Home » Evolution, News, Origin Of Life » Paper: “The origin and relationship between the three domains of life is lodged in a phylogenetic impasse”

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

Proceedings of the Royal Society B: Biological Sciences

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

  1. impasse is a drastic understatement, neo-Darwinists can’t even explain how ANY first ‘simple’ protein ‘naturally’ came to be, much less a ‘super’ LUCA, which apparently ‘sub-speciated’ into all the domains of life, and which, of course, they have no biogeochemical evidence of. (i.e. the first biogeochemical evidence we have for life on earth is of Photosynthetic and of sulfate reducing bacteria):

    ==================================

    OT:

    New video on Don Johnson’s book ‘Programming of Life’

    Programming of Life – video playlist
    http://www.youtube.com/user/Pr.....6iWX9nGocg

  2. news, the last common ancestor is not the same as the first common ancestor.

    Just because the last common ancestor was complex doesn’t mean the first was.

  3. And yet Elizabeth, besides your imagination, where does this evidence exist for a ‘simple’ first common ancestor, much less evidence for a ‘complex’ last common ancestor? ,,, you do not even have any evidence for prebiotic chemistry. The oldest sedimentary rocks we find on earth already have signatures of ‘specialized’ bacterial life in them!

    notes:

    The Sudden Appearance Of Photosynthetic Life On Earth – video
    http://www.metacafe.com/watch/4262918

    Team Claims It Has Found Oldest Fossils By NICHOLAS WADE – August 2011
    Excerpt: Rocks older than 3.5 billion years have been so thoroughly cooked as to destroy all cellular structures, but chemical traces of life can still be detected. Chemicals indicative of life have been reported in rocks 3.5 billion years old in the Dresser Formation of Western Australia and, with less certainty, in rocks 3.8 billion years old in Greenland.
    http://www.nytimes.com/2011/08......html?_r=1

    Life – Its Sudden Origin and Extreme Complexity – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4287513

    The evidence scientists have discovered in the geologic record is stunning in its support of the anthropic hypothesis. The oldest sedimentary rocks on earth, known to science, originated underwater (and thus in relatively cool environs) 3.86 billion years ago. Those sediments, which are exposed at Isua in southwestern Greenland, also contain the earliest chemical evidence (fingerprint) of ‘photosynthetic’ life [Nov. 7, 1996, Nature]. This evidence had been fought by materialists since it is totally contrary to their evolutionary theory. Yet, Danish scientists were able to bring forth another line of geological evidence to substantiate the primary line of geological evidence for photo-synthetic life in the earth’s earliest sedimentary rocks.

    U-rich Archaean sea-floor sediments from Greenland – indications of +3700 Ma oxygenic photosynthesis (2003)
    http://adsabs.harvard.edu/abs/2004E&PSL.217..237R

    Moreover, evidence for ‘sulfate reducing’ bacteria has been discovered alongside the evidence for photosynthetic bacteria:

    When Did Life First Appear on Earth? – Fazale Rana – December 2010
    Excerpt: The primary evidence for 3.8 billion-year-old life consists of carbonaceous deposits, such as graphite, found in rock formations in western Greenland. These deposits display an enrichment of the carbon-12 isotope. Other chemical signatures from these formations that have been interpreted as biological remnants include uranium/thorium fractionation and banded iron formations. Recently, a team from Australia argued that the dolomite in these formations also reflects biological activity, specifically that of sulfate-reducing bacteria.
    http://www.reasons.org/when-di.....pear-earth

    Thus we now have fairly conclusive evidence for bacterial life in the oldest sedimentary rocks ever found by scientists on earth.

    On the third page of this following site there is a illustration that shows some of the interdependent, ‘life-enabling’, biogeochemical complexity of different types of bacterial life on Earth.,,,

    Microbial Mat Ecology – Image on page 92 (third page down)
    http://www.dsls.usra.edu/biolo.....nit2.2.pdf

    Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. – Paul G. Falkowski – Professor Geological Sciences – Rutgers

    ,,,Please note, that if even one type of bacteria group did not exist in this complex cycle of biogeochemical interdependence, that was illustrated on the third page of the preceding site, then all of the different bacteria would soon die out. This essential biogeochemical interdependence, of the most primitive different types of bacterial life that we have evidence of on ancient earth, makes the origin of life ‘problem’ for neo-Darwinists that much worse. For now not only do neo-Darwinists have to explain how the ‘miracle of life’ happened once with the origin of photosynthetic bacteria, but they must now also explain how all these different types bacteria, that photosynthetic bacteria are dependent on, in this complex biogeochemical web, miraculously arose just in time to supply the necessary nutrients, in their vital link in the chain, for photosynthetic bacteria to continue to survive for long periods of time. As well, though not clearly illustrated in the illustration on the preceding site, please note that the long term tectonic cycle, of the turnover the Earth’s crustal rocks, must also be fine-tuned to a certain degree with the bacterial life and thus plays a important ‘foundational’ role in the overall ecology of the entire biogeochemical system that must be accounted for as well.

  4. All I’m saying, ba77, is that evidence that the LCA was complex is irrelevant to the question as to whether the first one was.

    So the answer to Denyse’s implied question:

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

    Is simply that the ancestors of the LUCA were simpler than the LUCA.

  5. And Elizabeth all I am saying is that the only hard physical evidence that you have, for your atheistic neo-Darwinian view, that ‘the ancestors of the LUCA were simpler than the LUCA’ is in your imagination. Whereas ID has hard physical evidence of a extremely complex web of biogeochemical ‘terraforming’ on the Earth, to eventually make the Earth hospitable for higher life-forms, as soon as we have evidence for water on the face of the earth from the earliest sedimentary rocks found on earth!!! Pretty much, it is a ‘Big Bang’ of specialized interdependent bacterial life suddenly appearing on the face of the Earth as soon as was possible!!!

    Bring Me To Life
    Lyrics Excerpt: Oh, only You are the life among the dead

    Evanescence – Bring Me To Life – video
    http://www.youtube.com/watch?v=3YxaaGgTQYM

  6. Yes, the terraforming thing is interesting. But your idea of “specialized interdependent bacterial life suddenly appearing on the face of the Earth as soon as was possible” is just as much (actually more) “imagination” than the idea that the LUCA had simpler ancestors.

    At least we have some promising testable hypotheses abiogenesis.

  7. Elizabeth, this is simply a bald face lie!!!

    ‘But your idea of “specialized interdependent bacterial life suddenly appearing on the face of the Earth as soon as was possible” is just as much (actually more) “imagination” than the idea that the LUCA had simpler ancestors.’

    For I have already listed several lines of evidence establishing the case for sudden appearance and interdependence, whereas you have merely asserted that what you imagine to be true for your atheistic conjectures is true! Moreover, your ‘promising testable hypotheses’ has already been tested to death and is in fact a wild goose chase!!!

  8. No, it isn’t a “bald-faced lie”. There is plenty of evidence for interdependence, but not for “sudden appearance”.

    You are mistaking lack of evidence for one thing for positive evidence for another. Also complete ignoring what data we do have in support of abiogenesis theories.

    Please don’t assume that people you disagree with are lying.

  9. There isn’t any data in support of abiogenesis.

  10. Yes there is. How do you think abiogenesis labs work if they don’t have data?

  11. Please reference these alleged “promising testable hypotheses abiogenesis”.

    And what is the evidence that demonstrates that the ancestors of the LUCA were simpler than the LUCA.

    You do realize that with evolution organisms can become more simple and there isn’t any evidence that blind, undirected chemical processes can make the functionally simple functionally more complex.

  12. Strange that you cannot reference any of that data.

  13. Course I can.

    Here’s output from just one lab:

    http://genetics.mgh.harvard.ed.....tions.html

  14. Nice literature bluff. Unfortunately there isn’t any evidence that a living organism can arise from non-living matter via blind, undirected chemical processes.

  15. It’s not a “literature bluff”. You said there wasn’t any data – I just gave you links to loads of data.

    Just repeating “there isn’t any evidence” doesn’t make it true. We still don’t know how it happened, or, indeed, yet, whether it happened, but that doesn’t mean “there isn’t any evidence”. It just means that there are still a lot of unsolved questions.

  16. There isn’t any data on that page that supports abiogenesis.

    That is why you posted a literature bluff.

    But please feel free to post the best one or two from that page and I will show you what I mean.

  17. First paper in that link doesn’t help you

  18. From The Origins of Cellular Life:

    Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, de?ned as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that de?nes a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information.

    Note two key words: plausible and proposed. Plausibility in particular is subjective, and leads to yet more clever circular reasoning. It seems reasonable because it seems reasonable. And in this case the authors are proposing what seems plausible to them.

    I don’t object to any of that, but rather to the implication that they have provided any evidence of abiogenesis whatsoever. Let them muse and speculate all they wish without confusing people about the facts.

    Which leads back to the first sentence. Since they cannot explain the origin of cellular life on Earth, how can they begin their paper by stating what is required to understand it? Having not demonstrated even the possibility of abiogenesis, how can they use it as a starting point for research into the origins of life?

    Perhaps they should append to the title of the paper, ” – Our Best Guess and Why We Think It Might Be Right.” Stripping away the veneer of certainty would be refreshingly honest.

  19. It’s not a “literature bluff”. But you can’t see the data unless you actually read the literature!

    geez!

    Joseph, how can you say “there isn’t any data” then when someone shows you a whole load of scientific papers, full of data, you just say it’s a “literature bluff”!

    Perhaps you disagree that the data support abiogenesis, but in that case, make the argument – say why it doesn’t. But don’t just keep saying “there isn’t any data”!

  20. The second paper on that link doesn’t deal with abiogenesis

  21. The first two papers do not support your claim, Liz.

  22. Well, I look forward to reading your critique of the paper.

  23. Yes, it does. It’s about the emergence of lipid membranes.

  24. It’s about the alleged evolution of some speculative primitive membrane.

  25. Well by your “logic” there is data supporting the claim that mother nature built Stonehenge because mother nature can make stones.

  26. I am still trying to figure out how it supports abiogenesis- you sure as heck don’t know…

  27. I’m interested in what people here regard as “evidence”.

    There seems to me to be a hint of burden-of-proof-shifting here. ID, as I understand it, as an inference depends on the lack of a plausible “natural” explanation for life.

    However, presented with any explanation that claims to be “plausible”, the response is dismissal of the explanation as “imagination” or “speculation”.

    As I see it, it the party basing a case on lack of a plausible pathway bears the burden of showing that the pathway is not plausible.

    Whereas the party basing the case on plausibility has a much more straightforward task – putting the hypothesis to the test. No hypothesis is ever proven in science, but the more evidence that supports it, the more plausible it becomes.

    Nobody is claiming that abiogenesis has been explained, and many would say that it never will be, definitively. However, if plausible mechanisms can be proposed, then that is a problem for those who base a case on the lack of a plausible mechanism. It’s not a problem for those of us who are content merely to say “we don’t know”.

    That’s the issue with Matzke’s flagellum hypothesis as well: it may be right or it may be wrong. That doesn’t matter to those of use who know that many things will remain unexplained by science, but remain curious about finding as many explanations as we can. But it does matter to those who base their case on bacterial flagella being unevolvable. If someone says that a mountain is unclimbable, and so the people observed on the top of it must have got their by helicopter, the finding of any path to the top, whether the path is the one they actually took, is enough to undermine the helicopter inference(though it could still be true). That’s the problem with any inference that depends solely on the lack of an explanation, not on positive evidence for the hypothesis.

  28. Yes, Joseph. It’s about a hypothesis, supported by data, about how a primitive membrane might have come about.

    So please stop saying there are no data and no evidence.

    Science works by testing hypotheses against data. If the data support the hypothesis then the hypothesis is retained. No scientific hypothesis is ever “proved”; all conclusions are provisional.

    Your position seems to be that because science hasn’t proved that abiogenesis occurred, and explained how, that there is no evidence that it occurred, nor supported hypothesis regarding how.

    It seems to me that you have fundamentally misunderstood the nature of scientific claims.

  29. There seems to me to be a hint of burden-of-proof-shifting here. ID, as I understand it, as an inference depends on the lack of a plausible “natural” explanation for life.

    Blind, undirected processes- design is natural.

    And ID is not anti-evolution.

    And just what is a plausible mechanism and how was it determined that it is plausible?

  30. Scott Andrews: any scientific paper could be entitled “Our Best Guess and Why We Think It Might Be Right”. In fact you could argue that every single scientific paper has that essential format.

    It’s a hugely powerful approach, and the basis of the scientific method.

    It’s put men on the moon, and doubled our life-expectancy. It works :)

  31. Elizabeth you try to work damage control for the lie I caught you in by stating;

    ‘There is plenty of evidence for interdependence (and this helps your atheistic neo-Darwinism how?), but not for “sudden appearance”.’

    Yet, Despite what you wish were true to comfort your atheistic delusions, the fact is that their is very strong physical evidence for sudden appearance of life on Earth, as soon as it was possible on Earth 3.8 bya, from carbon 12 to carbon 13 ratio analysis:

    Origin of Life Paradox – Hugh Ross – video
    http://www.metacafe.com/watch/.....hugh_ross/

    Elizabeth, as to your origin of life ‘research’ (ahem) papers, please show the exact paper that falsifies Abel’s null hypothesis, then you will at least have a empirical leg to stand on as far a real science is concerned. Until then, if you still claim that you have any real evidence for solving the ‘origin of life ‘problem’, you are merely, whistling in the dark, telling lie after lie trying to placate your materialistic/atheistic delusions!!!:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8 ) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    http://www-qa.scitopics.com/Th.....iency.html

    Programming of Life – Information – Shannon, Functional & Prescriptive – video
    http://www.youtube.com/user/Pr.....3s1BXfZ-3w

  32. A “plausible mechanism” is one supported by well-researched and well-established processes. And you test its validity by deriving a testable hypothesis, making predictions and testing those predictions against new data.

  33. Elizabeth you try to work damage control for the lie I caught you in by stating;

    ‘There is plenty of evidence for interdependence (and this helps your atheistic neo-Darwinism how?), but not for “sudden appearance”.’

    I did not and do not lie.

    And my tolerance for conversations in which I am accused of doing so is limited. I’m taking a break.

  34. Hi Joseph,

    Citation bluffing is a reliable indicator that our opponents have abandoned any further pretence towards being susceptible to things like reason and evidence. Casey Luskin wrote an excellent article about a citation bluffer. In it, he said:

    Proponents of undirected evolution have long employed a strategy to overcome weaknesses in their arguments. This strategy preys on those who are overly impressed or intimidated by citations to technical scientific papers. It’s called citation (or literature) bluffing, and the tactic goes something like this:

    •First, make a controversial claim in favor of evolution.
    •Then list a bunch of impressive-sounding technical papers that appear to support that claim.
    •Do not quote from or describe the contents of the papers. That wouldn’t be a bluff, because it would require actually dealing with the evidence. Instead, just enumerate the references in laundry-list fashion, as if they all supported the point.
    •Count on no one taking the time to dig up the obscure references and fact-check the claims. (Subscription-required journal access often makes it nearly impossible for readers to fact-check anyway.) Otherwise, readers would discover the papers are either irrelevant to the claim being made or contradict one another and don’t support a coherent argument.
    •If the bluff works, those who place unjustified faith in the infallibility of the peer-review process will be impressed, gloating that the juggernaut of science has rolled over the skeptics. Meanwhile, the mass of people who aren’t familiar with the technical literature–or don’t have access to it–will be intimidated from further comment.

    Unfortunately the original article can only be accessed via Google Cache at the moment, here hopefully:

    http://webcache.googleusercont.....#038;gl=uk

    The search result can be found by Google searching:

    “Has Hurd’s viewpoint biased him to make irrelevant citation bluffs”

    Too many atheists here have a hopelessly biased viewpoint and it is destroying any prospect of a constructive debate.

