Recently in Intelligent Design Category

Note: this turned into kind of a rough draft of an essay, and I think the part about the origin of life and complexity of the cell would be publishable in perhaps an education journal. So I welcome any comments on the argument, supporting or undermining points, etc. I don’t have my references folders handy at the moment but I have references in mind for all of the factual assertions, although more are always welcome. I’m very happy to acknowledge commentators if this does get published, or even have a coauthor if someone else is interested in working on this. Thanks!

I have not been able to blog much lately, due to minor distractions like grad school and actually having a social life for once (don’t everyone gasp at once an suck all of the air out of the room). But now it is summer and I am in a coffee shop, and I am feeling frisky. I just came across blogs by Jeff Shallit and PZ Myers responding to an essay in The Scientist entitled “What neo-creationists get right” by Gordy Slack, journalist and author of an excellent book on the Dover trial, The Battle Over the Meaning of Everything: Evolution, Intelligent Design, and a School Board in Dover, PA. (And Slack’s reply to PZ and PZ’s surreply.) Slack argued that part of the reason for the persistence of creationism is that evolutionists often react with “ridicule and self-righteous rage” on some issues where creationists might have a point, or are at least not so clearly wrong.

I consider both Slack and his critics friends and colleagues, and both sides make some valid points. But I think many of the arguments that both Slack and his critics make in this particular instance don’t work.

“Intelligent design” creationist Paul Nelson was bragging recently on “Uncommon Descent” about getting a presentation accepted at a conference in the UK, the Ian Ramsey Center for Science and Religion at Oxford’s “God, Nature and Design: Historical and Contemporary Perspectives”. Apparently, the fix is in for IDC advocates, and several openly pro-IDC abstracts have been accepted.

There seem to be about five that have been spotted so far, Paul Nelson’s included. Nelson’s presentation is titled, “The Logic of Dysteleology”. Having attended the 1997 “Naturalism, Theism, and the Scientific Enterprise” conference and heard Nelson’s talk there, if I were attending the Ian Ramsey conference now I could go visit a snack bar during Nelson’s talk and not miss much. It looks to be the same topic, just with a few more recent references tossed in.

Now, as to the rigor of this conference, let’s look at another abstract that was deemed worthy by the reviewers, submitted by one Don Booker of Pace University.

J.B.S. Haldane, when asked “What has the study of biology taught you about the Creator, Dr. Haldane?”, replied

“I’m not sure, but He seems to be inordinately fond of beetles.”

Discovery Institute Fellow Dr. Paul Nelson is inordinately fond of ORFans, genes unique to one species that appear to have no relatives in other species. He feels that these unique genes represent a significant challenge to evolutionary biology. However, he has not noticed that the distribution of ORFans implies that the designer is more enamoured of viruses than humans.

Michael Le Page at New Scientist discusses Evolution: 24 myths and misconceptions.

Shared misconceptions:

Everything is an adaptation produced by natural selection
Natural selection is the only means of evolution
Natural selection leads to ever-greater complexity
Evolution produces creatures perfectly adapted to their environment
Evolution always promotes the survival of species
It doesn’t matter if people do not understand evolution
“Survival of the fittest” justifies “everyone for themselves”
Evolution is limitlessly creative
Evolution cannot explain traits such as homosexuality
Creationism provides a coherent alternative to evolution

Read on for the much longer list of Creationist myths

T Ryan Gregory at Genomicron who is an evolutionary biologist specializing in genome size evolution at the University of Guelph in Canada educates us (and perhaps some ID proponents) about some of the common pitfalls in phylogeny. In this case, the posting discusses the findings in a recent paper which argues that the comb jellies and not sponges are the earliest branch.

The core concept of Dr. Michael Behe’s recent book “The Edge of Evolution” (Behe, 2007) is that protein-protein binding sites are extremely unlikely to have developed by natural means, and therefore were designed by unknown intelligent agents. There is a lot of interest in this concept, as the tag cloud at PT indicates. A recent paper (Grueninger et al., 2008) on human design of binding sites undermines some of his key assumptions, but what is more interesting is an old paper cited in Grueninger that shows researchers have known for some time that evolution of protein-protein binding sites is not as difficult as Behe makes out. Indeed, his very premise was invalid from the beginning.

