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Prominent NAS member trashes neo-Darwinism

Natural selection …is not the fundamental cause of evolution.

Masatoshi Nei

Science continues to destroy Darwinism. A prominent member of the National Academy of Sciences, Masatoshi Nei, trashed neo-Darwinism in the recent peer-reviewed article: The new mutation theory of phenotypic evolution.

Haldane’s dilemma showed mathematically that natural selection could not be the major driving force of evolution. Haldane’s dilemma lead in part to the non-Darwinian theory of molecular evolution known as the “neutral theory of molecular evolution”. Neutral theory asserted natural selection was not the principal driving force of molecular evolution. However, when molecular neutral theory was presented to the world in the 1960′s, it was politically incorrect to assert the obvious consequence of the neutral theory of molecular evolution, namely: morphology, physiology, and practically anything else made of molecules would NOT be principally shaped by natural selection either.

In What are the speed limits of naturalistic evolution?, I pointed out:

And if Haldane’s dilemma were not enough of a blow to Darwinian evolution, in the 1960′s several population geneticists like Motoo Kimura demonstrated mathematically that the overwhelming majority of molecular evolution was non-Darwinian and invisible to natural selection. Lest he be found guilty for blasphemy, Kimura made an obligatory salute to Darwin by saying his non-Darwinian neutral theory “does not deny the role of natural selection in determining the course of adaptive evolution”. That’s right, according to Kimura, adaptive evolution is visible to natural selection while simultaneously molecular evolution is invisible to natural selection. Is such a position logical? No. Is it politically and intellectually expedient? Absolutely!

But now 4 decades later, the inevitable consequence of Haldane’s dilemma and Kimura’s neutral theory may be ending the uneasy truce between neo-Darwinists and neutralists.

Nei writes:

For the last six decades, the dominant theory of evolution has been neo-Darwinism, which was developed by the three founders of theoretical population genetics, Fisher (1), Wright (2), and Haldane (3), and was later supported by various evolutionists (4). Neo-Darwinism asserts that natural selection is the driving force of evolution,
….
In the last four decades, the study of molecular evolution has shown that a majority of amino acid substitutions in proteins are neutral or nearly neutral

However, most evolutionists still believe in neo-Darwinism with respect to phenotypic evolution and are not interested in neutral evolution (19,22).

Mayr (23) stated that neutral mutations apparently occur at the molecular level, but because they do not affect phenotypic characters, they are of little interest to evolutionists.
….

By contrast, Nei (17, 24, 25) argued that because phenotypic characters are ultimately controlled by DNA sequences, both molecular and phenotypic evolution must occur in similar [non Darwinian] ways. He also suggested that a considerable portion of morphological evolution is caused by neutral or nearly neutral mutations, and the driving force of evolution is mutation at both molecular and phenotypic levels.
….
As mentioned in the introduction, a majority of current evolutionists believe in neo-Darwinism. In one of the most popular textbooks on evolution, Futuyma (ref. 20, p. 10) states that evolutionary change is a population process in which one genotype replaces other ones, and for this process to occur, mutation is quite ineffective because of its low rate of occurrence, whereas even the slightest intensity of natural selection can bring about substantial change in a realistic amount of time. He also states “Natural selection can account for both slight and great differences among species, and adaptations are traits that have been shaped by natural selection.” Although this type of statement is quite common in the evolutionary literature, it is obvious that any advantageous genotype is produced by mutation including all kinds of genetic changes. Natural selection occurs as a consequence of mutational production of different genotypes, and therefore it is not the fundamental cause of evolution.

Historically, the word mutationism was used to refer to William Bateson’s saltationism or similar ideas, in which natural selection plays little role. Later Morgan (109) presented a more reasonable form of mutationism taking into account the role of natural selection. His view was abstract and based on a few lines of speculative arguments. However, recent molecular studies of phenotypic evolution support the basic ideas of his view and have extended it to a more comprehensive view presented in this article. If the new form of mutation theory described here is right, even in its crudest form, more emphasis should be given on the roles of mutation in the study of evolution.

Notes:

1. ID sympathizer Dr. John Davison, who has spent much of his recent life promoting the works of William Bateson, should be much encouraged with these developments. It was through Davison I learned of Bateson’s wonderful ideas.

2. Richard Dawkins wrote of Kimura in Blindwatchmaker. Dawkins argued Kimura’s ideas wouldn’t overturn Darwinism since Darwinism operated at the higher level of adaptation whereas Kimura’s non-Darwinian theory operated at the lower level of molecules. But the reductionists are now getting taste of their own medicine. If the Darwinism doesn’t operate at the molecular level, then why should we expect it to operate at much higher levels like morphology and physiology either?

3. Lewontin gives a powerful example of neutral evolution at the morphological level. Rhinos have either 1 horn or 2 horns. Did natural selection cause the evolution of one horn in one case, and 2 horns in another? Unlikely.

4. Salthe pointed out a fundamental contradiction in Fisher’s fundamental theorem of natural selection. Selection is the enemy of diversity. Salthe realized the obvious problem of trying to account for the abundance of diversity through a mechanism which reduces diversity.

5. At least 3 signatories of the Discovery Institute’s Dissent from Darwin list anticipated these recent developments. Davison, Salthe, and Ho. Ho managed to present echoes of these ideas 30 years ago in a peer-reviewed journal. See: An eloquent but bogus non-review by Dawkins.

a relative lack of natural selection may be the prerequisite for major evolutionary advance

Mae Wan Ho

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201 Responses to Prominent NAS member trashes neo-Darwinism

  1. Great post Sal.

    Watching the evolutionists run around in circles spouting mutually exclusive axioms brings to mind a scene from my favorite movie, Princess Bride. After listening to Vizzini spew his pseudo-intellectual analysis for several minutes, the man in black (Wesley) replies, “Truly you have a dizzying intellect.” Vizzini, on whom Wesley’s irony is completely lost, shouts back, “Wait ‘till I get going!”

  2. I wonder if Nei stayed close enough to the “evolutionary canons” to avoid being called a hack like Philip Skell. After all, Nei did not call evolutionary biology useless. But then again, I give it 24 hours before some PTer or P-Zed spews venom at Nei.

    hmmm, maybe NAS should have a “Dissent from Darwin” petition going, too. Skell, Nei, anyone else?

    Princess Bride: Classic! Love it! Question: who would play Prince Humperdink? (I vote for Dawkins) ;)

  3. TOO GOOD Barry!

  4. As mentioned in the introduction, a majority of current evolutionists believe in neo-Darwinism.

    I’ve been looking for a comprehensive poll of the positions of evolutionists/Darwinists for a while now. They’re divided into camps and I figured the Neo-Darwinist camp was still the largest but I’d still like to know the percentage for each camp. It’s quite confusing when you’re debating someone and it turns out they’re not even in the Neo-Darwinist camp.

  5. [...] From Uncommon Descent As mentioned in the introduction, a majority of current evolutionists believe in neo-Darwinism. In one of the most popular textbooks on evolution, Futuyma (ref. 20, p. 10) states that evolutionary change is a population process in which one genotype replaces other ones, and for this process to occur, mutation is quite ineffective because of its low rate of occurrence, whereas even the slightest intensity of natural selection can bring about substantial change in a realistic amount of time. He also states ‘‘Natural selection can account for both slight and great differences among species, and adaptations are traits that have been shaped by natural selection.’’ Although this type of statement is quite common in the evolutionary literature, it is obvious that any advantageous genotype is produced by mutation including all kinds of genetic changes. Natural selection occurs as a consequence of mutational production of different genotypes, and therefore it is not the fundamental cause of evolution. [...]

  6. Sal – can you give a reference for Lewontin’s comments in your point 3?

    Folks – Nei is hardly going to deny evolutionary biology. This is more of a discussion about the relative strengths of the different forces. Nei is arguing that we should stress mutation and contingency more. As an evolutionary biologist, I find nothing disturbing: I think he’s only looking at evolution over a long time-scale, but this is a detail that is obvious from the context. And like any good (or, round here, evil?) evolutionary biologist, he does stress the blind nature of the evolutionary process: one of his conclusion is (p12241, middle column):

    The prospective view of evolution suggests that evolution occurs without purpose by mutation and adaptation to new environmental
    conditions, and therefore it is intrinsically unpredictable.

    Bob

  7. JJS, better question. Who would play the albino dungeon keeper? I vote for Daniel Dennett.

  8. Bob – you bring up a good point. However, from a layman’s point of view, NDE seems to rest on the foundations of NS+RM. If NS is “not the fundamental cause of evolution”, as Nei states, then NDE can almost be equated with a game of Yahtzee. Also, if the fundamental cause of evolution is RM, what is left of NDE? I am not trying to be difficult, I would just like to know what the implications are (with views from both sides of the fence).

    Also, does this mean that Dawkins will be pushed to the side since he sees NS as having such awesome creative powers?

    Barry – excuse me for a second while I clean my monitor. LOL

  9. Bob OH:

    Sal – can you give a reference for Lewontin’s comments in your point 3?

    I got it second hand from Arch Darwinist, Larry Moran here.

    If Moran got it wrong, I’d appreciate being alerted. Thanks.

    [update: I just corrected the link]

  10. Bob,

    Appreciate your comments. For my benefit and the reader’s benefit, given that you are probably the best poplulation geneticist in our UD community, I have theoretical question.

    Selection coefficients are rated from 0 to 1, with 1 being the maximum possible for a trait.

    In general, if an organism has 10,000 possible selectable traits, can the AVERAGE selection co-efficient be greater than 1/10,000? The more traits an organism has, the more selection is diluted per trait. Is that a valid interpretation?

    I realize there might be some math circumstances that might allow the AVERAGE to be greater than 1/10,000, but if in general 1/10,000 would be the general limit on the Average, then it seems to me that approximate neutralism of all traits has substantial theoretical soundness, since on average, many traits would have to be close to being selectively neutral. I welcome your thoughts on this.

  11. 11

    Darwinists always try to dance around the fact that they are bound by random mutations for any creative process. That is to put it simply that a random mutation of some sort must occur first and foremost on the molecular level before natural selection has anything to select from on the macro level. I’ve seen all sorts of obfuscation from darwinists surrounding this one very simple point. The empirical evidence testifying against gross beneficial morphological changes from random molecular mutations is overwhelming. Yet darwinists must claim that evolution is constantly occurring so they must divorce it from the actual evidence we are finding on the molecular level.
    I swear, who issued those guys science degrees?

  12. “who issued those guys science degrees?”

    Birds of a feather flock together

  13. NS cannot account for molecules to man evolution, as the first organisms which existed on our planet (bacteria) where already fitter and better adapted to liveable environments than all the organisms which supposedly evolved from them.

    How in other words can NS direct the evolution of higher organisms when it correlates to a reduction in fitness? At some point, for example, NS would have to select for longer gestation times, longer generation times, reduced population sizes, sexual reproduction etc, etc.

    a relative lack of natural selection may be the prerequisite for major evolutionary advance

  14. For the UD readers benefit, regarding the reference to Vizzini, here is a 5-minute clip of Wesley vs. Vizzini. Enjoy.

  15. What is more important in causing phenotypic evolution? Mutations which have shown to be at least 99.9% of the time to be disadvantageous to an organisms survival, or natural selection which may or may not eliminate any of those those harmful mutations? What they are arguing over is what type of theoretical scenario has the best chance of theoretically being correct even though the odds of either theory actually being able to have relevance to speciation in known reality within known probabilities are so infinitesimally small as to make the whole debate nothing more then an ironic exercise in begging the question and circular reasoning. They want everyone to believe that the “scientific” choices which are available to explain life are evolution and nothing else. Evolution is accepted as true then they try and convince us that the real question on life is how evolution works, not if it can work. Their approach is in reality unscientific because they completely neglect actual known probabilities concerning mutations and their probabilistic effects on an organism. Therefore they are accepting as conclusive truth a theory which is based on an imagined power of RM and NS on speciation and then using that imagined power of RM and NS to try to prove that evolution is true.

  16. The paper by Nei is a tough read, not because of the technical content, but because the paper on the whole is something of a random walk (just like neutral evolution LOL!).

    In strongly selective environments (pesticice and antibiotic resistance), the evolution of ceratain traits is predictable and repeatable.

    In contrast, in neutral evolution, there are no predictions as to what the evolved form will look like.

    We observe neutral evolution in nature, and it appears more ubiquitous than selective evolution.

    The prospective view of evolution suggests that evolution occurs without purpose by mutation and adaptation to new environmental conditions, and therefore it is intrinsically unpredictable

    M. Nei

    Thus a mutation pops up, we get something of saltation which PRE-adapts the organism to an new environment. If the organism happens to have access to the new environment. All the better. The old line is preserved and so is the new line, hence diversity (and recall, diversity is a problem for Darwinism).

    There are numerous views of evolutionary mechanisms:

    1. Competetion (Darwin)
    2. Neutral random walk (Kimura, Nei, so many others)
    3. Cooperation (Goodwin)
    4. Structuralism/Self Organization
    5. Front Loaded evolution

  17. Long live Margulis — one of the few who actually has a real mechanism for speciation — the generation of new symbioses.

    See my reviews here:

    http://baraminology.blogspot.c.....lanet.html
    http://baraminology.blogspot.c.....rs-to.html
    http://baraminology.blogspot.c.....ation.html
    http://baraminology.blogspot.c.....-devo.html

  18. Selection coefficients are rated from 0 to 1, with 1 being the maximum possible for a trait.

    I’ve no idea where you got this from. There’s nothing to stop a selection coefficient being >1.

    In general, if an organism has 10,000 possible selectable traits, can the AVERAGE selection co-efficient be greater than 1/10,000? The more traits an organism has, the more selection is diluted per trait. Is that a valid interpretation?

    No, I don’t see any reason for a limit on the average selection coefficient.

    I think you’ve mis-understood selection coefficients. Or you’re asking about something other than selection coefficients (i.e. the s in the population genetics equations of Haldane et al.).

    I’ll comment more on the Nei paper later: I’m still reading it.

    Bob

  19. Bob OH wrote:

    I’ve no idea where you got this from. There’s nothing to stop a selection coefficient being >1.

    I got it from Evolution by Mark Ridley, 3rd Edition:

    He writes:

    The coefficient of selection is usually taken to be a measure of the extent to which natural selection is acting to reduce the relative contribution of a given genotype to the next generation.

    Denoted as s, the selection coefficient is a number between zero and one. If s = 1, selection against the genotype is total, and it makes no contribution to the next generation. If s = 0, the genotype is not selected against at all. In this case gene frequencies will lapse into the Hardy-Weinberg case, unless there is neutral drift.

  20. Bob OH wrote:

    No, I don’t see any reason for a limit on the average selection coefficient.

    I went back to geneticist John Sanford’s book Genetic Entropy where I got the idea. Rather than the way I phrased it (which was rather clumsy), let me state the result he concluded based on Kimura’s cost analysis in his 1983 publication Neutral Theory of Molecular Evolution pp. 30-31.

    In Kimura’s publication, 138 nucleotide sites can be selected simultaneously when s = .01, and C=.50.

    C = Total selective cost to a population, the fraction of the poulation that is NOT allowed to reproduce in order to achieve all selection.

    For example, assume on average humans have 4 kids, if on average 2 of the kids effectively don’t reproduce but are selected against, the C value is 2 / 4 = .5

    In contrast, plants that bear 100 seeds can afford to have 99 not reproduce, so their C value is 99/100 = .99

    This of course is an idealization, but an optimistic one for evolution. There are many non selective reasons for no reproduction (i.e. accidental death, etc.). So these are rather generous idealizations to begin with.

    There is the Additive Model and the Multiplicative Model in calculating cost. For the sake of brevity, given an optimisitc C=.5 for humans and a selection coefficient of s = .001, Sanford gives the number of simultaneous “traits” that can be selected for:

    Additive Model
    500 traits

    Multiplicative Model
    700 traits

    This implies, if indeed a large amount of the 4 gigabase pair human genome is functional, only about 700 nucleotides can be positively selected at one time, the majority of molecular evolution must surely be NOT influenced by natural selection. Whether my line of reasoning here is correct is less important than the fact neutral molecular evolution is an accepted fact by many evolutionists. I have only given my take on it here.

    Sanford

    Notes:

    1. trait is often meant to tie to phenotype, however, there is a generalization where the idea of an inhereted nucleotide is still a “trait”

  21. Just a question for whoever wants to answer. Can anyone explain to me how evolution based on neutral mutations and/or genetic drift is supposed to work? (I mean, withour NS, or with only a small contribution by it).

