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Are Fitness Valleys Too Deep?

Over at PhysOrg.com, there’s a new news item about a computer program that was run simulating evolutionary characteristics. What’s interesting about it are two things: (1) who the people are that are running this program, and (2) one of the results—which is being downplayed, it would seem.

First, one of the people associated with this new program is Christoph Adami, who, with others, gave us the touted “Avida” evolutionary algorithm. So, this isn’t just anybody doing this simulation.

Second, here’s what the lead author had to say:
“These fitness landscapes simply could not be traversed with mutations that did not interact.”

This wasn’t a ‘main conclusion’ of the study; however, I don’t know about you, but this sounds to me like any ‘single’ mutation cannot get you across any fitness valley, and, therefore, seems to rule out having a single mutation ‘sweep’ across a population to fixation.

IOW, without epistatic effects, evolution cannot move forward. This is unexpected. It makes simple neo-Darwinian evolution that more complex with more hurdles to get over. And, it is another nail in the coffin of neo-Darwinism. That is: “Another day, another bad day for Darwinism.”

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72 Responses to Are Fitness Valleys Too Deep?

  1. PaV, as to

    ‘IOW, without epistatic effects, evolution cannot move forward.’

    ,,,But yet we learned a few weeks ago,,,

    New Research on Epistatic Interactions Shows “Overwhelmingly Negative” Fitness Costs and Limits to Evolution – Casey Luskin June 8, 2011
    Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn’t run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
    http://www.evolutionnews.org/2.....47151.html

  2. Is there a mathematically rigorous defintion of “fitness”?

  3. Is there a mathematically rigorous definition of “fitness”?

    Why is one needed?

    The whole idea behind a fitness landscape is that fitness is like a landscape.

    You want a mathematical definition for a landscape? What’s the formula for the Grand Canyon?

  4. Two quick comments:

    (1) For this kind of post, it would be very helpful if an actual link were provided to the news item that the post reports on.
    (2) Maybe it is because I am not a biologist, and am therefore unaware of the internal deliberations of the secret Darwinist cabal, but I find what you describe to be about what I would have expected and therefore not at all surprising. I am not understanding why you would see it as a problem for evolution.

  5. 5

    Pav,
    I found another quote.

    “In reality, many mutations that affect different traits interact with each other, and a single mutation also can affect multiple traits,” he said. “Multiple mutations may actually cooperate to give the organism a bigger boost in fitness than the individual mutations would on their own.”

    http://www.physorg.com/news/20.....d-bad.html

    Interestingly Bjorn Ostman (author of the paper in question I believe) also has this to say:

    When creationists continue to reiterate that evolution is not happening, they are perpetuating some serious misunderstandings of the science involved. Either they honestly do not understand how these things work, or they are knowingly misrepresenting them for the laymen, and I don’t know which is worse.

    The arguments against evolution – obviously based on the faith that Genesis must be true, lest the Bible loses all relevance – are foolish inasmuch as they have been stated many times, but have all been countered by scientists. Some people of faith purposely elect to disregard these arguments, but hopefully other people are more willing to hear what the true workings of evolution are, as much as we know them at this time.

    Among the most foolish ones is the argument that biological complexity cannot increase by way of random changes in DNA. This is completely false, which is quite easily seen, and yet the argument is continually cited in creationist literature (do a google news search for ‘evolution’).

    This argument is made leaving out a crucial factor, namely natural selection. The argument goes that random changes (mutations in the genome/DNA) are most likely to have a deleterious effect on the organism, which will therefore die as a result, and no change in the genome will be perpetuated. For every beneficial mutation, there are many deleterious ones, and overall the effect of beneficial mutations will drown in the adverse effects of deleterious mutations. As a consequence, no new variation can evolve.

    Or so they say. But this is false, and there are no two ways about it.

    The process of acquiring beneficial mutations, many of which will add up in effect to cause a population of organisms to evolve, depends on a second factor – the process of natural selection. Not all the organisms are hit by deleterious mutations. Some are lucky enough to have beneficial mutations – random changes that happen to make them slightly better suited for reproduction. And exactly because they reproduce a little more than average, there will be a higher fraction of organism in the population with that particular change in their genome in the following generations. This is natural selection, and it precisely explains how complexity can increase by the process of random change. Natural selection transforms the random process of mutation into a deterministic process.

    The problem in this debate is of course that science claims as its domain anything that the scientific method can be applied to. This means there is an overlap with a literal reading of the Bible (specifically Genesis 1 and 2). Those who have the faith (i.e. a strong belief in God, which can be overcome by no amount of rationality) will of course not let this happen, and only because of this technicality do the creationists object in the first place. Not because they were doing science, which happened to show that evolution does not occur. They got the conclusion first, and have secondly gathered their so-called scientific evidence to arrive at this predetermined conclusion in numerous books and papers, and recently in a creationist museum.

    This debate so tedious, there is no denying that. But it will go as with Galileo and the heliocentric system: eventually everybody in their right mind will come around, and this will no longer be something sane people will spend any time debating any more.

    Bjorn Ostman

    http://www.bestsyndication.com.....lution.htm

    So I guess if you asked him about his work that you present in this thread he’d disagree with your conclusions!

  6. 6

    I heard a rumor that neo-Darwinism has got itself a job selling nails!

    It gets them for free after all.

  7. 7
    Elizabeth Liddle

    Well, no, it a “bad day for Darwinism”, PaV.

    I assume the paper you are referring to is this one:

    http://rspb.royalsocietypublis.....f7b3ba276c

    Firstly, yes, fitness landscapes can (and do) have deep valleys. But it’s a great mistake to think of a “fitness landscape” as a landscape in only 1 or 2 dimensions (well, 2 or 3 if you include the vertical dimension).

    As a way of envisaging this: imagine 1D “landscape, with one dimension along the horizontal axis, and height (fitness) on the vertical. If a population moves along the horizontal axis (perhaps it represents “ability to detect shadows”, it may climb a little hill – then across a deep valley there is a tall cliff. It cannot hope to scale the cliff, even if it could traverse the valley.

    Now add a second horizontal dimension – perhaps the ability to protect its light sensitive patches with a translucent gel. And the landscape (possibly) may be very different – instead of the only route to being down a valley then up a sheer cliff, there may a gentle ramp from the top of the little hill, back into the picture, and up to the cliff top – the landscape is now revealed to be a combe (or that’s what we call them here).

    Now, imagine (which is hard) many many dimensions. Yes there will be valleys, but there are many ways of getting across them by traversing different dimensions.

    However, this is all very abstract.

    The paper itself (lucky me, I have access to the whole thing – if you want a copy, PM me at Talk Rational (I’m Febble) with your email) is an investigation, using computer modeling, about the kind of fitness landscape that best promotes fitness in asexually reproducing organisms (recall that most multicellular organisms reproduce sexually) where mutations can have epistatic effects (interact with other genes) and pleiotropic effects (affect more than one trait). Once you include these effects in your model, you get a much more complex fitness landscape.

    Interestingly, they find that, contrary to expectations (and as in my simplistic example above), highest fitness was obtained in a moderately rugged landscape – better than in a smooth, ramped landscape. Above a certain value of “ruggedness”, there was a slight decline in max fitness, though not to baseline.

    So actually the conclusion isn’t that valleys are a problem, but that they actually help. To quote from the discussion section:

    Ruggedness is normally viewed as an impediment to adaptation, because the presence of valleys means that a lineage has to suffer a decrease in fitness before it can gain a fitness advantage. However, in the NK model, increased ruggedness not only translates into more peaks to ascend and more valleys to cross, but also increases both the fitness difference between the peaks and the valleys (amplitude) and the height of the global peak. The attained fitness is maximal atK ¼ 3 to 5, from which we infer that an intermediate amount of epistasis and pleiotropy is most conducive to adaptation.

