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

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

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

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

Why would I want to silence you? You're too entertaining. paragwinn

It makes even more sense now. ScottAndrews

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

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

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

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

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

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

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

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

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

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

paragwinn, care to quote Nick's comment directly preceding that comment? bornagain77

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

Our knowledge is a receding mirage in an expanding desert of ignorance. - Will Durant ScottAndrews

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

You can lead them to the water, but you can't make them drink... NickMatzke_UD

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

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

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

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

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

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

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

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

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

You know Nick your link on point 3 doesn't work, which is just as well since I am fairly certain that it is a sequence comparison instead of an actual demonstration of the almighty power of evolution, further down Your light dark colored moth example of preexisting information variation within kind is a friggin joke as to demonstrating the power of darwinism to create anything new. But hey Nick, I try to be a fair guy, so let's see if i can help you see what an actual SCIENTIFIC demonstration of Darwinian evolution might actually look like: The search for the 'Edge of Evolution'; What can neo-Darwinism really do???
Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species… (Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).) http://www.evolutionnews.org/2010/12/peer-reviewed_research_paper_o042191.html
Four decades worth of lab work is surveyed here:
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Michael Behe talks about the preceding paper in this following podcast:
Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00
How about the oft cited example for neo-Darwinism of antibiotic resistance?
List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria: Excerpt: Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” ,,, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding. http://www.trueorigin.org/bacteria01.asp
That doesn't seem to be helping! How about we look really, really, close at very sensitive growth rates and see if we can catch almighty evolution in action???
Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010 Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html
Shoot that doesn't seem to be helping either! Perhaps we just got to give the almighty power of neo-Darwinism ‘room to breathe’? How about we ‘open the floodgates’ to the almighty power of Darwinian Evolution and look at Lenski’s Long Term Evolution Experiment and see what we can find after 50,000 generations, which is equivalent to somewhere around 1,000,000 years of human evolution???
Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information – September 2011 Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html
Now that just can’t be right!! Man we should really start to be seeing some neo-Darwinian fireworks by 50,000 generations!?! Hey I know what we can do! How about we see what happened when the ‘top five’ mutations from Lenski’s experiment were combined??? Surely now the Darwinian magic will start flowing!!!
Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations) 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
Now something is going terribly wrong here!!! Tell you what, let’s just forget trying to observe evolution in the lab, I mean it really is kind of cramped in the lab you know, and now let’s REALLY open the floodgates and let’s see what the almighty power of neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal??? Surely now almighty neo-Darwinian evolution will flex its awesomely powerful muscles and forever make those IDiots, who believe in Intelligent Design, cower in terror!!!
A review of The Edge of Evolution: The Search for the Limits of Darwinism The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-michael-behe-edge-of-evolution Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.” http://www.evolutionnews.org/2009/05/swine_flu_viruses_and_the_edge020071.html
Now, there is something terribly wrong here! After looking high and low and everywhere in between, we can’t seem to find the almighty power of neo-Darwinism anywhere!! Shoot we can’t even find ANY power of neo-Darwinism whatsoever!!! It is as if the whole neo-Darwinian theory, relentlessly sold to the general public as it was the gospel truth, is nothing but a big fat lie!!! bornagain77

As to this lie, ahem, I mean comment of yours:
The very fact that protein sequences fit into a neat phylogenetic tree, with every amount of percentage difference between sequences, from 0 to 90%+, is evidence of this, and not just dismissible as “its only evidence of common ancestry”. * * (Note: and, to head off the usual ID bafflegab on tree congruence, observed congruence between different genes and proteins is always or almost always statistically very strong congruence. This is a universal problem with creationist/IDist arguments about congruence and incongruence in phylogenetic trees: the IDists have no concept of the fact, well-known in phylogenetics, that congruence and incongruence are quantatively measurable, and even the “incongruence” that biologists themselves often highlight is quite minor disagreement in a very tiny region of Possible Tree Space.
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/article/mg20527511.400-accidental-origins-where-species-come-from.html?page=2 Congruence Between Molecular and Morphological Phylogenies - Colin Patterson Excerpt: "As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology." http://www.arn.org/docs/odesign/od171/sampler171.htm Bones, molecules...or both? Excerpt: Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology. Can the two ever be reconciled?,,, When biologists talk of the 'evolution wars', they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging (between Darwinists) within systematics. http://www.nature.com/nature/journal/v406/n6793/full/406230a0.html The universal ancestor - Carl Woese Excerpt: No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves. http://www.pnas.org/content/95/12/6854.full Evolution: Charles Darwin was wrong about the tree of life - 2009 Excerpt: "We have no evidence at all that the tree of life is a reality," Eric Bapteste, an evolutionary biologist http://www.guardian.co.uk/science/2009/jan/21/charles-darwin-evolution-species-tree-life Uprooting The Tree Of Life - W. Ford Doolittle Excerpt: as DNA sequences of complete genomes have become increasingly available, my group and others have noted patterns that are disturbingly at odds with the prevailing beliefs. http://people.ibest.uidaho.edu/~bree/courses/2_Doolittle_2000.pdf Do orthologous gene phylogenies really support tree-thinking? Excerpt: We conclude that we simply cannot determine if a large portion of the genes have a common history.,,, CONCLUSION: Our phylogenetic analyses do not support tree-thinking. http://www.ncbi.nlm.nih.gov/pubmed/15913459 The tree of life, one of the iconic concepts of evolution, has turned out to be a figment of our imagination, says Graham Lawton http://www.thedivineconspiracy.org/Z5221S.pdf Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009 Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html
bornagain77

