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

I'd love to see a guest post by Dr Meyer here, if there have been any in the past could somebody link me up?kellyhomes_{September 30, 2011
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Elizabeth: "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." No self-replicating RNA has been demonstrated. If you are thinking of a couple of the papers on Szostak's site or if you are thinking of the Lincoln & Joyce work or similar work, you are mistaken. It is simply false that self-replicating RNA has been demonstrated.Eric Anderson_{September 29, 2011
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Peter, An important addition. I think by environmental pressure we should mean not only physical conditions (humidity, temperature, etc.) but also the harshness of competition for the resources in the same ecological niche.Eugene S_{September 26, 2011
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Hi Peter, The only rational explanation I have is that all different species have the same Designer. Evolutionists assert that such a difference in the pace at which evolution occurs for various species can be explained by the differences in environmental pressure on them. Where there is no pressure for survival, natural selection acts conservatively, otherwise competition presses for change. I am happy with this explanation only as far as minor changes are concerned, i.e. microevolution within already existing species. Maybe it is even possible to get something like rudimentary speciation (it all depends on the definition of this or that particular species and how much biological novelty we are talking about). But, and it is a great "but"... Both macroevolution and theories of spontaneous origin of life have information theoretic hurdles that are impossible to get over without intelligence.Eugene S_{September 26, 2011
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Hi Eugene, I watched a documentary, sometime last week, on mainstream television, about the development of the modern day Racehorse. Not too long into the programme the presenter of the show introduced Richard Dawkins who produced a collection of horses hoofs, dating back some 65million years, and explained how they had evolved slowly over that time from having ‘3 toes’ to a ‘single hoof’. Anyone watching that programme would have been convinced that ‘evolution’ had indeed taken place; after all they had the evidence to prove it, but I was left somewhat baffled as to why the horse should undergo such a minor change, when during this same time frame a land dwelling creature swimming in the shallows became the modern day whale, a primate became Homo Sapiens etc? We could go further back and ask why a small ‘rat type creature’ could evolve into the Elephant, tiger, monkey, horse, giraffe etc, when scurrying around at their feet are lots of small ‘rat type creatures’ who have undergone very little change? Why should ‘evolution’ for instance so affect one creature, when living in a burrow down the hill a little, exposed to the same environmental pressures, it virtually misses out something else? I’m just curious as to why this should be. Do you have any thoughts on this?PeterJ_{September 26, 2011
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Elizabeth, Thanks for the link. BTW, before you write a response, don't forget two important things: (1) Darwin himself acknowledged the fact that the fossil record was the hardest argument against his theory. But he conjectured that future findings would indeed fill in the gaps. (2) 150 years after he formulated the classical TOE, the more fossils are found, the less certain the picture is in terms of its plausibility. The classical TOE postulates massive tiny changes over time. Consequently, the fossil record must be able to present a great many transitional forms. Understandably, this is what was not observed in the days of Darwin, and, remarkably, it is even less certain now that a lot more paleontological data is available.Eugene S_{September 26, 2011
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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.
Actually Szostak is proposing something not far from a Darwinian model. Obvious, for definitional reasons, you cannot say the "first" replicator evolved via Darwinian selection. But the Szostak model involves what might be regarded as accidental replicators. Ones not having metabolism or "information." I'm not aware of any chemistry that is off the table. One can never predict where basic research will lead, but increases in knowledge are always interesting and frequently useful.Petrushka_{September 24, 2011
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Well, Elizabeth, I get the sense you are pulling my chain, as I find it hard to believe that you believe some of the positions you take, but we have made some minor progress on a couple of points. At this stage there may not be a lot of value in further discussion, as we have so many tangential items going, but I’ll try one last time to round out some of the discussion on a few of the key points. Elizabeth: “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.” I typically see this kind of comment from someone who has no engineering background and no idea what is involved in building complex functional machines. It is yet another version of the logical fallacy of “bad design.” Elizabeth: “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.” Thank you. I fully agree that we don’t know how the alleged optimization worked, hardly at any level. Now please consider this: don’t shoot off a quick response, but contemplate this in the coming days: if you don’t know how your mechanistic theory did something, how do you know that it in fact did? This is a very key point and a large part of where the disconnect comes in the debate. To slightly reword the question: What if this mechanistic theory (which you acknowledge is poorly understood at this stage) *didn’t* create the optimization/design that we see in life? Are you even ready to consider this possibility? Elizabeth: “The ID argument seems to me to be that this [undirected abiogenesis] 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.” That is not the ID argument, so, unfortunately, you have misunderstood