    Joseph: Yes there is a mathematically rigorous definition of “fitness”. It comes in two flavours: absolute; and relative. The “absolute fitness” of a genotype is defined as the ratio between the frequency of the genotype in one generation the frequency in the next. “Relative fitness” is defined in as the ratio between the average number of surviving progeny of one genotype and the average number of another.

    So an “absolute fitness” of 1 means that the genotype is neutral. A value between zero and 1 means it is deleterious and a value greater than 1 means that it is beneficial.

    For “relative fitness”, a value of one means the two genotypes have equal fitness.

    It is always calculated between one generation and the next, because fitness is always (whether relative or absolute) calculated for the current environment. Because changes in allele frequency in the population is itself a change in the environment, what is beneficial in one generation may be neutral, or even deleterious, in the next.

    Also “fitness” doesn’t mean anything about how much fun you have :) It is just to do with how many progeny you leave. So having lots of accidental pregnancies may not make the individual woman fitter (it may be a real nuisance) but if a good number survive, she is, in population genetics terms, “fitter” then the woman next door who has one child then got her tubes tied rather than have any more.

    Hope that helps. I’m not trying to argue for evolution here (though I do elsewhere) just trying to explain some of the concepts :)

  8. WilliamRoache, perhaps you can get your guy to falsify this:

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

  9. I’d say that neo-Darwinism has ‘deep valleys’

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

    Evolution vs. Functional Proteins – Doug Axe – Video
    http://www.metacafe.com/watch/4018222

    Doug Axe Knows His Work Better Than Steve Matheson
    Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance.
    http://www.evolutionnews.org/2.....35561.html

    ID Scientist Douglas Axe Responds to His Critics – June 2011 – Audio Podcast
    http://intelligentdesign.podom.....9_43-07_00

    etc.. etc.. etc..

  10. WilliamRoache, while you are getting your guy to try to falsify ID by traversing universe wide oceans of sequence space looking for those sparse islands of functional proteins, perhaps you can get him, in his spare time if he is not too busy, to explain the finding of ‘non-local’ quantum information in molecular biology in neo-Darwinian terms.

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

    Falsification of neo-Darwinism;

    First, Here is the falsification of local realism (reductive materialism).

    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:

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

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

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

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    And yet, quantum entanglement, which rigorously falsified local realism (reductive materialism) as the complete description of reality, is now found in molecular biology on a massive scale!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    Untangling the Quantum Entanglement Behind Photosynthesis – May 11 2010
    Excerpt: “This is the first study to show that entanglement, perhaps the most distinctive property of quantum mechanical systems, is present across an entire light harvesting complex,” says Mohan Sarovar, a post-doctoral researcher under UC Berkeley chemistry professor Birgitta Whaley at the Berkeley Center for Quantum Information and Computation. “While there have been prior investigations of entanglement in toy systems that were motivated by biology, this is the first instance in which entanglement has been examined and quantified in a real biological system.”
    http://www.sciencedaily.com/re.....151356.htm

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time
    and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!
    ,,,To refute this falsification of neo-Darwinism, one must falsify Alain Aspect, and company’s, falsification of local realism (reductive materialism)!

    ,,, As well, appealing to ‘non-reductive’ materialism (multiverse or many-worlds) to try to explain quantum non-locality in molecular biology ends up destroying the very possibility of doing science rationally;

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    ,,,Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.

    “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook

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

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

  11. To dovetail into Dembski and Marks’s work on Conservation of Information;,,,

    LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information
    William A. Dembski and Robert J. Marks II
    http://evoinfo.org/publication.....ation-law/

    ,,,Encoded classical information, such as what we find in computer programs, and yes as we find encoded in DNA, is found to be a subset of ‘transcendent’ quantum information by the following method:,,,

    This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy.
    Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    And here is the empirical confirmation that quantum information is ‘conserved’;

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

  12. William Roache:

    So I guess if you asked him about his work that you present in this thread he’d disagree with your conclusions!

    First of all, the link is fixed.

    Second, I was focusing on what the lead author said, not his conclusions in the paper.

    Third, the finding that the fitness valleys could not be “traversed” is significant.

    You’ve placed a rather extended quote in your post (which will be deleted the next time it happens—we don’t need anything of that length that doesn’t apply directly) which simply tells us of the bias of the lead author. That only makes his concession all that more remarkable.

    Just think about what he has said: a mutation occurs; it’s a beneficial mutation; and, yet, one cannot get from one fitness peak to another. IOW, it cannot lead the way to a subspecies being formed. To you this may not be a big thing, but this is NOT how evolution has always been thought to work.

    This is a big concession. A newer, presumably more probing, simulation is run. And, normal, easy, straightforward steps cannot be taken.

    As BA77 has shown, we just recently have seen that epistasis is limited in its effects.

    In toto, this means that fitness “islands” remain “fitness islands”.

    Our authors may want to tell us how important epistasis and pleiotropy is, but not being able to cross over to another fitness landscape with a single, non-interacting mutation, is a limitation of neo-Darwinism. And, as is usual, they are only willing to talk about it because they think other parts of their work are interesting.

  13. EL:

    Now, imagine (which is hard) many many dimensions. Yes there will be valleys, but there are many ways of getting across them by traversing different dimensions.

    However, “crossing” any of these “dimensions” cannot be brought about by any single, non-interacting mutation. This runs counter to simplistic neo-Darwinian thought wherein single mutations sweep through populations, and, as these mutations become ‘fixed’, increases in ‘fitness’ until such time that a ‘new species’ arises.

    This doesn’t help the Darwinian model.

  14. I want to know how, having gone into another dimension, they get back into this one.

  15. 15
    Elizabeth Liddle

    But PaV, I’m not sure where you’re getting that “simplistic neo-Darwinian” thought from!

    It’s nothing like any evolutionary theory I’ve ever heard of!

    Do you really think that “Darwinian” (or “neo-Darwinian”) theory posits that:

    single mutations sweep through populations, and, as these mutations become ‘fixed’, increases in ‘fitness’ until such time that a ‘new species’ arises.

    ?

    Because if so, I’m not surprised that you think it’s bunk!

    It is!

    Do you have any source for the position you described? I’d dearly like to know where you got it!

  16. BA 77:

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

    That’s a couple of galaxies over.

    GEM of TKI

  17. F/N: Co-ordinated mutations to gain a benefit? Isn’t that just a tad suspicious?

  18. Why Elizabeth, Dr. Sternberg speaks of such right here:

    Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology – video
    http://www.metacafe.com/watch/4165203/

  19. 19
    Elizabeth Liddle

    Sorry, ba77, that video won’t play for me. Can you link me to Dr Sternberg’s written papers?

  20. 20
    Elizabeth Liddle

    OK, I found it – Dr Sternberg is not saying that

    single mutations sweep through populations, and, as these mutations become ‘fixed’, increases in ‘fitness’ until such time that a ‘new species’ arises

    .

    From the sound of it, he isn’t even a neo-Darwinist.

    I would like to know where PaV got the idea that the above was an example of “neo-Darwinist thought”.

    I have never heard anyone propose that, let alone a neo-Darwinist. Dr Sternberg certainly isn’t proposing it.

    So who is?

  21. EL:

    Do you have any source for the position you described? I’d dearly like to know where you got it!

    The reality is that Darwinists don’t have a way of explaining how speciation takes place in any kind of mathematically rigourous fashion. I have found no explanation for how new species arise given neo-Darwinian thinking.

    Perhaps you can point me in that direction. Give me some sort of resource.

    Now, there are lots of attempts at explaining how new species arise; but they all end up floundering. So, surprise me!