Biola University’s ‘Christian Apologetics’ program announced a showing of Ben Stein’s movie ‘Expelled’ for $10. However, when Troy Britain showed up, he discovered that the event was a ‘backstage’ event only.

It gets “better” though. After listening to Stein practically foam at the mouth (he almost seemed like he had a pulse for a minute there) about the horrible injustices supposedly documented in his film and a bunch of stuff about God, this despite the fact that one of the clips from the film was one of the Discovery Institute muckety-mucks prattling on about how they want to talk about science and that it’s the “people with no argument” who keep bringing up the “red-herring” of religion, the night was topped off with Stein receiving the Orwellianly titled “Phillip E. Johnson Award for Liberty and Truth” for 2008. All of this to no less than three standing ovations from the crowd.

While the DI is working hard to differentiate ID from its religious foundations, Ben Stein and other ‘Expelled’ people seem to be quite clear that this is all about God.

Thank God, I say, for their honesty even though they are quite misguided about evolutionary theory and Intelligent Design and are doing science and religion a disfavor.

We got the following story via a dedicated reader in Kentucky, who says its from the newsletter of the ACLU of Kentucky.

When the Discovery Institute and other professional intelligent design apologists talk about wanting to just “teach the controversy”—which everyone knows is in direct opposition to “teach the science”—you should remember this example of a DI-inspired curriculum.

Bloomfield Middle School - Intelligent Design
by William E. Sharp, Staff Attorney

This case also represents a significant pre-litigation victory that is due in large part to the dedication and courage of a committed ACLU of Kentucky member. Specifically, this member contacted us about a particular teacher’s inclusion of Intelligent Design components into a 7^th grade science curriculum at Bloomfield Middle. Upon further investigation, we learned that the teacher not only incorporated Intelligent Design’s critiques of Darwinism, but the teacher also disseminated a chart containing Intelligent Design’s rationale for the earth’s short existence. This chart provided a timeline that included (and dated) Noah’s Ark and the Biblical flood story. This teacher also provided students with a five page “fact sheet” on Intelligent Design’s Model of Origins, its critique of the big bang theory, and its theory that dinosaurs coexisted with humans.

When we presented school officials with our objections to Intelligent Design as a reformulated version of Creationism and the substantial legal authority establishing the illegality of teaching a religious doctrine within a science curriculum. Bloomfield officials decided to remove all Intelligent Design components from the science curriculum.

(emphasis ours)

The cdesign proponentsists at the Discovery Institute spend a lot of hot air trying to convince the courts that they have noting to do with those creationdesign proponentsists from the 80s—just like the “scientific” creationists from the 80s claimed to have nothing to do with the “biblical” creationists from the 60s.

However, their grassroots supporters never seem to get the memo.

At the NewScientist blog, we find a posting which raises more questions than it answers

After confirming the news that the movie is without much of any scientific content, and makes ill chosen references to Nazis, Amanda Gefter, opinion editor, describes the Q&A that followed.

We learn at the Discovery Institute Blog about a recent lecture tour in Spain by ID creationists

Over an eight day period last January, Physicians and Surgeons for Scientific Integrity (aka DoctorsDoubtingDarwin.com, a rapidly growing, 277-member, physician group from 17 countries) sponsored a lecture tour in Barcelona, Malaga, Madrid, Leon and Vigo. It was titled “Lo Que Darwin No Sabia,” or “What Darwin Didn’t Know.” Tom Woodward, Ph.D. (author of Doubts About Darwin and Darwin Strikes Back) and myself (author of What Darwin Didn’t Know and Billions of Missing Links) lectured on eight occasions to exceptionally large audiences. Santiago Escuain was our translator extraordinaire. Rich Akin, the CEO of PSSI, put in enormous hours into making this trip a huge success.

El Pais reports on the ‘successful’ Spain Tour of ‘Lo que Darwin no sabía’. Of course, the DI does admit later on that the success was limited.

Intelligent Design Creationists like Bill Dembski have argued that Woese’s work contradicts evolutionary theory or more specifically common descent and Darwinian theory. See for instance “Woese: Life could have started “millions of times”” or this old posting of mine.