it. Lots of people, including people who are not friendly toward ID have noticed that there is nothing even approaching a plausible account of abiogenesis. That point can be made forcefully without reference to ID, per se. What ID additionally brings to the table is: (i) a positive case that if we find complex specified information in a system it is affirmative evidence for design (you can argue about whether ID has successfully made its case here, but you cannot dismiss ID on rhetorical grounds just by claiming it is only a negative case against evolution, because it isn’t), and (ii) the related corollary that, yes, operates as a negation of any purely mechanistic hypotheses (evolution or otherwise), by rightly pointing out that purely mechanistic processes have not been shown to create complex specified information. Elizabeth: “[Identifying how the designer did 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.” That is a logical fallacy. Let’s test your reading comprehension for a moment. (1) Was object x designed? (2) Who designed object x? (3) How did the designer design object x? I hope you notice these are separate, distinct questions. The first question can be asked *and* answered without asking the subsequent questions. This is a matter of pure logic. ID *does not* claim to identify the designer, nor to outline a mechanistic scenario of how a designer did the work. The fact that ID appropriately limits itself to questions it can answer is a strength, not a weakness (and something that other theories, ahem, might want to consider implementing). ID does not claim to be a theory of everything. You may be bothered by the fact that ID does not go past question 1 into question 2, question 3 and so on, but that is a problem of your personal preference, not a limitation of the theory. ID rightly, appropriately, and correctly limits itself to the specific question it can answer, namely whether something was designed. You may desire ID proponents to go further, but that is your bias, not a problem with ID as a tool for answering question 1. Elizabeth: “Yes, [self-replicating entities] 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.” I don’t know why miracles are being brought up. You are absolutely bluffing to say that generation of complex specified information via Darwinian principles is well-supported by field, lab and other research. Surely you realize that this is an area of extreme interest for evolutionary proponents. This is the holy grail. If you were right, we would have seen Nobel prizes all around by now. Please support your assertion by providing at least a concrete example or two. Incidentally, you are perhaps confused about what needs to be explained here (which is probably why you keep exhibiting a misunderstanding of the concept of information and those “dodgy” information laws throughout several threads). As to your last sentence, I’ll respond in mathematical form so that it is more explicit: reproducing better *does not equal* more information content. BTW, just to go back to where we started for a moment. All this came up in the context of our discussion of abiogenesis. You provided us with a model that is currently being pursued at Harvard, and I appreciate you pointing us to Szostak’s work. Several of us were able to see huge holes in the model with even a cursory review, but fine, I’m all in favor of abiogenesis research, so I’m glad they are carrying on. Your repeated view has been that once we get this self-replication off the ground (which the model will not be able to do, but oh well), then Darwinian principles (by which we simply mean chance, filtered by reproductive success) will somehow bring complex specified information into being. That is an assertion without any support. Or perhaps I’m wrong, Elizabeth? Please give us a couple of the very best examples of this taking place that you are aware of (no literature bomb, please). Anderson: “Further, the design inference, properly applied, does not throw up false positives and false negatives.” Elizabeth: “Yes, it does. Or at least: let me challenge you to demonstrate this claim.” Sorry, Elizabeth, you are the one claiming that the design inference, as articulated by prominent ID proponents, throws up both false positives and false negatives. This is your, as-yet-unsupported, assertion. As you apparently think this is a pervasive problem which excludes the design inference from serious consideration, and since I’m sure you wouldn’t just be parroting an NCSE talking point, you must be aware of many examples of these false positives and negatives. Please provide at least a couple to substantiate your allegation.Eric Anderson_{September 23, 2011
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Oh dear, Elizabeth. Another post from you, filled with words and yet devoid of evidence. You deny the fact that gene-pools are pre-existing and yet fail to detail any evidence that a gene pool has been improved, or even permanently altered, through neo-darwinistic processes. You ridiculously insist that epigenetics is “specified” by the gene pool when much better-informed evolutionists than yourself concede that “there is no unequivocal empirical basis for believing the frequent assertion that DNA contains all necessary hereditary information.” Indeed, “It is possible that DNA-based heredity will ultimately find a more modest role in our thinking about inheritance in the course of this new century”. It is also, once again, noted that you have failed to name a single “transitional fossil”. Using intelligently-designed software, created, by a programmer, to achieve a designated goal, using intelligently-designed hardware, to prove that intelligent design is not needed for FSCI outputs is about as self-contradictory as you can get. You deny this. Without substantiation. Again. You’re wrong but, conveniently, you’ve “gotta run shortly”. Which is the same line you used to excuse yourself from the conversation about the Galapagos finches, the one that you now appear to have conveniently forgotten about. After one final, and I must say, desperate, appeal to “the concept of a continuum” where it is obvious that no continuum exists you then try to change the subject, complaining that you have been personally affronted or something. If you want to discuss your personal issues with me, you can send me an e-mail. Here on Uncommon Descent, it’s time for you to put up (the evidence for you atheistic evolutionist position) or shut up (and give others a chance to succeed where you have failed).Chris Doyle_{September 23, 2011
