Home » Intelligent Design » Why Up When Down is Just As Good And A Lot Easier?

Why Up When Down is Just As Good And A Lot Easier?

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?

  • Delicious
  • Facebook
  • Reddit
  • StumbleUpon
  • Twitter
  • RSS Feed

106 Responses to Why Up When Down is Just As Good And A Lot Easier?

  1. That is a fantastic question, indeed. I am curious to see what the responses are to it.

  2. Surely evolution is a story about the rise of more and more complex organisms.

    Nope, that just happened to happen here on this planet. Evolution can make things less complex too. Whatever works.

    That is the whole thing- stuff happens and what doesn’t die may get the chance to reproduce. Reproduction is just “Rinse and repeat”.

  3. SLT: The precise meaning of ‘fitness’ has yet to be settled, in spite of the fact — or perhaps because of the fact — that the term is so central to evolutionary thought” (Beatty 1992). This is, if anything, even more emphatically true today. The concept remains troubled, as it has been from the very beginning, with little agreement on how to make it a workable part of evolutionary theory. Indeed, the “consensus view,” as Roberta Millstein and Robert Skipper, Jr., write in The Cambridge Companion to the Philosophy of Biology (2007), is that “biologists and philosophers have yet to provide an adequate interpretation of fitness.” And Lewontin, together with University of Missouri philosopher André Ariew, expressed the conviction that “no concept in evolutionary biology has been more confusing” than that of fitness (Ariew and Lewontin 2004). Yet the neo-Darwinian theory of natural selection hinges, “as empirical science,” upon a reasonable understanding of what fitness means (Bouchard and Rosenberg 2004).

  4. First a comment about rules of engagement. My rate of posting to this thread might be slow. I have other things that I do in life, and right now the IRS thinks that filing a tax return is of some importance. I won’t be responding to everyone who comments. But I will try to discuss the gist of what is in the OP (opening post), though not all in one comment.

    I’ll note that I don’t much like the title.

    Phinehas ask how evolution can get from point A to point B. I think I can best respond with an analogy.

    Suppose that I want a vacation trip to the mountains. I go to a travel agent, and ask for advice. The travel agent asks me the destination. I have heard of Denver, so maybe I name that as the destination. And the travel agent then draws up plans. That’s a kind of intelligent design at work, and Denver is the point B that Phinehas is asking about.

    However, maybe I skip the travel agent. Instead, I decide to just drive to the mountains and follow my whims as I go. I see a mountain route that looks interesting, so I head there. Part way there, I see a quaint inn with a vacancy sign, so I stop in and make arrangements to stay there for the night. Having arranged where to sleep, I continue following that mountain route, and maybe I stop to take photographs as I go.

    I follow a similar procedure for several days. And I take pictures and make notes as I go. With a little luck, I will have a great vacation. And, when I get back home, I’ll describe it to my friends. They are probably going to ask me what travel agent designed the vacation, and how I came up with the particular ideas on where I was going. That’s the appearance of design. But, in fact, the vacation just evolved as I went along. There was no specific destination, no point B, no plan. It will just look as if there was a destination in an after-the-fact report.

    Of course, there’s a risk that things will go awry, and I will have an unpleasant vacation. In that case, my friends probably won’t hear about. That’s natural selection at work. Only the good results finish up in the report.

    A comment on complexity. My vacation trip was probably quite complex. In fact, it was probably a lot more complex than anything that a travel agent would have designed. It is simplicity, rather than complexity, that is an indicator of design.

    If I had taken my vacation in the Sahara desert, it probably would not have been very complex. But in the Rockies, it would be a lot more complex. The complexity reflects the nature of the world. For evolution, complexity appears to increase. But that’s because the world is becoming more complex due to all of those other evolving creatures. There is nothing about the principles of evolution that require increasing complexity, apart from what is the result of an increasingly complex world.

    That’s it for this post.

    Phinehas asked a lot of questions related to natural selection. I have not said much about NS. That’s because I am not a big fan of Darwinism. I’m inclined to think that NS is overrated. I would like to see more research emphasis on mutation and recombinant DNA.

  5. And here I thought travel agents were so 20th century.

    Methinks Neil’s adventure wasn’t as blind and mindless as he wants us to think…

  6. 6

    Neil @ 4:

    Your analogy fails at many levels and does not shed the slightest light on the Darwinian account. I may come back to this later in detail, but I want to focus on this comment:

    “It is simplicity, rather than complexity, that is an indicator of design.”

    This comment is just astonishing.

    So the international space station is simple? Your statement is exactly opposite of the facts.

    It is not simplicity that indicates design. On the other hand, “complexity” standing alone also does not indicate design. High complexity combined with a specification indicates design.

  7. Would it not be stunning that ‘evolution’ theory as developed by countless scientists over decades, the mechanisms, its operation – are essentially correct but headed in the complete opposite direction!? It certainly is. Error, degradation, information loss are the reality.

  8. Your analogy fails at many levels and does not shed the slightest light on the Darwinian account.

    That’s being generous

  9. 9

    Phinehas ask how evolution can get from point A to point B. I think I can best respond with an analogy.

    Suppose that I want a vacation trip to the mountains. I go to a travel agent, and ask for advice… I skip the travel agent… I decide to just drive… I see a mountain route… I stop in… I continue…

    Yup. Now there’s a real skeptic.

  10. Something I have trouble understanding comes from the precision of the end result.
    i.e. nature seems to solved a large number of “fitness” problems with what appears to be optimal (or at least near optimal) solutions. Take for instance the impressive mimicry of many animals, the amazing chromatic filters in the eyes of kingfishers, feather structure etc…
    Path-finding was mentioned, and having a programming background I have written such algorithms myself and they are, in my view, a poor representation of how evolution works even with natural selection acting upon it.
    In order to achieve the best solution, the route has to be able to back-track (undo mistakes if you like) something current models of evolution seem not to allow. This is because if one move towards the optimal target leads to a fitness increase that does NOT fall in line with the optimal solution then you will never reach it, a new optimal has been defined with a new limiting factor that is imposed by the last fitness increase.
    Not all changes might make the perfect solution impossible but some will, and if these have a fitness gain in their own right (or potentially even a neutral effect) then the optimal solution may have been changed forever! I am interested in the maths around this dilemma. So much in the natural world has found it’s solutions, many indeed that we would struggle to improve upon.

    So my point is I suppose why do I not see more people questioning the fact that millions upon millions of changes/adaptations so frequently add up to optimal solutions. When logic suggests the more simple and basic solutions are the more likely found. I would not be surprised if simulations of a more realistic fitness model (where some changes can rule out others – potentially even permanently) you rarely achieve the optimal solution for a set of conditions, especially if optimal solutions are complex ones involving more than a couple of mutations (slight sarcasm as I was thinking some will require a vast amount of coding for).

    b

    Unrelated but was pointed at this today and thought it might be interesting:
    Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

    Sorry if none of that makes any sense to anyone, am pretty groggy at the mo. Hi to all, I just wanted to quickly add that I appreciate the contributors to blogs such as this by both writers and the comment box folk.

  11. as to “When Down is Just As Good And A Lot Easier?”

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    and though I certainly like the detail and clarity with which Phinehas fleshed this question of ‘fitness’ out better than I’ve seen it fleshed out before, here is my crude, and not so detailed, realization of the ‘what is fitness?’ question a few weeks ago:

    Since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but successful reproduction ever be realistically ‘selected’ for? Any other function besides reproduction, such as sight, hearing, thinking, etc.., would be highly superfluous to the primary criteria of successfully reproducing, and should, on a Darwinian view, be discarded as so much excess baggage since it would slow down successful reproduction.
    http://www.uncommondescent.com.....ent-448416

    In a Tadpole’s Eye: Another Case of Darwinism’s Plasticity Problem – David Klinghoffer – March 1, 2013
    Excerpt: Organisms of all sorts are capable of intelligent, goal-directed, adaptive behavior that cannot possibly be accounted for on the basis of the theory of natural selection.
    *Never in the evolutionary history of human beings was there selection for “seeing” with the tongue.
    *Never in the evolutionary history of fruit flies was there selection for adaptation to an inverted visual field.
    *Never in the evolutionary history of ferrets was there selection for the brain reorganization necessary to see with the auditory cortex.
    *And never in the evolutionary history of the slime mold was there selection for solving mazes.
    Of course, the Darwinist will say that there is no need to posit past selection for plasticity. Instead, we will be invited to view plasticity as a “spandrel” — an accidental side effect of other abilities that were selected for.
    But that would be entirely ad hoc. There is absolutely no evidence to support such a claim.
    http://www.evolutionnews.org/2.....69691.html

  12. supplemental notes:

    Can Darwin’s enemy, math, rescue him? – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is.
    (On a job description from Oxford seeking a mathematician to ‘fix’ the problems within population genetics)
    http://www.uncommondescent.com.....escue-him/

    With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory – November 2011
    Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,,
    http://www.evolutionnews.org/2.....52821.html

    The next evolutionary synthesis: Jonathan BL Bard (2011)
    Excerpt: We now know that there are at least 50 possible functions that DNA sequences can fulfill [8], that the networks for traits require many proteins and that they allow for considerable redundancy [9]. The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate – it is really only half a theory!
    http://www.biosignaling.com/co.....X-9-30.pdf

  13. Barry,

    Neil doesn’t accept darwinism so he isn’t going to support it. However his use of the word “evolved” as in the vacation just evolved as I went along. is misleading. Developed is more like it.

    Now if he repeated the trip, ie reproduced it, left out the bad, kept the good and added something new. Then perhaps he would have an evolving trip, by design ;).

  14. How to make judgments about fitness?

    A zebra having longer leg bones that enable it to run faster than other zebras will leave more offspring only if escape from predators is really the problem to be solved, if a slightly greater speed will really decrease the chance of being taken and if longer leg bones do not interfere with some other limiting physiological process. Lions may prey chiefly on old or injured zebras likely in any case to die soon, and it is not even clear that it is speed that limits the ability of lions to catch zebras. Greater speed may cost the zebra something in feeding efficiency, and if food rather than predation is limiting, a net selective disadvantage might result from solving the wrong problem. Finally, a longer bone might break more easily, or require greater developmental resources and metabolic energy to produce and maintain, or change the efficiency of the contraction of the attached muscles. Richard Lewontin.

