Intelligent Design

How Darwinian Logic Works

Spread the love

In this post we discover: According to Darwinian theory, new species emerge when mutations produce individuals who can outperform the stock they came from…

This statement, and so many like them, reveal how Darwinian “logic” is based primarily upon hyper-imaginative speculation, and not anything that could be described as science. Here’s how Darwinian logic works:

Given #1: A certain feature of a living system exists. (Let’s try a trivial example, like Mozart’s ability to write symphonies.)
Given #2: Since this feature exists, it must have a survival advantage.
Given #3: Since it is known (scientifically) that Darwinian mechanisms can explain everything about the history of life, there must have been a gradual pathway such that random mutations and natural selection could turn a microbe into Mozart. How could this not be obvious?

The ID proponent challenges the Darwinist with some obvious questions:

Which random mutations would be required to turn a microbe into Mozart? How long would this take? What is the probability that these beneficial mutations could take place, and what is the probability that they could be fixed in the population with the available reproductive and probabilistic resources? What about the fact that the simplest living cell is the most sophisticated and functionally-integrated information-processing system ever discovered?

The universal and entirely predictable Darwinist response to such challenges:

Are you a religious fanatic who wants to destroy science?

148 Replies to “How Darwinian Logic Works

  1. 1
    Neil Rickert says:

    Given #2: Since this feature exists, it must have a survival advantage.

    I sometimes wonder whether some evolutionary psychologists think that. As far as I know, most evolutionary biologists would disagree.

  2. 2
    Petrushka says:

    I can’t think of a movie that got anything about evolution right. Certainly not the X-Men.

  3. 3

    Neil, I think you’re correct that the wildest stories come from the evolutionary psychologists. But are you saying that evolutionary biologists would generally disagree that particular features have a survival advantage?

    So would they say, for example, that wings, hearts, lungs, eyes, brains, didn’t arise because they conferred a survival advantage?

  4. 4
    markf says:

    I think most biologists would say that #2 is not always true.  Some features may be neutral or mildly disadvantageous.  Nevertheless it is clearly true that it makes sense in biology to ask of any feature “what does it do for the this organism?” – bearing in mind the answer might be “nothing much”.

    But surely even the most ardent IDist agrees with #1 and probably agrees with #2 even more than a biologist.  So the dispute is about #3 – what is the best explanation.  The biologist is challenged to give detail about an evolutionary explanation and does so to greater or less extent depending on the data available (and often changes the detail in the light of data).  The IDist says “you can’t challenge me to provide detail because ID is not about how it happened”.

  5. 5
    wd400 says:

    Probably a good to not get your evolutionary biology from people that oppose evolution


    According to Darwinian theory, new species emerge when mutations produce individuals who can outperform the stock they came from

    Nope. (That’s actually adaptation)

    Since this feature exists, it must have a survival advantage.

    Nope. That’s the kind of hyper-adaptationism that hyper-adaptationists laught at.

  6. 6
    wd400 says:

    err.. “Probably not a good idea to get your…”

  7. 7
    gpuccio says:

    Mark:

    #2 could be re-written, for all darwinists to accept it, this way:

    Given #2: Since this feature exists, it must have originated thorugh ramdom events plus natural selection of a survival advantage.

    I would definitely say that I don’t agree with #2, however stated. Mozart’s genius exists bevause it was intentionally designed, not because it gives a survival advantage, not because it is neutral. It is an intelligent feature whose purpose is to express some potentialities of consciousness.

    But you are right, the main dispute is about #3. And obviously, I absolutely dispute the way you represent the dispute 🙂

  8. 8
    gpuccio says:

    wd400:

    Could you please, being probably a moderate adaptationist, explain what is in your opinion the general mechanism by which new complex information (such as a new basic protein domain) emerges, according to darwinian theory?

    You see, I am taking your counsel. I am trying to get my darwinian nonsense directly from a darwinist…

  9. 9
    markf says:

    I didn’t think of Mozart’s genius as a feature as it would be the result of combination of nature and nuture. But let is put it this way – I doubt there is much disagreement in practice between IDists and biologists over whether a particular feature has a survival advantage (not that #2 does not say whether a particular feature arose because it had a survival advantage).

    Is it not true that IDists do not attempt to provide any detail whatsoever about how features evolved? And indeed resist any such attempt as being beyond the scope of ID?

  10. 10
    gpuccio says:

    Mark:

    No. I have discussed those things openly and in detail, even with you, I believe.

    There is often this misunderstanding.

    a) It is true that the details about inplementation of design are not required for the procedure of design detection, as it is outlined in ID.

    b) It is perfectly true, however, that details of design implementation can certainly be the object of scientific research, once ID is accepted as best explanation, or at least as possible explanation.

    Maybe some IDists prefer not to deal with the second point. I have no problems about that, and I have openly discussed possible mechanisms that can in principle be recognized from observed facts in natural history.

    I maintain, however, like all IDists, that the design inference needs not the details about design implementation.

  11. 11
    Eugene S says:

    GPuccio,

    “I have openly discussed possible mechanisms that can in principle be recognized from observed facts in natural history”.

    Could you point me to the discussion. I have been wondering about the question of ID entailments lately. So that discussion would be of help. Thanks.

  12. 12
    Eugene S says:

    Is it possible to get it right even between two evolutionary biologists?

  13. 13
    markf says:

    Gpuccio

    You are one of the few IDists that has openly discussed possible mechanisms but these are only a few informal conjectures at very high level. I don’t think you mention any specific transition – not even at the phylum level (most IDists would refuse to go even that far).

    Contrast that with the detailed hypotheses that are proposed (and sometimes disproved) by biologists about the evolution of specific proteins, species, and higher taxons. And the even more detailed proof that the ID community demand of biologists – lack of which is taken as evidence for ID.

  14. 14
    paragwinn says:

    Gil,

    You appear to provide three premises (indicated by the term ‘Given’) but you dont lay out any logic operations on those premises to arrive at a conclusion with a truth value. Is this really your idea of ‘Darwinian Logic’?

  15. 15

    We now know that drift is responsible for many “particular features” and selection may play a less critical role.

    More to the point, the ability to write Mozart symphonies is not highly heritable, and, to the extent that it is, there are extremely important gene-environment interactions.

    What is heritable, of course, are many of the component abilities, many of which may well have had a survival advantage. But these are likely to be polygeneic.

  16. 16
    gpuccio says:

    Mark:

    I would really like to see the “detailed hypotheses” you speak of. Most evolutionary hypotheses are just about lines of descent, without any trace of causal explanation. Those hypotheses are an attempt at reconstructing natural history, not explaining it, and they are as good for design research as they are for darwinism.

    Reconstructing natural history as precisely as possible is the basis for any attempt at explaining it, be it from a design poiny of view or from a darwinist point of view.

    But darwinists have never explained the emergence of even a single protein. They explain nothing. They can’t, because their theory is wrong, and will never find support in natural hystory.

    What ID demands is an explanatory model, not just smoke and mirrors. ID has an explanatory model, and facts about natural history can and must be viewed in the light of that model.

    We have to answer to specific and important questions:

    a) How and when do new proteins emerge?

    b) Is the pattern gradual or discontinuous?

    c) How much new information seems to appear without any trace of step by step paths?

    d) Can we reconstruct a more or less detaile map of the emergence of new information in natural history?

    e) What can we really say about LUCA? When did it live? How old are the proteins which were already present in it?

    f) Can we define more in detail the fundamental transitions in natural history? OOL, emergence of eukaryotes, emergence of multicellular phyla? And try to objectively chracterize them in terms of time, space and information?

    Science must try to give objective amswers to these and other questions, getting rid of the delusion that darwinist theory is the only possible answer. Existing data must be viewed also from a design point of view, with open mind and sincere desire for truth.

  17. 17
    Joseph says:

    According to Darwinian theory, new species emerge when mutations produce individuals who can outperform the stock they came from

    wd400

    Nope. (That’s actually adaptation)

    Nope, adaptation is when they are (best) suited to their environment.

  18. 18
    Petrushka says:

    I find it interesting that domain invention seems to be mostly the work of microbes, and seems to have slowed down over time.

    Whatever the actual history of new domains, it seems associated with very high numbers of organisms.

    Can you offer an ID explanation for this trend?

  19. 19
    Petrushka says:

    Do you consider domain shuffling to be the creation of new information?

    How about incremental changes in gene expression?

  20. 20
    gpuccio says:

    Eugene:

    I have discussed those points many times, but it is difficult for me to find where.

    There is something recent here:

    http://www.uncommondescent.com.....ent-402266

    and here:

    http://www.uncommondescent.com.....ent-402272

    My idea is: whatever the designer is, its interaction with physical reality must be explorable, to a point, in a bottom up way, starting from physical reality.

    Natural history, as it can be inferred form the traces we have now, is fundamental both to infer design and to reason on the modalities of implementation of the design.

    At the origin of design is always a conscious representation. That’s what makes design design. But the process of design is an implementation of that representation on a physical plane. The designer does specific things to implement his representation. He has to “configure switches”, to give them the desired form.

    The configuration of material switches must be explorable.

    ID gives us a powerful tool the computation of dFSCI (or any equivalent metrics). Applied to natural history, that can tell us when important informational outputs were realized. We must narrow our time windows.

    The big bang theory of protein evolution, to which I have often given reference, is IMO an important tool to understand what really happens in the proteome in the course of natural history.

    Darwinists continuoslu boast their “theories”, but the truth is that they are blinded by the necessity of justifying a wrong theory. That’s why they cannot see the obvious.

    The obvious is that new protein information emerges suddenly in the course of natural history, after having emerged much more suddenly and in huige quantities at OOL.

    The obvious is that such information changes gradually in the course of natural history, probably because of neutral evolution, while retaining the same function.

    The obvious is that in other cases the same basci information is tweaked and adapted to generate families of slightly different functions.

    We have to keep those facts well separated.

    The emergence of new basic information cannot be explained by darwinist theory. There can be no possible doubt about that. It is the best tool to trace important design events, and to investigate their modalities: time distribution, and possibly ways of implementation (guided mutations, or intelligent selection, or both), the existence of intermediaries, and so on.

    We must try to understand if the differences between the same functional proteins in far species are due only to neutral evolution in the island of functionality, or if they have a functional value.

    We have to better define the informational thrsholds of minor protein evolution within families, which is potentially in an intermediate range, and could be explained in principle by both RV and NS and design.

    And so on. A lot of good questions. But until research will be interpreted only in the light of darwinism, answers will be difficult to be found.

  21. 21
    Neil Rickert says:

    But are you saying that evolutionary biologists would generally disagree that particular features have a survival advantage?

    They would not say that just because a feature exists, therefore it has a survival value. Rather, they would make judgments about survival value based on actual evidence.

  22. 22
    gpuccio says:

    Petrushka:

    Domain shuffling, like any other form of variation, must be quantitatively analyzed. In principle, it could be explained by RV and NS, or by design.