  22. Sorry Elizabeth, you’ll just shrug it off anyway as you always do, so I think I’ll go have a bite instead!

  23. 23
    Elizabeth Liddle

    PaV:

    The reality is that Darwinists don’t have a way of explaining how speciation takes place in any kind of mathematically rigourous fashion. I have found no explanation for how new species arise given neo-Darwinian thinking.

    Perhaps you can point me in that direction. Give me some sort of resource.

    Now, there are lots of attempts at explaining how new species arise; but they all end up floundering. So, surprise me!

    OK, fair enough! But first let’s deal with a couple of straw men:

    The idea that beneficial mutations sweep through populations in sequential waves until they become “fixed” is simply not a hypothesis I’ve ever met, and is certainly not supported by any evidence.

    Yes, eventually some mutations do become fixed (as, interestingly, do some neutral mutations as well as slightly deleterious ones, but beneficial ones are more likely to go to fixation).

    A better mental picture of the neo-Darwinist (if I must use that term! Not sure I like it because I’m not anti-Margulis for instance) is of lots of nearly-neutral mutations occurring all the time i.e. new alleles appearing all the time, some of which result in a slightly fitter genotype, some a slightly less fit genotype, but, as I tried to convey in my response to Joseph above, the concept of fitness is always in relation to a single generation, and what is slightly beneficial in one generation may be slightly deleterious in another.

    Not only that, but as the article in your OP illustrates (nice article by the way!) the fitness conferred by a single mutation doesn’t just depend on the current external environment, it also depends on the genes it shares an organism with. And while the article referenced in the OP concerns asexually reproducing species (which are a rather special case) things get rather more complicated in sexually reproducing species, because they have the great advantage of being able to “mix and match” genes within genotypes.

    So what we have, in a given population, is a great many genotypes (i.e. lots of alleles, none of which are, by definition, “fixed”) all being swapped around with each new generation, and the ones that tend to promote successful progeny become more common and the ones that don’t become less common, although which ones do what will tend to change even from generation to generation, and certainly as the external environment changes.

    So the kind of “sweep” that occurs is not that a single mutation “sweeps” through the population, but that there are lots of different alleles, and that the frequency distribution of each allele changes from generation to generation, the ones that tended to be associated with more progeny increasing in frequency, and the ones that tended to be associated with fewer, reducing.
    And so the mean fitness of the population tends to optimise with the alleles that contribute to the most successful gene cocktails (aka genotypes) in that environment, at that time, becoming the most frequently. Over time, the least successful alleles may drop out of the gene pool altogether, and, if they are ever needed again, will have to mutate ab initio (which occasionally happens).
    But that isn’t “speciation” – that’s simply adaptation.
    Speciation happens when a population diverges for some reason, into two populations that don’t, or rarely interbreed, for example if they become separated by a mountain range, or a stretch of water. When that happens, adaptation continues, but the environmental history of the two populations will change – one side of the mountain may be drier than the other, or there may be different predators.

    And, because the two populations are now adapting independently to environmental changes, they will not only tend to differ from their ancestral populations, but also from each other, to the point where they could not interbreed even if the barrier between them was removed.

    And it is this divergent adaptation that we call “speciation”.
    Adaptation is what happens down a single lineage; speciation is the process by which one population lineage diverges into two.

    Again, I’m not trying to convince you that this happens – merely explain what it is that “evolutionists” actually envisage happening :)

  24. “As BA77 has shown, we just recently have seen that epistasis is limited in its effects.”

    Wait, is that in reference to the paper “Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population,” which Tim Cooper himself posted here to correct the misunderstanding of?

    http://www.uncommondescent.com.....ent-384735

    You might want to read the paper, and dialogue with the authors. I say this because I have read the paper, and find this post somewhat puzzling. There are some unjustified leaps in logic.

    Bjørn Østman blogs here:

    http://pleion.blogspot.com/201.....cross.html

  25. Elizabeth Liddle:

    I would like to know where PaV got the idea that the above was an example of “neo-Darwinist thought”.

    I review of your own posts might be informative.

    Do you dispute that beneficial mutations occur?

    Do you dispute that those mutations which increase in frequency in future generations of the population are by definition beneficial. (Except when they aren’t.)

    Do you dispute that according to population genetics models these mutations will increase in the population to the point where they become fixed?

    Do you dispute that this is the process by which one species is changed into another species?

    Do you dispute that all the above is neo-darwinian theory?

    Give us break Elizabeth, really.

  26. Yet another note on the incoherence of modern evolutionary theory

    ME: Do you dispute that those mutations which increase in frequency in future generations of the population are by definition beneficial. (Except when they aren’t.)

    Elizabeth: Yes, eventually some mutations do become fixed (as, interestingly, do some neutral mutations as well as slightly deleterious ones, but beneficial ones are more likely to go to fixation).

    Now since it is clear that both neutral and deleterious mutations can become fixed, one cannot simply look at the frequency of a mutation and whether it is increasing to determine that a mutation is beneficial.

    One cannot simply assume from the presence of a fixed mutation that it was fixed because it was beneficial.

    So what then is a beneficial mutation? How do we tell?

  27. arg, i just read that over. It makes it look like Elizabeth was answering yes to a question I was asking. That is not the case. Sorry about that.

  28. And DrREC, in your ‘unbiased’ neo-Darwinian world-view, exactly how are we to take these results???

    Mutations : when benefits level off – June 2011
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    ,,,so DrREC, in your ‘unbiased’ neo-Darwinian world-view, these 5 mutations, which were gathered after 50,000 generations (equivalent to 1,000,000 years of proposed human evolution) when combined, producing ‘less’ of a benefit, is not a problem at all??? Does the fact that they were not truly ‘beneficial’ in terms of building functional molecular complexity matter to you at all???

    Michael Behe’s Quarterly Review of Biology Paper Critiques Richard Lenski’s E. Coli Evolution Experiments – December 2010
    Excerpt: After reviewing the results of Lenski’s research, Behe concludes that the observed adaptive mutations all entail either loss or modification–but not gain–of Functional Coding ElemenTs (FCTs)
    http://www.evolutionnews.org/2.....41221.html

    Lenski’s e-coli – Analysis of Genetic Entropy
    Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment.
    http://www.answersingenesis.or.....n-bacteria

    Moreover DrREC, for those of us not predisposed to look at the world through Darwinian glasses, this negative return on ‘benefit’ is to be expected because of the poly-constraint to evolvability brought on by the poly-functionality of the classical information encoded onto DNA;

    Poly-Functional Complexity equals Poly-Constrained Complexity
    http://docs.google.com/Doc?doc.....Zmd2emZncQ

    DNA – Evolution Vs. Polyfuctionality – video
    http://www.metacafe.com/watch/4614519

  29. 29
    Elizabeth Liddle

    Mung:

    Elizabeth Liddle:

    I would like to know where PaV got the idea that the above was an example of “neo-Darwinist thought”.

    I review of your own posts might be informative.

    Do you dispute that beneficial mutations occur?

    No, of course not. However, I would point out (AGAIN!) that a “beneficial” means “in relation to the current environment.

    Therefore, the same allele may be beneficial in one generation and deleterious in the next. It isn’t a property of an allele, but of an allele-within-the-current-environment.

    Hence the concept of “adaptation”.

    Do you dispute that those mutations which increase in frequency in future generations of the population are by definition beneficial. (Except when they aren’t.)

    Yes, I do dispute that. You said “generations” plural. Beneficial only refers to the change in frequency between two generations. So your parenthesis is irrelevant. Some alleles may oscillate between beneficial and deleterious by the generation (read The Beak of the Finch if you haven’t already).

    You are seeing inconsistencies in my posts not because they are inconsistent but because you consistently misread them :)

    Do you dispute that according to population genetics models these mutations will increase in the population to the point where they become fixed?

