Birth and death of genes in a hybrid frog genome

De novo genes¹ are quite rare but genome duplications are quite common. Sometimes the duplicated regions contain genes so the new genome contains two copies of a gene that was formerly present in only one copy. "Common" in this sense means on a scale of millions of years. Michael Lynch and his colleague have calculated that the rate of fixed gene duplication is about 0.01 per gene per million years (Lynch and Conery, 2003 a,b; Lynch 2007). Since a typical vertebrate has more than 20,000 genes, this means that 200 genes will be duplicated and fixed every million years.

The initial duplication event is likely to be deleterious since there will now be redundant DNA in the genome. The slightly deleterious allele (duplication) can be purged by negative selection in species with large population sizes (e.g. bacteria). But in species with smaller populations, natural selection is not powerful enough to eliminate slightly deleterious alleles so the duplication persists and may become fixed in the population.

Gert Korthof reviews my book

Gert Korthof thinks that the current view of evolution is incomplete and he's looking for a better explanation. He just finished reading my book so he wrote a review on his blog.

Scientists say: 90% of your genome is junk. Have a nice day! Biochemist Laurence Moran defends junk DNA theory

The good news is that I've succeeded in making Gert Korthof think more seriously about junk DNA and random genetic drift. The bad news is that I seem to have given him the impression that natural selection is not an important part of evolution. Furthermore, he insists that "evolution needs both mutation and natural selection" because he doesn't like the idea that random genetic drift may be the most common mechanism of evolution. He thinks that statement only applies at the molecular level. But "evolution" doesn't just refer to adaptation at the level of organisms. It's just not true that all examples of evolution must involve natural selection.

I think I've failed to explain the null hypothesis correctly because Korthof writes,

It's clear this is a polemical book. It is a very forceful criticism of ENCODE and everyone who uncritically accepts and spreads their views including Nature and Science. I agree that this criticism is necessary. However, there is a downside. Moran writes that the ENCODE research goals of documenting all transcripts in the human genome was a waste of money. Only a relatively small group of transcripts have a proven biological function ("only 1000 lncRNAs out of 60,000 were conserved in mammals"; "the number with a proven function is less than 500 in humans"; "The correct null hypothesis is that these long noncoding RNAs are examples of noisy transcription", or junk RNA"). Furthermore, Moran also thinks it is a waste of time and money to identify the functions of the thousands of transcripts that have been found because he knows its all junk. I disagree. The null hypothesis is an hypothesis, not a fact. One cannot assume it is true. That would be the 'null dogma'.

That's a pretty serious misunderstanding of what I meant to say. I think it was a worthwhile effort to document the number of transcripts in various cell types and all the potential regulatory sequences. What I objected to was the assumption by ENCODE researchers that these transcripts and sites were functional simply because they exist. The null hypothesis is no function and scientists must provide evidence of function in order to refute the null hypothesis.

I think it would be a very good idea to stop further genomic surveys and start identifying which transcripts and putative regulatory elements are actually functional. I'd love to know the answer to that very important question. However, I recognize that it will be expensive and time consuming to investigate every transcript and every putative regulatory element. I don't think any lab is going to assign random transcripts and random transcription factor binding sites to graduate students and postdocs because I suspect that most of those sequences aren't going to have a function. If I were giving out grant money I give it to some other lab. In that sense, I believe that it would be a waste of time and money to search for the function of tens of thousands of transcripts and over one million transcription factor binding sites.

That not dogmatic. It's common sense. Most of those transcripts and binding sites are not conserved and not under purifying election. That's pretty good evidence that they aren't functional, especially if you believe in the importance of natural selection.

There's lot more to his review including some interesting appendices. I recommend that you read it carefully to see a different perspective than the one I adocate in my book.

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IDiots Don't Understand Punctuated Equilibria

Intelligent Design Creationism is a movement dedicated to discrediting evolution and attacking the rational explanation of nature.¹ The evidence is in the books and blogs and the propaganda distributed to local school boards and state legislators. The attack on science and scientists makes up about 99% of their activities.

Given their dedication to disproving evolution, you'd think that the IDiots must at least understand it. Maybe not all of them—because there are some really, really, stupid IDiots—but certainly some of the most prominent IDiots should know what they're talking about? Right? Doesn't that seem reasonable?

The facts say otherwise. Off hand, I can't think of a single IDiot who has an adequate understanding of the science they attack. Believe me, I've tried harder than most to find an intelligent believer.

Does Disbelieving Evolution Reflect a Lack of Understanding of It?

 
Bill Dembski is troubled by the latest report in Science that shows a correlation between acceptance of evolution and education. [See PZ Myers' summary on Pharyngula.] The data suggests that the more educated you become the more likely you are to accept evolution. In other words, the data suggests that IDiots are, well, idiots.

You can see why Dembski is upset [Does understanding coerce belief?]. The truth hurts. Dembski then goes on to give us a good demonstration of the negative correlation between intelligence and belief in intelligent design.

But why should disbelieving evolution reflect a lack of understanding of it? Alternatively, does understanding evolution automatically force one to believe it? I remember speaking at the University of Toronto in 2002 when a biologist challenged me about how holding to ID renders one a nonscientist. I asked him if that disqualified Isaac Newton from being a scientist. His instant response was, “but he didn’t know about evolution.”

I don't know if Dembki is referring to me or to one of my colleagues who was at the meeting. I recall accusing Dembski of stupidity and of not being a good scientist, but there were so many of us making the same point that I don't know which one Dembski remembers. (Dembski has mentioned this meeting many times. It must have been very traumatic for him.)

At the risk of boring anyone with an IQ over 80, let me make the point that Dembski is deliberately missing. In 2002, if you rejected evolution you were an idiot. That's because the evidence for evolution is overwhelming. The same correlation holds today, only more so.

To answer the question posed in the title; yes, disbelieving in evolution reflects a lack of understanding of evolution. That's an empirical observation. There are very, very few IDiots who understand evolution. (Don't believe me? Read Uncommon Descent and Evolution News & Views.) Dembski sure aint' one of them. He didn't understand the basic principles of evolutionary theory in 2002 and he's given no indication of having learned anything since then.

Newton didn't know about evolution so he couldn't have rejected it. He wasn't stupid and he wasn't a bad scientist. He also didn't know about general relativity and plate tectonics but that didn't mean he was stupid either. If Newton were alive today you can be sure he would accept evolution, continental drift and general relativity. In the 21st century, anyone who rejects these fundamental concepts in science doesn't deserve to be called a scientist.

