Let me say, right from the beginning, that Michael Behe's book The Edge of Evolution is very interesting and provocative. Many of my colleagues think that Behe's main argument can be easily dismissed as the work of an uninformed IDiot who is blinded by his religion. There's some truth in that, but only a little.
The main thesis of the book is that there are some combinations of mutations that could theoretically be beyond the reach of evolution during the 3 billion years that life has evolved on Earth. Behe refers to this combination as a double CCC (1040). It's his estimate of the probability of a particular combination of four specific mutations arising by chance. Since we know that such combinations have arisen, Behe concludes that god(s) must have been involved.
There are many ways of exploring Behe's calculations in order to see if he has a point. The first problem is that the meaning of his conclusion is very unclear. Let's think about it this way ...
Apparently I flunked the Behe challenge [Laurence Moran's Sandwalk Evolves Chloroquine Resistance]. Let's review what happened.
In his book, The Edge of Evolution, Michael Behe calculated the odds of a malaria parasite developing resistance to chlorquine by assuming that two separate mutations were necessary. Here's what he said on page 57 ...
How much more difficult is it for malaria to develop resistance to chloroquine than to some other drugs? We can get a good handle on the answer by reversing the logic and counting up the number of malarial cells needed to find one that is immune to the drug. For instance, in the case of atovaquone, a clinical study showed that about one in a trillion cells had spontaneous resistance. In another experiment, it was shown that a single amino acid change at position number 268 in a single protein, was enough to make P. falciparum resistant to the drug. Se we can deduce that the odds of getting that single mutation are roughly one in a trillion.
The debate over the existence of human races has heated up recently with the publication of a book by science writer Nicholas Wade. The book is ridiculous, by all accounts (I haven't read it). In fact, it is so wrong that a group of geneticists have written an open letter refuting the claims [see Geneticists decry book on race and evolution].
There are several aspects of this controversy that interest me greatly. One of them has to do with the reputation of science writers. Nicholas Wade was a science writer for Nature (1967-1971), Science (1972-1982), and the New York Times (1982-2012). I've often heard heard him being referred to as one of the best science writers, particularly by other science writers. That's an opinion that I've never shared and I'm glad to see him get his comeuppance.
Science writers aren't doing so well these days.
Micheal Behe came to Toronto a few years ago and gave three talks on the campus of the University of Toronto. One of them was in the big lecture hall in my building (Medical Science Building). I went to all three lectures and enjoyed them immensely even though I disagreed with what he was saying [Michael Behe in Toronto: "What Are the Limits of Darwinism?"] [Michael Behe in Toronto: "Evidence of Design from Biology" ]. It was fun meeting him again and talking to him about his views. You can learn a lot about what people think by attending a lecture and seeing how they respond to questions and debate.
That's what a university is all about. I also greatly enjoyed a lecture by William Dembski a few years ago. I got to meet him and I got to ask a question at his lecture. It was a very valuable experience. Over the years I've heard several creationists speak on my campus, even Hugh Ross. Attending those lectures has put me in touch with many creationist sympathizers in my area and I've formed a number of friendships. Some of them read my blog.
Vincent Joseph Torley (vjtorley) has several degrees listed on his website. Quoting ...
- Bachelor of Science, completed in 1981, at the Australian National University, Canberra. Major: Pure Mathematics. Other subjects studied: Physics (2 years), Chemistry (2 years), Geology (1 year) and Science German (1 year).
- Bachelor of Arts, completed in 1986, at the Australian National University, Canberra. Majors: Philosophy and Computing Science.
- Bachelor of Economics, completed in 1987, at the Australian National University, Canberra. Majors: Economics and Accounting. Other subjects studied: Statistics (2 years).
- Master of Arts in Philosophy, completed in 1994, at the University of Melbourne, Australia. Thesis topic: Laws of Nature (Scientific Laws). Grade: 2A.
- Ph.D. in philosophy, which I received in August 2007 from the University of Melbourne, Australia. Thesis topic: The Anatomy of a Minimal Mind.
.... end quote.
He hasn't studied much biology and his undergraduate science degree, obtained 26 years ago, was a major in pure mathematics.
That hasn't prevented him from writing extensively about biology and evolution. His latest contribution is a critique of Keith Blanchard's article on Why you should stop believing in evolution: You don't believe in it — you either understand it or you don't. That article has attracted attention from evolution supporters who think he got some things wrong [see Glenn Bransch's Five Quibbles for Blanchard]. I agree with them. Blanchard does not present the best case for evolution and he seems to lack a deep understanding of evolution.
Vince Torley's article is worth reading because it illustrates some of the confusions in the minds of IDiots as they struggle to catch up with 21st century biology [see Why Keith Blanchard really doesn’t understand evolution]. However, that's not the point I want to make today. Instead, I want to quote a paragraph from near the end of Vincent Torley's article ....
I could go on, but I’d like to conclude this article with a final observation: Keith Blanchard doesn’t have a science degree. His LinkedIn profile lists him as having a two year tech degree in Electronic Technology, which he obtained in 1975. Let us freely grant that the man’s skill set looks quite impressive. Nevertheless, the fact remains that a man without a science degree has no place writing an article on evolution in a popular online magazine like The Week. It’s simply presumptuous.
I wonder if there are any prominent Intelligent Design Creationists who don't have real science degrees?
I love watching "Who Do You Think You Are." The latest episode features Rachel McAdams and her sister Kayleen who search for their Canadian ancestors. They discover a family who settled on the shores of Lake Champlain in the mid-1700s and got caught up in the Revolutionary War. Their ancestors supported the government (Great Britain) against the revolutionaries and when General Burgoyne's invasion from Canada was stopped at the Battles of Saratoga (1777) the loyalists had to flee to Canada with the retreating army.
The McAdams ancestors spent a year or so at a refugee camp near St. Johns in Quebec, near the American border. The sisters visit the site during the show. It looks like one of the young sons of their ancestors died during the stay in the refugee camp—probably because the conditions were pretty horrible.
One of my ancestral families was Isaac Montras and his wife Tamar Betts. They had a farm near Saratoga and they supported the British side during the revolution. They also had to leave their farm and flee to Canada after the Battles of Saragota. They were settled at another refugee camp in Machiche, Quebec where they stayed for a year before moving on to settle in Nova Scotia.
