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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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

No, the idea is that you don't get Darwinian processes until you have your self-replicator. It's the necessary condition for Darwinian evolution. So what we need is evidence for a self-replicating polymer to have arisen simply from chemistry. That is one of the areas of OOL research, but as several candidate molecules have already been created artificially, it seems that researchers are on their way to do so using conditions that might have existed on early earth.Elizabeth Liddle_{September 23, 2011
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I will repeat- there STILL isn't any evidence that Darwinian processes can construct new, useful multi-part systems. And there isn't anything in your reference that demonstrates darwinian processes didit.Joseph_{September 23, 2011
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Elizabeth, There isn't any evidence for a self-replicating polymer arising via Darwinian processes. Self-replication is your downfall...Joseph_{September 23, 2011
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Elizabeth, Please do not mention paleontology. Paleontological "evidence" is far from clear. What we do see is not a gradual process of accumulating infenitesimal changes over vast periods of time but sudden gaps in complexity, e.g. in Cambrian strate, hence the name Cambrian explosion. In any case, it is decidedly counter-Darwin.Eugene S_{September 23, 2011
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There is quite a lot of literature on the evolultion of multi-cellular organisms. There's a review paper here: http://www.nature.com/scitable/topicpage/volvox-chlamydomonas-and-the-evolution-of-multicellularity-14433403Elizabeth Liddle_{September 23, 2011
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Thanks Joseph - yes indeed there is. But the theory is a multi-component theory, and the idea is that one of the "parts" - the lipid vesicle - co-evolves with other parts - its polymer content. So if you count a primitive cell, with membrane and self-replicating polymeric contents as a "living thing" then, yes, there is data supporting that. As for Stonehenge - as I've pointed out, several times: there is no evidence that Stonehenge can self-replicate! So no Darwinian mechanism could possibly account for Stonehenge. Which is just as well, because we have plenty of evidence for intelligent human designers and artisans (don't forget the artisans!)Elizabeth Liddle_{September 23, 2011
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Elizabeth yet again claims that neo-darwinian evolution is “extremely well supported by field, lab, palaentological, genetic, and computational evidence. And is in any case no more than simple logic.” However, in all the months she has been active here, she has not made a single serious attempt to substantiate this claim. Nor has any other participating atheistic evolutionist.
Of course I have, and so have many others. Repeatedly. And people here agree that the field and lab evidence supports it - but insist that it only applies to "micro-evolution". However, palaeontological evidence also demonstrates exactly the incremental changes that we observe in what is called "micro" evolution" but over much longer time scales, and the genetic evidence tells us just how that variance arises and what it does. Computational evidence shows us that if a population of extremely simple virtual organisms is allowed to "breed" with variance, it will adapt to the fitness landscape provided, so well, that the resulting evolved critters often solve problems that human engineers have failed to solve. That is a "serious attempt to substantiate this claim". Self-replication with heritable variance in reproductive success results in adaptation. Statistically, it can't not. What's more, it's a very similar mechanism to the mechanism by which human designers design things, so it's not surprising that there's a family resemblance in the products.
Now, as Richard Dawkins himself puts it: “Biology is the study of complicated things that give the appearance of having been designed for a purpose.” This indisputable fact cannot be explained away with terms like ‘optimisation’.
I don't know why Richard Dawkins earns himself a "himself" - as in "the pope himself"? :) There is no "explaining away" being done here by the word "optimisation". It's just a more precise term. If something is optimised, it looks as though it has "been designed for a purpose" and, indeed, it has, if that purpose can include persisting and self-replicating. But optimisation algorithms are not confined to the outputs of intelligent intentional external designer. Populations of things optimise all by themselves, from the simplest sorting systems (resulting in sorted ebbles on a beach) to populations of self-replicators whether Galapagos finches or virtual critters in a GA. They do so because it is self-evidently true that if a populations of self-replicators that replicate with heritable variance in reproductive success, then the best self-replicators will become more prevalent in the population. I assume you agree that this is true?
There is a vast gap between amino acids and a self-replicating molecule. Self-replication is not just a molecule splitting itself in half then being lucky enough to find another complementary half floating around: at best, such a molecule would simply split into two halves and then those two halves would re-connect to each other again. That isn’t self-replication.
No it's not "being lucky enough" - it's chemistry. And self-replicating molecules that self-replicate identically are extremely common - any molecule that catalyses its own formation will do that. What is more interesting are molecules such as polymers where the sequence of monomers itself is replicated so that where there was one polymer of given sequence there are now two. But such molecules exist, and at least one artificially created molecule actually evolves: http://www.newscientist.com/article/dn16382-artificial-molecule-evolves-in-the-lab.html And here's another interesting report: http://www.newscientist.com/article/dn755-early-replica.html Sure, there are still many unknowns, but the principle is already established - that some molecules catalyse their own synthesis. What the first one was, may never be known, but there seems no a priori reason to expect that we won't find a candiate. The important thing is that a) the replication is not 100% faithful and b) that the variants vary in reproductive success. Once you've got that, you've got the necessary conditions for Darwinian processes to begin, just as happened in case above (first link).
There is an even greater gap between mere improvements in reproductive efficiency and explaining the existence of biochemistry, organs and body parts and all of the remarkable diversity we see in nature: all of it bursting with the sort of precision engineering and sophistication that mankind can only dream about imitating. This gap cannot be bridged by simple logic, on the contrary it is completely illogical to suggest it can be!
Not at all, and much is known about how those improvements came about. As for "the existence of biochemistry" - biochemistry is just chemistry, and how that chemistry came about is a completely different question. If the ID argument was that the ID designed a universe with the kind of chemistry that would eventually produce life, I'd have a bit more respect for it! (Although I still think the "fine-tuning" argument has some serious problems). And as for "engineering and sophistication that mankind can only dream about imitating" = exactly. Intelligent agents aren't all that good at optimising solutions, which is why they are smart enough to use GAs! The great thing about optimisation algorithms is that they "reach the parts other beers cannot reach" as the old Heineken ad went. Intelligent agents work faster, because they take short-cuts; however, in taking shortcuts they do a much less thorough search than blind optimisers who will follow their noses down pathways that an intelligent agent may reject a priori. This is why, even in my field, we increasingly devise optimisation algorithms to solve problems that we as "intelligent agents" cannot easily solve. And those algorithms tend to be essentially Darwinian (there are probably some that aren't but the ones that I use all are).