See the IDiots Gloat over Jonathan Wells

This is part of my discussion about The Myth of Junk DNA by Jonathan Wells. I still haven't read the book—it won't be released in Canada until May 31st.

Over on Evolution News & Views (sic) David Klinghoffer is already counting his chickens [Junk DNA and the Darwinist Response so Far].

Over the weekend, Jonathan Wells's The Myth of Junk DNA broke into the top five on Amazon's list of books dealing with genetics -- a list normally dominated at its pinnacle by various editions of Richard Dawkins' The Selfish Gene. Not bad, Jonathan.

Not bad indeed, except I can't tell if it's true. When I check the top selling recently published books I don't see The Myth of Junk DNA in the top five. Never mind, I'm sure there will be many skeptics like me who will buy the book just for a good laugh.

UPDATE: The latest information shows that Wells' book is ranked 23rd under "Genetics." I'm sure the IDiots just made a simple arithmetic error when they said it had broken into the top five.

The juxtaposition with Dawkins' Selfish Gene is appropriate, notwithstanding the demurrals of biochemist Larry Moran et al. Dawkins and other Darwinists, such as Jerry Coyne, have indeed posited that neo-Darwinian theory predicts that swaths of the genome will turn out to be functionless junk. The Junk DNA argument has been a pillar of the Darwin Lobby's efforts to seduce public opinion and influence public policy. Professor Moran wants to imagine that Dawkins never held that neo-Darwinism predicts junk DNA. But that's not how other Darwinists see it. (Compare, for example, Dennett's Darwin's Dangerous Idea, page 316.)

The IDiots have a bit of a problem. In order to make this book look important they have to first establish that the concept of abundant junk DNA in our genome was a "pillar" of support for evolution. That's hard to do when their understanding of evolution is so flawed that they don't see the difference between "Darwinism" and evolution by random genetic drift.

Their claim that evolutionary theory PREDICTED the presence of huge amounts of junk DNA in our genome is just plain false. They been told this but they keep repeating their error. There's a word for that kind of behavior.

It's easy to see how they got confused. It's because they're IDiots. It's partly because they don't understand that an argument for inheritance of a few pseudogenes is not the same as an argument that more than 50% of our genome is junk. There are plenty of scientists who will use the pseudogene argument to challenge Intelligent Design Creationism but who don't believe that MOST of our genome is junk.

It's also partly because the IDiots don't know the difference between selfish DNA and junk. Here's what Daniel Dennett says on page 316 of Darwin's Dangerous Idea.

The presence of functionless DNA in the genome is no longer regarded as a puzzle. Dawkins (1976) selfish-gene theory predicts it, and elaborations on the idea of "selfish DNA" were simultaneously developed by Doolittle and Sapeinza (1980) and Orgel and Crick (1980) (see Dawkins 1982, ch. 9, for the details).

Selfish DNA is not junk DNA. The classic examples of selfish DNA are active transposons and integrated viruses. These bits of DNA have a function—even if it's only to propagate themselves. As you can see from my summary [What's in Your Genome?]. I don't count them as junk.

It's remarkable that Klinghoffer quotes Chapter 9 of The Extended Phenotype (1982) since Dawkins take pains to point out that much of the junk DNA in our genome could have a function. This is exactly the sort of skepticism one would expect from a Darwinist.

This does not mean, however, that the so-called junk DNA is not subject to natural selection. Various 'functions' for it have been proposed, where 'function' means adaptive benefit to the organism.

He goes on to describe several of the proposals that are common arguments against junk DNA. If the DNA has a function and it's adaptive, then it is not junk. Selfish DNA is not junk.

Let's be very clear about one thing. The scientific dispute is not over the existence of junk DNA. That's well established. The dispute is over how much of our genome is junk (DNA with no function). In order to refute the idea that MOST of our genome is junk, you have to show that most of it has a function of some sort. I'm looking forward to Jonathan Wells' book where he is going to prove to us that >50% of our genome has a function. (Not holding my breath!)

So far, with none of them having actually read the book (though P.Z. Myers threatens to do so), the Darwin apologists' response to The Myth of Junk DNA has followed along four lines of defense.

1) The usual insults. In his blog Larry Moran of the Department of Biochemistry at the University of Toronto, a grown man and from the looks of him not a young one either, repetitively derides Jonathan as an "IDiot." (How embarrassing for this mature gentleman, you might think. Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as "Larry Moron" or similar? The question is self-answering and tells you a lot about how desperation kindles anger among these people.)

You know, there's one sure way to prove you're not an idiot. The IDiots have been trying for over twenty years to show that they understand science. I'll gladly stop calling them idiots as soon as they deserve it.

Speaking of insults. There's one sure way to ensure that you aren't going to be insulted and that's to stop calling evolutionary biologists "Darwinists" and stop saying that they don't understand their own discipline. I find that extremely insulting and I'm not going to refrain from responding in kind.

I don't know what Jonathan Wells is going to say in his latest book but here's a few examples of insults in Icons of Evolution.

There is a pattern here, and it demands an explanation. Instead of continually testing their theory against the evidence, as scientists are supposed to do, some Darwinists consistently ignore, explain away, or misrepresent the biological facts in order to promote their theory. One isolate example of such behavior might be due simply to overzealousness. Maybe even two. But ten? Year after year? (p. 230)

Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it? (p. 234)

If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and use their position of dominance to censor dissenting viewpoints. (p. 235)

The truth is that a surprising number of biologists quietly doubt or reject some of the grander claims of Darwinian evolution. But—at least in America—the must keep their mouths shut or risk condemnation, marginalization, and eventual expulsion from the scientific community. This happens infrequently, but often enough to remind everyone that the risk is real. (p. 239)

Klinghoffer continues with his four lines of defense that we "Darwinists" apparently use to defend the existence of abundant junk DNA (>50%) in our genome.

2) Denying that junk DNA ever figured preeminently in the Darwinist's quiver of arguments against design. Moran, for example, asserts, "There was never a time when knowledgeable molecular biologists equated 'junk' DNA and 'noncoding' DNA." Huh, that's strange. I'm not aware of anyone who has scientifically polled the community of professional biologists on the subject. But I do know that in the struggle for public opinion over the question of Darwin versus Design, junk DNA has again and again been employed, by all the most eminent protagonists on the Darwinian side, as a bludgeoning weapon against intelligent design. Never mind The Selfish Gene, in his most recent book, The Greatest Show on Earth (2009), Dawkins observed that "the greater part...of the genome might as well not be there, for all the difference it makes," and that this fact is "useful for...embarrassing creationists."