Since many creationists have come to misunderstand Woese’s arguments, the impact on Darwinian evolutionary theory, let’s start exploring Woese’s argument

Dembski’s article which references (and fully reproduces) an article by Ronald Kotulak claims that Woese commented in 2002 that life could have started “millions of times”, a statement I have not been able to track back to his scholarly work.

The 2002 paper is likely: Carl Woese On the evolution of cells PNAS June 25, 2002 vol. 99 no. 13 8742-8747

The New York Times reports in an article titled Disinvited to a Screening, a Critic Ends Up in a Faith-Based Crossfire how a critic was invited and then disinvited from attending the screening of Expelled and how the critic still attended the showing.

Shortly before he was to attend a screening in January of the documentary “Expelled: No Intelligence Allowed,” which is about alternatives to the theory of evolution, Roger Moore, a film critic for The Orlando Sentinel, learned that his invitation had been revoked by the film’s marketers.

But Roger Moore decided to attend anyway

On Uncommon Descent William Dembski claims that Richard Dawkins has admitted that life could be designed and thus wonders: “Is ID therefore scientific?”. As I will show this is a logically flawed conclusion.

First of all lets point out Intelligent Design does not claim merely that life is designed but that such design can be detected via scientific methods. In this aspect if differs from science which admits that design always remains a logical possibility, however science also accepts that if such design is ‘supernatural’ no scientific method can detect such design.

The Board of Regents met to hear Gonzalez’s appeal this morning. It’s worth noting that they rarely take a differing view on tenure decisions from the tenure committee itself. So sorry Tara, you got it wrong… the decision is already out, and it’s not a shocker:

The Iowa Board of Regents has denied Guillermo Gonzales’, associate professor of physics and astronomy, appeal for tenure. After a private deliberation, the Board voted down the appeal which has already been denied by Iowa State University and ISU President Gregory Geoffroy.

No details at this point. But look for the Discovery Institute Spin Room to start kvetching at any moment, if they haven’t already. At least Casey Luskin will have something to whine about besides his inability to figure out internet image copyright stuff. Might I suggest that he just pretend that Gonzalez was actually thrice denied tenure– once by the tenure board, once by the Preznident, and once by the Board of Regents– for maximum martyrhood?

It’s practically Biblical.

Edit in: A more detailed news release can be found here

Well, the Intelligent design Challenge is over, and we have a winner(s). It was interesting looking at the various methods people used, and I’ll discuss this below the fold. One thing stood out though.

No one used the explanatory filter, or any of the various methods proposed by Intelligent Design proponents. Not one person.

Determining where a genome has been produced or altered by an intelligent designer is a matter of some importance. Consider the claims that the HIV virus was engineered as a biowarfare weapon, or the concern that virulence genes from other organisms could be inserted into viruses and bacteria to “weaponise” them. For example the engineered mouse pox virus that turned lethal (Nature. 2001 May 17;411(6835):232-5 see also Nat Genet. 2001 Nov;29(3):253-6) and limits on the sequencing of the 1918 strain of the flu to stop flu from being weaponised (Fed Regist. 2005 Oct 20;70(202):61047-9,). A method that could reliably detect the action of human intelligent design in the genomes of microorganisms would be of significant advantage.

Thus we issue the “Intelligent Design Challenge”. Below the fold are 6 gene sequences. At least one of them has been produced by a human designer. All you have to do is to determine which one(s) have been acted on, what the designed sequence does, and explain the method you used to determine this (in sufficient detail to replicate your determination eg. if you used an approximation of Chaitin information, a brief description of the algorithm you used).

I’ve re-written the contest rules slightly as some people were confused as to what designer they were supposed to detect.

To win, you have to:

1) Identify which sequences have been produced by a human designer
2) Describe how you identified the sequence as being designed (eg. I used PKZip to compress the sequences as an approximation of Chaitin information and ordered the output according to the following criteria etc. etc.)
3) Describe what the sequence does (eg. “This is the active site of a triose phosphate isomerise engineered into a riboprotein – this due to the catalytic triad signature” real example BTW: this isn’t as hard as it sounds once you have the designed sequences)

Obviously, the groups who produced these sequences are not eligible to enter, and if you walked down the corridor and asked the groups who produced these sequences what they did, you are also not eligible. You need to have done some actual work related to the sequences presented here. Simply looking up all journal references to “designed sequences” in Pubmed doesn’t count (obviously this is all public domain, I’m not going to release the engineered killer mousepox virus sequence am I).

