Intelligent Design

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.

124 Replies to “Can a Lowly Lawyer Make a Useful Contribution?  Maybe.

  1. 1
    Robert Byers says:

    Good points here.
    Cladistics is case in point of assumed evolutionary relationships and not demonstrating relationships are from evolution.

    YES a top lawyer is and should be better able to see the merits of arguments regardless of expertise.
    Indeed a top biologist should be able to evakluate law stuff if being intellectually careful about how data is used.
    IN short anyone who has trained themselves to think carefully about contentions in anything should be credible to take on any contention.
    So knowledgable (anyone but here lawyers) easily have the intellectual right to contend with evolutionist well degree-ed as long as the conversations demonstrate this.
    Surely on uD this is demonstrated excellently and fot a long time.
    From authors and posters on all sides if not all who post. Not all!!
    No voting either. Especially the historic prejudice against canadians or I assume that to explain lack of support for me.
    Yeah thats it.

  2. 2
    Gordon Davisson says:

    Coming at this from the other side…

    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. […]

    I’d fully agree with that so far; however:

    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.

    While I’ve also seen this equivication, I think it may be less common than you think. I may be a little sensitive about this, because on another thread kairosfocus just (falsely) accused me of a very similar mistake. I said:

    There are some parts of evolutionary theory that are so well supported that they can be considered facts. Widespread (if not necessarily universal) common ancestry. Mutation, selection, and drift all happen; we see ’em in the lab, we see ’em in the wild, and we see their effects in genomes.

    Other things are not well established. The one you’re particularly concerned with, materialism, is neither well-established nor part of evolutionary theory. I’m not going to say anything at all like “fact, Fact, FACT” about it, because I don’t consider it one. I think it (or some variant, like physicalism) is the best available guess at the nature of reality, but I consider that a (semi-educated) guess, not fact.

    then KF quoted the first paragraph (highlighting the bits about common ancestry and mutation, selection, and drift) and replied:

    Do you not see the error of conflation and halo of factual character by close rhetorical association you just fell into?

    What we see in the lab is small changes in populations, often by loss of prior function or in Lenski’s case apparent recovery of ability to use an existing mechanism under aerobic conditions. What we have definitely not actually seen is observation of common ancestry of body plans by blind watchmaker chance and/or necessity via chance non foresighted variations of the 47 or whatever kinds, followed by differential reproductive success and descent with modification leading to the rise of divergent major body plans from a common unicellular ancestor. We have not even seen the rise of humans diverse from chimps or whatever from a common population what 6 – 10 MYA.

    Note that I said mutation, selection, and drift all clearly happen; I didn’t say they were the whole story. In fact, they clearly aren’t: at the very least, endosymbiosis is also involved. I didn’t claim that we know the whole story (we don’t). I didn’t claim that the whole story (when/if we figure it out) will involve only natural processes; I think it will, but I’ll freely admit that I don’t have a solid case for it. (I just haven’t been impressed by the case against it.)

    But that still has important implications for ID: it means the only plausible ID hypotheses are those involve intelligent input in addition to (rather than instead of) mutation, selection, drift, etc. Genetic front-loading, guided mutation, guided selection, front-loaded fitness function (“active information”), etc are the ID hypotheses that fit with this evidence. Independent creation of different “kinds”, on the other hand, is pretty much out.

    I also have to turn the accusation around, since you do something like the reverse (in the section I omitted above):

    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.

    Just as it’s invald to use certainty about some aspects of evolution to imply certainty about all aspects, it’s also invalid to use uncertainty about some aspects of evolution to imply uncertainty about all aspects. There’s some controversy(*) about whether Napoleon died of arsenic poisioning, but that doesn’t imply any uncertainty at all about whether he died. Similarly, there’s some controversy about exactly how all the various mechanisms of evolution mesh together, but that doesn’t imply any uncertainty about whether they happen.

    (* Actually, the Napoleon controvery seems to have settled out in the last decade; but the question of whether he was dead was settled way before that.)

    I should also probably address your point about cladistics. I’ll start by pointing out that it’s not just the existence of cladistics that’s signicant, it’s the success of cladistics at grouping organisms with similar characteristics together. Your training as a lawyer may actually be a problem here, because you’re thinking like lawyer, not like a scientist.

    (A qualification: I’m not a scientist either. But my father was a physicist, as were an uncle and aunt, grandfather, great-uncle, several friends… I also studied a fair bit of science [esp physics] in college. So I’m fairly familiar with how scientists — especially physicists — reason.)

    Science involves a form of inference called abduction, or inference to the best explanation. This doesn’t necessarily mean the explanation you like best, it means the one that does the best job of predicting (and in this case that includes retrodicting) the evidence. Essentially, it means the explanation that does the best job of explaining why the evidence is the way that it is.

    Take planetary orbits: Kepler worked out that the were eliptical, with the sun at one focus of the ellipse. Then Newton came along and proposed a theory of universal gravitation that said they had to be elliptical. It also explains why, for example, heavy objects have to fall at the same rate as lighter object. That’s why elliptical orbits and equal fall rates are considered evidence for the theory of gravity. (It’s also an oversimplification, but I’ll get to that…)

    The situation with cladistics is similar. Linnaeus worked out that living organisms fell naturally into a nested hierarchy of similarity. Common ancestry explains why they have to fall into such a hierarchy (as well as why extinct organisms violate these rules in certain ways).

    But wait, I hear you cry, organisms also violate the strict nested hierarchy! Doesn’t that mean that common ancestry is actually refuted? Well, no, no more than the fact that planetoids with sort of kidney-bean-shaped orbits exist, or that feathers fall slower than bowling balls, refute gravity. The strict predictions I mentioned (eliptical orbits, objects falling at the same rate, strict nested hierarchy) all follow only when there are no other factors interfering to complicate things.

    In the case of orbits, you may need to take the effect of other planets (and maybe other forces) into account. In the case of falling objects, you might need to include wind resistence, buoyancy, electromagnetic forces, and anything and everything else that happens to be acting on the falling object. In the case of the nested hierarchy, you need to take into account not just common ancestry, but also endosymbiosis, horizontal genetic transfer, convergence, and anything and everything else that happens to have influenced the pattern of similarity of organisms.

    This is one of the things that make science difficult. And interesting.

    But it doesn’t make things hopeless; in all these cases you can pick out the most common pattern (ellipses, equal fall rate, nested hierarchy) and explain that, then look for anomalies and find explanations for them (wind resistence, horizontal transfer, etc), then look for still-unexplained anomalies and find explanations for them… making more and more complete pictures of all the contributing factors as you make better and better matches to the data.

    Realistically, any good explanation of why things fall at the rate they do is going to have something like gravity as the dominant factor. Likewise, any good explanation of the pattern of similarity among organisms is going to have to have something like common ancestry as the dominant factor.

    The nested hierarchy of similarity is something that needs to be explained, and any theory that hopes to replace common ancestry will need to explain it at least as well, and will also have to allow additional factors to explain the anomalies at least as well as endosymbiosis, HGT, etc do for common ancestry. I haven’t seen anything that comes even slightly close.

    (If anyone is thinking of disputing that the nested hierarchy is real, I have a challenge: try arranging different cars into a nested hierarchy. If you organize them by, say, manufacturer and model, you’ll find sedans, coupes, hatchbacks, and wagons splattered all over with no correspondence to the tree. Same with auto vs manual transmissions, and front/rear/4-wheel drive, and various engine layouts, and Diesel vs gas, and with/without satellite radio, and… And any other tree you pick will be at last bad. Organisms mostly fit in a nested hierarchy, cars almost completely don’t.)

  3. 3
    Andre says:

    It is easy to build a tree on the similarities. Try doing it on the differences. Personally I have no beef with CD but I’m not convinced yet because there are other explanations that fit the data too.

  4. 4
    Box says:

    Gordon,

    Gradual evolution predicts a smooth blending of traits and therefore does not predict a nested hierarchy.

    Joe:
    Branching descent will not produce a nested hierarchy. Darwin, Mayr, Denton, Knox and Wagner have all explained why this is true. (…)
    A family tree is an example of branching descent and you cannot create a nested hierarchy of traits from a family tree. OTOH the US Army has nothing to do with branching descent and it is constructed as a nested hierarchy.

  5. 5
    kairosfocus says:

    GD,

    did you notice that you spoke to “evolutionary theory” and not to micro-evolutionary adaptations?

    Are you aware that the extrapolation from the micro to the macro is a material and commonly made shift shift and one that is highly questionable on the issue of origin of FSCO/I by blind watchmaker thesis needle in haystack search?

    That, the failure to make a clear distinction therefore implies much?

    You go on to cite yourself from 173:

    Other things are not well established. The one you’re particularly concerned with, materialism, is neither well-established nor part of evolutionary theory. I’m not going to say anything at all like “fact, Fact, FACT” about it, because I don’t consider it one. I think it (or some variant, like physicalism) is the best available guess at the nature of reality, but I consider that a (semi-educated) guess, not fact.

    The problem here is of course that there is a commonly observed stalking horse that effectively implies commitment to metaphysics level evolutionary materialism by imposing a censoring rule on thought about origins.

    Namely, so called methodological naturalism, which in effect boils down to only those entities acceptable to metaphysical naturalism etc will be acknowledged in science as we dominate it. Cf Rational Wiki and US NSTA and NAS etc for cases in point across a broad spectrum.

    Yes, it is possible to formally deny this link between seemingly reasonable methodological constraints and linked metaphysical commitments and still be influenced by or even locked into the relevant ideological agenda; the implication is all that is needed (or even just the tendency), and/or the going along with the flow.

    A long time ago, that was a routine problem with those influenced and controlled by marxism. Sometimes to the point of being puppets and agitprop false front operations that seemed to be grassroots but were in fact what in more recent times is termed astroturf.

    A very good sign of such is something like I am one of you guys BUT . . . , and here comes the agitprop. Slightly less common is, I don’t agree with those extremists BUT . . .

    Judging by the obvious success of cultural marxist disinformation pushes and the taqiyya of the IslamIST propaganda front men, such can work very well indeed, at the level of rhetorical manipulation.

    I put it to you, that much the same obtains today for methodological vs metaphysical naturalism.

    And in that wider context, when you say something like:

    There are some parts of evolutionary theory that are so well supported that they can be considered facts. Widespread (if not necessarily universal) common ancestry. Mutation, selection, and drift all happen; we see ’em in the lab, we see ’em in the wild, and we see their effects in genomes . . . .

    Methodological naturalism is part of science, but philosophical naturalism is not . . .

    — you are giving off some pretty strong signs of underlying ideological influences.

    Now, the onward context is that I had highlighted the challenge essay on the ToL, in the context of the common Darwinist claim it’s a fact:

    170 kairosfocus November 12, 2015 at 5:43 pm

    GD, pardon, but if the Darwinism proponents had the goods as they often project (fact, Fact, FACT) that essay would be all over the Internet in many forms as survey feature articles. The ABSENCE is what is so telling. Later. KF

    171 kairosfocus November 12, 2015 at 5:46 pm

    PS: The actual thread focus is the grip of evolutionary materialist ideology, from the title on.

