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The Incredible Shrinking Genome

Soulskill posted more than 5 years ago | from the hey-it's-cold-alright dept.

Science 113

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.'"

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Indeed (0)

Anonymous Coward | more than 5 years ago | (#28542187)

"Unlike flies, mammals are still cleaning up."

Unlike what you may expect, the flies are actually doing something rather disgusting on that crap, rather than cleaning it up.

Bigger mammals! (1, Funny)

Anonymous Coward | more than 5 years ago | (#28542215)

bigger genome.... bigger mammals! that's it. The woolly mammoth was big because his dna was big! guess size does matter.

Genome size (4, Informative)

MindKata (957167) | more than 5 years ago | (#28543665)

"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 [genomesize.com]

Re:Genome size (1, Funny)

Anonymous Coward | more than 5 years ago | (#28544947)

I was in the genome pool! I was in the genome pool! There was shrinkage ...

Re: The Incredible Shrinking Genome (-1, Troll)

Anonymous Coward | more than 5 years ago | (#28542223)

We still haven't shed the genes that make some people become Republicans...

Re: The Incredible Shrinking Genome (3, Insightful)

Lifyre (960576) | more than 5 years ago | (#28542507)

We still haven't shed the genes that make some people become Politicians...

There fixed that for you...

CAREFUL! (0)

Anonymous Coward | more than 5 years ago | (#28543777)

Slashdot is full of whiny partisan Republicans. Good thing you posted anonymously because you would lose huge amounts of karma.

Re:CAREFUL! (1)

The End Of Days (1243248) | more than 5 years ago | (#28546177)

replace "Republicans" with assholes, because the whining knows no party lines around here.

Re:CAREFUL! (0)

Anonymous Coward | more than 5 years ago | (#28546975)

replace "Republicans" with assholes

You mean like this guy? [slashdot.org] Or this guy? [slashdot.org] Yeah, you're right!

Re:CAREFUL! (0)

Anonymous Coward | more than 5 years ago | (#28547059)

That would have made more sense if you linked to comments of mine where I whined.

Still, give yourself a pat on the back for almost being clever. I'm sure it's the closest you've ever come.

Re: The Incredible Shrinking Genome (1)

Eudial (590661) | more than 5 years ago | (#28543969)

Politicians don't shed their genes, they shed their genitalia.

refactoring (4, Funny)

farker haiku (883529) | more than 5 years ago | (#28542251)

I blame it on increased use of design patterns and better tools for refactoring ;)

Re:refactoring (1)

Fenris Ulf (208159) | more than 5 years ago | (#28542771)

I was going to make a similar joke.

No coincidence that I'm halfway through Fowler's book at the moment.

Re:refactoring (0)

Anonymous Coward | more than 5 years ago | (#28542849)

It's all natural selection, versus survival. Where species that are being preyed upon need to be small in order to be faster. Versus dominance in choice of partner of small mammals, most females are smaller anyway.

The larger the other subject is the more cumbersome the appearance would be to a smaller specimen. That's basically why Chuck Norris is ye bigger than Bruce Lee.

Not quite. (3, Informative)

BrokenHalo (565198) | more than 5 years ago | (#28544897)

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.

Re:Not quite. (0)

Anonymous Coward | more than 5 years ago | (#28546667)

If there were a god, viruses would be my foremost evidence for its existence. I wouldn't go that far, but since viruses by definition splice host genes, I believe it is highly likely that viruses are the driving force behind evolution. The question is, can you attribute any intelligence on the part of the viruses as contributing to this process? More likely it is a random unintended consequence of their simple attempts to propagate themselves.

Re:Not quite. (2, Interesting)

BrokenHalo (565198) | more than 5 years ago | (#28546767)

The question is, can you attribute any intelligence on the part of the viruses as contributing to this process?

No. I was merely postulating that their chemistry is way beyond cool, and that if I were a God, I would be fucking proud to have come up with them. :-)

Re:refactoring (1)

MindKata (957167) | more than 5 years ago | (#28543159)

"I blame it on increased use of design patterns and better tools for refactoring"

So its taken us 65 million years to become more optimal?!.

Still it helps explains politicians, they must be running an earlier version?

So if its taken us 65 million years, then I can't wait for Windows 6502009 !

