Monthly Archives: January 2008

Signs of function in non-coding RNAs in mouse brain.

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Over on his blog, Greg Laden points to some new work by John Mattick’s group on non-coding RNA expression in mouse brains. It’s interesting stuff, and worth a look. Please bear in mind as you do, however, that non-protein-coding but functional RNA is nothing new. Ribosomes are made of non-coding RNA, for one thing. Sadly, Greg seems to have bought into the distortions (several promoted by Mattick) about what people have said about non-coding DNA.

The “Junk DNA” story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don’t know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of “non-coding DNA.” It does really seem that scientists assumed for too long that there was no function in the DNA.

As I have noted, people have been proposing functions for non-coding DNA since the beginning. As I noted in one of my first Genomicron posts,

Those who complain about a supposed unilateral neglect of potential functions for non-coding DNA simply have been reading the wrong literature. In fact, quite a lengthy list of proposed functions for non-coding DNA could be compiled (for an early version, see Bostock 1971). Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).

I am not about to claim that the study hasn’t shown evidence of function for these non-coding regions. I think it’s quite interesting, and it wouldn’t surprise me if lots of non-coding RNA turned out to have a regulatory function. But let’s be realistic with this. The authors consider a “long” non-coding RNA transcript to be >200bp. So let’s just round up and say 1,000bp for convenience. They identified around 850 potentially functional sequences (and ~500 that do not show evidence of functional expression, at least in the brain) and estimate that there are 20,000 of them all told. 1,000bp x 20,000 = 20Mb. The mouse genome is about 3Gb. In other words, this study, even read generously, has identified possible function for 0.7% of the mouse genome.

In summary, cool research. Important question, neat result. But let’s not start the usual extrapolationfest that normally accompanies such publications.


Course evaluations.

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There is more than enough discussion about the usefulness (or not) of student evaluations of courses. I will refer you to Larry Moran‘s recent discussion where you can find one perspective as well as links to other articles. More recently, there is an interesting piece in University Affairs by Brett Zimmerman of York University.

Course evaluations – students’ revenge?

To some extent, the issue appears to be that anonymous evaluations are not particularly helpful. I don’t know how it is done at most universities, but at Guelph evaluations are now done online on a volunteer basis (so the problem becomes getting them to participate) and only comments that are signed count in T&P reviews. I personally find the comments useful, if in no other way than to provide confidence that some of the new approaches I try to implement are successful.

I don’t think we want to abolish student feedback, and I think this should be part of T&P reviews, especially in disciplines like science where there can be a tendency to consider oneself a researcher first and an educator a distant second. However, unsigned comments, especially when they allow students to make insulting statements without consequences, are not useful and should be updated.


Junk DNA and ID redux.

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Just a reminder, these are the important points under discussion:

* Proponents of ID themselves clearly suggest that “junk DNA” will mostly or all be functional.

* No unambiguous explanation has been given for why ID must assume that non-coding DNA is functional, especially since they say nothing can be known about the designer or the mechanism.

* The existence of much non-functional DNA would not necessarily refute the idea of design, as many human-designed structures have redundant, non-functional, or even counterproductive characteristics. It would, however, challenge certain assumptions about the designer and the mechanism, which again is why these must be made explicit if the junk DNA argument is to be invoked. Therefore, this is only a useful prediction if one includes details about the mechanism of design.

* The demonstration that all or most non-coding DNA is functional would not support ID to the exclusion of evolution, because a strict interpretation of Darwinian processes has always been taken to propose function as well.

* The demonstration that all or most non-coding DNA in the human genome is functional would still leave the question unanswered as to why the designer put five times more in onion genomes.

* Many functions that have been proposed or demonstrated are dependent on the process of co-option, the same process that is involved in the evolution of complex features.

* Evidence for function in non-coding DNA comes from analyses using evolutionary methods. Other approaches, such as deleting some, have not supported the hypothesis that it is functional.

* The current evidence for function, and other details about how non-coding DNA forms, both suggest that most non-coding DNA is non-functional, or at least that this is the most plausible condition pending much more evidence.

Feel free to comment, but please address these points directly.


