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

_{Denyse O'Leary

September 18, 2011

Evolution, News, Origin Of Life}

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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

oops "have you never seen" should have ended "a lava lamp?"Elizabeth Liddle_{September 22, 2011
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it is not at all clear that the monomers will join up in nice chains as depicted in the video; specifically, if the monomers can join either on side-bonds or opposing-bonds, which is indeed required for the later copying to work, there is no reason to expect a nice chain to form – more likely a jumbled mess
Depends on the monomer. This is chemistry. Polymers form. This is testable, and subject to testing.
- similar problem when trying to replicate; even if the chain/clump gets broken apart with heat, there is no way to avoid interferring cross-reactions and a jumbled mess with new monomers coming into the scene
How do you know? Again, this is exactly the sort of question with empirical answers
- then there is the unlikely repetitive heat, cool, heat, cool cycle that would be required for the copying to even function
Why is a convection current unlikely? Have you never seen
- it doesn’t appear that the vesicles replicate (unless I missed something in the model), the idea being simply that the vesicles simply grow bigger until, presumably, they either stop growing or burst spilling their contents
Yes, you missed something. The vesicles grow, and when they grow they elongate. When they divide the don't spill their contents. I'm not sure which video shows this, but at least one of them does. Again, this is based on empirical evidence.
- assuming the vesicles are meant just to be a temporary housing to get the first self-replicating molecule to form, which I assume must be the idea with the vesicles, there is no reason why, chemically, a vesicle with more monomers and growing polymers would be favored over one without; there is no “selection” going on in any sense — just a growing glob of monomers
No, the vesicles are not "meant just to be a temporary housing". They are the antecedents of cell membranes. One of the two top articles on that page reports an experiment that demonstrates how early simple lipid vesicles could evolve into tougher phospholipid membranes.
- finally, and most importantly, even if the model succeeds in showing how the monomers create nice chains of polymers and how those chains are faithfully replicated (which is exceedingly doubtful, given the above considerations and probably a dozen others if we were to examine it in more detail), the central problem remains: where does the elusive information-rich molecule ultimately come from?
From the above processes!!!! It tells you quite specifically! And the "information" comes from the environment, as is the case with all Darwinian systems.
The model doesn’t have any capability of generating a functional polymer that can actually do any work. Thus, the model is relying on pure chemical chance to come up with a functional chain of nucleotides. (So I take back my statement that OOL researchers have rejected chance, at least in the sense of the component parts! :) )
No, the polymer does work. In the early stages, all it does is increase the chance the vesicle will grow, later it does more.
And then there was the gratuitous anti-religious stuff at the beginning of the youtube video, which you presumably do not endorse.
Yes, that was annoying. Although it did itemise some wrong ideas. Unfortunately it also peddled a canard - that abiogenesis isn't Darwinian evolution. The whole point of the Szostak model is that it pushes back the first Darwinian-capable entity to much earlier than we'd normally call "life". There really isn't a hard-and-fast dividing line between the two, or rather, the threshold is self-replication. The simpler the entity that can self-replicated with heritable variance in reproductive success, the more likely it is to have arisen "by chance" and got the Darwinian engine going.Elizabeth Liddle_{September 22, 2011
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As I've said several times that Szostak's model could turn out to be completely wrong, I'm not sure that "overselling" is the apt term! And yes, natural selection is a truism. Which is why it's so weird that people think it doesn't work. It pretty well has to work: if things self-replicate with heritable variance in reproductive success, the variants that replicate best will become more prevalent. It's hard to see how anyone could argue with it!Elizabeth Liddle_{September 22, 2011
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Hi Elizabeth, You might find the following papers useful: http://www.evolutionnews.org/2011/08/new_scientist_weighs_in_on_ori049621.html http://www.evolutionnews.org/2011/08/the_rna_world_a_response_to_ni049871.html Incidentally, have you ever thought of contacting Dr. Stephen Meyer? I know he's busy, but I think he would probably respond to you, given your background. http://www.stephencmeyer.org/contact.phpvjtorley_{September 22, 2011
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Well, Elizabeth, you are misunderstanding Meyer's point, and also *way* overselling Szostak's model, which has many, likely unsurmountable problems (see my comment above from a few minutes ago in response to video you referred us to). BTW, thanks for acknowledging in passing that natural selection is a "truism". We could have a lot of fun with that point, but it is OT for this thread. :)Eric Anderson_{September 22, 2011