    (I intended to come back on technicalities but local events plus news on a biopsy elsewhere are intervening. I will just note here that he search for a golden search is in a power set to the direct config space so that we face thereafter exponentially harder searches for searches in higher order spaces. So, no the oh you mean flat random spaces is irrelevant. And hoping for a convenient forcing law of bias in nature that in effect solves the problem of OOl in absence of actual empirical observation of same, is questionable. Where the genome and the vast diversity of proteins points to the fact that there is no good reason to infer forced patterns or conveniently easy search spaces or strategies. At higher organisational level, it is even more evident that the organisation of he cell is highly contingent. The needle in haystack search challenge at OOL and thereafter for origin of body plans, remains. The fact is, the only actually empirically grounded source of FSCO/I is design, and that is exactly the issue we are looking at for the world of life from LUCA to us.)

    And yes, notice that I spoke explicitly to what Darwinists all too commonly say, that the macroevolutionary picture of origins is fact not theory, even comparing to the roundness of the earth or the like. In the context that if they had the goods, the essay would be everywhere. Your hot retort, but I have not said that is at best tangential, especially when it leads straight to what I excerpted.

    Now, too, no-one including informed YECs denies micro-evolution and linked empirically supported factors, so that suggestion on what the only viable ID would be is a strawman by suggestion.

    The key clue I responded to, is the distinctions you fail to make, and the conflation of what should not be conflated.

    Let me further clip what I responded to:

    [GD, 173:] There are some parts of evolutionary theory that are so well supported that they can be considered facts. Widespread (if not necessarily universal) common ancestry. Mutation, selection, and drift all happen; we see ’em in the lab, we see ’em in the wild, and we see their effects in genomes . . . .

    Methodological naturalism is part of science, but philosophical naturalism is not . . . .

    Everyone here is falling all over themselves accusing those of us on the science side of being hopelessly biased, irrational, etc. All I can really say is, have you looked in a mirror lately? The level of irrational bias on the ID side is completely ridiculous. Do you have all have any self-awareness at all?

    I here highlight two key points, first to show that you have joined the party of We are the Scientists [ which is used by evolutionary materialist ideologues and their fellow travellers, by way of disqualifying and dismissing those who differ] and an explicit affirmation of methodological naturalism while trying to distance oneself from the implied philosophical naturalism.

    Just as a reminder, I again cite Rational Wiki (noting that here is plenty of back-up for the expressed sentiment):

    >“Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses.”

    Of course, this ideological imposition on science that subverts it from freely seeking the empirically, observationally anchored truth about our world pivots on the deception of side-stepping the obvious fact since Plato in The Laws Bk X, that there is a second, readily empirically testable and observable alternative to “natural vs [the suspect] supernatural.” Namely, blind chance and/or mechanical necessity [= the natural] vs the ART-ificial, the latter acting by evident intelligently directed configuration. [Cf Plantinga’s reply here and here.]

    And as for the god of the gaps canard, the issue is, inference to best explanation across competing live option candidates. If chance and necessity is a candidate, so is intelligence acting by art through design. And if the latter is twisted into a caricature god of the gaps strawman, then locked out, huge questions are being oh so conveniently begged.

    See what I mean when I talk about dressing up evolutionary materialist scientism (and its fellow travellers) in the holy lab coat?

    And, going back to the original point, the missing essay speaks volumes. So should the primary focus of the macro evo is a “fact” claim.

    So, on balance I suggest that in the first instance I pointed to a common claim, I did not personalise to you. You took it up and then showed a pattern of advocating methodological naturalism, which I then pointed out is tantamount to the implicit influence of metaphysical naturalism. This, I think you need to address, along with the underlying point on why that essay is so missing.

    Gotta get going now.

    Sorry, I have to cut off.

    More later.

    KF

  6. 6
    kairosfocus says:

    PS: Johnson, replying to Lewontin:

    For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence.

    [–> notice, the power of an undisclosed, question-begging, controlling assumption . . . often put up as if it were a mere reasonable methodological constraint; emphasis added. Let us note how Rational Wiki, so-called, presents it:

    “Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses.”

    Of course, this ideological imposition on science that subverts it from freely seeking the empirically, observationally anchored truth about our world pivots on the deception of side-stepping the obvious fact since Plato in The Laws Bk X, that there is a second, readily empirically testable and observable alternative to “natural vs [the suspect] supernatural.” Namely, blind chance and/or mechanical necessity [= the natural] vs the ART-ificial, the latter acting by evident intelligently directed configuration. [Cf Plantinga’s reply here and here.]

    And as for the god of the gaps canard, the issue is, inference to best explanation across competing live option candidates. If chance and necessity is a candidate, so is intelligence acting by art through design. And if the latter is twisted into a caricature god of the gaps strawman, then locked out, huge questions are being oh so conveniently begged.]

    That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

  7. 7
    kairosfocus says:

    PPS: We tend to forget what Lewontin so clearly put on the table:

    . . . to put a correct view of the universe into people’s heads [==> as in, “we” have cornered the market on truth, warrant and knowledge] we must first get an incorrect view out [–> as in, if you disagree with “us” of the secularist elite you are wrong, irrational and so dangerous you must be stopped, even at the price of manipulative indoctrination of hoi polloi] . . . the problem is to get them [= hoi polloi] to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations,

    [ –> as in, to think in terms of ethical theism is to be delusional, justifying “our” elitist and establishment-controlling interventions of power to “fix” the widespread mental disease]

    and to accept a social and intellectual apparatus, Science, as the only begetter of truth

    [–> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]

    . . . . To Sagan, as to all but a few other scientists [–> “we” are the dominant elites], it is self-evident

    [–> actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . . and in fact it is evolutionary materialism that is readily shown to be self-refuting]

    that the practices of science provide the surest method of putting us in contact with physical reality [–> = all of reality to the evolutionary materialist], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [–> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . .

    It is not that the methods and institutions of science somehow compel us [= the evo-mat establishment] to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [–> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [–> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [–> irreconcilable hostility to ethical theism, already caricatured as believing delusionally in imaginary demons]. [Lewontin, Billions and billions of Demons, NYRB Jan 1997,cf. here. And, if you imagine this is “quote-mined” I invite you to read the fuller annotated citation here.]

  8. 8
    Zachriel says:

    Barry Arrington: Can a Lowly Lawyer Make a Useful Contribution? Maybe.

    Sure. If a patent clerk can, then maybe a lawyer can to.

    Barry Arrington: Johnson is saying that attorneys are trained to detect baloney.

    Generally, attorneys are better known for making baloney.

    Box: Gradual evolution predicts a smooth blending of traits and therefore does not predict a nested hierarchy.

    Trees grow gradually, but the leaves still form a nested hierarchy when grouped by branch and stem.

  9. 9
    Barry Arrington says:

    Zach,

    Generally, attorneys are better known for making baloney.

    True, and that is exactly why we are trained to detect it.

  10. 10
    Zachriel says:

    Barry Arrington: 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.

    Analysis of traits, including molecular data, shows that the tree structure is an objective pattern — regardless of baloney, er, rhetoric.

  11. 11
    Collin says:

    Gordon,

    I don’t mean to pile on, but I wanted to take issue with just one thing. You said we observe mutation. We certainly do. I understand that the vast majority of mutations are harmful and that even the mutations that confer an advantage also cause harm. See here at 53:00 https://www.youtube.com/watch?v=V_XN8s-zXx4

  12. 12
    Collin says:

    Zach.,

    Don’t the genome and the phenome give us conflicting trees though?

  13. 13
    REC says:

    “I understand that the vast majority of mutations are harmful”

    Generally, the vast majority of mutations are neutral. Behe’s trying to trick you a bit here. Notice his slide says “Of those that affect the organism,” in an attempt to hide this fact. Neutral mutations don’t affect the organism.

    The lack of references should tell you something.

    Try this one: “Adaptive mutations in bacteria: High rate and small effects. Science 317: 813-815.”

    “Don’t the genome and the phenome give us conflicting trees though?”

    Could you point us to a phenome-based tree of life? Does the data to construct such a thing even exist?

  14. 14
    Zachriel says:

    Collins: Don’t the genome and the phenome give us conflicting trees though?

    Until the age of genetics, phenetics based on morphology was the primary method of tree-building. It’s still used in palaeontology and in species-level classification.

    Trees constructed on genomes and those constructed on phenomes give largely the same pattern. Humans group with great apes, great apes group with primates, primates group with placentals, placentals group with amniotes, regardless of whether you look at phenomes or genomes. However, highly derived organisms can be difficult to classify on morphology alone. While everyone agreed that cetaceans are mammals, there was disagreement as to which branch of mammals they grouped with. Genomic data pointed to Artiodactyla, and eventually this was confirmed from the morphology of fossils. In other words, molecules predicted what would be found in geological strata.

  15. 15
    Jack Jones says:

    The Philosophy of evolution accommodates whatever is found.

  16. 16
    Larry Moran says:

    When I open a page of Darwin I immediately sense that I have been ushered into the presence of a great mind. I have the same feeling when I read RA Fisher and with GC Williams. When I read Phillip Johnson, I feel that I have been ushered into the presence of a lawyer.

    Robert Pennock in “Intelligent Design Creationism and Its Critics” (p. 549)

  17. 17
    Mapou says:

    Darwin, a great mind? That’s a laugh. Isaac Newton, Gottfried Leibniz, Rene Descartes, Max Planck were great minds. Darwin was a mental midget in comparison, a moron.

  18. 18
    Jack Jones says:

    Larry Moran thinks Darwin had such a great mind that he takes it as an insult to be called a Darwinist.

    hahaha

  19. 19
    bornagain says:

    Anti-Science Irony
    Excerpt: In response to a letter from Asa Gray, professor of biology at Harvard University, Darwin declared: “I am quite conscious that my speculations run quite beyond the bounds of true science.”
    When questioned further by Gray, Darwin confirmed Gray’s suspicions: “What you hint at generally is very, very true: that my work is grievously hypothetical, and large parts are by no means worthy of being called induction.” Darwin had turned against the use of scientific principles in developing his theory of evolution.
    http://www.darwinthenandnow.co.....nce-irony/

    An Early Critique of Darwin Warned of a Lower Grade of Degradation – Cornelius Hunter – Dec. 22, 2012
    Excerpt: “Many of your wide conclusions are based upon assumptions which can neither be proved nor disproved. Why then express them in the language & arrangements of philosophical induction?” (Sedgwick to Darwin – 1859),,,
    And anticipating the fixity-of-species strawman, Sedgwick explained to the Sage of Kent (Darwin) that he had conflated the observable fact of change of time (development) with the explanation of how it came about. Everyone agreed on development, but the key question of its causes and mechanisms remained. Darwin had used the former as a sort of proof of a particular explanation for the latter. “We all admit development as a fact of history;” explained Sedgwick, “but how came it about?”,,,
    For Darwin, warned Sedgwick, had made claims well beyond the limits of science. Darwin issued truths that were not likely ever to be found anywhere “but in the fertile womb of man’s imagination.”
    The fertile womb of man’s imagination. What a cogent summary of evolutionary theory. Sedgwick made more correct predictions in his short letter than all the volumes of evolutionary literature to come.
    http://darwins-god.blogspot.co.....ed-of.html

    SKEPTICS OF DARWINIAN THEORY
    Sedgwick to Darwin
    “…I have read your book with more pain than pleasure. Parts of it I admired greatly, parts I laughed at till my sides were almost sore; other parts I read with absolute sorrow, because I think them utterly false and grievously mischievous.”
    Adam Sedgwick (1785-1873) – one of the founders of modern geology. – The Spectator, 1860
    http://veritas-ucsb.org/librar.....itics.html

    Here is the letter from Adam Sedgwick to Charles Darwin:

    Sedgwick, Adam to Darwin – 24 Nov 1859
    Excerpt: There is a moral or metaphysical part of nature as well as a physical. A man who denies this is deep in the mire of folly.,,
    http://www.darwinproject.ac.uk/entry-2548

    Was Darwin a Scholar or a Pitchman? – Michael Flannery – October 20, 2015
    Excerpt: By and large, the scientists of his day were not much impressed with Darwin’s theory. John Herschel called natural selection “the law of higgledy-piggledy,” and William Whewell thought the theory consisted of “speculations” that were “quite unproved by facts,” so much so that he refused to put the book on the shelves of the Trinity College Library.
    http://www.evolutionnews.org/2.....00191.html

    Someone tries telling the truth: Darwin wasn’t that great but he met an elite need – July 29, 2014
    Excerpt: , he (Charles Darwin) devoted almost every bit of his magnum opus (Origin Of Species) to tedious examples of artificial selection in domestic animals. He brushed away the glaring advantage of artificial over natural selection with rhetoric along the lines of “I see no reason why” natural selection might not have fashioned the eye or any other organ or living thing. For such schoolboy ineptitude he was roundly criticized by his contemporaries, all of whom are now consigned to history’s dustbin, regardless of their skills and biological competency.
    http://www.uncommondescent.com.....lite-need/

    In fact, Darwin’s book contains far more (bad) theology than it contains anything of what may be considered proper science.