As has been stated over and over again, we know of only one explanation for the existence of “complicated things that give the appearance of having been designed for a purpose”: Intelligent Design.
Nope, there is also Darwinian evolution! We know that it results in “complicated things that give the appearance of having been designed for a purpose” or rather "that actually are fitted for their own intrinsic purpose of persisting, and in some cases, also for our own". It is fundamental property of self-replication with heritable variance in reproductive success. Once you have that, then the population will adapt/optimise in such a way that the individuals' chances of successful reproduction are maximised, whether that's by having flagella, wings, fancy lines of code or simply a longer polymer chain.
The onus is on atheistic evolutionists like Elizabeth to provide detailed evidence for an alternative explanation like natural selection acting upon random mutations.
Which I just did for the umpteenth time. And please stop with the "atheistic evolutionist". I'm not an "atheistic evolutionist". I don't believe we have an afterlife, because I don't see that minds can exist without bodies; because I do not think that minds can exist without bodies, I don't see how a mind can precede bodies, therefore I reject the idea of a creator with a mind. That has absolutely nothing to do with my views on evolution, indeed, in the days when I thought that minds could exist without bodies, I gave credit to the creator mind for having dreamed up such a cool scheme for creating intelligent life.
Rhetoric and evasion are no substitute for reason and evidence.
Indeed. Which is why I have been giving clear reasons and citing actual evidence.
Given the duration of this discussion, it is now plainly obvious that the atheistic evolutionists participating in this discussion are completely incapable of providing detailed evidence for a neo-darwinistic explanation of “complicated things that give the appearance of having been designed for a purpose.”
Well, clearly we are incapable of providing evidence that you regard as evidence. I submit that the problem may be on your side.
Indeed, the more honest atheistic evolutionists are (albeit carefully) increasingly abandoning neo-darwinism precisely because there is no evidence whatsoever that natural selection acting upon random mutations has the creative power required to produce, amongst millions of other amazing life-forms, a human being from a single-celled eukaryotic ancestor.
Yes, there is a great deal of evidence. As I said, it's genetic, palaeontological, empirical and even logical. Throughout this thread, people have said "there is no evidence whatsoever for...." and I have provided evidence. That evidence is then dismissed for various reasons, each of which I have countered. If you want to discuss the evidence, let's discuss the evidence. But it's time you guys stopped accusing anyone who presents any evidence of dishonesty. Clearly we find it persuasive. Clearly you don't. Time to move past the honesty thing.
Wherever we seek continuity in species, we find only discontinuity. Wherever we seek evolutionary change, we find only stasis (or, at best, genetic homeostasis).
No, we find continuity - google "transitional fossils" (though it's a bad term because all organisms are transitional). And far from "stasis" even if we look at populations that oscillate about a point, like the Galapagos finches, we find not "stasis", but indeed oscillations that are correlated with oscillations in the environment. In other words, evolution works to keep populations at an optimum, and it has measurable effects even from generation to generation. There is no stasis - there is just variation in rates of change.
So, the time for our regular atheistic evolutionist participants to put up, or shut up, is long overdue. If they can’t put up, then they should shut up by doing the decent thing and withdrawing from the debate. Hopefully, this will encourage others to champion neo-darwinism and make a case for it that is actually based upon reason and evidence instead. For a change.
I'm almost speechless. I have been "putting up" throughout this thread. Oh, and Chris, are you going to "put up or shut up" about my alleged moral failings? I'm pretty annoyed with you right now! I think you owe me a few beers.Elizabeth Liddle_{September 23, 2011
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Elizabeth, For some reason, my internet connection is sluggish so there may be other inadvertant double posts occasionally... "so to account for the origin of life, we have to account for the earliest and simplest Darwinian-capabile self-replicating entity" I am afraid, this is simply wrong. To account for abiogenic OOL one has to demonstrate how a number of constituents started organising themselves into a complex entity spontaneously *without* extraneous instructions. In order to have a game between agents, rules must be defined before anything else. Instruction comes FIRST. Unwilingness to recognise that is a major logical flaw behind all abiogenesis thinking. Remarkably, Friedrich Engels was prone to the same flaw when he conjectured that it what physical labour that made humans out of apes. This reasoning is simply nonsensical, because in order to do something one must first have an idea of that something and an idea of how he can bring it into existence, instead of starting to sporadically, without any plan, hit one stone against another to try and see what will come out of it. Biological and artificial systems alike are amenable to information theoretic analysis, which has clear findings: rich information content cannot be generated spontaneously, in other words, self-organisation is not plausible. I asked you earlier on to provide at least one demonstrably clear example of such self-organisation. Do you have any such examples? Self-organisation in the rigorous sense implies spontaneous emergence of formal relationships between components. In reality such relationships in complex systems *always* comply with some sort of a priori defined interface. In biosystems, such an interface also exists. Just like in every other type of complex system, this interface in biosystems is not a by-product of some mysterious spontaneous process but a prerequisite for the existence of self-replication. This is clear from information theoretic analysis, which you seem decidedly not to notice. You appear to disregard the distinction between inferring design and making claims about how the object was designed. Why do you think that proper design inference must necessarily involve inferring particular ways of its realisation? The two are logically *distinct*. I don't know what causes you not to notice the difference.Eugene S_{September 23, 2011
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So it looks like there is data supporting the claim that some of the components that make up a living organism can arise via blind, undirected chemical processes. SOME OF THE PARTS- yet there still isn't any sata supporting the claim that a living organism is a sum of those parts. OTOH Stonehenge is a sum of its parts- stones no less and we know mother nature can produce stones. Yet no one would ever say that since mother nature can produce stones then that is evidence that mother nature produced Stonehenge. However that is exactly what Elizabeth and others are doing. Strange, that...Joseph_{September 23, 2011
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EL:
However, what I am arguing for is perfectly simple: that Darwinian mechanisms are capable of producing entities optimised aka adapted to thrive (persist; self-replicate) in their environment, and so to account for the origin of life, we have to account for the earliest and simplest Darwinian-capabile self-replicating entity, and that is exactly what various labs, with varous degrees of success in producing models supported by data, are doing.