If you are in an emergency ward, trying to discover if the superflu screaming through the population is a bioweapon, you won’t find the answer that way. And you won’t have the luxury of having a full viral sequence to BLAST against known genes [thus discovering that the M2 ion channel had been replaced with the amandatine-insensitive Vpu ion channel, so that your antiviral drugs won’t work], but short sequences like the ones above.

Remember, in a real biowarfare situation, everyone will be short of time and resources. A simple, reliable procedure to determine if a sequence has been human-engineered is of the utmost importance.

So, in the spirit of the Robot Soccer Challenge and the NASA Spacecraft Challenge, look at the sequences below the fold and off you go.

The first successful determination of the designed sequence(s) and their function will win a copy of OpenLab 2007.

Comments will be will be opened for your entries at 10:30 pm Australian Central Daylight Saving Time (GMT +10:30), 1 February.

The comments are now live, write in your entries. The first correct answer fulfilling the conditions will receive a copy of OpenLab 2007. As tonight is my sons’ birthday, and I have an occultation to observe as well, don’t expect much input from me for a while.

Speaking of brazen antics, PT commenter Glen Davidson over on the AtBC forum blew the whistle by posting the “Expelled Challenge” FAQ. Apparently, these folks are running scared that their project will be little more than one step up from “direct to video” projects, and are coordinating mass attendance of students and their parents from literalist-Christian schools. They are providing what amounts to a kickback to school administrators for movie ticket stubs from attendees who go to the “Expelled” movie during its first two weeks in the local theater.

(Continue reading at the Austringer.)

The Union of Concerned Scientists has released a six section overview on Science, Evolution, and Intelligent Design

Section 1: Science as a Way of Knowing
Section 2: Science and Society
Section 3: Evolution, Creationism, and Intelligent Design
Section 4: Why Intelligent Design is not Science
Section 5: Science Education and Intelligent Design
Section 6: Fairness and Balance in the Classroom and Beyond

I would add another section on the scientific vacuity or infertility of Intelligent Design. Ask yourself this simple question: What non-trivial contribution has Intelligent Design made to our scientific understanding? And ask you then a follow-up question: For those systems which ID claims to be designed, how does ID explain these systems?

The answers, or lack thereof, may surprise you.

HT: NCSE

William Dembski and Jonathan Wells authored the successor to “Of Pandas and People”, titled “The Design of Life”. The Foundation for Thought and Ethics (FTE) released the book on November 19^th. Since then, Dembski has made a point of bragging about five-star reviews on the The Design of Life: Discovering Signs of Intelligence In Biological Systems Amazon.com website.

But that’s not all that the IDC advocates are doing concerning Amazon. They managed, for a time, to suppress a critical review by a Top 50 Amazon.com reviewer, John Kwok. For those who gave credence to the notion that IDC advocates were serious when they said that they wished to foster discussion and “teach the controversy”, this should be a reminder that actions do sometimes speak louder than words. Abbie Smith at ERV wrote an entertaining treatment of a number of issues involved here.

I’ve published book reviews before, primarily concerning things in the evolution/creation socio-political controversy. My review of Dembski’s “The Design Inference” back in 1999 even got notice in some of the antievolution venues as a serious review.

So on December 6^th, I emailed the contact address for the Foundation for Thought and Ethics (FTE) and requested a review copy of the new book by William Dembski and Jonathan Wells, “The Design of Life”. I provided my work address at Michigan State University for shipping. So far, neither a review copy of the book nor any correspondence concerning my request has appeared there, nor even a note in email.

But apparently FTE does have a message for those it believes will provide critical reviews of their book: ‘Buy it yourself.’

Of course, not all of the reviews posted in the first month have been as exuberant as those above; some are venomous. We are receiving numerous requests for review copies from people we know intend to try to destroy it. (We do not intentionally send complimentary review copies to these people.) But we are greatly encouraged and delighted by the extremely positive reviews and accolades coming in from highly respected research scientists and science teachers across the country and from overseas.

