Junk DNA: The original ‘onion test’ is a biological non-sequitur

_{Denyse O'Leary

October 10, 2011

'Junk DNA', Darwinism}

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Probably in response to Nick Matzke here and here, proposing among other things an onion test. A friend of UD News writes to say,

Those who employ “the onion test” should recall that the test — as originally formulated by geneticist T. Ryan Gregory — asks for a “universal function” for non-coding DNA. Is this a biologically reasonable question to ask? No. As Jonathan Wells writes, in The Myth of Junk DNA (pp. 85-86):

The “onion test,” according to Gregory, “is a simply reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?” [1]

Gregory directs his challenge to “anyone who thinks they have come up with a universal function for non-coding DNA.” Yet there probably is no such person. As we have seen, scientists know of many functions for non-protein-coding DNA. Nobody claims that there is “a universal function” that applies both to mammals and to onions. Based on the evidence, scientists have proposed that non-protein-coding intronic DNA helps to regulate alternative splicing in brain cells, and that non-protein-coding repetitive DNA plays a role in placental development. Why should those scientists justify their proposals by referring to onions, which have neither brains nor placentas?

See also: Thoughts on the “C-Value Enigma”, the “Onion Test” and “Junk DNA”

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Comments

With evos you can't even lead them to water...Joseph_{October 12, 2011
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Wring again, Nick. 1- Neither Creationists nor IDists say "X can't evolve" 2- Evolutionists NEVER show how X can evolve via blind, undirected chemical processes- they just say it- as in they use teir imagination to "show" how it can evolve. IOW Nick evos = wankers.Joseph_{October 12, 2011
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Nick Matzke:
If you agree that evolution can do things like change mucilage secretion levels, then the argument about the origin of the snap trap is over, because I (well, the sources I cited) explained the origin of the snap trap *from* a glue trap with quantitative changes like changes in levels of mucilage secretion.
They cannot do that if tey do not know the genes involved. Also if tey ent into a lab and produced a snap-trap from a glue-trap that would help their case. And without that they don't have any science...Joseph_{October 12, 2011
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As far as I can tell, the main complaint is that a comprehensive, detailed account of a specific evolutionary event/process is not provided. Is it possible to provide those details with the design inference as the tool?Cabal_{October 12, 2011
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Why would I want to silence you? You're too entertaining.paragwinn_{October 11, 2011
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It makes even more sense now.ScottAndrews_{October 11, 2011
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Guess who?
Although I am fully convinced of the truth of the views given in this volume under the form of an abstract, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as the `plan of creation,' `unity of design,' &c., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject my theory. A few naturalists, endowed with much flexibility of mind, and who have already begun to doubt on the immutability of species, may be influenced by this volume; but I look with confidence to the future, to young and rising naturalists, who will be able to view both sides of the question with impartiality. Whoever is led to believe that species are mutable will do good service by conscientiously expressing his conviction; for only thus can the load of prejudice by which this subject is overwhelmed be removed. Several eminent naturalists have of late published their belief that a multitude of reputed species in each genus are not real species; but that other species are real, that is, have been independently created. This seems to me a strange conclusion to arrive at. They admit that a multitude of forms, which till lately they themselves thought were special creations, and which are still thus looked at by the majority of naturalists, and which consequently have every external characteristic feature of true species, -- they admit that these have been produced by variation, but they refuse to extend the same view to other and very slightly different forms. Nevertheless they do not pretend that they can define, or even conjecture, which are the created forms of life, and which are those produced by secondary laws. They admit variation as a vera causa in one case, they arbitrarily reject it in another, without assigning any distinction in the two cases. The day will come when this will be given as a curious illustration of the blindness of preconceived opinion. These authors seem no more startled at a miraculous act of creation than at an ordinary birth. But do they really believe that at innumerable periods in the earth's history certain elemental atoms have been commanded suddenly to flash into living tissues? Do they believe that at each supposed act of creation one individual or many were produced? Were all the infinitely numerous kinds of animals and plants created as eggs or seed, or as full grown? and in the case of mammals, were they created bearing the false marks of nourishment from the mother's womb? Although naturalists very properly demand a full explanation of every difficulty from those who believe in the mutability of species, on their own side they ignore the whole subject of the first appearance of species in what they consider reverent silence.
NickMatzke_UD_{October 11, 2011
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We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable.