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Eugene: I just composed a lengthy reply that seems to have got lost. Unfortunately I'm going to be very tied up for the next couple of weeks, so we may have to leave it there I hope to talk to you again when things are less busy. In the mean time, I give you this link again: http://www.pnas.org/content/97/9/4426.fullElizabeth Liddle_{September 23, 2011
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Elizabeth,
So what we need is evidence for a self-replicating polymer to have arisen simply from chemistry.
I believe that's what we've been trying to say. And as every OOL experiment is quite deliberate, every accomplishment in the field supports Intelligent Design just as much as it supports unintelligent self-organization. More, in fact, because of the deliberate, planned nature of the experiments. For example, OOL researchers are demonstrating how one might intentionally create self-replicating fatty vesicles. The intelligent manipulation to produce the results will always be a certainty, while the question of whether those results could occur without that intelligent cause will always be an uncertainty. You've sold me on the validity of their research. If, as you claim, ID must supply specific mechanisms, then it's time to start calling these people what they are, ID researchers.ScottAndrews_{September 23, 2011
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Elizabeth,
There is nothing in that mechanisms that says that the process requires “vast periods of time”, and indeed, as we know from the Grants’ work in the Galapagos, it is in fact it enables populations to show detectable optimisation within a generation to an environmental change.
I've seen living things that can adapt visibly to their environments within seconds. How does anyone know whether the changes in finches' beaks was caused by some sort of variation and selection or by some other mechanism that adapts them to their needs? That the change occurs across generations tells us nothing of its mechanism. Variation and selection are the "narrative gloss" applied to the observations.ScottAndrews_{September 23, 2011
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Elizabeth, 31.1.1.1.3 "I am not redirecting the question." Yes, you are. I use Darwin's own definition from "On the origin of species". Classical Darwinism is contrary to geological evidence, which is an established fact. We will not be on the same page until you do accept it as fact. The Cambrian explosion is called an explosion in the geological sense of this word. It is a geologically sudden emergence of biological novelty unaccounted for by the classical Darwinian model. Dating from 544-505mya, the Cambrian Period began with what has been called a "Cambrian Explosion" for the large diversity in animals seen over such a geologically short period in time. There suddenly appeared animals with the ability to swim and crawl, with more acute senses of smell and taste and vision. Trilobites e.g. aquired vision as advanced as the best insect sight of today.Eugene S_{September 23, 2011
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I am not redirecting the question. Of course the palaeontolical recored is scanty. What part of it that we do have do you think is "clearly counter-Darwinian"? And if by "Darwinian" you mean "gradual change over vast periods of time as a result of tiny advances" then you are not using the word as I am using it, which is to denote the mechanism that Darwin proposed, namely: self-replicators with heritable variance in reproductive success. There is nothing in that mechanisms that says that the process requires "vast periods of time", and indeed, as we know from the Grants' work in the Galapagos, it is in fact it enables populations to show detectable optimisation within a generation to an environmental change. What you are calling "sudden change" in the fossil record is over far vaster spans than a generation! The fossil record isn't "gradual" because there are gaps. Within contiguous parts that we do see, we see incremental change, including the Cambrian period itself. I'm sure there was a great radiation at the beginning of the Cambrian, that doesn't run counter to the Darwinian mechanism at all - and what there was, specifically, was the beginning of readily fossilisable forms. There's a good review in PNAS here: http://www.pnas.org/content/97/9/4426.fullElizabeth Liddle_{September 23, 2011
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Elizabeth, 32.1.2.1.4 I was asking for clear unequivocal answers, i.e. those that do not need endless re-reading or thinking between the lines. I am afraid there is something going wrong in my communication with you as I feel there exists some basic problem of understanding. It is hard to maintain this kind of exhange of opinions because I constantly feel you are always trying to say "something else" apart from what you write. Is it because you are trying to get as far as possible with zero information "A && ¬(A)" assertions a lot of times? You have essentially no examples of self-organisation. My QED related to my example of self-replicating mutating artificial viruses that show no tendency to spontaneus gradual complexity increase. The example is an existence proof of self-replicating systems for which self-replication may not be enough for Darwinian evolution to initiate. Computer viruses do not evolve by themselves even though they self-replicate. In other words, computer viruses do not spontaneously acquire extra levels of function/complexity, but only mutate as much as they are preprogrammed to. I think a lot of people here have clearly and unambiguously shown sheer lack of evidence and complete futility of attempts to explain OOL as a spontaneous/contingent event or a lucky number of such.Eugene S_{September 23, 2011
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The real challenge of OOL researchers is for them to have enough moral strength to acknowledge that their ultimate aim is scientifically ungrounded.
