Intelligent Design

Why KeithS’s bomb is a damp squib

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In this short post, I’d like to explain what’s wrong with KeithS’s argument for unguided evolution. The argument, in a nutshell, goes like this:

1. We observe objective nested hierarchies (ONH)
2. Unguided evolution explains ONH
3. A designer explains ONH, but also a trillion alternatives.
4. Both unguided evolution and a designer are capable of causing ONH.
Conclusion: Unguided evolution is a trillion times better at explaining ONH.

The first thing I’d like to point out is that while KeithS, in his post over at TSZ leans heavily on the evidence assembled by Dr. Douglas Theobald in his article, 29+ Evidences of Macroevolution, it is very odd that Dr. Theobald himself does not put forward this argument anywhere in his article. On the contrary, he expressly declares, in his reply to creationist Ashley Camp’s critique:

This is not to say that God could not have created species independently and miraculously, yet gradually. While there currently is absolutely no scientific evidence for such an idea, gradual Divine direction of evolution is indeed consistent and compatible with common descent.

It is possible for a theist to see the theory of common descent, and the hierarchy which it predicts, as a reflection of the Creator’s divine plan—much as Sir Isaac Newton saw his laws of motion, and the ellipses and parabolas which they predict, as evidence of the Creator’s hand in our universe…

In fact, no theological assumptions or arguments are made at all in the essay. The “29 Evidences” is not an argument against creation—it is the scientific argument for common descent, no more, no less…

I personally believe that an omnipotent, omniscient Creator could have created in any manner that he chose. For a theist, the pertinent question is not “what is an omnipotent Creator capable of?” but rather “how exactly did/does the Creator create?”. The first question is purely theological, and as such is left unaddressed in the “29 Evidences”; in contrast, the second question is one that science can answer (given the assumption of a Creator).

The second point I’d like to make – and here I’m basically restating a point that William J. Murray made earlier, in mathematical language – is that KeithS has misapplied Bayes’ Theorem, which states: P(A|B) = P(A).[P(B|A)/P(B)],
where A is a proposition and B is the supporting evidence,
P(A), the prior probability, is the initial degree of belief in A,
P(A|B), the conditional probability, is the degree of belief in A, having taken B into account, and
the quotient P(B|A)/P(B) represents the support B provides for A.

A better way of stating Bayes’ Theorem is to expand the denominator, P(B). We can say that P(B) is equal to [P(B|A).P(A))+(P(B|~A).P(~A)], since if B is true, then either A is also true or A is false (and thus ~A is true). Hence:
P(A|B) = [P(A).P(B|A)]/[P(B|A).P(A))+(P(B|~A).P(~A)]
Where P(~A) is the probability of the initial degree of belief against A, or 1-P(A)
P(B|~A) is the degree of belief in B, given that the proposition A is false.

The problem is that KeithS has conflated two hypotheses: the hypothesis of common descent (which is very well-supported by the evidence that objective nested hierarchies exist in living things), and the hypothesis of unguided design (which he also claims is well-supported by the evidence that objective nested hierarchies exist in living things).

The first hypothesis is indeed well-supported by the evidence, as the only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. The probability that any other process would generate such hierarchies is vanishingly low.

But if KeithS wishes to argue against intelligently guided evolution, then the two alternative hypotheses he needs to consider are not:
A: a branching evolutionary process (also known as a Markov process) generated the objective nested hierarchies we find in living things; and
~A: an Intelligent Designer generated these objective nested hierarchies,

but instead:

A: an unguided process generated the objective nested hierarchies we find in living things; and
~A: an intelligently guided process generated these objective nested hierarchies.

The point KeithS makes in his essay is that on hypothesis ~A, the likelihood of B (objective nested hierarchies in living things) is very low. However, it is also true that on hypothesis A, the likelihood of B is very low, as the vast majority of unguided processes don’t generate objective nested hierarchies.

My third point is that KeithS’s argument assumes that the genetic and morphological features on the basis of which living things are classified into objective nested hierarchies were generated by the same process as the (unguided, Markovian) processes which generates the branches in the hierarchies. This is unlikely, even on a standard evolutionary view: features take time to evolve, and therefore would presumably have appeared at some time subsequent to the branch nodes themselves. Thus it could well be the case that while unguided processes explain the existence of objective nested hierarchies in the living world, guided processes are required to explain some or all of the features in these hierarchies.

My fourth point is that KeithS’s exclusion of the origin of life from his argument limits the force of his conclusion. At most, he can argue that objective nested hierarchies are best explained by unguided processes; but that is not the same as saying that living things themselves are best explained by these processes, or that the origin of life is due to an unguided process.

Finally, I’d like to point out that KeithS’s argument against Dr. Douglas Axe is factually mistaken. Nowhere in his paper, “The Case Against a Neo-Darwinian Origin of Protein Folds” does Dr. Axe make the argument KeithS imputes to him.

My time at the Internet cafe is up, so I shall stop here.

408 Replies to “Why KeithS’s bomb is a damp squib

  1. 1
    keith s says:

    Thanks for your OP, Vincent.

    I’ll comment more tomorrow, but for now, let me repost a comment I just made on the other thread:

    Box,

    It’s astonishing to me that you still don’t get this, but let me try once more.

    Suppose you have two objects:

    1. A coin with ONH stamped on both sides.
    2. A trillion-sided die with ONH engraved on one and only one side.

    A friend of yours takes both objects into another room, out of your sight. She randomly picks one of the two objects and flips it.

    “I randomly picked one of the objects and flipped it, and it landed with ONH up,” she shouts to you.

    Your job is to guess which of the objects she flipped — the coin with ONH on both sides, or the trillion-sided die with ONH on only one side.

    If you can’t figure out the best answer, I’m afraid there’s little hope that you will ever understand my argument.

  2. 2
    keith s says:

    Oh, and one other thing before I go to bed, Vincent.

    You wrote:

    Finally, I’d like to point out that KeithS’s argument against Dr. Douglas Axe is factually mistaken. Nowhere in his paper, “The Case Against a Neo-Darwinian Origin of Protein Folds” does Dr. Axe make the argument KeithS imputes to him.

    You’re looking at the wrong paper. The argument I criticized is in a different Axe paper, co-authored with Ann Gauger:
    The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway

    Talk to you later.

  3. 3
    Andre says:

    Keith S

    Even Dr Theobald disagrees with you lol!

  4. 4
    Andre says:

    Keith S

    So the coin is loaded…. ONH/ONH (aka designed)
    The other is a trillion side dice with one ONH on it…… (also designed but for the sake of your argument lets ignore that)

    It lands on ONH and I have to guess? which one? Dice or coin?

    Well it would obviously be the coin that is loaded. The other one is only a 1 in a trillion chance……. so its unlikely…. But I know the loaded dice (designed one) will give me the outcome 100% of ONH side up every single time!

  5. 5
    kairosfocus says:

    VJT:

    I’d note, on points:

    >> 1. We observe objective nested hierarchies (ONH)>>

    Not quite, the homology/ resemblance implies relationship by descent principle even at gross level (eyes, wings etc) leads to “except where it doesn’t” and the diverse molecular trees undercut this claim. Diverse embryological development paths for obviously close creatures, also raise questions. Molecular structures and embryological development programs will be at least as important as gross ones.

    >>2. Unguided evolution explains ONH>>

    Begs the question of origin of FSCO/I on blind chance + mechanical necessity, in the teeth of strong evidence that the only observed source is design. So, we see a red herring and a question-begging assumption that plays to an indoctrinated gallery. Where origin/ source of FSCO/I is a bridge between OOL and origin of body plans requiring novel cell types, tissues, organs, arrangements and regulatory programs (esp. in embryological development). So, start at the root, OOL. No empirically grounded needle in haystack challenge plausible answer save design. How design is effected is secondary to that it credibly was effected.

    >>3. A designer explains ONH, but also a trillion alternatives.>>

    The word trillion is patently put in to rhetorically counter the fact that there are now — thanks to the Internet — trillions of cases in point of the observed source of FSCO/I, design; the only such observed source. That rhetorical device of distraction needs to be noted.

    The next issue is the second diversion, from design — intelligently directed configuration — detected on tested empirically reliable sign, to the rhetoric of the Designer is God and evocation of the train of thoughts, we fear, loathe and hate God and think of followers of God with contempt — Dawkins’ recent writings being exhibit A. Multiplied by the radical attempt to question-beggingly redefine science on a priori materialism, warping its inferences on the past of origins through demanding that we substitute for the longstanding inference on natural [= chance plus necessity] vs the ART-ificial [= intelligently configured] spoken of by Plato and Newton alike, to natural vs supernatural. Where the latter is caricatured and dismissed as beyond science.

    In fact, per empirically tested reliable signs, we routinely infer intelligently directed configuration on FSCO/I as sign — no one here thinks posts in this thread came about by lucky noise instead. The difference being exerted on cases of origins boils down to ideologically motivated selective hyperskepticism.

    Next, tree-patterns shaped by design constraints and purposes are a commonplace pattern of designs. That is the existence of a treelike pattern is empirically known to be a result of design.

    Linked, there is the problem of systematically missing transitionals, known since Darwin’s day. He hoped that future work would fill in but with 1/4 million species, millions of cases in museums and billions seen in the ground, the same pattern of distinct and separate forms without smooth incremental transitions remains. The idea of an organic incrementally branching pattern is projected unto the evidence not drawn out from it. But as those familiar with the problem of ideologically loaded misreading of situations backed by the fallacy of the closed mind know, undoing this error is very difficult.

    Psychologically, it normally takes breakdown, at personal or community level. Just ask former cultists and former Marxists willing to speak plainly.

    What is warranted, then, is just this: A designer explains ONH, but also a trillion alternatives

    And with that, the rest of the anti-design argument collapses.

    >>4. Both unguided evolution and a designer are capable of causing ONH.>>

    Therefore, there is no reason to use tree patterns (and note again the dynanmics challenges above) to try to distinguish the two.

    The argument collapses, pfft, like a stabbed tyre.

    >>Conclusion: Unguided evolution is a trillion times better at explaining ONH. >>

    This does not follow from the above chain of argument.

    As has been pointed out in several ways from several directions.

    It is time for KS et al to do some serious re-thinking.

    KF

  6. 6
    kairosfocus says:

    PS: I point to my FTR on the KS argument here, now updated with the point by point from 5 above.

  7. 7
    Joe says:

    keith s doesn’t know what a nested hierarchy is let alone an objective nested hierarchy.

  8. 8

    Theobald states:

    The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes.

    The problem is that it is those very evolutionary processes that are under debate; you cannot assume evolutionary processes are either natural or designed.

    Yet keiths claims that IF we assume natural forces capable of generating the nested hierarchy (assumedly) found in living systems, then natural forces are the best explanation for the nested hierarchy.

    However, assuming natural forces can produce the nested hierarchy is not the same as assuming that a nested hierarchy is the only biological system configuration natural forces are capable of producing.

    Keith’s makes two entirely different sets of assumptions about the two categorical candidates. He assumes natural forces can produce the nested hierarchy configuration, and assumes that is the only configuration natural forces can produce.

    On the design side, kieths assumes that design can produce the nested hierarchy configuration and trillions of other configurations.

    His conclusion (which is still erroneous) is built into his assumptions, as I and others have pointed out several times.

  9. 9
    kairosfocus says:

    F/N: I have taken time to address, here, the Theobald claims and the Wiki claims in the context of the now 2 years and one month plus pro-darwinism essay challenge, which on fair comment has never been cogently answered from the darwinist side. I did so by pulling together some previous discussions and links, as a point of reference for further discussion in threads such as this one. KF

    PS: WJM, you are dealing with an ideological circle of thought, the whole has to break down before it is going to be seen for what it is, as happened with Marxism.

  10. 10
    Andre says:

    And he keeps ignoring PCD….

  11. 11
    Box says:

    Keith #1,

    Your nonsense has been rebutted in the appropriate thread.

  12. 12

    kf,

    As long as they are willing to post such nonsense, I’m happy to continue to point it out. I guess on the one hand letting them post here has the value of being able to expose them for the sake of onlookers. Unfortunately, we also have to put up with their Darwinian Debate Tactics & Disorders. I’m not really sure it’s a good trade-off.

  13. 13
    kairosfocus says:

    WJM: These days, there is the emergency of the day pressure. Though I just ponied up and had a long distance chat with my dad to tap his longstanding expertise on macro, fiscal policy & thought on business cycles. He added something I didn’t know while we were chatting on Solow and tech-influenced growth — J’can unis are now making strides in Computer Science and robotics . . . my fight on the future of tech edu curriculum in emerging native unis fifteen years ago is paying off and I think will tell long term; they need to lop off a couple of zeros on the J$ when it stabilises though so the Sangster “bill” will be about US$ 1 and the GWG coin, the dime, with the Busta 1 cent. (When I was a kid, a fav sweet was called the Busta and went for about that.) Wish I could write that phone call off as a business expense but he is not at arms-length. The developing development policy battle closer to where home base now is, means I don’t have a lot of time for point by point exchanges at UD just now. But, I have taken time to provide backdrop stuff for what exchanges do happen surrounding the core ID issues — and it is interesting to contrast visit statistics and the studious ignore and dismiss tactic. My thought remains, FSCO/I is pivotal, and it cuts hard on cell molecular biology, OOL and unfolding of body plans embryologically and in the tree of life. Notice in the linked FTR how Wiki has had to admit that it’s not so clearly a classic tree anymore too. Which BTW means KS et al need to address their CV-NS model in the context of not quite cleanly rooted and branching trees. KF

  14. 14
    mahuna says:

    I wouldn’t push the “common descent” thing too far. We have too many examples, including whales and bats (and humans), where there is no known STRING of ancestors prior to the appearance of the species alive today or known from fossils.

    So, yes, we know from fossils that there were animals with backbones a very long time ago. And by simple calculation, we know which particular backboned animal is currently the oldest we have yet found. But that is entirely separate from an argument that proposes that humans (of which there has only ever been 1 species) have some direct and necessary link to ancient cave-dwelling saber-toothed wombats.

    If you look at airplanes or cars, machines designed by the same engineer look a LOT alike. The lineage of the Corvette is a popular example, but the A-7 Corsair II (made by Vought) looks a LOT like the F-8 Crusader (also made by Vought). And of course there is the problem for the design engineer of what powerplants, etc., are available while the machine is still in design.

    So if we accept The Theory of Intelligent Design, then tree-like structures can be explained by a Designer exploring one basic design, getting bored with the options inherent in that basic design, and then starting a fresh design that uses the same basic frame and powerplant.

  15. 15
    bornagain77 says:

    I would like to point out, once again, that Darwin’s tree of life is not supported by either the fossil record or genetic evidence. In other words, the empirical evidence itself, when taken at face value, away from all the rhetoric and ‘statistical analysis’, does not support Universal Common Descent.
    First and foremost, as Dr. Wells points out in this following video,,,

    Cambrian Explosion Ruins Darwin’s Tree of Life (2 minutes in 24 hour day) – video
    http://www.youtube.com/watch?v=bQKxkUb_AAg

    ,,,Darwin predicted that minor differences (diversity) between species would gradually appear first and then the differences would grow larger (disparity) between species as time went on. i.e. universal common descent as depicted in Darwin’s tree of life. What Darwin predicted should be familiar to everyone and is easily represented in the following graph.,,,

    The Theory – Diversity precedes Disparity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/F.gif

    But that ‘tree pattern’ that Darwin predicted is not what is found in the fossil record. The fossil record reveals that disparity (the greatest differences) precedes diversity (the smaller differences), which is the exact opposite pattern for what Darwin’s theory predicted.

    The Actual Fossil Evidence- Disparity precedes Diversity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/G.gif

    Timeline graphic on Cambrian Explosion from ‘Darwin’s Doubt’ (Disparity preceding Diversity)
    http://www.evolutionnews.org/2.....74341.html

    Moreover, there are ‘yawning chasms’ in the ‘morphological space’ between the phyla which suddenly appeared in the Cambrian Explosion,,,

    “Over the past 150 years or so, paleontologists have found many representatives of the phyla that were well-known in Darwin’s time (by analogy, the equivalent of the three primary colors) and a few completely new forms altogether (by analogy, some other distinct colors such as green and orange, perhaps). And, of course, within these phyla, there is a great deal of variety. Nevertheless, the analogy holds at least insofar as the differences in form between any member of one phylum and any member of another phylum are vast, and paleontologists have utterly failed to find forms that would fill these yawning chasms in what biotechnologists call “morphological space.” In other words, they have failed to find the paleolontogical equivalent of the numerous finely graded intermediate colors (Oedleton blue, dusty rose, gun barrel gray, magenta, etc.) that interior designers covet. Instead, extensive sampling of the fossil record has confirmed a strikingly discontinuous pattern in which representatives of the major phyla stand in stark isolation from members of other phyla, without intermediate forms filling the intervening morphological space.”
    Stephen Meyer – Darwin’s Doubt (p. 70)

    Moreover, this top down pattern in the fossil record, which is the complete opposite pattern as Darwin predicted for the fossil record, is not only found in the Cambrian Explosion, but this ‘top down’, disparity preceding diversity, pattern is found in the fossil record subsequent to the Cambrian explosion as well.

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.”
    TS Kemp – Fossils and Evolution,– Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.”
    Robert L Carroll (born 1938) – vertebrate paleontologist who specialises in Paleozoic and Mesozoic amphibians

    etc.. etc.. etc..

    Thus, contrary to the keith s’s claim that the fossil record supports Universal Common Descent as is predicted by Darwin’s theory ‘trillions of times better’ than any theory of Intelligent Design, the fact of the matter is that the fossil evidence itself reveals keith s’s claim to be bogus!
    As well, the genetic evidence offers no support for keith s’s claim for Universal Common Descent as it is predicted by Darwin’s theory:
    Casey Luskin did an overview of the genetic evidence here:

    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

    etc.. etc..

    Thus, despite keith s’s ‘black knight’ impersonation, (which is quite good actually), when the evidence itself is looked at clearly, without trying to force the fossil or genetic evidence into any artificial ‘statistical’ model, (i.e. ‘imaginary’ model), the empirical evidence itself testifies very strongly against keith s’s bogus claims for UCD as predicted by Darwin’s theory.

  16. 16
    Bob O'H says:

    (my apologies in advance if I’m about to make the thread drift off too far from the OP: I’ll understand if you want to curtail this digression)
    mahuna @14 –

    So if we accept The Theory of Intelligent Design, then tree-like structures can be explained by a Designer exploring one basic design, getting bored with the options inherent in that basic design, and then starting a fresh design that uses the same basic frame and powerplant.

    I’m interpret you as saying that an intelligent designer can mimic evolution, which is fine. But then how would you falsify the theory of intelligent design?

  17. 17
    Zachriel says:

    Douglas Theobald: While there currently is absolutely no scientific evidence for such an idea, gradual Divine direction of evolution is indeed consistent and compatible with common descent.

    That is correct. The evidence from the nested hierarchy strongly supports common descent, however, the evidence doesn’t directly impact whether that process is guided or not. For instance, here’s a simple tree structure that is guided:
    http://etc.usf.edu/clippix/pix.....medium.jpg

    What we can say is that the evidence strongly supports that the branching process is *intrinsic*. Other evidence has to be marshaled to explain the shape of the tree.

    vjtorley: The first hypothesis is indeed well-supported by the evidence, as the only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes.

    Of course, we could suppose a designer with an inordinate fondness for beetles nested hierarchies, but that is a scientifically vacuous claim unless you ascribe testable properties to the designer that imply such a fondness.

    mahuna: If you look at airplanes or cars, machines designed by the same engineer look a LOT alike.

    Vehicles don’t form a nested hierarchy.

    bornagain77: I would like to point out, once again, that Darwin’s tree of life is not supported by either the fossil record or genetic evidence.

    “The first hypothesis is indeed well-supported by the evidence”

  18. 18
    kairosfocus says:

    F/N: In a pause, I decided to go back in and add a few illustrations and links to today’s FTR, here. Let’s see if the objectors to design can answer on the merits to the OOL gap, the issue that FSCO/I is about finding shorelines of islands of function in huge config spaces . . . and yes requisites of tightly coupled correctly organised interacting components to achieve function lead directly to the islands pattern . . . and this holds first at OOL the root of the tree of life. But it then extends across the tree, insofar as a branching tree model is applicable. So, the premise that CV + NS –> DWIM can account for branching tree macro evo is on the table from the root on up. Nope, we don’t spot you that claimed power of your naturalistic mechanisms, show that they are up to the job of creating FSCO/I required at the root and for major body plan branches. Minor adaptations like finch beaks or blindness in cave fishes or the like don’t count. KF

    PS: The darwinism 6000 word essay challenge, after 2 years, is still open . . . the composite I had to cobble together a year ago was grossly inadequate and earlier both Wiki and Theobald failed the tests of sitting in for the empty chair. (Which, newbies, gives some of the backstory for the sort of namecalling smears and general trollish nastiness we saw in the past few days targetting us here at UD.)

  19. 19
    kairosfocus says:

    Z, if you are forced to refer to Theobald as your point of reference, I am afraid you are stumbling in the starting gate — start with OOL and address origin of FSCO/I, and please don’t get into the it’s fact, fact FACT blunder that lies behind KS’ skeletal argument responded to on points in 5 above. Later. KF

  20. 20

    Zachrieal,

    If nature can produce a biological system that is not a nested hierarchy, then assuming it had other possibilities available but generated an ONH is no different than assuming that a designer had other options but chose an ONH.

    If nature is predisposed by natural law and molecular tendency to produce an ONH in biological systems, the questions that follow are: (1) Why would any designer attempt to thwart natural law and tendency when he could just work</strong with such natural forces, and (2) How could any designer circumvent such a system if nature itself is assumed incapable of producing anything else, as keith’s argument assumes?

  21. 21
    bornagain77 says:

    Anyone who thinks that the Cambrian Explosion, and the subsequent ‘top down’ pattern in the fossil record, supports Darwin’s tree of life seriously needs to consider entering a rehab program to get off of whatever drugs they are smoking:

    Timeline graphic on Cambrian Explosion from ‘Darwin’s Doubt’ (Disparity preceding Diversity)
    http://www.evolutionnews.org/2.....74341.html

  22. 22
    Zachriel says:

    kairosfocus: Z, if you are forced to refer to Theobald as your point of reference

    Um, it’s the basis of the original post.

    kairosfocus: KS’ skeletal argument

    Um, we’re disagreeing with KeithS’s conclusion. The reasons you give, such as the mystery of the origin of life, don’t address the nested hierarchy.

    William J Murray: If nature can produce a biological system that is not a nested hierarchy, then assuming it had other possibilities available but generated an ONH is no different than assuming that a designer had other options but chose an ONH.

    “Nature” is too vague to be a suitable mechanism for scientific consideration. The hypothesized mechanism is branching descent. The entailment is the nested hierarchy.

    bornagain77: Timeline graphic on Cambrian Explosion from ‘Darwin’s Doubt’ (Disparity preceding Diversity)
    http://www.evolutionnews.org/2.....74341.html

    The diagram of the Cambrian Explosion is consistent with a branching process.

  23. 23
    bornagain77 says:

    “The diagram of the Cambrian Explosion is consistent with a branching process.”

    Save for the fact that the branches only exist in the imagination of Darwinists you may have had a point.

    Challenging Fossil of a Little Fish
    Excerpt: “I think this is a major mystery in paleontology,” said Chen. “Before the Cambrian, we should see a number of steps: differentiation of cells, differentiation of tissue, of dorsal and ventral, right and left. But we don’t have strong evidence for any of these.” Taiwanese biologist Li was also direct: “No evolution theory can explain these kinds of phenomena.”
    http://www.fredheeren.com/boston.htm

    “We go from single cell protozoa. which would be ameoba and things like that. Then you get into some that are a little bit bigger, still single cell, and then you get aggregates, they’re still individual cells that aggregate together. They don’t seem to have much in the way of cooperation,,, but when you really talk about a functioning organism, that has more than just one type of cell, you are talking about a sponge and you can have hundreds, thousands, tens of thousands of cells. So we don’t really have organisms that function with say two different types of cells, but there is only five total. We don’t have anything like that.”
    – Dr. Raymond G. Bohlin – quote taken from 31:00 minute mark of this following video
    Natural Limits to Biological Change 2/2 – video
    http://www.youtube.com/watch?v=vo3OKSGeFRQ

    Dr. Stephen Meyer: Darwin’s Dilemma – The Significance of Sponge Embryos – video
    http://www.youtube.com/watch?v=JPs8E7y0ySs

    Deepening Darwin’s Dilemma – Jonathan Wells – Sept. 2009
    Excerpt: “The truth is that (finding) “exceptionally preserved microbes” from the late Precambrian actually deepen Darwin’s dilemma, because they suggest that if there had been ancestors to the Cambrian phyla they would have been preserved.”
    http://www.discovery.org/a/12471

  24. 24
    bornagain77 says:

    What Types of Evolution Does the Cambrian Explosion Challenge? – Stephen Meyer – video
    https://www.youtube.com/watch?v=AaF7t5wRFtA&list=UUUMhP2x7_7psVO-H4MJFpAQ

  25. 25
    keith s says:

    Zachriel:

    Um, we’re disagreeing with KeithS’s conclusion.

    Zachriel and I disputed this in the comments of my original thread. Interested readers can find our discussion starting here.

  26. 26
    Moose Dr says:

    Kieth S: “A friend of yours takes both objects into another room, out of your sight. She randomly picks one of the two objects and flips it.”

    How illogical is it to decide that the designer(s) choose(s) which option to go with at random. Could the designer(s) look at the available options and consider which is best for his/their purpose(s)?

    There are exactly two models that I could see the designer using if his purpose was to make it clear to all that there is only one designer, not many. The model chosen does a rather good job of that. As all organisms originate from an initial ancestor, they all have the same root. The number of designers is now limited to none or one. (There is a possibility of many designers working as a unity, but they can be treated as one.)

    Another option of course is “poof” 6,000 years ago. Evidence of such would be incredibly strong support of a Biblical view, and very much a science stopper. However, the fact that life was developed over eons makes for a much more interesting blow-by-blow account of life’s development. Maybe the designer likes it that way. It certainly is more, well, interesting. It also produces a position where the validity of God is not in your face obvious — something I think the designer may want. ‘Would be nice if the first few chapters of the Bible were written differently though.

  27. 27
    Barry Arrington says:

    Bob O’H @ 16. I am sure you will agree that the phrase “common descent” (about which he was speaking) is not coterminous with the word “evolution.”

  28. 28
    Phinehas says:

    Zachriel:

    William J Murray: If nature can produce a biological system that is not a nested hierarchy, then assuming it had other possibilities available but generated an ONH is no different than assuming that a designer had other options but chose an ONH.

    Zachriel: “Nature” is too vague to be a suitable mechanism for scientific consideration. The hypothesized mechanism is branching descent. The entailment is the nested hierarchy.

    No, the hypothesized mechanism is unguided branching descent. “Nature” is a decent enough label for keeping the “unguided” part in view. Without keeping this in view, you are saying nothing at all about whether or not design was involved.

  29. 29
    Joe says:

    Zachriel:

    The evidence from the nested hierarchy strongly supports common descent,

    Only if transitional forms are not allowed. And a family tree is an example of common descent yet it doesn’t form a nested hierarchy based on defined characteristics.

    OTOH the US Army is a nested hierarchy, by design. Common descent not required. Also a branching tree can be put into a nested hierarchy depending on the criteria used.

    Just because a nested hierarchy can be depicted as a branching tree pattern does not mean all branching tree patterns are nested hierarchies. Yet evos think that they are. Strange

  30. 30
    Joe says:

    Zachriel:

    The hypothesized mechanism is branching descent.

    So you are discussing baraminology and the fact the nested hierarchy is evidence for a common design. Cool

  31. 31
    keith s says:

    Barry,

    We’re still awaiting your response to my challenge.

  32. 32
    Joe says:

    LoL! keith s gets spanked and ignores it. keith s, a special type of Black Knoght

  33. 33
    Joe says:

    LoL! keith s gets spanked and ignores it. keith s, a special type of Black Knight LoL

  34. 34
    bornagain77 says:

    semi related: Among Theistic Evolutions, Still No Consensus on What’s Wrong with Stephen Meyer’s Argument – Casey Luskin – November 5, 2014
    http://www.evolutionnews.org/2.....90921.html

  35. 35
    nullasalus says:

    I’m repeating what others, particularly WJM, have already said – but that’s because the responses from ID critics don’t seem to get it.

    Saying ‘we have this particular pattern, which is explained by evolution / common descent / etc’ doesn’t get you an inch in the direction of saying that pattern was the result of an unguided process in the broad sense – and the broad sense is exactly what’s under discussion here.

    Just about every tool in the evolutionary toolbox – common descent, reproduction with variation, selection, and more – are also tools in the designer’s toolbox. It’s not enough for you to point to those tools. You need some way to argue that the tools have no guidance by any designer behind them. None whatsoever.

    The ID proponent, meanwhile, has a lot more freedom. It actually doesn’t matter if one or another event in nature was unguided – if it was even partly guided, however remotely and ultimately, then ID is correct. And using science, the ID skeptic can’t provide evidence that much of anything at all is unguided in the relevant sense.

    Now, it’s possible to try and turn this around – and I see some people are already attempting this – by arguing, ‘Well, you haven’t proven that God/a designer/designers was involved in evolution!’ Let’s put all of the argued ID inferences to the side for one moment and accept, for the sake of argument, that the ‘haven’t proven’ claim is true. Okay – the resulting conclusion is that science is absolutely silent on the presence or lack of design in evolution at any stage, at any level. It leaves the topic untouched, with neither “evolution is guided” nor “evolution is unguided” having scientific merit.

    But to concede that would just be to concede a victory to most skeptics of naturalism and naturalistic evolution. It turns out that Darwin never discovered anything that should shake people’s belief that nature was designed. He discovered a system under which nature was possibly not-designed – but ‘possibly not designed’ was never new, and was possible before.

    As Barry said – there is no bomb. A whole lot of smoke, sure. Mirrors too. But no bomb.

  36. 36
    Mapou says:

    Darwin predicted a strictly nested tree of life. The evidence proved him dead wrong. Intelligent design predicts a nested hierarchy with horizontal gene sharing sprinkled everywhere. Guess what? This is precisely what is observed in nature.

    Zachriel has been repeating the same lies for years. No hall pass for you, Zachriel.

  37. 37
    Box says:

    Based on the quote in the OP, one has to wonder if Theobald is to be regarded as a leading light.

    Dr. Theobald: For a theist, the pertinent question is not “what is an omnipotent Creator capable of?” but rather “how exactly did/does the Creator create?”. The first question is purely theological, and as such is left unaddressed in the “29 Evidences”; in contrast, the second question is one that science can answer (…)

    How on earth can science answer the question, “how exactly did/does the Creator create?” Theobald’s optimism is only grounded when he has received an invitation to visit the designer’s lab.

  38. 38
    Joe says:

    If Darwin couldn’t say anything about the origin of life he couldn’t say how many trees there would be.

  39. 39
    kairosfocus says:

    Z, in a pause. The OP is reporting where KS took his stance. My point from two years past and counting is that Dr T stumbled in the starting gate once he entertained notions of categorising the evolutionary materialist narrative as “fact” — the fact, fact, FACT error. Wiki goes worse by suggesting self-evident. There is need to ground the claimed powers of blind chance and mechanical necessity from OOL through the whole branching tree system, and particularly on the origin of functionally specific complex organisation and associated information, in the context of interacting arranged pasts to achieve function. FSCO/I in short. Absence of showing that blind watchmaker mechanisms in our observation can and does create FSCO/I leads to a failure of showing vera causa, and to a question begging fail for KS as noted at 5 above (which KS has not adequately resolved). Cf here for details. KF

  40. 40
    Zachriel says:

    Phinehas: No, the hypothesized mechanism is unguided branching descent.

    The hypothesis in Theobald’s paper is branching descent. That’s what was subjected to testing.

    Phinehas: Without keeping this in view, you are saying nothing at all about whether or not design was involved.

    That’s correct. The paper only concerns the evidence for branching descent.

    nullasalus: Saying ‘we have this particular pattern, which is explained by evolution / common descent / etc’ doesn’t get you an inch in the direction of saying that pattern was the result of an unguided process in the broad sense

    That’s correct. The paper only concerns the evidence for branching descent.

    nullasalus: Just about every tool in the evolutionary toolbox – common descent, reproduction with variation, selection, and more – are also tools in the designer’s toolbox.

    Good. Then we agree on branching descent. That’s important because it provides the historical context necessary for understanding mechanisms of adaptations.

    Mapou: Darwin predicted a strictly nested tree of life.

    That’s not correct. For instance, Darwin was well aware of hybridization about which he wrote extensively. Also, convergence leads to traits which don’t fit the nested hierarchy, such as dolphins and fish both having fins. In any case, Theobald’s paper demonstrates monophyly.

  41. 41
    Zachriel says:

    kairosfocus: Dr T stumbled in the starting gate once he entertained notions of categorising the evolutionary materialist narrative as “fact” — the fact, fact, FACT error.

    No. Theobald *hypothesized* branching descent, then tested the entailment, the nested hierarchy.

    hypothesis, a claim provisionally accepted for the purpose of testing its empirical implications (entailments).

    kairosfocus: There is need to ground the claimed powers of blind chance and mechanical necessity from OOL through the whole branching tree system, and particularly on the origin of functionally specific complex organisation and associated information, in the context of interacting arranged pasts to achieve function.

    That is irrelevant to the particular hypothesis being tested. Perhaps someone shaped the tree, or forced branches into particular shapes, but the branching is still evident. We’d have to look at other evidence to determine that, but any competing hypothesis would probably have to be consistent with branching descent, or at least explain why the data has the signature of branching descent.

  42. 42
    keith s says:

    A challenge for the IDers here.

  43. 43
  44. 44
    kairosfocus says:

    KS, you plainly have not read Theobald’s argument, and why I said that. Please read here, right at the beginning of his 29 points argument he committed exactly the blunder I highlighted. That undermines his system. Further you need to note what appears at 5 above in regards to your own argument, which is based on question begging as again shown. When you show us how you resolve that and linked concerns, then we can begin to make actual progress towards a reasonable view. KF

  45. 45
    Mapou says:

    Zac:

    Mapou: Darwin predicted a strictly nested tree of life.

    That’s not correct.

    Of course, it is correct. Darwin never anticipated horizontal gene transfers. To suggest that he did is insulting to the readers. It’s a lie.

    For instance, Darwin was well aware of hybridization about which he wrote extensively. Also, convergence leads to traits which don’t fit the nested hierarchy, such as dolphins and fish both having fins. In any case, Theobald’s paper demonstrates monophyly.

    For someone as fanatically dishonest as you to insinuate that “convergent evolution”, let alone hybridization, is anything like horizontal gene transfers, is tantamount to flinging feces through the fence at the onlookers. You need to be hosed down with a firehose. There is no way that random mutations and natural selection are going to arrive at the exact same code sequences in distant species. You’re a superstitious voodoo practitioner masquerading as a scientist. Pathetic.

  46. 46
    Moose Dr says:

    Box (37): How on earth can science answer the question, “how exactly did/does the Creator create?”

    The only point where there may be validity to your rhetorical is in the word “exactly”. As science pursues a log of the history of the earth and its biology, a pattern of the designer’s activity unfolds.
    > It seems clear that the designer did his thing over millions of years.
    > It seems clear that one mechanism used by the designer is to load balance and purify using a tool we have called natural selection.
    > Evidence seems to support the idea that the designer caused biological diversity by twiddling with existing, living organisms along the way (UCD).
    > The designer seems to have liked to work one level at a time. (During the early cambrian, the designer was fiddling with the phyla. Once he had so fiddled, he abandoned fiddling at that level, and began fiddling on the level of the classes.)
    > The designer seems to like to inject whole working genes. At least that is the conclusion I come to as I see how many de novo genes are being found. (Something that NDE can’t achieve in my opinion.)

    So far we don’t know “exactly” how the designer injects a new gene into an organism. We may never know. However, as time and research continue our picture of how the designer designs becomes clearer and clearer.

  47. 47
    Zachriel says:

    Mapou: Darwin never anticipated horizontal gene transfers.

    That wasn’t your previous claim, which was that Darwin “predicted a strictly nested tree of life”. That was incorrect. While Darwin was unaware of horizontal gene transfer, he was aware of other mechanisms that would lead to imperfections in the nested hierarchy, including hybridization and convergence.

  48. 48
    Joe says:

    Zachriel is full of it, as usual. Family trees are examples of branching descent and they do not form objective nested hierarchies. The hypothesis fails.

  49. 49
    Box says:

    Moose Dr #46,

    You may have some points there. BTW I find it questionable to place the designer in our space-time frame.

    What I had in mind when I asked my question was the designing/creative part of creation. Science cannot know how the designer comes up with molecular machines, body plans etc. Obviously, his muses are out of our reach, so to speak.

  50. 50
    keith s says:

    Hi Vincent,

    You write:

    The first thing I’d like to point out is that while KeithS, in his post over at TSZ leans heavily on the evidence assembled by Dr. Douglas Theobald in his article, 29+ Evidences of Macroevolution, it is very odd that Dr. Theobald himself does not put forward this argument anywhere in his article.

    I don’t find it odd at all. Here are a few plausible explanations:

    1. Theobald’s stated purpose was to present the evidence for common descent, so that’s what he did.

    2. He is a methodological naturalist, so for him any discussion of a Designer is off-limits. Also, he is not an atheist, so he may not be particularly motivated to pursue an argument with atheistic implications. (See this commentary.)

    3. His primary audience is creationists who doubt common descent, so making an explicit anti-designer argument might lead them to reject his argument out of hand. Leaving room for God makes common descent easier for creationists to swallow.

    4. He might also wish to avoid alienating believers who see God as involved in the evolutionary process.

    5. He may not have realized that the evidence he was presenting could be used to argue against guided evolution. A lot of evolutionists are surprised by my argument when they hear it for the first time.

    I don’t know which, if any, of those explanations is correct. My point is simply that you needn’t be surprised that Theobald didn’t make the same argument that I do.

    Read your Theobald quote again, keeping those plausible explanations in mind:

    This is not to say that God could not have created species independently and miraculously, yet gradually. While there currently is absolutely no scientific evidence for such an idea, gradual Divine direction of evolution is indeed consistent and compatible with common descent.

    It is possible for a theist to see the theory of common descent, and the hierarchy which it predicts, as a reflection of the Creator’s divine plan—much as Sir Isaac Newton saw his laws of motion, and the ellipses and parabolas which they predict, as evidence of the Creator’s hand in our universe…

    In fact, no theological assumptions or arguments are made at all in the essay. The “29 Evidences” is not an argument against creation—it is the scientific argument for common descent, no more, no less…

    I personally believe that an omnipotent, omniscient Creator could have created in any manner that he chose. For a theist, the pertinent question is not “what is an omnipotent Creator capable of?” but rather “how exactly did/does the Creator create?”. The first question is purely theological, and as such is left unaddressed in the “29 Evidences”; in contrast, the second question is one that science can answer (given the assumption of a Creator).

  51. 51

    Perhaps he doesn’t make the same argument because he cannot vet the process as unguided.

    “Microevolution creates ONH’s” is not the same statement as “unguided microevolution creates ONH’s”.

  52. 52
    keith s says:

    William,

    Theobald is a methodological naturalist, so guided evolution has no place in his scientific thinking.

  53. 53
    Andre says:

    I don’t think the lights will go on for Keith S but it is worth talking about it. The problem is right there methodological naturalism. You see Keith naturalism cannot explain PCD.

    You haver to be able to demonstrate how an unguided process built a guided process that prevents unguided processes from happening. You see Keith once PCD breaks unguided processes do in fact happen and always at the detriment of the organism. We know PCD is evolutionary conserved, we also know its vital for unicellular and multicellular organisms, but how did it get there? By an unguided process? Really?

  54. 54
    Andre says:

    And it is ok for you to concede that point, but you can’t hammer on about unguided evolution being the best explanation for the diversity of life if we know empirically that unguided processes, first have multiple mechanisms that prevent them from happening and when they fail we know its catastrophic to the organism. So you see Keith your unguided argument just does not fit the evidence we have.

  55. 55
    Andre says:

    Do you understand the problem that PCD presents to your argument Keith?

    If unguided evolution is the reason why everything in the biological world exist, then we have to give this a thought….

    At which point did unguided evolution “decide” (and I use this word loosely) to construct a mechanism that will prevent any other unguided processes from happening and prevent any type of “tampering” with the optimal state of the organism? How did unguided processes know the organism is optimal? And further how is it that unguided evolution managed to build not one but multiple stability control mechanisms for this?

    Was it by sheer dumb luck?

    Stuff happens?

    Keith please you need to address this issue if you are to convince me.

  56. 56
    Andre says:

    That is all I ask,

    Don’t point to the OP at TSZ, I really don’t care about it, I know what that is just a trap to have me battered with foul language and belittling, you set the tone yourself when you called me a little twerp……

    Answer it here and do so honestly.

  57. 57
    AVS says:

    Hey Andre, what “mechanism that will prevent any other unguided processes from happening and tampering” are you referring to?

  58. 58
  59. 59
    Andre says:

    Here is the paper’s conclusion….. and Keith S cannot skirt this issue……

    “Apoptosis is regarded as a carefully regulated energy-dependent process, characterized by specific morphological and biochemical features in which caspase activation plays a central role. Although many of the key apoptotic proteins that are activated or inactivated in the apoptotic pathways have been identified, the molecular mechanisms of action or activation of these proteins are not fully understood and are the focus of continued research. The importance of understanding the mechanistic machinery of apoptosis is vital because programmed cell death is a component of both health and disease, being initiated by various physiologic and pathologic stimuli. Moreover, the widespread involvement of apoptosis in the pathophysiology of disease lends itself to therapeutic intervention at many different checkpoints. Understanding the mechanisms of apoptosis, and other variants of programmed cell death, at the molecular level provides deeper insight into various disease processes and may thus influence therapeutic strategy.”