    In other words, I don’t believe in the power of NS for two reasons:
    1) Behe’s arguments have definitely demonstrated that NS cannot select complex new functions, because complex new functions are IC and cannot be selected in a step by step way (the only way open to NS).
    2) Dembski’s work shows clearly that no really blind selection can improve the efficiency of a search. In other words, in all the examples of true selection, either natural or artificial, a new complex function can be selected only if the “selecting agent” has some specific information about what to select. Otherwise, no CSI can arise from random variation.

    That’s a brief summary of why NS cannot explain biological information. But my point is, at least the theory of RM + NS is “trying” to explain something, even if it fails.

    But neutral mutations? Genetic drift? These are, by admission of their proponents, completely random and blind phenomena. How are they supposed to explain CSI? How are they supposed to explain any complex function? Are the proponents of this kind of “evolution” completely unaware of the mathematical impossibilities of obtaining CSI by purely random methods? Have they never read any serious ID source? Or are they simply not interested in the question?

    I am not implying that neutral mutations and/or genetic drift don’t exist, or that they are not frequently observable in nature. Of course hey are. My question is: how can they help in explaining biological functional complexity?

  22. gpuccio asked:

    How are they supposed to explain CSI? How are they supposed to explain any complex function? Are the proponents of this kind of “evolution” completely unaware of the mathematical impossibilities of obtaining CSI by purely random methods? Have they never read any serious ID source? Or are they simply not interested in the question?

    Though it’s rather hard to glean it in the somewhat rambling paper by Nei, the explanation for CSI or the appearance of progress is that it is an artifact of our post-dictive projections, much like us projecting and seeing human faces in the sky.

    To some like Nei, asking why certain clouds evolved to look like human faces is like asking why neutral mutations evolved to look like functional machines.

    The teleological view of evolution has been out of fashion for more than a century. Yet, human minds appear to be susceptible to this view consciously or unconsciously. In the evolutionary literature,
    it is not uncommon to see such
    phrases as ‘‘making of Homo sapiens’’

    M. Nei

    The Universal Probability Bound (UPB) suggested by Dembski actually refutes much of the post-diction arguments, but how UPB does this when combined with a 500-bit specification is a bit subtle and probably beyond the scope of this thread.

    But briefly, there are only so many 500-bit (or more than 500-bit) specifications humanity can conceive of because of memory storage issues. These specifications are patterns. If the patterns can be demonstrated to be independent and not post-dictive and are 500 or more bits, then Nei’s arguments are refuted.

    One way to demonstrate a pattern is not post-dicitve is to see how these patterns emerged independently in the engineering discipline or even every day life. The lock/key or login/password metaphor is an independently given pattern. Why do we see these patterns in biology. We call such things protein-protein binding sites, but this analogy would not be possible if biology were a product of neutral evolution.

    This of course is a very difficult and subtle math argument, but I believe ultimately correct.

    The neutralists (even though wrong) are much less wrong than the Darwinists. It takes a more subtle argument to refute the tenets of neutralism. Heck, most people don’t even know there exists neutralism, much less an argument to refute it.

  23. Natural selection …is not the fundamental cause of evolution.

    Masatoshi Nei

    I’ve surveyed the Darwinist blogsphere. They haven’t done their usual and accuse me of quote mining yet. They’re becoming slackers. What’s taking them so long. By now I would have expected to hear venom and vitriol spewing forth.

    Man, I’m dissappointed with their non reaction. :-)

  24. OK, Sal. Now I see where you’re coming from. A couple of comments:

    1. (this is trivial) Usually the selection coefficient is calculated relative to the least fit allele. Hence my confusion.
    2. Is there any evidence that there are 700 genes where there is an allele reducing viability like this? It sounds high to me, although that is just my intuition – I don’t have any evidence.

    OK, I’d better get back to Nei before this thread is totally derailed.

    Bob

  25. gpuccio,

    Just a comment. Natural Selection is over hyped as a force in evolution. All it can do is select among already existing alleles. It cannot create any new information, only select amongst the information structure already present. And over time actually decrease information by eliminating alleles. So in no case can NS, by definition, ever increase information. This is basic NDE 101.

    Increasing information can only come from the origin of new alleles through some mechanism. So the real Achilles heel of gradualism is the origin of new alleles. Mutations are the gradualist’s only hope and as Behe just showed, this is a forlorn hope.

    Where are they to go. Hype a meaningless process such as NS or pray for more meaningful mutations. The answer is “prayer.”

  26. On Nei, he’s just adding to the debate over the relative strengths of different evolutionary forces. It’s actually a debate that my PhD supervisor was involved in (in a different context) about 15 years ago.

    Nei wants to argue that mutation is important, and we should pay more attention to it. I’m not convinced by his arguments, partly because I don’t think he makes a strong case: there’s too much arm-waving, but also because it’s not clear what exactly he thinks we should be looking for.

    At one level, he’s right that mutation is important: novelty has to arise through mutation. Hence, a lineage may become dominant simply because the key novelty arose by mutation in that lineage, and not another one (I think this is the message of his discussion about humans and chimps). But one could argue from the same data that selection is important, because that is what will fix most mutations that have a phenotypic effect.

    So, it’s more a problem of which perspective you want to take. And a lot of that will depend on the sorts of problems you are looking at, and aspects such as the time scales you are looking over: he criticises Fisher, Wright and Haldane, but they were mainly thinking over shorter timescales, and not so much about the long-term evolution of novelty. I think we’ve moved on a lot since then, and the sorts of problems Nei raises are being studied much more now, and we’re getting quite a good understanding of the processes.

    So, the bottom line: this is nothing to get excited about, unless you’re interested in the details of the subject: it’s part of the process of assimilating the new empirical process.

    Bob

  27. Bob,

    As you say NS can never create novelty. The process only selects, not creates. All novelty must come from some mechanism as yet undetermined and NS just chooses from what is presented and then eventually eliminates possibilities.

    So why should anyone really study NS for anything other than the obvious or the trivial? It is only a study of what is potentially in a genome. Sort of like intellectual dog breeding.

  28. I’ll probly mess this up but here goes:

    gpuccio asks:
    Can anyone explain to me how evolution based on neutral mutations and/or genetic drift is supposed to work?

    Neutral mutations- those which do not convey an advantage or disadvantage- are then free to accumulate.

    This accumulation will then lead to DNA sequences that will then do something good or bad for the organism.

    That is when NS takes over. The good is kept and the bad dies with its owner.

    Budda-bing, budda-boom, a novel function is created.

  29. “Budda-bing, budda-boom” is technical evolutionary jargon…

    :)

  30. I genuinely would love to know how NS can direct the evolution of higher organisms, all of which process a reduced level of fitness – compared to their first primitive ancestor. For example, at some point NS must select these traits:

    1. Reduced reproductive fecundity (i.e. reduced numbers of offspring)

    2. Reduced population size (from tillions to, for example, pandas)

    3. Reduced resistance to poisons, temperature and environmental changes/conditions

    4. Increased generation times (bacteria can reproduce every 20 minutes)

    5. Increased gestation times (i.e. elephants 22 months)

    6. A reduction in livable environments (bacteria live virtually everywhere)

    7. Sexual reproduction (a 50% hit in fitness alone)

    If NS really did direct the process of evolution then it must, at some point, have selected traits which lead to one or more of these effects.

    How therefore does NS select in the direction of higher complexity, when it appears that higher complexity necessitates a reduction in fitness?

    In regards to NS without constructive mutations, then clearly all it can do is take generalizations and produce specializations, which eventually go extinct though lack of, you guessed it – generalization.

    The panda is a fine example. Becoming more specialized for its peculiar lifestyle it has totally lost generalization – if the bamboo (which consists of well over 90% of its diet) goes extinct, it goes extinct.

  31. So basically what I’m saying is that even if we grant Darwinists NS and RM the likelihood is that NS would only direct RM in producing traits which further increase fitness. So its doubtful NS would ever go beyond simple, fast reproducing organisms such as bacteria.

    Of course the Darwinists would contend that this argument is flawed because, you guessed it – higher organisms with reduced fitness do exist. Spot the circular nature of that response, which I’ve had many times.

  32. On a side point, NS, let’s remember, can only select a trait once it adds some selective value, which means functionality. So if it’s one chance in 10^130 to get a specific protein molecule by RM, it will still be one chance in 10^130 even when NS is factored in. All NS can do is potentially fixate the trait into the population once it has arisen, and even that’s not a given.

  33. Acquiesce,

    You raise valid points concerning Darwinism. I have wondered myself, for example, how anything other than bacteria (super-replicators) can be expected from RM/NS, since going from uni-cellularity to multi-cellularity results in a fitness hit, as does moving to sexual reproduction (even when factoring in possible benefits from recombination…the short-term 50% hit is way too high to overcome with a subtle, long-term benefit).

    On a side-note, your last comment makes reference to a specific protein (1 in 10^130 chance) and NS. The reason NS is brought in is because if any sub-set of that protein has function/selection value, it will spread and allow cumulative selection to help get the final product. It is easier to get the protein in many small steps, if each step is indeed selectable, than getting it all at once.

    PS Has anyone read Jon Saboe’s The Days of Peleg advertised on the side-bar? I’m reading it right now and it is a verrrry good, fun read. I had the opportunity to build with Jon as well, a very nice guy.

  34. Finally, someone has accused me of misrepresentation!

    I point to a good critique (though I disagree) by Dr. N. Wells, a geologist/paleontologist at ARN here.

    He argues neutral theory can be absorbed into Neo Darwin synthesis. I took some pains to point out there is a quantitative estimate which proceeds from one of the founders of neo-Darwin synthesis (Haldane) which puts a limit on how much an organism is shaped by natural selection. I pointed out about 700 of the 4 Billion base pairs might be subject to selection at any time for creatures like humans, and this is being generous. Natural selection explains only about 700/4 billion of what makes us human…

    With those figures it’s like trying to say a piece of canvas car cover can cover a Corvette (or Lamborghini), therefore isn’t the canvas wonderful, and the canvas can explain the entire Corvette. This is what is done when arguments are made that Neo Darwin synthesis can accommodate any possible stream of new and inconvenient facts — just argue Natural Selection influences all of biolgical reality, therefore one gives the impression it therefore explains biological reality. Gravity influences all of biological reality, it certainly doesn’t explain it.

    In fact, a canvas is too generous. Saran wrap is a better metaphor.

  35. Acquiesce,

    I’ve been pondering the same issue, only from a different perspective.

    As a video game designer, I am familiar with various path-finding algorithms. Some algorithms, such as Dijkstra’s, do a comprehensive search of the space in order to discover the shortest path from one spot to another. An algorithm like A* differs from Dijkstra’s in that it has a heuristic that helps direct the search. For instance, a simple heuristic will give preference to nodes that are closer to the goal point (as the crow flies, so to speak, even though there could be intervening barriers).

    So, I’ve tended the think of NS as a kind of heuristic, helping narrow the search space, or helping direct the search toward a specific direction.

    But then I stumble on the realization that the NS heuristic only moves toward life.

    If we take a look at Dawkins’ Mount Improbable, we see an analogy that purports to show how gradualism solves the problems that Darwinian evolution faces in taking life from bacteria to man. Setting aside CSI for the moment, I’m not sure I really see how gradualism is such a great solution. I keep wondering why Dawkins assumes life will climb Mount Improbable in the first place, as opposed to rolling down the gradual slope.

    Surely the Darwinist would say that it is NS that propels life up Mount Improbable. But isn’t the mountain one of complexity? I can see how NS can function as a heuristic guiding toward life, but how does it function as a heuristic guiding toward complexity? It seems to me that at any point up on that gradual slope of Mount Improbable, you have life to the left, to the right, and down the slope behind you. So why must NS lead straight ahead, up the slope? What heuristic is it that pushes toward the complex life that is man vs. toward the simple life that is bacteria?

    And if you don’t have NS as a heuristic guiding toward complex man, aren’t you left with a comprehensive search of the problem space?

    I would really like to understand the Darwinists perspective on this. Anyone?

  36. The problem is Blindwathcmaker heuristics lead down the wrong path. An arm must be a bad arm first before becoming a good wing. NS does not have the foresight to overcome such problems.

  37. An arm must be a bad arm first before becoming a good wing. NS does not have the foresight to overcome such problems.

    Indeed. And it doesn’t seem to me that appealing to flying squirrels is much help in this regard, since at some point on the continuum between arm and wing, it seems likely that you will have something that doesn’t function very well as either. And the something would be selected against by NS.

    So, it seems to me that there are two sides to the NS problem for Darwinists. (1) NS as a heuristic cannot seem to account for how a baboon is more fit than bacteria, and (2) NS would likely cull the vast majority of those changes that might have proved helpful in moving toward a novel function, but not yet providing it.

  38. An arm must be a bad arm first before becoming a good wing. NS does not have the foresight to overcome such problems.

    Sal, Sal, Sal.

    A bad arm riding the NS wave of good legs, good sight and good everything else, will survive because the deficiancy it raises is outweighed by the over-performance of other innovations. ;)

    To Acquiesce:

    Please read Wobbling Stability

    To Phinehas:

    There isn’t any direction.

    Natural selection is the simple result of variation, differential reproduction, and heredity—it is mindless and mechanistic. It has no goals; it’s not striving to produce “progress” or a balanced ecosystem.

    http://evolution.berkeley.edu/.....ndom.shtml

  39. There isn’t any direction.

    Right. And there isn’t any heuristic that would seem to bias evolution toward a baboon instead of toward bacteria. So, how is NS useful in the process again?

    And yet Dawkins’ Mount Improbable seemed to assume that evolution would climb toward the peak.

    Still, with no direction and no heuristic, that seems to leave us with a comprehensive search of the problem space, in which case, man is just an incredibly lucky guess.

    What am I missing?

  40. What are you missing?

    Magical mystery mutations!

    But anyway:

    From the “Contemporary Discourse in the Field Of Biology” series I am reading Biological Evolution: An Anthology of Current Thought, edited by Katy Human (perhaps related to Mike Gene ;) ).

    The old, discredited equation of evolution with progress has been largely superseded by the almost whimsical notion that evolution requires mistakes to bring about specieswide adaptation. Natural selection requires variation, and variation requires mutations- those accidental deletions or additions of material deep within the DNA of our cells. In an increasingly slick, fast-paced, automated, impersonal world, one in which we are constantly being reminded of the narrow margin for error, it is refreshing to be reminded that mistakes are a powerful and necessary creative force. A few important but subtle “mistakes,” in evolutionary terms, may save the human race. -page 10 ending the intro

    Can evolution make things less complicated?:

    Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand.
    Penny, who worked on the research with Chuck Kurland of Sweden’s Lund University and Massey University’s L.J. Collins, acknowledged that the results might come as a surprise.
    “We do think there is a tendency to look at evolution as progressive,” he said. “We prefer to think of evolution as backwards, sideways, and occasionally forward.”

  41. All novelty must come from some mechanism as yet undetermined…

    Mutation.

  42. Acquiesce – you’re evidently not aware of the idea of a trade-off. Just to give one example, a reduction in the number of offspring can lead to a higher fitness if the offspring are more likely to survive. Another example: specialisation (e.g. on one food source) can be advantageous if it means you can exploit it better, and that you don’t loose out too much in trying to eat everything.

    Incidentally, point 6 is silly: it’s not the same bacteria that live everywhere. You don’t find viable populations of E. coli on the skin of humans, for example.

    Bob

  43. Bob [42] Acquiesce – you’re evidently not aware of the idea of a trade-off. Just to give one example, a reduction in the number of offspring can lead to a higher fitness if the offspring are more likely to survive.

    Actually, I’m fully aware of it, that’s why I specifically made the point that not only are bacteria the fittest organisms on our planet, but are the fittest organisms in whatever environment they live in. So your point that a reduction in the number of offspring can lead to higher fitness seems strange.

    Maybe you name me an organism, other than bacteria, which are fitter than bacteria in any particular environment? In other words, what offspring are more likely to survive than those of bacteria? This is precisely the point I’m making.

    Bob [42] Incidentally, point 6 is silly: it’s not the same bacteria that live everywhere. You don’t find viable populations of E. coli on the skin of humans, for example.

    That’s why I just said bacteria. Whats the point your making here? Bears are quite diverse, the polar, the grizzely, the panda – they’re not the same bear. But they’re still a bear, and you wouldn’t find them living near sea vents with temperatures around 600F.

    Bob [42] specialisation (e.g. on one food source) can be advantageous if it means you can exploit it better, and that you don’t loose out too much in trying to eat everything.

    Now, I didn’t say it wasn’t advantageous. I said that increasing specialzation, such as predominance to a certain food source, in the case of the panda, shows how NS takes generalizations, produces specializations. which lead ultimately to extinction through lack of generalization. I think that’s common sense.