It's not "scientifically" ungrounded at all. Right now it's not grounded in robust evidence, but there's nothing wrong with the science. Why should there be?Elizabeth Liddle_{September 23, 2011
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Thanks, I interpret your answer number 3 as NO. Right? So computer viruses are an example of self-replicating mutating systems incapable of evolving into substantially more complex systems without intelligent interaction. Their extraneously imparted ability to adapt means mutation (microevolution) is feasible. However, computer viruses to date have not shown any tendency to spontaneously evolve to exhibit gradually more sophisticated structure and cleverer behaviour. So no spontaneous evolution scenarios of the type: “Hello, World” to Windows XP have been observed so far. QED.
Well,I'm not sure what Quod you think you've Demonstrated, but it seems you need to re-read my reponse to your third question. :DElizabeth Liddle_{September 23, 2011
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The real challenge of OOL researchers is for them to have enough moral strength to acknowledge that their ultimate aim is scientifically ungrounded.Eugene S_{September 23, 2011
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Simply not good enough, Elizabeth. 1. Micro-evolution : sub-specific variety with-in a pre-existing gene pool – does not even attempt to explain where all of the information for organs and body parts came from in the first place. As for body plans, it appears that an epigenetic explanation is increasingly required and so has nothing to do with the gene pool!
Not a "pre-existing gene pool". You are making a categorical distinction where none exists. Genetic variation is being drip-fed into the population all the time, most of it neutral, half of it spreading by drift. As for "organs and body parts" I've already linked to a paper on the evolution of multicellularity, and the entire field of evo-devo is devoted to "organs and body parts". And I'm not at all why you say that "an epigenetic explanation" has "nothing to do with the gene pool"! Of course it has! What do you think specifies the epigenetics?
2. Palaeontological evidence: you appeal to this without naming a single fossil. And you describe this as a “serious attempt to substantiate” your claims?
As I said, just google "transitional fossils". The entire field of phylogenetics is founded on them.
3. Computational evidence: Requires sophisticated engineering just to create the computer, never mind Intelligent Design to write and execute the sophisticated simulation. Show me a computer that made itself by accident (after a whirlwind swept through a junkyard or something) and a program that wrote itself without any programmer, then – and only then – can you appeal to “computational evidence” for neo-darwinism.
This is tantamount to saying you have to throw your computer out of the window to simulate gravity. But I'm happy to talk about this in more detail. Gotta run shortly.
4. Pebbles on a beach: Charles Darwin might have been excused for comparing this low-level ‘optimisation’ with the highest-level ‘optimisation’ we find in the cell alone. No-one alive today has any excuse for such unacceptably inadequate over-simplification.
What is wrong with the concept of a continuum? Does it falsify the concept of length to note the size of a beetle and the size of the sun?
5. Galapagos finches: Dealt with here months ago. Getting excited about less than a 2mm oscillation in beak-size says nothing about neo-darwinism and everything about the straw-clutching that is required when atheistic evolutionists try to justify their beliefs.
