Paper: “The origin and relationship between the three domains of life is lodged in a phylogenetic impasse”

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September 18, 2011

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And you can download it for free from the Royal Society until September 24, here.

Transitional forms between the three domains of life and evolutionary implications

Emmanuel G. Reynaud1,* and Damien P. Devos2,*

The question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. The dominant paradigm is to see the three domains as separated. However, the recently characterized bacterial species have suggested continuity between the three domains.

Here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. The existence of intermediate steps between the three domains discards the need for fusion to explain eukaryogenesis and suggests that the last universal common ancestor was complex.

We propose a scenario in which the ancestor of the current bacterial Planctomycetes, Verrucomicrobiae and Chlamydiae superphylum was related to the last archaeal and eukaryotic common ancestor, thus providing a way out of the phylogenetic impasse.

If the last universal common ancestor was complex, as the researchers reasonably suggest … and how long ago was that? Then how did … ?

They got the impasse part right.

Hat tip: Pos-Darwinista

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Comments

Yes, we can "test the claim that teh bacterial flagellum evolved via Darwinian processes". And no "Darwinian processes" don't "work to break things". You are thinking of deleterious mutations, I think. Darwinian processes work to filter out breakages, and retain improvements. That's why populations adapt incrementally to their environment.Elizabeth Liddle_{September 19, 2011
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Darwinian mechanisms work to break things- so what are these alleged predictions based on Darwinian processes? Heck you have already admitted that we cannot test the claim that teh bacterial flagellum evolved via Darwinian processes- so what do you have?Joseph_{September 19, 2011
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It supports the plausibility of one step in of one theory of abiogenesis, clearly stated in the paper. And it seems to me that you do "need a lecture on 'how science works'" because you seem to have a very odd idea about it. As for "the obviously hoped for conclusion" - yes, it is pretty "obvious" that if you have a hypothesis that makes a prediction that you "hope" the data will support it. As I said, there's not much point in thinking up a hypothesis that you don't think your data will support. You make your best stab at a hypothesis, then you test it. And "obviously" if your data support it, then you have a positive finding, and you publish it.Elizabeth Liddle_{September 19, 2011
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Elizabeth: "What is your evidence that it didn't occur?" (Presumably, meaning by purely naturalistic and materialistic processes.) Ummm, lesseee . . . Math; chemistry; physics; information theory; our uniform and repeated experience about how information-rich structure some into being.Eric Anderson_{September 19, 2011
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And as I said there is evidence to support abiogenesis in the same manner there is evidence to support mother nature building Stonhenge.Joseph_{September 19, 2011
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Umm primitive cells emans living organisms already exist and this is post-abiogenesis. Cell membranes is also post-abiogenesis. shrug, sighJoseph_{September 19, 2011
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On the contrary, what you suggest is essentially the UK science national curriculum, which mandates the teaching of hypothesis testing. It isn't implemented as successfully as it should be, IMO, but that's the principle. I blame widespread misunderstanding about the provisional nature of all scientific conclusions and a fundamental misunderstanding about the nature of scientific knowledge, which is not about proof, but about how well models fit the data. And it's precisely that misunderstanding, and the resulting straw men, I find myself trying to hack my way through on this thread! But it seems I have at least one ally in you :) This essay should be required reading in all science classes IMO.Elizabeth Liddle_{September 19, 2011
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The authors do NOT "fail to tell us WHY the data support" their hypothesis, or, indeed, their conclusion (which, being a conclusion is not a given, but follows their finding). The why is clearly stated in the papers (if it hadn't been, it wouldn't have got past peer-review, because it's the sine qua non for publication). Now you may think that their given reasons are not adequate, but that's different from saying that they don't give them. They do. But this conversation is getting a bit weird. Clearly we must be talking about different things (why else would you look at a paper that clearly spells out how the data support the hypothesis and say that it doesn't attempt to do so?). So I'm curious as to what you actually mean. Are you saying they don't say why their data supports the case that abiogenesis happened? No, they don't, because that isn't what the paper is about. The paper (at least the first one) is about their theory of abiogenesis, which postulates the co-evolution of lipid vesicles. However, this presents some problems - why would low levels of phospholipids be advantageous? And they find the answer - low levels of phospholipids are advantageous because they accelerate the growth of the membrane (and they go into great detail as to how this happens). Read the paper, it's interesting. And it reports data that support a hypothesis derived from a theory of abiogenesis. So Joseph's statement that there are no such data is incorrect.Elizabeth Liddle_{September 19, 2011