    No, but that is because many population genetics models make gross simplifying assumptions (like setting a selection coefficient as a fixed property of an allele, rather than as a variable that may itself be modulated by allele frequency.

    Certainly some alleles do become fixed. But many (most?) genes have polymorphisms. What is far more important is the other end – that some alleles drop right out of the gene pool.

    Do you dispute that this is the process by which one species is changed into another species?

    Yes. One species is never “changed into another species”. You are confusing speciation with adaptation.

    Populations speciate when they diverge (and, usually, adapt as well). Populations adapt when their allele frequencies adjust to optimise survival in a changing environment.

    You can have adaptation over time without speciation; you can have speciation where one lineage undergoes conservative evolution (i.e. remains very similar to the ancestral population) while the other adapts to become very different.

    But that doesn’t mean that “one species changed into another”. It means, simply, that the population split and adapted independently.

    Do you dispute that all the above is neo-darwinian theory?

    Most of it. But, as my then-eight-year-old once said about his teacher who knew less about zoology than he did, “fortunately I was able to put her right”.

    Now, I’m happy to defend any of the above against challenges to its likelihood, but I hope that at least we have put to rest the straw man of evolution that I’m supposed to have espoused :)

    Give us break Elizabeth, really.

    Glad to have been able to help :)

  30. El,

    ‘Yes, eventually some mutations do become fixed (as, interestingly, do some neutral mutations as well as slightly deleterious ones, but beneficial ones are more likely to go to fixation).’

    and yet in the real world we have,,,:

    spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

  31. El,, ‘No, of course not. However, I would point out (AGAIN!) that a “beneficial” means “in relation to the current environment.’

    Of course you mean that for you have no evidence of ‘beneficial’ in regards to actually building functional complexity!!!!

  32. 32
    Elizabeth Liddle

    Mung:

    So what then is a beneficial mutation? How do we tell?

    Excellent question. The short answer: we can’t easily, we can only infer, statistically, that there must be a distribution from very beneficial to very deleterious. But near neutrality you can’t tell which is which, and of course most mutations are near neutrality.

    The only method I know of to do it unambiguously is Lenski’s with E-coli, because not only does he have lots of lineages from a single ancestral population, but he can actually thaw out clones from that ancestral population and compare each lineage with its forebears.

    Other than that, linkage studies are the only way I know.

  33. El,

    shoot let’s really expand the research and see what evolution can do for the biggest ‘worldwide’ experiments that can be performed:L

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....hes_t.html

    The Sheer Lack Of Evidence For Macro Evolution – William Lane Craig – video
    http://www.metacafe.com/watch/4023134

  34. Kairosfocus, actually a ‘couple of galaxies away’ is far too generous for it only takes into consideration a single protein fold,, whereas:

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    ,,, Kairos, the closest comparison I could find for putting any meaning to the number 1 in 10^159 is this;

    The Case for Jesus the Messiah — Incredible Prophecies that Prove God Exists By Dr. John Ankerberg, Dr. John Weldon, and Dr. Walter Kaiser, Jr.
    Excerpt: But, of course, there are many more than eight prophecies. In another calculation Stoner used 48 prophecies (even though he could have used 456) and arrived at the extremely conservative estimate that the probability of 48 prophecies being fulfilled in one person is one in 10^157.
    How large is the number 10^157? 10^157 contains 157 zeros! Let us try to illustrate this number using electrons. Electrons are very small objects. They are smaller than atoms. It would take 2.5 times 10^15 of them, laid side by side, to make one inch. Even if we counted four electrons every
    second and counted day and night, it would still take us 19 million years just to count a line of electrons one inch long.
    But how many electrons would it take if we were dealing with 10^157 electrons? Imagine building a solid ball of electrons that would extend in all directions from the earth a length of 6 billion light years. The distance in miles of just one light year is 6.4 trillion miles. That would be a big ball! But not big enough to measure 10^157 electrons.
    In order to do that, you must take that big ball of electrons reaching the length of 6 billion light years long in all directions and multiply it by 6 x 10^28! How big is that? It’s the length of the space required to store trillions and trillions and trillions of the same gigantic balls and more. In fact, the space required to store all of these balls combined together would just start to “scratch the surface” of the number of electrons we would need to really accurately speak about 10^157.
    But assuming you have some idea of the number of electrons we are talking about, now imagine marking just one of those electrons in that huge number. Stir them all up. Then appoint one person to travel in a rocket for as long as he wants, anywhere he wants to go. Tell him to stop and segment a part of space, then take a high-powered microscope and find that one marked electron in that segment.
    What do you think his chances of being successful would be? It would be one in 10^157.
    Remember, this number represents the chance of only 48 prophecies coming true in one person (there are 456 total prophecies concerning Jesus).
    http://www.johnankerberg.org/A.....1103-3.pdf

  35. 35

    When the strawman tactics of Bjorn Ostman are striken, his argument settles back down to earth, to something actually debatable, that many find demonstrably lacking in certain aspects. Notice that the strawmen are loaded into the top, and bottom of the post, nicely insulating the actual argument. Quaintly tucking it away so that by the time you get to it, many of the laymen will have already concluded the he is the man of reason and his opponents are ignorant fanatics.

    Strawmen Strucketh:

    When creationists continue to reiterate that evolution is not happening, they are perpetuating
    some serious misunderstandings of the science involved. Either they honestly do not understand
    how these things work, or they are knowingly misrepresenting them for the laymen, and I don’t
    know which is worse.

    The arguments against evolution – obviously based on the faith that Genesis must be true,
    lest the Bible loses all relevance – are foolish inasmuch as they have been stated many times,
    but have all been countered by scientists. Some people of faith purposely elect to disregard
    these arguments, but hopefully other people are more willing to hear what the true workings of
    evolution are, as much as we know them at this time.

    Among the most foolish ones is the argument that biological complexity cannot
    increase by way of random changes in DNA. This is completely false, which is quite easily seen,

    and yet the argument is continually cited in creationist literature (do a google news search for ‘evolution’).


    This argument is made leaving out a crucial factor, namely natural selection. The argument
    goes that random changes (mutations in the genome/DNA) are most likely to have a deleterious
    effect on the organism, which will therefore die as a result, and no change in the genome
    will be perpetuated. For every beneficial mutation, there are many deleterious ones, and
    overall the effect of beneficial mutations will drown in the adverse effects of deleterious
    mutations. As a consequence, no new variation can evolve.

    Or so they say. But this is false, and there are no two ways about it.

    The process of acquiring beneficial mutations, many of which will add up in effect to cause
    a population of organisms to evolve, depends on a second factor – the process of natural
    selection. Not all the organisms are hit by deleterious mutations. Some are lucky enough
    to have beneficial mutations – random changes that happen to make them slightly better
    suited for reproduction. And exactly because they reproduce a little more than average,
    there will be a higher fraction of organism in the population with that particular change
    in their genome in the following generations. This is natural selection, and it precisely
    explains how complexity can increase by the process of random change. Natural selection
    transforms the random process of mutation into a deterministic process.

    The problem in this debate is of course that science claims as its domain anything that the
    scientific method can be applied to. This means there is an overlap with a literal reading
    of the Bible (specifically Genesis 1 and 2). Those who have the faith (i.e. a strong belief
    in God, which can be overcome by no amount of rationality) will of course not let this happen,
    and only because of this technicality do the creationists object in the first place. Not because
    they were doing science, which happened to show that evolution does not occur. They got the
    conclusion first, and have secondly gathered their so-called scientific evidence to arrive at
    this predetermined conclusion in numerous books and papers, and recently in a creationist
    museum.

    This debate so tedious, there is no denying that. But it will go as with Galileo and the
    heliocentric system: eventually everybody in their right mind will come around, and this will
    no longer be something sane people will spend any time debating any more.

