Friday, May 23, 2008

Fugu, Pharyngula, and Junk

 
PZ Myers writes about Random Acts of Evolution in the latest issue of Seed magazine. The subtitle says it all.
The idea of humankind as a paragon of design is called into question by the puffer fish genome—the smallest, tidiest vertebrate genome of all.
The genome of the puffer fish (Takifugu rubripes or Fugu rubripes) has about the same number of genes as other vertebrates (20,000) but its genome is only 400 Mb in size [Fugu Genome Project]. This is about 12.5% of the size of mammalian genomes.

THEME

Genomes & Junk DNA

Total Junk so far

    53%
The Fugu Genome Project was initiated by workers who wanted to sequence a vertebrate genome with as little junk DNA as possible in order to determine which sequences are essential in vertebrate genomes. The small size of the fugu genome suggests that more than 80% of our genome is non-essential junk.

Many of you might recall the results of my Junk DNA Poll from last January. In case you've forgotten the results, I'll post them again. The question was: "How much of our genome could be deleted without having any significant effect on our species?" The question was designed to find out whether Sandwalk readers believed in junk DNA or whether they were being persuaded by some scientists to think that most of our genome was essential. (Modern creationists are also promoting the death of junk DNA.) There was some dispute about the interpretation of the question but most readers took it to be a question about the amount of junk DNA.




Astonishingly, almost half of Sandwalk readers think that we need more than half of our genome to survive. This would be a surprise to a puffer fish.

I began a series of postings in order to explain what our genome actually looks like. So far we've determined that about 2.5% is essential and 53% is junk. Now it's time to finish off this particular theme and have another vote.

PZ points out that most of what we call junk DNA is not controversial. It consists of LINEs and SINES, which are (mostly) defective transposons. The pufferfish genome has a lot less of this kind of junk DNA than we do. This accounts for a good deal of the reduction n genome size that we see in modern pufferfish.

PZ also points out that we need to think differently about evolution ...
In the world of genomic housekeeping, the puffer fish is a neatnik who keeps the trash under control, while the rest of us are pack rats hoarding junk DNA.

There's a lot of thought these days going into trying to figure out some adaptive reason for such a sorry state of affairs. None of it is particularly convincing. We'd be better off reconciling ourselves to the notion that much of evolution is random, and that nothing prevents nonfunctional complexity from simply accumulating.
Well said PZ!!1

Watch for a few more postings on the remaining 45% of our genome then get ready to vote again. I'm hoping for a better result next time!


1. I used to know someone named Paul Myers who would never had said such a thing on talk.origins. Any relation?

[Image Credit: The junk DNA icon is from the creationist website Evolution News & Views.]

8 comments :

  1. With due respect, I don't think polls means what you think they mean.

    There was some dispute about the interpretation of the question but most readers took it to be a question about the amount of junk DNA.

    You can't know that (without polling :-), but the dispute shows that interpreting the result is dubious.

    "How much of our genome could be deleted without having any significant effect on our species?"
    Astonishingly, almost half of Sandwalk readers think that we need more than half of our genome to survive.

    And now you are confirming the problem. Significant change and survival are two different things.

    ReplyDelete
  2. I think what is amazing is that fugu and some other extraordinary cases have almost no junk. How does this happen? Why don't they accumulate any new junk?

    Do we even know why bacteria have no junk?

    ReplyDelete
  3. I think the theory is that bacteria can't handle the overhead of replicating junk, so it's heavily selected against.

    ReplyDelete
  4. This accounts for a good deal of the reduction n genome size that we see in modern pufferfish.

    What evidence do we have that an ancestor of Fugu rubripes had significantly more DNA per haploid cell than the modern species? You seem to be implying a trend through time of reduction in genome size. Who has reconstructed the ancestral state? For which ancestor? How long has this supposed trend been going on?

    The idea of humankind as a paragon of design is called into question by the puffer fish genome—the smallest, tidiest vertebrate genome of all.

    That's disengeneous. We DON'T KNOW which vertebrate species has the smallest genome. Fugu might be the smallest measured to date, but our sample across vertebrates is far from complete.

    ReplyDelete
  5. FWIW, I believe I originally voted that 11-49% could be deleted with no significant effect. I admit that's a guess, but I'd be surprised if there's sufficient data to do anything other than guess.

    If you asked how much of the genome could be replaced with random sequence, I'd vote greater than 90%.

    ReplyDelete
  6. getzal says,

    FWIW, I believe I originally voted that 11-49% could be deleted with no significant effect. I admit that's a guess, but I'd be surprised if there's sufficient data to do anything other than guess.

    If you asked how much of the genome could be replaced with random sequence, I'd vote greater than 90%.


    Let's see if I understand your position.

    Up to 49% of the genome is junk by any reasonable definition of the word "junk." On the other hand, 40% of the genome cannot be deleted without significant effect but the sequence of that part of the genome is irrelevant.

    Have I got that part right?

    Assuming that I do, can you recognize the 40% by looking at how the genome is organized? In other words, can you point to the parts that can be deleted and distinguish them from the parts that can't?

    Or, is this just a question of total bulk? Maybe it doesn't matter which parts you delete and which parts you keep as long as you don't get rid of more than 50% of the total?

    I distinguish between speculation and "guess" so I wouldn't say that the answer to the question is just a "guess." What I expect is that people will offer good arguments in favor of their position.

    In your case, I'm interested in arguments for why particular large parts of the genome are essential even though their sequence is irrelevant, or why the total size of the genome is important for the survival of the species.

    ReplyDelete
  7. FWIW, catching up on old threads:

    I'm interested in arguments for why particular large parts of the genome are essential even though their sequence is irrelevant, or why the total size of the genome is important for the survival of the species.

    That followed from an excellent reformulation of the question. I assume that gene regulation and cell sizes are bothering people - they are bothering me.

    ReplyDelete