    Again the problem is: how likely is it that existing protein domains are subkect to casual shuffling that produces a functional result?

    We should apply here the same methodology as for protein sequences, but it can be more difficult. That’s why I rarely discuss this aspect.

    Anyway, we should know the combinatorial search space, and the target space of functional shufflings, and the probabilistic resources. And, if we want to invoke NS, we must provide some evidence that the results for which we compute probabilities are naturally selectable.

    My opinion is that domain shuffling can be bets explained as a form of modular programming. It is object oriented programming at its best. IOWs, it is a form of highest design.

    But at present I have not the resources to give a detailed analysis of that scenario, and I prefer to stick to basic protein domains as a model for ID.

    On the other hand, I doubt that there is any credible quantitative darwinist analysis of the domain shuffling model from a darwinian point of view.

  23. 23
    Petrushka says:

    The concept of most proteins as systems of domains exemplifies the new combinatorial thinking frequently emphasized in this book. It makes good sense a priori to expect that a protein will make a successful functional change by acquiring an existing intact binding or catalytic capability. Intuitively, this has a far higher probability of proving effective than does a random process of changing one amino acid at a time and gradually selecting modest improvements in catalysis or binding specificity. In many cases, existing sequences do not provide suitable starting material for evolving new functions one amino acid at a time, because those novel functions require entirely different polypeptide structures. But this restriction does not apply to the process of acquiring an entire new domain, which already comes appropriately configured. The fact that artificial protein evolution in the laboratory often works far better by domain-swapping methods than by localized mutagenesis is yet another indication that the former is a more effective protein innovation strategy than individual or multiple independent amino acid changes [746].

    The systems view of proteins implies that they evolve by natural genetic engineering rather than by localized mutation. Is there experimental evidence that the requisite processes for swapping domain-coding sequences actually occur in living cells? Some of the earliest molecular genetics experiments in bacteria involved the formation of hybrid proteins by deletion events that eliminated termination signals and joined two coding sequences into one (for example, [747]). My late colleague Malcolm Casadaban developed a generalized in vivo technique using a DNA transposon that could fuse any E. coli protein coding sequence to the enzymatically active domains of LacZ beta-galactosidase [748]. Mammalian tissue culture experiments have demonstrated the domain-swapping capabilities of non-LTR retrotransposons through retrotransduction, either of upstream sequences (SVA elements) or downstream sequences (LINE elements) [522, 749, 750].

    In addition to domain swapping by retrotransduction, genome sequences in plants and animals have begun to document protein-coding regions where new exons have been incorporated by different classes of DNA transposons (so-called “Pack-MULEs” in rice and helitrons in maize [213, 751–754]). So the capacity of living cells to carry out the requisite natural genetic engineering operations for protein evolution by domain swapping is unequivocally established.

    Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 1771-1784). FT Press. Kindle Edition.

  24. 24
    Joseph says:

    Umm if you have genes then you are starting with that which needs explaining in the first place.

  25. 25
    gpuccio says:

    Petrushka:

    My answer is simple. To establish life in the beginning, a lot of basic protein information was necessary. About half of basic protein domains were implemented at that level.

    That information has remained available for higher taxa. New information is inputted only whne it is really necessary to implement some completely new function.

    For instance, the hundreds of proteins, very complex proteins, that are necessary for basic processes like transcription and translation were alreadythere, in LUCA, and are still working in pretty much the same way in us humans.

    It is also true that, with the development of evolution, new information is inputted much more at the regulatory level (a level we still poorly understand). New information at protein level is less necessary.

  26. 26
    Petrushka says:

    What I asked was:

    Do you consider domain shuffling to be the creation of new information?

    How about incremental changes in gene expression?

    I asked if they qualify as new information. It’s asking for a definition of terms.

  27. 27

    Well, that is a nice idealistic thought. Perhaps when pressed and when being careful they would not say that a feature has survival value just because it exists. Personally, however, I have seen many interviews, press releases and the like with biologists who make precisely that kind of statement. I’d invite everyone to just keep a watch when you see articles/stories about particular features of life. The kind of circular statements Gil is referring to come up quite often.

  28. 28

    Well, if a feature exists, the likelihood is strong that at some point it provided survival, or rather reproductive, value.

    But we don’t always know how, or even at what stages, it did. For example a peacock would probably survive better without that cumbersome tail, if all that mattered was survival. Similarly, peahens would probably have more successful offspring if they chose peacocks with nice trim tails than big cumbersome tails.

    But things don’t always pan out that way, and nowadays, peacocks have to breed in an environment populated by peahens who will only mate with you if you have a cool tail, and peahens have to breed in an environment where only the healthiest individuals have the kind of tails that tickle their fancy.

    So feedback loops seem to have conspired to endow the peacock with a tail that is only of use in attracting peahens, and peahens with a fancy only for peacocks with beautiful tails.

    It is difficult to demonstrate a clear selective advantage of any one allele in any lineage, because a) we don’t know what the environment was at the time or since it appeared, and b) because we don’t necessarily know what other alleles (or environmental factors) it needs to interact with to confer selective advantage.

    What we can do, easily, is demonstrate that these processes can, and do, result in the kind of feedback loops of advantage that generate complexity, function, and, indeed, beauty.

    Which is what makes the ID inference untenable. We know there is a mechanism that can produce the kinds of phenomena we observe that does not involve an ID.

    Whether it did or not in any given case is another question.

  29. 29
    Eugene S says:

    “if all that mattered was survival”

    I think this lacks the necessary amount of “pathetic detail”. What else matters? Sexual selection? But why at the cost of this much redundancy? In fact so much as to obviously endanger the poor peacock?

    For example, one can argue that to ensure a high mating success a crow’s cry is perhaps more efficient than a nightingale’s song. Why is there such a difference?

  30. 30

    What else matters is reproduction, Eugene. “Survival of the Fittest” is less important than “reproduction of the fittest”.

    And in this case, sexual selection is probably very important – indeed we know that tail-display is an important courtship behaviour.

    Why at the cost of so much redundancy? Because that’s the kind of rabbit hole evolutionary processes tend to go down. Evolutionary processes produce some stunning designs, but not always the most functional!

    Because they are full of feedback loops, it’s a chaotic (in the mathematical sense) system, and like many chaotic system, results in astonishing, complex, but unpredictable structures.

    Again, this is relatively easy to demonstrate mathematically or by simulation. I have produced some amazing patterns simply by building iterative programs with feedback loops, where the output of one iteration is an important input into the next iteration.

    There’s a wiki piece on it here:

    http://en.wikipedia.org/wiki/S.....preference

  31. 31

    Sure, but science is an iterative, dialectic process. That’s why it’s so much fun.

  32. 32

    To establish life in the beginning, a lot of basic protein information was necessary. About half of basic protein domains were implemented at that level.

    On what evidence are you asserting this?

    You do know that the Last Universal Common Ancestor was not necessarily the First?

  33. 33

    What about the fact that the simplest living cell is the most sophisticated and functionally-integrated information-processing system ever discovered?

    In what sense is said cell “the simplest” if it is also “the most sophisticated and functionally-integrated information-processing system ever discovered”?

    Are all biological systems as simple as the simplest cell, or are some simpler?

    What about the human brain? Do you not think that the human brain is a more functionally-integrated information-processing system than the simplest cell? After all, it consists of billions of cells, all interconnected by countless synapses.

    I think you made a logical slip there 🙂

  34. 34
    Neil Rickert says:

    Perhaps when pressed and when being careful they would not say that a feature has survival value just because it exists. Personally, however, I have seen many interviews, press releases and the like with biologists who make precisely that kind of statement.

    You are probably thinking of features that appear to have led to speciation. In such a case, they do have a lot more evidence than the mere existence of a feature.

  35. 35
    gpuccio says:

    Elizabeth:

    I was referring to the number of basis protein domains supposedly present in LUCA. This is the reference:

    http://www.plosone.org/article.....ne.0008378

    You do know that the Last Universal Common Ancestor could well have been the First?

    You do know that Wikipedia, just as an example, states that LUCA “is estimated to have lived some 3.5 to 3.8 billion years ago”?

    You do know that there is no evidence at all that a FUCA, different form LUCA, ever existed?

  36. 36
    gpuccio says:

    Petrushka:

    Combining existing domains to work together for a new function certainly implies new information. How much functional information should be analyzed by the methods I mentioned.

    Anyway, it is obvious that the information for the individual blocks must already be present.

    Incremental changes in gene expression imply new information. How much depends on how those changes are implemented at molecular level, and if the intermediate steps are selectable or not, and so on. Whatever the system, the principles of design detection are always the same.

  37. 37
    gpuccio says:

    And so?

  38. 38
    wd400 says:

    Could you please, being probably a moderate adaptationist, explain what is in your opinion the general mechanism by which new complex information (such as a new basic protein domain) emerges, according to darwinian theory?

    1. You should drop the Darwinian business, because how ever you define it there is more than evolutionary biology than Darwinian forces.

    2. I’m not sure there is a general mechanism by which complexity arises. It will often be the result of selection on point mutations (in the case of portein domains over a very long time). But it can also arise form, say, exon shuffling . I’m also convince some of the things we think of as complexity at the level of genome-level are really just emergent properties or even the result of a lack of selection preventing redundancies etc adding up (a la Lynch 2011

  39. 39
    wd400 says:

    No, you don’t get to define a word completely different than everyone else that uses it.

  40. 40
    Joseph says:

    No, you don’t get to baldly declare I am defining a word completely different than everyone else uses it.

  41. 41
    Petrushka says:

    Anyway, it is obvious that the information for the individual blocks must already be present.

    But that is irrelevant to my question, which is based on the understanding that the last half billion years of evolution has been mostly one of recombination and changes in regulation. Not my idea: it seems to be a point of common ground between mainstream and ID friendly theorists.

    You are making a point that creation of new protein domains is difficult and rare, and my understanding of mainstream biology is that there are few such instances among eukaryotes. Very few among vertebrates and fewer still among mammals.

    So it almost appears that the occurrence of biological invention follows a power law based on population size and time.

    Several people, including Shapiro and Koonin make the point that the invention of protein domains seems mostly to have occurred in the firs billion years of life on earth.

    One might speculate that as living things became more competitive, it became less possible for weak functionality to succeed. One might also look for evidence that modern domains are modifications of earlier domains.

  42. 42
    wd400 says:

    Ahem

    1,2,3

    Adaptation is the process by which creatures fit their environment, and also the name given to a particular trait which is teh result of adaptation. It certainly isn’t about the “best” fit – since evolution doesn’t know about global optima.

  43. 43
    Joseph says:

    wd400:

    Adaptation is the process by which creatures fit their environment,

    That is what I said:

    adaptation is when they are (best) suited to their environment.

    How is THAT COMPLETELY DIFFERENT from what you posted?

    Did you note I put best in ()? Or do you like being obtuse?

