Barry Arrington Part II: questions from Phinehas

A very nice post by Barry at UD struck me as worth reposting here (as I can’t post there), inspired by Neil Rickert:

Phinehas asks Neil Rickert a fascinating question about the supposed direction of evolution.  Neil says he will address it in a separate thread, and I started this one for that purpose.  The rest of the post is Phenehas’ question to Neil:

@Neil I also appreciate the professional tone. I am a skeptic regarding what evolution can actually accomplish. In keeping with your demonstrated patience, I’d be grateful if you would give serious consideration to something that keeps tripping me up. I’ve often thought of natural selection as the heuristic to random mutations’ exhaustive search.

A path-finding algorithm can be aided in finding a path from point A to point B by using distance to B as a heuristic to narrow the search space. Without a heuristic, you are left to blind chance. It is said that evolution has no purpose or goal, so there is no point B. It is also claimed that evolution isn’t simply the result of blind chance, so a heuristic would seem to be required. Somehow, natural selection is supposed to address both of these concerns. Nature selects for fitness, we are told, so somehow we have a heuristic even without a point B.

But what is fitness? How does it work as a heuristic? How is it defined? Evidently, it is all about reproductive success. But how does one measure reproductive success? This is where things get fuzzy for me. Surely evolution is a story about the rise of more and more complex organisms. Isn’t this how the tree of life is laid out? Surely it is the complexity of highly developed organisms that evolution seeks to explain. Surely Mt. Improbable has man near its peak and bacteria near its base. But by what metric is man more successful at reproducing than bacteria? If I am a sponge somewhere between the two extremes, how is a step toward bacteria any less of a point B for me than a step toward man? Why should the fitness heuristic prefer a step upward in complexity toward man in any way whatsoever over a step downward in complexity toward bacteria?

It seems that, under the more obvious metrics for calculating reproductive success, bacteria are hard to beat. Even more, a rise in complexity, if anything, would appear to lead to less reproductive success and not more. So how can natural selection be any sort of heuristic for helping us climb Mt Improbable’s complexity when every simpler organism at the base of the mountain is at least as fit in passing on its genes as the more complex organisms near it’s peak? And without this heuristic, how are we not back to a blind, exhaustive search?

 

Excellent questions.

273 thoughts on “Barry Arrington Part II: questions from Phinehas

  1. Phinehas: whether I ever change anyone’s mind or not

    I don’t understand? What are you trying to change my mind about?

    If you are trying to make me change my mind about what evolution can accomplish then I don’t see how you’ve attempted to do that. Rather you’ve asked some questions, and got some answers.

    I’ve always preferred dialectic methods, especially when addressing skepticism, since I typically find myself with lots of questions.

    My point is then that you are asking questions to learn about this subject, not putting forth arguments against what evolution can accomplish? If you consider your skepticism about what evolution an accomplish and your questions to be potential triggers for skepticism in those that are answering them, then fine.

    But this does not address the technical data.

    It even seems possible to me that the added complexity could be viewed as a very slight decrease in fitness that (for the present) would not adversely affect reproductive success, allowing it to spread through the population, but as the described process repeated and complexity grew without increasing fitness, rising brittleness and fragility could reach a point where the accumulation of slight decreases in fitness would reach a tipping point.

    Great. Many things are possible. I’m no expert, just an interested amateur. But the fact is that what you are talking about here is not new nor some amazing insight.

    http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution

    The neutral theory of molecular evolution states that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants (not affecting fitness).[1] The theory was introduced by Motoo Kimura in the late 1960s and early 1970s. Neutral theory is compatible with Darwin’s theory of evolution by natural selection: adaptive changes are acknowledged as present and important, but hypothesized to be a small minority of all the changes seen fixed in DNA sequences.

    I don’t see how you can reasonably think that someone who professes no particular expertise in the subject (I believe you’ve said as much) can reveal some facet of the argument that people who have spent their lives looking at this have failed to reveal.

    Or perhaps I’ve misread your intent 🙂

  2. Lizzie,

    The domain name is not the issue, it’s pointing correctly. The problem is telling the system what to do when a file name is not specified. http://www.theskepticalzone.com/wp/index.php works fine because the file name is specified. You may have lost your .htaccess files in the great hack. Connect to your host with FTP or equivalent. In public_html/wp there should be a file named .htaccess (that’s right, a period is the first character of the file name) that should at least contain:

    # BEGIN WordPress
    
    RewriteEngine On
     RewriteBase /
     RewriteCond %{REQUEST_FILENAME} !-f
     RewriteCond %{REQUEST_FILENAME} !-d
     RewriteRule . /index.php [L]
    
    # END WordPress

    If that doesn’t help, assuming you don’t have other sites hosted at the same place, you need to have:

    # BEGIN WordPress
    
    RewriteEngine On
    RewriteBase /wp/
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule . /wp/index.php [L]
    
    # END WordPress

    in public_html/.htaccess.

    “.htaccess” is case-sensitive, and can be created in any plain-text editor.

  3. Phinehas,

    OK, but how long do we suppose that potentially rich but currently useless patch will hang around waiting for Gould’s “almost, but not quite, never?”

    In the case of gene duplication and variation, the duplicate is not subjected to purifying selection. In the case of Lensky;s experiment, the answer is, long enough.

    My question for gpuccio and friends is, how does a designer know which neutral mutations to create and preserve so that they might, in combination with some future mutation, enable a new function?

    Lensky’s answer, supported by observation, is that a population of bacteria can “test” every possible point mutation in a reasonable amount of time.

    It might also be relevant that other researchers have demonstrated that about two-thirds of the bases on a protein coding gene can be modified to any arbitrary value without significantly altering the fold. And that some mutations enable dual functionality, making a transition to new protein possible without losing old functionality.

    All relevant research supports the standard model of duplicate and diverge as adequate to explain the origin of new proteins. Which doesn’t change the fact that in the entire biosphere, new proteins occur only every one or two million years.

    That’s a tough experiment to replicate. But then we have yet to observe a full orbit of Pluto either.

