Proto-world and the primordial globule
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An editorial by Miranda Robertson in the latest Journal of Biology, "Of primordial genomes and cooperative kittens", discusses the problems that horizontal gene transfers pose for phylogenetic analysis of bacterial genomes:
The extraction of tree structures from the web of gene transfers requires that transferred genes be subtracted by some means from the database of genes used to construct the trees. […]
Whether because of horizontal gene transfer or the compression of branching events early in the evolution of prokaryotes, the lines of vertical descent […] defy resolution, at least for now and perhaps for ever. There is a character in the comic opera The Mikado, by WS Gilbert and Arthur Sullivan, who claims: 'I can trace my ancestry to a protoplasmal primordial atomic globule. Consequently my family pride is something inconceivable.' Inconceivable and probably misplaced, it would seem. The character is named, more appropriately even than Gilbert could have imagined, Pooh-Bah.
As you'll see if you read the editorial and the articles it references, the analogies between the evolution of species and of languages are closer than Charles Darwin knew when he first suggested the metaphor. Like languages, species exhibit the borrowing of traits ("horizontal gene transfer"), and also areal features ("false vertical signals reflecting preferential gene transfer between bacterial species from quite separate branches of the phylogenetic tree and that happen to share a habitat").
One difference: horizontal gene transfer, as I understand it, is much less common as you look higher up in the evolutionary tree of species. (Though I guess there are some theories according to which rates and even types of linguistic "horizontal transfer" might have been strikingly different in different historical periods.)
As for the cooperative kittens,
Sleeping kittens are invoked to explain the Monod-Wyman-Changeux model for cooperative binding of oxygen by hemoglobin, in which it is assumed that oxygen binding to one subunit has no effect on the affinity of the other subunits for oxygen, but that the conformational changes that increase or decrease oxygen affinity occur in unison. Readers who find the behavior of kittens easier to understand than the behavior of molecules may be encouraged by the analogy to read the non-kitten paragraphs too.
There are linguistic analogies here as well, but I'll leave those for another day.
Carl Zimmer said,
July 21, 2009 @ 10:04 am
Horizontal gene transfer is rare between distantly related species, but only if you look at the odds of one organism picking up DNA from one other organism. Because there is a vast number of organisms on Earth, as well as a vast span of time that life has been on Earth, horizontal gene transfer has had a huge impact on the make-up of genomes. In fact, biologists use another lovely metaphor to describe a typical genome of a bacterial species: a mosaic.
Mark Liberman said,
July 21, 2009 @ 10:30 am
And then there's the theory of symbiogenesis, especially associated with Lynn Margulis, which sees evolution as being sometimes (or even mostly) driven by species-level mergers and acquisitions.
This idea is now generally accepted, as I understand it, with respect to the origins of mitochondria and plastids, but remains controversial with respect to the origin of cilia, and even more controversial with respect to the idea that the various metamorphic stages of invertebrates represent the successive expression of what were originally entirely separate genomes.
On this theory, the crucial steps in the evolution of the animal kingdom were, in effect, "creole organisms" (at least on some theories of the nature and origin of creole languages).
Carl Zimmer said,
July 21, 2009 @ 11:25 am
Yes, endosymbiosis is clear for plastids and mitochondria (take a deep breath of oxygen, thanks to your bacterial symbionts). Not much support for cilia anymore, or the invertebrates. Horizontal gene transfer is the shuttling of a few genes or even a single one, via viruses, or slurping up loose DNA in the environment.
Jonathan Badger said,
July 21, 2009 @ 11:30 am
It isn't "controversial" in regard to cilia — it just isn't accepted, period. People accept that mitochondria and plastids are related to bacteria because in the 1980s people sequenced individual genes from these organelles and found that they were related to alphaproteobacterial and cyanobacterial genes respectively. In more recent years, entire mitochondrial and plastid genomes have been sequenced, further solidifying their relationship to bacteria. But cilla don't *have* genes of their own — their information is in the nucleus, as one would expect. Margulis would have it that they once had genes but lost them all — an argument which is unconvincing because it could be used for *anything*.