Similarly, in Why Evolution Is True (2009), Jerry Coyne offers it, again, as a "prediction" of neo-Darwinian theory that we'll find the genome littered with useless "vestigial genes."

I said that knowledgeable scientists never said that all non-coding DNA is junk. Klinghoffer says, blah, blah, blah, not even addressing my statement.

You can't make this stuff up. At every single opportunity the IDiots demonstrate that they deserve the title.

3) When not denying that junk DNA is a prime, staple argument for Darwin apologists, Professor Moran wants to have it the opposite way. In the same series of blog posts attacking "the IDiot" Jonathan Wells, Moran maintains his own belief that the genome is indeed overwhelmingly useless junk. "Some (I am one)," he writes, "still think that as much as 90 percent could be junk." He insists that "it's not sufficient to show that a few bits of repetitive DNA have gained a function in some species."

Dr. Moran's problem is that he has neither read Jonathan's book nor, it seems, followed the cascade of evidence from the scientific publications. It's a heck of a lot more than just "a few bits of repetitive DNA" that have been shown to be functional. In a brief (and enviably readable and accessible) 115-page book, Jonathan Wells offers over 600 references to recent peer-reviewed literature.

Twenty-five thousand studies further down the road from where we are now, no one knows how much of the genome will turn out to be truly functionless and therefore genuinely worthy of the appellation "junk." But for Darwinists, the speedily mounting evidence against junk DNA is an ominous portent. As Casey Luskin and others have put it, it's the trend that stands out prominently here, on which the likes of Larry Moran have so far been in denial.

Theme

Genomes
& Junk DNAI've tried and tried to get the IDiots to have a serious, scientific, discussion about the evidence for and against abundant junk DNA in our genome. Some of them have tried but their arguments soon degenerate into insults about my lack of knowledge of the scientific literature. This is in spite of the fact that I have dozens of postings on the subject over the past few years and nobody has ever shown that I've been ignorant of the science behind the controversy. We may disagree about the interpretation but that's not what I'm being accused of here.

As soon as I read the book I'll post a bunch of articles pointing out why it's wrong. That will give the IDiots, like Jonathan Wells, a chance to debate the points I make and show that he is right and I am wrong. I'm looking forward to it.

4) Finally, in my own small contribution to this debate, I made a facetious comment here about how the identification of Osama bin Laden's corpse by DNA fingerprinting, using his "junk DNA" as the media habitually referred to it, provided a welcome news hook for the publication of Jonathan's book. This provoked braying responses from the Darwin Lobby. For example, our journalist friend Lauri Lebo, challenged as ever in her reading-comprehension skills, somehow understood that I was saying the usefulness of non-coding DNA for this forensic purpose proved it isn't junk.

P.Z. Myers tried to show that the usefulness of non-coding DNA for genetic fingerprinting is another demonstration that the stuff really is junk, being "subject to random changes at a higher rate than coding DNA, because it is not subject to functional constraints."

Every now and them some IDiots get something right—even if it's just by accident. One example is when Klinghoffer describes his posting as "my own small contribution."

But whether "junk DNA" is functional is exactly the question at issue, isn't it? The fact that our DNA is pervasively transcribed, as Jonathan Wells points out in Chapter 3 of his book, itself suggests pervasive functionality. As has become clear, too, DNA may serve in various functions even if it does not code for functional RNA.

It will be fun to read how Wells deals with the issue of spurious transcription based on his understanding of how RNA polymerase and transcriptional activators bind to DNA. I'm certainly looking forward to learning about the reliability of those genome studies on transcription and I'm sure Wells is going to discuss conflicting data in the scientific literature. After all, Wells has a Ph.D. in molecular biology so he must know about the real scientific controversy, right?

As for functions that don't require transcription, I highly recommend my short summary of these in What's in Your Genome. We've known about them for decades but apparently the IDiots think this is a new discovery.

So far, the Darwinist response fails to appreciate that Jonathan is in the act of very seriously blunting a Darwinian icon. What, in this context, is an icon? It's a mainstay in the public debate about Darwinian evolution that turns out, on inspection, to be based not on solid science but on puffery, illusion or deception.

This is another icon that, as Jonathan shows, was in the process of being blunted by biologists who are not ID advocates, well before Dr. Wells gathered the evidence together so concisely and conveniently in these pages.

Whatever. Wells' first book, Icons of Evolution was full of lies and I suspect this one will be too. Only one of the ten so-called icons was "blunted" by Wells and that one was the Haeckel drawings. Even then, Wells seriously distorted the significance of those fake drawings by claiming that there was now no evidence of similarities in the development of all mammals.

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Advice to New Creationist Students

We're getting close to the beginning of the semester in the northern hemisphere. That means a lot of high school students will be experiencing university for the first time.

In many cases, students will have graduated from high school with only a rudimentary knowledge of some important topics. This isn't necessarily a bad thing as long as they realize that they still have lots to learn. It becomes a bad thing when they think they know the subject but what they know is wrong.

Universities are places that challenge your beliefs and force you to think. New students should embrace this challenge and look forward to giving up misconceptions and ideas that can't stand up to critical analysis. The last thing you want to do as a new student is to begin university with the idea that your high school ideas are always right.

Which brings us to creationism. A large number of students enter university with little or no knowledge of evolution but they are convinced that it's wrong. They will soon encounter teachers who try to convince them that evolution is true. How should students react to this challenge?

David Klinghoffer¹ proposes one solution on the Intelligent Design Creationist blog Evolution News & Views. Here's his advice [A Piece of Unsolicited Advice to Students].

The practical question is nearly self-answering. You should be very, very circumspect about even hinting at your views to people who will end up giving you grades. But beyond that fairly obvious and uninteresting advice, I wanted to add that you should, in your own mind, strive to give respect to your Darwinist teachers no matter how firmly convinced you are that they are wrong.

If I were a professor and had a student who walked into my class intending to inform me that my fundamental views on the subject of my professional training were in error, I can well imagine thinking the kid deserved a good smack. Unfair? Yes, but true. Overturning scientific theories is not the job of an undergraduate student. A student's job is to learn what his teacher has to teach him, so that perhaps later when the student is intellectually ripened, he can lead or participate in a revolution. It's not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.

At an emotional and personal level, I can sympathize with the Darwinist prof who resents his openly Darwin-doubting student. What arrogance, it must seem, to imagine that what I spent decades mastering, you a little pipsqueak think you're ready to discard half-way into the semester. Imagine yourself in your teacher's place. To him, this is about you, in your ignorance and arrogance or at best innocence, sitting in judgment of the system to which he's devoted his professional life.

