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Is nature really a struggle in which natural selection is the key factor?

British physicist David Tyler comments:

In a perceptive essay, Daniel Todes focuses attention on the reactions of Russian biologists to Darwin’s writings. Many of these naturalists “were evolutionists before 1859″, so they did not dissent from common ancestry. However, their experiences of the living world were quite different from Darwin and Wallace, who drew their inspiration from densely populated tropical forests and related habitats. They witnessed a struggle for existence that matched the description Thomas Malthus had given of human communities. Using the same logic, Darwin and Wallace were stimulated to think about winners and losers in populations of animals and plants. The Russian scientists lived in a different world.

[They] “investigated a vast under-populated continental plain. For them, nature was not an “entangled bank” – the image Darwin took from the Brazilian jungle. It was a largely empty Siberian expanse in which overpopulation was rare and only the struggle of organisms against a harsh environment was dramatic.”

The Russian response to living in a harsh environment was to develop “the language of communalism – stressing not individual initiative and struggle, but the importance of cooperation within social groups and the virtues of social harmony.” The analysis of Malthus did not match the biological communities in their part of the world, so Darwin’s metaphor of the “struggle for existence” was not, in their view, well grounded.

That’s always what bothered me. I see competition in nature, to be sure, but also lots of cooperation. Otherwise, life could not survive against non-life. There is much more non-life than life. That much should be obvious. For more, go here.

Tyler also points out that the modern synthesis that is supposed to save Darwinism is gone.

Earlier this year, Eugene Koonin published a masterly analysis of the impact of genomics on evolutionary thinking. This proved to be too meaty a study for a concise blog, and my initial draft was abandoned. Happily, a shorter overview has now been published, and this abstracts salient points from the research paper. Koonin notes that the 1959 Origin centennial was “marked by the consolidation of the modern synthesis” but subsequent years have witnessed great changes which have undermined its credibility. “The edifice of the modern synthesis has crumbled, apparently, beyond repair.”

Koonin uses the metaphor of “the landscape of evolutionary biology”. There are three distinct revolutions have occurred over the past half-century: the molecular, the microbiological and the genomic revolutions.

“[T]his year is the perfect time to ask some crucial questions: how has evolutionary biology changed in the 50 years since the hardening of the modern synthesis? Is it still a viable conceptual framework for evolutionary thinking and research?”

The molecular revolution culminated, says Koonin, in the neutral theory, which means that purifying selection is more common than positive selection. The microbiological revolution brought the world of prokaryotes into the domain of evolutionary biology, but it then became apparent that the concepts of Darwinism and the modern synthesis “applied only to multicellular organisms”. The genomic revolution revealed that the living world was “a far cry from the orderly, rather simple picture envisioned by Darwin and the creators of the modern synthesis”. In particular, it is now interpreted as an “extremely dynamic world where horizontal gene transfer (HGT) is not a rarity but the regular way of existence, and mobile genetic elements that are vehicles of HGT are ubiquitous”. “The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the tree of life as we knew it but also another central tenet of the modern synthesis inherited from Darwin, namely gradualism. In a world dominated by HGT, gene duplication, gene loss and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.”

Koonin is serious in saying that all the concepts of the modern synthesis are in need of a fundamental overhaul. “Moreover, with pan-adaptationism gone forever, so is the notion of evolutionary progress that is undoubtedly central to traditional evolutionary thinking, even if this is not always made explicit. The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking. In the postgenomic era, all major tenets of the modern synthesis have been, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the modern synthesis is gone.”

Koonin tentatively identifies two candidates to fill the vacuum left by the discarded modern synthesis. The first of these appears to emphasis the role of chance; the second appears to emphasise law. “The first is the population-genetic theory of the evolution of genomic architecture, according to which evolving complexity is a side product of non-adaptive evolutionary processes occurring in small populations where the constraints of purifying selection are weak. The second area with a potential for major unification could be the study of universal patterns of evolution such as the distribution of evolutionary rates of orthologous genes, which is nearly the same in organisms from bacteria to mammals or the equally universal anticorrelation between the rate of evolution and the expression level of a gene. The existence of these universals suggests that simple theory of the kind used in statistical physics might explain some crucial aspects of evolution.”

It is not difficult to predict that Koonin’s analysis will not be received quietly by the very vocal leaders of evolutionary biology. They are still entrenched in neoDarwinism and show no signs of conceding any ground to anyone.

Go here for more.

Actually, Koonin is just as likely to be ignored as not quietly received. The fantasy creation story of fashionable atheism is in many places, government policy. Its proponents often have tenure and get their pay every month. The only solution is eventual retirement parties, followed by a big revaluation – = what do we really know? How much is mere propaganda?

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104 Responses to Is nature really a struggle in which natural selection is the key factor?

  1. I think it’s also very questionable whether populations geometrically increase and that it is this “too many” competing for the “too few” resources that drives natural selection.

    So the fundamental Malthusian basis can be questioned on two accounts:

    1. The assertion of scarce resources.

    2. The assertion of uncontrolled population expansion.

  2. How much is mere propaganda?

    I think this may be the most important thing to arm the next generation of students with, namely the tools to determine if what they are being taught is mere propaganda or is worth listening to.

  3. Mung

    I think it’s also very questionable whether populations geometrically increase

    In fact you can observe it yourself quite simply, as the number of microorganisms in a culture broth will grow exponentially until an required nutrient is exhausted.

    Of course, we are not talking about an empty Siberian expanse in that example, quite a different situation.

    More on exponential growth here
    http://en.wikipedia.org/wiki/Exponential_growth

  4. “Actually, Koonin is just as likely to be ignored as not quietly received.”

    Someone pointing out that the edifice of the modern synthesis is crumbling is running a big career risk. Bravo to Dr Koonin for standing up and we can only pray that it works out well for him.

  5. In fact you can observe it yourself quite simply, as the number of microorganisms in a culture broth will grow exponentially until an required nutrient is exhausted.

    No one was asserting that a population of organisms cannot grow exponentially.

    What I wrote was:

    I think it’s also very questionable whether populations geometrically increase and that it is this “too many” competing for the “too few” resources that drives natural selection.

    However, I have questions about your example.

    What if this “required nutrient” was not present from the start?

    Does the experiment still show the exponential growth?

    What happens when the population has grown so large that the “required nutrient” has been consumed?

  6. Interesting; both Will Provine and I have been saying “the modern evolutionary synthesis is dead” for years. Indeed, the phrase noted in the OP — “hardening of the synthesis” — was coined by Will Provine to describe the narrowing of focus in evolutionary theory during the first half of the 20th century to concepts entirely reducible to mathematical models, especially theoretical population genetics (see
    http://www.uncommondescent.com.....ment-69014
    and
    http://evolutionlist.blogspot......onary.html
    and
    http://evolutionlist.blogspot......-gene.html

    Ironically, John Sanford and William Dembski (among others in the ID camp) have not moved beyond this narrow focus on theoretical population genetics, and so have apparently missed the fact that evolutionary biology has evolved far beyond the narrow theoretical focus of the mid-20th century.

    As for people like Dr. Koonin taking a “big career risk” in stating the obvious, both Will and I have been saying all this about the “modern synthesis” for a very long time, yet both of us are respected members of the faculty at Cornell and neither of us have “suffered” in any way of which I’m aware. Yes, some of our colleagues disagree with us, some of them quite strenuously. That’s what makes a life in academics so much fun! And when it’s all over, we all go to Will’s farmhouse for a beer (several actually) and an exhilarating slide down his bobsled run (that’s all of us; EBs, TEs, IDs, and YECs…at least the one’s who respect the rules of academic courtesy and no-holds-barred intellectual debate).

    Maybe that’s because we have also pointed out that the “modern evolutionary synthesis” has itself evolved to the point that evolutionary biology today is broader, more generally applicable, and less narrowly focused than at any time since the publication of the Origin of Species 150 years ago. That’s why I’ve titled my forthcoming book The Darwinian Revolutions — there’s been more than one “evolution revolution”, with plenty more coming. As Will is fond of saying, it’s an incredibly exciting time to be an evolutionary biologist. Indeed, it’s like being a physicist in 1905; a whole new world of theoretical and practical empirical research is opening up, with new discoveries being made every day.

    As just one example, Kyoto-prize-winning evolutionary biologists Peter and Rosemary Grant have reported on something that Darwin could only speculate about: the systematic empirical documentation of the “origin” of a new species (see http://evolutionlist.blogspot......olved.html ). Creationists have of course moved the goalposts, arguing that “they accepted all along that new species could arise from existing ones, it’s just “microevolution”, which everyone accepts. This despite the fact that speciation has always been considered to be the first (and perhaps most important) stage in macroevolution, and that less than two decades ago creationists were confidently stating that “true” speciation had not only never been observed, it couldn’t ever be observed because it can’t happen.

    Now the leaders of the ID movement — people like Dr. Michael Behe and Dr. William Dembski — publicly state that they fully accept that descent with modification (i.e. evolution) has happened (despite the name of this blog), that microevolution (i.e. natural selection, sexual selection, and genetic drift) are also fully accepted, and the “real” focus of disagreement is over the “engines of variation” that produce the raw material upon which the “engines of micro and macroevolution” operate. They’ve come a long way, but they’ve missed the parade by a couple of decades. So it goes…
    As for the OP, I would say that Tyler’s essay on where evolutionary biology is today is quite close to the the mark. The concept of natural selection as the foundation of evolutionary change has been largely “superseded”, mostly through the work of Motoo Kimura, Tomoko Ohta, and others, who have shown both theoretically and empirically that natural selection has little or no effect on the vast majority of the genomes of most living organisms.

    However, ID supporters should find this sea change in evolutionary biology to be cold comfort. The overall effect of the advances in our understanding of how genomes and phenotypes change over time has had the same effect on evolutionary theory that the rise of quantum mechanics had on classical physics. Einstein famously asserted that “God does not play dice”, but a century of physics research has shown him to be more wrong about how the universe works at the quantum level than ever.

    The same is true for the “evolving synthesis”. Rather than revert to a neo-Paleyan paradigm (as proposed by Behe, Dembski, and their supporters), evolutionary biology has gone in the same direction as quantum mechanics. According to the “modern synthesis” of the last century, the genome was “homeostatic”, “organized”, and “regulated” primarily by natural selection. Sure there were purely random processes also going on (such as genetic drift), but most evolutionary change was both adaptive and coherent over time.

    Oops.