  35. There isn’t any plausible stochastic mechanism for the origin of life, nor the bacterial flagellum. And darwinism doesn’t have a testable hypothesis nor does it make predictions.

  36. It is NOT about abiogenesis. We are talking about abiogenesis.

    Now what are these alleged hypotheses?

  37. Elizabeth,

    Stating wild guesses as certain facts did not put men on the moon. It would have killed them.

    Don’t forget how the paper came into discussion. You cited it as data supporting abiogenesis, not as a plausible guess. That mistake is made often. It’s almost as if we’re supposed to think that someone knows something about the origin of cells.

  38. Correction – you did not cite the paper directly. You referenced a selection of papers, and I picked this one. Which is reasonable, since you didn’t reference all the papers on the page except this one.

  39. Well Elizabeth you stated:

    ‘But your idea of “specialized interdependent bacterial life suddenly appearing on the face of the Earth as soon as was possible” is just as much (actually more) “imagination” than the idea that the LUCA had simpler ancestors.’

    Yet I indeed did provide physical evidence just prior to that statement, where you had provided nothing, and still have provided nothing solid save for a literature bluff that comes no where near falsifying Abel’s null hypothesis!!!. Thus you are either telling bald face lies or you are incredibly blind to what is right in front of you! And just to make matters that much worse for your atheistic/materialistic delusions, trying to wrap themselves in the garb of scientific integrity, I remind you once again that neo-Darwinism, as currently formulated to the reductive materialistic framework is falsified by the finding of ‘non-local’ quantum information in life, since it is IMPOSSIBLE for non-local quantum information to arise a ‘local’ materialistic basis!!!

  40. to arise FROM a ‘local’ materialistic basis!!!

  41. “Data supporting abiogenesis” and “plausible guess” are not different things, is my point.

    And “stating wild guesses as certain fact” is not something anyone should be doing, least of all scientists, and certainly not me.

    There are data supporting abiogenesis. That is NOT the same thing as “stating [abiogenesis] as certain fact”.

    And a plausible, testable hypothesis is certainly not the same thing as a “wild guess”.

    Nor are “data supporting plausible hypotheses” the same thing as “no evidence”.

  42. Well, I understand you think I am blind, ba77. But then I think you are, so that makes us even, I guess. I think you are ignoring very important facts.

    I also think that you are failing to understand the nature of scientific claims.

  43. Elizabeth,

    Your position seems to be that because science hasn’t proved that abiogenesis occurred, and explained how, that there is no evidence that it occurred, nor supported hypothesis regarding how.

    That first part is quite true. There is no evidence that abiogenesis occurred other than the very existence of living things. As for “supported,” that’s a bit vague. A hypothesis is only useful when tested and discarded if necessary. It’s not much good when used by itself as evidence of its own plausibility.

  44. Well, you don’t use a hypothesis as evidence of its own plausibility! You need to test it against data. That’s what the papers on the Szostak papers are mostly about.

    That doesn’t mean that the problem is solved, or even that the solutions proposed are on the right lines. But it certainly doesn’t mean there is no evidence supporting them.

    I think that a lot of the problems in these conversations arise from equivocation between conclusions drawn by a few polemicists (on both sides of the debate) and what scientists themselves conclude. Most scientists probably think that abiogenesis occurred, but no-one would say that it had been demonstrated conclusively, or even that we know how it must have happened. We don’t.

    The problem, as I see it, is on the other side – in the absence of actual evidence that it didn’t happen, you can’t infer ID. The only sensible position to take on it is that there is still a mystery about how life got from non-life to complex life, that we have some ideas about it, some of which are supported by lab and field data, but that we still don’t know, and may never know for sure.

    If you want to take the view that the absence of an explanation leaves open the possibility of miraculous intervention, that’s fine, but my point is that you can’t conclude it from the fact that we don’t know how the gap was bridged, if it was, especially in view of the fact that we have a rather nice set of clues.

    Although we’ve moved a long way from the OP, and my original point about it, which is that the inference that the LUCA was complex tells us nothing about the FUCA.

    That’s just a simple error on news’s part.

  45. Well, obviously you don’t find the current hypotheses plausible. Others do.

    And yes, many testable hypotheses can be derived from “darwinism”, together with predictions, and have indeed been tested and supported.

    Again, I have to say: repeating that something is not the case does not make it not the case. Evolutionary theories are very well-supported, and even anti-evolutionists agree that Darwinian mechanisms work. It’s pretty well undeniable, actually, precisely because you can make testable hypothesis and watch the predictions being fulfilled.

  46. Elizabeth,

    Allow me to clarify. By “certain fact” I mean science tested sufficiently that men will repeatedly strap themselves to it and launch themselves into space.
    Admittedly, most science is never put to such an extreme test. But that’s a far cry from abiogenesis research in which an untested hypothesis is offered as evidence.

  47. It is NOT about abiogenesis. We are talking about abiogenesis.

    Now what are these alleged hypotheses?

    Well, decide what you mean by abiogenesis. If you mean how life got from non-replicating non-life to LUCA, yes, it’s about abiogenesis. If you mean how simpler forms of life got to LUCA, then it isn’t, but in that case, it’s about how LUCA wasn’t FUCA.

    Either way, it’s evidence for the thing you keep saying there’s no evidence for.

  48. “The ancestors were…”

    Should really read “might have been”, to be exact. Multiple repetitions of a statement cannot make it sound more plausible without evidence.

  49. Well, it’s a continuum. I certainly wouldn’t want to strap myself to an amino acid and hope I ended up in a protein :)

    But I still take issue with your formulation: an “untested hypothesis” is not being “offered as evidence”.

    Or not that I can see. What is being offered is evidence in support of testable (and tested) hypotheses about abiogenesis.

    So to say there is no evidence in support of abiogenesis is in correct. The hypotheses aren’t evidence, but the evidence that supports the hypotheses are evidence.

    When you see bits of what looks like a path, that is evidence that there may indeed be a path, even if you haven’t connected up all the bits yet, and even if some of the bits may still turn out to be sheep tracks.

  50. Elizabeth,

    Fair enough. We do hear plenty of rhetoric placing much more certainty on abiogenesis, often on the basis that there is supposedly no possible alternative.

    And I see that belief as driving acceptance of what looks like scant evidence. Each hypothesis contains certain unsupported narrative elements and relies on unexplained preconditions. Less attention would be paid to them if not for a philosophical drive to believe in the underlying premise.

    If you want to take the view that the absence of an explanation leaves open the possibility of miraculous intervention, that’s fine, but my point is that you can’t conclude it from the fact that we don’t know how the gap was bridged

    It’s intelligent intervention, and it’s inferred from what’s at this end of the bridge, not from the gap.

  51. Elizabeth Liddle, LOL,,, you make materialistic/atheistic ‘scientific’ claims all day long but, when demanded for specific hard evidence by UDers for your claims, you never back any of them up with ANY hard evidence, but always play long winded word games. And at the end of the day, after all is said and done, all your materialistic ‘scientific’ claims turn out to be nothing but wishy, washy, mush, with no hard ‘scientific’ evidence to actually back them up,, and are, in reality, nothing but you personally trying to defend a bankrupt materialistic philosophy. And you have done this in so far that you may retain your religion of atheism, for whatever severely misguided reason you have chosen to keep such a hopeless, and pointless, philosophy. Did I mention that materialism was bankrupt??? Well just to show you how ‘scientific claims’ actually work Elizabeth, here is my empirical evidence to back up my claim!!

    “As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter.”
    Max Planck – The Father Of Quantum Mechanics – Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944)

    Colossians 1:17
    “He is before all things, and in Him all things hold together.”

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007
    http://henry.pha.jhu.edu/aspect.html

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    Why the Quantum? It from Bit? A Participatory Universe?
    Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.” Anton Zeilinger – a leading expert in quantum teleportation:
    http://www.metanexus.net/Magaz.....fault.aspx

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. (This experiment provides experimental proof that the teleportation of quantum information in this universe must be complete and instantaneous.)
    http://www.physorg.com/news/20.....tally.html

    John 1:1-3
    In the beginning, the Word existed. The Word was with God, and the Word was God. He was with God in the beginning. Through Him all things were made; without Him nothing was made that has been made.

    The Word – Sara Groves – music
    http://www.youtube.com/watch?v=0ofE-GZ8zTU

  52. Exactly, Eugene. In fact, it would make more empirical sense to say that LUCA’s ancestors were more complex than LUC. We only have evidence for (extremely limited) change brought about by elimination/degradation of genetic information: not creation of genetic information.

  53. “Might have been” more complex, to be exact!

  54. “Lie” is a pretty strong word. It indicates intent to deceive. If I change my mind and accept abiogenesis or darwinisn, nobody gets a free vacation to Mexico or even a toaster. So I don’t think anybody has a motive to lie.

  55. But some people lie to themselves, Scott. And atheists especially have to lie to themselves if they seek meaning, morality and an understanding of origins.

  56. Yes, indeed, people lie to themselves, and it’s difficult to be sure one isn’t lying to oneself.

    But I certainly do not lie deliberately, and as I would very much rather not lie to myself, I do my best to discern whether I am inadvertently doing so. I trust the same is true of everyone here.

    As for your last sentence, obviously I disagree profoundly.

  57. Citation bluffing is a reliable indicator that our opponents have abandoned any further pretence towards being susceptible to things like reason and evidence.

    Oh, for goodness’ sake.

    Joseph claimed there are no data supporting abiogenesis. I simply linked to the output from one prominent abiogenesis lab. The very first two papers listed are data papers supporting abiogenesis theories.

    Ergo, there are data supporting abiogenesis theories.

    If you want to critique the paper, and say why in your view, those data don’t support the theory they are advanced to support, feel free, but at least bear in mind that the very first requirement for a peer-reviewed paper is that in the opinion of the referees, the data support the study hypothesis.

    But don’t accuse me of “bluffing” unless you are prepared to do so. Because I’m right now calling yours.

  58. What “claims” ba77?

    I’m not claiming that abiogenesis occurred, merely that, contrary to Joseph’s assertion, that there is some evidence in support.

    What is your evidence that it didn’t occur?

  59. It’s intelligent intervention, and it’s inferred from what’s at this end of the bridge, not from the gap.

    OK, fair enough :)

    My point was about the gap. Clearly I also disagree with your inference, but I do agree it is a different argument :)

    Thanks for the exchange.

  60. Elizabeth,

    I can remember seeing a video on youtube with Jon Wells demonstrating a very simple thing. He had a living cell in a test tube happy, alive and kicking. Then he pierced the cell’s membrane and all of a sudden (surprise!) the cell stopped functioning and died despite the fact that:

    (a) the environment was friendly to the cell prior to the experiment;
    (b) all parts of the cell that was just functioning a second ago were nicely situated together with all thinkable favourable conditions for it to reintegrate.

    And yet it decided to die.

    Do you or anybody else supporting abiogenesis as a plausibility have anything like that to demonstrate that would have the long-awaited wow factor?

    I seriously doubt that…

  61. A strong indication that you are lying to yourself is when you can’t substantiate your claims (citation bluffing is not a substitute for substantiation) or can’t engage with arguments (plenty of threads have come to an end here on Uncommon Descent because you disappeared instead of providing evidence for your position or even a detailed, cogent counter-argument).

  62. Fair enough – my point was just that the complexity of the LUCA simply says nothing about the complexity of its own ancestors, because there is no a priori reason for assuming that the LUCA was the FUCA.

    Chris: no it wouldn’t make a lot more empirical sense, although of course it is perfectly possible that the LUCA had more complex ancestors. Sometimes things do evolve in the direction of simplicity, and, indeed, will, if simplicity confers a greater chance of reproductive success.

    However, I disagree with your statement that “We only have evidence for (extremely limited) change brought about by elimination/degradation of genetic information: not creation of genetic information”. We know that genetic information can be duplicated; we also know that it can be changed; we can therefore say that if those changes turn out to confer increased reproductive success in a given environment, they will embody new “information” about what succeeds in that environment, and if the change is in a duplicated part of the genome, nothing useful need have been traded for it.

    Unless you mean something else by “creation of genetic information”. Perhaps you could explain.

  63. The first two papers do not support your claim, Liz.

    What claim, Joseph?

  64. Elizabeth,

    As to data supporting theories… Well, how many curves can you think of that would pass through a given point on a plane? I mean, one can happily invent any number of theories around the given data. The question is though:

    (a) how complex they are explaining available data;
    (b) whether these theories can stand more empirical data without becoming more complex;

    So it is not a surprise we can see all sorts of theories around. But what is their scientific worth is another matter.

  65. I’ll revisit the first paper I looked at, The Origins of Celluar Life.

    If anything what’s misleading are the title and opening paragraph. If this were positioned as a hypothesis on the formation of fatty vesicles then there would be no controversy. And, most likely, no one would be interested in it at all.

    The paper constantly reminds us of the possible connections between its subject matter and the origin of cells while honestly admitting that there might be none. A few actual experiments are overlaid with speculation regarding what else may or may not be possible and what has yet to be explained.

    The question is not whether it says anything inaccurate, but rather, what does it say about the origin of cellular life? The answer is nothing. It doesn’t even really claim to except by its vague title.

  66. Joseph, I said that there were data in support of abiogenesis theories. You said there weren’t. I linked to the publication output of an abiogenesis lab that includes data papers.

    You said they don’t support my claim. So I can only conclude that you have read the papers and think that either the data don’t support the hypotheses, or the hypotheses aren’t to do with abiogenesis.

    Well, the first paper on the list cites data that support the hypothesis that “that functional structures could evolve from mosaic nucleic acids, despite the presence of nonheritable variation in the sugar-phosphate backbone”. So it’s an abiogenesis hypothesis, or at least a pre-LUCA hypothesis. So if you disagree that it supports my claim that there are data that support abiogenesis, you’d better show how the data don’t support the hypothesis.

    The second paper on the list cites data that support the hypothesis that “low levels of phospholipids, potentially
    synthesized by genomically encoded catalysts (e.g., ribozymes), could also drive competitive growth and therefore provide a clear selective pressure for the evolution of modern cell membranes”. Again, it’s an abiogenesis paper (or at least a pre-LUCA paper) and so if you disagree that it supports my claim that there are data that support abiogenesis, again, you’d better show how the data don’t support the study hypothesis.

    Unless you are using a different definition of abiogenesis.

  67. Except that I wasn’t “citation bluffing”.

    And if you want me to pick up an argument you think I have “disappeared” from, here, please link to it.

    It’s a fast-moving site, and I’ve been very busy recently (as well as being on holiday).

    And, actually, Chris, this is pretty rich from you – I was delighted that you came over to my own site, where things move a bit more slowly, but not only did you “disappear” from the discussions you were having there, but, as far as I can tell, you deleted all your posts AS WELL as all the counter-arguments that had been made to you!

    Pots and kettles come to mind :)

    Anyway, I’d be delighted to see you back, only please don’t delete any more posts!

  68. You most certainly were citation bluffing, Elizabeth. That stunt combined with your recent “Trust me, I’m a scientist” tactic and your general, repeated unresponsiveness at crucial moments in various discussions are all clear indicators that you are wasting our time.

  69. You most certainly were citation bluffing, Elizabeth. That stunt combined with your recent “Trust me, I’m a scientist” tactic and your general, repeated unresponsiveness at crucial moments in various discussions are all clear indicators that you are wasting our time.

    No, I was NOT, Chris. I simply posted a link (making it perfectly clear what I was doing) to a page of the Szostak lab’s publications. The lab is an abiogenesis lab (so the papers are about abiogenesis) and the output clearly includes data papers.

