Are Fitness Valleys Too Deep?

_{June 30, 2011

Intelligent Design}

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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.”

Comments

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.PaV_{June 30, 2011
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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/publications/lifes-conservation-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/releases/2011/06/110601134300.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/2011-03-quantum-no-hiding-theorem-experimentally.htmlbornagain77_{June 30, 2011
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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/2010-11-physicists-loopholes-violating-local-realism.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/releases/2009/07/090722142824.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.com/2010/09/15/quantum-entanglement-holds-together-lifes-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/releases/2010/05/100510151356.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/releases/2011/03/110331104014.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/news/2010/oct/1/hawking-irrational-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 2007bornagain77_{June 30, 2011
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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/2010/06/doug_axe_knows_his_work_better035561.html ID Scientist Douglas Axe Responds to His Critics - June 2011 - Audio Podcast http://intelligentdesign.podomatic.com/entry/2011-06-01T15_59_43-07_00 etc.. etc.. etc..bornagain77_{June 30, 2011
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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/pdfbornagain77_{June 30, 2011
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Well, no, it a "bad day for Darwinism", PaV. I assume the paper you are referring to is this one: http://rspb.royalsocietypublishing.org/content/early/2011/06/18/rspb.2011.0870.abstract?sid=0a3330be-63d8-4beb-ae47-61f7b3ba276c 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 :)Elizabeth Liddle_{June 30, 2011
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I heard a rumor that neo-Darwinism has got itself a job selling nails! It gets them for free after all.WilliamRoache_{June 30, 2011
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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/2011-06-evolutionary-kings-hill-good-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/?q=052907_evolution.htm So I guess if you asked him about his work that you present in this thread he'd disagree with your conclusions!WilliamRoache_{June 30, 2011
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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.Neil Rickert_{June 30, 2011
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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?Mung_{June 30, 2011
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Is there a mathematically rigorous defintion of "fitness"?Joseph_{June 30, 2011
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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/2011/06/new_research_on_epistatic_inte047151.htmlbornagain77_{June 30, 2011
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