The tale of the Matrix Beetle.

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Gather ’round, and I will tell you the tale of the Matrix Beetle.

It began in England — London, to be precise — during the second half of my two-year NSERC postdoc. I had spent the first year in New York at the incredible American Museum of Natural History, and decided to spend the second in the UK at the equally remarkable Natural History Museum. Time well spent in both cases. In London, I joined the lab of Alfried Vogler, an expert on tiger beetles, accomplished molecular systematist, and all-around excellent person. Alfried is, like many of my colleagues, interested in the applications of molecular tools to the problem of identifying the probable 10 million species on the planet. He takes it a step farther in some cases and would like to see a “DNA taxonomy” and not just “DNA barcoding” (there is a big difference, folks), but the basic point remains that he is interested in exploring how modern genetic methods can inform the identification of life.

Every Friday at the NHM, people would gather for inexpensive (by UK standards), though certainly not cheap, beer; it was here that I discovered Leffe, which, to my delight, is also available in Canada (at the LCBO, not the Beer Store, in case you’re looking for it in Ontario). One evening whilst enjoying said brew, Alfried remarked that someone in the lab had shown him a DNA sequence that morning, and that he had looked at it and said “That’s not from a tiger beetle”. He then noted — jokingly, of course — that if he had seen the real beetle he may not have been so sure. “What are you, like the Matrix?,” I snorted, “You just see DNA sequences raining down all over?”.

Deciding to follow up on this amusing notion, I created an image of a tiger beetle as seen in a Matrix world of DNA sequences. I put this on the computers in the lab, and hilarity ensued. Someone joked that it would be funny if we managed to get that on a journal cover. I agreed, but left it at that.

For those of you who follow the literature, you’ll know that there is a vocal opposition to DNA barcoding. Most of this comes from (some) taxonomists who see barcoding as a threat to their discipline. A debate on this issue was held at the PEET meeting in 2004 (watch the video), with a follow-up “discussion” to be held in the pages of Systematic Biology. By this time, I was back in Guelph, and Paul Hebert and I were neck deep in writing a multi million dollar Genome Canada grant (which, incidentally, took exactly $0.00 from the pockets of taxonomists and delivered a sizable chunk of funds to many non-molecular types). As a result, Paul was regretfully planning to withdraw from submitting his paper to the journal issue. I thought this would be a mistake, busy though he was, because it would have let the anti-barcoding side have the only word. We agreed to work on the paper together, which consisted of answering a series of questions that had arisen from the PEET meeting.

When the papers were accepted, the journal editors asked if anyone had ideas for a cover image. On a lark, I sent in the “Matrix Beetle” — and they wanted it.

And so, from the beer gardens of the NHM to the cover of Systematic Biology Volume 54 Number 5, I give you… the Matrix Beetle:

Cover Illustration: The recent proposal to use short, standardized gene sequences as unique identifiers of species – known as DN barcoding – has generated both strong support and vocal opposition in certain biological circles. The potential impact of DNA barcoding as either a help or a hindrance to taxonomic research represents an especially polarizing point of contention. A debate on the issues of DNA barcoding was held at the fifth biennial conference of the Partnerships for Enhancing Expertise in Taxonomy (PEET) in September 2004 at the University of Illinois at Urbana-Champaign. The debate was moderated by Vincent Smith, and involved Paul Hebert, the lead proponent of DNA barcoding, and Kipling Will, a vocal barcoding opponent. As a follow up to this debate, two contrasting position papers dealing with DNA barcoding are provided in this issue, moderated once again by a contribution from Smith. On the pro-barcoding side, Hebert and Gregory outline what they consider to be the beneficial aspects of DNA barcoding for taxonomy and other biological disciplines, where as Will et al. provide an opposing perspective in which they argue that DNA barcoding will be detrimental to taxonomic science. Neither set of authors has been permitted to read the others’ contribution prior to publication. Image © 2005 by T. Ryan Gregory.

Discovery wants to "demote" fungi.

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Here’s an interesting story from the Discovery Channel.

Plants and animals: long lost relatives?

“Yes,” I know you’re thinking, “next question?”.

But wait, the story takes a different approach.

Plants and animals may occupy distinct branches on the tree of life, but they could be more alike than we think.

In fact, green plants and animals enjoy a relatively close evolutionary relationship that has been obscured by a narrow focus on DNA sequences to find relatedness, says biologist John Stiller of East Carolina University.

Plants, fungi and animals are all in a group called the eukaryotes — distinguished by their advanced cellular machinery. But some eukaryotes, most notably the fungi, have long been considered more closely related to animals than plants are.

Stiller’s theory suggests organisms such as fungi should be given a demotion — placed further from animals on the tree — while green plants should get a leg up.

Say again???