    Kimura, Ohta, Jukes, and Crow dropped a monkey wrench into that idea, and then Gould and Lewontin finished the job with their famous paper on “the spandrels of San Marco and the Panglossian paradigm”. The rise of evo-devo over the past two decades has laid the groundwork for a completely new and empirically testable theory of macroevolution, a theory that is currently facilitating exponential progress in our understanding of how major evolutionary transitions happen. And iconoclasts like Lynn Margulis, Eva Jablonka, Marian Lamb, Mary Jane West-Eberhard, and David Sloan Wilson are rapidly overturning our understanding of how evolutionary change happens at all levels, and how it is inherited.

    So, as I have said many times before, when ID supporters set their sights on “neo-Darwinism” as a target for criticism, they set their sights on a model that has been all but abandoned. The carnival has moved on, folks, and ID supporters are fighting battles that evolutionary biologists left behind a half century and more ago.

  7. 7
    EndoplasmicMessenger

    Hello All,

    In his book Darwinian Fairytales, David Stove looks deeply at the Malthusian/Darwinian theory in the context of the life of man and human society, and not only finds it severely wanting, he finds it impossible. A very important and highly recommended book.

  8. I doubt ID proponents are going to find the sea change “cold comfort”, Allen. If anything it’s yet another vindication, a demonstration that the broad thrust of ID – particularly, that when it comes to evolutionary biology there’s a tremendous amount of exaggeration (in terms of what we know about biology and species, what we don’t know, how adequate our current state of knowledge is, what said knowledge indicates about our world, etc) – is correct. You’re pointing out that ID proponents are out of date, but if that’s true, all it means is they’re fighting a battle they’ve already won, and simply don’t realize it. (Indeed, that’s my own position more and more.)

    You may as well dismiss ID proponents for their deep criticisms of materialism, on the grounds that materialism is an untenable and increasingly abandoned position anyway. That just a gripe-laden way of admitting “Well, you guys were right after all.” And I say that well aware that you apparently reject materialism yourself.

  9. 9

    nullasalus at 8,

    I doubt ID proponents are going to find the sea change “cold comfort”

    Your doubts are not well-founded. Mr. MacNeill’s analogy with quantum mechanics is well founded. Just as natural selection explained much empirical evidence of evolution, Newtonian mechanics explained many observations of physical processes. Neither was a complete explanation. Quantum mechanics extends Newton’s work to the infinitesimally small, and the work of Kimura, Ohta, Jukes, Crow, and others extends the modern synthesis to a broader range of empirical evidence.

    Neither quantum mechanics nor the latest evolutionary biology theories require abandoning methodological naturalism. In fact, both demonstrate that the underlying philosophy of science is sound, and leads to greater explanatory power.

    This is indeed cold comfort for ID proponents.

  10. Mustela Nivalis,

    Quantum mechanics did not merely “extend Newton’s work” – it showed the previous, classical-mechanistic view of the world to be deeply flawed and flat-out wrong in some ways. Materialism took a savage beating as a direct result of this (one which was never really recovered from).

    Similarly, the advances which one may say are ‘extending Darwin’s work’ are extending it by utterly contradicting him. We have Allen MacNeill saying that “neo-Darwinism” – the horse ID proponents have been wailing on with both fists for quite some time – is actually a dying or dead horse anyway. That model is dead, and is being superseded.

    Keep in mind, it isn’t like Denyse O’Leary here has only just discovered discussions like these: She’s been covering Margulis’ and others views, with some considerable sympathy, for a while on her blog. People who think that the aims of ID proponents only advance if MN is eschewed in name are like those who think ID proponents universally insist that evolution is not true: Deeply misinformed about the concept and “movement” at large.

    But hey, believe what you want. To hear you guys talk, tomorrow the New Scientist could have a cover story (again) of “Darwin Was Wrong”, and – so long as no one said “methodological naturalism”, that lovable mirage, had to be dumped – it would be “cold comfort to ID proponents”. Color me skeptical. And amused, while you’re at it.

  11. A simplistic view might be that Newton’s work confirmed that gravity is a fact and that advances in QM have not in any way lead to abandonment of the main scientific paradigm: We are not able to detect any designers at work in nature and until that unlikely discovery is made we cannot take such considerations seriously.

    IMHO, just as gravity is a fact even though AFAIK we have not been able to develop and test a complete theory of gravity, evolution also is an established fact even if there may be many facets of mechanism we have not yet fully understood.

    Just as we do not see any need for introducing supernatural forces in order to explain gravity, we don’t see any need for them in any other field of science including evolution.

    That some people wish such forces would be detectable is another matter.

  12. Cabal,

    The inability to detect designers at work in nature is not a “scientific paradigm” whatsoever. The whole point of the opposition to ID is that science, properly defined, is incapable of such detections one way or the other. Such talk is philosophy and metaphysics, whether you detect design’s presence or lack. But if you want to say that such detection is in the realm of science, good work – you’ve just legitimized ID.

    As for the lack of necessity for “supernatural forces”, what nonsense. The fact that panpsychism, non-physicalistic metaphysics, multiverses, simulated/created universes, are now popping up as “scientific possibilities” puts the lie to that claim. The only difference is that what used to be recognized as the supernatural is now being called “natural” out of desperation.

    Rather like how neo-darwinism’s death by criticism is now being shrugged off as of no interest to ID proponents. Almost as if this entire debate is less about science and more about metaphysics anyway.

  13. Mr Nullasalus,

    Rather like how neo-darwinism’s death by criticism is now being shrugged off as of no interest to ID proponents.

    I think Mr Macneill’s point was not that neo-Darwinism died by criticism, rather it was replaced by another material explanation even less familiar and less comforting than the survival of the fittest.

    We can understand an explanation in which good works are rewarded easily, because it matches the rough outline of our human experience. It is the same explanation of success we like to think is at work in a political democracy or freemarket capitalism, or the marketplace of ideas.

    However, easy analogy to human experience says more about how easy it will be to market an idea than how good it is an explanation. (po-mo science, yay!)

    But being the best possible finch doesn’t make you more likely to be the founder of a new species of finch. Being a poor finch, and forced into a marginal territory, which is then cut off from the parent territory, or being forced to eat different foods, or being blown across the sea in a storm are examples of success by a shlemiel that finds the winning lottery ticket on the ground.

    While good things do happen to the poor heroes of our folk tales, they usually have virtues that outweigh their poverty. The subtext of the folk tale is that these virtues such as honesty, cleverness, trustworthiness, etc are being rewarded.

    The analogy to QM as an explanation is that Einstein was being profoundly human when he stated a preference for a fair game – dice rolled in public. Survival of the fittest was at least a fair game. Neutral drift and founder effects, profoundly less so.

    As a familiar and comfortable opponent, it is fine to tilt at the windmill of neo-Darwinism. That sadly ignores the wind turbine now thirty kilometers offshore.

  14. In comment #8 nullasalus wrote:

    “You’re pointing out that ID proponents are out of date, but if that’s true, all it means is they’re fighting a battle they’ve already won, and simply don’t realize it.”

    Then how do you reconcile this with the following quote from Eugene Koonin (which David Tyler conveniently overlooked in his blogpost):

    There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation.” [emphasis added]

    So much for CSI, or any kind of “C”.

    Seems to me that Tyler performed a rather classical quotemine on Dr. Koonin, selecting those bits of the abstract of his papers that supported a viewpoint that was exactly the opposite of the actual content of the articles.

    Here’s what Dr. Koonin actually wrote:

    Darwinian evolution in the light of genomics.
    Nucleic Acids Research, 37(4), 2009, pp. 1011-1034.

    ABSTRACT: Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.[emphasis added]

    In other words, the evolving evolutionary synthesis of the 21st century is de-emphasizing adaptation. But, since adaptation is the heart and soul of ID (which is all about how things become purposeful in evolution), then the new discoveries are cutting the heart and soul out of ID. ID, like its mirror image “the modern synthesis” has always been relentlessly pan-adaptationist. According to ID, even those things that evolutionary biologists assert do not have a purpose actually do, we’re just ignorant of what those purposes might be. The Intelligent Designer ® does nothing by accident: “not a sparrow falls but that Thou art mindful of it”.

    But the emerging picture of the genome (and the phenome for which it is at least partially responsible) is that, rather than being a coherent, homeostatic, apparently “rationally designed” entity, it is a frothing ocean of randomly varying nonsensical and furiously selfish genetic entities, none of which give a tinker’s dam about the phenome.

    Indeed, rather than producing the exquisitely perfect adaptations of living organisms, it is becoming clear that natural selection may be important only as that process that prevents the accelerating disintegration of the genome in the face of increasing chaos. In other words, evolution isn’t a steady climb toward greater and greater complexity nor a process designed to produce perfection. No, it’s a process out of which adaptation and complexity arise almost as an afterthought in the “mind” of a universe bent wholly on self-annihilation.

    Looks like “biological quantum mechanics” to me…

  15. In comment #13 Nakashima-san wrote:

    “I think Mr Macneill’s point was not that neo-Darwinism died by criticism, rather it was replaced by another material explanation even less familiar and less comforting than the survival of the fittest.”

    As usual, Nakashima-san has it exactly right, and expressed it much more concisely than I have. The “evolving synthesis” is steadily moving away from where both ID supporters and the supporters of the “modern synthesis” thought was the heart of evolutionary biology.

    It’s a new world out there, where design and purpose are steadily being overwhelmed by chaos and disintegration. Maybe the most appropriate religion for an up-to-date evolution denier would be Norski:

    The One-Eyed God has heard the future whispered in His ear by Huginn and Muninn, and proclaims to the world,

    Ragnarok is coming!

  16. Nakashima in comment #13:

    I bow down to you, sir. What you have written here is brilliant stuff.

    ’nuff said!

  17. Allen MacNeill,

    From the beginning the debate has been about blind and undirected processes vs purposeful and directed processes.

    And what your position has failed to do is to demonstrate that blind and undirected processes can build new and useful protein machinery and change body plans.

    BTW no one is debating “evolution”.

    And your list of mechanisms does not mean they are all blind and undirected processes.

  18. 18

    nullasalus at 10,

    Quantum mechanics did not merely “extend Newton’s work” – it showed the previous, classical-mechanistic view of the world to be deeply flawed and flat-out wrong in some ways. Materialism took a savage beating as a direct result of this (one which was never really recovered from).

    There is nothing immaterial or non-material about quantum mechanics, it just shows that reality is far more complex than Newton was able to see. Newtonian mechanics is still useful, as is the modern synthesis, it just isn’t the whole story.

