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. 

Karl Giberson: 2014 Revenge of the Creationists

Karl Giberson has written a post for the Daily Beast called “Revenge of the Creationists,” in which he outlines all of the recent developments in the land of young-earth creationism, although he lumps in climate change as well, a related and often correlative movement.  Aside: I am currently working on a post involving the examination of young earth creationism as a natural theology-based heresy.  Anyway, back to Giberson.  Of course, leading the charge is Ken Ham.  Giberson writes:

America’s leading science denialist is Ken Ham, head of the Answers in Genesis organization that built the infamous $30 million Creation Museum in Kentucky. He also put up a billboard in Times Square to raise funds for an even more ambitious Noah’s Ark Theme Park. Ham’s wacky ideas went primetime in February when he debated Bill Nye. An estimated three million viewers watched Ham claim that the earth is 10,000 years old, the Big Bang never happened, and Darwinian evolution is a hoax. His greatest howler, however—and my top anti-science salvo of 2014—would have to be his wholesale dismissal of the entire scientific enterprise as an atheistic missionary effort: “Science has been hijacked by secularists,” he claimed, who seek to indoctrinate us with “the religion of naturalism.”

It is quite clear from his writings that Ham has absolutely no idea how science actually operates and, as further evidence of his bad judgment in this area, relies on writers who know little to nothing of the areas in which they write.  This creates a two-fer-one bad science punch, giving your average scientist (and even most reasonably educated people) yet another reason to think Christianity is stupid. 

I differ from Giberson in his analysis of his point number four:

Climate change is arguably the most serious form of science denial. Creationism may be wrong, but embracing it won’t wreck the planet.  The last few years have seen many howlers on climate change including Senator Inhofe’s claim that humans cannot possibly influence the climate because “God’s still up there." 

There are plenty of examples of people who have embraced the young earth model who believe that the climate will be just fine because all of the changes recorded in the geological record are only six thousand years old.  The corollary to this is that, because earth is only six thousand years old, God must be returning soon, so why should we care how we treat the environment?  I saw that argument made a few years back (cannot find the post at the moment).  Albert Mohler gets a spot, as well as the Discovery Institute's Stephen Meyer, for this skewed analysis of the Cambrian explosion.  The only people missing are Kirk Cameron and Banana Ray Comfort.  Read the whole thing.  His tone is dismissive, but he is largely correct in his assessments.

Meanwhile, In Scotland...

On November 11, a hearing will take place in Glasgow to air a petition that will call for official guidelines that would bar teaching of creationism and ID in Scottish schools.  A local organization, C4ID (Centre for Intelligent Design) has responded to this petition.  The Scotland Herald writes:

The petition, to be heard on November 11, calls for official guidance to be issued in schools barring the presentation of creationist and Young Earth doctrines as viable alternatives to the science of evolution.

It has been backed by three Nobel-winning British scientists - Sir Harold Kroto, Sir Richard Roberts and Sir John Sulston.

Alastair Noble, director of C4ID, said his organisation believed the petition was based on imposing a "particular world view".

He ­acknowledged the idea of teaching "for and against" evolution would be controversial, but claimed it was consistent with scientific method.

But Paul Braterman, an honorary senior research fellow in chemistry at Glasgow University and committee member of the British Centre for Science Education (BCSE), a campaign to keep religion out of science classes, said C4ID was using "tired" arguments that were "merely a stalking horse for creationism".

Spencer Fildes, chairman of the Scottish Secular Society, said its concerns were about protecting science. "If you are in religious and moral education, then by all means you can philosophise about this," he said. "Students and children are welcome to discuss it, as long as it is contextual.

"Unfortunately, this does not happen, hence the reason why we have raised the petition."

This is more the David Klinghoffer arm of the ID argument, than the Stephen Meyer arm—and it tends not to carry as much traction because it specifically relies on the morality argument, which carries no weight in the science classroom.  This argument seems to regard science as some sort of "truth," to be compared to religious truth and it is nothing of the sort. 

Thoughts On Jared Diamond, Creationism and Lies

Jared Diamond, professor of geography at UCLA, was interviewed for TES Magazine.  Adi Bloom writes:

Jared Diamond , author of The Third Chimpanzee, which discusses evolution and human development, said people often assumed that advocates of creationism were ignorant. “One might be tempted to think that creationism is based on lack of exposure to science,” he told TES, during an interview to mark a new edition of the book for school-age children.