(My old programmer brain just threw an interrupt when I wrote down the numbers 6502 ... ahh ... memories ... maybe it means Windows will be so optimal by then, that it'll run on a 6502!).

Re:refactoring (1)

HTH NE1 (675604) | more than 5 years ago | (#28547851)

(My old programmer brain just threw an interrupt when I wrote down the numbers 6502 ... ahh ... memories ... maybe it means Windows will be so optimal by then, that it'll run on a 6502!).

If it's good enough for a T-800....

Re:refactoring (0)

Anonymous Coward | more than 5 years ago | (#28544857)

Oh, those "pattern" nuts drive me crazy: they force fit stuff.

entropy is winning (0)

Anonymous Coward | more than 5 years ago | (#28542255)

the genome in mammals is losing information. This is Devolution.

Re:entropy is winning (4, Insightful)

DigiShaman (671371) | more than 5 years ago | (#28542305)

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.

Re:entropy is winning (0)

Anonymous Coward | more than 5 years ago | (#28542487)

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).
Keeping humans alive that should have died at a young age, helping people that have troubles creating offspring, create offspring, ...
will certainly affect the 'natural' evolution.

Re:entropy is winning (4, Informative)

mcvos (645701) | more than 5 years ago | (#28542657)

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.

Re:entropy is winning (1)

tyrione (134248) | more than 5 years ago | (#28546461)

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.

If it survives and produces, it's prospers. If it dies before reproduction, it fails.

Re:entropy is winning (5, Insightful)

spun (1352) | more than 5 years ago | (#28542707)

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.

Re:entropy is winning (0)

Anonymous Coward | more than 5 years ago | (#28543681)

Um, you realize your second paragraph flat out contradicts your first?

Re:entropy is winning (1)

spun (1352) | more than 5 years ago | (#28544091)

No, it doesn't. Sure, today's genetic parasite might be tomorrow's genetic savior, which is why I said 'tends to muck things up.' We're talking about transposons, sections of DNA that (apparently) don't do anything except jump around and mess up other sections of the genome.

To put it another way, throwing this stuff away has been advantageous. Whether it will be in the future remains to be seen. We could be walking down a dead end street here, and the other critters, who haven't been cleaning house, could be the ones who have gotten it right.

Evolution and progress (1)

ACorrosionOfDeviants (877893) | more than 5 years ago | (#28545471)

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.

The philosopher of science Daniel Dennet [wikipedia.org] argues quite persuasively that evolution does indeed result in real progress, beyond fleeting temporary advantage. His arguments are best articulated in Darwin's Dangerous Idea [wikipedia.org] and his talks (e.g. TED2009 [ted.com] , TED2006 [ted.com] , TED2003 [ted.com] , and TED2002 [ted.com] ).

The jury is still out on whether Dennet is right on this point, but it has support from some evolutionary biologists, and the debates continue...

Re:Evolution and progress (3, Insightful)

spun (1352) | more than 5 years ago | (#28546393)

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.

Re:Evolution and progress (1)

HiThere (15173) | more than 5 years ago | (#28546413)

I think he's wrong. It's a drunkards walk kind of thing, except the drunk occasionally bifurcates, and the two copies walk in different directions.

OTOH, there are two definite biases in the situation:
1) We are biased in what we notice. If it's larger and lives on top of the ground, e.g., we are more likely to notice it.
2) There's a smallest size. Things can only get so small and remain alive. So that's a boundary of one kind. (There's also a large end boundary...but it's fuzzier, somewhere around the size of a blue whale. Probably nothing larger than twice that size is possible with a standard genome. )

It's worth noting, however, that almost all life on the planet it single cellular...mainly bacteria, blue-green algae, and their kin. Eukaryotes are a minority.

Re:entropy is winning (4, Insightful)

Artifakt (700173) | more than 5 years ago | (#28542903)

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.

Re:entropy is winning (2, Insightful)

LEMONedIScream (1111839) | more than 5 years ago | (#28544799)

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?

Re:no progress (1)

presidenteloco (659168) | more than 5 years ago | (#28545037)

Actually, evolution is progressing toward "increased sustained negentropy" in the matter and energy patterns exhibited in a local spacetime region.