    Physicists are still using the scientific method, based on methodological naturalism, to investigate quantum phenomena, just as biologists are using the scientific method to investigate and explain phenomena not explained by the modern synthesis. Reports of the death of materialism have been greatly exaggerated.

    Similarly, the advances which one may say are ‘extending Darwin’s work’ are extending it by utterly contradicting him. We have Allen MacNeill saying that “neo-Darwinism” – the horse ID proponents have been wailing on with both fists for quite some time – is actually a dying or dead horse anyway. That model is dead, and is being superseded.

    The model is not dead, merely incomplete. Any model that replaces it will have to explain exactly the same observations, as well or better, and the observations it does not explain. That’s how science works. Methodological naturalism has proven to be a powerful underlying philosophy of science, leading to theories with great explanatory power. It’s in no danger of being abandoned.

  19. “So, as I have said many times before, when ID supporters set their sights on “neo-Darwinism” as a target for criticism, they set their sights on a model that has been all but abandoned. The carnival has moved on, folks, and ID supporters are fighting battles that evolutionary biologists left behind a half century and more ago.”

    Nonsense Allen and you know it. The choice is between 100% naturalistic and not 100% naturalistic changes in life forms. Nothing anyone has said on the planet has undermined that divide and the techniques of ID are just as appropriate to your scenario as to any of the evolutionary syntheses that have been put forth. So you can go on how the Darwinian paradigm is a false one, and we agree, but the questions thrown at it are just as applicable to anything you brought up. If there is to be an intelligent dialogue here then you should stop throwing your ad hominems and let’s discuss the science. There is nothing new in what you have said so why try to denigrate those who oppose naturalistic evolution as out of touch. I have read Jablonka and Lamb’s book and there is zero in it that contradicts ID. Zero, nothing, zilch, zip, nada, diddly-squat. That is not out of touch.

    You are also attacking nearly all the anti ID people on this blog with your comments. I suggest you proceed with a calm rational discussion and not imply that those here who support Darwinian processes are some how challenged in this debate. We agree that the anti ID people here appear challenged but your barbs are not appropriate for many on the pro ID side. We all want to learn, so let’s see what we can learn from you.

    As an aside, why don’t you go on Panda’s Thumb and make your claims and let’s see where it goes. It might be interesting and educational to observe.

  20. 20

    Jerry at 16,

    The choice is between 100% naturalistic and not 100% naturalistic changes in life forms.

    That sums up much of the underlying disagreement very well (although I believe there are some ID proponents who claim that ID is a scientific endeavor, even with the constraint of methodological naturalism).

    The dichotomy you note leads immediately to the question of how we could, even in principle, obtain objective, empirical evidence of non-naturalistic changes. Arguments from incredulity are unconvincing — positive evidence for non-natural mechanisms is required. What might that look like? How could we investigate it using the tools of science?

  21. “Arguments from incredulity are unconvincing”"

    Nonsense. Not when the examples pile up and the rationale for the findings are backed up by good science and logic. The term “incredulity” is used to convey a pejorative meaning to something but has no basis in the dichotomy referenced. It is all an argument based on likelihood. All the positive examples are piling up one one side while the other side has yet to provide a coherent example. Witness the latest debacle on bats.

    “positive evidence for non-natural mechanisms is required.”

    Again nonsense. The ideologue may say this because they are on the losing end of the argument and must clasp as straws to discredit what they do not like. But to the logical person, the current evidence is persuasive. They are just not allowed to be exposed to it in the curriculum. Instead they are exposed to lies. What does that tell you? It tells you the weak position the anti ID side is in.

  22. MacNeill (#14): “Indeed, rather than producing the exquisitely perfect adaptations of living organisms, it is becoming clear that natural selection may be important only as that process that prevents the accelerating disintegration of the genome in the face of increasing chaos. In other words, evolution isn’t a steady climb toward greater and greater complexity nor a process designed to produce perfection. No, it’s a process out of which adaptation and complexity arise almost as an afterthought in the “mind” of a universe bent wholly on self-annihilation.”

    Selection seems to still be the only known naturalistic directional force in adaptation. All the other sources of variation and other mechanisms now being uncovered are random with respect to reproductive fitness. If natural selection is only an “afterthought” in an overall process being seen as more and more chaotic, much more pressure is then being placed upon it to explain the origin of biological complexity, cell types, body plans, IC structures, etc. In modern evolutionary theory (whatever that is), it is still the only directional filtering force arising from natural law, and there is nothing fundamentally new in the debate. Otherwise it must be being proposed in a new MET that purely random change directly results in organized, adaptive complexity without even the filtering of selection.

  23. MacNeill,

    The concept of natural selection as the foundation of evolutionary change has been largely “superseded”, mostly through the work of Motoo Kimura, Tomoko Ohta, and others, who have shown both theoretically and empirically that natural selection has little or no effect on the vast majority of the genomes of most living organisms.

    I would have thought Kimura et al. had lost the neutrality-selection controversy. Consider this abstract:

    Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19-26% on the autosomes and 12-40% on the X chromosome. The overall trends are broadly consistent with “background selection” or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events.

    From McVicker et al. (2009), PLOS Genetics.

    Doesn’t this slightly contradict your view?

  24. Allen,

    But, since adaptation is the heart and soul of ID (which is all about how things become purposeful in evolution), then the new discoveries are cutting the heart and soul out of ID.

    Do you really think that adaptation is the heart and soul of ID? ID in biology deals with abiogenesis, which has nothing to do with adaptation, cellular machinery, motor neurons etc., and ID on the cosmological level has nothing to do with adaptation whatsoever. This is a baseless false dilemma you’ve created. And are you saying that things that arise in biological systems are not “purposeful”? I mean, clearly, they are, for they serve purposes, such as we understand now with epigenetics and supposedly junk dna that have a sort of meta-narrative when instructing the functional genes.

    But the emerging picture of the genome (and the phenome for which it is at least partially responsible) is that, rather than being a coherent, homeostatic, apparently “rationally designed” entity, it is a frothing ocean of randomly varying nonsensical and furiously selfish genetic entities, none of which give a tinker’s dam about the phenome.

    Nonsensical and selfish at the same time? Nonsensical and doesn’t give a damn about something at the same time?

    In other words, evolution isn’t a steady climb toward greater and greater complexity nor a process designed to produce perfection. No, it’s a process out of which adaptation and complexity arise almost as an afterthought in the “mind” of a universe bent wholly on self-annihilation.

    Tell “climbing mount improbable” Richard Dawkins that. So do you think the universe has a mind that has afterthougts?

  25. Clive,

    ID in biology deals with abiogenesis

    Does it? What does ID tell us about the origin of life, specifically?

    I thought ID was about the detection of design. Not the origin of life.

    Tell me something about the origin of life that can only be true if ID is required for the origin of life. Tell me something that can be tested.

  26. Allen MacNeill @6

    That’s why I’ve titled my forthcoming book The Darwinian Revolutions — there’s been more than one “evolution revolution”, with plenty more coming.

    Looking for any feedback on it before it’s published?

    So the “hardening” was the attempt to make it more mathematically rigorous, i.e., more scientific.

    And people were opposed to this. Like you and Will. But I’m sure that they jsut wanted to show how utterly compelling and inescapable it all is, to a mathematical certainty.

    For if it’s less than certain that genes get fixed in populations, and this is what drives evolution, what are you left with? Maybe it happens, maybe it don’t? And this is science?

    Ironically, John Sanford and William Dembski (among others in the ID camp) have not moved beyond this narrow focus on theoretical population genetics, and so have apparently missed the fact that evolutionary biology has evolved far beyond the narrow theoretical focus of the mid-20th century.

    There is nothing wrong with this narrow focus. For if Darwinian evolution is wrong at it’s core, then it’s still wrong, no matter how many bells and whistles (and ad hoc additional theories) you add to “the theory.”

    The fact is, that there are still unresolved problems, even with population biology. Evolutionary theory can “evolve” if it likes, but just like the vaunted “nested hierarchy,” if certain characteristics are lost over time, well, it just ain’t nested anymore, and it sure isn’t the same theory being sold to the public as “fact.”

  27. … we have also pointed out that the “modern evolutionary synthesis” has itself evolved to the point that evolutionary biology today is broader, more generally applicable, and less narrowly focused than at any time since the publication of the Origin of Species 150 years ago.

    Walter ReMine calls it a “smorgasbord.” You sort of pick and choose from it depending on the particular circumstance. I think he’s correct.

    Maybe one day evolutionary theory will have it’s own GUT(oE), but I am not holding my breath.

    It may be more “general” because you have more theories now than before, but that’s not what most scientists think of when you talk of a general theory. Adding additional ad hoc theories on to an existing theory does not make it more general, it just makes more theories. Does this simple fact truly escape you?

    What is it that unifies the various and sundry “theories of evolution”?

    Is it that “ev0olution is a fact”?

    Is it that, “no designer would have done it like this”?

    Really, I’d like to know.

    Say one thing about evolution that is true in all cases, and show me how it’s part of modern evolutionary theory.

  28. Just as we do not see any need for introducing supernatural forces in order to explain gravity, we don’t see any need for them in any other field of science including evolution.

    Color me stunned! I missed the most amazing discovery!! The explanation of gravity!!! Who won the Nobel?

    But I agree, supernatural explanations are not needed. For God is the most natural being that could ever exist, for non-existence is not in his nature. Why, he could not NOT EXIST, if he wanted to. What could possibly be more natural than an entity which has no choice in the matter?

  29. The “evolving synthesis” is steadily moving away from where both ID supporters and the supporters of the “modern synthesis” thought was the heart of evolutionary biology.

    It’s only “moving away” from it in the sense that a tree “moves away” from it’s roots, which is why so many of us remain skeptical.

    After all, it’s not like it has “moved away” from home and taken on a life of it’s own.

    Evolutionary theory may gain more branches, it may gain more leaves, but it is still firmly rooted in the same soil, and it still draws it’s nutrients from the same place that it always has.

  30. Mr MacNeill,

    Your words are very kind. I would be thrilled beyond measure if my remarks ever found a use in instructing your students.

  31. Allen MacNeill,

    You ask me how I reconcile Eugene Koonin’s quote. But that’s the funny thing – neither I, nor any other ID proponent, needs to “reconcile” anything with Koonin’s stated view. Just as it would be inane to ask Margulis how she can “reconcile” her view of evolution as cooperative with quotes from colleagues that stress evolution as competitive. She can look at the data herself, give her own explanations of it, and justify an out and out denial her colleague’s perspective, or even a broad denial with proper qualifications.