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011
    Excerpt: The Origin supplies abundant evidence of theology in action; as Dilley observes:
    I have argued that, in the first edition of the Origin, Darwin drew upon at least the following positiva theological claims in his case for descent with modification (and against special creation):

    1. Human beings are not justified in believing that God creates in ways analogous to the intellectual powers of the human mind.
    2. A God who is free to create as He wishes would create new biological limbs de novo rather than from a common pattern.
    3. A respectable deity would create biological structures in accord with a human conception of the ‘simplest mode’ to accomplish the functions of these structures.
    4. God would only create the minimum structure required for a given part’s function.
    5. God does not provide false empirical information about the origins of organisms.
    6. God impressed the laws of nature on matter.
    7. God directly created the first ‘primordial’ life.
    8. God did not perform miracles within organic history subsequent to the creation of the first life.
    9. A ‘distant’ God is not morally culpable for natural pain and suffering.
    10. The God of special creation, who allegedly performed miracles in organic history, is not plausible given the presence of natural pain and suffering.
    http://www.evolutionnews.org/2.....46391.html

    “Religious views were mixed, with the Church of England scientific establishment reacting against the book, while liberal Anglicans strongly supported Darwin’s natural selection as an instrument of God’s design.”
    http://en.wikipedia.org/wiki/R.....of_Species

    Moreover, Darwin introduced no math whatsoever in his theory of origin of species. In fact, Darwin said he found math to be ‘repugnant’:

    “During the three years which I spent at Cambridge my time was wasted, as far as the academical studies were concerned, as completely as at Edinburgh & at school. I attempted mathematics, & even went during the summer of 1828 with a private tutor (a very dull man) to Barmouth, but I got on very slowly. The work was repugnant to me, chiefly from my not being able to see any meaning in the early steps in algebra.”
    Charles Darwin, 1887 – Recollections of the Development of my Mind & Character, the work which Darwin himself referred to as his autobiography

  20. 20
    Jack Jones says:

    Born, did you ever hear the radio debate that Bob Enyart had with Eugenie Scott?

    I think you will like it.

  21. 21
    Jack Jones says:

    @19 Born

    It is the same when William lane Craig debated Ayala about Darwinism and Ayala wanted to talk theological arguments against God while Craig wanted to talk about what the Darwinian processes were or were not capable of.

  22. 22
    bornagain says:

    Born, did you ever hear the radio debate that Bob Enyart had with Eugenie Scott?

    not yet, thanks for pointing it out.

    Bob Enyart has commented on UD once or twice that I know of.

  23. 23
    Jack Jones says:

    It was about the junk dna idea, She was pretty firm about it, i think it was from 2001. She is a darwinist is she not?

    I will try and dig it up for ya.

  24. 24
    Jack Jones says:

    Apparently it was from 1998, they play a clip of it.

    http://kgov.com/journal-nature.....enie-scott

  25. 25
    brian douglas says:

    Joe: “The Philosophy of evolution accommodates whatever is found.”

    Do you have an argument or just an unsupported ascertain?

    If you mean that the theory of evolution adapts itself to better fit the evidence, you are absolute correct. As does every good scientific theory.

    Or are you going to claim that there is no theory of evution and demand that we link to it?

  26. 26
    Mapou says:

    For someone who has been elevated to divine status by atheists and materialists, Darwin seemed to have had a surprisingly intimate knowledge and understanding of God’s mind and intentions.

    But the truth is simpler than all that. Darwin was a mental midget and his followers and admirers are even bigger morons.

  27. 27
    Andre says:

    Brian

    Have you ever wondered how evolutioniory theory can explain a round worm, a flat worm, a long worm, a short worm, a fat worm, a skinny worm, a green worm, a brown worm.

    Don’t you wonder?

    A theory that explains everything explains nothing. Evolution did it is no different than God did it….

  28. 28
    Mapou says:

    If you mean that the theory of evolution adapts itself to better fit the evidence, you are absolute correct. As does every good scientific theory.

    Funny. I have studied Newtonian physics and I have never seen Newtonian gravity theory adapt to fit any evidence. It is still the same old Newtonian gravity theory. In fact, the current failure to find gravitational waves means that Newton was correct in supposing that the effect of gravity is instantaneous and nonlocal instead of traveling at the speed of light as Einstein claimed. Newton is reaching from the grave and falsifying a wildly acclaimed modern theory that came centuries after his death. Now, that’s a scientific theory. Darwinian evolution is chicken shit in comparison.

    Good scientific theories do not adapt. They are either wholly or partially replaced by new theories if found to be deficient.

  29. 29
    brian douglas says:

    Funny. I have studied Newtonian physics and I have never seen Newtonian gravity theory adapt to fit any evidence.”

    No, it was superceded by the theory of relativity. But Newton’s equations are such a good approximation that they are of still practical value.

  30. 30
    Larry Moran says:

    Collin says,

    I understand that the vast majority of mutations are harmful and that even the mutations that confer an advantage also cause harm. See here at 53:00 https://www.youtube.com/watch?v=V_XN8s-zXx4

    That’s a talk by Michael Behe in the lecture room two floors below my office. I was there—you can see him wave to me at 1:25:33 when he says, “… with some caveats due to stochastic effects …”

    At 52:10 he says “This is what observations demonstrate about random mutations … we’ve known for a long time that of those mutations that affect an organism, about 99% are detrimental.”

    This may or may not be true depending on what he means by “affect an organism.”

    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.

    Behe argues (in “The Edge of Evolution”) that this is possible in Plasmodium falciparum, the malaria parasite, because of its huge population size. It won’t be possible in most other species so this is the basis of his argument that there’s an “edge” to evolution.

    In other words, there are some things that random mutation just can’t achieve because a pathway requiring multiple mutations doesn’t include stepwise increases in fitness with each mutation. When you see things that required multiple mutations, this is evidence for guided mutation.

    Recent results show clearly that all of the pathways leading to chloroquine resistance involve multiple mutations but that all of them involve sequential mutation events where one of the mutations is neutral. In combination with a second mutation, the combined effect is chloroquine resistance. The intermediate population carrying the first mutation was not a “little bit resistant” and the mutation was not detrimental. It was neutral.

    Michael Behe’s final thoughts on the edge of evolution

    Behe is misleading you when he says that most mutations are detrimental.

    Here’s what a leading expert in molecular evolution says in his textbook.

    The neutral theory of molecular evolution holds that although a small minority of mutations in DNA or protein sequences are advantageous and are fixed by natural selection, and although many mutations are disadvantageous and are eliminated by natural selection, the great majority of those mutations that are fixed are effectively neutral with respect to fitness and are fixed by genetic drift.

    Douglas Futuyma in “Evolution” 2nd ed. p. 267

    If you don’t understand modern evolutionary theory, which includes Neutral Theory and random genetic drift, you won’t understand why Behe is wrong about the edge of evolution, even if you are a lawyer.

    You can’t detect baloney if you don’t understand the subject. Anyone who thinks they can make a contribution to the debate about evolution without investing a lot of time and effort into studying the subject, is fooling himself.

    He needs to call some expert witnesses to help him out.

  31. 31
    Larry Moran says:

    Mapou says,

    Darwin, a great mind? That’s a laugh. Isaac Newton, Gottfried Leibniz, Rene Descartes, Max Planck were great minds. Darwin was a mental midget in comparison, a moron.

    Have you read “Origin of Species” cover-to-cover?

    A simple “yes” or “no” will suffice.

  32. 32
    Larry Moran says:

    Barry Arrington says,

    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.

    Barry, one of your readers has linked to the following article …

    “Nature” Confirms Creationist Rejection of Junk DNA

    Can you use your training to expose the underlying assumptions and the lack of logic in that article?

    Or you you think it’s an accurate portrayal of the facts?

  33. 33
    bpragmatic says:

    Zachriel:

    “Box: Gradual evolution predicts a smooth blending of traits and therefore does not predict a nested hierarchy.

    Trees grow gradually, but the leaves still form a nested hierarchy when grouped by branch and stem.”

    Despite any point you think you are effectively making, we can observe the growth and the parts of an actual tree, from the tips of the leaves to the limbs to the branches to the tree trunk down to the roots. No need to make any assumptions there.

