Uncommon Descent Serving The Intelligent Design Community

Can a Lowly Lawyer Make a Useful Contribution?  Maybe.

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Dr. Moran has asked me to respond to some technical questions over at Sandwalk.  When I started writing this response I intended to put it in his combox.  Then I realized there is a lot in it that is relevant to our work at UD.  So I will put it here and link to it there.

Dr. Moran, before I answer your technical questions, allow me to make one thing perfectly clear.  I am not a scientist, much less a biologist.  I am an attorney, and being an attorney has some pluses and some minuses insofar as participating in the evolution debate goes.  Like many people in the last 25 years, I was inspired to become involved in this debate by Phillip E. Johnson’s “Darwin on Trial.”  Johnson is also an attorney, and he said this about what an attorney can bring to bear:

I approach the creation-evolution dispute not as a scientist but as a professor of law, which means among other things that I know something about the ways that words are used in arguments. . . . I am not a scientist but an academic lawyer by profession, with a specialty in analyzing the logic of arguments and identifying the assumptions that lie behind those arguments.  This background is more appropriate than one might think, because what people believe about evolution and Darwinism depends very heavily on the kind of logic they employ and the kind of assumptions they make.

Johnson is saying that attorneys are trained to detect baloney.  And that training is very helpful in the evolution debate, because that debate is chock-full of faulty logic (especially circular reasoning), abuse of language (especially equivocations), assumptions masquerading as facts, unexamined premises, etc. etc.

Consider, to take one example of many, cladistics.  It does not take a genius to know that cladistic techniques do not establish common descent; rather they assume it.  But I bet if one asked, 9 out of 10 materialist evolutionists, even the trained scientists among them, would tell you that cladistics is powerful evidence for common descent.  As Johnson argues, a lawyer’s training may help him understand when faulty arguments are being made, sometimes even better than those with a far superior grasp of the technical aspects of the field.  This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.

In summary, I am trained to evaluate arguments by stripping them down to examine the meaning of the terms used, exposing the underlying assumptions, and following the logic (or, as is often the case, exposing the lack of logic).  And I think I do a pretty fair job of that, both in my legal practice and here at UD.

Now to the minuses.  I do not claim personally to be able to evaluate technical scientific questions.  Like the vast majority of people, I rely on the secondary literature, which, by and large, is accessible to a layman such as myself.  When it comes to independent analysis of technical scientific questions, I have nothing useful to say.

Back to our cladistics example.  I have a very general understanding of how clads are made and what they mean.  But I do not claim to be an expert in the technical issues that arise in the field.  Of course, that is not an obstacle to spotting a faulty argument about cladistics, as I explained above.

Digging deeper – to the fundamental core of the matter – my baloney detector allows me to spot metaphysical assumptions masquerading as scientific “facts.”  This is especially useful in the evolution debate, because – to use KF’s winsome turn of phrase – evolutionists love to cloak their metaphysical commitments in the holy lab coat.

Consider the following claim:  Evolution is a fact.

Yes it is, and it most certainly is not, depending on what one means by the word “evolution.”  If all you mean is that living things were different in the past than they are now, then sure.  Even YEC’s believe that.  But if you mean that modern materialist evolutionary theory has been proven to such a degree that it would be perverse to withhold consent, then the statement is absolutely not a fact.  Even materialist evolutionists dispute such vital issues as the relative importance of natural selection.  This is quite aside from the fact that many people (especially ID proponents) do not believe the theory is even plausible, far less unassailable.

Yet I can’t tell you how many times I have caught materialists in this very equivocation.  I do not believe that materialists are always being intentionally misleading when they say this.  Some are but not all.  Those in the latter group have a commitment to materialist metaphysics that is so strong that they often cannot tell where their metaphysics ends and their empirical observations begin.  A person who allows his materialist metaphysical commitments to blind him, may truly believe that the mere fact that living things are different now than they were in the past is, on its face, evidence for materialist evolutionary theory.  Why?  Because if materialism is true, then materialist evolutionary theory must also be true as a matter of simple logic even before we get to the evidence.

And as a matter of strict logic, they are correct.  The conclusion follows from the premises.  The argument is valid.  But what materialist fundamentalists never stop to ask is whether the argument is also sound.  Is that crucial premise “metaphysical materialism is true” a false statement?  There are good reasons to believe that it is, and sometimes it takes someone with a good baloney detector – someone like a lawyer – to clue them in on this.  As astounding as it seems, it is very often the case that materialist evolutionists not only fail to acknowledge an unstated assumption that is absolutely critical to their argument; but also they fail to even know that they’ve made that assumption in the first place and that that assumption might possibly be false.  I can help them understand those things.