  44. Atom [33] It is easier to get the protein in many small steps, if each step is indeed selectable, than getting it all at once.

    Well that’s highly debateable after all we know proteins have an invariant core, rubisco (a protein used in photosynthesis) comprises 476 aminos, 105 of these are totally invariant. In edition 110 other animos can only be substituted by one alternative, and nearly 189 others by one of three alternatives.

    So for NS to produce this protein it must have a substantial amount of the sequence correct, which means it cannot proceed in ‘many small steps’. But the point I was making was merely an attack on NS. NS doesn’t make the arrival of a new trait any more likely, all it does is potentially fixate it into the population.

  45. joseph:

    “Neutral mutations- those which do not convey an advantage or disadvantage- are then free to accumulate.”

    I understand that’s the general idea. But the problem is, “any” neutral mutation is free to accumulate, or alternatively be lost. So, we are left with the whole configuration space, with the total of possibilities. At risk of being repetitive, Dembski’s UPB is of “only” 500 nucleotides, or roughly 100 aminoacids. And believe me, Dembski’s UPB is really, really a generous limit. Behe’s arguments, which deal with true mutations in real life, show that even a coordinated mutation of a few aminoacids is beyond any reasonable chance, if there is no step by step selection. And now neutralist are claiming that the whole genome, or most of it, derives from the accumulation of neutral mutations, totally random, without practically any relevant selection… I must miss something in their reasoning.

    Acquiesce:

    I agree with what you say. I have suggested myself, in a previous post somewhere in UD, that really evolution seems to implement more the need to “express” higher functions than the need for survival. There is no doubt that increasing complexity is, everywhere, a cause of incresing weakness. That is particularly true of information and of software. The more the complexity, the more the problems, errors, bugs, etc. But, indeed, complexity can perform “new” functions. That’s its real value. On the same line, it seems that evolution is constantly trying to express higher complexity, and an astonishing level of diversification, creativity and beauty, “in spite” of the inherent challenges to survival and fitness. While I remain convinced that the highest fitness belongs to stones, there is no doubt that bacteria are more fit than any other living being. And just try to compare mosquitos and rats with chimps and human beings…
    The whole idea that biological complexity arises from the need for survival is totally wrong. Biological complexity is an astonishing, utterly unlikely design through which some intelligent and artistic force is trying to express something new, some new interesting quality or function, some further creative adventure.

    Regarding NS, it is obvious that it can act only to select a new relevant function after it has appeared. That’s why its role is so limited, because complex functions are not deconstructable in step by step subfunctions. In other words, practically any significant new function, new protein, new network, is in essence IC.
    But there is more. Even if NS has a role, it cannot really be “heuristic” in any way. NS is, by definition, blind. That’s why it is, in reality, practically random. All the examples made by darwinists (see Methinks it’s a weasel and similar) are examples of intelligent selection, where a very definite knowledge of the aim to be obtained is already present in the “selector”. That’s why they can work.

    A very good example of “intelligent” selection is the mechanism by which antibody affinity is increased after an immune response. That’s an almost perfect model of how an intelligent mechanism can determine evolution through random mutation. A random mutation process (an intense and intentional random mutation process) is aimed at a target which is already near to the desired result in the configuration space (the low affinity antibody of the primary immune response, which is selected from a natural repertoire through its affinity with the antigen). The variations in affinity are then accurately tested against the available information (the antigen itself), and only the clones with higher affinity are selected, while the others are inhibited. That’s really intelligent selection. Even if the organism does not know which DNA/aminoacids sequence is the best to react with the antigen, it can use a random search and carefully select the results aaccording to a specific complementary information (the antigen). The procedure is higly purposeful, and it can succeed only because it has already most of the necessary information (the antigen itself).
    If the organism did not know the antigen, or if it had to test the efficacy of all the new anibodies “in the wild”, that is by darwinian mechanisms, waiting to see if any new variant of the antibody gives some survival advantage, no higher antibody spcificity could be found in million of years. Instead, the organism checks each result with a known target, by an informational algorithm performed by specific cells (probably the antigen presenting cells in network with other T cells, of the helper and suppressor kind), and useful results are reached in a short time, exactly like in the “methinks it’s a weasel” example. Intelligent selection can perform miracles: it only has to know in advance what it has to find.

  46. Bob,

    You said to my comment

    “All novelty must come from some mechanism as yet undetermined”

    “Mutation.”

    Any examples? Behe just shot down mutations; they do nothing but trivial stuff.

    Whay can you offer other than faith and a few simple examples?

  47. gpuccio,

    You said

    “and now neutralist are claiming that the whole genome, or most of it, derives from the accumulation of neutral mutations, totally random, without practically any relevant selection… I must miss something in their reasoning.”

    They never have any reasoning only conjecture and “just so stories”. Evolutionary biology is the only science without empirical backing. Whenever you ask for reasoning you get speculation. Whenever you ask for evidence you get silence or in its place rhetoric or sophistry or irrelevant answers. It is always fun to watch them ignore, evade or distract. That is all they can do other than their ad hominem comments.

    The real interesting question is what psychological make up leads to such an approach. For once it would be refreshing for them to admit that they don’t have anything but just beleive it will be forthcoming. My guess is to admit the obvious is like surrendering to an enemy.

  48. gpuccio:
    But the problem is, “any” neutral mutation is free to accumulate, or alternatively be lost.

    Even the most beneficial mutation has the chance of being lost.

    NS acts each and every day on each and every organism.

    Those which aren’t lost are then free to accumulate.

    (I am just giving you their version, not that I believe it)

    At risk of being repetitive, Dembski’s UPB is of “only” 500 nucleotides, or roughly 100 aminoacids.

    500/3=166.67 amino acids. Don’t want the anti-ID lurkers to think we have a problem doing division, do we?

    Behe’s arguments, which deal with true mutations in real life, show that even a coordinated mutation of a few aminoacids is beyond any reasonable chance, if there is no step by step selection.

    There isn’t any coordination. Just a bunch of lucky mistakes that happen to make something of themselves.

    And that is why the premise is unscientific.

    And now neutralist are claiming that the whole genome, or most of it, derives from the accumulation of neutral mutations, totally random, without practically any relevant selection… I must miss something in their reasoning.

    Magical mystery mutations.

    Magical because they do things that have never been directly observed. And mystery because they still elude us.

    When I first started studying electricity and electronics back in the early 70s we used to call it “friggin’ magic”. That term can now be aplied to the theory of evolution.

  49. Jerry:
    For once it would be refreshing for them to admit that they don’t have anything but just beleive it will be forthcoming.

    And what, exactly, is your problem with “science via promissory notes”?

    :)

  50. Joseph:

    500/3=166.67 amino acids. Don’t want the anti-ID lurkers to think we have a problem doing division, do we?

    I apologize. You are obviously right. I was writing in a hurry, and from (misled) memory. The number 500 is in reality the number of bits, not of nucleotides. Dembski’s UPB is 1 to 10^150, and corresponds roughly to 500 bits of information, which is the same as about 115 aminoacids (20^115), that would be, as you correctly remarked, 345 coding nucleotides (indeed, 4^345 is more than 10^200, but that’s because of the redundancy of the genetic code).
    Anyway, 115 aminoacids are really a very small quantity of biological information if their possible random computation would exhaust all the resources of the whole universe!

    Again, I apologize. And, please keep it secret and just don’t tell darwinists, but sometimes I do have problems doing division…

  51. ARN points out this by Dawkins:

    The crucial passage in The Edge of Evolution is this: “By far the most critical aspect of Darwin’s multifaceted theory is the role of random mutation. Almost all of what is novel and important in Darwinian thought is concentrated in this third concept.” What a bizarre thing to say! Leave aside the history: unacquainted with
    genetics, Darwin set no store by randomness. New variants might arise at random, or they might be acquired characteristics induced by food, for all Darwin knew. Far more important for Darwin was the nonrandom process whereby some survived but others perished. Natural selection is
    arguably the most momentous idea ever to occur to a human mind, because it – alone as far
    as we know – explains the elegant illusion of design that pervades the living kingdoms and explains, in passing, us.
    Whatever else it is, natural selection is not
    a “modest” idea, nor is descent with modification.

    Unfortunately for Dawkins, someone more knowledgeable says otherwise:

    Natural selection …is not the fundamental cause of evolution.

    Masatoshi Nei

  52. gpuccio:
    The number 500 is in reality the number of bits, not of nucleotides.

    From reading Spetner, Wm Dembski and Stephen Meyer, I was under the impression that one nucleotide = 1 bit.

    Lookslike I will have to re-read them…

  53. Salvador,

    Is Dawkins really saying this. The implications are that all the varieties for the various species are already in the genome (wings and all) and just has to be teased out by natural selection given the right environmental/ecological conditions.

    Does this mean that Dawkins believes in a form of front loading?

  54. jerry – Firstly, and this might surprise you, Behe’s work is not universally accepted. Indeed, his peer-reviewed stuff (i.e Snokes & Behe) shows nicely that mutation can act quickly enough.

    Secondly, there are several examples of mutations leading to novel features.

    Thirdly, what else is there other than mutation? We know they can happen. We can make changes in organisms with them, the differences in DNA we see look like they are due to mutation (I’m including things like gene duplication in this: it’s a population geneticist’s prerogative). So, we have direct and circumstantial evidence to back this up. What do you have that’s better?

    Bob

  55. Thirdly, what else is there other than mutation?

    A metaphorical touch of the finger of the telic entity.

  56. Dawkins said:
    Natural selection is
    arguably the most momentous idea ever to occur to a human mind,

    I wonder if he realizes that Edmin Blythe, a Creationist, came up with the idea before Darwin.

    To Bob O’H,

    What is that data which demonstrates any amount of mutations can account for the physiological and anatomical differences observed between chimps and humans?

    Yes natural selection and mutations occur. However all the scientific data we have demonstrate the best they can produce is wobbling stability.

    And it appears that the only way around that is to just ignore it.

  57. Indeed, his peer-reviewed stuff (i.e Snokes & Behe) shows nicely that mutation can act quickly enough.

    I disagree. Behe himself claims that EOE is an extension of the work done in that paper and that the empirical results confirm his theoretical work in that paper. (He said this in either EOE or in his replies to critics on his amazon blog – I can’t remember which it was.)

  58. Secondly, there are several examples of mutations leading to novel features.

    Would you be so kind as to point out which of the examples (Nylonase, etc.) is actually beyond Behe’s claimed EOE? (Or any EOE proposed, in print, by an ID theorist?)

    They all seem like basic changes, within the power of blind search. It is disingenuous to claim this as evidence for any sort of large-scale macro-evolution. It is like pointing to rust on my car and saying “See, changes have been documented to occur on a car by blind mechanisms. Therefore, internal-combustion engines could have been built by the same mechanisms.”

    Or even better, a wheel falling off, and you discovering a new “spark-shooting” function under my car (as it grinds on the road), then making the same claim about engines.

  59. In defense of Bob OH, it is true mutation leads to novel features, at the very base, the novel feature is at least the changes in the genome.

    Dawkins was correct to point out the diversity of mutation in dogs. The impression is that mutation can do enormous things and make varieties of new patterns. So can explosions…..

    But what is not so apparent is that Behe also asserts mutation does a lot of things. The malarial parasites have trillions of varieties today (much more than dogs). The issue is whether the mutation lead to coherent novelty.

    When one registers and computer account, one creates coherent novelty, a login and a coherently matching password. The systems that Behe describe that create demarcations for the edge of evolution, and those systems are those of coherent novelty. Mutants from radiation experiments are examples of incoherent novelty….

    So in defense of Bob OH, yes random mutations create novelty (albeit mostly incoherent), but in defense of my ID comrades, it is coherent novelty that may mark the edge of evolution.

    However, there is a subtlety. James Shapiro shows that many mutations may not be random and maybe adaptive. That is, the organism senses an environmental stress and then invokes mutational strategies to reinvent itself. These are adaptive mutations. I think there is a lot of evidence for these sort of mutations.

    The human immune system (which Behe describes) uses an adaptive mutational strategy to create protein binding sits for threatening substances which the body has never seen before. This is an adaptive mutation internal to the organism, but not at the popluation level. However, if populations are also designed, then there is nothing stopping the possibiliy of pre-programmed front loaded adaptive evolution. Shapiro’s work suggests evidence in that direction.

  60. Hello Joseph,

    One nucleotide = 2 binary digits (bits) of information.

    There are four possibilities of nucleotides which can be chosen. Assuming equal probability of choosing any nucleotide:

    2(since we are converting to BInary)^x(number of bits) = [or >] 4(number of nucleotides)

    “x” will give us the lowest number of bits necessary to represent the four nucleotides.

    x=2 so that 2^x=4

    Therefore, we need AT LEAST TWO binary digits in order to convert the group of four nucleotides into binary digits.

    Arbitrarily assigned:

    00 = a
    01 = c
    10 = t
    11 = g

    We can do the same for the english alphabet:

    at 26 letters, how many bits (binary digits) of information are “in” each letter.

    2^x= (or >)26

    x=5 which gives us 32, so that there is room to add 6 more letters
    (or symbols such as punctuation/spaces) and still need only 5 bits of information per letter/symbol.

    “does that help?” including spaces, quotation marks, and punctuation has
    85 bits of information.

    arbitrarily assigned:

    00000 = a
    00001 = b
    00010 = c

    11001 = z
    11010 = ?
    11011 = [space]
    11100 = ”
    … etc …

  61. Salvador:
    “Is Dawkins really saying this. The implications are that all the varieties for the various species are already in the genome (wings and all) and just has to be teased out by natural selection given the right environmental/ecological conditions.”

    Jerry:
    “Does this mean that Dawkins believes in a form of front loading?”

    If so, it would seem to coincide with my belief that the design space is front-loaded into the both the laws of nature and life and that life is programmed to NECESSARILY discover these designs.

  62. ATOM:
    “They all seem like basic changes, within the power of blind search. It is disingenuous to claim this as evidence for any sort of large-scale macro-evolution. It is like pointing to rust on my car and saying “See, changes have been documented to occur on a car by blind mechanisms. Therefore, internal-combustion engines could have been built by the same mechanisms.”

    Or even better, a wheel falling off, and you discovering a new “spark-shooting” function under my car (as it grinds on the road), then making the same claim about engines.”

    LOL! … “spark shooting function” excellent visual and completely appropriate.

    It’s rather interesting to see some scientists attempt to extrapolate from what information processing systems can do (including break down and yet provide a benefit as pointed out in EoE) to the necessary changes and mechanisms to build those information processing systems in the first place.

  63. 1 nucleotide implies 2 bits of information, but it takes 3 nucleotides to code an amino acid and Behe’s suggest a good minimum is 6 amino acides to create a novel protein binding site.

    However, 3 nucleotides because of synonymous codons in a 64 element genetic code span only 20 amino acids. The log2(20) = 4.32 bits.
    Log2(20^6) = 25 bits or about 1 in 64,000,000. This in itself may not seem like something too remote, but when one factors in the likelihood of a mutation occurring we get numbers on the order of 1 in 10^20.

  64. Bob,

    I don’t have anything that would explain the changes but just because mutations happen in large numbers, one cannot invoke them unless one has evidence for these mutations leading to positive changes that are not trivial in the field of evolutionary biology. Mutations happen to everyone and are certainly not trivial in disease and medicine.

    I prefer the term random variation to random mutation because that would allow all sorts of other modifications of the genome to be included such as gene duplication. But just because I think random variation is a better concept, it does not mean that I have seen anything convincing in terms of random variation to explain change.

    Until then the most honest position is that we have seen some very minor changes in genomes due to random variation but as of yet we have not see anything really novel take place because of it. Scientists should keep looking and maybe something will turn up but till then there is no mechanism for major positive changes that is known and this should be admitted.

    And whatever mechanism causes these changes to happen, NS can then have an effect but not before.

    I cannot imagine Behe getting a favorable review by anyone in the current crop of biologists. As soon as they did, their careers would be over. Have you read Behe’s responses to Coyne, Carroll and Miller? Where has Behe gone wrong that these authors got it right. For a more objective review, read Dawkins. He is the soul of fairness on this issue.

  65. For a more objective review, read Dawkins. He is the soul of fairness on this issue.

    The irony is I think Dawkins was the most honest. I have often felt that. He can be excused for his mistaken position because I genuinely think he’s somewhat clueless to the science (product of willful Darwin delusions).

    I’m having a hard time believing Miller doesn’t actually realize Behe is right.

    I suppose if I were Miller, I could view life as a stage (to quote Behe), and that this pro-Darwinism is merely playing the part. I mean, Behe caught Miller confusing lipids and proteins. C’mon, Miller, a Brown professor of biology couldn’t possibly make such a stupid mistake.