    Your presentation of ID is bizarrely off-base for someone who’s been buzzing around the sites for years. ID as insisting evolution is “a process designed to produce perfection”? Please – not when ID proponents constantly point out that imperfection or “bad design” not being arguments against design. ID as presenting a designer who does “nothing by accident”? Goodness, Allen – is that what Behe says ID is about? Dembski? Mike Gene? Steve Meyer? Or are those views ones which ID proponents consistently argue are *outside* of ID and science itself? Your depiction of ID is absurd (and I say this as a sometimes-critic of ID), and I really have to wonder if it’s due to ignorance or dishonesty.

    But here’s what I really love: None of your “Even though Neo-Darwinism is dead in the water ID proponents aren’t going to like this!” schtick gets by on the science. You’re relying desperately on narrative and poetics you gloss over the science with. But what’s comfort to ID is not determined by the energetic spin you personally give it (Disintegration! Chaos! Selfish! Nonsensical!), but the perspective ID proponents themselves bring to the table (Nanotechnology! Homeostatic! Biased! Brilliant!)

    So, sorry Allen. The “evolution is just sooooooo horrible a process that no designer would do it this way! We swear!” routine may work on YECs. But many ID proponents, many TEs, many people in general now see otherwise. Hell, as much as it bothers you, plenty of ID-leaning types see a lot of consonance between their views and evo-devo, Margulis’ views, even Lovelock-style views. In other words, the evo-devo crowd – God love ‘em! – are doing work on behalf of the ID crowd, in essence.

    So, thank you for the assistance, Allen. Thank you for helping to knock down neo-Darwinism. And thank you for the research. I’m sure many ID proponents and TEs alike will accept all these things gladly. Your shoddy “it’s all so chaotic!” narrative, however? That you can keep. It’s uninteresting, and an unpersuasive rendering of what’s being discovered.

    But then, perhaps you knew that.

  32. Mr Mung,

    Your lead comment is quite interesting, and has some imlications for our programming project.

    I think it’s also very questionable whether populations geometrically increase and that it is this “too many” competing for the “too few” resources that drives natural selection.

    So the fundamental Malthusian basis can be questioned on two accounts:

    1. The assertion of scarce resources.

    2. The assertion of uncontrolled population expansion.

    Consider that any population that succeeds in bringing (on average) more than one offspring per parent to reproductive age is increasing geometrically.

    Does this drive natural selection? No, it is only a method of delivering more variation to natural selection. A change in allele frequencies can still take place in a stable population or a shrinking population.

    There are also counter-examples such as cane toads in Australia evolving to invade new territories more quickly – though invasive species such as this also provide clear examples of geometric growth until a natural limit is reached.

    To your numbered points, I find it hard to believe that you seriously question the existence of scarce resources. Since it is obvious that no resource is infinite, is your point a more subtle one, such as ‘most resources are adequate and renewable in biology, not scarce’?

    I’ve already noted that any replacement rate above unity is exponential, the only question is what is the first scarce resource. Arctic black flies would breed until their number weighed more than the planet, but there are not sufficient warm days in Siberia to let them. Yak would cover the planet, except there are not enough plants to eat during the winter.

    The lesson of invasive species is that the control on geometric growth rests in the environment, not in some innate limit that the species imposes on itself.

  33. Nakashima,

    As with Allen, all you’re really offering here is poetic gloss. Except with the added weirdness of not even getting Einstein right.

    First, Einstein’s problem with QM as it was being offered had nothing to do with it being “fair” or “unfair”, and certainly not with a “public roll of the dice”. He had a philosophical commitment to determinism. If the dice rolls were not “public” but were still certain, determinism would be satisfied.

    Second, as for the poetic gloss – good God, you’re worse at this than Allen himself. Trying to pass off neo-Darwinism as the view the virtuous behavior (honesty, cleverness, trustworthiness) would be consistently rewarded is nothing short of insane. Neo-Darwinism as the explanation that “good works are rewarded easily”? Are you even reading what you’re writing?

    Why not try another poetic gloss? Say that, much like in other folk tales, the lowliest sparrow may – with a little bit of providence and some hard work – may play a vital role in the course of events.

    Oh, wait. Because that wouldn’t suit the aim of the moment. And what’s of central concern here is not the science, but the spin.

  34. Mr Nullasalus,

    Yes, I think both Mr Macneill and myself were speaking poetically about certain humanistic reasons why “survival of the fittest” Darwinism would be a more familiar and comforable opponent that the alien landscape of neutral drift, spandrels, and founder effects.

    However, you have misparsed my sentence, compared to my intention. I apologize for being ambiguous. “Survival of the fittest” can be analogized to “virtue is rewarded”, easily in our minds. Having apprehended the analogy, we might find it abhorrent. The point was how easy it was to grasp.

  35. Mr Nullasalus,

    Why not try another poetic gloss? Say that, much like in other folk tales, the lowliest sparrow may – with a little bit of providence and some hard work – may play a vital role in the course of events.

    Oh, wait. Because that wouldn’t suit the aim of the moment. And what’s of central concern here is not the science, but the spin.

    Ah, but that _is_ the science of the moment. The best finch in the forst is dead, and her descendants killed by deforestation, while the lowly finch, marginalized to some poor roost near the beach, has children all over the Galapagos that have become world famous. Substitute randomness for Providence and you are au courant.

  36. Nakashima,

    Wonderful. But poetics are not science, and the fact that you and Allen can put an anti-ID poetic gloss over the science replacing neo-darwinism is no more “cold comfort” to ID than someone being able to put a pro-ID poetic gloss over evo-devo should make the fall of neo-darwinism “cold comfort” for either of you.

    If your point of bringing up “virtue” and “darwinism” was merely to say “Well, darwinism was easier to understand. But the new understanding is more complicated.”, again – wonderful. Somehow I don’t think ID proponents are going to be distraught over the fact that biology and evolution is a far more complicated subject than we’ve previously been led to believe.

  37. Nakashima,

    Ah, but that _is_ the science of the moment. The best finch in the forst is dead, and her descendants killed by deforestation, while the lowly finch, marginalized to some poor roost near the beach, has children all over the Galapagos that have become world famous. Substitute randomness for Providence and you are au courant.

    No, Nak – that is not the science of the moment. It’s poetic gloss. And I can demonstrate as much.

    Compare my gloss to yours. Yours reads like a tragedy, mine reads like inspiration. In yours, you stress that the “best finch” (What in the world is such a thing?) is dead, while the “lowly finch”‘s death – I take it she is not immortal – goes unmentioned in favor of describing her success. In mine, a finch’s importance is not strictly determined – even lowly ones can achieve great things. My example stresses the potential and importance even for the disadvantaged.

    Why are we both, supposedly, describing the same thing – yet my story reads vastly different from yours? Because it’s not science. It is poetics. A type of extra-scientific description.

    Even your ending isn’t scientific. ID opponents repeatedly stress that identifying or ruling out guidance in nature is beyond science – so your distinction between “random” and “providence” is outside of science as well. Was it blind chance or divine intention? Don’t ask science – no answer can be provided.

    The fact that you seemingly cannot tell what is actual science and what is dramatics and extra-scientific exposition makes me wonder how much damage so many anti-ID “defenders of science” are really doing to what they so often claim to cherish.

  38. Allen @15

    It’s a new world out there, where design and purpose are steadily being overwhelmed by chaos and disintegration.

    Pure, utter, bullsh*t.

    On the other hand, someone paid by the state to re-enforce the accepted dogma might say something like this and expect to profit from it. Darwinism?

    What Allen (and others of his ilk) are loathe to admit, is that the cell exhibits “exquisite” and “ingenious” design.

    Where is the evidence for this “chaos and disintegration” which Allen asserts is so prevalent in biology?

  39. To your numbered points, I find it hard to believe that you seriously question the existence of scarce resources. Since it is obvious that no resource is infinite, is your point a more subtle one, such as ‘most resources are adequate and renewable in biology, not scarce’?

    I cannot recall a day where I have gone hungry and competed for resources unless it was my will to go hungry (e.g., fasting).

    So yes, I question whether it is competition for scarce resources which is driving human evolution.

    But I have also visited countries such as Kenya and India, where it can hardly be doubted by any reasonable person that individuals go hungry.

    Are they competing for scarce resources while I am not? Are they evolving while I am not?v Is it the “most fit” among them that is surviving and passing on theiur genes? And just what advantage are they passing on to their offspring? more poverty?

    Mr. Nakashima, I do not have any reason to doubt the existence of infinite resources, as evolutionary theory seems capable of an infinity of explanations.

    You appear to be concerned about my lack of faith. But I say to you, that evolutionary modeling does not take resources into account.

    I have to find your post. :(

  40. Mr Mung,

    But I say to you, that evolutionary modeling does not take resources into account.

    That is an interesting position, and one that will shape our discussion on creating just such a model. I would appreciate it if you could expand upon your thoughts.

    Earlier in this message, I saw that your objection to scarce resources had slipped from driving natural selection to driving human evolution. Rather than accuse you unhelpfully of ‘moving the goalposts’, I’ll just note that arguing a point about evolution from the current human condition, even averaged across all societies, is probably a bad idea.

    We are certainly still evolving, in the sense of our allele frequencies are changing, but the drivers of our evolution have little to with the classic drivers of metazoan evolution, I think. You probably need to go back to the Great Oxygen Catastrophe to find biota changing their own niche as much as we are.

  41. Evolutionary theory may gain more branches, it may gain more leaves, but it is still firmly rooted in the same soil, and it still draws it’s nutrients from the same place that it always has.

    Darwin, 1859: The Origin of Species
    by Means of Natural Selection,
    or
    The Preservation of Favoured Races in the Struggle for Life

  42. In comment #37 Mung wrote:

    “…someone paid by the state to re-enforce the accepted dogma might say something like this and expect to profit from it.”

    That might, indeed, be the case, but that wouldn’t be me. My paycheck comes from the “endowed” side of Cornell, not the “statutory” side, which means that I’m paid by my students via their tuition. And, since my evolution course is a voluntary elective, the only students taking it are the ones who want to do so (they’re also the ones who consistently rate my course as one of the best they’ve taken while at Cornell). And, oddly enough, slightly less than half of my students (when anonymously polled at the beginning and the end of the course) agree with this sentence:

    “Man has evolved over millions of years, but that process was guided [either by God or by some "intelligent force", identity unspecified].”