“It’s not that the creationists are ignorant of the arguments of evolution,” he said. “They’re aware of the evidence. They simply don’t believe it.”

For science teachers, therefore, it is not enough to counter the arguments of creationists – whether students or fellow teachers – with scientific fact. “Creationists have very slick one-liners, and you need to know the answers to these,” Professor Diamond said. “You have to know not only the science, but also the errors and the cheap one-liners of creationists.”

I am not sure that I agree with this section. Having read (and commented on) David Menton's diatribe against human evolution it was pretty clear that he thought he knew the evidence but really did not. His mistakes are elementary, both in examining the fossil record and in describing hominin anatomy.  In some instances, particularly in describing the fossil record, it was hard to tell if he was being ignorant or dishonest.

Duane Gish's book Evolution: The Fossils Still Say No! is rife with paragraphs in which he mis-characterizes the evidence for evolution particularly because he didn't know it as well as he thought he did (Gish passed away in March of last year).

In fact, it is usually not hard to blow these articles and books out of the water simply because the authors get basic facts wrong time after time.

What I find more of a problem rather than the slick one-liners is the persistent use of the "repeat a lie often enough and people will start to believe it" tactic.  One example of this is when ID supporters characterize the fossil record when they argue that lineages appear fully formed, when in fact, they do not.  Witness Stephen Meyer's recent book on the Cambrian explosion, in which he claims that this period is too short for evolution to have occurred and that the biotic proliferation is best explained by intelligent design processes.  As Don Prothero notes, the only reason Meyer comes to this conclusion is that he completely mischaracterizes the fossil record of the Cambrian.  Prothero writes:

Even more damning, Meyer completely ignores the existence of the first two stages of the Cambrian (nowhere are they even mentioned in the book, or the index) and talks about the Atdabanian stage as if it were the entire Cambrian all by itself. His misleading figures (e.g., Fig. 2.5, 2.6, 3.8) imply that there were no modern phyla in existence until the trilobites diversified in the Atdabanian. Sorry, but that's a flat out lie.

This notion that lineages appear fully formed can be found in any home school science book and hundreds of ID books as well. It is difficult to have any respect for people that repeat this falsehood when they ought to know better. Furthermore, in Meyer's case, he had every opportunity to avail himself of the evidence of the Cambrian expansion and chose to mischaracterize it, anyway.

Other examples of this meme are "evolution is untestable" and "there are no transitional fossils in the geological record,"  both are which are demonstrable falsehoods and yet are pervasive in the creationist and ID literature.  Even if you repeat a lie time and time again, it is still a lie, and it is not unChristian to point it out as such.

Discovery Institute Promoting New Book: Counting to God

The Discovery Institute is pushing a new book called Counting To God: A Personal Journey Through Science to Belief, a new attempt, by Doug Ell, an attorney (again?) with an undergraduate degree in math and physics,  to meld science and faith. It is purported to be a balanced and fair treatment of evidence for the “Seven Wonders of Science of the New Millennium.” That it is being promoted by the DI makes me wonder how fair the treatment of evolution will be, though, especially since one of the pillars is “New species appear suddenly in the fossil record.” The critiques of Darwin's Doubt (here and here, for example) apparently did not sink in.

In the book, he is said to address scientism (philosophical naturalism) and is quoted in the write-up thus: 

Do you think we live in a meaningless universe, and human beings were created by accident? Or do you think we live in a universe designed and created by a great intelligence, and human beings were designed? Accident or design -- that is the question.

This is a noble question and one that has been addressed by learned philosophers for centuries. And that is the point: it has been addressed by philosophers, not scientists. People can take swipes at evolutionary theory for the next two hundred years and it won't make modern design theory any more robust. You can construct tests to show that something fails to reject the null hypothesis, but you cannot use those results in support of a theory that does not have its own testable hypotheses.

That is where ID fails.

HuffPo: Intelligent Design's Final Days?

The intelligent design movement has labored under the premise that its attacks on evolution are not based on religion but on solid science and that arguments that promote intelligent design have no teleological motive.  This denial of religiosity on the part of the DI led, of course, to the church of the flying spaghetti monster, a parody based on the idea that the “intelligence” that was not attributable to God could, then, be attributable to any form of intelligence.