  66. Salvador,

    The old expression “Follow the money” drives this whole conflict. Anyone who is non tenured will face obvious tenure questions if they question Darwin. Anyone with tenure will face funding problems if they question a naturalistic mechanism for evolution.

    Some exceptions may be if the researcher/engineer has mojo for some unusual practical applications of biological engineering or medicine. You should look at the video on MIT’s website about synthetic biology and see if you can see where this guy is coming from. ID comes up in the discussion but not in the usual way…about 40 minutes into the video.

    http://mitworld.mit.edu/video/363/

    He talks about designing non evolvable genomes. I am not saying this guy is ID friendly but he doesn’t seemed to be hung up on the conventional wisdom because he is at the cutting edge of designing new genomes. And someone else with similar capabilities and the ability to generate significant money for a university would get a pass by the administration even if they believed an ID paradigm.

  67. Would you be so kind as to point out which of the examples (Nylonase, etc.) is actually beyond Behe’s claimed EOE? (Or any EOE proposed, in print, by an ID theorist?)

    The nylonase example keeps getting dragged up again and again.

    1. Went from 100% efficiency to 2% efficiency to metabolize.
    2. Lost genetic info as a result of a frameshift.
    3. Has a lower reproductive rate and efficiency.
    4. Cannot survive amongst the parent species.
    5. To go “beyond the edge” requires functional divergence without information loss. Going from metabolic function to metabolic function is not considered functional divergence. Going from, say, a sequence that codes for a metabolic function to a sequence that codes for oxygen transport would be considered “functional divergence.” This point is more debatable since it gets into definitions.

    Am I missing something? Why is TalkOrigins bothering with such an example? Seems within the bounds of EOE to me.

  68. Am I missing something? Why is TalkOrigins bothering with such an example? Seems within the bounds of EOE to me.

    The last time I checked TalkOrigins was using human babies born with “monkey tails” as a proof of common descent. How idiotic can you get? Talk Origins has no credibility whatsoever.

  69. Bob:

    “Firstly, and this might surprise you, Behe’s work is not universally accepted.”

    The problem is not if it is accepted. The problem is if it is true and convincing. And the answer is yes. For it to be accepted by the vast majority of scientists, there should be a complete shift of power and authority. If you are basing your argument on the fact that official science, on the basis of pure authority, rejects ID theory, then you are perfectly right. That will change, but we need some more time…

    “Secondly, there are several examples of mutations leading to novel features.”

    I have checked the links. A very short and very controversial list indeed. Anyway, to be correct, I am reading the (not very long) stuff and checking the references. For the moment, I am lost in the metaphysics of nylonase, and I must confess that I am a little bit bored… But, if there is time, we can discuss those very virtual examples in the future. I am always very pleased to verify how insignificant, abstract and unlikely are the “strong” examples which darwinists try to offer in defense of the most extraordinary scientific theory of all times.

    “Thirdly, what else is there other than mutation?”

    I suppose you mean “random” mutation, or random variation if you want. Well, there is a lot else. Design, for instance. OK, the final result is always a “mutation” or “variation”, but it is the implementation of a plan, of a design. Through what means? We don’t know, but two reasonable possibilities are: “directed” mutations; and “intelligent” selection.

  70. Lest I give the impression the neutralist like Nei and Kimura can get out of this unscathed, let me point out the ultra-Darwinist have found equally fatal issues with netural theory, namely, deeply “conserved” sequences. If evolution has been neutral at the molecular level, then why to we have huge stretches of DNA that are identical between mice and men.

    The ultra-Darwinists will argue that natural selection has purified out those regions, therefore natural selection has maintained hundreds of millions of base pairs. But then we knock these deeply conserved regions out, and what do we get? Normal mice! But in addition to that, we should see a bit more sequence divergence in these regions if neutral theory were true. “Something is rotten in the state of neutral theory” (to quote William Shakespeare).

    So the neutralists have found fatal flaws in Darwinian evolution, and the Darwinists have found fatal flaws in neutral theory. Collectively, they both managed to invalidate each others existence.

    But (wink, wink) one of them has to be right, because there is a third alternative that is unthinkable (wink, wink).

  71. Lest I give the impression the neutralist like Nei and Kimura can get out of this unscathed, let me point out the ultra-Darwinist have found equally fatal issues with netural theory, namely, deeply “conserved” sequences.

    From Nei’s paper (p12235, third column):

    The highly conserved genes stay in the genome not because of a low mutation rate but because of a high degree of purifying selection.

    Yes, there is this mysterious Third Way, where both selection and drift occur. This is the consensus position in evolutionary biology: the debates we have are over the relative strengths of the two forces.

    I’ll pre-empt one criticism by continuing Nei’s paragraph:

    The degree of purifying selection can be measured by comparing the number of synonymous nucleotide substitutions per synonymous site (dS) and the number of nonsynonymous substitutions per nonsynonymous site (dN) under the assumption that dS represents the number of neutral mutations.

    i.e. we can measure drift and selection: it’s not just guesswork, we have evidence.

    Bob

    BTW, Sal, I think you’ve got something in your eye.

  72. I see nobody has been able to come up with a workable solution to the problem of reduced fitness, so let me try and solve it myself – criticism wanted.

    Bob talks of trade-off, let’s put this in simple terms:

    Organism A produces 100 offspring – but only 1 survives. Mutated organism B on the other hand produces only 3 offspring but of this 2 survive. So despite B producing less offspring – more survive. B is then evolutionarily speaking – fitter.

    Fitness = the number of surviving offspring.

    Now coming back to bacteria. Bacteria not only produce a staggering number of offspring, but they can also produce a staggering number of surviving offspring. Without doubt bacteria are the fittest organisms we know of.

    It’s safe to say that complexity and fitness are linked – the more complexity the more of a fitness hit (for example, gestation time alone seems to correspond to an organism’s complexity and size). Therefore, any mutated organism which arose (exhibiting more complexity – therefore lacking fitness) must compete with the parent stock and would be rapidly filtered out.

    I propose a solution:

    Gradualism has many flaws, but in this respect because the changes are so small, mutated organisms must compete with the parent stock and win out. Consequently, complexity can never increase – at least not in the direction observed in the fossil record (i.e. from bacteria to man).

    Only when changes are so large that the mutated organism no longer competes with its parent stock (producing an entirely new type / lifestyle) can the organism remain despite its reduced fitness. This would obviously mean it bypasses NS.

    Criticism wanted.

  73. Bob [42] specialization (e.g. on one food source) can be advantageous if it means you can exploit it better, and that you don’t loose out too much in trying to eat everything.

    Now, I didn’t say it wasn’t advantageous. I said that increasing specialization, such as predominance to a certain food source, in the case of the panda, shows how NS takes generalizations, produces specializations, which lead ultimately to extinction through lack of generalization. I think that’s common sense.

    In fact, this seems to fit nicely with what we observe (i.e. organisms appearing at first generalized, then diversifying and ultimately going extinct). If NS is limited to gene shuffling and segregation then without the continue input of constructive mutations, species and ultimately genera and higher taxa are inevitably going to go extinct through the continued action of NS (this is not to say that new species can’t be formed by NS in the meantime).

  74. i.e. we can measure drift and selection: it’s not just guesswork, we have evidence.—Bob O’H

    If your theory is guesswork, but amenable to calculations, does the quantification of the theory necessarily remove it from the realm of guesswork?

    When Sal alludes to ultra-conserved regions of mice being removed yet resulting in normal mice, what meaning is there to “highly-conserved”? Surely you can’t say that NS is responsible for the conservation. Isn’t the straightforward and sensible deduction from all of this that the cell, itself, has mechanisms for conservation completely independent of NS?

  75. If your theory is guesswork, but amenable to calculations, does the quantification of the theory necessarily remove it from the realm of guesswork?

    Yes. well done.

    When Sal alludes to ultra-conserved regions of mice being removed yet resulting in normal mice, what meaning is there to “highly-conserved”? Surely you can’t say that NS is responsible for the conservation. Isn’t the straightforward and sensible deduction from all of this that the cell, itself, has mechanisms for conservation completely independent of NS?

    I can’t remember the details of this, so I can’t be sure to what extent the mice were “normal”. Can you give a reference?

    Acquiesce –

    It’s safe to say that complexity and fitness are linked – the more complexity the more of a fitness hit…

    A moment’s thought will make you realise that this is nonsense.

    To be honest, and my apologies for sounding arrogant, I would suggest you go back and learn the basics of evolutionary theory.

    It’s clear to me that you don’t understand the theory. I don’t have a problem with this: there are lots of things I don’t understand either. But if you wish to comment and criticise, I would heartily suggest you understand what you are criticising.

    There are many good textbooks available: I like John Maynard Smith’s Evolutionary Genetics, but you might find another text you prefer.

    Bob

  76. I can’t remember the details of this, so I can’t be sure to what extent the mice were “normal”. Can you give a reference?—-Bob O’H

    I can’t easily find the New Scientist citation where I originally read it, but here’s more or less the same article:

    http://www.medicalnewstoday.com/articles/9088.php

  77. I’m testing something here: please ignore.

  78. Testing again: here’s the link

  79. Bob OH taunted:

    BTW, Sal, I think you’ve got something in your eye.

    Nei may say purifying seleciton acts, but that is a bit of circular reasoning.

    You need:

    1. population resources to effect it

    2. deletion experiments of megabases of conserved regions suggests the selection pressure is not that great. That would be expected if these regions have redundancy somewhere. But then, that would cast doubt on the ability of purifying selection to act.

    Things like Nachman’s paradox put some question upon this. Something is in someone’s eye for sure.

  80. Bob OH taunted:

    BTW, Sal, I think you’ve got something in your eye.

    Sorry if that was mis-interpreted. It was meant as a silly joke, and not as a taunt at all.

    Bob

  81. Bob [75] To be honest, and my apologies for sounding arrogant, I would suggest you go back and learn the basics of evolutionary theory…It’s clear to me that you don’t understand the theory.

    Ok your right I know nothing – I’m stupid, insane, ignorant, wicked or whatever. I asked for criticism of my argument not criticism of my person. Do you want to try this again and address the issue (i.e. how NS can direct the evolution of higher complexity, when it corresponds to a massive reduction in fitness)?

    Would it help if I said I wasn’t a creationist?

    Acquiesce: It’s safe to say that complexity and fitness are linked – the more complexity the more of a fitness hit…

    Bob: A moment’s thought will make you realize that this is nonsense.

    Organisms of higher complexity (compared to bacteria) and size have longer gestation times, longer generation times, reduced reproductive fecundity, REDUCED NUMBERS OF SURVIVING OFFSPRING, reduced resistance to many poisons, environmental or temperature changes, reduced population sizes, not to mention they sexually reproduce. How is this not a fitness hit?

  82. I’m not going to question your understanding of evolution Bob; I trust you can explain to us all how NS can direct for higher complexity whilst simultaneously selecting for lower fitness.

    Maybe it’s in that book you suggested I purchase?

  83. Bob (to Acquiesce):

    “It’s clear to me that you don’t understand the theory.”

    I respectfully disagree with you (Bob). One thing is not to understand a theory, another thing not to accept it. I think Acquiesce has a very good point, with which I agree completely, and that point is that increasing complexity implies increasing “weakness”, in the sense of exposition to bugs, errors, incomplete control of function, and so on. The only real advantage of increased complexity is the possibility to perform something new. But, in terms of mere survival and fitness, simpler organisms are better, provided that the necessary complexity for efficient survival has been acquired (see bacteria). In other terms, what Acquiesce and I are trying to say is that, in our opinion, the whole evolutionary darwinian theory is based in a false assumption: that increasing complexity provides increasing survival. Our point could be wrong, but it is our opinion, and it does not imply that we don’t understand darwinian theory. It just means that we don’t agree with it.

    I don’t know, but I feel that beeing adviced to study a basic book seems to be the only answer that darwinists, in recent times, give to my posts. Is it a new discuddion ardument and strategy? That is, each time someone says something you don’t like, instead of answering with real counter arguments, just invite him to study grammar, or basic history, or anything else?

    (By the way, I apologize with Acquiesce for having enclosed him in my discussion without asking. I hope I have not misunderstood his thoughts.)

  84. Gpuccio [83]

    Our point could be wrong, but it is our opinion, and it does not imply that we don’t understand darwinian theory. It just means that we don’t agree with it.

    Well put.

    Bob, instead of just questioning our understanding of evolution, show us where our error lies; explain how NS can direct for higher complexity whilst simultaneously selecting for lower fitness. I’m not commited to this argument, if a solution can be found I will abandon it – I will not abandon it however just because someone thinks I lack understanding of evolution theory.

    The argument, I realise, cuts the heart out of orthodox evolution, but that doesn’t mean it’s wrong. If orthodox evolution theory is science, then it must be tentative. Arguments which go against it must not be ruled out for a circular notion that orthodox evolution theory is ‘truth’ and that all counter arguments are therefore ‘false’.

  85. Bob has been asked several times to defend the gradualist approach to evolution and has punted each time.

    When asked to justify or to point to other than a few trivial examples of mutations for NDE, Bob pointed to a TalkOrigin site with a few examples of trivial mutations. Thus, when we say that Darwinist only point to the trivial, Bob points to the trivial.

    Now the technical definition of evolution is a change in the allele frequency of a population over time and Bob’s examples are examples of a change in a population over time and also include the origin of new alleles but are only very small changes or micro-evolution. None of the debate that surround this issue really denies micro evolution or these trivial examples.

    So while the proposition of Acquiesce may or may not be true it seems reasonable as gpuccio has pointed out, namely complexity has more places where something can go wrong and also less offspring. Seems a reasonable proposition that they will be less fit in terms of survival. The fossil record seems to back this up. Lots and lots of extinctions but those hard little single celled creatures seem to go marching on like the Eveready Bunny.

    Acquiesce is also trying to understand how complexity arises and that is a fair question and he is also questioning the point mutation approach which I think is valid. We all question point mutations or any other type of mutation as the source of complexity of novelty. To suggest genetic books is a fatuous reply.

    Genetic books are excellent examples of micro-evolution but nothing more. They are great when applying some mathematical calculations to figure what happens to a population with all ready existing variations in the various alleles. And as such they are very useful and insightful.

    But genetics books are not of any use for macro evolution or understanding the origin of complexity. As I just said genetics only discusses how changes appear in a population when those changes are already in the alleles of the population members. There is no example of complexity of novelty arising within the field of genetics, only how what already exists changes proportions. If I am wrong on this then please provide the examples. (I expect there are a few trivial examples of changes such as the anti-freeze protein in Antarctic fish that increase fitness in that environment but trivial changes such as this hardly drive the amazing complexity we witness in the biological world.)

    If what we are saying is incomplete, then help us understand how to see beyond our blinders.

  86. Thanks CJYman.

    Let me chew on that for a day or two while I consult my resources.

  87. The argument simply stated is that NS hit a fitness peak with bacteria, and that NS is unable to descend from it, as required for evolution to higher organisms.

    NS could potentially increase complexity (with constructive mutations) but the direction would only be for further fitness (more surviving offspring).

    The argument therefore stands alone from the improbability of constructive mutations and does not require the tentative upper probability bound.

  88. Sorry if that was mis-interpreted. It was meant as a silly joke, and not as a taunt at all.

    Bob

    Quite all right. And for the record I appreciate the fact you are posting here. Though we disagree, I’ve appreciated your courage and willingness to participate in a weblog generally hostile to your ideas.

    I think the particpants can learn a lot by contact with those on the otherside and gain knowledge about the field. I think there is value in understanding something even if one does not agree.

    I salute you sir.

    Salvador

  89. Acquiesce – quite simply, there isn’t a reduction in fitness with increasing complexity. You seem to be thinking that fitness is a single global measure, so that one can compare any individual to any other, regardless of how similar they are. I’m afraid it simply doesn’t work like that: it makes no sense to compare the fitness of a human with (say) a bacterium. They’re not competing with each other (they live in very different ecological niches).

    Hence, you have to ask whether an increase in complexity leads to an increase in fitness as compared to individuals in the same population (i.e. the same species, in the same area).

    Bob

  90. But genetics books are not of any use for macro evolution or understanding the origin of complexity.

    For that, you need a book like Major Transitions in Evolution.

    Bob

  91. Acquiesce – quite simply, there isn’t a reduction in fitness with increasing complexity.

    Depends on how you define “fitness”. My guess is that you’re using it in a specialized sense and Acquiesce is using it in a generalized sense. As in, you’re talking past each other due to a difference in meaning.