"Fx of Junk DNA" or "Mondo hackitude-o-rama".

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I do not read the intelligent design blogs, but I do read the blogs of some people who read the intelligent design blogs. Today, Afarensis points to a series of “predictions” put forward by ID proponents at the behest of William Dembski on his blog Uncommon Descent for use in an upcoming interview or something. Curious to see what ID predicts (since, as noted, I don’t read their blogs and they don’t publish in the scientific literature), I took a look.

Apparently, many ID proponents don’t know what a prediction is, or at least not what a useful, testable, scientific prediction is. For example:

“Intelligent design can predict that science will never be able to explain how this complex life arose (homochirality). This prediction has been confirmed every year for decades.”

“That after “billions and billions” of generations of any particular biological entity no new morphology will occur due to random mutations and natural selection.”

“ID predicts that many, if not all, innovative technology achievements of human kind (read agency) will have direct parallels in, or derivation from, biological systems.”

And so on.

But here is what caught my attention.

“The single most important prediction of Intelligent Design is that, although there might be the occasional degeneration of either macroscopic or microscopic structure, most structures should serve a purpose. Thus most organs should not be vestigial, and most DNA should not be “junk DNA”.”

Others concurred that 1) junk DNA won’t be junk, and 2) this is a prediction of ID, and 3) this distinguishes ID from evolutionary science.

I have been over this many times, but of course ID proponents probably don’t read my blog (or the scientific literature). Here are the salient points:

1) There is good reason to believe that non-functional DNA is common. The mechanisms of formation — primarily things like transposable element multiplications, gene duplication and pseudogenization, replication slippage, and unequal crossing over — can add DNA without any requirement that it serve a function. Actual data from genome sequences confirms that the most substantial fraction of eukaryotic DNA is transposable elements, some of which are functional, some of which cause disease, and perhaps most of which are now inactive molecular vestiges. Evolutionary biologists do not simply assume non-function out of ignorance. The default assumption for much non-coding DNA is non-function because of what we do know about how it gets there.

2) I have yet to see a convincing, or even unconvincing, argument for why ID requires that non-functional features be rare or non-existent if indeed nothing can be known about the designer. Even very sophisticated products of design by humans have their redundancies and non-functional aspects. For a fun example, consider what was discovered when parts of the source code for Windows 2000 were leaked to the internet during development. It was laced with curse words, warnings of “hacks” that had to be written in to make parts work, and just general expressions of frustration. For example:

“ // We are morons. We changed the IDeskTray interface between IE4″

“ // TERRIBLE HORRIBLE NO GOOD VERY BAD HACK“

“ * The magnitude of this hack compares favorably with that of the national debt.”

“ // Mondo hackitude-o-rama.”

These are remarks that do not code for anything. You could take them all out and nothing would happen to the function of the software. Or, taking a larger view of this analogy, your computer hard drive probably has on it all sorts of redundant, partly deleted, or perhaps even malevolent bits of code, and yet it nonetheless was a designed structure.

Here is the argument I am making. Either IDists cannot say anything one way or the other about non-function, or they must provide information about the method and motive of the designer to justify the assumption.

3) One of the basic assumptions made by hardcore adaptationists is that non-coding DNA must be functional or it would have been deleted. So, this “prediction” is not exclusive, or even original, to ID — it is based firmly in the most rigid applications of Darwinian processes.

One commenter on the ID blog said this:

“As already mentioned, “junk-DNA” would completely undermine ID if it turned out to really be “junk”. But, of course it isn’t.”

I disagree on both fronts. The existence of truly non-functional DNA would not automatically indicate a conclusive refutation of intelligent design, it would only be evidence against design by a divine designer. One can have design with non-function. I also note that there presently is no convincing evidence that more than a small portion of the human genome is functional, let alone the many genomes that are much larger than that of humans.

IDists can consider “all or most non-coding DNA will have some function” their “single most important prediction” if they choose, but this is meaningless because it provides no specifics, it does not actually allow a test of ID unless they acknowledge the features of the designer, and it was already made by some evolutionary biologists decades ago.



The Dr. Credibility principle.