Tens of thousands of United Empire Loyalists came to Canada after the Thirteen Colonies gained their independence from Great Britain. Nobody knows how many of the residents of the Thirteen Colonies remained loyal to the government in Great Britain but it may have been as much as one-third of the total population. Only a small percentage of them left after the war was over.
You can watch a clip from "Who Do You Think You Are" featuring the McAdams sisters at: Rachel McAdams Learns Her Ancestors' Loyalties. If you want to watch an entire show, I recommend the British version that's been around for ten seasons. Here's one on J.K. Rowling.
Michael Behe is at it again. He has a freaky knack of taking scientific results that directly contradict his views and twisting them into confirmation that only god can explain the result.
This time he is revisiting an old issue. Joe Thornton's lab has published a series of papers showing that the evolution of the glucocorticoid receptor involved a number of neutral steps that were absolutely required before the receptor could acquire the ability to bind to cortisol. Each of the steps was contingent on earlier steps. This is evolution by accident.
This conflicts with Michael Behe's view of evolution because he maintains that there's an edge of evolution defined by pathways that involve multiple steps. According to Behe, all the multiple mutations have to take place at the same time because none of the intermediates are beneficial and most of them are detrimental.
I visited the Institute for Creation Research back in 1992 when it was still based in Santee, California (USA). I toured the museum and bought this wonderful poster in the gift shop. It now hangs on the wall outside my office. I relate to the pirates.
A much simpler black and white version (below) was shown to a high school class in Atlanta, Georgia, USA and it caused quite a stir [Flap over creationist cartoon shown in high-school class]. I can understand why. The color poster that I bought twenty years ago is much better. I can see why the Atlanta high school students weren't impressed with the pirates.
Seriously, I don't think evolution supporters should make a fuss about this [see Evolution vs. creationism: Does this cartoon belong in Grady High School biology class? ]. It may provide some comfort to the diehard fundamentalist Christian students in the class but lots of students are going to make fun of the cartoon and that may have a beneficial effect in the long run. We should be careful about putting up obstacles that prevent creationists from shooting themselves in the foot.
(I know about the so-called "separation of church and state" provision in the American Constitution. You don't need to lecture me on the legality of showing a religious cartoon in a public high school.)
Drugmonkey (@drugmonkeyblog) doesn't think there's a filter problem [There is no "filter problem" in science].
He writes,
Seriously.
It is your job as a scientist to read the literature, keep abreast of findings of interest and integrate this knowledge with your own work.
We have amazing tools for doing so that were not available in times past, everything gets fantastically better all the time.
If you are a PI you even have minions to help you! And colleagues! And manuscripts and grants to review which catch you up.
So I ask you, people who spout off about the "filter" problem.....
What IS the nature of this problem? How does it affect your working day?
I'm trying to keep up with a number of very broad and diverse fields. For example, as a textbook author, I need to keep abreast of just about everything that might be covered in an introductory biochemistry course. I'm also trying to keep informed about evolutionary biology; especially molecular evolution because I teach a course on that topic and I blog about it. I don't want to miss exciting developments in pedagogy (teaching) and the philosophy of science. Finally, I like to be up-to-date on the latest advances in other disciplines.
Here's the problem. There's a lot of junk out there. It's a waste of time to scan all of the science journals that might possibly have something of interest to me and it's a waste of time to get any "tools" to do it for me. Most of the time I wouldn't even know what to ask for. For example, I don't want to see all the papers on photosynthesis but I need to see the one that's going to change my textbook. I don't want to see all the papers on mutation rates but I do want to see the ones that are worth blogging about.
There were times when I could sit down for a few hours every week and scan the tables of contents of the leading journals in my field. Those days are long gone and my "field" has expanded enormously. I need to filter but I'm pretty sure I'm missing some important papers. In fact, I know this because just about every month I hear from others about things that I've missed months, or even years, ago.
I have a filter problem. I'm filtering out some important things and reading far too much junk. My filter problem can't be solved. If it wasn't for blogs, I'd be in bigger trouble.
We're in the middle of a discussion about the function wars. It's obvious to me that members of the ENCODE Consortium also have a filter problem. They've filtered out all kinds of information about the organization of the human genome. They don't understand the evidence for junk DNA, for example, and they don't have a good grasp of evolution. On the other hand, they've probably read every recent paper on the methodology of RNA-Seq, ChIP, and data analysis algorithms.
I'm glad that drugmonkey doesn't have a filter problem. Or, should I say, I'm glad that he THINKS he doesn't have a filter problem. It must be comforting to believe that he's keeping abreast of everything relating to his interests. I've never felt like that.
The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.
Stephan Jay Gould (1982)This is my fourth post on the function wars.
The first post in this series covered the various definitions of "function" [Quibbling about the meaning of the word "function"]. In the second post I tried to create a working definition of "function" and I discussed whether active transposons count as functional regions of the genome or junk [The Function Wars: Part II]. I claim that junk DNA is DNA that is nonfunctional and it can be deleted from the genome of an organism without affecting its survival, or the survival of its descendants.
In the third post I discussed a paper by Rands et al. (2014) presenting evidence that about 8% of the human genome is conserved [The Function Wars: Part III]. This is important since many workers equate sequence conservation with function. It suggests that only 8% of our genome is functional and the rest is junk. The paper is confusing and I'm still not sure what they did in spite of the fact that the lead author (Chris Rands) helped us out in the comments. I don't know what level of sequence similarity they counted as "constrained." (Was it something like 35% identity over 100 bp?)
My position if is that there's no simple definition of function but sequence conservation is a good proxy. It's theoretically possible to have selection for functional bulk DNA that doesn't depend on sequence but, so far, there are no believable hypothesis that make the case. It is wrong to arbitrarily DEFINE function in terms of selection (for sequence) because that rules out all bulk DNA hypotheses by fiat and that's not a good way to do science.
So, if the Rands et al. results hold up, it looks like more that 90% of our genome is junk.
Let's see how a typical science writer deals with these issues. The article I'm selecting is from Nature. It was published online yesterday (Aug. 6, 2014) (Woolston, 2014). The author is Chris Woolston, a freelance writer with a biology background. Keep in mind that it was Nature that started the modern functions wars by falling hook-line-and-sinker for the ENCODE publicity hype. As far as I know, the senior editors have not admitted that they, and their reviewers, were duped.