Increased sustained negentropy is roughly more and more matter and energy in the region being describable (its form and disposition) by fewer bits of information (per joule or gram?) over time. The matter and energy are becoming more regular and more homeostatic (in overall larger chunks). The patterns govern more matter and energy in the region over time, and the patterns last longer (are instantiated for longer in matter and energy in the region) as evolution of the patterns progresses.

It is true that evolution "uses" unbiased methods (based on random variation and selection) in "accomplishing" this trend, but a trend it is indeed.

Another way of thinking about this is to say that selection processes shape their environment, and generally, the more long-lasting results of selection will be those which manage to lower the entropy in their surrounding environment, eventually essentially incorporating aspects of that environment into the functioning system that the evolving genome controls.

Re:entropy is winning (2, Insightful)

cool_story_bro (1522525) | more than 5 years ago | (#28542489)

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.

Re:entropy is winning (1)

Archangel Michael (180766) | more than 5 years ago | (#28542729)

On the other hand, a shorter DNA strand has less room for errors that might be non-life threatening.

Meaning duplication errors are magnified.

It is interesting to see how people view news like this, as people tend to fit the results into their own world views.

The way I view this is not "XOR" logic, as it could be BOTH. Yes, there is less chance of problems, but greater chance those problems are life threatening.

And, just like I view things, there is blessing and curses in everything. Read the following link if you want a better look into my world view.

http://www.crosswalk.com/careers/11583282/ [crosswalk.com]

Re:entropy is winning (4, Informative)

holmstar (1388267) | more than 5 years ago | (#28543407)

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.

Re:entropy is winning (0)

Anonymous Coward | more than 5 years ago | (#28545161)

[citation desired]

Re:entropy is winning (1)

DigiShaman (671371) | more than 5 years ago | (#28546277)

I've read (a post here on /. that "Junk DNA" is supposedly an agent to both protect vital genes and improve the odds that those vital genes don't be come corrupted in comparison to junk dns. IE, they act as the sacrificial lamb if you will.

Not sure if it's a valid explanation, but it makes sense to me.

Re:entropy is winning (1)

Archangel Michael (180766) | more than 5 years ago | (#28546855)

You are assuming that errors occur at a particular rate per base pair. If that assumption is off, then your whole premise is off.

Again, it may be better, or it may be worse. We don't have ENOUGH INFORMATION to do anything but guess based upon assumptions. I'm not willing to assume much.

Re:entropy is winning (2, Interesting)

tomhudson (43916) | more than 5 years ago | (#28545339)

On the other hand, a shorter DNA strand has less room for errors that might be non-life threatening.

Meaning duplication errors are magnified.

... but since those duplication errors ARE life-threatening, they get removed from the gene pool more efficiently. So over time, the shorter genes would tend to have better duplication, since the ones that don't duplicate properly are culled much more ruthlessly (ok - "ruthlessly" is an anthropomorphism - but you know what I mean).

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.

Re:entropy is winning (1)

John Hasler (414242) | more than 5 years ago | (#28542767)

> All else being equal, Short DNA may logically be a defense against cancers and other
> genetic diseases.

And against useful mutations.

Re:entropy is winning (0)

Anonymous Coward | more than 5 years ago | (#28542801)

And against useful mutations.

such as shorter DNA strands?

Re:entropy is winning (1)

tomsomething (1553077) | more than 5 years ago | (#28545293)

"Devolution" is like "reverse racism". Really just evolution and racism (respectively).

Evolutionary Problems? (0)

Anonymous Coward | more than 5 years ago | (#28542257)

So there's less diversity possible today? Does that make evolution more difficult today than in the past?

Re:Evolutionary Problems? (1)

mcvos (645701) | more than 5 years ago | (#28542681)

No idea, but it's an interesting thought.

My Crazy Idea (2, Funny)

MarkPNeyer (729607) | more than 5 years ago | (#28542273)

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.

Re:My Crazy Idea (1)

ruin20 (1242396) | more than 5 years ago | (#28542411)

Everyone knows god programed in perl :) [xkcd.com]

It's the Right Idea (0)

Anonymous Coward | more than 5 years ago | (#28542415)

"God" could also be replaced by "evolution". It explains why late-stage man -- i. e., non-Africans -- is smarter and more accomplished than early-stage man -- i. e., Africans. As man migrated out of Africa and traveled to the endpoints of Europe and Japan, the harshness and variations of the environment eliminated the genomic variations exhibiting lesser intelligence.