  36. Elizabeth Liddle:

    Yes, eventually some mutations do become fixed (as, interestingly, do some neutral mutations as well as slightly deleterious ones, but beneficial ones are more likely to go to fixation).

    So, in addition to “beneficial” mutations sweeping through the population I should have said that “deleterious” and “neutral” mutations sweep through the population (but at lesser rates)?

    So, per this logic, Darwinian evolution depends on neutral (no selective value) and deleterious (negative selection factor) mutations. How does this help?

    Here’s what the lead author wrote per William Roache: The process of acquiring beneficial mutations, many of which will add up in effect to cause
    a population of organisms to evolve
    , depends on a second factor – the process of natural
    selection.

    A better mental picture of the neo-Darwinist (if I must use that term! Not sure I like it because I’m not anti-Margulis for instance) is of lots of nearly-neutral mutations occurring all the time i.e. new alleles appearing all the time, some of which result in a slightly fitter genotype, some a slightly less fit genotype, but, as I tried to convey in my response to Joseph above, the concept of fitness is always in relation to a single generation, and what is slightly beneficial in one generation may be slightly deleterious in another.

    I suspected you would come up with Kimura’s “Neutral Theory”. But, Lizzie, the neutral theory is not Darwinian. Kimura invented the neutral theory because of the radical inadequacy of Darwinian (Modern Synthesis) theory to explain newly discovered rates of polymorphism, rates which were staggeringly higher than ‘theory’ predicted.

    So the kind of “sweep” that occurs is not that a single mutation “sweeps” through the population, but that there are lots of different alleles, and that the frequency distribution of each allele changes from generation to generation, the ones that tended to be associated with more progeny increasing in frequency, and the ones that tended to be associated with fewer, reducing.
    And so the mean fitness of the population tends to optimise with the alleles that contribute to the most successful gene cocktails (aka genotypes) in that environment, at that time, becoming the most frequently. Over time, the least successful alleles may drop out of the gene pool altogether, and, if they are ever needed again, will have to mutate ab initio (which occasionally happens).
    But that isn’t “speciation” – that’s simply adaptation.
    Speciation happens when a population diverges for some reason, into two populations that don’t, or rarely interbreed, for example if they become separated by a mountain range, or a stretch of water. When that happens, adaptation continues, but the environmental history of the two populations will change – one side of the mountain may be drier than the other, or there may be different predators.

    And, because the two populations are now adapting independently to environmental changes, they will not only tend to differ from their ancestral populations, but also from each other, to the point where they could not interbreed even if the barrier between them was removed.

    And it is this divergent adaptation that we call “speciation”.
    Adaptation is what happens down a single lineage; speciation is the process by which one population lineage diverges into two.

    So, based on this argument, FIRST,there are no differences between adaptation and speciation. SECOND, it is purely qualitative and, so, speculative. And, THIRD, where is Natural Selection mentioned in any of this?

  37. Elizabeth Liddle:

    Certainly some alleles do become fixed. But many (most?) genes have polymorphisms.

    Ah. Thanks for reminding me. You’ve mentioned polymorphisms a number of times.

    Each time I’ve asked how you explain them.

  38. 38
    Elizabeth Liddle

    You mean explain what polymorphisms are? Or explain how they arise?

    I’ll assume the latter and get back to you later. There are lots of known mechanisms.

  39. Joseph @2:

    Fintess is understood as the degree of adaptation to the environment. I do not see any problem with this. One of the inherent problems of Darwinism in my opinion is not here but in the curse of dimensionality: the probabilistic resources of the world seemingly are not enough to explain the diversity of life. Stuart Kauffman talks about coevolving landscapes, i.e. he hypothesises that as time progresses the landscapes change, but that is too much to accept at such a grand scale. Microevolution is observed and consequently I can accept Kauffman’s theory of antichaos, but only to the extent of microevolution (microadaptations of available forms). You cannot get over the chasms of chaos and preserve life. There are other practical limits to macroevolution such as the number of mutations of paralogous genes.

  40. 40
    Elizabeth Liddle

    Eugene S:

    Fintess is understood as the degree of adaptation to the environment. I do not see any problem with this.

    Excellent :)

    One of the inherent problems of Darwinism in my opinion is not here but in the curse of dimensionality: the probabilistic resources of the world seemingly are not enough to explain the diversity of life.

    What does that have to do with “dimensionality”? We know that there are countless dimensions along which populations can evolve (size, camouflage, predictive ability, toxicity, energy efficiency, as well as feedback loops that involve evolution along such odd dimensions as “a more spectacular tail”). What resources do you consider limit these dimensions?

    Stuart Kauffman talks about coevolving landscapes, i.e. he hypothesises that as time progresses the landscapes change,

    Yes indeed. Sexual dimorphism is a good example of this.

    but that is too much to accept at such a grand scale.

    Why?

    Microevolution is observed and consequently I can accept Kauffman’s theory of antichaos, but only to the extent of microevolution (microadaptations of available forms). You cannot get over the chasms of chaos and preserve life.

    Why not? Are you sure? Which chasms are you thinking of?

    There are other practical limits to macroevolution such as the number of mutations of paralogous genes.

    Why is there a practical limit to the number of mutations of paralogous genes?

  41. junkdnaforlife @35:

    That is all fine with the exception of practical bounds on time and other resources available at time 0. In my opinion, this reasoning fits only microevolution. In other words, I am happy with the random mutation + natural selection scenario starting off in an initial state with some already existing forms.

    It could have been plausible on a greater scale (to allow for new species or higher taxinomic ranks), if it had been practically possible. Practical research shows insurmountable difficulties for macroevolution.

  42. Elizabeth,

    I hope comment #41 explains it already. In case it does not, basically, by the resources I mean time and the initial pool of genes (initial diversity, initial information). By the chasms I mean chaos. In biology chaos essentially means death or deleterious mutations. I can refer you to Stuart Kauffman “Antichaos and Adaptation”, Sci. American, 1991, pp.78-84. The paper is available online (you can find a link to it on Wikipedia).

    I am not a biologist, I have an engineering background which allows me to doubt the plausibility of macroevolution, esp. in light of the works of Behe, Axe (esp. the one where he showed tight limits on the number of deleterios mutations possible in bacteria), Gauger and others in biology and information theoretic work of Dembski.

    My thoughts laid out in detail can be found here:

    http://orthodoxchristian-blogg.....chive.html

    I am citing all the mentioned works there.

  43. Elizabeth,

    “Why is there a practical limit to the number of mutations of paralogous genes?”

    Possibly because various mutations do not go together well.

    Broadly speaking, I don’t know why such and other limits to macroevolution should exist. It just so happens.

    Practice is a good measure of the validity of any theory. E.g. speciation has not been observed in earnest at all: either in real time in bacteria or in retrospect in fossils.

    Of course, we can hypothesise to our hearts’ content but practical science must be realistic :)

  44. Elizabeth (29)

    One species is never “changed into another species”. You are confusing speciation with adaptation.

    I thought he meant something like a frog evolving into the next version (species) of that frog, not a frog evolving into a different frog that already exists.

    Certainly some alleles do become fixed. But many (most?) genes have polymorphisms. What is far more important is the other end – that some alleles drop right out of the gene pool.

    What do you mean by “far more important” in this context?

  45. 45
    Elizabeth Liddle

    uoflcard:

    Well, it’s an important distinction, I think – “species” is a horizontal concept, not a vertical one.

    The simplest definition of a species is an “interbreeding population”, and “two different species” are “species that do not interbreed”. Obviously a population cannot interbreed with its long-dead ancestors! But that doesn’t mean it is a different species to them. It’s just not a concept relevant to longitidinal differences.

    So a population of frogs that evolves into a rather different looking/behaving population of froggy things hasn’t “evolved into a new species of frog”. It has simply evolved. It has even evolved if it stays the same! (Evolutionary processes can also act to conserve optimal adaptive traits).

