Is Bio-Complexity Dead?

Is the Intelligent Design journal Bio-Complexity dead?  A visit to the web site indicates that no new articles have been published in 2015, after only four in 2014.  Panda's Thumb had a review of the 2014 “issue” last December.  They were not kind.  Jeffrey Shallit wrote:

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.

What happened to the claim that ID creationists stand for ideas? One research article a year is not that impressive. Where are all those ideas Klinghoffer was raving about? Why can't their own flagship journal manage to publish any of them?

As 2015 draws near, don't expect that we will get any answers to these questions. Heck, not even the illustrious Robert J. Marks II can manage to respond to a simple question about information theory. 

Ouch! As I noted to my wife last night, while it is a flawed approach, even young-earth creationism can generate hypotheses for testing (That none of them pan out is, somehow lost on the supporters of this view, however).  ID cannot even generate testable hypotheses.  Despite protests to the contrary, their methodological construct violates a basic principle of science:

“Even if I can show that your hypothesis to explain something cannot be supported, that does not automatically mean that mine can.  Mine has to be independently tested.”  

ID automatically assumes that if evolutionary theory cannot explain something then it can be explained miraculously.  Aside from Howard Van Till's observation—even if it was done miraculously, no explanation is provided for exactly how it was done—as we have seen from the work of Stephen Meyer (here and here) and Michael Behe, even the science behind this work is questionable.

Other problems abound, from Douglas Axe's fundamentally mistaken idea that if you can't evolve a modern protein into another modern protein, then evolution doesn't work, despite the fact that the two proteins represent the end points of long evolutionary sequences (a somewhat more sophisticated version of Kirk Cameron's “Crocoduck” argument) to William Dembski's mathematical assumptions that incorrectly model evolutionary behavior.

Unless I miss my guess, this is the last we will see of Bio-Complexity, as it disappears into the mists of time along with Progress in Complexity, Information, and Design which ceased publication in 2005, after a short run of four years. 

Another Conservative Drinks From the Wrong Bottle

Granville Sewell has written a piece for Human Events, titled Intelligent Design Theories Gaining Steam in Scientific Circles.  As nearly as I can tell, he has gotten everything wrong.  Lets start with who Granville Sewell is.  He is a mathematics professor at the University of Texas at El Paso and a long-time supporter of intelligent design.

First, the title is indefensible.  Whether or not he, himself, came up with it, there is no evidence whatsoever that intelligent design is gaining ground in scientific circles.  In fact, there is contra-evidence.  There have been no intelligent design-based articles published in any of the mainstream journals and the only journal that is devoted to it, Bio-Complexity, has had one article and two critical reviews published for the entire year of 2013.  The article is co-written by two members of the editorial staff, to boot.

 He writes:

Darwin thought he could explain all of this apparent design through natural selection of random variations. In spite of the fact that there is no direct evidence that natural selection can explain anything other than very minor adaptations, his theory has gained widespread popularity in the scientific world, simply because no one can come up with a more plausible theory to explain evolution, other than intelligent design, which is dismissed by most scientists as “unscientific.”

This is ignorant nonsense with an arrogant tone attached to it.  The theory of evolution has gained widespread popularity because, as a theory, it is incredibly robust, with over 150 years of evidence to back it up, coming from the fields of biology, palaeontology, biogeography, microbiology, molecular biology, geology and others.  Every year, the evidence for evolution continues to pile up as we fill in more pieces of the jigsaw puzzle.  Witness recent discoveries that have shown that the first tetrapods evolved in the late Devonian in shallow seas, that feathers evolved and diversified in dinosaurs as a means of insulation before they evolved into a means of flight, or that the femur of Orrorin tugenensis shows transitional characteristics between late Miocene apes and the earliest hominins.  These are not minor adaptations.  They show selection and evolution across taxonomic levels and reflect predictions about what would be found in the fossil record IF evolution were true.

He writes: 

But, in recent years, as scientific research has continually revealed the astonishing dimensions of the complexity of life, especially at the microscopic level, support for Darwin’s implausible theory has continued to weaken, and since the publication in 1996 of Darwin’s Black Box by Lehigh University biochemist Michael Behe, a growing minority of scientists have concluded, with Behe, that there is no possible explanation for the complexity of life other than intelligent design.

Really?

Contrast the publication record of Bio-Complexity with the journal Evolution which, in 2013 alone, published 200 articles. Furthermore, Journal Citation Reports lists 29 journals that have "evolution" in the title. This does not even count those that publish articles on evolution, such as The American Journal of Physical Anthropology, Cell and Systematic Biology to name just a few.