Yet there isn't any evidence that Darwinian processes can construct new, useful multi=part systems and living organisms are full of them.Joseph_{September 23, 2011
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Elizabeth yet again claims that neo-darwinian evolution is “extremely well supported by field, lab, palaentological, genetic, and computational evidence. And is in any case no more than simple logic.” However, in all the months she has been active here, she has not made a single serious attempt to substantiate this claim. Nor has any other participating atheistic evolutionist. Now, as Richard Dawkins himself puts it: “Biology is the study of complicated things that give the appearance of having been designed for a purpose.” This indisputable fact cannot be explained away with terms like ‘optimisation’. There is a vast gap between amino acids and a self-replicating molecule. Self-replication is not just a molecule splitting itself in half then being lucky enough to find another complementary half floating around: at best, such a molecule would simply split into two halves and then those two halves would re-connect to each other again. That isn’t self-replication. There is an even greater gap between mere improvements in reproductive efficiency and explaining the existence of biochemistry, organs and body parts and all of the remarkable diversity we see in nature: all of it bursting with the sort of precision engineering and sophistication that mankind can only dream about imitating. This gap cannot be bridged by simple logic, on the contrary it is completely illogical to suggest it can be! As has been stated over and over again, we know of only one explanation for the existence of “complicated things that give the appearance of having been designed for a purpose”: Intelligent Design. The onus is on atheistic evolutionists like Elizabeth to provide detailed evidence for an alternative explanation like natural selection acting upon random mutations. Rhetoric and evasion are no substitute for reason and evidence. Given the duration of this discussion, it is now plainly obvious that the atheistic evolutionists participating in this discussion are completely incapable of providing detailed evidence for a neo-darwinistic explanation of “complicated things that give the appearance of having been designed for a purpose.” Indeed, the more honest atheistic evolutionists are (albeit carefully) increasingly abandoning neo-darwinism precisely because there is no evidence whatsoever that natural selection acting upon random mutations has the creative power required to produce, amongst millions of other amazing life-forms, a human being from a single-celled eukaryotic ancestor. Wherever we seek continuity in species, we find only discontinuity. Wherever we seek evolutionary change, we find only stasis (or, at best, genetic homeostasis). So, the time for our regular atheistic evolutionist participants to put up, or shut up, is long overdue. If they can’t put up, then they should shut up by doing the decent thing and withdrawing from the debate. Hopefully, this will encourage others to champion neo-darwinism and make a case for it that is actually based upon reason and evidence instead. For a change.Chris Doyle_{September 23, 2011
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No problem :) Interestingly, from my PoV, the confusion seems all on the other side! Which may be why what I am arguing against seems unclear - there seem to be a large number or unrelated, and even contradictory, ID cases being made. However, what I am arguing for is perfectly simple: that Darwinian mechanisms are capable of producing entities optimised aka adapted to thrive (persist; self-replicate) in their environment, and so to account for the origin of life, we have to account for the earliest and simplest Darwinian-capabile self-replicating entity, and that is exactly what various labs, with varous degrees of success in producing models supported by data, are doing. And that therefore, any ID argument based on probability is circular (because it depends on the absence of a mechanisms rendering life probable) and any ID argument based on the conviction that optimisation requires an external volitional agent is flawed (because we know that self-optimisation occurs in populations of self-replicators). And ID arguments based on irreducible complexity, whether of a bacterial flagellum, or the LUCA, or the simplest complexity Darwinian-capable entity are simply arguments-from-gaps, not positive arguments. Any demonstration as to how a transitional state could have been selectable removes the irreducibility. But which post of mine were you referring to in your comment?Elizabeth Liddle_{September 23, 2011
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To answer your first question: both - there are clearly gaps and unsolved problems, but also, it is a fundamental principle of science that all models are at best incomplete.Elizabeth Liddle_{September 23, 2011
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Good, then perhaps we can make some progress in the discussion. Are you saying that it could turn out to be wrong, just as a matter of principle, or have you actually looked at it in enough detail to see any weaknesses? Can you articulate a couple of areas where you see the greatest weaknesses in his model? Some of us have actually taken time to look at it and can see a number of shortcomings right out of the gate. What weaknesses do you think it has?
It's not my field, so I'm really not qualified to critique it. But clearly there are a number of unsolved steps. And as I understand it, there is still some debate about whether proteins came first or RNA came first. Although self-replicating and evolving RNA has been produced in a lab. I think the lipid vesicle idea shows great promise though, as that has been fairly well tested, and solves at least some of the problems faced by OOL researchers, one of which is how you get a concentration of self-replicating polymers in one place, protected, in something resembling a cell, and in a context where specific sequences may promote faithful replication of the whole than others. In other words you have the beginnings of the genotype-phenotype relationship, without which you don't have the basis for Darwinian mechanisms. But whether it was amino acid sequences that came first, or nucleotide sequences, I'm not sure where the betting currently is. Conceivably both together.Elizabeth Liddle_{September 23, 2011
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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).