In other words, hide your views because your professor might punish you. Recognize that your professor thinks he/she knows more than you do but be confident that they're wrong. Realize that when you encounter professors in class they probably don't understand their subject even though they've devoted their lives to studying it. They might be a bit angry if you exposed them so keep you mouth shut.

Above all, resist the temptation to learn and to question your beliefs. You already know the right answer. University is not the a place for learning.

Here's my advice. It you don't want to learn then don't go to university. If your belief in creationism is really strong then don't ever take a biology class—it might turn you into an atheist and your parents will be very upset. If you need the grade, then take the class, but be prepared to fail. It takes courage to openly stand up for what you believe, especially if there might be consequences. But it's the Christian thing to do.

Most professors love it when students challenge their ideas in class. We prefer those kind of students even if they are wrong. You will never fail a course because of your ideas and beliefs as long as they don't conflict directly with scientific facts. If you believe that the Earth is 6000 years old then you will not pass a geology course or a biology, unless you lie. If you dispute the existence of junk DNA then you could get an excellent grade as long as you get your facts correct.

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1. I don't think Klinghoffer has ever been to university. None of the creationist websites mention any university degrees.

Creationists admit that junk DNA may not be a "myth" after all

Creationists in general, and Intelligent Design Creationists in particular, feel very threatened by the idea that most of our genome is junk. We know why they feel threatened: it's because a genome full of junk doesn't seem like something gods would design on purpose. It's pretty hard to reconcile junk DNA with with gods that spend so much effort designing bacterial flagella.

The creationists get very excited whenever a group of scientists publish evidence for function in junk DNA and they could hardly contain themselves when the ENCODE preliminary results were published in 2007 because the ENCODE Consortium said that most of the human genome was functional. You will recall that the creationists fell hook line and sinker for the ENCODE publicity hype in September 2012 when the ENCODE leaders came right out and said that their analysis of the entire genome shows there is almost no junk in the human genome.

The creationists, just like the ENCODE leaders, were very resistant to all of the scientific evidence for junk DNA. Both groups showed a remarkable ignorance of four decades of work leading to the conclusion that our genomes are full of junk DNA [see ENCODE, Junk DNA, and Intelligent Design Creationism ]. Creationists, and even some scientific opponents of junk DNA, quote Jonathan Wells' book The Myth of Junk DNA as an authority of the issue.

Now, I wrote a pretty extensive review of The Myth of Junk DNA showing where mistakes were made and why the evidence still favored lots of junk DNA in our genome [The Myth of Junk DNA by Jonathan Wells]. That was in 2011. Here's how Jonathan Wells responded ... [Jonathan Wells Sends His Regrets].

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

The ENCODE Consortium has decided that it had better backtrack a little on the subject of junk DNA. Their recent PNAS article (Kellis et al., 2014) pretends that the publicity hype of September 2012 never existed and, even if it did, they may have been right to conclude that 80% of our genome is functional. It all depends on how you define function. Apparently they have just discovered that lots of scientists define it in a way that the ENCODE Consortium overlooked in September 2012.

Now they just want to make sure that everyone knows they have done their homework and they acknowledge that there's a wee bit of a controversy—but they weren't wrong! They just have a different way of defining function.

This puts some of the creationists in a difficult position. Some of them are actually willing to conceded that there's a lot of junk DNA in our genome while other are only willing to concede that the case for function may not be quite as rock solid as they thought.

Here's how an anonymous creationist explains the backtracking of the ENCODE Consortium on Evolution News & Views (sic): Defining "Functional": The Latest from ENCODE.

He/she starts off with the obligatory snipe at "Darwinists" and the obligatory misrepresentation of the case for junk DNA. He/she is referring to the Kellis et al. paper ...

First, the paper is a remarkably restrained and balanced response to some of the rather intemperate criticisms of ENCODE from hard-core Darwinists who insist that (a) ONLY an evolutionary approach yields valid information about functionality, (b) evolutionary theory necessarily implies that most of our DNA is junk, and (c) junk DNA provides evidence that Darwinian evolution is a fact. In other words this paper is a model of rational and civil scientific discourse, in contrast to what we have come to expect from some hard-core Darwinists.

(See the quote above from Jonathan Wells for an example of "a model of rational and civil scientific discourse.")

The Evolution News & Views post concludes with ...

The authors conclude that all three approaches must be taken into account, though a simple intersection of the three (which would include only DNA sequences that meet the test of functionality for all three approaches) would be far too restrictive. Unfortunately, the authors do not specify exactly how the three approaches could be integrated to yield a single reliable estimate of the percentage of functional DNA.

So the debate continues.

Believe it or not, that last sentence ("So the debate continues") is pretty remarkable considering that the creationists have steadfastly refused to admit that there is a scientific debate. Over the past decade, they have consistently claimed that the evidence is in and it shows that gods did it after all most of our genome is functional.

Maybe I'm being overly optimistic but it looks to me like some creationists are actually disagreeing with Jonathan Wells. Stay tuned.

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Kellis, M. et al. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) April 24, 2014 published online [doi: 10.1073/pnas.1318948111 ]

Facts Supporting Intelligent Design Creationism?

 
We all know that the Intelligent Design Creationist movement consists almost exclusively of attacks on science. The idea seems to be that if you can cast doubt on evolution then this is evidence in favor of God.

Some unnamed Professor has challenged students to come up with facts that support Intelligent Design Creationism. The only criterion is; "fact can be any observation in biology that is substantiated by publication in a scientific journal,"

Casey Luskin attempts to meet the challenge over on the Discovery Institute propaganda site, Evolution News & Views: Helping Students Answer a Professor's Challenge to "Find a Fact" That Supports Intelligent Design (Part 2).

Here's a list of "scientific" publications submitted by Luskin. I haven't read all of them but, of the ones I've read, there isn't a single one containing a fact that supports the existence of God, let alone evidence that he/she designed anything at all. Furthermore, many of them aren't from a scientific journal. It looks like Casey Luskin has goofed, once again.

Let me know if any of these publications contain evidence of Intelligent Design Creationism. Is this the best they can do? (I've put asterisks in front of the ones I've read.)

*Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301:585-595 (2000)

*Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, 1-21 (2004)

*Michael Behe, Darwin's Black Box: The Biochemical Challenge to Evolution (Free Press, 1996)

*Michael J. Behe & David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, Vol 13:2651-2664 (2004)

Geoff Brumfiel, “Outrageous Fortune,” Nature, Vol. 439: 10-12 (Jan. 5, 2006)

Bract, "Inventions, Algorithms, and Biological Design," in Progress in Complexity, Information, and Design (Vol. 1.1, 2002)

*William A. Dembski, The Design Inference: Eliminating Chance Through Small Probabilities (Cambridge University Press, 1998)

a. William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success” (In publication, 2009)

b. William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search” (In publication, 2009)

*William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Living Systems, (FTE, 2008) (see www.thedesignoflife.net)

*Wayt T. Gibbs, “The Unseen Genome: Gems among the Junk,” Scientific American (November, 2003)

Guillermo Gonzalez and Jay Wesley Richards, The Privileged Planet: How our Place in the Cosmos is Designed for Discovery, (Regnery, 2004)

*Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009)

Hiroaki Kitano, ”Systems Biology: A Brief Overview,” Science, Vol. 295: 1662-1664 (March 1, 2002)

Wolf-Ekkehard Lönnig, "Dynamic genomes, morphological stasis, and the origin of irreducible complexity," in Dynamical Genetics pp. 101-119 (Valerio Parisi, Valeria De Fonzo, and Filippo Aluffi-Pentini eds., 2004)

Casey Luskin, “Human Origins and Intelligent Design,” Progress in Complexity and Design, (Vol 4.1, November, 2005)

Casey Luskin, "Intelligent Design Has Scientific Merit in Paleontology," part of the "Does Intelligent Design Have Merit?" debate at OpposingViews.com (September, 2008)

*Wojciech Makalowski, “Not Junk After All,” Science, Vol. 300(5623) (May 23, 2003)

Stephen C. Meyer, Marcus Ross, Paul Nelson & Paul Chien, "The Cambrian Explosion: Biology's Big Bang," in Darwinism, Design, and Public Education (John A. Campbell and Stephen C. Meyer eds., Michigan State University Press, 2003)

*a. Stephen C. Meyer, “The Cambrian Information Explosion,” in Debating Design (edited by Michael Ruse and William Dembski; Cambridge University Press 2004)

b. Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004)

Scott A. Minnich & Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (M.W. Collins & C.A. Brebbia eds., 2004)

Paul Nelson and Jonathan Wells, “Homology in Biology,” in Darwinism, Design, and Public Education, (Michigan State University Press, 2003)

*Richard v. Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981: 154–188 (2002)

J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, Vol. 28: 729-739 (2004)

D. L. Abel & J. T. Trevors, “Self-organization vs. self-ordering events in life-origin models," Physics of Life Reviews, Vol. 3: 211–228 (2006)

Øyvind Albert Voie, "Biological function and the genetic code are interdependent," Chaos, Solitons and Fractals, Vol. 28:1000–1004 (2006)

Jonathan Wells, "Using Intelligent Design Theory to Guide Scientific Research" Progress in Complexity, Information, and Design (Vol. 3.1.2, November 2004)

Jonathan Wells, "Do Centrioles Generate a Polar Ejection Force?," Rivista di Biologia / Biology Forum, Vol. 98:71-96 (2005)

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Waiting for multiple mutations: Intelligent Design Creationism v. population genetics

Casey Luskin is worried about university students. Apparently, they aren't getting enough correct information about intelligent design. Luskin uses the example of a student named Michael Heckle at Iowa State University. Mr. Heckel said; "So far, there has been no research done by intelligent design advocates that has led to any sort of scientific discovery."

This happens to be a true statement but Casey Luskin takes exception in a blog post that appeared the other day on Evolution News & Views (sic) [No ID Research? Let's Help Out This Iowa State Student].

Debating Darwin's Doubt

Today is the day that John Scopes was found guilty in Dayton, Tennessee (USA) 90 years ago. The Intelligent Design Creationists have marked the day with publication of a new book called Debating Darwin's Doubt [A Scientific Controversy That Can No Longer Be Denied: Here Is Debating Darwin's Doubt].

The book was necessary because there has been so much criticism of the original Stephen Meyer's book Darwin's Doubt. David Klinghoffer has an interesting way of turning this defeat into a victory because he declares,

... the new book is important because it puts to rest a Darwinian myth, an icon of the evolution debate, namely...that there is no debate, about evolution or intelligent design!

Jonathan Wells Sends His Regrets

Paulmc visited Uncommon Descent in order to defend junk DNA [Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives]. Now Wells has responded to several of paulmc's points [Jonathan Wells on Darwinism, Science, and Junk DNA].

We'll get to those issues in another post but right now I want to take note of something Wells said at the end of his article.

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

I can understand why Wells might decline to post a comment on Sandwalk. Many of us know what it's like to try and argue with the readers of the intelligent design blogs. Wells would meet the same reception here that we get over there.

But that doesn't preclude Wells from posting on Uncommon Descent or Evolution News & Views. If he really believes that my review of his book is an example of "confused thinking and malicious misrepresentations of my work"¹ then why not back up such a statement with a thoughtful response on a friendly blog? Evolution News & Views would be ideal since comments are banned.

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1. Wells has accused other scientists of misrepresentation. It's a common theme in The Myth of Junk DNA and in Icons of Evolution. I quoted this passage in Junk & Jonathan: Part 13—Chapter 10.

Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence. In fact, one of Coyne's colleagues at the University of Chicago is James Shapiro, co-author of the 2005 article cited in Chapter 6 that listed over 80 known functions for non-protein-coding repetitive DNA. [The other author is Richard (von) Sternberg ... LAM] But if Coyne and Avise were not ignorant of the evidence, then they misrepresented it—and they continue to do so. Like Dawkins, Shermer and Kitcher they have forfeited any claim they might have to be speaking for science.

I can understand why Wells is reluctant to defend such statements. It's because they are indefensible.

Evolution of Mammals

 
A paper in this week's issue of Nature presents a nice summary of recent work on mammalian evolution. Bininda-Emonds et al. (2007) have combined a lot of data from various studies in order to construct a supertree of mammalian evolution. The study incorporates fossil data with molecular sequence data to arrive at estimates of divergence times for 4,510 species of mammal out of a total of 4,554 extant species (99% complete).

This is a study of macroevolution. The authors are addressing questions about the mode, tempo, and pattern of speciation over a period of more than 150 million years. The main questions are when did mammals diversify and did it have anything to do with the mass extinction event at the Cretaceous/Tertiary (K/T) boundary. This is the event that resulted from an asteroid impact 65 million years ago.

The results are presented in the form of a large phylogenetic tree showing the major groups of mammals. The first split in the mammalian tree occurred 166 million years (My) ago when monotremes such as platypus and echidnas (black) split off from the other mammals. Marsupials such as opposums, kangaroos, and koalas (orange) separated from placental mammals 148 My ago.