Comments
Phinehas asks,
We can talk about potential beneficial changes ’til the cows come home, but what changes do we actually observe? For me, this is where Behe’s argument edges out his detractors. What he is proposing appears to line up with what we actually see. He may still end up being wrong, but at least he’s stepped out of the bubble where everything is about what could happen and into the reality of what has actually been observed to happen. Would that others would join him there!
In the case of chloroquine resistance, you should read my post where I point out that Behe's reliance on Nicholas White is misguided for several reasons. Taking the Behe challenge! Flunking the Behe challenge! He is wrong to assume that White's observation can be directly interpreted as due to just the mutation rate. What that means is that Behe actually didn't rely on "the reality of what has actually been observed to happen." As for the likelihood of any human gene acquiring two different mutations in the past few million years—something that Behe predicts can't happen—see ... CCC's and the edge of evolution Now let's see what we actually see ... what's actually observed in the development of chloroquine resistance in Plasmodium. The important paper is Summers et al. (2014).
Summers, R. L., Dave, A., Dolstra, T. J., Bellanca, S., Marchetti, R. V., Nash, M. N., Richards, S. N., Goh, V., Schenk, R. L., Stein, W. D., Kirk, K., Sanchez, C. P., Lanzer, M. and Martin, R. (2014) Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite’s chloroquine resistance transporter. Proceedings of the National Academy of Sciences. published online April 11, 2014. [doi: 10.1073/pnas.1322965111]
You can read about it on Sandwalk where I discuss why it is relevant to Behe's calculations. Michael Behe and the edge of evolution What Summers et al. did was to look at existing populations of chloroquine resistant Plasmodium to see which mutations were required for resistance. They discovered that multiple mutations were required but that most of them had no effect by themselves. Some strains required just two mutations while others required three or four. They all had the key K76T mutation. The authors show that this mutation by itself is neutral with respect to chloroquine resistance. It needs additional potentiating neutral mutations at other sites. They then look at natural populations of Plasmodium that were sensitive to the drug and found that single copies of these mutations were present in many of the populations. What presumably happened, according to the observations, is that neutral mutations arose in a populations and reached significant frequency by random genetic drift. Then a second mutation occurred on this background and the combination of the two mutations gave rise to chloroquine resistance. This is all based on actual observations of living populations of the malarial parasite. You do not need two particular mutations to happen simultaneously; therefore, it is incorrect to calculate the overall probability by just multiplying together the mutation rates for two single mutations. Why is this a problem for you? Why do you think that Behe's incorrect guesstimate based on White's observation is better than the actual sequence data of Summers et al.?Larry Moran
November 17, 2015
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LM:
Lots of potential beneficial changes involving several mutations are well within the edge of evolution once you realize that neutral alleles—and even deleterious alleles—can be fixed in a population by random genetic drift. That’s where Behe’s argument fails. He didn’t take that into account.
We can talk about potential beneficial changes 'til the cows come home, but what changes do we actually observe? For me, this is where Behe's argument edges out his detractors. What he is proposing appears to line up with what we actually see. He may still end up being wrong, but at least he's stepped out of the bubble where everything is about what could happen and into the reality of what has actually been observed to happen. Would that others would join him there!Phinehas
November 17, 2015
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Gordon Davisson actually since you cannot establish that unguided evolution is in the least bit feasible with real time empirical evidence then that refutes YOUR atheistic claim for common ancestry by unguided material processes. That you say ID is compatible with common ancestry is a shameless attempt by you to avoid having to deal with the gross empirical shortcoming of your preferred atheistic worldview. Most honest people would realize that this complete failure to empirically validate their atheistic worldview with real time evidence refutes their atheistic worldview as true and then drop atheism as their worldview. But you are not an honest atheist and just pretend as if this complete failure in validation is no big deal. You are wrong! It is, as far as science itself is concerned, a very big deal. You simply have no real time empirical basis whatsoever for the grand sweeping claims you are making for unguided material processes in the remote past. Integrity is certainly not a strong suit of atheists. Now if you want to argue common descent more honestly and admit that Intelligence is necessary to even explain life in the first place, as say gppucio and Torley honestly do, then you may have a more firm basis to stand on as far as CD is concerned. I personally consider the Theistic evolution position to be pathetically weak, but at least you would have a firmer foundation to stand on, as far as science itself is concerned, than you do now. Your foundation which I affectionately refer to as the 'feet firmly planted in mid air foundation'. :) Moreover, it is impossible for me to debate your philosophical position with 'you' since there is no 'you' to have an opinion one way or the other in the first place. There are only a bunch of neurons producing an illusion of a person named Gordon who thinks that his opinions matter. Given atheism, they don't matter since they, and the person holding them, don't even really exist. i.e. I don't object to, nor have arguments with, illusions. Just as I don't debate rocks. It is insane argue with rocks and with illusions. Only real persons can have real opinions! But "You" don't exist, ergo no debate is possible.bornagain
November 16, 2015
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bornagain@117:
Gordon Davisson, your idea of what constitutes real time empirical evidence and what real time empirical evidence actually is are two VERY different things. I’ve been looking for real time empirical evidence for Darwinian evolution for a long time now. I’ve found none
What's the relevance of "real time" empirical evidence? We are (or at least were) talking about common ancestry, which is a historical claim, and thus inherently cannot be tested in real time. You seem to have switched to talking about limits on the capabilities of evolution. But since as we're told over and over (and I agree) that ID is fully compatible with common ancestry, I don't see any relevance at all. Your objections to my philosophical views are even more irrelevant.Gordon Davisson
November 16, 2015
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Joe: "I asked Larry Moran what chemicals are free,..." Could you provide a link to where you asked Larry this question? I looked, but can't seem to find it. But I am using an iPhone and the search features are non-existant.brian douglas
November 16, 2015
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Excellent links Born. I asked Larry Moran what chemicals are free, you know, seeing as how he likes to judge other peoples reasoning and sees people as soul-less chemical bags in motion but he never did tell me which chemical elements that he teaches his students are free, Yet the materialist Moran likes to judge others as wrong. It makes no sense to say chemistry is acting incorrectly. These Materialists are very strange people.Jack Jones
November 16, 2015
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Gordon makes this humorous claim in 116:
So stick your fingers in your ears and your head in the sand for as long as you want, but it’s you, not I, that is ignoring reality.
Now this 'reality claim' is a very humorous claim for Gordon, a materialistic atheist, to make since, given the reductive materialistic premises that he believes in, Gordon himself does not even really exist as a real person, but is merely a neuronal illusion.