No, there is no "full stop". There is plenty of evidence of "self-ordering systems". That is precisely what is at issue. Simply stating that "the picture is clear" does not make it so. What we are faced with is that on your "side" you think that there are no "genuinely self-ordering systems" and our "side" we think there are. So the picture is NOT clear. So what is wrong with the picture? I suggest that what is wrong is imprecise definition of what either "side" actually means. However, when I raise the issue of definitions, I am usually accused of "playing word games". How to escape? Well, we need to keep drilling down until we reach what is actually separating the two camps. And what I think separates us is a simple error - a statistical error - on your side :) The assertion that " We have evidence that suggests that systems exhibiting complex enough organisation cannot be generated by chance and/or necessity. Full stop." is, I suggest, simply undemonstrated, not least because "chance" and "necessity" are not clearly specified (ironically) in the alleged demonstrations, for instance, Dembski's paper: Specification: The Pattern That Signifies Intelligence.
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.
And this is a glaring misuse of a statistical technique, on many counts, not least being the fundamental error of extrapolating beyond the range of your data. And I don't think anyone doubts that "ID does not contradict theistic world views!" You don't need a correlation to infer that! But then Darwinian evolution doesn't contradict theistic world views either (well, may be some - YEC, for instance). tbh, having been a devout theist for half a century, I always thought ID was a clunky, theologically. A designer who didn't need to tinker to produce life seems superior to me to one who does, especially one who, incomprehensibly, tinkers with bacterial flagella, so that bacteria may more efficiently kill small children.
A Of course, we are unable to test this hypothesis but it is in principle falsifiable provided enough unambiguous counter-ID evidence.
Did you mistype your hypothesis ("that ID does not contradict theistic world views")? I'm really not sure what you are saying here.
Science cannot go any further, so the mystery of Creation is duly revered and the principles of science stay where they should.
On what basis are you asserting that "Science can go no further?" What if it does? Where did that "should" come from"?
But in contrast to Darwinistic hypothesising, the ID based OOL hypothesis is well grounded.
On the contrary: "Darwinistic hypothesising" takes the form of empirical hypothesis testing, with some positive results. The "ID based OOL hypothesis" doesn't exist. It's just an inference drawn from the lack of an alternative explanation. There is only one empirically testable hypothesis for ID that I know of which is the "front-loading" hypothesis. We could derive testable predictions from that, which would differ from the predictions made for Darwinian mechanisms. But I don't see that being done anywhere. And I see absolutely no evidence that anyone is actively trying to figure out How The Designer Did It. Whenever I raise that question, I am told I do not understand ID, and that it's just about detecting design. That is an equivocation with the word "design". There are two things that produce design, that we know of: one is Darwinian mechanisms; the other is intentional agents. In the absence of self-replication we can are reasonably safe from false positives for intentional agents, just by looking at the thing; in the presence of self-replication, we need to use other criteria.Elizabeth Liddle_{September 23, 2011
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Dear Elizabeth, Sorry for the unintentional double post. My concern was to sound as friendly as possible :)Eugene S_{September 23, 2011
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Eric:
Boy, it is tiring to have to correct so many misconceptions about ID, especially from people who should know better, but I can’t let this stand. Elizabeth: “The evidence for ID is negative, not positive. It lies in the lack of an alternative explanation, it is not in itself an explanation.” I don’t know how to put this kindly, but I’ll try. Rather than assuming this is a flat-out lie, I’ll assume it results from a basic misunderstanding of the design argument. So back to Design 101.
Thank you for the assumption. There is, of course, a third possibility, but thank you for dismissing the first. You were correct to do so.
First, every theory that challenges another theory is, in a very practical sense, making a negative case against the other theory. There is absolutely nothing wrong with that. Indeed, the traditional evolutionary argument as put forth by Darwin was specifically proposed to make a negative case against design.
No, and no. However, perhaps I wasn't clear. By "negative" evidence for an argument I mean simply lack of evidence for the alternative. By positive evidence for an argument, I mean data that supports differential predictions arising from the hypothesis. Darwin's theory was not a "negative case against design". It was a positive proposal of a mechanism by which populations of organisms would adapt to their environment that required no intentional designer. It was not the argument: "there is no evidence for a designer". Indeed, Darwin posited that for his theory to work, life first had to be "breathed" by the Creator into "a few forms or one".
Further, prominent evolutionary proponents continue to acknowledge that life appears to be designed. In that sense, evolution is very much an attempt to negate our initial impression of design and show that the design is an illusion. Finally, even if the only point of ID were to be a negative case against evolution and bring some sanity back into the ridiculous evolutionary storytelling, it would be doing a tremendous factual and scientific service.
There is a real problem with the word "designed", as I've mentioned. We can use the word to mean "optimised", or we can uses the word to mean "done by an intentional agent". Those are quite different uses. Of course biological organisms are optimised. It's not that biologists are forced to continue to "acknowledge" this. The evolutionary issue is: by what mechanism did and does this optimisation occur? Darwin's answer, which demonstrably works (in what you all "micro-evolution") is by self-replication with heritable variance in reproductive success. It's not that "design is an illusion", it's that the appearance of intentional design is an illusion, and not a very good one. The pattern of living things looks far more like incremental optimisation than far-sighted (i.e. with a distal goal in mind) design by an intentional external agent. Hence Dawkins' phrase "the blind watchmaker" - there is indeed a "watchmaker" aka the optimisation of Darwinian mechanisms, but it is blind - can only "see" the next operation, not even the next-but-one. So: we know that Darwinian optimisation works; what we don't know is how, specifically, it worked in any given transition (bar a few, and then only partially) and, in particular, how it worked in the earliest days, to get from the earliest crude self-replicating molecules (or what those were) to the earliest modern type cell. But the mechanism itself is well-tested.
Second, ID makes a positive case for design. The entire point of ID is that some physical systems exhibit characteristics that identify, positively, the activity of an intelligent agent. There is nothing negative whatsoever in that formulation of design detection. It is perfectly legitimate, and is routinely used in SETI, forensics, archaeology, etc. Everyone is fine with those applications of design detection, but when it comes to life, outrage ensues. We can only conclude that this is not because the concept of design detection itself is a problem, but because someone’s philosophical toes are being stepped upon.