I will be discussing the book’s contents in the future, probably on a shorter time-frame than Michael Behe’s prospective perspective on being a co-author on the book (testifying to that effect in 2005). But for now, I will just take up the ethical dimension of FTE’s actions here.

We are all familiar with the creationist argument about the eye, an argument which Darwin already addressed in his original work. And while creationists are still in much of a denial about eye evolution, science keeps on closing gaps.

In the Australian a second paper addressing eye evolution is discussed.

Science literacy is increasingly seen as important for people to be effective participants in a society where the pace of scientific discovery and translation to products and processes is increased. Effective engagement with GM crops, stem cell therapies, burgeoning healthcare costs and global warming require a reasonable degree of science literacy.

The need for science literacy is emphasised by a recent post at Uncommon Descent by commentator Gil Dodgen, who makes this remarkable statement:

In the meantime, medical doctors should prescribe multiple antibiotics for all infections, since this will decrease the likelihood that infectious agents can develop resistance through stochastic processes. Had the nature of the limits of Darwinian processes been understood at the outset, the medical community would not have replaced one antibiotic with another in a serial fashion, but would have prescribed them in parallel.

As I’ve said before in a different context, to paraphrase Mr. Babbage[1], I cannot apprehend the confusion of mind that would result in the above statement. One would have to be ignorant of 60 years of biomedical research and medical practice to say that. Both Humble Monkey and The Sandwalk have already commented on this post, and it’s got a big helping of Respectful Insolence, but I want to discuss this from a pharmacological perspective.

Oops, someone pointed out to me that this publication preceded the DI’s press tour.

Poor Discovery Institute, after spending much time and effort on trying, unsuccessfully, to generate some media interest on the Gonzalez tenure case, all they got was a cynical response from Mac Johnson at the conservative site Human Events.com.

So in light of the issue’s new prominence and with a desire to improve the mental hygiene of others, I would just like to say that Intelligent Design is a really, really bad idea –scientifically, politically, and theologically. I say this as a dedicated conservative, who has on many occasions defended and espoused religion and religious conservatism. I also say it as a professional molecular biologist, who has worked daily (or at least week-daily) for years with biological problems to which the theory of evolution has contributed significant understanding – and to which Intelligent Design is incapable of contributing any understanding at all.

Intelligent Design is a career-killer. There’s just no two ways about it. And not because of how peers treat the ID supporter; they throw their own productivity under the bus, to use Casey Luskin’s overworked cliche. We saw the same thing with Behe and Dembski. Behe has published ONE peer-reviewed paper in the last decade. And Dembski… well, does anybody even know where he works these days?

All hyperbole aside, let’s look at Gonzalez’s publication track record…

Continue reading at Neurotopia

Yesterday the Discovery Institute held a press conference at the capitol building in Des Moines, to announce Guillermo Gonzalez’s plans to sue Iowa State University over their decision to deny him tenure. Supposedly the lawsuit will be filed pending the rejection of an appeal to the Board of Regents, which is virtually guaranteed simply for the fact that the Regents typically uphold tenure decisions. Joining Casey Luskin, Rob Crowther, Gonzalez’s attorneys, and a few other DI folk was state Senator David Hartsuch (R-District 41).

The core of the DI’s assertion is that there were “secret tenure deliberations” aka a plan to oust Dr. Gonzalez because of his ID views.

Continue reading at Neurotopia.

The Discovery Institute, after having realized that Intelligent Design is doomed to remain scientifically infertile and vacuous and after their devastating loss at the Dover trial, seems to have retreated to their fundamental opposition to materialism. Hopelessly confused by Phil Johnson’s misunderstanding of methodological and philosophical naturalism, the DI seems to be intent to blame evil Darwinists for immoral behaviors such as eugenics.

Let me start of by pointing out that any such attempt is doomed from the beginning for the simple reason that the Discovery Institute and other ID Creationists have claimed that Darwinism cannot provide foundation for morality, or in other words, Darwinism cannot serve as a principle on which to build a decision of what is ‘good’ and what is ‘bad’. This means that Eugenics cannot have a foundation in amoral scientific concepts lest there exists an external principle on which to base the decision as to what is good and bad for society.