  4. Lizzie,

    And an evolvable population is less brittle. Which seems to be important considering that geological eras seem to reflect mass extinction events.

    Just my intuition, but it seems like repeated sudden changes in the physical environment would favor evolvable populations.

  5. Phinehas:
    Lizzie:

    OK, but how long do we suppose that potentially rich but currently useless patch will hang around waiting for Gould’s “almost, but not quite, never?

    Well, non-coding sequences are not conserved, so the longer it hangs around, the further it will move from its original sequence, and probably, the further from something readily mutatable into something useful. But we know that at least some genes owe their origins to a duplication, and even duplicates, it turns out, tend to be conserved (something I learned, incidentally, from Joseph Bozorgmehr, of all people!). And many point mutations of coding sequence result in viable, sometimes identical, sometimes slightly different, proteins, so it may not have to hang around long before we have a useful additional gene.

    ”There’s also every chance that the resulting gene (should it ever manifest) will be negative, though we’d assume that organism would be weeded out and not significantly impact the population.

    Well, that’s really the point – once the duplication has happened, and has started to spread through the population (as it has a fair chance of doing, by drift, even if it is non-advantageous) then only near-neutral or beneficial mutations to it will tend to remain in the population. So while it does something, it will tend to be conserved in viable form. And there may be several viable forms.

    On the other hand, there’s an even greater chance that the resulting gene (should it ever manifest) would be neutral, in which case it could wellspread throughout the population.

    Yes.

    It even seems possible to me that the added complexity could be viewed as a very slight decrease in fitness that (for the present) would not adversely affect reproductive success, allowing it to spread through the population, but as the described process repeated and complexity grew without increasing fitness, rising brittleness and fragility could reach a point where the accumulation of slight decreases in fitness would reach a tipping point.

    Well, you are absolutely right that near neutral, including slightly deleterious genes or alleles can propagate through a population by drift. But in a sexually reproducing population, at least, genome segments that are in some deleterious way “weighted down” by non-functional junk will tend to decrease in prevalence – so if the “tipping point” is reached then the affected genomes will tend to drop out of the pool. Are you thinking of Sanford’s “Genetic Entropy” concept here? He makes a large number of mistakes in that book.

    So it seems to me that greater complexity without greater fitness is at least as likely an outcome as greater complexity with greater fitness, isn’t it?

    Well, no – for a given amount of complexity, the trait that confers greater fitness will become more prevalent than the trait that confers less. So let’s take four scenarios:

    1. more complex genome, fitter phenotype
    2. more complex genome, less fit phenotype
    3. less complex genome, fitter phenotype
    4. less complex genome, less fit phenotype

    We’ve agreed (I think) that A and B are more likely than B and C or D (there are more ways to complicate a thing, than simplify it). And of A and B, B will tend do drop out of the population, whereas A will tend to become more prevalent. Same is true for C and D. So the most prevalent genomes will be A, the next most prevalent C, and B and D will tend to drop out of the gene pool.

    Conceivably, greater complexity with a decrease in fitness is also a plausible outcome.(Not only plausible, but as pointed out before, something that seems pretty apparent when we take a high view of all organisms and compare their complexity and reproductive success.)All of which leads me back to trying to figure out how complexity and reproductive success could possibly be correlated.

    Well, as I keep saying, I think they are non-causally correlated! Time tends to complicate things (increase entropy/complexity); time tends to increase fitness (less fit variants leave fewer copies of their genome).

    So I ask you (nay, I beseech you :)):Does it appear that my skepticism, at least at this point, could possibly be reasonable?

    Yes, indeed. The key question you have raised is: are more complex variants more likely to be generated de novo than less complex ones? I think the answer is yes, but I don’t know the answer for sure. It’s certainly find-outable – Joe Felsenstein is the one to ask!

    Whether valid or not, are my objections at least understandable?Do I in any way demonstrate a lack of willingness to consider that I might be mistaken?Might my motivations be characterized by an honest search for the truth of the matter?

    Looks that way to me 🙂

    If I’ve given you cause to question your beliefs, not about evolution, but about those who are skeptical regarding what it can accomplish, then I would consider my visit here fruitful, whether I ever change anyone’s mind or not.I think it is often a lack of doubt rather than a lack of faith that tends to get in the way of progress in these sorts of discussions.I think there is more than enough faith on both sides to go around.

    Oh, I agree. And the fact is that none of us have any hope of becoming so expert on everything that we can verify findings for ourselves. Even peer-review is a very crude filter-outer of the frankly invalid. We all have, to some extent, to take some things on trust. Evaluating conflicting arguments and evidence isn’t easy. But it’s a necessary skill in science! In fact, one of the modules I teach is critical evaluation of scientific papers. It’s all too easy to read the intro and discussion and miss out the methodology and equations in the middle!

  6. @petrushka

    My question for gpuccio and friends is, how does a designer know which neutral mutations to create and preserve so that they might, in combination with some future mutation, enable a new function?

    I’m certainly not the expert that gpuccio is, but in my experience, designers plan for contingencies all the time.

    I’m also tempted to point out how useful the quality of being able to see the future as easily as the past might be for your theoretical designer, but will try to resist. 🙂

  7. Phinehas,

    Being omniscient would certainly be an advantage for a designer. In the case of biology I think it might be a prerequisite.

    But that would male biology rather unique among sciences. In every other field, science looks for explanatory regularities.

    Sometimes they are difficult to find. In the case of gravity, several hundred years have not been sufficient, even though irregularities occur only at size extremes.

    My point would be that science needs to be patient when facing the unexplained. there is no precedent in science for ID-like explanations becoming useful, except when the designer is visible and has known capabilities.

  8. OMagain:

    Then I would ask “what is your current personally accepted explanation for the issues being discussed in this thread”?