  44. 44
    Petrushka says:

    You seem to be hedging when you say recombination and changes in expression “imply” new information. If it is in fact new information, I’d like to see how you calculate it. An example of a calculation.

    Suppose we take as an example of gene expression the incremental change from jaw bone to middle ear bone. We don’t know how many specific mutations were involved, but you should be able to provide a formula that would allow plugging the number in, if it became available.

  45. 45
    wd400 says:

    Then the xmen quote is adaptation and you’re (surprise, surprise) a waste of time.

  46. 46
    gpuccio says:

    Petrushka:

    But that is irrelevant to my question, which is based on the understanding that the last half billion years of evolution has been mostly one of recombination and changes in regulation. Not my idea: it seems to be a point of common ground between mainstream and ID friendly theorists.

    You must be kidding. Almost half protein domains appeared after LUCA. It is true that the rate has been slowing down, but a lot of them appeared in natural history just the same.

    I link again a reference paper:

    http://www.plosone.org/article.....ne.0008378

    You are making a point that creation of new protein domains is difficult and rare, and my understanding of mainstream biology is that there are few such instances among eukaryotes. Very few among vertebrates and fewer still among mammals.

    What about:

    1984 in LUCA

    494 in bacteria and archea

    520 in eukaryota

    86 in fungi

    209 in metazoa

    So, it is true that a majority was formed near the beginning, but it is equally true that a lot of new protein domains emerged throughout evolutionary history.

    So it almost appears that the occurrence of biological invention follows a power law based on population size and time.

    It is much more credible that it follows the simple laws of what is necessary for engoneering of biological functions.

    I have already argued (and you have not commented) that most basci cellular functions were already present in LUCA, and that they have been reused by the designer in all following beings.

    One might speculate that as living things became more competitive, it became less possible for weak functionality to succeed. One might also look for evidence that modern domains are modifications of earlier domains.

    Be my guest. Look for that. And let me know.

  47. 47
    gpuccio says:

    Petrushka:

    I have already commented on that. See my post number 7, addressed to you.

  48. 48
    markf says:

    I would really like to see the “detailed hypotheses” you speak of. Most evolutionary hypotheses are just about lines of descent, without any trace of causal explanation.

    Well how about heomoglobin? There are any number of papers with hypotheses about the how it evolved.

  49. 49

    Why should I think that LUCA could well have been the FUCA?

  50. 50
    Joseph says:

    Wow, an evo can’t support its claims and has a hissy fit- surprise, surprise.

  51. 51
    Joseph says:

    Any paper that pertains to blind and undirected chemical processes? If not, then by evo “logic” (see Judge Jones) they don’t count.

  52. 52
    wd400 says:

    The xmen quote describes adaptation? Does it not?

  53. 53
    Joseph says:

    What xmen quote?

  54. 54
    ScottAndrews says:

    Like this one?

    At first this apparatus was quite primitive,
    probably limited to a caged metal atom capable of binding
    oxygen or tearing away its electrons, which are used in
    metabolism. But this basic chemical apparatus grew
    increasingly complex through time and evolution. At some
    point the metal atom was fixed inside a kind of flat
    molecular cage called a porphyrin ring, and later that
    porphyrin ring became embedded in larger organic
    compounds called proteins. These organic compounds
    themselves became increasingly varied through time and
    evolution.

    Then, sometime between one and two billion years ago,
    an amazing thing happened. Photosynthetic bacteria
    learned a new trick. Instead of carrying out photosynthesis
    with [H.sub.2]S, they used water, [H.sub.2]O. And instead
    of producing sulfur, this process produced molecular
    oxygen, [O.sub.2]. This remarkable event transformed the
    earth and all of the life on it.

    It is interesting to consider what the original function of the porphyrin ring may have been.

    In time, the hemoproteins could have been further
    modified to allow them to participate in other
    electron-transfer reactions or to take on entirely new
    functions.

    Okay, I just picked the first one I saw. But what sort of hypothesis is this? Every critical juncture is either what apparently happened with no explanation or what might have happened but we’re not sure. How does one test such a narrative? How does one falsify statements such as

    In time, the hemoproteins could have been further modified to allow them to participate in other
    electron-transfer reactions or to take on entirely new
    functions.

  55. 55
    wd400 says:

    The one, referring to the film, that started this?

    According to Darwinian theory, new species emerge when mutations produce individuals who can outperform the stock they came from

    If you out compete someone you so because you perform better in the given environment therefore…

  56. 56

    Joseph, please explain what you mean by “blind” and “undirected”.

    Because as used in evolution, “blind” means: new variants are generated regardless of whether they will be better or worse at replicating than their parents, and “undirected” means much the same thing. It doesn’t mean that the environment has no influence on whether a variant reproduces well or not. Quite the reverse. The environment has a huge influence on whether a variante reproduces well or not. So in another sense, you could say that the environment “directs” evolution – causes the population to adapt to optimise its reproduction rate within it.

    And exactly the same is true in an evolutionary algorithm – variants are randomly generated without regard for whether the result is a better or worse replicator than its parent (many will be neutral or worse, and the proportion that are neutral or worse will increase as the population gets better and better), and the process thus “blind” and “undirected” just as in nature.

    However, just as in nature, the environment determines to a large extent how well any given variant replicates, and so in that sense “directs” the evolution of the population.

  57. 57

    Do you agree, Joseph, that adaptation and speciation are different concepts, and that “when mutations produce individuals who can outperform the stock they came from” that is a definition of adaptation rather than speciation?

    (Not a very good one, though, IMO – populations evolve, not individuals)

  58. 58
    Joseph says:

    wd400 & Elizabeth:

    1- The “populations evolve” is nonsense. Natural selection is an individual thing. Mutations happen to individuals. OTOH populations tend to stifle change, unless there is some very strong (selective) pressure.

    2- Adaptation can and does lead to speciation. Ya see if I am not adapted for one environment I just move to another where I am and establish another population

    3- How do you think new species arise, that is according to Darwinism or neo-darwinism?

  59. 59
    Joseph says:

    In evolution “blind” means without foresight or any sight at all- no purpose, no plan and undirected means what you said.

    You seem to forget behaviour- that is much easier to change than waiting around for some undirected change to occur that may help you do better. That is how organisms best adapt, by changing their BEHAVIOUR, not their genes.

    That said there isn’t anything we have ever observed that supports your claims that blind and undirected processes can construct new, useful multi-part systems.

  60. 60
    wd400 says:

    Joseph.


    1- The “populations evolve” is nonsense. Natural selection is an individual thing. Mutations happen to individuals. OTOH populations tend to stifle change, unless there is some very strong (selective) pressure.

    Yes mutations happen to individuals, and it’s individuals that compete with each other. But individuals are in populations, and this, populations evolve as a result of those processes. individuals can’t evolve for obvious reasons.

    Even in the absence of any selective pressures, new mutations will fix at rate of muatation (that’s Kimura for ya) so change is actually the background against which all evolutionary pressures are playing out. Add selection to that and things will change more quickly


    2- Adaptation can and does lead to speciation. Ya see if I am not adapted for one environment I just move to another where I am and establish another population

    Well, I’d like to see evidence for this. Or that something maladaptive in one environment is likely to be adaptive in a another. Adaptation might play a role in speciation, but I don’t know of any evidence for this sort of thing.

    3- How do you think new species arise, that is according to Darwinism or neo-darwinism?

    I really think you guys should drop the Darwin Tourette Syndrome. Darwin’s theory of speciation was wrong, and the leading modern theory of speciation is quite un-darwinian. Populations stop sharing genes with each other, as a result changes in population A don’t effect population B and they are free to evolve away from each other. In time the differences that accrue during this reproductive isolation are such that if they were to be reunited that wouldn’t fall back into each other and we call those species.

    The prevailing (but not only) view is that the reproductive isolation is usually a result of geographical isolation. Tha changes that keep species apart from each other might be the result of adaptation, but don’t have to be.

  61. 61
    Timbo says:

    “Which random mutations would be required to turn a microbe into Mozart? How long would this take? What is the probability that these beneficial mutations could take place, and what is the probability that they could be fixed in the population with the available reproductive and probabilistic resources?”

    I would love to see ID offer an explanation for how this (microbe to Mozart) happened.

  62. 62

    Yes, organisms adapt by changing their behaviour, also, sometimes their physiology.

    Populations adapt by means of natural selection. One trait that may be selected is the ability of individuals to adapt. So if the tendency to tan in the sun, or to startle at surprise, both of which have genetic underpinnings, have selective advantage, the alleles that promote them will tend to become more prevalent.

    That said there isn’t anything we have ever observed that supports your claims that blind and undirected processes can construct new, useful multi-part systems.

    Give me an example of a useful multi-part system that you think can’t evolve.

  63. 63
    Eugene S says:

    Elizabeth, you haven’t persuaded me as yet that evolution is not story telling but science…

  64. 64
    Eugene S says:

    3.1.1.1.3

    GPuccio,

    Much appreciated. It makes a lot of sense.

  65. 65
    Joseph says:

    Elizabeth:

    Yes, organisms adapt by changing their behaviour, also, sometimes their physiology.

    Behaviour is something they can do now and by themnselves.

    Populations adapt by means of natural selection.

    Natural selection is a result and only a minor player.

    One trait that may be selected is the ability of individuals to adapt.

    By changing their behaviour? What if they were designed to adapt by changing their behaviour?

    Give me an example of a useful multi-part system that you think can’t evolve.

    There isn’t any evidence taht blind and undirected processes can produce any. ya see that is how science operates-> via positive evidence and you just don’t have any.

  66. 66
    Joseph says:

    wd400:

    Yes mutations happen to individuals, and it’s individuals that compete with each other. But individuals are in populations, and this, populations evolve as a result of those processes. individuals can’t evolve for obvious reasons.

    Individuals can evolve- evolution by conact, as in prions. Not only that if one individual has a different allele than the rest of the population then that individual is an evolved individual within that population.

    Populations can’t evolve for obvous reasons.

    Even in the absence of any selective pressures, new mutations will fix at rate of muatation

    It is still very unlikely for any mutation to become fixed- that’s reality for ya. And natural selection is still an oxymoron.

    2- Adaptation can and does lead to speciation. Ya see if I am not adapted for one environment I just move to another where I am and establish another population

    Well, I’d like to see evidence for this.

    That’s the standard evolutionary propaganda.

    3- How do you think new species arise, that is according to Darwinism or neo-darwinism?

    I really think you guys should drop the Darwin Tourette Syndrome.

    EVOLUTIONISTS use it! Are you really that obtuse?

    Populations stop sharing genes with each other, as a result changes in population A don’t effect population B and they are free to evolve away from each other.

    Yes, as I said- one population moves to an area that better suits them. Adaptation.

    The prevailing (but not only) view is that the reproductive isolation is usually a result of geographical isolation.

    Creationsits predicted reproductive isolation and again adaptation leads to geographical isolation.

  67. 67
    Joseph says:

    Timbo:

    I would love to see ID offer an explanation for how this (microbe to Mozart) happened.