Within the placental mammals, all of the extant orders appeared by 75 My ago. This includes the clades labelled on the outside of the circle plus other. For a compete list and a description of the species, see the NCBI Taxonomy website [Eutheria].


All of these orders were established at least 10 Myr before the mass extinction event (dashed circle on the circular tree). This is one of the main conclusions of the meta-analysis. The most significant diversification of mammals takes place well before the extinction of non-avian dinosaurs.

The other conclusion is that subsequent radiations at the level of families were not significant until after 50 Myr ago. This period of diversification lasted until about 10 Myr ago. There is no evidence to suggest that the radiations within each order were synchronous, ruling out global climate change as a mechanism.

Furthermore, the data clearly shows no connection between the mass extinction event at the K/T boundary (65 Myr ago) and subsequent radiations of mammalian groups. This effectively rules puts an end to the long held belief that mammals diversified after the devastation in order to fill up the niches left by dinosaurs. This is not the first paper to refute that belief but it may be the final nail in the coffin.

This summary serves as a warning to those who continue to associate evolution with environmental change. At this level of analysis there does not seem to be a connection between rates of speciation and climate change. This is most obvious with respect to the asteroid impact of 65 My ago. While it led to mass extinction, it did not lead to increases in the rate of evolution of the survivors. The branching pattern of cladogenesis in the figure is hardly affected by the cataclysm.

Similarly, there are no other speciation events that correlate with known climate change over the past 150 million years, including recent ice ages. There is growing recognition among evolutionary biologists that rates of speciation cannot be attributed to large-scale environmental change. (The data has not prevented speculation. Many reports on this paper attempt to manufacture some correlation between global environmental change and speciation. The old idea of a link between them is too entrenched to give up so easily.)

There's an interesting sidebar to this story. The paper clearly states the two main conclusions,

... the pivotal macroevolutionary events for extant mammalian lineages occur either well before the boundary (significant decrease in diversification rate at approximately 85 Myr ago, after establishment and initial radiations of the placental superorders and major orders at approximately 93 Myr ago) or well afterwards, from the Early Eocene onwards (when net diversification began to accelerate)....

Therefore, the demise of the non-avian dinosaurs, and the K/T mass extinction event in general, do not seem to have had a substantial direct impact on the evolutionary dynamics of the extant mammalian lineages.

However, in the title of the paper, The delayed rise of present-day mammals, the authors focus attention on the second conclusion at the expense of the first. Some of the press releases picked up on this emphasis, leading to the false impression that mammalian evolution is more recent than scientists thought [Did the Dino Die-Off Make Room for Mammals?] while others got it right [Mammals not such late developers, after all].

The point about early diversification is emphasized in the Nature News & Views commentary that's published with the article in the March 29th issue. David Penny and Matthew J. Phillips begin with a summary of the evidence for early evolution,

On page 507 of this issue, Bininda-Emonds and co-authors1 present an evolutionary tree of more than 4,500 mammals, and conclude that more than 40 lineages of modern mammals have survived from the Cretaceous, some 100 million to 85 million years (Myr) ago, to the present. This is paralleled by Brown and colleagues' analyses for birds, just published in Biology Letters: they claim that more than 40 avian lineages have likewise survived from before the extinctions at the Cretaceous/Tertiary (K/T) boundary 65 Myr ago. These numbers of surviving lineages push back the evolutionary history of many mammals and birds much further than earlier estimates based on smaller data sets. But strong claims need strong evidence to support them.

Later on they re-emphasize this point,

But the most challenging aspect of the phylogeny is the inference that more than 40 lineages of living mammals (and of birds, as described by Brown et al. 2007 ) survived from the Cretaceous to the present.

There are some quibbles about the data. Personally, I think the estimates for early divergence are too recent rather than too late . It all depends on the first fixed data point which is the separation of monotremes. This date (166 Myr ago) is a minimum estimate and there's evidence for an older date. The popular report on the Nature website [Disappearing dinos didn't clear the way for us] mentions this possibility. Mark Springer of the University of California, Riverside (USA) is interviewed and the article states,

"This is a reasonable first approximation," he [Springer] says. "Some of the dates and relationships are probably right on, and some are probably going to move around."

For example, says Springer, the team estimates that the deepest split in the mammals' family tree, between the egg-laying monotremes (such as the duck-billed platypus) and the rest happened 166 million years ago. But some molecular analyses suggest it happened more than 200 million years ago; Springer thinks this earlier date is probably closer to the truth. If that fundamental point changes, he notes, other things will have to shift too. "That date influences everything else through the tree," he says.

I suspect he's right and all the dates will move back in time. One wonders whether the late radiation at 50 My will then shift closer to the K/T boundary.

It's clear that more work needs to be done but the significance of this paper is that it assembles a lot of evidence into one place and publicizes a debate that's been smoldering among evolutonary biologists for over adecade.

Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., MacPhee, R.D.E., Beck, R.M.D., Grenyer, R., Price, S.A., Vos, R.A., Gittleman, J.L., and Purvis, A. (2007) The delayed rise of present-day mammals. Nature 446: 507-512. [PDF]

Penny, D. and Phillips, M.J. (2007) Evolutionary biology: Mass survivals. Nature News & Views, Nature 446: 501-502. [PDF]

Revisiting Michael Behe's challenge and revealing a closed mind

It's been twenty years since Michael Behe published Darwin's Black Box and Intelligent Design Creationists are flagellating themselves over the fact that it had so little impact on creationism. The USA is becoming more secular with each passing year. Religion is on the decline.

In their attempt to deal with their defeat, the main ID blog has been publishing "Behe's Greatest Hits," which is a euphemistic way of saying "Behe's Greatest Failures." The latest one caught my eye. It's Best of Behe: An Open Letter to Professors Kenneth Miller and PZ Myers.

It takes you back more than two years to July 21, 2014. That's when Michael Behe issued his challenge to PZ Myers and Ken Miller. The challenge was based on his book The Edge of Evolution and specifically on the development of chloroquine resistance in Plasmodium falciparum. Behe starts with the assumption that cloroquine resistance is extremely rare—it occurs with a probability of roughly 10^-20. He concludes that resistance requires at least two different mutations that must occur simultaneously in an individual suffering from malaria while being treated with chloroquine.

The first assumption is approximately correct. Chloroquine resistance is rare. He was criticized for the second assumption; namely, that the overall probability of chloroquine resistance is just the probability of two mutations occurring simultaneously (e.g. 10^-10 × 10^-10 = 10^-20).

Inside the mind of an Intelligent Design Creationist

The blog Evolution News & Views (sic) is part of the public outreach of The Center for Science and Culture, a subsidiary of the The Discovery Institute.