Do they define "nontrivial"? The classic pattern is that creationists declare X can't evolve, evolutionists show how X evolves, then the creationists declare X trivial and move to Y.NickMatzke_UD_{October 11, 2011
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Nick, now in realizing your superior intellect, and how you have humbled this IDiot with the massive molecular fluctuations of your brain that produce such superior thoughts of truth (though in my 'IDiotness' I still can see no reason to presuppose why your 'emergent' thoughts, from molecular fluctuations in your brain, should correspond to the truth, nor why you should think your fluctuations of emergent thought should not give you a completely different truth tomorrow), but anyways,,,, in being so humbled by such brilliance of molecular fluctuations of your brain, I was wondering if you could perhaps find the time to formally falsify Abel's null hypothesis? (There's a million dollar prize in it for you) You could probably do such trivial stuff while your brushing your teeth, or whatever,,, and just think of all the time you will save in the future by not having to tirelessly defend what seems to be so clearly evident to you, but is so clearly deficient to us poor lowly IDiots who were not blessed with such lucky configurations of brain molecules as to figure out why random configurations of material molecules never seem to generate functional information (except in our brains of course! :) ).
Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29 The Origin-of-Life Prize ® Excerpt: The annuity consists of $50,000.00 (U.S.) per year for twenty consecutive years, totaling one million dollars in payments.,,, The ability of the Foundation to underwrite these payments and to administer the Project is monitored by the well-known accounting firm of Young, Brophy & Duncan, PC, Certified Public Accountants. http://lifeorigin.info/
Music:
TobyMac - Lose My Soul http://www.youtube.com/watch?v=coHKdhAZ9hU
bornagain77_{October 11, 2011
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Nick, the crushingly beautiful thing about this study, against neo-Darwinism, is the incongrence with EACH individual tree to the theory of neo-Darwinism!!! We, in fact, despite attempts to dance around the implications, have 101 individual witnesses each testifying that the prevailing “TREE” view of a gradually branching neo-Darwinian ‘tree’ of gradual change into new species is completely wrong!!!., In fact this study, despite your name calling and stonewalling denial to the contrary, directly contradicts your initial comment, ‘quite minor disagreement in a very tiny region of Possible Tree Space’,
So apparently you don't even know what the word "incongruence" means, when referring to phylogenetic trees. I even put a link up that explained it. Wow. Just...wow. Anyone want to defend bornagain77's use of this paper? [birds chirping]NickMatzke_UD_{October 11, 2011
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Nick as to this rationalization of yours of the study:
They found statistically more support for #2 (which is what the author termed 'dropping out of the sky' speciation). Since a lot of biologists have had the opinion that geographic separation is the most common cause of speciation, this tends to support their position.
Yet these following studies find that this gut reaction rationalization of yours is severely wanting:
Amazing Insects Defy Evolution – October 2010 Excerpt: India spent tens of millions of years as an island before colliding with Asia. Yet the fossil record contains no evidence that unique species evolved on the subcontinent during this time, http://www.creationsafaris.com/crev201010.htm#20101026a Fantasy Island: Evolutionary Weirdness Does Not Favor Islands - July 2010 Excerpt: “We concluded that the evolution of body sizes is as random with respect to ‘isolation’ as on the rest of the planet,” he said. “This means that you can expect to find the same sort of patterns on islands and on the mainland.” http://www.creationsafaris.com/crev201007.htm#20100708b
This following article reveals how evolutionists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations:
More Biogeographical Conundrums for Neo-Darwinism - March 2010 http://www.evolutionnews.org/2010/03/sea_monkeys_are_the_tip_of_the.html
further notes:
A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html The Biological Big Bang model for the major transitions in evolution - Eugene V Koonin - Background: "Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable; http://www.biology-direct.com/content/2/1/21 Biological Big Bangs - Origin Of Life and Cambrian - Dr. Fazale Rana - video http://www.metacafe.com/watch/4284466 The million-year wait for macroevolutionary bursts - July 2011 Excerpt: Even though rapid, short-term evolution often occurs in intervals shorter than 1 Myr, the changes are constrained and do not accumulate over time. Over longer intervals (1–360 Myr), this pattern of bounded evolution yields to a pattern of increasing divergence with time. The best-fitting model to explain this pattern is a model that combines rare but substantial bursts of phenotypic change with bounded fluctuations on shorter timescales. https://uncommondescent.com/evolution/pnas-paper-studies-actual-pattern-of-evolution-doesnt-pretend-its-somehow-something-else/