Again, no. The difference is not philosophical at all. There are not one, but at least two systems known to produce the kinds of patterns you call "designs". One is intentional biological agents; the other is Darwinian optimisation, which occurs populations of biological organisms, i.e. populations of self-replicators. Both are biological, note, but one involves an external intentional agent, the other is a self-optimising process. In the case of archaeology, we know of external biological agents, and we are, in general, not talking about self-replicators. In the case of the hoped-for SETI signal, again, we are probably not talking about a self-replicating population, so it is reasonable to conclude an external intelligent agent. But note that "designs", to our knowledge, are always traceable to self-replicators, whether as external agents who design some other system, or whether as the design itself.
ID is most definitely not just a negative argument from ignorance. Anyone who says otherwise either does not understand the design argument or is being deceptive. Which one applies to you, Elizabeth?
As I've said, there is an excluded middle :) Which, in this case, is, IMO, that you have misunderstood the nature of your own argument, and, indeed, the nature of the evolutionary argument. To be specific: I am always seeing the "universal probability bound" quoted, and the argument made that as biological organism X is extremely unlikely to have arisen "by chance" in the time of the universe, then an ID is more likely than said "chance" - and, moreoever, that people who try to escape this inevitable conclusion by invoking multiverses are merely trying to get round the universal probability bound in order to save their "chance" hypothesis. That is a straw man: "evolutionists" do not propose that complex biological organisms, or even the LUCA, came about "by chance". What they propose is that the Darwinian mechanisms, by which, when self-replicators replicate with heritable variance in reproductive success, the better replicators will become more prevalent, only needs a minimally efficient self-replicating entity to get going, and that that minimally efficient self-replicator occurred "by chance" or rather, occurred in an environment in which its occurance was quite probable. The ID argument seems to me to be that this did not happen, for no good reason other than we do not have a precise and plausible account of how it did. Which means it is indeed, as I said an argument from lack of alternative, not an argument from evidence of an ID. And argument for an ID would involve, as I said, evidence of the kinds of forces the ID would have used, not simply to conceive the design, but to execute it. And not only is that nor forthcoming, ID proponents seem to think it isn't even necessary, insisting, as you are doing, that the fact of a complex optimised entity is evidence enough for an external intentional designer, even though we have to hand, a perfectly good internal optimisation algorithm.
Elizabeth: “If you want to find positive evidence for an Intelligent Designer, then you have to go looking for not merely for a designer but for an artisan – what forces were used to guide the atoms into position? What tools? What muscles? We have absolutely no evidence for any such forces or any such agent.” Complete red herring.
Far from it. It is critical. If you want to advance a positive case for a designer, as opposed to a negative case that the Darwinian mechanism cannot explain the observed optimisation of self-replicating biological entities, you need to provide an alternative mechanism.
It is possible to detect design. We do it all the time in life. If you want to go a further step and ask who the designer is, how the designer accomplished her work, etc., that is fine. But it in no way impacts the ability to detect design in the first place.
Yes it does, because we already have a self-designing mechanism, and we know it works. Not only that, but the pattern of living things suggests incremental self-design, not intentional far-sighted design, as I have argued above.
According to Elizabeth’s reasoning, if we find old paintings on a cave wall, but we don’t know who the artisan was or whether she used a reed or a hair brush or her finger, whether she used her left hand or her right hand or her toes, etc., then we have to reject design and assume the painting came about by natural forces. It’s painful to have to point this out, but that is just ludicrous.
Yes, it's ludicrous, and it's a straw man. Firstly, we know that there were painters, from other evidence; secondly we have proposed mechanisms for how the painting got on to the wall; thirdly we have no evidence that the painting is a population of self-replicators. In the case of a biological organism we have no evidence of a "painter"; we no evidence as to how the "paint" got on the "wall" (how the molecules were guided together); and clear evidence that the "painting" is a population of self-replicators. So in the first case we infer that the painting was painted by people; in the second case we infer that the population evolved by Darwinian mechanisms. The one tricky bit is how the self-replicators got going in the first place, but that's exactly what we've been talking about in this thread, specifically Szostak's theory.
Elizabeth: “And I agree that intentional, external design can sometimes be detected. But when it comes to self-replicators, I think the inference is flawed, and in any case, the detection system throws up both false positives and false negatives.” As though self-replicators somehow miraculously overcome laws of conservation of information, for example. The whole idea of self-replicators being able to somehow miraculously climb from the simple to the complex; from chaos to organization; from nonsense to information-rich systems is an unproven, unsubstantiated (and, frankly, preposterous) belief.
Yes, they do overcome "laws of conservation of information", and no miracle is required (they are, IMO, pretty dodgy laws, and inasfar as they make any sense, the additional "information" has very straightforward source - the environment). And far from being "unproven, unsubstantiated" or "preposterous", is extremely well supported by field, lab, palaentological, genetic, and computational evidence. And is in any case no more than simple logic. If self-replicators self-replicate with heritable variance in reproductive success, then variants that reproduce better must become more prevalent in the population.
Further, the design inference, properly applied, does not throw up false positives and false negatives.
Yes, it does :) Or at least: let me challenge you to demonstrate this claim.
Now, if someone doesn’t understand the design inference, in its conservative approach as proposed in recent years by key design proponents, and if they are simply thinking of design as “gee, some things are complicated so they must be designed,” then sure, they might think false positives and false negatives are a problem. However, if one understands the design argument, including the careful caveats and conservative parameters applied to it by leading design proponents (I’m not talking about every Tom, Dick and Harry who comments on blogs), then we don’t have false positives or false negatives.
Please demonstrate a set of design criteria with perfect (or near perfect) discriminability :)
Again, this accusation is not so much an accusation against ID as it is a litmus test for whether someone actually understands the design argument.