  15. @Neil

    Thank you for your response, especially given your busy schedule.

    I think the title does a decent job summing up my skepticism. In fact, it might be a bit closer to the mark than your analogy. Based on the analogy, I’m wondering whether my main point was too subtle or unclear. I’ll try to do better.

    It is simplicity, rather than complexity, that is an indicator of design.

    Perhaps you mean elegance? While I’m not that good at golf, I think I could probably get a golf ball from tee to hole with a bit more elegance than purely natural forces like wind, earthquakes, gophers, and the like. But to say my methods were less complex might be to take for granted the near-miraculous feats that a sentient, contingent agent can accomplish with seeming ease. Incidentally, this is where I tend to get hung up in the micro vs. macro debate. For some, it is simply a matter of quantity, but I see it as more of an issue of elegance or even accuracy.

    For evolution, complexity appears to increase.

    Yes! This gets more to the point of what I am trying to understand. When I look at evolution’s tree of life, it seems like the arrows point consistently toward greater complexity. Based on the evolutionary narrative and the way the data is organized and presented, it is almost as if you could overlay evolution with a big, fat arrow labelled “Increasing Complexity”.

    Yet if natural selection has any heuristic or any big, fat arrow of its own (labelled “Increasing Fitness,” natch) at best you could say that this arrow was orthogonal to an increase in complexity, and it certainly appears that it could actually be pointing in the exact opposite direction. So how can the second be any sort of an aid or explanation for the first? Is there some way to define increasing fitness such that increasing complexity would be a natural result?

    Unfortunately, I’m not really able to mine enough from your analogy to bring any real clarity to this particular issue. I also fear that trying to express my reservations in terms of your analogy might stretch it past its breaking point. Still, I appreciate the effort you put into it and hope you’ll find the time to zero in on what it is I’m trying to understand.

  16. Neil
    ” I see a quaint inn with a vacancy sign, so I stop in and make arrangements to stay there for the night.”

    Hopefully it’s not Bates Motel!

  17. @bw

    I’m a video game designer with just enough programming knowledge to make the thought of giving me code access terrify the engineers. Still, I wrote code for Djikstra, A* and various other methods for solving well defined problems while in school. I realize that these are probably poor analogies for natural selection, but for the life of me, I just can’t figure out how to view natural selection from any perspective that would save evolution from an exhaustive search of the problem space. I’m hoping someone can help me out with that.

  18. Here are a few questions that have been on mind for quite a while. I had hoped to get satisfactory answers but to no avail.

    1. How did “primitive” organisms evolve the complex ability to reproduce if this very ability is an essential prerequisite of the evolution process?

    2. Given that the number of deleterious random mutations is greater than the number of beneficial random mutations by orders of magnitude (ask any programmer), how did “primitive” organisms survive the onslaught of deleterious mutations without first evolving a gene repair mechanism?

    3. How does an evolved gene repair mechanism distinguish between a good and a bad mutation?

    These unanswered questions are why I maintain that evolution is really a superstitious, dirt-worshiping religion, i.e., a religion of cretins, created by cretins for cretins. Sorry to be so brunt. Just my opinion.

  19. semi related: Coming in June, a Game-Changing New Book: Darwin’s Doubt, by Stephen Meyer
    Excerpt: For now but not for long, exclusively at DarwinsDoubt.com, you can preorder your copy, receiving a steep discount, free shipping and four free digital books!
    http://www.evolutionnews.org/2.....70501.html

  20. 20

    “Yet if natural selection has any heuristic or any big, fat arrow of its own (labelled “Increasing Fitness,” natch) at best you could say that this arrow was orthogonal to an increase in complexity, and it certainly appears that it could actually be pointing in the exact opposite direction. So how can the second be any sort of an aid or explanation for the first? Is there some way to define increasing fitness such that increasing complexity would be a natural result?”

    This is an excellent question. Why should an increase in complexity correspond to an increase in fitness, viewing fitness as a measure of reproductive success? The question suggests that increased complexity, as observed, slows reproduction and makes survival more tentative. I suppose a putative answer would need to have something to do with environmental pressures, niches, fitness landscapes, etc., i.e., the usual suspects. However it should be addressed, that if fitness is measured by differential reproductive success, why should the complexity observed in multicellular, sexually reproducing organisms logically come about, when such organisms might be deemed less fit by the most useful definition of fitness.

    As corollaries, what slight successive changes can theoretically be introduced into bacterial organisms that would tend toward increased complexity while providing increased fitness along the way? What environmental pressures and factors may be introduced to bacterial colonies which would equate increasing complexity with reproductive success?

    Box @14, good quote! :)

  21. 21
    William J Murray

    I’ve made this same argument many times. If fitness means anything along the lines of “hardiness that increases ongoing reproductive success”, then evolution apparently started out with pretty much the most fit organism possible and everything went downhill from there.

    Human beings, then, don’t exist because of Darwinistic evolution; they exist in spite of it.

  22. 22

    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?

    Imagine a planet covered with only bacteria-like cells. If one cell were bigger, and thus more slowly reproducing, but was able to eat the other bacteria, would it persist in the ecosystem?

    Your argument says no. Which is why your argument is ridiculous.

    Reason for creationist silliness #2847285 — total failure to think about ecological niches.

    At least it’s a refreshing departure from reason for creationist silliness #1 — total failure to think statistically. Or #2: total failure to think over many orders of magnitude of timescale, geographic scale, organism size scales, etc.

  23. 23

    WJM @21, I also made the point at least once before, but never as a standalone challenge.

    From my perspective, if one begins with a stable self-replicator, then such an entity exists in a stable state, where perturbations to its configuration, namely mutations, are much more likely to damage its ability to reproduce than to enhance it. In this stable state, natural selection can be readily observed, imo, because offspring with mutations that cause deleterious effects are unlikely to reproduce effectively, and therefore will not usually pass along their genes. Now, assuming that our first self-replicator is not optimal, we can presume that some chance mutations might occur which help optimize it, allowing for increased reproductive success to gain a foothold in the overall population. But it seems to me that such optimizations only serve to push our putative protocell upwards on a local maximum, stranding it upon a peak of the functional landscape. One consequence of this view is that for unguided evolution to have occurred gradually, multiple disparate starting points are required for early organisms, so that they can all make their way to their respective peaks on the fitness landscape. It doesn’t appear that evolution by natural selection, acting necessarily upon slight changes, can jump between peaks. So either is required multiple starting points, which is reminiscent of special creation, or the ability to span great gaps of form and function, which is reminiscent of discrete miracles. The other option asks for us to imagine that increased complexity is collinear with increased fitness, at least in some environmental niche or another; and that increases in complexity can happen gradually enough for random variations to account for them, but not so gradually as to be invisible to natural selection.

  24. Nick @22:

    Way to go. You’ve misrepresented his argument.

    Of course your comment is evolutionist bluff #1.

    There are niches. They must get filled. Except when they don’t get filled. Reproduction might drive change. Except when it doesn’t. And so it goes . . .

    And you still haven’t provided the slightest reason for why anyone should believe that such a process would drive evolution toward greater complexity of structure, less reproduction, expenditure of resources on activities unrelated to reproduction, and so on. All decent questions related to Phineas’ larger inquiry.

    Because at the end of the day all you’ve got is that Great Evolutionary Explanation:

    Stuff Happens.

  25. Nick Matzke, would you care to give us your definition of ‘fitness’?

  26. Mr. Matzke you claim that a bigger and slower reproducing organism can be considered ‘more fit’ if the bigger organism eats the smaller but faster reproducing organism, but what prevents these faster, smaller, reproducing organisms from eating the larger, slower, reproducing ones?

    Richard Dawkins interview with a ‘Darwinian’ physician goes off track – video
    Excerpt: “I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly — a few hours sometimes, they can reproduce themselves — that they can evolve very, very quickly. And we’re stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?”
    http://www.evolutionnews.org/2.....62031.html

    A stunning example of that paradoxical scenario was played in HIV Mr. Matzke:

    Michael Behe defends the one ‘overlooked’ protein/protein binding site generated by the HIV virus, that Abbie Smith and Ian Musgrave had found, by pointing out it is well within the 2 binding site limit he set in “The Edge Of Evolution” on this following site:

    Response to Ian Musgrave’s “Open Letter to Dr. Michael Behe,” Part 4
    “Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane — not something to crow about after 10^20 replications and a greatly enhanced mutation rate.”
    http://behe.uncommondescent.co.....he-part-5/

    In fact, I followed this debate very closely and it turns out the trivial gain of just one protein-protein binding site being generated for the non-living HIV virus, that the evolutionists were ‘crowing’ about, came at a staggering loss of complexity for the living host it invaded (People) with just that one trivial gain of a ‘leaky cell membrane’ in binding site complexity.

    “the AIDS virus originated relatively recently, as a mutation from SIV, the simian immuno-deficiency virus. According to Wikipedia, this virus was also benign in its original form:.. Unlike HIV-1 and HIV-2 infections in humans, SIV infections in their natural hosts appear in many cases to be non-pathogenic. Extensive studies in sooty mangabeys have established that SIVsmm infection does not cause any disease in these animals, despite high levels of circulating virus.”
    http://www.uncommondescent.com.....ent-448372

    Thus the ‘evolution’ of the virus clearly stayed within the principle of Genetic Entropy since far more functional complexity was lost by the living human cells it invaded than was ever gained by the non-living HIV virus. A non-living virus which depends on those human cells to replicate in the first place. Moreover, while learning HIV is a ‘mutational powerhouse’ which greatly outclasses the ‘mutational firepower’ of the entire spectrum of higher life-forms combined, for millions of years no less, and about the devastating effect HIV has on humans with just that one trivial binding site being generated, I realized if evolution were actually the truth about how life came to be on Earth then the only ‘life’ that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the ‘fittest’ are allowed to survive.