    Honestly, if life were reduced down to simply a question of the origin of species, I would probably lean pretty strongly toward an “I don’t know” at this point. But I tend to view things from a more holistic perspective from which I also wonder about:

    – the origin of matter
    – the origin of universal constants that appear finely tuned
    – the origin of physics and natural laws
    – the origin of information
    – the origin of life
    – the origin of consciousness
    – the origin of reason
    – the origin of morality
    – the origin of love

    I feel no particular compunction to rule out the possibility that these things are what they are by design. In fact, I personally find this a more intellectually satisfying conclusion than any other on offer. Probably by a pretty decent margin. So, when it comes to considering the origin of species, though I try to have an open mind and follow the evidence wherever it leads, I’m also not inclined to ignore the previous conclusions I’ve tentatively reached. Even so, I definitely don’t feel that things like common descent are settled issues for me. I just tend to suspect, when all is said and done, that ultimate causes will end up being the work of design and not blind chance.

  9. Phinehas: Honestly, if life were reduced down to simply a question of the origin of species, I would probably lean pretty strongly toward an “I don’t know” at this point.

    Ok, given that there is a limited list of possibilities, please list those possibilities in order of likelihood, or plausability to you personally.

    We know that “Darwinian evolution” will not be at the top of that list. Or do we?

    Whatever is at the top of your list I won’t hold you to that! It’s just speculation. But I think you see the point I’m trying to make….

    Or to put it another way, out of all the options you are aware of what do you consider to be the one with the most support? The second on that list? The third?

    I feel that you are trying to get me to be skeptical about a thing that you yourself already accept and believe is right.

    Phinehas: So, when it comes to considering the origin of species, though I try to have an open mind and follow the evidence wherever it leads, I’m also not inclined to ignore the previous conclusions I’ve tentatively reached.

    But ignoring the evidence (more evidence that you actually support Darwinism as the explanation here) in preference to your prior beliefs is hardly an argument for skepticism is it?

    Phinehas: Even so, I definitely don’t feel that things like common descent are settled issues for me.

    What evidence would you need to see that would decide the issue of common descent?
    Is that evidence within the scope of science to provide?
    Given that the preponderance of evidence is for common descent, from multiple independent strands, what is the bit of evidence that is preventing you from accepting it? There must be some particular thing that you can point at as counter evidence? If not, why is it not settled?

  10. petrushka:

    Being omniscient would certainly be an advantage for a designer. In the case of biology I think it might be a prerequisite.

    I tend to agree.

    But that would male biology rather unique among sciences. In every other field, science looks for explanatory regularities.

    I’m not so sure. Without quibbling over definitions of science, most of the questions I posed above are germane to one area of the hard or soft sciences or another (or a simple desire to know what is true), and they seem pretty resistant to explanatory regularities to me.

    My point would be that science needs to be patient when facing the unexplained. there is no precedent in science for ID-like explanations becoming useful, except when the designer is visible and has known capabilities.

    I totally agree regarding science’s patience, and would suggest that humility might also be a useful characteristic. 🙂

    Also, to be honest, you throwing in “except when the designer is visible and has known capabilities,” engenders all sorts of skepticism in me. It implies that, well, yes, there is in fact a certain usefulness to some ID-like explanations. (To deny this would be to deny the kind of useful inferences made in forensics and archaeology.) To be frank, the inclusion of your qualifier appears, at best, arbitrary to me. (I want to believe the best and not start speculating about other motives.) I can think of no reason whatsoever to assume visible designers with known capabilities are more subject to ID-like explanations than are designers who are not currently visible and whose capabilities (beyond the capability to design the artifact that is being examined) are unknown.

  11. Phinehas has (here) asked:

    [quoting me]: Meanwhile advocates of ID repeatedly try to give their readers the impression that evolutionary biologists refuse to be quantitative.

    Quantitatively speaking, how do evolutionary biologists express the “fitness” of a man vs. a microbe?

    One can compute the Intrinsic Rate of Natural Increase of each, for example. That is the growth rate that would result from the measured age-specific birth and death rates. Man cannot reproduce (Man can when Woman is present, though). Human populations can roughly double every 30 years, while some bacterial populations can double every 20 minutes, under favorable conditions.

    However, as they are not competing perfectly for the same resources, one cannot project from this that bacteria will outcompete humans, or even that fast-growing species of bacteria are going to outcompete slower-growing species of bacteria. And that’s why there are multiple species around, including why there are both humans and monkeys around.

    The theory of population growth is quite quantitative and mathematical. It is part of Theoretical Ecology and part of Demography. If Phinehas’s point was that evolutionary biologists weren’t being quantitative, this should refute that: there are (many) thousands of scientific papers doing this theory, and quite a few books too. But then again, I don’t really understand what Phinehas’s point is.

  12. designers who are not currently visible and whose capabilities (beyond the capability to design the artifact that is being examined) are unknown.

    And herein lies the rub. Given that any event at all can be ascribed to the whim of such a “designer” it’s actually not useful at all as an explanatory device.

  13. OMagain:

    As to likelihood or plausibility, again, it depends on scope. There are some things about evolution that I find uncontroversial (microevolution), other things that I find plausible (speciation), and still other things that I find speculative (universal common descent). I know that evolution tries to avoid OOL questions, but I don’t feel particularly compelled to set aside the possibility that both origins might have the same, or a related answer. It seems to me that the answer to OOL may have major implications and ramifications on OOS.

    The most compelling support I’ve seen for at least some form of common descent has been (and please forgive my poor, layman’s attempt at this) what I understand to be the discovery of the same exact (viral?) insertions of DNA sequences apparently being inherited from what is believed to be an ancestral species. Even though I feel this could be explained away by appealing to an intelligent designer using “spare parts” or “code reuse” that happened to retain the insertion, I don’t really find that a very compelling objection.

    On the other hand, there is a lot of evidence presented in favor of evolution that I think can be explained just as readily by intelligent design.

    And on the third, mutated hand, I think that ID makes some very compelling points regarding things like the rise of information, semiotics, functional complexity, etc. Much of it rings true to me, though there are still areas where I think explanations are fuzzy, hopeful, or perhaps a bit forced.

    So, staying strictly within the scope of the origin of species, I don’t really know. I may lean slightly toward ID? Maybe? But I find things both compelling and skeptical on both sides.

    But when I widen the scope to include a general search for truth in all areas of life, appeals to design tend to win out over chance pretty consistently, and I’ve no doubt that this affects the ID vs. evolution debate for me.