The effects are quite pronounced. Non-Africans (notably, ethnic Jews) have an IQ that is 20% greater than that of Africans. The developers of computer technology -- including the computer that you are using to read Slashdot -- are nearly 100% European or Asian (including Americans of European or Asian ancestry).

Re:It's the Right Idea (0, Troll)

A nonymous Coward (7548) | more than 5 years ago | (#28542677)

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.

Re:It's the Right Idea (2, Insightful)

Anonymous Coward | more than 5 years ago | (#28543191)

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.

Re:It's the Right Idea (0, Offtopic)

A nonymous Coward (7548) | more than 5 years ago | (#28544561)

Fundamentalist Islam goes back 1300 years? Fundamentalist Christianity goes back 2000 years! Ha! The ignorant Christians beat the ignorant Muslims again.

Then there's the fact that the ignorant fundamentalist Christians don't even know their own bible, calling gay marriage an affront to traditional Christian marriage, ignoring the Mormons in their modern day midst who are more Christian in their views on marrying multiple wives (but not multiple husbands) and at a young age too. Yes, let's bring back traditional biblical marriage, widows being forced to marry their brother-in-laws, multiple young wives, all that good Christian marriage stuff.

Trolling the trolls is so much fun.

What a bummer (1)

A nonymous Coward (7548) | more than 5 years ago | (#28548287)

Original troll modded 0, my retroll modded -1 Troll, then his response +1 Insightful? and my reretroll modded -1 Offtopic?!? Come on, give me at least a -1 Flamebait. I stayed very clearly on the original poster's troll topic.

Buncha Fundamentalist Christians running around here, I swear. I'm surprised they have so much time to waste on slashdot with that ... thing ... in the formerly white house. On the other hand, good to get them riled up and venting their bile here rather than on talk radio.

Re:It's the Right Idea (0)

Anonymous Coward | more than 5 years ago | (#28543427)

IQ tests are a bad bad metric for proving there's a genetic difference in intelligence. If you want to explore genetic differences between the races, and not come across as a total asshole, then please, please, don't bring up IQ tests. Come up with a way to examine intelligence that isn't so subjective. That'd be productive even aside from the genetics issues.

Re:It's the Right Idea (1)

Kayden (1406747) | more than 5 years ago | (#28546963)

Why are people so terrified by the thought of the BREEDs (we're all that same race, just different breeds) of human being different? Do you honestly think the only difference between white, black and asian is skin color, big noses, and slanty eyes? Irish are more likely to have red hair and green eyes. Scandinavians are likely to be tall, blond, and blue eyed. Black people are prone to blood pressure issues, naturally develop muscle easier, and have a natural resistance to malaria. Asian people are good at math and are generally short. Is it really so hard to imagine that maybe there is something different about mental faculties between breeds? Why are IQ tests a bad metric? Are they a bad metric because people in general can have largely varying results or are they a bad metric because different breeds score consistently lower? If it's consistent, good or bad, it shows there is an obvious difference. You can argue that the learn different or you can just call them inferior. Different is different; just because we should all be equals doesn't mean we're all the same.

IQ tests are too narrow. (1)

Valdrax (32670) | more than 5 years ago | (#28552997)

Why are IQ tests a bad metric? Are they a bad metric because people in general can have largely varying results or are they a bad metric because different breeds score consistently lower? If it's consistent, good or bad, it shows there is an obvious difference.

IQ tests only measure a few, testing-friendly types of intelligence; they do not, by far, fairly measure the full range of human cognition. For example, they poorly test long-term memory and ability to categorize general knowledge (and not a particular, dominant culture's assumed shared knowledge), navigation and non-local spatial awareness, empathy and awareness of the emotional state of other humans, musical ability, kinetic learning, fluency with multiple languages and the ease of learning new ones, etc.

Most IQ tests are biased somewhat towards testing the kind of capability that formal schooling imparts to people. Naturally, the more schooling you've had, and the more schooling your parents had, the better you'll do on these tests. But that's not the kind of intellectual ability that necessarily thrives in a hunter-gatherer society. There are different social and environmental pressures in said societies.