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The title “Doctor” and the abbreviated prefix “Dr.” come from the Latin for “teacher”, and are traditionally bestowed on those who have earned a doctoral degree, the highest academic degree attainable. The suffix Ph.D. is an abbreviation for Philosophiæ Doctor (L. “Teacher of philosophy”), with “philosophy” from the Greek for “love or pursuit of wisdom”. The Ph.D. is awarded in most academic disciplines, including science (in many cases, the D.Sc., or Doctor of Science, is awarded as an honour for special accomplishment). Medical professionals may also hold the title “Doctor” even though they may do little or no teaching, with common suffixes being M.D. (Medicinae Doctor, or Doctor of Medicine), D.V.M. (Doctor of Veterinary Medicine), D.D.S. (Doctor of Dental Surgery), and so on. It is also possible to obtain the title “Doctor” in areas such as homeopathic medicine or chiropractic. In other words, the title alone does not provide much information about what the individual’s qualifications are. However, one can reasonably argue that the prestige attached to it comes from the fact that individuals such as medical doctors and scientists who hold the title are typically ranked among those with greatest prestige.

For the past several years, i.e., since completing my Ph.D. degree, my official title has been “Dr.” and not “Mr.”. Some people become upset if you call them “Mr.” (or “Ms.”) instead of “Dr.”, but I generally try not to make too much of this. In academic settings, I think a good rule is that people who do not hold the degree, or colleagues in formal settings, should address those with the degree by their official title of “Dr.”. On the other hand, in informal settings with colleagues who hold the same title, or with students with whom one is familiar (e.g., graduate students in one’s own group), using the title simply becomes awkward and first names are appropriate. I will admit that it did take me some time to get used to calling my advisors by their first names, and I have since observed this in several of my students. Outside of academic settings, I generally don’t correct people if they call me “Mr.”, and I don’t introduce myself with the title. I believe most of my colleagues take a similar approach, though of course there is some variation.

Two recent discussions on science blogs have prompted this post, in case you were curious as to why I was bothering to tell you this. Both relate to what I am calling the “Dr. Credibility principle”, which is an attempt to gain undeserved credibility simply through invoking the title.

The first is the example of Dr. Sharon Moalem, author of the book Survival of the Sickest. It appears Dr. Moalem has been misrepresenting his credentials, making it seem as though he has obtained a medical degree, when in fact he has not (though he his a med student). PZ Myers has already discussed the book, which seems to be largely based on non-scientific and pseudoscientific arguments. I had a feeling that this would be so right away. Why? Because he used the title “Dr.” on the cover.

You see, scientists almost never use the prefix “Dr.” on their book covers. It doesn’t matter if it is a popular book or a technical one. If you have science books, go see for yourself. We just don’t do it. In fact, I am willing to extend the “Dr. Credibility principle” to claim that whenever you see someone making a big deal out of their title, especially on a book cover, you can usually bet it is because the content of the book cannot stand on its own without a deflecting appeal to authority. Yet, as noted, those with real authority, and because of whom the title has some prestige, do not use it in that way.

The second case is the Discovery Institute’s public relations gimmick of having “scientists” sign the following “Dissent from Darwinism” statement:

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

As I tell my students, this is so benign that I could easily sign it, and I suspect any biologist could. I too am skeptical of claims that random mutation and natural selection account for everything. And careful examination of the evidence should be encouraged in all sciences, always. Nevertheless, as John Lynch has demonstrated, people with qualifications in evolutionary biology don’t sign this list because it is obviously intended to confuse the uninitiated.

Compare this with a statement that many biologists (though only those with the name Steve or its derivatives) are only too happy to put their names on:

Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to “intelligent design,” to be introduced into the science curricula of our nation’s public schools.

The Discovery Institute has managed to find only 700 signatories since 2001. The NCSE’s list, which is meant only as a parody, has 860 Steves.

Most of the individuals who have signed the Discovery Institute’s list have degrees in engineering (see the Salem conjecture), chemistry, physics, or computer science, though several at least have biological training, albeit in physiology or molecular biology. Some of them are not scientists of any sort. The only unifying feature appears to be that they hold a Ph.D. in something. Once again, it’s the “Dr. Credibility principle”: If one has the title, one must be an authority on the issue under discussion.