    A targeted search would suffice

  68. 68
    woodford says:

    b) It is perfectly true, however, that details of design implementation can certainly be the object of scientific research, once ID is accepted as best explanation, or at least as possible explanation.

    Wouldn’t it be more effective to focus on the details of the design implementation since it would bolster acceptance as best explanation? I think for many it’s the lack of these details that make ID unconvincing. In the end isn’t science as much about the “how” as the “what”?

  69. 69
    Petrushka says:

    I haven’t found anything regarding my speculation about origin of “recent” domains. Most of that is behind paywalls.

    But I notice that in metazoa there’s less than one new domain every two million years. How again are we supposed to witness one of these events?

    The overall rate of invention is about one every 12 million years. Fairly lethargic for a designer.

  70. 70
    Petrushka says:

    OK, you have an opinion. Shapiro also thinks genomic mutations increase due to environmental stress. He likens it to the immune system.

    However, the immune system does not have foresight. It does not produce variations targeted to need.

    I would suggest that ID advocates need to find some evidence that mutations and recombinations are skewed in favor of meeting needs.

  71. 71
    wd400 says:

    Just, for the record, do you now see that the quote that started this conversation was about adaptation?

    Can you show me the evidence that “if I am not adapted for one environment I just move to another where I am and establish another population”? Can you tell me how plants and microbes achieve this feet?

    Can you show me where such a process is part of mainstream evolutionary biology, which is what I presume you mean when you say “standard evolutionary propaganda” and the claim that the scenario I described is about “adaptation”. (It doesn’t need to be, if glaciation separates a population they become reproductively isolated without moving…)

    Can you show me where creationists predicted reproductive isolation, and explain to me what they means for that matter?

  72. 72
    Timbo says:

    Ok, cool. Can you break it down a bit more?

  73. 73
    gpuccio says:

    Mark:

    Well how about heomoglobin? There are any number of papers with hypotheses about the how it evolved.

    That was, explicitly, in response to my:

    “I would really like to see the “detailed hypotheses” you speak of. Most evolutionary hypotheses are just about lines of descent, without any trace of causal explanation.”

    Well, ScottAndrews has just shown an example of paper that goes beyond my wildest dreams of what a “gross unscientific fairy tale” can be.

    Would you call that a “detailed hypothesis”. I suppose that calling it a “just so story” would still be a gross understatement!

    So, as you are certainly a serious interlocutor, would you please suggest one paper about hemoglobin evolution that falsifies my statement (I repeat iy for your convenience):

    “”I would really like to see the “detailed hypotheses” you speak of. Most evolutionary hypotheses are just about lines of descent, without any trace of causal explanation.”

    As you say that there are “any number” of such papers about the evolution of hemoglobin, it should not be difficult.

  74. 74
    markf says:

    Gpuccio

    Well about this for an example:

    http://www.nature.com/ng/journ.....g.574.html

    To quote from the abstract:


    We have genetically retrieved, resurrected and performed detailed structure-function analyses on authentic woolly mammoth hemoglobin to reveal for the first time both the evolutionary origins and the structural underpinnings of a key adaptive physiochemical trait in an extinct species. Hemoglobin binds and carries O2; however, its ability to offload O2 to respiring cells is hampered at low temperatures, as heme deoxygenation is inherently endothermic (that is, hemoglobin-O2 affinity increases as temperature decreases). We identify amino acid substitutions with large phenotypic effect on the chimeric ?/?-globin subunit of mammoth hemoglobin that provide a unique solution to this problem and thereby minimize energetically costly heat loss.

    I don’t see how you could ask for anything more specific. The actual mutation and the resulting advantage.

  75. 75
    Joseph says:

    It could be a design feature and not a mutation…

  76. 76

    “Mutation” means a “change”.

    Perhaps the mutation was designed.

    Why would we think so?

  77. 77
    markf says:

    Every change might be designed – but there has to be some reason for supposing this. The paper hypotheses the exact mutations, their order, roughly when they happened and the resulting advantage. There is no requirement for more than a single point mutation at any point to get the resulting advantage. What more could you possibly ask? Does anything in ID even come remotely close to this. Note that this one of hundreds (maybe thousands) of papers on hemoglobin evolution.

  78. 78
    Joseph says:

    Why would we think all mutations are due to blind and undirected chemical processes?

    I will tell you why- an a priori world-view that refuses to allow design.

  79. 79
    Joseph says:

    No one said every change has to be designed. ID does not exclude darwinian mechanisms and it does not exclude random effects.

    Also the hypotheses have nothing to do with blind and undirected chemical processes and again ID is not anti-evolution.

  80. 80
    Joseph says:

    What, do you want me to write a genetic algorithm taht will accomplish this?

    Dawkins showed the power of a targeted search using cumulative selection- as have others.

  81. 81
    Joseph says:

    wd400:

    Can you show me where creationists predicted reproductive isolation, and explain to me what they means for that matter?

    That is in the Bible.

    As for moving- how do YOU think geographic isolation happens? A glacier moves too slowly to split a population. Perhaps a flash-flood would work.

    Plants move via their pollen and seeds. Microbes move on the backs of animals.

    That said if we have one population and some in that population become adapted to one thing , while others remain adapted to something else, then we can have sympatric speciation due to the differing adaptations. Then one part of teh population could possibly outprerform the others.

  82. 82

    Well, biochemistry, basically, and molecular genetics.

    But I’m glad that you are prepared to accept the evidence for a mutation, however caused.

  83. 83
    gpuccio says:

    Mark:

    Reality check: the paper is about 3 (three!) adaptative mutations. It has nothing to do with the emergence of the globin domain, which was (and always has been, as you should well know) my issue.

    I refer you to my post 3.1.1.1.3 to Eugene, in this thread. Please read it. I copy here the relevant part for your convenience:

    “The obvious is that new protein information emerges suddenly in the course of natural history, after having emerged much more suddenly and in huige quantities at OOL.

    The obvious is that such information changes gradually in the course of natural history, probably because of neutral evolution, while retaining the same function.

    The obvious is that in other cases the same basci information is tweaked and adapted to generate families of slightly different functions.

    We have to keep those facts well separated.

    The emergence of new basic information cannot be explained by darwinist theory. There can be no possible doubt about that. It is the best tool to trace important design events, and to investigate their modalities: time distribution, and possibly ways of implementation (guided mutations, or intelligent selection, or both), the existence of intermediaries, and so on.

    We must try to understand if the differences between the same functional proteins in far species are due only to neutral evolution in the island of functionality, or if they have a functional value.

    We have to better define the informational thresholds of minor protein evolution within families, which is potentially in an intermediate range, and could be explained in principle by both RV and NS and design.”

    So, I ask again, where are the detailed models about the original evolution of new basic protein domains?

  84. 84
    gpuccio says:

    Petrushka:

    The immune system is a bery intelligently designed system, with a lot of obvious targets. I will point to you the two main obvious targets of the system:

    a) Establishing a low affinity basic repertoire of antibodies to recognize possible antigenes in the future life of the organism. That is brilliantly achieved by a procedure which couples random variation to a small repertoire of genes, resulting in the only relevant systematic somatic modification of genetic structure in multicellular organisms, and in a basic “blind” repertoire of antibody specificities that cover quite well the search space of epitopes, altough with low level specificity.

    b) Transforming the low affinity antibodies of the primary immuine response into high affinity molecules. That is accomplished through a very sophisticated algorithm that couples RV targeted to the existing specificity (selected in the primary immune response), to intelligent selection where the random results are measured for their affinity to the memorized epitope, and selectively stimulated or suppressed accordingly.

    I could not think of a more intelligently designed, integrated, complex, efficient, purposeful system.

  85. 85
    gpuccio says:

    Elizabeth:

    I could just answer: why should I think that a FUCA, different from LUCA, ever existed?

    One can think any possible thing. The fact remains that we have scientific reasons to believe in the existence of LUCA, to localize it on time, and to make models of what it was (essentially, a prokaryote), and of which proteins allowed it to exist and live.

    About FUCA, we have absolutely nothing. So, you can think what you like, but I don’t like to think about and believe in things that very likely never existed.

  86. 86
    Petrushka says:

    That is brilliantly achieved by a procedure which couples random variation to a small repertoire of genes, resulting in the only relevant systematic somatic modification of genetic structure in multicellular organisms, and in a basic “blind” repertoire of antibody specificities that cover quite well the search space of epitopes, altough with low level specificity.

    I could not think of a more intelligently designed, integrated, complex, efficient, purposeful system.

    In other words there is no better way to evolve than by producing a blind repertoire of variants that cover the immediately adjacent search space. I think I get it.

  87. 87
    markf says:

    Gpuccio

    I was not responding to your request for a detailed description of the evolution of protein domains. I was just responding to your request for an example of a paper which gives a detailed hypothesis about the evolution of hemoglobin. Do you accept this is an example? Can you give me any example of any ID paper which comes close to this in trying to provide detail which can be assessed?

  88. 88
    gpuccio says:

    Petrushka:

    Just to explain. The establishment of the primary antibody repertoire has nothing to do with “evolution”. It is an intelligent algorithm to cover a big (but not huge) search space at low level, through targeted RV applied to very functional genes. In this way, some essential information is multiplied thorough RV plus a very specific algorithm.

    The search space of epitopes is big, but not huge, epitope length usually being 5 – 20 AAs. Still, that space cannot be efficiently covered even by the efficient algorithm embedded in the immune system, and the result is a low level coverage.

    That’s why the process of antibody maturation after the primary response is necessary. And that process is driven by the specific epitope information stored in Antigen Presenting Cells.

  89. 89
    gpuccio says:

    Mark:

    The “evolution of hemoglobin” is first of all the initial emergence of hemoglobin from something else. Or are you suggesting that all proteins appear from nothing, and that evolutionary theory is only about their successive small tweakings?

    You example is an example of what? Most research about protein structure is obviously done by those who have the resources. But basci research is neither darwinist nor ID. It is the interpretation of data that differs, not the data.

    So, mammuth hemoglobin differs at 3 AA sites, and that is probably a functional difference. That is an example, like many others, of those “tweakings” that, being in principle in the range of RV, could be explained by a darwinian mechanism, although that can still be discussed. Axe, in one of his recent papers, discussed exactly that.

    But the “successive evolution” in already existing protein families in certainly not the best field to discriminate between ID and darwinism, because the informational content here is usually borderline, and the causal reasoning is less clear cut.

    But the original “evolution” of each new protein, that is the right scenario.

    So, if you think that darwinists have “detailed papers” about the “original” evolution of hemoglobin, other than the bad fairy tales already shown here, please let us know.

  90. 90
    markf says:

    Gpuccio

    My point is one about methodology not about what particular problems have been solved or not. The fact remains that evolutionary biologists regularly make detailed hypotheses about various expects of evolution which can (and sometimes are) falsified by the evidence. IDists do not attempt any thing close to this. All they do is dwell on the difficulties that evolutionary biologists have in explaining some parts of evolution.

