Friday, May 28, 2010

Junk DNA and Genetics Textbooks

 
The latest issue of The GSA Reporter, published by the Genetics Society of America, is just out and they have an article on The Ins and Outs of Textbook Authorship. Here's something I agree with.
Anthony Griffiths (University of British Columbia, Vancouver) places more emphasis on core principles than on specific applications: “The goal is to show how genetic inference is made ... hence overall the emphasis is more on process than the discoveries.”
That's right. A textbook should emphasize concepts and principles and not facts. The goal is to show students how all of the knowledge we have fits into a coherent picture of the subject. Genetics, like all sciences, is based on models that represent the consensus view of the scientists in the field. It's important for students to see that these models are internally consistent and compatible with biology and biochemistry and all other sciences. It's important that students realize that there may be some controversy in the discipline but that they need to learn how to sort it out.

The next paragraph says, ...
[Scott] Hawley also places a heavy emphasis on core topics, because he “factor[s] in heavily the concept that so-called facts can be pretty ephemeral in science.” As Hawley explains, “Many of the ‘facts’ I was taught in college are either irrelevant now or wrong. For example, I heard many lectures as an undergrad asserting that a huge part of the genome was useless ‘junk’. We no longer look at things that way.”
I'm looking forward to seeing the next edition of The Human Genome by Julia Richards and Scott Hawley. It will be interesting to see what principles and concepts they advance to explain the absence of junk in our genome.

One of the things textbook authors have to careful of is discarding solid, well-established, models (like junk DNA) based on the results of a few modern experiments. Yes, it's true that new discoveries often overthrow old concepts, but it also true that when new "facts" disagree with established models it's usually the new facts that turn out to be wrong. The idea that theories are frequently overthrown by "nasty little facts" is a myth.

Rejecting the concept of junk DNA has consequences that will be difficult to handle in the next edition. It means re-writing the sections on the C-value Paradox, transposons (especially defective transposons), selfish DNA, pseudogenes, and genetic load. Also, the explanation for why this DNA is functional is going to have serious ramifications for other topics. I can't imagine how they'll put together a coherent picture of modern genetics if they reject junk DNA.

If you're looking for a good genetics textbook then here's my advice. Buy the one that supports the idea of copious amounts of junk in our genome and explains why it has to be junk. Ignore any textbook that rejects the notion of junk DNA—it will probably have other things wrong as well.


Thanks to a friend who alerted me to the article in The GSA Reporter.

9 comments :

  1. That's right! Anyone who does not believe in junk DNA can't be trusted on *anything*! :-)

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  2. Well, it's a very serious mistake (you are discarding a lot of fundamental cell and molecular biology plus most of the modern theory of molecular evolution if you decide that there is no such thing as junk DNA) which shows that the authors have been reading more editorials in Nature and Science then they have been reading the actual papers those editorials referred to...

    Which is probably the case for non-junk DNA topics too...

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  3. DK says,

    That's right! Anyone who does not believe in junk DNA can't be trusted on *anything*! :-)

    That's a bit of an exaggeration, but only a "bit"! :-)

    The point was mainly that you can't have your cake and eat it too. You can't claim to be writing a textbook that concentrates on core principles then demonstrate in the next sentence that you have fallen hook line and sinker for the latest hype in the scientific literature.

    To me, than calls into question the other "core" concepts that are being presented.

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  4. Hi,

    As a computer science professor interested in genetic algorithms a new(?) reason for junk DNA recently occurred to me. The question mark indicates the possibility that this idea may not be new. Please let me know.)

    A simple genetic algorithm operates through crossover and mutation. The issue is where the crossover point occurs. If it occurs within a gene, and if the crossover point is not exactly the same in both parents, the children will have two parts of that gene, which may not fit together correctly. On the other hand, if the crossover point is in the junk part--which is far more likely--the children will have a mixture of the parents' genes.

    This also suggests that evolution of the genes themselves occurs primarily through mutation and not through crossover.

    Is this a very naive suggestion--or one that biologists have already discussed? Or is it potentially interesting?

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  5. Blue says,

    A simple genetic algorithm operates through crossover and mutation. The issue is where the crossover point occurs. If it occurs within a gene, and if the crossover point is not exactly the same in both parents, the children will have two parts of that gene, which may not fit together correctly. On the other hand, if the crossover point is in the junk part--which is far more likely--the children will have a mixture of the parents' genes.

    First, let's deal with the differences between genetic algorithms and real biology. In real organisms, recombination occurs overwhelmingly between homologous sequences and the break points in each chromosome are at exactly the same place in the gene (or the junk). Thus, crossing over is not a common mechanism for generating new genes. It only shuffles existing alleles. It breaks up some combinations in one generation then puts them back together in the next generation.

    That's not usually what happens in genetic algorithms and it's one of many reasons why those algorithms do not reflect real evolution.

    The presence of extra junk DNA will have no effect on this mixing of alleles.

    Mistakes can occur in recombination where the crossover point is not at homologous sites. If one or both of the breakpoints are within a gene then this would probably be bad. If you have lots of junk DNA in your genome then the probability of disrupting a gene due to errors in homologous recombination would be lower.

    But that's not the only problem. These recombination errors will always lead to some offspring with less DAN than their parents and some with more DNA than their parents. That's just as serious a problem and having more junk DNA in your genome isn't going to solve that problem.

    As a matter of fact, most junk DNA consist of many copies of very similar sequence so it promotes recombination errors. This should be detrimental to an individual—not beneficial—but the effect of adding a small amount of extra DNA is not significant. If junk DNA accumulates gradually then the overall detrimental effect on a single individual is not going to stop the expansion of the genome.

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  6. "Rejecting the concept of junk DNA has consequences that will be difficult to handle in the next edition. It means re-writing the sections on the C-value Paradox, transposons (especially defective transposons), selfish DNA, pseudogenes, and genetic load. Also, the explanation for why this DNA is functional is going to have serious ramifications for other topics. I can't imagine how they'll put together a coherent picture of modern genetics if they reject junk DNA."

    Hoisted on their own petard.

    You all should have listened to me 10 years ago. I don't feel the least little bit of empathy for your pain.

    Does the word "schadenfreude" ring a bell?

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  7. "If you're looking for a good genetics textbook then here's my advice. Buy the one that supports the idea of copious amounts of junk in our genome and explains why it has to be junk. Ignore any textbook that rejects the notion of junk DNA—it will probably have other things wrong as well."

    WTF? I can't believe you as an alleged scientist would make such a closed-minded statement.

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  8. Charlie Wagner says,

    You all should have listened to me 10 years ago. I don't feel the least little bit of empathy for your pain.

    Does the word "schadenfreude" ring a bell?


    According to Wikipedia, "schadenfreude" means taking pleasure from the misfortune of others.

    That doesn't apply to me, Charlie. We have a long history and I can assure you that I've never taken any pleasure from your many mistakes.

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  9. "That doesn't apply to me, Charlie. We have a long history and I can assure you that I've never taken any pleasure from your many mistakes."

    Nor have I of yours.

    You've been gracious and tolerant and I appreciate that.

    ReplyDelete