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Computational Genomics
blamanj writes "Scientists at UC Santa Cruz have been using computational techniques to 'reverse engineer' the DNA of extinct species. David Haussler and colleagues created a hypothetical portion of ancestral mammalian DNA and let a computer model simulate the process of evolution. Then they made their algorithm work backward from these descendants, to see if it could recreate the original ancestor."
"Scientists at UC Santa Cruz have been using computational techniques to 'reverse engineer' the DNA of extinct species."
The scientists added that the Bush Administration's environmental policies will helpfully provide many more extinct species for the new techniques to be tested on.
Opinions on the Twiddler2 hand-held keyboard?
Does this seem like "we'll get the original order of a list based on the sorted order and knowing how the sort algorithm took to run" (in otherwords, bound to be so wrong as to be useless)?
Or is it just me?
--Ender
Loose things are easy to lose. You're getting your hair cut. They're going there to see their aunt.
From the article: "Then they made their algorithm work backward from these descendants, to see if it could recreate the original ancestor. The ancestor the algorithm came up with had a sequence that was 98% accurate..."
Human and chimpanzee DNA are about 98% similar, too. In that context, 98% similarity doesn't seem that impressive. Maybe someone needs to invent a new benchmark for sequence comparison for species that are already similar?
Apply this to birds and we'll get the gene sequence for raptors and other dinos..
Who's up for Jurassic Park? Anyone?
Wasn't "Computational Genomics" in the Sid Meier's Alpha Centauri Tech Tree?
Moo.
I read the Nature summary, but no real articles .. anyone know how they do the "working backwards" thing? I would've guessed some sort of Bayesian analysis, just like most people use to come up with phylogenetic trees, but it sounds like there's something more interesting going on here.
I don't know how well understood the lineage from dinosaurs to modern birds are, but I suspect you would need the genomes from a few species that are not descended from dinosaurs (say, mammals) as well, for interpolation rather than extrapolation of the dinosaur genome.
Even if we could recreate dinosaur DNA in this way, I doubt we have the technology to turn that DNA into a live animal, or even do a computer simulation of that process. Is anybody working on an open-source biochemical simulator?
- 1) Manually create a set of hypothetical data.
- 2) Run a mathematical algorithm to generate new data.
- 3) Run the converse of the algorithm on the generated data.
If an algorithm is truly reversable then, without the necessary randomization, such a process is likely to generate the original data with 100% accuracy. I'd have felt much better if they'd run two independent algorithms against each other: create descendants with ForwardA() and extract ancestors with BackwardB(), then do the same thing with ForwardB() and BackwardA().I figure by 2030 or so my 6-digit UID will be something to brag about.
Once we get things like this under control along with teraforming, we can seed barren planets. We can walk the universe like gods. Probably have to kick the old one's out first.
Someone hates these cans.
...Barclay's turned into a spider.
Theory and practice are the same in theory, but different in practice.
I believe the answer is in line with your explanation, but I still can't really visualize the process well enough to understand it. If the female rat is one year old and the human woman is 30, how come their respective egg cells are both 20 "cell generations" younger than those of their mothers?
While the entire rat population will experience a higher number of cell divisions (and thus a proportionally higher number of mutations) per unit time due to its size, those mutations will normally end up in different lineages rather than accumulate in the same lineage, and thus not contribute to a higher number of mutations in the same individual...
Ah! I think I get it now. Sykes was discussing mtDNA evolution, where lineages split, but never merge (as mitochondrial DNA is inherited along the maternal line only). This is of course different from nucleic DNA, which is combined from the DNA of two parents, thereby allowing mutations from both to merge in the same individual. The mutation rate is the same, but mtDNA mutations are more easily lost due to some mothers having sons only, no daughters. While any single nucleic mutation from either parent runs a 50% risk of being eliminated in a child, this is made up for by one couple having more than two children, whether male or female. This effect is way more noticeable with rats and their explosive reproduction.
It's late here, but I hope I didn't mess that reasoning up completely and there is still a grain of truth to it... :-)
Forget the 98% figure. It honestly doesn't mean anything at all. The tests are very accurate, but their results are meaningless. They amount to comparing two strings of binary written with a language and compiler that were lost 3 billion years ago, for a computer we don't understand. Measuring how every base pair matches up to every other base pair is useless. There are pieces of DNA that are far more important than others, like the ones that turn other genes on and off, or the ones that code for important enzymes.
The figure for how many identical base pairs we share doesn't mean much because we don't understand most of what the DNA is doing. A switch controlling production of an important chimp hormone could be switched off in humans, turning off the thousands of base pairs involved in creating that hormone. Read by this type of analysis, however, that system would read as only 1% different, rather than 100% different, because the base pairs stay on the chromosome even though they don't do anything.
Also, chimps don't even have the same number of chromosomes we do, so comparing the DNA strands in their 48 chromosomes to those in our 46 is to ignore significant changes in the overall organization of genes.
So please, stop asking for clarification on the percentage, because it just doesn't matter. All it tells us is that we are closely related, but not how close, or in what way.
-sig removed for tax purposes-
The percentage that doesn't matter is the similarity between human and chimp DNA, not the accuracy with which the artificial sequence was reconstructed after simulated mutations. While it's true that there is little if any correlation between DNA sequence similarity and similarity of the resultant physiologies, the simulation was only concerned with the DNA sequences themselves, not their manifestations as living creatures.
For all we know, the initial DNA sequence used for the simulation may have been entirely random, not related to the DNA of any organism alive today or in the past. The purpose of the experiment was to determine whether the reverse-engineering algorithm would be able to "undo" the simulated mutations, which it managed to do with 98% accuracy. This is a strictly quantitative measure, unrelated to the biochemical results of placing those DNA sequences in live cells.
One thing I doubt the simulated evolution can have taken into account is natural selection due to lethal mutations. Well, the simulation may have considered some percentage of mutations lethal and dropped them, but it may hardly have been able to predict which parts of the artificial DNA sequence would kill the embryo if they were mutated. Thus the resulting sequences were obviously even more artificial than the sequence they started with, but I doubt this mattered to the reverse-engineering algorithm. The scientists are merely comparing blueprints with each other, not the houses built from said blueprints. If you are interested in blueprint evolution, it doesn't matter what the houses look like or how similar they are to each other (assuming those blueprints are based on other blueprints only, not on actual houses previously built).
Of course, but this doesn't affect the mutation rate, and thus won't explain the differing mutation rates between rats and humans. A mutation in a rat's brain cell is no more likely to make it to the reproductive organs than a mutation in a human brain cell, in spite of the rat being a lot smaller (it supposedly has fewer of all kinds of cells, not smaller cells).
Instead, the number of mutations passed on to future generations relates to the number of times the DNA helix is split and copied between two successive conceptions, ignoring what happens in non-reproductive organs of the body. As others have explained, that number appears to be constant with mammals, resulting in faster mutation rates for species with shorter generation spans, although this theory is probably not cast in stone yet.