Ann Gauger is a researcher at The Biologic Institute, which is funded by The Discovery Institute. She wrote an article for Evolution News & Views entitled What If People Stopped Believing in Darwin? I think it's safe to assume that this is a common view of a leading Intelligent Design Creationist and close to the position of other members of that cult.

American scientists think science education is a problem

The results of the latest PEW/AAAS survey are getting a lot of attention [Public and Scientists’ Views on Science and Society]. Most people focus on the fact that the American public doesn't accept evolution and anthropogenic climate change. That's not news.

The real issue is what can we¹ do about it. Alan Leshner, Chief Executive Officer of AAAS and Executive Publisher of Science, thinks he has the answer. Here's what he writes in an editorial "Bridging the opinion gap" ...

Speaking up for the importance of science to society is our only hope [my emphasis, LAM], and scientists must not shy away from engaging with the public, even on the most polarizing science-based topics. Scientists need to speak clearly with journalists, who provide a great vehicle for translating the nature and implications of their work. Scientists should also meet with members of the public and discuss what makes each side uncomfortable. In these situations, scientists must respond forthrightly to public concerns. In other words, there needs to be a conversation, not a lecture.

Isn't that insightful? Here we are in 2015 and nobody ever thought of that before now! Can you imagine how much better off we'd be if scientists have only started speaking up 40 years ago, or even 10 years ago?

Scientists have been engaging with the American public about evolution for half a century and it has not worked. They've also been speaking to journalists.²

Fortunately, there are some people who have gone way past these naive views and actually thought seriously about the problem. Here's are the results of two questions from the survey.

• Only 16% of AAAS scientists and 29% of the general public rank U.S. STEM education for grades K-12 as above average or the best in the world. Fully 46% of AAAS scientists and 29% of the public rank K-12 STEM as “below average.”
• 75% of AAAS scientists say too little STEM education for grades K-12 is a major factor in the public’s limited knowledge about science. An overwhelming majority of scientists see the public’s limited scientific knowledge as a problem for science.

I agree with those scientists. We are part of the problem because we are not doing a very good job of educating students in the ways of science. The long term solution is to do a far better job of teaching about science. We should not be graduating students from university who reject evolution and climate change. We should not be giving out degrees to students who fall for pseudoscience gobbledegook like homeopathy and astrology. If we do that then we are not doing our job as educators and survey results like these are not going to change in the forseeable future.

Now, to be fair, Alan Leshner recognizes the problem even if he's wrong about the solution.

The public's perceptions of scientists' expertise and trustworthiness are very important, but they are not enough. Acceptance of scientific facts is not based solely on comprehension levels. It can be compromised whenever information confronts people's personal, religious, or political views, and whenever scientific facts provoke fear or make people feel that they have no control over a situation. The only recourse is to have genuine, respectful dialogues with people. Good venues are community clubs, science museums, science fairs, and religious institutions. Working with small groups is more effective than working with large groups.

Perhaps he and some other scientists can sit down in small groups with Republican members of Congress and change their minds. Maybe you could do it in their churches. (Remember to be respectful when dialoguing with John Boehner.) Meanwhile, I believe that's not the "only hope." I think educating our young people is a better investment in time and effort even though it won't pay off for a generation.

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1. I say "we" because the same problems exist in Canada.

2. Maybe Alan Leshner should have a little chat with Elizabeth Pennisi.

Is it impossible to educate Intelligent Design Creationists on evolutionary theory?

We all know how much creationists like to label their opponents as "Darwinists." What you don't know is that many of us have spent decades trying to teach creationists about modern evolutionary theory and why is is much more than just mutation plus natural selection. Some Intelligent Design Creationists seem to get it but then they quickly revert to the old rhetoric.

So, the question is whether the Intelligent Design Creationists really understand modern evolutionary theory or not. If they do, then they must be lying when they claim that it's just natural selection and "Darwinism." It can't be excused as ignorance in that case. Alternatively, if they don't understand modern evolutionary theory then they must be stupid.

Which is it?

Evolutionary Biologists Flunk Religion Poll

 
In a follow-up to previous studies, Gregory W. Graffin and William B. Provine surveyed prominent evolutionary biologists to find out what they thought about religion. The results are summarized in the latest issue of American Scientst [Evolution, Religion and Free Will]. (Click on the figure to see a larger version where you can read the fine print.)

Our study was the first poll to focus solely on eminent evolutionists and their views of religion. As a dissertation project, one of us (Graffin) prepared and sent a detailed questionnaire on evolution and religion to 271 professional evolutionary scientists elected to membership in 28 honorific national academies around the world, and 149 (55 percent) answered the questionnaire. All of them listed evolution (specifically organismic), phylogenetics, population biology/genetics, paleontology/paleoecology/paleobiology, systematics, organismal adaptation or fitness as at least one of their research interests. Graffin also interviewed 12 prestigious evolutionists from the sample group on the relation between modern evolutionary biology and religion.

A primary complaint of scientists who answered the earlier polls was that the concept of God was limited to a "personal God." Leuba considered an impersonal God as equivalent to pure naturalism and classified advocates of deism as nonbelievers. We designed the current study to distinguish theism from deism—that is to day a "personal God" (theism) versus an "impersonal God" who created the universe, all forces and matter, but does not intervene in daily events (deism). An evolutionist can be considered religious, in our poll, if he calls himself a deist. ...

Perhaps the most revealing question in the poll asked the respondent to choose the letter that most closely represented where her views belonged on a ternary diagram. The great majority of the evolutionists polled (78 percent) chose A, billing themselves as pure naturalists. Only two out of 149 described themselves as full theists (F), two as more theist than naturalist (D) and three as theistic naturalists (B). Taken together, the advocacy of any degree of theism is the lowest percentage measured in any poll of biologists' beliefs so far (4.7 percent).

No evolutionary scientists in this study chose pure deism (I), but the deistic side of the diagram is heavy compared to the theistic side. Eleven respondents chose C, and 10 chose other regions on the right side of the diagram (E, H or J). Most evolutionary scientists who billed themselves as believers in God were deists (21) rather than theists (7).

When asked directly whether they believe in God, almost 80% said no. I wonder how many of them think of themselves as atheists as opposed to agnostics?

Here's the bad news. 79% of these eminent evolutionary biologists say they believe in free will (option A on the question). Even the authors of the study were surprised by that one.