    “Carefully regulated” sounds just like the kind of thing unguided processes can accomplish….

    NOT!

  60. 60
    AVS says:

    But apoptosis serves an array of functions in multicellular organisms. I don’t think it in any way “prevents any other unguided processes from happening”or “prevents any type of tampering with the optimal state of the organism?”

    Apoptosis simply is the destruction of specific cells for a specific reason. Careful regulation of this process would be expected to evolve, just as careful regulation of every other process in the cell has evolved.

  61. 61
    Andre says:

    AVS

    Please can you demonstrate how unguided processes created a guided process to prevent unguided processes from happening? In addition there are multiple stability control mechanism like PCD……..

    Disease happens when PCD becomes unregulated, while PCD is optimal diseases are prevented. In addition PCD builds body plans too….

    You guys don’t seem to understand the issue here, PCD is also evolutionary conserved in unicellular and multi cellular organisms….. it does not evolve! It can not evolve and if it changes organisms Die!

  62. 62
    AVS says:

    Which unicellular organisms exhibit apoptosis?

  63. 63
    keith s says:

    Andre,

    Here’s an idea. See if you can convince one of your fellow IDers, with author privileges, that PCD is the whiz-bang evo-killer you say it is.

    Then they will enthusiastically post an OP on your behalf. Or not.

    If you can’t even convince your fellow IDers that it’s worth an OP, then you certainly aren’t going to convince anyone else.

  64. 64
    Andre says:

    AVS

    So let me see, just like Keith S, Rich and Thornton, you believe it just emerged?

    A Stability control system is an engineering solution that has a very specific function, it can not be created by ANY unguided process…… The mere fact that there are multiple stability control mechanisms make the claim that unguided evolution did it even more dubious……..

    When the stability control system becomes deregulated unguided processes take over and the organism dies!

  65. 65
    Andre says:

    Keith S

    I’m not trying to get an OP…. I’m trying to point out that unguided processes can not create guided processes to prevent unguided processes from happening! It is Impossible, these type of systems are engineering solutions……

  66. 66
    Andre says:

    So what am I saying to you?

    Unguided processes are not capable of solving problems! Because to solve a problem you need to know about it! Unguided evolution knows nothing about problems or how to solve them!

    To think it does makes you a believer in magic!

  67. 67
    AVS says:

    Andre, you are making the fatal flaw of assuming that because today’s organisms have complex machinery that cannot function with missing pieces, the evolution of this machinery is impossible. Much simpler systems were the ancestors of current cellular processes and more often than not they are offshoots of other processes that have already developed. The paper mentions autophagy, maybe apoptosis is related to this cellular process. We simply don’t know.

  68. 68
    Andre says:

    AVS

    http://www.ncbi.nlm.nih.gov/pubmed/15527405
    http://www.plantphysiol.org/content/132/1/99

    It’s there it’s conserved! But it I must protest it “evolved” and it transferred itself from unicellular organisms to multi cellular organisms by magic!

    The moment PCD becomes deregulated the organisms, both uni and multi cellular dies! It stops this unguided nonsense in its tracks!

  69. 69
    Andre says:

    AVS

    I’m not assuming anything, you are the one that assumes that such machinery could build itself….. I’m asking you to show me how!

    If you are to claim that unguided processes can do this you need to back your claim with evidence!

  70. 70
    Andre says:

    AVS

    Autophagy is another one of the stability control mechanisms of the cells, as pointed out there are multiple ones…… in normal English, REDUNDANCY……..

    mmmmmm redundancy just like stability control is another engineering solution to engineering problems…….

    Sheesh unguided processes sure are smart AVS! They can solve engineering problems without even thinking about it!

  71. 71
    Andre says:

    Autophagy

    http://www.ncbi.nlm.nih.gov/pm.....MC2990190/

    “Autophagy is a self-degradative process that is important for balancing sources of energy at critical times in development and in response to nutrient stress. Autophagy also plays a housekeeping role in removing misfolded or aggregated proteins, clearing damaged organelles, such as mitochondria, endoplasmic reticulum and peroxisomes, as well as eliminating intracellular pathogens. Thus, autophagy is generally thought of as a survival mechanism, although its deregulation has been linked to non-apoptotic cell death.”

    So we not only have apoptosis we also have another backup system to apoptosis called autophagy!

    If I was stupid I’d also say wow unguided processes sure are smart!

  72. 72
    AVS says:

    Did you read those papers? They actually talk about possible mechanisms of the evolution of apoptosis.
    I agree completely that the ability of nature to solve engineering problems is astounding, but you should really learn more about them and try to understand what they are capable of, before trying to tell people what they are incapable of.
    Evolution is not an “unguided process” in my opinion, it is guided by environmental conditions.

  73. 73
    AVS says:

    Autophagy is not really a back-up system to apoptosis. In some cases it may have a role in apoptosis, but generally autophagy is a mechanism for the cell to breakdown its own macromolecules in order to support regular cellular function.

  74. 74
    Andre says:

    AVS

    Yes Autophagy is non-apoptotic, but it is one of the pathways, which there are many of…..

    http://link.springer.com/chapt.....0_1#page-1

    They all work together and when they start failing the organism fails!

  75. 75
    Andre says:

    From the paper and this is important!

    “, evidence is accumulating that necrotic cell death in some cases can be as well controlled and programmed as caspase-dependent apoptosis. Autophagy is foremost a survival mechanism that is activated in cells subjected to nutrient or obligate growth factor deprivation. When cellular stress continues, cell death may continue by autophagy alone, or else it often becomes associated with features of apoptotic or necrotic cell death, depending on the stimulus and cell type. It is debatable whether autophagic cell death is an alternative way of dying, different from apoptotic and necrotic cell death, or whether failure of autophagy to rescue the cell can lead to cell death by either pathway.”

    These stability control mechanisms work together but each one is independently regulated.

  76. 76
    keith s says:

    Vincent,

    Regarding your second point, you write:

    The problem is that KeithS has conflated two hypotheses: the hypothesis of common descent (which is very well-supported by the evidence that objective nested hierarchies exist in living things), and the hypothesis of unguided design (which he also claims is well-supported by the evidence that objective nested hierarchies exist in living things).

    The first hypothesis is indeed well-supported by the evidence, as the only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. The probability that any other process would generate such hierarchies is vanishingly low.

    Okay, so we’re in agreement on common descent.

    But if KeithS wishes to argue against intelligently guided evolution, then the two alternative hypotheses he needs to consider are not:
    A: a branching evolutionary process (also known as a Markov process) generated the objective nested hierarchies we find in living things; and
    ~A: an Intelligent Designer generated these objective nested hierarchies,

    but instead:

    A: an unguided process generated the objective nested hierarchies we find in living things; and
    ~A: an intelligently guided process generated these objective nested hierarchies.

    That’s not true.

    In reality, mutation rates are low enough and vertical inheritance predominates enough that we can treat unguided evolution as a Markov process.

    That’s why Theobald can write this:

    Does Phylogenetic Inference Find Correct Trees?

    In order to establish their validity in reliably determining phylogenies, phylogenetic methods have been empirically tested in cases where the true phylogeny is known with certainty, since the true phylogeny was directly observed.

    Bacteriophage T7 was propagated and split sequentially in the presence of a mutagen, where each lineage was tracked. Out of 135,135 possible phylogenetic trees, the true tree was correctly determined by phylogenetic methods in a blind analysis. Five different phylogenetic methods were used independently, and each one chose the correct tree (Hillis et al.1992 ).

    In another study, 24 strains of mice were used in which the genealogical relationships were known. Cladistic analysis reproduced almost perfectly the known phylogeny of the 24 strains (Atchely and Fitch 1991).

    Bush et al. used phylogenetic analysis to retrospectively predict the correct evolutionary tree of human Influenza A virus 83% of the time for the flu seasons spanning 1983 to 1994.

    In 1998, researchers used 111 modern HIV-1 (AIDS virus) sequences in a phylogenetic analysis to predict the nucleotide sequence of the viral ancestor of which they were all descendants. The predicted ancestor sequence closely matched, with high statistical probability, an actual ancestral HIV sequence found in an HIV-1 seropositive African plasma sample collected and archived in the Belgian Congo in 1959 (Zhu et al.1998 ).

    In the past decade, phylogenetic analyses have played a significant role in successful convictions in several criminal court cases (Albert et al. 1994; Arnold et al. 1995; Birch et al. 2000; Blanchard et al. 1998; Goujon et al. 2000; Holmes et al. 1993; Machuca et al. 2001; Ou et al. 1992; Veenstra et al. 1995; Vogel 1997; Yirrell et al. 1997), and phylogenetic reconstructions have now been admitted as expert legal testimony in the United States (97-KK- 2220 State of Louisiana v. Richard J. Schmidt [PDF]). The legal test in the U. S. for admissibility of expert testimony is the Daubert guidelines (U. S. Supreme Court Case Daubert v. Merrell Dow Pharmaceuticals, Inc., 509 U.S. 579, 587-89, 113 S. Ct. 2786, 2794, 125 L. Ed. 2d 469, 1993). The Daubert guidelines state that a trial court should consider five factors in determining “whether the testimony’s underlying reasoning or methodology is scientifically valid”: (1) whether the theory or technique in question can be and has been tested; (2) whether it has been subjected to peer review and publication; (3) its known or potential error rate; (4) the existence and maintenance of standards controlling its operation; and (5) whether it has attracted widespread acceptance within the relevant scientific community (quoted nearly verbatim). Phylogenetic analysis has officially met these legal requirements.

    The Markov model is empirically verified, which means that ID is still at a trillions-to-one disadvantage with respect to unguided evolution.

  77. 77
    Andre says:

    So my question remains….

    How did unguided processes create a guided process to prevent unguided process from happening?

    Show me!

  78. 78
    AVS says:

    That’s not true, there are plenty of instances where autophagy fails and an organism continues to survive. As you said, there are many cases of redundancy in cells, and these allow the organims to carry on when certain systems fail.

  79. 79
    Andre says:

    AVS

    Thank you for stating my point….. I did not say if one fails the organism dies its when they all fail the organism dies…..

    That is why you have redundancy so that you’re not dependant on just one single system but the multiple systems as a whole…..

    Engineering at work here nothing else!

  80. 80
    Andre says:

    But your admittance

    there are many cases of redundancy in cells

    This begs the question? How did unguided evolution build not only a stability mechanism but multiple ones that are all self regulated but yet depend on each other?

  81. 81
    AVS says:

    Well like I said, evolution is not an “unguided process.” It is guided by the environment.
    And like the paper you quoted said, lets say the environment lacks nutrients to support large amounts of bacteria. An individual bacterial cell that develops a mechanism that leads to its premature death would be favorable to the population of bacteria. And through horizontal gene transfer, the bacteria can share this early form of apoptosis with nearby bacteria.
    The population would evolve to have this apoptotic pathway present in their genome for use whenever conditions were unfavorable, allowing death of some portions of the population.

    Just an idea.

  82. 82
    AVS says:

    How these systems evolved is an almost infinitely complex one question. But don’t you worry, there are many scientists working on answering it as we speak.

  83. 83
    Andre says:

    The environment guides evolution?

    Oh brother……. then how did this “guided environment” build these stability control mechanisms? How did it “choose” the best solution? How did it know that if it lobbed apoptosis, necrosis and autophagy together it would have the answer to prevent unguided processes from happening?

    Do you really believe what you wrote? Are you sure?

  84. 84
    Andre says:

    I’m not holding my breath that one of these finite scientists will ever be able to answer an infinitely complex question…..

    Are you?

  85. 85
    AVS says:

    The complex regulation of these systems is very difficult to tease apart, but in no way is it the “best solution.” Evolution does not find the best solution, it finds slightly better solutions. Evolution builds on what is already present. Often in this case, processes can be regulated together because they have evolved from each other as we have already talked about. As I have also already said though, these process are very separate from each other and while they may have some overlap, they have evolved to carry out their own functions under certain conditions. Intertwining of the functions is a common occurrence in biology.

  86. 86
    Andre says:

    Engineers never find a perfect solution either, the find the best solution…….

    Evolved together means what? The emerged? The Darwinian code world for magic happened!

  87. 87
    AVS says:

    First of all it is never “one” scientist, and second, I said “almost infinitely complex.”
    The devil is in the details my friend, pay attention to them.

  88. 88
    AVS says:

    The engineer of biology is the environment and the processes of evolution.
    And it’s not magic, it’s an awesome process that is extremely complex. You should look into it.

  89. 89
    keith s says:

    Vincent,

    Regarding your final points:

    You write:

    My third point is that KeithS’s argument assumes that the genetic and morphological features on the basis of which living things are classified into objective nested hierarchies were generated by the same process as the (unguided, Markovian) processes which generates the branches in the hierarchies. This is unlikely, even on a standard evolutionary view: features take time to evolve, and therefore would presumably have appeared at some time subsequent to the branch nodes themselves.

    I’m not sure why you think this is an issue. The taxa in a cladogram are always at the ends of the branches, never at the nodes.

    Thus it could well be the case that while unguided processes explain the existence of objective nested hierarchies in the living world, guided processes are required to explain some or all of the features in these hierarchies.

    It isn’t enough to show that guided processes might be involved. You need to show that they must be involved, because otherwise you are still at the trillions-to-one disadvantage.

    My fourth point is that KeithS’s exclusion of the origin of life from his argument limits the force of his conclusion. At most, he can argue that objective nested hierarchies are best explained by unguided processes; but that is not the same as saying that living things themselves are best explained by these processes, or that the origin of life is due to an unguided process.

    I’ve never claimed that my argument is relevant to OOL, so that isn’t a concern. It can’t be relevant to OOL, because you can only get an objective nested hierarchy after OOL.

    And, as you know, IDers care very much about God’s the Designer’s involvement after OOL as well as before.

    Finally, I’d like to point out that KeithS’s argument against Dr. Douglas Axe is factually mistaken. Nowhere in his paper, “The Case Against a Neo-Darwinian Origin of Protein Folds” does Dr. Axe make the argument KeithS imputes to him.

    I addressed that here. You were looking at a different paper from the one I was criticizing.

  90. 90
    Andre says:

    AVS

    The engineering of biology makes sense if there is an actual engineer, nothing engineers itself……

  91. 91
    AVS says:

    Again Andre, making another fatal flaw: comparing biological designs from adaptation, to the intelligent and conscious designs of humans.
    Apples and oranges my friend.

  92. 92
    Andre says:

    AVS

    The assumption that nothing (mindless processes) can build anything is your flaw……

    Do you know what type of universe we live in AVS?

  93. 93
    AVS says:

    But we see mindless processes build a whole organism from a single cell everyday, don’t we? Transcription factors don’t have minds, and neither do ribosomes or any other piece of cellular machinery, and yet here we are.

  94. 94
    Andre says:

    KF

    I think this article is for you 🙂

    “This is why the average person produces only a handful of ideas when brainstorming; whereas, a creative genius will produce great quantities of ideas. Thomas Edison, for example, created 3000 different ideas for a lighting system before he stepped back to evaluate them for practicality and profitability. All geniuses produce great quantities of ideas because they uncritically search for all possible alternatives. If you ask the average person to find a needle in a haystack, he or she will stop when they find a needle. Creative thinkers, on the other hand, will go through the entire haystack looking for all the possible needles.”

    http://www.creativitypost.com/.....jTmLw.dpuf

    Can unguided evolution really search the entire haystack for all possible needles?

  95. 95
    keith s says:

    vjtorley:

    1. We observe objective nested hierarchies (ONH)

    kairosfocus:

    Not quite, the homology/ resemblance implies relationship by descent principle even at gross level (eyes, wings etc) leads to “except where it doesn’t” and the diverse molecular trees undercut this claim.

    No, they don’t. The nested hierarchies inferred from the molecular and morphological data match to an astounding accuracy of 1 in 10^38. Read Theobald.

    vjtorley:

    2. Unguided evolution explains ONH

    kairosfocus:

    Begs the question of origin of FSCO/I on blind chance + mechanical necessity, blah blah blah…

    No, because we know that unguided microevolution produces ONHs, and you haven’t been able to demonstrate the existence of a barrier that would prevent microevolution from turning into macroevolution.

    Also, your ‘islands of function’ argument is in tatters (link, link).

    vjtorley:

    3. A designer explains ONH, but also a trillion alternatives.

    kairosfocus:

    The word trillion is patently put in to rhetorically counter the fact that there are now — thanks to the Internet — trillions of cases in point of the observed source of FSCO/I, design;

    No, the word “trillions” comes into play because of the astounding match between nested hierarchies mentioned above. It’s actually a significant understatement. I was being very conservative.

    Multiplied by the radical attempt to question-beggingly redefine science on a priori materialism, warping its inferences on the past of origins through demanding that we substitute for the longstanding inference on natural [= chance plus necessity] vs the ART-ificial [= intelligently configured] spoken of by Plato and Newton alike, to natural vs supernatural. Where the latter is caricatured and dismissed as beyond science.

    Um, KF — I’m not a methodological naturalist. I think science is perfectly capable of handling supernatural claims, as long as they’re testable. Oops.

    Next, tree-patterns shaped by design constraints and purposes are a commonplace pattern of designs. That is the existence of a treelike pattern is empirically known to be a result of design.

    KF, you don’t have the slightest idea of what we are discussing here. There is a difference between nested hierarchies and objective nested hierarchies. Until you understand that, you have no hope of participating intelligently in this debate.

    It is time for KS et al to do some serious re-thinking.

    It is time for KF to learn about the argument he is supposedly trying to refute.

  96. 96
    Andre says:

    AVS

    We see no such thing…….. that my friend is only in your imagination……

  97. 97
    Andre says:

    And where do those ribosomes come from? Built itself then? You are aware the idea that something can create itself is illogical right?

    to create yourself means you’ve existed before you’ve existed……

  98. 98
    AVS says:

    That post couldn’t be a more perfect description of evolution, Andre.
    No organim’s offspring is exactly identical to the original parent(s), this means that every single individual organism represents a single trial in evolution’s search for new adaptations, solutions, or “ideas,” whatever you want to call it. Think about it, every single organism that has ever lived was part of this never-ending experiment that is run by nature called evolution.

  99. 99
    Andre says:

    AVS

    WHAT? hahahahahahahaha ok I give up…. if what you said was true there would be homo infinity …. instead homo sapiens only exist. Sure we have different colours, sizes heights but we are 100% exactly homo sapiens all you’re describing is variation, who’s arguing about that?

  100. 100
    AVS says:

    How do you think you got here Andre? You were once a single cell.
    And actually there are molecules out there that can self-replciate, the origin of these molecules is another question in itself.

    Toodaloo for now.

  101. 101
    keith s says:

    William J Murray:

    Theobald states:

    The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes.

    The problem is that it is those very evolutionary processes that are under debate; you cannot assume evolutionary processes are either natural or designed.

    William,

    As you know, we actually observe microevolution producing ONHs, and microevolution does not require designer intervention, as even most YECs acknowledge.

    However, assuming natural forces can produce the nested hierarchy is not the same as assuming that a nested hierarchy is the only biological system configuration natural forces are capable of producing.

    See my reply to vjtorley above.

    Keith’s makes two entirely different sets of assumptions about the two categorical candidates. He assumes natural forces can produce the nested hierarchy configuration, and assumes that is the only configuration natural forces can produce.

    I don’t assume it. It is an empirical observation and an obvious consequence of gradual evolution with predominantly vertical inheritance.

    On the design side, kieths assumes that design can produce the nested hierarchy configuration and trillions of other configurations.

    Right, because we know absolutely nothing about the purported designer — including whether or not he/she/it exists, or existed at the time.

    Any IDer who wishes to add assumptions to the design hypothesis, in order to narrow down those trillions of possibilities, must justify them.

  102. 102
    Andre says:

    a single cell with the exact instructions on how to assemble. where did the instructions come from?

  103. 103
    AVS says:

    First of all, what I said is exactly true. But here is where your one-track mind becomes the issue. You do realize there are other species under the genus homo right? Just because they are extinct, doesn’t mean we just ignore them. How quickly you forget that if we were alive 150,000 years ago we would have walked among a number of the other species within our genus. Humans are the tip of a long line of descendants, with many branches. Exactly where these branches are, is difficult to say, in fact the definition of species isn’t even nailed down yet. But we are working on it.

  104. 104
    AVS says:

    We’ve inherited these instructions from our ancestors, with slight modifications over time. And they inherited them from their ancestors, also with slight modifications. This has gone on for the last few billion years, in the grand experiment of evolution and produced the variety of species we see, in the process.

    Have a nice day, maybe I’ll check back with you when I get a chance.

  105. 105
    Andre says:

    If you’re talking about Neanderthal….. I think you know as well as I do that they are not a different homo species, just another damn variation….

    The had speech, art, complex structures and of course they could interbreed with us…….

    But you knew this already yet ignored it…..

  106. 106
    Andre says:

    Where did the ancestors get the instructions from AVS?

  107. 107
    Andre says:

    I must say after this discussion with AVS I can say with certainty, materialists absolutely believe in magic!

  108. 108
    AVS says:

    So are you saying that homo neanderthalensis is the same species as homo sapiens?

    You do realize that by definition, neanderthalensis and sapiens are the names of the species and that entire field of evolutionary biology would disagree with you on that, right?

    But you probably know better.

    And as I said, the instructions have been passed on from generation to generation, with changes in them playing a big part in the divergence of species from their ancestors. Yes all humans follow virtually the same instructions, but the other species within our genus had slightly different instructions, and as you move further and further from our lineage, you see more an more variation in the instructions. This is the essence of evolution.

    You should do some more research on this whole biology thing before you get back to me.
    Bye now

  109. 109
    AVS says:

    Andre, you are exactly what I have come to expect from the UD crowd.
    I will sleep easy tonight knowing that our ID friends have people like you in their ranks.

    <3

  110. 110
    Andre says:

    AVS

    If Neanderthal and Sapiens interbred and made viable offspring then they can not be separate species…..

    http://phys.org/news/2014-04-m.....rbred.html

  111. 111
    Andre says:

    I wonder how many times, this story you believe in will be rewritten?

    Here is one from August 2014

    http://www.nature.com/scientif.....14-36.html

  112. 112
    kairosfocus says:

    KS,

    . . . The nested hierarchies inferred from the molecular and morphological data match to an astounding accuracy of 1 in 10^38. Read Theobald.

    Let me first cite the Wiki admission against interest in their article on evo, which I used in my empty chair stand-in 2 yrs past:

    . . . organisms can be classified using these similarities into a hierarchy of nested groups – similar to a family tree.[247] However, modern research has suggested that, due to horizontal gene transfer, this “tree of life” may be more complicated than a simple branching tree since some genes have spread independently between distantly related species. [–> burying the evidence of mutually incompatible molecular trees and the evidence of code libraries under an assertion; U/D Nov 5, 2014: I now add, and so much for nested hierarchies which necessarily show up as branching trees . . . ] [248][249]

    The 1 part in 10^38 just went up in a smoke of circularities, cherry-picked data and suppression of relevant contrary evidence that Wiki just gives the tip of the iceberg on. For, in fact, the matter is evidently a lot worse than that, and ENV aptly summarises:

    . . . a variety of studies — typically unmentioned when evolutionists promote common descent to the public — have recognized that evolutionary trees based upon morphology (physical characteristics of organisms) or fossils, commonly conflict with evolutionary trees based upon DNA or protein sequences (also called molecule-based trees).

    One authoritative review paper by Darwinian leaders in this field [Patterson et al.] stated, “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.”17 Another set of pro-evolution experts [Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch] wrote, “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.”18

    For example, pro-evolution textbooks often tout the Cytochrome C phylogenetic tree as allegedly matching and confirming the traditional phylogeny of many animal groups. This is said to bolster the case for common descent. However, evolutionists cherry pick this example and rarely talk about the Cytochrome B tree, which has striking differences from the classical animal phylogeny. As one article [Michael S. Y. Lee] in Trends in Ecology and Evolution stated: “the mitochondrial cytochrome b gene implied…an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.”19

    The widespread prevalence of disagreement and non-correspondence between molecule-based evolutionary trees and anatomy-based evolutionary trees led to a major article in Nature [Trisha Gura] that reported that “disparities between molecular and morphological trees” lead to “evolution wars” because “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”20 The article’s revelation of the disparities between molecular and morphological phylogenies was striking:

    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 within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species’ morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. … So can the disparities between molecular and morphological trees ever be resolved? Some proponents of the molecular approach claim there is no need. The solution, they say, is to throw out morphology, and accept their version of the truth. “Our method provides the final conclusion about phylogeny,” claims Okada. Shared ancestry means a genetic relationship, the molecular camp argues, so it must be better to analyse DNA and the proteins it encodes, rather than morphological characters that can end up looking similar as a result of convergent evolution in unrelated groups, rather than through common descent. But morphologists respond that convergence can also happen at the molecular level, and note there is a long history of systematists making large claims based on one new form of evidence, only to be proved wrong at a later date.21

    Likewise, a review article in the journal BioEssays [Matthew A. Wills] reported that despite a vast increase in the amount of data since Darwin’s time, “our ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years,” and that, “[d]espite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.”22 Strikingly, an article in Trends in Ecology and Evolution [W. W. De Jong] concluded, “the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.”23

    Despite the inaccurate claims of some evolutionists and their cherry picking of data, the truth is that there is great incongruence between these two different types of phylogenies, and that this incongruence is a huge issue, problem, and debate within systematics . . . .
    ________

    [17.] Patterson et al., “Congruence between Molecular and Morphological Phylogenies,” Annual Review of Ecology and Systematics, Vol 24, pg. 179 (1993) (emphasis added).

    [18.] 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 (Supplement 1, 1997) (emphasis added).

    [19.] See Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution, Vol. 14:177-178 (1999) (emphasis added).

    [20.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000) (emphasis added).

    [21.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000).

    [22.] Matthew A. Wills, “The tree of life and the rock of ages: are we getting better at estimating phylogeny,” BioEssays, Vol. 24: 203-207 (2002), reporting on the findings of Michael J. Benton, “Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century,” Proceedings of the Royal Society of London B, Vol. 268: 2123-2130 (2001).

    [23.] W. W. De Jong, “Molecules remodel the mammalian tree,” Trends in Ecology and Evolution, Vol 13(7), pgs. 270-274 (July 7, 1998).

    IDEA has summarised the common rhetoric-facts gap on the ToL icon, the subject of the sole illustration in original edns of Origin:

    When arguing for common descent, evolutionary scientists typically assert that the degree of genetic (or anatomical) similarity between two species indicates how closely they are related. But there are numerous cases where this assumption fails, and anatomical or molecular data yield evolutionary trees (called ‘phylogenies’) that conflict with conventional views of organismal relationships. The basic problem is that evolutionary trees based on one gene commonly differ strikingly from a phylogeny based on a different gene.

    Leading evolutionists are loath to admit this fact during public debate. During the 2009 Texas State Board of Education (TSBOE) hearings on evolution-education, University of Texas Austin evolutionary scientist David Hillis cited himself as a “world’s leading exper[t] on the tree of life” and told the TSBOE that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. Hillis’s self-proclaimed expertise makes it all the more disconcerting that he tried to mislead the TSBOE about the widespread prevalence of incongruencies between various molecular phylogenies within his own field.

    Indeed, the very day that Hillis testified before the TSBOE, the journal New Scientist published a cover story titled “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’s gross oversimplification of the case for common ancestry, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:

    “For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.1

    To reiterate, the basic problem is that one gene or protein yields one version of the “tree of life,” while another gene or protein yields an entirely different tree. As the New Scientist article stated:

    The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.2

    Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”3 Evolutionary biologists like Doolittle may claim that this problem is encountered when one tries to reconstruct the evolutionary relationships of microorganisms, such as bacteria, which can swap genes through a process called horizontal gene transfer, thereby muddying any phylogenetic signal. But this objection does not hold water, since the tree of life is challenged even among higher organisms where such gene-swapping is not observed. As the New Scientist article noted, “research suggests that the evolution of animals and plants isn’t exactly tree-like either.”

    Authority Carl Woese has also observed that these problems extend well beyond the base of the tree of life, stating: “Phylogenetic incongruities [conflicts] 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.”4 To reiterate, even among higher organisms, as the New Scientist article explains that “The problem was that different genes told contradictory evolutionary stories,” therefore leading one scientist to say regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.”
    _________________

    [1.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009) (emphasis added).

    [2.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009).

    [3.] W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science, Vol. 284:2124-2128 (June 25, 1999).

    [4.] Carl Woese “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998) (emphasis added)

    This article went on to note:

    A 2009 paper in Trends in Ecology and Evolution notes that: “A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome.”5 Similarly, a paper in the journal Genome Research studied the DNA sequences in various animal groups and found that “different proteins generate different phylogenetic tree[s].”6

    A study published in Science in 2005 tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” Again, the problem lies in the fact that trees based upon one gene or protein often conflict with trees based upon other genes. Their study tried to avoid this problem by using a many-gene technique, yet still found that “[a] 50-gene data matrix does not resolve relationships among most metazoan phyla.”7

    Striking admissions of troubles in reconstructing the “tree of life” also came from a 2006 paper in the journal PLoS Biology, entitled “Bushes in the Tree of Life.” The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” The paper even contends that “[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”8 Unfortunately one assumption they were not willing to re-evaluate is that of universal common ancestry.

    Another study published in Science found that the molecular data implied that six-legged arthropods, or hexapods (i.e. insects) are not monophyletic, a conclusion that differed strikingly from virtually all previous wisdom. The article concluded “Although this tree shows many interesting outcomes, it also contains some evidently untenable relationships, which nevertheless have strong statistical support.”9

    A paper in the Journal of Molecular Evolution found that molecule-based phylogenies conflicted sharply with previously established phylogenies of major mammal groups, concluding that this anomalous tree “is not due to a stochastic error, but is due to convergent or parallel evolution.”10 Likewise, a study published in Proceedings of the National Academy of Sciences USA explains that when evolutionary biologists tried to construct a phylogenetic tree for the major groups of birds using mitochondrial DNA (mtDNA), their results conflicted sharply with traditional notions of bird relationships. Strikingly, they even find “convergent” similarity between some bird mtDNA and the mtDNA of distant species such as snakes and lizards. The article suggests bird mtDNA underwent “multiple independent originations,” with their study making a “finding of multiple independent origins for a particular mtDNA gene order among diverse birds.”11
    ______________

    [5.] James H. Degnan and Noah A. Rosenberg, “Gene tree discordance, phylogenetic inference and the multispecies coalescent,” Trends in Ecology and Evolution, Vol. 24(6) (March, 2009).

    [6.] Mushegian et al., “Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes,” Genome Research, Vol. 8:590-598 (1998).

    [7.] Antonis Rokas, Dirk Krueger, and Sean B. Carroll, “Animal Evolution and the Molecular Signature of Radiations Compressed in Time,” Science, Vol. 310:1933-1938 (Dec. 23, 2005).

    [8.] Antonis Rokas and Sean B. Carroll, “Bushes in the Tree of Life,” PLoS Biology, Vol. 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).

    [9.] Nardi et al., “Hexapod Origins: Monophyletic or Paraphyletic?,” Science, Vol. 299:1887-1889 (March 21, 2003)

    [10.] Cao et al., “Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders,” Journal of Molecular Evolution, Vol. 47:307-322 (1998).

    [11.] Mindell et al., “Multiple independent origins of mitochondrial gene order in birds,” Proceedings of the National Academy of Sciences USA, Vol. 95: 10693-10697 (Sept. 1998).

    Rokas and Carroll, in “Bushes in the Tree of Life” — once one duly discounts the rosy spectacles view and digs in — have a significant admission:

    . . . we have focused on the emerging evidence from genome-scale studies on several branches of the TOL that sharply contrasts with viewpoints—such as that in the opening quotation [from Dawkins]—which imply that the assembly of all branches of the TOL will simply be a matter of data collection. We view this difficulty in obtaining full resolution of particular clades—when given substantial data—as both biologically informative and a pressing methodological challenge. The recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics . . . .

    In the course of evolution, the relative rates of cladogenesis and extinction have differed enormously across clades [14] [–> bye bye molecular clocks . . . ], resulting in different tree shapes (Figure 1A). For example, the occurrence of cladogenetic events at widely spaced intervals generates clades characterized by long stems, and as time elapses, the phylogeny acquires a tree-like shape. In contrast, a radiation where a series of cladogenetic events occurs within a short time span generates a clade characterized by short stems. As the elapsed time since the radiation increases, the external branches lengthen and the phylogeny becomes bush-like.

    The relative shape of clades is a key determinant of the prospects for the accurate reconstruction of their history [15]. This is because the amount of signal for a given stem is finite and proportional to the time span of the stem in question [16]. [–> here comes the poverty of evidence claim again, which in the teeth of 1/4 mn species on shelves with millions of specimens plus billions seen in the field is threadbare] In a parsimony framework—which we illustrate here for simplicity—the signal for a given stem essentially equals the number of parsimony-informative characters (PICs; Box 1) supporting that stem (Figure 1B).

    Because molecular characters typically have a few alternative states [–> 4 per DNA base, 20 per protein base, moving at 4^n or 20^n respectively, i.e. growing exponenially!], the probability of several species acquiring the same nucleotide or amino acid independently (homoplasy; Box 1) is significant and can overwhelm the true historical signal given sufficient time [–> but, not the chain, and of course there’s that kangaroo that after a branch-point said to be c 150 MYA, has in it large swathes of the human genome], irrespective of the phylogenetic method used [17]. Bush-shaped clades are characterized by longer external branches relative to the stems, and therefore more homoplastic changes are likely to occur on the external branches [18], thus generating characters that conflict with the true phylogenetic signal (Figure 1C).

    If you notice a built in circle on the assumption of blind watchmaker thesis evo and the linked assumption that FSCO/I can be accounted for incrementally, no need to be concerned about gaps between islands and limited search resources and/or challenges of irreducibly complex multi-part function, it is there.

    But, notwithstanding, we still see pulling, stretching and cutting to fit recalcitrant data pointing in other directions into the dominant view of a school of thought. To my mind, rather like how marxists used to treat economic, sociological, anthropological, psychological, historical and other evidence back in the day.

    Looks like not only smoke, but glaring fire.

    In short, the branching tree leading to nested hierarchies as core characteristics get permanently embedded in body plans concept is open to serious challenge at root/trunk [I recall, when looking for suitable illustrations, deciding not to use one that tried to turn the root/trunk into a sort of mesh network] and shoots level. The nested hierarchy premise you used is deeply questionable, and yes it is fair comment to say that the traditional TOL has been put to severe challenge based on molecular level trees, never mind the circularities involved in homologies imply relationships of descent with modification, except where we deem the case to be convergence. Convergence between whales and bats on genes for echolocation systems seems a particularly strange case. And the existence of “library of parts” mosaic animals such as the platypus, should give pause.

    So, KS, you have a bit of a problem addressing the real situation, which does not come down to one neat convergent picture of a simple branching tree leading to a nested hierarchy pivoting on conservation of core characteristics once acquired. Instead, it looks like tree-ish patterns with cross-links from re-use or transfer of a library of parts. A typical designer’s pattern leading to in the programming sense multiple inheritance.

    Theobald, as usual for Talk Origins, seems to be rather over-stating his case. Remember, he started with the fact, fact, FACT blunder.

    And, of course, your usual brush-asides of key issues fail. But, we are here dealing with deeply entrenched ideology such as Marxism was, seemingly impervious for many decades. Then, pfft, it collapsed and — apart from attempts to revive it under other guises — is dead.

    KF

  113. 113
    kairosfocus says:

    Oops, overlooked the ENV link.

  114. 114
    kairosfocus says:

    BTW, KS, do you think that whatever personal views and rhetoric you may put up, that suffices to rewrite the history [–> note, my always linked] of trying to redefine science as evolutionary materialist ideology in a lab coat and the ugly intimidation tactics used to push that on Boards of Education etc? Or, to change the fact that in a strawman ntactic, a 2350 year long history of inference between natural and ART-ificial has been transmuted by ruthless agit prop tactics into a caricature of how dare you inject the — shudder — irrational and superstitious supernatural into our Temple of Science? Please. KF

  115. 115
    kairosfocus says:

    F/N: For those curious to see what Camp said to Theobald on nested hierarchy years ago, let’s clip:
    ____________

    >> PREDICTION 1: THE FUNDAMENTAL UNITY OF LIFE

    [Th:] According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1) replication, (2) information flow in continuity of kind, (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.

    If every living species descended from an original species that had these four obligate functions, then all living species today should necessarily have these functions. Most importantly, they should have inherited the structures that perform these functions. The genealogical relatedness of all life predicts that organisms should be very similar in the particular mechanisms and structures that execute these basic life processes.

    [Ca:] The alleged prediction and fulfillment are:

    If universal common ancestry is true, then all organisms will have one or more traits in common.

    All organisms have one or more traits in common.

    Unless one inserts an additional premise imposing a limit on the degree to which descendants can vary (which would require specification of a mechanism of descent), the claim of common ancestry does not require that all of the descendants share one or more traits. There is no logical reason why completely novel organisms could not arise in one or more lineages. Absent specification of a mechanism of descent, which Dr. Theobald purposefully avoids, there is no way to tether the traits of the descendants to those of the common ancestor.

    The belief that evolution predicts biologic universals is “one of evolution’s major illusions.” (ReMine, 92.) As Walter ReMine says:

    First, evolution does not predict that life would arise precisely once on this planet. If there were two or more unrelated systems of life, then evolutionary theory would effortlessly accommodate that situation.[3]

    Second, even if life originated precisely once, then evolutionary theory would still not predict biologic universals. Shortly after life’s origin, nothing prevented life from branching and leading separate lineages to higher life forms entirely lacking the known biologic universals.

    Third, evolutionary loss and replacement processes could prevent biologic universals. If one organism is a distant ancestor to another, then nothing in evolution predicts the two must share similarities. If evolution were true, then distant ancestors and descendants (as well as sister groups) can be totally different.

    Evolution never did predict biologic universals, it merely accommodated them. (ReMine, 92-93.)

    Biophysicist Cornelius G. Hunter concurs. He writes:

    There is yet another reason that the universality of the genetic code is not strong evidence for evolution. Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all). In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature.

    Consider how evolutionists would react if there were in fact multiple codes in nature. What if plants, animals, and bacteria all had different codes? Such a finding would not falsify evolution; rather, it would be incorporated into the theory. For if the code is arbitrary, why should there be just one? The blind process of evolution would explain why there are multiple codes. In fact, in 1979 certain minor variations in the code were found, and evolutionists believe, not surprisingly, that the variations were caused by the continuing evolution of the universal genetic code. Of course, it would not be a problem for such an explanation to be extended if it were the case that there were multiple codes. There is nothing wrong with a theory that is comfortable with different outcomes, but there is something wrong when one of those outcomes is then claimed as supporting evidence. If a theory can predict both A and not-A, then neither A nor not-A can be used as evidence for the theory. When it comes to the genetic code, evolution can accommodate a range of findings, but it cannot then use one of those findings as supporting evidence. (Hunter, 38.)

    The fact that some leading evolutionists believe early life forms were biochemically distinct from modern forms confirms that evolution does not predict biologic universals. Robert Shapiro, for example, entertains the possibility of finding living relics of an original protein-based life form that lacked DNA and RNA. (Shapiro, 293-295.) Likewise, A. G. Cairns-Smith thinks that descendants of ancient crystalline clay organisms may be all around us. He states: “Evolution did not start with the organic molecules that have now become universal to life: indeed I doubt whether the first organisms, even the first evolved organisms, had any organic molecules in them at all.” (Cairns-Smith, 107.)

    On the other hand, ReMine argues that biologic universals are a prediction of his message theory of creation, which “says all life was constructed to look like the unified work of a single designer.” (ReMine, 94.) So evolution does not predict the unity of living things, but at least one theory of creation does.

    Of course, the biochemical similarity of living things fits easily within a creation framework. As biochemist Duane Gish explains:

    A creationist would also expect many biochemical similarities in all living organisms. We all drink the same water, breathe the same air, and eat the same food. Supposing, on the other hand, God had made plants with a certain type of amino acids, sugars, purines, pyrimidines, etc.; then made animals with a different type of amino acids, sugars, purines, pyrimidines, etc.; and, finally, made man with a third type of amino acids, sugars, etc. What could we eat? We couldn’t eat plants; we couldn’t eat animals; all we could eat would be each other! Obviously, that wouldn’t work. All the key molecules in plants, animals, and man had to be the same. The metabolism of plants, animals, and man, based on the same biochemical principles, had to be similar, and therefore key metabolic pathways would employ similar macromolecules, modified to fit the particular internal environment of the organism or cell in which it must function. (Gish, 277.)

    As for the alleged fulfillment, I do not doubt that all living things have carried out the basic functions of life in similar ways, but there are many organisms, past and present, about which we know nothing. It is impossible to be certain that none of these organisms is (or was) biochemically unique (witness the speculations of Shapiro and Cairns-Smith). The claim that all organisms have one or more traits in common is true in the sense that all living things necessarily have the traits by which life is defined, but that is simply a tautology—living things all have the traits of living things.

    PREDICTION 2: A “NESTED” HIERARCHY OF SPECIES

    [Th;}As you can see from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as “groups within groups.” This nested hierarchical organization of species contrasts sharply with the continuum of “the great chain of being” and the continuum predicted by Lamarck’s theory of organic progression. Few other natural processes would predict a nested hierarchical classification. Real world examples that cannot be classified as such are elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc. That certain organisms merely are similar to each other is not enough to support macroevolution; the nested classification pattern that satisfies the macroevolutionary process is very specific.

