Junk and genomes in The Scientist.

I used to subscribe to (and quite enjoy) The Scientist when it was a free publication, but have mostly stopped reading it now. Two stories in the latest issue were pointed out to me by readers of Genomicron, so I thought I should provide some brief comments.

The first relates to an editorial by Richard Gallagher entitled “Junk Worth Keeping“, which asks “Is it time to retire provocative descriptors such as ‘junk DNA’?”. The answer, says Gallagher, is “no”. Why? Because “junk DNA” is useful for… framing. He cites Nisbet, although as I have come to learn, framing, sensu Mooney and Nisbet, applies to conveying science in a particular way to help win an election. I’m not sure what “junk DNA” has to do with defeating the Republicans as per Mooney’s formulation of framing, and in any case, Greg Laden has already provided a very useful discussion of the fact that “junk DNA” is a frame that anti-evolutionists exploit because it allows them to obfuscate genetic knowledge to their own ends. They do, of course, get both the history and the science of the term totally wrong, but that’s not the point when it comes to spin. In other words, the term “junk DNA” is a horrible way to communicate the complexity of non-coding DNA to an audience with no background in evolution or genome biology. Granted, it does get them to talk about the issue, but I believe there must be better ways to do this than to set up the discussion to be oversimplified and confused.
[Hat tip: junkdna.com]

The second comes from a story by Melissa Lee Phillips reporting “Surprises in the Sea Anemone Genome“. Here are some statements of interest:

  1. “…the sea anemone, one of the oldest living animal species on Earth…”
  2. “The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution.”
  3. “It’s surprising to find such a ‘high level of genomic complexity in a supposedly primitive animal such as the sea anemone,’ Koonin told The Scientist.”

I will probably do an entire post on the common fallacy of describing one extant lineage as older than another (common descent dictates that all contemporary lineages are of exactly the same age, although some have undergone more branching and/or morphological change than others). But statement #1 is especially inaccurate because the age of a species is not the same thing as the age of a lineage (which is what the author meant to describe). This species (Nematostella vectensis) could, for all we know, be very young, and certainly there is no basis in evidence for calling it one of the oldest species on Earth. (The original paper in Science is at least clearer on this, describing the Cnidaria as “the oldest eumetazoan phylum”, though this is difficult to substantiate given that no unambiguous fossils exist for eumetazoa prior to the Cambrian, at which time early representatives of modern phyla were already present; they cite two papers that can, at best, only suggest that Cnidarians [and perhaps molluscs] were present among the Ediacaran biota). And, of course, “the” sea anemone is a misnomer as this name applies to the entire order Actinaria, within which there are several dozen families.

Statement #2 may refer to a widely held belief among the public (and perhaps among some genome sequencers), but the expectation that complexity always increases in evolution is a fallacy that was abandoned long ago by evolutionary biologists. (It also bears noting that organisms do not evolve, populations do). A huge amount of the diversity on this planet is composed of parasites, and their evolution often involves simplification. In this case, it is not morphological but genome evolution that is under discussion, and there is really no reason to expect an increase in complexity here either. Gene loss is a well known phenomenon, and in fact one could make a case that streamlining of the genome or having one gene do multiple things is related to increased morphological complexity whereas gene number is not. Take, for example, the sea urchin, whose immune system seams to involve a large number of genes, as compared to a vertebrate, whose immune system generates nearly endless variation by recombining a comparatively limited number of genes. (Incidentally, the anemone genome appears to contain 18,000 genes).

Statement #3 is not necessarily inaccurate, but I caution readers that it must be interpreted in a certain way. “Primitive” does not mean “less complex” or “less advanced”, it means “more like the last common ancestor of the groups being compared”. In this sense, a sea anemone is probably more like the last common ancestor of all animals than is, say, a fly. But this is also a modern species whose overall lineage has been around for exactly the same amount of time as that of the fly. The anemone lineage may have undergone fewer morphological changes (though still probably a lot) than the lineage that led to insects, but the anemone itself is not the common ancestor and in fact may bear only a modest resemblance to the ancestor. This is exactly the same confusion people face when thinking about humans and chimpanzees. Chimps were not the ancestor of humans, and may bear only a modest resemblance to the common ancestor of the two lineages — the two split millions of years ago, and both lineages have undergone considerable change since, with many species arising and disappearing in the meantime.

I like to see these interesting topics covered in The Scientist, but I must admit that these two pieces in particular do not inspire me to re-subscribe to the magazine.