With regard to the "growing minority of scientists,"  if he is referring to the "Dissent From Darwin" list put out by the Discovery Institute, that constitutes no evidence against evolution whatever.  When I analyzed the list a few years back, I found:

13 physicists, 1 plasma physicist, 10 biochemists, 24 chemists, 8 engineers, 7 mathematicians, 2 psychologists, 13 geneticists, and 5 medical doctors.

There are only five geologists on the list, and one lone palaeontologist on it. 

Like most ID writers such as David Berlinski, Cornelius Hunter and David Klinghoffer, he argues that there is dichotomy between accepting evolution and ID:

If you believe that a few fundamental, unintelligent forces of physics alone could have rearranged the basic particles of physics into Apple iPhones, you are probably not an ID proponent, even if you believe in God. But if you believe there must have been more than unintelligent forces at work somewhere, somehow, in the whole process: congratulations, you are one of us after all!

Here is one-dimensional, reductionistic thinking on display. it is either/or. There is no third option, the evolutionary creationist, who argues that the evidence for evolution of life, in all of its 3.5 billion year existence, can be explained as the work of a fantastically inventive and creative God, who took great joy in watching his creation unfold. It is also the thinking of someone who has taken no time to actually learn the basics of evolution and what the evidence is that supports it.  As long as this is the case, we will continue to be subjected to substandard prose such as this offering by Dr. Sewell. 

Jeffrey Shallit: The Sterility of Intelligent Design

Jeffrey Shallit notes, in Recursivity,  the lack of grounded research in the intelligent design community.  He writes:

Here is a perfect example of this sterility: Bio-Complexity, the flagship journal of the intelligent design movement. As 2012 draws to a close, the 2012 volume contains exactly two research articles, one "critical review" and one "critical focus", for a grand total of four items. The editorial board has 30 members; they must be kept very busy handling all those papers.  (Another intelligent design journal, Progress in Complexity, Information, and Design, hasn't had a new issue since 2005.)

By contrast, the journal Evolution has ten times more research articles in a single issue (one of 12 so far in 2012). And this is just a single journal where evolutionary biology research is published; there are many others.

But that's not the most hopeless part. Of the four contributions to Bio-Complexity in 2012, three have authors that are either the Editor in Chief (sic), the Managing Editor, or members of the editorial board of the journal. Only one article, the one by Fernando Castro-Chavez, has no author in the subset of the people running the journal. And that one is utter bilge, written by someone who believes that "the 64 codons [of DNA are] represented since at least 4,000 years ago and preserved by China in the I Ching or Book of Changes or Mutations".

I noted something like this a bit back. He is correct. It cannot generate new information or new testable ideas because its ultimate goal is to find the conclusion “God did it” which, while being satisfying on a rudimentary theological level is not on a scientific level. Further, it is deductive in the sense that it has a stated goal in mind.  This is antithetical to scientific research and, as such, it is not different from young earth creation “science.”  I have the Talking Heads' “Road to Nowhere” going through my head...

Checking in on BIO-Complexity

So, it has been a year and a half since the Center for Science and Culture, the wing of the Discovery Institute, inaugurated BIO-Complexity, the new journal devoted to objectively examining the evidence for intelligent design. At the time, I wrote the following, concerning the viability of the journal:

The only other way that this would work is if competent scholars in biological complexity were to submit papers. Then the journal would probably get a wide variety of papers, some supportive of ID (maybe) and some not. Even if some of them were not supportive, though, the board would be foolish not to publish them. If it only accepted ID friendly papers which were then reviewed by the biological community as a whole and found wanting, it would be another nail in the coffin for the scientific argument for ID.

The Discovery Institute have set themselves up a huge task here and are finally putting their cards on the table. Lets see what kind of hand they have.

Now we know what kind of hand they have. It is not very good. Since its debut, eighteen months ago, the journal has produced...

five research articles.

That is one article every 3½ months. Even brand new journals in the sciences have at least five to seven articles per month. Further, the current year, which is now in its waning days, has seen only two articles. That is slightly better than one article every six months.

It gets worse. Three of the five articles are either single-authored or co-authored by Douglas Axe, who is the managing editor and only four authors represented are not on the editorial board.

This is inbreeding if I have ever seen it. This level of production is every bit what I feared: the lack of impartiality has given rise to a journal that is slanted in one direction: support of ID. In April of this year, Todd Wood wrote the following:

In the larger scheme of things, I am sensing a discouraging pattern to BIO-Complexity publications. As I quoted above, the journal is supposed to be about "testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life," which is a great goal. But this is the fifth paper published by BIO-Complexity, and it's the fifth paper that focuses on perceived inadequacies of evolution. So when are we going to test "the scientific merit of the claim that intelligent design (ID) is a credible explanation for life?"