On most days I'm an optimist. I think that eventually the truth will win out and all you have to do is convince people that they are misguided. That's why I spend so much time discussing the view of Intelligent Design Creationists. On the good days, I firmly believe that if I can show them what science is all about then they will come around to accepting evolution.
I cherish a few modest successes over the years. For example, a few months ago I tried to teach David Klinghoffer and his friends about modern concepts of evolution and genetics. The example I used was the 98% sequence similarity between the human and chimp genomes. I showed him that the similarity is quite consistent with our understanding of Neutral Theory and random genetic drift [Why are the human and chimpanzee/bonobo genomes so similar?].
A remarkable thing happened. Some of the Intelligent Design Creationists on Evolution News & Views (sic) and Uncommon Descent actually agreed with me! They tried to explain to their fanatical friends that chimps and humans really do share a common ancestor and that the differences between them are explained by evolutionary theory. (I've included links to all the posts at the bottom of this post.)
Just when you think you are making some progress, the IDiots prove you wrong. Yesterday on Uncommom Descent there was a post on the topic of the similarity between chimps and humans [At last, a proposed answer re 98% human-chimpanzee similarity claim]. The author was probably Barry Arrington posting as "News." Here's the relevant part of that post ...
From this comment (by Gordon Davisson, in response to this post):
In other words, I’m agreeing with Denyse here:
BUT claimed 98% similarity due to a common ancestor (a claim that hundreds of science writers regularly make, in support of common descent) *undermines anything else they have to say on the subject.*
I do not know how to put the matter more simply than this: A person who does not see the problem is not a credible source of information.
He responds:
…just disagreeing about which side is not credible. Take the 98% similarity figure as an example: one of the basic principles of science is that you must follow the evidence. If the evidence supports the 98% figure, and that conflicts with your intuition, then you either have to throw that intuition into the trash bin, or stop claiming to be doing science.
No. Absolutely not.
One should never discard intuitions formed from experience, especially about vast claims. Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science.
This is called, among other things, wanting to have your cake an eat it too. The IDiots want you to believe that they accept all of modern science and that their "theory" is consistent with the evidence.
On the other hand, if the science of genetics leads to conclusions that contradict your "intuition" then the science must be wrong.
We've known for decades that this is how the IDiots really think but it's interesting to see someone like Barry Arrington express it so openly.
Now all we have to do is sit back and wait for the more intelligent IDiots to point out that we've been through all that a few months ago and Barry's intuition is wrong. Instead, what we're seeing is Barry Arrington doubling down [Sun orbits Earth vs. Chimps are people too – the differences].
This is not a good day. It's hard for me to remain optimistic.
An Intelligent Design Creationist explains why chimpanzees and humans are so similar
IDiots respond to the evidence for evolution of chimpanzees and humans
A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory
Breaking news: Creationist Vincent Torley lies and moves goalposts
Vincent Torley apologizes and claims that he is not a liar
Vincent Torley tries to understand fixation
On the frustration of trying to educate IDiots
Why creationists think they are more open-minded than scientists
What would happen if Intelligent Design Creationists understood evolution?
Branko Kozulic has questions about fixation
Branko Kozulic responds
Branko Kozulic responds: Part II
There are so many problems with Darwin's Doubt that one hardly knows where to begin. For me, the most important problem is that Meyer dismisses all the evidence for pre-Cambrian ancestors. These ancestors had most of the genes necessary to make all the animals that arose during the Cambrian explosion.
Our current model for evolution and development is that small changes in the regulation and timing of key developmental genes are responsible for big phenotypic differences, including new animal body plans. The data shows that all the animal phyla have similar genes and that there aren't very many genes whose origins can be traced to the Cambrian.
... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.
Stephen Jay Gould
Ontogeny and Phylogeny (1977)This model was popularized by Stephen Jay Gould in his 1977 book Ontogeny and Phylogeny. Meyer disputes this model. He claims that massive amounts of new information (= new genes) arose at the time of the Cambrian explosion. He claims that this cannot be explained by any naturalistic means; therefore, god(s) must have made those strange Cambrian animals. (Presumably, the gods are also responsible for making them go extinct.)
Charles Marshall, a paleontologist at UC Berkeley (USA) wrote a critical review of Darwin's Doubt [When Prior Belief Trumps Scholarship]. Here's part of what Marshal wrote in September 2012.
Gordon E. Mullings ("kairosfocus") just can't understand why scientists haven't become believers in a creator who designs life [BA77′s observation: "many influential people in academia simply don’t want Design to be true no matter what evidence . . ."]. He quotes BA77 (really!) ...
The inimitable BA77 observes:I [used] to think that if ID could only get its evidence to the right people in the right places then they would change their mind about Darwinian evolution and we would have a fundamental ‘paradigm shift’ from the ‘top down’. But after a few years of banging my head on that wall to no avail, I realized that it is not a head problem with these people so much as it is a heart problem. i.e. many influential people in academia simply don’t want Design to be true no matter what evidence you present to them. Indeed, in many educational institutions, there is a systematic effort in academia to Expel anyone who does not toe the Darwinian party line.
He concludes: "Thus the growth in popular support for ID has been more of a ‘bottom up’ affair."
Mullings presents a diagram that's supposed to demonstrate the evidence for Intelligent Design Creationism (right, above).
There are many reasons why "people in academia" have not been convinced by "evidence" like that presented by Bill Dembski. The most important reason is that the "evidence" isn't really evidence at all. It has been refuted repeatedly by people who know what they are talking about. There is no evidence for the existence of a creator who meddles in the affairs of living organisms.
But the real reason why people like BA77 and kairosfocus are puzzled has nothing to do with evidence. They believe in the existence of gods(s); therefore; they already believe in a creator so it's no big leap to "make sense" of biology in the light of god(s). What they don't understand is that for nonbelievers the "evidence" of Intelligent Design Creationism (if it existed) is only a small part of the path towards believing in a divine creator.
It's a heart problem. Intelligent Design Creationists are absolutely convinced that god(s) exist so they don't realize that Dembski's argument falls into category of "extraordinary claim" since it requires the existence of creators. It's not sufficient just to cast doubt on evolution and question scientific evidence. You also have to propose an alternative explanation and that hypothesis includes evidence for the designer. That kind of extraordinary claim requires extraordinary evidence and the IDiots haven't even come close to providing it.1
People like Gordon E. Mullings and BA77 have been trying to convince "infuential people in academia" for over 200 years. Generation after generation of academics have rejected their "evidence" and their logic. It's about time that the IDiots came to grips with the truth; namely, that they don't have any proof of the existence of god(s) and they never will.