:D Well, I've looked into it (in its variants - there are several, of course) and my conclusion is that they are flawed, for reasons I've given. I think the best argument it the Irreducible Complexity argument - that some features are "unevolvable" by Darwinian mechanisms. But again, that's a negative, and gets rapidly mired in yes it could/no it couldn't stuff, and is of course vulnerable to empirical evidence "that it could". The information argument I think is simply wrong. The "appearance of design" argument rests on an equivocation, and founders in the face of clear evidence and argument that Darwinian optimisation algorithms work. The "probability is too low" argument founders because it assumes there is no mechanism that renders the probability higher, and that is exactly what the Darwinian mechanism gives us.Elizabeth Liddle_{September 23, 2011
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Dear Elizabeth, Your argumentation is just amazing! I did not expect this mucho confusion of everything, from A to Z. Unfortunately, you seem to have no clear idea of what you are trying to argue against or even for. Perhaps it is time to step back a bit, take a breath and give it a bit more thought. I am sorry to have to say this. Please consider it friendly advice, not a personal offence.Eugene S_{September 23, 2011
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Elizabeth, Your argumentation is just amazing! I did not expect this mucho confusion of everything, from A to Z. Unfortunately, you seem to have no clear idea of what you are trying to argue against or even for. I am sorry to have to say this. I think perhaps it is time to step back a bit, take a breath and give it a bit more thought.Eugene S_{September 23, 2011
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Dr Liddle, you claimed that in order to give ID proper consideration, miracles would have to be tested. I then reminded you of something you already knew; the evidence for ID is purely material, physical, and observable. It requires no miracles to be tested, and to suggest otherwise is demonstrably false. You completely ignored that point, and immediately changed the subject to whether or not the evidence for ID is positive or negative. In that same exchange, I made the observation that you cannot validate/falsify your own controlling assumption (that OOL was a completely unguided event in chemical history). I believe it is an abuse of science/logic/honesty to enforce this unsupported, unsupportable assumption on the evidence, particularly in the face of substantial physical evidence to the contrary. Yet, this is the most obvious feature of your position. Your assumption cannot be tested(and is therefore non-scientific) and you know it. That is why in the 500 word response you gave, not a single one of those words dealt with this issue in a straightforward manner, which is the same number that dealt with it at all. The remainder of your reply is very much as expected. At one point you are telling me that you could not dismiss the evidence for ID just because it cannot explain everything, then at another point, you are telling me that ID must explain what “muscles” the designer used in order to “guide the atoms into position”. This rings very similar to your previous position, where you would attempt to falsify an ID argument while simultaneously claiming one doesn't exist. It is unfortunate to think that these gymnastics will have no impact on the way in which you defend your position.Upright BiPed_{September 22, 2011
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Elizabeth,
If you want to find positive evidence for an Intelligent Designer, then you have to go looking for not merely for a designer but for an artisan – what forces were used to guide the atoms into position? What tools? What muscles? We have absolutely no evidence for any such forces or any such agent. However, we do know of an optimisation system, namely Darwinian processes, which effectively “self-designs”, and we have lots of potential mechanisms for how it might have operated in the earliest days of living things. In contrast to absolutely none for a material designer/artisan.
When you say "we know," you're referring to the partial hypotheses that by their own admission may or may not have any relation to the actual formation of life. What do you hope to accomplish by comparing ID or anything else to such vague uncertainties? But that's fine. I'm going to provide for you a theory that proposes exactly how a designer or designers assembled life, atom by atom. The explanation is not complete and there are no certain conclusions. You see, all scientific conclusions are provisional. But they are peer-reviewed and supported by data, so you cannot say that they are only speculation. Enjoy. So perhaps we may leave that irrelevant distraction behind.ScottAndrews_{September 22, 2011
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Agreed! I can't think of anything more frustrating than to spend your life looking for an answer that doesn't exist. Of course, that is Being an OoL researcher must be one of the most depressing and frustrating jobs in the universe as Mt. Improbable continues to grow in height.tjguy_{September 22, 2011
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Boy, it is tiring to have to correct so many misconceptions about ID, especially from people who should know better, but I can’t let this stand. Elizabeth: “The evidence for ID is negative, not positive. It lies in the lack of an alternative explanation, it is not in itself an explanation.” I don’t know how to put this kindly, but I’ll try. Rather than assuming this is a flat-out lie, I’ll assume it results from a basic misunderstanding of the design argument. So back to Design 101. First, every theory that challenges another theory is, in a very practical sense, making a negative case against the other theory. There is absolutely nothing wrong with that. Indeed, the traditional evolutionary argument as put forth by Darwin was specifically proposed to make a negative case against design. Further, prominent evolutionary proponents continue to acknowledge that life appears to be designed. In that sense, evolution is very much an attempt to negate our initial impression of design and show that the design is an illusion. Finally, even if the only point of ID were to be a negative case against evolution and bring some sanity back into the ridiculous evolutionary storytelling, it would be doing a tremendous factual and scientific service. Second, ID makes a positive case for design. The entire point of ID is that some physical systems exhibit characteristics that identify, positively, the activity of an intelligent agent. There is nothing negative whatsoever in that formulation of design detection. It is perfectly legitimate, and is routinely used in SETI, forensics, archaeology, etc. Everyone is fine with those applications of design detection, but when it comes to life, outrage ensues. We can only conclude that this is not because the concept of design detection itself is a problem, but because someone’s philosophical toes are being stepped upon. ID is most definitely not just a negative argument from ignorance. Anyone who says otherwise either does not understand the design argument or is being deceptive. Which one applies to you, Elizabeth? Elizabeth: “If you want to find positive evidence for an Intelligent Designer, then you have to go looking for not merely for a designer but for an artisan – what forces were used to guide the atoms into position? What tools? What muscles? We have absolutely no evidence for any such forces or any such agent.” Complete red herring. It is possible to detect design. We do it all the time in life. If you want to go a further step and ask who the designer is, how the designer accomplished her work, etc., that is fine. But it in no way impacts the ability to detect design in the first place. According to Elizabeth’s reasoning, if we find old paintings on a cave wall, but we don’t know who the artisan was or whether she