    Yet instead of eating us, or just killing us outright, which is what one would rightfully expect in a Darwinian view of things, time after time these different types of microbial life are found to be helping us in essential ways that have nothing to do with their ability to successfully reproduce,,,

    NIH Human Microbiome Project defines normal bacterial makeup of the body – June 13, 2012
    Excerpt: Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival.
    http://www.nih.gov/news/health.....gri-13.htm

    We are living in a bacterial world, and it’s impacting us more than previously thought – February 15, 2013
    Excerpt: We often associate bacteria with disease-causing “germs” or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them.,,,
    I am,, convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens.”
    http://phys.org/news/2013-02-b.....tml#ajTabs

    The Microbial Engines That Drive Earth’s Biogeochemical Cycles – Falkowski 2008
    Excerpt: Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. -
    Paul G. Falkowski – Professor Geological Sciences – Rutgers
    http://www.genetics.iastate.edu/delong1.pdf

    Though most people think of viruses as being very harmful to humans, the fact is that the Bacteriophage (Bacteria Eater) virus, in the preceding video, is actually a very beneficial virus to man to keep certain populations of bacteria in check.

    Bacteriophage
    Excerpt: Bacteriophages are among the most common biological entities on Earth,,,They have been used for over 60 years as an alternative to antibiotics in the former Soviet Union and Eastern Europe.[5] They are seen as a possible therapy against multi drug resistant strains of many bacteria.,,,development of phage therapy was largely abandoned in the West, but continued throughout 1940s in the former Soviet Union for treating bacterial infections, with widespread use including the soldiers in the Red Army—much of the literature was published in Russian or Georgian, and unavailable for many years in the West. Their use has continued since the end of the Cold War in Georgia and elsewhere in Eastern Europe.,,,In August, 2006 the United States Food and Drug Administration (FDA) approved using bacteriophages on cheese to kill the Listeria monocytogenes bacteria, giving them GRAS status (Generally Recognized As Safe).[10] In July 2007, the same bacteriophages were approved for use on all food products.[11] Government agencies in the West have for several years been looking to Georgia and the Former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, e.g., Anthrax, Botulism.
    http://en.wikipedia.org/wiki/Bacteriophage

    Viruses: A Pirate Phage Commandeers the Immune System of Bacteria – Feb. 27, 2013
    Excerpt: The study provides the first evidence that this type of virus, the bacteriophage (“phage” for short), can acquire a wholly functional and adaptive immune system.
    The phage used the stolen immune system to disable — and thus overcome — the cholera bacteria’s defense system against phages. Therefore, the phage can kill the cholera bacteria and multiply to produce more phage offspring, which can then kill more cholera bacteria. The study has dramatic implications for phage therapy,,,
    http://www.sciencedaily.com/re.....134334.htm

    supplemental note:

    Doug Axe: Lignin & the Coherent Design of the Ecosystem – podcast
    Excerpt: Lignin provides a paradoxical case for the Darwinian method of evolution, but fits perfectly into a design oriented scientific paradigm. Thirty percent of non-fossil organic carbon on the planet is lignin, so in a Darwinian world, something should have developed the ability to consume lignin–but it hasn’t. Lignin binds together and protects plant cellulose, which is vital to all types of large plant life; “The peculiar properties of lignin therefore make perfect sense when seen as part of a coherent design for the entire ecosystem of our planet.”
    http://www.idthefuture.com/201.....ent_d.html

  27. 27

    Nick,

    If one prebiotic organization of some unknown sort didn’t benefit from a mechanism to establish the semiotic relationships required to record information into a medium (and then translate effects from it), and another did…which one would be able to evolve via changes to that information?

  28. ‘evolution is really a superstitious, dirt-worshiping religion, i.e., a religion of cretins, created by cretins for cretins.’

    Don’t put yourself down, Mapou. That must be the gold standard of epigrammatically dimissive eloquence. Brutally blunt though it be, within the context it has its own beauty.

    ‘a religion of cretins, created by cretins for cretins.’

    I believe the Greeks considered a circle, the perfect, shape, and there is a wonderful, circularity, parsimony and balance about that last phrase of yours.

    And ‘a dirt-worshipping religion’ is simply overkill, an embarrassment of riches. All worthy of the Encyclopaedia Britannica, although I am not absolutely certain the editors would concur. It meets Einstein’s aesthetic criterion for selecting hypotheses. Though it may be that I’m just dazzled by the euphony. But I don’t think so.

  29. 29
    William J Murray

    “Fitness” = “Whatever quality makes a Darwinian just so story sound the most plausible.”

  30. Nick Matzke:

    Imagine a planet covered with only bacteria-like cells.

    Who are you, Rod Serling?

    If one cell were bigger, and thus more slowly reproducing, but was able to eat the other bacteria, would it persist in the ecosystem?

    No, because I can imagine the other bacteria ganging up on that one and eating it.

  31. My final comment for today (Mar 25, Chicago time). I’ll be back tomorrow.

    There have been questions about Darwinism. Since I am not a Darwinist, I’m the wrong person to ask. But I’ll at least say a little.

    As I see it, a scientific theory serves two roles. One of those is as a guide to research. I’m not a biologist, however neo-Darwinism seems to be doing pretty well as a guide to research. It establishes technical terminology and gives direction to the research.

    A second role for a theory, is as a marketing instrument to sell the science to those outside the field. And, as I see it, Darwinism does that rather poorly. There’s a tendency to dismiss that problem, by blaming it on creationists. However, some non-religious folk have similar objections and similar misunderstandings of evolution, so I think it fair to say that Darwinism is not very effective at selling the theory to people outside of biology.

    Natural selection is often presented as a kind of filter that shapes the direction of evolution. As an analogy, imagine a cookie cutter that shapes the cookie dough. The trouble with a cookie cutter, is that it is passive. The cook has to force the dough through the cookie cutter before there is any shaping. Natural selection has a similar problem. And what forces biological populations through the shaping of natural selection, is the biological reproduction. I see too much emphasis on selection (sometimes criticized as pan-selectionism or pan adaptionism), and not enough emphasis on the importance of pressures caused by reproduction. Biologists know all about reproduction, but they make the mistake of not saying enough about its role when talking to the lay public.

    My own way of looking at evolution, is in terms of a population. I see the population as exploring the environment (or the fitness landscape, as it is sometimes called). I see the production of mutations as part of this exploration.

    I’m not sure why, but many scientists don’t want to look at it that way, because they think it looks too much like purposeful activity, and they want to avoid “purpose” and other terms in the intentional vocabulary. However, you cannot avoid the intentional vocabulary. Biology is loaded with apparently purposeful behavior.

    On the question of complexity vs. simplicity, I’m surprised at the disagreement. Yes, the space station is complex, because the problem is complex. But, given the complexity of the problem, the solution is relatively simple. Phinehas mentions a golf game, so I’ll suggest that the path that the ball takes from the tee-off to the hole will usually be more complex when a duffer is playing, than when a pro is playing.

    Since the topic of fitness has come up, I’ll comment on that tomorrow (again, as a non-biologist).

  32. bw(10)
    http://www.biomedcentral.com/1.....7/abstract

    CONCLUSIONS:

    We suggest that the overall trends of gene emergence are more compatible with a de novo evolution model for orphan genes than a general duplication-divergence model. Hence de novo evolution of genes appears to have occurred continuously throughout evolutionary time and should therefore be considered as a general mechanism for the emergence of new gene functions.

    Yup, Orphans. That whole evolutionary model of functional sequences being selected for in small increments is no good anymore. Evolution works by poofing new genes into existence, now. Blind natural forces are great at that sort of thing.

    This is the mother of all ad-hoc explanations.

    Anyone want to place bets on when we might be lucky enough to observe any new orphan genes popping into existence?

  33. well lifepsy, darwinists never had any evidence that genes and/or proteins could arise incrementally anyway! i.e. if substantiating evidence doesn’t really matter to your ‘scientific’ theory in the first place,, what difference is it if you just ‘randomly’ allow stuff to poof into existence?,, I mean as long as it is not Intelligence ever doing the ‘poofing’ it is still science is it not?? :)

    Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.
    Richard Lewontin’s January 9, 1997 article, Billions and Billions of Demons

  34. Neil, you may be happy to learn that I am not going to pile on about how lame your analogy is. I’ll with-hold my opinion of your analogy for now, in fact, for the sake of argument, I’ll try to track with it. In your analogy, the best you seem to be saying is that fitness is somehow analogous to your travelogue being shared. In other words, a longer pleasant trip is more likely to be recorded and shared than an unpleasant trip. We all get how there is no travel agent in your story, but what you haven’t explained is why there is travel in your story. Traveling is dangerous(!) even in your own analogy (cf. “unpleasant trips”).

    So, suppose you are an beer-swilling amoeba. An amoeba because it was mentioned earlier, and beer-swilling because it implies that you are fat, happy, and just ready to reproduce. I’d ask why in the world would you expend unimaginable resources to go climb Mount Improbable or any of the other Rocky Mountains. Your analogy suggests that you just got a wild hair and did it. This can only be analogous to a random mutation of some sort.

    But at 21, WJM writes, “If fitness means anything along the lines of hardiness that increases ongoing reproductive success, then evolution apparently started out with pretty much the most fit organism possible and everything went downhill from there. Human beings, then, don’t exist because of Darwinistic evolution; they exist in spite of it”

    I’d say he has hit the nail right on the head. Amoebas like to drink beer. It makes them better amoebas. Even it they “wanted” (mutated) to travel, they are better at beer.

    WJM used hardiness; I’ll use robustness. Fitness, whatever fitness is, requires them for enough time for organisms to reproduce. (I learned that in a BIOLOGY BOOK.) Robust amoebas are robust because they apply the resources they have appropriately; taking trips would not seem to fit.

    This is what people want you to address. Why would an amoeba sitting in a recliner with a beer on his belly, travel at all, risking death, spending resources that would otherwise be used on, well, beer, instead of just getting better at simply drinking beer?

    It isn’t enough to say that the rest of the world was getting more complex. First of all, that assumes facts not in evidence, and second of all, many species when faced with an increasingly complex environment merely drink more beer. It is what they know . . .

  35. Why Up When Down is Just As Good And A Lot Easier?

    Because the life giving Light comes down to Earth from the heavens and generates a Common Ascent of increasingly complex creations.
    #TMOG

  36. Phinehas – Coming from the field of physics I have always thought about this lack of direction in evolution in terms of the problem of the perpetual motion machine.

    A naive person can think. Oh let’s build a perpetual motion machine this way.

