New Post by Dennis Venema on Biological Information

Dennis Venema has a new post on the testing of an hypothesis by supporters of ID:

In previous posts in this series, we’ve explored the claim made by the Intelligent Design (ID) movement that evolutionary mechanisms are not capable of generating the information-rich sequences in genes. One example that we have explored is nylonase – an enzyme that allows the bacteria that have it to digest the human-made chemical nylon, and use it as a food source. As we have seen, nylonase is a good example of a de novo gene – a gene that arose suddenly and came under natural selection because of its new and advantageous function. Since nylonase is a folded protein with a demonstrable function, it should be beyond the ability of evolution to produce, according to ID.

It goes downhill from there for ID.Experiments routinely show that new proteins that appear can, very often, have functions and be incorporated into the genome. Further, this, apparently, happens at all stages of gene replication, transcription and translation.  As Venema notes at the end:

The importance of these results for ID arguments is clear. By direct experimental test, new biological functions have been shown to be common, not rare, within random sequences - and that these functions may be found in either RNA transcripts or de novo protein products. By Gauger’s own measure, ID advocates have been shown to be wrong. Since this particular ID claim undergirds a large proportion of the ID argument that biological information cannot have arisen through evolution, the consequences for ID are significant.

Stephen Meyer and Douglas Axe have, in the words of the Discovery Institute: “made this strong claim:”

[T]he neo-Darwinian mechanism — with its reliance on a random mutational search to generate novel gene sequences — is not an adequate mechanism to produce the information necessary for even a single new protein fold, let alone a novel animal form, in available evolutionary deep time.

From these experiments, we now know this to be completely wrong.

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. 

Donald Prothero Writes A Withering Review of Darwin's Doubt

On the Amazon page for the new Stephen Meyer book Darwin's Doubt, there is a review of the book by Donald Prothero, who is responsible for one of the best books on the fossil record in recent memory, Evolution: What the Fossils Say and Why it Matters.  Of creationists (sensu lato), he writes:

They either cannot understand the scientific meaning of many fields from genetics to paleontology to geochronology, or their bias filters out all but tiny bits of a research subject that seems to comfort them, and they ignore all the rest.
Another common tactic of creationists is credential mongering. They love to flaunt their Ph.D.'s on their book covers, giving the uninitiated the impression that they are all-purpose experts in every topic. As anyone who has earned a Ph.D. knows, the opposite is true: the doctoral degree forces you to focus on one narrow research problem for a long time, so you tend to lose your breadth of training in other sciences. Nevertheless, they flaunt their doctorates in hydrology or biochemistry, then talk about paleontology or geochronology, subjects they have zero qualification to discuss. Their Ph.D. is only relevant in the field where they have specialized training. It's comparable to asking a Ph.D. to fix your car or write a symphony--they may be smart, but they don't have the appropriate specialized training to do a competent job based on their Ph.D. alone.

This credential mongering was, of course, true with the modern progenitors of all subsequent creationist works, The Genesis Flood and Scientific Creationism, both written by Henry Morris, a hydraulic engineer with no training in any of the major earth or biological sciences.That they were accepted uncritically by masses of Christians is, to this day, astounding.  Onward.

Prothero, who is a palaeontologist, has found Meyer's book unimpressive:

Almost every page of this book is riddled by errors of fact or interpretation that could only result from someone writing in a subject way over his head, abetted by the creationist tendency to pluck facts out of context and get their meaning completely backwards. But as one of the few people in the entire creationist movement who has actually taken a few geology classes (but apparently no paleontology classes), he is their "expert" in this area, and is happy to mislead the creationist audience that knows no science at all with his slick but completely false understanding of the subject.

This is the same sort of experience I had with the abysmal Bones of Contention, written by Marvin Lubenow some years back, where every page had some sort of error on it.  I felt beaten down by the time I was finished and, despite having the best intentions of reviewing it, I never did because I couldn't stomach picking it up again.

Meyer's central focus of the book is the Cambrian "explosion," in which life seems to have proliferated and diversified during what Meyer argues is too short a time for evolution to have occurred.  After correcting Meyer's understanding of how long the Cambrian was, he addresses a persistent problem:

The mistakes and deliberate misunderstandings and misinterpretations go on and on, page after page. Meyer takes the normal scientific debates about the early conflicts about the molecular vs. morphological trees of life as evidence scientists know nothing, completely ignoring the recent consensus between these data sets. Like all creationists, he completely misinterprets the Eldredge and Gould punctuated equilibrium model and claims that they are arguing that evolution doesn't occur--when both Gould and Eldredge have clearly explained many times (which he never cites) why their ideas are compatible with Neo-Darwinism and not any kind of support for any form of creationism.

It is immensely disappointing to see this kind of problem over and over in ID writings. This example is similar to the lack of understanding of natural selection and adaptive valleys and peaks that William Dembski exhibits in his writings.  He seems to make the same errors consistently to the point where people don't even comment on what he has written because he won't address any of the criticisms. This is common of most ID writers.  I am currently piecing through Science and Human Origins by Luskin, Axe and Gauger and am encountering the same errors that I took Casey Luskin to task for three years ago.

You should read the whole review in all of its caustic glory.  I will probably get around to reading it but have too many other things to read right now. 

