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

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September 18, 2011

Evolution, News, Origin Of Life

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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

Elizabeth, I think the gentlemen are simply asking you to make the connection between the study (studies) that you cite and the substance of your claims. Example: The study in question explored this question: ....................................................... Based on the following data, ....................................................... the researchers drew the (1),(2),(3) conclusions: ....................................................... The researchers believe that the data supports those (findings) conclusions because ............................................................ These conclusions may be considered the equivalent of showing that life can emerge from chemicals because ........................................................... If you do not take us through the process, then it seems fair to suggest that you cannot take us through the process. That is why your adversaries are accusing you of bluffing. 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. Indeed, I could, standing on their shoulders, do it myself. Under the circumstances, then, it will not do for you to say, "Hey, I provided a link, what else do you want?"StephenB_{September 19, 2011
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Elizabeth, what your claim for 'some' evidence for abiogenesis is completely non-existent as far as falsifying Abel's null hypothesis for functional information generation. That you would cling to such a tortured imagination that life from non-life 'might have' occurred by purely materialistic means, in spite of odds that can't even be properly fathomed by the human mind, is not even on the same planet as far as hard science is concerned!! ,,,Your atheistic/materialistic dream-world ignores, besides thermodynamics as a whole (Sewell), the fact that reality is not even materialistic in its most foundational basis, but is indeed found to be a information theoretic Theistic basis of reality at its core,,, and this is true despite whatever flights of imagination Stephen Hawking and Lawrence Krauss, or other atheist with letters behind their name may try to sell you, or to sell to the public as a whole!!! The following are some of the probabilities against your position. Probabilities that are never properly addressed by your side, save to deny that they matter. (Denialism)
Programming of Life - Probability - Defining Probable, Possible, Feasible etc.. - video http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/8/kckv0wVBYpA The Universal Plausibility Metric (UPM) & Principle (UPP) - Abel - Dec. 2009 Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes.",,, c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108 c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96 c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85 c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70 http://www.tbiomed.com/content/6/1/27 Signature in the Cell - Book Review - Ken Peterson Excerpt: If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power. http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell In fact years ago Fred Hoyle arrived at approximately the same number, one chance in 10^40,000, for life spontaneously arising. From this number, Fred Hoyle compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Fred Hoyle also compared the chance of obtaining just one single functioning protein molecule, by chance combination of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously. Professor Harold Morowitz shows the Origin of Life 'problem' escalates dramatically over the 1 in 10^40,000 figure when working from a thermodynamic perspective,: "The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!" (Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University) Dr. Don Johnson lays out some of the probabilities for life in this following video: Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video a typical functional protein - 1 part in 10^175 the required enzymes for life - 1 part in 10^40,000 a living self replicating cell - 1 part in 10^340,000,000 http://www.vimeo.com/11706014 Programming of Life - Probability of a Cell Evolving - video http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/9/nyTUSe99z6o Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number: DID LIFE START BY CHANCE? Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias) http://members.tripod.com/~Black_J/chance.html The Theist holds the Intellectual High-Ground - March 2011 Excerpt: To get a range on the enormous challenges involved in bridging the gaping chasm between non-life and life, consider the following: “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU) http://www.faithfulnews.com/contents/view_content2/49631/rabbi-moshe-averick-the-theist-holds-the-intellectual-high-ground-apologetics-christian-apologetics-defending-gospel
bornagain77_{September 19, 2011
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You most certainly were citation bluffing, Elizabeth. That stunt combined with your recent “Trust me, I’m a scientist” tactic and your general, repeated unresponsiveness at crucial moments in various discussions are all clear indicators that you are wasting our time.