    That was all that was required to support my simple point that there are data supporting abiogenesis theories. I did not claim that abiogenesis had occurred, was proven, an accepted fact, or anything else. I simply pointed out that the statement that there are no data supporting abiogenesis is not true.

    There are quite a lot.

    As for “Trust me, I’m a scientist” jibe – where did I say, or imply that? Huh?

    It seems to me that I’ve been saying all through this thread that no, scientists shouldn’t be making claims that aren’t supported – and that they aren’t making the claims they are assumed to be making.

    So no, don’t trust scientists, because they, rightly, don’t trust themselves. Science is all about provisional conclusions based on provisionally supported hypotheses, and always subject to potential falsification.

    As for my “general, repeated unresponsiveness at crucial moments in various discussions” – well, I’ve asked you for links to what you are referring to.

    I do try to keep up with conversations, but RL does sometimes intervene.

    What’s got into you Chris? Where’s this coming from?

    As for your time – it’s your own to waste as you see fit. I post in good faith. I thought you did too.

  70. Elizabeth, what your claim for ‘some’ evidence for abiogenesis is completely non-existent as far as falsifying Abel’s null hypothesis for functional information generation. That you would cling to such a tortured imagination that life from non-life ‘might have’ occurred by purely materialistic means, in spite of odds that can’t even be properly fathomed by the human mind, is not even on the same planet as far as hard science is concerned!! ,,,Your atheistic/materialistic dream-world ignores, besides thermodynamics as a whole (Sewell), the fact that reality is not even materialistic in its most foundational basis, but is indeed found to be a information theoretic Theistic basis of reality at its core,,, and this is true despite whatever flights of imagination Stephen Hawking and Lawrence Krauss, or other atheist with letters behind their name may try to sell you, or to sell to the public as a whole!!!

    The following are some of the probabilities against your position. Probabilities that are never properly addressed by your side, save to deny that they matter. (Denialism)

    Programming of Life – Probability – Defining Probable, Possible, Feasible etc.. – video
    http://www.youtube.com/user/Pr.....ckv0wVBYpA

    The Universal Plausibility Metric (UPM) & Principle (UPP) – Abel – Dec. 2009
    Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, “Yes.”,,,

    c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108

    c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96

    c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85

    c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70

    http://www.tbiomed.com/content/6/1/27

    Signature in the Cell – Book Review – Ken Peterson
    Excerpt: If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.
    http://www.spectrummagazine.or.....ature_cell

    In fact years ago Fred Hoyle arrived at approximately the same number, one chance in 10^40,000, for life spontaneously arising. From this number, Fred Hoyle compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Fred Hoyle also compared the chance of obtaining just one single functioning protein molecule, by chance combination of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously.

    Professor Harold Morowitz shows the Origin of Life ‘problem’ escalates dramatically over the 1 in 10^40,000 figure when working from a thermodynamic perspective,:

    “The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!”
    (Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University)

    Dr. Don Johnson lays out some of the probabilities for life in this following video:

    Probabilities Of Life – Don Johnson PhD. – 38 minute mark of video
    a typical functional protein – 1 part in 10^175
    the required enzymes for life – 1 part in 10^40,000
    a living self replicating cell – 1 part in 10^340,000,000
    http://www.vimeo.com/11706014

    Programming of Life – Probability of a Cell Evolving – video
    http://www.youtube.com/user/Pr.....yTUSe99z6o

    Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number:

    DID LIFE START BY CHANCE?
    Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias)
    http://members.tripod.com/~Black_J/chance.html

    The Theist holds the Intellectual High-Ground – March 2011
    Excerpt: To get a range on the enormous challenges involved in bridging the gaping chasm between non-life and life, consider the following: “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU)
    http://www.faithfulnews.com/co.....ing-gospel

  71. Elizabeth, I think the gentlemen are simply asking you to make the connection between the study (studies) that you cite and the substance of your claims.

    Example:

    The study in question explored this question:
    ……………………………………………….

    Based on the following data,

    ……………………………………………….

    the researchers drew the (1),(2),(3) conclusions:

    ……………………………………………….

    The researchers believe that the data supports those (findings) conclusions because

    ……………………………………………………

    These conclusions may be considered the equivalent of showing that life can emerge from chemicals because

    …………………………………………………..

    If you do not take us through the process, then it seems fair to suggest that you cannot take us through the process.
    That is why your adversaries are accusing you of bluffing. I promise you that William Dembski, Paul Marks, and Michael Behe can take you through this process from an ID perspective with their eyes closed and one-half of their brain tied behind their backs. The clarity of their arguments and the transparent relationship between those arguments and the evidence are all there to be evaluated. Indeed, I could, standing on their shoulders, do it myself. Under the circumstances, then, it will not do for you to say, “Hey, I provided a link, what else do you want?”

  72. I didn’t even mention Abel, ba77.

    All I am saying is that it is not true that there are no data supporting abiogenesis theories.

    And I’m not very impressed with Abel, who totally mis-cites Monod. Nor with his null hypotheses.

  73. Elizabeth,

    What is being offered is evidence in support of testable (and tested) hypotheses about abiogenesis.

    How can you know whether it supports abiogenesis without presuming abiogenesis? Without knowing how it occurred, how can you know whether any test is relevant?
    In the case of the earlier cited paper, it admittedly may or may not support a premise which in turn may or may not even be true, with pretty good evidence suggesting it isn’t.

    I won’t argue that they aren’t following the scientific method. But they are clearly driven by their expectations of where this or some other path will lead.

    I’m curious – I honestly don’t know the answer – how many laboratories are funded to research phenomena other than abiogenesis that are both historical and never known to have occurred?

  74. The connection between the published studies that are posted on Szostak’s lab page and my claim that there are data that support abiogenesis theories is simply that the output of that lab includes data in support of abiogenesis theories.

    So Joseph’s claim that there are none, is false.

    Now, we can argue about the papers themselves, if you wish, but I’d have to read them properly, and they are very technical, and I don’t personally have the expertise to critique them. But if someone here is, fine. Let’s hear why the data in those studies do not support the hypotheses they are cited to support.

    But the burden, it seems to me, is on those who claim there is are no supporting data for abiogenesis to show why the published data in support of abiogenesis theories do not, in fact support it, and not merely to claim, repeatedly, that there are no such data.

    As for your specific questions, the PNAS papers are public access and you can easily read them yourself. The hypotheses are clearly stated, and the data in support of them are clearly described.

    Of course none of them “may be considered the equivalent of showing that life can emerge from chemicals” because no-one has shown that. As I’ve said, repeatedly. Even if we do manage to make life in a test-tube, it still won’t show that that is what actually happened.

    And right now do not know how (or even whether, for that matter) “life emerge[d] from chemicals”. What we do have, however, are data that support theories about how it may have done.

    Please do not assume that I hold positions that I do not in fact hold, and have not claimed to hold.

  75. And I’m not very impressed with Abel, who totally mis-cites Monod. Nor with his null hypotheses.’

    but of course Elizabeth, and your opinion for what matters is suppose to impress me, instead of you actually falsifying the null hypothesis, because???, because???, because???, because you are Elizabeth by golly!!! and evidence doesn’t matter if Elizabeth says it doesn’t matter!!! :)

  76. We really are at cross purposes here!

    A theory generates hypotheses. Those hypotheses generate predictions. Predictions are tested against data.

    There are a number of broad abiogenesis theories, and Szostak’s lab are pursing one in particular, namely that lipid vesicles are part of the story – in other words that the emergence of membranes was a key aspect.

    This theory has led to a number of testable hypotheses, and the published output of that lab, which I linked to, includes reports of the testing of those hypotheses.

    Some have been supported, some not. The lab certainly has not solved the problem of abiogenesis, and may even be barking up the wrong tree. But some of their work looks promising.

    So there are data in support of abiogenesis theories. They could be wrong, still, but that’s the way it goes in science.

    But of course they are “driven by their expectations” – you don’t derive a testable hypothesis without at least some expectation that your data will be as you, well expect! That’s why we talk about “predictive” hypotheses! You don’t bother to test a hypothesis you are pretty sure is wrong.

    I don’t know the answer to your last question (and I’m not even sure what it means!).

  77. Elizabeth, I simply asked you to take us through the process and explain why the evidence offered supports abiogenesis. What your dialogue partners on this site are trying to tell you, aside from their references to you, is that the authors of the study are, THEMSEVLES, bluffing. Since, as you acknowledge, you don’t really know what they are talking about, (they saw to it that almost no one would know by virtue of their obfuscating) then it seems evident that you cannot use their work to support your claim. All this confirms what we have been telling you. There is no credible evidence to support abiogenesis.

  78. Re this:

    I promise you that William Dembski, Paul Marks, and Michael Behe can take you through this process from an ID perspective with their eyes closed and one-half of their brain tied behind their backs. The clarity of their arguments and the transparent relationship between those arguments and the evidence are all there to be evaluated.

    Well, I’d much rather they did it with both eyes open and brain fully engaged!

    My own view is that if they did so, they’d find the flaws in their own arguments :p

    Seriously, I find Dembski’s argument seriously flawed. I haven’t read Behe’s The Edge of Evolution, but I certainly wasn’t impressed by Darwin’s Black Box, and what I’ve heard of the argument made by Behe in The Edge of Evolution, it doesn’t seem to me he’s found an Edge at all.

    There certainly are Edges to evolution, which is one of the reasons we can be pretty confident the theory is broadly correct, because life doesn’t seem to overstep those edges, whereas a Designer could.

  79. Elizabeth,

    But the burden, it seems to me, is on those who claim there is are no supporting data for abiogenesis to show why the published data in support of abiogenesis theories do not, in fact support it, and not merely to claim, repeatedly, that there are no such data.

    Fair enough. Again, from the oddly named The Origins of Cellular Life.

    Although such laboratory studies may not re?ect the speci?c pathways that led to the origin of life on Earth, they are proving to be invaluable in uncovering surprising and unanticipated physical processes that help us to reconstruct plausible pathways and scenarios for the origin of life.

    The authors openly admit that they do not know whether their studies are relevant to the actual origin of life. (The rest of the sentence attempts to mitigate that detail, but does not.)

    How can the paper provide data supporting abiogenesis when its own authors don’t know whether it does?

    And let’s revisit this sentence fragment: “may not re?ect the speci?c pathways that led to the origin of life on Earth.”

    Notice that they do not qualify this with any uncertainty, as in ‘pathways that may have led to the origin of life on Earth.’ While admittedly not knowing how it happened, they are quite certain that they did. It sounds like they are determined to find their keys under that streetlight.

    But I digress. The authors of this paper admit that they do not know whether their data supports abiogenesis or even what pathway it followed. Only that it happened.

  80. OK, and my response is: if people here think the authors are bluffing, then it’s up to them to say why they think so. They are the ones claiming that there are no data supporting abiogenesis theories.

    And there’s a huge difference between claiming that “the data advanced to support theories of abiogenesis don’t, and the authors obfuscate to stop you realising that” and “there are no data that support abiogenesis”.

    The first requires detailed justification, especially when the work is peer-reviewed in one of the highest-impact-factor scientific journals in the world.

    That doesn’t mean that the odd turkey doesn’t get through, but it certainly puts the burden on the challenger to show that it’s a turkey.

    As for the papers themselves – just read them. And if you think the data don’t support the hypotheses, write to PNAS. Or at least post the critique here.

  81. What I said, originally, to ba77 was that s/he was “complete ignoring what data we do have in support of abiogenesis theories”.

    I did not say that abiogenesis was supported by data. I said there were data in support of abiogenesis theories. There are many theories of abiogenesis, and at least some of them must be wrong, and at best, all are incomplete. It’s possible that they are all wrong and it didn’t even happen. That does not mean that there is no support for them.

    There really does seem to be a cultural chasm here, and I’m just not sure how to bridge it.

    I’ve even said myself that, even if we were to succeed in generating life from non-life in a test tube, that wouldn’t tell us whether the pathway we were observing was the pathway life actually took!

    Science is always provisional. From where I’m standing it’s as though you guys are so fixated on the straw man (as I see it) of scientific certainty that abiogenesis occurred that you simply cannot see that there is no such certainty on the part of scientists – that certainty is completely irrelevant to what scientists do. What there is is a gap, one that scientists are curious to fill (it’s a pretty interesting question).

    And, as you rightly said, you can’t infer ID from that gap.

    Let’s talk about the problem of the bridge :)

  82. Nope, I’m just telling you my opinion, ba77. A man who cites Monod as saying the opposite of what he actually did say, doesn’t inspire me with confidence.

    And I find his nulls badly specified.

    You can regard my views as worth what you paid for them.

  83. OK, let’s take the first of the Szostak papers on the list (hey, let’s make it a journal club!):

    http://genetics.mgh.harvard.ed.....1_PNAS.pdf

    Here is the abstract:

    To understand the emergence of Darwinian evolution, it is necessary to identify physical mechanisms that enabled primitive cells to compete with one another.

    So we know it’s about abiogenesis, because it’s actually about the emergence of a Darwinian-capable entity. So the subject matter is clear.

    Whereas all modern cell membranes are composed primarily of diacyl or dialkyl glycerol phospholipids, the first cell membranes are thought to have self-assembled from
    simple, single-chain lipids synthesized in the environment.

    Here they refer give the background to one of problems the lab has to solve in order to make their story – how do you get from simple lipid chains to more complex phospholipids ?

    We asked what selective advantage could have driven the transition from primitive to modern membranes, especially during early stages characterized by low levels of membrane phospholipid.

    And here they define the problem: what reproductive advantage could have been given by phospholipids at very low levels (“what use is half a phospholipid?” if you like :)) In other words they are testing the hypothesis that even low phospholipid levels must have had some survival advantage, if modern membranes were to have resulted from Darwinian processes.

    Here we demonstrate that surprisingly low levels of phospholipids can drive protocell membrane growth during competition for single-chain lipids. Growth results from the decreasing fatty acid efflux from membranes with increasing phospholipid content.

    And here they report the data that support their hypothesis, and the mechanism – that even low levels of phospholipids drive membrane growth even when the membraine is largely single-chain lipids.

    The ability to synthesize phospholipids from single-chain substrates would have therefore been highly advantageous for early cells competing for a limited supply of lipids. We show that the resulting increase in membrane phospholipid content would have led to a cascade of new selective pressures for the evolution of metabolic and transport machinery to overcome the reduced membrane permeability of diacyl lipid membranes. The evolution of phospholipid membranes could thus have been a deterministic outcome of intrinsic physical processes and a key driving force for early cellular evolution.

    And here they relate their finding to their broader theory about the role of lipids in abiogenesis.

    And that’s the way science works – you don’t suddenly find a bacteria spontaneously creating itself in a jar of peanut butter, and get your Nobel Prize, you painstakingly devise theories, derive hypotheses, spot a problem, solve the problem, or fail and derive a different hypothesis… and little by little you gain some kind of understanding of the kinds of processes that are possible, the kinds of feedback loops that might have operated etc.

    And it’s all provisional, all, literally, hypothetical, and could be wrong. But the great thing is that to make progress, your hypotheses have to be supported by data. And that data is what they report.

    It exists.

  84. Elizabeth,

    I did not say that abiogenesis was supported by data. I said there were data in support of abiogenesis theories.

    Do you mean hypotheses that explain some possible step in a process? Then perhaps we could clear up the confusion by not calling them “abiogenesis theories.” If research indicates that fatty vesicles can form in certain laboratory tests, then the data in the paper could support that.

    It’s possible that they are all wrong and it didn’t even happen. That does not mean that there is no support for them.

    To borrow from Dr. Hunter, there is support for geocentrism. Every day we see the sun going around us. That’s why we also need to look at the contradictory evidence.