used a reed or a hair brush or her finger, whether she used her left hand or her right hand or her toes, etc., then we have to reject design and assume the painting came about by natural forces. It’s painful to have to point this out, but that is just ludicrous. Elizabeth: “And I agree that intentional, external design can sometimes be detected. But when it comes to self-replicators, I think the inference is flawed, and in any case, the detection system throws up both false positives and false negatives.” As though self-replicators somehow miraculously overcome laws of conservation of information, for example. The whole idea of self-replicators being able to somehow miraculously climb from the simple to the complex; from chaos to organization; from nonsense to information-rich systems is an unproven, unsubstantiated (and, frankly, preposterous) belief. Further, the design inference, properly applied, does not throw up false positives and false negatives. Now, if someone doesn’t understand the design inference, in its conservative approach as proposed in recent years by key design proponents, and if they are simply thinking of design as “gee, some things are complicated so they must be designed,” then sure, they might think false positives and false negatives are a problem. However, if one understands the design argument, including the careful caveats and conservative parameters applied to it by leading design proponents (I’m not talking about every Tom, Dick and Harry who comments on blogs), then we don’t have false positives or false negatives. Again, this accusation is not so much an accusation against ID as it is a litmus test for whether someone actually understands the design argument. /soapboxEric Anderson_{September 22, 2011
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Liz "Can you be specific about these growing gaps?" 96% of the universe is now considered unobservable, and currently undetectable. 4% is observable. Of that 4%, the entire foundation of the standard model of physics is predicated on the idea that Higgs boson exists. However thus far, despite the multi-Billion dollar effort by Cern, the higgs boson has failed to signal at nearly all the low-low/mid ranges. Also nested within that tiny 4% sliver of observability, is the epic problem of OOL. Not to mention QM and the lack of any "theory of everything." And the fact that in the 1960's the equations of Feynman-Weinberg implied that a TeO may never be determinable even in principle anyhow. This is not gap, this may very well be an abyss. This is a much different state of affairs than the state of affairs as considered by many of the contemporaries in the late 19th century and early 20th century concerning scientific thinking. The gap has grown.junkdnaforlife_{September 22, 2011
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The evidence of ID regarding OOL is purely material, physical, observable evidence. It is therefore not subject to dismissal on the metaphysical (worldview) complaint that ‘the observations of bio-ID are invalid unless/until miracles can be tested’. There is nothing in that evidence that requires the testing of miracles (repeating: there is nothing in that evidence that requires the testing of miracles). You already know this to be true. Yet at the same time, you have failed to produce any test in which to validate the controlling assumption that unguided forces are all that exist in the cosmos, or more accurately in this instance, that OOL was a purely unguided event in chemical history.
You missed my point. The evidence for ID is negative, not positive. It lies in the lack of an alternative explanation, it is not in itself an explanation. If you want to find positive evidence for an Intelligent Designer, then you have to go looking for not merely for a designer but for an artisan - what forces were used to guide the atoms into position? What tools? What muscles? We have absolutely no evidence for any such forces or any such agent. However, we do know of an optimisation system, namely Darwinian processes, which effectively "self-designs", and we have lots of potential mechanisms for how it might have operated in the earliest days of living things. In contrast to absolutely none for a material designer/artisan. And if you claim that the designer was immaterial,then we are back with miracles.
You might try to understand how it appears to some here when you throw up these baseless diversions about testing miracles, while at the same time, you abuse the institution of science in order to protect your worldview from empirical/scientific scrutiny.
Because in my view they are not "baseless diversions" at all, they get to the heart of the matter. As for "in order to protect your worldview from empirical/scientific scrutiny! - :rolleyes:
The word “abuse” in this instance is directly related to there being no method to test or falsify your prior assumption regarding materialism.
You mean I should assume miracles are possible? Seriously, UBP, you can't have your cake and eat it! Either miracles or a "straw man" or "materialists" are at false for a priori leaving them off. Pick one.
And given that you cannot validate the assumption you wish to impose upon the evidence, it is too much to ask that you (at least) remember that no one in ID is challenging the methodologies of science by observing the evidence of ID? Again, since that evidence is purely material, and available for all to see, is it too much to ask to not be treated as if miracles must be tested in order to gain insight from those observations?
I have never said that ID is not scientific. I think simply that it is bad science. What would make it better science would be if someone went looking for evidence of that designer/artisan. Without such evidence, and with good evidence that self-replication with heritable variance in reproductive success results in optimisation and adaptation, I'll stick with the most likely option. It's not as though it rules out a creator God anyway, just gives her more credit for designing a bug-free system.
Or shall you treat me once again to the speech on methodologies, as if some gulf of sacred knowledge exists between us? Please spare me the insult.
OK, but you don't deserve it.

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.
Physical entailments are a part of the artifact, Dr Liddle, not the other way around. We don’t say that Stonehenge was caused by wind and rain because we don’t know how it was done.
No, we say it was caused by people because there is plenty of evidence for people, and none for self-replication with heritable variance in reproductive success.
In any case, you wish to dismiss the evidence of ID on the grounds that it does not fully explain how that evidence came to exist as it does – it cannot provide to you a mechanical description of first cause. What would you say to Pensias, for instance? Or to Clerk Maxwell, or even Newton? Does the observation of microwave background radiation offer a mechanical description of the cause of the cosmos? What other theories must offer such a description in order to be seen as a legitimate description of evidence? Quantum mechanics, for instance?
No, I do not "wish to dismiss the evidence of ID on the grounds that it does not fully explain how that evidence came to exist as it does", obviously. Nor does any scientific theory fully explain anything - all theories are incomplete. I don't dismiss any evidence of ID - I just don't see any that isn't inference from an explanatory gap in any alternative. Indeed, an inference made while dismissing much of the evidence that potentially fills that gap, in part.
And is it not true that the theory of evolution is a description of biological evidence, yet it is specifically separated from having to provide for the cause of that evidence? Why is that?
I don't understand the questions.
ID is a program of design detection (no less legitimate than any other science of design detection) and it makes the modest claim that design can be detected from the physical evidence observable to anyone.