They also need to stop fooling themselves about their "success" among the general public. Belief in god(s) is declining all over the world.
1. As most of you already know, the IDiots try to avoid talking about the Intelligent Design Creator. They claim that the "evidence" for his/her/their existence stands on it's own. All they want is for you to accept the "evidence" for the existence of god(s). What you do with that "evidence" is up to you. They aren't concerned about that part because they've already taken the leap.
Last year at this time I was in Copenhagean, Denmark. This is a country full of people who don't believe in god(s). At least they think they don't believe in gods. Turns out they are probably wrong according to Casey Luskin [Evolutionary Studies Suggest that Atheists, Whatever They Say to the Contrary, Really Do Believe in God].
Luskin thinks that evolution is true after all, especially when it supports his prejudices beliefs. He quotes some really silly articles that make a really silly claim; namely, that it's impossible for all those Danes to have abandoned belief in gods because lack of belief in gods is psychologically impossible. We have evolved to believe in Loki and Freyr and there's no escaping our evolutionary destiny.
Just when you think that the IDiots can't get any stupider, they come up with something like this.
Michael Behe thinks the main thesis of his book, The Edge of Evolution, has been vindicated by a recent paper (Summers et al., 2014). He is wrong, as I discussed in a previous post [Michael Behe and the edge of evolution].
PZ Myers and Ken Miller have already made the same points that I make but the IDiots never listen when their view are challenged. Instead, they go on the attack and claim that the latest publications refute evolution and support Intelligent Design Creationism.
Behe is certain that he's right. He's so certain that he has issued a challenge to Myers and Miller [An Open Letter to Kenneth Miller and PZ Myers]. I'm going to try and do some calculations to meet his challenge but I'm not certain if I'm doing them correctly. Please help me find any mistakes.
Michael Behe's book, The Edge of Evolution, is very interesting. His main thesis is that there are some genotypes that are beyond the reach of evolution. His examples include genotypes where two or three mutations have to occur simultaneously in order to achieve an effect. The probability to this happening is extremely remote but it could happen in some populations with very large effective population sizes.
The reason why mutations have to happen simultaneously in the same organism, according to Michael Behe, is because any one of them, by itself, is detrimental. This defines the edge of evolution because it's a result that cannot be achieved by mutation and selection (or by drift).
Behe is correct. If a given phenotype absolutely requires that two mutations happen simultaneously then this is going to be almost impossible in most species.
The IDiots at the Discovery Institute have evolved something that they think is a winning strategy. They publish a book that has lots of scientific-sounding words then they embark on a massive publicity campaign to promote it as the latest scientific breakthroughs showing that evolution is wrong (and, therefore, God did it). Then they wait for the bad reviews to come in and concentrate on rebutting the reviewers. They get as much publicity by pretending that the reviewers are biased as they do from selling the books in the first place.
They use four main tactics to avoid admitting that they are wrong [see What Do You Do When All the Reviews Are Bad?]. One of them is to claim that all the reviewers are ignoring the main arguments in the book. That's what Stephen Meyer does in the video below. It's titled, "The Biggest Failure of Critics." (Warning, this has been tested with the Mark X Irony Meter and it passes. I can't guarantee that earlier models will survive.)
This is Part III of several "Function Wars"1 posts.
How much of the human genome is conserved?
The first post in this series covered the various definitions of "function" [Quibbling about the meaning of the word "function"]. In the second post I tried to create a working definition of "function" and I discussed whether active transposons count as functional regions of the genome or junk [The Function Wars: Part II]. I claim that junk DNA is DNA that is nonfunctional and it can be deleted from the genome of an organism without affecting its survival, or the survival of its descendants.
The best way to define "function" is to rely on evolution. DNA that is under selection is functional. But how can you determine whether a given stretch of DNA is being preserved by natural selection? The easiest way is to look at sequence conservation. If the sequence has not changed at the rate expected of neutral changes fixed by random genetic drift then it is under negative selection. Unfortunately, sequence conservation only applies to regions of the genome where the sequence is important. It doesn't apply to DNA that is selected for its bulk properties.
I'm not a big fan of alternative splicing. I think it falls into the same category as pervasive transcrition—most of it is accidental [see Alternative Splicing and Why IDiots Don't Understand How Science Works and A Challenge to Fans of Alternative Splicing ]. The error rate for splicing is known to be high [Splicing Error Rate May Be Close to 1% ].
I just read a paper about alternative splicing in Science (Lo et al., 2014) and it annoys me that a key piece of data was left out. The missing data is the abundance of the rare transcripts that are presumed to be genuine, alternatvely spliced, variants. Are they present at more than one copy per cell?
We need to know this in order to decide whether the detection of alternatively spiced variant is biologically significant. You should not be able to publish a paper on this topic without presenting your data on relative and absolute abundance [see Extraordinary Claims about Human Genes and How to Evaluate Genome Level Transcription Papers]. Surely this is obvious, having just been through the ENCODE publicity hype disaster.
Lo, W.-S., Gardiner, E., Xu, Z., Lau, C.-F., Wang, F., Zhou, J. J., Mendlein, J. D., Nangle, L. A., Chiang, K. P. X-L, Yang, K-F. Au, W. H. Wong, M. Guo, M. Zhang, and P. Schimmel1 (2014) Human tRNA synthetase catalytic nulls with diverse functions. Science 345:328-332. [doi: 10.1126/science.1252943]
I just learned today that Walter Gehring died in a car accident in Greece on May 29th. I learned of his death from the obituary by Michael Levine in Science [Walter Gehring (1939–2014)]. There's another obituary on the Biozentrum (Basel, Switzerland) website [Obituary for Walter Gehring (1939 – 2014)]. He was only seven years older than me.
I first met Walter Gerhing when I was a post-doc in Alfred Tissières lab in Geneva (Switzerland) in the mid-1070s. The two labs collaborated on cloning and characterizing the major heat shock gene (Hsp70) of Drosophila melanogaster. Paul Schedl and Spyros Artavanis-Tsakonis made the library in Gehring's lab in 1976-1977 and Marc-Edouard Mirault and I isolated the mRNA for screening and then identified the genes we cloned. The result was three papers in Cell (see below). (John Lis, then in David Hogness' lab, was cloning the same gene.)