Well, now the mask is off.  Michael Zimmerman, the founder of the Clergy Letter Project, which can be thought of as a kind of response to the Discovery Institute's Dissent From Darwin list (but not to be confused with the hilarious Project Steve list) has written a piece for the Huffington Post titled Intelligent Design's Final Days?  He believes so.  This is why:

An article in the TFN Insider points out that Faith Bible Church in the Woodlands north of Houston will host a conference this weekend that explicitly links this form of creationism to "essential Christian doctrines." This is of particular significance because the most important talking point of those who promote intelligent design is that it has absolutely no link to Christianity in particular or to religion in general.
The description of the conference is clearly at odds with this perspective.

As Zimmerman points out, this conference is being attended by the movers and shakers of the intelligent design movement, with such luminaries as John West, Stephen Meyer and William Dembski. In fact, all but one of the speakers is a Discovery Institute senior fellow, with the sole exception being Melissa Cain Travis, who has written several books for the YEC-oriented publisher Apologia.While Zimmerman is quick to say that all of the main speakers have publicly distanced ID from Christianity, it should be pointed out that in 1999, William Dembski was quoted as saying that intelligent design was “the Logos of John’s Gospel restated in the idiom of information theory” and design leader Paul Nelson has publicly accepted the YEC perspective, co-authoring a book called A Case for Young-Earth Creationism: A Zondervan Digital Short.   Therefore, when these folks say that design is irrespective of Christianity, it is with a wink and a nudge.  The designer could be anybody but really, it is God.

Nonetheless, Zimmerman is correct in his observation that this conference represents a sea change of sorts in the movement.  They have, if you will, gone from latent to blatant.  Zimmerman puts it succinctly: “All three of these intelligent design stars are now comfortable moving away from their previous position and saying what all of us have known from the beginning: intelligent design is linked to “essential Christian doctrines.”  It now becomes clear that they have been “cdesign proponentsists” all along. 

And I Thought Don Prothero's Review of Darwin's Doubt Was Withering...

Nick Matzke has also written a review of Darwin's Doubt that has been posted on Panda's Thumb.  This is the nicest thing he has to say about it:

As I read through Meyer’s book, though, in case after case I see misunderstandings, superficial treatment of key issues which are devastating to his thesis once understood, and complete or near-complete omission of information that any non-expert reader would need to have to make an accurate assessment of Meyer’s arguments.

Matzke also points out that Meyer continually uses redrawn, dumbed-down illustrations, while ignorning detailed ones that would poke holes in his case and completely fails to understand the key events in the Pre-Cambrian and Cambrian periods. According to Matzke, Meyer also completely fails to understand phylogenetic analysis and the importance that it has to understanding patterns in the fossil record. It is this section for which he reserves his greatest scorn:

His main argument is basically that phylogenetic results sometimes conflict, therefore the whole thing is meaningless. This exhibits a jaw-dropping level of incompetence. It’s amateurish in the worst possible way, the opening-your-yapper-without-knowing-the-first-thing-about-what-you-are-discussing sort of amateurism.

Indeed, this seems to characterize much of the work that comes out of the DI these days.  One wonders why they don't just pick up a book on palaeontology and read it from cover to cover before writing these things.  This sort of reluctance to adapt their arguments to current data or respond to their critics is the kind of thing that leaves a bad taste in the mouth of your average scientist.  Reading reviews of Meyer's earlier work Signature in the Cell, it is clear that he has learned nothing in the intervening years. As I wrote over two years ago:

It is as if the concept of natural selection is completely foreign or is so repugnant as to be unacceptable and therefore, the DI writers continue to misunderstand it. The problem that I have with this perspective is that this misunderstanding of natural selection has not gone uncorrected. Kenneth Miller, Richard Dawkins, P.Z. Myers, Jerry Coyne, Steve Matheson and Darrel Falk, just to name a few have written treatises strongly rebutting this position held by Meyer, Dembski and Michael Behe. These have been ignored. Therefore, to continue to promote this misunderstanding of natural selection and its role in evolution constitutes, as they say, a terminological inexactitude. This would not be the first time the Discovery Institute was accused of that.

Why should your average scientist take this organization seriously when they continue to misunderstand basic evolutionary theory and repeat falsehoods time and time again?

What really pains me about this is that books that emanate from the Discovery Institute are being read by my kids in school. That has got to stop.

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. 