    That’s why dogs will never evolve into cats. In fact, dogs will never evolve into not-dogs, if “dog” is regarded as taxonomic category.

    What do you mean by “far more important” in this context?

    Good question. What I meant was that once an allele has vanished from a population (the last bearer has died) that allele has gone for good. And if it once conferred an advantage – perhaps it assisted night vision) – but stopped being beneficial because the population underwent an adaptation that involved sleeping through the night hours. So the allele is now not beneficial and so drifted out to extinction i.e. it is lost for good.

    That matters, because now, if the population finds itself in a environment where good night vision would have helped, it will either face extinction, or have to adapt in some other way.

    But there may be many other alleles of once-night-vision-conferring allele, and none of these may go to fixation because they are neutral, or even slightly beneficial for some other purpose. Or may simply be non-functional. So what matters is that the potentially useful allele was lost, not that some other allele of the same gene went to fixation (which it may or may not have done).

    Once an allele is gone, it is not “selectable” obviously. So the population then is ratcheted out of the zone in which that allele was potentially advantageous.

    The poster child of course is the Vitamin C gene – the good allele dropped out of the great ape gene pool, so if we ever find ourselves in an edible fruit-poor environment we may face extinction, unless another allele appears that does the same job, or we find a work-around.

    But so far, apes (which include us!) are stuck with fruit-dependency!

  46. Elizabeth,

    I have been carefully reading your comment #7 about fitness landscapes. Let me first ask a question about fitness landscapes. What does a steep cliff imply? Reading different resources, I seem to see two very different possibilities:

    1.) If seen as a 3-D graph, with the z-direction being vertical, the x-y plane can be seen as genetic mutations and the z-axis is the fitness. So if you’re standing at the base of a steep cliff, a slight change in the x-y plane (i.e. a slight change to a genome) can result in you now being on top of the cliff (i.e. a huge increase in fitness).

    2.) Translation within the 3-D system is accomplished with step-by-step changes, like hiking in a mountain range. You cannot “walk” up a cliff, therefore you need to find the gentle slopes to reach the higher elevations.

    I’ve always been under the impression that it is #2, but I wanted to confirm that you agreed with that before I went further. Thanks for the response, if you have the opportunity.

  47. 47
    Elizabeth Liddle

    Eugene S:

    Elizabeth,

    “Why is there a practical limit to the number of mutations of paralogous genes?”

    Possibly because various mutations do not go together well.

    Broadly speaking, I don’t know why such and other limits to macroevolution should exist. It just so happens.

    Well, that’s what I’m asking you about – how do you know it “so happens”? Because I don’t see any reason why it should NOR evidence that it does!

    What are you basing your claim on?

    Practice is a good measure of the validity of any theory. E.g. speciation has not been observed in earnest at all: either in real time in bacteria or in retrospect in fossils.

    Well, I notice you put “in earnest” in there :) Yes, speciation has been observed, both in the field and in the lab i.e. populations have been observed to diverge so far as to no longer be able to interbreed. That’s fairly “earnest”.

    And while speciation is difficult to observe in the inevitably gappy fossil record, we can still derive phylogenies that trace out a clear branching tree, even if data from around the actual branch point are going to be, necessarily, sparse (necessarily, because fossilisation is a rare event, and so small populations have an even lower probability of leaving fossils than large ones).

    As far as bacteria go, bacteria, are not, strictly speaking, divided into “species”, at least not in the sense that sexually reproducing organisms are. So although they are a wonderful resource for watching evolution in action, seeing as they reproduce so rapidly. we won’t see “speciation” in bacteria.

    What you need is fruitflies! And yes, speciation has been observed in fruitflies.

    Of course, we can hypothesise to our hearts’ content but practical science must be realistic

    Yes indeed. But where speciation and evolution can be observed on a human time scale (as in fruitflies and bacteria) both have been observed. Where it can’t be (because it happens too slowly) we have phylogenetic analysis, both of anatomical characters and genetic characters.

    So to make the case that evolution has limits and you can’t get macroevolution from microevolution we need an actual argument that it can’t happen.

    Behe has attempted to supply one of course, but it has serious problems.

    There are limits to evolution of course, but not in the direction of macroevolution over long periods of time.

    The big limits are imposed by common descent – once an allele is lost, as I said above, it’s gone, unless it coincidentally reappears, or an allele that does the equivalent appears in a different gene. So you don’t get transfer of adaptive “solutions” from one lineage to another.

    I find it one of the most persuasive arguments against Design, actually :)

  48. Elizabeth #45

    I still don’t see the significance of the distinction because, as you said, “Obviously, a population cannot interbreed with its long-dead ancestors”. Do you say “obviously” because frog 1.2 can’t travel back in time to mate with frog 1.1, or because even if you did put them together, they are now so different that they would not be able to breed? I’m talking about the 2nd disambiguation, and in that case, I fail to see how the two are not different species. Also, I understand speciation to be horizontal (the “moment” one species becomes two different ones), but I thought species was horizontal and vertical. But this is not a major quibble for me, so I’ll let it be.

    Regarding alleles dropping out of the population being “far more important”… I guess my main reason for bringing this up is because most ID advocates would tend to agree that natural selection is good at eliminating useless (or, at least, less useful) information. But the entire debate is about the generation of new material. Okay, an animal with night vision that now sleeps at night will probably lose its night vision; I understand that. .. How did the mutations add up to allow night vision in the first place? That is the type of question we are interested in

  49. You mean explain what polymorphisms are? Or explain how they arise?

    See PaV’s post @36.

  50. Fitness is understood as the degree of adaptation to the environment. I do not see any problem with this.

    The degree of adaptation by the individual? The degree of adaptation by the population? Both?

    How would one ever measure or calculate such a thing?

  51. What resources do you consider limit these dimensions?

    How do you define any limits on the undefinable? In your theory you’ve simply replaced God with another ineffable. That makes it science?

  52. That’s why dogs will never evolve into cats.

    So there ARE limits!

  53. 53
    Elizabeth Liddle

    Yes, there are. As I’ve said a few times :)

  54. 54
    Elizabeth Liddle

    Mung:

    Fitness is understood as the degree of adaptation to the environment. I do not see any problem with this.

    The degree of adaptation by the individual? The degree of adaptation by the population? Both?

    Population. Fitness, in the population genetics sense, is a population-level concept.

    How would one ever measure or calculate such a thing?

    You can’t measure the fitness (in the population genetics sense) of an individual. It’s a meaningless concept, like the mean and standard deviation of a population of one.

    You can only measure it in the sense that your Personal Trainer might measure it in the gym :)

  55. 55
    Elizabeth Liddle

    PaV:

    Elizabeth Liddle:

    Yes, eventually some mutations do become fixed (as, interestingly, do some neutral mutations as well as slightly deleterious ones, but beneficial ones are more likely to go to fixation).

    So, in addition to “beneficial” mutations sweeping through the population I should have said that “deleterious” and “neutral” mutations sweep through the population (but at lesser rates)?

    Well, as long as those rates can have a negative value! The “sweep” is a “drunkard’s walk”, but it’s a biased drunkard’s walk.

    All mutations drunkards start at the Tavern at the South end of Main Street. the street runs north-south. There is a police station just south of the Tavern. If the drunkard is a neutral mutation, each step he takes has a .5 probability of being in a Northern or Southern direction.

    So half of the neutral drunkards will end in the police station after one step. In fact, a lot of them will end up in the police station after just one step. But a few of them, just by chance, will make it a fair distance up Main Street, and some of them may even make the far end (fixation).

    This is called drift.

    If a mutation is deleterious, the city is built on a south facing slope, so the drunkard is far more likely to end up in the police station, than not, but if the slope is only very slight, some will “drift” up main street, and a few will actually make it to fixation, despite being deleterious.