We anticipated a much higher percentage for option B and a low percentage for A, but got just the opposite result. One of us (Provine) has been thinking about human free will for almost 40 years, has read most of the philosophical literature on the subject and polls his undergraduate evolution class (200-plus students) each year on belief in free will. Year after year, 90 percent or more favor the idea of human free will for a very specific reason: They think that if people make choices, they have free will. The professional debate about free will has moved far from this position, because what counts is whether the choice is free or determined, not whether human beings make choices. People and animals both certainly choose constantly. Comments from the evolutionists suggest that they were equating human choice and human free will. In other words, although eminent, our respondents had not thought about free will much beyond the students in introductory evolution classes. Evolutionary biology is increasingly applied to psychology. Belief in free will adds nothing to the science of human behavior.

There's one other surprise. 72% think that religion is part of evolution—it's an adaptation. One can only wonder what these evolutionary biologists think of themselves. Are they able to overcome their deterministic predisposition to God or are they mutants who lack the gene(s)? Maybe it explains why they believe in free will?

[Hat Tip: Denyse O'Leary]

Theme: Genomes & Junk DNA

Junk in Your Genome

Transposable Elements: (44% junk)

      DNA transposons:
         active (functional): <0.1%
         defective (nonfunctional): 3%
      retrotransposons:
         active (functional): <0.1%
         defective transposons
            (full-length, nonfunctional): 8%
            L1 LINES (fragments, nonfunctional): 16%
            other LINES: 4%
            SINES (small pseudogene fragments): 13%
            co-opted transposons/fragments: <0.1% ^a

^aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.

Viruses (9% junk)

      DNA viruses
         active (functional): <0.1%
         defective DNA viruses: ~1%
      RNA viruses
         active (functional): <0.1%
         defective (nonfunctional): 8%
         co-opted RNA viruses: <0.1% ^b

^bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.

Pseudogenes (1.2% junk)
      (from protein-encoding genes): 1.2% junk
      co-opted pseudogenes: <0.1% ^c

^cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.

Ribosomal RNA genes:
      essential 0.22%
      junk 0.19%

Other RNA encoding genes
      tRNA genes: <0.1% (essential)
      known small RNA genes: <0.1% (essential)
      putative regulatory RNAs: ~2% (essential) Protein-encoding genes: (9.6% junk)
      transcribed region:  
            essential 1.8%  
            intron junk (not included above) 9.6% ^d

^dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.

Regulatory sequences:
      essential 0.6%

Origins of DNA replication
      <0.1% (essential) Scaffold attachment regions (SARS)
      <0.1% (essential) Highly Repetitive DNA (1% junk)
      α-satellite DNA (centromeres)
            essential 2.0%
            non-essential 1.0%%
      telomeres
            essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above)
      conserved 2% (essential)
      non-conserved 26.3% (unknown but probably junk)

Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%

For references and further information click on the "Genomes & Junk DNA" link in the box

LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)

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November 11, 2006
Sea Urchin Genome Sequenced

The sea urchin genome is 814,000 kb or about 1/4 the size of a typical mammalian genome. Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. The preliminary count of the number of genes is 23,300. This is about the same number that we have in our genomes. Only about 10,000 of these genes have been annotated by the sea urchin sequencing team.

Why is a brain surgeon afraid of evolution?

Michael Egnor is a brain surgeon who doesn't like evolution. Egnor isn't a scientist so why does it matter so much to him?

Listen to this podcast where Casey Luskin interviews Michael Egnor: Dr. Michael Egnor on Debating Intelligent Design. You may want to turn off your irony meter.

Egnor is afraid of evolution for exactly the right reasons. It's because evolution (and science) threaten his worldview. Science tells us that we don't have free will—at least not the kind of free will that Christians demand. Science tells us that there's no such thing as moral absolutes that are dictated by god(s). Science is materialistic and it may be the only valid way of knowing.

No wonder he's scared. Michael Egnor is a Roman Catholic and he knows that evolution threatens his religion.

You'll probably enjoy hearing Egnor and Luskin talk about atheist blogs and about the high quality of science writing on Evolution News & Views. Casey Luskin (lawyer) and Michael Engor (physician) are responsible for some of that high quality science writing.

David Klinghoffer really likes the podcasts. Here's his review at: Listening to Neurosurgeon Michael Egnor on the Brain and Intelligent Design, Rubik's Cube and Jerry Coyne's Blog.

I've exchanged many emails with brain surgeon and ENV contributor Dr. Michael Egnor, but I had never actually heard his voice till now. It's a good voice, which is vital for a physician, mellow yet authoritative, with the correct pitch and timbre. Egnor's stellar academic and medical background aside, I've often thought that, if you had no other information about a healthcare provider, what you don't want is a doctor with the wrong kind of voice.

Now you can hear Egnor as I just did in this fascinating new series of podcasts in which he is interviewed by Casey Luskin. Their themes include evidence of intelligent design in the complexity of the brain, but no less so in the simplest creature, a bacterium. Dr. Egnor compares that design to the solution of a Rubik's Cube. It doesn't happen by chance.

Egnor also talks about the unusual window that Jerry Coyne provides into the mind of a materialist, which is why his name comes up here often. Coyne, unlike many Darwin apologists, doesn't self-censor. You don't have to wonder: What does he really think about, for example, personal responsibility. Because he tells you! Whatever else Coyne may be, he's no weasel. For that, Egnor expresses his gratitude and -- yes, appropriately.

I'm disappointed that Egnor said nothing about me even though he posts quite a few comments on Sandwalk. Guess I don't get much respect.

I wonder why David Klinghoffer didn't mention Casey Luskin's voice?

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Is Intelligent Design Creationism a Scientific Theory?

You should recall that Casey Luskin is one of those "serious science bloggers" who strikes fear into the hearts of evolutionary biologists. In fact, we are so afraid of people like Casey Luskin and Jonathan M that we go out of our way to avoid responding to their posts [see: A Reason to Doubt the IDiots].

Luskin's latest posting on Evolution News & Views (sic) is: How Do We Know Intelligent Design Is a Scientific "Theory"?. Here's the main argument ...

ID is a theory of design detection, and it proposes intelligent agency as a mechanism causing biological change. ID allows us to explain how aspects of observed biological complexity, and other natural complexity, arose. And it uses the scientific method to make its claims.

The scientific method is commonly described as a four-step process involving observations, hypothesis, experiments, and conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesize that if a natural object was designed, it will contain high levels of CSI. Scientists then perform experimental tests upon natural objects to determine if they contain complex and specified information. One easily testable form of CSI is irreducible complexity, which can be tested for by reverse-engineering biological structures through genetic knockout experiments to determine if they require all of their parts to function. When scientists experimentally uncover irreducible complexity in a biological structure, they conclude that it was designed.