A Review of Darwin's Doubt By Nick Matzke

Over at Panda's Thumb, Nick Matzke has written a review of Stephen Meyer's new book Darwin's Doubt.  To get an idea of what he thinks of the book, Matzke's post is called "Meyer's Hopeless Monster." For example:

As I read through Meyer’s book, though, in case after case I see misunderstandings, superficial treatment of key issues which are devastating to his thesis once understood, and complete or near-complete omission of information that any non-expert reader would need to have to make an accurate assessment of Meyer’s arguments.

He also chastises Meyer for his lack of understanding of unilineal versus collateral ancestry, and notes that this is a common problem with creationists:

Yet another confusion that Meyer exhibits relates to the idea of “ancestor”. As with all creationists, Meyer exhibits no understanding of the fact that phylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry, and, crucially, that this is neither a significant flaw, nor any sort of challenge to common ancestry, nor any sort of evidence against evolution. Distinguishing between a close sister-group relationship and an exact ancestor is just a level of precision that we cannot expect in most cases. It’s just a by-product of the method and the data available.

A common problem is the inability to understand that even if a species did not give rise to successor species, it can still be transitional by virtue of the number of derived and retained traits relative to its sister taxa.

The whole review is scathing and his examples devastating to the premises of the book.  Another ID hatchet job.  

Sigmund Comments on the BioLogos/Discovery Institute Rift

Jerry Coyne has a guest post on his blog by Sigmund.  Sigmund has noticed the bad feelings between the Discovery Institute and BioLogos and has seen fit to comment on it.  He writes:

The slow descent into irrelevancy of BioLogos continues apace. From its inception by Francis Collins in 1997, the BioLogos Foundation’s original emphasis on increasing the acceptance of science amongst evangelical Christians has been gradually replaced by a more traditional focus on ‘worship’ and an increasing defense of Christianity from the challenges of secular reason.

This is a mite peculiar since many of the posts recently that I have seen including my own don't deal with what he describes whatever. My series of posts deals with the evidence for human evolution and three days ago, Dennis Venema started a series of posts on the basics of evolutionary theory. While it is true that Pete Enns expends much energy writing excellent columns on the nature of biblical interpretation, there are quite a few posts about basic science and, ironically, Sigmund writes that BioLogos has gotten away from science yet the whole purpose of his post is to illuminate a rift between the two organizations that is science-based.

He comments on the recent reaction to Dennis Venema's review (which I thought was smack on the money) of Stephen Meyer's Signature in the Cell by the author.  Meyer argues that complex specified information such as that found in the cell can only come from intelligent causes, while Venema states that there are natural causes that can create complex specified information without the need to invoke a designer.  Meyer responds to this charge (in a way that Sigmund describes as “shifting the goalposts”) by arguing that he was only writing about biopoesis, not established life.  Darrel Falk responded to Meyer's article in a way that Sigmund finds baffling. Sigmund and Falk are both fully aware that Meyer moved the goal posts, however Sigmund writes: 

It was at this point that the real problems with the new BioLogos strategy become apparent. Falk, needing to see the best in every Christian, comes across as the theological equivalent of Woody Allen in the aftermath of the nymphomaniac scene in ‘Play it again Sam’. Falk spends almost the entire article wondering “How did I misread those signs?” and getting sidetracked into talking about “complex specified information” an imprecise term regarding complexity, only used by ‘Intelligent Design’ supporters.
While it is clearly a case of the usual dishonest creationist tactics of trying to be vague and then shifting the goalposts when caught out, Falk doesn’t seem to be able to state the obvious.

I feel for Darrel here, because, as Christians, we are called to see the best in people, even in a scientific setting. But Darrel has been on the receiving end of questionable Discovery Institute practices before at the Vibrant Dance conference.  Commenting on it at the time, Steve Matheson wrote: 

The question is not whether Christians should point to the things they agree on. It's not about whether affirmations of shared belief are beneficial or appropriate when Christians find themselves in disagreement. For me and, I suspect, most of the critics that Falk was referring to, the question is whether BioLogos should cosponsor a conference on faith and science with organizations that seek to mislead people about science.

Here, Steve is referring to both the Discovery Institute and Reasons to Believe, an organization that Todd Wood has dealt with. I have written about them as well.