"that “You”, your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules. As Lewis Carroll’s Alice might have phrased: “You’re nothing but a pack of neurons.” This hypothesis is so alien to the ideas of most people today that it can truly be called astonishing.” Francis Crick - "The Astonishing Hypothesis" 1994 “We have so much confidence in our materialist assumptions (which are assumptions, not facts) that something like free will is denied in principle. Maybe it doesn’t exist, but I don’t really know that. Either way, it doesn’t matter because if free will and consciousness are just an illusion, they are the most seamless illusions ever created. Film maker James Cameron wishes he had special effects that good.” Matthew D. Lieberman – neuroscientist – materialist – UCLA professor "What you’re doing is simply instantiating a self: the program run by your neurons which you feel is “you.”" Jerry Coyne The Confidence of Jerry Coyne - January 6, 2014 Excerpt: But then halfway through this peroration, we have as an aside the confession that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant: But more on that below.) Prometheus cannot be at once unbound and unreal; the human will cannot be simultaneously triumphant and imaginary. per NY TIMES
At the 23:33 minute mark of the following video, Richard Dawkins agrees with materialistic philosophers who say that:
"consciousness is an illusion"
A few minutes later Rowan Williams asks Dawkins
”If consciousness is an illusion…what isn’t?”. https://www.youtube.com/watch?v=HWN4cfh1Fac&t=22m57s
at 37:51 minute mark of following video, according to the law of identity, Richard Dawkins does not exist as a person: (the unity of Aristotelian Form is also discussed) i.e. ironically, in atheists denying that God really exists, they end up denying that they themselves really exist as real persons.
Atheistic Materialism – Does Richard Dawkins Exist? – video Quote: "It turns out that if every part of you, down to sub-atomic parts, are still what they were when they weren't in you, in other words every ion,,, every single atom that was in the universe,, that has now become part of your living body, is still what is was originally. It hasn't undergone what metaphysicians call a 'substantial change'. So you aren't Richard Dawkins. You are just carbon and neon and sulfur and oxygen and all these individual atoms still. You can spout a philosophy that says scientific materialism, but there aren't any scientific materialists to pronounce it.,,, That's why I think they find it kind of embarrassing to talk that way. Nobody wants to stand up there and say, "You know, I'm not really here". https://www.youtube.com/watch?v=rVCnzq2yTCg&t=37m51s
And in the following article Dawkins reluctantly admits that it is impossible for him to live as if his atheistic worldview were actually true
Who wrote Richard Dawkins's new book? - October 28, 2006 Excerpt: Dawkins: What I do know is that what it feels like to me, and I think to all of us, we don't feel determined. We feel like blaming people for what they do or giving people the credit for what they do. We feel like admiring people for what they do.,,, Manzari: But do you personally see that as an inconsistency in your views? Dawkins: I sort of do. Yes. But it is an inconsistency that we sort of have to live with otherwise life would be intolerable.,,, http://www.evolutionnews.org/2006/10/who_wrote_richard_dawkinss_new002783.html
Indeed, anybody who lived as if atheism were actually true would be considered psychopathic
The Heretic - Who is Thomas Nagel and why are so many of his fellow academics condemning him? - March 25, 2013 Excerpt:,,,Fortunately, materialism is never translated into life as it’s lived. As colleagues and friends, husbands and mothers, wives and fathers, sons and daughters, materialists never put their money where their mouth is. Nobody thinks his daughter is just molecules in motion and nothing but; nobody thinks the Holocaust was evil, but only in a relative, provisional sense. A materialist who lived his life according to his professed convictions—understanding himself to have no moral agency at all, seeing his friends and enemies and family as genetically determined robots—wouldn’t just be a materialist: He’d be a psychopath. http://www.weeklystandard.com/articles/heretic_707692.html?page=3
Although many atheists, because it refutes their atheistic worldview, try to claim that they still really exist as real persons even given materialistic premises, many prominent atheists actually do readily, and honestly, confess to this self-refuting absurdity, that is inherent to the materialistic philosophy, of denying that they really exist as real persons:
Darwin's Robots: When Evolutionary Materialists Admit that Their Own Worldview Fails - Nancy Pearcey - April 23, 2015 Excerpt: Even materialists often admit that, in practice, it is impossible for humans to live any other way. One philosopher jokes that if people deny free will, then when ordering at a restaurant they should say, "Just bring me whatever the laws of nature have determined I will get." An especially clear example is Galen Strawson, a philosopher who states with great bravado, "The impossibility of free will ... can be proved with complete certainty." Yet in an interview, Strawson admits that, in practice, no one accepts his deterministic view. "To be honest, I can't really accept it myself," he says. "I can't really live with this fact from day to day. Can you, really?",,, In What Science Offers the Humanities, Edward Slingerland, identifies himself as an unabashed materialist and reductionist. Slingerland argues that Darwinian materialism leads logically to the conclusion that humans are robots -- that our sense of having a will or self or consciousness is an illusion. Yet, he admits, it is an illusion we find impossible to shake. No one "can help acting like and at some level really feeling that he or she is free." We are "constitutionally incapable of experiencing ourselves and other conspecifics [humans] as robots." One section in his book is even titled "We Are Robots Designed Not to Believe That We Are Robots.",,, When I teach these concepts in the classroom, an example my students find especially poignant is Flesh and Machines by Rodney Brooks, professor emeritus at MIT. Brooks writes that a human being is nothing but a machine -- a "big bag of skin full of biomolecules" interacting by the laws of physics and chemistry. In ordinary life, of course, it is difficult to actually see people that way. But, he says, "When I look at my children, I can, when I force myself, ... see that they are machines." Is that how he treats them, though? Of course not: "That is not how I treat them.... I interact with them on an entirely different level. They have my unconditional love, the furthest one might be able to get from rational analysis." Certainly if what counts as "rational" is a materialist worldview in which humans are machines, then loving your children is irrational. It has no basis within Brooks's worldview. It sticks out of his box. How does he reconcile such a heart-wrenching cognitive dissonance? He doesn't. Brooks ends by saying, "I maintain two sets of inconsistent beliefs." He has given up on any attempt to reconcile his theory with his experience. He has abandoned all hope for a unified, logically consistent worldview. http://www.evolutionnews.org/2015/04/when_evolutiona095451.html Existential Argument against Atheism - November 1, 2013 by Jason Petersen 1. If a worldview is true then you should be able to live consistently with that worldview. 2. Atheists are unable to live consistently with their worldview. 3. If you can’t live consistently with an atheist worldview then the worldview does not reflect reality. 4. If a worldview does not reflect reality then that worldview is a delusion. 5. If atheism is a delusion then atheism cannot be true. Conclusion: Atheism is false. http://answersforhope.com/existential-argument-atheism/
Dr. Nelson weighs in here
Do You Like SETI? Fine, Then Let's Dump Methodological Naturalism - Paul Nelson - September 24, 2014 Excerpt: "Epistemology -- how we know -- and ontology -- what exists -- are both affected by methodological naturalism (MN). If we say, "We cannot know that a mind caused x," laying down an epistemological boundary defined by MN, then our ontology comprising real causes for x won't include minds. MN entails an ontology in which minds are the consequence of physics, and thus, can only be placeholders for a more detailed causal account in which physics is the only (ultimate) actor. You didn't write your email to me. Physics did, and informed you of that event after the fact. "That's crazy," you reply, "I certainly did write my email." Okay, then -- to what does the pronoun "I" in that sentence refer? Your personal agency; your mind. Are you supernatural?,,, You are certainly an intelligent cause, however, and your intelligence does not collapse into physics. (If it does collapse -- i.e., can be reduced without explanatory loss -- we haven't the faintest idea how, which amounts to the same thing.) To explain the effects you bring about in the world -- such as your email, a real pattern -- we must refer to you as a unique agent.,,, some feature of "intelligence" must be irreducible to physics, because otherwise we're back to physics versus physics, and there's nothing for SETI to look for.",,, http://www.evolutionnews.org/2014/09/do_you_like_set090071.html
And although Dr. Nelson alluded to writing an e-mail, (i.e. creating information), to tie his ‘personal agent’ argument into intelligent design, Dr. Nelson’s ‘personal agent’ argument can easily be amended to any action that ‘you’, as a personal agent, choose to take:
“You didn’t write your email to me. Physics did, and informed the illusion of you of that event after the fact.” “You didn’t open the door. Physics did, and informed the illusion of you of that event after the fact.” “You didn’t raise your hand. Physics did, and informed the illusion you of that event after the fact.” “You didn’t etc.. etc.. etc… Physics did, and informed the illusion of you of that event after the fact.” Human consciousness is much more than mere brain activity, - Mark Vernon - 18 June 2011 However, "If you think the brain is a machine then you are committed to saying that composing a sublime poem is as involuntary an activity as having an epileptic fit. ...the nature of consciousness being a tremendous mystery." http://www.guardian.co.uk/commentisfree/belief/2011/jun/17/human-consciousness-brain-activity
Dr. Craig Hazen, in the following video at the 12:26 minute mark, relates how he performed, for an audience full of academics at a college, a ‘miracle’ simply by raising his arm,,
The Intersection of Science and Religion – Craig Hazen, PhD – video http://www.youtube.com/watch?feature=player_detailpage&v=xVByFjV0qlE#t=746s
What should be needless to say, if raising your arm is enough to refute your supposedly ‘scientific’ worldview of atheistic materialism/naturalism, then perhaps it is time for you to seriously consider getting a new scientific worldview?bornagain
November 16, 2015
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Gordon Davisson, your idea of what constitutes real time empirical evidence and what real time empirical evidence actually is are two VERY different things. I've been looking for real time empirical evidence for Darwinian evolution for a long time now. I've found none The last four decades worth of lab work are surveyed here, and no evidence for neo-Darwinian evolution surfaces:
“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/
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. per True Origin
That doesn’t seem to be helping. How about we look really, really, close at very sensitive growth rates and see if we can find any evidence for neo-Darwinian evolution?
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
Well, that doesn’t seem to be helping either. How about if we just try to fix an unconditionally ‘beneficial’ mutation by sustained selection?
Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010 Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies
Well that’s certainly disappointing. How about if try to help neo-Darwinian evolution out a little and just saturate genomes with mutations until we can actually see some ‘evolution’ in action?
Response to John Wise – October 2010 Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html
Now this is starting to get a little frustrating. Perhaps we just have to give neo-Darwinian evolution a little ‘room to breathe’? How about we ‘open the floodgates’ 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 Lenski's Long-Term Evolution Experiment: 25 Years and Counting - Michael Behe - November 21, 2013 Excerpt: Twenty-five years later the culture -- a cumulative total of trillions of cells -- has been going for an astounding 58,000 generations and counting. As the article points out, that's equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski's project the best, most detailed source of information on evolutionary processes available anywhere,,, ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, - http://www.evolutionnews.org/2013/11/richard_lenskis079401.html
Now that just can’t be right. 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’ ‘beneficial 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. Isn’t neo-Darwinian evolution an established fact on par with gravity? 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, and let’s REALLY open the floodgates and let’s see what neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal. Surely now neo-Darwinian evolution will flex its awesomely powerful muscles for all to see 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 "The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable." - Michael Behe - The Edge of Evolution - page 146 Michael Behe - Observed (1 in 10^20) Edge of Evolution - video - Lecture delivered in April 2015 at Colorado School of Mines 25:56 minute quote - "This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not." https://www.youtube.com/watch?v=9svV8wNUqvA
Now, there is something terribly wrong here! After looking high and low and everywhere in between, we can’t seem to find any substantiating evidence for neo-Darwinism anywhere! 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! And that would make anyone who claims it is an established fact on par with gravity a LIAR!bornagain
November 16, 2015
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Gordon, Your just so stories are what they are. Just so stories. You have no empirical evidence.
Did you look at the graph that Hunter posted? The complete lack of overlap between the distances for the real vs. random sequences? THAT IS EMPIRICAL EVIDENCE. It's far from the only evidence on my side, but it's plenty to refute your claim that I have no evidence. So stick your fingers in your ears and your head in the sand for as long as you want, but it's you, not I, that is ignoring reality.Gordon Davisson
November 16, 2015
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Box said,
It is as if Moran did not read Behe’s rebuttal of his article “Understanding Michael Behe”. As far as I can see in #98 LM just rehashes points already addressed and which brought up nothing.
Of course I read Michael Behe's response. You can assume that I haven't changed my mind based on that reading and that's why I explained the correct facts in #98. It's pretty obvious that Behe and I disagree on a few of his claims in The Edge of Evolution. That shouldn't come as a big surprise. Your mission, should you choose to accept it, is to decide who's right. How are you going to do that? Ask Barry Arrington? My goal here is not to convince you that evolutionary biologists are always correct, although that would be a nice bonus. My goal is to make most of you understand that ID proponents are not always correct and you shouldn't always assume that everything they say is the truth. Be as skeptical about ID proponents as you are about evolutionary biologists. If you want to know the truth you are going to have to study the issue on your own.Larry Moran
November 16, 2015
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Gordon, Your just so stories are what they are. Just so stories. You have no empirical evidence. The severely discordant sequence data is far from your only problem. For instance, you have no evidence whatsoever that radical changes to body plans are even feasible by mutations to DNA as is held in neo-Darwinism (or mutations to anything else for that matter). Thus the sequence data, whether you agree with it or not, is moot and void anyway to the overall point you would like to make for your atheism:
'No matter what we do to a fruit fly embryo there are only three possible outcomes, a normal fruit fly, a defective fruit fly, or a dead fruit fly. What we never see is primary speciation much less macro-evolution' – Jonathan Wells Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs Response to John Wise - October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html Scant search for the Maker Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol. http://www.timeshighereducation.co.uk/story.asp?storycode=159282 Body plans, contrary to Darwinian presuppositions, simply are not reducible to DNA, period! That finding pretty much renders any Darwinian argument based on DNA alone moot and void: - Nov. 2015 https://uncommondescent.com/intelligent-design/are-some-of-our-opponents-in-the-grip-of-a-domineering-parasitical-ideology/#comment-587726
It would be nice if you guys ever actually followed the evidence where it leads instead of just making up flimsy excuses every time your hand is caught in the cookie jar. Friggin liars! All of ya!
THREE DOG NIGHT - LIAR (Rare Live 80s w / lyrics) https://www.youtube.com/watch?v=mq5_pEO8a8U
bornagain
November 16, 2015
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bornagain@110:
Gordon, the severely discordant sequence data is real. It is not an anomaly limited to just one study as you are pretending but is pervausive across all studies as my ‘spewed links’ clearly indicate. Your just so stories that try to explain away the one study are imaginary. I side with reality and against the usual Darwinian imagination that has no real data but only shallow excuses as to why the evidence does not ever really support Darwinian evolution.