    Science is always provisional. From where I’m standing it’s as though you guys are so fixated on the straw man (as I see it) of scientific certainty that abiogenesis occurred that you simply cannot see that there is no such certainty on the part of scientists

    Science is one thing. Scientists are another. In my previous post I quoted from a paper implying that there is a natural pathway even if we don’t know what it is. They know how to express uncertainty, but they sure don’t do it there.

    What would happen if a public school decided to teach evidence against abiogenesis alongside support for it? It would be on every news channel and respected scientists would come out of the woodwork to tell us how ignorant someone is to contradict that thing that they aren’t certain about. We both know what they would say: There’s lots of research supporting it.

  85. I am afraid you are not following me, Elizabeth. The authors’ fail to tell us WHY the data supports their conclusion. Anyone can claim that data supports a given conclusion. The task is to show the connection between the data and the conclusion (why the data justifies the conclusion). If they don’t provide the “why,” then they are bluffing. If you do not know why the data supports the conclusion, then you have no reason so say that evidence for abiogenesis exist. Since you, nor anyone else has ever produced that connection, then I am more than justified in saying that no such connection exists and that anyone who claims to have evidence for abiogenesis is bluffing.

  86. Well, I think we are getting on to the same wavelength, finally!

    But I’d point out that hypotheses are derived from abiogenesis theories – that’s how science works. The reason the Szostak lab has been pursuing lipid hypotheses so vigorously is that their theory is that membranes are really important – that without co-evolution of some kind of cell-membrane, you wouldn’t get robustly self-replicating polymers – so they see the very earliest proto-biological entities as a combination of lipid vesicles and polymers.

    But to support their theory they have to generate specific hypotheses and test them, and that’s what they do. That’s why I linked to their publication output! There’s a lot of it.

    And, while it’s no guarantee of brilliance, a Nobel Prize in science isn’t nothing :) Szostak is a bright guy. I find the research quite exciting.

  87. What would happen if a public school decided to teach evidence against abiogenesis alongside support for it? It would be on every news channel and respected scientists would come out of the woodwork to tell us how ignorant someone is to contradict that thing that they aren’t certain about. We both know what they would say: There’s lots of research supporting it.

    I don’t know that. I think it’s fine to teach Szostak’s theories as long as it’s clear that they are very tentative at this stage, if looking promising. There are some interesting problems IIRC and that would make for an interesting school topic.

    Tell me what you think the evidence against it is – what would you propose teaching?

  88. Why do you change subjects in this way? The issue I raised in this context has to do with the clarity of the argument being presented. Behe’s argument for Intelligent Design is based on the methodology of “irreducible compexity.” Everyone understands the argument, namely that the whole cannot work without all of the parts and that no evolutionary pathway can likely explain the finished product.

    Your author’s claims for abiogenesis contains no similar argument. It can’t be evalutated because it has no substance, as is clear from your inability to articulate it even after I asked you to do so several times (WHY does the data support the hypothesis).

  89. Good grief. What (and where) in these papers is the ARGUMENT that the data supports the plausibility of abiogenesis? I don’t need a lecture on “how science works.” I need an answer to the question, WHY does the data support the obviously hoped-for conclusion. Please!

  90. And that’s the way science works – you don’t suddenly find a bacteria spontaneously creating itself in a jar of peanut butter

    Gee, thanks for clearing that up. We wouldn’t even be having this discussion if there were a bit more humility regarding such research. When’s the last time we’ve heard that scientists were researching to determine whether it was possible for life to self-assemble and evolve into modern cells? Say what you will about the scientific method, this is presented as fact. It’s about how it happened, not if it happened. That is reality.

    Is it possible to minimize the importance of this research without being accused of minimizing or not understanding the scientific process? Each paper depends upon numerous assumptions made in other papers and then makes its own which become the premises for yet more papers. If they say they can synthesize fatty vesicles, great. I believe them. But there are too many assumptions and too much background ideology for any of it to credibly relate to anything that actually occurred.

  91. Would you say abiogenesis research is worth doing, or not?

  92. Elizabeth, it seems that you feel yourself expert enough to lecture others on establishing ‘certainty’ in science, (which in reality you are doing your level best to avoid a certainty about abiogenesis that has already been reached from the best scientific evidence now available; Meyer), yet the completely ironic thing in all this, in you lecturing others about establishing ‘certainty’ in science, is that if, as you hold in your materialistic atheism, life, and particularly consciousness, really did come about by purely materialistic/atheistic processes then there would be absolutely no way for any of us to know with 100% CERTAINTY if anything we believed was actually true or not. Thus you, by insisting on purely materialistic/atheistic causation for all of life, have basically completely undermined any argument for ‘certainty’ that you were trying to make in the first place.,,,

    notes:

    Should You Trust the Monkey Mind? – Joe Carter
    Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties.
    http://www.firstthings.com/ont.....onkey-mind

    “Atheism turns out to be too simple. If the whole universe has no meaning, we should never have found out that it has no meaning…”
    CS Lewis – Mere Christianity

    What is the Evolutionary Argument Against Naturalism? (‘inconsistent identity’ of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) – video
    http://www.youtube.com/watch?v=5yNg4MJgTFw

    Can atheists trust their own minds? – William Lane Craig On Alvin Plantinga’s Evolutionary Argument Against Naturalism – video
    http://www.youtube.com/watch?v=byN38dyZb-k

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.” J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.

    It is also interesting to point out that this ‘inconsistent identity’, pointed out by Plantinga, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to be able to account for objective morality, in that neo-Darwinists cannot maintain a consistent identity towards a cause for objective morality;

    The Knock-Down Argument Against Atheist Sam Harris – William Lane Craig – video
    http://www.youtube.com/watch?v=tvDyLs_cReE

    “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth.
    As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” Creation-Evolution Headlines
    http://creationsafaris.com/cre.....#20110227a

    But Elizabeth, I know where ‘certainty’ can be found!

    Solid Rock – the 5th service band Featuring TRU-SERVA
    http://www.youtube.com/watch?v=G4jD70Y-mQ0

  93. First, I would teach what you just said. Here’s a hypothesis, and it’s tentative.

    I wouldn’t teach ID. It’s way too controversial, and it’s new. Rather, I impress upon them the enormity of what takes place in the cell. That’s not something to gloss over. It’s astonishing and should be represented as such.

    In a separate lesson, using unrelated subject matter, I would teach them the limitations of science, including that it is practiced by humans, not Vulcans. I would provide simple examples of accepted knowledge that turned out to be wrong. (Everyone thought that bacteria could not survive inside the stomach.) I would tell them never to believe something just because they’re told that scientists do. And if something sounds wrong or outright ridiculous, look for the opposing viewpoint.

    But none of that should take up disproportionate time. Science class is for science.

    Such lesson plans could never be part of most official curricula because they are obviously slanted toward religious fanaticism.

  94. The authors do NOT “fail to tell us WHY the data support” their hypothesis, or, indeed, their conclusion (which, being a conclusion is not a given, but follows their finding).

    The why is clearly stated in the papers (if it hadn’t been, it wouldn’t have got past peer-review, because it’s the sine qua non for publication). Now you may think that their given reasons are not adequate, but that’s different from saying that they don’t give them. They do.

    But this conversation is getting a bit weird. Clearly we must be talking about different things (why else would you look at a paper that clearly spells out how the data support the hypothesis and say that it doesn’t attempt to do so?).

    So I’m curious as to what you actually mean.

    Are you saying they don’t say why their data supports the case that abiogenesis happened?

    No, they don’t, because that isn’t what the paper is about. The paper (at least the first one) is about their theory of abiogenesis, which postulates the co-evolution of lipid vesicles. However, this presents some problems – why would low levels of phospholipids be advantageous? And they find the answer – low levels of phospholipids are advantageous because they accelerate the growth of the membrane (and they go into great detail as to how this happens).

    Read the paper, it’s interesting. And it reports data that support a hypothesis derived from a theory of abiogenesis.

    So Joseph’s statement that there are no such data is incorrect.

  95. On the contrary, what you suggest is essentially the UK science national curriculum, which mandates the teaching of hypothesis testing.

    It isn’t implemented as successfully as it should be, IMO, but that’s the principle. I blame widespread misunderstanding about the provisional nature of all scientific conclusions and a fundamental misunderstanding about the nature of scientific knowledge, which is not about proof, but about how well models fit the data.

    And it’s precisely that misunderstanding, and the resulting straw men, I find myself trying to hack my way through on this thread! But it seems I have at least one ally in you :)

    This essay should be required reading in all science classes IMO.

  96. Umm primitive cells emans living organisms already exist and this is post-abiogenesis.

    Cell membranes is also post-abiogenesis.

    shrug, sigh

  97. And as I said there is evidence to support abiogenesis in the same manner there is evidence to support mother nature building Stonhenge.

  98. Elizabeth: “What is your evidence that it didn’t occur?” (Presumably, meaning by purely naturalistic and materialistic processes.)

    Ummm, lesseee . . . Math; chemistry; physics; information theory; our uniform and repeated experience about how information-rich structure some into being.

  99. It supports the plausibility of one step in of one theory of abiogenesis, clearly stated in the paper.

    And it seems to me that you do “need a lecture on ‘how science works’” because you seem to have a very odd idea about it.

    As for “the obviously hoped for conclusion” – yes, it is pretty “obvious” that if you have a hypothesis that makes a prediction that you “hope” the data will support it. As I said, there’s not much point in thinking up a hypothesis that you don’t think your data will support. You make your best stab at a hypothesis, then you test it. And “obviously” if your data support it, then you have a positive finding, and you publish it.

  100. Darwinian mechanisms work to break things- so what are these alleged predictions based on Darwinian processes?

    Heck you have already admitted that we cannot test the claim that teh bacterial flagellum evolved via Darwinian processes- so what do you have?

  101. Yes, we can “test the claim that teh bacterial flagellum evolved via Darwinian processes”.

    And no “Darwinian processes” don’t “work to break things”. You are thinking of deleterious mutations, I think. Darwinian processes work to filter out breakages, and retain improvements. That’s why populations adapt incrementally to their environment.

  102. I guess that your sixth evasive answer in a row means that you will never answer my inquiry. In any case, I will try yet again. I am asking you to provide an explanation about WHY the conclusion (abiogenesis is plausible) follows from the hypothesis and the data. Let me give you a template that you can work with: [A] This evidence (being specific, of course, numbers and all) [B] leads to the conclusion that abiogenesis is plausible BECAUSE C]……………

    Without [C], [A] and [B] are meaningless. Do you not understand this?

    Please fill in all three blanks.

  103. We can also blame such misunderstandings about science on the academic culture. Origins sciences seem to sit apart from others in that they are only partly provisional. The how is provisional, but the what is carved in a great big slab of marble. It is proven, with all sorts of verbal gymnastics tacked on to the effect that nothing is ‘proven,’ etc. Except that this is.

    That’s why there are forums like this in which these subjects are debated, politely at times and less so at others. Because science is not being permitted to take its course, certain supposedly provisional conclusions cannot be challenged without risking marginalization from mainstream science.

    If researchers and students could discuss alternatives without fear of needless consequences then surely the matter would run its course. If the challenges or alternatives were baseless then the scientific method could determine that. ID could get flushed away with a slew of other ideas that went nowhere.

    It reminds me of Animal Farm. The principles seem sound, but they tend to get corrupted. It’s just human nature.

  104. Dr Liddle et al have been having much the same exchange with me in another thread, where I drew attention to the exchange between Shapiro and Orgel on the claimed genes and metabolism first gradualist schemes discussed in IOSE. Mutual destruction. GEM of TKI

  105. Petrushka,

    Space research provided some technology that would be useful even if nothing had ever launched. Maybe some new technology will result from the manipulation of molecules in OOL experiments. Maybe someone will even engineer some new form of life.
    It’s like brainstorming. The idea is that you consider every idea, even the bad ones. Because if we reject seemingly bad ideas without even any consideration, then we inhibit their expression, which in turn means that people stop expressing ideas and something really good could get lost.

    If I’ve learned something from this thread (why does this feel like the end of Brady Bunch episode) it’s that perhaps I’m too dismissive of the research, even though I’m convinced that they’re looking for something that isn’t there. Nonetheless, I think that the polarization results from dogmatic beliefs regarding what fills in the so-called “gaps,” and notable defensiveness toward any challenges to those beliefs. Everyone just needs to chill out.

  106. I am asking you to provide an explanation about WHY the conclusion (abiogenesis is plausible) follows from the hypothesis and the data.

    That is not the conclusion – I’m astounded, just astounded at the the total failure to understand EL’s point, which has been made over and over again, or the contents of the paper.

    EL:

    they are testing the hypothesis that even low phospholipid levels must have had some survival advantage, if modern membranes were to have resulted from Darwinian processes.

    And in the conclusion as quoted by EL above:

    The ability to synthesize phospholipids from single-chain substrates would have therefore been highly advantageous for early cells competing for a limited supply of lipids. We show that the resulting increase in membrane phospholipid content would have led to a cascade of new selective pressures for the evolution of metabolic and transport machinery to overcome the reduced membrane permeability of diacyl lipid membranes. The evolution of phospholipid membranes could thus have been a deterministic outcome of intrinsic physical processes and a key driving force for early cellular evolution.

    Now where, StephenB, do they conclude that “abiogenesis is plausible”? They don’t, what they show is that the data supports their hypothesis, as stated in the paper, and that it fits into their own broader theory about abiogenesis.

  107. StevenB

    I am asking you to provide an explanation about WHY the conclusion (abiogenesis is plausible) follows from the hypothesis and the data.

    It doesn’t. I didn’t say that it did.

    I’ve explained this several times. Read Dr Bot’s post above, and see he is making the point more clearly than I appear to have done.

    The hypothesis was derived from atheory of abiogenesis, and the data support that theory. Therefore, at least one theory of abiogenesis has data to support it. Which was my original point.

    It doesn’t mean that “abiogenesis is plausible” because the theory in question (the lipid vesicle theory) is far from complete and many questions remain. But the papers on that site provide data that address at least some of the potential “implausibilities” in that theory.

    I hope that is now clear. I am not being evasive. You are simply reading into my earlier statement something that was never there, then reading my attempts to clarify what was there as evading your challenge to me to support a claim that I did not make!

    Communication is Hard Work :)

  108. I agree with most of this :)

    Certainly the polarization is a problem, and, worse, a self-perpetuating one.

    Good to hear a call for depolarization! Let me add my voice to it.

  109. as to their comment from the paper:

    ‘new selective pressures for the evolution of metabolic and transport machinery’

    and exactly how does postulating a ‘cascade of new selective pressures’ for ‘machinery’ (i.e. now needing a sequence particular molecular machines to be present or else) explain how the irreducibly complex molecular machines can arise in order to achieve self sustaining replication? It simply does not follow that needing particular molecular machines by a ‘cascade of selective pressure’, will make any required molecular magically appear. It is charitable, to the point of self-imposed intellectual poverty, to think that this experiment indicates anything more than merely ‘playing around’ in a extremely limited ‘thermodynamically uphill’ environment, that had results that are not at all surprising when considering the starting parameters they imposed on the experiment.

  110. Elizabeth Liddle:

    Yes, we can “test the claim that teh bacterial flagellum evolved via Darwinian processes”.

    Prove it by telling us how to do so. Or admit that you have no idea what you are talking about.

    And no “Darwinian processes” don’t “work to break things”.

    Then it is strange how we have evidence for that- mutations causing bad things and beneficial mutations being beneficial by causing a loss of functionality.

    And populations adapt by changing their behaviour, not by waiting for a mutation to come along.

    But anyway I am still waiting on those alleged predictions based on Darwinian processes.