    [Ca: . . . pattern continues] The alleged prediction and fulfillment are:

    If universal common ancestry is true, then organisms will be classifiable in a nested hierarchy.

    Organisms are classifiable in a nested hierarchy.

    It is not a corollary of the hypothesis of common descent that organisms will have features by which they can be classified as groups within groups. Common descent can explain or accommodate nested hierarchy (though not without difficulty in the specific case of Neo-Darwinism), but it does not predict it. There are mechanisms of descent from a common ancestor that would yield a different pattern. If common descent can yield either nested hierarchy or something else, then the presence of nested hierarchy does not count as evidence of common descent.

    Hunter puts it this way:

    It has been known since Aristotle that species tend to cluster in a hierarchical pattern, and in the eighteenth century Linnaeus saw it as a reflection of the Creator’s divine plan. Obviously this pattern does not force one to embrace evolution. Also, Darwin’s law of natural selection does not predict this pattern. He had to devise a special explanation—his principle of divergence—to fit this striking pattern into his overall theory. To be sure, evolution can accommodate this hierarchical pattern, but the pattern is not necessarily implied by evolution. (Hunter, 108.)

    Even a mechanism of descent that includes branching events does not ensure a nested pattern. As ReMine explains:

    The pattern of descent depends on the extent that evolved characters are later lost. Suppose losses are significant, and characters are replaced at a high rate. Then there is no reason to expect a nested pattern. Descendants could be totally different from their distant ancestors and sister groups, with little or no semblance of nested similarities linking them. (ReMine, 343.)

    Evolution does not predict a hierarchical pattern. Simple processes of loss, replacement, anagenesis, transposition, unmasking, or multiple biogenesis would prohibit such a pattern. Since hierarchical patterns (such as cladograms or phenograms) are not predicted by evolution they are not evidence for evolution. (ReMine, 444.)

    In fact, nested hierarchy raises some difficult issues within a Neo-Darwinian framework. As Michael Denton observes:

    In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed. There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology[4] and not evolution. How much easier it would be to argue the case for evolution if all nature’s divisions were blurred and indistinct, if the systema naturalae was largely made up of overlapping classes indicative of sequence and continuity. (Denton 1986, 136-137.)

    The notion that the nested hierarchy of organisms is incompatible with creation is based, not on science, but on the unprovable theological assumption that if God created life he would do it in some other way. As biologist Leonard Brand explains:

    The hierarchical arrangement of life illustrated in Fig. 9.6 has been used by Futuyma (1983) and others as evidence that life must have evolved. They believe that if life were created, the characteristics of different organisms would be arranged chaotically or in a continuum, not in the hierarchy of nested groups evident in nature. If we think of that concept as a hypothesis, how could it be tested? Actually, to state how a Creator would do things and then show that nature is or is not designed that way is an empty argument. Such conjecture depends on the unlikely assumption that we can decide what the Creator would be like and how he would function. (Brand, 155.)

    It may be that the nested hierarchy of living things simply is a reflection of divine orderliness. It also may be, as Walter ReMine suggests, that nested hierarchy is an integral part of a message woven by the Creator into the patterns of biology. (See, e.g., ReMine, 367-368, 465-467.) The point is that the hierarchical nature of life can be accommodated by creation theory as readily as by evolution. Accordingly, “[i]t is not evidence for or against either theory.” (Brand, 155.)

    Dr. Theobald’s claim that “specially designed objects like buildings, furniture, cars, etc.” cannot be classified in a nested hierarchy requires elaboration. In terms of mere classification, it is incorrect. Buildings and vehicles have both been used as examples of nesting (Ridley 1993, 52-54; Fastovsky and Weishampel, 51-53; Brand, 165-166). According to Mark Ridley:

    Any set of objects, whether or not they originated in an evolutionary process, can be classified hierarchically. Chairs, for instance, are independently created; they are not generated by an evolutionary process: but any given list of chairs could be classified hierarchically, perhaps by dividing them first according to whether or not they were made of wood, then according to their colour, by date of manufacture, and so on. The fact that life can be classified hierarchically is not, in itself, an argument for evolution. (Ridley 1985, 8.)

    PAGE TOP | OUTLINE
    PREDICTION 3: CONVERGENCE OF
    INDEPENDENT PHYLOGENIES

    If there is one true historical phylogenetic tree, all separate lines of evidence should converge on the same tree, our standard phylogenetic tree.

    The alleged prediction and fulfillment are:

    If universal common ancestry is true, then phylogenies constructed from any comparisons of organisms will “converge” on the standard phylogenetic tree.

    Phylogenies constructed from comparisons of certain biological molecules in organisms “converge” on the standard phylogenetic tree.

    There is an obvious disconnect between the alleged prediction and fulfillment. The fulfillment refers to only one basis of comparison (biological molecules), not all bases of comparison, and it refers to only some comparisons on the selected basis (some biological molecules), not all comparisons.

    The alleged prediction could, of course, be amended to conform to the statement of fulfillment. The important point is that it is not a prediction of the hypothesis of common ancestry that phylogenies[5] constructed from comparisons of biological molecules will match phylogenies constructed from comparisons of morphology. This is obvious from the fact molecular and morphological phylogenies often are inconsistent, and yet the hypothesis of common descent is not considered falsified. The discordant data are simply accommodated by the theory.

    The conflict between molecular and morphological phylogenies is a notorious problem in systematics. In fact, it was the focus of a recent article in Nature, subtitled: “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology. Can the two ever be reconciled, asks Trisha Gura.” (Gura, 230.) Ms. Gura states in the article:

    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 within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species’ morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. . . .

    Battles between molecules and morphology are being fought across the entire tree of life. Perhaps the most intense are in vertebrate systematics, where molecular biologists are challenging a tradition that relies on studies of fossil skeletons and the bones and soft tissue of living species. . . .

    So can the disparities between molecular and morphological trees ever be resolved? Some proponents of the molecular approach claim there is no need. The solution, they say, is to throw out morphology, and accept their version of the truth. “Our method provides the final conclusion about phylogeny,” claims Okada. Shared ancestry means a genetic relationship, the molecular camp argues, so it must be better to analyse DNA and the proteins it encodes, rather than morphological characters that can end up looking similar as a result of convergent evolution in unrelated groups, rather than through common descent. But morphologists respond that convergence can also happen at the molecular level, and note there is a long history of systematists making large claims based on one new form of evidence, only to be proved wrong at a later date. (Gura, 230, 232.)

    These conflicts have long been recognized. In 1986, biochemist Christopher Schwabe wrote:

    Molecular evolution is about to be accepted as a method superior to paleontology for the discovery of evolutionary relationships. As a molecular evolutionist I should be elated. Instead it seems disconcerting that many exceptions exist to the orderly progression of species as determined by molecular homologies; so many, in fact, that I think the exception, the quirks, may carry the more important message. (Schwabe, 280.)

    The incongruities of the molecular evidence led Schwabe to conclude that there were multiple evolutionary trees stemming from many separate origin-of-life events. In other words, he thought the evidence favored the existence of different genealogies instead of a unique one, i.e., polyphyletic evolution rather the traditional view of monophyletic evolution (universal common ancestry). He opined, “The quirks that will not submit to the neo-darwinian hypothesis are telling us that life had countless origins and that the chemistry of the origins of life has produced the diversity that has become a substrate for the evolution of biological complexity.” (Schwabe, 282.)

    Two years earlier, Schwabe and Gregory Warr were equally blunt in their criticism of molecular phylogenies. They saw the field of molecular evolution as being mired in subjectivity driven by an a priori commitment to universal common ancestry. They wrote:

    We believe that it is possible to draw up a list of basic rules that underlie existing molecular evolutionary models:

    All theories are monophyletic, meaning that they all start with the Urgene and the Urzelle which have given rise to all proteins and all species, respectively.
    Complexity evolves mainly through duplications and mutations in structural and control genes.
    Genes can mutate or remain stable, migrate laterally from species to species, spread through a population by mechanisms whose operation is not fully understood, evolve coordinately, splice, stay silent, and exist as pseudogenes.
    Ad hoc arguments can be invented (such as insect vectors or viruses) that can transport a gene into places where no monophyletic logic could otherwise explain its presence.

    This liberal spread of rules, each of which can be observed in use by scientists, does not just sound facetious but also, in our opinion, robs monophyletic evolution of its vulnerability to disproof, and thereby its entitlement to the status of a scientific theory.

    The absolute, explicit and implicit, adherence to all the monophyletic principle and consequently the decision to interpret all observations in the light of this principle is the major cause of incongruities as well as for the invention of all the genetic sidestepping rules cited above. (Schwabe and Warr, 467.)

    In 1993, Patterson, Williams, and Humphries scientists with the British Museum, reached the following conclusion in their review of the congruence between molecular and morphological phylogenies:

    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. . . .

    Partly because of morphology’s long history, congruence between morphological phylogenies is the exception rather than the rule. With molecular phylogenies, all generated within the last couple of decades, the situation is little better. Many cases of incongruence between molecular phylogenies are documented above; and when a consensus of all trees within 1% of the shortest in a parsimony analysis is published (e.g. 132, 152, 170), structure or resolution tends to evaporate. (Patterson and others, 180.)

    Citing many recent examples, Laura Maley and Charles Marshall wrote in 1998: “Animal relationships derived from the new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present.” (Maley and Marshall, 505.) An important issue is the nature of the assumptions under which this reconciliation will be pursued.

    The following year, biologist Carl Woese, an early pioneer in constructing rRNA-based phylogenetic trees, wrote: “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.” (Woese, 6854.)

    It should be noted that molecular phylogenies are constructed on the basis of certain evolutionary assumptions. The tree that is presented is chosen from a forest of alternatives, typically on the assumption of maximum parsimony. That is, the tree that is selected is the one that reflects the least amount of presumed evolutionary change. But if the assumption of maximum parsimony fails to fit the data, it can be jettisoned in favor of another. (Hunter, 40-41.)[6] The availability of such ad hoc adjustments for resolving incongruities makes the claim of falsifiability an illusion. Any result can be accommodated by the theory by revising one or more of the underlying assumptions.

    Even if a morphological phylogeny was matched closely by multiple molecular phylogenies, that would not prove that the groups in question descended from a common ancestor.[7] The molecular differences could be linked to the morphological differences for some other reason. Hunter illustrates the point this way:

    Penny[8] obtained his trees by culling those that were most parsimonious—that is, he selected the trees that showed the least amount of evolutionary change to represent the history of life. The first problem is that Penny’s method works perfectly fine on things we know did not come about via Darwinian evolution. For example, Penny’s method would also claim that automobiles evolved from one another. Consider a group of vehicles, beginning with a small economy car and increasing in size to larger cars and to minivans and large-sized vans. One could quantify several aspects of the vehicle designs, such as tire size, steering mechanism, engine size, number of seats and so forth. Presupposing the evolutionary paradigm and searching for parsimonious relationships, we would find that most of the design measures suggest the same relationship. The smaller vehicles have smaller tires, manual steering, smaller engines, and fewer seats. The larger vehicles have larger tires, power steering, larger engines, and more seats. In other words, the groupings suggested by the different design measures (tire size, steering mechanism, engine size, etc.) tend to be similar. But of course, the family of automobiles did not evolve from one another via random mutations. The groupings of the design measures are a natural result of engineering and have nothing to do with Darwinian evolution. How then can Penny’s results provide “strong support” for evolution? (Hunter, 40.)

    As Gish explains, it would not be surprising from a creation perspective to find that biochemical similarities increase in relation to other similarities of the creatures being compared. He writes:

    We know, for instance, that man is more similar to a chimpanzee than he is to a bat; that he is more similar to either a chimpanzee or a bat than he is to a crocodile or a flea. Man, chimpanzee, and the bat are mammals. The creationist would expect, therefore, that his protein, DNA, and RNA molecules, those macromolecules that are among the most important molecules in metabolism, would be more similar to those of the chimpanzee and to those of the bat than to those of the crocodile or the flea. . . . Creationists believe that all normal genes, the genes that account for the normal, healthy differences in plants and animals, were created. Each basic type of plant and animal was created with a sufficient genetic potential or variability (or gene pool, as geneticists say) to permit sufficient variability within the circumscribed boundaries of each kind, in order to adapt to various environments and conditions. (Gish, 277-278.)

    Biologist Leonard Brand concurs. “Anatomy is not independent of biochemistry. Creatures similar anatomically are likely to be similar physiologically. Those similar in physiology are, in general, likely to be similar in biochemistry, whether they evolved or were designed.” (Brand, 156.) He makes the same point with specific reference to phylogenies based on cytochrome c.

    An alternate, interventionist hypothesis is that the cytochrome c molecules in various groups of organisms are different (and always have been different) for functional reasons. Not enough mutations have occurred in these molecules to blur the distinct grouping evident in Fig. 10.1 [the cytochromes percentage of sequence difference matrix]. . . . If we do not base our conclusions on the a priori assumption of megaevolution, all the data really tell us is that the organisms fall into nested groups without any indication of intermediates or overlapping of groups, and without indicating ancestor/descendant relationships. The evidence can be explained by a separate creation for each group of organisms represented in the cytochrome c data. (Brand, 158-159.)

    Of course, failure to discern a relationship between morphology and a particular biological molecule does not prove the nonexistence of such a relationship. It may mean simply that the relationship is beyond our present understanding. The possibility of our ignorance is obvious, but even if it was not, earlier proclamations that most DNA is functionless “junk” illustrate the point. “Recent research has begun to show that many of these useless-looking sequences do have a function.” (Walkup, 19.)

    The cytochrome c data on which Dr. Theobald relies present some puzzles from a Neo-Darwinian perspective. First, the cytochromes of all the higher organisms (yeasts, plants, insects, fish, amphibians, reptiles, birds, and mammals) exhibit an almost equal degree of sequence divergence from the cytochrome of the bacteria Rhodospirillum. In other words, the degree of divergence does not increase as one moves up the scale of evolution but remains essentially uniform. The cytochrome c of other organisms, such as yeast and the silkworm moth, likewise exhibits an essentially uniform degree of divergence from organisms as dissimilar as wheat, lamprey, tuna, bullfrog, snapping turtle, penguin, kangaroo, horse, and human. (See matrices in Brand, 157 and Davis and Kenyon, 37.)

    Why would the sequence divergence of cytochrome c between bacteria and horses be the same as the divergence between bacteria and insects? The presumed evolutionary lineage from the ancestral cell to a modern bacterium differs radically from the presumed evolutionary lineage from the ancestral cell to a modern horse, both of which differ radically from the presumed evolutionary lineage from the ancestral cell to a modern insect. How could a uniform rate of divergence have been maintained through such radically different pathways? According to Michael Denton, a molecular biology researcher, “At present, there is no consensus as to how this curious phenomenon can be explained.” (Denton 1998, 291.)

    Moreover, the notion that the rates of divergence remain uniform regardless of evolutionary pathway does not fit all of the cytochrome c data. For example, referring to Dr. Theobald’s Figure 1 (reproduced above), lampreys, carp, and bullfrogs allegedly shared a common ancestor above the node labeled “vertebra.” Since that time, the branch leading to carp and bullfrogs evolved independently of the branch leading to lampreys. If the rates of cytochrome c divergence remain uniform regardless of evolutionary pathway, then the degree of sequence variance between the cytochrome c of lampreys and carp would be essentially the same as the degree of variance between the cytochrome c of lampreys and bullfrogs. That is not the case. The variance between the cytochrome c of lampreys and carp is 12%, whereas the variance between lampreys and bullfrogs is 20%. (See matrix in Davis and Kenyon, 37.)

    Second, the sequences of cytochrome c sometimes differ inversely to the presumed evolutionary proximity of the organisms being compared. For example, turtles and rattlesnakes, both being reptiles, are presumed to have shared a common ancestor with each other more recently than they shared a common ancestor with humans. So the evolutionist would expect the cytochrome c of a rattlesnake to be more similar to that of a turtle than to that of a human. That, however, is not the case. The cytochrome c of the rattlesnake varies in 22 places from that of the turtle but only in 14 places from that of a human. (See matrix in Brand, 134.)

    Humans and horses, both being placental mammals, are presumed to have shared a common ancestor with each other more recently than they shared a common ancestor with a kangaroo (a marsupial). So the evolutionist would expect the cytochrome c of a human to be more similar to that of a horse than to that of a kangaroo. Yet, the cytochrome c of the human varies in 12 places from that of a horse but only in 10 places from that of a kangaroo. (See matrix in Brand, 134.)

    Such discrepancies between traditional phylogenies and those based on cytochrome c are well known. Even Ayala could only bring himself to say that “[t]he overall relations agree fairly well with those inferred from the fossil record and other sources” (emphasis supplied). (Ayala, 68.) He then acknowledged:

    The cytochrome c phylogeny disagrees with the traditional one in several instances, including the following: the chicken appears to be related more closely to the penguin than to ducks and pigeons; the turtle, a reptile, appears to be related more closely to birds than to the rattlesnake, and man and monkeys diverge from the mammals before the marsupial kangaroo separates from the placental mammals. (Ayala, 68.)

    PAGE TOP | OUTLINE
    PREDICTION 4: POSSIBLE MORPHOLOGIES
    OF PREDICTED COMMON ANCESTORS

    Any fossilized animals found should conform to the standard phylogenetic tree. Every node shared between two branches represents a predicted common ancestor; thus there are ~30 common ancestors predicted from the tree shown in Figure 1. Our standard tree shows that the bird grouping is most closely related to the reptilian grouping, with a node linking the two (A in Figure 1); thus we predict the possibility of finding fossil intermediates between birds and reptiles. The same reasoning applies to mammals and reptiles (B in Figure 1). However, we predict that we should never find fossil intermediates between birds and mammals.

    The alleged prediction and fulfillment are:

    If universal common ancestry is true, then all fossilized animals will “conform”[9] to the standard phylogenetic tree.

    All fossilized animals “conform” to the standard phylogenetic tree.

    Universal common ancestry affirms only that all creatures descended from the same ancestor. There is nothing about that affirmation that requires conformity to the standard phylogenetic tree. A phylogenetic tree is merely a diagram that reflects current evolutionary thinking about the relationships of the taxa included. Branches are arranged on the tree on the assumption of evolution and according to perceived similarities in selected traits.[10] The relationships of some branches are viewed more dogmatically than the relationships of others, but none of the branches are set in stone.

    Since phylogenies are by nature provisional, the suggestion that the hypothesis of common descent would be falsified by “[a]ny finding of mammal/bird intermediates” is mistaken. Should a strikingly birdlike mammal be discovered, the standard tree simply would be modified to accommodate the new creature, after wrangling over its placement in the schema.

    The ease with which this precise adjustment could occur was illustrated two decades ago, when “[t]he reality of the ‘mammal-bird,’ a hypothetical common ancestor of birds and mammals, [was] a contentious issue in modern systematics.” (Mike Benton, 18.) Brian Gardiner’s cladistic analysis indicated that birds were most closely related to mammals, which relationship was supported by two Cambridge scientists’ analysis of molecular data. That view was readily accepted by some, even to the point that one French paleontologist “published a restoration of the hypothetical common ancestor between birds and mammals—a sort of warm-blooded, hairy/feathery climbing insect eater!” (Mike Benton, 18.) Branches can be rearranged, even between mammals and birds, without skipping a beat in terms of commitment to common ancestry.

    Of course, the discovery of a strikingly birdlike mammal would not necessarily force a shift in thinking about the relationship of mammals and birds (a placing of their branches next to each other). The birdlike features could be attributed to convergent evolution. Many organisms are believed by evolutionists to have evolved similar traits independently. (In fact, some experts believe that the birdlike features of dromaeosaurids, the dinosaurs considered by most experts to be the sister group to birds, arose independently rather than by inheritance from the ancestor of birds.) If the mammal’s birdlike traits were judged to be the result of convergent evolution, the species would be shown on the phylogenetic tree as a subset or side branch of mammals that was unrelated to birds.

    The shift in thinking over the last 30 years about the relationship of dinosaurs and birds is an example of a generally accepted phylogenetic adjustment, albeit at a lower taxonomic level. From the publication of Gerhard Heilmann’s The Origin of Birds in 1926, it was a matter of textbook orthodoxy that birds were more closely related to thecodonts (an order of reptiles) than to theropods (a suborder of a different order of reptiles). Thus, the discovery in 1964 of the birdlike theropod Deinonychus was contrary to phylogenetic expectations. Today, however, the standard phylogeny shows birds more closely related to theropods than to thecodonts.

    The assertion that all fossilized animals conform to the standard phylogenetic tree is unprovable, because one can never be sure that all fossilized animals have been discovered. But more importantly, the premise turns out to be merely a restatement of the claim of nested hierarchy. It adds nothing to the case for common ancestry.

    Conformity and nonconformity to the standard phylogenetic tree are defined in the article in terms of “intermediates.” It is stated that, given the standard phylogeny, one would expect “intermediates” between reptiles and birds and between reptiles and mammals (because these pairs are shown as sharing hypothetical common ancestors, A and B in Figure 1), but one would not expect “intermediates” between mammals and birds. It is then alleged that the fossils conform to this expectation, and thus “conform to the standard phylogenetic tree,” in that “intermediates” have been found between reptiles and birds (citing mainly dromaeosaurids) and between reptiles and mammals (citing synapsids) but not between mammals and birds.

    But according to the definition of “intermediate” given in the article, dromaeosaurids are not reptile-bird intermediates and synapsids are not reptile-mammal intermediates. An “intermediate form” is defined as “[a] fossil or modern species that displays characters definitive of two or more different taxa” (emphasis supplied). Dromaeosaurids do not display characters that are definitive of both reptiles and birds (which is why they are not considered birds), and synapsids do not display characters that are definitive of both reptiles and mammals (which is why they are not considered mammals).

    On the other hand, under the given definition, all taxa qualify as “intermediates” between themselves and the taxa in which they are shown as nested.[11] For example, all mammal species, including all monotremes and marsupials, are reptile-mammal “intermediates” because they all possess the traits that are definitive of both Reptilia and Mammalia.[12] That is, they are all amniotes with the definitive traits of Mammalia. (Reptilia is defined simply as amniotes that are not birds or mammals [Carroll, 193].) Likewise, all bird species, including the Kiwi (called an “honorary mammal”), are reptile-bird “intermediates” because they all possess the traits that are definitive of both Reptilia and Aves.

    But if taxa are intermediate by virtue of being nested, the existence of intermediates is not a separate argument for common ancestry. It is the argument of nested hierarchy under a different label. And if there are no intermediates between non-nested taxa, that means only that nested hierarchy is a pattern to which there are no known exceptions. As previously explained, that result could be accommodated by the theory of common descent, but it is not evidence for it.

    In citing dromaeosaurids as reptile-bird intermediates and mammal-like reptiles as reptile-mammal intermediates, Dr. Theobald is apparently defining “intermediates” as organisms that are morphologically between alleged ancestors and descendants (rather than using the specified definition of organisms that possess the definitive traits of the two relevant taxa). But if intermediates can occur by definition only between alleged ancestors and descendants, then they can occur by definition only in conformity to the phylogenetic tree.

    Consider the striking similarities between some marsupials and placentals. If the consensus were that a marsupial wolf evolved into a placental wolf, then the marsupial wolf would qualify as an intermediate under the definition being considered. That is, it would be morphologically between its alleged ancestor (an earlier marsupial) and descendant (the placental wolf). But since the consensus (which is reflected in the standard phylogeny) is that marsupial wolves and placental wolves arose independently, the marsupial wolf cannot qualify as a marsupial-placental intermediate, whatever its morphology. Conformity with the standard phylogeny is guaranteed by the definition.

    The assertions that there are “no morphological gaps” in the alleged dinosaur-to-bird transition and that there is an “exquisitely complete series of fossils” for the alleged reptile-to-mammal transition are debatable, to say the least. I have elsewhere tried to point out some of the limitations of those claims (see, “On the Alleged Dinosaurian Ancestry of Birds” and “Reappraising the Crown Jewel”).

    But even if one granted that reptiles evolved into a bird and a mammal, that would not establish that reptiles and all other organisms descended from a common ancestor, which is the proposition being argued. The difference between a bacterium and a reptile, not to mention the other organisms, is considerably greater than the difference between a reptile and a bird or a reptile and a mammal. So the fact a reptile could evolve into a bird or a mammal would not mean that a bacterium could evolve into a reptile and everything else. In fact, granting that reptiles evolved into a bird and a mammal would not even establish that all birds and all mammals descended from a reptile. That would be an assumption.
    PAGE TOP | OUTLINE
    PREDICTION 5: CHRONOLOGICAL ORDER
    OF PREDICTED COMMON ANCESTORS

    Fossilized intermediates should appear in the correct general chronological order based on the standard tree. Any phylogenetic tree predicts a relative chronological order of hypothetical common ancestors and intermediates between these ancestors. For instance, in our current example, the reptile/mammal common ancestor (B) [from Figure 1] and intermediates should be older than the reptile/bird common ancestor (A) [from Figure 1] and intermediates.

    The alleged prediction and fulfillment are:

    If universal common ancestry is true, then fossil intermediates will appear in the “general chronological order” reflected in the standard phylogenetic tree;

    Fossil intermediates appear in the “general chronological order” reflected in the standard phylogenetic tree;

    As pointed out above, “intermediate” is defined in the article as “[a] fossil or modern species that displays characters definitive of two or more different taxa” (emphasis supplied). Since, under that definition, a taxon is intermediate by virtue of being nested within another, the alleged prediction is that fossils will appear in the order of nesting reflected in Figure 1. In other words, a prokaryotic organism would appear first, followed successively (in the fungi/metazoan direction) by organisms with nuclei, multicellularity, organs, nervous and vascular system, and so on up the deuterostomic and protostomic branches.

    There is nothing about the hypothesis of universal common ancestry that requires organisms to have descended in the pattern depicted in the standard phylogeny. Common ancestry does not even require nested hierarchy, let alone any particular pattern of nesting. A phylogeny is simply a depiction of the order in which evolutionists believe taxa arose, not the order in which they were required to arise. (And even if it was believed that universal common descent could occur in only one way, that is an assertion about the mechanism of descent, a subject Dr. Theobald purposefully excluded from his case.)

    Moreover, while ancestral taxa must have existed before any taxa that descended from them, that does not mean the appearance of their fossilized forms must correspond to that order of existence. However unlikely the claim may be, it remains possible for a proponent of common descent to assert that select taxa appear in the fossil record contrary to the order in which they came into existence.

    Witness the fact dromaeosaurids, which are offered by Dr. Theobald as “reptile-bird intermediates,”[13] first appear in the fossil record some 25 million years after the first fossil bird. (If one accepts Protoavis, rather than Archaeopteryx, as the first fossil bird, the gap in appearance increases to about 100 million years.) Rather than disqualifying dromaeosaurids in Dr. Theobald’s eyes as “reptile-bird intermediates,” which he argues must appear in the order suggested by the standard phylogeny, it is simply assumed that dromaeosaurids lived tens of millions of years before there is any evidence of their existence. (The ambiguity of “general chronological order” prevents such nonconformities from falsifying the claim.)

    This same strategy could be employed if dromaeosaurids turned up in strata older/lower than that in which synapsids first appear. That is, it could be assumed that pelycosaurs and therapsids actually predated dromaeosaurids but for some reason did not appear in the fossil record until later. So the suggestion that the hypothesis of universal common ancestry would be falsified if dromaeosaurids first appeared in the fossil record before synapsids reptiles is incorrect.

    The fact synapsids appear before dromaeosaurids hardly constitutes proof (confirms the “prediction”) that “fossilized intermediates” appear in the general chronological order indicated in the standard phylogeny. They are only two data points. But more importantly, one must bear in mind that Figure 1 is of necessity a simplified and fragmentary phylogeny. The picture changes significantly when the scope of inquiry is broadened.[14] According to one Harvard-trained paleontologist:

    [T]he correspondence between phylogeny and the fossil record is not as strong as it might first seem. When the order of all kingdoms, phyla and classes is compared with the most reasonable phylogenies, over 95 percent of all the lines are not consistent with the order in the fossil record. The only statistically significant exceptions are the orders of first appearances of the phyla of plants and the classes of vertebrates and arthropods. Yet these three lineages also order organismal groups from sea-dwellers to land dwellers. The land-plant phyla, for example, are in a simple sequence from plants that need standing water to survive (e.g., algae and bryophytes) to those that can survive extreme desiccation (e.g., the cacti). The vertebrate classes go from sea-dwellers (fish) to land/sea creatures (amphibians) to land creatures (reptiles/mammals), to flying creatures (birds). The arthropod classes go from sea-dwellers (e.g., trilobites, crustaceans) to land dwellers (e.g., insects). So it’s not clear that macroevolution is a truly good explanation for the order of fossil first appearances of major groups of life. Such a radical idea as a global flood, for example, which gradually overcame first the sea and then the land, actually explains the primary order of major groups in the fossil record (sea to land) better than macroevolutionary theory. (Wise, 225-226.) >>
    _______________

    Food for thought, or at least second thoughts.

    Gotta run to put out a local fire.

    Later.

    KF

  116. 116
    Joe says:

    keith s:

    1. Theobald’s stated purpose was to present the evidence for common descent, so that’s what he did.

    No, he only thinks he presented evidence for Common Descent. There isn’t any way to verify his claims.

    As you know, we actually observe microevolution producing ONHs,

    Evidence please. We all know tat you are a liar.

  117. 117
    Joe says:

    VJT:

    The first hypothesis is indeed well-supported by the evidence, as the only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes.

    Evidence please. Nested hierarchies are purely artificial. Only intelligent agencies can produce them. That is in part because the levels and the sets on the levels require definitions. For example Animalia has a set of definitions that has to be met before an organism can be called an animal. Each Phyla under Animalia also has a set of definitions which also include the definitions of animal.

    With the nested hierarchy of the US Army the same rule applies.

    So what is VJT talking about?

  118. 118
    Joe says:

    AVS:

    That post couldn’t be a more perfect description of evolution, Andre.

    Evolution isn’t being debated. Grow up.

    No organim’s offspring is exactly identical to the original parent(s), this means that every single individual organism represents a single trial in evolution’s search for new adaptations, solutions, or “ideas,” whatever you want to call it

    Except unguided evolution isn’t a search.

  119. 119
    Andre says:

    Joe

    I give up…… They truly believe in magic!

  120. 120
    Andre says:

    I don’t think I’m wrong when I say that materialists are the most superstitious group of people in the world.

  121. 121
    Joe says:

    Asking for help from IDists- Richie has been booted but his ghost spews on. Richie sed:

    In the discussion* it shown that Barry wanted a demonstration of CSI being made by natural forces, whilst Demski defines CSI as only to be ‘counted’ in the absence of them.

    Can anyone reference Denmbski saying that or anything like that? From what I have read of Dembski CSI exists regardless of how it was produced, it is just that the only mechanism known to produce it is intelligent agency activity- deliberate activity. And if someone could demonstrate CSI arising without intelligent agency involvement then CSI would no longer be a hallmark of ID.

    Anyone?

  122. 122
    Box says:

    Keith,

    Keith: #76: which means that ID is still at a trillions-to-one disadvantage with respect to unguided evolution.

    Keith: #89: because otherwise you are still at the trillions-to-one disadvantage.

    Multiple times, I have soundly refuted your trillion-to-one nonsense. In post #11 I have linked to my latest rebuttal, where I explain that you make a category error when you compare a designer – a free agent – with a trillion-sided die.
    In post #243 of the ‘black-knight-taunt-thread’, I offer a more general summation of the problems with your trillion:

    Keith,
    What it boils down to is this: you state that there are trillions of options available for a designer and that he/she/it could have chosen either one, but we simply have no way of knowing. There is no grounding for your claim.

    We do not know if a designer is capable of producing trillions of different orderings of life – for all we know the designer’s capability is limited to only one option. But even if there are trillions of options available, we have no way of knowing if there are compelling reasons – any reasons – for the designer to choose for ONH. That is the problem with free agents …

    And what we certainly cannot know is – your implicit claim – that the designer is completely indifferent about the ordering of life and that he based his decision on the role of a die.

    What bothers me, is not so much that you won’t respond to my rebuttals, but that you keep repeating your fallacious claim that ID has a trillions-to-one disadvantage with respect to unguided evolution. Can you at least have the courtesy to dispense with this nonsense until you have addressed my refutations?

  123. 123
    Andre says:

    Box

    It’s not going to happen he refuses to discuss PCD here, instead he invites me to his viper pit to do so……

    Keith S does not give one iota about truth….

  124. 124
    Box says:

    Andre,

    A lot has been said about PCD lately. I’m trying to get your argument clear and simple.
    Are you saying that stability mechanisms, like PCD, are fundamental to life? They must be present before RM+NS can act on life? IOW the first cell must have stability mechanisms, otherwise is just falls apart?

  125. 125
    Silver Asiatic says:

    Joe 121

    From what I have read of Dembski CSI exists regardless of how it was produced, it is just that the only mechanism known to produce it is intelligent agency activity- deliberate activity. And if someone could demonstrate CSI arising without intelligent agency involvement then CSI would no longer be a hallmark of ID.

    Anyone?

    I have never seen that from Dembski and I suspect its a misreading. By taking his conclusion “only intelligent agency is known to produce it” as if it was the premise, he is criticized as giving a circular argument.

    Of course, natural forces could, in theory, produce CSI. That’s the evolutionary claim. CSI refers to specified sequences. The ID inference is ruled out if a pattern can be explained by natural forces. If the pattern contains CSI, then ID is falsified entirely.

    I hate to say it, but our opponents deliberately misunderstand that point. They work quite hard to twist the argument until the ID proposal is unrecognizable. The notion that we take the conclusion first and then fit the evidence to it, really is what evolutionists do. They assume common descent and the effective power of mechanisms and then claim evolution did it with whatever they observe.

    We are accused of the same thing, but it’s false.

    “IDers believe in God so they claim everything is designed”.
    “IDers must be told first that something has been designed, then they claim they detected design”.
    “The only examples of design that ID uses are cases where we already know the designer.”

    Those arguments are twisted and completely inaccurate. An honest opponent (and there are some) will recognize that and more directly attack the ID proposal.

  126. 126
    Joe says:

    Thank you Silver Asiatic.

  127. 127
    Silver Asiatic says:

    Evidence please. Nested hierarchies are purely artificial. Only intelligent agencies can produce them. That is in part because the levels and the sets on the levels require definitions. For example Animalia has a set of definitions that has to be met before an organism can be called an animal. Each Phyla under Animalia also has a set of definitions which also include the definitions of animal.

    With the nested hierarchy of the US Army the same rule applies.

    So what is VJT talking about?

    This is one of the rare cases where I disagree with VJT. I don’t see evidence that unguided evolution produces a nested hierarchy. Also, I don’t agree that it’s the only process that can produce such a thing.

    Take a drop of water – you can trace its history through a nested hierarchy.

    1. 1 cup of of rainwater
    2. Same cup of water on the ground with mineral from the soil
    3. Same cup of river water (with soil and river particles)
    4. Same cup of ocean water (with all the above and salt).

    There’s a branching hierarchy of descent with modification.

    But of course, there’s nothing in nature like that “objectively”. You’d have to isolate a cup of water and call it the same thing over time. Eventually, it is muddled with all the elements and other elements are lost.

    The hierarchy is an artificial construct.

    Evolution would have to be a deterministic cause (as it is claimed to be) starting from chemical/physical properties. That nested hierarchy I gave with a cup of water is more deterministic and certain than evolution and even that is muddled and impossible to detect.

    Supposedly, a chemical process causes living organisms to exist, and then causes them to “want to survive and reproduce”.

    What combination of chemicals causes that to happen?

    Chemicals don’t want to live. They don’t struggle to survive. They’re quite happy being inanimate molecules.

  128. 128
    Silver Asiatic says:

    Good posts and questions, Joe. Unfortunately, our opponents always seem to avoid the key points you raise. (E.g. Explain how you can even get from prokaryotes to eukaryotes ?)

  129. 129
    Joe says:

    Dr (Margulis) Sagan posited a hypothesis with respect to how some eukaryotic organelles developed. And other have said that prokaryotes may be a stripped-down version of uber single-celled eukaryotes. Opposite hypotheses based on the same evidence and neither support unguided evolution. And neither explain the origin of Eukaryota.

    But anyway, given the diversity of life and given the fact that unguided evolution cannot explain it, unguided evolution is a trillion times better at explaining the disease and deformities that exist in that diversity than Intelligent Design is. So keith s has that, anyway. 😛

  130. 130
    Zachriel says:

    KeithS: He is a methodological naturalist, so for him any discussion of a Designer is off-limits.

    Only a nebulous designer that has no entailments is off limits. Certainly humans are designers that are subject to study.

    KeithS: The Markov model is empirically verified, which means that ID is still at a trillions-to-one disadvantage with respect to unguided evolution.

    KeithS: the word “trillions” comes into play because of the astounding match between nested hierarchies mentioned above.

    The trillions-to-one number apparently comes from Theobald’s study. The study does not distinguish between guided and unguided evolution. It does, however, strongly support branching descent. Other evidence is required to determine the particular shape of the tree. However — and this is an important point —, once we establish common descent, then it provides a framework for understanding adaptation and other historical mechanisms.

    Andre: If Neanderthal and Sapiens interbred and made viable offspring then they can not be separate species….

    That is incorrect. Species interbreed all the time; otherwise, there would only be one species of duck/goose. The process is called hybridization, and is very common especially in plants. Species exist because there is limited gene flow such that they maintain their distinct characteristics, but they still may breed with related species.

    Silver Asiatic: There’s a branching hierarchy of descent with modification.

    Not sure you get the whole nested hierarchy thing. Try grouping organisms by trait. Which do you think are closest of the three; cat, dog, trout? If you continue this process, you will find that the vast majority of taxa fall neatly and objectively into groups within groups.

  131. 131
    bornagain77 says:

    The Cambrian explosion directly challenges Universal Common Descent and the ‘mechanism’ of Random Mutation/Natural selection

    What Types of Evolution Does the Cambrian Explosion Challenge? – Stephen Meyer – video – (challenges Universal Common Descent and the Mechanism of Random Variation/Natural Selection)
    https://www.youtube.com/watch?v=AaF7t5wRFtA&list=UUUMhP2x7_7psVO-H4MJFpAQ

    Cambrian Explosion Ruins Darwin’s Tree of Life (2 minutes in 24 hour day) – video
    http://www.youtube.com/watch?v=bQKxkUb_AAg

    , as Dr. Wells points out in the preceding video, Darwin predicted that minor differences (diversity) between species would gradually appear first and then the differences would grow larger (disparity) between species as time went on. i.e. universal common descent as depicted in Darwin’s tree of life. What Darwin predicted should be familiar to everyone and is easily represented in the following graph.,,,

    The Theory – Diversity precedes Disparity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/F.gif

    But that ‘tree pattern’ that Darwin predicted is not what is found in the fossil record. The fossil record reveals that disparity (the greatest differences) precedes diversity (the smaller differences), which is the exact opposite pattern for what Darwin’s theory predicted.

    The Actual Fossil Evidence- Disparity precedes Diversity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/G.gif

    Timeline graphic on Cambrian Explosion from ‘Darwin’s Doubt’ (Disparity preceding Diversity)
    http://www.evolutionnews.org/2.....74341.html

    Moreover, there are ‘yawning chasms’ in the ‘morphological space’ between the phyla which suddenly appeared in the Cambrian Explosion,,,

    “Over the past 150 years or so, paleontologists have found many representatives of the phyla that were well-known in Darwin’s time (by analogy, the equivalent of the three primary colors) and a few completely new forms altogether (by analogy, some other distinct colors such as green and orange, perhaps). And, of course, within these phyla, there is a great deal of variety. Nevertheless, the analogy holds at least insofar as the differences in form between any member of one phylum and any member of another phylum are vast, and paleontologists have utterly failed to find forms that would fill these yawning chasms in what biotechnologists call “morphological space.” In other words, they have failed to find the paleolontogical equivalent of the numerous finely graded intermediate colors (Oedleton blue, dusty rose, gun barrel gray, magenta, etc.) that interior designers covet. Instead, extensive sampling of the fossil record has confirmed a strikingly discontinuous pattern in which representatives of the major phyla stand in stark isolation from members of other phyla, without intermediate forms filling the intervening morphological space.”
    Stephen Meyer – Darwin’s Doubt (p. 70)

    Moreover, this top down pattern in the fossil record, which is the complete opposite pattern as Darwin predicted for the fossil record, is not only found in the Cambrian Explosion, but this ‘top down’, disparity preceding diversity, pattern is found in the fossil record subsequent to the Cambrian explosion as well.

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.”
    TS Kemp – Fossils and Evolution,– Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.”
    Robert L Carroll (born 1938) – vertebrate paleontologist who specialises in Paleozoic and Mesozoic amphibians

  132. 132
    Zachriel says:

    Z: duck/goose

    Should read duck or goose.