bornagain77_{October 11, 2011
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Nick, the crushingly beautiful thing about this study, against neo-Darwinism, is the incongrence with EACH individual tree to the theory of neo-Darwinism!!! We, in fact, despite attempts to dance around the implications, have 101 individual witnesses each testifying that the prevailing "TREE" view of a gradually branching neo-Darwinian 'tree' of gradual change into new species is completely wrong!!!., In fact this study, despite your name calling and stonewalling denial to the contrary, directly contradicts your initial comment, ‘quite minor disagreement in a very tiny region of Possible Tree Space’, for the plain fact is, no matter how 'scientific you perceive yourself to be, that we have 101 individual 'tree' witnesses testifying that there is quite a major disagreement between Darwinian theory and the ACTUAL evidence. The other studies I listed, that you merely hand waved off as old and outdated (even though some are recent), are in fact the icing on the cake and do you no good whatsoever, for they show that when trees are compared to each other, that, as one study put it, 50% of sequences will give you one history and 50% of sequences will give you another. Thus Nick, though you belittle me, and every one else who has the audacity to question the almighty power of evolution, the fact is you have no help from any study, whether they are done with individual trees or whether they are done by comparing trees with each other. Yet instead of you realizing that this study provides another line of evidence against neo-Darwinism, you attack me and then rationalize the results away as if they mean nothing, instead of dealing with the evidence forthrightly, as would anyone who was a true scientists would do, but you, apparently, are not so much concerned with calmly and cooly evaluating the evdence and coming to a correct conclusion as you are in protecting your beloved atheistic worldview, evidence be damned if it gets in they way!!!bornagain77_{October 11, 2011
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Nick, Apparently the diversity of life via mutation and selection boils down to an extrapolation through which the rest of the evidence is filtered. If there's anything more I'm never going to get it out of you. (Thank you for leading me to an empty ditch and waiting for me to drink.) That's quite a stretch of the imagination. Here's my extrapolation. I know that even hard-working scientists blow it once in a while. It's even easier in a field that lends itself to making up unverifiable stories. We've seen contradictory research on whether we should brush our teeth up and down, sideways, or in circles. It was once common knowledge that bacteria could never survive in our digestive tracts. Excess dietary calcium caused kidney stones. And so on. These people were not idiots. And these examples, while common, do not represent of pattern of scientific incompetence. They do however demonstrate a point. Scientists can be dead wrong, individually and collectively. That does not indicate whether an individual or group is right, wrong, or somewhere in between in any particular case. It simply indicates that such 'wrongness' is by no means rare or unheard of. So you may choose to extrapolate that limitless apparent but unintended ingenuity and engineering can arise from the tiniest of variations. And apparently you gain confidence from having the majority of the scientific community behind you. But, based on numerous examples, it's also easy to conceive that scientists, both individual and communities, can sometimes be off in left field, regardless of their passion and dedication, and that this is likely one of those cases. Which is a greater stretch of the imagination? The known phenomenon of group-think applied in this particular case, or tiny step-by-step variations leading lizards to grow wings, use them, and discover migration routes from North America to South America by way of air currents over the eastern Atlantic which would get them killed unless they already knew where they were going? Your extrapolation is a far bigger reach. And that's just based on considering which possibility is simpler and more plausible. It's not even factoring in that the science itself is crap.ScottAndrews_{October 11, 2011
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Like when a pair of monkeys is prevented from mixing offspring with the rest of their population by the ocean they just made a raft and sailed across? I believe the phenomenon is called genetic drift.
A matter of single, rare events — which might be expected if dispersal to new regions was the major cause of lineage splitting, e.g. when a species on rare occasions gets over a mountain range, out to a remote island, etc.