I never said discordant sequence data isn't real (although I think "severely" is an exaggeration), nor did I say or imply that it was limited to just one study. "Pervasive across all studies" -- have you looked at all studies? No, of course not, you've only looked at studies that appear to support your case; any that don't get discarded. I only commented on one study (mostly because I happened to have looked at it before), but that certainly doesn't mean that I think it's the only one that exists. However, what I explained clearly shows that at least one of the studies you claimed supports your side does nothing of the sort! Common ancestry does not imply exact concordance, any more than the theory of gravity requires that feathers should fall at the same speed as bowling balls. As I said back at #2, you need to take into account everything that is acting on the phenomenon in question. In the case of gravity, you can't pretend that gravity is the only force acting on a falling body and expect to get agreement with actual results. Similarly, you can't pretend that common ancestry is the only thing influencing similarity among organisms and expect to get agreement with actual results. What you can do is say, e.g. "ok, gravity explains why most things fall at approximately the same rate; let's look at the ones that don't, and try to figure out what else is acting on them." That's essentially what a lot of the studies you cite are: "ok, common ancestry explains why most things fall into approximately convergent nested hierarchies; let's look at where they don't and see if we can figure out what else is going on." (Hints: statistical noise, horizontal genetic transfer, endosymbiosis, convergence, maybe a tangled net at the beginning of life, etc...) I don't claim that all trees are exactly concordant, that's plainly false. What I do claim (and even your own citations support this) is that there's far too much convergence to happen by chance (again, look at that graph that Cornelius Hunter posted -- there's no overlap!). Concordance is real, and it needs explaining. You have no explanation. Discordance is real, and it needs explaining. We have explanations. Trying to use discordance to refute common ancestry is exactly as bogus as trying to use feathers and helium balloons to refute gravity. (And no, ORFans don't support your case either. Did you forget that Vincent Torley refuted that recently?) (I just noticed Jack's comment -- you're seriously accusing someone other than bornagain of argument ad nauseam?)Gordon Davisson
November 16, 2015
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'argument ad nauseam' Ha ha ha ha :)bornagain
November 16, 2015
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@94 "And there you have it Jack, no matter how many time Zach is corrected on a point he thinks if he can just repeat the same lie over and over again that he has somehow, in his twisted reasoning, won the argument. Somebody on UD referred to this dishonest debating tactic as the ‘I can still type so I must still have an argument’ tactic. :)" Born my friend, he is relying on the fallacy of argument ad nauseam.Jack Jones
November 16, 2015
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Gordon, the severely discordant sequence data is real. It is not an anomaly limited to just one study as you are pretending but is pervausive across all studies as my 'spewed links' clearly indicate. Your just so stories that try to explain away the one study are imaginary. I side with reality and against the usual Darwinian imagination that has no real data but only shallow excuses as to why the evidence does not ever really support Darwinian evolution. For example, Here is Nelson on severely discordant bacteria ORFan data:
,,,”Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size.” Paul Nelson – quoted from 103:48 minute mark of the following video Whatever Happened To Darwin's Tree Of Life? – Paul Nelson – video https://youtu.be/9UTrZX47e00?t=3820 You can see the pie chart that Dr. Nelson used in his talk here on page 108 (figure 2) of this following article: Estimating the size of the bacterial pan-genome Excerpt Figure 2 pg. 108: At the genomic level, a typical bacterial genome is composed of _8% of core genes, 64% of character genes and 28% of accessory genes,,, http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf Estimating the size of the bacterial pan-genome - Pascal Lapierre and J. Peter Gogarten - 2008 Excerpt: We have found greater than 139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered. http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf
bornagain
November 16, 2015
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bornagain, you haven't shown that I was off the mark; all you did was spew links without bothering to understand them. The only one directly relevant to my comment was an update from Dr. Hunter ("Here Are Those Incongruent Trees From the Yeast Genome – Case Study – Cornelius Hunter"), but it doesn't show what you (or Dr. Hunter) think it does. He says "In fact, as the figure above shows, the individual gene trees did not converge toward the concatenation tree"; I'm not sure what he means by "converge". Possibly he thought most of them should show short distances from the concatenation tree, i.e. that the distance graph should have its peak near 0 distance? If so, I think he's unfamiliar with how noise will show up in many-dimensional spaces. The average distance from the consensus tree (0.40) is quite a bit smaller than the distance between the individual trees (0.52), though, which is what I'd think "convergence" would refer to here. The graph he gives does show something much more significant, though, that you and Hunter missed completely. See the dotted line on the right? Those are the distances between 1000 random trees; they have an average distance of 0.98. The distribution of distances for the actual trees doesn't overlap the distribution of trees for random sequences! The actual distances are almost all under 0.7 (most are between about 0.3 and 0.6); as far as I can see from the graph, none of the random sequences have distances below 0.9 and almost all are barely below 1.0. In short, the actual trees are far from perfect matches (again, expected because of the small sample size), but they're far FAR better than would be expected from random data. That means there's a real pattern here. And that pattern needs explaining. Do you have an explanation that fits the data better than common ancestry + statistical noise?Gordon Davisson
November 16, 2015
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spin it baby spin it! You'll be a politician yet! :) Three Shell Game https://www.youtube.com/watch?v=IFLa_tl4Rk0bornagain
November 16, 2015
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bornagain: Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution Here is a picture of Koonin's Big Bang. http://www.zachriel.com/blog/BigBangCladogenesis.gif Now, compare to Darwin's original diagram. http://darwin-online.org.uk/converted/published/1872_Origin_F391/1872_Origin_F391_figdiagram.jpg Notice that Darwin did not posit that branching would always be through bifurcation. Each of his nodes has multiple branches — not unlike Koonin's diagram. (Odd that Koonin didn't discuss incomplete lineage sorting in his book, as that would seem to be an important mechanism obscuring branching order during adaptive radiations.)Zachriel
November 16, 2015
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Of note, since Gordon was so far off the mark on the sequence data (i,e, "Not Even Wrong!"), I will not even bother to read his diatribe against quantum non-locality which I suspect to be even worse. Much worse.bornagain
November 16, 2015
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Gene tree discordance, phylogenetic inference and the multispecies coalescent - 2009 Excerpt: Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates. http://www.sciencedirect.com/science/article/pii/S0169534709000846 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 'The theory makes a prediction (for amino acid and nucleotide sequence studies); we've tested it, and the prediction is falsified precisely.' Dr. Colin Patterson Senior Principal Scientific Officer in the Paleontology Department at the British Museum Bones, molecules...or both? - Gura - 2000 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 Shilling for Darwin — The wildly irresponsible evolutionist - William Dembski - Oct. 2009 Excerpt: The incongruence of gene and species trees is a standing obstacle, or research problem, in molecular phylogenetics. https://uncommondescent.com/evolution/shilling-for-darwin-the-wildly-irresponsible-evolutionist/#comments 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 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 “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent." (Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution, Vol. 44, pgs. S117-S120) Darwin's Predictions - Cornelius Hunter PhD. Excerpt: 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] http://www.darwinspredictions.com/#_4.2_Genomes_of
bornagain
November 16, 2015
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A few more notes in regards to the SEVERELY incongruent sequence data:
“The genomic revolution did more than simply allow credible reconstruction of the gene sets of ancestral life forms. Much more dramatically, it effectively overturned the central metaphor of evolutionary biology (and, arguably, of all biology), the Tree of Life (TOL), by showing that evolutionary trajectories of individual genes are irreconcilably different. Whether the TOL can or should be salvaged—and, if so, in what form—remains a matter of intense debate that is one of the important themes of this book.” Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 76-80). Pearson Education (USA). Kindle Edition. Statistics and Truth in Phylogenomics - 2011 Excerpt: reports of highly significant P values are increasing even for contrasting phylogenetic hypotheses depending on the evolutionary model and inference method used, making it difficult to establish true relationships. http://mbe.oxfordjournals.org/content/29/2/457.full More Fossil-Molecule Contradictions: Now Even the Errors Have Errors - Cornelius Hunter - June 2014 Excerpt: a new massive (phylogenetic) study shows that not only is the problem (for Darwinists) worse than previously thought, but the errors increase with those species that are supposed to have evolved more recently.,,, "Our results suggest that, for Aves (Birds), discord between molecular divergence estimates and the fossil record is pervasive across clades and of consistently higher magnitude for younger clades." http://darwins-god.blogspot.com/2014/06/more-fossil-molecule-contradictions-now.html Here Are Those Incongruent Trees From the Yeast Genome - Case Study - Cornelius Hunter - June 2013 Excerpt: We recently reported on a study of 1,070 genes and how they contradicted each other in a couple dozen yeast species. Specifically, evolutionists computed the evolutionary tree, using all 1,070 genes, showing how the different yeast species are related. This tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. Yet one of the fundamental predictions of evolution is that different features should generally agree. It was “a bit shocking” for evolutionists, as one explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.” In fact, as the figure above shows, the individual gene trees did not converge toward the concatenation tree. Evolutionary theory does not expect all the trees to be identical, but it does expect them to be consistently similar. They should mostly be identical or close to the concatenation tree, with a few at farther distances from the concatenation tree. Evolutionists have clearly and consistently claimed this consilience as an essential prediction. But instead, on a normalized scale from zero to one (where zero means the trees are identical), the gene trees were mostly around 0.4 from the concatenation tree with a huge gap in between. There were no trees anywhere close to the concatenation tree. This figure is a statistically significant, stark falsification of a highly acclaimed evolutionary prediction. http://darwins-god.blogspot.com/2013/06/here-are-those-incongruent-trees-from.html The Mystery of Extreme Non-Coding Conservation - No Plausible Speculations - Cornelius Hunter - Nov. 2013 Excerpt: Consider this new paper from the Royal Society on “The mystery of extreme non-coding conservation” that has been found across many genomes. Years ago an evolution professor told me, in defending the claim that evolution is falsifiable, that if functionally unconstrained yet highly similar DNA sequences were found in different species, then evolution would be false. A few years later that is exactly what was discovered. In fact, the DNA sequences were extremely similar and even identical in different species,,, Did the professor agree that evolution was false? Not at all. For the fact of evolution goes far deeper than scientific findings and failed predictions.,,, Here is how the paper summarizes these findings of extreme sequence conservation: "… despite 10 years of research, there has been virtually no progress towards answering the question of the origin of these patterns of extreme conservation. A number of hypotheses have been proposed, but most rely on modes of DNA : protein interactions that have never been observed and seem dubious at best. As a consequence, not only do we still lack a plausible mechanism for the conservation of CNEs—we lack even plausible speculations." http://darwins-god.blogspot.com/2013/11/the-mystery-of-extreme-non-coding.html "Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species." (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, "Understanding phylogenetic incongruence: lessons from phyllostomid bats," Biological Reviews of the Cambridge Philosophical Society, Vol. 87:991-1024 (2012).) (Shhhhsh!, maybe they won't notice) Theory Creep: The Quiet Shift in Evolutionary Thought - Douglas Axe June 25, 2012 Excerpt: But if we fast-forward two more decades, it becomes clear that the consistent picture that everyone expected -- all genes confirming the same pattern of species relationships -- is not to be. What we have instead is something of a mess, as James Degnan and Noah Rosenberg made clear in a paper published in 2009(3): "Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates." And despite consistent attempts to portray this as something less than a crisis for evolutionary theory, the news found its way into the popular press. That same year, The Telegraph jumped on the story with an article titled, "Charles Darwin's tree of life is 'wrong and misleading,' claim scientists"4. http://www.evolutionnews.org/2012/06/theory_creep_th_1061301.html Evolutionist: Plants Are “Driving Me Nuts!” - Cornelius Hunter - July 2012 Excerpt: Plants also don’t fit into the evolutionary tree very well. Their DNA comparisons are inconsistent with their visible features,,, “The old family tree was now in for a major pruning. Roses were found to be closely related to squash, strawberries to marijuana, this meat-eating pitcher plant to China's famous rhododendrons. For centuries water lilies were thought to be nearly twins with the lotus—no longer.” MARK CHASE: "This, believe it or not, is the closest living relative of the lotus. This is the London plane tree or sycamore. As you can see, this is not a little water plant, this is a big tree." ANDREW DARRAGH (Horticulturist, Kew Gardens): …”driving me nuts!” http://darwins-god.blogspot.com/2012/07/evolutionist-plants-are-driving-me-nuts.html Evolutionist: Plants Are “Driving Me Nuts!” - Cornelius Hunter - July 2012 Excerpt: Plants also don’t fit into the evolutionary tree very well. Their DNA comparisons are inconsistent with their visible features,,, “The old family tree was now in for a major pruning. Roses were found to be closely related to squash, strawberries to marijuana, this meat-eating pitcher plant to China's famous rhododendrons. For centuries water lilies were thought to be nearly twins with the lotus—no longer.” MARK CHASE: "This, believe it or not, is the closest living relative of the lotus. This is the London plane tree or sycamore. As you can see, this is not a little water plant, this is a big tree." ANDREW DARRAGH (Horticulturist, Kew Gardens): …”driving me nuts!” http://darwins-god.blogspot.com/2012/07/evolutionist-plants-are-driving-me-nuts.html UCEs - Another Big Failure (For Darwinism) - Cornelius Hunter Dec. 20, 2012 Excerpt: 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. [1],,, Reaction “It can’t be true” was one evolutionist’s reaction to the UCE findings in recent years. [6] The findings falsify predictions of evolution, but they are true and they have been verified independently.,,, http://darwins-god.blogspot.com/2012/12/uces-see-somethingsay-something.html 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
bornagain
November 16, 2015
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It is as if Moran did not read Behe's rebuttal of his article "Understanding Michael Behe". As far as I can see in #98 LM just rehashes points already addressed and which brought up nothing.Box
November 16, 2015
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bornagain@45:
As to another empirical falsification of Darwinian theory, I find another empirical falsification of Darwinism by the now empirically established fact that ‘non-local’, beyond space and time, quantum entanglement/information is now found in molecular biology on a massive scale. Darwinism holds information (as well as consciousness) to be emergent from a reductive material basis. Quantum non-locality falsified that assumption. [...] That ‘non-local’ quantum entanglement, which conclusively demonstrates that ‘information’ in its ‘quantum form’ is completely transcendent of any time and space constraints (Bell, Aspect, Leggett, Zeilinger, etc..), should be found in molecular biology on such a massive scale, in every DNA and protein molecule, is a direct empirical falsification of Darwinian claims, for how can the ‘non-local’ quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) cause when the quantum entanglement effect falsified material particles as its own causation in the first place?