Well Nick, as to:
There probably isn’t a single new protein fold between chimps and humans, for instance — based on what we know, all of mammalia or even vertebrates could have evolved without any new protein folds
And yet we find, at least, 1000 ORFan genes in humans alone that are not found in any other species. Completely unique ORFan genes that were thrown out of the human gene count, in one study, simply because the neo-Darwinists doing the study could not find the ORFan genes in any other species: This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 'ORFan' genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!
Human Gene Count Tumbles Again - 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes. Although this was strong evidence that the sequences were not true protein-coding genes, it was not quite convincing enough to justify their removal from the human gene catalogs. Two other scenarios could, in fact, explain their absence from other mammalian genomes. For instance, the genes could be unique among primates, new inventions that appeared after the divergence of mouse and dog ancestors from primate ancestors. Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm
The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true. If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins:
A survey of orphan enzyme activities Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles. http://www.biomedcentral.com/1471-2105/8/244 Dr. Howard Ochman - Dept. of Biochemistry at the University of Arizona Excerpt of Proposal: The aims of this proposal are to investigate this enigmatic class of genes by elucidating the source and functions of “ORFans”, i.e., sequences within a genome that encode proteins having no homology (and often no structural similarity) to proteins in any other genome. Moreover, the uniqueness of ORFan genes prohibits use of any of homology-based methods that have traditionally been employed to establish gene function.,,, Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins. https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-5/#comment-358868
In fact it turns out that the authors of the 'kick the ORFans out in the street' paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore it in favor of their preconceived evolutionary bias:
Comment by gpuccio on their analysis https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-4/#comment-358547
Moreover the 'anomaly' of unique ORFan genes is found in every new genome sequenced:
Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166
As well, completely contrary to evolutionary thought, these 'new' ORFan genes are found to be just as essential as 'old' genes for maintaining life:
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New genes in Drosophila quickly become essential. - December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages. http://www.sciencemag.org/content/330/6011/1682.abstract
I would like to reiterate that Darwinian evolutionists cannot account for the origination of even one unique gene or protein, much less the over one thousand completely unique ORFan genes found deeply imbedded within the 20,000 genes of the human genome:
Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." http://www.creationsafaris.com/epoi_c10.htm "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: - Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences." http://www.mendeley.com/research/estimating-the-prevalence-of-protein-sequences-adopting-functional-enzyme-folds/
bornagain77

Nick, I'm seeing a lot of personal attacks and attempts at character assassination on ID proponents. 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. bbigej

Nick, If you had explained it in previous threads we wouldn't be talking about it again.
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.
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. At best you offer a handful of genetic differences and hope that we'll give you credit for pointing out the obvious - that two different plants are bound to have identifiable genetic differences. You insist that such processes effect the change, but then you are unable to explain the changes in the very terms of those processes. You revert to more vague descriptions of phenotypic change. 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. ScottAndrews

Really Nick??? REALLY??? Does this include ‘confirmation’ for THE PRIMARY, and most important, claim of neo-Darwinism that purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present???
We've had, like, a million threads on the origin of new genes. They typically go like this: someone says "evolution can't explain how 'purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present'! I explain how gene duplication + mutation + selection can generate new genes with new functions, which is new information on any reasonable definition of "information". I also give lots of references. Pretty soon the IDists beat a hasty retreat to the origin of life and forget that their original claim was that evolution couldn't produce ANY new information. Re: Luskin -- his argument is so poor he couldn't even convince a longtime Telic Thoughts blogger. See guts's reply, and my reply, here, since Luskin bravely closed the DI thread: http://telicthoughts.com/casey-luskin-vs-kimura/ My reply to Luskin, which I'll quote here http://telicthoughts.com/casey-luskin-vs-kimura/#comment-277428
nickmatzke Says: September 29th, 2011 at 2:16 am Hmm, Luskin wrote a big reply and then closed comments, which sadly I noticed only after composing a reply. I'll post it here. Casey — very briefly as I am in London and will not spend too much time on this - 1. One of the points of Meyer's book was that his argument was different than Behe's and Dembski's, and added something to them. He says this several times, that he's not just rehashing their arguments. But, when you are defending the book, you retreat to IC-like arguments. So what was the point of the book and all of the subsequent rhetoric? We might as well have just ignored Meyer's book and should have just kept arguing about whether the IC argument works, since the "information" argument can't stand on its own without IC supporting it. As it stands, while playing defense you've walked Meyer's argument all the way back to "evolution can't produce new protein folds", which is dramatically less bold than claiming that evolution can't produce new genes and new information (which was what the main message of Meyer's book and all the propaganda surrounding it was — go back and read the promotional materials and the original taunts from the ID side, before you guys started playing defense and claiming that the book wasn't about intelligence being required to produce information). There probably isn't a single new protein fold between chimps and humans, for instance — based on what we know, all of mammalia or even vertebrates could have evolved without any new protein folds 2. Similarly, you keep going back to calculations based on the ASSUMPTION that IF it takes some moderately large number of mutations before some selectable function is achieved, THEN the expected waiting time for such events to occur is way to long occur in the history of the earth. But this is an unproven and unlikely "if". I'm sure you disagree, but that's the point — all of the probability calculations are just a smokescreen, because 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. Assessing this requires not more smokescreen calculations, but a fair assessment of whether or not it really in fact looks like multiple independent changes would ever be required to produce the kinds of changes that have occurred in biological history. My experience is that (a) this question is usually ignored by you guys, who just brazenly assume it is so and then proceed to snow your audience with calculations, and (b) whenever some case is investigated in detail, the features (sequences, proteins, whatever) that are supposed to be "required for function" are typically (1) not all universally required and/or (2) are known to be present, often widespread, in systems without the function. This has happened with the flagellum, the immune system, the wing, the malaria pfcrt resistance gene, etc. etc. Plus, over here in real biology, we know of lots of generic, basic facts that indicate that gradual, step-by-step paths through sequence space are a reasonable thing to believe in. The fact that a protein can have the same structure & function with essentially no sequence similarity is one piece of evidence. The very fact that protein sequences fit into a neat phylogenetic tree, with every amount of percentage difference between sequences, from 0 to 90%+, is evidence of this, and not just dismissible as "its only evidence of common ancestry". * * (Note: and, to head off the usual ID bafflegab on tree congruence, observed congruence between different genes and proteins is always or almost always statistically very strong congruence. This is a universal problem with creationist/IDist arguments about congruence and incongruence in phylogenetic trees: the IDists have no concept of the fact, well-known in phylogenetics, that congruence and incongruence are quantatively measurable, and even the "incongruence" that biologists themselves often highlight is quite minor disagreement in a very tiny region of Possible Tree Space. Another piece of evidence is that you can do histograms of the distance between homologous genes and get a nice bell curve, exactly what you expect if the differences between sequence pairs are due to gradual divergence through many independent point mutation events: http://www.talkorigins.org/faq... 3. Re: Sdic – I linked to a detailed graphic from a paper, I guess you missed that, here it is again: http://pandasthumb.org/archive... Please give us the equivalently detailed ID explanation of Sdic — doesn't matter if it's just a hypothesis, what would a "detailed ID explanation" of Sdic even look like? They become absurd as soon as you start proposing them in concrete fashion. 4. Origin of the Sdic promotoer. This gets us back to point #2 — IDists/creationists have this instinctual feeling that various sequence features that they see must be "highly specific" and "hard to evolve" — but that's all it is, subjective gut instinct, usually put forward camouflaged with irrelevant calculations and with a complete lack of the kind of responsible review of the literature you would have to do to even begin to make such claims. Over in actual biology, what is known is that promoter sequences are typically short, they occur throughout genomes and many of them aren't even being used, and they occur at random at high frequency even in randomly-generated sequence. ID/creationist instinctual feelings about scientific matters do no a rigorous argument make. 5. Re: detecting selection. You aren't getting what a selective sweep is. It's not the fact that everyone has the same allele — that applies to most of the human genome, for instance. It's the amount of polymorphism when you compare two or more homologous chromosomes. A gene under selection will sweep through the population, but adjacent sequence will be dragged along with it. At the end of the sweep, the whole region around the selected gene will have very low diversity across the population. The shape of the curve depends on the rate of crossing over and the strength of selection. Diversity gradually returns over time, depending on the mutation rate. It's not like this stuff is obscure, there are armies of population geneticists that work on just this stuff. The quote you keep using/abusing about the problems with computational detection of selection is about a rather different thing — trawling through entire genomes with a computer in an attempt to pick out evidence of selective sweeps, biases in nonsynonymous substitutions, etc. Because such projects are running millions of statistical tests, and there is random noise in any stochastic process such as mutation, crossing over, etc., and effects like population expansion and contraction can influence all this, it is trickier to be confident that every positive result picked up in one of these fishing expeditions is a real case of selection. Probably a lot of it is, but one has to estimate the rate of false positives etc. It's rather different when, a priori, you have a reason to think that a specific spot in the genome is of interest and may have been effected by selection — for instance, when an obvious new gene is found that is the fusion of two adjacent genes, as in Sdic, which is found in one species but not close relatives. In that context, seeing a classic signature of a selective sweep is highly suggestive. This isn't even abstract-theory-which-creationists-can-deny-because- theory-is-hard-and-they'd -rather-not think-about it. When they looked at the peppered moth genome and found the allele that causes dark bodies, guess what they found in the surrounding region of the chromosome? That's right, significant diversity dip, classic evidence of recent selective sweep. Bam. Even at Telic Thoughts they were surprised at your missing the boat on this point, Casey: http://telicthoughts.com/casey... It leads to the interesting question — if an ID commentator is unfamiliar with basic introductory material in a scientific field, yet nevertheless is engaged in announcing to the world that the entire field is bunk, why should scientists take ID seriously? There is other stuff that could be said but I'd rather go to Kew Gardens. Cheers, Nick Comment by nickmatzke — September 29, 2011 @ 2:16 am
NickMatzke_UD