And I agree that intentional, external design can sometimes be detected. But when it comes to self-replicators, I think the inference is flawed, and in any case, the detection system throws up both false positives and false negatives.
Without equivocation, what exactly then is the principle at work when we say that one theory must offer a mechanical description of first cause in order to describe evidence, but another does not?
First cause of the existence? Or first cause of life on earth?Elizabeth Liddle_{September 22, 2011
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Elizabeth: "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!" Good, then perhaps we can make some progress in the discussion. Are you saying that it could turn out to be wrong, just as a matter of principle, or have you actually looked at it in enough detail to see any weaknesses? Can you articulate a couple of areas where you see the greatest weaknesses in his model? Some of us have actually taken time to look at it and can see a number of shortcomings right out of the gate. What weaknesses do you think it has?Eric Anderson_{September 22, 2011
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Anderson: “it is not at all clear that the monomers will join up in nice chains as depicted in the video”. Elizabeth: “Depends on the monomer. This is chemistry. Polymers form. This is testable, and subject to testing.” This is pretty simple: Do the monomers have the ability to join via side bonds to create a chain? If not, then we don’t even get the model off the ground, so the answer must be yes. Do the monomers have the ability to join across with an opposing monomer? If not, then there is no copying of any sort, so the answer must again be yes. If the monomers can join with side bonds and with cross bonds, what keeps them sorted out? There has to be a mechanism. You cannot simple jumble everything into a vesicle and let the monomers go for it. (And we haven't even addressed the issue of whether there is actual copying going on, or just an unrelated group of monomers attaching to the first one.) Anderson: “there is no way to avoid interfering cross-reactions.” Elizabeth: “How do you know?” You are exactly right, this is the kind of thing that is subject to empirical investigation. And several decades of research have shown that interfering cross-reactions are a huge problem for naturalistic OOL scenarios. Szostak’s model gives absolutely no indication that it has solved this fundamental issue. Anderson: “finally . . . the central problem remains: where does the elusive information-rich molecule ultimately come from?” Elizabeth: “From the above processes!!!! It tells you quite specifically! And the “information” comes from the environment, as is the case with all Darwinian systems.” I don’t know where else we can go with this discussion. You are obviously a very smart person, so sometimes I can’t tell whether you are just pulling my chain or whether you seriously believe what you write. The information just comes from the above processes? Even assuming for a moment the ridiculous notion that your “Darwinian systems” can create complex specified information (as to which there is considerable doubt), what makes you think that it is applicable to the model you’ve shown us? What is being selected for? Longer chains? Faster copying? Don’t give us vague generalities about the information “coming from the environment” or some other such nonsense. Why don’t you just tell us that it comes from the pixie dust in the vesicles? Where does an aperiodic specifically-arranged functional polymer come from? Chance. That is it. That is your only option (unless you want to invoke some kind of law-like process, which we’ve already dispensed with). I would seriously recommend that you think through with more specificity what actually has to be explained for OOL and what the details are. Vague generalizations, which enjoy no empirical support whatsoever and which are contrary to information theory, are absolutely of no use other than to continue the smoke and mirrors.Eric Anderson_{September 22, 2011
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"...later it does more" lolUpright BiPed_{September 22, 2011
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Dr Liddle, question:
Why is “a miracle” a straw man?
answer:
When we don’t know something in how something happened in science we don't say “it might have been a miracle”, not because it we think it wasn’t, but because you can’t test miracles by science.
The evidence of ID regarding OOL is purely material, physical, observable evidence. It is therefore not subject to dismissal on the metaphysical (worldview) complaint that ‘the observations of bio-ID are invalid unless/until miracles can be tested’. There is nothing in that evidence that requires the testing of miracles (repeating: there is nothing in that evidence that requires the testing of miracles). You already know this to be true. Yet at the same time, you have failed to produce any test in which to validate the controlling assumption that unguided forces are all that exist in the cosmos, or more accurately in this instance, that OOL was a purely unguided event in chemical history. You might try to understand how it appears to some here when you throw up these baseless diversions about testing miracles, while at the same time, you abuse the institution of science in order to protect your worldview from empirical/scientific scrutiny. The word “abuse” in this instance is directly related to there being no method to test or falsify your prior assumption regarding materialism. And given that you cannot validate the assumption you wish to impose upon the evidence, it is too much to ask that you (at least) remember that no one in ID is challenging the methodologies of science by observing the evidence of ID? Again, since that evidence is purely material, and available for all to see, is it too much to ask to not be treated as if miracles must be tested in order to gain insight from those observations? Or shall you treat me once again to the speech on methodologies, as if some gulf of sacred knowledge exists between us? Please spare me the insult.
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.
Physical entailments are a part of the artifact, Dr Liddle, not the other way around. We don’t say that Stonehenge was caused by wind and rain because we don’t know how it was done. In any case, you wish to dismiss the evidence of ID on the grounds that it does not fully explain how that evidence came to exist as it does – it cannot provide to you a mechanical description of first cause. What would you say to Pensias, for instance? Or to Clerk Maxwell, or even Newton? Does the observation of microwave background radiation offer a mechanical description of the cause of the cosmos? What other theories must offer such a description in order to be seen as a legitimate description of evidence? Quantum mechanics, for instance? And is it not true that the theory of evolution is a description of biological evidence, yet it is specifically separated from having to provide for the cause of that evidence? Why is that? ID is a program of design detection (no less legitimate than any other science of design detection) and it makes the modest claim that design can be detected from the physical evidence observable to anyone. Without equivocation, what exactly then is the principle at work when we say that one theory must offer a mechanical description of first cause in order to describe evidence, but another does not?Upright BiPed_{September 22, 2011
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Elizabeth, growing vesicles that divide are no more self replicating entities than blowing soap bubbles or rocks tumbling down a hill side that split in half at the bottom. Cells dont replicate by outside mechanical forces. They use internal comtrol mechanisms and machinery. Growing vesicles are in no way analogous to cell replication.kuartus_{September 22, 2011
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