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First, I would teach what you just said. Here's a hypothesis, and it's tentative. I wouldn't teach ID. It's way too controversial, and it's new. Rather, I impress upon them the enormity of what takes place in the cell. That's not something to gloss over. It's astonishing and should be represented as such. In a separate lesson, using unrelated subject matter, I would teach them the limitations of science, including that it is practiced by humans, not Vulcans. I would provide simple examples of accepted knowledge that turned out to be wrong. (Everyone thought that bacteria could not survive inside the stomach.) I would tell them never to believe something just because they're told that scientists do. And if something sounds wrong or outright ridiculous, look for the opposing viewpoint. But none of that should take up disproportionate time. Science class is for science. Such lesson plans could never be part of most official curricula because they are obviously slanted toward religious fanaticism.ScottAndrews_{September 19, 2011
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Elizabeth, it seems that you feel yourself expert enough to lecture others on establishing 'certainty' in science, (which in reality you are doing your level best to avoid a certainty about abiogenesis that has already been reached from the best scientific evidence now available; Meyer), yet the completely ironic thing in all this, in you lecturing others about establishing 'certainty' in science, is that if, as you hold in your materialistic atheism, life, and particularly consciousness, really did come about by purely materialistic/atheistic processes then there would be absolutely no way for any of us to know with 100% CERTAINTY if anything we believed was actually true or not. Thus you, by insisting on purely materialistic/atheistic causation for all of life, have basically completely undermined any argument for 'certainty' that you were trying to make in the first place.,,, notes:
Should You Trust the Monkey Mind? - Joe Carter Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties. http://www.firstthings.com/onthesquare/2010/09/should-you-trust-the-monkey-mind “Atheism turns out to be too simple. If the whole universe has no meaning, we should never have found out that it has no meaning...” CS Lewis – Mere Christianity What is the Evolutionary Argument Against Naturalism? ('inconsistent identity' of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) - video http://www.youtube.com/watch?v=5yNg4MJgTFw Can atheists trust their own minds? - William Lane Craig On Alvin Plantinga's Evolutionary Argument Against Naturalism - video http://www.youtube.com/watch?v=byN38dyZb-k "But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?" - Charles Darwin - Letter To William Graham - July 3, 1881 “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.” J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209. It is also interesting to point out that this ‘inconsistent identity’, pointed out by Plantinga, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to be able to account for objective morality, in that neo-Darwinists cannot maintain a consistent identity towards a cause for objective morality; The Knock-Down Argument Against Atheist Sam Harris – William Lane Craig – video http://www.youtube.com/watch?v=tvDyLs_cReE "Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth. As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain." Creation-Evolution Headlines http://creationsafaris.com/crev201102.htm#20110227a
But Elizabeth, I know where 'certainty' can be found!
Solid Rock - the 5th service band Featuring TRU-SERVA http://www.youtube.com/watch?v=G4jD70Y-mQ0
bornagain77_{September 19, 2011
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Would you say abiogenesis research is worth doing, or not?Petrushka_{September 19, 2011
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And that’s the way science works – you don’t suddenly find a bacteria spontaneously creating itself in a jar of peanut butter
Gee, thanks for clearing that up. We wouldn't even be having this discussion if there were a bit more humility regarding such research. When's the last time we've heard that scientists were researching to determine whether it was possible for life to self-assemble and evolve into modern cells? Say what you will about the scientific method, this is presented as fact. It's about how it happened, not if it happened. That is reality. Is it possible to minimize the importance of this research without being accused of minimizing or not understanding the scientific process? Each paper depends upon numerous assumptions made in other papers and then makes its own which become the premises for yet more papers. If they say they can synthesize fatty vesicles, great. I believe them. But there are too many assumptions and too much background ideology for any of it to credibly relate to anything that actually occurred.ScottAndrews_{September 19, 2011
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Good grief. What (and where) in these papers is the ARGUMENT that the data supports the plausibility of abiogenesis? I don't need a lecture on "how science works." I need an answer to the question, WHY does the data support the obviously hoped-for conclusion. Please!StephenB_{September 19, 2011
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Why do you change subjects in this way? The issue I raised in this context has to do with the clarity of the argument being presented. Behe's argument for Intelligent Design is based on the methodology of "irreducible compexity." Everyone understands the argument, namely that the whole cannot work without all of the parts and that no evolutionary pathway can likely explain the finished product. Your author's claims for abiogenesis contains no similar argument. It can't be evalutated because it has no substance, as is clear from your inability to articulate it even after I asked you to do so several times (WHY does the data support the hypothesis).StephenB_{September 19, 2011
