Monday, October 05, 2009

IDiots and Telomeres

 
Today's Nobel Prize announcement has prompted the usual stupidity from the creationist crowd. They don't get things right very often but when they rush into print their track record is even worse. You'd think they would have learned by now.

Most, but not all, bacteria have circular chromosomes. This is undoubtedly the primitive condition of living cells—at least once life got underway.

The advantage of a circular chromosome is that it doesn't have any free ends. This is important for two reasons: (1) nucleases that chew up nucleic acids like to work on free ends so having a circular chromosome increases the stability of the chromosome, and (2) circular chromosomes avoid the problems with replicating the ends of DNA.

That last reason needs a little explanation. DNA replication is complicated because evolution has only produced one kind of polymerase enzyme—the kind that works exclusively in the 5′→3′ direction.1 This creates a problem when replicating double-stranded DNA because the strands run in opposite directions.

The DNA replication complex (replisome) has evolved a solution to this problem as illustrated in the diagram. As replication proceeds from right to left, one of the strands is copied directly by a DNA polymerase molecule. This new strand is called the leading strand. The other strand is copied by a separate DNA polymerase molecule but it has to run backwards. That strand, the lagging strand, is made in short pieces that have to be stitched together. Every now and then a new lagging strand fragment (Okazaki fragment) is initiated using a special RNA primer.

This is not a very good design but it's the only thing that could evolve given that polymerases can only go in one direction. Most of us could have easily designed an better way of replicating DNA if we were in charge. While we were at it we could have designed nucleases that don't attack genes.

The DNA replication complex may be messy but it works. At least it works with circular DNA. When you have free ends there's a bit of a problem. Look at the diagram. You can see that when the replication fork reaches the end on the left, the leading strand will be complete. However, there will likely be a gap at the very end where the lagging strand didn't initiate a new Okazaki fragment. When the replisome dissociates this gap will persist.

As strands continue to be replicated over and over there will be a progressive shortening of the chromosome because of the inefficiency of the replication process.

There are several ways of handling this problem. Some bacteriophage with linear chromosomes form circles during replication in order to avoid shortening. In bacteria, there are two different mechanisms for dealing with the problem. Either the ends of the two strand are covalently joined, creating a hairpin, or a protein is covalently attached to the end of one strand [see Bacterial Chromosomes]. Either way is effective in preventing chromosome shortening during replication.

Eukaryotes have evolved a third mechanism. The ends of eukaryotic chromosomes have extensive repeat segments called telomeres. This works because the repeats can be shortened for many generations before the "business part" of the chromosome is affected. The repeats can also be extended from time to time by telomerase. This restores the parts that are lost during replication. The copying is crude, but effective. It uses an RNA template that's part of the telomerase.

The net effect is that telomeres protect the ends of eukaryotic chromosomes. This protection is due to the fact that cells have nucleases that can chew up DNA and because the DNA replication machinery has a built-in flaw that doesn't allow it to copy the very ends of double-stranded DNA. All in all you'd have to say that if this was designed then it must have been Rube Goldberg who built it!

This year's Nobel Prize in Physiology & Medicine was awarded to Elizabeth Blackburn, Carol Greider and Jack Szostak for their work on telomeres and telomerase.

Within hours, DLH posted an article n Uncommon Descent [DNA Preservation discovery wins Nobel prize].
Were one to design the encoded DNA “blueprint” of life, would not one incorporate ways to preserve that “blueprint”? The Nobel prize in medicine has just been awarded for discovery of features that look amazingly like design to preserve chromosomes ....

These telomeres can probably be shown to be essential to survival, and are likely to be irreducibly complex. If so, how can macro evolution explain the origin of this marvelous preservation feature that appears to be an Intelligent Design?
Chromosome ends need "protection" because the designer couldn't figure out how to have safe nucleases in a cell and couldn't figure out how to replicate the ends of double-stranded DNA molecules. Several different mechanisms have evolved for dealing with these problems. Telomeres are one solution.

The telomeric repeats evolved from internal repeat sequences. Telomerase is a reverse transcriptase and it likely evolved from a retrovirus-encoded reverse transcriptase. In Drosophila there are no telomers and there isn't a telomerase, Instead, the chromosome ends are protected by multiple copies of defective transposons.

The IDiots are going to have to look elsewhere for evidence of God.


1. There are good reasons for this. They have to do with the acccuracy of DNA replication and proofreading, but that's a story for another posting.