ScottAndrews_{October 11, 2011
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That's not the research article, it's the news article summary. And either way, it has NOTHING to do with incongruence between phylogenetic trees! Do you even know what incongruence means? They used phylogenetic trees to do the study, for godssakes! Bolding random parts of a news article about a research paper you don't understand is not an argument. These kinds of shenanigans are why I mostly just ignore your posts, and why the scientific community will definitely, and rightly, never take the kind of stuff you put out seriously. Here's what the article was actually about -- using phylogenetic trees to test whether the most common mechanism of speciation was: 1. A matter of gradually building up many small changes -- which might be expected if natural selection of a long series of mutations was the major cause of lineage-splitting. 2. A matter of single, rare events -- which might be expected if dispersal to new regions was the major cause of lineage splitting, e.g. when a species on rare occasions gets over a mountain range, out to a remote island, etc. #1 predicts that the lengths of the branches between nodes on the phylogenetic tree will have a normal (bell curve) distribution, since if you add up the waiting times of a large number of exponentially-distributed events, you get a normal distribution. #2 predicts that the lengths of the branches between nodes on the phylogenetic tree will have an exponential distribution. They found statistically more support for #2. Since a lot of biologists have had the opinion that geographic separation is the most common cause of speciation, this tends to support their position. There are various criticisms one can make of the study, since e.g. estimating branch lengths is nontrivial, but that's neither here nor there. In short...what am I, as a scientist, supposed to think about the shenangians you are pulling here? I know you're not doing it dishonestly, you're doing it out of the confidence that you're correct, and your eagerness to show it -- but that's almost worse! Imagine what it looks like to a scientist who is already predisposed to dislike religion. Here's a guy who calls himself "bornagain77", who goes around telling people that a major scientific theory is a total fraud, yet he can't even get the first thing correct about a recent scientific paper, and his doubling-down on the mistake indicates he doesn't even care enough to double-check his claim once he is criticized about it. I'm just amused, because I've seen such shenanigans so many times from creationists, but a lot of scientists get pretty darn ticked off at the abuse of their work and their field by people who have high confidence, but no idea what they are talking about. This, not atheism, is what makes so many scientists so strongly opposed to creationism/ID. That and the fact that other creationists/IDists don't correct such mistakes, which are being made all the time. And, if the goal is to convert people to evangelical Christianity, imagine how your behavior looks from the scientists' perspective. Apparently, becoming born again involves throwing away your brain, naively misinterpreting the hard and careful work of scientists, and loudly proclaiming to the world that the scientists are wrong, when you don't even know what you are talking about. That's about the last thing that will ever appeal to a scientist, or to anyone who values science. Creationists are one of the biggest impediments to successful apologetics that exists in the modern world.NickMatzke_UD_{October 11, 2011
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But alas paragwinn, perhaps we can get past all this mud slinging, as if mud slinging is ever the high road to take, and focus directly on the science as bbigej suggested, Perhaps you care to take up bbigej's challenge to ;
Can you please cite any papers in support of your claims, especially pertaining to the claim that the Darwinian mechanism can produce copious amounts of complex, specified information? Thanks.
paragwinn, produce such evidence and you can forever silence us 'IDiots'!!!bornagain77_{October 11, 2011
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paragwinn, care to quote Nick's comment directly preceding that comment?bornagain77_{October 11, 2011
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bigej, Then you must have missed ba77's intro to his comment at 2.1.1.1.4:
Nick, It might interest you to know that I find you to be one of the most religious, intellectually dishonest, atheistic neo-Darwinists I’ve ever met!!! And I’ve met my fair share!!! In fact it is such shamelessly intellectually dishonesty on the part of religious atheists such as yourself who have made my faith in the truthfulness of the claims of Christianity that much stronger!!! Before I met people like you I pretty much thought everyone was basically fair minded. But I’ve certainly learnd differently! And for that I thank you, even though I certainly fear for the fate of your soul for trying to lead people away from the truth of God with such shameless, and persistent, deception!!!
paragwinn_{October 11, 2011
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Our knowledge is a receding mirage in an expanding desert of ignorance. - Will DurantScottAndrews_{October 11, 2011
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Further notes on tree incongruences:
Genomes of similar species Excerpt: There certainly are many genetic similarities between allied species, but we now know of dramatic differences and the list is growing. This prediction has been falsified as many unexpected genetic differences have since been discovered amongst a wide range of allied species. Even different variants within the same species have large numbers of genes unique to each variant. Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. And some of these genes have been found to have important functions, such as helping to construct proteins. [8] Massive genetic differences were also found between different fruit fly species. The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc... http://www.darwinspredictions.com/#_4.2_Genomes_of Genomes of distant species Excerpt: Even more remarkable are the recently discovered ultra-conserved elements (UCEs). Thousands of these DNA segments, hundreds of base pairs in length, have been found across a range of species including human, mouse, rat, dog, chicken and fish. Evolutionists were astonished to discover these highly similar DNA sequences in such distant species. In fact, across the different species some of these sequences are 100% identical. Species that are supposed to have been evolving independently for 80 million years were certainly not expected to have identical DNA segments. “I about fell off my chair,” remarked one evolutionist. etc.. etc.. http://www.darwinspredictions.com/#_4.3_Genomes_of
