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Monday, September 17, 2012

Stephen Jay Gould and Sydney Brenner Agree on Junk DNA

It's no secret that I'm a big fan of Stephen Jay Gould. I'm also a big fan of Sydney Brenner. Here's Gould writing in The Structure of Evolutionary Theory (pages 1269-1270). This is long and complicated but if you want to understand junk DNA and why it conflicts with Darwinism, then you've got to make the effort. I especially like the idea that Gould understands the difference between junk DNA, which can't be explained by any adaptive mechanism, and "selfish DNA," which isn't junk and has a Darwinian explanation. Many people don't get this.

Gould and Brenner are talking about repetitive DNA. This includes highly repetitive sequences of simple repeats and moderately repetitive sequences that include the transposons.
In some cases, of course, gene amplification originates as an immediate adaptation at the organismal level, especially when the availability of more gene product provides a selective advantage to the organism. But, more commonly, amplification occurs for causal reasons at the genic level itself, often by the conventional Darwinian mechanism of increased reproductive success, in this case by generating more copies of oneself, and inserting them into various places in one's surrounding totality—that is, in the genome itself. (Such an argument about direct Darwinian selection at the gene level provides the rationale, as previously discussed, for the important hypothesis of "selfish DNA"—see Orgel and Crick, 1980; and Doolittle and Sapienza, 1980 for the original publications.) Yet evolutionists have also recognized (see Ohno, 1970 for the classic statement) that those extra copies may strongly impact the evolutionary future of organisms by supplying flexibility for change through their redundancy. But this otherwise sensible argument also seems to raise a central dilemma in causality itself—since flexibility for future change cannot cause the current origin or maintenance of any feature! We can resolve this problem by recognizing augmented copies as nonadaptive ... spandrels at the time of their initial expression at the organismic level. Later recruitment and utilization of spandrels represents a perfectly sensible, indeed inevitable, concept under notions of constraint and hierarchical selection. I have, of course, and throughout this chapter, referred to such later utilization as exaptation—in this case by the cooptation of initially nonadaptive spandrels.

I have, in the past, objected to the usual terminology of such amplified elements as "junk DNA," feeling that such a dismissive term could only record an adaptational bias towards using such currently "superfluous" stuff as an insult to Darwinian optimality. I wrote (Brosius and Gould, 1992): "Genes duplicated or amplified by the tens of thousands ... have been named in an ambiguous or even derogatory manner (e.g., pseudogene or 'junk DNA'). Such names do not reflect the significance of the retroposed sequences as large valuable assets for the future evolvability of species; and, as a result, it is more difficult to contemplate their significance, impact and function."

But I have changed my mind after reading an insightful commentary by Sidney Brenner (1999) on my 1997 paper about the meaning and significance of spandrels and evolution. Benner begins by acknowledging the role of adaptational bias in our misunderstanding of the meaning and significance of amplified DNA:
There is a strong and widely held belief that all organisms are perfect and that everything within them is there for a function. Believers ascribe to the Darwinian natural selection process a fastidious prescience that it cannot possibly have and some go so far as to think that patently useless features of existing organisms are there as investments for the future...

Even today, long after the discovery of repetitive sequences and introns, pointing out that 25% of our genome consists of millions of copies of one boring sequence, fails to move audiences. They are all convinced by the argument that if this DNA were totally useless, natural selection would have removed it. Consequently, it must have a function that still remains to be discovered. Some think that it could even be there for evolution in the future—that is, to allow the creation of new genes. As this was done in the past, they argue, why not in the future?
But Brenner then defends the traditional terminology of junk DNA with an argument (based on the contrast of junk and garbage and vernacular English) that I had not considered, and it now strikes me as wise and useful:
Some years ago I noticed that there were two kinds of rubbish in the world and that most languages have different words to distinguish them. There is the rubbish we keep, which is junk, and the rubbish we throw away, which is garbage. The excess DNA in our genomes is junk, and is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it. Were the extra DNA to become disadvantageous, it would become subject to selection, just as junk that takes up too much space, or is beginning to smell, is instantly converted garbage.
Brenner then ribs my literary and terminological pretensions (and I except his criticism). But he also finds a resolution to the conceptual puzzles surrounding junk DNA in recognizing that such amplified sequences, when they arise causally at the gene level and then get propagated as effects to the organismal level, are non-adaptive spandrels with great potential for later expectation to utility. Therefore, their designation as junk—that is, as currently useless, but harmless (as opposed to garbage), and replete with potential future value—seems entirely appropriate, and I belatedly embrace this term as a proper implication flowing from the definition and meaning of spandrels:
The paper (Gould, 1997) has an important message and I strongly urge my readers to at least look at it even if all the words in it can't be understood. I offer this brief summary as a guide.

The term spandrel originates in architecture and is used to describe spaces left over as a consequence of some other design decision, such as triangles that remain behind when a rectangular wall is pierced by an arched opening. No self-respecting architect would simply leave such spaces, especially in a grand cathedral with a rich patron. Instead they would be decorated, as is the case of the four pendentives under the dome of San Marco in Venice, which are decorated with the four evangelists. This example is a good one, because the historical sequence of events is known. The spandrels are the consequence of the structural design decision, a by-product of placing an dome on rounded arches; three centuries later, mosaicists decorated these spaces. The spandrels are not primary adaptations, because they could have later uses, they come they become in Gould's terminology, exaptations.


  1. "I especially like the idea that Gould understands the difference between junk DNA, which can't be explained by any adaptive mechanism, and "selfish DNA," which isn't junk and has a Darwinian explanation. Many people don't get this."

    Count me among the many. Could you expand on this?

    1. Selfish DNA refers to stuff like transposons that have evolved means to increase their copy number - this is essentially adaptation within the 'ecosystem' of your genome.

      But there are other ways to bulk up on non-functional DNA, without transposons, all sorts of ways for duplications and expansions to happen. Especially in small populations, these DNA expansions can accumulate via the powerful, non-adaptive influence of genetic drift. In multicellular organisms, which have smallish population sizes, it is more difficult for selection to remove mildly deleterious DNA accumulation.

      Michael Lynch lays this out in his book 'The Origins of Genome Architecture'.

  2. Can you point to an article by Brenner where he talks about this? Thanks.

  3. The article is ‘Refuge of spandrels’(1999, Current Biology) and you can find it (free) here:

  4. In this world if anything that can clearly distinguish you from others or proves your identity is nothing but DNA testing, so whether it is in case of forensic lab requirement or anything research it becomes really important. Thanksssss……