  133. 133
    bornagain77 says:

    No Known Hominin Is Common Ancestor of Neanderthals and Modern Humans, Study Suggests – Oct. 21, 2013
    Excerpt: The article, “No known hominin species matches the expected dental morphology of the last common ancestor of Neanderthals and modern humans,” relies on fossils of approximately 1,200 molars and premolars from 13 species or types of hominins — humans and human relatives and ancestors. Fossils from the well-known Atapuerca sites have a crucial role in this research, accounting for more than 15 percent of the complete studied fossil collection.,,,
    They conclude with high statistical confidence that none of the hominins usually proposed as a common ancestor, such as Homo heidelbergensis, H. erectus and H. antecessor, is a satisfactory match.
    “None of the species that have been previously suggested as the last common ancestor of Neanderthals and modern humans has a dental morphology that is fully compatible with the expected morphology of this ancestor,” Gómez-Robles said.
    http://www.sciencedaily.com/re.....153202.htm

    Skull “Rewrites” Story of Human Evolution — Again – Casey Luskin – October 22, 2013
    Excerpt: “There is a big gap in the fossil record,” Zollikofer told NBC News. “I would put a question mark there. Of course it would be nice to say this was the last common ancestor of Neanderthals and us, but we simply don’t know.” –
    http://www.evolutionnews.org/2.....78221.html

    “A number of hominid crania are known from sites in eastern and southern Africa in the 400- to 200-thousand-year range, but none of them looks like a close antecedent of the anatomically distinctive Homo sapiens…Even allowing for the poor record we have of our close extinct kin, Homo sapiens appears as distinctive and unprecedented…there is certainly no evidence to support the notion that we gradually became who we inherently are over an extended period, in either the physical or the intellectual sense.”
    Dr. Ian Tattersall: – paleoanthropologist – emeritus curator of the American Museum of Natural History – (Masters of the Planet, 2012)

    The Red Ape – Cornelius Hunter – August 2009
    Excerpt: “There remains, however, a paradoxical problem lurking within the wealth of DNA data: our morphology and physiology have very little, if anything, uniquely in common with chimpanzees to corroborate a unique common ancestor. Most of the characters we do share with chimpanzees also occur in other primates, and in sexual biology and reproduction we could hardly be more different. It would be an understatement to think of this as an evolutionary puzzle.”
    http://darwins-god.blogspot.co.....d-ape.html

    Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity – Sternberg – 2009
    Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors.
    http://www.evolutionnews.org/2.....think.html

    If Modern Humans Are So Smart, Why Are Our Brains Shrinking? – January 20, 2011
    Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.”
    “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,,
    He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.”
    http://discovermagazine.com/20.....-shrinking

    “Neanderthals are known for their large cranial capacity, which at 1600cc is larger on average than modern humans.”
    http://en.wikipedia.org/wiki/Neanderthal#Anatomy

  134. 134
    bornagain77 says:

    Reproductive isolation and hybridization is not proof of universal common descent. Wolf-Ekkehard Lönnig a leading expert in genetics (especially plants), comments on how differences between closely related ‘sub species’ are generated

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

  135. 135
    Joe says:

    Zachriel:

    Certainly humans are designers that are subject to study.

    Certainly we cannot study the alleged humans who designed and built Stonehenge.

    It does, however, strongly support branching descent.

    No, it only supports what he thinks branching descent would look like.

    Try grouping organisms by trait.

    As we would do when classifying a common design.

  136. 136
    lifepsy says:

    Zachriel 130

    Not sure you get the whole nested hierarchy thing. Try grouping organisms by trait. Which do you think are closest of the three; cat, dog, trout? If you continue this process, you will find that the vast majority of taxa fall neatly and objectively into groups within groups.

    Maybe you can explain what Keith S couldn’t.

    If unguided evolution is true, why should we necessarily find identifiable distinct groupings of taxa that fall neatly into groups within groups?

    Why don’t we find a dominant pattern of blurred and indistinct character traits that can not be objectively classified into neat distinguishable groups?

    That type of signal is certainly expected if unguided evolution had really produced these character traits gradually through countless fine gradations.

    Is it just an evolutionary coincidence that we are only left with such orderly typological groupings?

  137. 137
    keith s says:

    Joe G:

    Asking for help from IDists- Richie has been booted but his ghost spews on. Richie sed:

    In the discussion* it shown that Barry wanted a demonstration of CSI being made by natural forces, whilst Demski defines CSI as only to be ‘counted’ in the absence of them.

    Can anyone reference Denmbski saying that or anything like that?

    Joe, you really should learn more about ID. Yes, Dembski says exactly that.

    His CSI equation contains a P(T|H) term, and he describes H as follows:

    Moreover, H, here, is the relevant chance hypothesis that takes into account Darwinian and other material mechanisms.

    Silver Asiatic:

    I have never seen that from Dembski and I suspect its a misreading. By taking his conclusion “only intelligent agency is known to produce it” as if it was the premise, he is criticized as giving a circular argument.

    It’s not a misreading, and yes, Dembski’s argument is hopelessly circular.

    This is why scientists laugh at ID. One of its leading lights, the so-called “Isaac Newton of information theory”, is making a freshman logic mistake.

    That makes his concept of CSI useless. Pitiful, isn’t it?

  138. 138
    Zachriel says:

    lifepsy: If unguided evolution is true, why should we necessarily find identifiable distinct groupings of taxa that fall neatly into groups within groups?

    This doesn’t directly relate to the original study, which only concerns whether or not the evidence supports branching descent. The evidence supports branching descent, even if we didn’t understand the mechanism or reason for this pattern.

    lifepsy: Why don’t we find a dominant pattern of blurred and indistinct character traits that can not be objectively classified into neat distinguishable groups?

    We do sometimes. There’s blurry edges between closely related species, especially with regards to bacteria. However, the branching pattern is still discernible, even amidst all the other goings-on.

    First, organisms which successfully reproduce are more likely to persist over time. To ensure true copies, organisms separate themselves from the environment and from other organisms. While chimera’s can occur, they tend to be maladaptive.

    In addition, reproductive isolation reinforces adaptation. Consider two populations of beetles, one is adapted to living on top of the rock, and one on the bottom. Hybrids would tend to be less successful than purebreds, being neither adapted to the top nor to the bottom of the rock. Reproduction is expensive, so beetles evolve incompatible sexual organs to prevent hybridization.

    Different taxa have different strategies in this regard. For instance, birds speciate through song, which gives them a great deal of adaptive flexibility.

  139. 139
    Joe says:

    LoL! @ keith s- If Dembski says that “H” is the relevant chance hypothesis that means what I said is correct and Rich is wrong. What is wrong with you?

  140. 140
    Joe says:

    ID is based on three premises and the inference that follows (DeWolf et al., “Darwinism, Design and Public Education”, pg. 92):

    1) High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.

    2) Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.

    3) Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.

    4) Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.

  141. 141
    bornagain77 says:

    “The evidence supports branching descent”

    The evidence supports “top down’ branching descent within distinct morphological kinds, the evidence does not support Darwin’s ‘bottom up’ descent/ascent from a single common ancestor,,

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    Dollo’s law and the death and resurrection of genes
    ABSTRACT: Dollo’s law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or “lost” developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints;
    http://www.pnas.org/content/91.....l.pdf+html

    The Cambrian’s Many Forms
    Excerpt: “It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.””From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” University of Chicago paleontologist Mark Webster; article on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.
    http://www.terradaily.com/repo.....s_999.html

  142. 142
    lifepsy says:

    Zachriel

    lifepsy: If unguided evolution is true, why should we necessarily find identifiable distinct groupings of taxa that fall neatly into groups within groups?

    This doesn’t directly relate to the original study, which only concerns whether or not the evidence supports branching descent. The evidence supports branching descent, even if we didn’t understand the mechanism or reason for this pattern.

    That was a dodge.

    I asked you a simple question. Why should branching common descent necessarily produce a discernible nested hierarchy?

    The answer, which perhaps you’re uncomfortable stating, is that it shouldn’t.

    Common descent may also produce a non-discernible nested hierarchy.

    lifepsy: Why don’t we find a dominant pattern of blurred and indistinct character traits that can not be objectively classified into neat distinguishable groups?

    We do sometimes. There’s blurry edges between closely related species, especially with regards to bacteria. However, the branching pattern is still discernible, even amidst all the other goings-on.

    Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy?

    It’s rather unscientific to be promoting X as direct evidence for something, when Not-X would also be acceptable. Wouldn’t you agree?

  143. 143
    keith s says:

    Joe:

    LoL! @ keith s- If Dembski says that “H” is the relevant chance hypothesis that means what I said is correct and Rich is wrong.

    Joe,

    p(T|H) has to be extremely small in order for CSI to be high. Rich is right.

    This isn’t rocket science.

  144. 144
    bornagain77 says:

    as to this claim: “There’s blurry edges between closely related species, especially with regards to bacteria.”

    Yet, different types of bacteria are now found to have a large percentage of ORFan genes, so the claim for ‘blurry edges’ is false,

    ,,,”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 8:53 minute mark of the following video
    Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references
    http://www.vimeo.com/17135166

    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

    As well, no one has ever evolved one bacteria into another bacteria, and the conservation of morphology in bacteria, throughout deep time, is more extreme than in multicellular organisms. Thus, the ‘bottom up’ branching pattern, once again, is found to only exists in the imagination of Darwinists,,,

    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

    AMBER: THE LOOKING GLASS INTO THE PAST:
    Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.
    http://bcb705.blogspot.com/200.....st_23.html

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;
    http://www.thefreelibrary.com/.....a014909330

    Moreover, bacteria do not act as was predicted by Darwin:

    Doubting Darwin: Algae Findings Surprise Scientists – April 28, 2014
    Excerpt: One of Charles Darwin’s hypotheses posits that closely related species will compete for food and other resources more strongly with one another than with distant relatives, because they occupy similar ecological niches. Most biologists long have accepted this to be true.
    Thus, three researchers were more than a little shaken to find that their experiments on fresh water green algae failed to support Darwin’s theory — at least in one case.
    “It was completely unexpected,” says Bradley Cardinale, associate professor in the University of Michigan’s school of natural resources & environment. “When we saw the results, we said ‘this can’t be.”‘ We sat there banging our heads against the wall. Darwin’s hypothesis has been with us for so long, how can it not be right?”
    The researchers ,,,— were so uncomfortable with their results that they spent the next several months trying to disprove their own work. But the research held up.,,,
    The scientists did not set out to disprove Darwin, but, in fact, to learn more about the genetic and ecological uniqueness of fresh water green algae so they could provide conservationists with useful data for decision-making. “We went into it assuming Darwin to be right, and expecting to come up with some real numbers for conservationists,” Cardinale says. “When we started coming up with numbers that showed he wasn’t right, we were completely baffled.”,,,
    Darwin “was obsessed with competition,” Cardinale says. “He assumed the whole world was composed of species competing with each other, but we found that one-third of the species of algae we studied actually like each other. They don’t grow as well unless you put them with another species. It may be that nature has a heck of a lot more mutualisms than we ever expected.
    “Maybe species are co-evolving,” he adds. “Maybe they are evolving together so they are more productive as a team than they are individually. We found that more than one-third of the time, that they like to be together. Maybe Darwin’s presumption that the world may be dominated by competition is wrong.”
    http://www.livescience.com/452.....f-bts.html

    The rest of Zach’s post on beetles and birds is either unsubstantiated conjecture or trivially true. i.e. so what!
    supplemental note:

    Darwin ‘Wrong’: Species Living Together Does Not Encourage Evolution – December 20, 2013
    Excerpt: Charles Darwin’s theory of evolution set out in the Origin of Species has been proven wrong by scientists studying ovenbirds.
    Researchers at Oxford University found that species living together do not evolve differently to avoid competing with one another for food and habitats – a theory put forward by Darwin 150 years ago.
    The ovenbird is one of the most diverse bird families in the world and researchers were looking to establish the processes causing them to evolve.
    Published in Nature, the research compared the beaks, legs and songs of 90% of ovenbird species.
    Findings showed that while the birds living together were consistently more different than those living apart, this was the result of age differences. Once the variation of age was accounted for, birds that live together were more similar than those living separately – directly contradicting Darwin’s view.
    The species that lived together had beaks and legs no more different than those living apart,,,
    ,,,there is no shortage of evidence for competition driving divergent evolution in some very young lineages. But we found no evidence that this process explains differences across a much larger sample of species.,,,
    He said that the reasons why birds living together appear to evolve less are “difficult to explain”,,,
    http://www.ibtimes.co.uk/darwi.....on-1429927

  145. 145
    keith s says:

    lifepsy, to Zachriel:

    Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy?

    I keep explaining this to you, lifepsy. From my OP:

    What about our third subset of IDers — those who accept the truth of common descent but believe that intelligent guidance is necessary to explain macroevolution? The evidence is a problem for them, too, despite the fact that they accept common descent. The following asymmetry explains why: the discovery of an objective nested hierarchy implies common descent, but the converse is not true; common descent does not imply that we will be able to discover an objective nested hierarchy. There are many choices available to a Designer who guides evolution. Only a tiny fraction of them lead to a inferable, objective nested hierarchy. The Designer would have to restrict himself to gradual changes and predominantly vertical inheritance of features in order to leave behind evidence of the kind we see.

    In other words, our ‘common descent IDers’ face a dilemma like the one faced by the creationists. They can force guided evolution to match the evidence, but only by making a completely arbitrary assumption about the behavior of the Designer. They must stipulate, for no particular reason, that the Designer restricts himself to a tiny subset of the available options, and that this subset just happens to be the subset that creates a recoverable, objective, nested hierarchy of the kind that is predicted by unguided evolution. Unguided evolution doesn’t require any such arbitrary assumptions. It matches the evidence without them, and is therefore a superior explanation. And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.

    Real evolution is gradual, with predominantly vertical inheritance. That kind of evolution produces ONHs, and this is confirmed empirically: see the Theobald quote in this comment.

    Thus the evidence of the ONH implies not only that common descent is true, but also that evolution is unguided.

    My comment #1 illustrates why:

    Box,

    It’s astonishing to me that you still don’t get this, but let me try once more.

    Suppose you have two objects:

    1. A coin with ONH stamped on both sides.
    2. A trillion-sided die with ONH engraved on one and only one side.

    A friend of yours takes both objects into another room, out of your sight. She randomly picks one of the two objects and flips it.

    “I randomly picked one of the objects and flipped it, and it landed with ONH up,” she shouts to you.

    Your job is to guess which of the objects she flipped — the coin with ONH on both sides, or the trillion-sided die with ONH on only one side.

    If you can’t figure out the best answer, I’m afraid there’s little hope that you will ever understand my argument.

  146. 146
    bornagain77 says:

    The empirical evidence itself shows keith s’s’ claim to be false! No where is this more clear than in the Cambrian Explosion:

    What Types of Evolution Does the Cambrian Explosion Challenge? – Stephen Meyer – video – (challenges Universal Common Descent and the Mechanism of Random Variation/Natural Selection)
    https://www.youtube.com/watch?v=AaF7t5wRFtA&list=UUUMhP2x7_7psVO-H4MJFpAQ

    i.e. There is no hope for your theory if it is directly contradicted by the evidence itself!

  147. 147
    Box says:

    Keith #145,

    Just stop with the nonsense, please.

    The trillions-claim in your argument and more specifically the trillion-sided die from post #1 have been soundly refuted – in this thread (#122) and in the ‘black-knight-taunt’ thread (e.g. post #243).

    What bothers me, is not so much that you won’t respond to my rebuttals, but that you keep parading the “trillion” around as if it means something. Can you at least have the courtesy to dispense with this nonsense until you have addressed my refutations?

  148. 148
    lifepsy says:

    Keith S 145

    I already dismantled your premise in the other thread:
    http://www.uncommondescent.com.....ent-525837

    To which you have failed to respond.

    And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.

    Wrong. Unguided evolution also predicts trillions of other patterns where traits are so blurred as to make the nested hierarchy indiscernible.

    How is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes? (the very criticism you launch at the design inference!)

    A straight answer, please.

  149. 149
    Zachriel says:

    lifepsy: I asked you a simple question. Why should branching common descent necessarily produce a discernible nested hierarchy?

    Your original question was “If unguided evolution is true, why should we necessarily find identifiable distinct groupings of taxa that fall neatly into groups within groups?” You seemed to be asking why organisms branch. Your revised question is actually more pertinent.

    lifepsy: Why should branching common descent necessarily produce a discernible nested hierarchy?

    It’s a deduction from geometry as grouping leaves by branch and stem form a nested hierarchy. Now consider a tree that grows, but there are occasional mutations that are inherited along a given branch. The end result will be a pattern of traits that form a nested hierarchy. This is true as long as the number of traits is large compared to the mutation rate. There’s a statistical relationship between the mutation rate, number of traits, and the fit to the nested hierarchy. Here’s a simple example with one mutation* per branch.

    Trunk: plain
    First branch: plain
    Second branch: red*

    First branch first stem: plain, plain
    First branch second stem: plain, rippled*
    Second branch first stem: red, plain
    Second branch second stem: red, serrated*

    Even at this point, you can see that they nest by traits into groups. It’s basic geometry with a bit of statistics involved to account for the degree of mutation.

    lifepsy: Common descent may also produce a non-discernible nested hierarchy.

    If you mean branching common descent, then that would happen if the mutation rate is very high compared to the number of traits. Indeed, if the mutation rate were high enough, the entire organism could be reshuffled in each generation. Of course, we know this doesn’t happen, and children closely resemble their parents.

    lifepsy: Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy?

    The hypothesis is fidelity in reproduction with only occasional mutation among many traits branching descent. We could probably expand on that some more, but then you would end up with something like Darwin’s “long abstract”.

    lifepsy: How is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes?

    That’s not our position. Theobald shows that branching descent is strongly supported, but says nothing about whether the process is guided or not.

  150. 150
    Zachriel says:

    bornagain77: The rest of Zach’s post on beetles and birds is either unsubstantiated conjecture or trivially true.

    Which is it?! Your lack of interest in beetle sex organs is understandable, but not much of an argument.

  151. 151
    bornagain77 says:

    Theobald is wrong! ,,, The tree of life as imagined by Darwinists simply does not exist in either the fossil record or the genetic evidence,,,,

    “It is hard for us paleontologists, steeped as we are in a tradition of Darwinian analysis, to admit that neo-Darwinian explanations for the Cambrian explosion have failed miserably. New data acquired in recent years, instead of solving Darwin’s dilemma, have rather made it worse. Meyer describes the dimensions of the problem with clarity and precision. His book is a game changer for the study of evolution and points us in the right direction as we seek a new theory for the origin of animals.”
    -Dr. Mark McMenamin – 2013
    Paleontologist at Mt. Holyoke College and author of The Emergence of Animals

    “The record of the first appearance of living phyla, classes, and orders can best be described in Wright’s (1) term as ‘from the top down’.”
    (James W. Valentine, “Late Precambrian bilaterians: Grades and clades,” Proceedings of the National Academy of Sciences USA, 91: 6751-6757 (July 1994).)

    “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas.”
    James W. Valentine – On the Origin of Phyla: Interviews with James W. Valentine

    The unscientific hegemony of uniformitarianism – David Tyler – May 2011
    Excerpt: The pervasive pattern of natural history: disparity precedes diversity,,,, The summary of results for phyla is as follows. The pattern reinforces earlier research that concluded the Explosion is not an artifact of sampling. Much the same finding applies to the appearance of classes. These data are presented in Figures 1 and 2 in the paper.
    http://www.arn.org/blogs/index.....niformitar

    “Darwin’s prediction of rampant, albeit gradual, change affecting all lineages through time is refuted. The record is there, and the record speaks for tremendous anatomical conservatism. Change in the manner Darwin expected is just not found in the fossil record.”
    Niles Eldredge and Ian Tattersall, The Myth of Human Evolution (New York: Columbia University Press, 1982), 45-46.

    Challenging Fossil of a Little Fish
    “In Chen’s view, his evidence supports a history of life that runs opposite to the standard evolutionary tree diagrams, a progression he calls top-down evolution.” Jun-Yuan Chen is professor at the Nanjing Institute of Paleontology and Geology
    http://www.fredheeren.com/boston.htm

    In Explaining the Cambrian Explosion, Has the TalkOrigins Archive Resolved Darwin’s Dilemma? – JonathanM – May 2012
    Excerpt: it is the pattern of morphological disparity preceding diversity that is fundamentally at odds with the neo-Darwinian scenario of gradualism. All of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later. On the Darwinian view, one would expect to see all of the major differences in body plan appear only after numerous small-scale speciation events. But this is not what we observe.
    http://www.evolutionnews.org/2.....59171.html

    As Roger Lewin (1988) explains in Science,
    “Several possible patterns exist for the establishment of higher taxa, the two most obvious of which are the bottom-up and the top-down approaches. In the first, evolutionary novelties emerge, bit by bit. The Cambrian explosion appears to conform to the second pattern, the top-down effect.”

    Erwin et al. (1987), in their study of marine invertebrates, similarly conclude that,
    “The fossil record suggests that the major pulse of diversification of phyla occurs before that of classes, classes before that of orders, orders before that of families. The higher taxa do not seem to have diverged through an accumulation of lower taxa.”
    Indeed, the existence of numerous small and soft-bodied animals in the Precambrian strata undermines one of the most popular responses that these missing transitions can be accounted for by them being too small and too-soft bodied to be preserved.
    http://www.evolutionnews.org/2.....67021.html

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    “With the benefit of hindsight, it is amazing that paleontologists could have accepted gradual evolution as a universal pattern on the basis of a handful of supposedly well-documented lineages (e.g. Gryphaea, Micraster, Zaphrentis) none of which actually withstands close scrutiny.”
    Christopher R.C. Paul, “Patterns of Evolution and Extinction in Invertebrates,” K.C. Allen and D.E.G. Briggs, eds., Evolution and the Fossil Record (Washington, D.C., Smithsonian Institution Press, 1989), 105.

    “It must be significant that nearly all the evolutionary stories I learned as a student from Trueman’s Ostrea/Gryphaea to Carruthers’ Zaphrentis delanouei, have now been ‘debunked’. Similarly, my own experience of more than twenty years looking for evolutionary lineages among the Mesozoic Brachiopoda has proved them equally elusive.’
    Dr. Derek V. Ager (Department of Geology & Oceonography, University College, Swansea, UK), ‘The nature of the fossil record’. Proceedings of the Geologists’ Association, vol.87(2), 1976,p.132.

    “The point emerges that if we examine the fossil record in detail, whether at the level of orders or of species, we find’ over and over again’ not gradual evolution, but the sudden explosion of one group at the expense of another.”
    Paleontologist, Derek V. Ager, “The Nature of the Fossil Record,” 87 Proceedings of the British Geological Association 87 (1976): 133. (Department of Geology & Oceanography, University College, Swansea, UK)

    “It is a feature of the known fossil record that most taxa appear abruptly. They are not, as a rule, led up to by a sequence of almost imperceptibly changing forerunners such as Darwin believed should be usual in evolution…This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large.”
    G.G.Simpson – one of the most influential American Paleontologist of the 20th century

    “A major problem in proving the theory has been the fossil record; the imprints of vanished species preserved in the Earth’s geological formations. This record has never revealed traces of Darwin’s hypothetical intermediate variants – instead species appear and disappear abruptly, and this anomaly has fueled the creationist argument that each species was created by God.”
    Paleontologist, Mark Czarnecki

  152. 152
    bornagain77 says:

    Zach, most people when shown there foundational claims were false would either try to defend them or humbly admit they were wrong and apologize. Why don’t you? You trying to hide in trivialities, instead of admitting you were grossly wrong, is evidence that you are not interested in truth but in pushing a dogma.

  153. 153
    Zachriel says:

    bornagain77: Theobald is wrong!

    Nothing in your post rebuts Theobald, which doesn’t address the pattern of branching, whether top-down or bottom-up. You still have a branching pattern. Do you agree? If not, on what basis?

    bornagain77: most people when shown there foundational claims were false would either try to defend them or humbly admit they were wrong and apologize.

    When we pointed out mechanisms of speciation in beetles in response to another poster, you said they were “either unsubstantiated conjecture or trivially true”. That’s quite funny, but hardly a valid objection.

  154. 154
    Vishnu says:

    Box: “What bothers me, is not so much that you won’t respond to my rebuttals, but that you keep repeating your fallacious claim that ID has a trillions-to-one disadvantage with respect to unguided evolution. Can you at least have the courtesy to dispense with this nonsense until you have addressed my refutations?”

    Don’t. Hold. Breath.

  155. 155
    keith s says:

    spamagain77:

    Zach, most people when shown there foundational claims were false would either try to defend them or humbly admit they were wrong and apologize. Why don’t you? You trying to hide in trivialities, instead of admitting you were grossly wrong, is evidence that you are not interested in truth but in pushing a dogma.

    Got a mirror handy, sa77?

  156. 156
    Joe says:

    LoL! @ keith s- H has to be low in ALL design inferences. That is in the EF and is the way scientific investigation proceeds. CSI exists regardless of what produced it and Dembski never says otherwise.

  157. 157
    Joe says:

    Zachriel:

    Theobald shows that branching descent is strongly supported,

    No, he doesn’t. He shows what he thinks is strong support for branching descent.

  158. 158
    gpuccio says:

    Zachriel:

    Hi, happy to see you! I really missed you. 🙂

    About the nested hierarchy, my view is very simple. It is a very good argument for common descent, although not necessarily the best.

    Nothing else.

  159. 159
    bornagain77 says:

    “Nothing in your post rebuts Theobald, which doesn’t address the pattern of branching, whether top-down or bottom-up. You still have a branching pattern. Do you agree? If not, on what basis?”

    So Theobald, in your ever twisted Darwinian reasoning, supports the fact that ‘all of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later?’??

    But the Darwinian view, one would expect to see all of the major differences in body plan appear only after numerous small-scale speciation events. But this is not what we observe.

    So if you are telling me that Theobald supports all of the major differences (i.e. the higher taxonomic categories such as phyla) appearing first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appearing later, then I say welcome to ID Zack and Keith, you guys are both flaming old earth creationists!

    Darwin’s Dilemma – video on the Cambrian Explosion
    https://www.youtube.com/watch?v=xxh9o32m5c0

  160. 160
    Zachriel says:

    bornagain77: supports the fact that ‘all of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later?’??

    Actually, it doesn’t address the question.

  161. 161
    lifepsy says:

    Zachriel 149

    lifepsy: How is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes?

    That’s not our position. Theobald shows that branching descent is strongly supported, but says nothing about whether the process is guided or not.

    I was responding to Keith S who was adamant about calling it “unguided evolution”. Switch out unguided evolution for “branching descent”. It is the same problem.

    lifepsy: Why should branching common descent necessarily produce a discernible nested hierarchy?

    It’s a deduction from geometry as grouping leaves by branch and stem form a nested hierarchy. Now consider a tree that grows, but there are occasional mutations that are inherited along a given branch. The end result will be a pattern of traits that form a nested hierarchy. There’s a statistical relationship between the mutation rate, number of traits, and the fit to the nested hierarchy. Here’s a simple example with one mutation* per branch.

    I’m aware of the principle. Notice the keyword “discernible”. I’m asking you why this nested hierarchy should necessarily be recognizable after the fact, instead of having its signal confounded by a blurring of indistinguishable traits.

    lifepsy: Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy?

    The hypothesis is fidelity in reproduction with only occasional mutation among many traits branching descent. We could probably expand on that some more, but then you would end up with something like Darwin’s “long abstract”.

    Your description does not address the problem in any way. You’re merely describing the branching principle again, while I’m telling you that whether or not the nested hierarchy is generated in principle, the nested hierarchy signal itself may potentially be masked.

    Darwin is in accord with my position.

    Darwin’s Origin p.510

    Extinction has only separated groups: it has by no means made them; for if every form which has ever lived on this earth were suddenly to reappear, though it would be quite impossible to give definitions by which each group could be distinguished from other groups, as all would blend together by steps as fine as those between the finest existing varieties, nevertheless a natural classification, or at least a natural arrangement, would be possible. We shall see this by turning to the diagram: the letters, A to L, may represent eleven Silurian genera, some of which have produced large groups of modified descendants.

    Every intermediate link between these eleven genera and their primordial parent, and every intermediate link in each branch and sub-branch of their descendants, may be supposed to be still alive; and the links to be as fine as those between the finest varieties. In this case it would be quite impossible to give any definition by which the several members of the several groups could be distinguished from their more immediate parents; or these parents from their ancient and unknown progenitor. Yet the natural arrangement in the diagram would still hold good; and, on the principle of inheritance, all the forms descended from A, or from I, would have something in common. In a tree we can specify this or that branch, though at the actual fork the two unite and blend together. We could not, as I have said, define the several groups; but we could pick out types, or forms, representing most of the characters of each group, whether large or small, and thus give a general idea of the value of the differences between them. This is what we should be driven to, if we were ever to succeed in collecting all the forms in any class which have lived throughout all time and space.

    If you cannot distinguish actual different groups, then you cannot assemble them into branching orders and nested hierarchies.

    Furthermore, if these finest of intermediate links include heavy losses or reversal of traits, then the nested hierarchy signal is certainly confounded.

    The conclusion is that the branching pattern of common descent is just as likely (if not more so) to result in a data scenario where traits are so blurred as to make the assembly of nested hierarchies impossible.

    Thus, as usual, you are accommodating to an outcome that opposes the one you offer as evidence. And lack of a discernible nested hierarchy signal would not falsify a branching descent model.

    It’s rather unscientific to be promoting “nested hierarchy” as direct evidence for a branching descent model, when “Not-nested hierarchy” could also be accommodated by a branching descent model.

    “… But surely no purely random process of extinction would have eliminated so effectively all ancestral and transitional forms, all evidence of the trunk and branches of the supposed tree, and left all remaining groups: mammals, cats, flowering plants, birds, tortoises, vertebrates, molluscs, hymenoptera, fleas and so on, so isolated and related only in a strictly sisterly sense.

    In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed. There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology and not evolution.

    How much easier it would be to argue the case for evolution if nature’s divisions were blurred and indistinct, if the systema naturae was largely made up of overlapping classes indicative of sequence and continuity… ” – Michael Denton

  162. 162
    Box says:

    Zachriel: The hypothesis is fidelity in reproduction with only occasional mutation among many traits branching descent. We could probably expand on that some more, but then you would end up with something like Darwin’s “long abstract”.

    Does this branching principle conform with a top-down tree; as in BA77’s question? It seems pretty obvious to me that you refer to the good ol’ bottom-up branching pattern.

  163. 163
    keith s says:

    Interesting that Denyse has closed comments on yet another thread that was going badly for IDers.

  164. 164
    bornagain77 says:

    Zach, you don’t actually address reality, so as to the Black Knight, ‘let’s call it a draw shall we?’

  165. 165
    Mung says:

    Love the title of the OP!

  166. 166
    Mung says:

    keiths @ 50:

    1. Theobald’s stated purpose was to present the evidence for common descent, so that’s what he did.

    What was Theobald’s position on whether the nested hierarchy was guided or unguided?

  167. 167
    Mung says:

    keiths:

    My point is simply that you needn’t be surprised that Theobald didn’t make the same argument that I do.

    So you were quote-mining.

  168. 168
    Mung says:

    keiths:

    Theobald is a methodological naturalist, so guided evolution has no place in his scientific thinking.

    Therefore, all his “evidences” for common descent and a single “objective nested hierarchy” are only evidence for unguided evolution.

    gee. really? how did you reach that conclusion?

  169. 169
    Mung says:

    keiths and his swiss cheese bomb. It’s yummy, but full of holes.

  170. 170
    Mung says:

    keiths:

    In reality, mutation rates are low enough and vertical inheritance predominates enough that we can treat unguided evolution as a Markov process.

    If we assume what we want to prove, we can prove what we want to assume! As if that was ever in doubt.

  171. 171
    Mung says:

    Zachriel @ 17:

    Douglas Theobald: … gradual Divine direction of evolution is indeed consistent and compatible with common descent.

    keiths: Things That IDers Don’t Understand, Part 1 — Intelligent Design is not compatible with the evidence for common descent

    whatever

  172. 172
    keith s says:

    Box and lifepsy,

    Don’t kid yourselves. Your objections don’t hold water.

    Box:

    Keith,

    What it boils down to is this: you state that there are trillions of options available for a designer and that he/she/it could have chosen either one, but we simply have no way of knowing. There is no grounding for your claim.

    Sure there is. There are trillions of logical possibilities, and we have no reason to rule any of them out. After all, we know absolutely nothing about the purported designer.

    Lacking that knowledge, the principle of indifference applies. Every possibility should be treated as having equal probability, which is why my trillion-sided die model is totally appropriate.

    What’s amusing is that ID proponents — who are usually screaming “Don’t tell us what the Designer would or wouldn’t do!” — are suddenly eager to do exactly that when their “theory” is threatened.

    If you want to add assumptions to the ID hypothesis, you have to justify them. Otherwise you’re making the embarrassing Rain Fairy mistake.

    lifepsy:

    How is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes? (the very criticism you launch at the design inference!)

    A straight answer, please.

    The fact that we’re talking about a purely hypothetical designer doesn’t mean that we are talking about some hypothetical form of evolution.

    Evolution — actual, observed evolution — proceeds gradually and with primarily vertical inheritance, and produces inferable objective nested hierarchies.

    It’s a fact. Deal with it.

    Here’s Theobald as a reminder:

    Does Phylogenetic Inference Find Correct Trees?

    In order to establish their validity in reliably determining phylogenies, phylogenetic methods have been empirically tested in cases where the true phylogeny is known with certainty, since the true phylogeny was directly observed.

    Bacteriophage T7 was propagated and split sequentially in the presence of a mutagen, where each lineage was tracked. Out of 135,135 possible phylogenetic trees, the true tree was correctly determined by phylogenetic methods in a blind analysis. Five different phylogenetic methods were used independently, and each one chose the correct tree (Hillis et al.1992 ).

    In another study, 24 strains of mice were used in which the genealogical relationships were known. Cladistic analysis reproduced almost perfectly the known phylogeny of the 24 strains (Atchely and Fitch 1991).

    Bush et al. used phylogenetic analysis to retrospectively predict the correct evolutionary tree of human Influenza A virus 83% of the time for the flu seasons spanning 1983 to 1994.

    In 1998, researchers used 111 modern HIV-1 (AIDS virus) sequences in a phylogenetic analysis to predict the nucleotide sequence of the viral ancestor of which they were all descendants. The predicted ancestor sequence closely matched, with high statistical probability, an actual ancestral HIV sequence found in an HIV-1 seropositive African plasma sample collected and archived in the Belgian Congo in 1959 (Zhu et al.1998 ).

    In the past decade, phylogenetic analyses have played a significant role in successful convictions in several criminal court cases (Albert et al. 1994; Arnold et al. 1995; Birch et al. 2000; Blanchard et al. 1998; Goujon et al. 2000; Holmes et al. 1993; Machuca et al. 2001; Ou et al. 1992; Veenstra et al. 1995; Vogel 1997; Yirrell et al. 1997), and phylogenetic reconstructions have now been admitted as expert legal testimony in the United States (97-KK- 2220 State of Louisiana v. Richard J. Schmidt [PDF]). The legal test in the U. S. for admissibility of expert testimony is the Daubert guidelines (U. S. Supreme Court Case Daubert v. Merrell Dow Pharmaceuticals, Inc., 509 U.S. 579, 587-89, 113 S. Ct. 2786, 2794, 125 L. Ed. 2d 469, 1993). The Daubert guidelines state that a trial court should consider five factors in determining “whether the testimony’s underlying reasoning or methodology is scientifically valid”: (1) whether the theory or technique in question can be and has been tested; (2) whether it has been subjected to peer review and publication; (3) its known or potential error rate; (4) the existence and maintenance of standards controlling its operation; and (5) whether it has attracted widespread acceptance within the relevant scientific community (quoted nearly verbatim). Phylogenetic analysis has officially met these legal requirements.

    None of what Theobald describes in that quote would be possible if evolution weren’t gradual with predominantly vertical inheritance.

  173. 173

    keiths:

    In reality, mutation rates are low enough and vertical inheritance predominates enough that we can treat unguided evolution as a Markov process.

    What I want to know is how did proponents of “unguided evolution” rule out the possibility that they are attempting to explain how a genetic cognitive system works, using an antique theory that can only lead to false conclusions in regards to what is or is not “intelligent”?

  174. 174
    keith s says:

    I posed a challenge in the other thread that only William was brave enough to address. Here is his attempt, and here is my rebuttal.

    All of the other commenters, including nullasalus, were afraid to try — and for good reason. Read the challenge and you’ll see what’s got them spooked.

    Here is the challenge:

    Just to hammer my point home, here is a comment of mine from TSZ:

    Some more questions for the ID supporters out there:

    1. Bob is walking through the desert with his friend, a geologist. They come across what appears to be a dry streambed. After some thought, Bob states that every rock, pebble, grain of sand and silt particle was deliberately placed in its exact position by a Streambed Designer. His friend says “That’s ridiculous. This streambed has exactly the features we would expect to see if it was created by flowing water. Why invoke a Streambed Designer?”

    Who has the better theory, Bob or his friend?

    2. Bob is invited to the scene of an investigation by a friend who is an explosive forensics expert. They observe serious damage radiating out in all directions from a central point, decreasing with distance, as if an explosion had taken place. Bob’s friend performs some tests and finds large amounts of explosive residue. Bob says, “Somebody went to a lot of trouble to make it look like there was an explosion here. They even planted explosive residue on the scene! Of course, there wasn’t really an explosion.”

    Who has the better theory, Bob or his friend?

    3. Bob and another friend, an astronomer, observe the positions of the planets over several years. They determine that the planets are moving in ellipses, with the sun at one of the foci. Bob says, “Isn’t that amazing? The angels pushing the planets around are following exactly the paths that the planets would have followed if gravity had been acting on them!” The astronomer gives Bob a funny look and says “Maybe gravity is working on those planets, with no angels involved at all. Doesn’t that seem more likely to you?”

    Who has the better theory, Bob or his friend?

    4. Bob is hanging out at the office of a friend who is an evolutionary biologist. The biologist shows Bob how the morphological and molecular data establish the phylogenetic tree of the 30 major taxa of life to an amazing accuracy of 38 decimal places. “There couldn’t be a better confirmation of unguided evolution,” the biologist says. “Don’t be ridiculous,” Bob replies. “All of those lifeforms were clearly designed. It’s just that the Designer chose to imitate unguided evolution, instead of picking one of the trillions of other options available to him.”

    Who has the better theory, Bob or his friend?

    Share your answers with us. Did your answers to the four questions differ? If so, please explain exactly why.
    And ponder this: If you are an ID supporter, then you are making exactly the same mistake as Bob does in the four examples above, using the same broken logic. Isn’t that a little embarrassing? It might be time to rethink your position.

    And don’t forget the Rain Fairy.

    I repeat:

    Share your answers with us. Did your answers to the four questions differ? If so, please explain exactly why.

    And ponder this: If you are an ID supporter, then you are making exactly the same mistake as Bob does in the four examples above, using the same broken logic. Isn’t that a little embarrassing? It might be time to rethink your position.

  175. 175
    Mung says:

    poor keiths is deluded. Who has the better theory?

  176. 176
    Mung says:

    keiths claimed that intelligent design is incompatible with the evidence for common descent.

    So much for integrity.

    Who cares who has the better theory for a claim that is demonstrably false.

  177. 177

    I honestly sense that all in the Darwinian camp are heading towards the most epic “oops” moment there ever was, in all of science history.

  178. 178
    Mapou says:

    Gaulin:

    I honestly sense that all in the Darwinian camp are heading towards the most epic “oops” moment there ever was, in all of science history.

    I don’t think an “oops” moment does it justice. When the fit hit the shan, there will be a mountain of crow for the Darwinists and materialists to consume. It will be fun to watch. The paradigm shift will be much more radical and it will happen much sooner than most people suspect. It’s kinda like some karmic law in action. There is no escaping it.

  179. 179
    Andre says:

    Box @124

    Hi Box that is correct……

    Here is a comprehensive review of PCD

    Some snippets!

    Apoptosis is considered a vital component of various processes including normal cell turnover, proper development and functioning of the immune system, hormone-dependent atrophy, embryonic development and chemical-induced cell death.

    The mechanisms of apoptosis are highly complex and sophisticated, involving an energy-dependent cascade of molecular events

    The role of apoptosis in normal physiology is as significant as that of its counterpart, mitosis. It demonstrates a complementary but opposite role to mitosis and cell proliferation in the regulation of various cell populations. It is estimated that to maintain homeostasis in the adult human body, around 10 billion cells are made each day just to balance those dying by apoptosis

    Alterations of various cell signaling pathways can result in dysregulation of apoptosis and lead to cancer.

    Apoptosis is regarded as a carefully regulated energy-dependent process, characterized by specific morphological and biochemical features in which caspase activation plays a central role. Although many of the key apoptotic proteins that are activated or inactivated in the apoptotic pathways have been identified, the molecular mechanisms of action or activation of these proteins are not fully understood and are the focus of continued research. The importance of understanding the mechanistic machinery of apoptosis is vital because programmed cell death is a component of both health and disease, being initiated by various physiologic and pathologic stimuli. Moreover, the widespread involvement of apoptosis in the pathophysiology of disease lends itself to therapeutic intervention at many different checkpoints. Understanding the mechanisms of apoptosis, and other variants of programmed cell death, at the molecular level provides deeper insight into various disease processes and may thus influence therapeutic strategy.

    http://www.ncbi.nlm.nih.gov/pm.....MC2117903/

    Keith S is most welcome to make his argument about unguided evolution but here is the take home, PCD is an unguided evolution killer, it prevents unguided processes from happening and once PCD and the other mechanisms become deregulated, the organism dies.

    PCD is not something that could or have evolved, any alteration to it and the organism dies.

  180. 180
    Andre says:

    Box

    Necrosis, Apoptosis and autophagy all work together to maintain the stability of cells…….

    There are some settings where autophagy and apoptosis seem to be interconnected and the idea of “molecular switches” between the two processes has been introduced (Piacentini et al., 2003). This is similar to the concept of the necrosis-apoptosis “continuum” or “paradox” which suggests that both apoptosis and necrosis represent morphologic expressions of a shared biochemical network in which the route of cell death depends on a variety of factors such as the physiologic milieu, developmental stage, tissue type, and the nature of the cell death signal (Hirsch et al., 1997; Zeiss, 2003). However, the core apoptotic pathway can be diverted to induce a necrotic phenotype by alteration of the availability of intracellular ATP and the availability of caspases.

