Complex speciation of humans and chimpanzees

_{Mario A. Lopez
March 12, 2008

Biology, Darwinism, Evolution

1}_{Categories
Biology
Darwinism
Evolution}

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John Wakeley¹

Abstract

Arising from: N. Patterson, D. J. Richter, S. Gnerre, E. Lander & D. Reich Nature 441, 1103–1108 (2006); Patterson et al.

Genetic data from two or more species provide information about the process of speciation. In their analysis of DNA from humans, chimpanzees, gorillas, orangutans and macaques (HCGOM), Patterson et al.¹ suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al.¹ do not statistically test their own null model of simple speciation before concluding that speciation was complex, and—even if the null model could be rejected—they do not consider other explanations of a short divergence time on the X chromosome. These include natural selection on the X chromosome in the common ancestor of humans and chimpanzees, changes in the ratio of male-to-female mutation rates over time, and less extreme versions of divergence with gene flow (see ref. 2, for example). I therefore believe that their claim of hybridization is unwarranted.

[Bold added]

Just curious…How does interspecific hybridization occur between a Pan & Homo ?

Comments

Another Trevors and Abel paper extending their FSC approach with concrete application to existing protein families: Measuring the functional sequence complexity of proteinsAtom_{March 26, 2008
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Jerry, of course I am familiar with Calvert and Harris' writings, although I haven't looked at any of them for the last couple of years. What I wanted to know was which article you were referring to as a good explanation of CSI. I take it now that you are referring to "Intelligent Design: The Scientific Alternative to Evolution." That's what I wanted to know.Jack Krebs_{March 26, 2008
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KF, No problem.
Special post Easter greetings to the luminous one
I'll be sure to let her know. Belated Easter greetings to your family as well.Atom_{March 26, 2008
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Atom: Thanks a mill -- as usual. GEM of TKI PS: Special post Easter greetings to the luminous one!kairosfocus_{March 26, 2008
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Jack: I don't think I have mischaracterized the TE's., indeed there is much more that could have been said. I simply summarized my argument in as few words as possible. Perhaps you could summarize your objection to my argument. You can begin by explaining why you think the distinction between conceiving design and perceiving design is unimportant.StephenB_{March 26, 2008
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The Trevors and Abel paper can be found here: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1208958 jerry, Thanks for the link.Atom_{March 26, 2008
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I am flabergasted that Jack Krebs is not aware of Calvert and Harris's publications.jerry_{March 26, 2008
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KF, The paper is on a thread here. The PDF is here: Is Intelligent Design Required for Biological Life? Also, I remember Trevors and Abel using FSC (which I expanded to FSCI), which in their usage stands for "Functional Sequence Complexity" - basically CSI.Atom_{March 26, 2008
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Atom, The discussion of CSI in within a document published by John Calvert and an associate, William Harris. They are not creationist and were very much involved in the discussion of the Kansas standards. The first two documents on their site are 1. the discussion of Intelligent Design and contains the CSI discussion. It is rather brief and easy to understand. 2. the second document contains the quote by Liz Craig. There are other documents there. Here is the link http://www.intelligentdesignnetwork.org/publications.htmjerry_{March 26, 2008
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I promise I'll help bring the thread to an end (by quitting posting), but could you provide a link to the piece by Calvert on CSI. ThanksJack Krebs_{March 26, 2008
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Jerry, if another similar thread is started, that would be great. But if the choice is between continuing this thread or abandoning the subject matter, then I would prefer to continue, snags and all.StephenB_{March 26, 2008
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Atom Could you please get someone to pull the Kalinsky paper together in one PDF or something, at one linked place? [BTW, the idea of functional information sounds just a bit familiar. And FSCI is my abbreviation not T and A's – I have forgotten what they use, was it something like algorithmic information? Maybe, too, my always linked notes can be helpful to at least some?] GEM of TKI PS: Jerry: You have a point on how long and how fruitlessly on the NDT side this thread has been – but that is in itself very, very telling on the actual balance on the merits. And, indeed I still yearn to hear on the origin of full opposable thumbs and the full verbal ability of humans, etc, in the context of protohumans allegedly hybridising with protochimps. [And who better to do that than one trained in Anthropology with at least some specialisation in evolution? Or will this be yet another line where he goes silent . . .] PPS: SB – I do not have TV anymore so I didn't know about any ads on us cave men! (I refuse to pay what it costs for what it delivers --- trash!) Yabba Dabba Dabba Dooo!kairosfocus_{March 26, 2008
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I haven't seen Calvert's explanation of CSI. Is it available online somewhere? Yeah, this thread is long, no argument here. :)Atom_{March 26, 2008