  92. I’ve finally had a look at the web reports on the conserved sequences. It’s difficult to say a lot about the work, because so little is reported (the web page of the PI is pretty useless, and it doesn’t seem to have been published yet). What I can say is that there are several hypotheses that would explain the results that wouldn’t be a problem for evolutionary biology. Science being science, this is going to be followed up further, so I expect a plausible explanation to be found that doesn’t overturn evolutionary biology. Of course, I expect people here to have a different view.

    Patrick – I agree it’s quite possible that Acquiesce is using a different definition of fitness. But I think it’s reasonable to expect the technical definition to be used in a discussion of evolution (or at least something close to it).

    Bob

  93. Bob,

    Thank you for looking into the issue of conserved sequences. My prediction is that the deep conservation issue will parallel what has happened in abiogenesis research: answers will at first look promising, and then a dead end appears.

    I realize we disagree, but I would welcome being alerted to any developments either way.

    Thanks.

    Sal

  94. quite simply, there isn’t a reduction in fitness with increasing complexity.

    Can this be shown in some objective way?

    According to the theory, simple life evolves into complex life due to environmental pressure in which the complexity imparts some advantage in surviability for the species.

    Where can this be shown to be true in nature?

  95. Trying to find a definition of fitness is like trying to grab hold of jello.

    Bob, here’s an exercise. I remember taking a class in Animal Behavior years and years ago. One of the articles we read had to do with rats. It seems that when the density of rats in a restricted area gets so high, they begin to kill one another. Now, here’s the exercise, if fitness is related to competing species, and, if fitness is essentially reproductive success, then how can a species of rats that has developed the tendency to kill its own (and, therefore, reduce the number of offsprings in the present generation and the ensuing generation as well) be considered more fit? And, if it’s not more fit, then how did it develop?

  96. tribune7 – there are some examples here. The Major Transitions book I linked to above (#90) probably gives more examples (my copy is at work, and I won’t be in that office today).

    PaV – you haven’t been reading your Dawkins, have you? :-)

    The rats that are killed won’t produce offspring, so therefore will be less fit. The level of selection is (usually) the individual, not (as you seem to imply) the population.

    Bob

  97. Bob, linking to TalkOrigins isn’t answering the question.

    And the link doesn’t even address the question.

    Saying the eye evolved — a famously contested claim in itself — does not explain how creatures that depend on eyes are more fitted to survival than creatures that don’t.

  98. tribune7 – I would disagree. Note this comment:

    The increments between these steps are slight and may be broken down into even smaller increments. Natural selection should, under many circumstances, favor the increments.

    Now, it may be that this is wrong, but the page show how the complex eye can evolve in stages, and how each stage is fitter than the last. i.e. there is no fitness trough to go through. I think you have to demonstrate that such a trough would exist (indeed, I notice nobody in this thread has tried to provide evidence for a fitness trough).

    Also note that the page gives references, so you can follow it up further if you want to.

    Bob

  99. Bob,

    It isn’t fitness troughs that are being discussed but what type of life is most optimized for survivability.

    It seems, contrary to TOE, that the simplist life is the fittest if the point is survival.

  100. Bob:

    I looked at the TO page and the onward links:

    –> TO gives a generic claim, not the substantiating details backed up by enough credible cases that would be satisfactory. [This is typical of TO, which is simply not a credible source, period. If that is your best quick online response, that does not measure up.]

    –> The first onward link goes to another generic link with generic remarks on artificial life “experiments.” Of course,these are computer simulations, NOT experiments. GIGO, anyone?

    –> Worse, the second, main linked reference is to the AVIDA paper, which of course is a case which substitutes intelligently designed software for real world natural environments.

    –> As to the just-so story on how the eye might evolve, this is a case of smooth words papering over serious technical difficulties for the proposed problem-solving algorithm of NDT. The reversing of the burden of proof attempt simply underscores the point.

    –> I am particularly underwhelmed by TO’s “argument from incredulity” claim. Sorry, this is not an appeal to “we don’t know and/or it does not seem believable to us, skeptics that we are.” We are looking at the need to do something we are very familiar with: create functionally specified, complex information based systems, and in this case arguably involving multiple interacting parts that for a core subset need to be functioning together before the whole will work properly. That we know how to do: intelligent design and development. And we have good reason to infer that random processes cannot reasonably deliver that degree of complexity on the gamut of the observable universe. Thus the fitness dropoff is obviously present, BTW — and it is vouched for by just how destructive mutations tend to be, overwhelmingly. [Behe's recent work on the empirical cases of 10^20 or so organisms tightens this up even more . . .]

    In short, Trib 7 is dead right — you have NOT seriously answered the question.

    To give you an idea of what ID thinkers are looking for, let’s cite a recent semi-popular article by Petersen, discussing Behe from 1996, so this is hardly news:

    Behe the biochemist . . . search[ed] the relevant scientific journals, books, and proceedings of meetings to find out what the Darwinists had really proven about the origin of complex biochemical systems . . . . “There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems” . . . Behe, recalling the “fierce resistance” he encountered after the publication of Darwin’s Black Box, remarks that much of it came from “internet fans of Darwinism who claimed that, why, there were hundreds or thousands of research papers describing Darwinian evolution of irreducibly complex biochemical systems.” Except that there aren’t.

    Miller’s tale on the TTSS notwithstanding [it uses a subset of the genes for the flagellum and so is at best derivative and an instance of double coding which makes the problem more intractable -- frontloading using interleaved codes!], that judgement still stands, over a decade after that book was published.

    The resort to computer simulations under grossly unrealistic conditions and the associated attempted redefinitions of life etc are simply revealing of the balance of the case on the merits. The eye case and associated try on reversing the burden of proof simply underscores this.

    On the point where this leads, the basic point is well known from engineering: KISS.

    Complexity means there is more room to go wrong and so it naturally reduces fitness for function – ask anyone who has had to design a robustly functional system. Only if a certain degree of complexity is in effect necessary and robustly protected, can we get away with making things complex.

    Sure, complex, self-assembling multicellular organisms are able to create and/or go into niches, but the stages to get there are incredibly complex, far beyond the credible reach of chance-based search mechanisms [the random mutations part of NDT, which has to be there before we get the natural selection part].

    Wheel and tun and come again . . .

    GEM of TKI

    PS: We are still waiting over at the July 6th explanatory sufficiency thread

  101. Bob,

    All the eyes now present were present in the Cambrian Explosion. There is no evidence of any gradual development since. And there was no evidence of an eye of any kind existing before the Cambrian Explosion. So eyes came out of nowhere. Probably one of the most complicated pieces of machinery known to man.

    The model provided by Nilsson and Pelger is nothing more than a just so story with no explanation of the complicated biological proteins/machinery/instructions that would have to accompany these artistic drawings. Anyone with Adobe Illustrator and a little artistic ability could design any sequence they want from one animal to another and then claim it took place in little steps. That is all you provided. That is all evolutionary biology provides.

    In what other science would such an approach be taken as science and incorporated into its subject matter? The answer is none, so the real question is why is it allowed in evolutionary biology.

    Why is it so difficult to admit this? In any other discipline scientist would be having a field day with people who presented such nonsense. They would be looked upon as superstitious know nothings that have to invoke magic to justify their hypotheses. Remind you of anything.

  102. Thus the fitness dropoff is obviously present,…

    I’ll ask again – can someone give me some evidence for this.

    Bob

  103. Thus the fitness dropoff is obviously present,… I’ll ask again – can someone give me some evidence for this.

    Would you agree that fitness is defined as a species’ ability to survive?

  104. Bob,

    An organism that passes on 50% of its genes is less fit than one that passes on 100%; an organism that has an average of 2.5 surviving offspring is less fit that has 100. These were the things brought up earlier and they are indeed valid points.

    For example, there are certain advantages to sexually reproducing; the problem is these advantages do not increase fitness by a whopping 50%, in order to offset the loss caused by switching to that mode of reproduction. At best we have long-term, forward-looking advantages, such as purifying the gene-pool over time – but what matters for selection is only the immediate reward or penalty. And a 50% reduction in fitness is a tough pill to swallow.

    As people who design things in the real world, not just in our fecund imaginations, we know empirically that more complexity equals more potential points of failure. As an engineer I deliberately make systems as simple as possible, since complex ones have more things that can (and statistically will) go wrong.

    So again, what would cause selection to make a trend towards more complex, less reproductive organisms? How would bacteria eventually turn into man? If you put an equal number of humans and bacteria in the same environment (a warm pond, for example) it is clear which organism will have more surviving offspring after a given period of time.

    It is ok to admit that this is an awkward set of facts for Darwinism to deal with. No one will look down on you for being an honest, questioning human.

  105. Bob: I’m afraid it simply doesn’t work like that: it makes no sense to compare the fitness of a human with (say) a bacterium. They’re not competing with each other (they live in very different ecological niches.

    What are you talking about?

    Can you not understand my point?

    I thought I made it clear that I’m talking about how NS can select organisms for higher complexity when every organism we know of produces less surviving offspring than bacteria. How did the first organism (of greater complexity) which evolved from bacteria come to be selected by NS when its number of surviving offspring (i.e. its fitness) was vastly reduced?

    Where did I say ‘compare the fitness between humans and bacteria’?

    I must have given you an idea, because only a few posts further up I talked about a potential solution to this problem (e.g. large jumps producing a totally different type of organism, no longer competing with the parent stock).

    I can only think you either understand my point but cannot answer it (so you try and divert attention somewhere else), or you really do not understand it. But it appears most other people on this forum do – and I suspect they can also see you side stepping my point.

    So let me ask you again, how can NS direct for higher complexity whilst simultaneously selecting for lower fitness?

  106. Bob: quite simply, there isn’t a reduction in fitness with increasing complexity.

    Fitness is a measure of the numbers of surviving offspring (nothing else). Thus you are totally wrong, less complex organisms are orders of magnitude fitter than higher organisms – which brings us back to how NS can direct for higher complexity whilst simultaneously selecting for lower fitness.

  107. Would you agree that fitness is defined as a species’ ability to survive?

    Is this relevant? Why is species-level selection relevant to the evolution of complexity?

    An organism that passes on 50% of its genes is less fit than one that passes on 100%; an organism that has an average of 2.5 surviving offspring is less fit that has 100. These were the things brought up earlier and they are indeed valid points.

    Only ceteris paribus. Which is why I brought up trade-offs.

    Acquiesce – You’re claiming that fitness is highest in bacteria, as compared to more complex organisms. That only makes sense if the organisms are competing.

    You’re still thinking that a more complex organism is less fit, but haven’t given any evidence for this, unless it’s by comparison with “all the organisms which supposedly evolved from them” (#13). So you were making the fitness comparison, which I think we now agree is invalid.

    I would still like to see some evidence for the claim that more complex organisms are less fit.

    Bob

  108. Folks, if you’re not happy with t.o., the take it up with them! I’ll admit that palaeontology isn’t my field, so I don’t have all the information at my fingertips (and I have too many other things to do, rather than trawl through the literature). If you want an example of fossil evidence for the evolution of a complex organ, try the mammalian ear.

    Acquiesce –

    Fitness is a measure of the numbers of surviving offspring (nothing else).

    No, that’s lifetime reproductive success. Fisher showed in 1930 that this wasn’t a sufficient measure for fitness. As a counter-example, imagine one type of individual that produces 2 offspring after 100 years, and another that produces 1 offspring after 1 year. Which individual will have more descendents after 1000 years? (assuming a constant environment, and that the individuals are of the same asexual species)

    kairosfocus – I gave up checking the other thread because it looked like Crandaddy wasn’t going to answer my original question. I’ve just checked and he hasn’t given any more responses.

    Bob

  109. Bob: As a counter-example, imagine one type of individual that produces 2 offspring after 100 years, and another that produces 1 offspring after 1 year. Which individual will have more descendents after 1000 years?

    The second one is fitter and would eventually win out. What on earth has this got to do with the argument? Are you seriously suggesting that NS would favour the one that produces only 2 offspring in a 100 years rather than the other that produces 1 per year?!

    So let me ask you again, how can NS direct for higher complexity whilst simultaneously selecting for lower fitness (lower numbers of surviving offspring).

  110. Bob, do you think if I had a trait which allowed me to produce 1 offspring per year, when all other humans managed merely 2 in a lifetime that my newly found trait wouldn’t be selected by NS? And then if my offspring had another new trait which enable them to produce 1 offspring per week this wouldn’t be selected? Then 1 offspring per day….Then 1 per hour…etc

    This Bob is fitness, and this is how NS would direct the process of evolution if constructive mutations weren’t so improbable.

    You seem to think that NS can direct the evolution of higher organisms despite that fact that at some point these newly evolved organisms would have possessed a trait which reduced its fitness. So we start with an organism that produces thousands or more surviving offspring all the way to humans, elephants and whales which produce surviving offspring measured in single numbers.

  111. Would you agree that fitness is defined as a species’ ability to survive? Is this relevant? Why is species-level selection relevant to the evolution of complexity?

    Remember what’s on the table: Is simple life better able to survive environmental pressure than complex life.

    If yes, Darwinian evolution is false since Darwinian evolution claims that life evolves complexity to better be able to survive environmental pressure.

    How would you define fitness?

  112. Acquiesce: Fitness is a measure of the numbers of surviving offspring (nothing else).

    No, that’s lifetime reproductive success.

    Is Bob playing word games with me or what?

  113. I also [see tribune 111] would like to know how Bob defines fitness (if is isn’t the numbers of surviving offspring).

  114. “An organism that passes on 50% of its genes is less fit than one that passes on 100%; an organism that has an average of 2.5 surviving offspring is less fit that has 100. These were the things brought up earlier and they are indeed valid points.”

    Only ceteris paribus. Which is why I brought up trade-offs.

    No, since I already qualified my statement with “surviving”. Two organisms, A and B, of the same species, one produces 100 surviving, viable, reproducing offspring the other 2 of the same. By what method of accounting would you say the organism that only produces 2 is “more fit” than the organism that produces 100 equally viable offspring?

    There is an actual issue here. Re-defining “fitness” is not going to solve the issue.

    Atom

    PS Our problem is with you referring us to TO as a reliable source of information, which it is most certainly not. So please upgrade your source material if you don’t want us to complain.

  115. Hence, you have to ask whether an increase in complexity leads to an increase in fitness as compared to individuals in the same population (i.e. the same species, in the same area).

    That’s precisely what I’m asking – I’m asking how, under a gradualistic scheme an increase in complexity –in the form of a new trait– if it doesn’t produce an entirely new type (which no longer competes with its parent population) can become fixed into the population because there is no trait beyond that contained by bacteria which in anyway increases fitness.

    For example, any new trait of any level of complexity, would take more time to develop – this in turn would lead to an increase in gestation time. If the new trait doesn’t enable that individual to out-compete other members of the population (i.e. produce more surviving offspring) the trait, however nifty and complex, would be weeded out by NS – not selected!

  116. any new trait of any level of complexity, would take more time to develop – this in turn would lead to an increase in gestation time

    To this I would add:

    -What I mentioned before, more complexity equals more potential points of failure. This is an objective fact.

    -More complexity means more informational content to be stored, copied, and proof-read during the replication process. This leads to greater energy needs and longer replication times.

    I believe Darwinists are completely on the wrong track with this one. I think it was Dawkins who performed experiments on virtual organisms (I’ll call them “vorgs” for short)and found a trend towards increasing simplicity: vorgs would cast off parts of their genomes in order to be leaner, meaner replication machines, which would give them an edge. Over time, the organisms would get simpler and simpler – the exact opposite of the actual biological trend towards greater complexity over time. Of course his results were still somehow held up as evidence for Darwinism (could he do anything else?), but the meaning of the experiment is clear to the casual observer.

  117. Acquiesce – Let me explain your argument. You wrote

    Fitness is a measure of the numbers of surviving offspring (nothing else).

    So, in the example where an individual produces 2 offspring after 100 years, as compared to one which produces 1 offspring after one year, if they both only reproduce once, you would claim that the one producing 2 offspring is fitter. Is that right?

    I hope people can see why lifetime reproductive success isn’t the same as fitness.

    The definition of fitness is more complex, in terms of life histories it’s defined as the Malthusian growth rate – for example, see my lecture notes from a couple of years ago (pdf). There are other definitions, but they’re similar enough for our purposes.

    Bob

  118. Here is the definition of fitness as used in population genetics from Wikipedia.

    http://en.wikipedia.org/wiki/Fitness_%28biology%29

  119. Yeah good post, anything un-relating to fitness would eventually be lost creating as you put it ‘a leaner meaner replication machine’. The question why/how NS first produced those traits must be questioned. I believe orthodox evolution has it totally backwards. If higher organisms evolved from lower ones, it couldn’t have done so by NS.