The Dr. Credibility principle finds it most extraordinary application in the Orwellian-entitled Physicians and Surgeons for Scientific Integrity. Who can join, you ask? “Any person with an M.D., D. O., D.D.S., D.M.D., D.V.M. or equivalent degree may become a physician/surgeon member of PSSI”. Personally, I don’t think anyone should take a medical doctor, dentist, or veterinarian as an authority on biology any more than they should let biologists like me prescribe drugs or perform a root canal. The only possible explanation is that this is another misguided appeal to authority. Unfortunately, many people are liable to buy into it, especially in groups like anti-evolutionists, where authority seems to trump data regularly.

Let me say it clearly. Having the title “Dr.” does not make anyone an authority on anything except, one would hope, the field in which they obtained a degree. Anything else is just playing doctor to gain undue credibility.


Almost the entire genome is made up of protein-coding genes*.

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*In bacteria.

But seriously, don’t you hate it when you read a headline that makes some intriguing claim that you think is about humans, only to discover that the research in question was based on mice, or yeast, or a computer simulation?

________

Update:

Here is a good example.

Aggression As Rewarding As Sex, Food And Drugs, New Research Shows

New research from Vanderbilt University shows for the first time that the brain processes aggression as a reward – much like sex, food and drugs – offering insights into our propensity to fight and our fascination with violent sports like boxing and football.

The study was based on mice.


The Moral Instinct by Steven Pinker in the New York Times.

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In my experience in dealing with anti-evolutionists, the fundamental motivation for dismissing evolution is not its adverse implications for religion itself (real or imagined, depending on your view), but the sense (definitely imagined) that accepting evolution subverts any basis for morality. One can go around and around with an anti-evolutionist only to discover in the end that he or she is really arguing from a moral perspective: “A naturalistic approach cannot show why it is absolutely wrong to kill someone, only divine moral laws can, thus evolution is unacceptable and hence incorrect.”

In this regard, it was with much interest that I read the piece by Steven Pinker in the New York Times on The Moral Instinct.

Now, I am not a major advocate of evolutionary psychology. Many of the “just-so stories” that come out of that circle make me either roll my eyes or cringe, depending on the usually overblown ratio of strength-of-claim to quantity-of-data. On the other hand, I would not argue that the human brain and the behaviours it exhibits are somehow exempt from the evolutionary processes that apply to every other organ in every other living species. However, that is not to say that all behaviours are adaptive — far from it. I suspect that some behaviours are (or were) adaptive, and some are not and never were.

Speaking specifically of innate human behaviours that are (or were) adaptive, I prefer to think of them as a series of “rules” or “guidelines” that are supplemented by details from culture. Nature via nurture. Language is a good example, and one that I use with students. The ability to learn a language is innate. Which language one learns is cultural. These are inseparable.

I have long thought that morality is rather similar. There is an innate moral compass that all normal humans possess (e.g., “the golden rule”, known to biologists as the basis of reciprocal altruism), but many of the specifics of what constitutes “good” versus “bad” are filled in by culture. Pinker takes a similar view, although he (I think correctly) distinguishes between societal conventions and moral principles, the former of which are especially culturally malleable. He also notes five basic themes that comprise the moral sense: harm, fairness, community (or group loyalty), authority, and purity (see also Haidt 2007). The proportions and expressions of these may vary among cultures, but they are universally identifiable in human beings. I quite like this formulation as a useful way to think about the differences and unities in moral judgments among people.

Finally, and perhaps most importantly, Pinker points out that studying and even explaining morality does not destroy it: if anything, it may help us to behave morally in a more effective way by adding some rationality to the equation.

The article is excellent, and I recommend it very highly.


Huckabee is right for all the wrong reasons.

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Over at Pharyngula, PZ points to an interview with former Arkansas Governor and presidential hopeful Mike Huckabee. As a Canadian, I have long been amused by Huckabee for reasons you can see here. The prospect of this guy becoming president is unnerving, but then so is the fact that our neighbours saw fit to elect (or at least, not not-elect) Bush. Twice.