Wrong on all counts. Firstly, if we take the definition of "Darwinism" that the ID side seems to have settled on in these discussions (essentially, the synthetic theory of evolution aka new-Darwinism), it has no particular metaphysical entailments. It certainly uses methodological naturalism, but (despite KF's ranting) that does not imply metaphysical naturalism. You disagree? Ok, vital question: Is Dr. Francis Collins a Darwinist? He's certainly not a philosophical naturalist; he's a Christian, and a theistic evolutionist. If you claim he's a Darwinist, you're contradicting your link between Darwinism and reductive materialism. If you claim he's not a Darwinist, you're saying Barry doesn't know what Darwinism is (since he's been using Collins as an example Darwinist). As I said, evolutionary theory (and maybe Darwinism, whatever definition you settle on for that) does stick to methodological naturalism; but then, so do all other branches of science: geology, chemistry, astronomy, physics, etc... Do you rant against these and their materialist assumptions? Why just evolution? Wait a minute... physics uses methodological naturalism; that includes relativity, thermodynamcs, quantum mechanics.... but you're busy claiming that QM supports some sort of supernaturalism! Which brings me to my second point: quantum mechanics is just as much based on naturalism as evolutionary theory is: they're both based on methodological naturalism, but do not require (or contradict) metaphysical naturalism. (I'll note, though, that QM can be regarded as inconsistent with a strict view of materialism; it seems to imply that something like quantum fields exist, despite not really being "material" themselves. Philosophers sometimes distinguish between "materialism" and "physicalism", where physicalism includes materials and other physical things like fields as real. Most interpretations of QM violate strict materialm, but are consistent with physicalism.) I've pointed out before that your claims about QM are nonsense, but last time we talked you said you thought that nonlocality was inherently supernatural. I didn't seriously reply to that, because frankly the claim made no real sense to me. My reaction was more "huh???" than anything else. I think I've figured out your reasoning, but if I have... it's wrong. Let me give you a little physics history. Fairly early on, people figured out that objects could interact without touching. The sun and planets could exert gravitational forces on each other without touching, magnets could repel or attract without touching, etc. Some people regarded this "spooky action at a distance" as supernatural, since how else could objects affect each other without touching? But physicists came to regard this as being mediated by fields: a magnet produces a magnetic field, that spreads through space, and then the field acts locally on the other magnet. Similarly, electric charges produce an electric field, and objects with mass produce a gravitational field, and those spread through space and interact with other objects. Supernaturalism purged, materialism (well, physicalism actually) was safe, everyone was happy (except those who wanted a supernatural explanation for why planets stayed in their orbits). (And then the Aharonov–Bohm effect came along and people freaked out again; but that's another story.) Quantum mechanics has brought in a whole new class of "spooky action at a distance," thanks to entanglement. It's not clear what's actually going on, but whatever it is has to violate some things that we think of as obviously true. One class of possibilities involve a measurement at one location influencing another measurement at a different location. (There are other possibilities; superdeterminism and some versions of many worlds evade this requirement.) So what's wrong with a similar explanation here? QM already includes a field-like thing, the quantum wavefunction, which can fully explain the effect. The big thing that's different about this vs. the older types of spooky action at a distance is that this can happen instantaneously across long distances. Changes in the electromagnetic and gravitational fields don't travel any faster than the speed of light, but whatever's behind these QM effects doesn't obey that speed limit. The reason this is significant is that according to relativity, time is not absolute. When you have two events (e.g. the two measurements) far enough apart in space but close enough in time that light couldn't get from one to the other, then it's undefined which is before the other. Some observers will say one event happened first, some will say that the other happened first, and according to relativity, both are equally correct. This means that faster-than-light causal influences are sort-of equivalent to backward-in-time causal influences. So, this leaves us with a number of possibilities for what could cause these long-distance spooky correlations: 1) Something like superdeterminism or many-worlds could be correct. I'll ignore these for present purposes, but keep in mind that they are possible explanations. 2) Relativity could be wrong. In fact, we pretty much know that relativity is wrong (it doesn't get along with quantum field theory), but this particular aspect of it is generally thought to be solid. Let's ignore this possibility as well. 3) The measurement events could be linked via the quantum wavefunction (or something similar to it) in a way that violates normal forward-in-time-only causality. 4) The measurement events could be linked via some spooky supernatural force/entity/whatever in a way that violates normal forward-in-time-only causality. You're assuming that option #4 is the only possible explanation. That's clearly wrong, but your case is actually even weaker than that because #4 doesn't have any advantage at all over #3. Once you've given up forward-in-time-only causality, there's no reason at all to think the thing that violates it is supernatural. In fact, I'll go considerably further than that: option #3 explains why we get the specific correlations that we actually see, while with #4 the spooky supernatural force/entity/whatever it could do pretty much anything it feels like. If you want to claim that #4 is the correct explanation, you have to explain why the correlations follow the specific predictions of QM so closely. In the particular case that you think the supernatural thing in #4 is God, then you have to explain why God would act like such a slave to the equations of QM. Pray, and God might decide to answer you; rotate the polarizer on your detector, and God will hear and obey. I really don't think you want that in your theology.Gordon Davisson
November 16, 2015
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bornagain@90:
No Zach, it is just YOU, all by your lonesome, that is purposely lying about the sequence data.
Zachriel didn't claim that they were exactly congruent, he said they were mostly congruent (‘The overall pattern is congruent’). Pointing out discrepancies here and there does nothing to refute this. Compare phylogenetic trees based on different genes, and you'll often find some differences. Now try the same thing with cars, as I suggested above. Make a tree based on transmissions, and another based on body style. They'll have almost nothing to do with each other! Now try one based on engine layout (V8, V6, flat 6, flat 4, boxer, etc) and it'll have nothing to do with either of the other trees. Make one based on manufacturer and model... again, completely different. Well, ok, there'll be some correlations, like Porsche and Subaru tend to use boxer engines. But you'll be finding little bits of correlation against a broad pattern of nothing-to-do-with-each-other. Whereas with organisms you're finding little bits of discrepancy against a broad pattern of agreement. Take the study you linked under the headline "Contradictory Trees: Evolution Goes 0 For 1,070" (via Dr. Hunter, original article here. The first thing to ask is, how different were they? If someone measures something 1000 times and gets 1000 different results, that sounds really bad; but if the results are 1.00002514, 1.00000729, 0.99999830 etc, that's not really bad at all. They're all different, but not very far different. Did you or Dr. Hunter bother to look at this at all? No, you got a headline that fit your opinion, and stopped there. Now, I haven't read it either, since it's paywalled. But I read the abstract, and I can tell a fair bit about it from that. First: this was a study about how to best handle statistical noise in reconstructing phylogeny. They looked at phylogenetic trees reconstructed based on different single genes. With a single gene, you expect to get pretty noisy data. In general, the amount of "signal" in the sequence differences is proportional to the length of the sequence you're looking at (not surprising), and the amount of noise to be proportional to the square root of the length; that means the signal to noise ratio is proportional to the square root of the length being used. That means that by looking at individual genes rather than all of them together, they were decreasing the signal-to-noise ratio by a factor of over 30 (actually, probably worse because some genes will be shorter than others, some evolve slower, etc). This means you should expect the data to be pretty noisy, and the inferred trees similarly