Nick, I thought we were talking about the evolution of a snap-trap from a glue trap. Why are you retreating to a variation in mucilage? It is both possible and likely. It’s also possible and likely that a variation might result in a rodent having longer forelimbs. That does not explain bats. When pressed to explain your extrapolation you retreat defensively to a safer position. That’s fine. If you want to say that evolution can increase or decrease the amount of mucilage on a leaf, so be it. We can leave it there and now we both agree on what type of changes evolution can produce.
Hmm, I guess you didn't read my previous posts on the other threads after all. 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. Pretty please, go back and read that stuff, we had several threads on it, I can't sit around typing out the origin of the Venus Flytrap over and over and over again. NickMatzke_UD

Nick Matzke:
Saying that epigenetics determines genome size is a contradiction in terms — epigenetics is what happens on top of the genome, e.g. methylation. If the genome size changes, that’s genetics, straight-up.
If the genome size changes due to factors beyond itself and the organism it occupies, then that's epigenetics, straight-up. Or, as Dr Spetner put it in "Not By Chance"- "built-in responses to environmental cues". Joseph

Nick, I thought we were talking about the evolution of a snap-trap from a glue trap. Why are you retreating to a variation in mucilage? It is both possible and likely. It's also possible and likely that a variation might result in a rodent having longer forelimbs. That does not explain bats. When pressed to explain your extrapolation you retreat defensively to a safer position. That's fine. If you want to say that evolution can increase or decrease the amount of mucilage on a leaf, so be it. We can leave it there and now we both agree on what type of changes evolution can produce. ScottAndrews

Nick matzke:
So, you really think that it’s unlikely that evolution can quantitatively increase or decrease the amount of mucilage secreted by a leaf?
Nice equivocation, Nick. It's as if you really believe your ignoirance is some sort of refutation. ID is not anti-evolution, Nick, so when you say:
So, you really think that it’s unlikely that evolution can quantitatively increase or decrease the amount of mucilage secreted by a leaf?
What "evolution" are you talking about? Are you talking about: A) Front-loaded evolution B) Intelligent Design evolution C) Blind Watchmaker evolution
Why should anyone believe this is unlikely? It’s a simple change in degree, and typically such changes are just a matter of upregulating or downregulating a pathway, which is just a matter of altering the binding strength of a promoter or some such.
Then you should have no problem going into a lab and conducting experiments to demonstrate your claim. In the absence of that you don't have any science. Joseph