Those of us who follow Jesus Christ want to believe the best in our fellow Christians but the sad fact is that we have examples in Christendom where scientific evidence is very poorly treated or misrepresented outright. I would never accuse Ken Ham of not being a Christian. But I would also never state that he honestly treats the scientific evidence.  It is our duty to point out these errors in the hopes of reaching our fellow Christians and informing them that honest scientific inquiry can go hand in hand with Christianity.  If the goal posts get moved, it is our duty to point that out as well.  Darrel has done this.  We might fault the force of his response, but we should not fault his intentions.   

Martin Gaskell and the University of Kentucky

The University of Kentucky just settled out of court a discrimination suit brought by Martin Gaskell who felt that he was denied a position because he was a Christian. Here is the story from Inside Higher Ed and here is the essay that got Dr. Gaskell into trouble. Two things come to mind when I read the story and the essay: first, the University of Kentucky acted shamefully in many ways during the whole episode and, second, if I had been relevant professors at the University, I would have been a bit nervous too.

First, the University:

But Gaskell says it was Kentucky’s biology department that sank his candidacy for the observatory directorship. Upon discovering his lecture notes online, several members of the search committee expressed curiosity, though not necessarily alarm. “Clearly this man is complex and likely fascinating to talk to -- but possibly evangelical,” wrote one committee member in an e-mail. “If we hire him, we should expect similar content to be posted on or directly linked from the department website.” Another, noting that he was aware of Gaskell’s religious disposition, responded, “Personally, I believe in freedom of religion, and have no problem with Martin as long as he does not use the classroom or official university sites as a pulpit.”

Gaskell says that the biology department, whose members had no astrophysical experience or training were allowed to influence the decision to hire him. Understandably, this was upsetting. There was, additionally, clearly some future projecting going on:

“[A non-committee member] suggested, in particular, that we might one day wake up to a [Lexington] Herald-Leader headline citing ‘UK hires creationist as Observatory Director,’” wrote one member of the search committee in an e-mail. “Such a headline would probably not be a fair representation of Martin’s personal views, which are not simple, but the headline could appear nonetheless.”

You cannot hire or not hire somebody based on something that may or may not happen that has little bearing on their position. One might just as easily say that they have a problem with hiring someone for a biology position because they go to church. God only knows what that church might teach some Sunday.

Second, Martin Gaskell. After setting up the various divisions within the church with regard to the teaching of evolution and the age of the earth, he uncorks this:

It is true that there are significant scientific problems in evolutionary theory (a good thing or else many biologists and geologists would be out of a job) and that these problems are bigger than is usually made out in introductory geology/biology courses, but the real problem with humanistic evolution is in the unwarranted atheistic assumptions and extrapolations. It is the latter that “creationists” should really be attacking (many books do, in fact, attack these unwarranted assumptions and extrapolations).

What exactly are these “significant problems?” He does not say (nor, I will warrant, would he be able to). The first thing that comes to my mind when I read something like this is “Discovery Institute party line” and red flags go up. Here is a man who complains that biologists who have no expertise in astrophysics are having an influence on his hiring and yet appears to feel perfectly free to denigrate a science of which he knows nothing. Further, the statement isn't just wrong, it is pejorative, implying that biologists are pulling the wool over people's eyes when they teach it or practice it. That is uncalled for and unprofessional. He continues:

A discussion of the current controversies over evolutionary theory and how Christians view these controversies, is beyond the scope of this handout, but the now extensive literature discussing and reviewing books such as those of Phillip E. Johnson (“Darwin on Trial”) and of biochemist Michael J. Behe (“Darwin's Black Box”) will give you some of the flavor of the diversity of opinion of Christian biologists (and geologists).

Why has he mentioned no books by mainstream biologists, such as Kenneth Miller or Francis Collins? They are both Christians and well-respected in the field of biology. The only flavor you will get with the list Gaskell provides is “Intelligent Design”.

So, was the University of Kentucky right in denying him the appointment? likely not. It is not clear that his views on biology would have made the slightest difference in the performance of his duties as an astronomer. It is also true that he should have known that if he hung a big sign around his neck reading “Discovery Institute” that problems would arise.

While most scientists have taken to ignoring the young earth creation groups such as the ICR and AiG, the Discovery Institute is viewed as a real threat because of the thin veneer of “science” that it promotes as well as the their suspect practices (See Steve Matheson's open letter to Stephen Meyer of the DI) involving their portrayal of scientists and their promotion of debatable legislation damaging to the teaching of evolutionary theory in public schools. It is not surprising that the biologists reacted the way they did.