    A similar relationship may occur between apoptosis and autophagy. It has been suggested that mitochondria may be central organelles that integrate both apoptosis and autophagy (Elmore et al., 2001). Moreover, some of the same signals that are involved in apoptosis may also be involved in autophagy. For example, in both apoptosis and autophagy, there is the coordinated regulation of Akt (protein kinase B) and p70S6 kinase.

    So what we have here is a verification of engineering principles that apply to cells…… Stability control and redundancy built into the system…….

    Chance did this? No Chance!

  181. 181

    Mapou:

    I don’t think an “oops” moment does it justice. When the fit hit the shan, there will be a mountain of crow for the Darwinists and materialists to consume. It will be fun to watch. The paradigm shift will be much more radical and it will happen much sooner than most people suspect. It’s kinda like some karmic law in action. There is no escaping it.

    I agree. The “oops” moment is only what happens in the very first second after another emperor realizes that their tailor left them parading butt-naked through their kingdom…

  182. 182
    kairosfocus says:

    KS, still not seeing that Theobald et al are falling into a grand, question-begging circle on the Tree of Life? BTW, that both involves that the single root node branching tree architecture is dubious — undermining the nested hierarchy claim starting with molecular evidence, and the problem of the root and branches on blind watchmaker thesis proposed mechanisms. Kindly cf 112 ff above and many things onwards. KF

  183. 183
    kairosfocus says:

    KS,

    kindly drop the strawmen. And, the demand to provide a universal decoder algorithm which is a selectively hyperskeptical demand of and alien imposition on design theory. Start with FSCO/I recognised and in hand then provide an empirically grounded inductive explanation.

    Blind watchmaker — FAIL.

    Design — routinely, reliably done. FSCO/I is an inductively reliable sign of design. learn to live with it.

    If you want a stumble across in the field story to take on why not start 200 years ago. First Paley stumbling across a rock in a field then a watch, then from Ch II discovering that the watch has both a time keeping and a self replicating function. He infers that you cannot say much about the rock, but can recognise contrivance in the watch. He then anticipated — but it seems was ignored — the claim that reproduction makes a difference.

    Let me clip his normally overlooked thought exercise in Ch II in his Nat Theol, where he makes a very interesting inductive argument:

    Suppose, in the next place, that the person who found the watch [in a field, cf the well known argument in Ch I] should after some time discover that, in addition to [–> a key point] all the properties which he had hitherto observed in it, it possessed the unexpected property of producing in the course of its movement another watch like itself — the thing is conceivable; that it contained within it a mechanism, a system of parts — a mold, for instance, or a complex adjustment of lathes, baffles, and other tools — evidently and separately calculated for this purpose . . . .

    The first effect would be to increase his admiration of the contrivance [first excited by observing a complex, functionally specific, time keeping mechanism based on correct interaction of correctly formed and arranged parts], and his conviction of the consummate skill of the contriver. Whether he regarded the object of the contrivance, the distinct apparatus, the intricate, yet in many parts intelligible mechanism by which it was carried on, he would perceive in this new observation nothing but an additional reason for doing what he had already done — for referring the construction of the watch to design and to supreme art . . . . He would reflect, that though the watch before him were, in some sense, the maker of the watch, which, was fabricated in the course of its movements, yet it was in a very different sense from that in which a carpenter, for instance, is the maker of a chair — the author of its contrivance, the cause of the relation of its parts to their use.

    I’d say, worlds different from convenient strawman caricatures.

    Back to sleep, later.

    KF

  184. 184
    keith s says:

    Two weeks ago, Barry issued his ill-advised “bomb” challenge. Within hours, I had supplied a bomb that UDers have been desperately trying to defuse ever since.

    My bomb has now been a topic on at least six threads at UD, and still no one has managed to come up with a refutation.

    Despite the feigned insouciance of post titles referring to “damp squibs”, “fizzling” bombs, and “Black Knight taunts”, it’s clear that my argument has hit a nerve at UD. People are spooked, and every day that goes by without a rebuttal is a further embarrassment to UD.

    This is remarkable. I post an argument on the premier Intelligent Design blog, showing that ID is trillions of times worse than unguided evolution at explaining the existence of the objective nested hierarchy of life. ID supporters rush to refute it. Two weeks later, no one has succeeded.

    That means that at this point, it is impossible to be a rational IDer. You know my argument is there; you know it hasn’t been rebutted; you know that it shows that ID is inferior to unguided evolution by a factor of trillions to one.

    An honest IDer has only one option at this point: give up ID. You can hope, or even pray, that someone will come up with a refutation of my argument, so that you can legitimately become an IDer again. But for now, the only honest option is to accept what you have been unable to refute.

    Think about it, think very hard about your relationship with the truth, and think about whether you are willing, as the saying goes, “to follow the evidence where it leads” — even if it leads to a place that is very uncomfortable, at least at first.

  185. 185
    keith s says:

    Tomorrow, I plan to post a summary of all the attempted refutations of my argument, with explanations of why they fail.

    See y’all tomorrow.

  186. 186
    keith s says:

    Based on this, it looks like we can add kairosfocus to the long list of people who are afraid to answer my four simple questions and justify their answers.

    I’m not surprised.

    Anyone else brave enough? How about you, Barry? You like issuing challenges. How about responding to one?

  187. 187
    Andre says:

    O Brohter, the black knight truly lives….

  188. 188
    Andre says:

    The chemicals in Keith’s brain has convinced him that he’s right even though he admitted that you can never be 100% certain…..

    The irony!

  189. 189
    kairosfocus says:

    Andre,

    You are right.

    But, it’s worse than that.

    KS et al don’t really care about the loss of the case on the merits, if they can make their mud slinging and spin tactics stick. (Cf here on that subject.)

    For the ideologically indoctrinated, closed minded, fundamentally hostile and ruthless, a rhetorical manipulation victory gives power, and power reduces restraints on doing what one pleases regardless of consequences to others.

    That is, we are dealing with strains of an ideological neo-marxist, Saul Alinsky “community organiser [disorganiser]”:

    The first step in community organization is community disorganization. The disruption of the present organization is the first step toward community organization. Present arrangements must be disorganized if they are to be displace by new patterns…. All change means disorganization of the old and organization of the new.” [Alinsky, 1970, Rules for Radicals, p.116]

    . . . mind-virus that has been allowed in the doors of our civilisation and its key institutions, and thus through ruthless cynicallly nihilistic tactics to displace genuine reasoning from first principles of right reason towards truth warranted through factual adequacy, coherence and balanced explanatory power.

    Knowledge anchored in cogent reason has been displaced by a world of pseudo-intuitive, question-begging, evolutionary materialism driven agenda driven perceptions, hidden assumptions, controlling beliefs and resulting warped, lab coat clad ideology pretending to be Science . . . i.e. Knowledge.

    And if you dare to disagree, you must be ignorant, stupid, insane or wicked.

    Worse, if there is the “taint” of Theism around you, you are a dangerous threat to the selfish and self destructive, self-centred chaos such would substitute for mutual respect, genuine rights and moral government that constitute liberty.

    In short a mutual recognition of dignity rooted in Imago Dei, has been displaced by the nihilist’s credo, might and manipulation make ‘right.’ And, ‘truth.’

    So, to him, who wins the debate boils down to who spins it and gets his perception to stick.

    That’s why we see accusations, smears and assertions without regard to truth, accuracy, genuine warrant, fair-mindedness, grounds. That’s why there is a zero concessions to IDiots policy — they refuse to be beholden to mere facts and logic, and their game is to domineer, accuse, twist, turnabout and project blame when corrected, insistently ignore and swarm down or drown out what hey cannot answer, bully and/or enable bullying through dirty “good” cop-bad cop games, speak and act with utter disregard to truth, dominate and rule through ruthless factional power games, not to be docile — properly, teachable — under the force of truth and logic and facts, much less fairness, the right and justice.

    Plato warned us about such 2350 years ago, and about what happens to societies that let such in the gate, in The Laws Bk X:

    >>Ath. . . .[The avant garde philosophers and poets, c. 360 BC] say that fire and water, and earth and air [i.e the classical “material” elements of the cosmos], all exist by nature and chance, and none of them by art . . . [such that] all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only [ –> that is, evolutionary materialism is ancient and would trace all things to blind chance and mechanical necessity] . . . .

    [Thus, they hold] that the principles of justice have no existence at all in nature, but that mankind are always disputing about them and altering them; and that the alterations which are made by art and by law have no basis in nature, but are of authority for the moment and at the time at which they are made.- [ –> Relativism, too, is not new; complete with its radical amorality rooted in a worldview that has no foundational IS that can ground OUGHT.] These, my friends, are the sayings of wise men, poets and prose writers, which find a way into the minds of youth. They are told by them that the highest right is might [ –> Evolutionary materialism — having no IS that can properly ground OUGHT — leads to the promotion of amorality on which the only basis for “OUGHT” is seen to be might (and manipulation = might in “spin”)], and in this way the young fall into impieties, under the idea that the Gods are not such as the law bids them imagine; and hence arise factions [ –> Evolutionary materialism-motivated amorality “naturally” leads to continual contentions and power struggles influenced by that amorality], these philosophers inviting them to lead a true life according to nature, that is,to live in real dominion over others [ –> such amoral factions, if they gain power, “naturally” tend towards ruthless abuse], and not in legal subjection to them. >>

    What they refuse to accept is that Alcibiades came to a very sticky end, and that the Athenians in the end would rather lose a decisive battle through making mistakes than trust his insights.

    What we face is a reformation challenge.

    And, we have to recognise what we are up against, including in halls of influence and power all across our civilisation.

    Where, one of the strongest weapons that such evil doers have is our propensity to postpone taking strong action in defense of the imperfect but workable and reformable in teh face of the utterly destructive but manipulative and often persuasive.

    If you doubt me just ask the over 100 million ghosts of victims of the Communist and Fascist kissing-cousin totalitarianisms of the past 100 years.

    Here is Martin Niemoller’s warning — after spending years in a concentration camp:

    First they came for the Socialists, and I did not speak out—
    Because I was not a Socialist.

    Then they came for the Trade Unionists, and I did not speak out—
    Because I was not a Trade Unionist.

    Then they came for the Jews, and I did not speak out—
    Because I was not a Jew.

    Then they came for me—and there was no one left to speak for me.

    The lessons of history were paid for in blood and tears, but sadly, we too often refuse to study and take them to heart. Only, predictably, to have to pay the same price over and over and over again.

    KF

  190. 190
    Steve says:

    keiths,

    1. No IDer claims there is a streambed designer. Strike one.

    2. Friend has only performed tests and made no theory. nothing to compare. Strike two.

    3. No IDer claims angels push planets or atoms around. That is just your lame cartoon caricature of what you imagine IDers think. Strike three.

    4. You are clever, but not that much so. Date doesn’t not establish your tree. It only supports the tree structure you have designed. But it can also support other structures. Just depends on what data you decide to use. Further no IDer claims that life is designed to appear unguided. Strike four.

    Keiths, I would be embarrassed if I were you. But it is clear that you are impervious to embarrassment.

    We’ve got most of you covered in sand now. We’ll be sure to leave you with a straw for your mouth (or nose if you prefer).

  191. 191
    Joe says:

    keith s:

    My bomb has now been a topic on at least six threads at UD,…

    And it has been refuted in each and every one.

  192. 192
    Joe says:

    keith s:

    Tomorrow, I plan to post a summary of all the attempted refutations of my argument, with explanations of why they fail.

    keith s plans a lie-filled, cowardly post for later today.

  193. 193
    kairosfocus says:

    KS, I notice the school yard taunt game again, and the insistence on strawman tactic caricatures of design thought in the teeth of abundant corrective to the contrary.

    You full well know that I have a period of extreme busyness connected to a major change locally, and that I therefore have limited time to deal with your spin tactics. But instead of respect, that is a “weakness” to be taken rhetorical advantage of. Complete with accusations and insinuations you know to be false.

    Also, every time you have been cogently corrected, you have ignored it, and rushed on to more talking points, as though noting is the matter with your core case.

    On that the biggest single sign is two years and counting on an open invitation to host right here at UD an essay that grounds the darwinist case across the tree of life, not seriously taken up.

    About par for the might and manipulation make ‘right’ ‘truth’ and ‘knowledge’ course.

    I have already put up a counter example at 183, which gives a real sample of the real arguments long raised by design thinkers — in this case one willfully ignored (those who took the lead in the caricature knew what Paley actually wrote, or should have known) and strawmannised for 150 years, Paley’s self replicating watch, which you — or most likely astute onlookers should pay heed to.

    I will clip your latest spin on your caricature of design argument and comment on slices:

    >>Some more questions for the ID supporters out there:

    1. Bob is walking through the desert with his friend, a geologist. They come across what appears to be a dry streambed. After some thought, Bob states that every rock, pebble, grain of sand and silt particle was deliberately placed in its exact position by a Streambed Designer.>>

    a –> Caricature, you substitute a strawman for the case of something very specific: FSCO/I and its inductively known cause on trillions of cases in point.

    >> His friend says “That’s ridiculous. This streambed has exactly the features we would expect to see if it was created by flowing water. Why invoke a Streambed Designer?”>>

    b –> The strawman continues, willfully dodging the issue of FSCO/I and its known source: design. Notice, there is no, utterly no response tot he challenge that there is need to actually warrant that the favoured blind watchmaker mechanisms can and do in our observation create FSCO/I.

    >>Who has the better theory, Bob or his friend?>>

    c –> Willfully distorts the design inference per aspect filter. A streambed would be understood through that process as explicable on blind chance and mechanical necessity, accepting the risk of a false negative by setting the threshold for inferring design so high that the chances of a false positive will be negligible. 500 – 1,000 bits of functionally specific complex organisation and associated information is a sufficient threshold, per the atomic resources of the solar system or the observed cosmos — as has been explained any number of times but routinely caricatured and/or ignored.

    d –> By sharp contrast, the power of blind watchmaker thesis chance and necessity in Darwin’s warm pond or the like to create cell based life has NEVER been empirically demonstrated, and of course the power of such forces of chance and necessity as are known to create FSCO/I has similarly never been shown. FSCO/I is of course, a key aspect of the living cell. All of this is a case of the insistent willful distortion of the design case, often in the teeth of specific correction.

    e –> Likewise, the power of such blind watchmaker forces to create novel body plans full of FSCO/I has never been empirically shown, just, that by a priori evolutionary materialism and/or its fellow travellers, any alternative has been locked out. Grand begging of the question.

    f –> Coming out the door, a strawman caricature, one laced as well with the insinuation that if you disagree with the borg, you are ignorant, stupid, insane or wicked.

    >> 2. Bob is invited to the scene of an investigation by a friend who is an explosive forensics expert. They observe serious damage radiating out in all directions from a central point, decreasing with distance, as if an explosion had taken place. Bob’s friend performs some tests and finds large amounts of explosive residue. Bob says, “Somebody went to a lot of trouble to make it look like there was an explosion here. They even planted explosive residue on the scene! Of course, there wasn’t really an explosion.”>>

    g –> Again, willfully strawmannises the design inference process. On such signs of an explosion, without FSCO/I the explanation would be the first and second defaults of the filter process: natural regularities explained on lawlike necessity and stochastic contingencies on chance.

    h –> Notice, the continuing underlying question-begging assumption that the target of all this, FSCO/I has been explained on blind chance and/or mechanical necessity, as well as that the origin of life and of its major body plans — both involving FSCO/I — have been similarly explained.

    >> Who has the better theory, Bob or his friend?>>

    i –> Strawman tactic resting on begged questions and utter want of evidence that blind watchmaker thesis forces can and do produce FSCO/I.

    >>3. Bob and another friend, an astronomer, observe the positions of the planets over several years. They determine that the planets are moving in ellipses, with the sun at one of the foci. Bob says, “Isn’t that amazing? The angels pushing the planets around are following exactly the paths that the planets would have followed if gravity had been acting on them!”>>

    j –> A strawman caricature that disrespects and denigrates the work of Newton, a design thinker and theist. Here is what Newton, discoverer of the law, had to say on worldview matters in the general scholium to Principia, the work in which he presented the laws of motion and gravitation (and BTW this is there all along in my always linked note, as a major objector at one of the penumbra of objector sites, KS has no excuse to distort Newton like this):

    . . . This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being. And if the fixed stars are the centres of other like systems, these, being formed by the like wise counsel, must be all subject to the dominion of One; especially since the light of the fixed stars is of the same nature with the light of the sun, and from every system light passes into all the other systems: and lest the systems of the fixed stars should, by their gravity, fall on each other mutually, he hath placed those systems at immense distances one from another . . . . We know him only by his most wise and excellent contrivances of things, and final cause [i.e from his designs]: we admire him for his perfections; but we reverence and adore him on account of his dominion: for we adore him as his servants; and a god without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. [i.e necessity does not produce contingency] All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being necessarily existing. [That is, implicitly rejects chance, Plato’s third alternative and explicitly infers to the Designer of the Cosmos.] But, by way of allegory, God is said to see, to speak, to laugh, to love, to hate, to desire, to give, to receive, to rejoice, to be angry, to fight, to frame, to work, to build; for all our notions of God are taken from. the ways of mankind by a certain similitude, which, though not perfect, has some likeness, however. And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy.

    k –> KS’ Newton is obviously nothing like the real one. The real one, having worked out the grand system of the heavens and the earth known as the Newtonian synthesis, including showing why Kepler’s laws obtained per the laws — notice the implications of that term that still remains in our talk on science — of Gravitation etc, leading to elliptical orbits etc, saw the whole system as the work of teh great architect of the cosmos. He then went on to look at perturbations and gave himself a headache. That is the context in which he suggested that God might occasionally stabilise the system. Later, perturbations seemed to allow a solution but in fact there are still open questions on solar system stability in the long term, compounded by the discovery of chaos as a dynamical factor. Let us not ever forget that even the three body problem has no general analytic solution.

    >> The astronomer gives Bob a funny look and says “Maybe gravity is working on those planets, with no angels involved at all. Doesn’t that seem more likely to you?”

    Who has the better theory, Bob or his friend?>>

    l –> Notice how the willful caricature insistently continues in the teeth of a duty of truth, accuracy and fairness to deal with the real issue not a caricature of it.

    >> 4. Bob is hanging out at the office of a friend who is an evolutionary biologist. The biologist shows Bob how the morphological and molecular data establish the phylogenetic tree of the 30 major taxa of life to an amazing accuracy of 38 decimal places.>>

    m –> KS here refuses to address the many problems with Theobald and the general evolutionary claim, assuming away the problems. Notice, how he refuses to address the fact that here is serious reason to doubt that there is in fact a branching tree structure leading to the nested hierarchy once molecular evidence speaks, and more, cf 112 and FF above.

    >> “There couldn’t be a better confirmation of unguided evolution,” the biologist says.>>

    n –> The sobering issues of the blind watchmaker thesis and its failure to ground its claimed powers from the root up are ducked and brushed aside, with utter disregard to truth. This is spin not truthfulness or responsible comment.

    >> “Don’t be ridiculous,” Bob replies. “All of those lifeforms were clearly designed. It’s just that the Designer chose to imitate unguided evolution,>>

    o –> Notice the dodge of implying that blind watchmaker thesis OOL and body plan origin level macro evo has grounded its claimed dynamics on observed evidence of being able to account for FSCO/I, which is false as just linked. So there is no designer imitation issue to be answered — had there been, the design filter would have drawn the inference that the FSCO/I in the world of life was the product of known capacities of blind chance and mechanical necessity.

    >>instead of picking one of the trillions of other options available to him.”>>

    p –> Of course, the fact that designers routinely produce systems of entities that fit in tree patterns, perhaps with cross links and multiple inheritance via libraries of standardised parts perhaps adapted to this case etc [as the real data point to], is dodged. As for the problem that WJM highlighted, that too is ducked. Let me remind those who have not taken time to read what he said, or how I clipped and endorsed him in my own response to an earlier fallacy riddled “challenge” from KS who seems to be doing a fallacy energiser bunny game:

    Ultimately, keiths asks the question of IDists (to paraphrase) – “why did the designer pick just one form of life and utilize just one lineage, when it could have utilized any number of alternate, non-nested systems?” – yet, keiths fails to ask the same question of the natural forces argument – why just one form of life, why one lineage, why one neat, nested hierarchy?

    Keiths attempted logical argument claims to make the same assumptions about both natural and artificial causal agencies – that natural forces and design are both capable of originating life and generating the evolutionary processes and patterns we find. However, this is obviously not the only assumption keiths makes when it comes to the “natural forces” side of the argument; he assumes that natural forces could not have generated anything other than a nested hierarchy leading back to a UCA when it comes to biological life forms.

    He simply asserts that this is what we should expect from natural forces and makes no case for it. If we provide the same assumptions on the ID side of the argument, then we must assume any designer could not have generated anything other than a nested hierarchy leading back to a UCA when it comes to biological life forms – which means that given the same assumptions on both sides of the ledger, keiths argument fails to produce a distinction between what we should expect to find if natural forces or if design agency generated life and evolution here on earth.

    >> Who has the better theory, Bob or his friend?>>

    q –> the trick here is to get you to nod yes, and to mock all along based on strawman caricatures, then you will nod at the end yes without realising you have been had.

    >> Share your answers with us. Did your answers to the four questions differ? If so, please explain exactly why.
    And ponder this: If you are an ID supporter, then you are making exactly the same mistake as Bob does in the four examples above, using the same broken logic. Isn’t that a little embarrassing? It might be time to rethink your position. >>

    r –> The strawman having been set up and knocked over, the truth having been lost in the ill-advised laughs and ridicule, the ad hominem comes into play.

    s –> Now, let us understand, KS is no newbie tot he design issue. If he actually does not know what the core design argument is or how the per aspect explanatory filter work, it is not because of want of explanation or opportunity to know better, it is because of willful disregard for the truth.

    t –> If he DOES know but refuses to acknowledge, the case is far, far worse.

    u –> This is what we are dealing with too often on even the seemingly polite and plausible objectors.

    v –> Who will then declare to one and all that they have “won” the debate.

    Sad.

    KF

  194. 194
    kairosfocus says:

    Joe, given what has happened, please note that you are capable of reasonable commentary, and do not have to slip off the wagon to be effective. Please do not allow yourself to slip off the wagon again. KF

  195. 195
    Box says:

    Keith #172

    Box: What it boils down to is this: you state that there are trillions of options available for a designer and that he/she/it could have chosen either one, but we simply have no way of knowing. There is no grounding for your claim.

    Keith #172: Sure there is. There are trillions of logical possibilities, and we have no reason to rule any of them out.

    No one rules them out. Indeed, there may be trillions of logical possibilities but the question is, how much of them is the designer capable of producing? Your assumption that the designer can produce all of them implies the implicit attribution of omnipotence to the designer.

    Keith #172: After all, we know absolutely nothing about the purported designer.

    Correct. We do not know if a designer has the unlimited capability of producing trillions of different orderings of life – for all we know the designer’s choice is restricted to only one option by a limited capability. We simply have no way of knowing.
    You just said: “we know absolutely nothing about the purported designer”, so why do you in effect assume omnipotence?

    Keith #172: Lacking that knowledge, the principle of indifference applies. Every possibility should be treated as having equal probability, which is why my trillion-sided die model is totally appropriate.

    First you assume an omnipotent designer, and now you want to argue that the principle of indifference applies wrt the choice of the designer …
    So, you are saying that we should accept the assumption that an omnipotent designer is completely indifferent about the ordering of life and that he based his decision on the role of a trillion-sided die.

    So we have an omnipotent designer who is completely indifferent about the ordering of life.

    Those are two baseless assumptions Keith! Nice job!

    Keith #172: What’s amusing is that ID proponents — who are usually screaming “Don’t tell us what the Designer would or wouldn’t do!” —

    We say this for a good reason: we are trying to do science here. Unlike you, we are not in the business of making unsubstantiated assumptions about the designer.

    Keith #172: If you want to add assumptions to the ID hypothesis, you have to justify them. Otherwise you’re making the embarrassing Rain Fairy mistake.

    “Embarrassing” is correct.

  196. 196
    lifepsy says:

    Keith S 172

    Evolution — actual, observed evolution — proceeds gradually and with primarily vertical inheritance, and produces inferable objective nested hierarchies.

    Nice deflection attempt. We’re not talking about “observed unguided evolution”… we’re specifically referring to recovering a signal of this supposed unguided evolution from the past when it could not be observed.

    This issue concerns not what you believe unguided evolution does, but what data it leaves behind to be studied.

    And you already partially conceded that the ONH signal of unguided evolution could become masked in the black knight thread

    Keith S: If evolution were fast enough, or if there was enough horizontal transfer going on, then yes, of course the ONH signal would become unidentifiable.

    Character traits don’t come with little tags that say how long they took to “evolve”, Keith. This must be inferred from the available data set. (and has historically been a great source of contention among evolutionists) Which brings us back full circle:

    If observable gradations between remaining character traits were too blurred and indistinct (as unguided evolution expects), and if there had been many losses and reversals of those traits, then the objective nested hierarchy signal would become unidentifiable.

    It’s as simple as that.

    Unguided evolution/branching common descent, predicts scenarios other than an identifiable objective nested hierarchy.

    Now we refer back to Keith S main argument in #1

    Suppose you have two objects:

    1. A coin with ONH stamped on both sides.
    2. A trillion-sided die with ONH engraved on one and only one side.

    A friend of yours takes both objects into another room, out of your sight. She randomly picks one of the two objects and flips it.

    “I randomly picked one of the objects and flipped it, and it landed with ONH up,” she shouts to you.

    Your job is to guess which of the objects she flipped — the coin with ONH on both sides, or the trillion-sided die with ONH on only one side.

    But as we know, unguided evolution could produce patterns that lack the ONH signal. so in actuality it could have accommodated all sorts of faces on the “trillion sided die”.

    So I ask again, in reference to your own argument, how is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes where the ONH signal has become masked beyond recognition?

    You dodged this in the other thread and you’re dodging it here. Appealing to the presence of an objective nested hierarchy does not avert from your above flawed logic in assuming unguided evolution best explains it.

    At best you can say unguided evolution accommodates a recognizable objective nested hierarchy (as it does the opposite). But unfortunately that ranks you no higher than the IDers or Creationists for that matter.

  197. 197
    lifepsy says:

    Keith S

    Tomorrow, I plan to post a summary of all the attempted refutations of my argument, with explanations of why they fail.

    See y’all tomorrow.

    Yawn. I’ve debunked your “coin/dice” analogy in post#1 for two days now and you absolutely refuse to address it, even when taking the time to respond to me. From what it appears, the underlying flawed logic behind the rest of your arguments has been effortlessly exposed as well. Over and over again.

    I guess tomorrow we can expect more of the same of you completely ignoring counter-arguments and repeating your bald assertions?

  198. 198
    Box says:

    Keith #174: I posed a challenge in the other thread that only William was brave enough to address. Here is his attempt, and here is my rebuttal.

    Keith fails to mention that his “rebuttal” has been torn to pieces by WJMurray here; one day before Keith’s post #174.

  199. 199
    Zachriel says:

    lifepsy: You’re merely describing the branching principle again, while I’m telling you that whether or not the nested hierarchy is generated in principle, the nested hierarchy signal itself may potentially be masked.

    We did address your point, but let’s look at the rest of your specific objections.

    lifepsy: If you cannot distinguish actual different groups, then you cannot assemble them into branching orders and nested hierarchies.

    The answer is right there, in the quote you provided from Darwin, “nevertheless a natural classification, or at least a natural arrangement, would be possible“. There would still be correlations; for instance, having mammary glands would still imply a four-chamber heart and a cranium. There would still be nesting and there would still be hierarchy, even though the edges of any larger groupings would be blurry. Cladistics would proceed apace, though, as it does not depend on arbitrary groupings.

    Indeed, if we had all the organisms that have ever (posited) to have lived, then our evidence for common descent would be even stronger. This is what happens when we find fossil organisms of extinct species. They often confound existing general classifications, but not the nested ordering due to the branching process itself.

    What’s really odd about your statement is that your claiming that if we found what the theory says we would find, it would falsify the theory. That doesn’t even begin to make sense.

    lifepsy: if these finest of intermediate links include heavy losses or reversal of traits, then the nested hierarchy signal is certainly confounded.

    This returns us to our previous comment. The nested hierarchy is not expected to be perfect, but there is a statistical relationship between the rate of change and the number of traits. We have evidence that reproduction tends to fidelity, that mutation is relatively rare compared to the size of genomes, and that the rate of evolution inferred from the fossil record is less than the observed rates of evolution in extant organisms.

    lifepsy: The conclusion is that the branching pattern of common descent is just as likely (if not more so) to result in a data scenario where traits are so blurred as to make the assembly of nested hierarchies impossible.

    No. It turns out that we have substantial evidence of extinction.

    Branching descent –> natural nested ordering
    Branching descent with extinction –> nested hierarchy

    Box: Does this branching principle conform with a top-down tree; as in BA77?s question?

    Theobald’s paper doesn’t address that question. However, the so-called top-down tree is called adaptive radiation, and is consistent with Theobald’s results, as well as evolutionary theory generally.

    bornagain77: ‘let’s call it a draw shall we?’

    You can call it what you like, but you said Theobald was wrong, but didn’t provide any rebuttal.

    Mung: If we assume what we want to prove, we can prove what we want to assume!

    Actually, we have evidence concerning heredity, including rates of morphological and genetic change.

    Box: Your assumption that the designer can produce all of them implies the implicit attribution of omnipotence to the designer.

    The problem is that without ascribing specific properties to the posited designer, there is no way to determine the entailments. As such, it’s a scientifically vacuous claim. Why would the designer choose a nested hierarchy arrangement rather than some other arrangement? (Of course, that question become moot when you start considering the temporal succession of fossils.)

    The designer may have her angels push the planets in elliptical orbits, or it may be that the elliptical orbits are indicators of some simple physical principle. While the former is not subject to testing, the latter can be tested a number of different ways. Similarly, we test branching descent each time we find a new organism, extant or extinct. But, if you insist, you can always ascribe each new result to a capricious god.

    “If one could conclude as to the nature of the Creator from a study of creation, it would appear that God has an inordinate fondness for stars and beetles the nested hierarchy.”

    lifepsy: Character traits don’t come with little tags that say how long they took to “evolve”

    No, but the hypothesis of branching descent provides a relative ordering, something we can compare to other evidence, such as fossils.

    None of this addresses whether the process is guided or unguided, however. The evidence from natural ordering does, however, strongly support branching descent.

  200. 200
    Barry Arrington says:

    Joe your 192 is beyond the pale. This is your last warning.

  201. 201
    Joe says:

    Barry, my apologies but watch as what I posted becomes reality. keith s has either ignored all refutations of his “bomb”, hand waved them away, and carried on as if nothing has happened. My post was a reflection of all of his actions and comments.

  202. 202
    Box says:

    Zachriel #199,

    Box: Your assumption that the designer can produce all of them implies the implicit attribution of omnipotence to the designer.

    Zachriel #199: The problem is that without ascribing specific properties to the posited designer, there is no way to determine the entailments.

    That is exactly the point I’m trying to get across. Ascribing specific properties to the posited designer, like ‘omnipotence’ and ‘indifference’ (see post #195), is without any ground. So, one should not do that.

    Zachriel #199: As such, it’s a scientifically vacuous claim.

    Attributing omnipotence and indifference to the designer(s) has no scientific base whatsoever.

    Zachriel #199: Why would the designer choose a nested hierarchy arrangement rather than some other arrangement?

    This question, assumes that the designer(s) can choose from several options – which we do not know. And on top of that it assumes that we can penetrate the mind of the designer in order to ascertain her/his/their/its reasons. This is clearly absurd.

    Zachriel #199: The designer may have her angels push the planets in elliptical orbits, or it may be that the elliptical orbits are indicators of some simple physical principle. While the former is not subject to testing, the latter can be tested a number of different ways.

    I must say that this is straw man of a disappointingly low level – the kind of thing that is right up Keith’s alley. The ID position would be that the “simple physical principle” finds its explanation in a designer.

  203. 203
    Barry Arrington says:

    Joe @ 192:

    keith s plans a lie-filled, cowardly post for later today.

    Barry

    Joe your 192 is beyond the pale. This is your last warning.

    Joe:

    Barry, my apologies but watch as what I posted becomes reality. keith s has either ignored all refutations of his “bomb”, hand waved them away, and carried on as if nothing has happened. My post was a reflection of all of his actions and comments.

    Joe, you are missing the point. Yes, he has ignored refutations of his bomb, hand waved them away and carried on as if nothing happened. And if he does it again commenters here will be free to point out the flaws in his arguments. Or not. I tend to ignore him.
    That is all beside the point of my warning. Keep it about the issues. I know that is very hard and I sometimes slip myself. But sometimes it seems like “vituperative” is all you do.

    Our opponents have noticed this too, and they are calling us hypocrites for not dealing with it. That criticism is not entirely unfair. Again, last warning.

  204. 204
    Phinehas says:

    I’d like to give this bomb thing a try. I’m thinking it will go something like this:

    Phin’s BOMB: IDCritic is a loony, therefore his “bomb” is a damp squid.

    IDCritic: That’s a non sequitur. It simply does not follow that my mental state necessarily precludes me from making a true and valid point.

    Phin: No one can lay a finger on my BOMB. They don’t even want to address it.

    IDCritic: What are you talking about? I just refuted it. I might add that it is also an ad hominem. You need to address the points I make. They stand or fall on their own merits.

    Phin: IDCritic is desperate to defuse my BOMB! Look how desperate he is!

    IDCritic: If you were capable of embarrassment, you’d be embarrassed right now.

    Phin: I’m invincible!

    IDCritic: You’re a loony.

    Am I doing it right?

  205. 205
    keith s says:

    Steve,

    1. No IDer claims there is a streambed designer. Strike one.

    2. Friend has only performed tests and made no theory. nothing to compare. Strike two.

    3. No IDer claims angels push planets or atoms around. That is just your lame cartoon caricature of what you imagine IDers think. Strike three.

    Steve,

    You have completely missed the point of my challenge.

    Of course IDers don’t believe in streambed Designers, explosion Designers, Rain Fairies, and angels that push the planets around. Those are ridiculous hypotheses, and every IDer knows it.

    The embarrassing question is: If IDers recognize the first three hypotheses as ridiculous, why don’t they acknowledge the fourth one — the ID hypothesis — as equally ridiculous? It uses the same bad logic.

    It’s an awkward question. That is why UDers are afraid to face my challenge.

  206. 206
    keith s says:

    kairosfocus,

    Your #189 is bizarre and has nothing to do with our topic here.

    Regarding your #193:

    Though your comment is lengthy, I note that you have failed to address the challenge, which was simply to answer the four questions and justify any differences in the answers you gave.

    q –> the trick here is to get you to nod yes, and to mock all along based on strawman caricatures, then you will nod at the end yes without realising you have been had.

    There’s no trick. Of course you will regard the first three hypotheses as ridiculous. Who wouldn’t?

    The question is simple: If the first three hypotheses are ridiculous, then why isn’t the fourth one ridiculous? It uses the same bad logic, after all.

  207. 207
    Box says:

    Keith #205: The embarrassing question is: If IDers recognize the first three hypotheses as ridiculous, why don’t they acknowledge the fourth one — the ID hypothesis — as equally ridiculous? It uses the same bad logic.

    It’s an awkward question. That is why UDers are afraid to face my challenge.

    And yet, in post #193, Kairosfocus not only faces your “challenge”, but also thoroughly takes it apart. As usual you have chosen to ignore this.

  208. 208
    Box says:

    I retract my claim in post #207. Keith post #206 bears testimony to the fact that he does not ignore the existence of Kairosfocus’ post #193.
    Now let’s see if what he says holds any water.

  209. 209
    Joe says:

    keith s- your 4th scenario is bogus because the evolutionary biologist cannot support his claim. It is nothing but a bald assertion. And only in your mind does Bob use the same logic in all 4 scenarios.

  210. 210
    Vishnu says:

    I am looking out of my office window right now, contemplating nested hierarchies. I spy a half dozen objects that exhibit nested hierarchies. I am certain that various random factors came into play while these nested hierarchies were being developed. I am certain that at the beginning of their development nobody could have predicted precisely where each “data point” would have appeared, yet general predictions at a certain threshold would have been “in the ballpark”, so to speak.

    No sane person would disagree that the physical processes that generated these nested hierarchies are highly specified. One could say that these nested hierarchies evolved randomly, due to exposure to various features of their environment, within certain constraints determined by the extremely sophisticated physical processes from which the nested hierarchies sprang.

    Then I recall…

    “Poems are made by fools like me,

    But only God can make a tree.” –Kilmer

  211. 211
    Mapou says:

    Box @202

    Excellent comment. The old “the designer is omnipotent and omniscient” canard is a recurring theme in Darwinist arguments. The very idea of intelligence assumes that intelligent entities, regardless of how advanced they are, learn through trial and error and are therefore not omniscient. There are processes that are so computationally intractable that the only way to figure them out is to let them run their course. The creation of life on earth took billions of years because the ecological consequences of introducing self-replicating organisms in an environment can only be known by actually doing it and waiting to see what happens afterwards. I suspect that many extinction events in the distant past happened by design, not chance.

  212. 212
    keith s says:

    Box,

    First you assume an omnipotent designer, and now you want to argue that the principle of indifference applies wrt the choice of the designer …
    So, you are saying that we should accept the assumption that an omnipotent designer is completely indifferent about the ordering of life and that he based his decision on the role of a trillion-sided die.

    Not at all. I am not assuming that the designer is omnipotent, or indifferent, or random. I am doing exactly the opposite by assuming none of these things, nor their opposites.

    Do you understand the principle of indifference? If I have no basis for making particular assumptions about the designer, then I have no basis for favoring (or disfavoring) the ONH outcome versus the other outcomes. In other words, I must grant equal probabilities to all of the possible outcomes, because I have no reason to favor some over others.

    Ascribing specific properties to the posited designer, like ‘omnipotence’ and ‘indifference’ (see post #195), is without any ground. So, one should not do that.

    By that reasoning, we also cannot assume that the designer has (or had) the capabilities required to produce the pattern of life that we see. Therefore, the ID hypothesis is untenable.

    Congratulations, Box. Your own (bad) logic has ruled out ID.

  213. 213
    lifepsy says:

    Zachriel 199

    lifepsy: If you cannot distinguish actual different groups, then you cannot assemble them into branching orders and nested hierarchies.

    The answer is right there, in the quote you provided from Darwin, “nevertheless a natural classification, or at least a natural arrangement, would be possible“.

    That’s not an answer. Anything that exists can be “naturally arranged”. Cars can be naturally arranged by chassis dimensions. Splattered paint can be naturally arranged by the size of each splatter.

    Indeed, if we had all the organisms that have ever (posited) to have lived, then our evidence for common descent would be even stronger.

    Agreed. But you wouldn’t need all of the organisms. Even a fraction of actual unambiguous smooth gradations between unique body plans and it would actually look like common descent had happened, instead of being largely the product of the evolutionist’s imagination as it is today.

    All this talk about nested hierarchies wouldn’t matter since you’d actually have tangible evidence.

    Focus on nested hierarchy discussions are where the evolutionist finally goes when no real tangible evidence has turned up. It’s what made taxonomists so initially reluctant to embrace cladistics. Now they have no choice. It’s the bottom of the barrel.

    What’s really odd about your statement is that your claiming that if we found what the theory says we would find, it would falsify the theory. That doesn’t even begin to make sense.

    Nah, just a misunderstanding on your part.

    It wouldn’t falsify the theory, that’s the whole point. An outcome completely opposing the one you offer as evidence (lack of a recognizable nested hierarchy) would not falsify the theory.

    It would be accommodated as an assumed nested hierarchy that had its signal masked by past evolutionary processes.

    There would still be correlations; for instance, having mammary glands would still imply a four-chamber heart and a cranium.

    Sure there would be correlations, but that doesn’t help you in distinguishing groups or identifying what nests within what. With loss/reversal of traits, correlations could just as easily be weakening the nested hierarchy signal as strengthening it.

    You would potentially have countless gradations both towards and away from mammary glands, both towards and away from a four-chambered heart, and all other associated traits. Each one of those gradation points would have their own multi-directional trajectories through morphospace. It would be fractal.

    By what rule of evolution should a four-chambered heart immutably persist until mammary glands come to nest within it? Why should a cranium immutably persist until both other traits come to nest within it? There are no such rules, and any number of traits could be reversed or lost before other traits are added.

    Not to mention convergence potentially cropping up everywhere.

    There would still be nesting and there would still be hierarchy,

    Nope. Not necessarily a recognizable one.

    We could say that there might always be fragments of identifiable nesting, but any recognizable semblance of an overall objective nested hierarchy could easily be lost.

    even though the edges of any larger groupings would be blurry.

    Sorry, but you need to first distinguish groupings before you can find the edges of groupings. That’s just common sense.

    Cladistics would proceed apace, though, as it does not depend on arbitrary groupings.

    Cladistics only maintains coherency when working with distinguishable groupings.

    Sure Cladistics could “proceed”, but it would return mostly incoherent results. You would only get sensible results from phenetics, or measuring distances between any chosen points. But this would not resolve a nested hierarchy.

    lifepsy: Character traits don’t come with little tags that say how long they took to “evolve”

    No, but the hypothesis of branching descent provides a relative ordering, something we can compare to other evidence, such as fossils.

    Fossils don’t help you for a similar and simple reason: Branching descent does not necessarily predict an orderly fossil record.

    Even today we have instances where evolutionists have to say that ancestors didn’t fossilize until after their descendents – that is the supergroup did not fossilize until after the subgroup.