    1. We line up bowls of water on a set of steps.
    2. We wait for the natural process of evaporation and condensation to move the water up the steps.
    3. We let the water flow back down to the bottom bowl through a turbine to create energy.
    4. We use this as an infinite source of energy.

    What the naive person fails to realize is the “natural process of evaporation and condensation” would be just as good at moving water from an upper bowl to a lower bowl as lower bowl to upper bowl. You get a random walk, not a directional flow.

    So if evolution is fine with a random walk, what they need is a series of fits and starts. First evolution builds up quite a bit of life, then the whole thing collapses. Then it builds up a little more, then it all collapses. The idea of a random walk having any direction to it is an inherent contradiction.

    This is why the “bowls of water on steps” fails as a perpetual energy source. And it is why evolution fails. An evolutionist who believes in a random walk of life must believe in a series of directionless steps ( some towards more complex life, some towards simpler life). The current situation of the biosphere is just a great big step in the “more complex” direction.

    The problem is that no evolutionist can actually believe this. There is little confidence that neo-Darwinist techniques can build up the current biosphere along a directed route in the short time allotted by the universe. How much less credible is the idea that the entire biosphere has been built up to the current level of complexity by some random oscillations about some equilibrium state.

    Evolution is nonsense and most people realize it. It takes obfuscation, special pleading, belief in directionless direction, and ignoring of large inherit self inconsistencies to accept it. No wonder the Psalmist wrote, “The fool has said in his heart, there is no God.”

  37. 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?

    Just wondering if you’d read “Climbing Mount Improbable”. As it happens, I was re-reading it a fe days ago and I didn’t notice Dawkins make any such point.

  38. I really like Tim’s story about the ‘beer-swilling amoeba’.

    You can easily see the advantage in reproduction that a beer swilling amoeba would have over a sober one. As the saying goes ‘I never went to bed with an ugly ameoba but have woken up with plenty’ ;)

  39. Mr. Fox as to:

    ,,“Climbing Mount Improbable”. As it happens, I was re-reading it a fe days ago,,

    Here is a excellent video excerpt from ‘Darwin’s Dilemma’ (also listed) which clearly gets to the thrust, and crushing critique, of Dawkins’ argument:

    “Climbing Mount Improbable” – Evolution Vs. Functional Proteins – Where Did The Information Come From? – Doug Axe – Stephen Meyer – video
    http://www.metacafe.com/watch/4018222/

    Darwin’s Dilemma – Excellent Cambrian Explosion Movie
    http://www.youtube.com/watch?v=KWEsW7bO8P4

    Just how ‘small’ are these steps up the ‘backside of ‘Mount Improbable’ that Dawkins envisions?

    Doug Axe PhD. on the Rarity and ‘non-Evolvability’ of Functional Proteins – video (notes in video description)
    http://www.metacafe.com/watch/9243592/

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://www.biologicinstitute.o.....nt-collide

    “Biologist Douglas Axe on Evolution’s (non) Ability to Produce New (Protein) Functions ” – video
    Quote: It turns out once you get above the number six [changes in amino acids] — and even at lower numbers actually — but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.
    http://intelligentdesign.podom.....5_14-07_00

    “a very rough but conservative result is that if all the sequences that define a particular (protein) structure or fold-set where gathered into an area 1 square meter in area, the next island would be tens of millions of light years away.”
    Kirk Durston

    Moreover, The “context dependency” of any particular sequence of amino acids is found to exponentially exasperate the incremental evolution of protein sequences for Darwinists:

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.
    http://powertochange.com/wp-co.....rtions.pdf

    “Why Proteins Aren’t Easily Recombined, Part 2″ – Ann Gauger – May 2012
    Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
    http://www.biologicinstitute.o.....ned-part-2

    Moreover, many proteins are multifunctional and, serendipitously, perform several different ‘context dependent’ tasks within the cell, thus further exasperating the problem for Darwinists:

    Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought:
    Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.
    http://www.sciencedaily.com/re.....134623.htm

    Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013
    Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”

    Throw in Dr. Behe’s work on HIV and Malaria, etc.., and the ‘context dependency’ problem becomes even worse for Darwinists. But Mr. Fox, what is all this ‘context dependency’ found for proteins really telling us about the inadequacy of the molecular reductionism of Darwinism? The following article gives us a strong clue as to how we should be actually be viewing the proteins within cells in the ‘context of life’:

    Epigenetics and the “Piano” Metaphor – January 2012
    Excerpt: And this is only the construction of proteins we’re talking about. It leaves out of the picture entirely the higher-level components — tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players.
    http://www.evolutionnews.org/2.....54731.html

  40. NR:

    As I see it, a scientific theory serves two roles. One of those is as a guide to research. I’m not a biologist, however neo-Darwinism seems to be doing pretty well as a guide to research. It establishes technical terminology and gives direction to the research.

    Except neo-darwinism isn’t even a theory. It can’t even muster a testable hypothesis.

    NR:

    Natural selection is often presented as a kind of filter that shapes the direction of evolution.

    If whatever survives to reproduce is a direction.

  41. Wow, an evo from another forum chimed in and sed:

    And here I thought it was the explanation for the prevalence of nested hierarchies

    Just about anything can be put into a nested hierarchy Henry J. For example an Army can be placed into a nested hierarchy. And an Army doesn’t have anything to do with common descent nor evolution.

  42. footnotes to post 39 as to the exponentially worse problem that ‘context dependency’ presents to the evolvability of novel functional protein sequences:

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini and Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73
    Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
    http://www.scimednet.org/quant.....d-protein/

    Here are two other ways to deduce ‘context dependent’ quantum information along the entire protein structure:

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from.
    To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
    Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.
    http://www.technologyreview.co.....f-protein/

    Proteins with cruise control provide new perspective:
    Excerpt: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.”
    http://www.princeton.edu/main/...../60/95O56/

    The preceding experiment is solid confirmation that far more complex functional information resides along the entire protein structure than meets the eye.,, For a sample of the calculus equations that must be dealt with to calculate ‘cruise control’ please see this following site:

    PID controller
    Excerpt: A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal.
    http://en.wikipedia.org/wiki/PID_controller

    It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale within proteins, for how can the quantum entanglement ‘effect’ in proteins possibly be explained by a material (matter/energy) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place?

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

    Qubits that never interact could exhibit past-future entanglement – July 30, 2012
    Excerpt: Typically, for two particles to become entangled, they must first physically interact. Then when the particles are physically separated and still share the same quantum state, they are considered to be entangled. But in a new study, physicists have investigated a new twist on entanglement in which two qubits become entangled with each other even though they never physically interact.,,
    http://phys.org/news/2012-07-q.....ement.html

    Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012)
    Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed.
    Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can’t stay hidden, or they must have infinite speed.,,,
    The remaining option is to accept that (quantum) influences must be infinitely fast,,,
    “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,,
    http://www.sciencedaily.com/re.....142217.htm

    Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has already been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

  43. @Nick

    Imagine a planet covered with only bacteria-like cells. If one cell were bigger, and thus more slowly reproducing, but was able to eat the other bacteria, would it persist in the ecosystem?

    Your argument says no. Which is why your argument is ridiculous.

    First of all, I’m not presenting an argument so much as asking questions. I honestly don’t understand, but would like to. Second, it appears once again that what I’m getting at is a bit too subtle, since it has obviously been misunderstood. I’ll try to clarify.

    I’m imagining your planet covered in bacteria-like cells. I’m also imagining a larger, predatory cell introduced into the environment. I have no problem imagining that predator persisting in the environment. I can also imagine it eating all of the other prey cells and then starving into extinction. Or eating only the local prey cells and then going extinct because it didn’t have the mobility to reach additional food sources. Or mutating to have the mobility and surviving. Or the prey cells also gaining mobility and the predator going extinct. I can even imagine predator an prey having a race to the top of the food chain. Or not. (As a video game designer, I have an active imagination. Seriously, I can do this all day.) In fact, I bet I could imagine an evolutionary story to fit just about any data.

    None of this really addresses my question, though it may suggest new ones. The main thing I still don’t get it how natural selection can save evolution from a blind/exhaustive search of the problem space.

    When all is said and done and all the stories have been told, lowly bacteria still exist, and by most if not all of the metrics for actually calculating reproductive fitness, they are more fit than the increasingly complex organisms that came after them.

    So how can selection via reproductive success save the evolution of complexity from a blind search at the macro level when more complex organisms appear to be, if anything, less successful? Why shouldn’t man be at the bottom of the tree of life and bacteria at the top, if the story of evolution is all about reproductive success?

    Even if we drop back to the micro level and consider that first predatory cell that we imagined, how did its ability to eat other cells arise, other than by blind chance? And if macroevolution is simply more microevolution, then how is it not blind chance all the way down?

  44. @John W Kelly

    Because the life giving Light comes down to Earth from the heavens and generates a Common Ascent of increasingly complex creations.

    (Some posts are difficult to interpret on the internet, where there is often little context from which to view a snippet like this, so please forgive me if I’ve got this all wrong.)

    It appears that you are trying to support Darwinian evolution by appealing to a negative argument of a religious nature. Is that right? This seems a strange choice if there are plenty of positive scientific arguments for Darwinism at hand.

  45. 45

    Michael Beha on Dollo’s Law and why evolution shouldn’t be expected to be time-asymmetric.

    http://www.evolutionnews.org/2.....26721.html

  46. @Neil

    My own way of looking at evolution, is in terms of a population. I see the population as exploring the environment (or the fitness landscape, as it is sometimes called). I see the production of mutations as part of this exploration.

    For me, the problem of the cookie cutter analogy isn’t that the dough has to be forced through the cookie cutter, but that the cookie cutter is designed to pretty much the same degree (and maybe more so?) that you would need to design the cookie itself in order to get the same shape.

    My apologies if the following is a weak analogy, but it is what springs to mind. (BTW, I thought your travel analogy was perfectly fine in explaining what you wanted to explain, I just didn’t think it helped me understand what I wanted to understand.)

    As I’ve said, it is the elegance and accuracy of macroevolution that I find difficult to understand from a purely chance-based or naturalistic perspective. While the appeal to natural selection seems a plausible heuristic at first blush, a closer examination reveals it to be lacking in explanatory power. So maybe it is the fitness landscape that provides accuracy where natural selection cannot?