    The finely balanced ecological system is also evidence against NS’s role in evolution (for example, imagine if higher organisms evolved the enzymes necessary to digest cellulose). Many traits, which would greater improve the fitness of an organism could potentially be apocalyptic to the overall survival of our ecosystem. It doesn’t take a genius to work out the implications of the example just given.

    Certain designs cannot be ‘too good’ – for example, whilst pitcher plants do a wonderful job of collecting flies, if they evolved an even better design they could potentially decimate our ecosystem by simply being too effective. Darwinists, of course would see all of life evolving in union, and no particular design ever becoming too good. They of course base this assumption on the fact that – you guessed it – our ecosystem is finely balanced.

  120. Let me ask you a question Bob

    We have a bacterial colony, they all reproduce every 20 minutes or so. One bacterium arises that, due to some mutation, can only reproduce once an hour. In this example (which is seen with bacteria that gain resistance to antibiotics etc, being introduced back into the parent population i.e. those not resistance to the antibiotic)

    Q1. Which is the fittest organism?
    Q2. Which will eventually win out in the battle for selection?

  121. Bob: Acquiesce – You’re claiming that fitness is highest in bacteria, as compared to more complex organisms. That only makes sense if the organisms are competing.

    I know that. I even made a possible solution to this problem using that [see - 72]. Lets not keep going over old ground and explain to us how NS can direct for higher complexity whilst simultaneously selecting for lower fitness.

    I propose a solution:

    Only when changes are so large that the mutated organism no longer competes with its parent stock (producing an entirely new type / lifestyle) can the organism remain despite its reduced fitness. This would obviously mean it bypasses NS.

  122. So, in the example where an individual produces 2 offspring after 100 years, as compared to one which produces 1 offspring after one year, if they both only reproduce once, you would claim that the one producing 2 offspring is fitter. Is that right?

    I believe he meant number of surviving offspring in relation to a set number of organisms over a given period of time. At least that is the charitable reading would render.

    Basically, reproduction interval length (between successive generations), robustness (ability of offspring to reach reproductive maturity) and fecundity (number of offspring per replication event) are the factors we’re examining.

    And unfortunately for Darwinism, in the real world, the simpler the organism, the better they do on all three counts (speaking generally).

    I believe you have all the information you need to now answer Aq’s questions.

  123. For the benefit of those lurkers not familiar with evolution theory, Bob is claiming that you cannot compare fitness (the number of surviving offspring) between bacteria and humans (for example) because they don’t compete. He is right – but that’s not my argument and Bob knows this. My argument compares the fitness between the parent bacterial population and a new mutant which does compete with the rest of the population.

    Bob first replied by attacking my understanding of evolution theory (we call this ad hominem – attacking the person not his argument).

    Then Bob suggested I learn from books written by famous, highly intelligent evolutionists who, by implication, know more about evolution than myself (we call this the argument from authority)

    Next he tried to solve this problem by reference to trade-off, which has no bearing on my argument (as my argument refers to surviving offspring, not just numbers of offspring) – this is the classic red-herring (i.e. dragging a red-herring through the argument).

    Since then he has resorted to using the strawman tactic (i.e. changing my argument into something it is not then attack his own made up version of my argument).

    Mix in a few word games about fitness, even though we can experimentally prove that organisms exhibiting reduced fitness quickly lose out in the battle for survival (like I mentioned above, those that gain resistance being reintroduced back into the parent stock – like introducing domesticated animals back into the wild stock).

  124. The rats that are killed won’t produce offspring, so therefore will be less fit. The level of selection is (usually) the individual, not (as you seem to imply) the population.

    —Bob

    Well, here’s where the jello comes in. If, after the in-fighting took place, there were 10 left out of an initial hundred, it would be said that they are the fittest. Now, if the 10 started to fight, and only five survive, they would be termed the fittest. Now, if the five fight, and only one survives, it is (since fitness is determined between members of the same competing species, and, apparently has nothing to do with populations), by the definition you want to use, the fittest of them all—and he/she can’t reproduce; viz., there’s no one to mate with. So the fitness of the fittest memeber of the species is zero. Admittedly, this is a reductio ad absurdum, but it makes a valid point about the fluid notion of fitness definitions. In the end, it can be whatever you want it to be. Just look at the survivors—and call them the fittest. Yes, this is the tautology I believe Philip Johnson points out: who survive? the fittest? who are the fittest? the ones that survive.

  125. PaV – what you’re describing is called “evolutionary suicide”. This sort of behaviour can evolve, if there is migration between populations. I would argue that the definition of fitness is the same: what’s happening is that the environment is changing: as population size decreases, this reduces the chance of finding a mate, so fitness decreases.

    The tautology claim is debunked here. Mathematically fitness is an expectation, not what is observed.

    Bob

  126. Next he tried to solve this problem by reference to trade-off, which has no bearing on my argument (as my argument refers to surviving offspring, not just numbers of offspring) – this is the classic red-herring (i.e. dragging a red-herring through the argument).

    I’m sorry, but whether you were referring to offspring or surviving offspring doesn’t matter for the trade-off argument. What matters is that fitness is affected by several life history characteristics, and a trait can affect more than one: it can increase one life history characteristic, and decrease another. This is the trade-off.

    If the overall effect is to increase fitness, then fitness is increased. Some people here have argued that an increase in complexity can lead to an increasing chance of failure. This, on its own, would decrease fitness. But if it also increased fitness by having a positive effect on life history traits, then he overall effect might still be to increase fitness.

    I’d still like to see evidence that the overall effect of an increase in complexity is to decrease fitness. Anyone?

    Bob

  127. H’mm:

    Let’s see, over in the July 6 Explanatory Adequacy thread, Bob diverted the focus and demanded an answer on his terms from one person. That person answered, and others substantiated, and then it was pointed out that the issue Bob raised was already addressed adequately in the original post, complete with an excerpt. [Sounds like subject shifting to me, I won't use the usual names for the fallacies involved -- cf 123; perhaps it is inadvertent.]

    It is thus interesting to excerpt from Sal’s original citation of the NAS member, Nei:

    In the last four decades, the study of molecular evolution has shown that a majority of [observed, naturally occurring . . . ?] amino acid substitutions in proteins [coded for in DNA] are neutral or nearly neutral …However, most evolutionists still believe in neo-Darwinism with respect to phenotypic evolution and are not interested in neutral evolution (19–22) . . . . By contrast, Nei (17, 24, 25) argued that because phenotypic characters are ultimately controlled by DNA sequences, both molecular and phenotypic evolution must occur in similar [non Darwinian] ways. He also suggested that a considerable portion of morphological evolution is caused by neutral or nearly neutral mutations, and the driving force of evolution is mutation at both molecular and phenotypic levels . . . . In one of the most popular textbooks on evolution, Futuyma (ref. 20, p. 10) . . . states ‘Natural selection can account for both slight and great differences among species, and adaptations are traits that have been shaped by natural selection.’’ Although this type of statement is quite common in the evolutionary literature, it is obvious that any advantageous genotype is produced by mutation including all kinds of genetic changes. Natural selection occurs as a consequence of mutational production of different genotypes, and therefore it is not the fundamental cause of evolution . . .

    In short, absent a credible SOURCE of successful – i.e. functionally superior [and in our context more complex] — new genetic information, natural selection has nothing to work on apart from stabilising the population as it is by eliminating unfit “sports.” NS eliminatres the unfit, but cannot credibly explain the ARRIVAL of the fittest, and random walk based “searches” as observed overhelmingly lead to neutral changes not the sort of innovative ones we would need to ground NDT. This is of course underscored by Behe’s recent note on malaria in the face of chloroquinone.

    [BTW, I am annoyed to see that Bob is till pointing us to TO “debunking” articles as late as no 125 just above. FYI Bob, the article says nothing and addresses nothing serious in say Johnson's 1991 notes on the tautology issue, and issue that has long since been acknowledged as cogent in the serious level literature. If “the fittest” are assessed based on differential reproductive success, then by definition those who reproduce themselves well are “the fittest.” And, this simply fails to explain the ARRIVAL of the complexity and information behind it we are speaking to. [There are ways around this, but as Johnson long ago noted, they undercut the force of arguments rooted in Natural Selection and there is sa tendency to drift right back to tautological formulations. Since Johnson 1991 is easily accessible, and Nei above underscores the basic point, I will not now go into further long excerpts.]

    Now, too, on this thread, I and others have had to point to problems such as improper burden of proof shifting, citation of highly questionable and tendentious sources, use of just-so stories, dismissal of relevant factors – i.e the KISS (keep it simple, stupid) principle and what we know about complexity in systems from our experience of such, the basic datum that complex, functionally specified information-rich systems in our experience invariably are the products of design. And more.

    The only real point I see Bob has made, as Acquiesce made first [121 relative 72], is that where complexity accesses a new ecological niche via a radically different body plan or reproductive isolation otherwise [e.g. founder principle], then it could be rewarded by sufficient reproductive success to thrive.

    But, that “exception” only gets us back to Nei’s point, and Behe’s point and Johnson’s point and Dembski’s point and . . . namely: where do such new SUCCESSFUL and complex body plans come from, in a world where there is such a thing as a configurational space for digital information systems [and analogue ones too . . . look at classical stat mechanics on phase space cells] which rapidly exhausts probabilistic resources. E.g. 500 bits relative to a unique state soon enough exhausts the number of quantum states in the known universe across its reasonable lifetime. And more broadly 1 in 10^150 is a reasonable threshold of such isolation of functional islands that they are not credibly findable on that gamut.

    Further, as Aq points out in 123, the issue is to account for gradualistc increments in complexity across generations in a population within a given ecological zone such that there is competition for passing on genes in the population across time, as manifested in phenotypes — in a context where as Atom has highlighted, that should use up more energy, more materials, more development and growth time, and has more that can go wrong. Those factors all point to reductions in reproductive success, and would tend to do what the fossil record reports: stabilise the phenotypes.

    Put the two issues together and you see the other issue come out: the stasis and suddenness of new types of organisms that is all over the fossil record, the paltry number of celebrated “links” notwithstanding. (I gather they are now fewer than in late C19, contrary to Darwin’s hopes, and contrary to what one would reasonably expect from the “almost unmanageably rich” fossil collections we now have and have had for decades.)

    So, let’s focus back on the core issues int his thread and the July 6 thread, which is materially related. [We are still waiting over there, and you have some serious explaining to do.)

    GEM of TKI

  128. Bob: I’d still like to see evidence that the overall effect of an increase in complexity is to decrease fitness. Anyone?

    Atom gave you this answer: increased reproduction interval length (between successive generations); lack of robustness (ability of offspring to reach reproductive maturity) and a reduction of fecundity (number of offspring per replication event). All of these factors mean that higher organisms compared to their distant relatives show a significant reduction in overall fitness.

  129. I add, re Acq in 128: recall that a major argument in gradualism, is that small increments in survival factors have significant population impacts across time, so the impacts of these factors have to kick in real early, long before we get to major body plan alterations . . .

  130. Acquiesce – you didn’t understand my point (I suspect you’re still not understanding the importance of trade-offs in thinking about these points). Yes, complexity can have adverse effects, but it can also have positive effects. If the positive effects more than offset all of the negative effects, then overall a more complex organism will have a higher fitness.

    So, show me that these adverse effects are not offset by the advantages of complexity.

    Bob

  131. So, show me that these adverse effects are not offset by the advantages of complexity.

    Bob, shouldn’t you be trying to show that the advantages of complexity offset its adverse affects?

    Why should it be considered axiomatic that complexity increases survivability?

  132. I’m going to propose something akin to Godwin’s Law.

    Linking to TalkOrigins results in automatic loss of the debate.

  133. Bob: So, show me that these adverse effects are not offset by the advantages of complexity.

    What advantages of complexity? So far, it looks like the only advantage proposed for complexity is that if enough complexity accumulates over time, then perhaps a new function will arise that hopefully isn’t so disadvantageous as to doom the organism outright so that maybe it will be able to survive in a new niche (thankfully not having to compete against its predecessors, since they are much more fit) which hopefully isn’t already inhabited.

    Of course, the problem is that while the complexity is accumulating to the point that a new function is available, it is difficult to imagine how their can be a trade-off. If the organism is saddled with complexity, but has yet to develop anything that would allow for their to be a trade-off, then it seems it would be quickly selected against by the preserving power of natural selection long before any new sort of functional advantage could arise.

    You’ve made an appeal to positive trade-offs. Why shouldn’t the burden of proof be upon you to show that complexity can truly be advantageous, especially during the period where it is not yet able to provide a new function that sufficiently separates it from its biological peers.

  134. err…there to be a trade-off…

    Sometimes my fingers just pick a word that sounds close….multiple times, evidently. :P

  135. Bob, shouldn’t you be trying to show that the advantages of complexity offset its adverse affects?

    No. I’m not the making a claim. It’s other people who are claiming that there is no selective advantage to complexity: I’m just asking for their evidence.

    Bob

  136. I would argue that the definition of fitness is the same: what’s happening is that the environment is changing: as population size decreases, this reduces the chance of finding a mate, so fitness decreases.

    —-Bob

    But this is what I mean about fitness being “jello”. You’re (1) now defining fitness in terms of the population; (2) saying that the “killer” extinct is less fit (so how did it evolve?); (3) and omitting the problem that if the “killer” trait is at first helpful (relative to the population), it then becomes unhelpful. (It’s as if the rats knew how to count: 100 is too many; but 10 is about right). This fluid notion of what fitness is makes it an almost useless concept. As I said before (I haven’t looked at your link), all’s you have to do as an evolutionary biologist is see which animals are alive, and figure out how they’re better than the ones that aren’t alive—you then define that as “fitness”. You have to admit, that’s a fairly easy task.

  137. No. I’m not the making a claim. It’s other people who are claiming that there is no selective advantage to complexity: I’m just asking for their evidence.

    —Bob

    Following what I just wrote about fitness, you’re taking refuge in what we see in the world. This makes Darwinism an “a posteriori” science, not an “a priori” one. It can’t make objective definitions about what fitness is, and thus, can’t make predictions about what we would expect to see. It’s in this way “unfalsifiable”.

    BTW, you need a shave! What’s that you’re drinking?

  138. No. I’m not the making a claim. It’s other people who are claiming that there is no selective advantage to complexity: I’m just asking for their evidence.

    We have shown how complexity is a hinderance and pointed out that only when a sufficient amount of functional complexity arises, can we even hope for a benefit. But even then, empirical evidence suggests (see Dawkin’s experiment with v-orgs) that simpler, minimal replicators will be selected for when NS operates on informational replication systems. The costs of increased complexity are high; unless the presumed benefits (which you have yet to outline at all) can offset the very real costs (already outlined for you) then Natural Selection will work to eliminate nascent complexity whereever it can.

    And indeed, this is what the experimental evidence bears out.

  139. And again, to ask the simple question that began this:

    How can NS select for increasing complexity when simpler mechanisms can (and do) replicate much quicker, more easily and robustly?

  140. Bob–

    As to the link your provide to TalkOrigins, I find their refutation of “survival of the fittest” to be quite inadequate. The first reason they give is that Darwin seemed to distance himself from that terminology. Yet, Darwinists today sure don’t distance themselves from it, nor did Thomas Huxley it Darwin’s time.

    The second refutation suggests that if it it has ever been conjectured that the “fittest” will perish, then obviously were not dealing with a tautology. But, of course, anyone can conjecture anything in the world they want to. How do unsubstantiated conjectures prove anything.

    Finally, in their third attempt, they begin this way:

    “The fittest, to Darwin, were not those which survived, but those which could be expected to survive on the basis of their traits.”

    Don’t you see how illogical this statement is on the face of it? Darwin didn’t think the “fittest” were “those which survived”. So, he then thought they were the ones that didn’t survive?

    This is again the same “a posteriori” thinking I was writing about: Darwin knows who “survived”; he know the “traits” of those who “survived”; he then defines “fitness” as the “traits” of those who “survive”. To me, this isn’t science, it’s just guesswork and “just-so” storytelling. Evolutionary biologists have been following suit ever since.

    Now, in those limited areas where NS (as it is now called; I think in will one day be simply called “adaptation”) is known to work—in bacteria, e.g., “fitness” is easy to predict, and easy to define. E.g., if we put a whole bunch of E. Coli on a culture dish that has only lactose, then only those bacteria that can metabolize lactose are ‘fit’. All others are ‘unfit’. And we can ‘predict’ that those bacteria which either can’t metabolize, or cannot change over to metabolize, will perish.

    But stray from these extremely limited instances, and “fitness” becomes “jello”.

  141. Darwin didn’t think the “fittest” were “those which survived”. So, he then thought they were the ones that didn’t survive?

