The Loom

The textbook explanation of DNA goes something like this: enzymes in our cells read a stretch of DNA and convert its code into a single-stranded RNA molecule, which is then used by ribosomes as a template for building a protein. That stretch of DNA biologists call a gene. The protein it encodes drifts off to do some job–building cell membranes, maybe, or switching off other genes, and so on.

This is a fairly accurate picture–for less than two percent of the human genome. The rest of our DNA does not encode proteins. Much of it may be made up of genetic material from viruses and disabled genes. That does not mean that this genomic dark matter is all useless to us. Scientists have known for decades that some small chunks of DNA act like switches for nearby genes. Proteins grab onto these switches to prevent our cells from making proteins from the genes, or to speed up the process.

Far more mysterious, however, are segments of DNA that our cells use to build RNA, without then turning that RNA into proteins. These RNA molecules are a shadowy network of molecules that quietly control much of the activity in a cell. They can interfere with other RNA molecules, blocking the construction of proteins. In some cases, they can act like sensors, able to grab onto particular kinds of molecules. When they sense a molecule, they may then stop a gene from being copied.

Scientists don’t know a lot about this shadow network, but new experiments on it are coming out every week. And now it turns out to have been very important in our own evolutionary history. In Nature today, scientists report that the fastest-evolving part of the human genome is an RNA gene…

Researchers have been gauging the effects of natural selection on the human genome for several years now. They’ve taken advantage of the growing supply of data on DNA from humans and other animals. By comparing those sequences, scientists can pinpoint parts of genes that have changed a lot, or changed a little. And with various statistical methods, they can figure out whether natural selection drove the changes they observe.

A lot of the studies until now have focused on good old protein-coding genes. They’re particularly well-suited to these sorts of studies. Some changes to these genes can cause significant changes to an animal, because they can change the structure of a protein. The rest of the genome is much harder to test. A change to a non-coding piece of DNA may be favored by natural selection, or it may just be neutral, spreading thanks to little more than chance.

In the new paper, an international team of scientists dove into that dark matter. They found 35,000 pieces of non-coding DNA that were very similar in chimpanzees, rats, and mice. Since these mammals are separated by 100 million years of evolution, their similarity suggests these segments may be playing an important function that has been conserved by natural selection. If they didn’t have a function, mutations would have built up in each lineage. They then looked at these segments (or rather, they had a computer look at them) in the human genome. They picked out segments in which the human versions had acquired a significant number of new mutations not found in other mammals. These mutations must have evolved since our ancestors split from chimpanzees.

The scientists found 49 candidate segments. These segments have evolved a lot in our lineage. The most drastically altered of all is a segment the scientists dubbed HAR1 (for human accelerated region). It is 118 base pairs long. Chimpanzees and chickens, separated by over 300 million years, carry versions of HAR1 that are identical except for two base pairs. In humans, on the other hand, 18 base pairs have changed since we split from chimps.

What’s HAR1 for? This is the sort of question that seems like it should be easy to answer unless you’re the scientist doing the answering. The scientists found that human cells make RNA molecules out of the HAR1 segment. Specifically, they found that brain cells do. Specifically, brain cells in the cortex, the hippocampus, and certain other regions. We do love our brains, and so it is reasonable to consider that HAR1 took on some new role in the brains of human ancestors. The sequence of HAR1 suggests that an RNA molecule produced from it would be stable enough to carry out some important job, such as regulating the activity of protein-coding genes. HAR1 probably plays several roles. It is not just active in the adult brain, but in development-guiding cells in the fetus.

In a commentary that also appears in Nature, two Oxford scientists point out that HAR1 is also active in the ovary and testis of adult humans. And it is true that genes associated with sex are fast-evolving. So they don’t want to rule out the possibility that selection has acted on HAR1 in connection with reproduction, rather than with thought. It’s a fair point, but I was struck by the fact that the expression of HAR1 is far smaller in the sex cells than in the brain.

Still, it’s a strange point that may be worth raising at your next party: we have genes that are only active in our brains and sex cells. Insert punchline here.

Comments

  1. #1 Mikey
    August 16, 2006

    The more I read, the more I’m beginning to come to the conclusion that there was some fundamental change in human sexuality that provoked our evolution of intelligence.

  2. #2 somnilista, FCD
    August 16, 2006

    For the “Slowest-Evolving Piece of Human DNA” I nominate Kent Hovind’s entire genome.

  3. #3 David B. Benson
    August 16, 2006

    But I thought love was all in the mind…

  4. #4 Russell
    August 16, 2006

    Why not social reinforcement, in a more general way than sexual? Once there is a certain level of social complexity, communicative ability starts to have a high payoff.

  5. #5 Emanuel Goldstein
    August 17, 2006

    Fascinating stuff. But I hope my fellow students will remember, as the school year begins, that while Intelligent Design advocates often have a religious agenda, so do advocates of mainstream evolution. They want you to support their atheistic agenda.

    They will tell you to question authority! But watch out, if you dare question the foundation of their theories…the mindless developement of all existence, life, mind, and reason itself…you will be branded as a fundie fanatic.

    Think about it! Quetion THEM too!

  6. #6 Sylvilagus
    August 17, 2006

    Emanuel – That “atheistic agenda” notion makes no sense at all when you consider the large number of evolutionary scientists who are Christians, Jews, or other non-atheists such as myself. You are perpetuating a myth that evolutionary science is somehow opposed to religion(s). It isn’t.