  111. Yes Elizabeth and by your “logoc” there is data supporting the claim that mother nature built Stonehenge because mother nature can make stones.

    There aren’t any testable hypotheses for abiogenesis and there aren’t any predictions.

    If you think I am wriong then please post them- hypotheses and predictions.

  112. As to address the overriding materialistic/atheistic bias that Elizabeth has repeatedly shown in clinging to any shred of evidence, no matter how paltry it is, for a purely materialistic/atheistic origin of life, I would like to point out this fairly recent paper on the Bacterial Flagellum which, though not directly related to molecular machinery that would be necessary for the simplest conceivable microbial life to exist, none-the-less, severely compromises any hope that Elizabeth may have had for rationally maintaining her preconceived materialistic/atheistic bias against the Theistic origin of life;

    INFORMATION AND ENERGETICS OF QUANTUM FLAGELLA MOTOR
    Hiroyuki Matsuura, Nobuo Noda, Kazuharu Koide Tetsuya Nemoto and Yasumi Ito
    Excerpt from bottom page 7: Note that the physical principle of flagella motor does not belong to classical mechanics, but to quantum mechanics. When we can consider applying quantum physics to flagella motor, we can find out the shift of energetic state and coherent state.
    http://www2.ktokai-u.ac.jp/~shi/el08-046.pdf

    The reason this finding of ‘quantum action’, in the molecular machine of the flagellum, severely compromises Elizabeth’s Materialistic/Atheistic bias is that, regardless of whether she believes life arose purely by ‘material’ accident or not, somewhere along the line a ‘non-local’ (beyond space a time) cause came to be introduced into some, (perhaps all?), of the molecular machinery of life. i.e. Without this ‘non-local’ cause, whatever this beyond space and time cause may be :) , this machinery could possibly operate in the first place!!! i.e. A ‘non-local’ cause allows the flagellum to have movement!!!

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    This following video illustrates just how ‘spooky’, to use Einstein’s description, this quantum action is:

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182

    And whereas the materialist/atheists is sorely vexed to provide any coherent ‘non-local’ cause, that does not collapse into complete absurdity, it is interesting to note that the Theists have, for centuries, postulated a non-local cause that would fit the bill quite nicely:

    “The ‘First Mover’ is necessary for change occurring at each moment.”
    Michael Egnor – Aquinas’ First Way
    http://www.evolutionnews.org/2.....first.html

    Further note:

    Myosin Coherence
    Excerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects.
    http://www.energetic-medicine......Page1.html

    The relevance of continuous variable entanglement in DNA – July 2010
    Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix.
    http://arxiv.org/abs/1006.4053v1

    Acts 17:28
    ‘For in him we live and move and have our being.’,,,

    ROYAL TAILOR – HOLD ME TOGETHER – music
    http://www.youtube.com/watch?v=vbpJ2FeeJgw

  113. Dr. Bot writes: “That is not the conclusion – I’m astounded, just astounded at the the total failure to understand EL’s point, which has been made over and over again, or the contents of the paper.”

    What should astound you is that you have forgotten the original claim, made @ 4.1.1.1 and 4.1.1.1, which was that evidence exists to support abiogenesis. Everything which followed was an exercise in reframing the issue so that the original claim would be forgotten. However, I am prepared to discuss the new claim since the old claim has been abandoned.

    —Elizabeth: “You are simply reading into my earlier statement something that was never there, then reading my attempts to clarify what was there as evading your challenge to me to support a claim that I did not make!”

    Responding to the point that no evidence exists for abiogenesis, you said this:

    “Yes there is. How do you think abiogenesis labs work if they don’t have data?” The clarification came later.

    Overlooking that little detail, what I want to know, though, is WHY do you think that the data supports supports the plausibility of one step in of one theory of abiogenesis.” Again, I will give you the template: The data supports the hypothesis BECAUSE………… Neither you nor the authors have made the case that the data supports the hypothesis. To say that it does not not SHOW that it does. Are we clear now?

  114. David Abel is a guy who knows what is talking about. Great stuff. Drs Stuart Kauffman and Richard Dawkins may rest assured.

  115. Elizabeth,

    If it did, chances are it would have been able to be repeated. Musings about changed conditions that preclude it from happenning now, do not really help… It must be observable, otherwise it is not responsible science but grant holding.

    If I let go of an object, chances are it will fall on the ground. That is observable and measurable.

  116. ba77, perhaps you misread me.

    My point was that we cannot be certain, not that we can.

    So I’m not quite sure what “argument for ‘certainty’” you thought I was making.

    I was making an argument for uncertainty. That scientific conclusions are always provisional, and subject to potential falsification.

    It’s pretty well been my point this entire thread.

  117. What I originally said was that there were data in support of abiogenesis theories (4.1.).

    I did indeed leave off the word “theories” when I responded to Joseph in 4.1.1.1, which, it seems, left room for ambiguity. So let me clarify:

    I originally said that ba77 was “complete ignoring what data we do have in support of abiogenesis theories”. Joseph said there was none. I said there was, and there are.

    Now, clearly, data that support a theory of abiogenesis are also, in some sense, support, if very weak, for abiogenesis. So my second formulation was not incorrect. However, the links I provided were to precisely the kind of published output I had had in mind when I responded to ba77 (and Szostak’s is not the only theory with data to support it) – data that support hypotheses arising from specific theories about abiogenesis.

    By doing so, it strengthens those theories, and contributes to the pool of possible mechanisms that may turn out to have played a likely role

    But of course there is, as yet, no persuasive single theory of abiogenesis, just a number of incomplete, and in some ways, competing theories, some of which are, indeed, supported by data.

    I hope this is now clear.

  118. Elizabeth, but of course you would argue for ‘uncertainty’ since it is in fact impossible, in your materialistic/atheistic worldview, to establish any certainty at all for whatever you may want to believe to be true, which was my whole point in the first place. You may think this mere semantics, but in reality it is just the tip of the iceberg as to revealing the sheer bankruptcy that materialism, your adopted worldview, has as a coherent philosophy!!

  119. So why did you say that I was arguing for certainty?

    Make up your mind!

  120. Elizabeth, and how can you be certain that you were arguing for uncertainty???

  121. gee, ba77, you make an excellent point!

    Maybe I wasn’t!

  122. “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.” J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.

  123. This is an interesting exchange. Joseph asserts that there is no evidence for abiogenesis. Elizabeth asserts that there is because people are working on it, and they are learning new things and, in some cases, answering minor specific questions about how things work.

    Having looked at OOL in some detail, I have to say I’m not impressed with the state of any supporting data. Indeed, as one prominent OOL researcher stated years ago, all our efforts have only underscored the enormity of the problem, rather than leading to answers.

    But is there data that supports abiogenesis, as Elizabeth suggests? Sure, if you have an exceedingly low threshold for what you mean by “support”. For example, there is evidence that some biologically-relevant molecules may exist in comets and meteorites. There is evidence that some ribozymes can perform simple catalytic actions. And so on.

    Thing is, there is also plenty of data that support the idea that the Earth is flat. If I look outside to the horizon, it looks flat. When I place a soccer ball on the field, it stays put and doesn’t roll off the face of the earth. When I drive all the way across the country the earth doesn’t seem to curve.

    In other words, there is “data” to support all kinds of notions. Especially when we are taking simply about data that is “not inconsistent with” the notion we are trying to support. So the issue is not whether there is some consistent data, but whether the overall data, taken as a whole, supports the idea. Despite what we see and experience around us every day, we accept that the earth is not flat because we have additional data that points in another direction.

    So, sure, there is data that is consistent with the idea of abiogenesis. Elizabeth thinks such data “strengthens those theories” of abiogenesis. In contrast, Joseph, (if I can be so bold as to put words in his mouth), is looking at the overall body of data and concluding that abiogenesis is not supported.

    The problem for naturalistic abiogenesis, is that all the data obtained so far, including those bits that are consistent with abiogenesis, are also consistent with a competing theory, namely design; so while they are consistent with abiogensis, they don’t support abiogenesis to the exclusion the alternative. At the same time, there is a lot of data that is inconsistent with abiogenesis and that does support design to the exclusion of a naturalistic process.

    I think it is pretty clear that the overall weight of the evidence points toward intelligent activity for OOL. But, yes, there is some data that would be consistent with a naturalistic abiogenesis story, just as there is data that would be consistent with a flat earth.

  124. Very well put Eric!!

  125. Thanks for this, Eric.

    I’ll just take issue with one point, which, though minor, may be a clue to where the misunderstandings lie:

    You say:

    But is there data that supports abiogenesis, as Elizabeth suggests? Sure, if you have an exceedingly low threshold for what you mean by “support”.

    In science, a hypothesis is said to be “supported” if we make a testable prediction, and the data agree with our prediction in contrast to the expectation or prediction under some other hypothesis (“significantly” by some statistical test).

    What I linked to weren’t data that are “consistent with” some hypothesis, but actually “support” it, in the above sense. However, as you say, that support my be only weak for the theory from which the hypothesis is derived. Other theories could be consistent with the mechanism that received support

    Nonetheless, IMO, it remains untrue to say that there are no data that support abiogenesis. It’s an area of active research, there are a number of theories, each with problems, but then that’s what science is about – figuring out how stuff happens/happened. Provisionally.

  126. This is the gap between the scientific method as taught to students and the reality of it.

    Science produces data which is not inconsistent with abiogenesis. I’m still a little fuzzy on how the observation of a certain chemical process can be considered support when first it’s unknown whether abiogenesis even occurred and second, if it did occur it’s unknown whether that process would have been involved.
    It’s a bit like designing a component and saying that it supports faster-than-light travel without knowing how FTL might work, on the basis that if FTL ever were possible it may or may not use such a component. Maybe the component is useful, but all things considered even a number of such components wouldn’t make a convincing case that FTL was possible. It’s too incoherent and disconnected. (And I’ve gone off track.)

    But I’ve yet to encounter anything in the media released by a laboratory or university even hinting that chemical OOL might not have occurred. There is not a trace of uncertainty. And at least in this country, to even suggest making students aware of that uncertainty is tantamount to blasphemy.

    The scientific method is irrelevant. Science is as science does. Neither abiogenesis nor darwinian evolution are provisional or subject to testing. They are unalterable facts. The rest is the scientific method for all the other stuff.

  127. I suppose after several hundred years of finding natural explanations for things that were previously attributed to intervention, the expectations are that this will continue.

  128. Maybe or maybe not…

    As my linear algebra lecturer used to say, the art of being able to make no mistakes is in formulating the most general statements.

    However, the amount of information that those statements convey is very low, isn’t it, Elizabeth?

  129. Thanks, Elizabeth. I guess the issue comes down to how we define “support.”

    Many people would look at that term as an overall assessment, in light of all the potentially supporting data, as well as all contrary data. Then they might feel justified in saying that the data doesn’t support the theory.

    I certainly haven’t read every OOL paper, but I do feel like I follow the field fairly closely. So far, every time I have looked into evidence supporting abiogenesis (from Miller-Urey to modern ribozyme experiments in the RNA World), upon closer inspection the takeaway lesson of the experiment, without exception, has been either: (i) nothing interesting happens without intelligent guidance, (ii) the results are utterly trivial or tangential to the real challenges of abiogenesis (for example, finding amino acids in meteorites), or (iii) the results point to problems with the theory (for example, it turns out that RNA nucleotide bases cannot, even in principle, fold into the numerous three-dimensional shapes needed to catalyze a wide range of reactions like proteins do, thus casting a significant new doubt on the RNA World hypothesis). At most, therefore, any “supporting” data (most of which is in category (ii) above), is really just “consistent with.” Call me a skeptic, but I’ve seen this pattern repeated enough times to not get too excited about the latest OOL “breakthrough.”

    (And this is the lesson from looking at just the “supportive” data and setting aside for a moment all the contrary data, which is extremely formidable.)

    As a live example, I’d be happy to look at whichever one of the papers you pointed to that you think is most supportive of abiogenesis and see if we agree upon what results of the research, if any, are supportive of abiogenesis.

    I would be as excited as anybody with a true breakthrough, and I understand your point that this is an ongoing area of current and future research. At some point, however, we should consider that the 60 years of research already under our belt might actually be telling us something.

  130. Does this mean that you are going to continue to tell me THAT the data supports the hypothesis and that you are never going to tell me, in spite of my multiple inquies, WHY the data supports the hypothesis. .

  131. The scientific method is irrelevant. Science is as science does. Neither abiogenesis nor darwinian evolution are provisional or subject to testing. They are unalterable facts. The rest is the scientific method for all the other stuff.

    Well, being a Brit, I can’t comment on what happens in American schools, but that certainly isn’t true of the way science is mandated to be taught in Britain.

    You can’t teach the scientific method, and then say that some things are exempt. It would be ludicrous, and I can’t imagine that any American science teacher would think differently.

    I think the real problem lies in your comment “…even hint that OOL might not have occurred”. Why should a science department do this? They don’t do it for any other area of science, why should they do it for OOL?

    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. If something is unexplainable, the best you can do is say “we can’t explain this”. And that’s no reason not to continue to try.

    This is why there is a problem with the “Divine Foot” in science – not because scientists are atheists (lots are not) but because you can’t test the supernatural by scientific methods.

    So the only way of making a really persuasive case for ID is to actually test Designer hypotheses, on the working assumption that the Designer(s) was(were) as natural a phenomenon as you or me.

    Gaps in explanatory narratives are bound to shrink, even though they will always exist.

  132. Stephen, you are as capable of reading the papers as I am. In each case, there is a clear background to the hypothesis, a clear statement of the hypothesis, a clear statement as to how the hypothesis was tested, and clear statement of the results.

    If you want to discuss either paper in detail, I suggest you write an OP on the subject. I already posted a fairly detailed post at 16 on the first of the papers. If you read the rest of the paper (which is open access) you will find the part you are looking for. It’s quite technical, and the biochemistry is above my pay grade, but the reasoning is perfectly clear, as it is with the second paper on the list.

    Both are tests of specific hypotheses arising from a broader theory of abiogenesis, and both are supported by the data.

    Which is why they got published. It’s a problem in science that it’s harder to get null results published.

  133. Why should a science department do this? They don’t do it for any other area of science, why should they do it for OOL?

    Are you actually asking why a science curricula should limit its assumptions to those things it can empirically demonstrate? Really?

    Ah, and then there is the blessedly useful strawman; miracles.

    There will be no need to inform students that other causal forces (volition, for instance) have physical entailments that can be examined just as readily as any other physical object, as is regularly done in other scientific disciplines.

    The only price you pay (in order to adorn yourself in the Flag of Scicnce) is to make your assumptions scientifically unfalsifiable – given that they are never forced to submit themselves to a test of adequacy.

    Not such a bad price to pay, is it Liz?

  134. You can’t teach the scientific method, and then say that some things are exempt. It would be ludicrous

    Yet you can teach the scientific method, then violate it with impunity – as long as conclude the approved assumption.

    There’s nothing ludicrous about that, is there?

  135. The reasoning is perfectly clear: a little bit of mud, a stroke or two of lightning and in 10^17 seconds you get a self-conscious biped. A scientific breakthrough indeed.

  136. Elizabeth,

    You can’t teach the scientific method, and then say that some things are exempt. It would be ludicrous, and I can’t imagine that any American science teacher would think differently.

    Again, it’s not what anyone says. It’s the practice.

    Is there an ounce of honesty in teaching students about OOL research and leaving out the detail that no one knows whether abiogenesis is even possible, or that there are significant reasons why it might not be? Of course they should mention it if their purpose is to educate rather than indoctrinate.

    This is why there is a problem with the “Divine Foot” in science – not because scientists are atheists (lots are not) but because you can’t test the supernatural by scientific methods.