Please link to where it was "dealt with". Not sure where the "neo" comes in here - the Grants' work was with straight Darwinism. Have you read the book? And, I've already asked you to stop this scoffing at "atheistic evolutionists". I have no idea whether the Grants were atheists or not, but there is nothing intrinsically atheist about Darwin's theory. Nor is there any "straw-clutching" going on - far from it, the Grants demonstrated, definitively, that Darwinian evolution takes place, measurably on the time scale of single generations. That is a problem for those who deny the power of his proposed mechanism, not for those who do not
6. “at least one artificially created molecule actually evolves” : there’s a self-defeating statement if ever I’ve seen one.
Well, read it in context.
Why should anyone regard any of the above as evidence? This is the best you can offer and you “submit that the problem may be on” my side? Unbelievable. I can only impress on you how sincerely underwhelmed and unimpressed I am by your “serious attempt to substantiate” your atheistic evolutionist beliefs. I know you will dismiss that as some sort of “problem on my side” but, one day, you will realise the problem is all yours. For what it’s worth, I’d like to think that you’ll remember this conversation when that realisation dawns upon you.
Well, I guess thanks for that. Yes, I do think the problem is on your side, but that makes us even I guess :)
The overwhelming majority of evolutionists are basically clueless and quickly get found out in debates. They have nothing to offer at all and their contributions do not remotely trouble or impress people who do not share their blind faith. You were supposed to be one of the rare few, Elizabeth, who was able to make a good case for neo-darwinism while cogently attacking ID. It turns out it just took a bit longer for you to be found out.
Excuse me? Please explain what you mean. Especially by "found out".
Did you ever finish reading “Signature in the Cell”?
Yes.
And, by the way, I’ve never once alleged any moral failings on your part. Do not confuse any moral judgment on my part with the fact that I demonstrated to you, without refutation, the failure of atheistic morality.
No, you did not, in my view. But we can't reference the conversation because you deleted it. Which was pretty cheeky!
I have not, and never will, express, or even form, personal moral judgements about you or anyone else in these discussions.
I don't care if people form moral judgements, as long as they make them clear and support them, allowing me to defend myself. I think you were pretty cheeky to delete the posts you wrote on my blog, together with the comments of a great many other people, whose words you had no right to delete. Not only that, but you deleted the threads from the trash as well, so that I could not resurrect them. If you had soft-deleted them, and contacted me, I'd have been willing to delete your own words and leave the others (though not very happy - I'm a fan of transparency, and of letting the record stand). So I'm making a judgement on you, and you have equal right to make one on me. However, you need to support it - these snide accusations of dishonesty - of "being found out" - of abandoning God for "the pleasures of this life":
Well said, Eugene. I would suggest there is a fourth type of person: those who, having previously found and served God, have now lost God and serve only themselves. They have left the straight path and gone astray, sacrificing wisdom for the pleasures of this life. Such people cannot be reasoned with, nor are they interested in following the evidence wherever it leads: first appearances to the contrary are almost always deceptive.
in which you clearly included me.Elizabeth Liddle_{September 23, 2011
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Thanks, I interpret your answer number 3 as NO. Right? So computer viruses are an example of self-replicating mutating systems incapable of evolving into substantially more complex systems without intelligent interaction. Their extraneously imparted ability to adapt means mutation (microevolution) is feasible. However, computer viruses to date have not shown any tendency to spontaneously evolve to exhibit gradually more sophisticated structure and cleverer behaviour. So no spontaneous evolution scenarios of the type: "Hello, World" to Windows XP have been observed so far. QED.Eugene S_{September 23, 2011
