Recently in Junk DNA Category

junk_DNA_front.pngThe SMBE meeting is coming up next week in Chicago, and I am going for the first time, in part to present some of my work combining fossils and molecular data in Bayesian dating analyses*, and partially because I wanted to see the junk DNA symposium in person: http://smbe2013.org/2013/Scientific[…]ymposia.aspx

Note: I am extremely busy this summer, finishing grad school and moving to a postdoc. But when I got this book, I realized I wouldn’t be able to focus on my real work without having gotten my 2 cents in. This is a rough-and-ready piece, so typos and missing references, and missing explanations of technical terms are to be expected, although I’m sure they can all be figured out with a wee bit of googling. I am off to Evolution 2013 tomorrow and will be incognito, writing, after that. So I may not comment much. However I expect commenters to be reasonable discussants and polite and will ban people who break the spirit of this expectation. Cheers, Nick

Review of Stephen C. Meyer’s Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design

This week, a new book came out by Stephen Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. Having followed the ID movement and specifically its arguments on the Cambrian ‘Explosion’ for a long time, as well being somewhat up on the recent literature, and especially on phylogenetics, I feel that I have a pretty good sense of what to look for in any work purporting to be a capable commentary on the topic. As I read through Meyer’s book, though, in case after case I see misunderstandings, superficial treatment of key issues which are devastating to his thesis once understood, and complete or near-complete omission of information that any non-expert reader would need to have to make an accurate assessment of Meyer’s arguments.

Junk in the Trunk

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Sadly I don’t have time for a full blog, but PT readers should read a caustic paper by Dan Graur et al. (Graur of chicken entrails fame), which is doing the most thorough take-down to date of the ENCODE project’s widely-advertised claim last year that 80% of the human genome is functional and that the junk DNA concept has been debunked. It’s open access, and the media is starting to pick it up: http://gbe.oxfordjournals.org/conte[…]ull.pdf+html

The major weakness is that Graur et al. do not discuss the huge variability in eukaryote genome size much, although they do cite Ryan Gregory’s Onion Test. And the tone is such that tone itself is becoming an issue. On the other hand, many of us feel that ENCODE steamrolled basic, well-known scientific facts when it shot the “80% functional” claim around the world’s media. Certainly there’s a lot to discuss!

The ENCODE delusion

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I can take it no more. I wanted to dig deeper into the good stuff done by the ENCODE consortium, and have been working my way through some of the papers (not an easy thing, either: I have a very high workload this term), but then I saw this declaration from the Electronic Frontier Foundation.

On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California's warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.

The science media exploded today with the claim from the ENCODE project that 80% of the genome is “functional”. The creationists are already beside themselves with joy. And the problem cannot be blamed on the science media, although I wish they were quicker to exercise independent skepticism – the 80% claim is right there in the abstract of the Nature article.

However, skepticism has arisen spontaneously from all over the scientific blogosphere, facebook, and twitter. You see, most of us scientists know that (a) ENCODE is using an extremely liberal and dubious definition of “function”, basically meaning “some detectable chemical activity”. People have pointed out that randomly generated DNA sequences would often be “functional” on this definition. (b) All the evidence for relative nonfunctionality which has been known for decades is still there and hasn’t really changed – lack of conservation, onion test, etc. But I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative biology.

Anyway, I’d write more, but I’m jammed and Ryan Gregory has said everything I would say, except better: http://www.genomicron.evolverzone.c[…]encode-hype/

See also Larry Moran: http://sandwalk.blogspot.com/2012/0[…]-of-our.html, especially the rather wry comments.

Hashtag: #oniontest

ResearchBlogging.org“The Selfish Gene.” “Selfish DNA.” Oh, how such phrases can get people bent out of shape.  Stephen Jay Gould hated such talk (see a little book called The Panda’s Thumb), and Richard Dawkins devoted more time to answering critics of his use of the term ‘selfish’ than should have been necessary. Dawkins’ thesis was pretty straightforward, and he provided real examples of “selfish” behavior of genes in both The Selfish Gene and its superior sequel, The Extended Phenotype. But there have always been critics who can’t abide the notion of a gene behaving badly.

