What is Digg?30 Comments
- Lane, on 10/12/2007, -4/+24God loves efficient coding!
- burkay, on 10/12/2007, -1/+10@dcoolidge
and then in two generations the human race would be extinct.
it is not about compression, it is about error recovery. - Langford, on 10/12/2007, -1/+7This creature does reproduce on it's own however. It may not produce all the proteins it needs to live, but neither do humans. What it lacks, it gets from it's food, which would be the insect's material. It still fulfills the requirements to be considered living, if only barely.
http://en.wikipedia.org/wiki/Life#A_conventional_definition
Some might say that a virus deserves to be called living too, but what can I say, untestable definitions are subject to interpretation, and the line has to fall somewhere. I don't think a viruse resonds to stimuli either, except for maybe chimical based stimuli. - bloodylip, on 10/12/2007, -2/+7You don't depend on errors, but you should be prepared for them when they happen. I'd hate to use whatever results from your code.
- Xirto, on 10/12/2007, -0/+5@Anpheus: Introns are not considered "junk DNA" anymore. There is now evidence that introns have many functions such as gene expression regulation.
- Matteos, on 10/12/2007, -0/+5The errors are necessary, its called evolution.
- Hegemony, on 10/12/2007, -0/+4Actually he's not very well versed in biochemistry, kakapu4u (your name makes me giggle).
@democracy
Where would you get these ideas? Have you taken a degree in biochemistry? I'd bet not since that was entirely wrong. Here are the main problems with your argument (which I suspect is copied and pasted). The conversion of L-Amino Acids to D-Amino Acids is not complete. In fact it's not close. It exists in an equilibrium governed by Le Chatelier's Principle. I have a jar of L-Arginine in my lab if you don't believe me.
Also, your assumption that an amino acid forms a bond every second is WAY off. An entire protein (even globular proteins) folds completely in about 1 microsecond. Most of the folding takes place in the first 60 nanoseconds. Things happen very fast on the molecular level.
Next, you completely ignore any catalytic action taken by any of these proteins. And you skipped right from your Amino Acid sea to 124 proteins with no explanation.
And finally, your misunderstanding the number of conformations a protein can have. Sure you can calculate all these different orientations (phi-psi angles) that amino acids can take on. But most of them are impossible because of steric hindrance. Only thermodynamically favored bonds will form and bonds can sample conformations at the rate of 10^13 per second. This is known as the energy surface model in which functional conformation is obtained as proteins approach their lowest energy state. - lordmetroid, on 10/12/2007, -0/+4The problem is... This organism is enslaved by it's host. I doubt it even can produce keyparts of it's metabloic chain to reproduce.
- mkayatta, on 10/12/2007, -0/+4@Xitro
introns are not the only nonexpressed part of genomes. what about promoter regions and histone recognition sequences that are not encoded. without these how would we regulate gene expression? and yes, there is of course a ton of crap that we could get rid of, but still exists (if it ain't broken don't fix it). - onwardknave, on 10/12/2007, -0/+3@Langford: Humans derive their external proteins from consumption of external materials, not from within another cell. Yes, they're two different scales of "external environments," technically, but since the external environment of a symbiont is, in this case, another cell, that inherently categorizes the lifeform differently than if it were able to survive outside. Semantics to a degree, yet still technically relevant.
For anyone interested, Lynn Margulis pioneered the endosymbiotic theory of evolution. She still teaches as a Distinguished Professor of Biology at the University of Massachusetts in Amherst, and she's smart as a whip. - kakapu4u, on 10/12/2007, -0/+3You sound pretty well versed in this biochemistry stuff, but your argument is poorly formatted visually because it's just a huge block of text. Dividing into smaller groups of closer related concepts would make it much easier to read.
For your calculation tho, you use one Earth's worth of water molecules as your planetary quantity of amino acids. How many water molecules is that? - YourTechSupport, on 10/12/2007, -1/+4Okay. Where can I download the source from?
- Altotus, on 10/12/2007, -1/+4To be fair, the bacterium is a symbiote. It need not have the full complement of genes that a free-living organism would require because it has a less variable environment and can rely on the host for a considerable amount of its metabolic balance.
You'd expect to find this sort of thing occurring in nature. You'd also expect this organism to not handle life outside the insect very well. - inactive, on 10/12/2007, -0/+2@lordmetroid,
You're right: it probably can't. But that's not the point, really. The point is that we possibly have a model organism in transition to becoming an organelle. This discover could allow the verification behind the hypotheses behind the formation of organelles, e.g. mitochondrion, chloroplasts. - VAXcat, on 10/12/2007, -0/+21 to 1078436? Those aren't that long odds...now did you mean 1 to the 1078436th power? That's equal to 1....even better odds...sure success...maybe you meant 1X10 to the 1078436....BTW, there is plenty else wrong with your argument...you totally don't understand how a system with gain in it works.