People should therefor not be surprised that eugenics has been a principle which preceded Darwinism. Equally unsurprised will be the well informed readers who are familiar with the eugenic history of Christian evangelicals in the United States.

But I digress. The Discovery Institute, after having come to the inevitable conclusion that Intelligent Design is likely to remain without scientific relevance has changed its approach. While I predict that their attempts will become an ever greater disaster than their attempts to introduce the concept of Intelligent Design into schools, there is an even greater concern. Namely by violating St Augustine’s fair warnings about Christians saying foolish things (about science), an observer may easily come to reject the whole teaching of Christianity as a similarly foolish enterprise.

From Mike Elzinga whose comments deserve their own posting

It doesn’t require a federal judge to figure out if ID/Creationism is a science or not.

Anyone can go through the list of activities of the ID/Creationists and pseudo-scientists and compare them to the activities of working scientists.

Do typical working scientists engage in the following activities when advancing new ideas?

Do they pitch them to naive audiences while complaining they can’t get a fair hearing in the science community? Do they form institutes that spend millions of dollars to crank out propaganda pushing their idea and criticizing the scientific community? Do they issue talking points to grass-roots organizations and political groups to be argued in churches and local newspapers around the country? Do they publish books on their ideas in the popular press and claim they are peer-reviewed?

There is a wonderful article in todays issue of Nature on bioluminescent organisms in the deep seas. We like to think of the deep seas as dark, since virtually no light filters into the abyssal depths from above. However, the deep sea abounds with bioluminescence, bacteria and sea life of all sorts glow gently in the depths, enough to seriously hamper the Antares deep sea neutrino telescope that is searching for the flashes of light the represent the rare interactions of neutrinos with other matter (subscription required).

As fascinating as bioluminescence is in its own right, the article links to an amazing paper. One that puts yet another dent (if that is possible) in Dr. Behe’s key thesis; that multi-amino acid binding sites are difficult to evolve. But how does the ability of a fish to see red refute a central argument of Dr. Behe’s “Edge of Evolution”

To summarize the recent Open Letters series, some time ago a student of HIV, Ms Smith posted a list of binding sites found in the HIV-1 protein Vpu that contradicted Dr. Behe’s assertion that HIV has evolved no new protein-protein binding sites. Central to this was the demonstration that HIV-1 Vpu had evolved into an ion channel, a viroporin. Over two months later, Dr. Behe wrote a response, which did a disservice to Ms Smith on many levels, most especially by ignoring the key argument about Vpu viroporin. I remonstrated with Dr. Behe about this in an Open Letter. Dr. Behe publishing a series of responses to this open letter, which I responded to post by post as they were published.

As you may realize, Dr. Behe has finally conceded that he was wrong, and Vpu viroporin represents a real example of protein-protein binding. I have suggested that he issue an erratum to this effect, thanking Ms Smith for bringing this example to his attention (and the HIV Vpx duplication, which he also claimed didn’t exist). This is the very stuff of science, we all at some stage support ideas that were wrong, but when we realize they are wrong, we give them up. I thank Dr. Behe for acknowledging his mistake.

Along the way we have also learned that Dr. Behe’s citations don’t actually support his statements in “edge of Evolution”, his estimation of HIV mutation rates and effective population numbers is off by orders of magnitude, and his rationale for excluding viral protein-cellular protein binding has no biological basis (and is inconsistent).

For ease of perusal, I have put the links for all the Open Letters into this one post.

The Original Open Letter, where I protest at Dr. Behe’s treatment of Ms Smith.
An Open Letter Part 2, where I detail Vpu viroporin and point out that Dr. Behe’s references do not support his assertions.
An Open Letter Part 3, where I chide Dr. Behe for his continuing poor treatment of Ms Smith.
An Open Letter Part 4, where I go into more detail about why Dr. Behe’s attempt to exclude certain binding sites is not valid.
An Open Letter Part 5, where I dig even deeper into binding sites, and show why Dr. Behe’s attempt to exclude certain binding sites is not valid in even more detail.
An Open Letter Part 6, where I point out that Dr. Behe’s population and mutation rate estimates for HIV are wrong by orders of magnitude.
An Open Letter Part 7, where I thank Dr. Behe for admitting he was wrong, point out that “impresessedness” is not a biologically valid standpoint, and show that yet another reason for excluding viral protein-cell protein interactions is invalid.