    Isn’t it somewhat disconcerting to find your most cherished prejudices undermined by the facts?

  43. Interesting: in comment #24, Clive Hayden wrote:

    “…ID in biology deals with abiogenesis, which has nothing to do with adaptation, cellular machinery, motor neurons etc….”

    while in comment #37 Mung wrote:

    “…the cell exhibits “exquisite” and “ingenious” design.”

    Hmm, looks like somebody didn’t get the memo. Which is it:

    • ID is not about the “exquisite and ingenious design of the cell”

    or

    • ID is about the “exquisite and ingenious design of the cell”?

    Somebody’s confused, here, and they’re confusing the rest of us.

    At the end of our notorious “evolution and design” seminar at Cornell in 2006, the participants (including the founders of the Cornell IDEA club) all agreed with Clive: that ID is almost entirely confined to abiogenesis and the origin of the genetic code (as hypothesized by William Dembski) and, perhaps, the origin of a very few biochemical pathways (as hypothesized by Michael Behe). Beyond these two issues, evolutionary biology (i.e. the three, inter-related but separate, empirically verified theories of descent from common ancestors, exaptation via natural selection, and genetic drift over deep evolutionary time via neutral mutation) was virtually untouched by ID.

    So, if I had to choose, I would choose Clive’s characterization about what ID is about: it’s not about biological evolution at all, it’s about how biology got started (i.e. abiogenesis), which is not part of the theory of biological evolution.

    Furthermore, I have stated many times that I believe that any theory of abiogenesis will remain forever speculative, as there cannot ever be empirical evidence (either direct or indirect) of any of the particulars of this process. Even if it eventually becomes possible to “model” abiogenesis in the laboratory, nothing guarantees that such a “model” process is how abiogenesis actually happened four billion years ago. And, since no record of what must have been a geochemical process remains in rocks dating from that time (indeed, there are no rocks dating from that time), I am fairly confident that this situation will always be the case.

    That’s why I’m not particularly interested in abiogenesis, I’m interested in biology.

  44. In comment #37 Mung asked:

    “Where is the evidence for this “chaos and disintegration” which Allen asserts is so prevalent in biology?”

    In the genome; have you read Dr. Koonin’s abstract (or, even better, his review paper)? It’s all there.

  45. Also, the empirical observation that over 99.9% of all of the species of living organisms that have ever existed (defined morphologically) are now extinct (see the books of David Raup for corroboration). If ID is about every increasing degrees of perfection, it’s doing a really lousy job…

  46. Allen,

    Interesting: in comment #24, Clive Hayden wrote:

    “…ID in biology deals with abiogenesis, which has nothing to do with adaptation, cellular machinery, motor neurons etc….”

    while in comment #37 Mung wrote:

    “…the cell exhibits “exquisite” and “ingenious” design.”

    Hmm, looks like somebody didn’t get the memo. Which is it:

    • ID is not about the “exquisite and ingenious design of the cell”

    or

    • ID is about the “exquisite and ingenious design of the cell”?

    Somebody’s confused, here, and they’re confusing the rest of us.

    Mung and I said the same thing. It’s confusing to me why you’re confused.

    So, if I had to choose, I would choose Clive’s characterization about what ID is about: it’s not about biological evolution at all, it’s about how biology got started (i.e. abiogenesis), which is not part of the theory of biological evolution.

    I was saying that ID is not solely a matter of adaptation, like your straw man was dressed up to show.

  47. Allen,

    Also, the empirical observation that over 99.9% of all of the species of living organisms that have ever existed (defined morphologically) are now extinct (see the books of David Raup for corroboration). If ID is about every increasing degrees of perfection, it’s doing a really lousy job…

    Why are you conflating perfection and survival? Is it because the Darwinian mindset demands it? That Darwinian idealism shouldn’t have any purchase as a mental framework when considering whether or not design is present.

  48. “Also, the empirical observation that over 99.9% of all of the species of living organisms that have ever existed (defined morphologically) are now extinct (see the books of David Raup for corroboration). If ID is about every increasing degrees of perfection, it’s doing a really lousy job”

    Allen, do you believe this 99.9%. Oh, I am sure you can give some reason to back it up other than Raup’s books. Given that any little variation seems to be classified as a species, over a million animal species currently on the planet, this would mean there has been approximately 1 billion animal species in the history of the planet. Of course this would not be true if the 99.9% did not apply to animals but only to such things as bacteria. Are you pointing to all the extinct bacteria species as bad design?

    Wikipedia says that there is currently 16,000 species of mushrooms. Does the 99.9% mean there has been 16 million mushroom species in the history of the planet. And all this indicates a lousy job for ID.

    You wonder why we do not take you serious some times when you spout these irrelevancies. There are supposedly 5400 mammal species on the planet, how many were there in total and how do we know that and how many were fossilized? And were they really separate species or just variations just as all the Galapagos finches are really one species and cows and bisons are one species but often are classified as several different species.

    If someone here had spouted that 99.9% you would have taken them apart for their ignorance.

  49. Isn’t it somewhat disconcerting to find your most cherished prejudices undermined by the facts?

    Nope. I never let the facts get in the way of my prejudices. :)

  50. Allen:

    It’s a new world out there, where design and purpose are steadily being overwhelmed by chaos and disintegration.

    Me:
    Where is the evidence for this “chaos and disintegration” which Allen asserts is so prevalent in biology?

    Allen:

    In the genome; have you read Dr. Koonin’s abstract (or, even better, his review paper)? It’s all there.

    Actually, what Allen had written earlier is the following:

    Indeed, rather than producing the exquisitely perfect adaptations of living organisms, it is becoming clear that natural selection may be important only as that process that prevents the accelerating disintegration of the genome in the face of increasing chaos. In other words, evolution isn’t a steady climb toward greater and greater complexity nor a process designed to produce perfection. here

    Now I’d really like to know how he gets from one to the other.

    Yes, I’ve read the abstract. I fail to see how it makes your point.

    It’s a new world out there, where design and purpose are steadily being overwhelmed by chaos and disintegration.

    I’ll read the entire paper soon.

    So all this chaos and disintegration is going on in the genome, and it’s somehow steadily overwhelming design and purpose.

    How? What is the effect of this chaos and disintegration in the genome on the purposeful functions of the cell?

  51. Koonin’s paper, and also Allen McNeill in this blog, nicely explain how the old concept of Darwinism has had its day, and insofar as ID argues against that it appears to be correct. What the OP does not do, though, is invoke any need for Intelligent Design as an alternative explanation. On the contrary, with the decrease in importance on natural selection, other equally natural mechanisms are discovered to account for speciation and macroevolution.

    To me it seems that just like quantum physics replaced Newtonian physics without the need to invoke ID, modern evolutionary biology has replaced Darwinism without the need for ID.

    As so many keep saying, for ID to make an impact it has to focus on researching ID, not on arguing against other theories. ID could be correct about a thousand things it argues against, but unless it demonstrates that is correct about ID it still counts for nothing.

    fG

  52. “On the contrary, with the decrease in importance on natural selection, other equally natural mechanisms are discovered to account for speciation and macroevolution.”

    You continually misstate the ID position which is starting to lead me to think you are not doing it naively. There is nothing that has replaced natural selection. There are no natural processes that explain macro evolution. Allen is misrepresenting what is happening. They found natural selection etc to be wanting. They have not found alternatives that explain anything of consequence. The main still viable alternative is intelligent input and that is anathema to Allen and all the atheists because of its metaphysical implications.

    They must load the dice so that ID cannot be a possibility and that is not science being practiced but ideological dictums. Intelligence is still the best scientific explanation for what has been observed. Till they come up with something, it will remain so and no amount of fog that is spread by those who oppose ID will change that.

    Faded Glory, the anti ID people here are intellectually bankrupt. When they can back up something they say with science, we will listen to them.

  53. Allen MacNeil (43):

    Even if it eventually becomes possible to “model” abiogenesis in the laboratory, nothing guarantees that such a “model” process is how abiogenesis actually happened four billion years ago. And, since no record of what must have been a geochemical process remains in rocks dating from that time (indeed, there are no rocks dating from that time), I am fairly confident that this situation will always be the case.

    But, Allen, where is the fossil evidence of all the intermediate forms that Darwin hypothesized? I’m not asking just for forms (I’m sure you’ll talk about Eohippus, or the putative line leading to modern-day whales–but these are few, and offer not real proof of what descended from what in what order), but a whole lot of intermediate forms. If evolution is ‘gradual’ as Darwin supposed, then there should be a veritable treasure-chest full of them. You remember he talked aobut this “difficulty on the theory”. If we could find these intermediates, the whole discussion would be over. So, on the one hand you want to say that there is no fossil evidence for origins–nor, per your hypothesis, will there ever be–and then, on the other, you simply go your merry way when it comes to the rather severe difficulty the lack of fossil intermediates poses to the theory of evolution in the first place. (And, BTW, invoking hox-genes and such is to me nothing more than begging the question: that is, “How did life evolve? By mutations to Hox-genes. How did Hox-genes come about? Through evolution!)

    Now, let me ask you a further question. Below the surface of what you’re propsoing is the supposition that once organisms are able to replicated themselves that “anything is possible”–evolution can do it all!! Well, we know that bacteria came about, what, over 2 billion years ago at least. And we know that nothing mutates faster than bacteria do. So you have a billion and a half years of bacteria just wildly mutating away, and what do you have??? At the end of this process, you have……bacteria. If evolution/(replication + NS) is so powerful, then what happened? Rather, why didn’t anything happen? If this process is so powerful, then how do you explain this grand impotence? Any suggestions?

  54. Allen MacNeil (6):

    Kimura, Ohta, Jukes, and Crow dropped a monkey wrench into that idea, and then Gould and Lewontin finished the job with their famous paper on “the spandrels of San Marco and the Panglossian paradigm”.

    Interestingly, Allen, this is how I became such a Darwinian critic. I began in 2000 to look for some kind of explanation for macroevolution. I read Kimura’s “Neutral Evolution” (which, to use Stanley and Jukes term, is “Non-Darwinian Evolution”), and Lewontin’s 1974 book, followed by Hoyle’s “Mathematics of Evolution”. It was clear then that neo-Darwinism (= Modern Synthesis) was dead.