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Elizabeth, I don't disagree that what you've referred us to is a model, but there are several things that jump out at me with a quick look. - the model is pretty vague in several areas; not necessarily a problem as a first effort, but as you mention, there are *lots* of details to fill in - the model is largely a non-starter from the outset for several other reasons: - it is not at all clear that the monomers will join up in nice chains as depicted in the video; specifically, if the monomers can join either on side-bonds or opposing-bonds, which is indeed required for the later copying to work, there is no reason to expect a nice chain to form - more likely a jumbled mess - similar problem when trying to replicate; even if the chain/clump gets broken apart with heat, there is no way to avoid interferring cross-reactions and a jumbled mess with new monomers coming into the scene - then there is the unlikely repetitive heat, cool, heat, cool cycle that would be required for the copying to even function - it doesn't appear that the vesicles replicate (unless I missed something in the model), the idea being simply that the vesicles simply grow bigger until, presumably, they either stop growing or burst spilling their contents - assuming the vesicles are meant just to be a temporary housing to get the first self-replicating molecule to form, which I assume must be the idea with the vesicles, there is no reason why, chemically, a vesicle with more monomers and growing polymers would be favored over one without; there is no "selection" going on in any sense -- just a growing glob of monomers - finally, and most importantly, even if the model succeeds in showing how the monomers create nice chains of polymers and how those chains are faithfully replicated (which is exceedingly doubtful, given the above considerations and probably a dozen others if we were to examine it in more detail), the central problem remains: where does the elusive information-rich molecule ultimately come from? The model doesn't have any capability of generating a functional polymer that can actually do any work. Thus, the model is relying on pure chemical chance to come up with a functional chain of nucleotides. (So I take back my statement that OOL researchers have rejected chance, at least in the sense of the component parts! :)) And then there was the gratuitous anti-religious stuff at the beginning of the youtube video, which you presumably do not endorse.Eric Anderson_{September 22, 2011
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Elizabeth, There aren't any self-replicating polymers nor monomers. Not only that there still isn't any evidence that living organisms are reducible to their chemical components.Joseph_{September 22, 2011
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Elizabeth, Yes, science is based on belief. First of all, by engaging yourself into science you believe that the outcome of your activity may be sensical and useful. Otherwise, being a scientist would be a bizarre thing. More importantly, each theory rests upon axioms. True, a richer theory may question the initial axioms but only by introducing more axioms. A classic example is Lobachevsky and Eucledian geometries. Your interpretation of Einstein overturning Newton I find strange. Einstein extended the Newtonian model, so the Newtonian mechanics became a special case of the more generic model. No overturning occured. Circular argumentation is a logical flaw that people may have irrespective of their religious beliefs. I just wanted to say that abiogenesis makes no sense to me in all respects, scientific included. How can something that does not exist yet start all of a sudden assembling itself? Give us at least one real life example of self-organisation. I also said that if such a thing had been possible in the past, chances are it would have been possible today unless we give a credible explanation of why it is the other way around. Without these things, it is not a science but alchemy or attempts to breed a homunculus.Eugene S_{September 22, 2011
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Dear Elizabeth, Again and again, we are not postulating anything of this sort. The picture is clear. We have evidence that suggests that systems exhibiting complex enough organisation cannot be generated by chance and/or necessity. Full stop. Up until today, there has been no evidence whatsoever of genuinely self-organising systems (not to be confused with self-ordering). So all we can do is based on massive evidence of a strong correlation between intelligent agency and information complexity, we can by induction hypothesise that ID does not contradict theistic world views. Of course, we are unable to test this hypothesis but it is in principle falsifiable provided enough unambiguous counter-ID evidence. Science cannot go any further, so the mystery of Creation is duly revered and the principles of science stay where they should. But in contrast to Darwinistic hypothesising, the ID based OOL hypothesis is well grounded.Eugene S_{September 22, 2011
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Elizabeth, In response to my statement:
I’m not saying we teach students that perhaps it was designed. I’m saying that we teach them that we don’t know whether it could have originated by itself.