As well Nick, it might interest you to know, (Actually it will probably be severely 'inconvenient' for you to know, since you fight so hard against the truth), that proof for non-locality, (beyond space and time causation), of 'material' reality was recently extended past the 'spooky action at a distance' effects of quantum entanglement (A. Aspect), to the 'material' particles themselves! i.e. Now, a transcendent 'non-local' (beyond space and time) cause must be supplied to explain the existence of 'material' particles in this universe in the first place:
'Quantum Magic' Without Any 'Spooky Action at a Distance' - June 2011 Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically.,,, Asher Peres, a pioneer of quantum information theory, once remarked jokingly in a letter to a colleague (Dagmar Bruß): Entanglement is a trick 'quantum magicians' use to produce phenomena that cannot be imitated by 'classical magicians'. When two particles are entangled, measurements performed on one of them immediately affect the other, no matter how far apart the particles are. What if, in an experiment, one considers a system that does not allow for entanglement? Will the quantum magicians still have an advantage over the classical magicians? Quantum physics beyond magic This is the question the team of quantum physicists led by Anton Zeilinger from the Faculty of Physics at the University of Vienna and from the IQOQI of the Austrian Academy of Sciences addressed in their experiment. The physicists used a "qutrit" -- a quantum system consisting of a single photon that can assume three distinguishable states. "We were able to demonstrate experimentally that quantum mechanical measurements cannot be interpreted in a classical way even when no entanglement is involved," Radek Lapkiewicz explains. The findings relate to the theoretical predictions by John Stewart Bell, Simon B. Kochen, and Ernst Specker. Quantum world versus everyday life Quantum physics is in stark contrast with what we perceive and experience in our everyday lives and what we understand as "classical physics." http://www.sciencedaily.com/releases/2011/06/110624111942.htm Why the Quantum? It from Bit? A Participatory Universe? Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: "In the beginning was the Word." Professor Anton Zeilinger - a leading expert in quantum teleportation and quantum information: http://www.metanexus.net/Magazine/ArticleDetail/tabid/68/id/8638/Default.aspx
Further notes: The following describes how quantum entanglement is related to functional information:
Quantum Entanglement and Information Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. http://plato.stanford.edu/entries/qt-entangle/
Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
Quantum Entanglement and Teleportation – Anton Zeilinger – video http://www.metacafe.com/watch/5705317/
A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:
Quantum Teleportation Excerpt: To perform the teleportation, Alice and Bob must have a classical communication channel and must also share quantum entanglement — in the protocol we employ*, each possesses one half of a two-particle entangled state. http://www.cco.caltech.edu/~qoptics/teleport.html
And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian worldview of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!
Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp Atom takes a quantum leap – 2009 Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,, “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second. http://www.freerepublic.com/focus/news/2171769/posts
Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments??? i.e. It is simply COMPLETELY IMPOSSIBLE for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles!!! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!! verse and music:
John 1:1-3 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. Casting Crowns - The Word Is Alive http://www.metacafe.com/watch/5197438/ Flyleaf - All Around Me http://www.youtube.com/watch?v=xN0FFK8JSYE
bornagain77

Nick you state:
Evolution, on the other hand, is confirmed by evidence almost every place you look, if you take a fair and thorough look at the primary evidence
Really Nick??? REALLY??? Does this include 'confirmation' for THE PRIMARY, and most important, claim of neo-Darwinism that purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present??? Seems to me your grand claims for such irrefutable proof for neo-Darwinism, from the 'primary evidence', were just recently shown to be non-existent!!!:
Leading Darwin Defender Admits Darwinism's Most "Detailed Explanation" of a Gene Doesn't Even Tell What Function's Being Selected - Casey Luskin - October 5, 2011 Excerpt: ...You (Nick Matzke) just admitted that the most "detailed explanation" for the evolution of a gene represents a case where: *they don't even know the precise function of the gene, *and thus don't know what exactly what function was being selected, *and thus don't know if there are steps that require multiple mutations to produce an advantage, *and thus haven't even begun to show that the gene can evolve in a step-by-step fashion, *and thus don't know that there are sufficient probabilistic resources to produce the gene by gene duplication+mutation+selection. In effect, you have just admitted that Darwinian explanations for the origin of genes are incredibly detail-poor. http://www.evolutionnews.org/2011/10/leading_darwin_defender_admits051551.html
Nick, how quickly you seem to forget this so as to move on the ever important onion argument? :) That episode with Casey Luskin is fairly embarrassing in itself as to shooting down your very own credibility for any claims you might make in the future (a boy crying wolf if you will),,,, yet you also stated this;
People messing with science, in the teeth of the facts, is what bothers me.
Really Nick??? REALLY??? I actually have such anger towards neo-Darwinian atheists for 'messing with science'! Moreover, It might interest you to know that, 'science' would not even be possible if neo-Darwinism were true! Thus if you truly loved science, as you claim you do, then you would in fact be angry with atheistic neo-Darwinists for perverting it so severely to their own personal agenda:
Should You Trust the Monkey Mind? - Joe Carter Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties. http://www.firstthings.com/onthesquare/2010/09/should-you-trust-the-monkey-mind What is the Evolutionary Argument Against Naturalism? ('inconsistent identity' of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) - video http://www.youtube.com/watch?v=5yNg4MJgTFw Can atheists trust their own minds? - William Lane Craig On Alvin Plantinga's Evolutionary Argument Against Naturalism - video http://www.youtube.com/watch?v=byN38dyZb-k "But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?" - Charles Darwin - Letter To William Graham - July 3, 1881 “Atheism turns out to be too simple. If the whole universe has no meaning, we should never have found out that it has no meaning...” CS Lewis – Mere Christianity “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.” J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.
This following site is a easy to use, and understand, interactive website that takes the user through what is termed 'Presuppositional apologetics'. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.
Proof That God Exists - easy to use interactive website http://www.proofthatgodexists.org/index.php
Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:
Dr. Bruce Gordon - The Absurdity Of The Multiverse & Materialism in General - video http://www.metacafe.com/watch/5318486/ John Lennox - Science Is Impossible Without God - Quotes - video remix http://www.metacafe.com/watch/6287271/
further notes:
Materialism compared to Theism within the scientific method: http://docs.google.com/Doc?docid=dc8z67wz_5fwz42dg9 Christianity Gave Birth To Each Scientific Discipline - Dr. Henry Fritz Schaefer - video http://vimeo.com/16523153
bornagain77