noisy. Certainly, much worse (30x worse) than even simply concatenating the genes would get you. But I asked about how different the trees were. The details are in the section I haven't read, but even just in the abstract there's an interesting detail: "Incongruence severity increased for shorter internodes located deeper in the phylogeny." There are two interesting facts here: - The incongruence wasn't so bad that they couldn't tell where it was. If you tried something like this with my car example, you'd find there wasn't enough matchup that you could point and say "there's a mismatch here"; instead you'd be saying "there's mismatch everywhere". Even though none of them matched exactly, there was still enough agreement to pick out where they disagreed. - The incongruence showed up exactly where I'd expect statistical noise to have the biggest effect: shorter internodes (there's another square-root effect here, similar to the one I mentioned earlier, so you expect shorter links to be noisier) located deeper in the phylogeny (where the inference is least direct, and thus likely to be most fragile). (Disclaimer: I'm not any sort of expert on data analysis, especially not phylogenetic analysis. But I've worked with enough data and am familiar enough with the principles to have a reasonably good idea how errors flow through an analysis and into the results.) So, we're seeing lots of statistical noise in a situation where we should see lots of statistical noise, behaving basically like statistical noise should behave. It appears the noise level was a bit higher than the researchers expected, but overall this isn't a particularly bad result, and certainly doesn't justify the OMG THIS IS ALL NONSENSE spin Dr Hunter put on it.Gordon Davisson
November 16, 2015
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Actually Behe is doing fine and well in regards to the empirical evidence and it is the Darwinian just so stories that are, as usual, in very poor health:
“The number I cite, one parasite in every 10^20 for de novo chloroquine resistance, is not a probability calculation. Rather, it is a statistic, a result, a data point. (Furthermore, it is not my number, but that of the eminent malariologist Nicholas White.) I do not assume that “adaptation cannot occur one mutation at a time”; I assume nothing at all. I am simply looking at the results. The malaria parasite was free to do whatever it could in nature; to evolve resistance, or outcompete its fellow parasites, by whatever evolutionary pathway was available in the wild. Neither I nor anyone else were manipulating the results. What we see when we look at chloroquine-resistant malaria is pristine data — it is the best that random mutation plus selection was able to accomplish in the wild in 10^20 tries.” Michael Behe - Rebuttal to Paul Gross https://uncommondescent.com/intelligent-design/can-a-lowly-lawyer-make-a-useful-contribution-maybe/#comment-588211
bornagain
November 16, 2015
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Box: In general an admission against interest, as Koonin did, is trustworthy. More so than the follow-up spin. Hey! Someone tried to actually respond to the point raised. What is the interest that involved lying on the one hand, and telling the truth on the other?Zachriel
November 16, 2015
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Phinehas asks,
But wasn’t part of his argument about two mutations being required based on the actual rate of the development of chloroquine resistance as demonstrated by the experimental data? You make it sound like it was only a prior commitment to mutations being either beneficial or deleterious that led him to his conclusions. But if the rate of chloroquine resistance actually observed lines up with what would be predicted if two simultaneous mutations were required, then what conclusion should he or anyone else draw from that?
It's complicated. Behe based his argument on mutation rates that were not correct and he failed to account for the probability of fixation and the probability of detection. The observed frequency of chloroquine resistance in wild-type populations should be far lower that the simple frequency that the mutations occur because not all occurrences will result in development of chloroquine resistance. (For example, in a patient who isn't being treated with chloroquine.) Understanding Michael Behe As it turns out, the actual probability of two mutations occurring simultaneously is about 1 in 10^20 in most species but likely an order of magnitude more probable in Plasmodium. If evolution were limited by the requirement that two mutations had to occur together (and become fixed) then these are pretty good ballpark numbers. Behe's calculations were incorrect but that's not really important. The important point is that chloroquine resistance arose by stepwise mutations and not by simultaneous mutations. More than two mutations were required. Lots of potential beneficial changes involving several mutations are well within the edge of evolution once you realize that neutral alleles—and even deleterious alleles—can be fixed in a population by random genetic drift. That's where Behe's argument fails. He didn't take that into account.Larry Moran
November 16, 2015
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Of related interest to the unhealthy 'denialism' that has infected Darwinian thought:
Fear of Intelligent Design Prevents Some Biologists from Accepting ENCODE's Results - Casey Luskin November 16, 2015 Excerpt: In his retrospective on ENCODE in Nature, Philip Ball acknowledges that there is an "anxiety that admitting any uncertainty about the mechanisms of evolution will be exploited by those who seek to undermine it."1 Likewise, pro-ENCODE biochemists John Mattick and Marcel Dinger observe that "resistance to [ENCODE's] findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design."2 Writing in a slightly different context, eight biologists published a Nature article in 2014 recognizing that scientists self-censor criticisms of neo-Darwinism because, "haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front."3 It's disturbing that scientists oppose empirically based research results or suppress their own doubts about the neo-Darwinian paradigm simply because they don't like the perceived alternative -- ID. These admissions show that evolutionary biology is in an incredibly unhealthy state, where devotion to the paradigm trumps the evidence. http://www.evolutionnews.org/2015/11/fear_of_intelli100881.html
also of note:
It's Really Not Rocket Science - Granville Sewell - November 16, 2015 Excerpt: In a 2005 American Spectator article, Jay Homnick wrote: “It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. It strikes me as urgent to insist that you not allow your mind to surrender the absolute clarity that all complex and magnificent things were made that way. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident... you have essentially "lost your mind."” ,,, Max Planck biologist W.E. Loennig once commented that Darwinism was a sort of "mass psychosis" -- then he asked me, is that the right English word? I knew psychosis was some kind of mental illness, but wasn't sure exactly what it was, so I looked it up in my dictionary when I returned home: "psychosis -- a loss of contact with reality." I wrote him that, yes, that was the right word…. Loennig and Homnick are still right. Once you seriously consider the possibility that all the magnificent species in the living world, and the human body and the human brain, could be entirely the products of unintelligent forces, you have been in academia too long and have lost contact with reality -- you have lost your mind. http://www.evolutionnews.org/2015/11/it_really_isnt100911.html
bornagain
November 16, 2015
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LM:
But here’s the problem. Many of Behe’s arguments about mutation and mutation rates depend on the idea that a mutation must be EITHER beneficial or deleterious. He argues, for example, that more than two mutations were required to get chloroquine resistance in malaria parasites. Since one of the mutations by itself was NOT beneficial (hence, it must have been deleterious) this means that the two (or more) mutations had to occur simultaneously in order for the parasite to develop resistance to chloroquine.
But wasn't part of his argument about two mutations being required based on the actual rate of the development of chloroquine resistance as demonstrated by the experimental data? You make it sound like it was only a prior commitment to mutations being either beneficial or deleterious that led him to his conclusions. But if the rate of chloroquine resistance actually observed lines up with what would be predicted if two simultaneous mutations were required, then what conclusion should he or anyone else draw from that?Phinehas
November 16, 2015
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In general an admission against interest, as Koonin did, is trustworthy. More so than the follow-up spin.Box
November 16, 2015
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