Dear. Dr. Behe

I am pleased that you have acknowledged Vpu viroporin represents a real, de novo binding site.

Now if you had engaged with this in your response to Ms Smith, my respect for you would have risen immeasurably. To those of you not familiar with graduate and post graduate education, we actually want graduate students to disagree with us, robustly. After all, they are the ones carrying the torch of critical enquiry when we are gone. We don’t want them to accept our say so, “just because”. As scientists and educators our brief goes beyond just those PhD students we supervise, but to all engaged in critical enquiry, regardless of how we feel about their actual mode of delivery [1].

By “playing the man”[2] Dr. Behe, rather than engaging with Ms Smith’s arguments, you abrogated our responsibility as mentors and educators. Imagine the difference if you had dealt with Vpu Viroporin straight up. How about apologizing to Ms Smith now?

I do hope that you will now publish an erratum for your book, where you acknowledge Vpu viroporin. But again you engage in the “unimpressed” rhetoric. It matters not whether we are impressed or not by the outcome of the binding, the fact is that you have claimed that binding of two (or more) proteins to each other is statistically unlikely. It doesn’t matter what they do when bound (after all, as I have repeatedly pointed out, your own example is the haemoglobin S point mutation, which just glugs things up).

Dear Dr. Behe

It is good to see that you agree that the Golgi targeting sequence is an example of a binding site. However, you don’t get to ignore it because “viral proteins are special”. As I showed in the post you are supposed to be replying to, this is nonsense. In your book you categorically state HIV has developed no new binding sites, the diagram on page 145 of “Edge of Evolution” has a big zero on it. Yet your own example of a binding site is the haemoglobin S mutation, a single amino acid mutation that just clumps up proteins. You don’t write in your book “HIV has evolved several binding sites, but they don’t count because they are viral-protein-host protein interactions” or “HIV has evolved several binding sites, but they don’t count because they are equivalent to the HbS mutation”, you just write zero

Which is wrong.

An again, you are inconsistent, you are perfectly happy to consider viral-protein binding to cellular protein interactions when you think there is no evidence of them evolving (the gp120-cell surface receptor binding, CXCR4 binding anyone). Still, let us accept that you will ignore any viral-protein-cell protein interaction.

Why did you ignore the viroporin section? An example of viral-protein –viral protein interaction that generates a new structure with important functional consequences. This is a direct challenge to the very heart of your argument.

Dear Dr. Behe

I have just read your first response to my open letter to you. Is this what your argument is reduced to? A list of examples of Ms Smiths alleged uncivility to you. I find this rather sad

Yes, science is about civil discourse. And we, as experienced scientists are guardians and upholders of this discourse. We teach by example. If someone is discourteous to us, we reply courteously, and continue to reply courteously in the face of adversity. We keep to the topic and discuss the substantiative issues raised. We do not engage in petty sexism, we do not completely ignore someone’s core argument and discuss trivialities.

This is my central disagreement with you [1]. You avoided the issue. As educators, we lead by example. What example do you think it sets to avoid the major substantiative issue that Ms Smith raised?

Dr. Behe, regardless of how you feel about the tone of Ms Smiths discourse, you need to engage with the fact that HIV-1 M Vpu is a viroporin, a new mini-“molecular machine” that has arisen since HIV evolved from SIV. In science, there can be no greater discourtesy than ignoring a key, substantial argument. Until you engage with Vpu viroporin, your professionalism is on the line.

Yours sincerely

A male featherless biped named Ian Musgrave[2,3]

[1] The casual sexism issue is important too, but I leave that to others. [2] As I said before I’m a Senior Lecturer in the Australian system. Even though it is roughly equivalent to a US professorial appointment, calling me a professor is misleading. Dr. Musgrave is my appropriate title. [3] Once again Dr. Behe. I invite you to be co-respondent on “The Vpu Debate” blog, to avoid all this backing and forthing.