For example, I score extremely well on tests that measure verbal and math ability and have a well above average IQ. However, I'm utterly incompetent at learning how to speak new languages whereas I know several people from my sister's church who were mediocre high school students (and who didn't go on to college) who speak 3-4 languages now. Different aptitudes; different IQ scores. But am I inherently more intelligent than them due to a higher IQ score and greater academic ability? As I get older and wiser, I really don't think so anymore. If I lived in a culture where traveling a mere 5-10 miles meant that no one spoke the same language as you, I'd be helpless.

I recommend you read the opening chapter of "Guns, Germs, and Steel." The author, who spent many years with tribesmen of Papua New Guinea, takes an aggressive stance against the notion that some races are just mentally "superior" to others. The people he spent time with were capable of many mental feats he wasn't -- traveling long distances through unfamiliar wilderness without getting lost, being able to identify thousands of plant and animal species at a glance, etc. These are forms in intelligence that IQ tests do not measure well, and in the eyes of the people who live in these societies, our most valued forms of intelligence might make us seem stupid in comparison.

Re:My Crazy Idea (1)

Artifakt (700173) | more than 5 years ago | (#28542935)

Or we should all become polytheists, because God has open-sourced the project, and it's getting small and streamlined because of the 'many eyes' effect.

Summary of the article (4, Informative)

Absolut187 (816431) | more than 5 years ago | (#28542303)

Mammals genomes are getting smaller, primarily by cleaning out viral DNA.
This "house cleaning" seems to have started about the time of the massive KT extinction that killed the dinosaurs. Nobody knows for sure how or why the cleaning is occuring, although some hypotheses are set forth. Nobody knows whether it has anything to do with the KT extinction..

Think of genes as living things (1)

Colin Smith (2679) | more than 5 years ago | (#28545903)

Eventually some outcompete the others by allowing their replication machines to replicate more successfully. The ones which don't, also die off because their replication machines are unable to reproduce.

The result is an averaging out of gene noise, leaving only the successful signal for a particular niche.

smaller code size without copy& paste (5, Informative)

sadtrev (61519) | more than 5 years ago | (#28542315)

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.

Re:smaller code size without copy& paste (1)

DirtyUncleRon69 (1492865) | more than 5 years ago | (#28542443)

maybe global warming is the cause?

does that mean that heat is shrinking out genes?

Re:smaller code size without copy& paste (1)

mcvos (645701) | more than 5 years ago | (#28543009)

Do I need to point this out?

Global warming is very recent. Also, the amazing shrinking genome is about mammals in particular, and mammals can control their own temperature, which means environmental temperature has little or no effect on genes. It's possible that warmbloodedness is shrinking our genome, though (which is what the GP is suggesting).

Re:smaller code size without copy& paste (1)

DirtyUncleRon69 (1492865) | more than 5 years ago | (#28543139)

genes = jeans

it was not a serious post, but a badly worded attempt at a joke

Re:smaller code size without copy& paste (0)

Anonymous Coward | more than 5 years ago | (#28543663)

> Global warming is very recent.

No. Lady Gaea has done the global warming (and global freezing) thing quite a few times.

Al Gore being around to tell you about global warming is very recent.

I'm not saying we should be ignoring the phenomenon, we can probably mitigate some portion... but lil critters have survived and adapted to global changes plenty of times, and they'll still be doing so after humanity is wiped out by our arrogance at believing we can control "global warming" rather than recognizing that the energy involved is ludicrous amounts and learning how to adapt our civilization to the cyclic changes that our planet will be delivering to us whether we like it or not.

The frog's descendants will be fine, just as his ancestors have been for longer than humanity has infected this rock.

Re:smaller code size without copy& paste (2, Informative)

mcvos (645701) | more than 5 years ago | (#28544005)

> Global warming is very recent.

No. Lady Gaea has done the global warming (and global freezing) thing quite a few times.

The current global warming trend (which is what is generally meant by the phrase) is very recent. In the last 65 million years, I bet the earth has several times been warmer than it is now.

Re:smaller code size without copy& paste (1)

MartinSchou (1360093) | more than 5 years ago | (#28551513)

In the last 65 million years, I bet the earth has several times been warmer than it is now.