Science & Human Origins: A Not So Positive Review by Paul McBride

Douglas Axe, Ann Gauger and Casey Luskin have a new book out called Science & Human Origins. I have not had a chance to pick it up yet but it looks like the authors have learned nothing from the recent exchanges with folks like Dennis Venema and PZ Myers. The same faulty ideas still hold sway. Paul McBride has reviewed the book here. McBride points out an immediate problem that seems to characterize the ID camp in general. Ann Gauger writes:

I personally am convinced that unguided, unintelligent processes can’t do the job, not only because the neo-Darwinian mechanism is utterly insufficient, but also because we are beings capable of intelligence and creativity.

This is argument from personal incredulity and has no place in scientific discourse. If this is indeed how she feels, then it must color how she does her experiments and how she gathers her conclusions. If she is not open to this possibility, she has no business writing this book.

McBride remarks that chapter two, which is written by Douglas Axe, discusses his and Gauger's recent work where it was found that the time necessary to get one protein to evolve into another, contemporaneous protein is longer than the universe has existed. Other researchers have pointed out the logical error in this experiment but McBride's statement is succinct:

If Gauger and Axe couldn't get a single protein to evolve a novel function of their choosing then surely massive evolutionary changes are impossible. Actually, no. Gauger and Axe's experiment is a profound misunderstanding of evolution. The real question is not "Can X be turned into Y?" because that sense of direction requires preordination, which is not theorised to be a part of evolution. If we remove this preordination, the question becomes "Can X turn into something else?".

It is more than a little ironic that Axe and Gauger argue that, left to its own devices, evolution cannot foster new genetic material due to its randomness and then, to show that this is so, introduce an experiment in which evolution is directed and non-random. Didn't any of the editors catch this? Axe and Gauger do not seem to understand the concepts of exaptation and neutral mutations.

Casey Luskin wrote the chapter on the fossil record. McBride quotes Luskin:

There are many gaps and virtually no plausible transitional fossils that are generally accepted, even by evolutionists, to be direct human ancestors. Thus, public claims of evolutionists to the contrary, the appearance of humans in the fossil record appears to be been anything but a gradual Darwinian evolutionary process. The Darwinian belief that humans evolved from apelike species requires inferences that go beyond the evidence and is not supported by the fossil record.

Luskin isn't listening. He has shut his ears and refuses to listen to what people are saying about the evidence. As I will remark in my next BioLogos posts (and something McBride points out), the earliest Homo erectus individuals have cranial capacities of around 700 cc³, while the later ones have cranial capacities of up to 1225cc³. Does this overlap those of modern humans? Barely. And the suite of characteristics that are on display in your average Homo erectus are not modern human in any way. They are getting there, but they are not there yet. Then we have archaic Homo sapiens, such as Kabwe from what is now Zimbabwe, which is obviously evolved over Homo erectus but not quite modern human either. These people show up in Asia (Dali and Mapa in China and Ngandong in Indonesia), Europe (Petralona, Swanscombe, Steinheim, Atapuerca, to name a few) and they are obviously intermediate between Homo erectus and Homo sapiens in some way. Are they direct ancestors? Maybe, maybe not, but they are transitional. Luskin is arguing unilineal ancestry without allowing for the possibility of collateral ancestry.

The earliest modern remains that we have are from the site of Herto, on the Bouri Peninsula in the Afar triangle, in Ethiopia and they date to around 160,000. Even so, there are a few characteristics that link these remains to earlier, archaic Homo sapiens. There may be no absolute evidence that these represent our ancestors, but who is to say they aren't? We know that we have modern humans in the Near East at 100,000 that still show some signs of not being quite like us. By 40,000 they do. If these are not transitional sequences, what would qualify?

McBride's conclusion contains the following paragraph:

I have been left wondering why the Discovery Institute, or intelligent design advocates in general, or biblical literalists feel a need to try and accommodate science when they have a belief in a supernatural entity capable of breaking natural laws. In the case of this book, it has left them needing to make all kinds of awkward criticisms of fields in which the authors clearly lack expertise. A lawyer is not the right guy to challenge the world's palaeoanthropologists, nor the world's geneticists. Certainly, he shouldn't be trying to take them all on at once. It will end with him trying to smear the reputation of scientists rather than engaging with their ideas. Accusations that the entire field of palaeoanthropology is driven by personal disputes and that Francis Collins is a bad Christian are simply not compelling reading in a book that is putatively about scientific argument.

Leaving aside the issue of miracles, since I believe they can and do happen and are not restricted to the physical, observable world, McBride is partly correct in his assessment about the abilities of these authors to address the material. The problem is deeper than that, however. At least in the case of Luskin, there is an unwillingness to alter one's viewpoints in the face of additional evidence to the contrary. Here, there is a distinct similarity to the young-earth creationist camp, who have little to no scientific integrity. As McBride points out, Luskin's views have not altered since 2006. I pointed out these problems two years ago in a BioLogos post. I know that he read the post because we corresponded briefly about it. It is therefore, doubly disconcerting that he would continue to hold onto this “no transitional fossils” idea as if it were still defensible.

This is a book I clearly need to pick up and read, although I am quite certain it will just make my blood boil to do so.

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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