Pharyngula

My recent Seed column…

… is now available online. It’s a brief introduction to some interesting observations about the pufferfish genome.

Comments

  1. #1 Glen Davidson
    May 30, 2008

    Does anyone know why the puffer fish has such an efficient little genome?

    I realize that bird genomes are believed to be smaller than, for instance, ours, because their cells are thereby smaller and lighter (or actually, it’s believed that bird ancestors already had smaller genomes–but presumably birds have “kept their genomes small” at least partially for adaptive reasons, while they remained fliers anyway). But I can’t see any similar reason for puffer fish genomes to be so small.

    Maybe the better question is, have puffers seemed to evolve less with such a small genome? Cause and effect would be hard to disentangle there, but it is often thought that expansive genomes allow for more evolutionary opportunities, and I’m wondering if the evidence bears this idea out.

    Glen Davidson
    http://tinyurl.com/2kxyc7

  2. #2 David Marjanovi?, OM
    May 30, 2008

    That’s how to write on this topic.

    (Except… were there space constraints that prevented you from mentioning that different onion species have wildly different amounts of junk DNA, even though all have much more than we do?)

  3. #3 David Marjanovi?, OM
    May 30, 2008

    I realize that bird genomes are believed to be smaller than, for instance, ours, because their cells are thereby smaller and lighter

    “Lighter” doesn’t matter, but the surface-to-volume ratio probably does — it allows a higher metabolism, and that’s what birds have.

    it is often thought that expansive genomes allow for more evolutionary opportunities

    How does having another ten million SINE copies allow for more evolutionary opportunities? You seem to be thinking of gene or genome duplications.

    But I can’t see any similar reason for puffer fish genomes to be so small.

    Maybe the effect that smaller genomes can be replicated faster, which means faster growth and reproduction (if the resources allow it, obviously), is enough, and the limiting factor is whether one happens to evolve the ability to cut junk out or not.

  4. #4 Nentuaby
    May 30, 2008

    SEED is a print magazine, David, and it *is* fairly tangential to his point. Even if the words could have fit, it certainly wouldn’t have been very good economy of language.

  5. #5 Glen Davidson
    May 30, 2008

    “Lighter” doesn’t matter, but the surface-to-volume ratio probably does — it allows a higher metabolism, and that’s what birds have.

    Well, lighter should matter for flight. I’ve seen “metabolic costs” mentioned as well, and sure, metabolic rate ought to matter as well. Here’s one biologist who mentions weight:

    Second, small genome size is intriguingly correlated with flight. Bats, compared to other mammals, have small genomes, and flightless birds, compared to other birds, have larger genomes. This has led to the proposal that small genome size might offer a selective advantage to flying animals, by reducing the energy cost associated with hauling all that debris around.

    sfmatheson.blogspot.com/2007/08/which-came-first-bird-or-smaller-genome.html

    it is often thought that expansive genomes allow for more evolutionary opportunities

    How does having another ten million SINE copies allow for more evolutionary opportunities? You seem to be thinking of gene or genome duplications.

    It’s not all SINE copies, yet these might provide opportunity as well, simply by allowing genes and regulatory sections to find their appropriate places. That is to say, length of chromatin should provide flexibility, for assocation, and thus for evolution. Also, transposons are thought by some to enhance evolution and genome length, although more transposon activity seems to be the cause, and genome length, the effect.

    It seems to me that various “junk”, from SINE repeats to pseudogenes, could be co-opted for gene regulation, thus for evolution.

    Anyhow, I was going off from a Science special on plant genomes, which considered shorter genomes to be more efficient, but longer genomes to be correlated with more evolution (if perhaps longer genomes are often effect, not cause).

    Maybe the effect that smaller genomes can be replicated faster, which means faster growth and reproduction (if the resources allow it, obviously), is enough, and the limiting factor is whether one happens to evolve the ability to cut junk out or not.

    Maybe. The problem is figuring out why the puffer and not us. I was wondering if relative stasis could be a reason for the puffer, but I don’t know that it has experienced relative stasis.