    But ignoring the evidence (more evidence that you actually support Darwinism as the explanation here) in preference to your prior beliefs is hardly an argument for skepticism is it?

    Indeed not! But I don’t think I would ever characterize my approach as ignoring evidence. From time to time, there will definitely be evidences that appears to contradict each other, so I suppose you might say that, providing you can find no way to reconcile the two, you will end up discounting one over the other, but I think of this more in terms of weighing evidence than ignoring it.

  14. Phinehas: On the other hand, there is a lot of evidence presented in favor of evolution that I think can be explained just as readily by intelligent design.

    This is the problem. It can all be explained by intelligent design. This is why intelligent design is so sterile.

    The Cambrian explosion. Intelligent design.
    The bacterial flagellum. Intelligent design.
    DNA. Intelligent design.

    So, staying strictly within the scope of the origin of species, I don’t really know. I may lean slightly toward ID? Maybe? But I find things both compelling and skeptical on both sides.

    You’ll have to fill me in then. What is the Intelligent Design explanation for the origin of species other then “species were designed by an intelligent designer?

    Darwin wrote a book all about his view. I don’t seem to remember the equivalent from the ID perspective. Yet you find that case compelling, despite the additional work since Origin was first published?

    But I don’t think I would ever characterize my approach as ignoring evidence.

    But that’s exactly what you are doing, like it or not. When you say that intelligent design “explains away” something that’s no different to simply ignoring it.

  15. Phinehas: But when I widen the scope to include a general search for truth in all areas of life, appeals to design tend to win out over chance pretty consistently, and I’ve no doubt that this affects the ID vs. evolution debate for me.

    Ah, I see, I think. You think the universe cares about you! I suspect if you were sitting in a different situation to being in front of a computer you might change your opinion quite quickly. If you were in a terrible situation would you ascribe that to “design” as quickly as you would good luck?

    I think that ID makes some very compelling points regarding things like the rise of information, semiotics, functional complexity, etc. Much of it rings true to me, though there are still areas where I think explanations are fuzzy, hopeful, or perhaps a bit forced.

    The “ring of truth” is a deceiver.

    We’ve learned from experience that the truth will come out. Other experimenters will repeat your experiment and find out whether you were wrong or right. Nature’s phenomena will agree or they’ll disagree with your theory. And, although you may gain some temporary fame and excitement, you will not gain a good reputation as a scientist if you haven’t tried to be very careful in this kind of work. And it’s this type of integrity, this kind of care not to fool yourself, that is missing to a large extent in much of the research in cargo cult science.

    https://en.wikiquote.org/wiki/Richard_Feynman

    This is why we don’t usefully explore the universe by virtue of what “rings true”. What seems right is often not. Which is one reason why humans were around for so very long without the spectacular ascent in technological power we see now. What “rung true” did not allow progress in that regard.

    I’m not sure what your point is and you’ve failed to make any kind of argument for ID that seems more useful then then equivalent.

  16. OMagain:

    Given that any event at all can be ascribed to the whim of such a “designer” it’s actually not useful at all as an explanatory device.

    My skeptical spidey sense is doing a full-on jitterbug over this one. 🙂

    Are you seriously claiming that if SETI received what appeared to be a transmission of the first 128 digits of pi beamed from a distant galaxy, that such an occurrence could not possibly explain anything of use to science, given that it could be ascribed to the whim of an unknown designer with unknown capabilities?

  17. Phinehas: Are you seriously claiming that if SETI received what appeared to be a transmission of the first 128 digits of pi beamed from a distant galaxy, that such an occurrence could not possibly explain anything of use to science, given that it could be ascribed to the whim of an unknown designer with unknown capabilities?

    No. What I’m saying is that when ID proponents claim that X is explained by intelligent design they can construct no test to show that is or is not in fact the case.

    For example. The claim is that cancer is caused, in part, by smoking.

    ID supporters can say “cancer is caused by intelligent design” and there is no way of disproving that. Even when shown evidence that smoking leads to increased levels of cancer “that is also by design”.

    For example, one of JoeG’s usual arguments is this

    Just because we observe mutations occurring doesn’t mean the blind watchmaker didit.

    The “Skeptical” Zone, Where You Can Be Skeptical of Anything (Except Currently Fashionable Intellectual Dogmas)

    We observe mutations. We note the fact that they appear to be random with respect to function. Joe uses this as evidence that we don’t in fact know that was by intelligent design.

    And he’s right, we can’t know that some unknown agent with unknown powers caused the result that we observe.

    And that’s why these ideas are not useful to science. They are not excluded, as ID proponents claim, because “scientists want atheism to be true”, they are excluded because adding “or it was by the whim of an intelligent designer” to the end of every scientific paper would get old quickly.

    So were we to find a signal from SETI as you describe we’d ascribe it to an unknown designer, sure. Would it explain anything useful to science? Not really, we know pi to more digits then that. But we’d know we are not alone.

    So your spidey sense needs to be re-calibrated. This is a well worn path.

  18. From earlier today, the question of why evolution would lead to complexity when simple does just fine was discussed. One thing I’ll note from my work in ecology is that in general terms, complexity buys organism populations flexibility when it comes to environmental perturbations. For a number of reasons, simple organisms can withstand significantly narrower variations in their environments without major population decreases than more complex organisms. For example, the more complex an organism is, the more ways it can move to a different environment, the quicker it can move to a different environment, and the better chance it has of being able to immediately utilize – however comparatively inefficiently – new resources in a new environment. In other words, more complex organisms are generally more adaptable. In other cases, more complex species can tolerate a greater array or wider range in environmental conditions – such as temperature, humidity, salinity, oxygen, light, resource renewal rates, and so forth.

  19. Phinehas:
    OMagain:

    My skeptical spidey sense is doing a full-on jitterbug over this one.:)

    Are you seriously claiming that if SETI received what appeared to be a transmission of the first 128 digits of pi beamed from a distant galaxy, that such an occurrence could not possibly explain anything of use to science, given that it could be ascribed to the whim of an unknown designer with unknown capabilities?