Thus Nick no matter how you try to twist and turn the evidence to fit your bias, the fact is that the evidence itself is what is falsifying your claims for neo-Darwinism!!! You can get us names and get mad all you want, but the simple fact is that it is the evidence you should be mad at NOT US!!!bornagain77_{October 11, 2011
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You can lead them to the water, but you can't make them drink...NickMatzke_UD_{October 11, 2011
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Nick as tempting as it is to have you completely 'ignore' me (since you don't really listen to anything I put to you anyway), alas I cannot let you deceive again as you have here; Here is the entire article that you incredulously stated: 'it has NOTHING to do with tree incongruence statistics at all!:'
Accidental origins: Where species come from - Bob Holmes - March 2010 ANTARCTIC fish deploy antifreeze proteins to survive in cold water. Tasty viceroy butterflies escape predators by looking like toxic monarchs. Disease-causing bacteria become resistant to antibiotics. Everywhere you look in nature, you can see evidence of natural selection at work in the adaptation of species to their environment. Surprisingly though, natural selection may have little role to play in one of the key steps of evolution--the origin of new species. Instead it would appear that speciation is merely an accident of fate. So, at least, says Mark Pagel, an evolutionary biologist at the University of Reading, UK. If his controversial claim proves correct, then the broad canvas of life--the profusion of beetles and rodents, the dearth of primates, and so on--may have less to do with the guiding hand of natural selection and more to do with evolutionary accident-proneness. Of course, there is no question that natural selection plays a key role in evolution. Darwin made a convincing case a century and a half ago in On the Origin of Species, and countless subsequent studies support his ideas. But there is an irony in Darwin's choice of title: his book did not explore what actually triggers the formation of a new species. Others have since grappled with the problem of how one species becomes two, and with the benefit of genetic insight, which Darwin lacked, you might think they would have cracked it. Not so. Speciation still remains one of the biggest mysteries in evolutionary biology. Even defining terms is not straightforward. Most biologists see a species as a group of organisms that can breed among themselves but not with other groups. There are plenty of exceptions to that definition--as with almost everything in biology--but it works pretty well most of the time. In particular, it focuses attention on an important feature of speciation: for one species to become two, some subset of the original species must become unable to reproduce with its fellows. How this happens is the real point of contention. By the middle of the 20th century, biologists had worked out that reproductive isolation sometimes occurs after a few organisms are carried to newly formed lakes or far-off islands. Other speciation events seem to result from major changes in chromosomes, which suddenly leave some individuals unable to mate successfully with their neighbours. It seems unlikely, though, that such drastic changes alone can account for all or even most new species, and that's where natural selection comes in. Species exist as more or less separate populations in different areas, and the idea here is that two populations may gradually drift apart, like old friends who no longer take the time to talk, as each adapts to a different set of local conditions. "I think the unexamined view that most people have of speciation is this gradual accumulation by natural selection of a whole lot of changes, until you get a group of individuals that can no longer mate with their old population," says Pagel. Until now, no one had found a way to test whether this hunch really does account for the bulk of speciation events, but more than a decade ago Pagel came up with an idea of how to solve this problem. If new species are the sum of a large number of small changes, he reasoned, then this should leave a telltale statistical footprint in their evolutionary lineage. Whenever a large number of small factors combine to produce an outcome--whether it be a combination of nature and nurture determining an individual's height, economic forces setting stock prices, or the vagaries of weather dictating daily temperatures--a big enough sample of such outcomes tends to produce the familiar bell-shaped curve that statisticians call a normal distribution. For example, people's height varies widely, but most heights are clustered around the middle values. So, if speciation is the result of many small evolutionary changes, Pagel realised, then the time interval between successive speciation events--that is, the length of each branch in an evolutionary tree--should also fit a bell-shaped distribution (see diagram). That insight, straightforward as it was, ran into a roadblock, however: there simply weren't enough good evolutionary trees to get an accurate statistical measure of the branch lengths. So Pagel filed his idea away and got on with other things. Then, a few years ago, he realised that reliable trees had suddenly become abundant, thanks to cheap and speedy DNA sequencing technology. "For the first time, we have a large tranche of really good phylogenetic trees to test the idea," he says. So he and his colleagues Chris Venditti and Andrew Meade rolled