    Glen D
    http://tinyurl.com/2kxyc7

  6. #6 imsd007
    May 30, 2008

    > Among its claims to fame is that it protects itself from being eaten by secreting a potent neurotoxin called tetrodotoxin that blocks nerve impulses and can kill a person in a high enough dose.<

    To be more specific, tetrodotoxin is produced by bacteria (such as Pseudomonas and Vibrio sp.) and not by the fish itself. The same is true for the blue-ringed octopus and other toxic animals.

  7. #7 windy
    May 30, 2008

    Sorry for nitpicking, but that looks like a porcupinefish in the picture :) I don’t know if some people include them in the pufferfish, but their genomes are actually not that small. More problems for the “evolutionary opportunities” hypothesis – there are more pufferfish species and they live in a larger variety of environments (marine, brackish and freshwater) than porcupinefish.

  8. #8 Castaa
    May 30, 2008

    I enjoyed the article PZ. I subscribed to Seed this month. I’m excited to get my first copy.

    I think there is needs to be more focus on the philosophy of biological evolution in general. It’s valuable.

  9. #9 spgreenlaw
    May 30, 2008

    Great article. I’m not a scientist myself (I’m a creative writing sort of fellow) but I do have a deep interest in our natural world and a huge amount of admiration for those who explore it in the field and the lab. This article was clear enough that I could easily understand it, stuffed full of exciting facts and insights, and the writing was crisp, a quality I’ve come to appreciate when in nonfiction. Thanks for giving us lay people a look inside.

  10. #10 Jim
    May 30, 2008

    If I took some puffer fish nuclease could I loose 20 pounds?

  11. #11 PZ Myers
    May 30, 2008

    The magic limit on the print column is 1200 words: I have to write something that makes sense that falls right into that amount of space. I think the columns so far have all ranged between 1100 and 1300 words, partly due to my laser-like aim, and most importantly thanks to the excellent editors at Seed. If I turn in something 1400 words long, they find something to cut.

  12. #12 Fifi
    May 30, 2008

    So much junk. But then, one question beacons: assuming this is technically feasible (probably not, yet), has anyone tried to take the genome of a moderately complex animal, clean it from its presumed junk and try it out?

  13. #13 albinosquid
    May 30, 2008

    Windy, I too questioned the species of puffer shown in the illustration…my best bet is it’s a Striped Burrfish, which looks similar to the porcupinefish but I *think* they can be differentiated by the burrfish’s permanently erect spines, while the porcupinefish’s spines are held flush against the body when it’s not inflated.

    I live in Florda so the striped burrfish are quite common around here. I’ve even kept a couple baby ones as pets over the years…they are very cute, entertaining creatures anyway, but REDICULOUSLY so when they’re the size of your thumbnail!

    I swear one day I’m going to have another pet puffer and train it to do tricks. They’re very intelligent and have a high food drive, so I think it would work.

  14. #14 Reed
    May 30, 2008

    Fifi #12
    Not a full “cleaning” but fairly large chunks have been removed without apparent ill effect: http://www.nature.com/nature/journal/v431/n7011/abs/nature03022.html

    @PZ kipple… perfect.

  15. #15 Ichthyic
    May 31, 2008

    totally and completely OT:

    I spend a bit of time repairing computers for fun and profit, and I’ve been noticing a LOT of machines infested with vundo/virtumonde lately:

    http://www.auditmypc.com/virtumonde-remove.asp

    It’s really a bitch to get rid of, and it appears to be running a lot of “free” download sites at the moment, so be sure to carefully scan everything you dl with a good spyware checker (virus checkers often WILL NOT catch it).

    If you find it, and your anti-spyware proggy can’t get rid of it, try the microsoft online version (there’s a link to it in the article I linked to above).

    carry on.

  16. #16 Fifi
    May 31, 2008

    Reed @ #14, thank you very much.

  17. #17 wazza
    May 31, 2008

    I find it amusing that an article about superfluous information being removed was itself subject to the same process…

    but then I also find great amusement in knitting flowers, so don’t read too much into that.

  18. #18 scooter
    May 31, 2008

    A gene cleaner. This is certainly evidence of Intelligent Design. Obviously the Intelligencor is trying out this geneBot on the pufferfish, and if it works out, he will bestow on us.