    I think the point is that we have two methods here:

    One is: find a criterion that reliably indicates a designer.
    The second is: predict what you would see if a designer designed something.

    Some IDproponents (Dembski for instance) claim to have a criterion that may produce false negatives (looks undesigned/was designed) but no false positives ( looks designed/was designed). If it worked, we wouldn’t have to worry about the second method.

    But it doesn’t work as it stands, because of the pattern in question is part of a self-replicator, we have an alternative explanation: Darwinian processes. So Dembski’s method gives false positives (I would argue – he would disagree, and so may you).

    And to distinguish between a false positive and a true positive, we could use method two: if this pattern was produced by a designer, what would we see? And if evolution, what would we see? We can do that for evolution, to some extent (there are things that evolution can’t easily do) but for a designer capable of doing anything for any reason, we can’t do it for the second.

    So, sure, if we find a convincing SETI signal, we can postulate an intelligent sender, and if the SETI signal doesn’t seem to be a self-replicator, that’s going to be the most likely explanation. Same goes for black monoliths on the moon. But if we find a signal that indicates design in a self-replicator we need to go to method two, which means that we need to make some hypotheses about the designer. If we can be bothered – after all, we have a viable hypothesis to hand, and Occam’s Razor would suggest that there isn’t a lot of point multiplying entities at this point.

  20. Robin:
    From earlier today, the question of why evolution would lead to complexity when simple does just fine was discussed. One thing I’ll note from my work in ecology is that in general terms, complexity buys organism populations flexibility when it comes to environmental perturbations. For a number of reasons, simple organisms can withstand significantly narrower variations in their environments without major population decreases than more complex organisms. For example, the more complex an organism is, the more ways it can move to a different environment, the quicker it can move to a different environment, and the better chance it has of being able to immediately utilize – however comparatively inefficiently – new resources in a new environment. In other words, more complex organisms are generally more adaptable. In other cases, more complex species can tolerate a greater array or wider range in environmental conditions – such as temperature, humidity, salinity, oxygen, light, resource renewal rates, and so forth.

    Indeed. Brains, for example, are pretty useful gadgets in a changing world 🙂

  21. OMagain:

    You’ll have to fill me in then. What is the Intelligent Design explanation for the origin of species other then “species were designed by an intelligent designer?

    It is not difficult to be dismissive. Someone could just as easily question, “What is the Darwinian explanation for the origin of species other than, ‘species arose randomly with perhaps some help from natural selection’?”

    But being dismissive is not anything close to the same thing as being skeptical, is it?

    But that’s exactly what you are doing, like it or not. When you say that intelligent design “explains away” something that’s no different to simply ignoring it.

    Why are you putting words in my mouth? When did I ever say that intelligent design “explains away” anything? That’s your claim, not mine, and I would add that I don’t think it is a valid one.

    Returning to the SETI example, would you say that inferring a transmission had been sent from a distant galaxy by an intelligent agent would somehow be explaining it away? Do you really think such an inference would stop science? I think exactly the opposite. I think it would likely introduce a veritable scientific renaissance! In fact, if it were then revealed that, oops, no, the “transmission” can actually be explained as naturally occurring phenomena and an inference to intelligence is not warranted, this would be what put a damper on scientific exploration.

  22. OMagain:

    Ah, I see, I think. You think the universe cares about you! I suspect if you were sitting in a different situation to being in front of a computer you might change your opinion quite quickly. If you were in a terrible situation would you ascribe that to “design” as quickly as you would good luck?

    You should remind yourself that you don’t know me. At all. At all, at all. Then you should refocus on topics more scientific than personal.

  23. OMagain:

    The “ring of truth” is a deceiver.

    So is the “ring of skepticism.” That’s why I always try to dig a bit deeper.

  24. OMagain: No. What I’m saying is that when ID proponents claim that X is explained by intelligent design they can construct no test to show that is or is not in fact the case.

    For example. The claim is that cancer is caused, in part, by smoking.

    ID supporters can say “cancer is caused by intelligent design” and there is no way of disproving that. Even when shown evidence that smoking leads to increased levels of cancer “that is also by design”.

    For example, one of JoeG’s usual arguments is this

    http://www.uncommondescent.com/intelligent-design/the-skeptical-zone-where-you-can-be-skeptical-of-anything-except-currently-fashionable-intellectual-dogmas/#comment-451129

    We observe mutations. We note the fact that they appear to be random with respect to function. Joe uses this as evidence that we don’t in fact know that was by intelligent design.

    And he’s right, we can’t know that some unknown agent with unknown powers caused the result that we observe.

    And that’s why these ideas are not useful to science. They are not excluded, as ID proponents claim, because “scientists want atheism to be true”, they are excluded becauseadding “or it was by the whim of an intelligent designer” to the end of every scientific paper would get old quickly.

    So were we to find a signal from SETI as you describe we’d ascribe it to an unknown designer, sure. Would it explain anything useful to science? Not really, we know pi to more digits then that. But we’d know we are not alone.

    So your spidey sense needs to be re-calibrated. This is a well worn path.

    Quite so OM. Similarly, if complexity is an indicative characteristic of a designer, what’s to keep a designer from making simple things as well? In other words, there’s no reason that a designer capable of designing DNA could not equally be responsible for sand. How then does the IDist propose to differentiate between things “designed” and things “not designed”? How can an ID proponent test and show that a rock is not designed?

    ETA: 4thespellz

  25. Lizzie: Indeed.Brains, for example, are pretty useful gadgets in a changing world

    …and then there would be THAT sort of flexibility as well. Yes, some complex organisms don’t even bother moving to or adapting to different environments; they just adjust their surroundings to be the environment they best thrive in.

  26. OMagain:

    What I’m saying is that when ID proponents claim that X is explained by intelligent design they can construct no test to show that is or is not in fact the case.

    And I’m saying that is pure, unadulterated rubbish. Do you really believe that SETI cannot possibly distinguish between natural phenomena and intelligent transmissions? That they can construct no test or filter that would aid them in making a correct determination regarding signals from space? That the entire scientific pursuit has no idea what it is looking for and no way to know whether or not they’ve found it?

