Early links in the chain of being

April 22, 2010 8:40 AM

First there was Ida, the first molecule to self-replicate. (that's one hypothesis, anyway.) From Ida, eventually, came the Last Universal Common Ancestor, or Luca. The first substance to store information about itself in the form of a genetic code. Luca may be the form of Life from which all Life has evolved.
posted by cross_impact (32 comments total)

Does it live on the second floor?
posted by It's Raining Florence Henderson at 8:43 AM on April 22, 2010 [7 favorites]

Wrong Luca.
posted by InfidelZombie at 8:46 AM on April 22, 2010

Yeah, thought about throwing in a reference, but thought it better to play the straight man.
posted by cross_impact at 8:54 AM on April 22, 2010

It's a fascinating article, cross_impact. Thanks!
posted by It's Raining Florence Henderson at 8:57 AM on April 22, 2010

We can deduce Luca must have existed because all life forms that we know of - from bacteria and viruses to T. rex, bananas and humans - share the same genetic code, with a few small exceptions.

That's interesting. What are these exceptions?
posted by dunkadunc at 8:59 AM on April 22, 2010

"May your foist child be a thermophilic child..."
posted by stenseng at 9:05 AM on April 22, 2010 [4 favorites]

Does it live on the second floor?

No, silly, the ocean floor . . . Luca sleeps with the fishes.
posted by FelliniBlank at 9:07 AM on April 22, 2010 [5 favorites]

If you think convincing creationists that evolution is true was hard, when you can point to actual things and events around them to prove it, imagine trying to convince them of the scientific factuality of stuff that happened 4 thousandbillion years ago. Although if we can do it in the laboratory, that'd be sweet.
posted by DU at 9:08 AM on April 22, 2010

For Lane, these reactions in all probability happened around the piping hot black smokers of the oceanic abyss, where the Earth's crust is wrenched apart by immense geological forces. "In environments like hydrothermal vents it is likely, but as yet experimentally unproven, that a range of amino acids and nucleotides would be formed by the laws of chemistry," he says. Local currents, he adds, would probably draw the molecules together, making it more likely that self-replicating chains of RNA could form and associate with amino acids.

One of neat building blocks of Peter Watts' Rifters trilogy was that Luca had a competitor form of replicator (βehemoth) that simply never got a toehold outside of its origin hydrothermal vent, but once it did was so much more efficient at the molecular level that it cut the bottom of the food chain right out from under it wherever it spread. It was a great apocalypse foundation.
posted by Drastic at 9:08 AM on April 22, 2010 [1 favorite]

The first substance to store information about itself in the form of a genetic code.

Not necessarily, or even probably. I suspect several attempts occurred before a robust one persisted.
posted by Mental Wimp at 9:09 AM on April 22, 2010

In other words, the genetic code is the inevitable consequence of affinities between the molecular building blocks of RNA and those of the proteins they code for. If he's right, it will explain why individual triplets always code for the same amino acids, whether in a virus or a human.

Yarus works with artificial RNA and has shown that these chemical affinities do exist. Mix strands of RNA with amino acids and the amino acids will more or less spontaneously nestle up to their corresponding triplets. "Yarus found that anticodons [a type of triplet found in some RNAs] were particularly good in this regard and bind the 'correct' amino acid with up to a millionfold greater affinity than other amino acids," says Nick Lane of University College London.

Hmm, people didn't know that before? I guess in ordinary protein syntheses the amino acids are connected to tRNA which match up with the mRNA, so the natural affinities don't appear to matter. Wikipedia has a good animation showing protein synthesis.
posted by delmoi at 9:13 AM on April 22, 2010 [1 favorite]

What are these exceptions?

Some of us actually like cilantro, but that's more of a mutation.
posted by Pollomacho at 9:14 AM on April 22, 2010 [5 favorites]

Although if we can do it in the laboratory, that'd be sweet.

James Trefil et al - The Origin of Life

On the experimental side, some researchers, such as George Cody at the Carnegie Institution of Washington, D.C., are trying to work out the basic rules of organic chemistry for exotic environments that might have been relevant to the origin of life. Cody, for example, has worked on unraveling organic interactions at the kinds of temperatures and pressures that obtain at deep ocean vents. Mike Russell at the Jet Propulsion Laboratory in Pasadena, California, (author of “First Life,” January–February 2006) is building a large chamber to model the geochemistry of those environments. Shelley Copley at the University of Colorado at Boulder has been sorting out the intermediate chemistry leading to the current nucleic acid–protein system of genetic coding, with an eye toward resolving the chicken-and-egg problem.

We're getting there.
posted by kuujjuarapik at 9:25 AM on April 22, 2010

That's interesting. What are these exceptions?

Some of this is addressed at my nicely-related AskMe question from a couple weeks ago.
posted by shakespeherian at 9:25 AM on April 22, 2010

...Luca. The first substance to store information about itself in the form of a genetic code.

Which scientists are saying this? As I understand it, Luca was just the last substance to be an ancestor of all life on Earth. Not necessarily the first anything. Please correct me if I'm wrong.
posted by Mapes at 9:27 AM on April 22, 2010

I suspect several attempts occurred before a robust one persisted

That's probably right, but the next question is - isn't it likely that after the first persisting one, there were more, assuming the conditions continued for some time or even still exist? Or are we simply talking about an extraordinarily unlikely chance event that happened once, during a period of several hundred billion years of ripe conditions? IOW, how do we know only one Luca arose 4 billion years ago, and no more since then? And if all life can be shown to come from a single Luca, what prevented any others from arising or succeeding, either before or since?
posted by beagle at 9:28 AM on April 22, 2010

prevented any others from arising or succeeding, either before or since

Hm interesting. According to wikipedia, the presence of atmospheric oxygen molecules is what prevents any abiogenesis from continuing.
posted by polymodus at 9:35 AM on April 22, 2010

"You share 60% of your chromosomes with the sea cucumber."