    He’s a bit more careful after that experiment in Sodom and Gommorah with the spirituality Gene. That didn’t work out too well. The brain eating zombies were bad enough but the father rapers were a real embarrassment.

    Oh well, Nobody’s perfect. The old boy had to nuke the place to wipe out the subsequent rogue virus.

    This stuff is obvious if you just think about it.

  19. #19 BaldApe
    May 31, 2008

    I just thought of a cool experiment that might or moght not be possible.

    The reason eukaryotes get away with such huge genomes consisting largely of repeated nonsense is that they have multiple replication forks in their DNA. IOW, the process of duplicating the DNA molecules does not start on one end and work it’s way along the whole molecule (which I believe I read would take a month) but rather, start replication all over the place within the molecule. Prokaryotes have only one origin of replication, so they are under selective pressure to keep the genome small.

    What if someone could remove whatever signal establishes some of the replication forks from some rapidly reproducing species, and let it go. Would it excise superfluous bits of DNA from its genome?

  20. #20 kai
    May 31, 2008

    At what rate do the SINEs and LINEs reinsert themselves in the genome—are they doing it all the time, so that the chromosomes in each cell are constantly growing, or does it preferentially happpen during some special circumstances?
    It seems to me that you should have an exponential growth of the genome if their activity was completely unchecked?

  21. #21 Rebecca
    May 31, 2008

    Prokaryotes have only one origin of replication, so they are under selective pressure to keep the genome small.

    Even though they have only one origin of replication, they may have multiple replication processes going on at once, so I am not sure that is a factor.

    http://sandwalk.blogspot.com/2008/05/dna-replication-in-e-coli-solution.html

  22. #22 David Marjanovi?, OM
    May 31, 2008

    Even if the words could have fit, it certainly wouldn’t have been very good economy of language.

    Given the space constraints that’s a moot point, but I still disagree. An ad-hoc answer to the Onion Test might be “well, we’re humans and they’re onions, we’re so horrendously different in so many ways that we should expect the genome to be different”, or maybe “there’s a tradeoff between efficiency of replication and whatever function the junk has, we’re at the optimum, and the onions can get away with not being there” — but the wild variation between the onions falsifies both of these.

    I think there is needs to be more focus on the philosophy of biological evolution in general.

    What philosophy?

  23. #23 Sili
    May 31, 2008

    I’m afraid my lack of knowledge of biology and biochem is gonna show pretty obviously here, but I wondered:

    Is there any correlations between phosphate availability and genome size? Are there actually any environments where phosphate is a limiting nourishment, now that I think of it? Or would the need of phosphate in ATP become an issue long before the possible gain from using less PO43- becomes an issue?

  24. #24 Malcolm
    June 1, 2008

    What role does ncRNA play?
    And how much of it, if any, comes from the junk regions?
    Inquiring minds need to know for their imminent exams.

  25. #25 Paper Hand
    June 1, 2008

    Given that there is often considerable variation between different related species in the amount of junk DNA, and given the overall wide range of how much junk DNA there is, could it be possible that there is a cyclic tendency? That is, that genomes tend to accumulate more and more junk over time, until some critical point is reached, at which point a “cleaning mechanism” begins working harder, removing some of this junk, until the junk is brought back down to a reasonable level, at which point it weakens.

    Of course, for this to be true, there’d have to be some kind of cost to the cleaning mechanism (perhaps it occasionally removes useful DNA as well?) but also a very real cost to the junk DNA itself. Thus, when the junk is at a sufficiently high proportion, the costs of having all that junk is greater than the cost of the cleaning mechanism, but once it comes back down, the cleaning mechanism becomes too expensive.

    Thus, the variation we see in junk DNA would simply represent different species happening to be at different points in this cycle.

  26. #26 windy
    June 2, 2008

    I live in Florda so the striped burrfish are quite common around here. I’ve even kept a couple baby ones as pets over the years…they are very cute, entertaining creatures anyway, but REDICULOUSLY so when they’re the size of your thumbnail!

    Actually I’m currently in Florida too. Where can you find these cute buggers, Gulf or Atlantic coast or both?