The number of papers that do address the merits of the ID explanation for life simply aren't there. Why not? Surely in eighteen months, at least two or three papers discussing research in this area would have been submitted for publication. Where are these papers? Where is this research?

Is it possible that the intention was never to address this laudable goal? Was it always to write papers trying to poke holes in evolutionary theory? It certainly seems that way. The problem is, based on their output and the lack of diversity in authorship, they cannot even do much of that.

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Todd Wood on BIO-Complexity

Remember when the Biologic Institute produced BIO-Complexity, a new journal that would investigate the scientific evidence for design. Here was the tag line:

BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics—viewed from all angles and perspectives—are central to the journal's scope.

Todd Wood writes that he was originally enthusiastic about the new journal and its mission. Today, within the context of a review of a paper in that journal, he writes the following:

In the larger scheme of things, I am sensing a discouraging pattern to BIO-Complexity publications. As I quoted above, the journal is supposed to be about "testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life," which is a great goal. But this is the fifth paper published by BIO-Complexity, and it's the fifth paper that focuses on perceived inadequacies of evolution. So when are we going to test "the scientific merit of the claim that intelligent design (ID) is a credible explanation for life?" I don't want to be too pessimistic, though, since I am a big fan of research and technical publications. I'm genuinely happy that BIO-Complexity exists and is publishing this sort of work. I just hope that in the future, we'll begin to see some positive research for ID rather than just anti-evolution work.

Why am I not surprised? It still is not clear to me that there can ever be research that can test the scientific merit of the ID claim. The principle problem is that no mechanism exists. Because no mechanism exists and, consequently, no theory exists, ID can only be shown to be a viable explanation when all other explanations have been shown to be false. It MUST focus on anti-evolution work because as long as the evolutionary framework exists to explain the genetic and biological diversity, there is no reason to accept the ID explanation. This, to me, is a critical failing in current ID research.

A Review of BIO-Complexity

Bounded Science reviews the new BIO-Complexity journal and its guidelines. He finds much wanting:

As long as scientists reject ID as supernaturalism, there will be none of the "scientific controversy over ID" referred to at BIO-Complexity. It seems that the forum is designed to get scientists, identified by their real names, to engage in highly restricted exchanges on ID that create the impression of genuine controversy. This could aid the Discovery Institute in its "teach the controversy" campaign, the objective of which is to get ID into the science curricula of public schools.

Barbara Forrest has identified four different tactics that are used by the intelligent design movement to further the goals of establishing the validity of intelligent design: 1. Teach the Controversy, in which it is asserted that there is disagreement within the scientific community about how effective evolutionary theory is at explaining past and present biodiversity, 2. Teach the full range of scientific views, in which it is asserted that both evolutionary theory and intelligent design are on equal footing and 3. critical analysis/thinking, in which teachers are encouraged to question the validity of evolution. As she correctly points out, we should always engage critical thinking in performing science. The goal here, though, is to poke holes in evolution while elevating ID, and 4. teach the strengths and weaknesses of evolution. This relies on usually specious arguments against evolution that have been rebutted time and again by the scientific community but which are continually promoted by ID supporters.

This new journal seeks to accomplish all of the goals at once. The ID community has long argued that since the scientific community is not willing to engage it in examining the strengths and weaknesses of evolutionary theory or to deign to debate ID as if it were on an equal footing with evolutionary theory that they have taken the moral high ground. The problem with this stance is that it relies on some patently false positions such as the claim that there is disagreement within the biological community about evolution (the dissent from Darwin list), there are no transitional fossils, that the Cambrian explosion reflects creation by divine fiat and not evolution, and that evolution lacks explanatory power. None of these have been shown to have any scientific merit and yet they are continually promoted by design supporters. As I mentioned in an earlier post, there are only two ways in which this would work and the Discovery Institute does not seem interested in pursuing either path.

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New Paper at BIO-Complexity

A new paper at BIO-Complexity is up. It is called "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness." It is heavily biochemical in nature and is going to take some time to digest. The paper is described by Jay Richards as a "take-home lesson." All of the authors are employed at the Biologic Institute.

BIO-Complexity: A New Journal

The Discovery Institute is promoting a new peer-reviewed journal, BIO-Complexity, which is funded by the Biologic Institute, an arm of the Center for Science and Culture. Here is the mission statement:

BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics—viewed from all angles and perspectives—are central to the journal's scope.

