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The Incredible Shrinking Genome
Shipud writes "Mammalian genomes have been shrinking for about 65 million years, roughly since the dinosaur extinction. Why? And why were ancient mammalian genomes three times larger than they are today? A new article in Genome Biology and Evolution tries to explain this bizarre finding, and why the genomes of mammals (but not of other living groups) are still shrinking. 'Once [the dinosaurs] were gone, mammals started to radiate, fill those niches, and a whole new level of competition arose. The selective advantage of not having a genome encumbered by potentially damaging mobile DNA elements has probably become critical at this "be ye fruitful and multiply; bring forth abundantly in the earth, and multiply therein" stage. In effect, the genomes of mammals has been shrinking by removing mobile DNA elements, just after the KT boundary. And according to the model presented in this study, this process is still ongoing: mammalian genomes are not at an equilibrium size. Unlike flies, mammals are still cleaning up.'"
I blame it on increased use of design patterns and better tools for refactoring ;)
Your sig(k) has been stolen. There is a puff of smoke!
God is a computer programmer who made the many species by writing in some high level language which is ultimately compiled into DNA. The similarities in DNA among different species are a result of code re-use, and mammals are his (her?) "flagship product." He's currently refactoring the code, to make it more efficient.
My blog
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There is no such thing as devolution. By virtue to change, that is evolution in progress. In other words, evolution is not biased toward *your* idea of progress.
Life is not for the lazy.
Body temperature control is very effective in reducing the number of different enzymes that need to be coded for.
Frogs, for example have ~8x more genes than humans - partly because they have lots of different enzymes that do the same thing but at different temperature.
Here's the actual scientific paper, rather than the blog.
further, the shorter the strand of DNA, the fewer chances exist for error when the strand is duplicated. All else being equal, Short DNA may logically be a defense against cancers and other genetic diseases.
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We still haven't shed the genes that make some people become Politicians...
There fixed that for you...
I'll meet you at the intersection of "Should be" and "Reality"
Some have over a hunred billion base pairs. There a tremendous amount of junk DNA and gene duplication.
Size does not matter.
Devolution is indeed still evolution in some way.
But I think by evolution we mean progress too something 'better' and devolution too something 'worse'.
While I'll leave defining better and worse as an excercise to the reader (try finding a concencus on thatone).
Evolution doesn't make any value judgement other than: if it survives and reproduces, it's good. If it dies before reproduction, it's bad. In that sense, there's no such thing as evolution towards something worse. No matter how degenerate an organism may seem to you, it's like that because that's what works in that particular niche.
Wrong. There is no better or worse in evolution. What is good one day sucks when the environment changes. Evolution is not directed towards anything, it can not progress or retreat. There is no 'should have died young.' There is no natural and unnatural. By helping people procreate who might not have, all we are doing is changing the selection criteria, which are changing all the time anyhow.
However, you got the first part wrong too (assuming you are the same AC) The mammalian genome is not losing information that is valuable, it is losing genetic parasites. The genome has been throwing out the trash that tends to muck things up.
- None can love freedom heartily, but good men; the rest love not freedom, but license. -- John Milton
As a thought experiment, imagine the genome to be a very big, very modular program, with lots of clusters of specialized subclasses of functionality that are occasionally or potentially useful.
This program is represented by a coding sequence of molecules; at essence a copyable and readable bitstring.
Time and living in a complex, energetic environment tend to break down complex structures which must be "binary-precise" to maintain their meaning. All else being equal, a longer program, a longer bitstring, has a higher probability of losing parts of itself to mutation. Longer programs; longer genomes, require cleverer techniques to preserve themselves over evolutionary time scales.
The cool thing is, longer programs are precisely those that have the capacity to implement cleverer strategies for keeping their own program information reliably preserved.
That is the essential battle that life and evolution wage against entropy;
More bits (longer genome) = more or better strategies for building bit-containers (organisms) and better strategies for taking advantage of environments or pacifying environments.
But more bits = harder to preserve without critical errors breaking the program.
The life bitstrings are in different states of adaptation to their environment as time passes and both environments and genomes change. In a dynamic environment (or a wide, general niche) more modules and subclasses (waiting in the wings, ready for activation if needed) is probably advantageous to a set of generations of the organism, whereas in a highly adapted state in a stable environment, and an environment with well established niches and in fact cross-supporting functions of those niches (a long-lived relatively stable ecosystem in relatively stable climate), the extra adaptability may carry costs of it being too difficult to retain that extra information reliably for the potential benefit it might have if things changed. The extra program bits can also be dangerous. Most organized variants of code-sections of the life-program are organism-killers, most of the time.
In summary, a longer bitstring at the core of life can only be supported by evolution if it earns its keep in life-preserving strategy execution.