You say,
If “perhaps it was designed” isn’t the same as “we don’t know whether it could have originated by itself”, can you give an alternative scenario to “designed” that covers “[did not] originate by itself”?
You're overlooking the fact that my statement - "we don’t know whether it could have originated by itself" - is correct, and that any attempt to mitigate that uncertainty would be misleading. One doesn't need to follow the logic, only to look at the conclusion. If the end result is that a misleading statement is preferable to an accurate one then either the logic is flawed or the the goal is something other than education.ScottAndrews_{September 22, 2011
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I’m not saying we teach students that perhaps it was designed. I’m saying that we teach them that we don’t know whether it could have originated by itself. That’s a very accurate statement, and by omitting it students are misled to think otherwise. If it’s not worth teaching accurately then it’s not worth teaching at all.
If "perhaps it was designed" isn't the same as "we don't know whether it could have originated by itself", can you give an alternative scenario to "designed" that covers "[did not] originate by itself"? If not, then the two statements are equivalent!
There is no evidence except for all of this stuff which bears more resemblance to things which were designed than to those which were not. Or we can rule that out because there’s a set of hypotheses that suggest there may be support for an idea that hasn’t been quite clarified implying that perhaps such things can appear on their own. And, oh yes, we’re making progress.
Well, interestingly, despite protestations by many pro-evolution people (including that otherwise excellent youtube video about the Szostak hypothesis), most of what OOL researcher do is push back the start time and form of Darwinian-capable entities (hey, we are finally talking about the OP!) to find out just how simple the remote ancestors of the LUCA could have been. Because we know (well, I know this is disputed here, but I am more than willing to defend it) that Darwinian processes are "self-design" processes, and that once you have a Darwinian-capable entity, i.e. a population of self-replicators that replicate with heritable variance in reproductive success, you will get adaptation, i.e. "design", in the small-d sense of the evolution of an entity optimised to survive/persist within itsl environment. So your characterisation of the Szostak theory as "a set of hypotheses that suggest there may be support for an idea that hasn’t been quite clarified implying that perhaps such things can appear on their own" is a cariacature (yes I know it was meant as one!) that really doesn't work. We know Darwinian evolution is an optimisation mechanism, and rather than the equivocatable work "design" (which can describe both an optimised entity, that need not have been intentionally designed, and the process of intentionally designing something), and the Szostak theory, though it my turn out to be the wrong approach, is, like all OOL theories, a theory as to how very very simple early proto-life forms could have had Darwinian capability. And so the hypotheses that it generates are all about whether various attributes of later forms (such as phospholipid membranes) could have provided reproductive advantage when things were much simpler (simple lipid membranes). And those are tested in those papers. The membrane paper is particularly important, because without an account of how highly permeable simple-lipid vesicles could have evolved into much less permeable phospholipid cell membranes, the theory pretty well fails. And the beauty of the vesicle story is that there is good evidence that lipids were present on early earth, and that they self-replicate, retaining their contents. Being permeable, if their environment included nucleotides, that would mean that the contents included polymerisable nucleotides, which, of course, are potentially self-replicating.Elizabeth Liddle_{September 22, 2011
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The chicken/egg syndrome refers to the question of which came first, the DNA that makes proteins or the proteins capable of replicating DNA. Hence, we have the RNA first hypothesis. You seem to be attributing the chicken/egg problem to natural selection, but there is no chicken/egg problem associated with that process because natural selection obviously cannot, under any circumstances, come first. According to the RNA world hypothesis, a self replicating system or self replicating molecule must evolve before prebiotic natural selection can come into play. That brings us to a key (though, by no means, the only) irony inherent in the RNA world hypothesis. Ribozyme engineering does not do what it claims to do--it does not simulate undirected chemical evolution. Every phase of the process is intelligently designed--modifying sequences of naturally occurring RNA catalysts, simulating natural selection in order to produce ribozymes with increased functional capacities, isolating molecules that perform particular functions, or selecting the most functional molecules—its all being directed in the name of undirected evolution. Any success these engineers enjoy in the lab indicates the need for an intelligent agent.StephenB_{September 21, 2011