  34. 34
    bornagain says:

    The Very Neutral Kenneth Miller – Michael Behe – January 15, 2015
    Excerpt: But is there any direct, positive, experimental evidence indicating whether a single, uncompensated K76T mutation is deleterious or neutral?
    Yes, there is. As I wrote earlier, to see if a mutation is harmful by itself, at the very least you have to test it without any other mutations present in the relevant organism. Lakshmanan et al. did this carefully in the lab in 2005:,,,
    Miller’s claim that the individual mutation is neutral is wrong.
    http://www.evolutionnews.org/2.....92721.html

    The Many Paths of Kenneth Miller – Michael Behe – January 16, 2015
    Excerpt: Suppose you were given a choice of a billion trillion roads to travel, but were told that only one of them led to safety; the others all led to certain death. You would likely feel pretty pessimistic about your chances.,,,
    The number of 1 in 10^20 against developing chloroquine resistance comes from estimating the number of malaria cells without resistance that it takes to produce and select one with resistance, no matter what genetic route is taken. So the number of routes that Miller emphasizes turns out to have no effect at all on the statistical likelihood of developing chloroquine resistance. Each route itself is actually less likely than the cumulative probability. All of the routes together add up to only 1 in 10^20.
    http://www.evolutionnews.org/2.....92761.html

    “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

    How Many Ways Are There to Win at Sandwalk? – Michael Behe – August 15, 2014
    Excerpt: ,, with chloroquine resistance in Plasmodium falciparum. The best current statistical estimate of the frequency of de novo resistance is Nicholas White’s value of 1 in 10^20 parasites. That number is now essentially fixed — no pathway to resistance will be found that is substantially more probable than that. Although with more data the value may be refined up or down by even as much as one or two orders of magnitude (to between 1 in 10^18-10^22), it’s not going very far on a log scale. Not nearly far enough to lift the shadow from Darwinism.
    What’s more, we can also conclude that the mutations that have already been found are the most effective available of any combination of mutations whose joint probability is greater than 1 in 10^20, since more effective alternatives would already have occurred and been selected if they were available.,,,
    The bottom line for all of them is that the acquisition of chloroquine resistance is an event of statistical probability 1 in 10^20.,,,
    http://www.evolutionnews.org/2.....88981.html

    Supplemental notes:

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (greater than 100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that (they think) did the trick, but rather a list of mutations that (actually) can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.”
    Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

    “Lynch and Abegg assumed [in their paper] that organisms will acquire a given complex adaptation by traversing a direct path to the new anatomical structure. Each mutation would build on the previous one in the most efficient manner possible – with no setbacks, false starts, aimless wandering, or genetic degradation – until the desired structure or system (or gene) is constructed. Thus, they formulated an undirected model of evolutionary change, and one that assumes, moreover, that there is no mechanism available (such as natural selection) that can lock in potentially favorable mutational changes on the way to some complex advantageous structure….
    Yet nothing in Lynch’s neutral model ensures that potentially advantageous mutations will remain in place while other mutations accrue. As Axe explains [in his reply to Lynch], “Productive changes cannot be ‘banked,’ whereas Equation 2 [one of Lynch’s equations] presupposes that they can.” Instead, Axe shows, mathematically, that degradation (the fixation of mutational changes that make the complex adaptation less likely to arise) will occur much more rapidly than constructive mutations, causing the expected waiting time to increase exponentially.”
    Stephen Meyer – Darwin”s Doubt (Harper One, 2013, p. 328, square brackets mine – VJT)

    Stephen Meyer on the inadequacy of neutral theory. [S.Meyer, ch.16, ‘Darwin’s Doubt’]
    http://www.uncommondescent.com.....ent-587770

    Moreover, the development of neutral theory (and junk DNA) are actually the result of a theoretical failure of Darwinian theory within mathematics and is not the result of any compelling empirical observation:

    Haldane’s Dilemma
    Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in response to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional.
    – Sanford

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

  35. 35
    Jack Jones says:

    @Mapou@28

    You are gonna get people that are deluded to thinking there is a universal “theory of evolution” that all evolutionists agree with.

    You have neo darwinist and those that reject it,etc

    Such people are welcome to that delusion, Just like they are welcome to believe life originated spontaneously in nature in the past and believe chemistry in the present was different in their past.

    hahahaha

    Just like you are gonna get Moran who hates being called a Darwinist and does not use the term Darwinism or Neo Darwinism for his faith, making out that old Charlie is his hero.

    While he really is a hero to Coyne who has no problem with using the term Darwinism to describe what he believes.

    Coyne calls punctuated equilibrium as bunk and sticks to his Darwinian faith but Moran hasn’t and seems to admire Gould.

    Some seriously odd people they are.

    hahaha

  36. 36
    bpragmatic says:

    Zachriel:

    “Trees constructed on genomes and those constructed on phenomes give largely the same pattern.”

    What about all of the inconsistencies between the genotype and phenotype. I am sure Born Again can supply a vast array of scientific literature discussing those.

    Also,
    Pardon my side comment but:

    Too bad no one can “scientifically” demonstrate how the usually invoked evolutionary “mechanisms” are capable of originating and developing a “genome” or “phenome”. Let alone what is required to do such things.

    Kind of reminds me of a point I took Barry Arrington to make regarding “evolutionary” arguments: (Barry, please correct this assumption if it is incorrect)

    (being) “chock-full of faulty logic (especially circular reasoning), abuse of language (especially equivocations), assumptions masquerading as facts, unexamined premises, etc. etc.”

    Not to worry though. You can always point to certain things in living systems and claim the good old standby argument that “God wouldn’t have done it that way, therefore unguided evolution did it” if you are inclined to invoke a common typical atheist religious argument into the mix.

  37. 37
    Mapou says:

    “Funny. I have studied Newtonian physics and I have never seen Newtonian gravity theory adapt to fit any evidence.”

    No, it was superceded by the theory of relativity. But Newton’s equations are such a good approximation that they are of still practical value.

    This is a lie, of course. Nothing superseded Newtonian physics. Newton’s gravity equation is still part of general relativity. In fact, Newton (and even Galileo before him) already understood perfectly that the attraction of gravity on a body worked equally on all objects regardless of mass. This is the reason that gravity attracts even massless light particles. We don’t need Einstein to teach us this.

    The only thing that Einstein did was to take the results of the Mickelson-Morley experiments and extended Newtonian theory to include the speed of light and clock slowing. Newtonian gravity is what NASA uses to send probes to the moon and the rest of the solar system. They simply factor the speed of light in their measurements and Newtonian theory works perfectly.

    Darwinian evolution, by contrast, is continually being falsified by the evidence and simple logic. The combinatorial explosion alone kills it dead. It’s a religion of cretins and morons. More like a cult.

  38. 38
    brian douglas says:

    Joe: “Such people are welcome to that delusion, Just like they are welcome to believe life originated spontaneously in nature in the past and believe chemistry in the present was different in their past.”

    Again, Joe lies about what other people say in order to make his point. Please point to the comment where anyone claimed that chemistry was different in the past than it is now.

    I must say, you have earned the name Joe. Or would you prefer to be called Virgil?

  39. 39
    bpragmatic says:

    From 36

    “What about all of the inconsistencies between the genotype and phenotype. I am sure Born Again can supply a vast array of scientific literature discussing those.”

    Correction to the above statement:

    What about all of the unexpected results (from an evolutionary perspective) in the data concerning the genotype and phenotype when utlizing comparisons or whatever to support assertions regarding evolution? BA could probably easily site relevant information on the topic. Or can be found online. Or otherwise in the scientific literature.

  40. 40
    bornagain says:

    bpragmatic, Casey Luskin did a piece on that:

    Problem 6: Molecular Biology has Failed to Yield a Grand “Tree of Life” – Casey Luskin – February 2, 2015
    Excerpt: When fossils failed to demonstrate that animals evolved from a common ancestor, evolutionary scientists turned to another type of evidence — DNA sequence data — to demonstrate a tree of life. ,,,
    At the end of the day, the dream that DNA sequence data would fit into a nice-neat tree of life has failed, and with it a key prediction of neo-Darwinian theory.
    http://www.evolutionnews.org/2.....91151.html

    Logged Out – Scientists Can’t Find Darwin’s “Tree of Life” Anywhere in Nature by Casey Luskin – Winter 2013
    Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors.
    Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,,
    Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance:
    • A 1998 paper in Genome Research observed that “different proteins generate different phylogenetic tree[s].”6
    • A 2009 paper in Trends in Ecology and Evolution acknowledged that “evolutionary trees from different genes often have conflicting branching patterns.”7
    • A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history to be.”8
    Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled “Why Darwin Was Wrong about the Tree of Life.”9 The author quoted researcher Eric Bapteste explaining that “the holy grail was to build a tree of life,” but “today that project lies in tatters, torn to pieces by an onslaught of negative evidence.” According to the article, “many biologists now argue that the tree concept is obsolete and needs to be discarded.”,,,
    Syvanen succinctly summarized the problem: “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” ,,,
    “battles between molecules and morphology are being fought across the entire tree of life,” leaving readers with a stark assessment: “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”10,,,
    A 2012 paper noted that “phylogenetic conflict is common, and [is] frequently the norm rather than the exception,” since “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.”12,,,
    http://www.salvomag.com/new/ar.....ed-out.php

    Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution” – Cornelius Hunter – February 27, 2014
    Excerpt: there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.”,,,
    the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”,,,
    “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”,,,
    he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”
    “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”
    And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.
    http://darwins-god.blogspot.co.....nyone.html

    Darwin’s Tree of Life is a Tangled Bramble Bush – May 15, 2013
    Excerpt: ,,, One whole subsection in the paper is titled, “All gene trees differ from species phylogeny.” Another is titled, “Standard practices do not reduce incongruence.” A third, “Standard practices can mislead.” One of their major findings was “extensive conflict in certain internodes.”
    The authors not only advised throwing out some standard practices of tree-building, but (amazingly) proposed evolutionists throw out the “uninformative” conflicting data and only use data that seems to support the Darwinian tree: “the subset of genes with strong phylogenetic signal is more informative than the full set of genes, suggesting that phylogenomic analyses using conditional combination approaches, rather than approaches based on total evidence, may be more powerful.”,,,
    ,,,tossing out “uninformative” data sets and only using data that appear to support their foreordained conclusion. Were you told this in biology class? Did your textbook mention this?
    http://crev.info/2013/05/darwi.....mble-bush/

    That Yeast Study is a Good Example of How Evolutionary Theory Works – Cornelius Hunter – June 2013
    Excerpt:,,, The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene.
    These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes or of the problem that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.”
    And how do we know that these genes have strong phylogenetic signal. Because they give the right answer.
    This is an example of a classic tendency in science known as confirmation bias.,,,
    http://darwins-god.blogspot.co.....f-how.html

    etc.. etc..

  41. 41
    J-Mac says:

    One of the most saddest examples of someone who wants to be considered an authority in a scientific field is someone, like professor Dr. Larry Moran, who in order to criticize an experimental scientist, like Dr. Behe, and his real experimental work, has to use other scientists’ experiments to do so.
    The funniest part of it all is that Larry often thinks that the very few experimental scientists he knows support his personal views.

    The Fukuyama example has recently changed from the world’s best expert in the field J. Coyne. When Larry learned that Coyne doesn’t support his personal views, he quickly switched to Fukuyama in the desperation for support.

    Larry, if your university lacks money for experimental work, I might be able to support to test some of your evolutionary delusions. What do you think? You could become a hero IF you emerge victorious.

  42. 42
    brian douglas says:

    “This is a lie, of course. Nothing superseded Newtonian physics.”

    The physicists might disagree with you. Newton’s work was definitely revolutionary. And Einsteins work took Newton’s work and expanded on them to explain aspects that Newton’s work can’t explain. Does that sound familiar? Like Darwin proposing a theory that is expanded on by The modern synthesis. Which is further expanded on by neutral theory, HGT, etc.

    We have not discarded Newton; after all, as you accurately state, that is all we need to put a man on the moon, and we have not discarded Darwin. But we know that neither of them told the complete picture.

  43. 43
    REC says:

    J-Mac–Out of curiosity, what do you find Behe’s most interesting evolutionary biology experiment published in the scientific literature to be?

  44. 44
    bornagain says:

    If I may butt in REC. I know of no experiment that Behe has personally done.

    But in regards to peer review, Dr. Behe surveyed laboratory evolution experiments of microbes going back four decades, and that review was published in peer review:

    “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.co.....evolution/

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

    Biological Information – Loss-of-Function Mutations by Paul Giem 2015 – video
    (Behe – Loss of function mutations are far more likely to fix in a population than gain of function mutations)
    https://www.youtube.com/watch?v=hzD3hhvepK8&index=20&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ

    In the book “Biological Information: New Perspectives” the chapter entitled “Getting There First: An Evolutionary Rate Advantage for Adaptive Loss-of-Function Mutations” looks at the likelihood of gain-of-function and loss-of-function mutations occurring in a given population and finds loss-of-function mutations to be more probable in general, both in theory and in practice.
    http://www.worldscientific.com.....08728_0020

    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.