    Again, at best you can say branching descent accommodates an orderly fossil record, but it doesn’t specifically predict it.

    The evidence from natural ordering does, however, strongly support branching descent.

    Nope.

    Back to the central problem – Evolution theory/branching descent can accommodate way too many opposing outcomes. Nothing we see today is specifically predicted by it.

  214. 214
    Zachriel says:

    Box: That is exactly the point I’m trying to get across. Ascribing specific properties to the posited designer, like ‘omnipotence’ and ‘indifference’ (see post #195), is without any ground. So, one should not do that.

    We agree. That’s why it’s scientifically vacuous. You can explain any pattern as the whims of the gods.

    Box: The ID position would be that the “simple physical principle” finds its explanation in a designer.

    Sure, but the orbits themselves are the result of that simple physical principle, rather than an inordinate fondness for beetles ellipses whereby the desiger moves each planet continuously into a particular curve by whim. — just like the nested hierarchy is the result of a simple biological principle, branching descent.

    Let’s try to draw a more careful distinction. Theobald’s study strongly supports branching descent as *intrinsic* to the history of life. It does not show whether that process was set in motion by a designer, or not. Nor does it show that the process isn’t pruned or shaped by a designer, or not. But it does show that there is an intrinsic branching process.

    Vishnu: I am looking out of my office window right now, contemplating nested hierarchies. I spy a half dozen objects that exhibit nested hierarchies

    You might want to be specific.

    Mapou: learn through trial and error and are therefore not omniscient.

    Evolution is usually seen as a type of trial and error process.

    Mapou: There are processes that are so computationally intractable that the only way to figure them out is to let them run their course.

    You seem to be talking about branching descent.

  215. 215
    Joe says:

    So if we come up with 3 ridiculous scenarios with an evolutionist as the patsy, and then throw in keith s’ 4th scenario, do we win? 😛

  216. 216
    Vishnu says:

    Zachriel: You might want to be specific.

    The last word in the poem specifies the nested hierarchies I’m talking about. Fairly obviously, I think.

  217. 217
    Zachriel says:

    lifepsy: Anything that exists can be “naturally arranged”.

    Anything can be artificially arranged.

    lifepsy: Cars can be naturally arranged by chassis dimensions. Splattered paint can be naturally arranged by the size of each splatter.

    There is no best-fit classification for vehicles. Arranging by size doesn’t result in a nested hierarchy.

    lifepsy: Focus on nested hierarchy discussions are where the evolutionist finally goes when no real tangible evidence has turned up.

    The nested hierarchy has been fundamental to evolutionary theory since Darwin. It has spawned entire fields of study.

    lifepsy: Sure there would be correlations, but that doesn’t help you in distinguishing groups or identifying what nests within what.

    Sure it does. We just pointed to one. Humans would be nested with organisms with mammary glands which would be nested with organisms with vertebrae which would be nested with organisms with crania, which would be nested with organisms with eukaryotic cell structure. This is a non-trivial correlation of traits that is explained by branching descent.

    lifepsy: Fossils don’t help you for a similar and simple reason: Branching descent does not necessarily predict an orderly fossil record.

    Indeed, we don’t expect an orderly fossil record. However, each fossil fits the nested ordering.

  218. 218
    Mapou says:

    Keith s:

    Do you understand the principle of indifference? If I have no basis for making particular assumptions about the designer, then I have no basis for favoring (or disfavoring) the ONH outcome versus the other outcomes. In other words, I must grant equal probabilities to all of the possible outcomes, because I have no reason to favor some over others.

    This is another Darwinist canard. A scientific hypothesis, by definition, is an assumption that can be tested. We have a valid reason for ascribing intelligence to the designers because we routinely observe that it takes intelligence to design irreducibly complex objects. We posit that all designers are intelligent by definition and we look for the signs of intelligence. We know a lot about intelligence by observing humans. Intelligent entities can predict the outcomes of their designs. This ability is the sine qua non of intelligent design.

  219. 219
    Zachriel says:

    Vishnu (quoting): But only God can make a tree.

    Precisely. A simple principle explains the nested hierarchy of leaves, a branching process.

  220. 220
    Joe says:

    Bob is out hunting with a top-notch mainstream geologist. They are deep into the New England woods and the geologist points out different rock formations to pass the time. As they were heading to an unknown area they come across a 3 foot high wall-type structure of stones, millions of stones stretching North to South. The wall top is flat and secure enough to walk on. The sides of the wall are also relatively flat with an occasional protrusion. 1/2 mile North of that position they find another wall exactly perpendicular to the first wall, heading west. It is roughly the same height and also has a flat top and flat sides.

    Bob says it must have been early pioneers clearing the land and making walls with what they plowed and dug up. The geologist laughed and said there aren’t any houses around, no tools and no human remains. These are just rocks and mother nature produces those in abundance. We know this are was visited by glaciers in the past and this is nothing but a glacial deposit.

    Who has the better hypothesis?

  221. 221
    Joe says:

    LoL! @ Zachriel- The leaves are part of the nested hierarchy of the tree.

  222. 222
    keith s says:

    lifepsy,

    So I ask again, in reference to your own argument, how is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes where the ONH signal has become masked beyond recognition?

    Please stop telling me what my argument is.

    I keep reminding you that we are talking about actual biological evolution of the kind we observe on earth. We are not talking about some hypothetical form of evolution on the planet Zargon in some alternate universe, nor are we talking about some abstract idea of unguided evolution.

    We are talking about actual biological evolution on the planet earth. We know, from actual observations, that mutation rates are low and that inheritance is primarily vertical, particularly in multicellular life forms. We know, from actual observations in real time, that evolution produces objective nested hierarchies. See the Theobald quote in this comment.

    These are not assumptions; they are observations.

    Please rein in your imagination and deal with my actual argument, which is that unguided evolution of the kind I have specified is trillions of times better than ID at explaining the existence of the ONH.

  223. 223
    Vishnu says:

    Zachriel: Vishnu (quoting): But only God can make a tree.

    Precisely. A simple principle explains the nested hierarchy of leaves, a branching process.

    A principle may be simple. But its implementation quite another matter. In my example, an extremely sophisticated, loaded-with-functional-information, goal-oriented process was involved. The trees are programmed (if you will) to evolve within certain constrains to an outcome that is highly predictable at the more macro levels, with “niche filling” details randomly determined.

  224. 224
    keith s says:

    Barry,

    Yes, he has ignored refutations of his bomb, hand waved them away and carried on as if nothing happened. And if he does it again commenters here will be free to point out the flaws in his arguments. Or not. I tend to ignore him.

    It’s safer than trying to refute me.

    But come on, Barry, you’re the President of UD. It says so at the bottom of this very page.

    Shouldn’t the President of UD be able to handle a challenge from a feckless, bombless evolutionist?

    The questions are here. The challenge is:

    Share your answers with us. Did your answers to the four questions differ? If so, please explain exactly why.

    And ponder this: If you are an ID supporter, then you are making exactly the same mistake as Bob does in the four examples above, using the same broken logic. Isn’t that a little embarrassing? It might be time to rethink your position.

  225. 225
    Box says:

    Keith #212: Not at all. I am not assuming that the designer is omnipotent, or indifferent, or random.

    Yes you are.

    Keith #212: I am doing exactly the opposite by assuming none of these things, nor their opposites.

    Yes you do.
    Only an omnipotent and indifferent designer would warrant your idea that all trillions of logical possibilities of the ordering of life are equally probable to happen if they are created.

    Keith #212: If I have no basis for making particular assumptions about the designer, then I have no basis for favoring (or disfavoring) the ONH outcome versus the other outcomes.

    Indeed! You have no basis for your assumptions. Do you get it now? You are not allowed to make baseless assumptions about the designer(s). Therfore you have no argument.

    Keith #212: In other words, I must grant equal probabilities to all of the possible outcomes, because I have no reason to favor some over others.

    No you must not, because you have no grounding for assuming that all probabilities are available to the designer. Sorry, but we have no way of knowing. Nor can we ascertain the reasons of the designer.

    The question by Zachriel #199, …

    Why would the designer choose a nested hierarchy arrangement rather than some other arrangement?

    … is simply the wrong one. Such a question, assumes that the designer(s) can choose from several options – which we do not know. And on top of that it assumes that we can penetrate the mind of the designer in order to ascertain her/his/their/its reasons. This is clearly absurd.

    Keith #212: By that reasoning, we also cannot assume that the designer has (or had) the capabilities required to produce the pattern of life that we see. Therefore, the ID hypothesis is untenable.

    Not at all. We do not assume anything. This is not how ID works. If we were to observe patterns in life – or the ordering of life – that are best explained by design then we infer design. We do not assume design.

  226. 226
    lifepsy says:

    Zachriel, mostly non-responsive to my arguments. Noted.

    Arranging by size doesn’t result in a nested hierarchy.

    Yep. That was the point. Neither does arranging by organic traits that have undergone heavy losses or reversals.

    Humans would be nested with organisms with mammary glands which would be nested with organisms with vertebrae which would be nested with organisms with crania, which would be nested with organisms with eukaryotic cell structure. This is a non-trivial correlation of traits that is explained by branching descent.

    Why are you describing the traits of humans? Irrelevant to the argument. It’s as if you believe the natural selection fairies were destined to maintain the crania for all time once it had manifested. This is Darwinian mysticism.

    Indeed, we don’t expect an orderly fossil record. However, each fossil fits the nested ordering.

    No they don’t. For example, advanced tetrapod trackways appear “tens of millions of years” before the fish-a-pod body types they are supposed to nest in.

    Which brings us back to the point. Nested branching does not predict a corresponding fossil record.

    Nested branching also predicts and accommodates a non-corresponding fossil record.

  227. 227
    Zachriel says:

    Vishnu: In my example, an extremely sophisticated, loaded-with-functional-information, goal-oriented process was involved.

    The branching process is algorithmically simple. With evolutionary history, as with the tree, the specifics of the branching process can be complex and convoluted.

    For instance, the human male y-chromosome forms a nested hierarchy. From that, we can infer branching descent. The specifics of human reproduction and child-rearing are highly complex, but the inference to the branching process is the same as it is for evolutionary branching.

    Vishnu: The trees are programmed (if you will) to evolve within certain constrains to an outcome that is highly predictable at the more macro levels, with “niche filling” details randomly determined.

    In this case, the leaves bend towards the light. (It’s interesting to note, that organisms tends to bend towards unoccupied niches.) However, Theobald’s results don’t distinguish between that and other mechanisms that may direct the shape of the tree.

  228. 228
    StephenB says:

    KeithS

    The question is simple: If the first three hypotheses are ridiculous, then why isn’t the fourth one ridiculous? It uses the same bad logic, after all.

    The first three examples do not reflect ID’s argument. You are simply beating your own strawman to death. No more needs to be said about it. However, if you would like to discuss it further, I will be happy to take up each strawman one at a time.

  229. 229
    Joe says:

    keith s:

    We know, from actual observations in real time, that evolution produces objective nested hierarchies.

    That is incorrect and borders on dishonesty.

  230. 230
    kairosfocus says:

    KS, predictably, you are in no concessions denial mode per the pomo community disorganiser modus operandi. Onlookers will see for themselves why the case of what a significant design thinker said on record but was strawman caricatured for 150 years is highly relevant. As to you didn’t respond, I did so, point by point through the argument, showing it to be successive repeats of the same basic misrepresentations of design thought. Your Bob is a cartoon, not any informed and responsible design thinker. You come across as either willfully and culpably ignorant of the ID design filter or else as willfully misrepresenting it. Game over. KF

  231. 231
    Zachriel says:

    Box: Only an omnipotent and indifferent designer would warrant your idea that all trillions of logical possibilities of the ordering of life are equally probable to happen if they are created.

    Even the artifacts of humans with somewhat limited capabilities don’t form nested hierarchies. Because they are intelligent, they borrow rampantly across lines.

    Box: Such a question, assumes that the designer(s) can choose from several options – which we do not know.

    That’s fine. That leaves us with a proposition with no entailments, so it is scientifically vacuous.

    lifepsy: Neither does arranging by organic traits that have undergone heavy losses or reversals.

    Notably, you have ignored our comments. As we pointed out above, the nested hierarchy is not expected to be perfect for any of a number of reasons, including hybridization, reversals, loss of function, and convergence.

    lifepsy: Why are you describing the traits of humans?

    They’re an example that you might be familiar with. Note the nesting pattern.

    lifepsy: It’s as if you believe the natural selection fairies were destined to maintain the crania for all time once it had manifested.

    And yet, there we are, with this highly non-trivial correlation!

    In any case, the nested hierarchy isn’t dependent on single traits, but the sum of traits. See Darwin 1859 for details.

    lifepsy: advanced tetrapod trackways appear “tens of millions of years” before the fish-a-pod body types they are supposed to nest in.

    A fossil doesn’t typically represent the first instance of an organism. In any case, that doesn’t challenge Theobald.

  232. 232
    keith s says:

    Does anyone else want to step in and try to explain this to Box? It’s getting tiring.

    Box,

    For ID to have a chance, you have to assume a nonzero probability that the designer would produce an ONH. If the probability were zero, then design would be ruled out.

    Once you assume a nonzero probability, as you must, then the question arises: what value do you assign?

    Since you wish to minimize the assumptions you are making about the designer, you cannot assume that the designer is more likely to design with an ONH motif versus the other possibilities. You also cannot assume that the designer is less likely to design with an ONH motif versus the other possibilities.

    That means you must assign equal probabilities to the ONH and the trillions of other possible outcomes.

    Once you do that, my argument kicks in, and ID is rejected because it is trillions of times worse at explaining the ONH versus unguided evolution.

    Think about it for a while, rather than dashing off another ill-considered reply.

  233. 233
    Joe says:

    Zachriel:

    For instance, the human male y-chromosome forms a nested hierarchy.

    Based on what criteria? Please be specific or retract your claim.

  234. 234
    Vishnu says:

    Zechrial: The branching process is algorithmically simple.

    A computer adding 1 + 1 to get 2 is algorithmically simple.

    Designing an computer program to produce a two dimensional tree-like structure on the display is not very challenging for a decent programmer.

    The rules by which living trees actually produce their trunks, branches, limbs and leaves are not difficult for intelligent humans to discern and simulate using computers.

    However, all of these cases are examples of the operation of sophisticated, extremely information rich, forwarding looking (that is to say, goal oriented), processes and systems.

    Was the ONH generated by such a system?

  235. 235
    Joe says:

    Does keith s realize that we do not see an objective nested hierarchy with prokaryotes?

  236. 236
    keith s says:

    kairosfocus,

    The challenge was to answer my questions and justify your answers, if they differed.

    You didn’t even answer my questions.

    Now step aside and allow some braver IDers to take the challenge, if any are willing.

    Bydand!

  237. 237
    Joe says:

    keith s, your challenge, like your arguments, is bogus and misleading.

    Bob is out hunting with a top-notch mainstream geologist. They are deep into the New England woods and the geologist points out different rock formations to pass the time. As they were heading to an unknown area they come across a 3 foot high wall-type structure of stones, millions of stones stretching North to South. The wall top is flat and secure enough to walk on. The sides of the wall are also relatively flat with an occasional protrusion. 1/2 mile North of that position they find another wall exactly perpendicular to the first wall, heading west. It is roughly the same height and also has a flat top and flat sides.

    Bob says it must have been early pioneers clearing the land and making walls with what they plowed and dug up. The geologist laughed and said there aren’t any houses around, no tools and no human remains. These are just rocks and mother nature produces those in abundance. We know this are was visited by glaciers in the past and this is nothing but a glacial deposit.

    Who has the better hypothesis?

  238. 238
    keith s says:

    Joe:

    Does keith s realize that we do not see an objective nested hierarchy with prokaryotes?

    Yes, because of horizontal gene transfer.

    Does Joe realize that my argument does not depend on the presence of an ONH among the prokaryotes? It depends only on the objective nested hierarchy among the 30 major taxa, illustrated in Theobald’s Figure 1.

    P.S. Joe, you’re doing well! It must be really hard for you to lay off the invective. Good job. Keep it up.

  239. 239
    Mapou says:

    keith @232,

    You keep missing the obvious flaw in your equal probabilities argument. There is no problem of assuming that there could have been many different types of design and designers. Who cares? The design hypothesis does not have that assumption. The ID hypothesis is that there was only one type of designer, intelligent ones. We can test this hypothesis because we know how intelligent entities (humans) design things. Objects intelligently designed over a long period of time invariably follow an ONH pattern. This is not an assumption. It is a fact. ONH is such an inescapable consequence of intelligent design that modern software design tools enforce a hierarchical organization in software design. The whole idea behind hierarchical design is that previous designs should be reused as much as possible. It’s very simple, really.

  240. 240
    Zachriel says:

    Vishnu: Was the ONH generated by such a system?

    That’s not part of Theobald’s study, which only concerns whether such a branching process occurred. Do you agree that such a process did occur? If not, why not?

  241. 241
    keith s says:

    Joe @237:

    Who has the better hypothesis?

    Bob, of course. What’s your point?

  242. 242
    Vishnu says:

    Zachriel: That’s not part of Theobald’s study, which only concerns whether such a branching process occurred. Do you agree that such a process did occur? If not, why not?

    I am persuaded that it probably did. What about you?

    So, again, was the ONH generated by such a system as I described?

  243. 243
    Box says:

    Keith #232: For ID to have a chance, you have to assume a nonzero probability that the designer would produce an ONH. If the probability were zero, then design would be ruled out.

    Once you assume a nonzero probability, as you must, then the question arises: what value do you assign?

    What do want Keith?

    The answer to the question “How many options are available for the designer to order life?” is “at least one”, after ID infers design as best explanation for the ordering of life.

    What ID does not address is religious questions like “Why would the designer choose a nested hierarchy arrangement rather than some other arrangement?” or questions regarding ‘omnipotence’ or ‘indifference’. That is religion Keith. There is no scientific way of knowing these things.

    Got it?

  244. 244
    lifepsy says:

    Keith S 222

    Please stop telling me what my argument is.

    I’m not. It’s on the first post of this thread.

    We are talking about actual biological evolution on the planet earth.

    We are talking about the potential outcomes biological evolution predicts. That is the whole crux of your “coin/dice” analogy in Post #1.

    If biological unguided evolution can accommodate opposing outcomes (which it can), then you can not logically use only one of those outcomes as direct evidence.

    And the simple fact is that unguided evolution as it is believed today on planet Earth also predicts a scenario where the signal of the objective nested hierarchy has been lost.

    I’m sorry if you don’t get that.

    We know, from actual observations, that mutation rates are low

    This isn’t much of a constraint since population levels, selection pressures, and specific durations associated with past evolutionary events are hypothetical and extremely plastic to whatever the evolutionist needs to harmonize Evolution theory.

    The populations of common ancestors of major taxa themselves are essentially imaginary. They have been conjured into being by storytellers.

    and that inheritance is primarily vertical, particularly in multicellular life forms.

    So what? If vertical inheritance is coupled with a pattern of extensive loss and reversals of traits than it will not necessarily produce a recognizable signal of the objective nested hierarchy.

    Maybe, like Zachriel, you’d like to appeal to the natural selection fairies which have a friendly predisposition to maintain inherited traits so that there will be a nice orderly typological nested hierarchy for scientists to study after they’ve evolved.

  245. 245
    Zachriel says:

    Vishnu: I am persuaded that it probably did.

    We’re in agreement, then.

    Vishnu: was the ONH generated by such a system as I described?

    It’s generated by the branching process.

    Vishnu: However, all of these cases are examples of the operation of sophisticated, extremely information rich, forwarding looking (that is to say, goal oriented), processes and systems.

    You haven’t provided any evidence of a “forward-looking” process, but that’s beyond the scope of the thread, which concerns branching descent. By the way, the branching process helps give us the historical context to understand the mechanisms of change.

    lifepsy: And the simple fact is that unguided evolution as it is believed today on planet Earth also predicts a scenario where the signal of the objective nested hierarchy has been lost.

    That’s clearly not the case. The nested hierarchy has been fundamental to the theory of evolution since Darwin.

  246. 246
    lifepsy says:

    Zachriel

    As we pointed out above, the nested hierarchy is not expected to be perfect for any of a number of reasons, including hybridization, reversals, loss of function, and convergence.

    I see, so you just want to assign some arbitrary magical limit on how distorted the signal could potentially become.

    If the factors you just listed were extensive enough, (and there is no rule of evolution which says they can’t be) it could potentially obliterate any substantial signal of a nested hierarchy.

    lifepsy: Why are you describing the traits of humans?

    They’re an example that you might be familiar with. Note the nesting pattern.

    lifepsy: It’s as if you believe the natural selection fairies were destined to maintain the crania for all time once it had manifested.

    And yet, there we are, with this highly non-trivial correlation!

    ok… Were we debating whether or not humans exist and fall into a nested hierarchy?

    It appears that, like Keith S, you are simply unwilling to examine what other data your theory can potentially accommodate, but simultaneously you want to claim the current data as a specific prediction of your theory.

    Both you and Keith S are committing a major fallacy of logic.

  247. 247
    Vishnu says:

    Zechriel,

    Regarding the ONH, it would probably be more fair to say that I am comfortable with the overall layout. I do not think it is evidence of a blind watchmaker sort of evolution.

    And I rather like what gpuccio said, “About the nested hierarchy, my view is very simple. It is a very good argument for common descent, although not necessarily the best.”

    Vishnu: was the ONH generated by such a system as I described?

    Zachriel: It’s generated by the branching process.

    What is the nature of the branching process? Does it feature the sort of information and processes I mentioned? Is it “forward looking”, that is, it is goal oriented?

    Zachriel: You haven’t provided any evidence of a “forward-looking” process, but that’s beyond the scope of the thread, which concerns branching descent.

    I don’t mind straying off the Reservation, if you don’t.

    So then, you don’t think a tree genome can be said to have a forward looking process? Perhaps that sort of language is a bit too harsh for your sensibilities. I don’t intend to say that a tree genome is consciously thinking about what it’s producing. Neither do the genetic algorithms that I create consciously think about that they are doing.

    So then, what about a goal (as in “goal posts”) oriented process? Is it not fair to say that the programmed information and systems of a tree genome is to produce a tree with certain properties within certain limits taking advantage of certain stocastic variables? Do you think “goal” is too strong a word here? If so, why?

  248. 248
    Zachriel says:

    Vishnu: I see, so you just want to assign some arbitrary magical limit on how distorted the signal could potentially become.

    Only if you consider statistics to be magic.

  249. 249
    Zachriel says:

    Oops. That should have been attributed to lifespy.

  250. 250
    Box says:

    Box: Such a question, assumes that the designer(s) can choose from several options – which we do not know.

    Zachriel #231: That’s fine. That leaves us with a proposition with no entailments, so it is scientifically vacuous.

    So, if the creator of a mousetrap had only one design option available, than a ID-proposition has no entailments and is scientifically vacuous.? Can you elucidate your reasoning?

  251. 251
    Vishnu says:

    Zachriel,

    Also, what is the fundamental difference between the information and processes we call a tree genome, and a genetic algorithm that I create towards a certain goal?

  252. 252
    Vishnu says:

    Zachriel @ 248

    I think you intended that for someone else.

  253. 253
    Zachriel says:

    Vishnu: <II don’t mind straying off the Reservation, if you don’t.

    We prefer to stay on topic.

    If you accept branching descent, it strongly constrains any possible history. The common ancestry of simians and sunflowers is a very profound finding concerning nature, a finding that puts you at odds with much of the ID community.

    Box: if the creator of a mousetrap had only one design option available

    But a knowledgeable designer creating each organism independently isn’t so constrained, but can mix and match features across lineages. That’s why human artifacts don’t form a nested hierarchy. You would be supposing a designer more limited than humans, and constrained in ad hoc ways.

  254. 254
    Box says:

    Zachriel #253: But a knowledgeable designer creating each organism independently isn’t so constrained, but can mix and match features across lineages.

    These are all fascinating religious ideas. But none of that is of interest to ID. Very sorry to disappoint you, but ID is strictly about science and does not speculate on the identity, capabilities and options available to a designer.

  255. 255
    Vishnu says:

    Zachriel: If you accept branching descent, it strongly constrains any possible history.

    Likewise for the nested hierarchies existing as trees out in my backyard. I have no problem with that.

    The common ancestry of simians and sunflowers is a very profound finding concerning nature,

    Assuming it’s reality, I don’t accept that blind watch maker evolution is soley responsible for ONH. It’s a minor player. So I’m unsure of the relevance of your consequent…

    …a finding that puts you at odds with much of the ID community.

    To the degree that it’s true, it’s not a concern of mine.

  256. 256
    keith s says:

    Box,

    What do want Keith?

    I’d like a reasoned counterargument, and if you can’t provide one, I’d like you to acknowledge that my argument stands unrefuted.

    The answer to the question “How many options are available for the designer to order life?” is “at least one”, after ID infers design as best explanation for the ordering of life.

    So then we ask, “We know at least one is available, if ID is correct. Which of the options are available, and which aren’t?” The answer is “We can’t rule any of them out on the design hypothesis”. That leaves us with trillions of options that the designer might have been able to choose from.

    Then we look at unguided evolution of the kind we have been discussing (Hi, lifepsy!). It actually predicts an ONH and rules out the trillions of alternatives.

    So we have an ID hypothesis that can’t eliminate any of the trillions of options, against an unguided evolution hypothesis that actually predicts an ONH over everything else.

    Unguided evolution is therefore trillions of times better, because it makes a correct prediction that is trillions of times more specific than ID’s “prediction” (which is useless since it doesn’t rule anything out).

    If you “follow the evidence where it leads”, you cannot honestly continue to believe in ID.

  257. 257
    Vishnu says:

    Zachriel: That’s why human artifacts don’t form a nested hierarchy.

    Some of them do. Airplanes, trains, automobiles, computers, musical instruments, textiles, clothing styles, architecture, just to name a few. Their common root source is “humanity”, and each group can be looked at as a branch from that root, with many subgroups, all forming a nested hierarchy.

    We don’t know the extent of the putative designer’s options and capabilities. For all we know there could radically different biological trees on a trillion planets out in the universe. But again, as Box said, fascinating religious ideas, but not science.

    ID (as I understand it) is about inferring to the best explanation, not discovering the options, capabilities and motives of the designer.

  258. 258
    Zachriel says:

    Box: But none of that is of interest to ID. Very sorry to disappoint you, but ID is strictly about science and does not speculate on the identity, capabilities and options available to a designer.

    If something is designed, there is a causal connection from the artifact to the art to the artist. In any case, the evidence strongly supports branching descent.

    Zachriel: If you accept branching descent, it strongly constrains any possible history.

    Vishnu: Likewise for the nested hierarchies existing as trees out in my backyard. I have no problem with that.

    That constraint eliminates many creationist claims.

    Vishnu: Assuming it’s reality

    It’s what the evidence supports. While Theobald’s results don’t address whether the branching process is guided or not, that all life shares common ancestry is certainly an important finding to biology.

  259. 259
    keith s says:

    lifepsy,

    And the simple fact is that unguided evolution as it is believed today on planet Earth also predicts a scenario where the signal of the objective nested hierarchy has been lost.

    No, it doesn’t.

    The signal is only lost under specific conditions, and those conditions are usually not met.

    That is why Theobald can list his examples of evolutionary processes that are observed in real time and from which accurate ONHs can be inferred.

    I understand that you hate the evidence, because it undermines ID, but the truth is the truth, lifepsy. You can’t rationally ignore it.

    ID is a hypothesis, and it failed.

  260. 260
    Vishnu says:

    Vishnu: Likewise for the nested hierarchies existing as trees out in my backyard. I have no problem with that.

    Zachriel: That constraint eliminates many creationist claims.

    I agree. Which ones do you have in mind?

    Vishnu: Assuming it’s reality [simians and sunflowers having a common “ancestor”]

    Zachriel: It’s what the evidence supports.

    To a certain extent, I agree. But not to the degree I suspect you have in mind.

    Would you say that a genetically modified (by humans) soy plant has the same “ancestry” as its non-GMO progenitor? Largely, it does. But in some sense it does not. To the extent that an artificial intervention with respect to the genome’s information set has been monkeyed with, it does not have the same ancestry in the normal sense of that word.

    While simians and sunflowers may share a common progenitor, the source of the divergences is largely unknown, which makes “ancestor” a bit misleading, IMO. I can deal with it, but I think it shows a bias which is based on an assumption not in evidence.

    While Theobald’s results don’t address whether the branching process is guided or not, that all life shares common ancestry is certainly an important finding to biology.

    I have no problem with that. Except for the term “ancestry.”

  261. 261
    keith s says:

    Vishnu:

    The rules by which living trees actually produce their trunks, branches, limbs and leaves are not difficult for intelligent humans to discern and simulate using computers.

    However, all of these cases are examples of the operation of sophisticated, extremely information rich, forwarding looking (that is to say, goal oriented), processes and systems.

    Was the ONH generated by such a system?

    Vishnu,

    You are committing the classic Gil Dodgen error (link, link) of confusing the simulation with the thing being simulated.

    It’s much more embarrassing in your case, however, because you’ve told us that you have a computer science PhD.

  262. 262
    Vishnu says:

    keiths @ 261

    Let me ask you this:

    What was the point of my post?

  263. 263
    keith s says:

    Hi, StephenB.

    I was wondering when you would join the fray.

    Please take my challenge so that we can discuss your answers.

    I also invite Eric Anderson and Upright Biped to take the challenge. I’ve noticed that they’re steering clear of discussions of my argument.

  264. 264
    keith s says:

    Vishnu:

    Let me ask you this:

    What was the point of my post?

    That’s what I’d like to know.

  265. 265
    Box says:

    Keith,

    Box: The answer to the question “How many options are available for the designer to order life?” is “at least one”, after ID infers design as best explanation for the ordering of life.

    Keith #259: So then we ask, “We know at least one is available, if ID is correct. Which of the options are available, and which aren’t?” The answer is “We can’t rule any of them out on the design hypothesis”. That leaves us with trillions of options that the designer might have been able to choose from.

    Well, ‘the designer might have been able to choose’ and that is just great Keith, but we do not know, do we? We can only speculate on religious stuff like that. We have no scientific way of knowing how many options are available to a designer.

    We have been through this already several times. Maybe the designer is powerful enough to produce trillion of orderings of life. Maybe the designer is left with just one option. Maybe the designer has compelling reasons to choose for one very specific ordering of life. Maybe the designer is completely indifferent about the ordering of life.

    We have no way of knowing!

    Again, you raise some fascinating religious questions, but none of that is of interest of ID. ID is interested in formulating useful questions for scientific research, not in the unsubstantiated metaphysical assumptions that you offer.

  266. 266
    Vishnu says:

    Keiths,

    So you don’t know what my point is, and yet come to the conclusion that I’ve committed some alleged error of Gil Dodgen’s. Okie dokie.

    Care to explain how I’ve “committed” some error, especially since you admit you don’t know what my point is?

  267. 267
    StephenB says:

    KeithS

    Apparently, you missed my comment @228. Your first three examples do not reflect the ID argument and are riddled with bad logic.

    For now, just take the first scenario:

    [a] You do not even describe the arrangement of parts that prompts Bob to make a design inference. Do they form a word? Are they structured? What pattern did Bob observe?

    [b] You do not say whether it is the pebbles, particles, grains of sand, or rocks that are supposed to form the pattern. On the contrary, you try to agglomerate all of them into a unified whole, which makes no sense.

    Your argument, therefore, bears no resemblance to the process of drawing an inference to design. Do you understand your errors? If not, why do you not think they are errors?

  268. 268

    keith said:

    Since you wish to minimize the assumptions you are making about the designer, you cannot assume that the designer is more likely to design with an ONH motif versus the other possibilities. You also cannot assume that the designer is less likely to design with an ONH motif versus the other possibilities.

    Having been called out on his additional designer-side assumptions, Keith is now attempting to salvage his argument using even more flawed logic.

    Here, keith attempts to hide is extra design-side assumption while framing it as if he was choosing the fewest assumptions.

    The only assumption necessary in the example is that the designer can make a diversity of life landscape in the form of an ONH. Everything beyond that is an additional assumption about the designer, which keith states we know absolutely nothing about.

    If keith asserts that are additional alternatives available to the designer, that is an unnecessary assumption. If someone else says there are no other alternatives available, that is an additional assumption.

  269. 269
    keith s says:

    Vishnu,

    I know what your error is; I just don’t know what your point is.

    Your error is in failing to distinguish between a simulation and the thing being simulated:

    Designing an computer program to produce a two dimensional tree-like structure on the display is not very challenging for a decent programmer.

    The rules by which living trees actually produce their trunks, branches, limbs and leaves are not difficult for intelligent humans to discern and simulate using computers.

    However, all of these cases are examples of the operation of sophisticated, extremely information rich, forwarding looking (that is to say, goal oriented), processes and systems.

    The programs may be “sophisticated” and “information rich”, but that doesn’t mean that the processes being simulated are.

  270. 270
    Vishnu says:

    Box: We have been through this already several times. Maybe the designer is powerful enough to produce trillion of orderings of life. Maybe the designer is left with just one option. Maybe the designer has compelling reasons to choose for one very specific ordering of life. Maybe the designer is completely indifferent about the ordering of life.

    Keiths’s argument assumes A) the production of the tree of life as we know it from unguided evolution is an actual possibility, B) that the designer had “trillions” of options.

    Why does he assume either? There is no evidence for either.

    WJM and Box have cogently dealt with this over and over. This is what WJM’s new thread is pointing straight at, and it seems (so far) that keiths is reticent to engage it head on. I hope he does.

    Keiths, please come on over to the WJM’s new thread and address the core issue head on. Thank you.

  271. 271
    keith s says:

    Box,

    I continue to be amazed that you don’t grasp this.

    You wrote:

    Well, ‘the designer might have been able to choose’ and that is just great Keith, but we do not know, do we? We can only speculate on religious stuff like that. We have no scientific way of knowing how many options are available to a designer.

    We have been through this already several times. Maybe the designer is powerful enough to produce trillion of orderings of life. Maybe the designer is left with just one option. Maybe the designer has compelling reasons to choose for one very specific ordering of life. Maybe the designer is completely indifferent about the ordering of life.

    We have no way of knowing!

    Let’s make a few simple changes to your comment:

    Well, ‘the Rain Fairy might have been able to choose’ and that is just great Keith, but we do not know, do we? We can only speculate on Fairy stuff like that. We have no scientific way of knowing how many options are available to a Rain Fairy.

    We have been through this already several times. Maybe the Rain Fairy is powerful enough to produce trillions of distinct weather patterns. Maybe the Rain Fairy is left with just one option. Maybe the Rain Fairy has compelling reasons to choose one specific weather pattern. Maybe the Rain Fairy is completely indifferent about the weather patterns.

    We have no way of knowing!

    Should we accept the Rain Fairy hypothesis, Box?

    Your argument looks pretty ridiculous when expressed in those terms, doesn’t it? But it’s the same bad logic that you used to support ID.

    Your objection doesn’t fly. Unguided evolution is the superior explanation, just as unguided meteorology is.

  272. 272
    Vishnu says:

    keiths: I know what your error is; I just don’t know what your point is…

    I’ll go ahead and spell out for you what my point is: some nested hierarchies found in nature, such as trees, are generated by sophisticated, information rich processes.

    Your error is in failing to distinguish between a simulation and the thing being simulated… The programs may be “sophisticated” and “information rich”, but that doesn’t mean that the processes being simulated are.

    I don’t fail to see that and I didn’t assert otherwise. Therefore, I’m not committing any error.

    So then are you implying that the genomic and cellular processes that generate a Magnolia tree and it’s nested hierarchy are not goal-oriented, information rich processes?

  273. 273
    Box says:

    Keith #271,

    You are no longer making any sense at all.

  274. 274
    Vishnu says:

    Pardon the bad formatting.

  275. 275
    keith s says:

    StephenB,

    For now, just take the first scenario:

    [a] You do not even describe the arrangement of parts that prompts Bob to make a design inference. Do they form a word? Are they structured? What pattern did Bob observe?

    [b] You do not say whether it is the pebbles, particles, grains of sand, or rocks that are supposed to form the pattern. On the contrary, you try to agglomerate all of them into a unified whole, which makes no sense.

    You’re making this harder than it needs to be. The streambed looks like any other dry streambed in the desert. There is nothing about it that makes it look designed.

    However, it might be designed. Someone with the requisite desire and capability could have arranged the rocks, pebbles, grains of sand and silt particles in such a way as to mimic the action of water.

    The same goes for the other three examples:

    2. It looks like there was an explosion, but someone might have carefully designed and planted the evidence to make it look that way.

    3. It looks like gravity is affecting the planetary orbits, but the angels might be pushing the planets in a way that makes it appear that gravity is operating.

    4. The objective nested hierarchy is exactly what we would expect if unguided evolution were operating, but maybe God the Designer chose, or was limited, or just happened to produce an objective nested hierarchy out of the trillions of possibilities.

    Now, please answer the four questions. If your answers differ, then explain exactly why.

  276. 276
    keith s says:

    Box:

    You are no longer making any sense at all.

    I think the problem is that I am making too much sense, and you don’t have a counterargument.

    That’s okay, Box. Think about it for a while, and if you can’t come up with a refutation, do the honest thing and admit it.

  277. 277
    Vishnu says:

    Box, notice what keiths does. He takes a matter which is speculative (the capabilities of a putative designer- a designer inferred to exist for sound evidential reasons) and turns it into a ridiculous caricature, as if the inferred designer and the Rain Fairy are on equal footing with regards to being live issues.matter.

    We have sound evidential reasons to infer intelligent input in the creation and diversity of life on earth.

    We have no good reason to infer Rain Fairies.

  278. 278
    keith s says:

    Vishnu,

    The challenge is open to everyone, including you.

    Answer my four questions, and if your answers differ, explain exactly why.

    If you think the ID hypothesis is superior to the Rain Fairy hypothesis, tell us exactly what the relevant differences are and why the logic isn’t the same in the two scenarios.

    If you can, that is.

  279. 279
    Vishnu says:

    Keiths, please come on over to the WJM’s new thread and address the core issue head on. Thank you.

  280. 280
    keith s says:

    Vishnu,

    Stop trying to change the subject. I will address William’s OP later.

    Right now we are discussing my challenge. Take the challenge, if you dare.

  281. 281
    Vishnu says:

    keiths: Answer my four questions, and if your answers differ, explain exactly why.

    They’ve been cogently answered over and over again. If you don’t get it by now, I’m not going to be the one who does it.

    If you think the ID hypothesis is superior to the Rain Fairy hypothesis, tell us exactly what the relevant differences are and why the logic isn’t the same in the two scenarios.

    Because there is sound evidential reasons for inferring that the creation and diversity of life on earth required intelligent input in the first place. It’s a live issue. There is absolutely no sound evidential reasons to infer a Rain Fairy. It’s not a live issue (to my knowledge.) Therefore there’s no reason to speculate on the nature and capabilities of the Rain Fairy.

  282. 282
    Zachriel says:

    Vishnu: Some of them do. Airplanes, trains, automobiles, computers, musical instruments, textiles, clothing styles, architecture, just to name a few.

    While anything can be arranged in a nested hierarchy, none of those form an objective nested hierarchy. There are multiple, equally rational ways to classify them. Try it with automobiles.

    Vishnu: ID (as I understand it) is about inferring to the best explanation, not discovering the options, capabilities and motives of the designer.

    Ignoring the obvious entailment isn’t scientifically constructive.

    Vishnu: Which ones do you have in mind?

    Any that don’t include common ancestry.

    Vishnu: Would you say that a genetically modified (by humans) soy plant has the same “ancestry” as its non-GMO progenitor?

    If the genes are natural, then they share a common ancestry, but it’s not branched descent.

    Vishnu: While simians and sunflowers may share a common progenitor, the source of the divergences is largely unknown, which makes “ancestor” a bit misleading, IMO.

    They branched from a common ancestor.

    Vishnu: I can deal with it, but I think it shows a bias which is based on an assumption not in evidence.

    It’s exactly what is in evidence. See Theobald 2010.

    Vishnu: I have no problem with that. Except for the term “ancestry.”

    That’s what branching means.

    Box: Well, ‘the designer might have been able to choose’ and that is just great Keith, but we do not know, do we?

    That means the conjecture is ad hoc and of no more scientific utility than saying the designer has an inordinate fondness for beetles the nested hierarchy, or stars elliptical orbits.

  283. 283
    Vishnu says:

    keiths: Right now we are discussing my challenge. Take the challenge, if you dare.

    I don’t dare, because I could add nothing that has not already been stated quite cogently by others.

    I will address William’s OP later.

    Thanks in advance. I’m all a-tingle.

  284. 284
    kairosfocus says:

    Onlookers, remember, this is the level of objections after years of criticising design theory. It is plain that the critics cannot and/or refuse to accurately summarise design thought . . . a familiar pattern. This then leads to strawman caricatures as noted on correctively (and as dismissed or ignored), and it is strongly associated with lab coat clad materialism-loaded question begging. KF

  285. 285
    keith s says:

    Vishnu:

    They’ve been cogently answered over and over again. If you don’t get it by now, I’m not going to be the one who does it.

    It’s okay. You’re not the only IDer who has chickened out of taking my challenge. Everyone but William has refused, so far.

    Because there is sound evidential reasons for inferring that the creation and diversity of life on earth required intelligent input in the first place. It’s a live issue.

    Says you. I’ve provided an argument that shows otherwise. If you disagree, you need to actually rebut my argument instead of merely asserting that design is a live option.

    There is absolutely no sound evidential reasons to infer a Rain Fairy.

    I agree, but the problem is that there are no sound evidential reasons to infer God the Designer, either.

    Unguided evolution explains the ONH trillions of times better than ID. Unguided meteorology explains the weather trillions of times better than the Rain Fairy hypothesis.