14 comments :

  1. Of course, circular genomes have had to solve a different intrinsic replication problem, the intertangling of the daughter chromosomes.

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  2. @Rosie,

    Linear genomes have to deal with that problem as well. Obviously, linear chromosomes can't be topologically linked the way circular ones can, but daughter chromosomes still get highly entangled. There simply isn't room in the cell for the daughter chromosomes to unwrap spontaneously. Some kind of topoII activity is required.

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  3. And worse, the circular genomes need to figure out if recombination has made their circular genome dimeric. See also: xer/dif

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  4. Regarding the problem of copying two oppositely oriented single strands of DNA as they unwind from the double stranded parent, the link below is to a fantastic animation that illustrates the process.

    http://www.youtube.com/watch?v=4jtmOZaIvS0

    (sorry, I don't know the geek code to make the URL clickable)

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  5. < They don't get things right very often but when they rush into print their track record is even worse.>

    http://bethelburnett.blogspot.com/2009/10/rottweiler-who-lost-his-teeth-his-mind.html

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  6. I would like to thank you for a clear and concise explanation of the DNA shortening problem. I had heard this happened before and never got the hang of why it happened. This is the first description I have read that I could understand (not being a Biologist). All I can say now is Doh!

    As for ID, really what did you expect?

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  7. In Drosophila there are no telomeres and there isn't a telomerase, Instead, the chromosome ends are protected by multiple copies of defective transposons.

    But this shows that IDiot DLH is correct! Who, after all, is Lord of the Flies? It ain't God! ;)

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  8. Is that lovely animation of the duplication accurate? I'd think it was impossible to 'spin' the effectively infinitely long doublestrand. Isn't it more physically/topologically sensible that the apparatus is spinning around the strand? (I know this would make for a poor picture, so I'm not complaining about the film, just the explanation.)

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  9. I just posted about telomeres as evidence against intelligent design a couple days ago! My description for why they are needed focuses more on why DNA has to be copied in the 5' to 3' direction. In case anyone's interested: http://jackal-eyes.blogspot.com/2009/09/unintelligent-design.html

    Divalent, thank for linking the animation - will add on to my post.

    Sili, an enzyme called topoisomerase takes care of the the unwinding long macromolecules problem: it breaks the DNA, lets the one part unwind, and then rejoins it.

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  10. Thank you, Jackie.

    I'm sorry I never paid better attention in biochem &c.

    At least I was right, that it would otherwise be a problem.

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  11. So the ID'ers are saying that telomeres are LIKELY to be irreducibly complexed, thus macroevolution can't occur . Was just curious if they are planning to do any personal research on telomeres or just throw out 'it is likely' and then jump to erroneous conclusions .How about just a smidge of research ? A days worth even.

    Brian Rutledge

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  12. I want to join one of the Anonymouses in thanking you for a very clear and interesting explanation. What I learned reading this post and Jackie's comment about topoisomerase will probably be my 'insight of the week' and I live for insights.

    This post and comments are an example of the value, at its very best, of debunking creationism.

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  13. Were one to design the encoded DNA “blueprint” of life, would not one incorporate ways to preserve that “blueprint”?

    A typical instance of the fallacy of affirmation of the consequent that infests IDiot-think. "If there were a God, he would have made the world the way it is. The world is as it is. Therefore there is a God." And once again they combine the major logic fail with ignorance about how the world is -- evidence that argues against it being a product of God.

    The Nobel prize in medicine has just been awarded for discovery of features that look amazingly like design to preserve chromosomes ....

    That's swell but, for the billionth time, IDiot, Darwin showed that design does not necessitate a designer.

    These telomeres can probably be shown to be essential to survival, and are likely to be irreducibly complex.

    Uh, its seems to me that we've dealt with this issue before. Apparently a functional memory is not essential to the survival of IDiots.

    If so, how can macro evolution explain the origin of this marvelous preservation feature that appears to be an Intelligent Design?

    Uh, by the antecedent of the conditional being false, for one thing.

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  14. Once you see the phrase "irreducibly complex", you can stop reading. You already know the paper is garbage.

    On another subject:
    Will there be PAYBACK for Dr. Tiller? Will there be COUNTERTERROR against right-to-lifers? When it happens, will it be murder, or JUSTIFIABLE HOMICIDE? WHO would be the most effective and deserving TARGETS for anti-right-to-lifist counterterror? WHERE do they LIVE?

    operationcounterstrike.blogspot.com

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