  27. Phinehas,

    I rather hesitate to stick my oar in, here, as this is a busy thread with a number of strands. I’ve rushed through it a bit, and I see a number of areas where your skepticism seems allied to an unfamiliarity with the biology underlying particular areas. It’s a big subject, difficult to convey via blog comments. I’m unsure whether to make my post about the areas of concern, or take the low route of an appeal to authority! To pursue the latter, it must give some pause for thought that an area – for example, common descent – is routinely used in all manner of ways by professional biologists, who devise and use complex statistical techniques as a matter of routine that allow very high degrees of probabilistic confidence to be placed upon the assumption of relationship. If DNA sequences were not in fact commonly descended, this would show up like a beacon in these analyses. It doesn’t (granted that there are complications of lateral transfer and signal degradation).

    As you say, viral insertions provide a particularly interesting piece of the puzzle, and there is simply no way to deal with these on a ‘design’ paradigm, other than one involving deceit. One effectively has a binary signal – say “flanking sequence” and “flanking se[viral insert]quence”. It is highly unlikely that the insert could be surgically excised again to leave an uncorrupted “flanking sequence”, so that missing the insert is almost certainly the ancestral state, and there is no way to ascribe a consistent functional role to the presence or absence of the signal across the organisms that possess or lack it. Take a whole bunch of these binary signals and you build a branching pattern that accords very well with that from ‘real’ genes, and pseudogenes, and silent substitution (base changes that lead to no change of amino acid). This data does not have to accord to a branching pattern unless it arose from descent with speciation. The whole points unequivocally to common descent, and there is no wiggle room for a Common Design, ‘re-use’ paradigm, whatever Casey Luskin might try and say.

    As to complexity, there are two mechanistic considerations I might mention that are game-changers: endosymbiosis and sex. Prokaryotes ruled the world for 2 billion years, and still do, but a numerically small but carbon-hogging clade of organisms was founded by endosymbiosis – the merger of two prokaryote cells into a new kind of organism. This is not really ‘Darwinian’, nothing to do with tiny steps but a huge ‘hopeful monster’ leap. It allowed the emergence of organisms that could eat instead of absorb, and whose energy budget lifted the lid that restrained those prokaryotes to replicating small genomes asap. Replication became less urgent; more leisurely. On a strict temporal measure, the organisms became less ‘fit’. But they were able to exploit new niches.

    And then there’s sex (with its attendant ‘complex’ enhancement, multicellularity) – again, not something that can arise gradually. The role of sex in the overall picture would fill a book, but I will short-change you by simply declaring that sexual multicellular organisms are essentially ‘shells’ – complex somas wrapped around germline genes. The role of the soma is principally to nurture, transport and amplify the germline, and it does this most effectively by differentiating into specialist cell types. These organisms ultimately discover that all that complexity is a waste of time – they burst forth squillions of gametes, but still only manage to maintain a steady state on the average. They are complex for sure, but they are an oddity, whatever they themselves think 🙂

  28. Phinehas:
    OMagain:

    It is not difficult to be dismissive.Someone could just as easily question, “What is the Darwinian explanation for the origin of species other than, ‘species arose randomly with perhaps some help from natural selection’?”

    Except that “species arose randomly with perhaps some help from natural selection” doesn’t begin to describe any sort of Darwinian explanation. Where, for instance, is anything about reproduction? Fitness? Common ancestry? Heritability? And so on?

    There in lies the difference between ID and evolution. Evolution has very specific confining and defining parameters; ID has none.

    So the question really is valid and points to the underlying weakness of ID: What is the Intelligent Design explanation for the origin of species other then “species were designed by an intelligent designer? None of the ID leaders have offered any particular confining parameters of which I’m aware. Can you provide any?

  29. Robin:

    Similarly, if complexity is an indicative characteristic of a designer, what’s to keep a designer from making simple things as well? In other words, there’s no reason that a designer capable of designing DNA could not equally be responsible for sand. How then does the IDist propose to differentiate between things “designed” and things “not designed”? How can an ID proponent test and show that a rock is not designed?

    While complexity is a necessary requirement to infer design, it is by no means a sufficient one.

    Maybe I’m assuming some things here that I shouldn’t. Perhaps we should take a step back. Can anyone here explain SETI and how it works? What it is looking for? How it will know whether it has been found?

  30. It’s not about “you”. It’s about the class of being that can sit in front of a computer. That includes us.

    Lucky us!

    ETA: But if you took offence at something I implied or said then I offer my apologies for that. It was not my intent to get at you at at personal level, rather just trying (failing?) to make a general point.

  31. Phinehas: Someone could just as easily question, “What is the Darwinian explanation for the origin of species other than, ‘species arose randomly with perhaps some help from natural selection’?”

    But that’s the difference. The Darwinian explanation is capable of being dismissed because it exists.

    The ID equivalent does not.

    Why are you putting words in my mouth? When did I ever say that intelligent design “explains away” anything? That’s your claim, not mine, and I would add that I don’t think it is a valid one.

    Well, I took from this:

    The most compelling support I’ve seen for at least some form of common descent has been (and please forgive my poor, layman’s attempt at this) what I understand to be the discovery of the same exact (viral?) insertions of DNA sequences apparently being inherited from what is believed to be an ancestral species. Even though I feel this could be explained away by appealing to an intelligent designer using “spare parts” or “code reuse” that happened to retain the insertion, I don’t really find that a very compelling objection.

    On the other hand, there is a lot of evidence presented in favor of evolution that I think can be explained just as readily by intelligent design.

    While you may not find the first form compelling, you then go on to endorse it anyway with the claim that there is “a lot” of evidence for evolution that has an equivalent explanation from an ID point of view.

    Well, for example?

    Returning to the SETI example, would you say that inferring a transmission had been sent from a distant galaxy by an intelligent agent would somehow be explaining it away? Do you really think such an inference would stop science? I think exactly the opposite. I think it would likely introduce a veritable scientific renaissance! In fact, if it were then revealed that, oops, no, the “transmission” can actually be explained as naturally occurring phenomena and an inference to intelligence is not warranted, this would be what put a damper on scientific exploration.