Another attribute shared by plants and animals, according to Stiller, is the way the genetic material RNA operates in both groups. In both plants and animals, RNA acts as an intermediary between DNA and the protein it codes for. The enzymes that put RNA to work in a cell are similar in plants and animals, but not present in fungi or other organisms, he said.

It is, of course, utterly inconceivable that the common ancestor to all three groups had this trait which was then lost in fungi. Because fungi are, of course, not a derived group that has been evolving for exactly the same amount of time as plants and animals by definition. Oh no.

Maybe the paper makes a good argument. Maybe plants and animals are sister taxa to the exclusion of fungi. But one thing’s for sure — no one’s getting “demoted” one way or another because this idea of rank was should have been abandoned 150 years ago.

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Update:

See Sex, Genes & Evolution for more insights on the actual hypothesis, which should not be judged on the basis of how it was reported in the press.


Proof that introns are functional… come again?

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I use Google Reader to aggregate not just blogs but science news, journal contents, and index searches. The feed for my weekly PubMed search turned up a real doozy. The record had been deleted by the time I got to PubMed, although I did manage to track it down.

Check this one out, it’s the zaniest abstract I have seen in some time:

The Genomic Structure: Proof of the Role of Non-Coding DNA
Bouaynaya, N. Schonfeld, D.

Engineering in Medicine and Biology Society, 2006. EMBS ’06. 28th Annual International Conference of the IEEE, Aug. 2006, pp. 4544-4547.

We prove that the introns play the role of a decoy in absorbing mutations in the same way hollow uninhabited structures are used by the military to protect important installations. Our approach is based on a probability of error analysis, where errors are mutations which occur in the exon sequences. We derive the optimal exon length distribution, which minimizes the probability of error in the genome. Furthermore, to understand how can Nature generate the optimal distribution, we propose a diffusive random walk model for exon generation throughout evolution. This model results in an alpha stable exon length distribution, which is asymptotically equivalent to the optimal distribution. Experimental results show that both distributions accurately fit the real data. Given that introns also drive biological evolution by increasing the rate of unequal crossover between genes, we conclude that the role of introns is to maintain a genius balance between stability and adaptability in eukaryotic genomes. (Emphasis added, in case that didn’t leap out at you already).

There you have it. Introns are ingenious decoy targets, and some fancy math PROVED it. As if a few pages of equations weren’t enough, they even provided a basic analysis of exon sizes in three species — and one wasn’t even a mammal. Sadly, no Dappers though.


Dog’s Ass Plots (DAPs).

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The word logodaedaly means “a capricious coinage of words”. It was coined by Plato in the 4th century BC (as “wordsmith”) and picked up by Ben Johnson in 1611 in its current English usage. That’s right, someone coined a term for the process of coining terms.

Sometimes new terms are very useful. Every profession has its own jargon, which for the most part helps experts to save time by having individual terms for specific items or ideas. On the other hand, the original meaning can be lost and the term can be badly misunderstood or misapplied when it moves from jargon to buzzword. “Junk DNA” is a case in point. Other terms may be coined to give a simple summary of a more complex idea. “The Onion Test” is an example: it’s not really about onions, but about providing a reminder that there is more diversity out there than one might otherwise have considered.

Finally, sometimes terms are coined just for fun. This is one of those times.

Several bloggers have drawn attention to the persistent assumption expressed by some authors that humans are the pinnacle of biological complexity, as reflected in certain graphical representations relating to non-coding DNA [Pharyngula, Sandwalk, Sunclipse, Genomicron]. Larry Moran’s discussion pointed to what must be the single worst figure of the genre, from an article in Scientific American. This figure forms the basis of a new term that I wish to coin.

Here is the figure in question:



In a previous post, I complained about the ridiculous division of groups (humans are vertebrates and vertebrates are chordates), the lack of labels on the X-axis, the ambiguous definition of “complexity” implied, and the blatant assumption, sans justification, that humans are the most complex organisms around.

I also noted the following issue:

The sloping of the bars within taxa suggests that this is meant to imply a relationship between genome size and complexity within groups as well, with the largest genomes (i.e., the most non-coding DNA) found in the most complex organisms. This would negate the goal of placing humans at the extreme, as our genome is average for a mammal and at the lower end of the vertebrate spectrum (some salamanders have 20x more DNA than humans). Indeed, the human datum would accurately be placed roughly below the dog’s ass in this figure if it included a proper sampling of diversity.

As a result, I hereby propose that all such figures, with unlabeled axes and clear yet unjustified assumptions about complexity, henceforth be dubbed “Dog’s Ass Plots”. “DAPs” or “Dappers” also are acceptable, as in “I’m surprised that the reviewers didn’t pick up on this DAP” or “Check out this figure, it’s a real Dapper”. (As an added bonus, “dapper” means “neat and trim” — which these figures certainly are; the problem is not that they don’t look slick, it’s that they are oversimplified).