  91. 91
    Acipenser says:

    But the original “evolution” of each new protein, that is the right scenario.

    Any calculations made on the ‘new’ protein are dependent on knowing the history of that protein. If new information is found pushing back the protein history by one step the entire dFCSI calculation collapses. It is a calculation based on ignorance of the history of the protein beyond some arbitrary point. New information does not increase the precision of the calculation it totally eliminates the product of the calculation. There is no other metric in science where this happens outside of the alleged calculation of dFCSI.

  92. 92
    gpuccio says:

    Mark:

    Basic research is one thing. It is not driven by darwinian theory. It is driven by the necessity to find facts.

    Ecolutionary biologists find good facts and they iterpret them in the light of a wrong theory, often forcin facts into unscientific conclusions. That’s very bad methodology.

    ID is a new paradigm, and it is trying to contrast a dogmatic scientistic religion which was never seen in scientific thought beofre neo darwinism and strong AI were declared revealed truth.

    We don’t “dwell on the difficulties that evolutionary biologists have in explaining some parts of evolution.”
    We dwell on the total failure of a paradigm.

    And we certainly don’t deny the good facts discovered by biologists, whatever their ideology. They are the main contributors to the falsification of darwinism.

  93. 93
    gpuccio says:

    Acipenser:

    The only think that would make the entire dFSCI calculation collapse would be a detailed deconstruction of the transition from a protein domain to a completely different one by simple naturally selectable steps.

    That will never come, because it is impossible to do that.

    Your “ignorance of the history of the protein beyond some arbitrary point” is only an excuse for not having to give scientific support to your dogmatic convicitons. Science does not work that way.

    And the point is not arbitrary at all. We know more or less when new domains arose in natural history (see the paper many times linked). That is the point you have to explain, and it is not arbitrary at all. It is the point when the thing to be explained first appears.

    Finally, “If new information is found pushing back the protein history by one step”, as you say, the calculation of dFSCI does not collapse at all. It can easily be adjusted by calculating two separate values of functional information.

    For instance, let’s say we calculate the dFSCI implied by a transition from A to B. Then you show some possible intermediate state, near to B, let’s call it -B, which is naturally selectable. Well, we can then calculate the dFSCI from A to -B, and ignore the functional information from -B to B, if it is small enough to be in the range of the random system we are considering.

    Easy, isn’t it? So, all you have to do is to show, in nature or in the lab, all the intermediaries, -B, –B, … ++A, +A, each of them explicitly shown to be naturally selectable, that trace the “evolutionary path” from A to B.

    Good luck. Until you (or anybody else) succeeds in that, possibly for many proteins, I will continue to be certain that the neodarwinist model is an intellectual fraud.

  94. 94
    gpuccio says:

    Can someone get rid of the unwanted “bold”?

  95. 95
    material.infantacy says:

    The offending tag looks like this: “<b />” and is located in comment 14.2; the comment id is 403415.

  96. 96
    Acipenser says:

    gpuccio, As you/we learn more of the history of a protein domain your calculations get pushed back into smaller increments until at some point you lose your UPB level of dFCSI. Then what?

    Your approach/belief is that there were no precursors to any protein domain and that these domains were created ex nihilo. That is the Divine foot stuck in the door and the only reason, IMO, you wish to stop the investigation at that point is because it supports your worldview. It certainly isn’t the science since that would dictate looking for what came before those protein domains that led to their formation before you declare you’ve reached the end of the research line. Lewontin was correct.

    Why would anyone need to demonstrate this possibility for ‘many proteins’ when one is sufficient to demonstrate feasability? Is that a means of hedging your bet?

  97. 97
    wd400 says:


    Then one part of teh population could possibly outprerform the others.

    That will lead to one ‘population’ supplanting the other, not speciation. Sympatric speciation, which is a very controversial idea among evolutionary biologists, happens when phenotypic extremes can out-compete intermediates, which is quite different. Even then, adaptation bu itself can’t make species because recombination scrambles the adaptive alleles in each generation if there isn’t some sort of reproductive isolatoin (assortative mating) going on.

    I don’t understand what you mean when you say the bible predicted reproductive isolation, but I’d sure like to hear.

    And reproductive isolation evolves in lots of ways. Glaciation certainly did drive isolation, it doesn’t matter how fast it happens: if you started off with a continuous population then half of it was covered in a couple of kilometres of ice you’ll end up with a sub-divided population! Likewise, on geological timescales rivers often change direction or flow into different catchments (google “river capture”) which isolate inhabitants from different drainages. In times of high sea-level oceanic islands can be partially inundated, and form small archipelagos. Then there is climate driven habitat changes, chance settlement of islands, mountain building, hell continental drift made species (which have since become families or orders)…

    And it doesn’t have to be isolation in space, flowering time in plants can be controlled by soil type which would isolate plants living on different soil.

  98. 98
    gpuccio says:

    Acipenser:

    As you/we learn more of the history of a protein domain your calculations get pushed back into smaller increments until at some point you lose your UPB level of dFCSI. Then what?

    I am still waiting for the first push back 🙂

    Your approach/belief is that there were no precursors to any protein domain and that these domains were created ex nihilo.

    No. My belief is that they were intelligently designed. Please read my posts before saying incorrect things about my beliefs.

    That is the Divine foot stuck in the door

    I never discuss religious arguments here. I stay completely empirical. I have been doing that for years. At most, I can sometimes discuss some issues of natural philosophy, but that happens rarely.

    My discussions here are almnost exclusively about the scientific approach to biological information and to the problem of conmsciousness. Nothing of what I say implies a religious approach.

    you wish to stop the investigation at that point is because it supports your worldview

    You must ne kidding! I don’t want to stop any investigation, at any point.

    Let’s remind what has happened here.

    You stated:

    It is a calculation based on ignorance of the history of the protein beyond some arbitrary point.

    I commented:

    “And the point is not arbitrary at all. We know more or less when new domains arose in natural history (see the paper many times linked). That is the point you have to explain, and it is not arbitrary at all. It is the point when the thing to be explained first appears.”

    What has that to do with “stopping the investigation”? Why can’t you undersatnd simple english?

    I am just making the point that darwinian theory has no explanation for the “natural history” of any basci protein domain “beyond the point of its first known appearance in natural history”. And that is not an arbitrary point.

    The appearance of a new domain is a well identifiable point. Those who believe that such a point was reached by gradual, naturally selectable steps, starting form a different protein domain that already existed before, have the duty to provide a model of that. I will not believe such a bizarre and unsupported view out of faith in the reductionist dogma.

    My point was only that the emergence of a new domain is not an arbitrary point. It is exactly the point we should look at carefully, and gather data about, ehatever our scientific theory. It is as important for ID as it should be for neodarwinist theory.

    Why would anyone need to demonstrate this possibility for ‘many proteins’ when one is sufficient to demonstrate feasability? Is that a means of hedging your bet?

    No. I am not betting. It’s a problem of scientific methodology.

    One thing is to show the feasability of a scientific theory (something that darwinism has never done for itself, and never will do). Another thing is to show credibly that the “feasable” theory can well explain all that we observe.

    Any theory about the origin of biological information must be able in principle to explain all the biological information we observe.

    Let’s say we have 4000 indepenmdent protein domains. Let’s say that, after decades of trying, darwinist succeed in showing a barely acceptable model of transition from one of them to another one, based on their theory (it will not happen, but let’s just pretend). Is that enough?

    No, it isn’t enough. You still have to show that your “feasable” model for one case is really a ggod model for the rest.

    That’s why I said: “many proteins”. I am reasonable. I am not asking that you give a feasable model for all 4000 known domains.

    Let’s say that, after you can show that your (non existing) hypothetical model can work in about 1000 cases, I will take it into serious consideration.

    Can you see how generous I am with my adversaries?

  99. 99
    GilDodgen says:

    I’ve appreciated all the comments so far.

    For the sake of argument I’ll grant the Darwinist his unassailable belief in spontaneous generation (although I thought this notion was disqualified by Pasteur in the 19th century). There has been no forthcoming evidence that such a process has taken place, or could have taken place, even given the most optimistic assumptions.

    Given the assumption that a self-replicating primordial cell actually did spontaneously generate from inanimate matter through chance and necessity, one must logically ask how the proposed Darwinian mechanism could create the incredible results that are attributed to it.

    The reason I used the microbe-to-Mozart example was not just for purposes of alliteration; it was to plant seeds of doubt (an apparently hopelessly futile endeavor) in the Darwinist mind, which is still frozen in the 19th century.

    In my opinion, microbe-to-Mozart materialistic philosophy requires a helluva lot of blind faith.

    I mention Mozart because human life is obviously so much more than just survival and passing on one’s selfish genes. It’s about purpose, meaning, ethics, values, art, music, mathematics, creativity of all sorts, and yes, science, which should be about pursuing the evidence wherever it leads.

    There is an obviously huge discontinuity between humans and all other life forms, which Darwinists seem to have a pathological obsession denying.

    Why is this?

  100. 100
    GilDodgen says:

    gp,

    “Evolution” fixed it! I used a genetic random mutation and natural selection search algorithm that hill-climbed and homed in on the goal of finding the offensive HTML tag.

    NOT! It was intelligent design.

  101. 101
    markf says:

    Gpuccio

    Do you admit that the paper I showed you gives a detailed non-design account of a small aspect of the evolution of a protein? Clearly you are looking for something more fundamental. Before I research  papers on this I want to know I am not wasting my time.  What would count as a “Darwinian” explanation?  Does it have to give an exact series of mutations and their fitness advantages that happened billions of years ago?  How far back does it have to go?  I can see me wasting an awful lot of time digging up papers only to have them dismissed as insufficiently detailed or insufficiently fundamental.

    Meanwhile can you point to a single ID paper that gives any account of the development of any aspect of any protein?

    I also struggle to see how you can disagree that IDists dwell on the difficulties that evolutionary biologists have in explaining some parts of evolution. Just look at the most recent posts on this forum.  For example,

    A Whale of a Problem for Evolution: Ancient Whale Jawbone Found in Antartica

    Darwinists censor writer re: Fish that jump onto land unaided complicate the water-to-land transition story

    New paper sets out the precise “Swiss clock” mechanism of embryo development

    Now find a recent post with a design hypothesis for how something evolved.

  102. 102
    Petrushka says:

    It is the best tool to trace important design events,

    Could yo list the details of a few design events, in specific detail, and your evidence that they were design events?

  103. 103
    Petrushka says:

    I would concede your generosity if you could supply even one specific design event in detail, along with your evidence.

    All I’m asking for is the time, place, the details of the event.

  104. 104

    Basic research is one thing. It is not driven by darwinian theory. It is driven by the necessity to find facts.

    All scientific research is driven by theory. The idea that “basic science” involves simply “find[ing] facts” is false. Scientific methodology consists of devising theories that might account for the existing data, then deriving testable hypotheses that make predictions about new data (which can in fact include data we already have, if they are not the data that generated the hypothesis).