Jay Richards has written a story about the new journal on the Discovery Institute's main site in which, along the way, they commit another terminological inexactitude.One of the major complaints voiced by those espousing ID is that they cannot get heard. Richards claims that the peer review process is a Catch-22 because, while an article has to face review and revision, if it has a hint of "design" it is rejected. He writes:

But surely, you might ask, there’s an open-minded editor at some journal somewhere who would give ID a fair shake? I do know of one such editor, Richard Sternberg, who several years ago sent out for review an article by some guy defending a design perspective and then, when the article passed peer-review, Sternberg published it. If there are any remaining open-minded editors willing to send out similar articles for peer-review, the Sternberg affair reminds them what will happen if they do.

This account is wholly and completely false. Here, in fact, is what happened.

• Stephen Meyer (some guy) wrote a paper on the Cambrian Explosion called The origin of biological information and the higher taxonomic categories, which showed up in the Proceedings of the Biological Society of Washington in 2004. The paper was reviewed quite negatively in many places, Panda's Thumb being one, the Paleontological Association being another.
  
• Richard Sternberg handled the entire editorial process himself. He claims that he sent the paper out to several individuals to read but has never identified who these people were.
• A statement issued by the Council of the Biological Society of Washington, the publishers of the journal states that the paper never would have made it through the review process had it been done so correctly. It reads:

  The Council, which includes officers, elected councilors, and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings because the subject matter represents such a significant departure from the nearly purely systematic content for which this journal has been known throughout its 122-year history.

  
  
• The paper was withdrawn subsequent to publication when it was pointed out that the quality of the science was unacceptable.
  

Following the Sternberg affair, the American Association for the Advancement of Science issued a statement on Intelligent Design. All the Sternberg affair should tell prospective article writers is what happens when the proper procedures for peer review aren't followed. The whole publication of the article has the appearance of having been done "under the table." It is not encouraging that a writer for the Discovery Institute cannot get the basic facts right regarding so prominent an incident.

Beyond this, however, there is a further, perhaps deeper problem inherent in this whole endeavor. Much of Richards' post (and indeed much of the writings of most ID supporters) laments the fact that intelligent design cannot get a "fair shake" in the academic community as a whole and that, with the advent of this new journal, things will be different.

Why, then, is the editorial board composed almost entirely of Discovery Institute fellows or people that are already known to be sympathetic to the intelligent design argument? The editorial board for the journal consists of thirty individuals. This list includes Michael Behe (Darwin's Black Box, The Edge of Evolution), Scott Minnich, William Dembski (No Free Lunch), Richard Sternberg, Robert Marks, Jonathan Wells (Icons of Evolution) and Douglas Axe to name a few.

This is how the review process is set up:

Manuscripts submitted as Research Articles or Critical Reviews that fall within the stated scope and adhere to the journal's standards of originality, clarity, format, and tone are assigned to a member of the Editorial Board for peer review. Two or more reviewers will be consulted for each reviewed manuscript. Authors are encouraged to suggest suitable reviewers, though the Editor may elect to use other reviewers.

Now here's the real catch-22 situation: in order to gain much needed credibility, the BIO-Complexity editorial board must employ reviewers that are well-known in the biological community and can competently vet (or not) a given paper. Without this assurance, the scientific community will have no way of knowing how any given ID-supportive paper was reviewed and no credibility will have been gained. This is exacerbated by the fact that the Discovery Institute does not have a good track record in published literature supporting intelligent design.

To give up the identity of the reviewers, on the other hand, compromises the "anonymous reviewer" aspect of the process. Compounding this might be the reluctance of many well-respected biologists to want to be known as having reviewed an ID-supportive paper.

This was all gone about the wrong way. One way that this could have worked is if an isolated researcher without ties to the Discovery Institute decided to start a new biocomplexity journal and recruited known experts in the field. Then, and only then, could papers be submitted in an impartial way and only then would ID stand on its own merits. The way BIO-Complexity is currently set up, with a heavily pro-ID editorial board, it already looks like the fix is in.

What would they do with a paper that is sent out to an anonymous reviewer who tears it up? The only paper in recent memory other than the Meyer 2004 paper that has attempted to support intelligent design in an academic setting is the Dembski/Marks paper from a few months back which was criticized (here and here) as having little bearing on biological systems and mathematically unsound.

The only other way that this would work is if competent scholars in biological complexity were to submit papers. Then the journal would probably get a wide variety of papers, some supportive of ID (maybe) and some not. Even if some of them were not supportive, though, the board would be foolish not to publish them. If it only accepted ID friendly papers which were then reviewed by the biological community as a whole and found wanting, it would be another nail in the coffin for the scientific argument for ID.

The Discovery Institute have set themselves up a huge task here and are finally putting their cards on the table. Lets see what kind of hand they have.