up their sleeves and got stuck in. The team gleaned more than 130 DNA-based evolutionary trees from the published literature, ranging widely across plants, animals and fungi. After winnowing the list to exclude those of questionable accuracy, they ended up with a list of 101 trees, including various cats, bumblebees, hawks, roses and the like. Working with each tree separately, they measured the length between each successive speciation event, essentially chopping the tree into its component twigs at every fork. Then they counted up the number of twigs of each length, and looked to see what pattern this made. If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve. This would take the form of either a normal curve if the incremental changes sum up to push the new species over some threshold of incompatibility, or the related lognormal curve if the changes multiply together, compounding one another to reach the threshold more quickly. To their surprise, neither of these curves fitted the data. The lognormal was best in only 8 per cent of cases, and the normal distribution failed resoundingly, providing the best explanation for not a single evolutionary tree. Instead, Pagel's team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution (Nature, DOI: 10.1038/nature08630). Happy accidents Like the bell curve, the exponential has a straightforward explanation--but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen. The time interval between successive telephone calls you receive fits an exponential distribution. So does the length of time it takes a radioactive atom to decay, and the distance between roadkills on a highway. To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak. Speciation becomes an arbitrary, happy accident when one of these events happens to you." All kinds of rare events could trigger the accident of speciation. Not just physical isolation and major genetic changes, but environmental, genetic and psychological incidents. The uplift of a mountain range that split a species in two could do it. So too could a mutation that made fish breed in surface waters instead of near the bottom, or a change in preference among female lizards for mates with blue spots rather than red ones. The key point emerging from the statistical evidence, Pagel stresses, is that the trigger for speciation must be some single, sharp kick of fate that is, in an evolutionary sense, unpredictable. "We're not saying that natural selection is wrong, that Darwin got it wrong," Pagel adds. Once one species has split into two, natural selection will presumably adapt each to the particular conditions it experiences. The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause. "I think what our paper points to--and it would be disingenuous for very many other people to say they had ever written about it--is what could be, quite frequently, the utter arbitrariness of speciation. It removes speciation from the gradual tug of natural selection drawing you into a new niche," he says. This has implications for one of the most contentious aspects of evolution: whether it is predictable or not. If Pagel is correct, natural selection shapes existing species in a gradual and somewhat predictable way, but the accidental nature of speciation means that the grand sweep of evolutionary change is unpredictable. In that sense his findings seem to fit with the famous metaphor of the late Stephen Jay Gould, who argued that if you were able to rewind history and replay the evolution of life on Earth, it would turn out differently every time. So far, other evolutionary biologists have been reluctant to accept Pagel's idea wholeheartedly. Some regard it as interesting but in need of further testing. "The single, rare events model is brilliant as an interpretation--as a potential interpretation," says Arne Mooers at Simon Fraser University in Vancouver, Canada. Others suspect Pagel's analysis has highlighted only part of the story. "It's telling you about one necessary but not sufficient component of speciation," says Daniel Rabosky at the University of California, Berkeley. "You have to have two things: something to cause isolation, and something to cause differentiation." And the latter process--through which the two isolated populations change enough that we recognise them as two distinct species--is likely to involve gradual, adaptive change under the hand of natural selection. The notion that the formation of a new species has little to do with adaptation sits uncomfortably with fundamental ideas about evolution. A particular stumbling block is what evolutionary biologists call "adaptive radiations". When ecological opportunities open up--as, for example, when finches from the South American mainland first colonised the Galapagos--species seem to respond by diversifying into a host of new forms, each adapted to a particular niche. These bursts of speciation suggest that organisms need not wait for some rare event to push them into speciating, but instead can be pulled there by natural selection. "I would take it that there is quite a bit more pull than push," says Leigh Van Valen at the University of Chicago. But is there? In his analysis, Pagel specifically looked for the signature of this kind of evolutionary exuberance. Bursts of speciation would manifest as trees with lots of branching at irregular intervals; in other words, a highly variable rate of change over time, giving rise to a subtly different curve. "It was the model that, going in, I thought would explain far and away the most trees," says Pagel. He was wrong. "When it works, it works remarkably well," he says. "But it only works in about 6 per cent of cases. It doesn't seem to be a general way that groups of species fill out their niches." This finding has independent support. Luke Harmon at the University of Idaho in Moscow and his colleagues have examined 49 evolutionary trees to see whether there are bursts of evolutionary change early in a group's history, when unfilled niches might be expected to be most common. There is little evidence for such a pattern, they report in a paper that has been accepted for publication in the journal Evolution. Why so many rodents? If speciation really is a happy accident, what does that mean