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What would happen if a public school decided to teach evidence against abiogenesis alongside support for it? It would be on every news channel and respected scientists would come out of the woodwork to tell us how ignorant someone is to contradict that thing that they aren’t certain about. We both know what they would say: There’s lots of research supporting it.
I don't know that. I think it's fine to teach Szostak's theories as long as it's clear that they are very tentative at this stage, if looking promising. There are some interesting problems IIRC and that would make for an interesting school topic. Tell me what you think the evidence against it is - what would you propose teaching?Elizabeth Liddle_{September 19, 2011
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Well, I think we are getting on to the same wavelength, finally! But I'd point out that hypotheses are derived from abiogenesis theories - that's how science works. The reason the Szostak lab has been pursuing lipid hypotheses so vigorously is that their theory is that membranes are really important - that without co-evolution of some kind of cell-membrane, you wouldn't get robustly self-replicating polymers - so they see the very earliest proto-biological entities as a combination of lipid vesicles and polymers. But to support their theory they have to generate specific hypotheses and test them, and that's what they do. That's why I linked to their publication output! There's a lot of it. And, while it's no guarantee of brilliance, a Nobel Prize in science isn't nothing :) Szostak is a bright guy. I find the research quite exciting.Elizabeth Liddle_{September 19, 2011
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I am afraid you are not following me, Elizabeth. The authors' fail to tell us WHY the data supports their conclusion. Anyone can claim that data supports a given conclusion. The task is to show the connection between the data and the conclusion (why the data justifies the conclusion). If they don't provide the "why," then they are bluffing. If you do not know why the data supports the conclusion, then you have no reason so say that evidence for abiogenesis exist. Since you, nor anyone else has ever produced that connection, then I am more than justified in saying that no such connection exists and that anyone who claims to have evidence for abiogenesis is bluffing.StephenB_{September 19, 2011
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Elizabeth,
I did not say that abiogenesis was supported by data. I said there were data in support of abiogenesis theories.
Do you mean hypotheses that explain some possible step in a process? Then perhaps we could clear up the confusion by not calling them "abiogenesis theories." If research indicates that fatty vesicles can form in certain laboratory tests, then the data in the paper could support that.
It’s possible that they are all wrong and it didn’t even happen. That does not mean that there is no support for them.
To borrow from Dr. Hunter, there is support for geocentrism. Every day we see the sun going around us. That's why we also need to look at the contradictory evidence.
Science is always provisional. From where I’m standing it’s as though you guys are so fixated on the straw man (as I see it) of scientific certainty that abiogenesis occurred that you simply cannot see that there is no such certainty on the part of scientists
Science is one thing. Scientists are another. In my previous post I quoted from a paper implying that there is a natural pathway even if we don't know what it is. They know how to express uncertainty, but they sure don't do it there. What would happen if a public school decided to teach evidence against abiogenesis alongside support for it? It would be on every news channel and respected scientists would come out of the woodwork to tell us how ignorant someone is to contradict that thing that they aren't certain about. We both know what they would say: There's lots of research supporting it.ScottAndrews_{September 19, 2011
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OK, let's take the first of the Szostak papers on the list (hey, let's make it a journal club!): http://genetics.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Trevino_et_al_2011_PNAS.pdf Here is the abstract:
To understand the emergence of Darwinian evolution, it is necessary to identify physical mechanisms that enabled primitive cells to compete with one another.
So we know it's about abiogenesis, because it's actually about the emergence of a Darwinian-capable entity. So the subject matter is clear.
Whereas all modern cell membranes are composed primarily of diacyl or dialkyl glycerol phospholipids, the first cell membranes are thought to have self-assembled from simple, single-chain lipids synthesized in the environment.
Here they refer give the background to one of problems the lab has to solve in order to make their story - how do you get from simple lipid chains to more complex phospholipids ?
We asked what selective advantage could have driven the transition from primitive to modern membranes, especially during early stages characterized by low levels of membrane phospholipid.
And here they define the problem: what reproductive advantage could have been given by phospholipids at very low levels ("what use is half a phospholipid?" if you like :)) In other words they are testing the hypothesis that even low phospholipid levels must have had some survival advantage, if modern membranes were to have resulted from Darwinian processes.
Here we demonstrate that surprisingly low levels of phospholipids can drive protocell membrane growth during competition for single-chain lipids. Growth results from the decreasing fatty acid efflux from membranes with increasing phospholipid content.
And here they report the data that support their hypothesis, and the mechanism - that even low levels of phospholipids drive membrane growth even when the membraine is largely single-chain lipids.