    If mutation is beneficial, the city is built on a north-facing slope, and although some will still end up in the police station, these guys have a much better chances of making it to the end of main street, or at least to another tavern.

    So “sweep” might not be the best term! “Stagger” seems more appropriate, but if a mutation is extremely beneficial (very steep North-facing slope) yes, the drunkard may simply roll down Main street without stopping and hit the Fixation buffers at the end :)

    So, per this logic, Darwinian evolution depends on neutral (no selective value) and deleterious (negative selection factor) mutations. How does this help?

    Well, no, it doesn’t. I hope I’ve clarified with my silly story :)

    Here’s what the lead author wrote per William Roache: The process of acquiring beneficial mutations, many of which will add up in effect to cause
    a population of organisms to evolve, depends on a second factor – the process of natural
    selection.

    Well, my analogy needs a bit adaptation here :) But essentially, what this means is that for some mutations, the phenotypic effect (which is what matters – the effect on the actual organism) may be enhanced by the presence of another. For instance an allele for glorious main of golden hair might not improve your chances of snagging a mate unless it was also coupled with an allele that ensured that you don’t go bald shortly after puberty!

    So my drunkard’s story ignores the complications of different slopes for different genes, and different slopes for different combinations of genes.

    A better mental picture of the neo-Darwinist (if I must use that term! Not sure I like it because I’m not anti-Margulis for instance) is of lots of nearly-neutral mutations occurring all the time i.e. new alleles appearing all the time, some of which result in a slightly fitter genotype, some a slightly less fit genotype, but, as I tried to convey in my response to Joseph above, the concept of fitness is always in relation to a single generation, and what is slightly beneficial in one generation may be slightly deleterious in another.

    I suspected you would come up with Kimura’s “Neutral Theory”. But, Lizzie, the neutral theory is not Darwinian. Kimura invented the neutral theory because of the radical inadequacy of Darwinian (Modern Synthesis) theory to explain newly discovered rates of polymorphism, rates which were staggeringly higher than ‘theory’ predicted.

    Yes indeed. Darwin did not envisage the role of drift. But we now know it is extremely important.

    So the kind of “sweep” that occurs is not that a single mutation “sweeps” through the population, but that there are lots of different alleles, and that the frequency distribution of each allele changes from generation to generation, the ones that tended to be associated with more progeny increasing in frequency, and the ones that tended to be associated with fewer, reducing.
    And so the mean fitness of the population tends to optimise with the alleles that contribute to the most successful gene cocktails (aka genotypes) in that environment, at that time, becoming the most frequently. Over time, the least successful alleles may drop out of the gene pool altogether, and, if they are ever needed again, will have to mutate ab initio (which occasionally happens).
    But that isn’t “speciation” – that’s simply adaptation.
    Speciation happens when a population diverges for some reason, into two populations that don’t, or rarely interbreed, for example if they become separated by a mountain range, or a stretch of water. When that happens, adaptation continues, but the environmental history of the two populations will change – one side of the mountain may be drier than the other, or there may be different predators.

    And, because the two populations are now adapting independently to environmental changes, they will not only tend to differ from their ancestral populations, but also from each other, to the point where they could not interbreed even if the barrier between them was removed.

    And it is this divergent adaptation that we call “speciation”.
    Adaptation is what happens down a single lineage; speciation is the process by which one population lineage diverges into two.

    So, based on this argument, FIRST,there are no differences between adaptation and speciation. SECOND, it is purely qualitative and, so, speculative. And, THIRD, where is Natural Selection mentioned in any of this?

    FIRST: adaptation and speciation are terms that refer to two different, but related aspects of evolution. “Speciation” is the term used for a process in which a single population diverges into two independentally adapting sub-population.

    “Adaptation” is the term used to describe the evolution down a single lineage.

    Speciation, if you like, is about cousins; Adaptation is about ancestry!

    You and your second cousins have (not literally) speciated – your two sets of descendents (unless they interbreed) will be less closely related in each generation.

    However, both you and your second cousin (and both your descendents and your cousin’s descendents) can both trace your ancestry as a single line (if we take, say maternal ancestry) to your shared great-great…great grandmother.

    That line is the line we are talking about when we talk about “adaptaton”. The distancing relationship between your own progeny and your second cousins is what we are talking about when we talk about “speciation”.

    SECOND:, no it’s not “purely qualitative” (and even it it were, that wouldn’t render it “speculative” necessarily!). Phylogenetics is a heavily quantitive field, even if the result come with confidence estimates and question marks. And what is measured can be anatomical features or DNA sequences.

    THIRD: Natural selection aka differential reproduction is the drunkard’s walk. North is more progeny, South is fewer. Mutations that tend to move the phenotype “north” become more prevalent, by definition. Those that tend to move it south become less prevalent, by definition.

    Adaptation is the process by which alleles, or combinations of alleles, that tend to maximise successful progeny in a given environment become most prevalent.

    Speciation is when the adaptation (or even neutral drift) occurs independently in two subpopulations that have diverged from an ancestral single population.

    (Sorry for the delay – missed your post even though it was white! H/T to Mung for the reminder.)

  56. Elizabeth,

    I know you’re having 3 or 4 different conversations in this thread alone, but please see my comment #46

  57. 57
    Elizabeth Liddle

    uoflcard:

    (how do you pronounce that thing?!)

    You wrote:

    Elizabeth,

    I have been carefully reading your comment #7 about fitness landscapes. Let me first ask a question about fitness landscapes. What does a steep cliff imply? Reading different resources, I seem to see two very different possibilities:

    1.) If seen as a 3-D graph, with the z-direction being vertical, the x-y plane can be seen as genetic mutations and the z-axis is the fitness. So if you’re standing at the base of a steep cliff, a slight change in the x-y plane (i.e. a slight change to a genome) can result in you now being on top of the cliff (i.e. a huge increase in fitness).

    2.) Translation within the 3-D system is accomplished with step-by-step changes, like hiking in a mountain range. You cannot “walk” up a cliff, therefore you need to find the gentle slopes to reach the higher elevations.

    I’ve always been under the impression that it is #2, but I wanted to confirm that you agreed with that before I went further. Thanks for the response, if you have the opportunity.

    Well, there are different ways of representing a fitness landscape, but actually, 1 is the most common, and tbh I’ve always found it easier to envisage with high fitness as the low points,rather than the high points! Simply because I find it easier to walk down hill than up.

    However that’s just me. The idea is that populations move readily upwards and tend to “climb” towards “fitness peaks”. However, moving horizontally, in straightforward Darwinian terms doesn’t work, because there is no “selection” to move the population along.

    This is essentially the problem identified by Behe – however enticing the Bacterial Flagellum looks at the top of that far cliff, it can’t get to it because it has to traverse a vast plain to get there.

    That’s where drift comes in. Drift allows mutations to wander across plains until they come to something they can climb. Although the more dimensions in which that plain exists, the tougher it is to cross.

    But things get even worse, at least in theory, when a potentially advantageous peak is not just across a plain, but across a deep valley from the peak the population is on, and the only way it can get to the higher peak is by going downhill first (and it doesn’t like going downhill).

    There are two ways it can reach the higher peak. One is, again, by drift – even deleterious mutations need not be fatal, and can still be replicated often enough that there enough survivors to reach the foot of the advantageous summit (although remember this is “blind search” – populations can only “feel” the next step, as it were).

    The other is via another dimension, and we know that evolutionary search space is multi-dimensional. That’s where the ramp comes in. What seems like a butte in a flat plane seen from a neighbouring smaller butte, may, in another dimension or three, have a gentle ramp from one summit to the next.

    But thinking in more than 3D makes my head hurt :)

  58. uoflcard:

    (how do you pronounce that thing?!)