Oh, shit, SeaWorld found out about that?
posted by Smedleyman at 9:44 AM on April 22, 2010 [8 favorites]

dunkadunc - I assume this reference is to RNA viruses and potentially prions (although I am not sure prions are considered life).
posted by batou_ at 9:45 AM on April 22, 2010

My kids were just asking about this the other day. Seriously, kids will ask you things like this all the time. I hope I can retool some of what I told them so it makes some sense to them.

Also: Thanks, great post!
posted by Mister_A at 9:50 AM on April 22, 2010

In other words, the genetic code is the inevitable consequence of affinities between the molecular building blocks of RNA and those of the proteins they code for. If he's right, it will explain why individual triplets always code for the same amino acids, whether in a virus or a human.

Yarus works with artificial RNA and has shown that these chemical affinities do exist. Mix strands of RNA with amino acids and the amino acids will more or less spontaneously nestle up to their corresponding triplets. "Yarus found that anticodons [a type of triplet found in some RNAs] were particularly good in this regard and bind the 'correct' amino acid with up to a millionfold greater affinity than other amino acids," says Nick Lane of University College London.

Why if these intrinsic affinities exist, do we automatically conclude there is a single abiogenesis event and therefore a LUCA? If this truly were the case, you would expect that the same triplets would code for the same amino acids even if there were multiple events, no? I guess the fact that almost all organisms use the same set of amino acids would suggest a single event, but that could have been dictated by abundance in the primordial soup or by the fact that these amino acids were more highly specific for the nucleotide triplet. What am I missing here? Is anyone familiar with Yarus' work? Were these specificities compared to non-biological amino acids? This is very interested, I guess I have some reading lined up for this evening.
posted by batou_ at 10:01 AM on April 22, 2010

Me, I prefer the traditional explanation for the origin of life on earth.
posted by Halloween Jack at 11:04 AM on April 22, 2010 [1 favorite]

batou_ I'm not seeing an argument for a single abiogenesis event. Ida is the first abiogenesis event ever, and Luca is the organism whose structure became the basis for nearly every organism alive today. I don't think there's any suggestion that Ida led to Luca, they're just different "organisms of interest". I imagine that new forms of life arise almost constantly even now, but get gobbled up by the already-well-established organisms. NOM NOM
posted by breath at 2:25 PM on April 22, 2010

Matter is finite, information is inflationary, thus the universe is forced to move towards increasing states of complexity to store information through forms capable of increased compression. Therefore life is the inevitable byproduct of time.
posted by humanfont at 3:48 PM on April 22, 2010

And internet posting is the inevitable byproduct of too much time.
posted by kuujjuarapik at 7:13 PM on April 22, 2010

Matter is finite, information is inflationary, thus the universe is forced to move towards increasing states of complexity to store information through forms capable of increased compression. Therefore life is the inevitable byproduct of time.

What? That sounds like a bunch of nonsense. The end-state for any entropic system is a completely uniform distribution of random stuff. What we consider "complex" is actually low entropy states, and high entropy states seem "simple". The reason we have life on earth is because energy is constantly being dumped into it from the sun.

Also, the universe doesn't need to "store" information. The information is just the positions of the atoms/velocity/spin/etc of the subatomic particles.
posted by delmoi at 7:33 PM on April 22, 2010

I was wondering the same thing, delmoi.

But yeah, it must just be that we didn't know that there was natural affinity. Which is interesting, since it's totally the kind of thing you (I) would assume -- especially given that the tRNA match to corresponding amino acids. But I guess that process/state is more complex than, say, codon-anticodon affinity. Cool.

Sure enough, when the pair looked at where amino acids sat in the ribosome, they found that 11 of 20 standard amino acids were far more likely than not to be positioned next to the "right" triplet according to the genetic code

So the rRNA anticodons sit next to their corresponding amino acids in the structure of the ribosome, I guess. Funny that the evidence was there all along.
posted by sentient at 9:39 PM on April 22, 2010

That's interesting. What are these exceptions?

Exceptions to the Genetic Code
posted by sentient at 9:42 PM on April 22, 2010

breath, my understanding is most people assume that a single abiogenesis event is responsible for all life on earth today. The primary argument for this relies on the fact that almost every organism uses the same genetic code. However, the Yarus work showing there are intrinsic affinities between nucleotide triplets and corresponding amino acids suggests that any abiogenesis event would have a high probability to yield the same genetic code. And if there are multiple abiogenesis events, there is no LUCA. There are additional reasons to suggests a single abiogenesis event is responsible for all present day life on Earth, but it seems to me this muddies the water a bit.
posted by batou_ at 7:07 AM on April 23, 2010

What are these exceptions?

This list of subcellular life forms is interesting reading along these lines. It covers viruses, viroids, satellites, plasmids, transposons, and prions. They're all kind of exceptions that prove the DNA rule, though. Related: Spiegelman's Monster.
posted by msalt at 11:06 AM on April 23, 2010

Oh, and

ShitMyDadSays "Science and Mother Nature are in a marriage where Science is always surprised to come home and find Mother Nature blowing the neighbor."
February 28 at 3:45pm via Ping.fm · View Feedback (10,149)Hide Feedback (10,149)

posted by Mental Wimp at 1:49 PM on April 23, 2010

Batou_, I don't actually know anything about this subject, but while there may have been multiple abiogeneses, if all of them eventually died out except 1, then there is a LUCA, right? Maybe I am missing something. I always thought that the Krebs Cycle basically proved that all (or at least, most) life on earth was descended from a single ancestor.
posted by synaesthetichaze at 1:58 PM on April 23, 2010