    Why not take the challenge? That will give you an opportunity to show, step by step, how ID is relevantly different from the Rain Fairy hypothesis — if you can.

  286. 286
    lifepsy says:

    Keith S 259

    The signal is only lost under specific conditions, and those conditions are usually not met.

    No, there are no special conditions. According to your own theory, it is all up to blind chance and selection pressures on what pace and direction through morphospace character traits will travel, and whether they will amplify a nested hierarchy signal, or progressively mask it.

    You and Zachriel apparently hold some mystical idea about natural selection having predisposition towards and subsequent immutability of specific character trait assemblages, i.e. evolutionary destinies.

    That is why Theobald can list his examples of evolutionary processes that are observed in real time and from which accurate ONHs can be inferred.

    Well duh… those “evolutionary” processes are observed in a relatively instantaneous timespan. Give them half a billion years and the ONH signal could be obliterated.

    I understand that you hate the evidence…

    The premises of all of your arguments have been logically flawed… I can’t say I am concerned about your opinions on “the evidence”.

  287. 287
    keith s says:

    Onlookers, note that KF has again refused to take my challenge.

    It betrays a rather telling lack of confidence in the design hypothesis, doesn’t it?

  288. 288
    Box says:

    Vishnu #277,

    You are right of course. What’s even more ridiculous is that Keith suddenly acts as if I was making a argument for ID – “Should we accept the Rain Fairy hypothesis, Box?”. I did no such thing.
    It should be obvious to anyone that I was simply pointing out that Keith made unsubstatiated assumptions about the designer.

  289. 289
    Vishnu says:

    Vishnu: Some of them do. Airplanes, trains, automobiles, computers, musical instruments, textiles, clothing styles, architecture, just to name a few.

    Zachriel: While anything can be arranged in a nested hierarchy, none of those form an objective nested hierarchy. There are multiple, equally rational ways to classify them. Try it with automobiles.

    The historically sequenced appearance of all the objects named above is a pretty objective and non-arbitrary way of arranging them, wouldn’t you say? If not, why not?

    Vishnu: ID (as I understand it) is about inferring to the best explanation, not discovering the options, capabilities and motives of the designer.

    Zachriel: Ignoring the obvious entailment isn’t scientifically constructive.

    What entailment is being ignored?

    V: Which [creationist ideas] do you have in mind?

    Z: Any that don’t include common ancestry.

    I agree, with the previously explained caveat.

    V: Would you say that a genetically modified (by humans) soy plant has the same “ancestry” as its non-GMO progenitor?

    Z: If the genes are natural, then they share a common ancestry…

    Why are you making an arbitrary distinction between natural genes and artificially created ones?

    …but it’s not branched descent.

    What would you call it?

    V: While simians and sunflowers may share a common progenitor, the source of the divergences is largely unknown, which makes “ancestor” a bit misleading, IMO.

    Z: They branched from a common ancestor.

    Given your definition of “branched descent” that arbitrarily disallows artificial genes being inserted by intelligent entities at a point of branching, how do you know they they branched from a common ancestor?

    V: I can deal with it, but I think it shows a bias which is based on an assumption not in evidence.

    Z: It’s exactly what is in evidence. See Theobald 2010.

    No. Your assumption, I gather, is that no intelligent agency was involved in the branching. That is a “fact” not in evidence, as Theobald himself acknowledges.

    V: I have no problem with that. Except for the term “ancestry.”

    Z: That’s what branching means.

    You arbitrary exclude intelligent intervention in branched descent. A branch is a branch regardless of cause.

  290. 290
    keith s says:

    Box,

    The challenge is open to you, as well.

    If you think the Rain Fairy hypothesis is ridiculous, as the rest of us do, then explain clearly and precisely what the relevant differences are between the Rain Fairy hypothesis and the ID hypothesis.

    I say that they use the same flawed logic. If you disagree, show precisely how they differ.

  291. 291
    Phinehas says:

    keiths:

    You’re making this harder than it needs to be. The streambed looks like any other dry streambed in the desert. There is nothing about it that makes it look designed.

    So what does this have to do with life? Even the most ardent IDCritic will admit that life looks like it was designed.

    So, you argument appears to be: Take something that has absolutely no evidence of having the smallest iota of design involved, has zero real information content, and that would trivially fail the design explanatory filter. Now, is design a better theory for its existence?

    Um, no. What’s your point again?

  292. 292
    keith s says:

    Phinehas,

    Even the most ardent IDCritic will admit that life looks like it was designed.

    Only superficially. If you look carefully at the scientific evidence, ID is a losing proposition, as my argument demonstrates.

    The challenge is open to you, too.

    Are you feeling brave today?

  293. 293
    Vishnu says:

    keiths:…the problem is that there are no sound evidential reasons to infer God the Designer, either.

    Says you.

    I disagree.

    I mention a few:

    1. Origin of Life

    2. Coded information

    3. Protein families

    4. Cambrian Explosion

    5. Fine Tuned Universe

    Just to name a few. Big subjects all. There are sound empirical reasons for inferring design. It’s a live issue amongst some very intelligent people. (I’m not at all interested in the fact that you disagree. I would bet dollars to donuts that your reasoning is just as tortured with respect to those subjects as they have been to the ones submitted here. But whatever.)

    Poor girl, the Rain Fairy has nothing going for her.

    Nothing at all.

    She’s not a live issue.

  294. 294
    Zachriel says:

    lifepsy: No, there are no special conditions. According to your own theory, it is all up to blind chance and selection pressures on what pace and direction through morphospace character traits will travel, and whether they will amplify a nested hierarchy signal, or progressively mask it.

    It’s largely due to the statistics involved, a large number of possible traits, and a slow mutation rate, both of which are observed.

    lifepsy: You and Zachriel apparently hold some mystical idea about natural selection having predisposition towards and subsequent immutability of specific character trait assemblages, i.e. evolutionary destinies.

    Actually, as Darwin pointed out, natural selection often clouds the nested hierarchy. Non-adaptive traits are often better for discerning evolutionary relationships.

    lifepsy: Well duh… those “evolutionary” processes are observed in a relatively instantaneous timespan. Give them half a billion years and the ONH signal could be obliterated.

    The historical rate of change is low compared to the timescales involved.

    Vishnu: The historically sequenced appearance of all the objects named above is a pretty objective and non-arbitrary way of arranging them, wouldn’t you say?

    That creates a linear sequence, not a nested hierarchy. In any case, we’re discussing organizing by traits.

    Vishnu: What entailment is being ignored?

    If there is an artifact, then there is a causal connection between the artifact, art, and artisan.

    Vishnu: Why are you making an arbitrary distinction between natural genes and artificially created ones?

    Artificial genes don’t share common ancestry obviously.

    Vishnu: What would you call it?

    It’s a cross. Branched descent means there is exactly one path from the leaf to the root.

    Vishnu: Given your definition of “branched descent” that arbitrarily disallows artificial genes being inserted by intelligent entities at a point of branching, how do you know they they branched from a common ancestor?

    See Theobald 2010.

    Vishnu: Your assumption, I gather, is that no intelligent agency was involved in the branching.

    That is not our assumption, nor is it an assumption of Theobald.

    Vishnu: You arbitrary exclude intelligent intervention in branched descent. A branch is a branch regardless of cause.

    That is not our assumption, nor is it an assumption of Theobald. The finding is that branched descent is *intrinsic*. This does provide the historical context necessary to understand the mechanisms which shape the tree, but that is not part of Theobald.

    IDers often try to play both sides of this issue, as if common ancestry is of no importance, when, in fact, it is a fundamental finding of biology, and provides the framework for any discussion of life’s history on Earth.

  295. 295
    Phinehas says:

    keiths:

    The challenge is open to you, too.

    Are you feeling brave today?

    I’m feeling sufficiently brave, and quite bored, but not nearly bored enough to address something that breaks down to, “Is design a good explanation for something that gives no evidence whatsoever of having been designed?”

  296. 296
    Vishnu says:

    Vishnu: The historically sequenced appearance of all the objects named above is a pretty objective and non-arbitrary way of arranging them, wouldn’t you say?

    Z: That creates a linear sequence, not a nested hierarchy.

    Automobiles can be classified in a nested hierarchy. It doesn’t run too deep, but it’s there.

    Car -> Make -> Model -> Variations in Model

    In any case, we’re discussing organizing by traits.

    OK

    V: What entailment is being ignored?

    Z: If there is an artifact, then there is a causal connection between the artifact, art, and artisan.

    Yes?

    V: Why are you making an arbitrary distinction between natural genes and artificially created ones?

    Z: Artificial genes don’t share common ancestry obviously.

    OK

    V: What would you call it?

    Z: It’s a cross. Branched descent means there is exactly one path from the leaf to the root.

    So then you consider horizontally gene transfer to be a cross? HGT and intelligent intervention both crosses?

    V: Your assumption, I gather, is that no intelligent agency was involved in the branching.

    Z: That is not our assumption, nor is it an assumption of Theobald.

    OK

    <V: You arbitrary exclude intelligent intervention in branched descent. A branch is a branch regardless of cause.

    Z: That is not our assumption, nor is it an assumption of Theobald. The finding is that branched descent is *intrinsic*. This does provide the historical context necessary to understand the mechanisms which shape the tree, but that is not part of Theobald.

    Do you think the mechanisms rule out intelligent intervention? Right, off topic.

  297. 297
    Box says:

    Andre #179, #180.

    Thank you very much for providing the information on apoptosis (pcd). Especially due to its presence in unicellular organisms makes it yet another inexplicable problem for our adversaries!

  298. 298
    StephenB says:

    KeithS

    The streambed looks like any other dry streambed in the desert. There is nothing about it that makes it look designed.

    If there is no empirical evidence to suggest that anything was designed, then there is no reason for Bob to say “that every rock, pebble, grain of sand and silt particle was deliberately placed in its exact position by a Streambed Designer.” He is not making an ID argument. Your objection is a strawman.

    However, it might be designed. Someone with the requisite desire and capability could have arranged the rocks, pebbles, grains of sand and silt particles in such a way as to mimic the action of water.

    So what? There is no evidence for or against design, so there is no reason for Bob to make a design inference. Again, this is a strawman argument.

    2. It looks like there was an explosion, but someone might have carefully designed and planted the evidence to make it look that way.

    There is evidence for an explosion and against the proposition that nature created the observed effects. Thus, the most reasonable inference is that an explosion occurred (by design). Even if someone planted the fake evidence, the observed effects cannot be reasonably attributed nature’s operation. Are you sure you understand the design inference? It appears that you do not.

    3. It looks like gravity is affecting the planetary orbits, but the angels might be pushing the planets in a way that makes it appear that gravity is operating.

    What does any of this have to do with the methods of drawing an inference to design from empirical evidence?

    4. The objective nested hierarchy is exactly what we would expect if unguided evolution were operating, but maybe God the Designer chose, or was limited, or just happened to produce an objective nested hierarchy out of the trillions of possibilities.

    Your argument is self contradictory. If the objective nested hierarchy exists because God guided nature to that end, then it cannot also have been caused by an unguided process.

  299. 299
    lifepsy says:

    Zachriel

    Lifepsy: No, there are no special conditions. According to your own theory, it is all up to blind chance and selection pressures on what pace and direction through morphospace character traits will travel, and whether they will amplify a nested hierarchy signal, or progressively mask it.

    It’s largely due to the statistics involved, a large number of possible traits, and a slow mutation rate, both of which are observed.

    According to your beliefs you have small, fully terrestrial deer-like creatures transforming into a fully aquatic whale-like creature in roughly 10-15 million years.

    This rate of change is more than enough to potentially mask the signal of nested traits in the event of sufficient trait losses/reversals/convergences, etc.

    If such a scenario is occurring regularly at branching nodes, your nested hierarchy signal is obliterated. Period.

  300. 300
    keith s says:

    Vishnu, from the other thread:

    Let’s say I provide you with two cladograms.

    Both cladograms are nested hierarchies.

    One cladogram comes from a biology textbook.

    The other cladogram comes from an intelligently designed random cladogram generator.

    Do you think you will be able to tell which is which?

    Are you up for it?

    The fact that you would suggest this tells me that you have no idea what I am arguing.

    My impression is confirmed by your exchange with Zachriel above.

    If you don’t learn the difference between a nested hierarchy and an objective nested hierarchy, you’ll remain hopelessly confused about what’s being discussed here.

    Read Theobald. He explains it quite nicely.

  301. 301
    keith s says:

    Kairosfocus,

    That applies to you, too.

  302. 302
    keith s says:

    Okay, we can add Phinehas to the list of people scared to tackle the challenge.

  303. 303
    Zachriel says:

    Vishnu: Automobiles can be classified in a nested hierarchy.

    Automobiles can be rationally classified in nested hierarchies in many different ways. With organisms, there is only a single rational nested hierarchy.

    Vishnu: So then you consider horizontally gene transfer to be a cross?

    That’s right. However, even with horizontal gene transfer, convergence, and hybridization we can still discern a strong signal of the nested hierarchy across most taxa. Darwin wasn’t aware of genes, but he was well aware of the latter two mechanisms, and discussed them in detail and their relationship to the nested hierarchy in “Origin of Species”.

    Vishnu: This rate of change is more than enough to potentially mask the signal of nested traits in the event of sufficient trait losses/reversals/convergences, etc.

    No. While we tend to think of the changes as large, they mostly affect only gross morphological structures. They are still mammals, from chemistry to organ function. This is especially evident during embryonic development.

  304. 304
    lifepsy says:

    Zachriel

    No. While we tend to think of the changes as large, they mostly affect only gross morphological structures. They are still mammals, from chemistry to organ function. This is especially evident during embryonic development.

    Nowhere did I suggest they are not mammals. You have a habit of completely avoiding the point.
    Try again.

  305. 305
    Vishnu says:

    Zachriel: Vishnu: This rate of change is more than enough to potentially mask the signal of nested traits in the event of sufficient trait losses/reversals/convergences, etc.

    I didn’t say that, lifepsy did.

  306. 306
    keith s says:

    StephenB,

    Why are you afraid to take the challenge?

    All you have to do is answer the four questions by indicating who has the better theory, Bob or his friend.

    Then, if your answers differ, you need to explain exactly why.

    That’s all.

  307. 307
    keith s says:

    nullasalus:

    You are proposing a fairy hypothesis: ‘The mindless fairy magically orchestrates nature, and it just so happens that nature results in all manner of things, some of which are living structures, microevolutionary successes, macroevolutionary successes, and more.’ Your fairy has never been observed, tested for or discovered by science – because it’s not a scientific posit to being with.

    That’s a bizarre assertion. Do you actually believe that microevolution requires Designer internvention?

    Which is why I keep asking you to provide the scientific evidence, the peer-reviewed research/experiment, that demonstrates that even microevolution – or anything else, for that matter – is ‘unguided’.

    So for you, the Rain Fairy is a live hypothesis? After all, we can’t prove that the weather is unguided.

    Good grief, null. You might want to give this some more thought.

  308. 308
    Box says:

    Zachriel #22: The diagram of the Cambrian Explosion is consistent with a branching process.

    Zachriel, this is all you have said about the Cambrian Explosion; as far as I can see. Would you expand on that, please? Are we talking about a top-down branching process?

  309. 309
    Edward says:

    After much pondering and thought here is my most humble answer to the four questions:


    https://www.youtube.com/watch?v=rsRjQDrDnY8

    Ed

  310. 310
    Box says:

    Keith: So for you, the Rain Fairy is a live hypothesis? After all, we can’t prove that the weather is unguided. Good grief, null. You might want to give this some more thought.

    Keith, can you at least acknowledge that there is a striking difference between life and the weather? If you cannot, then there is no sense in debating with you.

  311. 311
    Vishnu says:

    Of course, the earth’s weather system might very well be designed processes that operate along certain lines, harnessing and exploiting stochastic elements, as I think biological life is.

    Certainly keiths doesn’t think earth’s weather is completely random.

    Keiths just keeps getting bizarrer and bizarrer in his defense of the indefensible.

  312. 312
    Vishnu says:

    Or put differently, surely keiths doesn’t think that stochastic elements in earth’s weather systems are evidence that earth’s weather processes are completely unguided.

  313. 313
    keith s says:

    OK, so Edward goes on the list of people afraid to take the challenge.

    Box:

    Keith, can you at least acknowledge that there is a striking difference between life and the weather? If you cannot, then there is no sense in debating with you.

    There are plenty of differences between life and the weather, but that’s not my question.

    I asked:

    Box,

    The challenge is open to you, as well.

    If you think the Rain Fairy hypothesis is ridiculous, as the rest of us do, then explain clearly and precisely what the relevant differences are between the Rain Fairy hypothesis and the ID hypothesis.

    I say that they use the same flawed logic. If you disagree, show precisely how they differ.

    Take the challenge, Box! It’s just four harmless questions plus an explanation.

  314. 314
    Vishnu says:

    If you don’t learn the difference between a nested hierarchy and an objective nested hierarchy, you’ll remain hopelessly confused about what’s being discussed here.

    I understand it. And as I indicated to Zachriel, I accept it, except for one caveat.

    Read Theobald. He explains it quite nicely.

    I did. And I do have criticisms. Let me ask you: does Theobald himself agree with this non-scientific utterance of yours: “12. If we take that approach and assume, temporarily and for the sake of argument alone, that the designer is responsible for the diversity of life, we can see that ID does does not predict an objective nested hierarchy out of the trillions of possibilities.” ?

    How can we “see” that?

    ID neither predicts the ONH or the lack of it.

    ID is perfectly consistent with the ONH or its opposite.

    As it has been pointed out to you over and over, the “trillions of possibilities” for the designer is a non-scientific conjecture. Interesting religious question, but non-scientific. Therefore, worthless in any sort scientific argument.

    Your “bomb” remains a dud.

  315. 315
    Vishnu says:

    Zachriel: I am curious. Do you agree with keiths “bomb” and Rain Fairy arguments?

  316. 316
    Vishnu says:

    Keiths,

    “12. If we take that approach and assume, temporarily and for the sake of argument alone, that the designer is responsible for the diversity of life, we can see that ID does does not predict an objective nested hierarchy out of the trillions of possibilities.”

    What I mean to say is: how can we “see” this any better if we assume the premise, since ID makes no predictions at all regarding an ONH? The premise is unnecessary. The conclusion is irrelevant.

    I would tend to agree that evolutionary, niche filling processes would tend to build nested hierarchies. However does this obviate an intelligent design of the system?

  317. 317
    keith s says:

    Vishnu, with a slight alteration:

    The Rain Fairy neither predicts the actual weather nor its opposite.

    The Rain Fairy hypothesis is perfectly consistent with the actual weather or its opposite.

    As it has been pointed out to you over and over, the “trillions of possibilities” for the Rain Fairy is a non-scientific conjecture. Interesting religious question, but non-scientific. Therefore, worthless in any sort scientific argument.

    Praise be to the Rain Fairy! Modern meteorology is dead, and the Rain Fairy hypothesis triumphs!

    Your “bomb” remains a dud.

    Think again.

  318. 318
    keith s says:

    Folks,

    Don’t make Vishnu’s mistake.

    If you think you have a whiz-bang refutation of my argument, pause and ask yourself this question:

    Could my whiz-bang defense of ID be used equally well to defend the Rain Fairy hypothesis?

    If the answer is yes, you’ve got a problem — unless you are willing to convert to Rain Fairyism.

  319. 319
    Vishnu says:

    Zachriel: Of course, we could suppose a designer with an inordinate fondness for beetles nested hierarchies, but that is a scientifically vacuous claim unless you ascribe testable properties to the designer that imply such a fondness.

    The designer might wish to utilize designed, evolutionary niche-filling, variation-producing processes, that harness stochastic elements to achieve those ends.

    Nobody knows.

    As far as I know, ID is not based on, nor limited by the ONH. Personally, I’m fine with ONH, with one caveat. But it’s a trivial caveat. ONH is consistent with an intelligent designer.

    Then why suspect a designer? See #293.

    What’s laughable is keiths “bomb” and Rain Fairy arguments. (Assumptions masquerading as arguments, actually.)

    I am curious, Zachriel. Do you agree with keiths “bomb” and Rain Fairy arguments?

  320. 320
    Vishnu says:

    keiths: If you think you have a whiz-bang refutation of my argument, pause and ask yourself this question: Could my whiz-bang defense of ID be used equally well to defend the Rain Fairy hypothesis? If the answer is yes, you’ve got a problem — unless you are willing to convert to Rain Fairyism.

    The Rain Fairy has no sound rational arguments based on evidence. ID does, as mentioned in #293.

    You may disagree with ID’s assessment of the issues I have cited, and there are others, but that’s a whole different discussion with no parity whatsoever to your Rain Fairy.

    If you want to discuss ID, the merits and demeteris, that would be great. And a refreshing difference. But you’re not discussing ID. You merely assume ID is false, make unwarranted assertions, and think you have a compelling argument. You don’t.

  321. 321
    keith s says:

    keiths:

    12. If we take that approach and assume, temporarily and for the sake of argument alone, that the designer is responsible for the diversity of life, we can see that ID does does not predict an objective nested hierarchy out of the trillions of possibilities.

    Vishnu:

    What I mean to say is: how can we “see” this any better if we assume the premise, since ID makes no predictions at all regarding an ONH?

    I explained this to Box earlier:

    Does anyone else want to step in and try to explain this to Box? It’s getting tiring.

    Box,

    For ID to have a chance, you have to assume a nonzero probability that the designer would produce an ONH. If the probability were zero, then design would be ruled out.

    Once you assume a nonzero probability, as you must, then the question arises: what value do you assign?

    Since you wish to minimize the assumptions you are making about the designer, you cannot assume that the designer is more likely to design with an ONH motif versus the other possibilities. You also cannot assume that the designer is less likely to design with an ONH motif versus the other possibilities.

    That means you must assign equal probabilities to the ONH and the trillions of other possible outcomes.

    Once you do that, my argument kicks in, and ID is rejected because it is trillions of times worse at explaining the ONH versus unguided evolution.

    Think about it for a while, rather than dashing off another ill-considered reply.

    Vishnu:

    I would tend to agree that evolutionary, niche filling processes would tend to build nested hierarchies.

    Not just nested hierarchies, but objective nested hierarchies — provided that the mutation rate is low enough and inheritance is primarily vertical.

    However does this obviate an intelligent design of the system?

    Do you mean ‘obviate’, or ‘preclude’?

    If the former, then I would point out that all you need for the “system” to get started is replication with heritable variation and differential reproductive success.

    If the latter, then no, the existence of an ONH-producing evolutionary process does not preclude the possibility that the initial setup was done by design. But if you accept that the subsequent process involved random mutation plus natural selection, then congratulations — you’re a Darwinist!

  322. 322
    keith s says:

    Vishnu,

    The Rain Fairy has no sound rational arguments based on evidence. ID does, as mentioned in #293.

    Neither one does. They are both invoked merely to plug gaps, or presumed gaps, in our knowledge. And yes, meteorology has gaps — every science does!

    And they are both based on atrociously bad logic.

    The Rain Fairy hypothesis is laughable for the same reason that ID is laughable. If a natural explanation works a trillion times better, who would be crazy enough to invent a Rain Fairy or an Intelligent Designer?

  323. 323
    StephenB says:

    KeithS

    Why are you afraid to take the challenge?

    There is no challenge to it.

    All you have to do is answer the four questions by indicating who has the better theory, Bob or his friend.

    Is this supposed to be hard? In scenarios 1 through 3, Bob’s friend has the better argument since Bob’s arguments are totally irrational. Clearly, they are not ID’s arguments. In argument 4, its a tie since both arguments are irrational.

    Then, if your answers differ, you need to explain exactly why.

    The answers for 1 through 3 do not differ for reasons already explained.

    If you are an ID supporter, then you are making exactly the same mistake as Bob does in the four examples above, using the same broken logic. Isn’t that a little embarrassing? It might be time to rethink your position.

    The broken logic belongs to you exclusively. None of the arguments that you presented bear even the slightest resemblance to ID’s argument. Clearly, you do not understand the methods of design detection.

    That’s all.

    Is that your way of saying that you have no answer to my refutations:

    Scenario #1

    [a] You do not even describe the arrangement of parts that prompts Bob to make a design inference. Do they form a word? Are they structured? What pattern did Bob observe?

    [b] You do not say whether it is the pebbles, particles, grains of sand, or rocks that are supposed to form the pattern. On the contrary, you try to agglomerate all of them into a unified whole, which makes no sense.

    [c] If there is no empirical evidence to suggest that anything was designed, then there is no reason for Bob to say “that every rock, pebble, grain of sand and silt particle was deliberately placed in its exact position by a Streambed Designer.” He is not making an ID argument. Your objection is a strawman.

    Scenario #2. There is evidence for an explosion and against the proposition that nature created the observed effects. Thus, the most reasonable inference is that an explosion occurred (by design). Even if someone planted the fake evidence, the observed effects cannot be reasonably attributed nature’s operation.

    Scenario #3. Angels and gravity have nothing to do with the methods of drawing an inference to design from empirical evidence?

    Scenario #4 is self contradictory. If the objective nested hierarchy exists because God guided nature to that end, then it cannot also have been caused by an unguided process.

    All the arguments presented are strawman arguments. You have not addressed that issue at all, nor have you confronted my stated reasons for saying why they are strawman arguments.

  324. 324
    keith s says:

    StephenB,

    Okay, so you answer “Bob’s friend” for scenarios 1 through 3. Good. We agree on those.

    You had some trouble with #4:

    4. Bob is hanging out at the office of a friend who is an evolutionary biologist. The biologist shows Bob how the morphological and molecular data establish the phylogenetic tree of the 30 major taxa of life to an amazing accuracy of 38 decimal places. “There couldn’t be a better confirmation of unguided evolution,” the biologist says. “Don’t be ridiculous,” Bob replies. “All of those lifeforms were clearly designed. It’s just that the Designer chose to imitate unguided evolution, instead of picking one of the trillions of other options available to him.”

    Who has the better theory, Bob or his friend?

    You wrote:

    Scenario #4 is self contradictory. If the objective nested hierarchy exists because God guided nature to that end, then it cannot also have been caused by an unguided process.

    Your complaint doesn’t make sense. Bob thinks God guided evolution. His friend the biologist does not.

    Two different people, two different viewpoints. Nothing self-contradictory about that.

    Give it another shot.

  325. 325
    StephenB says:

    KeithS

    Okay, so you answer “Bob’s friend” for scenarios 1 through 3. Good. We agree on those.

    How could we not agree? Bob, as you describe him, is a nitwit. That you would try to characterize him as the embodiment of ID indicates, once again, that you are not acquainted with the principles of design detection..

    KeithS

    Your complaint doesn’t make sense.Your complaint doesn’t make sense. Bob thinks God guided evolution. His friend the biologist does not. Two different people, two different viewpoints. Nothing self-contradictory about that.

    It is Bob’s argument that is self-contradictory. On the one hand, he says that God guides evolution. On the other hand, he says that God imitated unguided evolution.

    This scenario is not only illogical it has nothing to do with ID’s argument. No ID proponent would ever say that God “imitates” unguided evolution. So, you are still promoting a strawman.

    I have answered all your “challenges,” but you have avoided all of mine. Very well, I will give you a pass on all but two of then:

    [a] Explain why all your scenarios misrepresent ID’s arguments and transform them into strawmen. Or, if you think they don’t misrepresent ID’s arguments, tell me why.

    [b] In your own words, describe ID’s argument to the best of your ability. If you are going to critique ID’s method of design detection you should at least be able to show that you understand it.

  326. 326
    keith s says:

    StephenB:

    How could we not agree? Bob, as you describe him, is a nitwit. That you would try to characterize him as the embodiment of ID indicates, once again, that you are not acquainted with the principles of design detection..

    I am not “characterizing him as the embodiment of ID” in those examples. He is supposed to appear ridiculous to everyone, including ID proponents, in the first three examples. And I think he succeeds. He is, as you say, a nitwit.

    The point of the last example is to show that the ID position is marred by the same atrociously bad logic.

    If you disagree, you need to show that the ID can explain the objective nested hierarchy without employing the same bad logic that Bob uses.

    Can you do that?

    It is Bob’s argument that is self-contradictory. On the one hand, he says that God guides evolution. On the other hand, he says that God imitated unguided evolution.

    Those ideas aren’t contradictory. It is possible for a designer to guide evolution in a way that mimics unguided evolution.

    No ID proponent would ever say that God “imitates” unguided evolution.

    They wouldn’t choose those words, I’m sure, but the idea is the same. Vincent Torley even posted an OP arguing that the Designer would produce an objective nested hierarchy of exactly the kind that unguided evolution would produce, were it operating.

    And for good reason. The ONH is real, so the ID proponent must explain it somehow.

    I have answered all your “challenges,” but you have avoided all of mine. Very well, I will give you a pass on all but two of then:

    [a] Explain why all your scenarios misrepresent ID’s arguments and transform them into strawmen. Or, if you think they don’t misrepresent ID’s arguments, tell me why.

    [b] In your own words, describe ID’s argument to the best of your ability. If you are going to critique ID’s method of design detection you should at least be able to show that you understand it.

    The topic of this thread is my argument, not ID’s purported methods of detecting design.

    Can you refute my argument?

  327. 327
    kairosfocus says:

    KS: It has been repeatedly poinrted out to you by several people, with reasons and evidence, that you are distorting the thought and work of design thinkers to the point of strawman caricature. To date, we find no good reason to see that you are willing to accurately summarise what design thinkers actually think. You have repeatedly set up loaded assertions in axioms for your “challenges” that beg big questions on the empirically warranted capacity of blind watchmaker chance and necessity driven mechanisms to address origin of body plans. You have pretended that OOL is not relevant to the power of these mechanisms. You have tried to suggest in the teeth of quantification and repeated examples that FSCO/I is ill defined and not quantifiable. And more. Where, for years you have been a prominent critic in the penumbra of objector sites, with particular reference to original posts at TSZ. None of this commends you, your views, or the seriousness of the claimed objections. I suggest to you that it is time for pretty serious change. KF

  328. 328
    kairosfocus says:

    PS: There is a point by point refutation of your latest caricatures of design theory at 193 above. You refused to deal with it seriously (or to make amends for some unworthy personalities), and continue in much the same vein with SB. At this stage, on fair comment, it seems quite clear that you will not respond appropriately to evidence or reason that runs contrary to your ideological indoctrination, and are not to be taken seriously save as an example of what has gone so sadly wrong with the intellectual culture of our day.

  329. 329
    kairosfocus says:

    F/N: I have expanded my response to KS on the caricaturing of Newton’s account of planetary orbits and his thought on God as Architect of the cosmos, here, including addressing the proper understanding of the ID explanatory inference filter. The Paley case also comes in for a mention. KF

  330. 330
    Joe says:

    Zachriel:

    With organisms, there is only a single rational nested hierarchy.

    So prokaryotes aren’t organisms? There isn’t an objective nested hierarchy with prokaryotes.

  331. 331
    Joe says:

    Bob was walking through the woods with his evolutionist friend who was dedrologist. They came to a stand of apple trees in which each row was evenly spaced. Bob said they must be in someone’s apple grove. His friend said nonsense these are trees and trees are natural. Besides there isn’t anyone around, no houses nearby, no tools and no other signs of humans.

    Who has the better hypothesis?

  332. 332
    Joe says:

    And lest we forget:

    Charles Darwin’s tree of life is ‘wrong and misleading’, claim scientists:

    Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: “For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.”

    Whoops

  333. 333
    Zachriel says:

    lifepsy: Nowhere did I suggest they are not mammals.

    You have a habit of completely avoiding the point. Even though cetaceans have been under rapid adaptive evolution, if we look at the entirety of traits, they still classify as mammals.

    lifepsy: Try again.

    Be happy to. Here’s your claim.

    lifepsy: According to your beliefs you have small, fully terrestrial deer-like creatures transforming into a fully aquatic whale-like creature in roughly 10-15 million years. This rate of change is more than enough to potentially mask the signal of nested traits in the event of sufficient trait losses/reversals/convergences, etc.

    It’s false. Even with the posited changes in cetaceans, they still clearly classify as mammals, amniotes, vertebrates, chordates, eukaryotes — in that hierarchical ordering.

    You also exhibit an ignorance of evolution even as of Darwin’s time, which we addressed above, but you must have missed.

    lifepsy: You and Zachriel apparently hold some mystical idea about natural selection having predisposition towards and subsequent immutability of specific character trait assemblages, i.e. evolutionary destinies.

    Zachriel: Actually, *as Darwin pointed out*, natural selection often clouds the nested hierarchy. Non-adaptive traits are often better for discerning evolutionary relationships.

    Box: this is all you have said about the Cambrian Explosion; as far as I can see. Would you expand on that, please? Are we talking about a top-down branching process?

    A top-down process is still a branching tree. Near the node, we have many branches, fewer later on, while some die out. That’s called adaptive radiation. It’s posited to occur when a new niche becomes available.

    Vishnu: Of course, the earth’s weather system might very well be designed processes that operate along certain lines, harnessing and exploiting stochastic elements

    There’s no evidence of that, and there are robust theories of weather that render a designer superfluous.

    Vishnu: ID is perfectly consistent with the ONH or its opposite.

    ID doesn’t entail the nested hierarchy. ID doesn’t entail elliptical orbits. Branching descent entails the nested hierarchy. Gravity theory entails elliptical orbits. That’s fine, as far as it goes; however, the entailments we do have strongly support branching descent and gravity theory.

    Vishnu: Do you agree with keiths “bomb”

    No. The word “trillions” is clearly referring to Theobald, so the mistake is in #2. It should be branching descent explains the objective nested hierarchy. There would still be nesting whether the tree grew naturally, or whether a gardener trimmed and shaped the tree.
    http://www.bonsai-made-easy.co.....lecare.jpg

    It takes additional evidence to determine whether the tree grew naturally or whether it was artificially shaped. Regardless, the evidence for the nested hierarchy strongly supports branching descent.

    Vishnu: and Rain Fairy arguments?

    That one doesn’t appear expressed on this thread, but fairies would either be an extraneous entity as far as explaining the weather, or one without entailments.

    Vishnu: I would tend to agree that evolutionary, niche filling processes would tend to build nested hierarchies. However does this obviate an intelligent design of the system?

    In and of itself, no. However, there is strong support for branching descent. Imagine, Poe and the raven share an ancestor! That is a profound finding, and one that helps understand the balance of the evidence.

    Indeed, once you begin to come to grips with common descent, then the support for the Theory of Evolution comes into focus. Any ID theory must explain the nested hierarchy, as well as explain all the other evidence that the vast majority of scientists consider convincing for the Theory of Evolution.

    Vishnu: The designer might wish to utilize designed, evolutionary niche-filling, variation-producing processes, that harness stochastic elements to achieve those ends.

    Sure. The designer has an inordinate fondness for beetles, er, the nested hierarchy, er, elliptical orbits. You can make any ad hoc claims you want, but providing testable entailments is what gives it scientific merit. And don’t forget, it has to be consistent with the evidence for branching descent. Waving your hands and saying it doesn’t matter is just, well hand waving.


    While I nodded, nearly napping, suddenly there came a tapping,
    As of some one gently rapping, rapping at my chamber door.
    “’Tis some visitor,” I muttered, “tapping at my chamber door—
    Only this and nothing more.”

  334. 334
    StephenB says:

    KeithS

    The point of the last example is to show that the ID position is marred by the same atrociously bad logic.

    But you would have no way of knowing if ID’s logic is bad since you are not familiar with ID’s logic.

    If you disagree, you need to show that the ID can explain the objective nested hierarchy without employing the same bad logic that Bob uses.

    There are three problems here. First, nested hierarchies are not what we are finding. Second, even granting nested hierarchies, ID’s designer could either use them or not use them. Third, you don’t understand ID’s methods, so you cannot really comment on the second point.

    SB: No ID proponent would ever say that God “imitates” unguided evolution.

    They wouldn’t choose those words, I’m sure, but the idea is the same.

    You are contradicting yourself. Earlier, you said,

    I am not “characterizing him as the embodiment of ID” in those examples. He is supposed to appear ridiculous to everyone, including ID proponents, in the first three examples. And I think he succeeds. He is, as you say, a nitwit.

    Now you say that the idea “is the same.” First, you falsely characterize Bob’s argument as ID’s argument. Then, when I call you on it, you say you didn’t do that. Now you return to the same claim.

    Try to take one position and stay with it. If nitwit Bob doesn’t represent ID, then there is no reason to even bring him into the discussion. It’s an unnecessary distraction.

    Vincent Torley even posted an OP arguing that the Designer would produce an objective nested hierarchy of exactly the kind that unguided evolution would produce, were it operating.

    ID has room for that position, but it is not committed to it. It would help a great deal if you understood ID’s position before presuming to critique it. For some reason, though, you seem to feel that it isn’t necessary to understand an argument in order to comment on it. This is a curious position to take.

    And for good reason. The ONH is real, so the ID proponent must explain it somehow.

    You are not entitled to claim nested hierarchies as an indisputalble fact. It isn’t. However, even if it is a fact, it could be incorporated into ID’s paradigm.

    SB:

    [a] Explain why all your scenarios misrepresent ID’s arguments and transform them into strawmen. Or, if you think they don’t misrepresent ID’s arguments, tell me why.

    [b] In your own words, describe ID’s argument to the best of your ability. If you are going to critique ID’s method of design detection you should at least be able to show that you understand it.

    The topic of this thread is my argument, not ID’s purported methods of detecting design.

    I understand. You cannot articulate ID’s argument because you don’t understand it. That is a problem.

    Can you refute my argument?

    Yes. Easily.

    The existence of nested hierarchies is not an indisputable fact. The evidence does not support that claim.

    Either way, it is not necessary to deny the existence of nested hierarchies in order to argue that certain features in nature are designed. A designer can use them or not use them.

    Again, we have the same problem. You are trying to argue against ID’s paradigms without first taking the trouble to become familiar with them. ID is not inherently anti-common descent.

  335. 335
    StephenB says:

    Joe

    Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: “For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.”

    That is correct.

  336. 336
    Adapa says:

    StephenB

    It would help a great deal if you understood ID’s position before presuming to critique it.

    What is ID’s position? The only position I’ve ever seen articulated is “Life is intelligently designed”. There are zero details beyond that. I certainly can be mistaken so can you please supply any details like a timeline or by what physical mechanisms ID operated? Thanks.

  337. 337
    Adapa says:

    StephenB

    That is correct

    Well no, it is incorrect. Bapteste was only making the observation that among single celled organisms things like HGT make the tree of life at the very base more like a bush. Once you get into multicellular life the OHN of the phylogenetic tree is not in question.

  338. 338
    keith s says:

    Joe G is not happy about his banning:

    Has Barry Arrington totally lost it?

  339. 339
    kairosfocus says:

    F/N: Complex, per AmHD — Consisting of interconnected or interwoven parts; composite. This directly fits Orgel and Wicken, and work on metrics seeks to understand and quantify relative degree of such. The basic approach, chain of y/n q’s to specify config relevant to membership in a separately specifiable zone T in W (especially on function), is a quantification and extension by that, not the sort of utterly disparate usage being suggested by objections above. I am beginning to think the conclusion, reject design theory or thought is primary and at the root (driven by worldview level a prioris), the only issue is to find a seemingly plausible lab coat clad rationalisation. KF

  340. 340
    lifepsy says:

    Zachriel 333

    lifepsy: According to your beliefs you have small, fully terrestrial deer-like creatures transforming into a fully aquatic whale-like creature in roughly 10-15 million years.

    This rate of change is more than enough to potentially mask the signal of nested traits in the event of sufficient trait losses/reversals/convergences, etc.

    It’s false. Even with the posited changes in cetaceans, they still clearly classify as mammals, amniotes, vertebrates, chordates, eukaryotes — in that hierarchical ordering.

    I wasn’t claiming cetaceans do not fall into a nested hierarchy but was using their alleged rate of change as a reference point.

    Anyways… let me make it simpler for you…

    If the traits that define a group undergo rapid loss and/or reversals then voila, that group’s nested hierarchy signal thereafter has been masked.

    Example: If identifiable vertebrate traits are lost then so is the signal that groups the organism in vertebrates. This obviously becomes a problem if vertebrates begin “evolving” away from vertebrate traits shortly after they obtain them.

    This is common sense. I don’t think it can be explained more clearly.

    lifepsy: You and Zachriel apparently hold some mystical idea about natural selection having predisposition towards and subsequent immutability of specific character trait assemblages, i.e. evolutionary destinies.

    Zachriel: Actually, *as Darwin pointed out*, natural selection often clouds the nested hierarchy. Non-adaptive traits are often better for discerning evolutionary relationships.

    You can call the traits random if it makes you feel better. However this only weakens your position as there is even greater potential for those traits to be lost.

    Again you must appeal to some mystical notion of immutability that preserves basal traits as the nested hierarchy is gradually pieced together.

    However the conclusion is that Evolution/branching descent, does not necessarily predict a nested hierarchy pattern.

  341. 341
    StephenB says:

    Adapa

    What is ID’s position?

    You can begin by consulting UD’s resource section concerning “frequently raised but weak objections to ID.”

  342. 342
    Adapa says:

    StephenB

    You can begin by consulting UD’s resource section concerning “frequently raised but weak objections to ID.

    I wasn’t raising objections. I merely asked if you could provide some details on ID’s position like a timeline or a physical mechanism.

    If the answer is no I’ll accept that.

  343. 343
    keith s says:

    lifepsy,

    You are like a weasel with a rag dipped in rabbit juice, to borrow rich’s memorable phrase.

    You’re hanging onto this idea as if it were your salvation:

    If the traits that define a group undergo rapid loss and/or reversals then voila, that group’s nested hierarchy signal thereafter has been masked.