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    NIST team proves ‘spooky action at a distance’ is really real – November 12, 2015
    Excerpt: Researchers showed the measured results not only were correlated, but also—by eliminating all other known options—that these correlations cannot be caused by the locally controlled, “realistic” universe Einstein thought we lived in.,,,
    The research team achieved this feat by simultaneously closing all three major “loopholes” that have plagued previous Bell tests. Closing the loopholes was made possible by recent technical advances, including NIST’s ultrafast single-photon detectors, which can accurately detect at least 90 percent of very weak signals, and new tools for randomly picking detector settings.
    “You can’t prove quantum mechanics, but local realism, or hidden local action, is incompatible with our experiment,” NIST’s Krister Shalm says. “Our results agree with what quantum mechanics predicts about the spooky actions shared by entangled particles.”,,,
    The NIST results are more definitive than those reported recently by researchers at Delft University of Technology in the Netherlands.
    In the NIST experiment, the photon source and the two detectors were located in three different, widely separated rooms on the same floor in a large laboratory building. The two detectors are 184 meters apart, and 126 and 132 meters, respectively, from the photon source.
    The source creates a stream of photon pairs through a common process in which a laser beam stimulates a special type of crystal. This process is generally presumed to create pairs of photons that are entangled, so that the photons’ polarizations are highly correlated with one another. Polarization refers to the specific orientation of the photon, like vertical or horizontal (polarizing sunglasses preferentially block horizontally polarized light), analogous to the two sides of a coin.
    Photon pairs are then separated and sent by fiber-optic cable to separate detectors in the distant rooms. While the photons are in flight, a random number generator picks one of two polarization settings for each polarization analyzer. If the photon matched the analyzer setting, then it was detected more than 90 percent of the time.
    In the best experimental run, both detectors simultaneously identified photons a total of 6,378 times over a period of 30 minutes. Other outcomes (such as just one detector firing) accounted for only 5,749 of the 12,127 total relevant events. Researchers calculated that the maximum chance of local realism producing these results is just 0.0000000059, or about 1 in 170 million. This outcome exceeds the particle physics community’s requirement for a “5 sigma” result needed to declare something a discovery. The results strongly rule out local realistic theories, suggesting that the quantum mechanical explanation of entanglement is indeed the correct explanation.
    The NIST experiment closed the three major loopholes as follows:
    Fair sampling: Thanks to NIST’s single-photon detectors, the experiment was efficient enough to ensure that the detected photons and measurement results were representative of the actual totals. The detectors, made of superconducting nanowires, were 90 percent efficient, and total system efficiency was about 75 percent.
    No faster-than-light communication: The two detectors measured photons from the same pair a few hundreds of nanoseconds apart, finishing more than 40 nanoseconds before any light-speed communication could take place between the detectors. Information traveling at the speed of light would require 617 nanoseconds to travel between the detectors.
    Freedom of choice: Detector settings were chosen by random number generators operating outside the light cone (i.e., possible influence) of the photon source, and thus, were free from manipulation. (In fact, the experiment demonstrated a “Bell violation machine” that NIST eventually plans to use to certify randomness.)
    To further ensure that hidden variables such as power grid fluctuations could not have influenced the results, the researchers performed additional experimental runs mixed with another source of randomness—data from popular movies, television shows and the digits of Pi. This didn’t change the outcome.
    The experiment was conducted at NIST’s Boulder, Colo., campus…
    http://phys.org/news/2015-11-n.....tance.html

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. 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. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

    Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

    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? Appealing to the probability of various ‘random’ configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply!
    In other words, to give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain an effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

    And although Naturalists have proposed various, far fetched, naturalistic scenarios to try to get around the Theistic implications of quantum non-locality, none of the ‘far fetched’ naturalistic solutions, in themselves, are compatible with the reductive materialism that undergirds neo-Darwinian thought.

    “[while a number of philosophical ideas] may be logically consistent with present quantum mechanics, …materialism is not.”
    Eugene Wigner
    Quantum Physics Debunks Materialism – video playlist
    https://www.youtube.com/watch?list=PL1mr9ZTZb3TViAqtowpvZy5PZpn-MoSK_&v=4C5pq7W5yRM

    Verse:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through Him, and without Him nothing was made that was made. In Him was life, and the life was the light of men.

  45. 45
    Collin says:

    REC.

    Doesn’t matter, even a little bit.

  46. 46
    REC says:

    @ 45

    “REC.

    Doesn’t matter, even a little bit.”

    What doesn’t? Truth? Facts? Rational thought?

  47. 47
    bornagain says:

    “Rational thought?” and exactly how is “Rational thought” to be grounded in a Darwinian worldview?

    Sam Harris’s Free Will: The Medial Pre-Frontal Cortex Did It – Martin Cothran – November 9, 2012
    Excerpt: There is something ironic about the position of thinkers like Harris on issues like this: they claim that their position is the result of the irresistible necessity of logic (in fact, they pride themselves on their logic). Their belief is the consequent, in a ground/consequent relation between their evidence and their conclusion. But their very stated position is that any mental state — including their position on this issue — is the effect of a physical, not logical cause.
    By their own logic, it isn’t logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order.
    http://www.evolutionnews.org/2.....66221.html

    (1) rationality implies a thinker in control of thoughts.
    (2) under materialism a thinker is an effect caused by processes in the brain.
    (3) in order for materialism to ground rationality a thinker (an effect) must control processes in the brain (a cause). (1)&(2)
    (4) no effect can control its cause.
    Therefore materialism cannot ground rationality.
    per Box UD

    ” Hawking’s entire argument is built upon theism. He is, as Cornelius Van Til put it, like the child who must climb up onto his father’s lap into order to slap his face.
    Take that part about the “human mind” for example. Under atheism there is no such thing as a mind. There is no such thing as understanding and no such thing as truth. All (Stephen) Hawking is left with is a box, called a skull, which contains a bunch of molecules.
    Hawking needs God in order to deny Him.”
    – Cornelius Hunter –

    Photo – an atheist contemplating his mind
    http://3.bp.blogspot.com/-H-kj.....0/rob4.jpg

  48. 48
    Axel says:

    Mapou @ your #17, yes, Darwin was strictly a dilettante. I believe there have been one or two scientific dilettantes of genius – I believe, aristocrats, with the time, money and a certain autonomy – but Darwin was surely a journeyman ‘stamp-collector’ of Kelvin’s famous, dismissive quip, concerning non-physicists.

    In fact, he actually stated, and it is sometimes quoted, that if something* turned out to be true, then it would very gravel undermine his conjectures. Conjectures they were, and indeed, did turnout to be false.

    But even if the significance of Darwin’s avowal were to be insisted upon with great vehemence, not enough scientists in that field have died yet, for it to be accepted. Well, the atheist tenure-baggers will never voluntarily accept it – never mind that it was Darwin, himself, who saw how hopelessly vulnerable his conjectures were.

    *I’m sorry. I can’t remember what it was, but you boffins will know it well enough.

  49. 49
    Mapou says:

    Moran:

    Have you read “Origin of Species” cover-to-cover?

    A simple “yes” or “no” will suffice.

    Man, I’m not your dog. I’m a free man and a free thinker. I will not let either you or a deranged bozo like Darwin do my thinking for me.

  50. 50
    brian douglas says:

    “Man, I’m not your dog. I’m a free man and a free thinker. I will not let either you or a deranged bozo like Darwin do my thinking for me.”

    A strange response to a simple question. All Larry asked is if you had read Origin of Species. Not if you agreed with it.

  51. 51
    Mapou says:

    douglas,

    I consider all Darwinists and materialists to be weavers of lies and deception. And they are not really all that smart about it. I simply refuse to play Moran’s stupid deceptive game. That’s all.

    You got a problem with that?

  52. 52
    Collin says:

    Rec,

    You got me. I am actually totally against rational thought. I certainly wasn’t referring to your implication that Behe has to do experimental biology in order to be correct in his criticisms of evolutionary theory. Nope, that couldn’t be it. I must have been saying that I don’t believe in rationality. If you are curious here are some of his journal articles and other publications according to wikipedia.
    https://en.wikipedia.org/wiki/Michael_Behe#Journal_articles I recommend you learn how to use google to find this kind of information.

  53. 53
    brian douglas says:

    “You got a problem with that?”

    If it makes you happy, knock your socks off. For me, life is too short to be so hateful.

  54. 54
    Mapou says:

    I’m not hateful. I’m just pissed. Understanding the origin of life and the universe is, IMO, the most important knowledge we can attain. You people just don’t realize how much harm you bring to humanity. You must be mocked and discredited at every opportunity.

  55. 55
    REC says:

    Collin @52

    Sorry, couldn’t tell if it was my posts above (e.g. @13) that you fled from or what it was you were replying to.

    But for what it is worth, it was your compadre J-Mac was the one who attacked Larry Moran and lionized Behe above based on their experience in experimental evolutionary biology. So take it up with him…..

  56. 56
    bpragmatic says:

    Zachriel:

    “Trees constructed on genomes and those constructed on phenomes give largely the same pattern.”

    So Zachriel, based on your comment above, to you, at least for discussion do you think there would be any value in assessing,commenting on and refuting at least some of bornagain’s references in his post at comment 40 that contradict what your conclusion probably is based on your statement? Genome and phenome studies significantly support your evolutionary assertions?

    If not, why not?

  57. 57
    Andre says:

    I’ve read:

    On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life

    I enjoyed Chapter 1, 6 and 9.

    Darwin’s observation about artificial selection is spot on, the moment he tries to apply this to unguided processes the whole book falls apart. What I am glad about is that he understood the problems with his own theory.

    Descent of Man

    This is the most racist book ever written. As the world tries to deal with racism we continually teach this nonsense as true. How on earth can you tell one race they are superior another they are inferior and expect everyone to get along? This book is trash.

  58. 58
    goodusername says:

    Descent of Man This is the most racist book ever written.

    An astonishingly ridiculous and ignorant statement.

    You should try checking out just about any of the other books from the era.
    Some of the leading books of the subject of human races prior to Darwin: Account of the Regular Gradation in Man by Charles White, The Races of Men by Robert Knox, Types of Mankind and Indigenous Races of the Earth by Nott and Gliddon, Inequality of the Races by Gobineau, and Cannibals All! by George Fitzhugh

    Many of the anti-Darwinian late 19th century books were equally ugly – such as Adamites and Preadamites by Alexander Winchell or The Negro a Beast by Charles Carroll.

    But I wouldn’t recommend reading any of those if you don’t have a strong stomach.

    In fact, one would be hard pressed to find a less racist book during Darwin’s time.

    Anyone who reads Descent might be puzzled at how much time he spends actually arguing at how similar the races of humanity are in mind and body. This is because the leading theory of the time was polygenism, and so a major challenge was convincing others of his time that the races are similar enough to be related!

    I also recommend Darwin’s Sacred Cause, which argues that combating slavery and the racism of his time was a major motivation for releasing his theory.