    Ecolutionary biologists find good facts and they iterpret them in the light of a wrong theory, often forcin facts into unscientific conclusions. That’s very bad methodology.

    It’s appalling methodology, and it is not what evolutionary biologists do. Or rather, I would like you to present an example of such a methodology used by an evolutionary biologist.

    Science consists of fitting models to data, not in fitting data to models. The whole edifice of scientific methodology, including null-hypothesis testing and other statistical techniques is designed to ensure that it is the model, not the data, that is adjusted to maximise fit.

    ID is a new paradigm, and it is trying to contrast a dogmatic scientistic religion which was never seen in scientific thought beofre neo darwinism and strong AI were declared revealed truth.

    I’d like to see actual evidence to support this assertion. I know it is a rhetorical claim, but even rhetorical claims need to be based in reality to be persuasive.

    Neither “strong AI” nor “neo Darwinism” are regarded as “revealed truth” by any scientist that I am aware of.

    The “Darwinian paradigm” has not “failed” in any sense that I can see, although our models of evolution are now more detailed than anything Darwin could have dreamed of.

    Can you give me an example of a Darwinian hypothesis that has been falsified? (I can, actually, but I’m interested to know what you might have in mind).

  105. 105
    Petrushka says:

    The appearance of a new domain is a well identifiable point.

    Actually, no.

    No more so than the appearance of a new species is an identifiable point.

    Perhaps you could contradict this by pointing to a specific point in the history of life, before and after the first appearance of a new domain. That would liven up the debate.

  106. 106
    Chris Doyle says:

    Just for a change, I’d be interested in hearing an atheistic evolutionist here detail an example of a Darwinian hypothesis that is actually true! That would settle the debate once and for all so why are they holding back the big guns?

  107. 107
    gpuccio says:

    Thak you, Gil! 🙂

    Another precious cintribution from you to this blog.

  108. 108
    gpuccio says:

    Petrushka:

    Maybe we cannot give the exact day, but there are maps of natural history, and tentative time frames for the appearance of new species. Do you deny that?

    If a new species is the first to exhibit a nea protein domain in its proteome, according to what we observe today, that is according to present knowledge the first appearance of that domain in natural history.

    It is obvious that our un derstanding and level of definition of natural history are constantly growing. Both the existing proteome and the fossil record are still there to explore. Further information will certainly come from molecular data in ancient DNA (like the mammouths quoted by Mark elsewhere). And from who knows what other sources.

    Our data are growing. Our theories have to grow too.

  109. 109
    markf says:

    Chris – there is more to this request than meets the eye.

    1) The only way we know if a hypothesis is true is if the evidence is strong enough. So I guess you are asking for a Darwinian hypothesis for which there is very strong evidence. But of course much of the dispute between us is over what counts as good evidence.

    2) What counts as a Darwinian hypothesis? Would “an example of a mutation that caused a significant change in phenotype that gave it a fitness advantage that lead to that mutation becoming fixed” be sufficient?

  110. 110
    GilDodgen says:

    gp,

    I just state the obvious, occasionally with tongue in cheek, or even justifiable sarcasm. Darwinists have a seemingly unlimited capacity for not recognizing the obvious.

  111. 111
    Petrushka says:

    Maybe we cannot give the exact day, but there are maps of natural history, and tentative time frames for the appearance of new species. Do you deny that?

    What exactly do you mean by new species?

    Varieties shade into each other, and we see many instances where populations the to not interbreed are biologically capable of interbreeding.

    So I ask again: Without having the molecular history, how do you know anything bout the exact origin of protein domains?

  112. 112

    Well, if you used a hill-climbing algorithm, Gil, no wonder you had to fall back on Intelligent Design!

    Try an evolutionary algorithm next time 😉

  113. 113

    I think there is a real confusion here, between the concepts of adaptation and speciation.

    I think it’s really important to distinguish between lateral change (two sub-populations diverging) and longitudinal change (adaptation of a single lineage over time).

    Of course both can occur without any new proteins, as you point out.

  114. 114
    markf says:

    I just looked over the comments above – especially those from Gpuccio (whom I still respect immensely).  It is really striking how this conversation and indeed almost every conversation on ID turns to the perceived failures of "Darwinism" to explain certain evolutionary events.  There is nothing about the failure of design to explain certain evolutionary events because there are no such explanations. Despite several challenges to describe  a design hypothesis about how a particular thing evolved there is no attempt to do so (see below for a list of challenges). The closest anyone can come is one of the following:

    * Describe even more vividly why they don’t think conventional random mutation could have achieved a particular evolutionary development.

    * Wax lyrical about how the resulting development was cleverly engineered

    * Describe the resulting development in detail (but make no attempt to show how that development was implemented by the designer)

    This isn’t surprising because it isn’t possible to describe a design event, or the evidence for it, without saying something about who/how/why.  While ID refuses to rise to this challenge it is condemned to assessing the implausibility of other people’s hypotheses rather than making its own. 

    List of challenges above (in reverse order):

    15.1.1.1 Petrushka

    I would concede your generosity if you could supply even one specific design event in detail, along with your evidence

    14.1.1.1 markf

    Meanwhile can you point to a single ID paper that gives any account of the development of any aspect of any protein?

    13.2.2 Pretrushka

    Could you list the details of a few design events, in specific detail, and your evidence that they were design events?

    11 Timbo

    I would love to see ID offer an explanation for how this (microbe to Mozart) happened.

    10.1.1 wd400

    Can you show me where creationists predicted reproductive isolation, and explain to me what they means for that matter

    (Note Joseph’s response was: “It in the Bible”)

    3.1.1.1.2 markf

    You are one of the few IDists that has openly discussed possible mechanisms but these are only a few informal conjectures at very high level. I don’t think you mention any specific transition – not even at the phylum level (most IDists would refuse to go even that far).

  115. 115
    gpuccio says:

    Mark:

    Sometimes darwinists really can’t see the obvious. Some possible answers (just the most important):

    1) OOL. Design scenario: In a relatively short span of time, at most a few million years adtre the planet becomes physically apt for life, LUCA appears on earth. It is probably a wholly functional prokaryote, with more than half the basic protein information necessary for life as it has always been observed. It is the product of a very intense design process, that allows the biggest leap in natural history, that from inanimate matter to life.

    Evidence: There is no evidence or convincing model of any precursor for LUCA. There is no example of life simpler than prokaryotes. There is no explanation for the almost sudden formation of most of basci protein information.

    Research must address the following issues:

    a) How old is really LUCA on earth.

    b) How unlikely is the origin of basic protein domains

    c) Can life exist in simpler, or completely different, forms?

    d) How could the higly syncrhonized information necessary for transcription and translation happen?

    e) What are the functional requirements for minimal life, and why?

    f) What were the immediate necessities solved by the initial design, and are they still valid now for all living beings?

    Well, I have no more time now. But try to think yourself to the transition to eularyotes and the Ediacara and Cambrian explosion, and to the successive appearance of each new basci domain, including the most recent, as obvious examples of design events to be investigated.

  116. 116
    kellyhomes says:

    Gpuccio,

    it is the product of a very intense design process

    And you know this how, exactly?

    Evidence: There is no evidence or convincing model of any precursor for LUCA.

    And therefore design? Hardly.

    There is no explanation for the almost sudden formation of most of basci protein information.

    And by “sudden” you mean what? What is “almost sudden”? We both know you are still talking about millions of years. Hardly sudden. Or even “almost sudden”.

    But try to think yourself to the transition to eularyotes and the Ediacara and Cambrian explosion, and to the successive appearance of each new basci domain, including the most recent, as obvious examples of design events to be investigated.

    And yet when I ask Kariosfocus about how these things can be investigated he get’s all huffy and tells me to stop looking to the past, design in the past has been confirmed (but he can’t tell me anything about it).

    So, why don’t you and KF get together and work out your differences with regard to what can and cannot be investigated and then perhaps then investigate what remains? Perhaps you could even publish a paper between you, if the Darwinist police are busy with OWS…

    d) How could the higly syncrhonized information necessary for transcription and translation happen?

    Well, even I know the answer to that one! “It was designed!”

    It seems to me that every question ever asked here is answered with “it was designed” with no actual detail following.

  117. 117
    Acipenser says:

    gpuccio, How do you know that the design process was intense? Where the designers short on ingredients? No clean glassware> Instruments on the fritz?

    What exactly led you to the conclusion that the design process was intense versus say trivial or perhaps even serendipitous from another of the designer(s) research projects?

    That’s quite a claim you make and we are all assuming that you can support it

  118. 118
    Petrushka says:

    Using the numbers supplied by gpuccio, there’s a sudden appearance of a new protein domain, on average, every 12 million years. Mostly in pre-eukaryotic microbes.

  119. 119
    Petrushka says:

    I’m not sure how one determines that a three billion year old event was sudden, or that it had no incremental precursors.

    That seems to be a mystery.

  120. 120

    For the sake of argument I’ll grant the Darwinist his unassailable belief in spontaneous generation (although I thought this notion was disqualified by Pasteur in the 19th century).

    No, it was not disqualified by Pasteur in the 19th century. What was falsified by Pasteur in the 19th century was the hypothesis that maggots were spontaneously generated in decaying meat.

    That has nothing to do with the hypothesis that simple Darwinian-capable self-replicators emerged spontaneously in an environment of non-replicators. But let’s accept your the point hypothetically, as you graciously offer 🙂

    There has been no forthcoming evidence that such a process has taken place, or could have taken place, even given the most optimistic assumptions.

    Yes, there is quite a lot of good evidence in recent OOL research.

    Given the assumption that a self-replicating primordial cell actually did spontaneously generate from inanimate matter through chance and necessity, one must logically ask how the proposed Darwinian mechanism could create the incredible results that are attributed to it.

    Sure.

    The reason I used the microbe-to-Mozart example was not just for purposes of alliteration; it was to plant seeds of doubt (an apparently hopelessly futile endeavor) in the Darwinist mind, which is still frozen in the 19th century.

    OK, but let’s drop the rhetoric and address your direct question about how Darwinian evolution can generate complexity.

    That is fairly straightforward, and is well-illustrated by evolutionary algorithms – you start with a population of simple self-replicators that replicate with heritable variance and place them in an environment in which their probability of reproducing is dependent on being able to exploit that environment in that way, or avoid its hazards, and very rapidly you find yourself with a population of individuals that can perform more functions and exhibit more complexity than the population you started with.

    Go a little further, and provide a rich enough environment, and speciation will tend to occur. One lineage may evolve the ability to exploit an resource not exploited by another lineage.

    Now take that up a level, and think in terms of lineage survival as well. Lineages in which the self-replication system generates an optimal rate of variance production – not too much, not too little, will tend to adapt to more environments, and this speciate more readily, as well as adapting longitudinally to environmental changes more readily. Those lineages are less likely to go extinct than other lineages, and even if some lineages are wiped out by catastrophe, some descendent lineages have a chance of surviving.