No, I was NOT, Chris. I simply posted a link (making it perfectly clear what I was doing) to a page of the Szostak lab's publications. The lab is an abiogenesis lab (so the papers are about abiogenesis) and the output clearly includes data papers. That was all that was required to support my simple point that there are data supporting abiogenesis theories. I did not claim that abiogenesis had occurred, was proven, an accepted fact, or anything else. I simply pointed out that the statement that there are no data supporting abiogenesis is not true. There are quite a lot. As for "Trust me, I'm a scientist" jibe - where did I say, or imply that? Huh? It seems to me that I've been saying all through this thread that no, scientists shouldn't be making claims that aren't supported - and that they aren't making the claims they are assumed to be making. So no, don't trust scientists, because they, rightly, don't trust themselves. Science is all about provisional conclusions based on provisionally supported hypotheses, and always subject to potential falsification. As for my "general, repeated unresponsiveness at crucial moments in various discussions" - well, I've asked you for links to what you are referring to. I do try to keep up with conversations, but RL does sometimes intervene. What's got into you Chris? Where's this coming from? As for your time - it's your own to waste as you see fit. I post in good faith. I thought you did too.Elizabeth Liddle_{September 19, 2011
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You most certainly were citation bluffing, Elizabeth. That stunt combined with your recent "Trust me, I'm a scientist" tactic and your general, repeated unresponsiveness at crucial moments in various discussions are all clear indicators that you are wasting our time.Chris Doyle_{September 19, 2011
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Except that I wasn't "citation bluffing". And if you want me to pick up an argument you think I have "disappeared" from, here, please link to it. It's a fast-moving site, and I've been very busy recently (as well as being on holiday). And, actually, Chris, this is pretty rich from you - I was delighted that you came over to my own site, where things move a bit more slowly, but not only did you "disappear" from the discussions you were having there, but, as far as I can tell, you deleted all your posts AS WELL as all the counter-arguments that had been made to you! Pots and kettles come to mind :) Anyway, I'd be delighted to see you back, only please don't delete any more posts!Elizabeth Liddle_{September 19, 2011
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Joseph, I said that there were data in support of abiogenesis theories. You said there weren't. I linked to the publication output of an abiogenesis lab that includes data papers. You said they don't support my claim. So I can only conclude that you have read the papers and think that either the data don't support the hypotheses, or the hypotheses aren't to do with abiogenesis. Well, the first paper on the list cites data that support the hypothesis that "that functional structures could evolve from mosaic nucleic acids, despite the presence of nonheritable variation in the sugar-phosphate backbone". So it's an abiogenesis hypothesis, or at least a pre-LUCA hypothesis. So if you disagree that it supports my claim that there are data that support abiogenesis, you'd better show how the data don't support the hypothesis. The second paper on the list cites data that support the hypothesis that "low levels of phospholipids, potentially synthesized by genomically encoded catalysts (e.g., ribozymes), could also drive competitive growth and therefore provide a clear selective pressure for the evolution of modern cell membranes". Again, it's an abiogenesis paper (or at least a pre-LUCA paper) and so if you disagree that it supports my claim that there are data that support abiogenesis, again, you'd better show how the data don't support the study hypothesis. Unless you are using a different definition of abiogenesis.Elizabeth Liddle_{September 19, 2011
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I'll revisit the first paper I looked at, The Origins of Celluar Life. If anything what's misleading are the title and opening paragraph. If this were positioned as a hypothesis on the formation of fatty vesicles then there would be no controversy. And, most likely, no one would be interested in it at all. The paper constantly reminds us of the possible connections between its subject matter and the origin of cells while honestly admitting that there might be none. A few actual experiments are overlaid with speculation regarding what else may or may not be possible and what has yet to be explained. The question is not whether it says anything inaccurate, but rather, what does it say about the origin of cellular life? The answer is nothing. It doesn't even really claim to except by its vague title.ScottAndrews_{September 19, 2011
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Elizabeth, As to data supporting theories... Well, how many curves can you think of that would pass through a given point on a plane? I mean, one can happily invent any number of theories around the given data. The question is though: (a) how complex they are explaining available data; (b) whether these theories can stand more empirical data without becoming more complex; So it is not a surprise we can see all sorts of theories around. But what is their scientific worth is another matter.Eugene S_{September 19, 2011
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The first two papers do not support your claim, Liz.
What claim, Joseph?Elizabeth Liddle_{September 19, 2011
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Fair enough - my point was just that the complexity of the LUCA simply says nothing about the complexity of its own ancestors, because there is no a priori reason for assuming that the LUCA was the FUCA. Chris: no it wouldn't make a lot more empirical sense, although of course it is perfectly possible that the LUCA had more complex ancestors. Sometimes things do evolve in the direction of simplicity, and, indeed, will, if simplicity confers a greater chance of reproductive success. However, I disagree with your statement that "We only have evidence for (extremely limited) change brought about by elimination/degradation of genetic information: not creation of genetic information". We know that genetic information can be duplicated; we also know that it can be changed; we can therefore say that if those changes turn out to confer increased reproductive success in a given environment, they will embody new "information" about what succeeds in that environment, and if the change is in a duplicated part of the genome, nothing useful need have been traded for it. Unless you mean something else by "creation of genetic information". Perhaps you could explain.Elizabeth Liddle_{September 19, 2011
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A strong indication that you are lying to yourself is when you can't substantiate your claims (citation bluffing is not a substitute for substantiation) or can't engage with arguments (plenty of threads have come to an end here on Uncommon Descent because you disappeared instead of providing evidence for your position or even a detailed, cogent counter-argument).Chris Doyle_{September 19, 2011
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Elizabeth, I can remember seeing a video on youtube with Jon Wells demonstrating a very simple thing. He had a living cell in a test tube happy, alive and kicking. Then he pierced the cell's membrane and all of a sudden (surprise!) the cell stopped functioning and died despite the fact that: (a) the environment was friendly to the cell prior to the experiment; (b) all parts of the cell that was just functioning a second ago were nicely situated together with all thinkable favourable conditions for it to reintegrate. And yet it decided to die. Do you or anybody else supporting abiogenesis as a plausibility have anything like that to demonstrate that would have the long-awaited wow factor? I seriously doubt that...Eugene S_{September 19, 2011
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It’s intelligent intervention, and it’s inferred from what’s at this end of the bridge, not from the gap.