Nick: "And atheist philosophy? Puh-lease. The Gnu Atheists bash me worse than you guys for not being on their side." Nick, this is good to know, and thank you for clarifying your position. At least you're in good company! "Evolution, on the other hand, is confirmed by evidence almost every place you look . . ." This statement, however, is possible only by the rhetorical trick of conflating wildly different meanings of "evolution," from the obvious and well-supported to the outrageous and wildly-speculative. Once a person escapes from the intellectual trap of thinking that "evolution" is a single process that operates across the whole of reality, the evidence for "evolution" looks a whole lot more modest. Eric Anderson

Do you really need me to cite you saying that glue traps evolved into snap-traps by a series of incremental, selected variations? If you don’t think you said that, just tell me. This is your central dogma, and one of the primary reasons why critical thinkers ridicule darwinism. Having asserted it, why would you ever think the demands for evidence would stop unless you produced it, yielded, or just gave up and went away?
So, you really think that it's unlikely that evolution can quantitatively increase or decrease the amount of mucilage secreted by a leaf? That's where we left the discussion on the last CP thread. Why should anyone believe this is unlikely? It's a simple change in degree, and typically such changes are just a matter of upregulating or downregulating a pathway, which is just a matter of altering the binding strength of a promoter or some such. NickMatzke_UD

Nick Matzke you deliver priceless commenting gold to have on display here. Please do not stop schooling us ID/creasionist. butifnot

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!!!
LOL -- then you ought to be able to find plenty of times where I've argued for atheism. I bet you can't find *any*. It's not something I do -- I am actually pretty profoundly disinterested in theism vs. atheism. I doubt it's resolvable on objective evidence. Evolution, on the other hand, is confirmed by evidence almost every place you look, if you take a fair and through look at the primary evidence, and don't rely on misinterpretations of news stories, wishful thinking based on superficial study, etc. People messing with science, in the teeth of the facts, is what bothers me. NickMatzke_UD

Onions have lotsa DNA, therefore, all of biology of have been one massive fluke. The evidence is overwhelming... bbigej

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!!! notes:
coast to coast – Blind since birth – Vicki’s Near Death Experience http://www.youtube.com/watch?v=e65KhcCS5-Y Kenneth Ring and Sharon Cooper (1997) conducted a study of 31 blind people, many of who reported vision during their Near Death Experiences (NDEs). 21 of these people had had an NDE while the remaining 10 had had an out-of-body experience (OBE), but no NDE. It was found that in the NDE sample, about half had been blind from birth. (of note: This 'anomaly' is also found for deaf people who can hear sound during their Near Death Experiences(NDEs).) http://findarticles.com/p/articles/mi_m2320/is_1_64/ai_65076875/
It is also very interesting to point out that the 'light at the end of the tunnel', reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as an observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences: (Of note: This following video which was made by two Australian University Physics Professors with a supercomputer.)
Traveling At The Speed Of Light - Optical Effects - video http://www.metacafe.com/watch/5733303/
Here is the interactive website, with link to the relativistic math at the bottom of the page, related to the preceding video;
Seeing Relativity http://www.anu.edu.au/Physics/Searle/
Here are some 'typical' Near Death Experiences from Judeo-Christian cultures
The NDE and the Tunnel - Kevin Williams' research conclusions Excerpt: I started to move toward the light. The way I moved, the physics, was completely different than it is here on Earth. It was something I had never felt before and never felt since. It was a whole different sensation of motion. I obviously wasn't walking or skipping or crawling. I was not floating. I was flowing. I was flowing toward the light. I was accelerating and I knew I was accelerating, but then again, I didn't really feel the acceleration. I just knew I was accelerating toward the light. Again, the physics was different - the physics of motion of time, space, travel. It was completely different in that tunnel, than it is here on Earth. I came out into the light and when I came out into the light, I realized that I was in heaven.(Barbara Springer) Near Death Experience – The Tunnel, The Light, The Life Review – video http://www.metacafe.com/watch/4200200/
further note:
Science and Theism: Concord, not Conflict* – Robert C. Koons IV. The Dependency of Science Upon Theism (Page 21) Excerpt: Far from undermining the credibility of theism, the remarkable success of science in modern times is a remarkable confirmation of the truth of theism. It was from the perspective of Judeo-Christian theism—and from the perspective alone—that it was predictable that science would have succeeded as it has. Without the faith in the rational intelligibility of the world and the divine vocation of human beings to master it, modern science would never have been possible, and, even today, the continued rationality of the enterprise of science depends on convictions that can be reasonably grounded only in theistic metaphysics. http://www.robkoons.net/media/69b0dd04a9d2fc6dffff80b3ffffd524.pdf
bornagain77

Perhaps someone should start a Please Be Nice to Me I Only Came To Ridicule You But I Get Sad When You Ask Difficult Questions thread. Perhaps the simple question won't haunt you there. ScottAndrews

Sorry, Nick. It's just that you're so busy and I thought I'd catch you while you have time. Somehow the time always flies away talking about onions and there's never time to address the central question of how you can know that incremental genetic variations are selected to produce significant diversity in living things when you have not determined or even bothered to imagine a detailed pathway. You know, that one critical piece of information that either validates the theory or leaves it blowing in the wind. Do you really need me to cite you saying that glue traps evolved into snap-traps by a series of incremental, selected variations? If you don't think you said that, just tell me. This is your central dogma, and one of the primary reasons why critical thinkers ridicule darwinism. Having asserted it, why would you ever think the demands for evidence would stop unless you produced it, yielded, or just gave up and went away? ScottAndrews