    I find the game of golf and getting a ball from the tee to the hole a decent analogy for understanding the elegance and accuracy that I’m talking about. (As an aside, I still think I would describe the duffer’s game as less elegant than the pro’s, and might point to the hours spent on the practice tees as an indication to the behind-the-scenes complexity of the pro’s game.)

    From a microevolutionary perspective, I can imagine the Darwinist setting a golf ball on the side of a hill, carefully propped up by a single blade of grass. After a while, a gust of wind starts the ball rolling down hill, naturally. “See,” says the Darwinist, “Now imagine more of that!” OK. I can imagine more wind, earthquakes, hills, etc. But it is the accuracy of the overall tale of the ball getting from the tee to the hole that still nags at me.

    “No problem,” says the Darwinist, “its not so much about random forces like the wind as it is about the landscape.” So he sets about constructing a mini-golf-course hole with windmills and water hazards and carefully calculated angles. He sets the ball on the tee, and after another gust of wind, sure enough, the ball rolls down a hill, around the water hazard, through the windmill, bounces off the angled brace, and drops into the hole.

    You see, whenever I start thinking about fitness landscapes and environmental niches and the like, the only way I can get any sort of accuracy out of it (like the accuracy of a big, fat arrow pointing unerringly toward greater complexity) is if the fitness landscape itself is designed for that accuracy. In other words, the “mutations” in the external environment would appear, under purely natural circumstances, to be just as random as those in the cell. So appealing to the environment looks like it just moves the problem back a step. And in the end, I end up right back at pure, blind chance performing an exhaustive search.

    Where am I going wrong?

  47. @Alan Fox

    Interesting. So, what does Dawkins place at the peak of Mt. Improbable? And what is at its foot?

    If I should be talking about a Mt. Even More Improbable with man near its peak and bacteria near its foot in order to avoid confusion, I’m happy to do so.

  48. @JDH,

    Nice analogy!

    I could very well be a naive person. When you talked about condensation being distributed equally between the bowls, I immediately started thinking about some sort of plastic tent above the bowls that could catch the condensation which would then run down an angled fold to drop back into the top bowl. But then my skeptic clicked in and started thinking there’s probably good reasons why that would never work. :)

    How much less credible is the idea that the entire biosphere has been built up to the current level of complexity by some random oscillations about some equilibrium state.

    This sums up the issue rather elegantly. I’m now going to mess up the elegance with another analogy.

    You know the visualization on many equalizers that outputs the amplitude of various frequencies as a song plays? Often, there is a little line that hangs around a moment at the peak of each frequency even after it has changed? It seems to me that that little line is about the best that natural selection can be seen to accomplish. It might allow a peak in the random oscillations to hang around for a bit, but I don’t see how it can give any sort of direction that would allow random frequencies to climb ever higher without some additional designed element thrown into the mix.

  49. So, what does Dawkins place at the peak of Mt. Improbable? And what is at its foot?

    The theory of evolution posits common decent from a universal ancestor (LUCA)and proposes variation and selection as the mechanism of change. So Dawkins’ analogy covers the various paths from LUCA to any existent orextinct descendant, depending on what lineage is being considered. Homo sapiens is only one of many of the myriad species that are the end result of evolution. Each species sits on its own peak.

  50. My own way of looking at evolution, is in terms of a population. I see the population as exploring the environment (or the fitness landscape, as it is sometimes called). I see the production of mutations as part of this exploration.

    I don’t find Neil’s way of thinking about evolution compelling. There is no active search for solutions. Living organisms just get on with their lives. Plant evolution is a better illustration of the passive nature of evolutionary processes. Organisms are subject to the pressure for change brought about by the niche environment that they find themselves in. And the environment is dynamic and ever-changing, involving many factors, not all easy to spot. Continental drift, island formation, meteor strike, volcanic eruption, climate, weather, predators, prey, parasites etc etc.

  51. @Alan Fox

    So every organism sits atop its own Mt. Improbable with LUCA at its foot?

    Based on that, I suppose I am talking about the particular Mt. Improbable that has Homo sapiens at its peak and LUCA at its foot. Does that make a big difference in the questions I am asking?

  52. @Alan Fox

    Organisms are subject to the pressure for change brought about by the niche environment that they find themselves in. And the environment is dynamic and ever-changing, involving many factors, not all easy to spot. Continental drift, island formation, meteor strike, volcanic eruption, climate, weather, predators, prey, parasites etc etc.

    Sure, but which of these dynamic and chaotic forces gives evolution its accuracy or heuristic such that it moves toward greater complexity in some manner that doesn’t require a random, blind, and exhaustive search of the problem space?

  53. Alan Fox:

    The theory of evolution posits common decent from a universal ancestor (LUCA)and proposes variation and selection as the mechanism of change.

    Reference please.

    Seeing that this alleged theory allegedly doesn’t say anything about the origin of life, it should be perfectly OK if there wasn’t a LUCA as the OoL could have occurred many times, meaning many seeds to plant many trees.

    BTW passive isn’t going to get the diversity of life from some prokaryotic-like population.

  54. You know what is really strange, Alan? Ten and a half months later you babies are still mumbling about it.

    Do you realize how good that makes me feel? :)

  55. Other Mouth sez:

    But that’s what this is all about Joe.

    It’s about YOU. After all that post to YOU, in response to all your belligerent cowardice.

    So that is what it is all about. How Lizzie lets losers like you belligerently attack people at will and only intervene to save your cowardly butt from retaliation.

    Thank you for clearing that up mouthy…

  56. Does that make a big difference in the questions I am asking?

    Well, there seemed to be a misconception that there was some sort of goal in the mix, with humans as the ultimate target of a search. I don’t personally think searching is a good analogy for reiterated “vary and test”, which is how I think of the evolutionary process. Of course, I am a layman and no authority on the details of evolution. There are many people better informed and better qualified than me to answer questions on evolution and a wealth of literature available.

  57. Do you realize how good that makes me feel?

    No and I have not the slightest curiosity. Even contemplating for a second what goes on in the brain of Joe Gallien gave me the collywobbles! :)

  58. Sure, but which of these dynamic and chaotic forces gives evolution its accuracy or heuristic such that it moves toward greater complexity in some manner that doesn’t require a random, blind, and exhaustive search of the problem space?

    Evolution produces organisms that work as they are. If you could reproduce every intermediate from LUCA to Homo sapiens each of those organisms would have to function well enough to sustain itself and survive to reproduce. Each link in the line of organisms could only be a little different from its immediate antecedent and descendant. There is no prerequisite for an increase in complexity per se and modern cyanobacteria are still single-celle like their remote ancestors. Viruses are thought to have evolved as stripped down parasitic minimalists from more complex free-living ancestors.

    And “searches do not need to be “exhaustive”. Current life in all its diversity only uses a tiny proportion of the theoretically available DNA sequences. For all we know, there are vast possibilities for functional life-forms still yet to be stumbled upon.

  59. 59

    The evolution of complexity:

    “Under Darwin’s concept, variation is (nearly) completely random, whereas selection introduces order and creates complexity. In this respect, Darwin is diametrically opposed to Lamarck, whose worldview essentially banished chance.”

    Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 207-209). Pearson Education (USA). Kindle Edition.

    “Modern Synthesis shuns progress as an anthropomorphic concept but nevertheless maintains that evolution, in general, proceeds from simple to complex forms.

    Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 410-411). Pearson Education (USA). Kindle Edition.

    The beneficial changes that are fixed by natural selection are infinitesimally small (in modern parlance, the evolutionarily relevant mutations are supposed to have infinitesimally small fitness effects), so evolution occurs via the gradual accumulation of these tiny modifications. Darwin insisted on strict gradualism as an essential staple of his theory: “Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications, each profitable to the preserved being. …If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”

    Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 412-417). Pearson Education (USA). Kindle Edition.

    Evolution supposedly proceeds from simple to complex by gradual, undirected modifications which ultimately must introduce complexity by very slight increments. Natural selection is supposed to be the heuristic that guides the search. But NS doesn’t account for complexity, only fitness, relative to the rest of the population. So the general correlation between fitness and complexity is pretty clear.

    Now just because we can say that different organisms, like bacteria, occupy different ecological niches, it does not dismiss the notion that for a large variety of available niches, complexity is the result of some measure of fitness; and such a progression, from simple to complex, is the espoused arrow of evolution.

  60. Natural selection is supposed to be the heuristic that guides the search.

    Supposed by whom? There is no guided search (if evolution is true). By the way, I have no difficulty with someone who believes that life the universe and everything was the work of a supreme and loving God. What is today could have been wrought by such a being but maybe the Almighty choose to work within the properties of the universe he created. Maybe God, though omnipotent, can only bring about what he intends in his natural universe within the parameters of that universe.

    (I do have a problem when some extrapolate from this a set of authoritarian rules by which they they want others to abide – don’t get me stated on Islam or the Roman Catholic Church – but that’s probably off-topic. :) )

  61. @ Phinehas

    I see Dr. Liddle has posted a much better reply to your questions here and Professor Felsenstein has added a comment. Please have a look.

  62. Nick,

    Have any textbooks on Macro-Evolutionary Theory been recently published? Or is Macro-Evolutionary Theory still a field that has no recognized standard texts?

    No results found for “Degree in Macro-Evolutionary Theory”.

    Imagine that.

  63. I’m back for today’s posts in this thread.

    My analogy

    Several people have commented on the analogy that I used. No analogy is perfect. An analogy is used to illustrate a few points, and can be a useful tool. But I certainly don’t claim that it proves anything. It’s an illustration, not a demonstration.

    The point of my analogy was to distinguish between a plan and a random walk. It was also to illustrate that there is no search. If there were a pot of gold hidden somewhere in them thar hills, a random walk would be a terrible way of finding it, with little chance of success. However, as illustrated by the vacation analogy, there can be many possible alternative rewards (satisfactory vacations). So there isn’t a search, but there is a good chance of a satisfactory outcome for many of the possible paths of a random walk. The critics of evolution often miss this point.

    The difficulties of communication

    In #50, Alan Fox says:

    I don’t find Neil’s way of thinking about evolution compelling.

    Alan then goes on to give his preferred view. The funny thing is that I agree with almost all of that, with the exception of the word “passive”.