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Complexity Can Evolve Without High Cost

Was R.A. Fisher wrong? It has always been thought that with complexity comes a general lack of evolutionary adaptability. The consensus about human evolution is that early primates were able to exploit their environments because they had a generalized bauplan and could adapt to whatever came down the road. This was true from the teeth to the skeletal structure. Now, in an article for Phys.Org, research by Jianzhi "George" Zhang and colleagues has challenged the idea that the evolution of complexity carries a high cost:

When Fisher first wrote about the cost of complexity, he argued that random mutations---which, along with natural selection, drive evolution---are more likely to benefit simple organisms than complex organisms.

"Think of a hammer and a microscope," Zhang said. "One is complex, one is simple. If you change the length of an arbitrary component of the system by an inch, for example, you're more likely to break the microscope than the hammer."

Looking at pleiotropy, the idea that individual genes can affect a range of traits, the authors found something surprising:

For simplicity, mathematical models of pleiotropy have assumed that all genes in an organism affect all of its traits to some extent. But Zhang's group found that most genes affect only a small number of traits, while relatively few genes affect large numbers of traits.

What's more, they found a "modular" pattern of organization, with genes and traits grouped into sets. Genes in a particular set affect a particular group of traits, but not traits in other groups.

In addition, the researchers learned that the more traits a gene affects, the stronger its effect on each trait.

And how does this relate to the topic of this blog? The author writes:

The new findings help buffer evolutionary biology against the criticisms of intelligent design proponents, Zhang said. "The evolution of complexity is one thing that they often target. Admittedly, there were some theoretical difficulties in explaining the evolution of complexity because of the notion of the cost of complexity, but with our findings these difficulties are now removed."

One of the general complaints that has been made against those who espouse ID is that there is either a persistently simplistic model of evolution employed or an incorrect one. Recent works by Michael Behe, William Dembski and Stephen Meyer have focused on the presumed inability of evolutionary models to account for "specified complexity." They also make the specious argument that there can never be an increase in information under these models. Studies like these, which operate out of a predictive model, show otherwise.

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Win a Free Copy of Signature in the Cell

Anyluckyday.com is sponsoring a contest in which you can win a copy of Signature in the Cell, the book by Stephen Meyer promoting the idea that the molecular genetics of the cell show the handiwork of a designer. Here is the promo video:



As you know, there is a lively discussion going on right now about the book between Meyer and Steve Matheson, up at Calvin College. He reviewed it chapter by chapter in his blog and the latest installment can be found here.

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Steve Matheson Writes an Open Letter to Stephen Meyer

Steve Matheson has posted on his blog an open letter to Stephen Meyer following their colloquium/debate at Biola University. Subsequent to the event, a posting on the Discovery Institute's blog Evolution News and Views claimed that Dr. Matheson had conceded that design was the best explanation for origins of life questions. In a previous post, he writes that this isn't so. Here, he takes the gloves off:

Your Discovery Institute is a horrific mistake, an epic intellectual tragedy that is degrading the minds of those who consume its products and bringing dishonor to you and to the church. It is for good reason that Casey Luskin is held in such extreme contempt by your movement's critics, and there's something truly sick about the pattern of attacks that your operatives launched in the weeks after the Biola event. It's clear that you have a cadre of attack dogs that do this work for you, and some of them seem unconstrained by standards of integrity. I can't state this strongly enough: the Discovery Institute is a dangerous cancer on the Christian intellect, both because of its unyielding commitment to dishonesty and because of its creepy mission to undermine science itself. I'd like to see you do better, but I have no such hope for your institute. It needs to be destroyed, and I will do what I can to bring that about.

As Glenn Reynolds would say: Ouch! It is quite clear that those writing for the Discovery Institute have a fairly minimal grasp on the discipline (evolution) that they so seek to denigrate. This is clear from the writings of William Dembski, Michael Behe, Jonathan Marks, Jonathan Wells and Philip Johnson. It is also true that many posts or press releases from the Discovery Institute are either misleading or false (here, here, here, here and here just to name a few). All told, this gives one pause as to whether this organization is really involved whatever in a scientific enterprise and that it seeks to address the debate in an honest way.