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Thanks, Elizabeth, for your detailed response. “However, Chance has been “abandoned” by OOL (if it was ever current) in the sense that fully-fledged modern-type-celluar life emerged from non-life by chance assembly of the right atoms and molecules by (remembering Disney) a lightning strike in a mud puddle. Which is why I have made the point, repeatedly, on this thread, that probability calculations that show that this could not have happened are straw men. Nobody thinks that. It has, as you rightly say, been “abandoned”. Which is why it is odd that that “universal probability bound” keeps being produced.” No, probability calculations are not a straw man, for two reasons. First, the probability calculations are still very relevant to the various constituent parts. Even if no-one thinks that a “modern-type-cellular life” cell emerged all at once, the models invariably still rely on an assemblage of parts, whether we are dealing with a DNA-first, proteins-first, RNA first, or whatever model. The probability bound is absolutely relevant to forming, for example, a single protein of modest length. Second, absent a law-like process (whether stochastic or absolute) that can account for the assemblage of the various parts, the probability calculations are still relevant for the subsequent assemblage. “Nobody in science, that I know of, is arguing that modern-type cells emerged as a Vastly Improbable fluke. What OOL researchers, and indeed evolutionary biologists argue is that there are mechanisms that render such a fluke unnecessary. The Darwinian mechanism is one such.” Well, the Darwinian mechanism certainly isn’t applicable to the formation of the first self-replicating molecule, which is the holy grail of OOL research right now. It is also doubtful it would get us very far after self-replication, but I’m willing to leave that off the table now as a separate issue. “Well, it depends on that definition [of necessity]! But I can’t right now think of a definition that would make your statement true, and certainly not if we include stochastic processes.” There isn’t a reasonable definition that would make my statement untrue. Law-like processes, whether absolute or stochastic, simply do not create aperiodic complex specified information. Let’s get away from generalities and look at a specific example. Suppose we’re trying to get a functional RNA strand formed in the RNA World scenario (same principle applies with amino acids in a protein-first model). If we have an absolute chemical law that says, for example, C always attaches to G, then we end up with a largely repeating chain like a crystal that does not convey any information. I take it you agree with this. However, even with a stochastic process, for example C attaches to G with 70% probability, we might end up with a more complex pattern, but we still do not get the aperiodicity required, because all we get is a slightly-expanded stochastic pattern of repeating nucleotides; and we certainly don’t get the required specificity from a stochastic process itself. For that, we would have to fall back on pure luck, or chance. The concept of law-like processes operating at the chemical level, whether absolute or stochastic, is simply anathema to the creation of aperiodic specified information. This is a very well-understood principle in information theory. “But where is the evidence for a volitional agent 3.5 billion or so years ago?” Um, Elizabeth, that is the whole point of the inquiry. We have a complex information-rich system, which, based on our uniform and repeated experience and our current understanding of the cause and effect processes in the world, always and only comes from an intelligent agent. That is the evidence. You can’t avoid it by appealing to a circular statement: “we don’t know x, therefore we can’t consider x and can never come to a conclusion of x until we know x.” Historical sciences are in the business of identifying past causes, which, until identified, are not known. It is singularly unhelpful to say that we can’t consider something as a possible cause until we know that it was the cause.Eric Anderson_{September 21, 2011
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Elizabeth, I'm not saying we teach students that perhaps it was designed. I'm saying that we teach them that we don't know whether it could have originated by itself. That's a very accurate statement, and by omitting it students are misled to think otherwise. If it's not worth teaching accurately then it's not worth teaching at all.