While I’m at it, let me register a small complaint about the story by Elizabeth Pennisi in Science [Sea Anemone Provides a New View of Animal Evolution]. I have become mostly resigned to the fact that science writers will insist on describing genome sequencing as “decoding” a genome, and this story is no exception. What bothers me more is that Pennisi is so sloppy in characterizing evolution as a “progressive” process. Thus, she argues that “genome sequencers have just jumped down to a lower branch on the tree of life“, and that “until now, researchers have relied heavily on the sequenced genomes of the fruit fly, nematode, and that of a few other invertebrates to understand genome evolution leading up to the vertebrates“. (Update: Apparently the authors the paper cautioned Pennisi about this, but to no avail!).

Evidently, we have a lot of work to do in clearing up the basic details of how evolution occurs.



6 comments to Junk and genomes in The Scientist.

  • Chris Harrison

    I’ve often found the term “higher taxa” to be a possible point of confusion as well, since it seems to imply a ladder effect. It’s not, of course, but it just goes to show that appropriate terminology can sound a lot like other nonsense phrases(“lower branches”).

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  • TR Gregory

    “Higher taxa” usually refers to higher levels of the taxonomic hierarchy from a classification perspective. So, phylum and class are “higher taxa” compared to genera and species.

    “Lower branches” makes no sense. I can see what the author *might* have been thinking that is not progressionism-based, namely that if you draw a phylogeny with terminal nodes at the top, this would be an early branch. But you can rotate all nodes on a phylogeny, which means that this would only work if you drew with one of many equally accurate topologies. In other words, this would not be correct either, but at least it would be a misunderstanding about phylogenies and not of the entire history of life.

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  • Chris Harrison

    Right. Higher taxa is a valid term, it just sounds as though we’re talking about organisms above others on some linear scale.

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  • Andras

    Thanks for the “hat tip” to junkdna.com on Editor Richard Ghallager’s “Obituary of Junk DNA” on occasion of the 35th Anniversary of his introduction of the term. I suggested to him to write “The Scientist” article – and he finished his draft about a week before ENCODE came up (no change).

    There is one very strong positive about his posting; that he (IMHO very properly) characterizes the late Dr. Ohno’s term as “framing”. We know that it was intentional, since as you point out elsewhere, Ohno even tried two years prior to 1972 “trash DNA” (but that did not stick).

    For just in case science journalists truly care about science (not only sensationalism) I wrote up an “Obituary” which points out that such “framing” is not uncommon at all. (I quoted my experience with Marvin Minsky’s framing AI to exclude Neural Nets, thereby setting back funding for NN for at least 15 years).

    Since “Junk DNA” (whose journalistic value I also keep) is an extremely harmful “frame” (keeps people affected with “junk DNA diseases” dying: http://www.junkdna.com/junkdna_diseases.html ) I urge you and readers of your blog that we gently try to steer journalists towards better directions.

    Ultimately, this paradigm-shift of the gene/junk conceptual meltdown will bring up a new crop of science writers, who are both ready to discard old cliches and take some time to understand the issues as well as implications.

    It is important, since we should be mindful of the public opinion (and those shaping public opinion), as a good amount of funding may (should) come from tax-dollars.

    A collective effort is made by International PostGenetics Society; http://www.postgenetics.org

    pellionisz_at_junkdna.com

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  • Nick

    Woo hoo, the junkDNA.com crank guy showed up in the comments again!

    My 2 cents on the piece in The Scientist:

    I think the point of the “pro-junk-DNA terminology” argument in The Scientist was that the term was simple and expressed the “no function” position in a provocative way, such that scientists were encouraged to debate and investigate it. So the “framing” aspect was brought up in that specific context, not for debating Republicans or whatever.

    It is still debatable whether the “junk DNA” term is useful overall since it creates so much opportunity for confusion/obfuscation. But I think The Scientist made at least an interesting argument.

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  • Andras

    “Nick” is not telling the truth. Chief Editor of The Scientist (Richard Gallagher) openly admitted in his July editorial that “junk DNA” as a *scientific term* was dead as a doornail.

    [verbatim quote of the term]…”undermined by discoveries of the complexity of gene structure, the sophisticated nature of translational controls (which includes a role for Alu repeats, on the face of it the most meaningless junk of all), and the reach and scope of transposons. Recently, and damningly to the concept of junk, we’ve had the revelation of regulatory RNA networks.”

    Of course, it is quite uncomfortable for those who discarded (and contrary to ENCODE evidence) would like to go on discarding 98.7% of the (human) genome.

    “Nick” is probably not a scientist – and if he maintains such a dogmatic attitude probably never will be.

    For an analysis, see “the Obituary of Junk DNA” at

    http://www.junkdna.com/#obituary_of_junk_dna

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