[(myl) I don't have any dog in this fight, but isn't the verdict for the endosymbiosis theory of cilia more like "unproven and perhaps unprovable", not "definitely false"?
In that sense, it would be like some of the "long ranger" hypotheses about deep-time language relationships (like Nostratic or Austric), which are not generally accepted because of lack of evidence, rather than (say) the theory that Mandan is derived from Welsh, which is generally rejected because it's obviously false.
It seems possible that the genome-fusion theory of metamorphosis could be similarly shown to be false as opposed to simply unproven, by analysis of the gene-expression patterns in the various stages, or by evidence for an alternative and incompatible theory of the evolutionary origin of metamorphosis — but I haven't been able to find a clear version of such an argument (though this may be a combination of my unfamiliarity with the literature and the lack of uptake of Margulis's ideas in this area). ]
Carl Zimmer said,
July 21, 2009 @ 12:48 pm
One could imagine a situation in which a bacterium evolved into the cilium and lost all its genes. Those genes wouldn't actually vanish, but would be transferred to the nucleus. That, in fact, is what happened to some genes from mitochondria. And in some species, mitochondria have lost most of their functions (genes have been deleted), and their only surviving functions are encoded by genes that have been transferred to the nucleus. But we know that happened because the genes show clear kinship to genes from a certain group of bacteria, and not to the host genes (eukaryotes). No one has found any evidence that genes encoding cilia are bacterial. At least that I know of.
(I'm in the middle of writing a piece on all this, so I'm a bit obsessed…)
[(myl) Is it clear that the genes encoding cilia in multi-cellular animals evolved independently from the genes encoding cilia in ciliate protists? That would be the strongest form of argument against the endosymbiosis hypothesis.
Alternatively, all multi-cellular animals might have evolved from ciliates, I guess.
Margulis's idea (about morphogenesis as well as cilia) is obviously that the genomes merged, not that the organelles or developmental stages or whatever retained physically segregated genomes. Perhaps this can be disproved (as opposed to being unproven), but I haven't been able to find the argument. Maybe in your forthcoming article? ]
Nathan Myers said,
July 21, 2009 @ 2:42 pm
I wonder about other re-purposings. For example, bacteriophages, the viruses that look like an unholy cross between a mosquito and a hypodermic needle, seem implausible as original parasites: parasites rarely innovate structures. They make perfect sense as communication devices, used the way bacteria use plasmids, or as weapons, the way some wasps use virus-like structures. The step from weapon to actual virus is a trivial matter of substituting payload. To discover the origin of phages we probably need only find bacteria still using them. Use of virus-like structures among bacteria could be extremely common, yet easy to miss.
Aside from simple word borrowings, we have larger structures shuttling between languages. The notion of revenge as a comestible prepared hot but better eaten cold (like jello?), explored recently here, is speculated to have originated in Pashto but seems on the evidence to have entered English via French in the first half of the 19th century. How it might have got into French from Pashto has not been elucidated.
Q. Pheevr said,
July 21, 2009 @ 3:25 pm
I can't quite figure out what Robertson means by "more appropriately even than Gilbert could have imagined." The OED's entry for Pooh Bah indicates that the word means what it does today only because it was the name W. S. Gilbert gave to the Lord High Everything Else; how can horizontal transfer, or anything else, retrospectively make Pooh Bah more like himself than his creator knew?
[(myl) Reverse semantic transcriptase?]
Garrett Wollman said,
July 21, 2009 @ 11:26 pm
I thought it was fairly well understood that language, as an item of culture, exhibits Lamarckian evolution (through inheritance of acquired traits), as compared to Darwinian evolution of species (through Mendelian inheritance of random genetic variation, a mechanism unknown to but prefigured by Darwin). Lateral gene transfer, although both interesting and of real significance in the unicellular world, is insignificant outside that realm compared to Mendelian inheritance.
[(myl) While the basic mechanisms of inheritance are obviously different, historical linguists make a clear distinction between borrowed traits and those that persist or develop within a speech community; and they see the latter as changing through a process of random variation and selection. The selective processes may be cultural (i.e. fashion) as well functional — but biological evolution has the equivalent thing in sexual selection.