As Michael Levine puts it ...
An amazing group of students and postdocs was attracted to the Gehring lab over the years: Eric Wieschaus (Nobelist), Christianne Nüsslein-Volhard (Nobelist), David Ish-Horowicz, Spyros Artavanis-Tsakonas, Paul Schedl, Alex Schier, Georg Halder, Hugo Bellen, and Markus Affolter, to mention just a few. I worked closely with two of my future lifelong friends and colleagues: Ernst Hafen and Bill McGinnis. The lab was an absolute blast, but a strange mix of anarchy and oppression. Walter permitted considerable independence, but was hardly laissez-faire. He could be confrontational, and did not hesitate to call us out (particularly me) when he felt we were misbehaving.
I found Walter to be a complicated character. He had the mannerisms of an authoritative Herr Doktor Professor, but was also folksy and unaffected and always ready to laugh and joke. He sometimes felt competitive with his students and postdocs, but was also highly supportive and proud of our independent careers. In short, I believe the key to Walter's success was his yin and yang embodiment of old-world scholar and modern competitive scientist. He was able to exude charm and empathy, but nothing we did seemed to be quite good enough. In other words, tough love, possibly the perfect prescription for eliciting the very best efforts from his students and postdocs.
Walter Gehring was one of a small group people who changed the way I think about science.
Artavanis-Tsakonas, S., Schedl, P., Mirault, M.-E., Moran, L. and J. Lis (1979) Genes for the 70,000 dalton heat shock protein in two cloned D. melanogaster DNA segments. Cell 17, 9-18. [doi: 10.1016/0092-8674(79)90290-3]
Moran, L., Mirault, M.-E., Tissières, A., Lis, J., Schedl, P., Artavanis-Tsakonas, S. and W.J. Gehring (1979) Physical map of two D. melanogaster DNA segments containing sequences coding for the 70,000 dalton heat shock protein. Cell 17, 1-8. [doi: 10.1016/0092-8674(79)90289-7]
Schedl, P., Artavanis-Tsakonas, S., Steward, R., Gehring, W. J., Mirault, M.-E., Goldschmidt-Clermont, M., Moran, L. and A. Tissières (1978) Two hybrid plasmids with D. melanogaster DNA sequences complementary to mRNA coding for the major heat shock protein. Cell 14, 921-929. [doi: 10.1016/0092-8674(78)90346-X]
How many genes in the human genome? There's only one correct answer to that question and that's "we don't know."
The main problem is counting the number of genes that produce functional RNA molecules. The latest Ensembl results are based on build CRch37 from February 2009 and the GENCODE annotation from last year (GENCODE 19) [see Human assembly and gene annotation and Harrow et al., 2014]
The most recent estimates are 20,807 protein-encoding genes, 9,096 genes for short RNAs, and 13,870 genes for long RNAs. This gives 43,773 genes. Nobody knows for sure how many of the putative genes for RNAs actually exist. They may only be a few thousand functional genes in this category.
It's a lot easier to figure out whether a gene really encodes a functional protein so most of the annotation effort is focused on those genes. I want to draw your attention to a recent paper by Ezkurdia et al. (2014) that discusses this issue. The authors begin with a bit of history ...
I'm curious about how different people read the scientific literature. My way of thinking about science is to mentally construct a model of how I think things work. The more I know about a subject, the more sophisticated the model becomes.
When I read a new paper I immediately test it against my model of how things are supposed to work. If the conclusions of the paper don't fit with my views, I tend to be very skeptical of the paper. Of course I realize that my model could be wrong and I'm always on the lookout for new results that challenge the current dogma, but, in most cases, if the paper conflicts with current ideas then it's probably flawed.
This is what people mean when they talk about making sense of biology. The ENCODE papers don't make sense, according to my model of how genomes work so I was immediately skeptical of the reported claims. The arseniclife paper conflicted with my understanding of the structure of DNA and how it evolved so I knew it was wrong even before Rosie Redfield pointed out the flaws in the methodology.
I got an email message yesterday from a student who is taking a summer course in biochemistry. His professor asked the class to find "most efficient enzyme known to man." The professor gave them a hint by telling them that the enzyme had something to do with nucleotide biosynthesis. The student contacted me because some of my blog posts popped up on Goggle. He (the student) was a bit confused about how to define the "perfect" enzyme.
There are two different ways of defining the "perfect" enzyme and both of them are wrong because there's no such thing. The common textbook definition picks up on the idea that the "perfect" enzyme catalyzes a reaction every time it encounters a substrate(s). These enzyme rates are referred to as "diffusion-controlled" rates since the rate is limited only by the rate at which substrate diffuses into the reaction site on the enzyme. Some enzymes can even catalyze reactions that are slightly faster than the diffusion-controlled limit.
Here's what Voet & Voet (4th edition) say (page 490) ...
You may never have heard of Riken. Here's what they say on their website [Riken] ...
RIKEN is Japan's largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Founded in 1917 as a private research foundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing a network of world-class research centers and institutes across Japan.
They've published a video on the Central Dogma. Here's how they describe it ...
The 'Central Dogma' of molecular biology is that 'DNA makes RNA makes protein'. This anime shows how molecular machines transcribe the genes in the DNA of every cell into portable RNA messages, how those messenger RNA are modified and exported from the nucleus, and finally how the RNA code is read to build proteins.
The video was made by RIKEN Omics Science Center (RIKEN OSC) for the exhibition titled 'Beyond DNA' held at National Science Museum of Japan. RIKEN OSC has published in Nature Genetics on the regulation of RNA expression in human cancer cells.
Most of you know that I have a different view of The Central Dogma of Molecular Biology but that's not what I want to discuss here. Watch the video. Do you think it's a good idea to show this process as well-designed little machines and ships? It sure gets the IDiots excited {RIKEN’s 10-minute antidote to atheism: see for yourself].
This month's Carnival of Evolution is hosted by none other than the King of the Carnival, Bjørn Østman Pleiotropy . Read it at 73rd Carnival of Evolution: World Cup Edition .
Welcome to the 2014 Carnival of Evolution World Cup of evolution blog posts.
We have an exciting post ahead of us today where we will find the winner of the inaugural CoE World Cup. Entered posts will be scored based on several parameters, and matches will be determined probabilistically.