    No. Read the full sentence. Then note that the “expected” refers to a mathematical expectation: I don’t know how familiar you are with probability theory.

    Atom – we’re not getting anywhere. How about survival? How about an actual example where a more complex organism is less fit than its simpler counterpart?

    Bob

  142. Bob: Atom – we’re not getting anywhere. How about survival? How about an actual example where a more complex organism is less fit than its simpler counterpart?

    Bob, what do you mean by “counterpart?” I’m assuming your use of the word precludes comparing, say, polar bears with bacteria? (If not, then the exercise becomes rather simple, doesn’t it?) So, what are we allowed to compare in order for it to meet your “counterpart” standard?

  143. I’m assuming your use of the word precludes comparing, say, polar bears with bacteria?

    Indeed.

    You would have to compare individuals of the same species competing in the same niche (OK, we can relax the “same” a bit, to allow for complex individuals invading new niches for example).

    Bob

  144. How about an actual example where a more complex organism is less fit than its simpler counterpart?

    Depends on the complexity being looked at it, does it not? Let’s take a look at TO’s example of people with “monkey tails”. I have no problem calling that “complexity” in a generalized sense (as in, not CSI). I’m not sure what positive effects they do have. From what I remember they’re not articulated and cannot serve as an additional limb. But I’m pretty sure they’d act as the opposite of a peacock’s feathers, dramatically reducing those individual’s chances of reproducing. Ditto goes for additional/non-functioning mammary nipples and other examples that turn off the opposite sex.

    I see your point, though. The situation is complicated enough that there can’t be blanket statements. There can be increments in complexity where the tradeoff is more positive than negative. But that’s why ID doesn’t have blanket statement…there is a complexity threshold. And that’s why Behe is trying to find an “edge of evolution”. While an estimate has been arrived at I don’t think that “edge” has been found yet. Personally I think it “might” be greater than where some ID proponents envision it to be. But I could be wrong.

    As an aside, the problem with these loose definitions comes about when any type of complexity itself is rewarded for the sake of complexity…then you get things like AVIDA.

  145. “Then note that the “expected” refers to a mathematical expectation”—Bob

    Expected on what basis? And, of course, the basis is………they’re more “fit”. (s=selection coefficient=fitness.) Circle now complete.

    Q. “Why do you expect them to survive?” A. “Because they have traits that are more ‘fit’.” Q. “What do you mean by they’re more ‘fit’?” A. “They have traits that make you “expect” them to survive.”

    Round, and round, we go.

  146. You would have to compare individuals of the same species competing in the same niche (OK, we can relax the “same” a bit, to allow for complex individuals invading new niches for example).

    Bob

    If I am correct, the more unecessarily complex will be weeded out by NS before they can gain a foothold, unless they move to an entirely new niche as Aq suggsted, in which case you’d say their fitness cannot be compared.

    Where do we draw the (artificial) line of comparison? Can two different strains of a bacteria be compared? How about a bacteria and algae in the same habitat? How about rats and humans, both mammals, inhabiting the same village, competing for grain?

  147. I don’t want to lose focus of the basic point, so let’s go back to simple facts. Tell me which of these you disagree with:

    1) Simpler organisms reproduce in greater numbers than more complex organisms. (In general.) Bacteria vs. insects vs. rodents vs. man

    2) According to NDE, the general trend of life development in earth history is from simple organisms to more complex ones.

    3) If NS only selects for survivability and reproductive success, and the simpler the organism the better they do in both respects (see 1 above), then we should expect a trend towards increasing simplicity of organisms.

    4) Experimental evidence suggests this is indeed the case when replicators are allowed to mutate and are subject to NS, being selected by reproductive success.

    Please tell me which of those points is in error.

    and please get around to answering Aq’s intial question about how NS can form a trend of increasing complexity while selecting based on increasing reproductive success…

  148. “Then note that the “expected” refers to a mathematical expectation”—Bob

    Expected on what basis? And, of course, the basis is………they’re more “fit”. (s=selection coefficient=fitness.) Circle now complete.

    Ah, OK. You’re not familiar with basic terminology in probability theory. I hope you don’t mind if I pass on explaining this: it really would take us off-topic. There’s an explanation here. Sorry it’s not from TalkOrigins. :-)

    I’ll just point out that fitness isn’t a tautology, because we can predict fitness (e.g. as I did here). In essence, we can assign fitness to individuals, based on heredity (i.e. estimates of fitness of their ancestors). This would obviously be impossible if it were a tautology.

    Bob

  149. Atom – I’ve tried to answer Acquiesce’s point repeatedly, but you’re repeating many of the same mis-conceptions. You can’t compare the fitnesses of different species (competition between species is primarily a problem for ecologists to study). Even Acquiesce agrees with that. So your first point in wrong.

    You’re obviously not understanding what I’m writing: in post 146 you quote me saying that we can only compare individuals of the same species, and then ask if we can compare rats and humans. Now, I’m not up on thought in baraminology, but I suspect even they don’t think rats and humans are that closely related.

    Bob

  150. Bob,

    I’ve appreciated your patience in answering question. I have a technical one pertaining to mutation rates.

    There is the jukes-cantor model for neutral mutation and divergence. At some point two identical sequences become fully divergent (well really 75%).

    But one problem I’ve not been able to resolve. If we have a 1 mutation per 10 million years per nucleotid position. Should the sequences be pretty much fully divergent in 10 million years.

    I can’t seem to reconcile the math with the decaying explonential in the Juke-Cantor model.

    Any insights? The question related to neutral mutation in pseudo-genes.

    If the mutation rate is 1 nucleotide per 1 position per 10 million years, shouldn’t the pseudo gene be trashed in 10 million years?

    Salvador

  151. Sal – assuming a Poisson process, then the proportion that didn’t have a mutation would be e^-1 = 0.37. So there should still be some signal.

    Bob

  152. Atom [147]: I don’t want to lose focus of the basic point, so let’s go back to simple facts. Tell me which of these you disagree with:

    1) Simpler organisms reproduce in greater numbers than more complex organisms. (In general.) Bacteria vs. insects vs. rodents vs. man

    2) According to NDE, the general trend of life development in earth history is from simple organisms to more complex ones.

    3) If NS only selects for survivability and reproductive success, and the simpler the organism the better they do in both respects (see 1 above), then we should expect a trend towards increasing simplicity of organisms.

    4) Experimental evidence suggests this is indeed the case when replicators are allowed to mutate and are subject to NS, being selected by reproductive success.

    Please tell me which of those points is in error.

    and please get around to answering Aq’s intial question about how NS can form a trend of increasing complexity while selecting based on increasing reproductive success…

    Bob: In point 1 Atom was merely asking you whether you accept that simple organisms reproduce in greater numbers than more complex organisms. Don’t try and evade the point. Insects, rodents and man were merely put there to give examples of higher organisms and their trend towards decreased fitness.

    BTW, bacteria (under favourable conditions) could produce enough offspring to equal the mass of our planet in around a week. Point 1 is a no-brainer.

    Now can you answer those points listed by Atom? And also my initial question: How can NS form a trend of increasing complexity while selecting based on increasing reproductive success. We are 150 posts on and you still cannot put forward any workable solution (at least I have tried – see 72).

  153. H’mm:

    Onlookers — it seems Bob will not directly respond to me here or in the July 6th thread — it seems we have made little or no progress. (Other than to highlight that natural selection as a concept tends to fall into tautology/ circular argument, and that there are excellent reasons to think that simpler systems have obvious advantages.)

    As to the “you don’t understand mathematical expectation and/or probability theory”:

    –> Atom is an Engineer/Software Engineer.

    –> I am an Applied Physicist who also holds an MBA (as well as a third u/grad major in Math), who among other things has helped to design engineering undergraduate curricula, in partnership with people designing BSc computing curricula — we had one of those Faculties that blended engineering and computing.

    –> Others here will have comparable exposure to the relevant mathematics and sciences generally.

    –> Many of us have significant design and development experience with hardware and/or software systems, in academic, military or commercial contexts. (That is a big part of why when we see the sorts of complexity being discussed, we know the hard way just how hard it is to make something complicated work by intent much less through random generation and probabilistic filtering.)

    Speaking for myself, I first met expectation in sixth form, before going to University proper, decades ago.

    In designing u/grad engineering curricula, the relevant statistics and probability would be covered in the first level course in that area, soon after doing the basic calculus or in the part of the computer people, intro discrete math sequence.

    In short, your remarks evidently betray a lack of understanding of the level of the people you are addressing.

    Our concern is not as to whether sum across outcome payoffs times probabilities will yield an expectation, but on [1] what the credible probabilities are and [2] what the likely payoffs to increments in complexity compatible with what mutations are observed to do will be.

    In particular, as already excerpted, there is a serious question as to whether body-plan level innovations of the sort of scope in the Cambrian revolution are within reasonable reach of NDT.

    Then, when we look at the mechanism that is held to generate the sort of complexity implied by that revolution and the rest of the fossil record and what we see in current life forms and ecosystems, we have a big problem with the idea that the incrementalist approach in NDT will credibly generate such diversification, starting with the basic issue of more complexity step by step leads to greater competitive fitness to the environment thus differential reproductive success.

    The bacteria – insects – man example is just one case in point of the trend, and the simulations on the matter underscore the point too.

    All of this gets back to what Nei highlights, as was excerpted in 127 above.

    GEM of TKI

  154. Acquiesce – we’re no further because people are still bringing up irrelevant details. It doesn’t matter if bacteria produce more offspring that, say, polar bears. What matters is whether a bacterium (say) that mutates to something more complex (perhaps it gets a gene with a new function) is fitter than the non-mutants without the added complexity.

    I’m still waiting for someone to show that there is actually a problem: if there is no problem, there is no need for a solution.

    Bob

  155. Bob:

    Enough has long since been said — several times — to show why many of us note several problems with the assumption that we can credibly get enhanced functionality through random mutation [etc], and that we can then see such an incrementally ever more and more complex organism competing with their parent populations and establishing itself in the ecological zone.

    Then, there is the problem that such incrementalism has to account for the onward fact of the implications of the weight of the fossil record: sudden appearances [and disappearances] and stasis. Cf here, Lonnig, 2004:

    examples like the horseshoe crab are by no means rare exceptions from the rule of gradually evolving life forms . . . In fact, we are literally surrounded by ‘living fossils’ in the present world of organisms when applying the term more inclusively as “an existing species whose similarity to ancient ancestral species indicates that very few morphological changes have occurred over a long period of geological time” [85] . . . . Now, since all these “old features”, morphologically as well as molecularly, are still with us, the basic genetical questions should be addressed in the face of all the dynamic features of ever reshuffling and rearranging, shifting genomes, (a) why are these characters stable at all and (b) how is it possible to derive stable features from any given plant or animal species by mutations in their genomes? . . . .

    A first hint for answering the questions . . . is perhaps also provided by Charles Darwin himself when he suggested the following sufficiency test for his theory [16]: “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.” . . . Biochemist Michael J. Behe [5] has refined Darwin’s statement by introducing and defining his concept of “irreducibly complex systems”, specifying: “By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning” . . . [for example] (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans . . . .

    One point is clear: granted that there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time. For, if “several well-matched, interacting parts that contribute to the basic function” are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because “the removal of any one of the parts causes the system to effectively cease functioning”) such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist. And this could mean no less than the enormous time periods mentioned for all the living fossils hinted at above. Moreover, an additional phenomenon would also be explained: (3) the equally abrupt disappearance of so many life forms in earth history . . . The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, which prima facie could be an improbable process — or perish . . . .

    According to Behe and several other authors [5-7, 21-23, 53-60, 68, 86] the only adequate hypothesis so far known for the origin of irreducibly complex systems is intelligent design (ID) . . . in connection with Dembski’s criterion of specified complexity . . . . “For something to exhibit specified complexity therefore means that it matches a conditionally independent pattern (i.e., specification) of low specificational complexity, but where the event corresponding to that pattern has a probability less than the universal probability bound and therefore high probabilistic complexity” [23]. For instance, regarding the origin of the bacterial flagellum, Dembski calculated a probability of 10^-234[22].

    While of course Darwin indulged in a a bit of selective hyper-skepticism above [he was only going to accept absolute proof in a context where only abductive explanations are possible] but the point is clear enough.

    GEM of TKI

  156. What matters is whether a bacterium (say) that mutates to something more complex (perhaps it gets a gene with a new function) is fitter than the non-mutants without the added complexity.

    Bob, has a bacterium ever been observed mutating into something more complex?

  157. tribune7 – yes. Surely any bacterium that gains a function is more complex.

    I’ll let you search Talk Origins for the relevant pages. :-)

    Bob

  158. yes. Surely any bacterium that gains a function is more complex.

    Resistence to antibiotics? The ability to eat oil? How are they more complex than other bacteria.

    Let’s say you are right and these new functions increase complexity. Acquiesce points out in post 120 that these new functions cause a loss of fitness — once the antibiotic is removed from the environment — if fitness is defined as as the average number of surviving progeny of a particular genotype compared with average number of surviving progeny of competing genotypes after a single generation as per Jehu’s wiki link.

  159. I don’t think anyone is denying the basic ability to produce trivial complexity but not CSI. There’s only a certain level of plasticity and personally depending on the design of system I think that plasticity can vary. An example is multiple GAs all designed to reach the same goal but only some are capable of it. Here’s the question ID proponents have been asking for years: where’s the evidence that underlies the assumption that trivial changes will somehow compound and get beyond the “edge”?

  160. Patrick – as far as I can tell, people are arguing about the inability to produce complexity – see tribune7′s post just before yours.

    I think tribune7 now has to show that all increases in complexity are responses to a change in the environment that can be reversed if his argument is to stand. If he wants to bring more conditions in, I think it’s up to him to show that they always hold.

    Bob

  161. ok…so who here believes that Darwinian processes are incapable of producing complexity?

  162. Bob,

    Notice, in my last post I am talking about reproductive success (producing offspring in greater numbers), not your vague and shifting “fitness” (since you seem to want to play word games with that term.) I am simply making a factual point about which organisms produce offspring faster: simple vs. complex. I use examples of different organisms (bacteria, insects, rodents, man) to show that the general trend does in fact exist. There is no scientific law against comparing the reproductive output of two different kinds of replicators.

    It is becoming clear that you won’t tackle the issue directly, so I won’t press you any more on it. I am confident that this issue will remain in your mind after this. Whenever you see experimental results showing that simpler replicators outreproducing more complex ones, this thread will come to memory and eventually you will have to deal with the issue.

    Atom

  163. ok…so who here believes that Darwinian processes are incapable of producing complexity?

    I’ll raise my hand.

    Actually, it’s not so much that I think they are “incapable” of producing complexity but wondering why it should be assumed that they can based on the non-illustrations provided by Bob.

    Bob seems to be defining complexity as simple change. Are bacteria that acquire resistance to antibiotics more complex than those that don’t?

    Do they have more working parts?

  164. “Then note that the “expected” refers to a mathematical expectation”—Bob

    PaV responds:
    ‘Expected on what basis? And, of course, the basis is………they’re more “fit”. (s=selection coefficient=fitness.) Circle now complete.’

    Bob:
    “Ah, OK. You’re not familiar with basic terminology in probability theory. I hope you don’t mind if I pass on explaining this: it really would take us off-topic.”

    I’ve studied quantum mechanics. I know what an expected value is. But you’re assuming fitness values for various outcomes.
    From Wikipedia: “In probability theory the expected value (or mathematical expectation, or mean) of a discrete random variable is the sum of the probability of each possible outcome of the experiment multiplied by the outcome value (or payoff).”

    Those values are all “a posteriori”. That is the point I’m making. The values you “input”, are drawn from experience. Thus, the input simply reproduces the output. Now, I suppose you could do a simulation using initial values, and you could say that’s a prediction. But, if it doesn’t match what is seen “a posteriori”, then I suspect the temptation would be to change the “initial values” until you did get a match. IOW, circular reasoning.

    I’ll just point out that fitness isn’t a tautology, because we can predict fitness (e.g. as I did here).

    —Bob

    I’m reading your paper right now. But from the abstract, it appears you could make no conclusions about fitness. I don’t see how that answers my assertion.

  165. Atom – I’ve already given an example to show that reproductive success does not necessarily predict fitness. And also explained (several times) that you can’t compare fitness of different species.

    Bob seems to be defining complexity as simple change. Are bacteria that acquire resistance to antibiotics more complex than those that don’t?

    Do they have more working parts?

    Yes. Some of them are carried in plasmids.

    PaV – fitness is there. Check the Red Queen stuff. Also, I hope you’re aware of the tight connection between selection coefficients and fitness.