Leaving aside silly bickering about the attribution of selfishness or moral competence to little pieces of DNA, let’s consider what we might mean if we tried to imagine a really selfish piece of DNA. I mean a completely self-centered, utterly narcissistic little piece of DNA, one that not only seeks its own interest but does so with rampant disregard for other pieces of DNA and even for the organism in which it travels. Can we imagine, for example, a piece of DNA that deliberately harms its host in order to propagate itself?

How to afford a big sloppy genome

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Blogging on Peer-Reviewed Research

My direct experience with prokaryotes is sadly limited — while our entire lives and environment are profoundly shaped by the activity of bacteria, we rarely actually see the little guys. The closest I've come was some years ago, when I was doing work on grasshopper embryos, and sterile technique was a pressing concern. The work was done under a hood that we regularly hosed down with 95% alcohol, we'd extract embryos from their eggs, and we'd keep them alive for hours to days in tissue culture medium — a rich soup of nutrients that was also a ripe environment for bacterial growth. I was looking at the development of neurons, so I'd put the embryo under a high-powered lens of a microscope equipped with differential interference contrast optics, and the sheet of grasshopper neurons would look like a giant's causeway, a field of tightly packed rounded boulders. I was watching processes emerging and growing from the cells, so I needed good crisp optics and a specimen that would thrive healthily for a good long period of time.

It was a bad sign when bacteria would begin to grow in the embryo. They were visible like grains of rice among the ripe watermelons of the cells I was interested in, and when I spotted them I knew my viewing time was limited: they didn't obscure much directly, but soon enough the medium would be getting cloudy and worse, grasshopper hemocytes (their immune cells) would emerge and do their amoeboid oozing all over the field, engulfing the nasty bacteria but also obscuring my view.

What was striking, though, was the disparity in size. Prokaryotic bacteria are tiny, so small they nestled in the little nooks between the hopper cells; it was like the opening to Star Wars, with the tiny little rebel corvette dwarfed by the massive eukaryotic embryonic cells that loomed vastly in the microscope, like the imperial star destroyer that just kept coming and totally overbearing the smaller targets. And the totality of the embryo itself — that's no moon. It's a multicellular organism.

Junk DNA is still junk

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Blogging on Peer-Reviewed Research

The ENCODE project made a big splash a couple of years ago — it is a huge project to not only ask what the sequence of a strand of human DNA was, but to analyzed and annotate and try to figure out what it was doing. One of the very surprising results was that in the sections of DNA analyzed, almost all of the DNA was transcribed into RNA, which sent the creationists and the popular press into unwarranted flutters of excitement that maybe all that junk DNA wasn't junk at all, if enzymes were busy copying it into RNA. This was an erroneous assumption; as John Timmer pointed out, the genome is a noisy place, and coupled with the observations that the transcripts were not evolutionarily conserved, it suggested that these were non-functional transcripts.

Of late the IDists have been complaining about the dearth of reviews by ID skeptics of Stephen Meyer’s book Signature in the Cell. I agree, it would be nice if there were more reviews out there, but (a) the arguments boil down to the same old fallacious “improbability of assembly of functional sequence all at once from scratch by brute chance” creationist argument that dates back to at least the 1960s creation science literature, and (b) the book is tedious and repetitive, basically making the same unsupported assertions again and again in slightly different ways. I.e. information comes from intelligence and is too improbable to explain by chance, therefore intelligence! The actual known origin of the vast majority of genetic “information” – DNA duplication followed by mutation and selection is (1) almost completely ignored by Meyer and (2) directly refutes Meyer’s key claim, which is that the only known explanation of new information is intelligence. So in one sense, there is not a heck of a lot to review in Meyer’s book. If you are a sufficient wonk about the ID debate, there is some interesting stuff about Meyer’s highly revisionist account of his own history and the history of the ID movement, and there is an interesting study to be made of the science that Meyer left out of his book, but that makes for a big project, so it will be awhile before I or someone else get it out there.