  59. 59
    Andre says:

    Those Negroes are like Gorillas

    “The inability to move the ears in man and several apes is, however, partly compensated by the freedom with which they can move the head in a horizontal plane, so as to catch sounds from all directions. It has been asserted that the ear of man alone possesses a lobule; but “a rudiment of it is found in the gorilla”;*(4) and, as I hear from Prof. Preyer, it is not rarely absent in the negro.”

    “The great break in the organic chain between man and his nearest allies, which cannot be bridged over by any extinct or living species, has often been advanced as a grave objection to the belief that man is descended from some lower form; but this objection will not appear of much weight to those who, from general reasons, believe in the general principle of evolution. Breaks often occur in all parts of the series, some being wide, sharp and defined, others less so in various degrees; as between the orang and its nearest allies- between the Tarsius and the other Lemuridae- between the elephant, and in a more striking manner between the Ornithorhynchus or Echidna, and all other mammals. But these breaks depend merely on the number of related forms which have become extinct. At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate, and replace, the savage races throughout the world. At the same time the anthropomorphous apes, as Professor Schaaffhausen has remarked,* will no doubt be exterminated. The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilised state, as we may hope, even than the Caucasian, and some ape as low as a baboon, instead of as now between the negro or Australian and the gorilla.”

    The prevailing views by the authors you list all stems from the Darwin family views in the Victorian era.

    It’s called scientific racism and its deplorable!

  60. 60
    Zachriel says:

    bpragmatic: Despite any point you think you are effectively making, we can observe the growth and the parts of an actual tree, from the tips of the leaves to the limbs to the branches to the tree trunk down to the roots. No need to make any assumptions there.

    Huh? The very reason to use the tree as an example is because we can watch it grow over time.

    bpragmatic: What about all of the inconsistencies between the genotype and phenotype.

    The overall pattern is congruent.

    Axel: Darwin was strictly a dilettante.

    That’s hardly the case. Darwin published extensively, including original observations and experimentation.
    http://darwins-god.blogspot.co.....2205882625

    bpragmatic: do you think there would be any value in assessing,commenting on and refuting at least some of bornagain’s references in his post at comment 40 that contradict what your conclusion probably is based on your statement?

    Bornagain is not willing or able to discuss any of his links. When queried, he merely spews more links. Perhaps you could choose one for discussion.

  61. 61
    bornagain says:

    Zachriel spewing more of his lies:

    “Huh? The very reason to use the tree as an example is because we can watch it grow over time.”
    &
    “The overall pattern is congruent.”

    and yet there is no ‘tree’ as Zach falsely claims:

    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

    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/ar.....-life.html

    Phylogeny: Rewriting evolution – Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. – Elie Dolgin – 27 June 2012
    Excerpt: “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree,” he says. “…they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist – Kevin Peterson)
    Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says.
    Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.
    http://www.nature.com/news/phy.....on-1.10885

    “The study had sought to determine the evolutionary history of the animal phyla by analyzing fifty genes along seventeen taxa. He hoped that a single, dominant phylogenetic tree would emerge. Rokas and his team reported that “a 5-gene data matrix does not resolve relationships among most metazoan phyla” because it generated numerous conflicting phylogenies and historical signals. Their conclusion was candid: “Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved.”,,,
    Sean B. Carroll went so far as to assert that “certain critical parts of the TOL [Tree of Life] may be difficult to resolve, regardless of the quantity of conventional data available.” This problem applies specifically to the relationships of many of the animal phyla, where “[m]any recent studies have reported support for many alternative conflicting phylogenies.” Investigators studying the animal tree found that “ a large fraction of single genes produce phylogenies of poor quality” such that in one case, a study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom”,,,
    Their article brings the discussion of the Cambrian explosion full circle from an attempt to use genes to compensate for the absence of fossil evidence to the acknowledgment that genes do not convey any clear signal about the evolutionary relationships of the phyla first preserved by fossils in the Cambrian.”
    Steve Meyer – Darwin’s Doubt (pp. 120–21)

    A New Model for Evolution: A Rhizome – Didier Raoult – 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.co.....izome.html

    etc.. etc..

    as to:

    “Bornagain is not willing or able to discuss any of his links. When queried, he merely spews more links. Perhaps you could choose one for discussion.”

    Translation,

    I, Zach, can’t honestly answer these papers that BA77 presents, that expose my lies so clearly, and so I will stick my head in the sand and pretend that my lies are more ‘authoritative’ than the actual evidence presented”

    There you go Zach, all better. You can thank me later for translating your words into what they actually mean.

  62. 62
    Zachriel says:

    bpragmatic: do you think there would be any value in assessing,commenting on and refuting at least some of bornagain’s references in his post at comment 40 that contradict what your conclusion probably is based on your statement?

    Zachriel: Bornagain is not willing or able to discuss any of his links. When queried, he merely spews more links.

    Case in point @61. Here’s what bornagain quotes:

    Koonin: 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.

    Reading further, it’s clear there is a signal of several trees converging, but the points of convergence may not form a simple monophyletic relationship.

    Koonin: Here, I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees {emphasis added}.

    The author is clearly arguing for evolutionary descent. He suggests that there are two modes of descent, the usual tree, and a big bang period which involves rapid and tangled cladogenetic events. Most of the tangle in metazoa is probably due to incomplete lineage sorting on a grand scale. The tangle on the origin of domains is probably due to horizontal mechanisms, but there is still a lot unknown.

    Nonetheless, the overall branching pattern remains.

  63. 63
    kairosfocus says:

    Thought-provoking reading: https://www.andrew.cmu.edu/course/76-327A/readings/Campbell.pdf Note especially the implicit significance of speaking to Ch 1 of Paley but not Ch 2 on the thought exercise of a self replicating, time keeping watch, in light of the significance of OOL.

  64. 64
    bornagain says:

    Zachriel, what you just dishonestly did is called ‘cherry picking’.

    The fact of the matter is that the main point that Koonin admits to in the paper is exactly the point that refutes your claim that a tree is largely congruent from the data. Namely,

    “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”
    – Koonin

    That is, to put it mildly, and no matter how much you try to lie about it, NOT a minor problem for the Darwinian narrative!

    Moreover, it further exposes your inherent, and blatant, dishonesty towards the evidence when you brush aside glaring deficiencies in your preferred atheistic worldview to focus on whatever remains after such a stunning confession by Koonin.

    Moreover, even on the point that Koonin tries to say is non-problematic to the Darwinian narrative, we still have ample reason to believe that the data, (even in this limited instance after ‘major groups’ are conceded by Koonin as being ‘non-Darwinian), to believe that the data is being ‘cherry picked’ by Darwinists to accord to the Darwinian narrative:

    In fact, many times evolutionists will scan molecular sequences using computer algorithms to find a hypothetical Tree Of Life (TOL), but this is very problematic because of the inherent bias of researchers to look solely for evidence that accords to a preconceived evolutionary conclusion whereas ignoring all sequences that disagree with their inherent bias:,,,

    Pattern pluralism and the Tree of Life hypothesis – 2006
    Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.
    http://www.pnas.org/content/104/7/2043.abstract

    “The computer programs that analyze the sequence similarities, or differences, are programmed in advance to generate a tree-like pattern. In other words, the assumption of a common ancestor is built into the way in which the analysis is performed. So there is no way you would get anything other than the conclusion,,, It’s a question begging assumption.”
    Stephen Meyer – on the Cambrian Explosion – podcast (15:25 minute mark)
    http://intelligentdesign.podom.....3_15-07_00

    Contradictory Trees: Evolution Goes 0 For 1,070 – Whif
    Excerpt: One of evolution’s trade secrets is its prefiltering of data to make it look good, but now evolutionists are resorting to postfiltering of the data as well.,,,
    Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden.
    But even prefiltering cannot always help the theory.,,,
    http://darwins-god.blogspot.co.....oes-0.html

    Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% by Jeffrey Tomkins on February 20, 2013
    Excerpt: there is a great deal of preferential and selective treatment of the data being analyzed. In many cases, only the most promising data such as gene-rich sequences that exist in both species (homologs) is utilized from a much larger data pool. This pre-selected data is often further subjected to more filtering before being analyzed and discussed. Non-alignable regions and large gaps in DNA sequence alignments are also typically omitted, thus increasing the levels of reported similarity.
    https://answersingenesis.org/answers/research-journal/v6/comprehensive-analysis-of-chimpanzee-and-human-chromosomes/

    Do Molecular Clocks Run at All? A Critique of Molecular Systematics – Jeffrey H. Schwartz, Bruno Maresca
    Abstract: Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”.. For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central …
    http://www.pitt.edu/~jhs/artic.....clocks.pdf

    Fudging Evolution to Avoid Falsification – March 12, 2015
    Evolutionary theory follows Finagle’s Rule #4: “Draw your curves, then plot your data.”
    Excerpt: “The fact that the clock is so uncertain is very problematic for us,” David Reich of Harvard said at a recent meeting where no consensus was reached. “It means that the dates we get out of genetics are really quite embarrassingly bad and uncertain.” The solution for some has been to invoke “rate heterogeneity”: mutations rates that speed up or slow down as needed to keep the theory intact. –
    http://crev.info/2015/03/fudging-evolution/

    Evolution Makes No Sense on This Molecular Clock Problem – Cornelius Hunter – June 15, 2015
    Excerpt: The theory-laden measurements are based on evolutionary theory. The theory-neutral measurements do not entail evolutionary thinking. In other words, making measurements based on evolutionary theory leads to problems. The resulting DNA mutation rates are not even close to what we can measure more directly, free from theoretical assumptions.
    As is often the case, these discrepancies between the evidence and the theory leave evolutionists unsure and of differing opinions. As one evolutionist admitted:
    “The fact that the clock is so uncertain is very problematic for us, It means that the dates we get out of genetics are really quite embarrassingly bad and uncertain.”
    http://darwins-god.blogspot.co.....-this.html

    Moreover, even if molecular sequences did accord to the Darwinian narrative, it still is of absolutely no use for Darwinists since you can mutate DNA ‘until the cows come home’ and you are not going to effect body plan morphogenesis

    ‘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 not 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) (52:57 minute mark)
    https://youtu.be/7yqqlZ29gcU?t=3177

    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
    http://www.uncommondescent.com.....ent-587726

  65. 65
    Zachriel says:

    Case in point @61. Instead of responding to our comments, bornagain hurls insults, waves his hands, and spews more links.

    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 doesn’t mean there is no tree signal. It means that there are multiple trees converging, but that the point of convergence is not simple monophyly.

    Koonin: Here, I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees {emphasis added}.

    However, let’s be clear. Do you support Koonin’s hypothesis? That life evolved from common ancestors through two modes of cladogenesis?

  66. 66
    bornagain says:

    Zacheriel, I quoted Koonin to expose you as a liar about the tree being congruent’.

    That was your claim. Your claim was shown to be false. You do not concede the point. Ergo, you are a liar!

    i.e. Calling you a liar is not an insult but is, in fact, merely a statement of fact. I can’t help it that you do not like that fact.

    Perhaps, if you do not like it, you should ‘evolve’ into being honest towards the evidence instead of being a liar?

