Part of what makes us human may be what’s missing

Here’s one of those scientific questions that contains a highly suggestive fact: Why is it that the tiny water flea (Daphnia pulex) has a record 31,000 genes and the human – the infinitely more complex human – has only 23,000 genes? Here’s another similar question: How is it that the human species is so different from other primates when they have 96% of their DNA in common? These questions, or ones like them, are so prominent that it becomes a major stimulus, a challenge, to find answers. Some answers, or at least steps in that direction, are beginning to appear.

A team of biogeneticists working with David Kingsley at the Howard Hughes Medical Institute and Stanford University (USA) and published in the journal Nature, 9 March 2011, [Human-specific loss of regulatory DNA and the evolution of human-specific traits] used computer techniques to scan the genome of humans, chimpanzees, macaques (monkeys) and mice looking for differences in the genetic sequences. They came up with 510 short segments of DNA that were in the other animals but not in humans. In other words, rather than having extra genes to support human complexity, in this case we are missing genes. This was actually what the researchers expected, having seen similar DNA effects in other experiments with stickleback fish. However, for many biologists the results will be, to put it mildly, surprising. Scientists live for surprises.

There was more: Of the 510 missing DNA segments, only one affected a specific gene directly. That happens to be the gene that prohibits the growth of brain cells. That is powerfully suggestive – although don’t push the connection too hard at this point. More importantly: Of the other 509 DNA segments, all of it is associated with how genes are regulated and expressed. This enters the realm of epigenetics and the so-called ‘junk DNA,’ which concern the 98% of the genome that does not direct the production of specific proteins (what genes do).

I won’t go into lengthy background on epigenetics; here are some posts at SciTechStory:

Small steps toward understanding the epigenome
Oh Daphnia, why so many genes?
New for epigenetics: Active pseudogenes and RNA as gene regulator

After finding the 500+ DNA deletions came the hard part: What are these deletions and what does their absence mean. The researchers opened their work to dozens of specialists, asking them to submit analysis and explanations. The result was identification of a few sequences that were near or known to be related to genetic activity for specific human traits. Kingsley and colleagues then went hunting for these sequences in chimps and mice to see what they did in those animals. Two segments of DNA stood out: One segment I mentioned above that affects cell growth in the brain, the other is associated with what is called the androgen receptor, a transcription factor responsible for expression of male traits (like men have beards). With this segment of DNA missing, human beings (males) lack some traits found in chimps and mice such as facial whiskers and penis spines.

Ah…did you know this is a story about human males not having penis spines? You certainly would think so if you saw most of the coverage, even in science reporting such as Nature News How the penis lost its spikes, the same outfit that published the scientific paper. Sex sells, weird sex sells even better…dontcha know? It’s true that this story about missing elements of DNA includes the fact that somewhere along our evolutionary line human males (and that includes homo sapiens and Neanderthals) dropped a set of sensitive hairs at the end of the penis, which in primates helps trigger rapid ejaculation. Lots of bloggy speculation has flowed from this factoid about human males having more time to establish loving bonds with monogamous mates. It’s a factoid that may be a counterfactual surprise to many women.

As dull as it may sound, the moral of this story is not what humans are missing. It’s that our genetic inheritance is a whole lot more complicated than the DNA code. Some scientists have suspected this for quite a while, now the evidence is mounting. In this case, I think the media release gets it about right:

The finding mirrors accumulating evidence from other species that changes to regulatory regions of DNA – rather than the genes themselves – underlie many of the new features that organisms acquire through evolution.

[Source: EurekAlert]

The findings of this research continue to point in the direction of a re-evaluation of the role of epigenetics in evolution. This is not saying that DNA isn’t important or that the role of DNA in evolution isn’t paramount; but it does say, at the very least, that DNA is not the sole determinant of evolution. There are other factors that mediate between the environment and gene expression – such as the ‘missing’ DNA structures, and of course, those DNA structures that exist but are of unknown purpose – for which a lot more research will be needed to explain. How, when and why did the DNA sequences ‘go missing?’ What are other sequences that help determine human specific traits? Great questions. Scientists love great questions.

Research Spectrum

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