for the way biologists study it? By focusing on the selective pressures that drive two species into different ecological niches, as they currently do, they may learn a lot about adaptation but not much about speciation. "If you really want to understand why there are so many rodents and so few of other kinds of mammals, you should start to look at the catalogue of potential causes of speciation in an animal's environment, rather than take the view that there are all these niches out there that animals are constantly being drawn into," Pagel says. Rodents adapted to cool climates, for example, would be prone to isolation on mountain tops if the climate warmed. That could make them more likely to speciate than mammals adapted to warm temperatures. Likewise, marine animals whose larval stages live on the sea floor might be more likely to split into separate isolated populations and therefore speciate more often than those with free-floating larvae. Indeed, this is exactly what palaeontologist David Jablonski of the University of Chicago has found among marine snails. Similarly, species with narrow habitat requirements or finicky mate-choice rituals may also be prone to accidental splits. What other possible accidents might there be? No one knows yet. "We'd like people to start compiling the lists of these things that might lead to speciation, and start making predictions about who's going to have a high rate of speciation and who's going to have a low rate," says Pagel. If these lists help us understand the broad sweep of evolutionary history--the rise of mammals, why there are so many species of beetles, or the remarkable success of flowering plants--then we will know Pagel is onto something fundamental. In the meantime, though, Pagel's take on speciation may help explain another puzzling feature of the natural world. Over and over again, as biologists sequence the DNA of wild organisms, they find that what appears superficially to be a single species is actually two, several or even many. The forests of Madagascar are home to 16 different species of mouse lemurs, for example, all of which live in similar habitats, do similar things, and even look pretty much alike. These cryptic species complexes are difficult to explain if speciation is the end result of natural selection causing gradual divergence into different niches. But if new species are happy accidents, there need be no ecological difference between them. Pagel's own epiphany in this regard came in Tanzania, as he sat at the base of a hardwood tree watching two species of colobus monkeys frolic in the canopy 40 metres overhead. "Apart from the fact that one is black and white and one is red, they do all the same things," he says. "I can remember thinking that speciation was very arbitrary. And here we are--that's what our models are telling us." Bob Holmes is a consultant for New Scientist based in Edmonton, Canada http://postbiota.org/pipermail/tt/2010-April/007178.html
bornagain77_{October 11, 2011
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Eric, How true. I don't know how many times people including Nick have linked papers which supposedly detail the evolution between two organisms, but in reality only mention a few genetic differences. One of my favorites showed a difference in how forelimb growth was regulated between rodents and bats. There is never an attempt to explain the differences. What varied? Why was it selected? Why do I have a bird feeder outside my window and not a bat feeder? The answer is always 'well-known evolutionary' processes. Read the papers referenced by the papers I reference which explain why it's plausible. Come back tomorrow and don't look behind the curtain.ScottAndrews_{October 11, 2011
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Nick, You can't seem to answer the question without changing it. I'm asking for evidence that this is a valid explanation, and you're backtracking to "plausible." What is plausible? Plausibility is subjective. You express certainty that variation and selection are the engine of diversity. You have to be pretty sure of something to mock anyone who disagrees. But pressed for examples, observations, or specifics you present some toothless corroboration and ask, 'Isn't it obvious? Isn't is plausible?' It's neither. And what's up with linking to one of your previous posts in which you proclaim that you explained everything in another previous post? I have a sense of humor, but I don't think you're joking. It's turtles all the way down. Michael Flatley couldn't dance like this. It's pointless but it's fun to watch.ScottAndrews_{October 11, 2011
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ScottAndrews, you will never get a "detailed account of such a transformation" from Nick. He is not an engineer and doesn't think like one. Nick swoons very easily when he sees sequence similarities or homologous proteins (like with the bacterial flagellum). Since blind purposeless processes obviously brought everything about, there is no point is discussing the actual details of the transformation. Noting a few similarities between organisms is wholly sufficient to solidify the built-in confirmation bias.Eric Anderson_{October 11, 2011
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You lose: https://uncommondescent.com/intelligent-design/youtubes-c0nc0rdance-re-assures-us-that-the-evolution-of-chemotaxis-is-well-in-hand/comment-page-1/#comment-402002 https://uncommondescent.com/intelligent-design/youtubes-c0nc0rdance-re-assures-us-that-the-evolution-of-chemotaxis-is-well-in-hand/comment-page-1/#comment-402110 Read the papers and explain why the evolution of a snap trap from a glue trap is implausible, or else you haven't got a case at all. I'm not going to type them out for you, sorry.NickMatzke_UD_{October 11, 2011
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Nick, My position is consistent. I'm sure that a single genetic change can move the amount of mucilage secretion up and down. I do not extrapolate from that every variation in all of biology. I don't demand proof that you can glue two popsicle sticks together. But if you tell me you can make a space shuttle out of them I'll be a bit more demanding. That was a rather weak attempt.