unless we are postulating a miraculous director (or “supernatural” if you prefer) then there is no reason to posit such a thing, because there is absolutely no evidence of any director
There is no evidence except for all of this stuff which bears more resemblance to things which were designed than to those which were not. Or we can rule that out because there's a set of hypotheses that suggest there may be support for an idea that hasn't been quite clarified implying that perhaps such things can appear on their own. And, oh yes, we're making progress. But if we turn a blind eye to that evidence then the whole charade is over. It's willful ignorance, like when a man sees the signs that his wife is cheating but he tunes them out. It's not about our intellect or reason or education. It's about filtering out what we prefer not to know. As Friedrich Schiller said, against it the gods themselves contend in vain.ScottAndrews_{September 21, 2011
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I find this post difficult to make sense of. Clearly it is true that much modern science has Christian roots, in the sense that many great scientists were Christian by culture, and probably faith (although by no means all - some has Islamic roots, for instance, and of course pagan roots). But correlation is not causality, and you could equally argue that modern science has its roots in an empiricism that challenged faith, Galileo being the poster child. And I would profoundly disagree that science is "based on belief". Yes, science proceeds by resting on a priori assumption, but an assumption, or premise, is not a "belief". All scientific assumptions are that - mere assumptions, and the assumptions can, and are, questioned. That's how Einstein overturned Newton - by challenging the "assumption" that the universe was Euclidean. As for "science believes in our ability to develop a progressively better understanding of reality" - well, maybe so, but that isn't an a priori belief. And sometimes, in science, find that reality is more mysterious than we thought, not less. Although I guess that's progress of a kind :) But most importantly, I don't actually understand your main point. You say that the you considered that "chance and necessity...by themselves are impotent as far as OOL is concerned" based on your Christian faith. The reason I said that that means we are not talking about science is that you are basing your position on a non-negotiable premise. So any argument for your position based on that premise will be circular. This is quite different to scientific assumptions, which are always provisional, and always subject to potential falsification.Elizabeth Liddle_{September 21, 2011
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Well, I can see Meyer's problem! He doesn't seem to have read Szostak's papers, including the first two on that list! He seems to think, bizarrely, that natural selection can only operate once "RNA world" exists. This is completely false. Natural selection can, and will, operate wherever something self-replicates with heritable variance in the reproductive success, and a key element of Szotak's theory is, as I said, lipid vesicles (which self-replicate, but without heritable variance reproductive success) that are permeable enough to allow entry of monomers that assemble into polymers that then cannot escape, and which self-replicate, the cycle being driven, not by an enzyme, but by a thermocline. As a result, the lipid vesicles grow and divide, retaining their contents, which include copies of those polymers. The polymer contents vary, and that is the variance that results in variance in reproductive success, because some polymer sequences will promote division/replication. It's all in that video, but you'd have to read the science papers to get the details. But the Whole Point of the Szostak model is that competition between variants of self-replicating entites (aka "natural selection") sets in very early, long before you've got anything as fancy as an enzyme. Meyer seems to have missed this point, and accuses Szostak of circularity when there is no such circularity! That seems to be Meyer's problem generally - he keeps posing "chicken or egg first?" conundrums, forgetting, apparently, the concept of "bootstrapping". Or, at best, forgetting that the concept of natural selection is extremely simple, and almost a truism: that if things self-replicate with heritable variance in reproductive success, variants that reproduce better, will become more prevalent.Elizabeth Liddle_{September 21, 2011
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Well, it is "in model form". Did you look at that youtube video? It explains the model in substantial detail.Elizabeth Liddle_{September 21, 2011
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OK, here goes:
Elizabeth, Chance has been abaondoned by most OOL researchers, who realize that it doesn’t have the required resources to accomplish the necessary task. If you think chance is still a viable alternative, we can get back into the probability calculations.