    Moreover, I do not accept his, nor any other Darwinist’s dishonest attempt to ‘explain away’ the incongruences in molecular data and hold that the incongruences, which are rampant, to be yet another falsification of Darwinism than merely an anomaly as Koonin treats them. (By the way, do you like Koonin’s many worlds model which sought to ‘explain away’ the OOL?) 🙂

    You simply have no real time empirical evidence to explain, by unguided material processes, such dramatic jumps in the genetic Data (jumps which are pervasive in the data)

    “Charles Darwin said (paraphrase), ‘If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.’ Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way. – Doug Axe PhD.

    Nothing In Molecular Biology Is Gradual – Doug Axe PhD. – video
    http://www.metacafe.com/watch/5347797/

  67. 67
    Zachriel says:

    bornagain: Moreover, I do not accept his, nor any other Darwinist’s dishonest attempt to ‘explain away’

    So if Koonin is dishonest, why are you citing him as authoritative?

    bornagain: I quoted Koonin to expose you as a liar about the tree being congruent’.

    The phenetic and genomic trees are largely congruent across most taxa — as Koonin states.

  68. 68
    bornagain says:

    Zachriel, repeating a lie does not suddenly make it true:

    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?”
    per new scientist

    Phylogeny: Rewriting evolution – Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. – Elie Dolgin – 27 June 2012
    Excerpt: “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree,” he says. “…they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist – Kevin Peterson)
    Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says.
    Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.
    per Nature

  69. 69
    Zachriel says:

    bornagain,

    Try to deal with one citation at a time. So if Koonin is dishonest, why are you citing him as authoritative?

  70. 70
    goodusername says:

    Andre,

    The prevailing views by the authors you list all stems from the Darwin family views in the Victorian era.

    ?
    The prevailing view of the western world that humanity is comprised of unrelated species separately created by God, with some races created to be slaves, came from “Darwin family views”?

  71. 71
    bornagain says:

    Zachriel, I hold no man in science to be ‘authoritative’ but hold the empirical evidence itself to have the final word.

    i.e. Koonin’s 2007 observation of the incongruent sequence data (like the latter 2009 and 2012 papers I cited) is, I hold, accurate to the empirical evidence. His attempt to explain it away is what is clearly lacking in empirical support and is thus what lacks ‘authority’.

    The Scientific Method – Richard Feynman – video
    Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
    https://www.youtube.com/watch?v=OL6-x0modwY

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

  72. 72
    Zachriel says:

    bornagain: Koonin’s 2007 observation of the incongruent sequence data

    You didn’t point to the data, but to Koonin’s interpretation of the data. He didn’t provide any novel empirical observations in the paper, and you already said he was dishonest.

  73. 73
    Jack Jones says:

    Zach, You are missing the point of what Born is saying.

    An evolutionist could honestly admit something about the data but then still try and dishonestly spin away the data afterwards.

    The second point does not negate the first point.

    Why are you having problems understanding that?

  74. 74
    Zachriel says:

    Jack Jones: An evolutionist could honestly admit something about the data but then still try and dishonestly spin away the data afterwards.

    Koonin stated that the tree structure holds for most taxa. That’s not spin, nor is it a negligible finding.

  75. 75
    Jack Jones says:

    Zach “Koonin stated that the tree structure holds for most taxa. That’s not spin, nor is it a negligible finding.”

    Craig Venter said there is no tree but a bush and yet he is still an Evolutionist.

    Will Provine came out against the idea of there being a tree pattern.

    Evolutionists can agree or disagree whether there is a tree pattern and it does not hurt the philosophy of evolution one jot, they will accommodate any pattern.

    The philosophy of Evolution will accommodate any pattern, a tree, a web or a bush etc, It makes no difference to an evolutionist.

    That is why it is pointless of evolutionists trying to claim that any pattern supports their position, They will accommodate any pattern within the Philosophy of evolution.

  76. 76
    bornagain says:

    Zach tries to spin and lie again and again:

    Zach’s original fraudulent claim that he never acknowledged was wrong:

    “Huh? The very reason to use the tree as an example is because we can watch it grow over time.”
    &
    “The overall pattern is congruent.”

    Koonin:

    Koonin: Here, I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees

    Koonin on where the divisions are

    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

    Zach’s original fraudulent claim, even by the cherry picked quote he used, is shown to be false.

    I rest my case, Zach LIED when he said the ‘The overall pattern is congruent’.

    Moreover, he refuses to admit that he was wrong on his claim and is thus now shown, by that refusal, to be pathologically dishonest in regards to the evidence in hand. i.e. “denialism”

  77. 77
    Zachriel says:

    Jack Jones: Craig Venter said there is no tree but a bush and yet he is still an Evolutionist.

    Darwin knew the tree wasn’t perfect, so pointing out that the tree isn’t perfect doesn’t undermine evolutionary theory. Venter accepts the standard branching up to the origin of domains. Before then, horizontal mechanisms may have held sway.

    bornagain: Koonin on where the divisions are…

    You’ve already said Koonin is dishonest, so not sure why you keep referring to his opinion.

  78. 78
    Jack Jones says:

    Zach in his reply said “Darwin knew the tree wasn’t perfect”

    You sound like a politician spinning zach.

    Venter didn’t say that the tree wasn’t perfect when talking about Darwin’s tree of life.

    He said there is no tree not that it is imperfect, if it was just an imperfect tree then he wouldn’t need to throw the whole idea out and say there is a bush pattern.

    A bush does not show the linear pattern but evolutionists can come up with all kinds of reasons, hgt, convergent evolution etc to excuse the pattern away.

    The philosophy will allow any pattern.

    Dawkins was flabbergasted at Venter’s claim of no tree pattern.

    Provine said that it was a false prediction of the modern synthesis of there being a tree.

    It was one of the reasons that he rejected the modern synthesis.

    “You’ve already said Koonin is dishonest, so not sure why you keep referring to his opinion.”

    Zach, the person that is showing his dishonesty here with your spinning like a politician is yourself.

    I explained to you Born’s words in context and you are doubling down and still misrepresenting him.

  79. 79
    bornagain says:

    Zachriel, I made clear my distinction where I disagreed with Koonin, i.e. when he went beyond the evidence to try to ‘explain away’ the incongruent data, I considered that intellectually ‘dishonest’.

    That level of ‘dishonesty’ is somewhat understandable since he was trying to, however inadequately, give a naturalistic reason for the incongruent sequence data.

    But that level of minor ‘intellectual dishonesty’ is nothing compared to the purposeful deception that you were originally trying to convey, i.e. ‘The overall pattern is congruent’.

    That claim you made is an outright LIE to the evidence in hand! And you are a liar for repeatedly making that claim as I have seen you do in the past. There is nothing understandable or minor about the lie you are telling and refuse to admit you are wrong on. At least Koonin, in his honesty, willingly admitted the data is incongruent. I have seen, and expect, no such honesty coming from you.

    Of related note, Koonin, though not an ID proponent, readily admits that neo-Darwinism is false.
    In fact, he is one of the founding members of Shapiro’s “The Third Way”

    “The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone. ”
    Koonin
    (The Origin at 150: is a new evolutionary synthesis in sight? Trends Genet. Nov 2009; 25(11): 473–475)
    http://www.thethirdwayofevolut.....ene-koonin

  80. 80
    Zachriel says:

    Jack Jones: Venter didn’t say that the tree wasn’t perfect when talking about Darwin’s tree of life.

    Venter called it a bush. It’s branched trees that become tangled near the trunk. Koonin hypothesizes that this is because there are two types of cladogenesis.

    Jack Jones: He said there is no tree not that it is imperfect

    The tree structure for eukaryotes doesn’t go away because of a stray or out of context quote.

    Jack Jones: Dawkins was flabbergasted at Venter’s claim of no tree pattern.

    Because it was an overstatement. There are multiple branching trees which appear to converge. The question is how they connect, and whether they show the same branching pattern or not. However, the individual branches are still trees.

    Jack Jones: I explained to you Born’s words in context

    Bornagain wants to refer to Koonin’s authority when he agrees with bornagain, and wants to reject Koonin’s authority as dishonest when he disagrees with bornagain.

    bornagain: That claim is an outright LIE to the evidence in hand!

    You haven’t referred to the evidence, but a hypothesis proposed by Koonin. Please note that Koonin makes clear where he thinks the standard branching pattern breaks down. So dinosaurs still form a branching pattern, as do hominids.

  81. 81
    bornagain says:

    Zachriel, I made perfectly clear my distinction with Koonin. That you would try spin that clear distinction is yet another evidence of your inherent dishonesty.

    Then you claim ‘You haven’t referred to the evidence,’ which is yet another outright lie. I, in fact, referred to several papers after Koonin’s paper that go further than Koonin did in saying the tree does not exist.
    http://www.uncommondescent.com.....ent-588281

    Then you say Koonin infers ‘dinosaurs still form a branching pattern, as do hominids.’

    So what?

    I was not even contesting that point at this time! I was contesting your original fraudulent claim:

    ‘The overall pattern is congruent’

    That claim you originally made is false! And you are a liar for making it and for not apologizing for making it.

  82. 82
    Jack Jones says:

    “Venter called it a bush. It’s branched trees that become tangled near the trunk. Koonin hypothesizes that this is because there are two types of cladogenesis.”

    Venter said there is no tree and not a bush of life, he said it was a false idea. He didn’t say some parts are tree like and others are not, he rejected a tree outright.

    “The tree structure for eukaryotes doesn’t go away because of a stray or out of context quote.”

    And when evolutionists fail in argumentation they lie and claim something is out of context. People can see the video for themselves of Venter saying there is no tree, not that some parts are not tree like, he rejected that there is a tree and said you could say there is a bush of life.

    “Because it was an overstatement. There are multiple branching trees which appear to converge. The question is how they connect, and whether they show the same branching pattern or not. However, the individual branches are still trees.”

    Provine said there is no tree pattern, he said the idea of all life going back to one orgin producing a tree pattern is a failed prediction of the modern synthesis.

    “Bornagain wants to refer to Koonin’s authority when he agrees with bornagain, and wants to reject Koonin’s authority as dishonest when he disagrees with bornagain.”

    So, You can accept part of what somebody says without having to accept all of it, to say that Born has to accept the whole and cannot accept a part of what is said, is the fallacy of composition, because Koonin may have been partially honest does not mean that he was not spinning later on.

    If you accept a part then you do not have to accept the whole.

    Because Born accepts that Koonin admitted one thing truthfully does not mean that he has to accept the spin on that truth afterwards.

    Koonin can admit what the data shows and then try and spin away the problem, there is no contradiction in pointing that out.

  83. 83
    Zachriel says:

    Jack Jones: Venter said there is no tree and not a bush of life, he said it was a false idea.

    And in the same talk, he discusses standard branching patterns. Do you have more from Venter than an off-hand comment?

    Jack Jones: So, You can accept part of what somebody says without having to accept all of it, to say that Born has to accept the whole and cannot accept a part of what is said, is the fallacy of composition

    Bornagain cited Koonin as authoritative while saying he was dishonest. The latter undermines the former.

  84. 84
    bornagain says:

    Zachriel, I rest my case. I’m satisfied that it is perfectly clear to unbiased readers exactly what I meant with Koonin. And that it also perfectly clear you are doing your dishonest best to spin it.