OK, fair enough :) My point was about the gap. Clearly I also disagree with your inference, but I do agree it is a different argument :) Thanks for the exchange.Elizabeth Liddle_{September 19, 2011
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What "claims" ba77? I'm not claiming that abiogenesis occurred, merely that, contrary to Joseph's assertion, that there is some evidence in support. What is your evidence that it didn't occur?Elizabeth Liddle_{September 19, 2011
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Citation bluffing is a reliable indicator that our opponents have abandoned any further pretence towards being susceptible to things like reason and evidence.
Oh, for goodness' sake. Joseph claimed there are no data supporting abiogenesis. I simply linked to the output from one prominent abiogenesis lab. The very first two papers listed are data papers supporting abiogenesis theories. Ergo, there are data supporting abiogenesis theories. If you want to critique the paper, and say why in your view, those data don't support the theory they are advanced to support, feel free, but at least bear in mind that the very first requirement for a peer-reviewed paper is that in the opinion of the referees, the data support the study hypothesis. But don't accuse me of "bluffing" unless you are prepared to do so. Because I'm right now calling yours.Elizabeth Liddle_{September 19, 2011
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Yes, indeed, people lie to themselves, and it's difficult to be sure one isn't lying to oneself. But I certainly do not lie deliberately, and as I would very much rather not lie to myself, I do my best to discern whether I am inadvertently doing so. I trust the same is true of everyone here. As for your last sentence, obviously I disagree profoundly.Elizabeth Liddle_{September 19, 2011
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But some people lie to themselves, Scott. And atheists especially have to lie to themselves if they seek meaning, morality and an understanding of origins.Chris Doyle_{September 19, 2011
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"Lie" is a pretty strong word. It indicates intent to deceive. If I change my mind and accept abiogenesis or darwinisn, nobody gets a free vacation to Mexico or even a toaster. So I don't think anybody has a motive to lie.ScottAndrews_{September 19, 2011
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"Might have been" more complex, to be exact!Chris Doyle_{September 19, 2011
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Exactly, Eugene. In fact, it would make more empirical sense to say that LUCA's ancestors were more complex than LUC. We only have evidence for (extremely limited) change brought about by elimination/degradation of genetic information: not creation of genetic information.Chris Doyle_{September 19, 2011
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Elizabeth Liddle, LOL,,, you make materialistic/atheistic 'scientific' claims all day long but, when demanded for specific hard evidence by UDers for your claims, you never back any of them up with ANY hard evidence, but always play long winded word games. And at the end of the day, after all is said and done, all your materialistic 'scientific' claims turn out to be nothing but wishy, washy, mush, with no hard 'scientific' evidence to actually back them up,, and are, in reality, nothing but you personally trying to defend a bankrupt materialistic philosophy. And you have done this in so far that you may retain your religion of atheism, for whatever severely misguided reason you have chosen to keep such a hopeless, and pointless, philosophy. Did I mention that materialism was bankrupt??? Well just to show you how 'scientific claims' actually work Elizabeth, here is my empirical evidence to back up my claim!!
"As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter." Max Planck - The Father Of Quantum Mechanics - Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944) Colossians 1:17 "He is before all things, and in Him all things hold together." Alain Aspect and Anton Zeilinger by Richard Conn Henry - Physics Professor - John Hopkins University Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the "illusion" of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one's own mind is sure to exist). (Dr. Henry's referenced experiment and paper - “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 - “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007 http://henry.pha.jhu.edu/aspect.html Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn't quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable - it is enforced by the laws of quantum mechanics, which stipulate that you can't 'clone' a quantum state. In principle, however, the 'copy' can be indistinguishable from the original (that was destroyed),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp Atom takes a quantum leap - 2009 Excerpt: Ytterbium ions have been 'teleported' over a distance of a metre.,,, "What you're moving is information, not the actual atoms," says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second. http://www.freerepublic.com/focus/news/2171769/posts Why the Quantum? It from Bit? A Participatory Universe? Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: "In the beginning was the Word." Anton Zeilinger - a leading expert in quantum teleportation: http://www.metanexus.net/Magazine/ArticleDetail/tabid/68/id/8638/Default.aspx Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. (This experiment provides experimental proof that the teleportation of quantum information in this universe must be complete and instantaneous.) http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html John 1:1-3 In the beginning, the Word existed. The Word was with God, and the Word was God. He was with God in the beginning. Through Him all things were made; without Him nothing was made that has been made. The Word - Sara Groves - music http://www.youtube.com/watch?v=0ofE-GZ8zTU
bornagain77_{September 19, 2011
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Elizabeth, Fair enough. We do hear plenty of rhetoric placing much more certainty on abiogenesis, often on the basis that there is supposedly no possible alternative. And I see that belief as driving acceptance of what looks like scant evidence. Each hypothesis contains certain unsupported narrative elements and relies on unexplained preconditions. Less attention would be paid to them if not for a philosophical drive to believe in the underlying premise.