    U of L Cards

  59. Elizabeth Liddle:

    That’s where drift comes in. Drift allows mutations to wander across plains until they come to something they can climb.

    Following the analogy, how does one ascend from the valley or descend from the peak in order to reach the plain such that the neutral mutation can wander across it?

    Without selection how does one either descend or ascend?

    And if selection is taking place, it’s either towards the depth of the valley or towards the peak of the mountain. It’s never towards the plain.

    I’m sorry, but the theory you present just isn’t believable.

  60. Elizabeth Liddle:

    How do neutral mutations “drift” across the fitness landscape? Don’t they stay at the same location, since the x-y plane presumably represents genetic configuration. The occurrence of a new mutation would move the organism

  61. 61

    Hi. Just want to clear up a few things. If anyone feels like discussing evolutionary theory, I invite you to take it to my own post about my paper. I will not be posting on this thread again.

    #5 For the record, that is indeed my article quoted.

    #46 If the fitness landscape (really, fitness function) has a steep slope, it means that a small change in genotype (or phenotype) can change fitness a lot. I.e., your 1) is correct, while 2) is not.

    #50 and #54 One can talk about both individual and population fitness. In simulations (as the one the OP is about), fitness is known, and it determines the probability that the individual will have offspring. In biological organisms individual fitness can be measured in different ways; for bacteria it is often done by measuring the growth rate (yes, of an individual). Other proxies for fitness are used, such as the number of offspring.

    #60 Neutral mutations do not “drift across the fitness landscape,” as you seem to correctly imply. Drift refers only to fixation or loss of mutations or alleles. however, part of the fitness landscape (really, think of it just as a function) may be flat, so that a population in a flat part of the fitness landscape can experience mutations that are neutral: changes in genotype/phenotype results in organisms with the same fitness, and so those changes are equal in fitness, and can thus drift.

  62. Elizabeth Liddle:

    That’s where drift comes in. Drift allows mutations to wander across plains until they come to something they can climb. Although the more dimensions in which that plain exists, the tougher it is to cross.

    I don’t have time now to give a full answer. If I did, I would look at what individual genomes might look like after 100′s of thousands of generations.

    But to the point here: to invoke “drift” is to invoke stochastic/chance mechanisms. The argument that Dawkins makes is that, indeed, the ‘stuff’ of evolution is of chance origins, but that NS is what makes the random ultimately non-random.

    So here we are, as critics of Darwinism, being told that NS is indispensable; and then that it only comes in at the end (when the fitness peak needs to be climbed).

    How does one falsify a theory that wants it both ways?

  63. Elizabeth,

    1. Could you point to papers showing speciation of fruitflies please. What I read as of 2004 strongly suggested that poor fruitflies remained fruitflies: healthy, mutants or dead. Even a fruitfly with its legs sticking out of the eyes is a fuitfly. So no speciation was observed. Maybe I read the wrong papers.

    When I said “in earnest”, I meant the fuzziness of taxonomy in bacteria. What is also important when we speak about speciation, is how these experiments were conducted and whether what is done in the lab can happen in nature.

    2. I do find time a mightily limiting factor for evolution. You tacitly acknowledge this as well when you say it is hard to traverse a plateau when a lot of things are involved (the curse of dimensionality as I put it :)

    Overall, Darwinism does not stand practice. Even IF we accept speciation, I hazard a guess that 13 billion years are nowhere near to allow for what we can see flourishing around.

  64. Elizabeth,

    In addition to #62.

    I mean by speciation the emergence of populations unable to interbreed. According to my very limited knowledge, experiments on fruitflies end up in (a) dead flies, (b) severely mutilated flies unable to produce any offspring, (c) healthy flies with minor differences from ancestry where the scale of these differences does not lead to reproductive isolation.

    Maybe I am missing something…

  65. Eugene this recent summary paper on fruit flies may be of interest:

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

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

    f/n

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

  66. Elizabeth,

    I just remembered a friendly argument between two biologists (both of University of Manchester, UK), of which I was a witness. One of them insisted that the definition of “species” should include not only the aspect of just being able to produce offspring but that the offsping should be big enough in size.

    We can have a mule but does it mean that horses and asses are one species?

    By the way, as far as I remember both agreed that speciation has NOT been observed.

    I am afraid that, as is unfortunately usual with Darwinism, actual observations are in this case interpreted in its favour. But I may be wrong.

  67. Bornagain77,

    Many Thanks for this. I would have thought so.

  68. Regarding #65, I meant to say “in numbers”, of course.

  69. 69
    Elizabeth Liddle

    Eugene:

    Elizabeth,

    I just remembered a friendly argument between two biologists (both of University of Manchester, UK), of which I was a witness. One of them insisted that the definition of “species” should include not only the aspect of just being able to produce offspring but that the offsping should be big enough in size.

    We can have a mule but does it mean that horses and asses are one species?

    I don’t think the category is a binary one, Eugene! i.e. I don’t pairs of populations are cleanly “either” the same species or “not the same species”. Speciation is a gradual process, and even many generations after speciation began, and the two populations no longer interbreed in the wild (lions and tigers, for instance) hybridisation (even with fertile offspring) remains possible.

    So I’d say it was true to say that speciation processes have been observed, but that “complete” speciation processes (if that requires that hybridisation with fertile offspring is impossible) hasn’t, because, clearly, as the existence of ligers and tigons shows, hybridisation can still occur many generations later.

    By the way, as far as I remember both agreed that speciation has NOT been observed.

    I am afraid that, as is unfortunately usual with Darwinism, actual observations are in this case interpreted in its favour. But I may be wrong.

    BTW, interesting paper here, not sure if it’s open access or not:

    http://www.sciencedirect.com/s.....4707002868

  70. 70
    Elizabeth Liddle

    oops messed up the tags. Penultimate and antepenultimate paragraphs above are Eugene S’s words, not mine!

    Sorry!

  71. Elizabeth,

    Well, that does make sense as regards graduality. Thanks for this. Anyway, this graduality must terminate at the point of the new species emerging. So the main claim remains that speciation has NOT been observed.

    The effect of RM+NS is really there BUT it is marginal as has been shown experimentally (see “The Edge of Evolution” by Behe). And that I find very convincing. It is there to enable a certain degree of adaptation of species to make them survivable.

    Unfortunately, what evolutionists keep saying extrapolating the results too far to include speciation or formation of higher taxonomic entities, I find implausible. In theory it may look nice (but even that is questionable and the theory becomes clumsier as new data comes in). Unfortunately, as soon as the talk is down to business, Darwinists fail to present convincing evidence.

  72. 72

    Hi. Just want to clear up a few things. If anyone feels like discussing evolutionary theory, I invite you to take it to my own post about my paper. I will not be posting on this thread again.

    #5 For the record, that is indeed my article quoted.

    #46 If the fitness landscape (really, fitness function) has a steep slope, it means that a small change in genotype (or phenotype) can change fitness a lot. I.e., your 1) is correct, while 2) is not.

    #50 and #54 One can talk about both individual and population fitness. In simulations (as the one the OP is about), fitness is known, and it determines the probability that the individual will have offspring. In biological organisms individual fitness can be measured in different ways; for bacteria it is often done by measuring the growth rate (yes, of an individual). Other proxies for fitness are used, such as the number of offspring.

    #60 Neutral mutations do not “drift across the fitness landscape,” as you seem to correctly imply. Drift refers only to fixation or loss of mutations or alleles. however, part of the fitness landscape (really, think of it just as a function) may be flat, so that a population in a flat part of the fitness landscape can experience mutations that are neutral: changes in genotype/phenotype results in organisms with the same fitness, and so those changes are equal in fitness, and can thus drift.

    P.S. I submitted this comment on 7/2, but it didn’t make moderation.

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