    Now keep going, and lineages that hit on some method of swapping and recombining during reproduction, so that instead of cloning themselves, they “mate” in some way, exchanging genetic material. Now evolution can speed up, because beneficial sequences can be propagated independently of deletious ones, resulting in the concentration of beneficial alleles in individual organisms, as well as the maintenance of a pool of variance that enables the population to adapt to changing environmental conditions, and to speciate to exploit new niches.

    Now consider lineages that have evolved some basic motility, and resource/hazard detection mechanism, perhaps initially a mere reflexive response to chemical signals, but hugely enhancing survival. We have the beginnings of predictive ability, with survival-enhancing behavioural responses to threat and promise.

    Also the beginnings of the capacity to respond to chemical signals from organisms of their own species, laying the foundations for multi-cellular organisms.

    Keep going, and you start to get predation behaviour, and simple behavioural planning.

    We’ve come along way towards Mozart already! I think I’ll stop there, and say “the rest is history”.

    In my opinion, microbe-to-Mozart materialistic philosophy requires a helluva lot of blind faith.

    No, just straightforward logic and an unimaginably large number of generations and organisms.

    I mention Mozart because human life is obviously so much more than just survival and passing on one’s selfish genes. It’s about purpose, meaning, ethics, values, art, music, mathematics, creativity of all sorts, and yes, science, which should be about pursuing the evidence wherever it leads.

    Of course. With forward modelling and the ability to select actions based on remote goals, organisms started to free themselves from what I call “the tyranny of the immediate”. And with language capacity came the opportunity to bootstrap ourselves into a state where those goals could be represented symbolically, and not only were we free from the “tyranny of the immediate” but could command a representation of time itself, with abstract learning, abstract planning, understanding of consequences, theory of mind capacity, andn with it, the ability to understand the minds of others, and their feelings, and the capacity for compassion. And the capacity to reify beauty, and create it for sheer pleasure.

    There is an obviously huge discontinuity between humans and all other life forms, which Darwinists seem to have a pathological obsession denying.

    Not at all. There is certainly a very obvious point of deflection, I wouldn’t call it a discontinuity, and we know, from the skulls of our forbears, that our brain evolution was incremental, if not linear. But I’d say that the huge non-linearity was the ability to transmit culture, and especially by way of language. Once you have cultural transmission, you have a whole new vector for inheritance. And once you have language you not only have a whole new vector for culture, but an environment in which language capacity itself will be hugely beneficial, in terms of reproduction.

    That’s what I mean by “bootstrap”. Yes, I think humans are qualitatively different from all other animals, in that the magnitude of the quantitative difference between our cognitive capacity and that of our nearest primate relatives is colossal. And specifically, allows us to do supremely well some things that the smartest of them can only do to very slighlty degree, namely represent events in time symbolically, and abstract concepts including the theory that minds exist and are possessed by others (“Theory of Mind capacity”)

    Those are the capabilities that gave us Mozart, IMO, and Gil 🙂

    It was a long journey, but worth it:)

  121. 121
    markf says:

    OOL. Design scenario: In a relatively short span of time, at most a few million years adtre the planet becomes physically apt for life, LUCA appears on earth. It is probably a wholly functional prokaryote, with more than half the basic protein information necessary for life as it has always been observed. It is the product of a very intense design process, that allows the biggest leap in natural history, that from inanimate matter to life.

    This is a design event in detail! Suppose I were to speculate:

    In a relatively short span of time, at most a few million years adtre the planet becomes physically apt for life, LUCA appears on earth. It is probably a wholly functional prokaryote, with more than half the basic protein information necessary for life as it has always been observed. It is the product of chance combination of chemicals, that allows the biggest leap in natural history, that from inanimate matter to life.

    Would you not think I had failed to explain anything?

  122. 122
    gpuccio says:

    Guys,

    I find some of our questions rather strange, but I will try to answer just the same.

    Kellyhomes:

    And therefore design? Hardly.

    I really don’t follow here. We have a full proteome that appears evidently to be designed (even Dawkins admits that concept). We have no model or evidence for a non designed origin of that information. The only existing model, neo darwinism, comnpletely fails, and can find no support both in logic and evidence.

    Of course design is a very goos explanation, in this context. Why shouldn’t it be? Of course we have the cognitive and moral duty, as scientists, to try to interpret existing data in a design perspective. It is really obvious. It si only the dogmatism of the new reductionist religion that evokes such fiery objections from all of you. Good for you, it’s your choice, but I am certainly not impressed by your “arguments”.

    I suppose that the “and therefore design” objection expresses again a very common mistake: the design inference is not a logicl deduction, but an empirical inference. I have already discussed that many times.

    And by “sudden” you mean what?

    I mean at most a few hundred million years for the generation of about 1984 new independent basic protein domains out of 3464, acoording to this paper:

    http://www.plosone.org/article.....ne.0008378

    in a context where lvining and reproducing prokaryotes did not yet exist, and the mechanism of DNA storage for biological information, transcription, translation and protein synthesis could not exist, because they need exactly many of those domains.

    While, in the remaining 3 billion years, and with a full prokaryotic world alredy in existence, only about 1500 new domains have been added.

    That is a really sudden accumulation of complex functional information.

    So, why don’t you and KF get together and work out your differences with regard to what can and cannot be investigated

    KF is a friend and a great contributor to this blog. I sgare with him a lot of views. But, obviously, each of us responds for himself. So, please be kind and ask him your questions about what he says, and ask me your questions about what I say.

    Perhaps you could even publish a paper between you, if the Darwinist police are busy with OWS…

    The darwinist police is busy enough. But the simple fact is, I am a MD, i am not going to publish or do research in the lab about these things. Am I allowed to discuss on a blog such as this? Or do I need your permission?

    Behe, Axe, and others have published. Let’s make a deal: give us the resources and money, and we in ID will publish much more.

    Well, even I know the answer to that one! “It was designed!”

    Now you are reasoning!

    with no actual detail following

    But the details will follow. If the academic world just accepts the design scenario as a legit scientific hypothesis, and if a serious effort is done by the biological community to interpret existing data in a design framework, you will see…

  123. 123
    gpuccio says:

    Petrushka:

    Using the numbers supplied by gpuccio, there’s a sudden appearance of a new protein domain, on average, every 12 million years. Mostly in pre-eukaryotic microbes.

    Correct. And so?

    I’m not sure how one determines that a three billion year old event was sudden, or that it had no incremental precursors. That seems to be a mystery.

    It is not a mystery that LUCA has left traces in the proteome, and is a supported scientific hypothesis.

    It is not a mystery that there is no trace at all of precursors for LUCA, neither in proteome or fossils, or simply in credible lab models.

    Life as we can observe it requires the prokaryotic design, with all its basic functions. That is a fact.

    The rest is unsupported speculation.

    Science can certainly speculate, but it has the duty to reason primarily on existing facts.

  124. 124
    gpuccio says:

    Mark:

    It is the product of chance combination of chemicals, that allows the biggest leap in natural history, that from inanimate matter to life.

    It’s strange that you still miss the point.

    Let’s try again:

    a) A chance combination of chemicals cannot generate that kind of functional information. That can be demonstrated, and is at the core of ID theory.

    b) An input of outer information from a conscious intelligent being, in any form, can generate huge amounts of comlex functional information. Human artifacts, including all GAs, and huma protein engineering, are an obvious demonstration of that.

    So, a design scenario can explain complex functional information. Obviosuly, many questions remain, as you correctly say: how, when, with what purpose, in what times was the information inputted?

    Those are all legitimate questions, and in time they will be answered, if we really look for the answers including the design hypothesis in our interpretational framework.

    But there is no doubt that the design hypothesis has the explanatory power to explain dFSCI. While neo darwinism has not that explanatory power.

  125. 125
    gpuccio says:

    Acipenser:

    How do you know that the design process was intense?

    Because it produced almost 2000 basic protein domains in a few hundred million years, plus all the higher information necessary to structure prokaryotes. That is intense, compared to the following natural history, at least in terms of basic protein information, as Petrushka correctly reminds us every day.

    For higher levels of information, we cannot really say, because we lack most of the molecular basis for them.

    What exactly led you to the conclusion that the design process was intense versus say trivial or perhaps even serendipitous from another of the designer(s) research projects?

    The information in prokaryotes in certainly not trivial or serendipitous. If you have any personal information that it came from other research projects (probably intense in themselves too), please let us know. Otherwise, I will stick to what we know: prokaryotes did not exist at the beginning of our planet’s life, and they were designed in the first few hundred million years (maybe much less).

    That’s quite a claim you make and we are all assuming that you can support it

    I think I have supported it. Why do I believe that you will not agree?

  126. 126
    Acipenser says:

    “I think I have supported it. Why do I believe that you will not agree?”

    Likely because you recognize the weakness of your support in comparison to the magnitude of the claim.

    “Behe, Axe, and others have published. Let’s make a deal: give us the resources and money, and we in ID will publish much more.”

    A much better deal is for the IDists to respond to requests for grant proposals by submitting proposals that outline their proposed methodology for researching some aspect of design. There are ample resources available but the IDists need to submit the proposals in order to get the funding.

    “But the details will follow.”

    When? The academic world doesn’t have to accept anything that is as lacking in rigor and cannot produce on it’s promises of producing results using the methods they consider robust and appropriate to the task. The only example I know of is Dembski’s attempt at the calculation for the flagella and that went terribly bad. No wonder so great a period of time has passed with no one else even making the attempt.

  127. 127
    Petrushka says:

    Explain again exactly how you know that protein domain sequences have no precursors. Show me the evidence.

  128. 128
    Acipenser says:

    The paper gpuccio cites certainly suggests that there were likely precursors to the domains found in LUCA. I don’t know why he doesn’t acknowledge that portion of the paper.

  129. 129
    markf says:

    Gpuccio

    It’s strange that you still miss the point.

    That is because we are talking about different points. I am well aware of the argument

    (A) Life contains huge amounts of information and that only intelligent agents can produce information.

    I don’t think it is true but I am not seeking to cover that ground again.

    My point is that ID has not provided a detailed explanation of a single specific evolutionary event (and this impossible without specifying who, why and how). That you have still failed to do. All you have done is repeat A.

    It is important – because without this level of detail we cannot assess wether the ID hypothesis is credible. We know that humans can create things full of information but we do not know of any intelligent being that is remotely capable of creating a prokaryotic cell – particularly 4 bilion years ago.

  130. 130
    gpuccio says:

    Acipenser:

    because I am interested in the facts of the papers, not in the speculations unsupported by facts.

  131. 131
    gpuccio says:

    Acipenser:

    I quote myself:

    “Why do I believe that you will not agree?”

    And the answer is not the one you suggest. Try again.

  132. 132
    gpuccio says:

    Mark:

    we do not know of any intelligent being that is remotely capable of creating a prokaryotic cell – particularly 4 bilion years ago.