The ability to synthesize phospholipids from single-chain substrates would have therefore been highly advantageous for early cells competing for a limited supply of lipids. We show that the resulting increase in membrane phospholipid content would have led to a cascade of new selective pressures for the evolution of metabolic and transport machinery to overcome the reduced membrane permeability of diacyl lipid membranes. The evolution of phospholipid membranes could thus have been a deterministic outcome of intrinsic physical processes and a key driving force for early cellular evolution.
And here they relate their finding to their broader theory about the role of lipids in abiogenesis. And that's the way science works - you don't suddenly find a bacteria spontaneously creating itself in a jar of peanut butter, and get your Nobel Prize, you painstakingly devise theories, derive hypotheses, spot a problem, solve the problem, or fail and derive a different hypothesis... and little by little you gain some kind of understanding of the kinds of processes that are possible, the kinds of feedback loops that might have operated etc. And it's all provisional, all, literally, hypothetical, and could be wrong. But the great thing is that to make progress, your hypotheses have to be supported by data. And that data is what they report. It exists.Elizabeth Liddle_{September 19, 2011
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Nope, I'm just telling you my opinion, ba77. A man who cites Monod as saying the opposite of what he actually did say, doesn't inspire me with confidence. And I find his nulls badly specified. You can regard my views as worth what you paid for them.Elizabeth Liddle_{September 19, 2011
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What I said, originally, to ba77 was that s/he was "complete ignoring what data we do have in support of abiogenesis theories". I did not say that abiogenesis was supported by data. I said there were data in support of abiogenesis theories. There are many theories of abiogenesis, and at least some of them must be wrong, and at best, all are incomplete. It's possible that they are all wrong and it didn't even happen. That does not mean that there is no support for them. There really does seem to be a cultural chasm here, and I'm just not sure how to bridge it. I've even said myself that, even if we were to succeed in generating life from non-life in a test tube, that wouldn't tell us whether the pathway we were observing was the pathway life actually took! Science is always provisional. From where I'm standing it's as though you guys are so fixated on the straw man (as I see it) of scientific certainty that abiogenesis occurred that you simply cannot see that there is no such certainty on the part of scientists - that certainty is completely irrelevant to what scientists do. What there is is a gap, one that scientists are curious to fill (it's a pretty interesting question). And, as you rightly said, you can't infer ID from that gap. Let's talk about the problem of the bridge :)Elizabeth Liddle_{September 19, 2011
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OK, and my response is: if people here think the authors are bluffing, then it's up to them to say why they think so. They are the ones claiming that there are no data supporting abiogenesis theories. And there's a huge difference between claiming that "the data advanced to support theories of abiogenesis don't, and the authors obfuscate to stop you realising that" and "there are no data that support abiogenesis". The first requires detailed justification, especially when the work is peer-reviewed in one of the highest-impact-factor scientific journals in the world. That doesn't mean that the odd turkey doesn't get through, but it certainly puts the burden on the challenger to show that it's a turkey. As for the papers themselves - just read them. And if you think the data don't support the hypotheses, write to PNAS. Or at least post the critique here.Elizabeth Liddle_{September 19, 2011
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Elizabeth,
But the burden, it seems to me, is on those who claim there is are no supporting data for abiogenesis to show why the published data in support of abiogenesis theories do not, in fact support it, and not merely to claim, repeatedly, that there are no such data.
Fair enough. Again, from the oddly named The Origins of Cellular Life.
Although such laboratory studies may not re?ect the speci?c pathways that led to the origin of life on Earth, they are proving to be invaluable in uncovering surprising and unanticipated physical processes that help us to reconstruct plausible pathways and scenarios for the origin of life.
The authors openly admit that they do not know whether their studies are relevant to the actual origin of life. (The rest of the sentence attempts to mitigate that detail, but does not.) How can the paper provide data supporting abiogenesis when its own authors don't know whether it does? And let's revisit this sentence fragment: "may not re?ect the speci?c pathways that led to the origin of life on Earth." Notice that they do not qualify this with any uncertainty, as in 'pathways that may have led to the origin of life on Earth.' While admittedly not knowing how it happened, they are quite certain that they did. It sounds like they are determined to find their keys under that streetlight. But I digress. The authors of this paper admit that they do not know whether their data supports abiogenesis or even what pathway it followed. Only that it happened.ScottAndrews_{September 19, 2011
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Re this:
I promise you that William Dembski, Paul Marks, and Michael Behe can take you through this process from an ID perspective with their eyes closed and one-half of their brain tied behind their backs. The clarity of their arguments and the transparent relationship between those arguments and the evidence are all there to be evaluated.