But, while reading across the book, you do occasionally come across some examples of truly bizarre argumentation. Here an example which I just posted in response to a Telic Thoughts challenge:

By Don Prothero http://faculty.oxy.edu/prothero/index.htm

Don Prothero is a paleontologist and Professor of Geology at Occidental College in Los Angeles, and Lecturer in Geobiology at the California Institute of Technology in Pasadena, and author of Evolution: What the Fossils Say and Why it Matters, in my opinion the very best book on fossils and evolution for the general reader. Last night, Monday, November 30, Prothero debated (along with Michael Shermer) ID advocates Stephen Meyer (longtime head of the Discovery Institute’s Center for the Renewal of Science and Culture) and Richard von Sternberg (the former editor who in 2004 published Meyer’s pro-ID article in the last issue of the Proceedings of the Biological Society of Washington (D.C.) which Sternberg was scheduled to edit, despite the article being wildly off-topic for an alpha taxonomy journal, substantially copied from other Meyer publications, badly inaccurate, and just weird in several ways). Sternberg is now, I believe, an employee of the Discovery Institute.

Prothero wrote these remarks directly after the debate and emailed them to me. I have added links where relevant. — Nick Matzke

My mind is a bit fuzzy from the loss of sleep, and the two hours of “debate” went by very quickly, so I cannot recall all the details, let alone recount them. Here are my morning-after thoughts about last night’s “Battle in Beverly Hills.” I don’t know when they’ll release the video recording of the event, but when it does come out, hopefully it will be possible to post it so you can all see for yourself how it went. My subjective summary of it is that our side did very well: I caught them off-guard with new arguments they had no answer for; Shermer pushed them hard repeatedly to state who the “Designer” was (and Meyer finally conceded it was God), while we both pushed them hard on the fact that neither of them ever addressed the topic of the debate, “Origins of Life.” I could tell that they were rattled a number of times, and I definitely shook up Meyer and got under his skin with my answers. Several times Meyer and Sternberg were arguing with each other, leaving the moderator, our side, and the audience wondering who runs their show. The best sign of my effect on them was Meyer trying to challenge MY credentials, or dodging a tough question by playing the sympathy card and calling me “condescending” — and the virulent post on the Discovery Institute site this morning, full of lies and spin. Of course, the event is staged so that no one will really “win”. Their supporters turned out and dominated the audience, but I had a LOT of people come up to me during the book signing (we sold a LOT of books) and congratulate me, or discuss points further with me. And we got just as much applause and sympathetic laughter at our well-turned phrases as they did.

Hunter vs. Hunt on Turf-13

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As a last treat for the 150th anniversary of the Origin, have a look at young-earth creationist creationist Cornelius Hunter [Update: Hunter has stated he is not a young-earth creationist on his blog, so I guess he’s not, although that position directly follows from his stated theology/philosophy], author of the “Darwin’s God” book and blog. Hunter’s basic argument against virtually any common pro-evolution argument is, basically, “But you evolutionists are claiming that God wouldn’t have done it this way! You’re making an unscientific theological argument!”

In previous essays (here and here), we learned that genes encoding new proteins can and do, often, arise de novo in the course of evolution, contradicting one of the central tenets of ID proponents. The means by which these genes arise are many. One of these, suggested by Cai at al. (the subject of one of the earlier essays), involved the adaptation of a gene encoding an evolutionarily-conserved non-coding RNA via the appearance, by mutation, of appropriate translation initiation and termination (“start” and “stop”) codons. This mechanism represents an intersection of sorts between the subject of protein evolution and another matter of discussion on these blogs, namely the existence, evolution, and “function” of junk DNA. In this essay, I review a 2007 study by Debrah Thompson and Roy Parker (“Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae”, Mol. Cell. Biol. 27, 92-101) that adds a great deal of clarity to this mode of gene and protein evolution.

Junk to the second power

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The ID blogosphere is much agog, and has been for some time, about recent (and not so recent) results that suggest some sort of functionality in what has long considered to be nonfunctional (junk) DNA in eukaryotes. The most recent buzz centers on studies (such as ENCODE ) that indicate that large swaths of so-called junk DNA are “expressed” by RNA polymerase II. Apparently, the fact that RNA polymerase transcribes alleged junk DNA is a blow to Darwinism, and a feather in the cap of ID. Their excitement in this regard, I suspect, will wane greatly once they learn some of the true implications of these results. For the matter of “expression” in junk DNA is one wherein ID meets, and gets swallowed by, the Garbage Disposal.

What follows is a discussion of a relatively recent report that rains on the ID parade. As is my habit, I’ll summarize the essay for those with short attention spans – the bottom line is that the so-called “function” that so excites the ID proponents may be little more than manifestations of quality control in gene expression, and that the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase). In a nutshell, junk piled on top of junk.

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