    An intelligent non physical being is a viable hypothesis. You may not believe that intelligent non physical beings do exist, but you will admit that the issue has always been controversial in the history of human thought.

    And however, as I have said, the events are there. We must certainly look for the details. I am not repeating the genral principle. I have suggested many fields of research whose results are very likely to be heavily significant for a design – non design debate. OOL is one example. I have given others.

    If researchers gave at least part of the resources which are given to speculating about imaginary RNA worlds to other fields of research, such a serious exploration of the functional protein space, without any prejudice, and a serious definition of minimal life requirements, without any prejudice, the scenario of informational biology could expand.

    Regarding new protein domains which appeared more recently, it could be easier to try to determine with more precision tehir distribution in the genome and the time of their first appearance, and to verify or falsify explicit models for their possible gradual evolution. Or try to understand, in a design perspective, which functional implementations really required the new protein information.

    There is a big differemce even in the approach to the functional study of natural history: darwinists always try to explain things (if and when they try) in terms of reproductiove advantage, because that is the only accepted model. A design analysis needs not do that: it can try to explain things in terms of pure functional requirements, without having to pass through the irrational limitiaiton of reproductiove advantage. That means that we can try to build a hyerarchy of fucntion expression and informational content, and try to explain natural history, and the history of protien information, in those terms.

  133. 133
    Petrushka says:

    LOL. You are interested in facts.

    What facts support your assertion that there are no precursors? What facts support your assertion that some part of a living thing arose spontaneously?

    You have witnessed a living thing arising spontaneously. You have some precedent?

  134. 134
    Petrushka says:

    You may not believe that intelligent non physical beings do exist, but you will admit that the issue has always been controversial in the history of human thought.

    Let’s just say that non-physicality has been extensively searched for, as in decades of research on ESP, and centuries of attempts to communicate with the dead. Aside from occasional anecdotes and vast quantities of fraud, there is not positive evidence and huge quantities of negative evidence.

    Nor is there any conceptual basis for the interaction of physical and non-physical.

    But there is evidence that the physical world accessible to science has unexpected features, such as entanglement, that make it silly to talk about materialism as somehow limited compared to the wholly imaginary spiritual world.

    You have no basis for arguing that mere materialism can’t account for anything. You have no way of setting limits to what science can or cannot study.

    Even (Judeo-Christian) religions implicitly acknowledge the requirement for a physical body in its scripture and creeds, which promise the Resurrection of the body.

    If find it risible that you think you can make claims for the existence of things without evidence, that you can assert that things are inaccessible to evolution, all mathematical evidence to the contrary, and that you assert you know the detailed history of the beginning of protein domains, also without evidence.

    What a joke.

    If ID supporters want to argue about the mathematical ability of programs like Avida to model evolution, how about they make their own programs that better model the math. Publish them for open discussion.

  135. 135
    Joseph says:

    Just show us those precursors then.

    And no one has ever witnessed a living thing arising spontaneously- THAT is the whole problem- no evidence for it.

    BTW you do realize that “spontaneously” means without agency involvement…

  136. 136
    Joseph says:

    markf:

    My point is that ID has not provided a detailed explanation of a single specific evolutionary event (and this impossible without specifying who, why and how).

    Neither has your position. And we don’t have to know who, why nor how before determining design. We figure out those by studying the design.

    But anyway ALL of your objections about ID apply to your position.

    Strange that you don’t realize that…

  137. 137
    gpuccio says:

    Petrushka:

    As I said, it’s controversial.

    I really like when you abandon any pretence at resonable discussion, and just express your blind faith. That’s true passion!

  138. 138
    gpuccio says:

    Petrushka:

    Don’t go on changing subject. I am interested in facts. Or in the lack of them.

    In the paper I quoted there were facts, such as the application of some metrics to protein domains to establish a cronology of the. Facts and theories quantitatively applied to those facts. theories that can be right or wrong, but are anyway interesting, because they are derived from observable facts and try to analyze and explain them.

    But if the same paper, as Acipenser suggests (but I am not sure what part he is referring to), “suggests that there were likely precursors to the domains found in LUCA”, that is a speculation, which is not founded on the data and type of analysis presented in the paper.

    In biological papers we often find those tww things mixed up: interesting data, and ofte interesting analysis, and then completely unwarranted suggestions that all that strngthens darwinist theory.

    As I am really interested in the facts and the realistic analysis of them, I always try to keep the two things separated.

    Darwinists often object: but if you quote that paper, why don’t you accept also the conclusions of the authors?

    The reason is simple: because I don’t agree with the conclusion. Still, I am free, like anybody else, to use the facts, and those parts of the analysis that I find correct, in my reasons and in my discussions.

    That’s called critical thinking, and it is the basis of science.

    You ask: “What facts support your assertion that there are no precursors? ”

    It’s simple: the absolute absence of facts pointing to precursors. And some simple logic.

    The absence of facts is a fact in itself.

  139. 139
    markf says:

    Gpuccio

    An intelligent non physical being is a viable hypothesis. You may not believe that intelligent non physical beings do exist, but you will admit that the issue has always been controversial in the history of human thought.

    It is a hypothesis.  Whether it is open to scientific study depends on its properties (as Lizzie has often pointed out). My point is simply that we have no observable evidence of anything with the ability to do something so extraordinary as create the first prokaryotic life form.

    And however, as I have said, the events are there. We must certainly look for the details. I am not repeating the genral principle. I have suggested many fields of research whose results are very likely to be heavily significant for a design – non design debate. OOL is one example. I have given others.

    If researchers gave at least part of the resources which are given to speculating about imaginary RNA worlds to other fields of research, such a serious exploration of the functional protein space, without any prejudice, and a serious definition of minimal life requirements, without any prejudice, the scenario of informational biology could expand.

    Regarding new protein domains which appeared more recently, it could be easier to try to determine with more precision tehir distribution in the genome and the time of their first appearance, and to verify or falsify explicit models for their possible gradual evolution. Or try to understand, in a design perspective, which functional implementations really required the new protein information.

    There may be less resources going into ID but there is the discovery centre with several full-time fellows working there. There is at least one qualified ID bio-chemist.  And yet not one single paper on how a specific evolutionary event happened

    But what would such a paper look like?  Evolutionary biologists form hypotheses based on mutations, insertions, gene duplications, endo-symbiosis, even epigenetics.  They describe what they think actually happened at varying levels of detail.  Because they make the details explicit the hypotheses can be assessed (as we see repeatedly on this very forum).

    Suppose you come up with a detailed description of how protein domains appeared over time – and even find that they are almost instantaneous.  All this does is raise a question.  How could this have happened? It is not a hypothesis about how they appeared.  There is no hypothesis to be assessed as there is for biologists.  The only way such a hypothesis can be “falsified” is by providing an alternative explanation.

    A design analysis needs not do that: it can try to explain things in terms of pure functional requirements, without having to pass through the irrational limitiaiton of reproductiove advantage.

    But the functional requirements are requirements for reproductive advantage!  How does this ID analysis differ from a list of evolutionary developments and how they help with reproductive advantage? 

  140. 140
  141. 141
    kairosfocus says:

    First, reliable design detection is not detection of designer’s methods. Judge a theory by what it sets out to do. Besides, design methods are not lacking, in general and in the world of life; ranging from genetic engineering, to breeding.

  142. 142
    Petrushka says:

    Because it produced almost 2000 basic protein domains in a few hundred million years

    One thing is obvious. The rate of invention has declined. The rate of invention is always higher in new, unexploited niches. It’s true of human designs. How many new auto companies are starting up compared to the first few decades of automobiles. How many phone companies? there is nothing mysterious about a declining rate of invention.

    But you have simply fabricated an entity with no physical existence, no basis at all in any kind of experience no philosophical support for its mode of interaction with the physical world, no known specific instances, no specific instances of action, no actual need.

    And you expect to be taken seriously.

    How about you actually prove that protein domains sprang fully formed from the head of Zeus and have no precursors?

  143. 143
    Petrushka says:

    So here’s what the rate of new domains looks like:

    4 per million years in the first half billion years.
    1 per 3 million years in microbes
    1 per 2.5 million years in eukaryotes

    Looking at the rate change, it seems likely that the rate was high at first and tapered off pre-LUCA. Give me a reason why this isn’t likely.

    Then give us proof that the new domains were poofed into existence without precursors.

  144. 144
    markf says:

    Joseph

    Right at the moment I am not concerned whether an explanation is true. I am just considering the possibility of making a hypothesis about how an evolutionary event happened. Whether you think they are plausible or not you cannot deny that biologists offer many hypotheses of how evolutionary events happened in varying levels of detail. ID has not offered a single hypothesis about how a specific thing evolved.

    You may argue that is not what ID is about. But the trouble is without an explanation of “how” there is no way of falsifying ID except by demonstrating an alternative explanation is true. If you can think of another way please tell me.

  145. 145

    reliable design detection is not detection of designer’s methods.

    And this is at the heart of the whole disagreement. I think this premise is itself faulty.

  146. 146
    Joseph says:

    Elizabeth,

    Unfortunately for you it happens to be true and is not faulty.

  147. 147
    Joseph says:

    Sorry markF evolutionary biology lacks all detail. For example pertaining to universal common descent no one knows if the transformations required are even possible- that is because there isn’t any detail- none whatsoever.

    Your position cannot muster a testable hypothesis.

    That said the way to falsify any design inference is by demonstrating chance and necessity can produce it. Tat is how it has been throughout history. That conforms with Newton’s first rule.

    And in the absence of direct observation or designer input the only possible way to make any scientific determination about the design or the designer(s), is by studying the design in question.

    That is how it is done in forensics and archaeology.

  148. 148
    markf says:

    Joseph

    Sorry markF evolutionary biology lacks all detail. For example pertaining to universal common descent no one knows if the transformations required are even possible- that is because there isn’t any detail- none whatsoever.

    The paper I linked to in 13 above describes exactly which mutations lead to the development of one type of haemoglobin from another and the associated adaptive advantage.  This is just one of thousands of papers describing hypothesised evolutionary paths for various proteins in similar levels of detail.  You may disagree with them – but if you think they lack detail then what kind of level of detail are you asking for?

    Your position cannot muster a testable hypothesis.

    That said the way to falsify any design inference is by demonstrating chance and necessity can produce it. Tat is how it has been throughout history. That conforms with Newton’s first rule.

    Not sure what you mean by Newton’s first rule but I am glad you confirm my point that the only way to disprove a design hypothesis is demonstrating a non-design alternative.  Design hypotheses get a free pass from the kind of scrutiny that a scientific hypothesis is subject to.

    And in the absence of direct observation or designer input the only possible way to make any scientific determination about the design or the designer(s), is by studying the design in question.

    That is how it is done in forensics and archaeology.

    That is just not true.  In forensics and archaeology you reconstruct how it might have happened and test the plausibility of the reconstruction.

Leave a Reply