The scoring system works like this:
+1 for mentioning "evolution" or "evolve"
+1 for posts about biological evolution
-1 for saying "develop" or "development" when meaning "evolve" or "evolution"
-1 for being very short
-2 for being very long
0 to +5 points based on the interest of the referee (the CoE host)
+2 for posts about peer-reviewed articles
+4 for posts whose authors clearly present opinions of their own
+1 per picture (up to three) included in the post
+1 for attracting any comments
+1 extra for each original picture (max 3)
+3 for showing videos
+25 for reports on rabbit fossils from the Cambrian
-5 for any hint of panadaptationism
-2 for each logical fallacy
-4 for any mention of aquatic ape theory
-7 for agreeing with Lynn Margulis that everything is endosymbiosis
-3 if talking about the work of others without citation
-5 to -1 for any wrong statements about evolution - See more at: http://pleiotropy.fieldofscience.com/2014/07/73rd-carnival-of-evolution-world-cup.html#sthash.75w1XHA6.dpuf
It was a tough battle. My own entry, The Function Wars: Part I, had a fairly low score but managed to squeak out a victory in the early rounds in spite of the fact that it had a severe disadvantage (too long).
My post beat out Was Fisher (W)right? in the semi-final thanks to an own goal in extra time. In the final, Function Wars was up against a better post Of Population Structure and the Adaptive Landscapes but Function Wars won on penalty kicks. Yeah!!!!
If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.
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This is Part II of several "Function Wars"1 posts. The first one is on Quibbling about the meaning of the word "function" [The Function Wars: Part I].
The ENCODE legacy
I addressed the meaning of "function" in Part I It is apparent that philosophers and scientists are a long way from agreeing on an acceptable definition. There has been a mini-explosion of papers on this topic in the past few years, stimulated by the ENCODE Consortium publicity campaign where the ENCODE leaders clearly picked a silly definition of "function" in order to attract attention.
Unfortunately, the responses to this mistake have not clarified the issue at all. Indeed, some philosophers have even defended the ENCODE Consortium definition (Germain et al., 2014). Some have opposed the ENCODE definition but come under attack from other scientists and philosophers for using the wrong definition (see Elliott et al, 2014). The net effect has been to lend credence to the ENCODE Consortium’s definition, if only because it becomes one of many viable alternatives.
Some of you are probably watching Saturday morning cartoons but for those of you looking for other forms of entertainment I offer a list of six "old facts" that Ann Gauger says have been proven to be wrong [Why Does Biology Still Have the Ability to Surprise Us?].
Since I'm at least as old as Ann Gauger, I offer my own interpretation under each one. If you want to see how she interprets them you'll have to go to the IDiot website.
1. Old fact: DNA is stable and genes don't hop around.
I suppose there was a time when scientists might have thought that "DNA was stable." I was taught about "jumping genes" in my second year genetics class in 1965. I think that's before many of you were born so it's a pretty old fact.
2. New "old" fact: Mobile genetic elements are selfish DNA that replicate themselves without benefit to the organism, thus cluttering the genome with garbage.
That's still pretty much true today.
3. Old fact: A gene is an uninterrupted stretch of DNA that encodes a single protein. Genes are arranged like beads on a string.
I learned in 1965 that some genes produced tRNA and ribosomal RNA. I learned in 1975 that some protein-encoding genes had introns. (That one was a surprise.) I still think that genes are lined up one-after-another on their chromosomes although there are some minor exceptions. I learned about overlapping genes, for example, when the φX174 genome was sequenced in 1978. That's how old her facts are.
4. Old fact: There are only 3 forms of RNA: messenger RNA, transfer RNA, and ribosomal RNA.
Scientists have known about RNA viruses for at least 70 years. That's long before the discovery of messenger RNA and tRNA. It wasn't until the early 1970s that molecular biologists became aware of regulatory RNAs, RNA primers on Okazaki fragments, and antisense RNAs. This was followed quickly by the discovery of many other types of RNAs. Ann Gauger says these are "new" discoveries. I guess that depends on whether something that's been known for forty years (or seventy years) counts as "new."
5. Old fact: Pseudogenes are useless broken remnants of former genes.
Still true today. The fact that some of the sequence of one-in-a-million pseudogenes may have secondarily acquired another function doesn't change the fact that it is a pseudogene.
6. Old fact: The genome is full of junk, the remnants of wasteful evolutionary processes and selfish DNA (see #1, #2 and #5 above).
Still a fact in the 21st century.
My son, Gordon, ran in a 19km race at Whistler (British Columbia) last weekend. There were lots of obstacles and a 10,000 volt electric shock at the end. He said it was "Super fun!"
I remember when playing in the mud meant something a lot different.
UPDATE Ms. Sandwalk has posted more pictures, and more words at: Oh My Goodness.
This is Part I of the "Function Wars: posts. The second one is on The ENCODE legacy.1
Quibbling about the meaning of the word "function"
The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.
Stephan Jay Gould (1982)The ENCODE Consortium tried to redefine the word “function” to include any biological activity that they could detect using their genome-wide assays. This was not helpful since it included a huge number of sites and sequences that result from spurious (nonfunctional) binding of transcription factors or accidental transcription of random DNA sequences to make junk RNA [see What did the ENCODE Consortium say in 2012?]..
I believe that this strange way of redefining biological function was a deliberate attempt to discredit junk DNA. It was quite successful since much of the popular press interpreted the ENCODE results as refuting or disproving junk DNA. I believe that the leaders of the ENCODE Consortium knew what they were doing when they decided to hype their results by announcing that 80% of the human genome is functional [see The Story of You: Encode and the human genome – video, Science Writes Eulogy for Junk DNA]..
The ENCODE Project, today, announces that most of what was previously considered as 'junk DNA' in the human genome is actually functional. The ENCODE Project has found that 80 per cent of the human genome sequence is linked to biological function.
[Google Earth of Biomedical Research]
We were at our local supermarket yesterday and I wanted to buy some large Kaiser rolls. Unfortunately, the bins were empty.
I guess the customers couldn't resist the bargain if they bought half-a-dozen buns. 
The people of Ontario (Canada) voted in a provincial election yesterday and the Liberal Party won a majority of the seats. The leader of the party is Kathleeen Wynne and she becomes the first woman to be elected Premier of Ontario. (She has been Premier for the past sixteen months since she became leader of the Liberal Party.) Not only is she the first woman, she is the first openly gay politican to be elected Premier of any province in Canada. (According to Wikipedia, she is the first openly gay head of any government in the Commonwealth.)