Do you mean in Celsius, Fahrenheit or Kelvin?

Currently it's about 15 C/59 F/288 K
Double that in C is 30 C/86 F/303 K
Double in F is 118 F/47 C/320 K
Double in K is 576 K/302 C/577 F

Even if you meant Celsius I rather doubt the Earth has had that kind of average temperature going back that short a period. But I can't seem to find any lists of estimated global temperatures that far back. Hell, couldn't even find one for the ice ages.

Re:smaller code size without copy& paste (0)

Anonymous Coward | more than 5 years ago | (#28552393)

"has several times been", not "has been several times"...

Re:smaller code size without copy& paste (2, Interesting)

lavaforge (245529) | more than 5 years ago | (#28543169)

Are we seeing the same tendency in other warm blooded creatures, such as birds?

Re:smaller code size without copy& paste (1)

CrimsonAvenger (580665) | more than 5 years ago | (#28543831)

Are we seeing the same tendency in other warm blooded creatures, such as birds?

Since birds are dinosaurs, I'd expect not.

Re:smaller code size without copy& paste (1)

jae471 (1102461) | more than 5 years ago | (#28544779)

We should, if enzyme temperature range is a legitimate reason for the change.

We should also expect to see less of an effect in monotreme mammals (the platypus and echidna genera). They don't exhibit as much thermal stability as plancentals and marsupials, so they should need a wider range of enzymes. But 3 living genera makes a poor sample size, and the fossil record for monotremes is very poor.

Re:smaller code size without copy& paste (1)

Tablizer (95088) | more than 5 years ago | (#28544725)

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.

But the downside is that mammals have to eat a lot more to maintain a constant temperature. Amphibians and reptiles can go a lot longer without food. This is partly why mammals have a bigger brain: we have to catch more food per hour, and this requires a more complicated life-style and a wider diet. Amphibians and reptiles mostly sit around and wait for the right kind of food to come their way. Mammals instead have to move, dig, poke, prod, etc. to eat everything they can. Bigger brains are also expensive to feed, which puts even more pressure on food volume.

Mammal teeth is also different because we have to eat faster by chewing the food first. Most carnivorous reptiles swallow their prey almost whole, then sit around hidden for days or weeks slowly chemically digesting the victim. Thus, reptile teeth are pointy for capture, but not very useful for grinding for size reduction. Mammals tend to rely on social coordination to capture relatively large prey, not so much spiky teeth. But this social coordination also requires a bigger brain.
     

Design paterns? (0, Redundant)

line-bundle (235965) | more than 5 years ago | (#28542359)

Perhaps the genome is being optimized by design patterns instead of procedural programing.

Actual paper (5, Informative)

drunken_boxer777 (985820) | more than 5 years ago | (#28542477)

Here's [oxfordjournals.org] the actual scientific paper, rather than the blog.

Re:Actual paper (0)

Anonymous Coward | more than 5 years ago | (#28543257)

Thank you!

I can code that human in 44, maybe 42 chromosomes (1, Insightful)

Anonymous Coward | more than 5 years ago | (#28542529)

Sounds like some (open) source I hacked on years ago -- kept finding ways to take (stupid) things out without losing functionality.

Re:I can code that human in 44, maybe 42 chromosom (0)

Anonymous Coward | more than 5 years ago | (#28546369)

Do you imply that the universe is just a half-baked hacking project in some divine geek's basement ?
Oops - I see the fnords now. Nevermind.

X-Files was right!! (0)

Anonymous Coward | more than 5 years ago | (#28542577)

There is then still a chance that those strange branches of species we here about in the movies and X-Files tv series could still be or become reality.

Ameoba is ten times larger than human (4, Informative)

peter303 (12292) | more than 5 years ago | (#28542579)

Some have over a hunred billion base pairs. There a tremendous amount of junk DNA and gene duplication.

Size does not matter.

Re:Ameoba is ten times larger than human (0)

Daimanta (1140543) | more than 5 years ago | (#28542755)

"Size does not matter."

That's what SHE said!

Re:Ameoba is ten times larger than human (1)

Eddy Luten (1166889) | more than 5 years ago | (#28543383)

No, it's what guys tell themselves.