If you want to take the view that the absence of an explanation leaves open the possibility of miraculous intervention, that’s fine, but my point is that you can’t conclude it from the fact that we don’t know how the gap was bridged
It's intelligent intervention, and it's inferred from what's at this end of the bridge, not from the gap.ScottAndrews_{September 19, 2011
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Well, it's a continuum. I certainly wouldn't want to strap myself to an amino acid and hope I ended up in a protein :) But I still take issue with your formulation: an "untested hypothesis" is not being "offered as evidence". Or not that I can see. What is being offered is evidence in support of testable (and tested) hypotheses about abiogenesis. So to say there is no evidence in support of abiogenesis is in correct. The hypotheses aren't evidence, but the evidence that supports the hypotheses are evidence. When you see bits of what looks like a path, that is evidence that there may indeed be a path, even if you haven't connected up all the bits yet, and even if some of the bits may still turn out to be sheep tracks.Elizabeth Liddle_{September 19, 2011
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"The ancestors were..." Should really read "might have been", to be exact. Multiple repetitions of a statement cannot make it sound more plausible without evidence.Eugene S_{September 19, 2011
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It is NOT about abiogenesis. We are talking about abiogenesis. Now what are these alleged hypotheses?
Well, decide what you mean by abiogenesis. If you mean how life got from non-replicating non-life to LUCA, yes, it's about abiogenesis. If you mean how simpler forms of life got to LUCA, then it isn't, but in that case, it's about how LUCA wasn't FUCA. Either way, it's evidence for the thing you keep saying there's no evidence for.Elizabeth Liddle_{September 19, 2011
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Elizabeth, Allow me to clarify. By "certain fact" I mean science tested sufficiently that men will repeatedly strap themselves to it and launch themselves into space. Admittedly, most science is never put to such an extreme test. But that's a far cry from abiogenesis research in which an untested hypothesis is offered as evidence.ScottAndrews_{September 19, 2011
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Well, obviously you don't find the current hypotheses plausible. Others do. And yes, many testable hypotheses can be derived from "darwinism", together with predictions, and have indeed been tested and supported. Again, I have to say: repeating that something is not the case does not make it not the case. Evolutionary theories are very well-supported, and even anti-evolutionists agree that Darwinian mechanisms work. It's pretty well undeniable, actually, precisely because you can make testable hypothesis and watch the predictions being fulfilled.Elizabeth Liddle_{September 19, 2011
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Well, you don't use a hypothesis as evidence of its own plausibility! You need to test it against data. That's what the papers on the Szostak papers are mostly about. That doesn't mean that the problem is solved, or even that the solutions proposed are on the right lines. But it certainly doesn't mean there is no evidence supporting them. I think that a lot of the problems in these conversations arise from equivocation between conclusions drawn by a few polemicists (on both sides of the debate) and what scientists themselves conclude. Most scientists probably think that abiogenesis occurred, but no-one would say that it had been demonstrated conclusively, or even that we know how it must have happened. We don't. The problem, as I see it, is on the other side - in the absence of actual evidence that it didn't happen, you can't infer ID. The only sensible position to take on it is that there is still a mystery about how life got from non-life to complex life, that we have some ideas about it, some of which are supported by lab and field data, but that we still don't know, and may never know for sure. If you want to take the view that the absence of an explanation leaves open the possibility of miraculous intervention, that's fine, but my point is that you can't conclude it from the fact that we don't know how the gap was bridged, if it was, especially in view of the fact that we have a rather nice set of clues. Although we've moved a long way from the OP, and my original point about it, which is that the inference that the LUCA was complex tells us nothing about the FUCA. That's just a simple error on news's part.Elizabeth Liddle_{September 19, 2011
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Elizabeth,
Your position seems to be that because science hasn’t proved that abiogenesis occurred, and explained how, that there is no evidence that it occurred, nor supported hypothesis regarding how.
That first part is quite true. There is no evidence that abiogenesis occurred other than the very existence of living things. As for "supported," that's a bit vague. A hypothesis is only useful when tested and discarded if necessary. It's not much good when used by itself as evidence of its own plausibility.ScottAndrews_{September 19, 2011
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Well, I understand you think I am blind, ba77. But then I think you are, so that makes us even, I guess. I think you are ignoring very important facts. I also think that you are failing to understand the nature of scientific claims.Elizabeth Liddle_{September 19, 2011
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