The results are:
Liberals: 59 seats, 39% of the vote
Progressive Conservatives: 27 seats, 31%
New Democratic Party: 21 seats, 24%
Green Party: 0 seats, 5%.
The results are going to be poured over with a fine-tooth comb in the next few weeks but it's clear that the Tea-Party agenda of the Progressive Conservatives did not work. (He hired American Republican strategists to help with his campaign.) They should have won the election handily after 11 years of Liberal government plagued by scandal but, instead, they lost 10 seats and their leader Tim Hudak resigned last night when the results became clear.
Today is the 70th anniversary of D-Day—the day British, Canadian, and American troops landed on the beaches of Normandy.1
For baby boomers it means a day of special significance for our parents. In my case, it was my father who took part in the invasions. That's him on the right as he looked in 1944. He was an RAF pilot flying rocket firing typhoons in close support of the ground troops. During the initial days his missions were limited to quick strikes and reconnaissance since Normandy was at the limit of their range from southern England. During the second week of the invasion (June 14th) his squadron landed in Crepon, Normandy and things became very hectic from then on with several close support missions every day.
I have my father's log book and here (below) are the pages from June 1944. The red letters on June 6 say "DER TAG." It was his way of announcing D-Day. On the right it says "Followed SQN across channel. Saw hundreds of ships ... jumped by 190s. LONG AWAITED 2nd FRONT IS HERE." Later that day they shot up German vehicles south-east of Caen where there was heavy fighting by British and Canadian troops. The next few weeks saw several sorties over the allied lines. These were attack missions using rockets to shoot up German tanks, vehicles, and trains.
The photograph on the right shows a crew loading rockets onto a typhoon based just a few kilometers from the landing beaches in Normandy. You can see from the newspaper clipping in my father's log book that his squadron was especially interested in destroying German headquarter units and they almost got Rommel. It was another RAF squadron that wounded Rommel on July 17th.
The log book entry (above) for June 10th says, "Wizard show. Recco area at 2000' south west of Caen F/S Moore and self destroyed 2 flak trucks, 2 arm'd trucks, and i arm'd command vehicle, Every vehicle left burning but one. Must have been a divisional headquarters? No casualties."
Here's another description of that rocket-firing typhoon raid [Air Power Over the Normandy Beaches and Beyond].
Intelligence information from ULTRA set up a particularly effective air strike on June 10. German message traffic had given away the location of the headquarters of Panzergruppe West on June 9, and the next evening a mixed force of forty rocket-armed Typhoons and sixty-one Mitchells from 2 TAF struck at the headquarters, located in the Chateau of La Caine, killing the unit's chief of staff and many of its personnel and destroying fully 75 percent of its communications equipment as well as numerous vehicles. At a most critical point in the Normandy battle, then, the Panzer group, which served as a vital nexus between operating armored forces, was knocked out of the command, control, and communications loop; indeed, it had to return to Paris to be reconstituted before resuming its duties a month later.
My father was awarded the Distinguished Flying Cross (DFC) for his efforts during the war.
1. The British landed at Sword Beach and Gold Beache, the Canadians at Juno Beach, and American troops landed at Omaha and Utah Beaches.
Stephanie Keep is the new editor of Reports of the National Center for Science Education at NCSE (National Center for Science Education).
She tells an interesting story in her first post on the Science Laegue of Amercia blog [A New Finger in the Pie].
An editor friend of mine asked me the other day to read an activity she’s developing for middle school, one of the soon-to-be plethora of activities aligned to the Next Generation Science Standards. This particular one was about evolution, and asked kids to look for variation in a number of human traits and then infer adaptive explanations. For example, they could measure finger lengths and then come up with a reason that longer fingers are more adaptive than shorter ones. What followed was a half-hour conversation in which I tried my best to explain why that was a terrible idea for an activity. And here’s the thing—this friend of mine, she’s super-smart and has an advanced degree in biology from Harvard University. Now, she completely understood, once we discussed it, why that kind of activity will reinforce misconceptions about evolution (that every feature is adaptive, that you can infer a structure’s adaptive value from its current function, etc.), but we still had to have the discussion.
I have worked for the past decade-plus with scientists, science writers, and science educators, all of whom have the best intentions in the world, all of whom would have no problem declaring their allegiance to the cause of an authentic science education grounded in evolution. But—and I don’t want to point fingers at anybody here—many of them would have not batted an eye if that activity had come across their desks. And this, I believe, is one of the most important truths we have to face: many of us don’t really get evolution. It’s such a beautiful, simple, and powerful idea, but it’s also finicky, demanding vigilant attention to detail to be properly explained and explored.
Most of you will be familiar with this idea since I've been complaining about adaptationism for decades. In order to "get" evolution, you need to know about Neutral Theory and random genetic drift—and that's just for starters. We need to work much harder to dispel misconceptions about evolution.
Lot's of people don't really "get" evolution but, in fairness, they don't study it either. But if you are going to write about evolution—or teach it—then you'd better make sure you understand it. Unfortunately, there are far too many people like Stephanie Keep's friend. We have to fix that.
There's one group that spends an extraordinary amount of time "studying" evolution without ever "getting" it. I'm referring to creationists, especially the Intelligent Design Creationists, otherwise known as IDiots. They've been told time and time again that there's much more to evolution than just adaptation. Recently, some of them actually seemed to "get" the ideas of Neutral Theory and random genetic drift although that turned out to be an illusion. They still don't get evolution.
Bear in mind, too, that the very educators who don't get evolution are also the ones who fuss and complain whenever a state legislator or science standards committee member proposes language about "teaching the strengths and weaknesses" of evolution. From the way they kvetch, you would think there are no weaknesses in evolutionary theory. But if many of them don't get evolution in the first place, how would they know?
Keep says that evolution is a "beautiful, simple, and powerful idea, but it's also finicky, demanding vigilant attention to detail to be properly explained and explored." Perhaps Keep could provide a helpful list of exactly what those details are so educators like her Harvard-trained friend can stay on the straight and narrow Darwinian path, lest they join the chorus calling for a new theory of evolution.
This is ironic and confused on so many levels that I'm not even going to try and point them out. I just post it here for your amusement.
