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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.'"
"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 genome.... bigger mammals! that's it. The woolly mammoth was big because his dna was big! guess size does matter.
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!
the genome in mammals is losing information. This is Devolution.
So there's less diversity possible today? Does that make evolution more difficult today than in the past?
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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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.
Perhaps the genome is being optimized by design patterns instead of procedural programing.
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).
Here's the actual scientific paper, rather than the blog.
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"
Sounds like some (open) source I hacked on years ago -- kept finding ways to take (stupid) things out without losing functionality.
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.
Some have over a hunred billion base pairs. There a tremendous amount of junk DNA and gene duplication.
Size does not matter.
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?
The selfish genes are deleting themselves
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....
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?
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.
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 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.
"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.
Slashdot is full of whiny partisan Republicans. Good thing you posted anonymously because you would lose huge amounts of karma.
Politicians don't shed their genes, they shed their genitalia.
GAAH! MY PRINTER IS ON FIRE!!! PUT IT OUT! PUT IT OUT!
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?
"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...
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?
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.
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.
Where are we going and why are we in a handbasket?
The philosopher of science Daniel Dennet 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 and his talks (e.g. TED2009, TED2006, TED2003, and TED2002).
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...
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.
Deleted
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.
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.
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?
Tsukasa: All I really want, is to be left alone...
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.
Infuriate left and right
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.
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"mammals started to radiate"
The question of whether a computer can think is no more interesting than the question of whether a submarine can swim.
Wait, how is this different than gotos and blocks (functions, objects, etc)?
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.
If it's for-profit but free, you're not the customer -- you're the product (e.g., the Slashdot Beta's "audience").
I recently watched a video where this was predicted.
I did a Google Search to find it again just for you guys:
YouTube - Polyworld: Using Evolution to Design Artificial Intelligence
Anyway, the author had an interesting theory to why this happened in his simulation. He thought that once the peak of the DNA complexity was reached, evolution started removing the unnecessary parts. Weather this is called evolution or devolution is debateable.
Mammalian still refactoring their code. And still practicing Extreme programming too.
That might change things by a small and near-constant factor, but the essence of the argument remains; that you need more bits of information to encode more strategies and more complex strategies for organism construction and maintenance.
Technically, the DNA is not encoding directly in binary anyway, it is something closer to base-4 with some symbols not useable. However, this is still very close to pure binary information representation, and is probably about as close as the requirements for chemical stability, transcription, copying-by-complement-creation etc allow. Only a small representation conversion factor is needed to represent the genome as binary information; the most "pure" and artifact-free, and theoretically, if arranged correctly, able to be the most compact representation of any information.
We will learn a lot about evolution, I believe, if we start applying Kolmogorov Complexity theory (formal descriptions of the complexity of an individual, particular bitstring) to analysis of genomes,
and specifically, if we consider what the relative Kolmogorov Complexity between two instances of a genome is.
Relative Kolmogov complexity asks how short a program (i.e. description of a set of changes) would it take to produce this bitstring (genome instance) if we had that bitstring (genome) originally. This factor must be highly related to the probability of producing this genome from that genome by mutations and evolutionary processes.
Where are we going and why are we in a handbasket?
Energetic systems will always loose energy. Evolutionary Information systems will do likewise. Complexity does not mean more information, it means that the information is better structured and free from redundancy. I.e. Simpler is better. K.I.S.S. (?), hardly a surprise that all levels of reality comply. The Universe is Consistent when viewed as an Energetic Information System- not as balls of gas and stone strung along by gravity.
i hope one day DNA invents SHA1 hashing so invalid duplicates are throw away.
then we can get rid of cancer plus live forever.
DNA isn't encoded in binary, but lengths are still referred to in "kb" (kilobases).
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These aren't loops. You might make an argument that they're like loop unrolling, except there's no loops. It's entirely possible to have a smaller protein with an entirely different structure, composition and function encoded in the same region as a larger protein. Plus, there's a complementary DNA strand; you can have DNA that encodes something in one direction and something different in the other!
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