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Atom, I started to read it and got sidetracked. The best exposition of CSI I have seen is by Calvert who led the ID people at the Kansas standards. It limits its scope and it becomes comprehensible. My problem with Dembski's approach is that it is too universal or general and thus to deal with every possible situation becomes very abstract and essentially unknowable except to a select few. But someone should stop this thread because like Dembski's exposition of CSI it is only accessible to a few people who are intent on following the mini threads going on within it. Each may make interesting discussions if separated.jerry_{March 26, 2008
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Stephen, your characterization of what TE's believe is incorrect. However, given both the length of this thread, the difficulty of the topic, and my past experience discussing this here at UD, I'm not going to try to explain why I think you're wrong. You might check out Keith Miller's book "Perspectives on an Evolving Creation" or look for some essays on the topic at ASA. And I agree that this thread has gone on long enough (although I said that once before, and recanted.)Jack Krebs_{March 26, 2008
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echos = echoes*Atom_{March 26, 2008
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I for one would like to see someone post a coherent exposition of it all.
Hey Jerry, Have you checked out KD Kalinsky's paper posted by idnet.com.au? Kalinsky deals with the CSI question from a "functional information" angle, which is a much simpler way than dealing with general "specifications." This method is more specific (forgive the unintended pun) but is a concrete application of Dembski's broader framework. It echos the approach of Trevors and Abel, with their FSCI.Atom_{March 26, 2008
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-----kairosfocus: “Marcus Tullius Cicero — cf 500 — though in 50 BC, was not exactly a cave-man! ; -)” That is very true. My objective was to dramatize the point that calculating the “specified complexity” of a written paragraph is a reasonably easy thing to do. Thus, it serves as a good example for those who could not follow the math in another context. My “cave man” reference was meant to evoke images of a television commercial that ends with, “so easy a cave man could do it.” I didn’t mean to suggest that there was little wisdom in antiquity. Quite the contrary. A little ancient wisdom would fulfill a desperate need for some of our more logically challenged friends.StephenB_{March 26, 2008
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I will put my two cents in again. First - This thread should be stopped. It often takes a minute to load which is an indication that there is too much here to actually make a coherent statement because of the inability of looking at the various comments. Second - I have never seen Jack Krebs make a comment of substance about the evolution debate. He avoids it like the plague which is interesting because he said he has a background in evolutionary theory. He did make one comment here and it was irrelevant which indicates he either does not understand the debate or admits he doesn't have anything of substance to provide. Some moderator should start a thread about the Kansas science standards and maybe the debate could continue there. I said I have no problem with the Kansas standards but that Darwinian evolution should be eliminated from the curriculum because it does not live up to them. We have had several threads on CSI and they all seem to end up in a morass. I for one would like to see someone post a coherent exposition of it all. Don't say it exists because each time it is debated we get into the same quicksand. Don't try to convince me of the value of CSI. I understand the probabilities are so outlandish they could never happen which out intelligent input but I fail to see a real clear and comprehensive approach. Don't point to Dembski's books because I read one and could not understand it and several commenters with technical backgrounds have said the same about the other books suggested. The mathematics are too complex for any mortals to deal with. Until such a document exists and moderators and commenters here can address all the inane comments such as congregate's rocks and the CSI of a vole we will always have the morass. It gives the Darwinists some joy as they can make up these inane examples and we run around trying to deal with them. It allows them to avoid their conundrum of not having any empirical evidence for their pet theory. Hey what happened to the chimps and humans?jerry_{March 26, 2008
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SB: Just to make a point, let me quote the General Scholium to Principia, by of course Newton: _____________ . . . 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. This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called Lord God pantokrator , or Universal Ruler; for God is a relative word, and has a respect to servants; and Deity is the dominion of God not over his own body, as those imagine who fancy God to be the soul of the world, but over servants. The Supreme God is a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: these are titles which have no respect to servants. The word God usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God: a true, supreme, or imaginary dominion makes a true, supreme, or imaginary God. And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done. He is not eternity or infinity, but eternal and infinite; he is not duration or space, but he endures and is present. He endures for ever, and is every where present; and by existing always and every where, he constitutes duration and space. Since every particle of space is always, and every indivisible moment of duration is every where, certainly the Maker and Lord of all things cannot be never and no where. Every soul that has perception is, though in different times and in different organs of sense and motion, still the same indivisible person. There are given successive parts in duration, co-existent puts in space, but neither the one nor the other in the person of a man, or his thinking principle; and much less can they be found in the thinking substance of God. Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. God is the same God, always and every where. He is omnipresent not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved [i.e. cites Ac 17, where Paul evidently cites Cleanthes]; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. It is allowed by all that the Supreme God exists necessarily; and by the same necessity he exists always, and every where. [i.e accepts the cosmological argument to God.] Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure, and can therefore neither be seen, nor heard, or touched; nor ought he to be worshipped under the representation of any corporeal thing. [Cites Exod 20.] We have ideas of his attributes, but what the real substance of any thing is we know not. In bodies, we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the savours; but their inward substances are not to be known either by our senses, or by any reflex act of our minds: much less, then, have we any idea of the substance of God. 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. [Cf also his Rules of Reasoning.] _______________ That should make it pretty clear how the greatest scientist of all time – and author of the most powerful synthesis of a deterministic system of dynamics -- thought. GEM of TKI PS: This excerpt is of course the heart of appendix 4 my always linked.kairosfocus_{March 26, 2008
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PO: First, let us clear off the plainly incorrect notion that through the magic of RV + NS, we can account for the complexity of life. Then maybe Berra's blunder offers a clue: he tried to present the Corvette family 1953 to the 1980's as an illustration of evolution. But, he forgot the real common factor: common design. How that design was done is an onward exercise [in reverse engineering – and with an eye to forward engineering, i.e ID is not at all a science or technology stopper; cf my exchanges on really intelligent robots a few months back . . .], but first let us understand that we are looking at quite evident design, as the FSCI simply is vastly beyond reach of RV + NS, but FSCI of the relevant quantity is well within the reach of intelligent agents. Just, we have not yet mastered the QUALITY of the engineering to do it – YET! And yes, I am unabashedly optimistic that we will one day be able to do R Daneel Olivaaw and co, but probably with electronic brains. The very thought makes my handy soldering iron hand itch. [A lot better than reading the reports that have kept me pinned to the PC this morning. At least, the reports have relatively good -- but it seems expensive -- news.] GEM of TKIkairosfocus_{March 26, 2008
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-----Jack Krebs: "The confusion here is in the use of the word design. Such scientists believe that the rational order we find in the universe is because God designed it so. However that is different than the position of ID, which says that certain things show detectable signs of having been specifically designed. Many religious scientists believe in design in the theological sense but are opponents, on both scientific and religious grounds, of Intelligent Design and the arguments put forth by the ID movement." I am gratified that you would use the word confusion and design in the same sentence, because you have identified the very nature of the problem. Let us now consider the cosmological/biological schizophrenia involved in positing undetectable theological design. You refer, of course, to the theistic evolutionists, better characterized as Christian Darwinists. As we know, TE’s begin by accepting the Darwinian formulation of chance and then they plug God into that paradigm as a kind of footnote. To make it work, they insist that God stacked the deck so that life would evolve solely by chance. Somehow, God “designed” a non-design universe, except that the design is inherent in the evolutionary process. As a result, teleology gets twisted like a pretzel: life is designed, except that it isn’t; evolution is directed, except that it isn’t; biology has a purpose; except that it doesn’t. It is important to understand the epistemology that supports this whole notion in order to grasp its novelty-like nature. For ID, design is PERCEIVED, meaning that it can be APPREHENDED; For TE, design is CONCEIVED, meaning that it can only be COMPREHENDED. Now, as it turns out, every TE that takes this position violates his own ethic as a Christian Darwinist. Biblical Christianity holds that design can be both perceived and apprehended; Darwinism holds that design is totally illusory. Take note of the way the cognitive dissonance and self-contradictory composite resolves itself. In the end, TE’s reject Biblical teleology totally and accept Darwinistic non-teleology totally. That means of course that there Christianity is not RECONCILED WITH but rather SUBORDINATED TO their Darwinism. Thus, these religious folks that you allude to do not, in fact, believe in design at all. They simply smuggle design language into their rhetoric so that they can seem, oh, so reasonable. They want their God and the Darwin too; but they want a quiet God and a loud Darwin. Now, I clarify these things to illuminate yet another issue. You have suggested that scientists of the past practiced something similar to today’s methodological naturalism. Kairosfocus and I have already refuted that point several times. But I will confirm it yet again from yet another perspective. We know that methodological naturalism, when practiced by a TE, consists of believing that design is CONCEIVED and COMPREHENDED. Yet, we also know that all the great scientists of the past held that design is PERCEIVED and APPREHENDED. That means, of course, that they would have had nothing to do with your intrusive novelty. So, again we discover that this methodological naturalism that you are foisting on the world is totally alien to traditional science, and would clearly have offended Sir Isaac Newton and company.StephenB_{March 26, 2008