Nick this is OT, but in case your interested, Holly Ordway, a former atheist, is interviewed by Apologetics315 here; http://www.youtube.com/watch?v=uA4pho7QfVw
Wow, trying to convert me? And here I thought this ID stuff was just about science, not apologetics. Listening to this while running a program -- she started out being an English Ph.D. by hating Christians, then found out her nice fencing coach was one. This doesn't really speak to me, as I don't hate Christians. I was raised religious but am not particularly now, although I'm not anti-religious either. But, would you like know the biggest thing than made me agnostic about religion? Creationists and their continual, unabated, shameless, eternally uncorrected shenanigans. Once you've seen creationists distort scientific evidence, distort the views of scientists, etc., once you've seen them refuse to correct such mistakes in themselves and others, once you've seen them do this on an industrial and institutional scale, all the while insulting hardworking scientists and blaming them for pretty much every bad thing that has ever happened, it's hard to not be more than little skeptical of their critical thinking abilities, intellectual honesty (not in the sense of lying, but in the sense of doing "due diligence" before opening one's big fat mouth about some technical topic), and the rest. If creationists/IDists want to evangelize people like me, they should start correcting each other's mistakes before I do, they should start criticizing widespread but indefensible creationist views (like young-earthism), and they should start making arguments that are not shot down by a few minutes on Wikipedia and Google Scholar. NickMatzke_UD

Re: carnivorous plants, "information", etc. -- start a new post if you want to talk about off-topic stuff, there is no point to discussing a million things at once. And, it would be nice if you quoted my previous remarks on those topics and explained why they are wrong, rather than just inviting me to rehash the same basic case I've made several times already. NickMatzke_UD

Got it, Nick, the genome sizes of onions are an effect of their population size. That would explain why raspberries have a genome about 8% the size of ours. Or does it? And that would explain the difference in genome sizes within onions of the same population. Or does it?
Dude, you are just being angry, not making any sense. Raspberries could well have a larger historical population size than humans. You also have to factor in generation time, growth rate, number of offspring per generation, etc. It seems that fast-growing, fast-reproducing critters tend to have smaller genomes. And it's just a hypothesis in any case. Might be wrong, but it's dang well better than "Let's just brazenly assume everything is functional, despite all the evidence against this idea, and let's call all the scientists who are aware of the evidence idiots while we're at it."
And that would explain the difference in genome sizes within onions of the same population. Or does it?
The onions with different genome sizes are not in the same population, they are different species. Take a deep breath and think before you write, dude! NickMatzke_UD

Nick, if Mr Andrews hasn't worn you out, I could always use another refresher course on the rise of information. Upright BiPed

Better audio to music video:
The Police – Spirits in the Material World http://www.youtube.com/watch?v=cDs9zbiumDc
bornagain77

Got it, Nick, the genome sizes of onions are an effect of their population size. That would explain why raspberries have a genome about 8% the size of ours. Or does it? And that would explain the difference in genome sizes within onions of the same population. Or does it? If you ever have time to explain it to me, don't. Use it to describe to me the incremental genetic steps, both the variation and selection, leading from a glue trap to a flypaper trap. Sadly you've used up all your precious time telling me what you don't know about onions and once again you have none left to illustrate how the cornerstone of biology works. Come up with that and with your newfound credibility I'll just take your word for all the rest. ScottAndrews

Well Nick, perhaps we should just go a little deeper into exactly what kind of epigenetic information we are dealing with; A few comments as to 'non-local' epigenetic information: Though when many people speak of epigenetic information they are mainly focused on information flow in the cell that is not DNA centric in its basis, such as the many examples of epigenetic information flow Dr. Shapiro lists on page 22 of this following paper: ,,,
Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009 http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
,,,There is a particular type of extra ‘epigenetic’ information in life, that is not listed in Dr. Shapiro’s paper, that is very important for people to consider. To give a little background on this ‘extra’ epigenetic information, Dr. Stephen Meyer comments at the end of this following video,,,
Stephen Meyer – Functional Proteins And Information For Body Plans – video http://www.metacafe.com/watch/4050681/ ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009)
So exactly where does this mysterious information, that Dr. Meyer illustrates the necessity of, that controls the overall ‘biological form’ of a organism, actually reside if not in DNA coding??? I think a very strong case can be made that it is ‘non-local’, beyond space and time, quantum information, which is not reducible to a material basis (A. Aspect), that is what is actually in control of, and orchestrating, the biological forms of organisms to be in the particular ‘3D shapes’ we find them in.,,, To show the plausibility of this, first we find that DNA itself would not even have its necessary helical shape/structure if it were not for ‘non-local’ quantum information/entanglement holding it in that particular shape;
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. “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/
As well, DNA is shown to do ‘chemically impossible’ things here, thus, once again, demonstrating 'non-local' information's overarching control of '3-D form' in molecular structures:
Does DNA Have Telepathic Properties?-A Galaxy Insight Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to. Explanation: None, at least not yet.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible. http://www.dailygalaxy.com/my_weblog/2009/04/does-dna-have-t.html
As well, At the 6:05 minute mark, of this following video, cells are witnessed as they pull themselves together, from a distance, to form 'flawless' blood vessels. The commentator on the video refers to the 'at a distance' action of the cells as a 'miracle';
Fearfully and Wonderfully Made - Glimpses At Human Development In The Womb - video http://www.metacafe.com/watch/4249713 Psalm 139:13-14 For you created my inmost being; you knit me together in my mother's womb, I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.
Next we also find that non-local, beyond space and time, quantum information/entanglement is also necessary for dictating the final shape that proteins will take upon protein folding;
Quantum states in proteins and protein assemblies: The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign. http://www.tony5m17h.net/SHJTQprotein.pdf
Another very interesting piece of evidence, that 'non-local’ quantum information/entanglement is dictating the shape of a organism, comes forth when we realize that the ‘4-Dimensional shape’ of a organism fairly quickly disintegrates to 3-dimensional thermodynamic equilibrium upon the death of the organism:
“Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection." Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 The Unbearable Wholeness of Beings – Steve Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
As well it is very interesting to note that this quantum information/entanglement, which will assuredly be 'totally missing’ from the organism, once the organism disintegrates to complete thermodynamic equilibrium, is shown to be ‘conserved’. i.e. This transcendent non-local quantum information, though missing from the dead, and now disintegrated, organism must reside somewhere 'in the universe':
Quantum no-deleting theorem Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist. http://en.wikipedia.org/wiki/Quantum_no-deleting_theorem#Consequence
It is clear that a very strong case is now evident, that ‘non-local’ quantum information/entanglement is in fact the ‘highest level’ of epigentic information in organisms, and that it is this non-local, beyond space and time, epigentic information that is, in fact, ‘shaping’ 4 dimensional creatures in this 3-Dimensional world!!! Music:
The Police - Spirits in the Material World http://www.youtube.com/watch?v=-LtN7evu-eI Matthew 16:26 What good will it be for a man if he gains the whole world, yet forfeits his soul? Or what can a man give in exchange for his soul?
bornagain77