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Steve Matheson Fires Back

Steve has posted a response to the Discovery Institute's claim that he admitted design was the best alternative. It is here. One of the key arguments that design proponents (or "cdesignproponentsists" if you prefer) put out is that evolutionary theory does not have a good explanation for origins of life questions. Stephen Meyer, author of The Signature in the Cell, believes that this is where design comes in. Matheson responds:

It may be the case that we don't have a complete account of the origin of life, and it's certainly true that we don't have a complete account of the origin of genetic information control systems. But such an admission implies nothing about whether such an account is possible or even likely, and that's where Meyer would have to do his philosophical work in order to help his case. In other words, to assert that "we haven't explained X" is most assuredly not to assert that "we cannot explain X." Think about it: there would be no such thing as science if this were the case. Scientists are all about asserting that "we haven't explained X," then proposing a way to change that.

Origins of life questions have never been a center of evolutionary biology studies. During the formation of the synthesis, these question were largely ignored and it was not until the Miller-Urey experiments in 1953 that these question were associated with evolutionary theory. These question are, in a sense, like those governing those of the Big Bang. One can theorize back only so far until it becomes a conjecture. Evolution deals primarily with the changes in established life forms and with common descent issues. One can look at the fossil record and see that, as one moves through time, there is greater diversity of life from simpler forms to more complex forms and that transitional fossils (fishapods, frogamanders) exist at junctures that, chronologically, precede in one case, teleost fish and tetrapods and in the other case, frogs and salamanders. This is very largely corroborated by DNA studies, which reflect the similarities and differences in organisms and have given rise to divergence trees. That these trees mirror, to a very large extent, the fossil record is not exactly a smoking gun for universal common descent but it is pretty good model from which to work.

Hi experience was not entirely positive, however:

Anyway, Meyer spent a lot of time explaining why it matters that certain origin-of-life postulates are ineffective, but he never bothered to show that the current theories are in fact ineffective. What he did instead was attack a strawman (random flying-together of biological structures) at length, then erect a second one (a crude caricature of self-organization ideas) and attack it more briefly. Current thought focuses on the RNA World, and Meyer completely omitted any discussion of it. He meant to mislead the audience, and I think he was successful.

This straw man argument is not so unusual. While the Discovery Institute continually claims that evolutionary biologists put up straw men arguments about design, every single argument against evolution made by the writers there, from Phillip Johnson to William Dembski, takes the form of one. Steve's second and third posts should be up soon.

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David Klinghoffer: Signature of Controvery

David Klinghoffer has taken it upon himself to defend Signature in the Cell, the book by Stephen Meyer on Intelligent Design. In a new online book Signature of Controversy, he has collected rebuttals of different individuals, including Stephen Meyer to the criticisms of the book. The Discovery Institute is providing it as a free download here. More on this later.

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Stephen Meyer Faces His Critics: Update 2

I received this note from the Apologetics Department at Biola University about the possibility of getting a transcript of the panel discussion on May 14. Here is what they say:

Hello James,

Thank you for your note. While we will not have a transcript of the evening available, we are recording the event and it will be available to purchase as a DVD. To place your order, please call our office at 562.906.4570. Let me know if you have any questions!

Kristen Anderson
Administrative Assistant
M.A. in Christian Apologetics
Biola University
(562) 906-4570

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.

Stephen Meyer to Face His Critics: Update

Somehow, I linked to the wrong description of the event that I posted about yesterday. Here is the correct announcement:

Dr. Stephen Meyer has written a book that is shaking the evolutionary establishment like “Darwin’s Black Box” and “Evolution: A Theory in Crisis” did in previous decades. Meyer has assembled a set of ideas based on the latest research on living cells that must be answered if traditional Darwinism is to survive. So we have assembled a powerful group of credentialed critics of Meyer’s “Intelligent Design” position to let him have it with both barrels. No hiding in dark libraries or murky laboratories - if Meyer has the goods, he needs to debate his toughest critics face to face! In addition, we will be screening some clips of the latest Illustra Media DVD titled “Darwin’s Dilemma” and providing free copies to each family who attends.

I have just heard from Steve Matheson, who will be on the panel. Steve is no friend of Signature in the Cell, Stephen Meyer's most recent book, so I suspect it will be a lively time.

BTW, the event description that I accidentally linked to takes place the following day and is called "The Cambrian Explosion: The Data Behind Darwin's Dilemma." It is hosted by "Paul Nelson, Rick Sternberg, Doug Axe, Stephen Meyer, John Bloom, and more."

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