Re:Ameoba is ten times larger than human (1)

MaXintosh (159753) | more than 5 years ago | (#28543353)

Exactly. I have to wonder, if mammals' radiation is the cause of their shrinking genome, what powerful radiation did pufferfish undergo to shed so much of theirs? And where's all the left over diversity from that radiation?
Every now and then people publish papers announcing they've solved the C-value paradox. I think it's like a bunch of undergrads who think they've solved the problem of induction the first time they hear about it. Except these guys have Ph.Ds, and get slashdot stories for their whole-lot-of-nothing...

Re:Ameoba is ten times larger than human (0)

Anonymous Coward | more than 5 years ago | (#28543881)

...who think they've solved the problem of induction the first time they hear about it...

[sarcasm]But -their- model illustrates conclusively why it works... it fits the data perfectly![/sarcasm]

It's really sad how many PhDs don't even understand what induction is.

Fugu (1)

drunken_boxer777 (985820) | more than 5 years ago | (#28542615)

It's interesting that the authors looked at the Fugu genome when determining 'shrinkage'. The Fugu genome has roughly the same number of genes as the human genome, but is only 1/8th the size, meaning it is quite 'cleaned up'.

In fact, this is especially interesting because the Fugu genome isn't exactly representative of fish genomes in general, as most fish genomes are several times longer than the Fugu genome, and presumably don't contain a proportionate increase in the number of genes. There are other fish genomes out there (zebrafish, tetraodon, etc), so why choose one that is so devoid of non-coding DNA?

Obviously (0)

Anonymous Coward | more than 5 years ago | (#28542665)

The selfish genes are deleting themselves

NOP sledge anyone? (1)

js_sebastian (946118) | more than 5 years ago | (#28542723)

Organisms can acquire DNA from other organisms by inserting bits of foreign DNA, known as mobile DNA, into the genome. One way this is done is by viral infections. Some viruses integrate genomic material of their own, and sometimes of other host organisms into the hosts they infect. If those viruses happen to also infect germ cells â" sperm or ova â" those insertions or retrotransposons would be passed on to subsequent generations. It is quite easy to identify these viral insertions: they are flanked by characteristic DNA stretches called Long Terminal Repeats or LTRs. During the infection and insertion process, LTRs serve as âoeinsertion hooksâ

Easy to detect? wait till they start using polymorphism....

General difficulty of preserving a "life-program" (3, Insightful)

presidenteloco (659168) | more than 5 years ago | (#28542825)

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".

Re:General difficulty of preserving a "life-progra (1)

xenocide2 (231786) | more than 5 years ago | (#28551441)

But you're missing a key point: DNA translates into protein in chunks of 3. Depending on where the translation starts, one chunk of DNA can translate into several different proteins. You don't actually need to grow the genome to increase the amount of proteins around, and it's probably the case that genomes will shrink over time as natural selection finds these random overlaps.

To put it in computing terms, you can have two or three programs in one binary just by changing the word alignment. The only way I can think of to get a complier to do that would be one based on genetic programming, funnily enough.

Re:General difficulty of preserving a "life-progra (0)

Anonymous Coward | more than 5 years ago | (#28551991)

Wait, how is this different than gotos and blocks (functions, objects, etc)?

Better immune system? (1)

hey (83763) | more than 5 years ago | (#28543481)

I suppose this could be because mammals have developed a better immune system that stops DNA insertions. Once the insertions stop of course then number will decrease as they are naturally cleanup up -- just as they are cleaned up in other animals.

But don't worry something will come along that will figure out how to do DNA insertions in mammals eventually.

Re:Better immune system? (1)

Mr. Firewall (578517) | more than 5 years ago | (#28545127)

But don't worry something will come along that will figure out how to do DNA insertions in mammals eventually.

Yes, I seem to recall having inserted my DNA into several mammals (which I was able to identify because they had mammaries) when I was younger....

mystery why mitochondria keep any DNA at all (1)

peter303 (12292) | more than 5 years ago | (#28543611)

Mitochrondia merged with eukaryote cells about a billion years ago. This allowed eukaryotes to increase metabolic power an order of magnitude over bacteria and evolve locomotive animal life.