Nick, I did read it. You can't have it both ways. It's junk. It has no function. It does have a function, but one that doesn't technically count as a function. The more you carry on about what you think you might know about genes, their purpose or lack of it, the more it underscores that most of of it over your head. I don't mean that as bad as it sounds, because you clearly know a great deal. I know what it sounds when someone tries to sound even smarter by stating what they don't know. It sounds like this:
The only interesting question is whether or not some higher-level factor like selection favors particular genome sizes, and thus spreads insertions in some genomes, and deletions in others, or whether genome size is just a byproduct of e.g. population size, where extra DNA is always deleterious, but very mildly so, such that only in very large populations with rapid generation time is selection strong enough to favor the very weakly beneficial deletions.
Notice how you admit to not knowing why there is a difference in genome size (no problem there) but then lay it on pretty thick as you suggest that you've got it narrowed down to two distinct possibilities while leaving the door open for other unnamed 'higher-level factors.' Most people only need a few words to say they have no idea, and then I trust them more when they say they do know something. I had a friend who talked like you. I can hear it a mile away. ScottAndrews

For this stuff to make any sense to you, you would have to understand the influence of population size on selection/drift balance, I don't have time to explain it, maybe someone else will. NickMatzke_UD

That's right! Quit tossing around words starting with "e" that mean just about anything and everything! (Except "everything.") ScottAndrews

You haven't been reading what I've written, I've already laid out the two major ideas in the scientific community, see here: https://uncommondescent.com/junk-dna/thoughts-on-the-c-value-enigma-the-onion-test-and-junk-dna/comment-page-1/#comment-402595 and here: https://uncommondescent.com/darwinism/the-original-onion-test-is-a-biological-non-sequitur/comment-page-1/#comment-402687 NickMatzke_UD

Nick that is far from the ONLY question, and in my view is secondary to the question of what epigenetic mechanism is driving the variance.
You can't just toss around the word "epigenetics" like it means whatever poorly-specified notion is in your head. Saying that epigenetics determines genome size is a contradiction in terms -- epigenetics is what happens on top of the genome, e.g. methylation. If the genome size changes, that's genetics, straight-up. NickMatzke_UD

Nick this is OT, but in case your interested, Holly Ordway, a former atheist, is interviewed by Apologetics315 here; http://www.youtube.com/watch?v=uA4pho7QfVw bornagain77

Nick,
The only interesting question is whether or not some higher-level factor like selection favors particular genome sizes, and thus spreads insertions in some genomes, and deletions in others
You've just finished calling it junk. Maybe you're right. But why would selection favor either junk or specific genome sizes? If that were the case, then by definition the extra genes would be advantageous, therefore functional. This is true even if you overlook the circular logic that cannot distinguish between advantage and selection. Are you redefining natural selection so that it can "select" was does not affect differential reproduction? Or are you admitting that it's a tautology, defined as whatever survives, including enlarged genomes? Or are you saying that the enlarged genomes actually do provide a selectable advantage, contradicting everything you've just said before? ScottAndrews

Here's the answer to the onion test: Namely, that not all introns are functional. Many introns are functionless. Nevertheless, under a teleological perspective, the first introns were functional. Not all introns are functional because of whole-genome duplications. Let's say we have an onion with a small genome size. That genome is duplicated. There is no selective pressure to preserve the function of the duplicated introns (just like duplicated genes can often tolerate far more mutations than the original gene), and so the duplicated introns become functionless. Repeat this process several times and you have an onion population with a large genome size and large chunks of functionless introns. Nevertheless, the first introns were functional. This answers the onion test from a teleological context. LivingstoneMorford

Now who is being the lawyer Nick??? bornagain77

as to this comment:
The only interesting question is whether or not some higher-level factor like selection
Nick that is far from the ONLY question, and in my view is secondary to the question of what epigenetic mechanism is driving the variance. For you to presuppose the variance is completely random is to completely ignore where the cutting edge science is at right now (Shapiro for one cite), And indeed I would hold you position to be a science stopper! bornagain77

I am just opposing the numerous statements of the ID movement to the effect that junk DNA was a stupid idea, that the genome is "chock-full" of digital code, and that most/all of the genome is functional. Gregory is making a narrow point about the confusing history of the term. He certainly does not, though, think it is valid to declare or assume that most/all of the genome has organismal function, especially some kind of sexy, informational function, which is what IDists usually imply. When I use the word "junk", I am referring to the "no very important function" position. The primary, and very, very, good, evidence for this position, is that it is manifestly true that some organisms have way more DNA than is really required to build them, and we know this for a fact because basically similar organisms (even the same genus, or sister species) have much, much less DNA. And atheist philosophy? Puh-lease. The Gnu Atheists bash me worse than you guys for not being on their side. NickMatzke_UD

This is true, but I believe the onion genome sizes are all haploid values, i.e. it is not a matter of diploids vs. tetraploids vs. hexaploids etc. The usual explanation for dramatic differences in genome size is self-replication of the repetitive elements. LINES, SINES, etc. can easily get copied again and again in the genome, blowing up its size. Genome size is determined by a balance between genome-growing elements such as LINES and SINES, and removal mechanisms like deletion. The only interesting question is whether or not some higher-level factor like selection favors particular genome sizes, and thus spreads insertions in some genomes, and deletions in others, or whether genome size is just a byproduct of e.g. population size, where extra DNA is always deleterious, but very mildly so, such that only in very large populations with rapid generation time is selection strong enough to favor the very weakly beneficial deletions. NickMatzke_UD