  85. 85
    bornagain says:

    It is interesting to note why Dawkins almost had a cow when Venter denied common descent in front of him:

    Venter vs. Dawkins on the Tree of Life – and Another Dawkins Whopper – March 2011
    Excerpt:,,, But first, let’s look at the reason Dawkins gives for why the code must be universal:
    “The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.” (2009, p. 409-10)
    OK. Keep Dawkins’ claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code).
    Simple counting question: does “one or two” equal 23? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.
    http://www.evolutionnews.org/2.....44681.html

    The bottom line is that if any code is ‘randomly changed’ in part, it throws a huge monkey wrench into the code and will be ‘instantly catastrophic’, to use Richard Dawkins most appropriate term, to the species thus rendering gradual change to the code impossible.
    In other words, the entire code must be implemented ‘top down’!
    Please note, this is not randomly changing sequences within the code that we are talking about, this is talking about making changes to a code itself.

    The reason I bring this ‘non-evolvability’ of codes up is because of alternative splicing codes.
    Namely, alternative splicing codes are now found to be ‘species-specific’.

    The ‘species-specific’ alternative splicing code:
    https://docs.google.com/document/d/1UMbNM8V2b7mRzPJt05mlev3UO4SG1bMTV5wkNunezjY/edit
    Excerpted references:

    Thirdly, the alternative splicing code is ‘species specific’

    Canadian Team Develops Alternative Splicing Code from Mouse Tissue Data
    Excerpt: “Our method takes as an input a collection of exons and surrounding intron sequences and data profiling how those exons are spliced in different tissues,” Frey and his co-authors wrote. “The method assembles a code that can predict how a transcript will be spliced in different tissues.”
    http://www.genomeweb.com/infor.....issue-data

    And yet these supposed ‘junk intron sequences’, that Darwinists use to ignore, that were used to decipher the splicing code of different tissue types in an organism, are found to be exceptionally different between chimpanzees and Humans:

    Modern origin of numerous alternatively spliced human introns from tandem arrays – 2006
    Excerpt: A comparison with orthologous regions in mouse and chimpanzee suggests a young age for the human introns with the most-similar boundaries. Finally, we show that these human introns are alternatively spliced with exceptionally high frequency.
    http://www.pnas.org/content/104/3/882.full

    Characterization and potential functional significance of human-chimpanzee large INDEL variation – October 2011
    Excerpt:,,, we categorized human-chimpanzee INDEL (Insertion, Deletion) variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression.
    Results: Extensive, large INDEL (Insertion, Deletion) variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them.
    http://www.mobilednajournal.co.....3-2-13.pdf

    Jonathan Wells comments on the fallacious ‘Darwinian Logic’, within the preceding paper, that falsely tried to attribute the major differences that were found in INDEL variation to unguided Darwinian processes:

    Darwinian Logic: The Latest on Chimp and Human DNA – Jonathan Wells – October 2011
    Excerpt: Protein-coding regions of DNA in chimps and humans are remarkably similar — 98%, by many estimates — and this similarity has been used as evidence that the two species are descended from a common ancestor. Yet chimps and humans are very different anatomically and behaviorally, and even thirty years ago some biologists were speculating that those differences might be due to non-protein-coding regions, which make up about 98% of chimp and human DNA. (In other words, the 98% similarity refers to only 2% of the genome.) Now a research team headed by John F. McDonald at Georgia Tech has published evidence that large segments of non-protein-coding DNA differ significantly between chimps and humans,,,, If the striking similarities in protein-coding DNA point to the common ancestry of chimps and humans, why don’t dissimilarities in the much more abundant non-protein-coding DNA point to their separate origins?
    http://www.evolutionnews.org/2.....52291.html

    This following, more recent, paper also found that Alternative Splicing patterns to be ‘species specific’:

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013
    Excerpt: Although humans and chimpanzees share,, similar genomes, previous studies have shown that the species evolved major differences in mRNA (messenger RNA) expression levels.,,,
    http://www.sciencedaily.com/re.....144632.htm

    ,,,Alternative splicing,,, may contribute to species differences – December 21, 2012
    Excerpt: After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns—which determine the segments of those genes included or excluded—vary from species to species.,,,
    The results from the alternative splicing pattern comparison were very different. Instead of clustering by tissue, the patterns clustered mostly by species. “Different tissues from the cow look more like the other cow tissues, in terms of splicing, than they do like the corresponding tissue in mouse or rat or rhesus,” Burge says. Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says,,,
    Excerpt of Abstract: To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified;
    http://phys.org/news/2012-12-e.....wires.html

  86. 86
    Jack Jones says:

    “And in the same talk, he discusses standard branching patterns. Do you have more from Venter than an off-hand comment? ”

    it’s not an offhand comment, he dismissed that there is a tree.

    “The tree of life is an artifact of some early scientific studies that aren’t really holding up…So there is not a tree of life.”

    “Dawkins is Flabbergasted

    Fast forward to 11:23, when moderator Roger Bingham turns the microphone over to Dawkins:

    “I’m intrigued,” replies Dawkins, “at Craig saying that the tree of life is a fiction. I mean…the DNA code of all creatures that have ever been looked at is all but identical.”

    WHOPPER. Venter just told the forum that Mycoplasma read their DNA using a different coding convention than other organisms (for “stop” and tryptophan). But Dawkins is undaunted:

    “Surely that means,” he asks Venter, “that they’re all related? Doesn’t it?”

    As nearly as we can tell from the video, Venter only smiles.”

    https://www.youtube.com/watch?v=MXrYhINutuI

    Here is the whole video and I have seen it in the past, nothing was taken out of context.

    http://thesciencenetwork.org/p.....life-panel

    “Bornagain cited Koonin as authoritative while saying he was dishonest. The latter undermines the former.”

    No it does not follow, To say that you have to accept all of something because you accept some part as true is the fallacy of composition.

    “The fallacy of composition arises when one infers that something is true of the whole from the fact that it is true of some part of the whole (or even of every proper part).”

    This was Will Provine on the tree.

    “every assertion of the evolutionary synthesis below is false“:

    10. Evolution is a process of sharing common ancestors back to the origin of life, or in other words, evolution produces a tree of life.

    William Provine, Random Drift and the Evolutionary Synthesis, History of Science Society HSS Abstracts.

    Provine said it was false and still, he remained an Evolutionist.

    Tree of life or no Tree of life, The philosophy of evolution will accommodate it.

  87. 87
    Zachriel says:

    bornagain: I’m satisfied that it is perfectly clear to unbiased readers exactly what I meant with Koonin.

    You were clearly relying on Koonin as authoritative. Let’s try this:

    Joe Blow: 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.

    Just doesn’t have the same panache, does it? An appeal to authority is only valid if it represents a consensus in the field. Note that Joe Blow Koonin makes clear that the dominant description is still the tree pattern, and that his is a tentative hypothesis.

    What you haven’t done is actually discuss the evidence, which would raise your argument beyond an appeal to authority.

  88. 88
    bornagain says:

    Zach, baby put that thing on spin cycle you shameless liar.

    http://ryanpolly.com/wp-conten.....estuck.jpg

  89. 89
    Zachriel says:

    Jack Jones: “The fallacy of composition arises when one infers that something is true of the whole from the fact that it is true of some part of the whole (or even of every proper part).”

    Disregarding what a liar says is not a fallacy of composition. What the liar says may be true, or it may be false, but the utterance itself is not convincing.

    Bornagain made an appeal to authority. Because Koonin said something, it must be true, and those that disagree with him must be wrong, unless, of course, they disagree with bornagain, in which case they are lying.

  90. 90
    bornagain says:

    No Zach, it is just YOU, all by your lonesome, that is purposely lying about the sequence data.

    Jon Lovitz Appears as the Pathological Liar on Johnny Carson’s Tonight Show
    https://www.youtube.com/watch?v=pkYNBwCEeH4

  91. 91
    Jack Jones says:

    @88 Born “Zach, baby put that thing on spin cycle you shameless liar.”

    You get more spin from Zach than a Laundromat.

  92. 92
    Jack Jones says:

    “Disregarding what a liar says is not a fallacy of composition.”

    it’s a fallacy of composition to say what is true of a part is true of the whole.

    Because you accept Koonin’s spin does not mean that Born has to.

    You can accept part of what somebody says without having to accept the spin for that they have admitted.

    You claim otherwise but it is a non sequitur.

    Your conclusion does not follow.

  93. 93
    Zachriel says:

    Jack Jones: it’s a fallacy of composition to say what is true of a part is true of the whole.

    But that’s not the argument. If Joe Blow is a liar, some of what he says may be false. Some of what he says may be true. But what you can say is that you can’t rely upon what Joe Blow says.

    Jack Jones: You can accept part of what somebody says without having to accept the spin for that they have admitted.

    Bornagain said Koonin was being dishonest with the science, not merely wrong.

    Do you think Koonin would reject the branching descent of theropods, for instance?

  94. 94
    bornagain says:

    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. 🙂

  95. 95
    Box says:

    In general an admission against interest, as Koonin did, is trustworthy. More so than the follow-up spin.

  96. 96
    Phinehas says:

    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?

  97. 97
    bornagain says:

    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/2.....00881.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/2.....00911.html

  98. 98
    Larry Moran says:

    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.

  99. 99
    Zachriel says:

    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?

  100. 100
    bornagain says:

    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
    http://www.uncommondescent.com.....ent-588211

  101. 101
    Gordon Davisson says:

    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.

  102. 102
    Gordon Davisson says:

    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.

  103. 103
    Box says:

    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.

  104. 104
    bornagain says:

    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/.....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.co.....s-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.co.....-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.co.....oding.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/2.....61301.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.co.....-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.co.....-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.co.....thing.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/ar.....tml?page=2

  105. 105
    bornagain says:

    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/s.....4709000846

    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/odesig.....ler171.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/j.....230a0.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.
    http://www.uncommondescent.com...../#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/scie.....-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.....e_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

  106. 106
    bornagain says:

    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.

  107. 107
    Zachriel says:

    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/B.....enesis.gif

    Now, compare to Darwin’s original diagram.
    http://darwin-online.org.uk/co.....iagram.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.)

  108. 108
    bornagain says:

    spin it baby spin it! You’ll be a politician yet! 🙂

    Three Shell Game
    https://www.youtube.com/watch?v=IFLa_tl4Rk0

  109. 109
    Gordon Davisson says:

    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?

  110. 110
    bornagain says:

    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-conte.....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-conte.....genome.pdf

  111. 111
    Jack Jones says:

    @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.

  112. 112
    bornagain says:

    ‘argument ad nauseam’

    Ha ha ha ha 🙂

  113. 113
    Gordon Davisson says:

    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?)

  114. 114
    bornagain says:

    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/2.....38811.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.timeshighereducatio.....ode=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
    http://www.uncommondescent.com.....ent-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

  115. 115
    Larry Moran says:

    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.

  116. 116
    Gordon Davisson says:

    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.

  117. 117
    bornagain says:

    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.co.....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/20.....teria.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.....ruit_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/2.....38811.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/2.....51051.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/2.....79401.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-mic.....-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!

  118. 118
    bornagain says:

    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/2.....02783.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/.....tml?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/2.....95451.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/exis.....t-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/2.....90071.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/comm.....n-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?f.....qlE#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?

  119. 119
    Jack Jones says:

    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.

  120. 120
    brian douglas says:

    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.

  121. 121
    Gordon Davisson says:

    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.

  122. 122
    bornagain says:

    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.

  123. 123
    Phinehas says:

    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!

  124. 124
    Larry Moran says:

    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.?

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