1. Here's his profile on the Discovery Institute website.Donald McLaughlin joined Discovery Institute in August 2013, as a Development Officer and Regional Representative in the upper Midwest and Northeast regions. His areas of responsibility include cultivating and stewarding major gifts, and planned giving. Donald has had a successful career in development, including 8 years as a Regional Director of Advancement for Prison Fellowship Ministries, 2 years as National Director of Major Gifts for Teen Mania Ministries and 5 years as Regional Director of Advancement for Taylor University.
Donald is a 1975 graduate of Taylor University where he earned his BA in Speech and Drama. In 1977, he earned an MA in Clinical Audiology from Ball State University in Muncie, IN. While at Prison Fellowship, Donald also participated in the Centurions Program. Prior to his work in Development, Donald spent more than twenty years in financial services with both AG Edwards and Merrill Lynch. Donald lives in Granger Indiana, near South Bend, with his wife of 35 years, Elizabeth, who is Chair of the Communications Department at Bethel College in Mishawaka, IN. Donald enjoys reading, traveling, and music.
He also has a religious profile at: Donald McLaughlin.
The latest issues of ASBMB Today contains an article by Brent R. Stockwell and Michael Cennamo with a provocative title: Reimagining the undergraduate science course.
It describes an undergraduate course in biochemistry at Columbia University. Apparently, this course used to be taught in a way that's similar to many biochemistry courses. The lecture consisted of PowerPoint slides and a description of basic facts such as metabolic pathways. Stockwell and Cennamo want to redesign the course to allow more time in the classroom for debate and discussion. This is an admirable goal.
They decided to "flip the classroom."
What does it mean to flip the classroom?
When we say we flipped the classroom, we mean that we had students watch recorded videos before class, freeing classroom time for discussion, group work and solving problems. But this is not something you can do overnight.
We took time to define our goals: Obviously, we wanted the students to be better prepared for each class, allowing them to engage more fully in class discussion. But we also wanted to have students put lecture material into action by tackling practical biochemistry problems.
Last summer, we had a number of meetings to design a new course that not only would get students thinking and problem solving in a new way but would provide instant feedback on how well they understood the material.
What they did was to create a video with their PowerPoint slides and a recording of the lecturer explaining what's on the slides. The students were supposed to watch the video before class and, to ensure that they did, there was a quiz at the end of the video presentation. For example, at the end of the lecture on amino acid metabolism, the students were asked to identify the product of the deamination of alanine.1
Here's the part I don't understand. What's the value of having students watch a video presentation when they have a textbook? (The recommended textbook is Lehninger, Principles of Biochemistry by David Nelson and Michael Cox (6th edition, 2013)).
Why not just assign readings from the textbook? I assume that most lecturers are not very knowledgeable about the content of most lectures in an introductory biochemistry course so they probably rely on a textbook anyway.
And what are the students supposed to do when they watch the video? In the new version of the course, students are divided into groups and they deal with problems that "required students to synthesize and apply the information from the textbook, videos and class discussion" (i.e. "problem-based learning," according to the authors). One of the question is ....
If glucose labeled with 14C at C-1 were the starting material for amino acid biosynthesis, the product(s) that would be readily formed is/are:
A. Serine labelled at alpha carbon
B. None of these
C. All of these
D. Serine labelled at the carboxyl carbon
E. Serine labelled at the R-group carbon2
I assume that the students would have to take notes while watching the video and/or download the PowerPoint slides in order to answer this question during class. Or, they could bring their textbook to class.
Do PowerPoint video presentations add anything to the course that can't be found in the textbook?
1. Pyruvate and glutamate?
2. I assume the instructors are thinking about organisms that regularly utilize glucose as a carbon source so that amino acids like serine are mostly derived from intermediates in glycolysis (e.g. humans). In that case, the students have to understand the distribution of carbon atoms in the aldolase reaction. I had to look this up to determine that the correct answer is "E." I hope I'm right. For species that use the pentose-phosphate pathway, I think the correct answer is "B." (This doesn't seem to me like a fundamental principle or concept based on an evolutionary approach to biochemistry.)
Back in 1997, James Shapiro wrote an article for the Boston Review entitled "A Third Way." It was a very confusing article. His main point seemed to be that conventional neo-Darwinism wasn't a complete picture of modern evolutionary theory.
That part wasn't news since by 1997 the ideas of Neutral Theory and random genetic drift had been around for thirty years. Apparently, Shapiro was three decades behind in his understanding of evolution.
Shapiro doesn't demonstrate that he understands population genetics and random genetic drift. This just one (of many) criticisms that I mentioned in my review of Shapiro's book Evolution: A View from the 21st Century in NCSE Reports [Evolution: A View from the 21st Century]. Shapiro responded to my review at: Reply to Laurence A Moran’s review of Evolution: A View from the 21st Century] and I discussed his response on my blog [James Shapiro Responds to My Review of His Book].
The "third" way, according to Shapiro's 1997 article, is not classic Darwinism and it's not creationism. Instead, it's a new way of looking at evolution.
What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation. We can speculate what some of these more manageable questions might be: How can molecular control circuits be combined to direct the expression of novel traits? Do genomes display characteristic system architectures that allow us to predict phenotypic consequences when we rearrange DNA sequence components? Do signal transduction networks contribute functional information as they regulate the action of natural genetic engineering hardware?
Questions like those above will certainly prove to be naive because we are just on the threshold of a new way of thinking about living organisms and their variations. Nonetheless, these questions serve to illustrate the potential for addressing the deep issues of evolution from a radically different scientific perspective. Novel ways of looking at longstanding problems have historically been the chief motors of scientific progress. However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.
Now Shapiro has joined forces with some other "revolutionaries" and started a new website called "The Third Way." It has grandiose goals ....
The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.
There's only one problem. I'm familiar with Shapiro's ideas and with the ideas of most of the other people listed on the website and I don't think any of them (except Eugene Koonin) have anything significant to say about evolutionary theory. Futhermore, most of them don't seem to understand that there's already been a revolution and population genetics, Neutral Theory, etc. won the day. They seem to have completely missed that revolution.
They are advocating a fourth way that skips right from adaptationism to something else.
They are like a group of would-be revolutionaries marching up Rue de Lyon in Paris only to discover that the Bastille has been replaced by an open square and an opera house.
Note: There aren't many biologists that are interested in this "Third Way" but the creationists are lapping it up [A Group of Darwin-Skeptical Scientists Seeking a "Third Way" in Biology Have Launched a New Website; Welcome to Them!].