For a start, pace Monod, I don't think it's terribly helpful to consider "Chance" and "Necessity" as discrete categories. Rather, there is a continuum of contingency. If we take, hypothetically, a deterministic universe (one without quantum uncertainty), an initial configuration will lead to final state with 100% certainty, however complex that final state is, and however haphazard the events might seem to an inhabitant of that universe. However, within that universe, some events will appear to obey laws of "necessity" (things reliably fall to earth; things keep moving in a straight line at constant velocity unless acted on by a force), i.e. you can predict with near 100% certainty what will happen, whereas other things will only be predictable probabilistically (meteors will strike the earth; earthquakes will occur) and "chance" will appear to determine what damage is done to what. However, because the universe is deterministic, all these things are the result of "necessity". Re-run the universe from its starting conditions, and you will necessarily get the same result. In other words, in a deterministic universe, there is a sense in which "chance" does not exist (everything that happens "necessarily" happens) and also a sense in which it does (some things are highly predictable, given relatively little data; other things are highly unpredictable, even given a great deal of data). And things aren't that different in an non-deterministic universe such as the one we seem to have. Some things are highly predictable; other things are highly unpredictable. So it doesn't make a lot of sense to me to talk about Chance as something different from "Necessity" unless we are very clear about what we mean. Now, most scientific models of phenomena are stochastic, in other words they allow for events that are unpredictable in specifics, but predictable statistically. In other words, rather than modelling laws of "necessity", the models incorporate probability distribution functions. So in that sense, most models are "Chance" models, i.e. stochastic models. And, indeed, all the OOL models I know of are stochastic. So "Chance" has not been "abandoned" by OOL researchers in that sense. However, Chance has been "abandoned" by OOL (if it was ever current) in the sense that fully-fledged modern-type-celluar life emerged from non-life by chance assembly of the right atoms and molecules by (remembering Disney) a lightning strike in a mud puddle. Which is why I have made the point, repeatedly, on this thread, that probability calculations that show that this could not have happened are straw men. Nobody thinks that. It has, as you rightly say, been "abandoned". Which is why it is odd that that "universal probability bound" keeps being produced. Nobody in science, that I know of, is arguing that modern-type cells emerged as a Vastly Improbable fluke. What OOL researchers, and indeed evolutionary biologists argue is that there are mechanisms that render such a fluke unnecessary. The Darwinian mechanism is one such. The Szostak lab (and others) are investigating additional possibilities.
Necessity, or law-governed processes, cannot *by definition* create the aperiodic specified information found in the cell, such as a simple protein or strand of DNA.
Well, it depends on that definition! But I can't right now think of a definition that would make your statement true, and certainly not if we include stochastic processes.
Of course there is a cause which is fully capable of generating this kind of specified information, and which we regularly witness doing so. But we shan’t consider that possibility, because it would violate our philosophical sensibilities, right?