    So, as I have said many times before, when ID supporters set their sights on “neo-Darwinism” as a target for criticism, they set their sights on a model that has been all but abandoned. The carnival has moved on, folks, and ID supporters are fighting battles that evolutionary biologists left behind a half century and more ago

    Evo-devo doesn’t really solve anything, Allen. Take the origin of just one gene: whence does it come? Some kind of mechanism has to be prescribed. You seem content to just simply say: “That’s a problem for those working on abiogenesis. For me, once ‘life’ began, the mechanisms for variation were there and there must be some laws that dictate how these changes come about, and eventually we’ll discover them. In fact, we’re well on the road to such discoveries.”

    This is convenient. But it is just simply an effort to completely sidestep the problems we face; namely, how did these complicated mechanisms of interaction arise in biology. Evo-devo appears to be no more than saying that if you push a particular set/combination of buttons on a computer, you’ll get rich information as output (the analogy being that Hox-genes represent no more than ‘buttons’ that ‘evolution pushes’), and, if you push a different combination of buttons, then you’ll get a completely different form of information, though it still continues to be rich in complexity. But what about the pink elephant in the room? Where did the computer come from in the first place? The Modern Synthesis was supposed to give us this answer, but now its dead and being buried. So what then takes its place?

    Somehow you are intellectually comfortable in suspending these kinds of questions from critical analysis. This, then, becomes a question of whether or not proper logic is being applied to the raw facts that are, and have been, uncovered—which seems to me to run more along the lines of philosophy than pure biology.

    Just one more thing, if I may. You also write this:

    Creationists have of course moved the goalposts, arguing that “they accepted all along that new species could arise from existing ones, it’s just “microevolution”, which everyone accepts. This despite the fact that speciation has always been considered to be the first (and perhaps most important) stage in macroevolution, and that less than two decades ago creationists were confidently stating that “true” speciation had not only never been observed, it couldn’t ever be observed because it can’t happen.

    Now I’m not a creationist—and never have been, if we’re talking about the literal interpretation of Genesis. I do believe that God is the author of life, and that life reflects God’s creative power. Now many might also see this same creative power at work and choose to interpret it along the lines of what is called ‘theistic evolution’, your TE above. That’s how I used to think. But now having looked around a bunch, I see an emperor without clothes. In your quote, for example, you say that the Grants have ‘documented’ the generation of a new species. Well, wonderful. But when it comes to Darwinism, that’s not the real question. The real question is whether or not this new organism is a “species” or a “variety”. That is the central question. Darwin saw “varieties” as “incipient species”; that is, that which, compared to cultivated, broadly-based, known species, was formerly considered to be simply a “variety”, was now, in fact, to be considered, per his theory, an “incipient species”, destined to “evolve” more and more until it became a full-blown “species” on its own. And not only that—and this is critical because Darwin didn’t publish the “Origins” until Wallace wrote his paper describing the “principle of divergence”—this “incipient species” might be on its way in “displacing” the original “parent” species. If we view what the Grant’s have done—or may have done (I haven’t looked at their work yet, so I’ll suspend judgment)—what we really need to know is if this ‘new species’ is on its way to displacing other species, and eventually being the source of countless new species, which, taken together, will form a ‘family’ or a ‘class’. I surely have my doubts about this because no one has ever seen anything like this ever happen. And if this phenomena of “divergence” cannot be documented, then Darwinism is dead— an admission you studiously shrink away from. So, Allen, we need much, much more than what the Grants are giving us. Remember the lizards on those Adriatic islands that basically formed a new speices in less than 35 generations? We know about new species being formed. But we’ve never seen what might be termed “progressive evolution”. I await.

  55. and, if you push a different combination of buttons, then you’ll get a completely different form of information, though it still continues to be rich in complexity. But what about the pink elephant in the room?

    That’s correct. We have a description of how we get different results by pushing a button, but that does not in the least explain all the downstream activities, nor how this particular switch came to control them.

    Consider an assembly line, where throwing a single switch changes the end product that is produced. Someone might marvel at the ability of the switch to produce macro-evolutionary changes.

  56. jerry: ‘You continually misstate the ID position which is starting to lead me to think you are not doing it naively.’

    Come on now, I am not even trying to state the ID position here, so where am I misstating it? Is this just a prelude to the predictable flaming that always seems to happen when someone asks questions that ID-ers are uncomfortable with?

    Your position seems to be ‘natural mechanisms of evolution are lacking, therefore ID’. Here is a paper that provides a nice summary of the natural mechanisms as currently understood, so how can you possibly claim that they don’t exist?

    fG

  57. faded_glory,

    The inference goes like this:

    1- We make an observartion.

    2- We try to figure out what can account for it.

    3- If chance and necessity do not suffuce AND it has some specification only then do we infer design.

    Now to refute that design inference all YOU have to do is to then demonstrate that either chance and necessity can account for it OR no specification exists.

    However all you can do is whine.

    Go figure…

  58. 58

    Jerry at 21,

    “Arguments from incredulity are unconvincing””

    Nonsense. Not when the examples pile up and the rationale for the findings are backed up by good science and logic.

    It doesn’t matter how many logical fallacies are piled together, they’re still fallacies and therefore unconvincing.

    “positive evidence for non-natural mechanisms is required.”

    Again nonsense.

    Without positive evidence for a particular hypothesis (and a clear articulation of that hypothesis), there is no rational reason to consider it. Even if one were to demonstrate that no known material processes could account for a particular observation, that would not constitute support for non-material explanations. There could well be a currently unknown material explanation, for example.

    If one wants to posit a non-material explanation, one must provide positive, objective, empirical evidence. I’d be interested in hearing how one could do that, even in principle.

  59. Faded Glory,

    No one and I mean no one has ever presented any naturalistic mechanism that has been shown to create novel complex capabilities on any consistent basis. We have had more than one evolutionary biologist and several regular biologist come here. We are talking all the changes from a simple prokaryote cell to human beings so there is a lot of change that went on.

    We been asking here for over five years that I have observed and nothing yet. People always claim it exists but somehow never seem to be able to tell us what it is. I would think that would tell you something. If you disagree, be our guest and educate us.

    So cite all you want but until you or someone else can bring up something relevant, then I suggest you remain quiet about people knowing the causes for evolution.

  60. “Without positive evidence for a particular hypothesis (and a clear articulation of that hypothesis), there is no rational reason to consider it. ”

    Nonsense. Intelligent actions can modify life to a large extent now and most in the biological community believe it will soon be able to create life from scratch. So the capability is not disputed. So we have a known capability for creating and modifying life. What you want is a video tape or a copy of the plans from 3.5 billion years ago. Don’t be absurd.

    “Even if one were to demonstrate that no known material processes could account for a particular observation, that would not constitute support for non-material explanations. There could well be a currently unknown material explanation, for example.”

    Another stupid comment. First of all who said non-material and do you consider intelligence non material. It does not obey the natural laws. If there are only two possibilities and one has been eliminated, then hello, doesn’t that support the other possibility. Only in an Alice in Wonderland world would you find people taking the bet that it doesn’t. Yes, there is always the possibility of some unknown process accounting for life but speculating on some unknown process when all the probable ones have been eliminated does not make it a 100% probability as you and every anti ID person want. I would assume that the possibility of the alternative gets higher and higher as each alternative possibility is eliminated.

    Now most of those who challenge ID have an a priori attachment to an ideology that must be adhered to so logic and common sense go out the window. When the anti ID people start making some sense, we will pat attention to them. But arguments such as yours have been tried over and over again and are bogus. So I suggest if you are going to challenge ID, then do so with empirical evidence. Your arguments are non sequiturs.

  61. Jerry, Cornelius Hunter, a fellow ID advocate, just showed you one such example in a post made today.

    fG

  62. Mustela Nivalis,

    Nice talk but what is your hypothesis pertaining to blind and undirected processes?

  63. 63

    jerry at 60,

    “Without positive evidence for a particular hypothesis (and a clear articulation of that hypothesis), there is no rational reason to consider it.”

    Nonsense.

    You keep repeating this word. It’s quite rude and has no place in polite discourse.

    Intelligent actions can modify life to a large extent now and most in the biological community believe it will soon be able to create life from scratch. So the capability is not disputed. So we have a known capability for creating and modifying life. What you want is a video tape or a copy of the plans from 3.5 billion years ago. Don’t be absurd.

    All I’m asking for is a clearly articulated hypothesis and some objective, empirical evidence for non-materialistic behavior or mechanisms.

    “Even if one were to demonstrate that no known material processes could account for a particular observation, that would not constitute support for non-material explanations. There could well be a currently unknown material explanation, for example.”

    Another stupid comment.

    Another (extremely) rude comment. One might get the impression that you have so little confidence in your own arguments that you need to bluster instead. “When the facts are on your side, pound on the facts. When the facts aren’t on your side, pound on the table.”

    First of all who said non-material

    You did, up at 16:
    “The choice is between 100% naturalistic and not 100% naturalistic changes in life forms.”

    and do you consider intelligence non material.

    As far as is known, intelligence is an emergent phenomena of a complex, physical brain. Destroy the brain and the intelligence is no longer detectable. No non-material supposition required.

    It does not obey the natural laws.

    Please describe a natural law you can violate with your brain.

    If there are only two possibilities and one has been eliminated, then hello, doesn’t that support the other possibility.

    Your arguments from incredulity do not eliminate the possibility of unknown material mechanisms. In fact, the history of science suggests that the scientific method is very good at identifying the mechanisms responsible for initially unexplained phenomena.

    Yes, there is always the possibility of some unknown process accounting for life but speculating on some unknown process when all the probable ones have been eliminated does not make it a 100% probability as you and every anti ID person want.

    Thus far, not all known chemical processes have been eliminated, by a long shot. Abiogenesis is an active area of research. If you want to posit a non-material explanation, you need to provide some hard evidence in favor of it rather than taking potshots at science.

  64. “Cornelius Hunter, a fellow ID advocate, just showed you one such example in a post made today”

    We are at one and counting. Till we get to about two or three million examples, it really can’t be taken seriously. Actually that is hyperbole, it is really around two or three hundred thousand.

    PS – That example has been around for almost a year now and is very interesting. Take one down and pass it around, 199,999 more genes to go. (I am sure there are several more but the number required to show an on going process is closer to the 200,000 than one)

  65. “Please describe a natural law you can violate with your brain.”

    Please explain the natural laws responsible for the clothes you have on you.

  66. 66

    jerry at 65,

    “Please describe a natural law you can violate with your brain.”

    Please explain the natural laws responsible for the clothes you have on you.