- rbowes, on 10/12/2007, -1/+3The human genome is about 3 BILLION base pairs long. Good luck compressing that to 150,000, thats a 20,000 fold compression.
- inactive, on 10/12/2007, -0/+1Chloroplasts and mitochondria are symbiotic bacteria living inside eukaryote cells, much like this reported bacterium does. The mitochondrion genome is about 15000 bases, one tenth of this "smallest genome".
Also, as has been pointed out, these organisms have minute genomes because they a) have no redundancy in the genome and b) have outsourced a lot of their protein production to the host cell.
Has anyone managed to get DNA out of a nanobacterium yet? - tmcdigg, on 10/12/2007, -0/+1there is still alot we don't know about the requirements of life, much less to say "ultimate minimum requirements"
NoOne has invented equipment to see micro life, much less understand how it works or issue wonderfully intelligent ideas on the subject - madsci, on 10/12/2007, -4/+5It's interesting how they characterized this bug as "living" because of the need to depend on some genetic material of the host for life. I believe that is why viruses are not classified as being alive because of the dependence of the infected cell for viral reproduction.
- ollj, on 10/12/2007, -1/+2If you search for genomes on the internet you will find them, most are "open source" (and relatively small filesize) in one of a dozen catalogues.
But do not tempt to open the complete E-coli.txt genome in word or wordpad, it takes some time and then your is likely to crash. - asoulrebellion, on 10/12/2007, -0/+0ID troll Dug Down
- lisuebie, on 10/12/2007, -0/+0Me, I think the most interesting part of this story is the small number of genes and small number of proteins they determine. Makes this bacteria a prime candidate for studying gene expression or whatever it's called, no? And maybe for more on the topic of how genes interact in determining proteins.
But maybe not. I don't know much about all this. Just looks to me like a simple system, closer to an interpretable model than more complex critters are. - Anpheus, on 10/12/2007, -4/+2While that's doubtless not true, merely because of the amount of redundancy used by the human genome, it is true that the vast majority of DNA in most creatures is 'extra' and never used.
- unloud, on 10/12/2007, -3/+1God believes in security through obscurity....that's why we're vulnerable to these viruses.
- inactive, on 10/12/2007, -3/+1Does anyone really care?
- musntSurfatWork, on 10/12/2007, -5/+2We earthlings are tiny genomes to those living at large in the universe.
- Buddhist, on 10/12/2007, -5/+2Tiny bugs = Tiny genomes, apparently?
- democracysucks, on 10/12/2007, -5/+2Theoretically, the smallest living organism would consist of 124 proteins. This is much smaller than what we've actually found, but this is what scientists guess would be the smallest. Now, living organisms consist ONLY of L-amino acids, and no D-amino acids (just has to do with orientation). Outside of a living thing, the proteins change to 50% L and %50 D, no matter what we do to try to stop them. Even if we START with all L-forms, they change to D-forms. So somehow, without intelligence (even though we can't do it today WITH intelligence), 100% L-forms would have to be found and maintained and put together just right to create a chemical similarity to living organisms. So let's say we had 1031 earths in the universe. That's 100000000000000000000000000000000 earths in the universe, each with oceans of, instead of water, amino acids. EVERY molecule in these oceans, we'll say, is an amino acid. Let's say every single amino acid in each ocean of each earth combined with another amino acid every second for 10 billion years, non-stop. The likelihood that 100% L-amino acids would ever form to create the smallest 124 proteins is 1 to 1078436 against. I don't have enough time to type all those zeros, but you get the picture. And that's not even being picky about which proteins you get (very few of the thousands of proteins we know could be used in these living organisms that supposedly formed). Now, the law of probability says anything that is 1 to 1050 against will never happen, though it's been recently accepted that anything 1 to 1020 against will never happen, no matter what. Looks like even just L-proteins could never form. That's forgetting about D-sugars, cell organelles, atmospheric conditions that would destroy anything that DID form the instant it happened, etc.
- dcoolidge, on 10/12/2007, -7/+2The current human gemone could be replaced with a well written genome of about 150,000 base pairs.
- dcoolidge, on 10/12/2007, -8/+2@burkay
Depending on errors to happen is the worst code I've ever worked with.
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