Well, I'd much rather they did it with both eyes open and brain fully engaged! My own view is that if they did so, they'd find the flaws in their own arguments :p Seriously, I find Dembski's argument seriously flawed. I haven't read Behe's The Edge of Evolution, but I certainly wasn't impressed by Darwin's Black Box, and what I've heard of the argument made by Behe in The Edge of Evolution, it doesn't seem to me he's found an Edge at all. There certainly are Edges to evolution, which is one of the reasons we can be pretty confident the theory is broadly correct, because life doesn't seem to overstep those edges, whereas a Designer could.Elizabeth Liddle_{September 19, 2011
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Elizabeth, I simply asked you to take us through the process and explain why the evidence offered supports abiogenesis. What your dialogue partners on this site are trying to tell you, aside from their references to you, is that the authors of the study are, THEMSEVLES, bluffing. Since, as you acknowledge, you don't really know what they are talking about, (they saw to it that almost no one would know by virtue of their obfuscating) then it seems evident that you cannot use their work to support your claim. All this confirms what we have been telling you. There is no credible evidence to support abiogenesis.StephenB_{September 19, 2011
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We really are at cross purposes here! A theory generates hypotheses. Those hypotheses generate predictions. Predictions are tested against data. There are a number of broad abiogenesis theories, and Szostak's lab are pursing one in particular, namely that lipid vesicles are part of the story - in other words that the emergence of membranes was a key aspect. This theory has led to a number of testable hypotheses, and the published output of that lab, which I linked to, includes reports of the testing of those hypotheses. Some have been supported, some not. The lab certainly has not solved the problem of abiogenesis, and may even be barking up the wrong tree. But some of their work looks promising. So there are data in support of abiogenesis theories. They could be wrong, still, but that's the way it goes in science. But of course they are "driven by their expectations" - you don't derive a testable hypothesis without at least some expectation that your data will be as you, well expect! That's why we talk about "predictive" hypotheses! You don't bother to test a hypothesis you are pretty sure is wrong. I don't know the answer to your last question (and I'm not even sure what it means!).Elizabeth Liddle_{September 19, 2011
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And I’m not very impressed with Abel, who totally mis-cites Monod. Nor with his null hypotheses.' but of course Elizabeth, and your opinion for what matters is suppose to impress me, instead of you actually falsifying the null hypothesis, because???, because???, because???, because you are Elizabeth by golly!!! and evidence doesn't matter if Elizabeth says it doesn't matter!!! :)bornagain77_{September 19, 2011
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The connection between the published studies that are posted on Szostak's lab page and my claim that there are data that support abiogenesis theories is simply that the output of that lab includes data in support of abiogenesis theories. So Joseph's claim that there are none, is false. Now, we can argue about the papers themselves, if you wish, but I'd have to read them properly, and they are very technical, and I don't personally have the expertise to critique them. But if someone here is, fine. Let's hear why the data in those studies do not support the hypotheses they are cited to support. But the burden, it seems to me, is on those who claim there is are no supporting data for abiogenesis to show why the published data in support of abiogenesis theories do not, in fact support it, and not merely to claim, repeatedly, that there are no such data. As for your specific questions, the PNAS papers are public access and you can easily read them yourself. The hypotheses are clearly stated, and the data in support of them are clearly described. Of course none of them "may be considered the equivalent of showing that life can emerge from chemicals" because no-one has shown that. As I've said, repeatedly. Even if we do manage to make life in a test-tube, it still won't show that that is what actually happened. And right now do not know how (or even whether, for that matter) "life emerge[d] from chemicals". What we do have, however, are data that support theories about how it may have done. Please do not assume that I hold positions that I do not in fact hold, and have not claimed to hold.Elizabeth Liddle_{September 19, 2011
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Elizabeth,
What is being offered is evidence in support of testable (and tested) hypotheses about abiogenesis.
How can you know whether it supports abiogenesis without presuming abiogenesis? Without knowing how it occurred, how can you know whether any test is relevant? In the case of the earlier cited paper, it admittedly may or may not support a premise which in turn may or may not even be true, with pretty good evidence suggesting it isn't. I won't argue that they aren't following the scientific method. But they are clearly driven by their expectations of where this or some other path will lead. I'm curious - I honestly don't know the answer - how many laboratories are funded to research phenomena other than abiogenesis that are both historical and never known to have occurred?ScottAndrews_{September 19, 2011
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I didn't even mention Abel, ba77. All I am saying is that it is not true that there are no data supporting abiogenesis theories. And I'm not very impressed with Abel, who totally mis-cites Monod. Nor with his null hypotheses.Elizabeth Liddle_{September 19, 2011
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