    Non sequitur. You made the claim that “[Intelligence] does not obey the natural law.” It is incumbent upon you to support that assertion or retract it.

  67. Mustela @ 63
    “Thus far, not all known chemical processes have been eliminated, by a long shot. Abiogenesis is an active area of research. If you want to posit a non-material explanation, you need to provide some hard evidence in favor of it rather than taking potshots at science.”

    The search for a perpetual motion machine is probably still an active area of research but that’s hardly an argument in its favor. The problem is not chemical processes. The problem, on any naturalistic/materialistic account of life, is that chemical processes, driven by the laws of physics, are conceptually inadequate to explain what really needs to be explained, and that is biological information. Information is the distinguishing characteristic of all life so that is what needs to be explained. Not brains or feathers or claws or fins.

    The existence of information in any context requires the existence of a language (symbols and rules for the manipulation or organization of those symbols into terms which are then combined in various ways defined by the rules of the language so as to encode, transmit, and decode information). But the problem for the materialist/naturalist is that neither physics nor chemistry have anything to say about why “it is raining” and “es regnet” both mean the same thing. And they never will because they deal with the physical world. But information is abstract. It is encoded in a physical substrate but it is apart from that substrate.

    It is a blatant category mistake to try to explain the abstract only in terms of the material (and denying the existence of the abstract entity in the process). This is a typical move of the naturalist. I can’t explain design in terms of physics so I deny the existence of design and it becomes “apparent design.” I can’t explain the existence of a moral law in terms of physics so I deny the existence of a real moral law. But that move is unavailable now because information cannot be denied without using information. Checkmate. The materialist is painted into a corner from which he cannot escape.

    So what is the answer? Just a thought, we always know that information reduces to, or is explained by, mind. Only a mind, something “outside” of the physical world, although “encoded,” if you will, in the physical world, can deal with symbols, the representation of one thing for another. Or the rules which govern those symbols. You can’t begin to explain the contents of this post in terms of the laws of physics but a mind provides a very satisfying explanation.

    Let me put it this way. If a book is something that contains information encoded in a language then perhaps you would agree with me that all books have authors. Take that as a major premise. Seems pretty undeniable to me. Since the idea of a book without an author is ludicrous in the extreme. Then let’s take as the minor premise that biological information encoded in the genetic language is a book. Let’s call it the book of life. No one disputes this. That biological information is encoded in DNA by the rules of a genetic language. The conclusion is readily apparent. The book of life has an author.

    This categorical syllogism is valid and it is sound. Therefore its conclusion is necessarily true.

  68. 68

    tgpeeler at 67,

    The search for a perpetual motion machine is probably still an active area of research but that’s hardly an argument in its favor.

    Perpetual motion machines are not an active area of research because they have been demonstrated to inherently violate the laws of thermodynamics. Abiogenesis, on the other hand, suffers from no such fatal flaw. In fact, considerable progress is being made. While I usually hesitate to recommend Wikipedia, it’s abiogenesis page is a reasonable overview with some good links to chase down the original research.

    If a book is something that contains information encoded in a language then perhaps you would agree with me that all books have authors. Take that as a major premise. Seems pretty undeniable to me. Since the idea of a book without an author is ludicrous in the extreme. Then let’s take as the minor premise that biological information encoded in the genetic language is a book.

    Calling a dog’s tail a leg doesn’t mean that a dog has five legs.

    Tell me the rigorous mathematical definition of information you are using and we may be able to have an interesting discussion.

  69. Mustela @68

    If you’ll allow me to cite a few authors:

    Francis Crick:
    “In spite of our differences we all use a single chemical language, or, more precisely, as we shall see, two such languages, intimately related to each other.” Life Itself, page 39.

    “A protein is like a paragraph written in a twenty-letter language, the exact nature of the protein being determined by the exact order of the letters. With one trivial exception, this script never varies. Animals, plants, microorganisms and viruses all use the same set of twenty letters although, as far as we can tell, other similar letters could easily have been employed, just as other symbols could have been used to construct our own alphabet.” Life Itself. pages 44-45.

    Richard Dawkins:
    “You can treat the genetic code as a dictionary in which sixty-four words in one language (the sixty-four possible triplets of a four-letter alphabet) are mapped onto twenty-one words in another language (twenty amino acids plus a punctuation mark).” River Out of Eden, page 11.

    “Life is just bytes and bytes and bytes of digital information.” River Out of Eden, page 19.

    “Indeed, the whole DNA/protein-based information technology is so sophisticated – high tech, it has been called by the chemist Graham Cairns-Smith – that you can scarcely imagine it arising by luck, without some other self-replicating system as a forerunner.” River Out of Eden, page 150.

    “We have seen that DNA molecules are the centre of a spectacular information technology.” The Blind Watchmaker, page 126.

    Bernd-Olaf Kuppers:
    “To start with, a brief introduction to modern evolution theory is given (chapter 1). A central and fundamental concept of this theory is that of “biological information,” since the material order and the purposiveness characteristic of living systems are governed completely by information, which in turn has its foundations at the level of biological macromolecules (chapter 2). The question of the origin of life is thus equivalent to the question of the origin of biological information.” Information and the Origin of Life, from the introduction.

    “The term “biological information” requires clarification, and this is the purpose of part II. It will be shown that three dimensions of information can be distinguished: its syntactic, semantic, and pragmatic aspects.”

    “In contrast to this (syntactic), the semantic aspect is essential, since the elements of an organism that are governed by information have a special purpose and a meaning in the context of the maintenance of its life functions (chapter 4).” Information and the Origin of Life, From the introduction.

    Hubert P. Yockey:
    “The existence of a genome and the genetic code divides the living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” Information Theory, Evolution, and the Origin of Life, page 2.

    “The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.” page 5.

    “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” page 6.

    “The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter or energy.” (my emphasis) page 7.

    “Life is guided by information and inorganic processes are not.” page 8.

    It is in this sense that I refer to information. I don’t think I’m out on a limb here. Looking forward to our discussion.

  70. Mustela Nivalis,

    The latest in abio research says it takes quite a bit of agency intervention just to get an RNA molecule that will catalyze ONE bond.

    And please tell us about any of the rigor in any definitions used by evolutionists.

    Heck you can’t even provide a testable hypothesis for your position.

    What does that say about you?

  71. 71

    tgpeeler at 69,

    If you’ll allow me to cite a few authors:

    You’re allowed. ;-)

    Now, how about that mathematically rigorous definition of information? Until we agree on one, there is little to discuss.

  72. faded-Glory and jerry:

    I just posted over at Cornelious’ thread. Turf-13 appears to represent a “loss of function”, and hence a “loss of information”. So, if fG’s comment about Cornelius Hunter refers to this, then we’re back to zero I suspect.

  73. Hell, you give me one. I use information as the term is generally used and as is cited by these authors, all of whom are neo-Darwinists. The concept of information is rich and therefore difficult to pin down into a formula or equation but perhaps if we just assume for the moment that life and ‘information,’ whatever that turns out to be, exactly, are inextricably linked, then we can proceed anyway. If you disagree that ‘information’ and life are inseparable perhaps you can cite some example of a living thing that doesn’t have DNA/RNA. Otherwise, I still think I’m on pretty solid ground here.

    My other point is that it is impossible to have (create, transmit, understand) information apart from a language. No one can deny that since the denial would necessarily involve language and therefore create an internal self-contradiction. Rendering the claim nonsense. Literally.

    I am trying to look at this problem in the most fundamental way. If Kupper is right, and I believe he is (about this), that the problem of the origin of life is the problem of the origin of information, that is akin to saying that the problem of the origin of life is the problem of the origin of language. I say this, again, because you can’t have life without information and you can’t have information without language. And since ALL languages are a system of symbols and rules what must ultimately be explained are the symbols and rules if you are going to explain life. Darwin’s idea, no matter how “plausible” it sounded, doesn’t even begin to address the real issue.

    This is a devastating argument, I believe, to naturalism and its story of life, neo-Darwinian evolutionary theory. I expect a lot of resistance to it but I don’t expect good counter-arguments and I have never received good counter-arguments.

    In order to counter my claims, it seems to me that you must either separate life from information or information from language or language from symbols and rules. None of those things are possible. If you think it is possible then one example will be enough to falsify my claim. Or, you can show how some algorithmic process based on physical law can create information. But before you could do that, you would have to show how physics can describe some set of symbols and rules, i.e. a language, but physics has nothing to say, and will never have anything to say, about why some particular arrangement of symbols means something. Heck, the laws of physics are themselves written in the language of mathematics. I’m pretty sure that it is not even coherent to attempt to explain how “the laws of physics,” can possibly explain language. But you are welcome to try. If someone cannot explain the origination of symbols and rules within their metaphysical framework, they are dead in the water. I, not being a materialist, can easily explain information and language. I have “mind” and “Mind” in my metaphysical explanatory tool kit. The naturalist does not. All he has is physics. You can’t get to information from “there.” You just can’t.

  74. p.s. This is why I believe Michael Behe’s irreducible complexity argument is irrelevant. It’s elegant, but it addresses the physical ‘machines.’ Therefore it has nothing to say about how they were built in the first place. Behe’s argument is better than Darwin’s by orders of magnitude, in my estimation, but neither of them explain what needs to be explained. Apologies to Dr. Behe. Bill Dembski and Stephen Meyer are on the right track. Not that I am anybody to make such pronouncements but they seem correct to me.

  75. 75

    tgpeeler at 73,

    Hell, you give me one.

    Potty mouth. There are Christians reading this. ;-)

    I use information as the term is generally used and as is cited by these authors, all of whom are neo-Darwinists.

    It’s the “generally used” that’s the problem. If we don’t have a precise definition of a measurable quantity, we have no real way of discussing the amount of information in a particular biological system, no way to compare amounts of information, no way to determine if a mechanism creates or destroys information, indeed no way to tell if information is present at all.

    Too often in these discussions I’ve seen people switch from one definition to another. That, often unintentional, equivocation leads to confusion.

    The concept of information is rich and therefore difficult to pin down into a formula or equation but perhaps if we just assume for the moment that life and ‘information,’ whatever that turns out to be, exactly, are inextricably linked, then we can proceed anyway.

    Without a clear definition, I couldn’t possibly agree. In fact, this seems to be your conclusion, rather than a premise.

    For the sake of discussion, would you be willing to use Shannon’s definition of information or would you prefer Kolmogorov complexity?

