob O'H on 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.......
---------------------QUOTE-------------------


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.
Posted by: Occam's Aftershave on 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.......
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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
Posted by: The whole truth on 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.......
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------



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?
Posted by: J-Dog on Aug. 31 2015,16:13



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



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.
Posted by: Henry J on Aug. 31 2015,16:30

Maybe notpologies?
Posted by: Leftfield on Aug. 31 2015,18:53

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




Notractions?
Posted by: k.e.. on Aug. 31 2015,19:11

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




Notractions?
---------------------QUOTE-------------------


Well as a vanity publication peer review free, it's mainly missing vanity.
Posted by: Dr.GH on 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?
---------------------QUOTE-------------------




Notractions?
---------------------QUOTE-------------------


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


And publication.
???
Posted by: Henry J on Aug. 31 2015,22:42

Wonder how many submissions they rejected?
Posted by: k.e.. on 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?
---------------------QUOTE-------------------




Notractions?
---------------------QUOTE-------------------


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


And publication.
???
---------------------QUOTE-------------------


By definition one follows the other, either word is redundant.
Posted by: Bob O'H on Sep. 01 2015,03:36

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


Clearly they're trying to rival the Journal of Universal Rejection.
Posted by: OgreMkV on 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?
---------------------QUOTE-------------------


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


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.
Posted by: KevinB on Sep. 01 2015,09:30

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


Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"
Posted by: k.e.. on 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?
---------------------QUOTE-------------------


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


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!
Posted by: NoName on 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?
---------------------QUOTE-------------------


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


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!
---------------------QUOTE-------------------


And they say it at great, nigh unto interminable, length.
Posted by: Henry J on Sep. 01 2015,14:13

Yeah, isn't it funny how the ones with the least to say use the most words?
Posted by: rthearle on 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):1‚ąí16". 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
Posted by: Henry J on Nov. 11 2015,20:26

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

Surely not!
Posted by: Bob O'H on 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.
Posted by: REC on 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 TEMőĒ. What actually remains may be much less. In addition to the deletion, TEMőĒ 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.


Posted by: stevestory on 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.
---------------------QUOTE-------------------


....uh...hmm.....um.....
Posted by: rthearle on 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?
---------------------QUOTE-------------------

Answers on a postcard please.
Posted by: sparc on 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.


Posted by: timothya on 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.
---------------------QUOTE-------------------


Since when does a user guide for a piece of software qualify as a scientific paper?
Posted by: NoName on 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.
---------------------QUOTE-------------------


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


Oh, don't ask that where Gary can hear you.
Next thing you know you'll be accused of bashing 'real-science'.
Posted by: sparc on 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 |
---------------------QUOTE-------------------


Posted by: sparc on 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 > …
---------------------QUOTE-------------------


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).
---------------------QUOTE-------------------


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.


Posted by: sparc on 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.


Posted by: Henry J on 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?
Posted by: JohnW on 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 > …
---------------------QUOTE-------------------


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).
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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.
Posted by: Henry J on Nov. 09 2016,10:11

Isn't "single couple" an oxymoron?
Posted by: Acartia_Bogart on 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.
Posted by: Henry J on 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.)
Posted by: sparc on 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 > …
---------------------QUOTE-------------------


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).
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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.
---------------------QUOTE-------------------


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 >)
Posted by: clamboy on Dec. 10 2016,12:16

Thanks for the link, sparc. I took a few minutes to look around the site - looneytunes central.
Posted by: Dr.GH on 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.
---------------------QUOTE-------------------


Did you see this little charmer, < "Has Science Shown That We Evolved from Ape-like Creatures?" by Casey Luskin >
Posted by: clamboy on 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.
---------------------QUOTE-------------------


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


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)...
Posted by: Dr.GH on 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)...
---------------------QUOTE-------------------


:D  :D  :D  :D  :D  :D  :D
Posted by: khan on 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.
---------------------QUOTE-------------------


One of the articles I read was anti-vaccine.
Posted by: clamboy on 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"!
Posted by: sparc on Feb. 13 2018,09:09

Just opened Bio-Complexity and found the following from 2014

---------------------QUOTE-------------------
This document doi:10.5048/BIO-¬≠‚ÄźC.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-¬≠‚ÄźComplexity 2011(1):1-¬≠‚Äź
17. doi:10.5048/BIO-¬≠‚ÄźC.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-¬≠‚Äźlisted ¬†candidates ¬†by BioF ‚ÜíKbl mutation are now irrelevant, as they discuss the essential role ¬†of ¬†an ¬†amino-¬≠‚Äźacid ¬†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‚ÜíBioF 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‚ÄĒShared evolutionary history or shared design? A study of the GABA-¬≠‚Äźaminotransferase family. BIO-¬≠‚ÄźComplexity
2014 (4). doi:10.5048/BIO-¬≠‚ÄźC.2014.4.
---------------------QUOTE-------------------


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.
Posted by: sparc on May 01 2018,11:46

G√ľnter 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].
---------------------QUOTE-------------------


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