Petrushka, let's assume for a moment this is correct. What does it tell us about junk DNA generally? Not much. No-one disputes that duplications occur. This issue is that the iconic myth of "junk DNA" in humans has been shouted from the rooftops, over and over and over again, as a wonderful example of bad design and a confirmation of Darwinian evolution. That assessment has turned out to be spectacularly wrong, which, according to the Darwinists' own logic then, must operate as a *refutation* of the Darwinian mechanism. You can't have it both ways. Either junk DNA is irrelevant and never did support Darwinism in the first place, or it is relevant and has refuted Darwinism in the case of human junk DNA. Now the Darwinist lobby moves on to another example of what they think is junk DNA, in Nick's case, apparently misrepresenting what Gregory intended to say and making pronouncements without having the faintest idea whether the DNA is junk or not. The real kicker is that ID proponents don't dispute that machines break down, that code can get messed up, that errors can occur in the history of life. In contrast, the materialist cannot accept even a single example of design in the history of life, or his whole materialistic enterprise goes up in smoke. Some of us are willing to look at the world, realize some things are designed and others aren't, and then delve into the interesting question of whether and how we can detect which things are designed. The materialist can never even grasp this interesting question, because it lies beyond his philosophical blinders. Eric Anderson

Then why in blue blazes are you using the word 'junk DNA' to further your atheistic philosophy, instead of using “non-coding DNA” so Gregory suggests. But then again it is not about the science is it Nick??? It is about your religion!!! bornagain77

I myself noted this on the other thread: https://uncommondescent.com/junk-dna/thoughts-on-the-c-value-enigma-the-onion-test-and-junk-dna/comment-page-1/#comment-402596 NickMatzke_UD

Blas, as with Petrushka's cite, all you are ever going to get from neo-Darwinists is misdirection that never addresses core questions such as what is the functionality for why the genome size is at it is. bornagain77

Perhaps a little thinking outside of the 'central dogma' box?
Picture: Thinking Outside The Box http://www.crystalinks.com/outsidebox.jpg
Notes:
Modern Synthesis of Neo-Darwinism (Genetic Reductionism) Is Dead - Paul Nelson - video http://www.metacafe.com/watch/5548184/
Also of interest in the following paper other than the quote that is excerpted, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis) model of neo-Darwinism.
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
Eugene Koonin also agrees that the modern evolutionary synthesis (Genetic Reductionism/Central dogma) is devastated.
The Origin at 150: is a new evolutionary synthesis in sight? - Koonin - Nov. 2009 Excerpt: The edifice of the modern synthesis has crumbled, apparently, beyond repair. http://www.arn.org/blogs/index.php/literature/2009/11/18/not_to_mince_words_the_modern_synthesis
Dr. Sternberg has also come out very hard against 'neo-Darwinian narratives';
On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. - Richard Sternberg Excerpt: It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes. http://www.ncbi.nlm.nih.gov/pubmed/12547679
Further notes:
Deep Genomics: In the Case of DNA, the Package Can Be as Important as Its Contents, New Work With Fruit Flies Reveals - January 2011 http://www.sciencedaily.com/releases/2011/01/110113102158.htm Gene Regulatory Networks in Embryos Depend on Pre-existing Spatial Coordinates - Jonathan Wells - July 2011 Excerpt: The development of metazoan embryos requires the precise spatial deployment of specific cellular functions. This deployment depends on gene regulatory networks (GRNs), which operate downstream of initial spatial inputs (E. H. Davidson, Nature 468 [2010]: 911). Those initial inputs depend, in turn, on pre-existing spatial coordinate systems. In Drosophila oocytes, for example, spatial localization of the earliest-acting elements of the maternal GRN depends on the prior establishment of an anteroposterior body axis by antecedent asymmetries in the ovary. Those asymmetries appear to depend on cytoskeletal and membrane patterns rather than on DNA sequences,,, http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=7751 “Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340
verse and music:
Psalm 139:13 For you created my inmost being; you knit me together in my mother's womb. Live - Heaven (official video) http://www.youtube.com/watch?v=Ff3NUP-xzqQ
bornagain77

Whole genome duplications are common in plants, and have occurred in animals. http://en.wikipedia.org/wiki/Polyploid Petrushka

Shouldn´t darwinist explain first how one onion specie has 7 times the genome size of other onion specie from a common ancestor via RM + NS? Blas

Nick, Your statements are deeply rooted in assumptions. Maybe they are accurate assumptions. But why not question them?
If you’re going to claim, as ID advocates have again and again and again, that junk DNA is a crock, scientists were idiots for ever believing in such a thing, and most/all DNA is functional, you need to explain why some onions need multiple human genome’s worth of DNA more than other onions
You assume that there are only two possibilities. Either the onion needs the extra DNA to function, or it is junk. That assumption naturally follows from other assumptions. Maybe you're right on both counts. But it's odd that in a field dependent on boundless imagination that's all you can come up with. ScottAndrews

This is a interesting comment from Gregory, the originator of the onion test, at the bottom of the page:
The onion test. by T. Ryan Gregory, on April 25th, 2007 Excerpt: 1) I do not endorse the use of the term “junk DNA”, which I think has deviated far too much from its original meaning and is now little more than a loaded buzzword; the descriptive term “non-coding DNA” is what I use to refer to the majority of eukaryotic sequences (of various types) that do not encode protein products. - http://www.genomicron.evolverzone.com/2007/04/onion-test/
Are you listening Nick??? bornagain77

Interesting. When the facts start getting inconvenient, bring out the lawyerly hair-splitting. Unfortunately the facts are still inconvenient for you. Most of the difference in genome sizes is typically due to repetitive elements. Gene counts etc. don't change very much even between genomes with hugely different sizes. If you're going to claim, as ID advocates have again and again and again, that junk DNA is a crock, scientists were idiots for ever believing in such a thing, and most/all DNA is functional, you need to explain why some onions need multiple human genome's worth of DNA more than other onions, and why onions in general have genomes many times the size of the human genome. Otherwise, the argument that a lot of the DNA in organisms with large genome isn't doing much is pretty strong. After all, you can build an onion with a few human genomes worth of DNA, so clearly building an onion with 20 human genomes worth of DNA is not strictly necessary. NickMatzke_UD

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