I have no doubt that plenty of examples can be found in subjects besides genomics, so please feel free to use it as needed in your own field.



Worst figure of all.

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Larry Moran has provided a good discussion of complexity and genome size, and of the confusions that surround their relationship — rather, their lack of a relationship — to one another [Genome size, complexity, and the C-value paradox]. He links to my earlier story about figures that provide a misleading suggestion of a link between complexity and genome size, and in the process he tops the figure I mentioned [What’s wrong with this figure? see also Genome size and gene number]. In fact, the one he notes is easily the worst one I have ever seen like this, for all kinds of reasons. It is from a 2004 article in Scientific American by John Mattick entitled The hidden genetic program of complex organisms.

Where does one begin? For one thing, humans are vertebrates and vertebrates are chordates, so this is just downright ridiculous. “Invertebrates” is paraphyletic as echinoderms are more closely allied to vertebrates than to other non-vertebrate animals. Some fungi are single-celled, and some people consider unicellular algae to be plants. The X-axis in these figures is never labeled, but the obvious implication is that it represents an increasing scale of “complexity”. It is probably unlabeled because otherwise one would have to provide units of complexity, and I doubt that would be straightforward at all. It certainly would be a challenge to justify ranking humans as more complex than dogs — I can not think of any way that one could defend such a position objectively. The sloping of the bars within taxa suggests that this is meant to imply a relationship between genome size and complexity within groups as well, with the largest genomes (i.e., the most non-coding DNA) found in the most complex organisms. This would negate the goal of placing humans at the extreme, as our genome is average for a mammal and at the lower end of the vertebrate spectrum (some salamanders have 20x more DNA than humans). Indeed, the human datum would accurately be placed roughly below the dog’s ass in this figure if it included a proper sampling of diversity.

__________

Updates:

  • An astute, anonymous, commenter has pointed out a further distortion, namely that the disparate heights of the various organisms causes the eye to artificially exaggerate the differences among the bars.
  • This figure has led to the coining of a new term .


Global warming: how do scientists know they’re not wrong?

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Back in July, LiveScience ran a piece by Andrea Thompson entitled Global warming: how do scientists know they’re not wrong? Although one could argue that there is too much straining to seem “balanced” (the two deniers quoted receive a vastly disproportionate bit of page space relative to the consensus in science), it is generally a very interesting look at how science deals with politically controversial areas of inquiry, particularly when they involve questions that are not easily amenable to laboratory experimentation or direct observation or which involve extrapolation from available, smaller-scale observations. The parallels with evolution are clear. The lesson: science operates according to a set of principles, and if you reject those principles because some of the conclusions they produce are distasteful to you, you may do so at your own (and everyone else’s) peril.


Mus aureus!

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Bertalan Meskó of ScienceRoll, fellow DNA Network member and founder of the Gene Genie carnival, has very graciously awarded Genomicron the “Golden Mouse Award”. As he says,

This is the second time I present the Golden Mouse Award to a blogger. From time to time, I’ll present this award to bloggers who educate people in high quality and write hardcore scientific/medical articles with plenty of references, so to bloggers who make science or medicine more readable for laypeople and for even specialists. Now, the winner is T. Ryan Gregory of Genomicron who proved his enthusiasm and professionalism with posts like these:

What can I say? I’m flattered!

(Yes, I know the golden mouse is Ochrotomys nuttalli and there is no Mus aureus — I was being clever.)


Genome Technology Online is confused.

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From Genome Technology Online:

Perhaps They Should’ve Called It “One Man’s Treasure” DNA
September 17, 2007

It seems people are a little touchy about the use of the term “junk DNA.” On his Genomicron blog, TR Gregory attempts to put an end to the debate by harking back to the origins of the term, along with an exegesis of how it has been used over time and in various settings.

While GTO doesn’t doubt the accuracy of Gregory’s information, we have to say: his argument that scientists referred to these genomic regions as “junk” all while understanding how very important they were leaves us a little, well, dubious. But maybe we’re just naturally cynical.

Let me help you out. Comings (1972), who provided the first detailed exposition of the “junk DNA” idea (his article appeared in print before Ohno’s), wrote: “Being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded.” Orgel and Crick (1980), who developed the idea of “selfish DNA”, wrote: “It would be surprising if the host organism did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another. This seems more than plausible.” Both approaches emphasized non-function based on proposed mechanisms of non-coding DNA increase. And both sets of authors noted that some of it would be functional.

Why people seem incapable of a) understanding a mildly complex history, and b) reading the literature is inexplicable to me. Given how much interest there is in non-coding DNA in the press and among anti-evolutionists, I think it is worth getting it straight.