It's true that linguistic variation can originate later in life as well as at the time of primary language learning — and is exhibited in the behavior of each individual, as well as across the population of speakers — which might seem somewhat Lamarckian. And this makes change go faster relative to the cycle of biological generations. But it doesn't change the conceptual difference between linguistic traits that are inherited "genetically" (in the original sense, which existed long before Darwin) and those that are borrowed across "genetic" (i.e. tree-structured) lineages.
As for the insignificance of lateral transfers outside the unicellular world, that's what I thought as well, but Carl Zimmer seems to be suggesting that some biologists have a different opinion, which I look forward to reading about in his forthcoming article. ]
Tim said,
July 22, 2009 @ 3:15 am
I'm finding the phrase "higher up in the evolutionary tree of species" to be somewhat ambiguous. Does this refer to older or newer species? On the one hand, "higher" in a real tree would put you among the branches, far from the original stem. That would imply newer species. Then again, a "tree" of species is likely to be drawn with the newer species at the bottom, since they descend from the older species. My guess is that this was the intended meaning, and the reference was to older species. But, it's hard to be certain.
[(myl) The usual way of drawing evolutionary trees, I believe, is as real trees usually grow, with the root below and the leaves above. But linguists draw syntax trees upside down, so I understand that this could be confusing.
It's confusing for another reason, namely that modern bacteria are just as much leaves of the tree as we are; and it's not just the original bacteria that engage in promiscuous lateral transfers, it's bacteria through the ages and up to the present. So it was a lousy way to put things all around.
Also, as Carl Zimmer observed, it's not even necessarily true, as a fact about populations of (say) insects or mammals rather than individuals.]
Sili said,
July 22, 2009 @ 3:47 am
I assumed that the authors were unaware that the use of 'grand poobah' these days came from The Mikado.
Just as discussed here a whiles back when some biologists thought they were innovative when couching historical linguistics in terms of Darwian evolution. Completely missing the fact that languages inspired Darwin in the first place (not to mention their utter and complete failure to understand anything about the structure of language and properly apply their tools to them).
Picky said,
July 22, 2009 @ 6:19 am
re the Lord High Everything Else: Of course both Pooh and Bah predate Sir WSG, with similar meanings.
James Wimberley said,
July 22, 2009 @ 8:14 am
Why do you, Wikipedia and everybody else write "WS Gilbert" (or more usually "W.S. Gilbert") but "Arthur Sullivan"? This looks the sort of quirky preference that people can impose during their lives, as a matter of courtesy, but has no purchase after death. We could write "William S. Gilbert" on the very rare occasions we might need to disambiguate. We also write "P.G. Wodehouse", never "Wm. Shakespeare". Other examples? "V.I. Lenin" doesn't count as this is SFIK a standard Russian usage. A name for the phenomenon?
Chris said,
July 22, 2009 @ 9:40 am
I don't get the jab at Gilbert – was it insufficiently clear that Gilbert was satirizing, not endorsing, the custom of family pride based on ancestry? Being proud of your descent from a protoplasmal primordial atomic globule is ridiculous, but ISTM that Gilbert's point is that being proud of your descent from William the Conqueror is just as ridiculous. Satire by exaggeration has a long and hilarious tradition (although perhaps not quite going all the way back to protoplasmal primordial atomic globules).
Ken Brown said,
July 22, 2009 @ 11:47 am
[(myl) "Is it clear that the genes encoding cilia in multi-cellular animals evolved independently from the genes encoding cilia in ciliate protists? That would be the strongest form of argument against the endosymbiosis hypothesis."
No its not clear at all. In fact the opposite is true. It looks pretty certain that animal and protist cilia are homologous.
All the eukaryotic cilia/flagellae have the same basic structure. What we call the 9+2 cilium – there is a sheath of 9 protien rods around a core of 2 of them, which is attached to a basal body inside the cell membrane. The proteins it is made of are the same general type as the cytoskeleton, and also the proteins used to move chromosomes around during cell division. Its the same in animals, plants, and all sorts of other things.
(Bacterial flagellae are quite different)