  7. #7 Robert Maynard
    August 17, 2006

    “They will tell you to question authority! But watch out, if you dare question the foundation of [evolutionary] theories…you will be branded as a fundie fanatic.”

    Well, yeah..
    Unless your completely non-politically-motivated curiosity *cough* can actually produce testable predictions or evidence that could cast doubt on these well-established ideas, you’re mostly just wasting people’s time. :P

    There’s progress to be made!

  8. #8 G
    August 17, 2006

    Remember, Sylvilagus and Robert: Every time you feed a troll, God kills a kitten.
    http://www.emezeta.com/weblog/troll-gatito.jpg

  9. #9 Joshua
    August 17, 2006

    Fight world hunger! Stop feeding trolls!

  10. #10 Paul Maybury Jr.
    August 17, 2006

    Emmanuel, I am an atheist, but I don’t have any secret agenda. I don’t hate religious people, unless they act in hateful ways. I love science because it is just so darn interesting! On the other hand, gods are boring, and the phrase from that old collection of phrases ecclesiastes that says there are no new things under the sun is just how I feel about religions and religious people. I assure you that it is quite possible to love mankind and work for its future welfare without doing it out of some kind of fear of some invisible being’s anger. What is there to admire in doing good to either stay out of ‘hell’ or get into ‘heaven’ when you die? Altruism is a successful strategy that was being used by our ancestors for millions of years (yes, millions)because without acting for the benefit of those around you, you might as well have remained an amoeba. Atheists do good, for goodness’ sake. Religion is bad for you, and sunday school is, in my opinion, child abuse. Take that ;{)

  11. #11 Invigilator
    August 19, 2006

    Paul — I actually think that Gods are quite interesting — especially interesting in that their origins and development are governed by laws of cultural evolution that are in many ways analogous to those of biological evolution. Consider this Father/Jesus Christ/Holy Spirit God in three persons, a fusion of genomes that included the Jewish (did Akhenaton have a hand?) supreme God YHWH; an adaptation of a number of Gods that were sacrificed for our salvation (Osiris, Mithra); and the Holy Spirit which I can only imagine to be an adaptation of some kind of Platonic essence that also happened to be needed to explain the incarnation of Jesus in matter.

    And of course this tripartite amalgam has turned out to be spectacularly successful, giving rise to any number of genera and species, ranging all the way from the mighty Catholic Church to small, extinct groups like the Shakers. Plenty of room for thought and research there — don’t be close-minded!

  12. #12 Paul Maybury Jr.
    August 19, 2006

    Dear Invigilator, actually I should have said that gods are relatively boring. I actually have done a lot of reading about gods and religions, most recently some older works such as “they wrote in clay” which is a book of translations of the earliest babylonian cuneiform writings on the various creation myths or stories, tiamat and Marduk,the struggles of the early gods, and the creation of man which which was accounted for as fulfilling the usual need of gods for worshippers. Truly I don’t find anything completely boring, and my main regret is that I will not live long enough to read and study every subject available to our ever curious species. I suppose my main beef is that people who spend all of their time on ‘one book’ and who try to limit the thinking of others are doing actual harm to their fellows, thus my crack about sunday schools. Even though I have been on the internet since around 1995, it still surprises me with the wealth of knowledge available. This blog in particular is a source of great pleasure to me, and I am in the process of reading many of Carl Zimmer’s books. I think it was Alexander Pope who said that the proper study of man is mankind, I think it is more accurate to say that to study is to be human.

  13. #13 Chuck the Lucky
    August 19, 2006

    “The more I read, the more I’m beginning to come to the conclusion that there was some fundamental change in human sexuality that provoked our evolution of intelligence.”

    Posted by: Mikey | August 16, 2006 02:31 PM

    Language may be the common thread. Once women invented names for themselves men’s memories had to improve. Once men invented excuses women’s memories had to improve.

    While I agree that trolls must not derail a discussion, their points (so to speak, tongue in cheek) need to be addressed clearly and quickly so that people who are new to creationist clap trap don’t get the idea that people are unable or unwilling to address their “points”.

    Boys and girls, what Emanuel Goldstein has done is to try to encourage dismissing evolution without bothering to understand it by making the same criticism of it as has been made of creationist clap-trap (i.e. that it is religiously based). He knows that by a certain age people who doubt evolution are not going to make an exhaustive study of both modern biology and geology and chemistry and probability so if both sides look equally biased there is a better chance that “being open minded” will mean you will go with the belief that makes you feel comfortable in church. Let us ignore the fact that the “religious motivation” claim is false. He no doubt hopes that someone will say that this is irrelevant which would open the question as to why the religious motivation of Intelligent Designers is relevant. This would be a good point if:

    A) Both Evolution and ID were both based on equal bodies of evidence and equally sound methodology.

    B) The supposed “religious agenda” of evolution were in some way relevant to the theory and it’s mechanism the way the religious agenda of ID is to that movement. [Absent the desire of the evil scientists to convert the world there is still the theory and the evidence. Absent the religious need to have God be compatible with the theistic, interventionist micro-managing, biblical God of the middle-east's "holy scribbling", where is ID? With Scientology, that's where.]

    In other words, it is not a good point. fortunately he is probably not still on the discussion to make it explicitly but if you follow the creationism/ID movement to any degree you will see the point made. One falsehood plus one unfounded insinuation equals one good reason to make reasoning and critical thinking a separate, specific and mandatory subject in every school, everywhere in the western world, by force if necessary – which at this point it probably is.

    Learn logic kids. It is being denied you for a reason.

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