    We know that this has not happened in the case I am relying on, which is Theobald’s Figure 1, the cladogram of the 30 major taxa.

    If the signal had been lost, that objective nested hierarchy could not have been inferred. It was inferred, to an astounding accuracy of 1 in 10^38.

    Your objection is irrelevant. The evidence has spoken — loudly.

    (This goes for you, too, StephenB.)

  344. 344
    keith s says:

    StephenB @334,

    Your comment is full of confusions and misconceptions.

    1. You don’t understand the difference between nested hierarchies and objective nested hierarchies.

    2. You assert that “nested hierarchies are not what we are finding.” That’s incorrect for nested hierarchies, and it’s also incorrect for objective nested hierarchies.

    3. You write

    Either way, it is not necessary to deny the existence of nested hierarchies in order to argue that certain features in nature are designed. A designer can use them or not use them…

    ID is not inherently anti-common descent.

    Of course it isn’t, and my argument takes that into account. It is just as fatal to guided evolution as it is to creationism or common design.

    To have any hope of refuting my argument, you’ll need to understand it first. Here’s my OP. I would suggest reading it and Theobald, too.

  345. 345
    lifepsy says:

    lifepsy: If the traits that define a group undergo rapid loss and/or reversals then voila, that group’s nested hierarchy signal thereafter has been masked.

    keith s

    We know that this has not happened in the case I am relying on, which is Theobald’s Figure 1, the cladogram of the 30 major taxa.

    If the signal had been lost, that objective nested hierarchy could not have been inferred. It was inferred, to an astounding accuracy of 1 in 10^38.

    Epic fail again, Keith.

    The premise of your entire argument (see post #1) is that unguided evolution NECESSARILY PREDICTS a nested hierarchy pattern. Read it again if you’ve already forgotten.

    That is how you claim to be able to correctly infer unguided evolution in the first place – a double-sided coin that only results in an objective nested hierarchy remember?

    Getting it yet? Your argument has imploded on itself.

    It is not my fault if you cannot understand something so simple.

  346. 346
    StephenB says:

    KeithS

    2. You assert that “nested hierarchies are not what we are finding.” That’s incorrect for nested hierarchies, and it’s also incorrect for objective nested hierarchies.

    If you mean a nested hierarchy of shared traits, I agree. There is no question that they exist. The issue is that they are not found consistently and that they do not prove the “tree of life.” model. More importantly, their existence poses no problems for ID.

  347. 347
    StephenB says:

    From your OP

    KeithS

    There are many choices available to a Designer who guides evolution. Only a tiny fraction of them lead to a inferable, objective nested hierarchy. The Designer would have to restrict himself to gradual changes and predominantly vertical inheritance of features in order to leave behind evidence of the kind we see.

    This assertion needs to be argued for, and even it is true, why should it be a problem for ID? It’s really no more profound than saying the designer must use a gradual process to produce a result that leaves evidence of a gradual process.

    In other words, our ‘common descent IDers’ face a dilemma like the one faced by the creationists. They can force guided evolution to match the evidence, but only by making a completely arbitrary assumption about the behavior of the Designer.

    ID doesn’t need to force anything because ID is not committed to a world view. If there is evidence against common descent, so be it. That is only a problem for those who are committed to common descent and can’t bear the thought countervailing evidence.

    Unguided evolution doesn’t require any such arbitrary assumptions. It matches the evidence without them, and is therefore a superior explanation. And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.

    There isn’t a shred of evidence to support the proposition that an unguided process of gradual changes can produce biodiversity.

    This is a big problem for IDers. They concede that unguided evolution can bring about microevolutionary changes, but they claim that it cannot be responsible for macroevolutionary changes. Yet they give no plausible reasons why microevolutionary changes, accumulating over a long period of time, should fail to produce macroevolutionary changes. All they can assert is that somehow there is a barrier that prevents microevolution from accumulating and turning into macroevolution.

    If you don’t understand the difference in scale and complexity between increasing the size of a bird’s beak and transforming one body plan into another again and again, then I cannot help you.

  348. 348
    jstanley01 says:

    lifepsy @ 345

    Getting it yet? Your argument has imploded on itself.

    Ha-ha-ha-ha-ha-ha-ha-ha-ha-ha-ha, WIPEOUT!

  349. 349
    StephenB says:

    KeithS

    All they can assert is that somehow there is a barrier that prevents microevolution from accumulating and turning into macroevolution.

    Actually, ID does not claim that any such barrier exists. The point is that there is nothing in the cause that could reasonably be expected to produce the effect.

  350. 350
    Adapa says:

    StephenB

    KeithS

    All they can assert is that somehow there is a barrier that prevents microevolution from accumulating and turning into macroevolution.

    Actually, ID does not claim that any such barrier exists.

    That’s interesting. VJtorley has a whole thread claiming that such a barrier does exist.

    Barriers to macroevolution: what the proteins say

    Who are we to believe?

  351. 351

    Adapa:

    Who are we to believe?

    The premise/definition has no moving goalposts:

    The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

    Hopefully you know what a “premise” is.

  352. 352
    Zachriel says:

    lifepsy: I wasn’t claiming cetaceans do not fall into a nested hierarchy but was using their alleged rate of change as a reference point.

    That’s right. You provided an example which contradicted your position.

    lifepsy: If the traits that define a group undergo rapid loss and/or reversals then voila, that group’s nested hierarchy signal thereafter has been masked.

    That’s correct. However, we know the rate of mutation is low compared to the number of possible traits. Cetaceans are a good example. They have fins like fish, but a close look reveals their affinity to mammals, not fish.

    Again, this subject was discussed by Darwin back in the nineteenth century. “It is incredible that the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation.”

    lifepsy: Again you must appeal to some mystical notion of immutability that preserves basal traits as the nested hierarchy is gradually pieced together.

    Turns out we have actual evidence of the nested hierarchy. You provided an excellent example. Cetaceans went through rapid change, but not enough to cloud their essential mammalian ancestry.

    lifepsy: However the conclusion is that Evolution/branching descent, does not necessarily predict a nested hierarchy pattern.

    As we pointed out, there is a statistical relationship between the expected nested hierarchy and rates of change.

  353. 353
    lifepsy says:

    Zachriel

    Interesting that you quoted me on everything except what I bolded for you. Here it is again in case you missed it. I’m trying to help you out here.

    Example: If identifiable vertebrate traits are lost then so is the signal that groups the organism in vertebrates. This obviously becomes a problem if vertebrates begin “evolving” away from vertebrate traits shortly after they obtain them.

    Zachriel’s denial notwithstanding, it’s quite clear to see how easily a branching order could potentially produce a non-nested hierarchy pattern of traits.

  354. 354
    Zachriel says:

    lifepsy: Example: If identifiable vertebrate traits are lost then so is the signal that groups the organism in vertebrates. This obviously becomes a problem if vertebrates begin “evolving” away from vertebrate traits shortly after they obtain them.

    Darwin: “It is incredible that the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation.”

  355. 355
    lifepsy says:

    Zachriel is unable to form a cogent rebuttal.

  356. 356
    Zachriel says:

    lifepsy: If identifiable vertebrate traits are lost then so is the signal that groups the organism in vertebrates.

    You seem to think that phylogeny is based on single characteristics. Rather, scientists look at multiple traits. See Darwin 1859.

    A simple example is tetrapods. Cetaceans are considered tetrapods because they derive from vertebrates that first walked on land on four legs. Notably, embryonic cetaceans have four limb buds, but their classification depends on far more than just the existence of embryonic limb buds.

  357. 357
    lifepsy says:

    Zachriel

    You seem to think that phylogeny is based on single characteristics. Rather, scientists look at multiple traits.

    Branching descent does not simultaneously spawn multiple trait assemblages. Each trait must evolve sequentially. If a trait is lost then the descendent cannot nest within that trait. Simple logic.

  358. 358
    StephenB says:

    SB: Actually, ID does not claim that any such barrier exists.

    ADapa

    That’s interesting. VJtorley has a whole thread claiming that such a barrier does exist.

    Barriers to macroevolution: what the proteins say

    Who are we to believe?

    The question was whether ID or its design detection methods pose barriers to macro-evolution. It doesn’t; they dont. That doesn’t prevent VJTorely from using other methods to find barriers to macro-evolution.

  359. 359
    Mung says:

    keiths:

    So we have an ID hypothesis that can’t eliminate any of the trillions of options, against an unguided evolution hypothesis that actually predicts an ONH over everything else.

    ID doesn’t eliminate all imaginable alternatives. That’s your objection?

    Unguided evolution does eliminate all imaginable alternatives. That’s your claim?

  360. 360
    Adapa says:

    StephenB

    The question was whether ID or its design detection methods pose barriers to macro-evolution.

    That wasn’t the question at all. Here is your exchange with KeithS again.

    KeithS

    This is a big problem for IDers. They concede that unguided evolution can bring about microevolutionary changes, but they claim that it cannot be responsible for macroevolutionary changes. Yet they give no plausible reasons why microevolutionary changes, accumulating over a long period of time, should fail to produce macroevolutionary changes. All they can assert is that somehow there is a barrier that prevents microevolution from accumulating and turning into macroevolution..

    StephenB

    Actually, ID does not claim that any such barrier exists

    Your attempt to spin the question is very peculiar indeed.

    I’m also sure vjtorley will be quite surprised to learn the position he is arguing isn’t ID.

  361. 361
    StephenB says:

    Adapa

    Your attempt to spin the question is very peculiar indeed.

    Your inability to comprehend the point is very peculiar.

    I’m also sure vjtorley will be quite surprised to learn the position he is arguing isn’t ID.

    What part of VJTorley’s argument do you think constitutes an ID argument?

  362. 362
    Mung says:

    keiths: All they can assert is that somehow there is a barrier that prevents microevolution from accumulating and turning into macroevolution.

    StephenB: Actually, ID does not claim that any such barrier exists.

    Adapa: That’s interesting. VJtorley has a whole thread claiming that such a barrier does exist.

    SteohenB: The question was whether ID or its design detection methods pose barriers to macro-evolution. It doesn’t; they dont.

    Adapa: That wasn’t the question at all.

    *sigh*

  363. 363
    Adapa says:

    StephenB

    Your inability to comprehend the point is very peculiar.

    If your point was to cover your mistaken claim then it was fully comprehended.

    What part of VJTorley’s argument do you think constitutes an ID argument?

    Why don’t you ask him if he’s making an ID argument or not.

  364. 364

    StephenB:

    Actually, ID does not claim that any such barrier exists.

    Yes, (although the mechanisms of “macroevolution” are not at all explained by Darwinian Theory or are fully understood by even Gene Theory) the premise for the Theory of Intelligent Design says nothing about that at all.

    ID protesters are again fabricating their own premise/definition. As you may already know PNAS allows it too:

    From: Footprints of nonsentient design inside the human genome
    http://www.pnas.org/content/10.....9.abstract

    Intelligent design (ID)—the latest incarnation of religious creationism—posits that complex biological features did not accrue gradually via natural evolutionary forces but, instead, were crafted ex nihilo by a cognitive agent.

    The journal article should have been rejected (and at this point in time retracted) unless the above reads this exactly:

    The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

  365. 365
    Zachriel says:

    lifepsy: Branching descent does not simultaneously spawn multiple trait assemblages. Each trait must evolve sequentially. If a trait is lost then the descendent cannot nest within that trait.

    Not even sure what situation you are thinking about, unless it’s a population during incipient speciation. A toy example might look like this:

    AAAAAAAAA
    AAAAAAAAB
    ZZZZZZZZZ
    (out-group)

    Let’s say the B mutation is accompanied by reproductive isolation, i.e. a branch. After some time, the two lineages might look like this:

    AAyzAxAAA
    AArAsAtAB
    ZZZjZkZZZ

    Now, the B reverts, and we have this.

    AAyzAxAAA
    AArAsAtAA
    ZZZjZkZZZ

    Notice that we can still group the first two into their proper placement, with ZZZ being the out-group. Furthermore, we can easily distinguish any descendants of the second string because they will inherit the r,s,t mutations. We might even call this lineage the B-lineage for historical reasons, even though one sub-branch no longer has the B trait. With longer sequences, it’s even more obvious. This is easy to simulate algorithmically.

    As per your example, modern tetrapods share many traits. Even if one lineages loses the their limbs (Cetaceans), we can still discern their position within the nested hierarchy.

  366. 366
    StephenB says:

    SB: What part of VJTorley’s argument do you think constitutes an ID argument?

    Why don’t you ask him if he’s making an ID argument or not.

    I am asking you. You are the person who claimed that ID creates a barrier to macro-evolution (mindlessly following KeithS). You are the person who accused me of trying to camouflage my “error.” You are the person who said that VJTorley disagrees with me. Now you want me to bail you out? No thanks. Make your case.

  367. 367
    StephenB says:

    Gary S. Gualin

    ID protesters are again fabricating their own premise/definition.

    Precisely. They don’t even want to grant ID scientists the due privilege of providing their own definitions. Hence, when the ID researcher says, “here is what I mean by “X,” the Darwinist response is, “No, you don’t.” Incredible.

    The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

    Isn’t that interesting. I find no mention of the word “macro-evolution,” or “common descent” in that formulation.

  368. 368
    StephenB says:

    Mung @362. Good summary. Thanks.

  369. 369
    StephenB says:

    Apologies to Gary S. Gaulin who I clumsily addressed as [Gary S. Gualin].

  370. 370

    Close enough Steven. 😀

  371. 371
    Adapa says:

    StephenB

    You are the person who claimed that ID creates a barrier to macro-evolution

    I said no such thing, please stop making false statements. I merely pointed out your claim ID says no barrier exists which prevents microevolution from accumulating and turning into macroevolution is directly contradicted by other ID proponents here. That you can’t get your story straight is your problem, not mine.

  372. 372

    I had no problem understanding what Stephen was saying, Adapa.

    Perhaps you need to be a victim, to know what your victims are experiencing?

  373. 373
    Me_Think says:

    Stefen B @366

    You are the person who claimed that ID creates a barrier to macro-evolution (mindlessly following KeithS). You are the person who accused me of trying to camouflage my “error.”

    Although Question is for Adapa,I will give my opinion – I am surprised by your ID stand. Prominent ID proponents claim micro-evolution can’t aggregate to form macro evolution. Meyer has a whole book explaining why macro evolution can’t be a result of micro evolution aggregation.He uses explanations like Body plans, protein folds etc.

  374. 374
    StephenB says:

    Me_Think

    Prominent ID proponents claim micro-evolution can’t aggregate to form macro evolution. Meyer has a whole book explaining why macro evolution can’t be a result of micro evolution aggregation.He uses explanations like Body plans, protein folds etc.

    Of course. I have made that same point on this thread. I quote myself @347

    There isn’t a shred of evidence to support the proposition that an unguided process of gradual changes can produce biodiversity.

    and again @347

    If you don’t understand the difference in scale and complexity between increasing the size of a bird’s beak and transforming one body plan into another again and again, then I cannot help you.

    There is no evidence to support the proposition micro-evolution and time will provide macro-evolution. ID proponents

    That is not at all the same thing as saying that ID’s paradigms are not compatible with macro-evolution. There is no ID initiated barrier to macro-evolution. ID’s design detection methodologies do even address the subject.

    That doesn’t prevent ID proponents from exposing Darwinism’s unjustified claim that micro-evolution can become macro-evolution given enough time.

  375. 375

    From my personal experience ID arguments that present barriers (or hurdles) are useful for understanding the weaknesses of Darwinian Theory and what the Theory of Intelligent Design I’m developing needed to help explain in regards to speciation.

    This is the same as a group of evolutionary biologists who problem solve by sharing their personal opinions. It is scientifically unethical to cherry pick from all their personal opinions in order to fabricate an easy to argue against strawman premise, to replace the premise that already exists.

  376. 376
    StephenB says:

    Adapta

    I merely pointed out your claim ID says no barrier exists which prevents microevolution from accumulating and turning into macroevolution is directly contradicted by other ID proponents here.

    Barrier
    noun
    noun: barrier; plural noun: barriers

    a fence or other obstacle that prevents movement or access.
    synonyms: fence, railing, barricade, hurdle, bar, blockade, roadblock
    “the barrier across the entrance”
    a circumstance or obstacle that keeps people or things apart or prevents communication or progress.
    “a language barrier”
    synonyms: obstacle, obstruction, hurdle, stumbling block, bar, block, impediment, hindrance, curb
    “a barrier to international trade”

    In arguing against Darwinian evolution, ID proponents do not argue that a “barrier” (obstacle, impediment, hindrance, or stumbling block) exists that would prevent micro-evolution from becoming macro-evolution. What they do argue is that the natural process of random variation and natural selection can produce small changes, but there is no evidence that these small changes can accumulate into macro-evolution.

    They do not say that a “barrier” exists (though there is nothing to prevent someone from using the word as a metaphor). They simply say that, according to the evidence time and micro changes will likely not accumulate into macro-evolution.

    The reason for making this distinction is to point out that the cause does not have the necessary means to produce the effect. To suggest that a real, yet undefined, barrier exists is to imply that the micro changes could have become macro changes if only some “barrier” did not get in the way.

    To say that a real barrier exists is also to suggest that ID is including an important factor in their argument that they didn’t even bother to define. What is the barrier any reasonable person might ask? ID proponents do not make that argument. That is why KeithS’s argument is so bizarre. First, he invents the existence of a barrier, then he turns right around and says that ID is being mysterious about what this barrier might be. incredible.

  377. 377
    lifepsy says:

    Zachriel

    lifepsy: Branching descent does not simultaneously spawn multiple trait assemblages. Each trait must evolve sequentially. If a trait is lost then the descendent cannot nest within that trait.

    Not even sure what situation you are thinking about, unless it’s a population during incipient speciation. A toy example might look like this:

    I gave you a specific example before. Which you avoided. If a basal vertebrate evolves away from traits that define vertebrates, then its descendent traits will not nest within vertebrates. Simple.

    Notice that we can still group the first two into their proper placement, with ZZZ being the out-group.

    Um, of course you can. Your example began and ended with two distinct groups. Why wouldn’t you be able to distinguish them?

    If shared traits stay generally conserved, while new unique traits are lost shortly after they’ve evolved, then the descendent cannot nest within that trait, thus the nested hierarchy pattern is broken. It’s as simple as that.

  378. 378
    Zachriel says:

    StephenB: I find no mention of the word “macro-evolution,” or “common descent” in that formulation.

    No, however, this thread concerns strong support for branching descent. Any competing theory has to be consistent with this finding.

    lifepsy: I gave you a specific example before.

    You seem to be echoing everything on two threads. That makes it hard to follow for readers. Please respond on one or the other thread. You might want to respond to the specifics of the toy example. If you like, we can create a simple algorithm to explore your claims, but having done many such simulations in the past, it’s clear that for reasonable rates of change, it is easy to reconstruct nested hierarchies, even given the occasional reversion.

    lifepsy: Your example began and ended with two distinct groups.

    Because that’s how it works. A lineage diverges, then they change for a while, then they diverge again.

    AAyzAxAAA
    AArAsAtAB
    ZZZjZkZZZ

    Let’s show it in a bit more detail. The first and second populations diverge.

    AAyzAxAAA
    AAywAxAAA

    AArAsAtAB
    AArAsAtAA

    ZZZjZkZZZ

    That they diverged creates a nested hierarchy which reflects the ancestral relationship, even with the reversion.

    lifepsy: Branching descent does not simultaneously spawn multiple trait assemblages.

    That’s not necessarily the case. Divergence is a process, and not usually instantaneous. Rather, collections of traits are sorted through the population. When divergence occurs, let’s say one lineages pushes itself up above the water to look for prey, many traits may be involved; a flexible neck, a stronger wrist, the position of the eyes and nares. And as fossils only provide snapshots, we may find a fishapod, but not every individual event connecting the fishapod to fish and tetrapods. Indeed, the fossil will be very unlikely to be a direct ancestor of tetrapods, but will much more likely be one of many cousin lineages.

  379. 379
    lifepsy says:

    Zachriel

    You seem to be echoing everything on two threads. That makes it hard to follow for readers. Please respond on one or the other thread.

    I agree… (you started copy/pasting your responses first though actually). The problem is I keep finding you making the same erroneous claims about the nested hierarchy in multiple threads. But for now we can try to limit the discussion to the more recent thread here:

    http://www.uncommondescent.com.....ent-526786

    And good luck trying to distract from self-evident logical truths by appealing to algorithms.

  380. 380
    Box says:

    Zachriel,

    Does Stephen Meyer’s argument, presented in his book ‘Darwin’s Doubt’, that there is no Darwinian explanation for Cambrian organisms, pose a problem for Theobald’s position?
    If not, why not?

  381. 381
    Adapa says:

    StephanB

    In arguing against Darwinian evolution, ID proponents do not argue that a “barrier” (obstacle, impediment, hindrance, or stumbling block) exists that would prevent micro-evolution from becoming macro-evolution. What they do argue is that the natural process of random variation and natural selection can produce small changes, but there is no evidence that these small changes can accumulate into macro-evolution.

    Of course ID proponents claim there’s a barrier that prevents micro-e from accumulating into macro-e. Meyer wrote a whole book with that as the theme. Axe wrote a paper with that theme

    Axe: The Case Against a Darwinian Origin of Protein Folds

    Four decades ago, several scientists suggested that the impossibility of any evolutionary process sampling anything but a miniscule fraction of the possible protein sequences posed a problem for the evolution of new proteins. This potential problem—the sampling problem—was largely ignored, in part because those who raised it had to rely on guesswork to fill some key gaps in their understanding of proteins. The huge advances since that time call for a careful reassessment of the issue they raised. Focusing specifically on the origin of new protein folds, I argue here that the sampling problem remains. The difficulty stems from the fact that new protein functions, when analyzed at the level of new beneficial phenotypes, typically require multiple new protein folds, which in turn require long stretches of new protein sequence. Two conceivable ways for this not to pose an insurmountable barrier to Darwinian searches exist. One is that protein function might generally be largely indifferent to protein sequence. The other is that relatively simple manipulations of existing genes, such as shuffling of genetic modules, might be able to produce the necessary new folds. I argue that these ideas now stand at odds both with known principles of protein structure an with direct experimental evidence. If this is correct, the sampling problem is here to stay, and we should be looking well outside the Darwinian framework for an adequate explanation of fold origins.

    You attempts to spin your misunderstanding are getting really silly. Even your fellow IDers have called you on it. Just admit you made a mistake and move on.

  382. 382
    Adapa says:

    Box

    Does Stephen Meyer’s argument, presented in his book ‘Darwin’s Doubt’, that there is no Darwinian explanation for Cambrian organisms, pose a problem for Theobald’s position?
    If not, why not?

    No because Meyer’s claim has been falsified by the genetic evidence which shows the branching origin of the Cambrian biota from common ancestors in Precambrian times. Read the Peterson paper you keep avoiding.

  383. 383
    Zachriel says:

    Box: Does Stephen Meyer’s argument, presented in his book ‘Darwin’s Doubt’, that there is no Darwinian explanation for Cambrian organisms, pose a problem for Theobald’s position?

    Adapa: No because Meyer’s claim has been falsified by the genetic evidence …

    What Adapa said. Evidence is also found in the paper that formed the basis of this series of posts, Theobald 2010.

  384. 384
    Box says:

    Zachriel (and Adapa), are you aware of the fact that Stephen Meyer wrote extensively on Theobald’s claim?

    S.Meyer, from ‘Darwin’s Doubt’:

    And according to some scientists, studies of molecular homologies have confirmed expectations about the history of the animal phyla derived from studies of comparative anatomy. After citing Pauling and Zuckerkandl’s test, Douglas Theobald claims in his “29+ Evidences for Macroevolution” that “well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance.”26
    In reality, however, the technical literature tells a different story. (…)

    [and Meyer goes on for several pages providing arguments and information from dozens of studies]

    Can you link to Theobald’s response to Stephen Meyer?

  385. 385
    Adapa says:

    Box

    Zachriel (and Adapa), are you aware of the fact that Stephen Meyer wrote extensively on Theobald’s claim?

    I’m aware of the fact that Stephen Meyer egregiously quote-mined the Peterson paper on Precambrian genetic evidence while totally ignoring the technical content.

  386. 386
    Zachriel says:

    Box: “In reality, however, the technical literature tells a different story.” [and Meyer goes on for several pages providing arguments and information from dozens of studies]

    We have found an old discarded scroll of Meyer’s book, “Darwin’s Doubt”. Can you point to a chapter wherein he makes those claims? If not, can you quote specifics?

  387. 387
    Box says:

    Adapa #385: I’m aware of the fact that Stephen Meyer egregiously quote-mined the Peterson paper

    That is just dandy – although it’s interesting to point out that you are unable to provide a single sentence from Peterson’s paper that contradicts the quotations used by Stephen Meyer – but it is not an answer to my question.

    Let me ask again: “are you aware of the fact that Stephen Meyer wrote extensively on Theobald’s claim?”

  388. 388
    Adapa says:

    Box

    Let me ask again: “are you aware of the fact that Stephen Meyer wrote extensively on Theobald’s claim?

    Stephen Meyer has written a lot of pseudo-scientific Christian apologetics in his day. Ignoring the actual scientific data except for the occasional quote-mining foray is what he’s well known for in the scientific community. Is there a point?

  389. 389
    Box says:

    Zachriel: We have found an old discarded scroll of Meyer’s book, “Darwin’s Doubt”. Can you point to a chapter wherein he makes those claims?

    “Old discarded scroll”? Only a cub would call Meyer’s book (2013) “old”.
    In my e-book version of Stephen Meyer’s, ‘Darwin’s Doubt’ addressing and dissecting of Theobald’s erroneous claims starts here: Part One: The Mystery of the Missing Fossils; 6. The animal tree of life; Molecules vs. Anatomy.

    What follows is: many links to scientific studies, several diagrams and cogent valid argumentation.

    Happy reading!

  390. 390
    Box says:

    Zachriel,

    I have to ask you again: “Can you link to Theobald’s response to Stephen Meyer?”

  391. 391
    Zachriel says:

    Box: “Old discarded scroll”?

    Yes, it was found on the discard pile. Perhaps it wasn’t old. Didn’t look like it had been opened before.

    Box: Part One: The Mystery of the Missing Fossils; 6. The animal tree of life; Molecules vs. Anatomy.

    Ugh. He starts out with an analogy, the birth order of the children of Darwin, then mangles it by suggesting that you have to know everything in order to know anything.

    If we can find birth records on nine of Darwin’s ten children, then even though we don’t know everything, we don’t have to have to one true and complete history to have significant knowledge of the birth order. Indeed, we will have reduced the uncertainty from one of more than three million possibilities to just ten. The entire article rests on this faulty understanding of how evidence is evaluated.

    Really, Meyer’s Gap argument is that, sure, maybe we have a phylogeny showing humans evolved from primitive deuterostomes, but what about them arthropods!

    The scientific problem is one of resolution, that is, trying to discern the branches of a tree at a distance of hundreds of millions of years, one where the branching was occurring relatively rapidly, and fossils are rare. So what does Meyer do? He waves his hands. What do working biologists do? They build a better telescope and collect more data.

    Edgecombe et al., Higher-level metazoan relationships: recent progress and remaining questions, Organisms Diversity & Evolution 2011: “A stable core of the tree for bilaterian animals is now at hand, and instability and conflict are becoming restricted to a key set of important but contentious relationships.”

  392. 392
    Zachriel says:

    Box: Can you link to Theobald’s response to Stephen Meyer?

    Have no idea.

  393. 393
    StephenB says:

    Adapa

    Just admit you made a mistake and move on.

    Far be it from me to deny the evidence. Thank you for providing it.

  394. 394
    Box says:

    Zachriel #391: Ugh. He starts out with an analogy, the birth order of the children of Darwin, then mangles it by suggesting that you have to know everything in order to know anything.

    Zachriel, I have told you exactly where Meyer addresses Theobald’s claim (see post #389), but you seem to have some trouble finding it.
    Contrary to your claim, Meyer starts out like this:

    After citing Pauling and Zuckerkandl’s test, Douglas Theobald claims in his “29+ Evidences for Macroevolution” that “well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance.”26
    In reality, however, the technical literature tells a different story. Studies of molecular homologies often fail to confirm evolutionary trees depicting the history of the animal phyla derived from studies of comparative anatomy. Instead, during the 1990s, early into the revolution in molecular genetics, many studies began to show that phylogenetic trees derived from anatomy and those derived from molecules often contradicted each other.
    Probably the most protracted conflict of this type concerns a widely accepted phylogeny for the bilaterian animals. This classification scheme was originally the work of the influential American zoologist Libbie Hyman.27 Hyman’s view, generally known as the “Coelomata” hypothesis, was based on her analysis of anatomical characteristics, mainly germ (or primary tissue) layers, planes of body symmetry, and especially the presence or absence of a central body cavity called the “coelom,” which gives the hypothesis its name. In the Coelomata hypothesis, the bilaterian animals were classified in three groups, the Acoelomata, the Pseudocoelomata, and the Coelomata, each encompassing several different bilaterian animal phyla.28 (See Fig. 6.1a.)
    Then, in the mid-1990s, a very different a Then, in the mid-1990s, a very different arrangement of these animal groups was proposed based on the analysis of a molecule present in each (the 18S ribosomal RNA; see Fig. 6.1b). The team of researchers who proposed this arrangement published a groundbreaking paper in Nature with a title that surprised many morphologists: “Evidence for a Clade of Nematodes, Arthropods and Other Moulting Animals.”29 The paper noted the conventional wisdom, based on Hyman’s hypothesis, that arthropods and annelids were closely related because both phyla had segmented body plans.30 But their study of the 18S ribosomal RNA suggested a different grouping, one that placed arthropods close to nematodes within a group of animals that molt, which they called “Ecdysozoa.” This relationship surprised anatomists, since arthropods and nematodes don’t exactly look like kissing cousins. Arthropods (such as trilobites and insects) have coeloms, whereas nematodes (such as the tiny worm Caenorhabditis elegans) do not, leading many evolutionary biologists to believe nematodes were early branching animals only distantly related to arthropods.31 The Nature paper explained how unexpected this grouping of arthropods and nematodes was: “Considering the greatly differing morphologies, embryological features, and life histories of the molting animals, it was initially surprising that the ribosomal RNA tree should group them together.”32
    [and S. Meyer goes on several pages building his case based on several distinct arguments and many references to scientific papers]

    Now I ask you: where, in here, do you read about the analogy ‘the birth order of the children of Darwin’?

    Zachriel: So what does Meyer do? He waves his hands. What do working biologists do? They build a better telescope and collect more data.

    Edgecombe et al., Higher-level metazoan relationships: recent progress and remaining questions, Organisms Diversity & Evolution 2011: “A stable core of the tree for bilaterian animals is now at hand, and instability and conflict are becoming restricted to a key set of important but contentious relationships.”

    It will probably come as a surprise to you that Stephen Meyer shows diagrams from Edgecombe’s paper and cites him multiple times in the next couple of pages. Anyway, you seem to know everything about Stephen Meyer’s book already ….
    Good luck with that.

  395. 395
    Zachriel says:

    Box: Contrary to your claim, Meyer starts out like this …

    Box: Now I ask you: where, in here, do you read about the analogy ‘the birth order of the children of Darwin’?

    Um, at the start of the chapter. Meanwhile, you ignored our reply. Meyer starts the chapter by making an egregious error concerning scientific knowledge, that is we don’t know everything, we don’t know anything.

    As for the specifics. We observe vast trees of deuterostomes, arthropods, and nematodes. They are clearly nested within bilateria. The only question, out of thousands of known branches, is which branched from bilateria first. When we look at the vast amount of data that we have, the tree is strongly supported, even if we can’t always resolve certain branchings.

    Then Meyer mangles another analogy, the family reunion.

    “the majority of attendees and all the strangers you engage in conversation exhibit no discernible family resemblances. Nor does anyone seem to share any personal relationships with anyone else at the reunion”.

    But this is exactly contrary to what we observe concerning the biological tree! Indeed, the vast majority of people at the reunion can clearly find both close and distant relatives. Even the arthropod, deuterostome, and nematode branches share a common ancestor, Grandpapa Bilateria. The only question is which of Grandpapa Bilateria’s children was born first. But of the thousands upon thousands there at the reunion, the vast majority find themselves surrounded by people sharing a family resemblance, and who are relatives with known relationships.

    Meyer’s Gap argument is that, sure, maybe we have a phylogeny showing humans evolved from primitive deuterostomes, but what about them arthropods!

    Edgecombe et al., Higher-level metazoan relationships: recent progress and remaining questions, Organisms Diversity & Evolution 2011: “A stable core of the tree for bilaterian animals is now at hand, and instability and conflict are becoming restricted to a key set of important but contentious relationships.”

  396. 396
    Box says:

    Box: Now I ask you: where, in here, do you read about the analogy ‘the birth order of the children of Darwin’?

    Zachriel: Um, at the start of the chapter. Meanwhile, you ignored our reply. Meyer starts the chapter by making an egregious error concerning scientific knowledge, that is we don’t know everything, we don’t know anything.

    You must be talking about some other chapter, than the chapter I referred to (see post #389) – where S.Meyer actually addresses Theobald’s claim. Why did you not provide the title of this chapter? Thank you.
    Can you also provide the quote where Meyer states that “if “we don’t know everything, we don’t know anything”?

    I would be quite surprised to learn that Stephen Meyer actually said that.

  397. 397
    Zachriel says:

    Box: You must be talking about some other chapter, than the chapter I referred to (see post #389)

    It’s chapter 6. The animal tree of life.

    Box: Can you also provide the quote where Meyer states that “if “we don’t know everything, we don’t know anything”?

    It’s encapsulated in his two analogies.

    Concerning the birth order of Darwin’s children, he said “No one would consider the problem solved if you came back with more than one order.” And yet, if we find birth records for nine of the ten children, we have learned a great deal, and have reduced the possibilities from over three million to just ten. This faulty understanding of science is the basis of the rest of the chapter. He points to things we don’t know or don’t know with certainty, in order to then claim we don’t know anything. Yet this is the very strength of the scientific method, that we can learn some things while remaining ignorant of the vastness of the universe.

    Concerning the family reunion, it’s the same problem, only Mayer makes it explicit, saying we would be in a room with strangers because we don’t know the birth order of GrandPapa Bilateria’s children. It’s simply not the case.

  398. 398
    Box says:

    Zachriel,

    Box: Can you also provide the quote where Meyer states that “if “we don’t know everything, we don’t know anything”?

    Zachriel: It’s encapsulated in his two analogies.
    Concerning the birth order of Darwin’s children, he said “No one would consider the problem solved if you came back with more than one order.” And yet, if we find birth records for nine of the ten children, we have learned a great deal, and have reduced the possibilities from over three million to just ten.

    There is little doubt in my mind that Stephen would agree with you if you would be referring to reality. But you got it all wrong. Meyer goes on arguing that – in line with the Darwin family analogy – there is no agreement on the birth records at all. There is just a wide variety of conflicting lists.
    You see, it is the measure of the conflict that makes it very close to “we don’t know anything.”
    Now do you understand the analogy?

    Zachriel: This faulty understanding of science is the basis of the rest of the chapter. He points to things we don’t know or don’t know with certainty, in order to then claim we don’t know anything. Yet this is the very strength of the scientific method, that we can learn some things while remaining ignorant of the vastness of the universe.

    You are probably right that this is true for Darwinism. Obviously this needs correction: dogma and wildly conflicting papers should not provide ground for certainty. That should be considered unscientific by any rate.

    Zachriel: Concerning the family reunion, it’s the same problem, only Mayer makes it explicit, saying we would be in a room with strangers because we don’t know the birth order of GrandPapa Bilateria’s children. It’s simply not the case.

    Again you misrepresent Meyer. Meyer never said such a thing.

    Stephen Meyer: (…) imagine being invited to an event billed as an extended-family reunion where you’ve been told you will encounter hundreds of your relatives, most of whom you have never met.

    Stephen Meyer:
    Of course, my family reunion illustration breaks down as an analogy to the history of animal life, because if we could trace the history of all the people at the reunion back far enough we would find that they are all related by common ancestry. Though we can choose to assume that the same is true of the Cambrian animals, neither the fossil evidence nor the evidence of genetics and comparative anatomy actually establishes that. These three classes of evidence either provide no compelling evidence for Precambrian animal ancestors (in the case of fossils), or they provide question-begging and conflicting evidence (in the case of genes and anatomy).
    And that is the point of my story. Since there can be only one true history of the Cambrian animals, the evidence should converge on a common family tree—if indeed we are looking at evidence of true history. The picture given by the evidence should be stable, not constantly changing. But the evidence from a variety of quarters has instead continually generated new, conflicting, and incoherent pictures of the history of animal life. As with the “cousins” in my illustration, there seems to be no consistent and coherent way to organize the animal groups into a family tree.

  399. 399
    Zachriel says:

    Box: Meyer goes on arguing that – in line with the Darwin family analogy – there is no agreement on the birth records at all.

    But that’s false. There is a great deal of support for the overall phylogenetic tree. That there are areas of disagreement concerning some parts of the tree doesn’t imply we have no agreement at all.

    Box: Meyer never said such a thing.

    We quoted him directly.

    “the majority of attendees and all the strangers you engage in conversation exhibit no discernible family resemblances. Nor does anyone seem to share any personal relationships with anyone else at the reunion”.

    And he is clearly saying no one would recognize a family resemblance with anyone else. That’s simply false. Indeed, everyone would have close and distant relatives in a great tree of relationships.

    What you quote by Meyer, on the other hand, emphasizes that Meyer is arguing that a lack of knowledge in some areas of the tree translates into having “no consistent or coherent way to organism animals groups into a family tree.” That is simply false. Furthermore, that’s exactly what Theobald shows, that the mathematics of the overall nested hierarchy are strongly supported in spite of the areas of uncertainty.

    While Meyer waves his hands in the direction of the so-called gaps, biologists continue to fill in those gaps.

    Telford et al., The evolution of the Ecdysozoa, Phil. Trans. R. Soc. B 2008.

  400. 400
    Box says:

    Zachriel,

    Box: Meyer goes on arguing that – in line with the Darwin family analogy – there is no agreement on the birth records at all.

    Zachriel: But that’s false. There is a great deal of support for the overall phylogenetic tree. That there are areas of disagreement concerning some parts of the tree doesn’t imply we have no agreement at all.

    Don’t be uncharitable by taking it as a general statement about the phylogenetic tree as a totality, Zachriel. The statement pertains to the Cambrian only. That is what Meyer’s book is all about. Remember?
    And don’t tell me that there is general agreement on the Cambrian as well, because that is obviously not true.

    Zachriel: We quoted him directly.

    S.Meyer: “the majority of attendees and all the strangers you engage in conversation exhibit no discernible family resemblances. Nor does anyone seem to share any personal relationships with anyone else at the reunion”.

    And he is clearly saying no one would recognize a family resemblance with anyone else. That’s simply false.

    That would be false, right Zachriel? Well, the thing is that you stopped reading a little bit too early:

    S.Meyer: As the day goes on, however, something seems amiss. Here and there, you see familiar facial features—“Yes,” you think, that person could be my cousin”—(…)

    To be honest Zachriel, it’s no fun reading Darwin’s Doubt “together” with you. I think we are about done.

    Zachriel: What you quote by Meyer, on the other hand, emphasizes that Meyer is arguing that a lack of knowledge in some areas of the tree translates into having “no consistent or coherent way to organism animals groups into a family tree.” That is simply false. (…)
    While Meyer waves his hands in the direction of the so-called gaps, (…)

    Yeah. Sure. Whatever.
    Zachriel, I think we are done.

  401. 401
    Zachriel says:

    Box: The statement pertains to the Cambrian only.

    Sure, maybe we have a phylogeny showing humans evolved from primitive deuterostomes, but what about them arthropods!

  402. 402
    Box says:

    Zachriel: we have a phylogeny showing humans evolved from primitive deuterostomes

    Someone with your reading skills should have no trouble finding his way in here:
    Human Evolution

  403. 403
    Mung says:

    keiths runs from his damp squid as if it were a real bomb.

  404. 404
    Reality says:

    Keith hasn’t run from anything and you know it, Mung. Just because he doesn’t respond to every comment and question from you and other IDists within seconds of them being posted doesn’t mean that he’s running away. He has responded many times and continues to do so on more than one thread, even though most or all of the comments and questions directed at him are incredibly ignorant and rude and have already been answered by Keith and a few other knowledgeable people multiple times. You’re just a poor loser. If it weren’t for the unwarranted banning that is rampant here there would be more knowledgeable people responding to comments and questions from IDists.

  405. 405
    Andre says:

    Reality

    Keith S did run…..

    I asked about PCD, got my own OP at TSZ but no answer from Keith S…….

    The Question again, Reality perhaps you should try and answer it?

    How did unguided processes create a guided process that prevents unguided processes from happening?

  406. 406
    Andre says:

    Zachriel

    hahahahahahahahahaha…..

    we have a phylogeny showing humans evolved from primitive deuterostomes

    Then why is the story being rewritten again? And again…. and AGAIN!

    http://www.scientificamerican......rewritten/

  407. 407
    Zachriel says:

    Andre: Then why is the story being rewritten again?

    Hey, you discovered a new cousin. That must mean the theory of how babies are made must be wrong.

  408. 408
    Joe says:

    REality:

    Keith hasn’t run from anything and you know it

    Yes, keith is running from my refutations of his arguments. Heck he doesn’t even seem to know what a nested hierarchy is.

    If it weren’t for the unwarranted banning that is rampant here there would be more knowledgeable people responding to comments and questions from IDists.

    That was proven to be false. There aren’t any knowledgeable ID critics who have posted here. There aren’t any knowledgeable evolutionists who have posted here- ever.

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