Here is what Huckabee has to say about evolution. I have omitted the bit about teaching non-scientific alternatives in science class that preceded it, because it’s too silly to repeat (he says “all views”, but presumably he means “one other view” only).

Because, frankly, Darwinism is not an established scientific fact. It is a theory of evolution, that’s why it’s called the theory of evolution.

He’s right. “Darwinism” — a term used mostly by creationists, but also historically (e.g., Wallace) and to an extent today (e.g., Dawkins), especially in Britain — refers to natural selection as a mechanism of evolution. And it is a theory. In science, a theory is an explanation for an observed or inferred condition of the natural world that is well established through multiple lines of empirical evidence (i.e., a fact). Darwin’s theory of natural selection is one explanation for the fact that species are related through descent, which in turn has been well established in science for well over a century on the basis of fossils, biogeography, embryology, morphology, and genetics. Darwinian natural selection is not the only available explanation, and therefore represents a subset of modern evolutionary theory. That natural selection happens is an established fact (witness antibiotic resistance), but what its role is in causing large-scale evolution remains a subject of discussion among biologists.

So “Darwinism,” in the sense of meaning that the majority of evolution occurs via natural selection, is indeed not an established fact, it is a theory. Huckabee’s words are correct, even if his intent is terribly muddled. Scientific theories explain facts. If there is no established fact, then there is no theory needed.

I invite Gov. Huckabee to read more about this in a recent paper that is freely available here.


Is most of the human genome functional?

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I first became interested in genome size because of its tie-ins with important evolutionary questions in which I was (and still am) interested, such as punctuated vs. gradual patterns, levels of selection, and adaptive vs. non-adaptive processes. What I didn’t realize was that one component of the question, the quantity of DNA that is non-functional (but not necessarily inconsequential) with regard to the phenotype of the organism, is such a hot-button issue. I had vague inklings at first that young-earth creationists would object to the idea of non-functional DNA — because God, as they say, don’t make no junk. (Why intelligent design proponents, who purport to take a strictly scientific view of the question, also assume that non-coding DNA cannot be non-functional remains unstated). And of course there has always been a persistent undertone in biology that non-coding DNA must be doing something or it would have been deleted. This latter view, which derives directly from a hardcore adaptationist approach, destroys the argument by creationists that “Darwinism” has prevented researchers from considering functions for non-coding DNA. Indeed, the main motivation for the early papers on “selfish DNA” was to counter this adaptationist assumption (Doolittle and Sapienza 1980).

Creationist nonsense about DNA does not surprise me. What has intrigued me much more is the debate among biologists about this, and the rather questionable claims, suppositions, and extrapolations that get made not just by the media but by various scientists themselves.

Take Francis Collins. He’s a major player in genome biology and led the charge by the public Human Genome Project. And yet, he makes claims that non-coding DNA may be present in the genome “just in case” it needs to be put to use in the future. This makes no sense from an evolutionary perspective. It would be tempting to attribute this to Collins’s adherence to the notion of theistic evolution, but in fact one can find this sort of fuzzy foresight argument being brought up by lots of authors. I suppose it’s just disappointing that there is not better communication between genome biology and evolutionary biology.

The case that frustrates me most is that of John Mattick. He of the worst figure ever is one of the primary promulgators of the view that scientists have overlooked possible function for non-coding DNA and that this is “one of the biggest mistakes in the history of molecular biology” that can only be corrected by a “new paradigm”, and so on. Basically, the argument seems to be that much of the non-coding portion of a given genome is involved in regulation and such. In the past, Mattick has refrained from pinning down an estimate of how much non-coding DNA he believes is functional, but his presentation of (extremely selective) data left little doubt that he considers more non-coding DNA to be correlated with greater complexity. But now we’re starting to get some more explicit and increasingly bold claims.

As Check (2007) pointed out in a news article in Nature,

Mattick thinks scientists are vastly underestimating how much of the genome is functional. He and Birney have placed a bet on the question. Mattick thinks at least 20% of possible functional elements in our genome will eventually be proven useful. Birney thinks fewer are functional.