Well, if you mean volitional agents, sure. That wouldn't violate my philosophical sensibilities at all. But where is the evidence for a volitional agent 3.5 billion or so years ago? The only ones we know of are biological, and you can't invoke a biological agent as the cause of biological agents!Elizabeth Liddle_{September 21, 2011
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Elizabeth: "The trouble there, Scott, as I see it, is that unless we are postulating a miraculous director (or “supernatural” if you prefer) then there is no reason to posit such a thing, because there is absolutely no evidence of any director, nor of any forces that the director might have used to do the assembling. This, as I see it, is the most profound problem with ID. Either you posit a supernatural designer, in which case, there are no tests we can use to generate positive evidence for such a hypothesis, or you posit a natural designer, in which case, the hypothesis has no evidence to support it, whereas at least some “undirected” hypotheses do." Elizabeth, get real. You are the one who is happy to count vague, mildly relevant, wildly speculative observations as "evidence" for abiogenesis, but then you turn around and say there is "no evidence" to support design? Please. At least be somewhat intellectually equal in your treatment of competing hypotheses. Also, as to no evidence for design, you've got to be kidding. Surely it counts as "evidence" that every time, without exception, when we see complex specified information arise and are able to ascertain the cause, it always, without exception, turns out to be intelligence. Couple that with the fact that in no instance has undirected chance or law ever, not once, been observed to create complex specified information. Look, we understand you have a philosophical hangup with the idea of life being designed, but let's at least acknowledge your issue for what it is. It isn't a problem with the evidence. Shoot even folks like Dawkins acknowledge that life looks designed. It is the evolution camp which is trying mightily (and so far, futily) to muster evidence that the design so apparent in life is just an illusion.Eric Anderson_{September 21, 2011
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It was a general comment (you are not the first, nor will you be the last, to abandon the straight path) but naturally you are the sort of person, Elizabeth, who falls into that category. That you disagree in the strongest personal terms, shouldn’t be reinterpreted as an ‘accusation’, I wasn’t ‘accusing’ you of anything. The record speaks for itself. Let’s not waste time pretending it doesn’t.
I cannot parse this. You say you were not "accusing" me of anything. Yet you talk about my being the "sort of person" who "abandon[s] the straight path" and that "the record speaks for itself". What on earth are you talking about? It appears I have offended you in some way, and I have no clue why. Yet when I ask for clarification, you imply further accusations, yet decline to give any details. I'm afraid I find this intolerable. Please call a spade a spade and tell me what I am supposed to have done wrong, with links, preferably. Otherwise, please retract your insinuations. Thanks.Elizabeth Liddle_{September 21, 2011
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Well, clearly we are not understanding each other. I suggest you explain exactly what you think a theory of abiogenesis entails, then we might understand better what you are asking of us. Because clearly right now we are at an impasse.Elizabeth Liddle_{September 21, 2011
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No, I'm not playing word games. I'm trying to figure out what you mean. That means figuring out what the words mean. But if the key concept here is "undirected", fair enough. Now I understand. You are saying that we should tell students that it's possible that the assembly of life was "directed"? The trouble there, Scott, as I see it, is that unless we are postulating a miraculous director (or "supernatural" if you prefer) then there is no reason to posit such a thing, because there is absolutely no evidence of any director, nor of any forces that the director might have used to do the assembling. This, as I see it, is the most profound problem with ID. Either you posit a supernatural designer, in which case, there are no tests we can use to generate positive evidence for such a hypothesis, or you posit a natural designer, in which case, the hypothesis has no evidence to support it, whereas at least some "undirected" hypotheses do. Unless your position is that the supernatural designer simply designed the universe so that life would inevitably emerge from non-life ("frontloading", if you will, but not at the OOL, stage, but the Big Bang stage), but in that case we should be able to work out the physics and chemistry of the process just as we can work out the physics and chemistry of the rest of the phenomena we observe in the universe.Elizabeth Liddle_{September 21, 2011