    Fitness

    I said that I would comment on fitness today. So here goes.

    If the next generation has the same size as the current generation, then the fitness is 1. Population wide, the fitness is the ratio of the next generation size to this one. We usually think of the population fitness as being made up of the fitness contributions of each member of the population. As a crude approximation, if a person has two children that survive to maturity, that would be a fitness of 1. The crude estimate for humans would be the number of childred that survive to maturity, divided by two (because it takes two biological parents).

    If you look at honey bees, where the queen has thousands of offspring, and the worker bees have none, then it gets a lot more complex. We can’t say that the worker bees have zero fitness, because the queen’s ability to reproduced depends on the workers. So the contribution of each bee to the next generation is a lot harder to estimate, and is not merely counting.

    If we come back to humans, it is really more complex there than the crude estimate suggests. School teachers and physicians might contribute to many of the next generation. And maybe grandparents contribute more than zero, also, so they do not lose all fitness when they age.

    So fitness is hard to actually measure.

    I’m not a biologist. I’m a mathematician. If I want to mathematically model evolution or population genetics, then fitness will be an important part of that model. It doesn’t matter that it might be hard to actually measure. It shows up readily as an important variable in any mathematical modeling of population genetics. So, at least from my point of view, fitness is mainly important for its role in theory.

    The other important point about fitness, is that we have to be aware that it is relational. We should not talk about the fitness of an organism. Rather, we should talk about the fitness of an organism in a particular ecological niche. As the environmental conditions change, the fitness changes. Environmental change is one of the drivers of evolution.

    An example often given, is that of antibiotic resistant bacteria. If we were not using antibiotics, such bacteria might never have evolved. Some antibiotic resistant mutations might have cropped up, but it is unlikely that it would show up as other than the odd mutation. However, because we do use a lot of antibiotics, we have created an environment for bacteria where antibiotic resistance confers increased fitness. And that change in the environment is part of what drives the evolution of antibiotic resistant strains.

  64. 64

    “There is no guided search (if evolution is true).”

    Yes, “guided” is a loaded word, isn’t it Alan, just as “selected” is.

    Substitute whatever word you like. Natural selection is a required component of evolutionary theory, and is supposed to provide a way for evolution to climb hills of fitness and complexity as opposed to descending them. That may not provide a target, but it’s most certainly a direction. To say that NS guides variation is to state the obvious, unless you disagree with the quotes I provided in #59. If selection favors fitness, then it guides (constrains) the results of variation, just as gravity and the constraints of a landscape guide running water by meandering paths to lower elevations.

  65. Alan Fox:

    There is no guided search (if evolution is true).

    So there’s an unguided search?

    Phinehas:

    None of this really addresses my question, though it may suggest new ones. The main thing I still don’t get it how natural selection can save evolution from a blind/exhaustive search of the problem space.

    1. Deny that evolution is an exhaustive search.

    2. Deny that evolution is a blind search.

    3. Deny that evolution is any sort of search at all.

    4. Develop an evolutionary search algorithm and implement it in a computer simulation to demonstrate that evolution must be a fact.

    5. Ignore the cognitive dissonance.

  66. 66

    Alan @49,

    “The theory of evolution posits common decent from a universal ancestor (LUCA)and proposes variation and selection as the mechanism of change. So Dawkins’ analogy covers the various paths from LUCA to any existent orextinct descendant, depending on what lineage is being considered. Homo sapiens is only one of many of the myriad species that are the end result of evolution. Each species sits on its own peak.”

    And at the top of most peaks are species that are significantly more complex than single-celled organisms, suggesting a correlation of fitness with complexity, which was the point of the OP:

    “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?”

    So do you notice that there is an apparent and implied correlation between fitness and complexity with regard to evolutionary theory and the presumed Darwinian progression from simple to complex life forms? Do you understand that the questions being posed essentially ask how fitness entails complexity in most environmental conditions, and how that can be the case with a definition of fitness that equates with reproductive success?

  67. Hi Neil

    This is the bit that doesn’t gel with me:

    I see the population as exploring the environment

    In discussions on evolution, the plant kingdom is often overlooked. Yet the power of selection as demonstrated by plant husbandry (the humble cabbage, diversity personified!)for example. The process of environmental design that resulted in insect pollination of flowering plants is, I think, entirely passive from the perspective of the plant and, I would argue, from the insect too. Perhaps the culmination of environmental design in flowering plants where insect pollination happens is the symbiosis that links the fig to its fig wasp such that neither species can survive without the other.

  68. So do you notice that there is an apparent and implied correlation between fitness and complexity with regard to evolutionary theory and the presumed Darwinian progression from simple to complex life forms?

    It follows from how niches are available and get filled. Prokaryotes are enormously successful in terms of biomass, filling all the niches that are available to them. Exploitation of novel niches may indeed involve additions to (shall we say) the original design. It is just not a prerequisite, nor is it inevitable. (I’m tempted to add, otherwise, why are there still bacteria, but I’ll resist!)

  69. Alan Fox:

    The process of environmental design that resulted in insect pollination of flowering plants is, I think, entirely passive from the perspective of the plant and, I would argue, from the insect too.

    Can you plrease reference this alleged process of environmental design? Or could you at least admit that you just made it up and it has no basis in reality?

  70. Richie cupcake Hughes sez:

    This is established science.

    Your position doesn’t have anything to do with science.

    So unfortunately you wont get to make up your own acronyms and pretend you can measure without providing any….numbers.

    Unfortunately for YOU. YOU cannot provide any numbers. Your position doesn’t have anything to measure with.

  71. petrushka:

    Skepticism is reluctance to believe without evidence.

    And that is why you ain’t a skeptic. You accept unguided evolution and it doesn’t have any eb=videntiary support.

  72. Petrushka:

    Do you understand the infinite regress implied in:

    Skepticism is reluctance to believe without evidence.

    I suggest you try here on for a start on warrant for cases in the context of the underlying worldviews. In a nutshell, to accept A one demands warrant B, but why accept B, leads to C, D . . . So to infinite regress, or to circularity, or else to a context of warrant on comparative difficulties across live worldview options. Where also, we cannot but have a view of basic reality as a framework for science, history, issues, etc.

    In addition, the issue of the self referential absurdity of radical skepticism, and the extension to selective hyperskepticism — being overly dismissive of what you don’t want to accept while being by direct implication overly credulous about what you want to accept — will repay reflection.

    I would suggest instead of the undue and ill-advised glorification of “skepticism,” that to be critically aware, accepting that worldviews should rest on more or less reasonable faith that stands on first plausibles that stand comparative difficulties analysis on factual adequacy, coherence and explanatory power and elegance, and to see also that as a finite, fallible, morally struggling/fallen, too often ill willed thinker, we will make errors, is a better overall balance. In that context, warrant should be consistent in standard relative to what the cases allow.

    KF

  73. PS: I should also add that the tendency to dismiss what one does not wish to hear, as having “no evidence,” is all too common, and that to often it reveals a want of attending to duties of care to the actual evidence, to fairness and to the requirement that every tub must in the end stand on its own bottom. In some cases it is a case of speaking wantonly without regard to truth, and in the hope of profiting from what is said being taken as true. Such behaviour is in fact a species of being irresponsible and outright deceitful.

  74. 74

    So, according to Mr. Rickert, “fitness” is a post-hoc description that means nothing more than “how many offspring happened to survive”.

    Fitness, then, isn’t a quality of the organism lineage/species (as “survival of the fittest” would imply), but rather an accounting term that only compares relative survival rates.

    Indeed, since “fitness” only means “survival rate”, “survival of the fittest” simply means “survival of those with the highest survival rate.”

    Now THERE’S a significant scientific principle if I ever heard one.

  75. WJM @74:

    You have hit the nail on the head.

    “Fitness” is an after-the-fact label applied to the results of a process which, in most cases, we don’t understand or at least don’t have full details of.

    Most people don’t like to talk about it, even critics of evolutionary theory, but when we peel away the layers we find that in most discussions of survival of the fittest we are dealing with a tautology.

    A decade ago I addressed this issue on my (now defunct) website:

    http://web.archive.org/web/200.....0Avoid.htm

  76. William,

    Biological fitness is indeed an after-the-fact assessment and shouldn’t be confused with physical fitness.

    One can be very physically fit and have nothing wrt biological fitness.

  77. Can anyone please explain to me how the analogy of climbing up Mt. Improbable is supposed to prove Darwinian Evolution?

    Has anyone even attempted to climb a mountain without intelligence, skills/tools, awareness of each and every single step etc…?

    Are there simply so many paths (infinite perhaps?) to reach the “top” which renders it highly probable?

    It doesn’t seem likely that an unguided and/or undirected random process that relies explicitly on the condition “if survive” or no destruction (how niwrad puts it) would be capable of climbing Mt. Improbable even once.

    Each step would likely be a “death step”.

    Where does Darwinism fill in this gap where it increases its own probability?

    We are obviously not dealing with an easy path up Mt. Improbable which is attainable by simple incremental steps.

  78. WJM 74, I dropped a full plate of food when I read:

    “survival of those with the highest survival rate.”

    hilarious …

  79. Alan Fox:

    There is no guided search (if evolution is true).

    Only wrt unguided/ blind watchmaker evolution. If Intelligent Design Evolution is true then evolution is guided, with random effects sprinkled about.

  80. OT:

    Hey Lizzie, if you happen to be monitoring this thread, I’m suddenly getting…

    Forbidden

    You don’t have permission to access /wp/wp-comments-post.php on this server.

    Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.

  81. 81

    Alan Fox @68

    I wrote:

    So do you notice that there is an apparent and implied correlation between fitness and complexity with regard to evolutionary theory and the presumed Darwinian progression from simple to complex life forms?

    You replied,

    “It follows from how niches are available and get filled. Prokaryotes are enormously successful in terms of biomass, filling all the niches that are available to them. “

    So niches get filled by the process of evolution. We know a given niche exist by which species fills it. If there is a species, then there is an ecological niche which it fills.

    “Exploitation of novel niches may indeed involve additions to (shall we say) the original design.”

    So evolution proceeds by exploitation of niches. We can know an ecological niche by the fact that a species fills it. If complexity is observed, then we know that it was required by that niche.

    “It is just not a prerequisite, nor is it inevitable.”