Now consider this quote by Comings (1972), who was the first person to use the term “junk DNA” extensively (even before Ohno’s (1972) coinage appeared in print):

These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.

So, even if Mattick is right about 20% of the human genome being functional, which is considered a rather high estimate on the basis of available data, he still would be merely agreeing with the author of the first major discussion about junk DNA.

Now, I should point out that I do not have a vested interest in how much of the human genome is functional. 5%? Fine. 20%? Fine. 50%? Ok. I will go where the data indicate. My reason for rejecting the notion of “more complexity means more DNA” is comparative: I refer you to the “onion test” for a simple illustration. However, as readers of Genomicron already know, I find it rather irksome when people take any new finding about (potential) function in some part of the human genome and extrapolate this to mean that all DNA in every genome must be serving some role.

Anyway, back to what Mattick suggests. As noted, for the most part he has gone about arguing for large-scale function more by hint than by direct claim. However, finally he says the following (Phaesant and Mattick 2007).

Thus, although admittedly on the basis of as yet limited evidence, it is quite plausible that many, if not the majority, of the expressed transcripts are functional and that a major component of genomic information is rapidly evolving regulatory DNA and RNA. Consequently, it is possible that much if not most of the human genome may be functional. This possibility cannot be ruled out on the available evidence, either from conservation analysis or from genetic studies, but does challenge current conceptions of the extent of functionality of the human genome and the nature of the genetic programming of humans and other complex organisms. [Emphasis added]

It seems to me that “we can’t rule this out” is not a reason to think that something is plausible, let alone true. In fact, the existence of mechanisms such as transposable element spread and the pseudogenization of duplicate genes suggests that there is good reason to expect much (probably most) of the genome to be non-functional unless data show otherwise. Some TEs have taken on a function, some cause disease, some are merely benign or only slightly detrimental. The proportions of non-coding elements in each of these categories remain to be determined, but they are not all equally likely by default.

The question of which sequences are functional, and in what way, is one of the more contentious and therefore interesting ones in genome biology. On the one hand, new information from various sources including the ENCODE project indicates that much non-coding is transcribed, though it remains an open question whether this has to do with function or noise. On the other hand, a recent analysis has suggested that as many as 4,000 sequences within the human genome initially thought to be genes are not really genes after all (Clamp et al. 2007), bringing the total count down to around 20,000.

Some people, mostly creationists and strict adaptationists (strange bedfellows, I agree) desperately want the vast non-coding majority of eukaryote DNA to have a function. They latch onto any new discovery of function in some segment of the genome or another (or indeed, any mere restatement of what many authors have been saying since the 1970s) and consider their position supported. The rest of us will just have to wait and see.

________________

References

Check, E. (2007). Genome project turns up evolutionary surprises. Nature 447: 760-761.

Clamp, M., B. Fry, M. Kamal, X. Xie, J. Cuff, M.F. Lin, M. Kellis, K. Lindblad-Toh, and E.S. Lander (2007). Distinguishing protein-coding and noncoding genes in the human genome. Proceedings of the National Academy of Sciences USA 104: 19428-19433.

Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.

Doolittle, W.F. and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.

Ohno, S. 1972. So much “junk” DNA in our genome. In Evolution of Genetic Systems (ed. H.H. Smith), pp. 366-370. Gordon and Breach, New York.

Phaesant, M. and J.S. Mattick (2007). Raising the estimate of functional human sequences. Genome Research 17: 1245-1253.


News stories of interest.

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In keeping with my recent minimalist approach to the blog, here are some links to stories by others that I think you may find interesting.

US ‘doomed’ if creationist president elected: scientists (PhysOrg)

I think this is a great line:

“The logic that convinces us that evolution is a fact is the same logic we use to say smoking is hazardous to your health or we have serious energy policy issues because of global warming,” University of Michigan professor Gilbert Omenn told reporters at the launch of a book on evolution by the National Academy of Sciences (NAS).

Evolutionary idea
Scientists rally to explain and defend the cornerstone of biological study
(Houston Chronicle)

An interesting piece (especially given the venue), and I am happy to say that it makes a note of the new journal Evolution: Education and Outreach, which I hope you’re all planning to read.