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Why is "a miracle" a straw man? I thought that one problem with science was supposed to be its "a priori commitment to materialism"? That it cannot allow a "Divine Foot in the door"? If you do not hold this view, great, but there seems to be a fair bit of it about. And no, I don't think a science curriculum should "limit its assumption to those things it can empirically demonstrate". It's not what I said, and not what I meant. And of course volition has "physical entailments that can be examined just as readily as any other physical object". Again, I didn't say it didn't. But volition doesn't have "physical entailments" unless it is coupled to some motor system. Unless we are talking about miracles. Which you say is a straw man. So, to regroup: We know OOL/abiogenesis "occurred" in the sense that we know that there is life now, and there once wasn't. So we know that at some point, life emerged from non-life. Whether some volitional agent guided them into the right molecules or not makes no difference to the question as to whether it occurred. What we don't know is how it occurred. And we have absolutely no evidence of any volitional agent that might have done so (barring a miraculous agent, and even there, the only evidence is negative i.e. dearth of non-miraculous explanation) whereas we do have some evidence in support of some non-volitional theories, such as Szostak's. Not sure what you are getting at with your apparent jibe about unfalsifiable assumptions. Perhaps you'd like to clarify.Elizabeth Liddle_{September 21, 2011
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BTW, are you suggesting that abiogenesis researchers are hypothesizing that life was deliberately created? I didn't see that in any of those papers. I think 'abiogenesis' is the right word and there's no need to split hairs over it.ScottAndrews_{September 21, 2011
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Elizabeth, Now we're playing word games. Give me a word for 'spontaneous, undirected self-assembly of life' and I'll use it. I just don't want to type all that several times in one post.ScottAndrews_{September 21, 2011
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Sorry! But there is an important point here. We know that life exists now; we know at one time it didn't. So at somem point, life emerged from non-life - aka "abiogenesis". What alternative are you proposing to "chemistry" of some sort of another? Surely even if you postulate a designer, that designer must have assembled chemicals? Unless you are really are talking about a miracle, but Upright BiPed has just called that a "straw man".Elizabeth Liddle_{September 21, 2011
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---Elizabeth: "StephenB: from my PoV, I have answered your question in detail many times. Clearly you think I haven’t." I was simply asking you to articulate that this is an attempted partial defense of the RNA World Hypothesis (It does have a name, after all) so that we can examine its weakness from a paradigmatic perspective, since the study itself ignores the mean weakness of the theory. Stephen Meyer says it best: "Ribozyme engineers tend to overlook the role that their own intelligence has played in enhancing the functional capacities of their RNA catalysts. ... RNA-world advocates envision ligases evolving via undirected processes into RNA polymerases that can replicate themselves from freestanding bases, thereby establishing the conditions for the beginning of natural selection. In other words, these experiments attempt to simulate a transition that, according to the RNA-world hypothesis, would have taken place before natural selection had begun to operate. Yet in order to improve the function of the ligase molecules, the experiments actually simulate what natural selection does. ... But what could have accomplished these tasks before the first replicator molecule had evolved? Szostak and his colleagues do not say. They certainly cannot say that natural selection played this role, since the origin of natural selection as a process depends on the prior origin of the self-replicating molecule that Szostak and his colleagues are working so hard to design. ... [E]ngineers perform a role in simulating natural selection that undirected natural processes cannot play prior to the commencement of natural selection." Do you see the problem?StephenB_{September 21, 2011
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Of course it must be a model. All theories are models. And from a theory you derive testable hypotheses, and you test them against data. The Szostak model is clearly described on their lab web page, together with sub-theories, and hypotheses derived from those sub theories, and papers reporting tests of those hypotheses. Some of the specific sub-theories and hypotheses that go to make the model are shown in these movies: http://genetics.mgh.harvard.edu/szostakweb/movies.html http://exploringorigins.org/ Clearly, any theory that explains how cells emerged from non-replicating molecules is going to have a series of stages, and the each of these postulated stages raises hypotheses that need to be tested. The theory is nicely animated in this youtube video: http://www.youtube.com/watch?v=U6QYDdgP9eg From which you will see that there are a lot of details to be filled in and tested. Some parts of the postulated process may turn out not to work, and the the theory modified. The top two papers on that list test, respectively, a hypothesised solution to the polymer backbone problem, and a hypothesised solution to the problem of how phospholipid vesicles might have evolved from simple lipid vesicles. But of course there are many more problems to solve.Elizabeth Liddle_{September 21, 2011
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As in, there are two known sources of X, A and B. B is routinely observed to produce a certain sub-class X1, and in relevant cases A is not a credible source. Is or is not X1, then a signature of B at work, even though B may be unpalatable?kairosfocus_{September 21, 2011
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Oh golly. OK, I'll be back later to address this. Could you perhaps re-read my posts in the mean time?Elizabeth Liddle_{September 21, 2011
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