A mystery is why mitochondia kept enough DNA to code for about 10% of their proteins after all these eons. They get the other 90% of proteins from nuclear DNA of the host cells. Nick Lane [amazon.com] suggests in his mitochondria book this DNA codes for the most essential emzymes such as those that break down free-radical waste which could quickly kill the mitchrondia.

Re:mystery why mitochondria keep any DNA at all (1)

Anonymous Coward | more than 5 years ago | (#28544759)

Presumably because there's no longer any selective pressure moving DNA from mitochondria to the nucleus. To make up a hypothesis, assume that if a mitochondrion has 100% of its "original" (ie, when it was still an independent, exogenous lifeform) then it is able to leave its host cell and resume independence, resulting in the host cell's death. This would select for those freak events involving transfer of mitochondrial DNA to the host cell (which, at this point in evolution, may or may not actually possess a proper nucleus), as the mitochondria would then be dependent on the host cell for survival. Once you have enough to ensure complete codependence, there's no selective pressure to bring any more over.

Alternately, there may be a point at which it is disadvantageous to the host cell to control all aspects of the mitochondria's reproduction and so forth. Perhaps it would reduce variation in a cell's mitochondrial population (undesirable), or perhaps it would simply be too complicated, and evolution hasn't quite figured out how to do it yet without killing the host or the mitochondrion or both.

Re:mystery why mitochondria keep any DNA at all (1)

HiThere (15173) | more than 5 years ago | (#28546955)

There is definite active pressure to move genes from the mitochondria to the nucleus. The environment inside the mitochondria is hostile to DNA because of the number of free radicals produced during the construction of ATP. (If I've got that bit wrong, during the release of energy.)

One result of this is that mitochondrial DNA evolves considerably faster than nuclear DNA. (Evolves here just means changes. I think it's usually neutral drift.) This may also be one of the reasons for aging. Too many cells mitochondria accumulate too many mutations, and become ineffective. I hypothesize that this is also one of the reasons for so many miscarriages at a very early stage (i.e., usually before the mother is even aware of anything). This is a remarkably high number that needs some kind of explanation, and this, it seems to me, may be the reason. (In this light it's strange that the mitochondria should be carried by the ova and not by the sperm, which would have a built-in selective mechanism in how efficiently they could generate energy while swimming. OTOH, evolution only has to be "good enough", and perhaps the sperm would find it easy to cheat. Just storing ATP, e.g., rather than generating it en-route.)

Summary (1)

AnotherBlackHat (265897) | more than 5 years ago | (#28544007)

About the time of the KT extinction, mammals starting spreading and evolving into new niches.
Around this same time, their genome expanded.
Then, after they had spread into lots of niches, their genome switched from expanding to shrinking.

And this is surprising?

As Blaise Pascal put it... (4, Insightful)

backwardMechanic (959818) | more than 5 years ago | (#28544123)

"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...

How do they know? (1)

MiniMax988 (1461911) | more than 5 years ago | (#28544425)

Does anyone know where they are getting 65 million year old mammal DNA? Can a full set of DNA really last that long? Are all the assumptions for the very long extrapolations of LTRs valid?

Re:How do they know? (1)

drunken_boxer777 (985820) | more than 5 years ago | (#28546289)

Does anyone know where they are getting 65 million year old mammal DNA?

They aren't using 65 million year old DNA. The authors are drawing conclusions about the size of the genome 65 million years ago from calculations of the rate at which mobile DNA elements have changed.

Can a full set of DNA really last that long?

It's unlikely, but possible. There has been recovery of dinosaur DNA, but not an entire genome.

Are all the assumptions for the very long extrapolations of LTRs valid?

Yes and no. The authors compared their observations to two different models. The observations fit somewhere in between both models, indicating that rates of change in genome size are not constant. This means that during time span A model one is correct but at time span B model two is correct.

Because our environment is stable (2, Interesting)

naasking (94116) | more than 5 years ago | (#28546491)

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.

Reason the dinosaurs died out? (1)

jameskojiro (705701) | more than 5 years ago | (#28548105)

Was it ultimately because their DNA was incapable of radiating because it had lost so much of it's "junk DNA" that it couldn't have pulled any information out to help it adapt to changes?

Love the pun from OP... (1)

vikstar (615372) | more than 5 years ago | (#28551827)

"mammals started to radiate"

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