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Atom: Excellent point -- as usual. GEM of TKI PS: C -- 250 base pairs in 3-letter DNA code is about 80 protein monomers [about 1/4 of the average protein chain length], and takes us to 500 bits of information to code for it. The 10^150 configs get eaten up real fast, LOOONG before we get to body-plan level information capacity ~ 100 million base pairs if fruit flies are any useful metric.kairosfocus_{March 26, 2008
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"The missing links at that level have been missing for 150+ years now." Kairofocus, what do you propose in place of common ancestry?PannenbergOmega_{March 26, 2008
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FTK Thanks. GEM of TKI PS: C, the OOL issue -- before there was life to reproduce -- sorts out the initial claim you make, and in the context of body-plan level biodiversity, we have to get a LOT of bio-information in before we can get TO the bio-function. The missing links at that level have been missing for 150+ years now.kairosfocus_{March 26, 2008
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OK, and thanks for the discussion, Atom.Jack Krebs_{March 26, 2008
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Onlookers, We are of course by now well on a red herring track currently, leading out to an ad hominem soaked strawman. In the interests of getting back to the substantial and important issues being distracted from, I therefore cite from the relevant smoking gun statement by Ms Liz Craig -- evidently an officer of and media and PR contact for KCFS -- on February 10, 2005 at 7:35 pm. This message outlines the PR strategy as practised by KCFS since 1999:
My strategy at this point is the same as it was in 1999: notify the national and local media about what's going on and portray them in the harshest light possible, as political opportunists, evangelical activists, ignoramuses, breakers of rules, unprincipled bullies, etc. There may no way to head off another science standards debacle, but we can sure make them look like asses as they do what they do. Our target is the moderates who are not that well educated about the issues, most of whom probably are theistic evolutionists. There is no way to convert the creationists. The solution is really political. . . . Posted by Liz Craig, Member no 70 KCFS .org Discussion Forum
Let us observe: 1 --> The strategy is fundamentally a political, attack the man, public relations one, and has been sustained since 1999. 2 --> Its target is especially theistic evolutionists and “moderates” who of course are unlikely to realise that they are seeing a very slanted view of what is going on. (Of great help is the fact that the media amplifiers are predominantly dominated by those who will sympathise with or actively take the side of the party attempting to redefine science as in effect the best evolutionary materialist account of the cosmos from hydrogen to humans. Earlier failures of education systems to equip us to think critically and to truly understand the foundations and core praxis of science don't help matters.) 3 --> Ms Craig is evidently the PR person, and is not just giving her private opinion (Take note LNF): she is outlining STRATEGY, a strategy that had by 2005 long been in use, and one that plainly continues to be in use. 4 --> The strategy ducks away form the matters of substance, to try tot discredit the persons associated with particular views. [Observe that I have this AM taken time to address well over a dozen points of substance – and observe what instead is the focus for attempted debate from the side of those who champion darwinism.] Let us return to the core issues, instead of letting ourselves rep[eatedy get side tracked through destructive PR spin tactics. GEM of TKIkairosfocus_{March 26, 2008
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Good morning all, I think my point is clear, as I've made it several times: there are interactions and these interactions will either increase the likelihood of seeing certain types of events (a claim that needs to be substantiated with evidence and quantified) or you are making appeals to magical, unknown ordering principles. I can do the same: I can claim that all these posts were not designed by me, but that they were the lucky conincidence of random fluctuations and interactions of electrons. Electrons interact in the real world and they may in fact result in messages such as this. (Sure it is a big claim, but apparently we can invoke ordering principles without evidence of how they quantitatively change a situation...so I claim it here.) Let's not stop at electrons. Dice interact with air molecules, so a 'pure chance' scenario that does not take molecular air movements into account is irrelevant. We cannot calculate the expected outcomes of dice rolls unless we can calculate the incredibly complex interactions of the air molecules involved when the dice are thrown. You seeing the irrelevance of your protests yet Jack? Either the interactions affect likelihoods in a measurable way (in which case you need to show the measurements to back up this claim), or they don't. If they do, then you'd have the measurements in hand and the EF is safe. If not, then we are stuck with likelihoods the same as chance, by definition. I don't need to repeat my point further.Atom_{March 26, 2008
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If you really want to know where the ID community stands on issues. Read the Design of Life & the Privileged Planet. Don't play intellectual mind games.PannenbergOmega_{March 26, 2008
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"Oh, good grief…kf, don’t let Jack BS you." Thank you, FTK.PannenbergOmega_{March 26, 2008
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