    I’m re-reading my own post to see if I mentioned a divine foot or the supernatural. I didn’t.

    So the only way of making a really persuasive case for ID is to actually test Designer hypotheses, on the working assumption that the Designer(s) was(were) as natural a phenomenon as you or me.

    Did ID suddenly incorporate the supernatural while I wasn’t looking? I don’t even want to get into what “natural” is. For the sake of discussion let’s say the designer is either a really smart alien civilization or it’s made of dark matter and Higgs-Boson particles. Are those natural enough?

    Earlier today you made a reasonable case to explain why abiogenesis researchers perform tests without even having an actual hypothesis, in the hope (or belief) that enough results will enable them to piece one together.

    That’s fine, but it sets the bar pretty low. ID is testable. Read about it on this site. What are you looking for?

    Gaps in explanatory narratives are bound to shrink, even though they will always exist.

    I thought they were hypotheses. By what assumption do we know that the gaps will shrink? This is what I mentioned earlier, the unwarranted assumption that the evidence will lead toward a particular conclusion. It’s so pervasive you don’t even notice it or hear yourself expressing it.

  137. Elizabeth: “Gaps in explanatory narratives are bound to shrink, even though they will always exist.”

    Actually, the gaps have grown significantly, rather than shrinking. There is very good reason to think the naturalistic explanatory narratives are simply going down the wrong path altogether.

  138. —Elizabeth: “Stephen, you are as capable of reading the papers as I am. In each case, there is a clear background to the hypothesis, a clear statement of the hypothesis, a clear statement as to how the hypothesis was tested, and clear statement of the results.”

    Yes, I read the report and found that it begins with a number of anti-scientific assumptions, phrased in such equivocal terms as “it is thought.” The middle part is impressive for its rigorous analysis of the implications that might follow from a number of remarkably convenient assumptions.

    However, the most meaningful part is its admirably succint summary: “We conclude that far from representing an evolutionary dead end, MNA could have provided a source of heritable functionality for early organisms.”

    Actually, this exercise is fun because it challenges me to keep asking the same question in different ways until I receive a straight answer. Let’s try it yet another way.

    Please tell me which theory of abiogenesis this conclusion supports and why you think so.

  139. How do you test for ID? Let’s say you have a piece of round stone, how do you test whether it was designed that way or was a product of natural forces?

  140. Yes, I read the report and found that it begins with a number of anti-scientific assumptions, phrased in such equivocal terms as “it is thought.” The middle part is impressive for its rigorous analysis of the implications that might follow from a number of remarkably convenient assumptions.

    Are you reading the first two papers from the link I gave to output from the Szostak lab?

    The only use of the phrase “it is thought” I can find in either paper is in the abstract of the first one (“Whereas all modern cell membranes are composed primarily of diacyl or dialkyl glycerol phospholipids, the first cell membranes are thought to have self-assembled from simple, single-chain lipids synthesized in the environment.”

    References are not usually given in abstracts. However, statement is referenced in the very first two references of the paper, at the end of the first sentence.

    The middle part is impressive for its rigorous analysis of the implications that might follow from a number of remarkably convenient assumptions.

    What “remarkably convenient assumptions”?

    However, the most meaningful part is its admirably succint summary: “We conclude that far from representing an evolutionary dead end, MNA could have provided a source of heritable functionality for early organisms.”

    Right. So they tackled a problem in their theory, and found that it was not, in fact, a problem. Cool. What is your point?

    Actually, this exercise is fun because it challenges me to keep asking the same question in different ways until I receive a straight answer. Let’s try it yet another way.

    Please tell me which theory of abiogenesis this conclusion supports and why you think so.

    The theory being pursued by the Szostak lab. Essentially, the theory is that lipid vesicles were an important component of the process, and that the earliest forms of self-replicating entities were lipid vesicles entrapping self-replicating polymers, circulating in thermal currents.

    The details are on their site.

    StephenB: from my PoV, I have answered your question in detail many times.

    Clearly you think I haven’t.

    Clearly, it follows, there is a communication difficulty. The possibilities, as I see it, are these:

    I have misunderstood your question
    You have misunderstood my answers
    We are somehow starting from very different positions about the nature of scientific enquiry.

    Probably the answer is closest to that last thing. What do you think?

  141. Can you be specific about these growing gaps?

  142. Is there an ounce of honesty in teaching students about OOL research and leaving out the detail that no one knows whether abiogenesis is even possible, or that there are significant reasons why it might not be?

    OOL stands for “the origin of life”. Clearly life had an origin, because we are here! So it’s “possible”, indeed, it must have happened.

    We don’t know how. Maybe it was a miracle. Maybe it was chemistry. By telling students that we don’t have a persuasive chemical theory, we are telling them that we don’t know whether a chemical theory is possible.

    As for “significant reasons why it might not be” – I’m not aware of any, merely of a current lack of a persuasive explanation.

    It would be dishonest to tell students we know how something happened when we don’t. But I’m not aware of any curriculum in which a theory of abiogenesis is given as fact.

    Again, I think we are misconnecting. In fact, we must be, because you say:

    Earlier today you made a reasonable case to explain why abiogenesis researchers perform tests without even having an actual hypothesis, in the hope (or belief) that enough results will enable them to piece one together.

    No, I did not!!!!!

    You can’t perform a hypothesis test without a hypothesis!

    Oh boy.

    The Szostak lab have a broad theory about abiogenesis. The theory has quite a lot of parts, sub theories, if you will. From each of these, testable hypotheses can be derived, and are. Some of the publications on the list on their webste are data papers that report the results of tests of those hypotheses. So gradually, parts of their theory receive support. Others don’t, and have to be rethought.

    Think of it like a detective story – there’s a broad theory, with sub-theories, but alibis that must either be broken, or the theory modified. That’s what the Szostak lab is doing. It may turn out they are barking up the wrong tree completely, and that the answer is the Least Likely Person (a Designer? :))

    But right now, the work seems to be going quite well. Long way to go though.

  143. Yes, there is a great deal ludicrous about it.

    duh.

  144. In my opinion, all these theories will only do science an indirect favour, if at all. They will never be persuasive enough to explain the emergence of life by chance and necessity. These two by themselves are impotent as far as OOL is concerned. But if abiogenesis results in inventing some kind of useful polymer or anything like that, it will be good enough.

  145. They will never be persuasive enough to explain the emergence of life by chance and necessity. These two by themselves are impotent as far as OOL is concerned.

    Why? Seriously, on what do you base that assertion?

    Clearly not on the lack of current persuasive explanations, because that would be assuming your conclusion! And clearly not on the basis life sits on a “functional island”, because that would also be assuming your conclusion!

    So, on what?

  146. Elizabeth,

    I meant to say persuasive enough to me. I assert this based on my Christian faith. I simply do not believe that abiogenesis will ever be proven to have been the case. Apart from this, even scientifically this idea is ridiculous: something all of a sudden started assembling itself. Why, what for?

    You know what Elizabeth. I am so happy I can agree with Pascal who said:

    “There are only three types of people; those who have found God and serve him; those who have not found God and seek him, and those who live not seeking, or finding him. The first are rational and happy; the second unhappy and rational, and the third foolish and unhappy.”

    I wish you to be able to say so, too.

    You see, to me, the objective to prove the world is a meaningless burp of some fatum necessity is futile in all respects: philosophical, scientific, practical. The world has a meaning that shouts at us at every corner. And it takes an enormous amount of effort not to hear it.

    But let them try, maybe they will find out something really useful, as I said, maybe a polymer or some other substance to make outdoor clothes more durable or doormats stronger.

  147. 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.

    Genomes are sophisticated data storage organelles integrated into the cellular and multicellular life cycles of each distinct organism. Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations.

    James Shapiro, (spinning the fact that it is now established beyond any doubt that natural selection acting upon random mutations is incapable of explaining life.)

  148. Chris, I’d like you to be frank here. If you are talking about me, as you appear to be, please support your accusations.

    Alternatively, please stop.

  149. I meant to say persuasive enough to me. I assert this based on my Christian faith.

    That’s fine, and I thank you for your honesty. But in that case we are not talking about science.

  150. It was a general comment (you are not the first, nor will you be the last, to abandon the straight path) but naturally you are the sort of person, Elizabeth, who falls into that category.

    That you disagree in the strongest personal terms, shouldn’t be reinterpreted as an ‘accusation’, I wasn’t ‘accusing’ you of anything.

    The record speaks for itself. Let’s not waste time pretending it doesn’t.

  151. Chris Doyle:

    The record speaks for itself. Let’s not waste time pretending it doesn’t.

    And what about when such records are removed from publication? Does that mean it didn’t happen?

  152. Elizabeth,

    “But in that case we are not talking about science.”

    Yes, we are.

    Modern science has Christian roots, not only because a majority of really outstanding minds in science were believers but in principle.

    1. Science as faith is based on belief. Methodologically, every theory rests on initial assumptions taken for granted. Moreover, science believes in our ability to develop a progressively better understanding of reality (maybe up to a certain point).

    2. We bear an image of God, who created everything. Consequently, we can explore and understand it to a reasonable degree, to be able to use it for our own sakes and for the sake of the world. And secondly, because we bear an image of our Creator, we are responsible for this world (hence our motivation to explore it).

    So my scientific position is in agreement with my faith. When I say something I need not bisect my mind, as if I was wanting to say one thing as an engineer and another as a believer.

  153. What should astound you is that you have forgotten the original claim, made @ 4.1.1.1 and 4.1.1.1, which was that evidence exists to support abiogenesis.

    I am still astounded at you inability to comprehend clear and simple english – let me walk you through it, starting with EL @ 4.1:

    No, it isn’t a “bald-faced lie”. There is plenty of evidence for interdependence, but not for “sudden appearance”.

    You are mistaking lack of evidence for one thing for positive evidence for another. Also complete ignoring what data we do have in support of abiogenesis theories.

    Please don’t assume that people you disagree with are lying.

    Joseph replies in 4.1.1:

    There isn’t any data in support of abiogenesis.

    To which EL replies in 4.1.1.1:

    Yes there is. How do you think abiogenesis labs work if they don’t have data?

    So the conversation starts with EL claiming that there is data “in support of abiogenesis theories”, a point which she repeats time and again, along with references and arguments that back up the claim so when you say:

    Everything which followed was an exercise in reframing the issue so that the original claim would be forgotten.

    you are totally, and demonstrably, wrong.

    You are also making an utter fool of yourself.

  154. Actually, this exercise is fun because it challenges me to keep asking the same question in different ways until I receive a straight answer. Let’s try it yet another way.

    Good grief! I think you are a very confused and conflicted man! EL has provided answers over and over again, all straight, clear and correct. Perhaps you should attempt to understand the conversation you are engaged in, it may move things along.

    Please tell me which theory of abiogenesis this conclusion supports

    ROTFL – Stephen, the people who wrote the conclusion have developed a theory of abiogenesis, so they developed a hypothesis from that theory, did some experiments, got a positive result and published a research paper that explained the hypothesis, their experiment and how it supports their conclusions, and consequently their theory.

    StephenB: “Please explain which theory of relativity Einsteins conclusion supports?”

    DrBot: “That would be the theory of relativity that Einstein has proposed, the same one that he claims his conclusion supports!”

    Like I said ROTFL!

  155. OOL stands for “the origin of life”. Clearly life had an origin, because we are here! So it’s “possible”, indeed, it must have happened.

    I know, I know. That’s why I use the word “abiogenesis” even though it sounds so clunky. I hoped you would follow what I meant rather than seizing on the expression.

  156. Elizabeth,

    It would be dishonest to tell students we know how something happened when we don’t. But I’m not aware of any curriculum in which a theory of abiogenesis is given as fact.

    I’m not aware of any texts that state that explicitly. The claims are more along the lines that scientists believe that life originated from chemicals.

    Now I realize that at this point I’m deviating somewhat from the subject matter and addressing the content of school textbooks. But it raises some relevant questions:

    1) Do scientists believe that? Why, since it’s only a hypothesis?
    2) Why teach students what scientists believe? Isn’t it prejudicial and misleading, especially when it’s omitted that some scientists don’t believe, or believe there’s good reason not to believe?
    3) What misunderstandings do school board members have regarding the scientific method and the current state of research if they approve such misleading content?

    Again, these are just school books. But they are reflections of prevailing scientific thinking. They are an indication that abiogenesis as a hypothesis is lip service to the scientific method. It’s like darwinism. The what is settled, and they’ve moved on the how.

  157. Do you understand what a theory of abiogenesis must explain in model form? Do you understand that it must, indeed, be a model? If you do understand, then [a] articulate the criteria necessary to support a model, [b] explain how this paper meets that standard, [c] identify the model, and [d] tell me why the data supports it.

  158. —Elizabeth: “Essentially, the theory is that lipid vesicles were an important component of the process, and that the earliest forms of self-replicating entities were lipid vesicles entrapping self-replicating polymers, circulating in thermal currents.”

    That statement does not qualify as a theory. A theory of abiogenesis must explain how life comes from non-life in model form.

  159. I don’t think you understand what a theory of abiogenesis entails. Do you labor under the illusion that all scientific hypotheses are theories? Apparently so.

  160. Just a few, off the top of my head:

    - protein-first scenarios (long the preferred approach) have floundered, based on problems of getting a suite of specified proteins formed by chance

    - self-organizational theories have floundered and are now not seriously in contention, based on a realization that emergent systems formed by law-like processes cannot, even in principle, create the kind of functional, specified information found in life

    - RNA World is running into more problems all the time, such as the new recognition that due to the hydrophilic nature of the nucleotides an RNA structure cannot, even in principle, fold into the shapes necessary to carry out a wide range of enzymatic function

    - Some of the early ideas about how easy it would be for life to start on Earth have gone by the wayside; for example, the Miller-Urey experiment, which was heralded in its time as getting us so much closer to an answer, has now been tempered by newer understanding of atmospheric constituents and a growing realization of the intervention needed to even make and maintain biologically relevant molecules

    - Increasing understanding of cellular function and what is required for self-replication has placed far more constraints on what is required, than originally thought

    We could go on and this isn’t just me. OOL researchers, when you catch them in a candid mood, acknowledge the enormity of the problem and that the questions keep arising faster than the answers. I realize that some people have an unbounded hope that some as-yet-undiscovered law will break the horizon soon that will make the problem tractable. Unfortunately, that is an unfounded wish with no basis in reality. A close look at OOL efforts to date brings out the strong lesson that we are *not* getting closer to a naturalistic and materialistic answer for the origin of life. Rather, the efforts shed light on new problems and suggest, for those wiling to see the evidence, that perhaps we are looking in the wrong place altogether.

  161. Elizabeth,

    Chance has been abaondoned by most OOL researchers, who realize that it doesn’t have the required resources to accomplish the necessary task. If you think chance is still a viable alternative, we can get back into the probability calculations.

    Necessity, or law-governed processes, cannot *by definition* create the aperiodic specified information found in the cell, such as a simple protein or strand of DNA.

    Of course there is a cause which is fully capable of generating this kind of specified information, and which we regularly witness doing so. But we shan’t consider that possibility, because it would violate our philosophical sensibilities, right?

  162. Oh golly.

    OK, I’ll be back later to address this. Could you perhaps re-read my posts in the mean time?

  163. As in, there are two known sources of X, A and B. B is routinely observed to produce a certain sub-class X1, and in relevant cases A is not a credible source. Is or is not X1, then a signature of B at work, even though B may be unpalatable?

  164. Of course it must be a model. All theories are models.

    And from a theory you derive testable hypotheses, and you test them against data.

    The Szostak model is clearly described on their lab web page, together with sub-theories, and hypotheses derived from those sub theories, and papers reporting tests of those hypotheses.