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F/N: Re Stonehenge and von Neumann self-replicating facilities 1 --> All the evidence we actually observe tells us is that once an FSCI-rich system that embeds a vNSR -- which is both irreducibly complex and a necessary condition of self-replication -- it is capable of transmitting info stored in its control tapes; here, DNA etc. Slight mods, mostly by breaking things that are not fatal, are also possible. 2 --> So, we see that DNA is no more capable of replicating itself than Stonehenge, so this strawman crashes in flames. DNA requires an elaborate set of cellular machinery to be replicated, and to be maintained in working order. Prescriptive information [starting with your operating system on your PC] is dynamically inert, and requires executing machinery -- replicated on said stored info per the requisites of a vNSR, in the cell -- to function. 3 --> Yes, I am very aware of rather exaggerated claims on how RNA can spontaneously form and how it has catalytic capabilities etc. Show us credible evidence that this formation happens under realistic prebiotic conditions, empirically. Then, show us how this leads to the spontaneous formation of self-replicating cell based life using a code based, algorithmic vNSR facility. 4 --> We are back at the key problem in Meyer's Signature in the Cell: origin of self-replicating life is the signature of the design of life. 5 --> And, once we see the FSCI hurdle involved, at 100,000 - 1 mn bits of required functionally specific, algorithmic, coded, complex info, we readily see that the best and indeed blatantly obvious explanation absent imposed a priori materialism, is design. 6 --> So, the problem is not the evidence nor the cogency of inferences on that evidence to design as credible cause; it is a mind-closing, question-begging a priori imposition that has censored and warped the very meaning of science, convincing many to swallow the most patent absurdities as they must be scientific and science "must" "only" explain by "natural[ISTIC] causes." 7 --> Which a priori censored, question-begging explanations are then presented tot he unwary or ill-informed as practically certain truth, truth that one dares not dispute on pain of being pilloried as ignorant, stupid, insane or wicked. As we can now see all over our TV screens as a triumphant gotcha question by various media airheads. 8 --> So, the real issue is not evidence or reasonableness of the inference on that evidence to its obviously best explanation. It is institutionalised closed-mindedness and hostility to those who would point out that the emperor is stark naked. The proper answer to that is not to try to present evidence that will be rejected out of hand based on closed minded question begging, but exposure of the fallacy, and how it undermines the integrity of science and indeed of basic rationality, not to mention morality, leading to absurdity, nihilism and chaos. 9 --> Not to mention thought-police bully-boy tactics, threats and worse. If you doubt me on this, then explain why my family is being held hostage and why targetting pics of me have been posted, with nary a correction from the other side. 10 --> I call it in one direct word: WICKEDNESS. 11 --> Anyway, back on track. Once we see the best explanation for OOL is obvious, the next step is simple: novel body plans credibly need 10 - 100 mn or more bits of addiitonal FSCI. The best explanation for that is design, and the ability to then modify design to spontaneously adapt to niches is a no-brainer. Designers tend to want robust and flexible designs. 12 --> So, what is happening is that a mortally wounded establishment is trying hard to keep itself in power. And, it is slowly fading and failing. In twenty years, it will all be over, and we will look back and wonder why it took so long. GEM of TKIkairosfocus_{September 23, 2011
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vesical=vesicleElizabeth Liddle_{September 23, 2011
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Elizabeth, Would you mind me asking a few questions.
Not at all. 1. Take a cyber virus for example. Has it come about spontaneously or via human intervention? Human intervention.
2. Can it self-replicate?
Yes. I believe some also mutate in some ways.
2. If yes, do you still think it is amenable to Darwinian evolution? Please state clearly, concisely and unambiguously why you think this way or the other.
Only if it self-replicates with heritable variance in reproductive success. That's possible, in principle, as virtual critters do this, but whether anyone has done it for a virus I don't know. Life could get very complicated if they do!
3. Has there been any traces of evidence that it can evolve its code without intelligent intervention or pre-programmed ability to adapt?