Then quote my model for the origin of the Venus flytrap, and reference it with a link to the original, like decent posters are supposed to.
What? I'm telling you that you've never posted or referenced any detailed, meaningful explanation, and you want me to link to it? Link to what? I can quote it for you in its entirety:

Let me repeat what you are trying to avoid: You claim that an accumulation of individual genetic changes can, over time, evolve a glue trap into a fly trap, or something else into something else. But your proverbial 'mountain of evidence' contains anything but a detailed account of such a transformation. I'd be impressed if you just made something up. What makes you think that a model or a narrative covers that base? You cannot with any degree of certainty attribute countless changes to a mechanism that apparently has never been observed well enough to document or test. The challenge is so simple, and with every post you try to distract from it. I don't think you have anything, and you make my case with every post.ScottAndrews_{October 11, 2011
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bornagain77 writes/spams:
Yet contrary to your deceptive claim of ‘quite minor disagreement in a very tiny region of Possible Tree Space’. The truth is;
Accidental origins: Where species come from – March 2010 Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel’s team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation – but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: “It isn’t the accumulation of events that causes a speciation, it’s single, rare events falling out of the sky, so to speak.” http://www.newscientist.com/ar.....tml?page=2

bornagain77 -- dude! Where do you get this stuff?? We discussed this paper in my seminar at Berkeley, it has NOTHING to do with tree incongruence statistics at all! I know exactly what the paper is about -- do you, or are you just posting massive amounts of random spam? Why should I even talk to you if you are not a serious discussant and just a link spammer? Unless you go look up this paper, read it, and give a decent explanation of what it is about, and tell me why you posted it, I'm going to go back to ignoring your posts completely. Hint: it involves the difference between exponential distributions and normal distributions. Cheers! Nick PS: Other random quotes, some of them ancient and outdated, about congruence don't mean squat unless they are statistical statements. Statistics of tree congruence: http://www.talkorigins.org/faqs/comdesc/incongruent.html ORFans -- these will occur at a reasonable frequency at random when you have billions of nucleotides as in humans, there is no particular reason to think they are functional. All you need is a start codon followed by a stop codon. Furthermore, the human genome is more completely sequenced than most other "complete" genomes (genome sequencing is never literally 100% complete), so there may be a few cases where the region just hasn't been sequenced in chimp or monkey yet. But most of them are artefacts. The bacterial case which Ochman writes about is completely different from the human case, since many bacteria have no close relatives sequenced, and they acquire genes from the environment etc., although many of those ORFans may be artefacts as well.NickMatzke_UD_{October 11, 2011
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No. They. Did. Not. If the explanation is series of genetic changes which were selected, then it must actually include a pathway of specific genetic changes and describe how or why they were selected.
But, but...you JUST admitted that mutation-by-mutation detail was not required to produce a plausible pathway, when you conceded that it was reasonable to think that natural evolutionary processes could move the amount of mucilage secretion up and down. Can you make a consistent argument for two consecutive posts please?
I’m actually paying attention, so you can’t fake it by telling me that you already told me. This is at the foundation of the theory, and you are plainly hiding from it.
Then quote my model for the origin of the Venus flytrap, and reference it with a link to the original, like decent posters are supposed to. I'm not going to re-type it AGAIN just because you're too lazy to look it up and you prefer to just assert it doesn't exist.NickMatzke_UD_{October 11, 2011
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Nick,
the key factor determining whether or not the ID critique of evolution has any merit is whether or not the ASSUMPTION that multiple mutations are required to produce anything interesting is correct.
Nearly anything "interesting" requires, at a minimum, both a physical and behavioral change. It's not an absolute truth, but you could spend the rest of your life counting examples. In a nutshell, living organisms have things and use things. They cannot use what they do not have, and, according to theory, they do not pass on modifications which are literally useless. You're whistling along in your "happy day" scenario where phenotypic changes can accumulate without any cooperation from the rest of the organism, including its behavior. Theory, this is reality. Say hello. Would you care to explain how any such developments could result from single mutations? You haven't even attempted to explain how any of them arose from multiple mutations. You just compare two genomes and bridge the gap with assumed mutations and selection. Before I distract from the question, please explain yourself. Please provide a relevant example of something "interesting" that happened from a single mutation and that can reasonably be extrapolated to all other diversity. And if you have time explain why it isn't in every high school science book between the peppered moths and whale tales.ScottAndrews_{October 11, 2011
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