    Some of the specific sub-theories and hypotheses that go to make the model are shown in these movies:

    http://genetics.mgh.harvard.ed.....ovies.html
    http://exploringorigins.org/

    Clearly, any theory that explains how cells emerged from non-replicating molecules is going to have a series of stages, and the each of these postulated stages raises hypotheses that need to be tested.

    The theory is nicely animated in this youtube video:

    http://www.youtube.com/watch?v=U6QYDdgP9eg

    From which you will see that there are a lot of details to be filled in and tested. Some parts of the postulated process may turn out not to work, and the the theory modified. The top two papers on that list test, respectively, a hypothesised solution to the polymer backbone problem, and a hypothesised solution to the problem of how phospholipid vesicles might have evolved from simple lipid vesicles.

    But of course there are many more problems to solve.

  165. —Elizabeth: “StephenB: from my PoV, I have answered your question in detail many times.

    Clearly you think I haven’t.”

    I was simply asking you to articulate that this is an attempted partial defense of the RNA World Hypothesis (It does have a name, after all) so that we can examine its weakness from a paradigmatic perspective, since the study itself ignores the mean weakness of the theory.

    Stephen Meyer says it best:

    “Ribozyme engineers tend to overlook the role that their own intelligence has played in enhancing the functional capacities of their RNA catalysts. …

    RNA-world advocates envision ligases evolving via undirected processes into RNA polymerases that can replicate themselves from freestanding bases, thereby establishing the conditions for the beginning of natural selection. In other words, these experiments attempt to simulate a transition that, according to the RNA-world hypothesis, would have taken place before natural selection had begun to operate. Yet in order to improve the function of the ligase molecules, the experiments actually simulate what natural selection does. … But what could have accomplished these tasks before the first replicator molecule had evolved? Szostak and his colleagues do not say. They certainly cannot say that natural selection played this role, since the origin of natural selection as a process depends on the prior origin of the self-replicating molecule that Szostak and his colleagues are working so hard to design. … [E]ngineers perform a role in simulating natural selection that undirected natural processes cannot play prior to the commencement of natural selection.”

    Do you see the problem?

  166. Sorry! But there is an important point here. We know that life exists now; we know at one time it didn’t. So at somem point, life emerged from non-life – aka “abiogenesis”. What alternative are you proposing to “chemistry” of some sort of another?

    Surely even if you postulate a designer, that designer must have assembled chemicals? Unless you are really are talking about a miracle, but Upright BiPed has just called that a “straw man”.

  167. Elizabeth,

    Now we’re playing word games. Give me a word for ‘spontaneous, undirected self-assembly of life’ and I’ll use it. I just don’t want to type all that several times in one post.

  168. BTW, are you suggesting that abiogenesis researchers are hypothesizing that life was deliberately created? I didn’t see that in any of those papers. I think ‘abiogenesis’ is the right word and there’s no need to split hairs over it.

  169. Why is “a miracle” a straw man? I thought that one problem with science was supposed to be its “a priori commitment to materialism”? That it cannot allow a “Divine Foot in the door”?

    If you do not hold this view, great, but there seems to be a fair bit of it about.

    And no, I don’t think a science curriculum should “limit its assumption to those things it can empirically demonstrate”. It’s not what I said, and not what I meant.

    And of course volition has “physical entailments that can be examined just as readily as any other physical object”. Again, I didn’t say it didn’t. But volition doesn’t have “physical entailments” unless it is coupled to some motor system. Unless we are talking about miracles. Which you say is a straw man.

    So, to regroup: We know OOL/abiogenesis “occurred” in the sense that we know that there is life now, and there once wasn’t. So we know that at some point, life emerged from non-life. Whether some volitional agent guided them into the right molecules or not makes no difference to the question as to whether it occurred. What we don’t know is how it occurred.

    And we have absolutely no evidence of any volitional agent that might have done so (barring a miraculous agent, and even there, the only evidence is negative i.e. dearth of non-miraculous explanation) whereas we do have some evidence in support of some non-volitional theories, such as Szostak’s.

    Not sure what you are getting at with your apparent jibe about unfalsifiable assumptions. Perhaps you’d like to clarify.

  170. No, I’m not playing word games. I’m trying to figure out what you mean. That means figuring out what the words mean.

    But if the key concept here is “undirected”, fair enough. Now I understand. You are saying that we should tell students that it’s possible that the assembly of life was “directed”?

    The trouble there, Scott, as I see it, is that unless we are postulating a miraculous director (or “supernatural” if you prefer) then there is no reason to posit such a thing, because there is absolutely no evidence of any director, nor of any forces that the director might have used to do the assembling.

    This, as I see it, is the most profound problem with ID. Either you posit a supernatural designer, in which case, there are no tests we can use to generate positive evidence for such a hypothesis, or you posit a natural designer, in which case, the hypothesis has no evidence to support it, whereas at least some “undirected” hypotheses do.

    Unless your position is that the supernatural designer simply designed the universe so that life would inevitably emerge from non-life (“frontloading”, if you will, but not at the OOL, stage, but the Big Bang stage), but in that case we should be able to work out the physics and chemistry of the process just as we can work out the physics and chemistry of the rest of the phenomena we observe in the universe.

  171. Well, clearly we are not understanding each other.

    I suggest you explain exactly what you think a theory of abiogenesis entails, then we might understand better what you are asking of us.

    Because clearly right now we are at an impasse.

  172. It was a general comment (you are not the first, nor will you be the last, to abandon the straight path) but naturally you are the sort of person, Elizabeth, who falls into that category.

    That you disagree in the strongest personal terms, shouldn’t be reinterpreted as an ‘accusation’, I wasn’t ‘accusing’ you of anything.

    The record speaks for itself. Let’s not waste time pretending it doesn’t.

    I cannot parse this. You say you were not “accusing” me of anything. Yet you talk about my being the “sort of person” who “abandon[s] the straight path” and that “the record speaks for itself”.

    What on earth are you talking about?

    It appears I have offended you in some way, and I have no clue why. Yet when I ask for clarification, you imply further accusations, yet decline to give any details.

    I’m afraid I find this intolerable. Please call a spade a spade and tell me what I am supposed to have done wrong, with links, preferably. Otherwise, please retract your insinuations.

    Thanks.

  173. Elizabeth: “The trouble there, Scott, as I see it, is that unless we are postulating a miraculous director (or “supernatural” if you prefer) then there is no reason to posit such a thing, because there is absolutely no evidence of any director, nor of any forces that the director might have used to do the assembling.

    This, as I see it, is the most profound problem with ID. Either you posit a supernatural designer, in which case, there are no tests we can use to generate positive evidence for such a hypothesis, or you posit a natural designer, in which case, the hypothesis has no evidence to support it, whereas at least some “undirected” hypotheses do.”

    Elizabeth, get real. You are the one who is happy to count vague, mildly relevant, wildly speculative observations as “evidence” for abiogenesis, but then you turn around and say there is “no evidence” to support design? Please. At least be somewhat intellectually equal in your treatment of competing hypotheses.

    Also, as to no evidence for design, you’ve got to be kidding. Surely it counts as “evidence” that every time, without exception, when we see complex specified information arise and are able to ascertain the cause, it always, without exception, turns out to be intelligence. Couple that with the fact that in no instance has undirected chance or law ever, not once, been observed to create complex specified information.

    Look, we understand you have a philosophical hangup with the idea of life being designed, but let’s at least acknowledge your issue for what it is. It isn’t a problem with the evidence. Shoot even folks like Dawkins acknowledge that life looks designed. It is the evolution camp which is trying mightily (and so far, futily) to muster evidence that the design so apparent in life is just an illusion.

  174. OK, here goes:

    Elizabeth,

    Chance has been abaondoned by most OOL researchers, who realize that it doesn’t have the required resources to accomplish the necessary task. If you think chance is still a viable alternative, we can get back into the probability calculations.

    For a start, pace Monod, I don’t think it’s terribly helpful to consider “Chance” and “Necessity” as discrete categories. Rather, there is a continuum of contingency. If we take, hypothetically, a deterministic universe (one without quantum uncertainty), an initial configuration will lead to final state with 100% certainty, however complex that final state is, and however haphazard the events might seem to an inhabitant of that universe. However, within that universe, some events will appear to obey laws of “necessity” (things reliably fall to earth; things keep moving in a straight line at constant velocity unless acted on by a force), i.e. you can predict with near 100% certainty what will happen, whereas other things will only be predictable probabilistically (meteors will strike the earth; earthquakes will occur) and “chance” will appear to determine what damage is done to what. However, because the universe is deterministic, all these things are the result of “necessity”. Re-run the universe from its starting conditions, and you will necessarily get the same result.

    In other words, in a deterministic universe, there is a sense in which “chance” does not exist (everything that happens “necessarily” happens) and also a sense in which it does (some things are highly predictable, given relatively little data; other things are highly unpredictable, even given a great deal of data). And things aren’t that different in an non-deterministic universe such as the one we seem to have. Some things are highly predictable; other things are highly unpredictable.

    So it doesn’t make a lot of sense to me to talk about Chance as something different from “Necessity” unless we are very clear about what we mean.

    Now, most scientific models of phenomena are stochastic, in other words they allow for events that are unpredictable in specifics, but predictable statistically. In other words, rather than modelling laws of “necessity”, the models incorporate probability distribution functions. So in that sense, most models are “Chance” models, i.e. stochastic models. And, indeed, all the OOL models I know of are stochastic. So “Chance” has not been “abandoned” by OOL researchers in that sense.

    However, Chance has been “abandoned” by OOL (if it was ever current) in the sense that fully-fledged modern-type-celluar life emerged from non-life by chance assembly of the right atoms and molecules by (remembering Disney) a lightning strike in a mud puddle. Which is why I have made the point, repeatedly, on this thread, that probability calculations that show that this could not have happened are straw men. Nobody thinks that. It has, as you rightly say, been “abandoned”. Which is why it is odd that that “universal probability bound” keeps being produced.

    Nobody in science, that I know of, is arguing that modern-type cells emerged as a Vastly Improbable fluke. What OOL researchers, and indeed evolutionary biologists argue is that there are mechanisms that render such a fluke unnecessary. The Darwinian mechanism is one such. The Szostak lab (and others) are investigating additional possibilities.

    Necessity, or law-governed processes, cannot *by definition* create the aperiodic specified information found in the cell, such as a simple protein or strand of DNA.

    Well, it depends on that definition! But I can’t right now think of a definition that would make your statement true, and certainly not if we include stochastic processes.

    Of course there is a cause which is fully capable of generating this kind of specified information, and which we regularly witness doing so. But we shan’t consider that possibility, because it would violate our philosophical sensibilities, right?

    Well, if you mean volitional agents, sure. That wouldn’t violate my philosophical sensibilities at all. But where is the evidence for a volitional agent 3.5 billion or so years ago? The only ones we know of are biological, and you can’t invoke a biological agent as the cause of biological agents!

  175. Well, it is “in model form”. Did you look at that youtube video? It explains the model in substantial detail.

  176. Well, I can see Meyer’s problem! He doesn’t seem to have read Szostak’s papers, including the first two on that list!

    He seems to think, bizarrely, that natural selection can only operate once “RNA world” exists. This is completely false. Natural selection can, and will, operate wherever something self-replicates with heritable variance in the reproductive success, and a key element of Szotak’s theory is, as I said, lipid vesicles (which self-replicate, but without heritable variance reproductive success) that are permeable enough to allow entry of monomers that assemble into polymers that then cannot escape, and which self-replicate, the cycle being driven, not by an enzyme, but by a thermocline. As a result, the lipid vesicles grow and divide, retaining their contents, which include copies of those polymers. The polymer contents vary, and that is the variance that results in variance in reproductive success, because some polymer sequences will promote division/replication.

    It’s all in that video, but you’d have to read the science papers to get the details.

    But the Whole Point of the Szostak model is that competition between variants of self-replicating entites (aka “natural selection”) sets in very early, long before you’ve got anything as fancy as an enzyme.

    Meyer seems to have missed this point, and accuses Szostak of circularity when there is no such circularity! That seems to be Meyer’s problem generally – he keeps posing “chicken or egg first?” conundrums, forgetting, apparently, the concept of “bootstrapping”. Or, at best, forgetting that the concept of natural selection is extremely simple, and almost a truism: that if things self-replicate with heritable variance in reproductive success, variants that reproduce better, will become more prevalent.

  177. I find this post difficult to make sense of.

    Clearly it is true that much modern science has Christian roots, in the sense that many great scientists were Christian by culture, and probably faith (although by no means all – some has Islamic roots, for instance, and of course pagan roots). But correlation is not causality, and you could equally argue that modern science has its roots in an empiricism that challenged faith, Galileo being the poster child.

    And I would profoundly disagree that science is “based on belief”. Yes, science proceeds by resting on a priori assumption, but an assumption, or premise, is not a “belief”. All scientific assumptions are that – mere assumptions, and the assumptions can, and are, questioned. That’s how Einstein overturned Newton – by challenging the “assumption” that the universe was Euclidean. As for “science believes in our ability to develop a progressively better understanding of reality” – well, maybe so, but that isn’t an a priori belief. And sometimes, in science, find that reality is more mysterious than we thought, not less. Although I guess that’s progress of a kind :)

    But most importantly, I don’t actually understand your main point. You say that the you considered that “chance and necessity…by themselves are impotent as far as OOL is concerned” based on your Christian faith.

    The reason I said that that means we are not talking about science is that you are basing your position on a non-negotiable premise. So any argument for your position based on that premise will be circular.

    This is quite different to scientific assumptions, which are always provisional, and always subject to potential falsification.

  178. Elizabeth,

    I’m not saying we teach students that perhaps it was designed. I’m saying that we teach them that we don’t know whether it could have originated by itself. That’s a very accurate statement, and by omitting it students are misled to think otherwise. If it’s not worth teaching accurately then it’s not worth teaching at all.

    unless we are postulating a miraculous director (or “supernatural” if you prefer) then there is no reason to posit such a thing, because there is absolutely no evidence of any director

    There is no evidence except for all of this stuff which bears more resemblance to things which were designed than to those which were not. Or we can rule that out because there’s a set of hypotheses that suggest there may be support for an idea that hasn’t been quite clarified implying that perhaps such things can appear on their own. And, oh yes, we’re making progress.

    But if we turn a blind eye to that evidence then the whole charade is over. It’s willful ignorance, like when a man sees the signs that his wife is cheating but he tunes them out. It’s not about our intellect or reason or education. It’s about filtering out what we prefer not to know.

    As Friedrich Schiller said, against it the gods themselves contend in vain.

  179. Thanks, Elizabeth, for your detailed response.

    “However, Chance has been “abandoned” by OOL (if it was ever current) in the sense that fully-fledged modern-type-celluar life emerged from non-life by chance assembly of the right atoms and molecules by (remembering Disney) a lightning strike in a mud puddle. Which is why I have made the point, repeatedly, on this thread, that probability calculations that show that this could not have happened are straw men. Nobody thinks that. It has, as you rightly say, been “abandoned”. Which is why it is odd that that “universal probability bound” keeps being produced.”

    No, probability calculations are not a straw man, for two reasons. First, the probability calculations are still very relevant to the various constituent parts. Even if no-one thinks that a “modern-type-cellular life” cell emerged all at once, the models invariably still rely on an assemblage of parts, whether we are dealing with a DNA-first, proteins-first, RNA first, or whatever model. The probability bound is absolutely relevant to forming, for example, a single protein of modest length. Second, absent a law-like process (whether stochastic or absolute) that can account for the assemblage of the various parts, the probability calculations are still relevant for the subsequent assemblage.