I think life bitstrings (genomes) on Earth have GENERALLY been growing by 1 or 2 bits a year since life began (give or take an enormous waffle factor). But in some, relatively stable, organism-environment pairings, temporary program shortening trends may be advantageous prunings of the more wild-ass life mechanism "ideas".
Where are we going and why are we in a handbasket?
No, we don't mean progress towards something 'better'.
Evolution proceeds only towards a local optimum, never towards anything abstractly 'better' or 'more perfect'. Evolution has no interests, long term goals, or overall arrow of direction. That's standard. That's the version of the theory Darwin and Wallace framed, that's what Sir Francis Crick assumed to be true doing his work, that's what Richard Dawkins would argue right now.
Those same people would tell you evolution is not affected in the slightest by people changing environmental conditions so that some things which were once major disadvantages are not anymore, and that there is no 'should have died' in the theory.
I say this, because I disagree with some ideas people, including some prominent scientists, legitimately think are part of the theory. But usually if I bring that up on slashdot, I get negative modded to oblivion by people just like you. It's like being modded down for disagreeing with the "Standard Democratic Party" line, only to find out that the guys doing it also claim that party-line is "Strong spending for defense, no money for social programs". I never get to debate or discuss any real issues relating to Evolution, because by the time somebody who understands and agrees with the real theory is reading this thread, the whole topic will have drowned under dozens of mods from people who think they are defending Evolution from "Weirdo Creationists", when what they are defending is a weirdo theory with progress, devolution, and a bunch of other kerfluffle that has nothing to do with science.
Who is John Cabal?
This explains why the Vikings conquered the Mediterranean where the Assyrians, Hittites, Egyptians, Greeks, and Romans failed so miserably to make much of any kind of impression on history, and how the North Americans, who came from Asia and were the farthest removed from Africa, conquered the Europeans who were so much closer to Africa and had interbred with the dirty Neanderthals. Ditto for the Australians, who were also so far removed from Africa and conquered Europe too.
Don't laugh.
Look at how far we go to make sure medeival thugs who want to drag us all back about 1300 years don't get "offended".
Yeah, I'm talking about fundamentalist Islam.
Go ahead, mod me down. Kowtow to political correctness and chalk up stoning gays and subjugating women as "diversity" while you mock "ignorant Christians" and congratulate yourself on how "tolerant" you are.
On the other hand, a shorter DNA strand has less room for errors that might be non-life threatening.
Meaning duplication errors are magnified.
No, the odds of any given base pair being transcribed incorrectly is the same regardless of how long the chain of DNA is. Thus you will have exactly the same numbers of errors in vital genes as you would if mobile DNA is thrown in around those genes.
"bigger genome.... bigger mammals! that's it. The woolly mammoth was big because his dna was big! guess size does matter."
...
Sounds like you are insecure about your shrunken genome!
Meanwhile back in reality, here's some statistics
http://www.genomesize.com/statistics.php
There are 10 kinds of people in the world... those who understand binary and those who don't.
"I made this letter longer than usual because I lack the time to make it short." Blaise Pascal, 1656.
The watchmaker has had more time...
But usually if I bring that up on slashdot, I get negative modded to oblivion by people just like you.
Why on Earth would this bother you at all?
This is all beside the point.
A bigger genome != a more complex organism. What we seem to be finding is all sorts of funky ways for genes to be expressed. For those here who don't know, this is incredibly cool and froody. All that DNA formerly regarded as "junk" seems to be no such thing. We share lots of DNA sequences with rats and cockroaches, but expression is what counts.
But if you really want the ultimate in compact DNA with obfuscated (and self-modifying) code, I would recommend viruses. (Incidentally, a significant portion of our own DNA is of viral origin.) If there were a god, viruses would be my foremost evidence for its existence. And that god would definitely have to qualify as a really l337 geek.
So then we have the competition being between longer gene strands that aren't as efficient in duplicating, allowing more errors, and shorter genes that are better at making near-perfect copies of themselves. The shorter ones would tend to dominate - sort of like an evolutionary "principle of parsimony" - the shortest gene sequence that gets the job done wins.
Quoted from the wiki page on Darwin's Dangerous Idea:
The first chapter of part II, "Darwinian Thinking in Biology", asserts that life originated without any skyhooks, and the orderly world we know is the result of a blind and undirected shuffle through chaos.
That's all I'm saying. Adaptation is a continual process. As creatures adapt, they change their environment, which changes the selection criteria. Are wings 'progress?' Not to a worm. Are eyes? Not to a cave fish. Any thing in evolution that you can point to as 'progress,' I can point to a counter example where the exact same thing would be a liability.
- None can love freedom heartily, but good men; the rest love not freedom, but license. -- John Milton
The genome is shrinking because there is a selective advantage to a smaller genome when the environment is stable. Fewer errors can occur when copying for example. In unstable environments, having a larger genome with more adaptive mutations is a selective advantage. Shorter genomes marks species that are highly specialized to their environment.
Higher Logics: where programming meets science.