In order to make a critter that can undergo Darwinian evolution you need some kind of differentiation between genotype and phenotype. The genotype is subject to mutation when it self-replicates, and, ideally, mates. However, the phenotype needs to be robust - in other words changes to the genotype must result in a substantial proportion of viable phenotypes. A virtual critter designed with this property could be said to have a "pre-programmed ability to adapt", although that would be a misnomer. What would be more accurate would be to say that a virtual critter (or population of critters) had been designed (note I do not flinch :)) in such a way that the population will tend to evolve, and I just don't know if that is likely to be feasible with computer viruses (probably - hackers seem to be able to do anything) However, we know it is feasible with living things, because we know that phenotypes are highly robust to incremental changes in genotype. This tells us that if the Darwinian account extends right to the early days of proto-life, self-replication itself must have been robust, very early on. Once you have robust-self-replication you have reached mainland, as far as Darwinian mechanisms go, because only variants that improve matters will be retained, variants that make matters worse will tend to be lost. So the challenge for OOL researchers is to posit mechanisms by which robust self-replicators got started. That's where the lipid vesical story gets interesting :)Elizabeth Liddle_{September 23, 2011
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Simply not good enough, Elizabeth. 1. Micro-evolution : sub-specific variety with-in a pre-existing gene pool – does not even attempt to explain where all of the information for organs and body parts came from in the first place. As for body plans, it appears that an epigenetic explanation is increasingly required and so has nothing to do with the gene pool! 2. Palaeontological evidence: you appeal to this without naming a single fossil. And you describe this as a “serious attempt to substantiate” your claims? 3. Computational evidence: Requires sophisticated engineering just to create the computer, never mind Intelligent Design to write and execute the sophisticated simulation. Show me a computer that made itself by accident (after a whirlwind swept through a junkyard or something) and a program that wrote itself without any programmer, then – and only then – can you appeal to “computational evidence” for neo-darwinism. 4. Pebbles on a beach: Charles Darwin might have been excused for comparing this low-level ‘optimisation’ with the highest-level ‘optimisation’ we find in the cell alone. No-one alive today has any excuse for such unacceptably inadequate over-simplification. 5. Galapagos finches: Dealt with here months ago. Getting excited about less than a 2mm oscillation in beak-size says nothing about neo-darwinism and everything about the straw-clutching that is required when atheistic evolutionists try to justify their beliefs. 6. "at least one artificially created molecule actually evolves" : there’s a self-defeating statement if ever I’ve seen one. Why should anyone regard any of the above as evidence? This is the best you can offer and you “submit that the problem may be on” my side? Unbelievable. I can only impress on you how sincerely underwhelmed and unimpressed I am by your “serious attempt to substantiate” your atheistic evolutionist beliefs. I know you will dismiss that as some sort of “problem on my side” but, one day, you will realise the problem is all yours. For what it’s worth, I’d like to think that you’ll remember this conversation when that realisation dawns upon you. The overwhelming majority of evolutionists are basically clueless and quickly get found out in debates. They have nothing to offer at all and their contributions do not remotely trouble or impress people who do not share their blind faith. You were supposed to be one of the rare few, Elizabeth, who was able to make a good case for neo-darwinism while cogently attacking ID. It turns out it just took a bit longer for you to be found out. Did you ever finish reading “Signature in the Cell”? And, by the way, I’ve never once alleged any moral failings on your part. Do not confuse any moral judgment on my part with the fact that I demonstrated to you, without refutation, the failure of atheistic morality. I have not, and never will, express, or even form, personal moral judgements about you or anyone else in these discussions.Chris Doyle_{September 23, 2011
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06:24 AM
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Yes, to both of those. Neither is inconsistent with what I said.Elizabeth Liddle_{September 23, 2011
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Elizabeth, Please do not redirect the question. My point is that the paleontological record is scanty and yet what we do have is clearly counter-Darwinian. I remind you that by Darwinian a lot of people (biology laymen like myself) mean gradual change over vast periods of time as a result of tiny advances as opposed to a sudden change. "We also have plenty of evidence for pre-Cambrian organisms." So? Again, all I am saying is the fossil record is *not* gradual. The Cambriam explosion is the geologically sudden emergence of a whole raft of novel body plans in Cambrian strata. It presents clear evidence against the classical Darwinian scheme.Eugene S_{September 23, 2011
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The vast majority of the fossil record is of marine invertebrates and we do not see any evidence for universal common descent in that vast majority.Joseph_{September 23, 2011
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Elizabeth:
No, the idea is that you don’t get Darwinian processes until you have your self-replicator.
1- darwinian processes are NOT the only possibility after you get a self-replicator 2- Living organisms are far more than replicatorsJoseph_{September 23, 2011
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Elizabeth, Would you mind me asking a few questions. 1. Take a cyber virus for example. Has it come about spontaneously or via human intervention? 2. Can it self-replicate? 2. If yes, do you still think it is amenable to Darwinian evolution? Please state clearly, concisely and unambiguously why you think this way or the other. 3. Has there been any traces of evidence that it can evolve its code without intelligent intervention or pre-programmed ability to adapt? Thanks.Eugene S_{September 23, 2011
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We see gaps, but then the fossil record will be, inevitably, gappy. However, within parts of the record we do have, we see continuity. We also have plenty of evidence for pre-Cambrian organisms. Is it your contention that the Cambrian organisms were created, fully formed? If so, by what physical mechanism (even supposing them to have been designed by an external intentional designer)?Elizabeth Liddle_{September 23, 2011
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05:46 AM
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