    I don’t know what you are talking about here. Lizzie responds better then I can and says what I would have like to say. It’s a different thing!

  32. Phinehas:
    OMagain:

    And I’m saying that is pure, unadulterated rubbish.Do you really believe that SETI cannot possibly distinguish between natural phenomena and intelligent transmissions?That they can construct no test or filter that would aid them in making a correct determination regarding signals from space?That the entire scientific pursuit has no idea what it is looking for and no way to know whether or not they’ve found it?

    SETI certainly has a way to determine the difference between non-biological, non-replicating, non-changing signals from noise. What are the odds that their tools will work for determining the whether biological, reproducing, inexact replications are intelligent products or “noise”?

    I don’t see the two concepts as being analogous. For one thing, SETI has noted that its analysis is based on pattern comparison. SETI has identified and cataloged a series of common stellar signals and compares signal captures to that catalogue. To my knowledge, no one in ID has a similar identification and catalogue that incorporates biological arrangements. So, on what are you basing the idea that ID has any baseline of comparison for biological entities being designed?

  33. Phinehas: And I’m saying that is pure, unadulterated rubbish. Do you really believe that SETI cannot possibly distinguish between natural phenomena and intelligent transmissions? That they can construct no test or filter that would aid them in making a correct determination regarding signals from space? That the entire scientific pursuit has no idea what it is looking for and no way to know whether or not they’ve found it?

    And therein lies the difference between SETI and ID.

    It’s a scientific pursuit with clearly defined goals and mechanisms.

    Can they distinguish between distinguish between natural phenomena and intelligent transmissions? I’m sure that in some cases they can! In others it’ll be recorded but not recognized for what it is. Perhaps high bandwidth FTL comms channels will manifest as seemingly random static in our 3 dimensions. Will we recognize that as designed? Probably not for a long time, if ever.
    Here’s my version.

    Intelligent design proponents can construct no test or filter that would aid them in making a correct determination regarding the detection of design in biology, which they nonetheless contend is designed

    You explain how finding design in biology relates to SETI if you please.

  34. Phinehas:
    Robin:

    While complexity is a necessary requirement to infer design, it is by no means a sufficient one.

    I understand, but that not relevant to my question. To try this from a different angle, why is complexity a requirement at all? Ever? Is there some reason that you can think of that a designer who could design DNA could not design water? If not, what prevents water from being intelligently designed?

    Maybe I’m assuming some things here that I shouldn’t.Perhaps we should take a step back.Can anyone here explain SETI and how it works?What it is looking for?How it will know whether it has been found?

    See above. Here’s a pretty good summary: http://www.seti.org/node/662

    Here’s the basis of the radio search hypothesis:

    “Many radio frequencies penetrate our atmosphere quite well, and this led to radio telescopes that investigate the cosmos using large radio antennas. Furthermore, human endeavors emit considerable electromagnetic radiation as a byproduct of communications such as television and radio. These signals would be easy to recognize as artificial due to their repetitive nature and narrow bandwidths. If this is typical, one way of discovering an extraterrestrial civilization might be to detect non-natural radio emissions from a location outside our Solar System.”
    http://en.wikipedia.org/wiki/SETI

    Over the years, new programs have come online, but the basic hypothesis remains the same – intelligent activity creates a very specific signal pattern that looks nothing like artificial signal patterns that have been catalogued for comparison.

  35. Allan:

    As you say, viral insertions provide a particularly interesting piece of the puzzle, and there is simply no way to deal with these on a ‘design’ paradigm, other than one involving deceit. One effectively has a binary signal – say “flanking sequence” and “flanking se[viral insert]quence”. It is highly unlikely that the insert could be surgically excised again to leave an uncorrupted “flanking sequence”, so that missing the insert is almost certainly the ancestral state, and there is no way to ascribe a consistent functional role to the presence or absence of the signal across the organisms that possess or lack it.

    I happen to be a designer. I take various objects and connect them together with messages that fire on certain state changes in order to produce particular functionality. Some arrangements of objects are useful enough that I create what we call a template out of them. I can save that template off and then create multiple instances of it. This saves time and helps me be more productive. I can even create new templates using other templates and objects. Sometimes, I only want a useful part of a template I’ve created and in these cases, I often make an instance of the template, break the instance, grab the part of it that I want to use, and delete the rest.

    Sometimes, I make mistakes and introduce a bug into my templates. (Or a bug gets inserted upstream that I’m not aware of.) If you were to examine my templates, you might be able to use the information gleaned to figure out which pieces of my design are “ancestral” to others. You might be able to figure out which templates I created first and which likely came later. Not all of the templates created later will be more complex than those created earlier, but all of the really early templates will tend to be the simpler ones.

    If you were to look at my work as a whole and infer some sort of common descent, you’d have a really good argument. I certainly wouldn’t object to the inference. (And I’ve said much the same about some form of common descent in the evolution of the species.) On the other hand, if you started trying to rule out intelligent design or began to appeal to purely natural or mechanical forces as an explanation, I’d certainly want to intervene and point out a possible alternative to your theory. And none of this would involve any ‘deceit’ on my part.

    This is not really ‘Darwinian’, nothing to do with tiny steps but a huge ‘hopeful monster’ leap.

    And then there’s sex (with its attendant ‘complex’ enhancement, multicellularity) – again, not something that can arise gradually

    Indeed. And I don’t feel particularly committed to the notion that these huge and hopeful leaps were accomplished by sheer, dumb luck. I am quite skeptical regarding what sheer, dumb luck can accomplish. And I am open to allowing an intelligent foot in the door, Divine or otherwise.

    Hopefully, none of this makes me insane, stupid, or wicked.

  36. I too was a designer once, Phinehas (architecture, urban design, and I guess musical composition, if that counts as design), and you are making a point very like one I have been making for years! That the products of human designers, including their “lineages” have a lot in common with the lineages we observe in biology.