    So evolution is completely directionless. It proceeds in no definite direction, or any direction, or whichever direction it needs to proceed in. What we observe is explicable in terms of evolution, which is a process capable of creating what we observe.

    ” (I’m tempted to add, otherwise, why are there still bacteria, but I’ll resist!)”

    Well it’s a good thing you didn’t mention it then.

    In summary, it is not necessary nor likely for evolution to produce complexity. It just happened to do so because certain ecological niches favor complex species over simple ones. This makes sense. We can then, for example, say that aquatic creatures have complex features specific to being viable in aquatic environments, because those features were required in order for species to fill those niches. This sort of raw explanatory power is intoxicating.

  82. How to test the claim that unguided evolution produced humans:

    Humans exist by way of evolution and evolution is unguided.

    Brilliant in it’s simplicity…

  83. TSZ seems unresponsive at the moment. I suppose I can try to continue the conversation here for now.

    OMagain:

    It is improbable. It’s very improbable. Likewise, the chance of any given atom being exactly where it is right now is also improbable.

    Yet all atoms are somewhere, despite that improbability.

    Again, I’m not an expert on probabilities, but this doesn’t sound quite right to me. I’d think that any given atom being exactly where it is right now is awfully close to a 100% probability. :) Similarly, if I deal you five random cards, I would think the odds of you having five random cards is pretty well guaranteed. On the other hand, the odds of you having a specified set of cards will depend on the specification (i.e. a “flush”, a “full house”, etc.)

    At first, it might seem unintuitive to talk about probabilities after the fact, since, as you say, we get dealt the cards we get dealt. But when you start trying to explain how someone got dealt the cards in their hand, probability becomes helpful once again. For instance, if I sit down with you for a game of poker and (somehow) get dealt three royal flushes in the first three hands, you’d be forgiven for turning back to probabilities to try to consider exactly how I ended up with these cards, even though you knew that any other particular set of cards would have been just as improbable.

    I’ll ask again, have you actually read Dawkin’s book CMI?

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

  84. TSZ seems unresponsive at the moment.

    What do you mean “at the moment”?

  85. In #67, Alan Fox explains where he disagrees with me.

    I still think this is mainly miscommunication. What Alan does not like, is my statement “I see the population as exploring the environment.” And he wants to illustrate this using plants as an example.

    When I look around, I notice seedlings trying to grow in the most unlikely places, such as between paving blocks or in cracks in the driveway. This is an example of what I consider exploring. The plant population has evolved means of randomly dispersing its seed in way that would seem to work for finding new fertile places to grow.

  86. 86

    Phinehas,

    “Again, I’m not an expert on probabilities, but this doesn’t sound quite right to me. I’d think that any given atom being exactly where it is right now is awfully close to a 100% probability. Similarly, if I deal you five random cards, I would think the odds of you having five random cards is pretty well guaranteed. On the other hand, the odds of you having a specified set of cards will depend on the specification (i.e. a “flush”, a “full house”, etc.)”

    You are correct. One needn’t be an expert on probability to see that if we define a specification for a poker hand as “any 1 of the possible 2,598,960 poker hands” then we’ve defined a set of events that is equal to the set of all poker hands. In this case, it’s certainly no surprise that such a hand is dealt, since the probability for the event is exactly 1. This differs entirely from the probability of being dealt a flush for instance.

    I’m quite surprised that an argument with regard to the certainty of an improbable event is still frequently employed to argue against the improbability of a specific event. By the logic implied in the quote you provided, we should be no more surprised to see a royal flush than we are to see any other hand, since all five-card combinations are equally improbable. This reasoning ignores specification; and whenever it goes unchallenged by proponents of Darwinian evolution, we are reminded that no argument against design inferences is too ridiculous. One has to wonder why these categorically improper applications of certain improbabilities, in answer to specification, are not embarrassing to our opponents, and dealt with on their side.

    BTW argument was used by Ken Miller: Video

  87. Nick @22 wrote:

    Or #2: total failure to think over many orders of magnitude of timescale, geographic scale, organism size scales, etc.

    This got me to thinking about science, mathematics, and just when/how we are justified in extrapolating from our data. Clearly no statistician would graph data, draw a line through the points, and then extend that line 7 orders of magnitude to the right and expect to have anything useful as a result. (I take it that since Darwin is ~150 years ago, and life supposedly began 3.8 Gya, that we’re talking about extrapolating ~7 orders of magnitude back in time from our ability to closely observe.)
    I’m not just asking where scientists deal with quantities over that range. Physicists and astronomers do that all the time. I’m asking in what areas do investigational/empirical scientists observe at one level, and validly extrapolate to things they cannot empirically confirm that are many orders of magnitude beyond.

    As a possible response, I can imagine an evolutionist arguing that “we have observed for more than 150 years. We have good evidence of small-scale change over the last few thousand years. The evidence is more scant as time scales grow, but the picture remains consistent. Therefore all our extrapolating is valid and there is evidence that it is correct.” But that’s not entirely satisfactory, because as the evidence thins out, they’re filling in more of the gaps with their stories. The weight of the evidence shrinks rapidly as the time scales increase. Yes, I can extrapolate. But at some point, that becomes little more than my ability to imagine. Or the ability of thousands of scientists to collectively imagine.

    So as a serious question for the varied readers out there: In what other areas of human inquiry do we extrapolate over 7 orders of magnitude from our direct observations to things we cannot directly confirm, and not even bat an eye at the conclusions?

  88. Evolutionary
    Extrapolation
    Defended

    Seven orders by Maggie to punch Darwin’s tickets?
    No problem at all . . . you pathetic hick, it’s
    so common, you goof,
    and here is our proof –
    Um, let’s see, . . uh . [chirping crickets]


  89. Actually they are not all random wrt function and being random wrt function does not = blind and undirected.

    other mouth

    For the benefit of Phinehas, could you describe if it is possible, even if only in theory, to determine if a single mutation was random or if the intelligent designer was in fact involved?

    Nice strawman- however Phnihas, please read “Not By Chance” by Dr Lee Spetner. It does what the other mouth requests.

    OTOH the other mouth cannot describe, even if only in theory, to determine if a single mutation was random or directed.

    The evo position doesn’t have any methodology.

  90. For example Phinehas, transposons carry within their sequence the coding for two of the enzymes it requires to move around. It is all in one nice package.

    And then there are many mutations which occur only when instructed to by the cell. Dr James Shapiro calls it “natural genetic engineering”- Dr Spetner calls it “built-in responses to environmental cues”.

  91. Phinehas,

    If you want to know about evolutionism, just ask. I will not only answer your questions but I will also provide supporting references as required.

    The ilk over on TSZ isn’t interested in an open and honest discussion. All they care about is protecting their dogma.

  92. Joe, I think you raise some interesting points about the possibility of “evolution” being guided in some instances. It is important, however, to distinguish between the mere possibility of guidance (which, arguably could exist across a vast spectrum) and those cases in which we are justified, on the evidence of inferring design (according to the probability calculations — say 500-1000 bit threshold).

  93. Eric,

    I am reading James Shapiro’s “Evolution: A View from the 21st Century”- it appears that genetic change is guided in many instances. But he thinks all that evolved too- the guidance system.

    But anyway- “Not By Chance” is a must read for IDists and evos. It puts the whole debate into perspective, ie it demonstrates that those who oppose evolutionism do not oppose evolution. We just oppose the idea that the blind watchmaker is behind all the changes.

    And Shapiro’s book expands on Spetner’s ideas with more data. Yeah, he didn’t mean to and he thinks it all evolved but I know if Spetner reads Shapiro he will be all smiles.

  94. 94

    This got me to thinking about science, mathematics, and just when/how we are justified in extrapolating from our data. Clearly no statistician would graph data, draw a line through the points, and then extend that line 7 orders of magnitude to the right and expect to have anything useful as a result.

    That kind of bogus extrapolation is exactly what creationists/IDists/whatevers are doing when they sit on the couch, think about evolution for a moment, decide that since they haven’t personally observed X, X must be effectively impossible even over millions/billions of years.

    (Where X is the evolution of new genetic “information”, or whatever.)

  95. 95

    As a possible response, I can imagine an evolutionist arguing that “we have observed for more than 150 years. We have good evidence of small-scale change over the last few thousand years. The evidence is more scant as time scales grow, but the picture remains consistent. Therefore all our extrapolating is valid and there is evidence that it is correct.” But that’s not entirely satisfactory, because as the evidence thins out, they’re filling in more of the gaps with their stories. The weight of the evidence shrinks rapidly as the time scales increase.

    That’s not really true. For example, we now have good chains of transitional fossils for a great many major transitions. So what scientists are doing is interpolation more than extrapolation. It’s the creationists that are inappropriately extrapolating, namely extrapolating from their pitifully tiny, incredibly biased and poorly researched third-hand knowledge base.

  96. Nick Matzke:

    That’s not really true. For example, we now have good chains of transitional fossils for a great many major transitions.

    But still no genetic evidence to support the transformations.

    Ya see Nick, your position’s problem is that you think DNA is some sort of magical molecule that you can change to get new body plans tat require new body parts. Unfortunately evo-devo hasn’t borne that out.

  97. And BTW fossils do NOT say anything about a mechanism. IOW you falsely extrapolate the fossil evidence to equal blind watchmaker evolution.

    Nice job, ace.

  98. 98
    William J Murray

    Nick Matke appears immune to correction on this matter. I’ve already directed him to the FAQ on this site that clearly states that ID and common descent are fully compatible.

  99. 99
    William J Murray

    Excuse me, I meant Matzke.

  100. Mr. Matzke claims:

    That’s not really true. For example, we now have good chains of transitional fossils for a great many major transitions.