    Bob

  166. I’ve already given an example to show that reproductive success does not necessarily predict fitness.

    Excuse me? You’re trying to get back into the fitness word game?

    I’m not playing that game with you.

    As I made clear, we’re only talking about reproductive (replication) success now. (See my post 162) This can be compared across any class of replicators. And again you dodge the issue.

  167. Do they have more working parts? Yes. Some of them are carried in plasmids.

    More working parts or different working parts?

  168. Again:

    Tell me which of these you disagree with:

    1) Simpler organisms reproduce in greater numbers than more complex organisms. (In general.) Bacteria vs. insects vs. rodents vs. man

    2) According to NDE, the general trend of life development in earth history is from simple organisms to more complex ones.

    3) If NS only selects for survivability and reproductive success, and the simpler the organism the better they do in both respects (see 1 above), then we should expect a trend towards increasing simplicity of organisms.

    4) Experimental evidence suggests this is indeed the case when replicators are allowed to mutate and are subject to NS, being selected by reproductive success.

    BTW If you say 3, then you have to show how NS can select for organisms that produce fewer offspring per unit of time…

  169. EDIT: BTW If you say 3, then you have to show how NS can select for organisms that survive better than their competitors and produce fewer offspring per unit of time…

    (Before Bob serves up another uncharitable reading, I’ll make myself crystal clear)

  170. EDIT TO THE EDIT: BTW If you say 3, then you have to show how NS can select for organisms that survive less well than their competitors and produce fewer offspring per unit of time…

    (This I got it with that one)

  171. We could go on forever with Bob shifting the terminology.

    The greater the environmental hardship, the more organisms of higher complexity (or anything other than bacteria) struggle in the battle for survival. In the long run, highly complex organisms will perish due to their lack of fecundity, robustness and the shear amount of time between generations.

    Moreover, NS does not merely select on the basis of reproductive success, but being a blind force is unable to foresee potential problems (which intelligence does) and thus (acting upon shuffling and segregation) evolves organisms down an ever narrowing cone of generalization – leading ultimately to extinction.

    [Re: my comments on the panda – Post 30]

  172. The fact of the matter is that Bob cannot explain how NS can evolve bacteria, which occupy every liveable environment, into organisms of higher complexity, which along the way must have lost their environmental adaptability, robustness, fecundity, rapid generation / gestation times, and asexual reproduction.

    These are not minor losses, some bacteria, under favourable conditions, can produce around 100,000,000,000,000,000,000 offspring in a single day! Also, over the course of evolution NS must have turned a blind eye to an increase by some 10,000,000 minutes plus in generation times and some 300,000 minutes plus in gestation times.

    So let me ask you again. How can NS direct for higher complexity whilst simultaneously selecting for lower fitness?

  173. Bob: Do you really think that if I put a mutated ‘more complex’ bacterium – which due to this ‘higher complexity’ reproduced considerably less surviving offspring – into a sample with its parent population that the new trait it carries would fixate into the parent population?

    A simple yes/no would be fine.

  174. Out of curiosity, does anyone know of any data on extinctions categorized by complexity? My hunch is that the extinction rate for more complex organisms is much higher than for less complex organisms, but I am wondering if there have been any studies on this.

  175. Phinehas, that’s a good question.

  176. Acquiesce – with the information you’ve given me, the answer is I don’t know. It depends what other effects the complexity had.

    Look folks, we’re going round in circles, and getting nowhere. I’ve explained why reproductive output isn’t always the best predictor of fitness. I’ve even given you an example where it makes the wrong prediction. I’ve explained about trade-offs: i.e. a reduction in some contributions to fitness can be more than offset by increases in other contributions. Despite much repetition, it’s evident that none of this is sinking in. I’m therefore not going to waste any more time on this.

    I should, though, acknowledge Patrick’s attempt to move the debate on: he at least tried to help the discussion and I appreciate that.

    Bob

  177. Gentlemen:

    Re Bob’s:

    we’re going round in circles, and getting nowhere . . . I’m therefore not going to waste any more time on this.

    Actually, first, the proper image is not a circle but a spiral. We CAN make progress by revisiting key issues and themes incrementally, over and over. (Indeed, this is my favourite curriculum architecture. To see why, reflect on the classic saying that “practice [with correction and learning] makes perfect.”)

    Second, in a debate-type forum, such objective progress may be in a direction that some will not like.

    In this case, that seems to have happened. For, the progress has substantiated the point that NDT has very little robustness relative to challenges from a design-oriented perspective that factors in the implications of the observed functionally specified complex information that is at the heart of life forms.

    So, we can plainly see the above, that there is a reason for this second resort to evasions and distractors, followed by a second walkaway in a matter of a few weeks. The debate on the merits has in effect again been conceded without openly acknowledging that fact.

    So, let us learn from and build on this success.

    [Why not let's itemise lessons learned? My starter: the incrementalist model of complexity through RM + NS runs into trouble once we begin to take apart the underlying assumptions, terms used and proposed dynamics, to look at them closely. The gap between the model dynamics and the fossil record and empirical/simulation data, as well as the issues of information generation through random processes -- as Nei says, in effect NS is not about the arrival of the fittest and so is a secondary force. It is therefore very significant to note how often NDT thinkers promote NS to the primary force level.]

    GEM of TKI

  178. Acquiesce: Do you really think that if I put a mutated ‘more complex’ bacterium – which due to this ‘higher complexity’ reproduced considerably less surviving offspring – into a sample with its parent population that the new trait it carries would fixate into the parent population?

    Bob: with the information you’ve given me, the answer is I don’t know. It depends what other effects the complexity had.

    What ‘other’ effects (i.e. apart from numbers of surviving offspring) are important for NS? In other words, what ‘other’ effects can NS ‘see’ and ‘select’ if they do not impact on the numbers of surviving offspring? What are you talking about?

  179. Bob — I’ve explained why reproductive output isn’t always the best predictor of fitness.

    Bob, the main reason this argument keeps going in circles is because you refuse to provide a definition of what you think is the best predictor of fitness and hence allow us to weigh our notions on your terms.

  180. Another point — some materialists (not necessarily you, Bob) — try to rebut ID with the “no design is bad design” argument.

    Well, it seems that bacteria are basically a perfect means of maintaining the existence of DNA. I guess bacteria should be accepted as slam-dunk proof of a designer for those making the “bad design” claim.

    I’m confident the rest of us will understand that there is beauty in complexity (albeit not fitness) and there is a point to our existence beyond survival of the species.

  181. that should be “bad design is no design”

  182. acquiesce

    I’ve often raised the point that bacteria are the fittest organisms on the planet by nearly any metric – biomass, number, persistence, or ability to survive in environmental extremes.

    Ultimately however bacteria’s long term survival requires space travel. The earth has a finite span of time where it can support life. When that time is up even bacteria will perish. Their survival beyond that time requires locating a suitable new planet and transportation to it.

    So the way I see it humanity is here to provide relocation services so that life doesn’t end when the earth does. I believe this is a cycle that repeats ad infinitum – the earth is neither the first nor the last planet in this cycle. Not only that but it is no accident either. Phyogenesis proceeding to a technological space-faring species is a biological imperative.

  183. Bob,

    In the other thread that kairosfocus has mentioned, you seemed more interested in playing gotcha with word games than in addressing the real issues. Here in this thread, you have hidden behind varying meanings of “fitness” and trying to not only shift the burden of proof, but raise it to a level that doesn’t even make sense. It is difficult to imagine how anyone who is honestly seeking truth would not be able to take a step back and evaluate these two threads and realize that there are some serious questions being asked of NDT, and only evasions are being given in response. I’m just wondering when your love of science and desire to be intellectually honest is going to bring you around to start considering this. Or are presupposed religious beliefs getting in your way?

  184. When that time is up even bacteria will perish.

    There are those who claim they can ride on light beams and live in comets.

  185. What ‘other’ effects (i.e. apart from numbers of surviving offspring) are important for NS? In other words, what ‘other’ effects can NS ‘see’ and ‘select’ if they do not impact on the numbers of surviving offspring? What are you talking about?

    Ditto. Bob?

  186. c’mon Bob. Questions on the table. What say you?

    How about we go for 200 posts?

  187. Sal – assuming a Poisson process, then the proportion that didn’t have a mutation would be e^-1 = 0.37. So there should still be some signal.

    Bob

    THANK YOU!

  188. Bob OH,

    Casey Luskin was soliciting input on that very question (pseudogenes) in his review of Sean Carroll’s Book.

    The Evolutionary Gospel According to Sean B. Carroll

    He would welcome commentary on his pseudogene calculation. I have been unable to reconcile the linear model Casey uses versus something like Jukes-Cantor or the formula you gave.

    My inability to reconcile it tells me there is a subtlety in this part of evolutionary theory which was deep enough in the weeds I did not realize it till now.

    I would welcome your input on Casey’s pseudogene calculation as it does have bearing on our discussion of Nei’s paper.

    I express again my gratitude for your willingness to spend time here at UD defending the non-ID position.

    Though we disagree, I value your input.

    Thanks again!

    Salvador

  189. Hi Trib:

    [Re 179]:

    Bob, the main reason this argument keeps going in circles is because you refuse to provide a definition of what you think is the best predictor of fitness and hence allow us to weigh our notions on your terms.

    Actually, it seems the argument is making spiral-progress at another level: that B seemingly is locked in circles when challenged on terms, assumptions and dynamics implies — or at least strongly suggests – that the NDT patterns of thought are . . . circular.

    For, if there were simple, direct examples of functionally specified complexity and/or irreducible complexity in the Dembski and Behe senses incrementally emerging from the evidence of the fossil or current worlds, they would long since have been trumpeted and placed prominently all over the Internet. This, we do not see, but instead we hear of computer simulations [which are both intelligently designed and do not in fact generate complexity through RM + NS or the like; the smarts being front-loaded by the designers . . .] or else trivial things such as industrial melanism or Finch-beaks on drought-pluvial cycles. Then, a deeper look at the cases usually turns up more questions than answers, sometimes even outright manipulation and/or evident misrepresentation – cf. here, Wells’ Icons. (And note how the issues he raised were responded to – heavy on rhetoric, light on actual credible evidence and reasoned argument, joined to a quiet de-emphasis of the most notorious cases over time.)

    And so, when someone from the Design view publishes on the matter at professional level, e.g. Meyer, we see further evidence that the case is not as advertised: the Editor of the Journal suffered slander and persecution amounting to unjustifiable and indefensible [but not recanted of] career-busting – and he is not even really a Design thinker!

    This sounds more and more like an old Sci Fiction story on how “The Gostak distims the Doshes.” [The protagonist tries to figure out what each term means and only gets as far as finding that each is interpreted in terms of the others, in a circle. Of course it was originally meant as a parody on religion and religious wars, but instead it is telling with ever greater force against the NDT paradigm.]

    Finally as to “bad design is not design . . .” or the like, well, design is design, and we are in no position to assess its “optimality” absent sufficient understanding of the objectives and constraints. E.g. a design that is optimal for one situation may be very brittle once the environment shifts, so some degree of “slack” and even tolerance for defects that come in through random noise may well be wise.

    So, we are moving ever outward on the loops of the spiral . . .

    Having said all that, I join with Sal in expressing appreciation that Bob has tried to engage the issue and has been willing to go through a few loops of the spiral with us.

    GEM of TKI

  190. H’mm: mod piled – was it the link to Icons?

    I note in summary, that we should indeed appreciate Bob’s willingness to go through a few loops of the learning-spiral with us. Also, observing that his lock-in to a circle is evidence that perhaps the root problem is that NDT’s pop genetics models are circular, once their assumptions, dynamics and terms are questioned, and once they are put up against real world evidence from the fossil record and current life in ecosystems.

  191. we are in no position to assess its “optimality” absent sufficient understanding of the objectives and constraints.

    That is true.

    BUT

    For those that claim proof of design requires good design and “good design” requires efficiency, survivability and (hee hee) simplicity — bacteria should be more than enough evidence for them of a designer.

    And dittos for hoping Bob sticks it out.

  192. Dave Scot, that’s an interesting belief. Although without another directional mechanism which foregoes fitness to select for higher complexity, these space travelling bacteria aren’t going to be evolving into humans for the next saga.

    I still await a response from Bob [see post – 178 & 185]

  193. Acquiesce

    I’m just going where the evidence leads. Life surviving by moving to more suitable locations when necessary is universal. The stage was perfectly set for the arrival of an industrial species and we seem to have an instinctive desire for building telescopes, spacecraft, and exploration. Seems a little too pat for an unplanned happenstance.

    Directional mechanisms are inherent in DNA. The single celled egg that you once were contained a plan to diversify itself into scores of cell types, tissue types, and organs with nothing left to chance. That’s ontogenesis – a one-way, pre-planned, self-terminating process of diversification. I propose that phylogenesis was the same kind of process and it has terminated.

  194. Hi DaveScot and Acquiesce,
    Funny Denyse reviewing Tipler right now, as yesterday I wrote (and discarded) a reference to him in response to this conversation.
    Dave’s idea that humanity is a necessity of this universe and our survival reminds me of Tipler’s ideas. He says that humans must and will develop technologies to halt the expansion of the universe. This is a necessity of the future because without it the expansion would entail breaking the laws of physics. Because the laws of physics cannot be broken, the expansion will be stopped, and humans will arrive at the ability to facilitate this.
    The future determines the past in that the necessary and decided outcome must be accommodated by what comes before it.

    As Dave says:

    So the way I see it humanity is here to provide relocation services so that life doesn’t end when the earth does.

    Nothing but teleology and design there.

  195. Returning to the ongoing debate:

    Cancer provides us a good example of both problems with NS I mentioned earlier in this thread. Namely, the selection of abnormal (more reproductively successful – fitter) cells, which have lost the ability to control their own reproduction – they have lost complexity and consequently become fitter. It also provides us evidence that NS leads ultimately to extinction through a blind (especially in foresight) approach to selection.

    In a previous post I mentioned the consequences of a higher organism evolving the enzyme needed to efficiently digest cellulose and convert this into offspring – the long-term results would likely end up producing the extinction of all higher organisms including itself (for the short-term benefit of the species). NS, being unintelligent in its selection policy would blindly select this new trait because the selective value (the numbers of surviving offspring) would increase dramatically.

    Thus, without constructive mutations, basic types of organisms are lost because NS evolves them (through their sub categories) to become increasingly specialized for a certain ecological niche at the expense of their overall generalization. With constructive mutations, NS evolves organisms to greater levels of fitness, producing imbalance and ultimately a total collapse of our ecosystem.

    I still await a response from Bob [see post – 178 & 185]

  196. The trouble with the blind-watchmaker analogy, is that he’s not just blind, but totally devoid of intelligence and foresight: lacking the materials (in the form of constructive mutations) to produce the watch: lacking the functional continuums (requiring his first blind move to produce function – when it cannot): and lacking even the inclination to produce a watch (favouring much simpler, more evolutionarily efficient designs).

  197. [...] Masatoshi Nei is extending Kimura’s ideas to domains outside of molecular evolution. See: Prominent NAS member trashes neo-Darwinism These icons link to social bookmarking sites where readers can share and discover new web [...]

  198. [...] But such baloney goes stale quickly, and after Kimura passed away, Masotoshi Nei came along and dispensed with it. He pointed out if molecular evolution is mostly neutral, so also must be most of evolution! In carefully guarded and diplomatic language he stated it, but essentially trashed Darwinism. See: Prominent NAS member trashes Neo-Darwinism. [...]

  199. [...] But such baloney goes stale quickly, and after Kimura passed away, Masotoshi Nei came along and dispensed with it. He pointed out if molecular evolution is mostly neutral, so also must be most of evolution! In carefully guarded and diplomatic language he stated it, but essentially trashed Darwinism. See: Prominent NAS member trashes Neo-Darwinism. [...]

  200. […] The bottom line is molecular evolution at the nucleotide level must in principle be mostly neutral which means it must be non-Darwinian in principle. If most molecular evolution is non-Darwinian, this strongly suggests most other kinds of evolution must be non-Darwinian! Why should other levels of evolution higher than the molecular level be exempt from the mathematical considerations just laid out? The view that almost all evolution must be non-Darwinian has been advocated by Masotoshi Nei, a fact I pointed out here. […]

  201. […] The bottom line is molecular evolution at the nucleotide level must in principle be mostly neutral which means it must be non-Darwinian in principle. If most molecular evolution is non-Darwinian, this strongly suggests most other kinds of evolution must be non-Darwinian! Why should other levels of evolution higher than the molecular level be exempt from the mathematical considerations just laid out? The view that almost all evolution must be non-Darwinian has been advocated by Masotoshi Nei, a fact I pointed out here. […]

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