    “Nobody in science, that I know of, is arguing that modern-type cells emerged as a Vastly Improbable fluke. What OOL researchers, and indeed evolutionary biologists argue is that there are mechanisms that render such a fluke unnecessary. The Darwinian mechanism is one such.”

    Well, the Darwinian mechanism certainly isn’t applicable to the formation of the first self-replicating molecule, which is the holy grail of OOL research right now. It is also doubtful it would get us very far after self-replication, but I’m willing to leave that off the table now as a separate issue.

    “Well, it depends on that definition [of necessity]! But I can’t right now think of a definition that would make your statement true, and certainly not if we include stochastic processes.”

    There isn’t a reasonable definition that would make my statement untrue. Law-like processes, whether absolute or stochastic, simply do not create aperiodic complex specified information. Let’s get away from generalities and look at a specific example. Suppose we’re trying to get a functional RNA strand formed in the RNA World scenario (same principle applies with amino acids in a protein-first model). If we have an absolute chemical law that says, for example, C always attaches to G, then we end up with a largely repeating chain like a crystal that does not convey any information. I take it you agree with this. However, even with a stochastic process, for example C attaches to G with 70% probability, we might end up with a more complex pattern, but we still do not get the aperiodicity required, because all we get is a slightly-expanded stochastic pattern of repeating nucleotides; and we certainly don’t get the required specificity from a stochastic process itself. For that, we would have to fall back on pure luck, or chance. The concept of law-like processes operating at the chemical level, whether absolute or stochastic, is simply anathema to the creation of aperiodic specified information. This is a very well-understood principle in information theory.

    “But where is the evidence for a volitional agent 3.5 billion or so years ago?”

    Um, Elizabeth, that is the whole point of the inquiry. We have a complex information-rich system, which, based on our uniform and repeated experience and our current understanding of the cause and effect processes in the world, always and only comes from an intelligent agent. That is the evidence. You can’t avoid it by appealing to a circular statement: “we don’t know x, therefore we can’t consider x and can never come to a conclusion of x until we know x.” Historical sciences are in the business of identifying past causes, which, until identified, are not known. It is singularly unhelpful to say that we can’t consider something as a possible cause until we know that it was the cause.

  180. The chicken/egg syndrome refers to the question of which came first, the DNA that makes proteins or the proteins capable of replicating DNA. Hence, we have the RNA first hypothesis. You seem to be attributing the chicken/egg problem to natural selection, but there is no chicken/egg problem associated with that process because natural selection obviously cannot, under any circumstances, come first. According to the RNA world hypothesis, a self replicating system or self replicating molecule must evolve before prebiotic natural selection can come into play.

    That brings us to a key (though, by no means, the only) irony inherent in the RNA world hypothesis. Ribozyme engineering does not do what it claims to do–it does not simulate undirected chemical evolution. Every phase of the process is intelligently designed–modifying sequences of naturally occurring RNA catalysts, simulating natural selection in order to produce ribozymes with increased functional capacities, isolating molecules that perform particular functions, or selecting the most functional molecules—its all being directed in the name of undirected evolution. Any success these engineers enjoy in the lab indicates the need for an intelligent agent.

  181. I’m not saying we teach students that perhaps it was designed. I’m saying that we teach them that we don’t know whether it could have originated by itself. That’s a very accurate statement, and by omitting it students are misled to think otherwise. If it’s not worth teaching accurately then it’s not worth teaching at all.

    If “perhaps it was designed” isn’t the same as “we don’t know whether it could have originated by itself”, can you give an alternative scenario to “designed” that covers “[did not] originate by itself”?

    If not, then the two statements are equivalent!

    There is no evidence except for all of this stuff which bears more resemblance to things which were designed than to those which were not. Or we can rule that out because there’s a set of hypotheses that suggest there may be support for an idea that hasn’t been quite clarified implying that perhaps such things can appear on their own. And, oh yes, we’re making progress.

    Well, interestingly, despite protestations by many pro-evolution people (including that otherwise excellent youtube video about the Szostak hypothesis), most of what OOL researcher do is push back the start time and form of Darwinian-capable entities (hey, we are finally talking about the OP!) to find out just how simple the remote ancestors of the LUCA could have been.

    Because we know (well, I know this is disputed here, but I am more than willing to defend it) that Darwinian processes are “self-design” processes, and that once you have a Darwinian-capable entity, i.e. a population of self-replicators that replicate with heritable variance in reproductive success, you will get adaptation, i.e. “design”, in the small-d sense of the evolution of an entity optimised to survive/persist within itsl environment.

    So your characterisation of the Szostak theory as “a set of hypotheses that suggest there may be support for an idea that hasn’t been quite clarified implying that perhaps such things can appear on their own” is a cariacature (yes I know it was meant as one!) that really doesn’t work. We know Darwinian evolution is an optimisation mechanism, and rather than the equivocatable work “design” (which can describe both an optimised entity, that need not have been intentionally designed, and the process of intentionally designing something), and the Szostak theory, though it my turn out to be the wrong approach, is, like all OOL theories, a theory as to how very very simple early proto-life forms could have had Darwinian capability.

    And so the hypotheses that it generates are all about whether various attributes of later forms (such as phospholipid membranes) could have provided reproductive advantage when things were much simpler (simple lipid membranes).

    And those are tested in those papers. The membrane paper is particularly important, because without an account of how highly permeable simple-lipid vesicles could have evolved into much less permeable phospholipid cell membranes, the theory pretty well fails. And the beauty of the vesicle story is that there is good evidence that lipids were present on early earth, and that they self-replicate, retaining their contents. Being permeable, if their environment included nucleotides, that would mean that the contents included polymerisable nucleotides, which, of course, are potentially self-replicating.

  182. Elizabeth,

    In response to my statement:

    I’m not saying we teach students that perhaps it was designed. I’m saying that we teach them that we don’t know whether it could have originated by itself.

    You say,

    If “perhaps it was designed” isn’t the same as “we don’t know whether it could have originated by itself”, can you give an alternative scenario to “designed” that covers “[did not] originate by itself”?

    You’re overlooking the fact that my statement – “we don’t know whether it could have originated by itself” – is correct, and that any attempt to mitigate that uncertainty would be misleading. One doesn’t need to follow the logic, only to look at the conclusion. If the end result is that a misleading statement is preferable to an accurate one then either the logic is flawed or the the goal is something other than education.

  183. Dear Elizabeth,

    Again and again, we are not postulating anything of this sort. The picture is clear. We have evidence that suggests that systems exhibiting complex enough organisation cannot be generated by chance and/or necessity. Full stop. Up until today, there has been no evidence whatsoever of genuinely self-organising systems (not to be confused with self-ordering).

    So all we can do is based on massive evidence of a strong correlation between intelligent agency and information complexity, we can by induction hypothesise that ID does not contradict theistic world views. Of course, we are unable to test this hypothesis but it is in principle falsifiable provided enough unambiguous counter-ID evidence.

    Science cannot go any further, so the mystery of Creation is duly revered and the principles of science stay where they should.

    But in contrast to Darwinistic hypothesising, the ID based OOL hypothesis is well grounded.

  184. Elizabeth,

    Yes, science is based on belief. First of all, by engaging yourself into science you believe that the outcome of your activity may be sensical and useful. Otherwise, being a scientist would be a bizarre thing.

    More importantly, each theory rests upon axioms. True, a richer theory may question the initial axioms but only by introducing more axioms. A classic example is Lobachevsky and Eucledian geometries.

    Your interpretation of Einstein overturning Newton I find strange. Einstein extended the Newtonian model, so the Newtonian mechanics became a special case of the more generic model. No overturning occured.

    Circular argumentation is a logical flaw that people may have irrespective of their religious beliefs. I just wanted to say that abiogenesis makes no sense to me in all respects, scientific included.

    How can something that does not exist yet start all of a sudden assembling itself? Give us at least one real life example of self-organisation. I also said that if such a thing had been possible in the past, chances are it would have been possible today unless we give a credible explanation of why it is the other way around.

    Without these things, it is not a science but alchemy or attempts to breed a homunculus.

  185. Elizabeth,

    There aren’t any self-replicating polymers nor monomers.

    Not only that there still isn’t any evidence that living organisms are reducible to their chemical components.

  186. Elizabeth, I don’t disagree that what you’ve referred us to is a model, but there are several things that jump out at me with a quick look.

    - the model is pretty vague in several areas; not necessarily a problem as a first effort, but as you mention, there are *lots* of details to fill in

    - the model is largely a non-starter from the outset for several other reasons:

    - it is not at all clear that the monomers will join up in nice chains as depicted in the video; specifically, if the monomers can join either on side-bonds or opposing-bonds, which is indeed required for the later copying to work, there is no reason to expect a nice chain to form – more likely a jumbled mess

    - similar problem when trying to replicate; even if the chain/clump gets broken apart with heat, there is no way to avoid interferring cross-reactions and a jumbled mess with new monomers coming into the scene

    - then there is the unlikely repetitive heat, cool, heat, cool cycle that would be required for the copying to even function

    - it doesn’t appear that the vesicles replicate (unless I missed something in the model), the idea being simply that the vesicles simply grow bigger until, presumably, they either stop growing or burst spilling their contents

    - assuming the vesicles are meant just to be a temporary housing to get the first self-replicating molecule to form, which I assume must be the idea with the vesicles, there is no reason why, chemically, a vesicle with more monomers and growing polymers would be favored over one without; there is no “selection” going on in any sense — just a growing glob of monomers

    - finally, and most importantly, even if the model succeeds in showing how the monomers create nice chains of polymers and how those chains are faithfully replicated (which is exceedingly doubtful, given the above considerations and probably a dozen others if we were to examine it in more detail), the central problem remains: where does the elusive information-rich molecule ultimately come from? The model doesn’t have any capability of generating a functional polymer that can actually do any work. Thus, the model is relying on pure chemical chance to come up with a functional chain of nucleotides. (So I take back my statement that OOL researchers have rejected chance, at least in the sense of the component parts! :))

    And then there was the gratuitous anti-religious stuff at the beginning of the youtube video, which you presumably do not endorse.

  187. Well, Elizabeth, you are misunderstanding Meyer’s point, and also *way* overselling Szostak’s model, which has many, likely unsurmountable problems (see my comment above from a few minutes ago in response to video you referred us to).

    BTW, thanks for acknowledging in passing that natural selection is a “truism”. We could have a lot of fun with that point, but it is OT for this thread. :)

  188. Hi Elizabeth,

    You might find the following papers useful:

    http://www.evolutionnews.org/2.....49621.html
    http://www.evolutionnews.org/2.....49871.html

    Incidentally, have you ever thought of contacting Dr. Stephen Meyer? I know he’s busy, but I think he would probably respond to you, given your background.

    http://www.stephencmeyer.org/contact.php

  189. As I’ve said several times that Szostak’s model could turn out to be completely wrong, I’m not sure that “overselling” is the apt term!

    And yes, natural selection is a truism. Which is why it’s so weird that people think it doesn’t work. It pretty well has to work: if things self-replicate with heritable variance in reproductive success, the variants that replicate best will become more prevalent.

    It’s hard to see how anyone could argue with it!

  190. it is not at all clear that the monomers will join up in nice chains as depicted in the video; specifically, if the monomers can join either on side-bonds or opposing-bonds, which is indeed required for the later copying to work, there is no reason to expect a nice chain to form – more likely a jumbled mess

    Depends on the monomer. This is chemistry. Polymers form. This is testable, and subject to testing.

    - similar problem when trying to replicate; even if the chain/clump gets broken apart with heat, there is no way to avoid interferring cross-reactions and a jumbled mess with new monomers coming into the scene

    How do you know? Again, this is exactly the sort of question with empirical answers

    - then there is the unlikely repetitive heat, cool, heat, cool cycle that would be required for the copying to even function

    Why is a convection current unlikely? Have you never seen

    - it doesn’t appear that the vesicles replicate (unless I missed something in the model), the idea being simply that the vesicles simply grow bigger until, presumably, they either stop growing or burst spilling their contents

    Yes, you missed something. The vesicles grow, and when they grow they elongate. When they divide the don’t spill their contents. I’m not sure which video shows this, but at least one of them does. Again, this is based on empirical evidence.

    - assuming the vesicles are meant just to be a temporary housing to get the first self-replicating molecule to form, which I assume must be the idea with the vesicles, there is no reason why, chemically, a vesicle with more monomers and growing polymers would be favored over one without; there is no “selection” going on in any sense — just a growing glob of monomers

    No, the vesicles are not “meant just to be a temporary housing”. They are the antecedents of cell membranes. One of the two top articles on that page reports an experiment that demonstrates how early simple lipid vesicles could evolve into tougher phospholipid membranes.

    - finally, and most importantly, even if the model succeeds in showing how the monomers create nice chains of polymers and how those chains are faithfully replicated (which is exceedingly doubtful, given the above considerations and probably a dozen others if we were to examine it in more detail), the central problem remains: where does the elusive information-rich molecule ultimately come from?

    From the above processes!!!! It tells you quite specifically! And the “information” comes from the environment, as is the case with all Darwinian systems.

    The model doesn’t have any capability of generating a functional polymer that can actually do any work. Thus, the model is relying on pure chemical chance to come up with a functional chain of nucleotides. (So I take back my statement that OOL researchers have rejected chance, at least in the sense of the component parts! :) )

    No, the polymer does work. In the early stages, all it does is increase the chance the vesicle will grow, later it does more.

    And then there was the gratuitous anti-religious stuff at the beginning of the youtube video, which you presumably do not endorse.

    Yes, that was annoying. Although it did itemise some wrong ideas. Unfortunately it also peddled a canard – that abiogenesis isn’t Darwinian evolution. The whole point of the Szostak model is that it pushes back the first Darwinian-capable entity to much earlier than we’d normally call “life”. There really isn’t a hard-and-fast dividing line between the two, or rather, the threshold is self-replication. The simpler the entity that can self-replicated with heritable variance in reproductive success, the more likely it is to have arisen “by chance” and got the Darwinian engine going.

  191. oops “have you never seen” should have ended “a lava lamp?”

  192. 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.

  193. 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?

  194. “…later it does more”

    lol

  195. 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.

  196. 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?

  197. 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?

  198. 198

    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.

  199. 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.

    /soapbox

  200. 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.

  201. 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.

  202. 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.

  203. 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.

  204. 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.

  205. 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.

  206. Dear Elizabeth,

    Sorry for the unintentional double post. My concern was to sound as friendly as possible :)

  207. 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.

  208. 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.

  209. 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.

  210. 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?

  211. 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.

  212. 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.

  213. 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…

  214. 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.

  215. 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/ar.....e-lab.html

    And here’s another interesting report:

    http://www.newscientist.com/ar.....plica.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.

  216. 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!)

  217. 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.....y-14433403

  218. 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.

  219. Elizabeth,

    There isn’t any evidence for a self-replicating polymer arising via Darwinian processes.

    Self-replication is your downfall…

  220. 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.

  221. 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.

  222. 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)?

  223. 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.

  224. 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 replicators

  225. 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.

  226. 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.

  227. Yes, to both of those. Neither is inconsistent with what I said.

  228. 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.

  229. 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 :)

  230. vesical=vesicle

  231. 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 TKI

  232. 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.

  233. 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.

  234. The real challenge of OOL researchers is for them to have enough moral strength to acknowledge that their ultimate aim is scientifically ungrounded.

  235. 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. :D

  236. 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?

  237. 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.

  238. 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.full

  239. 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.

  240. 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.

  241. 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.

  242. 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.full

  243. 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).

  244. 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.

  245. 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.

  246. 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.

  247. 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?

  248. 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.

  249. 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.

  250. 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.

  251. 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?

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