    That’s simply not true. For instance, the infamous whale transitionals that Darwinists keep touting are found to be bogus:

    Whale Evolution vs. The Actual Evidence – video – fraudulent fossils revealed
    http://vimeo.com/30921402

    same for birds:

    Bird Evolution vs. The Actual Evidence – video and notes
    http://vimeo.com/30926629

    further notes:

    Bat Evolution? – No Transitional Fossils! – video
    http://www.metacafe.com/watch/6003501/

    The Unknown Origin of Pterosaurs – video
    http://www.youtube.com/watch?v=XP6htc371fM

    Fish & Dinosaur Evolution vs. The Actual Evidence – video and notes
    http://vimeo.com/30932397

    More of Nature’s Dusty Evolutionary Gems – podcast (debunking whale evolution, feathered dinosaurs, and Tiktaalik)
    http://intelligentdesign.podom.....6_06-07_00

    In the following video, from 15:05 minute mark to 19:15 minute mark, Phillip Johnson notes a very strange inconsistency in where the Darwinian fossil evidence is found:

    Phillip Johnson – “Gould and Eldridge were experts in an area where the fossil record is most complete, “marine invertebrates”, and developed the theory of Punctuated Equilibrium in response to what they saw in the fossil record in that area of research. Whereas, interestingly, the greatest claim for transitional fossils, such as ape-men, comes primarily from the area where fossilization is rarest, from land animals – April 2012 – video
    http://www.youtube.com/watch?v.....age#t=903s

    Here are some quotes by leading paleontologists on the true state of the fossil record:

    “The point emerges that if we examine the fossil record in detail, whether at the level of orders or of species, we find’ over and over again’ not gradual evolution, but the sudden explosion of one group at the expense of another.”
    Paleontologist, Derek V. Ager (Department of Geology & Oceonography, University College, Swansea, UK)

    “It must be significant that nearly all the evolutionary stories I learned as a student from Trueman’s Ostrea/Gryphaea to Carruthers’ Zaphrentis delanouei, have now been ‘debunked’. Similarly, my own experience [sic] of more than twenty years looking for evolutionary lineages among the Mesozoic Brachiopoda has proved them equally elusive.’
    Dr. Derek V. Ager (Department of Geology & Oceonography, University College, Swansea, UK), ‘The nature of the fossil record’. Proceedings of the Geologists’ Association, vol.87(2), 1976,p.132.

    “A major problem in proving the theory has been the fossil record; the imprints of vanished species preserved in the Earth’s geological formations. This record has never revealed traces of Darwin’s hypothetical intermediate variants – instead species appear and disappear abruptly, and this anomaly has fueled the creationist argument that each species was created by God.”
    Paleontologist, Mark Czarnecki

    “There is no need to apologize any longer for the poverty of the fossil record. In some ways, it has become almost unmanageably rich and discovery is outpacing integration. The fossil record nevertheless continues to be composed mainly of gaps.”
    T. Neville George – Professor of paleontology – Glasgow University

    “Evolution requires intermediate forms between species and paleontology does not provide them.”
    David Kitts – Paleontologist – D.B. Kitts, Paleontology and Evolutionary Theory (1974), p. 467.

    “The long-term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists” –
    Stephen Jay Gould – Harvard

    “Given the fact of evolution, one would expect the fossils to document a gradual steady change from ancestral forms to the descendants. But this is not what the paleontologist finds. Instead, he or she finds gaps in just about every phyletic series.” -
    Ernst Mayr-Professor Emeritus, Museum of Comparative Zoology at Harvard University

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.”
    Robert L Carroll (born 1938) – vertebrate paleontologist who specialises in Paleozoic and Mesozoic amphibians

    “Now, after over 120 years of the most extensive and painstaking geological exploration of every continent and ocean bottom, the picture is infinitely more vivid and complete than it was in 1859. Formations have been discovered containing hundreds of billions of fossils and our museums now are filled with over 100 million fossils of 250,000 different species. The availability of this profusion of hard scientific data should permit objective investigators to determine if Darwin was on the right track. What is the picture which the fossils have given us? … The gaps between major groups of organisms have been growing even wider and more undeniable. They can no longer be ignored or rationalized away with appeals to imperfection of the fossil record.”
    Luther D. Sunderland, Darwin’s Enigma 1988, Fossils and Other Problems, 4th edition, Master Books, p. 9

    “The evidence we find in the geological record is not nearly as compatible with Darwinian natural selection as we would like it to be …. We now have a quarter of a million fossil species but the situation hasn’t changed much. The record of evolution is surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than in Darwin’s time … so Darwin’s problem has not been alleviated”.
    David Raup, Curator of Geology at Chicago’s Field Museum of Natural History

    “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.” Fossils and Evolution, TS Kemp – Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

    “Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences.”
    George Gaylord Simpson (evolutionist), The Major Features of Evolution, New York, Columbia University Press, 1953 p. 360.

    “No wonder paleontologists shied away from evolution for so long. It seems never to happen. Assiduous collecting up cliff faces yields zigzags, minor oscillations, and the very occasional slight accumulation of change over millions of years, at a rate too slow to really account for all the prodigious change that has occurred in evolutionary history. When we do see the introduction of evolutionary novelty, it usually shows up with a bang, and often with no firm evidence that the organisms did not evolve elsewhere! Evolution cannot forever be going on someplace else. Yet that’s how the fossil record has struck many a forlorn paleontologist looking to learn something about evolution.” -
    Niles Eldredge , “Reinventing Darwin: The Great Evolutionary Debate,” 1996, p.95

    “Enthusiastic paleontologists in several countries have claimed pieces of this missing record, but the claims have all been disputed and in any case do not provide real connections. That brings me to the second most surprising feature of the fossil record…the abruptness of some of the major changes in the history of life.”
    Ager, D. – Author of “The Nature of the Stratigraphical Record”-1981

    “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology.”
    Stephen Jay Gould

  101. That kind of bogus extrapolation is exactly what creationists/IDists/whatevers are doing when they sit on the couch, think about evolution for a moment, decide that since they haven’t personally observed X, X must be effectively impossible even over millions/billions of years.

    That would be an argument from incredulity I suppose, more than an actual extrapolation. But the evolutionist asks me to extrapolate (and sometimes to use my imagination!) from what we can directly observe to what we have not directly observed. That’s the part I’m questioning–and at the moment, the magnitude of the extrapolation request.

    For relatively simple things such as the motion of a body in space, we can extrapolate over many orders of magnitude and have few concerns. (Although it might be worth noting that even Newtonian physics, which works great for human-sized systems, breaks down when you get 10-15 orders of magnitude away, requiring relativistic and quantum modifications to remain applicable.)

    But as the complexity of the system in question goes up, our ability to predict rapidly goes down. Meteorology, computer science, any area of physics featuring chaotic behavior, and probably many other areas, are each a totally different ball game at scales only a couple of orders of magnitude away from another that we think we understand. I cannot think of an area of science that features the complexity of living things, where we have a demonstrable ability to extrapolate as far back as evolutionists do beyond the directly observable.

    The following perspective will have to save the day:

    For example, we now have good chains of transitional fossils for a great many major transitions. So what scientists are doing is interpolation more than extrapolation.

    Yes, having made the necessary assumptions about molecular malleability (i.e., their unobserved ability to change as much as necessary) and then lining up the fossils neatly, it looks as if interpolation is all that’s left to do. Many careers rest on that. But at the foundation is an extrapolation. It had to come first.

    Even in a house of cards, some cards are closer to the bottom.

  102. Nick @ 94

    That kind of bogus extrapolation is exactly what creationists/IDists/whatevers are doing when they sit on the couch, think about evolution for a moment, decide that since they haven’t personally observed X, X must be effectively impossible even over millions/billions of years

    While your description of Darwin-skepticism rises only to the level of a crude caricature, it is true that many (including myself) place great stress on the empirical foundation (or lack thereof) of Neo-Darwinism. This is not wrong. On the contrary, this is what healthy skepticism looks like. The grand claims of Neo-Darwinism are positively staggering from an engineering viewpoint. It maintains that an unplanned, purposeless, largely stochastic process (and before you say it, yes we all know that natural selection is nonrandom, but it can only work with what random mutation provides for it, so the stochastic part of the equation really has to do much of the heavy lifting) can construct sophisticated systems for processing digital information, build intricate and tightly balanced micro-machinery, produce signal transduction systems that operate at the outer limits of what is physically possible in our universe, and so on and so on ad nauseam. Necessarily the Neo-Darwinian explanation for the diversity of the biosphere requires that something like an amoeba can gradually become a cheetah or a giant squid or an albatross. This is said to take place step by infinitesimal step, each one not only maintaining but improving fitness. Has anyone anywhere at any time ever witnessed anything that would give sufficient empirical grounding to such claims? If so, I would love to know what that observation is. If not, then what requires me to affirm the truthfulness of those claims? For that matter, why on earth would any rational, critical thinker accept those claims without very compelling evidence? Further, how do you reconcile your belief in the practically infinite plasticity of biological forms with the mountains of empirical data from breeding experiments that suggest that there seem to be limits to how far populations can change? There certainly is “bogus extrapolation” going on. It is in your willfully-blinded mind.

  103. It maintains that an unplanned, purposeless, largely stochastic process (and before you say it, yes we all know that natural selection is nonrandom, but it can only work with what random mutation provides for it, so the stochastic part of the equation really has to do much of the heavy lifting) can construct sophisticated systems for processing digital information, build intricate and tightly balanced micro-machinery, produce signal transduction systems that operate at the outer limits of what is physically possible in our universe, and so on and so on ad nauseam.

    To bring this full circle, even if natural selection saves the process from being random, it can only nudge organisms toward fitness, which may well run counter to the complexity of more intricate and sophisticated systems, making the arrival of such through largely stochastic means even more unlikely.

  104. In what way is natural selection non-random?

    Is it non-random in the sense that every time you have differential reproduction due to heritable chance variation, you have natural selection? That type of “non-random”?

    Ernst Mayr said whatever is good enough, and when sexual selection is involved, opinions on what is good enough vary a great deal. :) Is that non-random? You know the type of non-random you get with bird shot from a sawed-off shotgun. Not that I would know what that is. ;)

    Non-random in the sense that fatal and severely deletrious variations get weeded out? That type of non-random?

    Or non-random in the sense that no one can really ‘splain it, they just know it is?

    Anyone?

  105. Hi Nick,

    Can I read about “transitional fossils” in that textbook on Macro-Evolutionary Theory that you seem incapable of producing?

    Aren’t all fossils transitional?

  106. Why, I had a fossil I was holding transition into dust just the other day. Ain’t transitional fossils just grand proof of Macro-Evolutionary Theory?

    Pile up enough itty-bitty transitional fossils and you get proof of Nick’s relevance!

Leave a Reply