    But what I am trying to say is: the fact that the two processes leave similar footprints means that in order to make a differential prediction we need to postulate something about the putative designer – specifically, his/her/its limitations. We know something about the limitations of evolution, and so if we found something that really didn’t fit, we’d have to seriously rethink the theory. But with an unspecified designer of unlimited power, nothing can’t fit, and therefore there’s no predictive hypothesis to differentiate it prediction made by evolutionary theory.

    Evolutionary theory is certainly, and will always be, incomplete, and the data can never rule out a designer. The problem is that ID proponents actually want to rule a designer in. That would only be possible with a “natural” designer hypothesis. A putative non-natural designer generates no hypotheses.

  37. Many radio frequencies penetrate our atmosphere quite well, and this led to radio telescopes that investigate the cosmos using large radio antennas. Furthermore, human endeavors emit considerable electromagnetic radiation as a byproduct of communications such as television and radio. These signals would be easy to recognize as artificial due to their repetitive nature and narrow bandwidths. If this is typical, one way of discovering an extraterrestrial civilization might be to detect non-natural radio emissions from a location outside our Solar System.

    So SETI infers design by identifying the hallmarks of intelligent activity and ruling out natural causes.

    Over the years, new programs have come online, but the basic hypothesis remains the same – intelligent activity creates a very specific signal pattern that looks nothing like [natural?] signal patterns that have been catalogued for comparison.

    Indeed. But this isn’t just about signals, since archaeologists and forensic scientists use other methods to make similar inferences in their particular fields. To an archaeologist, an arrowhead will show signs of design where a rock or grain of sand will not. Why would it not be a valid and potentially useful scientific pursuit to see if you could identify what is common about the inference to intelligent involvement in these various scientific endeavors? And how can such inferences be said to have no use to science when they are quite obviously being used by science?

  38. Lizzie:

    We know something about the limitations of evolution, and so if we found something that really didn’t fit, we’d have to seriously rethink the theory. But with an unspecified designer of unlimited power, nothing can’t fit, and therefore there’s no predictive hypothesis to differentiate it prediction made by evolutionary theory.

    But Lizzie, are you outlining a positive reason to dismiss the viability of inferring a designer? Or merely an unfortunate shortcoming inherent in the way we currently do science?

  39. Also, if you don’t dismiss the very possibility of design outright, a study of what may (or may not) have been designed from the standpoint of an experienced designer may end up giving you insight into the limitations of the designer that would suggest even more areas of study in the search for truth.

    Why not view reality from every perspective to see what shakes out? Why dismiss certain perspectives outright? C’mon Lizze, let’s be skeptical together! 🙂

  40. Phinehas: Also, if you don’t dismiss the very possibility of design outright, a study of what may (or may not) have been designed from the standpoint of an experienced designer may end up giving you insight into the limitations of the designer that would suggest even more areas of study in the search for truth.

    Except it never has, has it when we talk about the topics that ID makes claims for? Unless you can give an example?

    Why not view reality from every perspective to see what shakes out? Why dismiss certain perspectives outright? C’mon Lizze, let’s be skeptical together!

    But who is doing that?

    Tell me, what actually useful perspective has to your mind been unfairly dismissed?

    That there *might* be an intelligent designer behind “it all”?

    Fine, bring that into the fold.

    Now what?

  41. Infer a designer!

    Now what?

    Keep doing science? Keep searching for truth? Consider what implications there may be for how we look at life and the universe? Consider whether you can discern the designer’s thoughts and motives? Consider the issues the designer faced and how they were overcome?

    How is this any worse than:

    Assert no designer!

    Now what?

  42. Phinehas: Why would it not be a valid and potentially useful scientific pursuit to see if you could identify what is common about the inference to intelligent involvement in these various scientific endeavors?

    It is! It’s a great idea! You could probably also use some metric, like, um, something like functional complex information or somesuch to measure that somehow!

    But you know what, sure, there’s a set of things that the natural universe acting without intelligence like us can achieve. What that is, I don’t know. Get started 🙂

    I think the thing is that fundamentally nobody really disagrees much with what the IDers claim, it’s their right to claim it. It’s a free world, hopefully. It’s rather the misuse of mathematics, logic etc to make their case (and claim victory already!) that is somewhat offensive, compounded with their resistance to venture out of the echo chamber to have their ideas tested against all comers. That’s what I don’t like about ID.

    The inference to design and all that is great. You know, if we have a video camera on every space probe in the future it’d would be great to have a “is it designed” plugin to run that video through to ensure we don’t slag a billion year old message sitting in an asteroid field just because it happened to be made of a valuable metal!

    It’s a worthy cause, their seeking of the truth. It’s just they’ve already found it , it seems, and when it’s questioned they are wont’ to respond with “that’s those immoral materialists for you” (KF etc) rather then respond to the actual argument made. You’ve noticed that about KF’s style by now I’m sure. Amazing how many different points can be responded to by repeating the same few text blocks.

    So there you have it, take it or leave it. But for an ID supporter I’m hearing a compelling lack of actual reasons that ID is more useful then any alternative from you. Lots of “potentially useful”, sure, but you’ve (ID) been saying that for a while now.

  43. Try out a little exercise that is a routine part of every scientist’s working life; i.e., write a research proposal and submit it for peer review and funding.

    Submit a research proposal that will determine whether or not the universe – or life, if you like – is designed and by whom (or what).

    Outline the research issues to be addressed and spell out in detail your research methods and how they will address the issues you have outlined. You will have to tell what your “signal” will be, how large it must be, and what level of precision you will need in order to discriminate design from non-design.

    You will also need to submit a budget outlining the equipment you will need to buy or design and build, how many people will be required, and a rough time schedule.

    I suspect you may be aware of the fact that ID/creationism has been around since the early 1970s and no research proposals have ever been submitted – even when requested by organizations like the Templeton Foundation. Dembski has not submitted any proposals; nor have anyone at the Discovery Institute. David L. Abel hasn’t done it, nor has Michael Behe.

    So the coast is clear; you have no competition.

    Do any ID/creationist advocates know how to write a research proposal to explore ID?

    Research proposals are where “the rubber hits the road;” you either know what the issues are and how to address them with a research program or you don’t.

Leave a Reply