    If you disagree that ‘information’ and life are inseparable perhaps you can cite some example of a living thing that doesn’t have DNA/RNA. Otherwise, I still think I’m on pretty solid ground here.

    Without rigorous definitions, there is no solid ground.

    My other point is that it is impossible to have (create, transmit, understand) information apart from a language.

    Mechanisms identified by modern evolutionary theory routinely transfer information (for a particular definition of the word) from the environment to subsequent populations of organisms, with no language involved. If you deny this, we’re probably using different definitions.

  76. “Now, how about that mathematically rigorous definition of information? Until we agree on one, there is little to discuss.”

    Is this the case? Really?

    Is is possible that all these authors, and literally scores of dozens upon dozens of others are all completely capable of sharing ideas with each other under the terribly incoherent phrase of “information” right up until the point where their thoughts are meant to establish some meaning by which be intend to communicate with each other – and at that incredibly obvious moment – everything they’ve said becomes hopelessly meaningless because they have utterly failed to provide a rigorous mathematical model of what they had been intendeing to say?

    …or is Mustela just FOS?

  77. Mustela Nivalis,

    According to Dr Meyer in “Signature in the Cell” the standard and accepted dictionary definition of information works just fine.

    As he points out the mathematical version can only point out mere complexity and cannot deal with content.

    You should probably read the book.

    Now how about a testable hypothesis for your position?

  78. —-Mustela Nivalis: “It’s the “generally used” that’s the problem. If we don’t have a precise definition of a measurable quantity, we have no real way of discussing the amount of information in a particular biological system, no way to compare amounts of information, no way to determine if a mechanism creates or destroys information, indeed no way to tell if information is present at all.”

    Darwinists crack me up. On the one hand, they claim that unguided forces can produce information and insist that the evolutionary pathway to get us there exists, even though they acknowledge that they have not yet found it.

    On the other hand, when ID explains WHY those unguided forces cannot climb that improbable mountain, Darwinists suddenly change tactics and claim not to know what it is.

    You’ve gotta to love it.

  79. Mustela, what Upright, Joseph, and StephenB said. I told you I’ve never received a good argument against. Your evasion keeps the record intact.

    At the risk of being pedantic, because you may possibly be someone who actually thinks about things, let me quickly offer you the only possible ways to defeat my argument.

    1. If naturalism doesn’t entail that physics is the ultimate explanation for everything. But it does. That is part of the definition of naturalism. See The Cambridge Dictionary of Philosophy or the Oxford Guide Philosophy or any number of authors I could cite.
    2. If you can separate information from life, or life from information. Just come up with one example of something living without DNA/RNA.
    3. If you can communicate information without using a language. As I said before, I don’t think you can even make that concept coherent.
    4. Show me a language that doesn’t have symbols and rules. Just one will do, of any kind.
    5. Show me how a valid form of argument, in this case modus tollens, with true premises (it’s sound), can be false.

    If P then Q. ~Q. Therefore, ~P.
    If naturalism is true (and the naturalistic story of life is true), then physics can explain everything. (True by definition.)
    But physics cannot explain language, information, or life. (see explanation above)
    Therefore, naturalism (and the naturalistic story of life) are false. Not only are they false, it’s not even possible that they are true. Evolutionary “theory” is the biggest intellectual fraud of all time. Well, in science, anyway.

    Please attack the argument, if you like, and spare us all the bobbing and weaving. I’ve given you the cheat sheet as to how to make me/us look foolish. I think you’d jump at the chance. :-)

  80. 80

    tgpeeler at 79,

    I’m not trying to be obtuse, but I genuinely fail to understand how you think we can have a rational conversation without defining our terms. “Information” has a couple of common mathematical definitions. Are you willing to use Shannon Information for the rest of this discussion? The colloquial definition of information does not permit measurement, an essential characteristic of the scientific method.

    As an example of the problems with failing to clearly define terms, you yourself use the word “language” above in a vague and equivocal manner (not deliberately, I’m sure). The “language” of DNA is vastly different from human language, so drawing parallels is unlikely to lead to knowledge.

    Shannon information, then?

  81. Mustela Nivalis,

    Shannon does not deal with “information” per se.

    Rather Shannon was only dealing with mere complexity.

    This is all discussed in “Signature in the Cell”.

    You should read it as opposed to agruing from ignorance as if that ignorance is meaningful discourse.

    As for measurement- that leaves your position out of it.

  82. 82

    Joseph,

    For the record, I have observed your participation here on several threads and it is my personal opinion that you lack both a basic understanding of biology and the desire to acquire the required education.

    Regrettably, I will refrain from responding to you again, hopefully saving both of us considerable frustration.

  83. Pardon the intrusion, but I don’t see how tgpeeler’s claims hold up, even under the colloquial usage of information.

    For instance, animals without language capabilities observe their environment, thus taking in information. Why does this not count as communication of information without language?

    Or even simpler, information about an object includes its momentum. If the object collides inelastically with another object, e.g. two billiard balls, the second object takes on the first object’s momentum. Is this not a case of information being communicated?

    As to languages without rules, I already provided one to tgpeeler in a previous thread. The language of positive integers over the alphabet {0,1,2,3,4,5,6,7,8,9} has no syntax rules — every string is grammatical.

    I suspect that tgpeeler will respond to my counterexamples by disputing semantics. Thus Mustela’s request for a univocal and quantitative definition. Why is it not reasonable for Mustela to try to nip the impending semantic problems in the bud?

  84. Mustela @ 80

    “Are you willing to use Shannon Information for the rest of this discussion?”

    Yes. I am. Even though Shannon Information, as far as I can tell, only deals with the statistical aspect of information and ignores the syntactic and semantic aspects. But those aspects can safely, I believe, be ignored for the purposes of our discussion. You still have the same problem. Even at the statistical level you have symbols (0s and 1s) and rules for why a particular sequence of 0s and 1s means something and another does not, and why this is. Now explain to me solely in terms of physical laws why this is and which physical law addresses each component of the problem. Problem 1 – symbols. Problem 2 – rules. Thanks.

  85. 85

    tgpeeler at 84,

    Thank you for your agreement to use Shannon Information as our definition.

    As it turns out, an increase in Shannon Information has been demonstrated in a simulation of simple evolutionary mechanisms corresponding to a real world organism. I recommend Thomas Schneider’s ev papers and software as an excellent description of this process.

    Schneider’s work clearly demonstrates that information can be generated by known evolutionary mechanisms, with no intelligence involved.

  86. ROb @ 83

    “For instance, animals without language capabilities observe their environment, thus taking in information. Why does this not count as communication of information without language?”

    Thanks for the opportunity to clarify my position on this. I am talking about information at a conceptual level. The cases that you describe do count as communication of information but there are still symbols and rules. Let’s say that a lion is charging me, a zebra. That communicates to me, the zebra, that I best be getting my a$$ in gear or I’m history. As opposed to, say, a lion lying on the ground and paying no attention to me, in which case that communicates something else. In either case, the symbol is the lion’s behavior and the rule is “lion charging = not good” and “lion not charging = good for now.” The “natural selection” move won’t work here because ns denies teleology so there would be no reason for anything to mean anything if one has a genuine intellectual commitment to the concept of ns. Which I say is nonsense but that is an entirely different conversation.

    To use another example, honey bees communicate with each other, by means of an elaborate dance, where the food is. Some dance steps mean go here and other dance steps mean go there. Why is this so? And why does it “mean” anything to other honey bees? It’s because one set of movements (symbols) means one thing and another set of movements means another (rules). Without these symbols and rules no communication takes place. If all of a sudden I started writing this in German and you didn’t understand the rules (vocabulary, syntax, and grammar) then no communication could take place. For communication to take place, as far as I can tell, it takes symbols and rules, under all circumstances, and an understanding of those rules on both the transmitting end (where the encoding takes place) and the receiving end (where the decoding takes place). The medium is irrelevant as long as it does not garble the message and this, I believe, was the focus of Shannon. How many bits can you jam through a pipe and have them come out on the other side as they went in.

    This is the problem for materialism and materialists. Nothing in the laws of physics has anything to say about why this is so. Only a mind or living thing can associate one thing with another. In the case of a bee, you may say, well, does the bee have a mind? I’d have to say no. But obviously the ability to recognize the symbols and understand the rules is either “learned” somehow or is pre-loaded into the DNA of the bee. A very interesting question but one that would never be addressed if the information question is ignored. I hope this helps or stimulates further questions.

  87. Mustela @ 85

    It will take me a little while to review Thomas Schneider’s work. In the meantime, I wonder what these evolutionary “mechanisms” are and again, I say, how is it possible for the information Schneider says is created by “evolution” to exist apart from some set of symbols that are arranged according to some set of rules?

    And how did Schneider’s program come into existence? Did it write itself or happen by accident? What if I randomly changed a piece of code? Would you think that would improve his program or crash it? And if I changed it randomly again? And if his code could error correct itself wouldn’t that make it even more obvious that it didn’t arise by accident? Or by any conceivable “evolutionary process”?

  88. #86

    tgpeeler

    Your comment illustrates the need to clarify how the word “information” is being used – even when not defined mathematically.

    The zebra will flee when the lion charges. It is possible that this is because the zebra has some kind of process that associates charging lions with being killed and eaten, or it could be because zebras just instinctively flee when large animals charge at them. In either case it is not logically different as far as the zebra is concerned from a zebra fleeing when it hears a loud rumbling preceding an earthquake. It is not material that the lion happens to be a living threat. All that has happened is that the zebra has associated phenomenon X which is observed with phenomenon Y which is not (yet) observed. In this sense lightening is information about thunder and dark clouds information about rain. Indeed we say that clouds are a sign of rain (but not a symbol of rain). Physics has no problem producing signs of this type.

    The bee example is only different because it is harder to explain how the position of the food causes the behaviour of the bees. But it is within the scope of physics to do so.

    There are subtler uses of information. The response of the zebra and the bee is pretty much hard-wired but of course some species respond to signs because they have learned the association between sign and signified. For Pavlov’s dogs the bell was a sign of food.

    A further development is confined to humans. I will use an example that the philosopher Grice famously used. Suppose I wish to communicate to you that your wife has been having an affair with someone else. If I send you a compromising photograph then that is little different from clouds giving information about rain. There is clear causal relationship between the compromising position and the photograph. The photograph would be incriminating and tell you about the affair even if you found it on the street. But if I draw a picture of your wife and her lover behaving improperly this only gives you information if you make some assumptions about my intention in drawing the picture – what Grice would call non-natural meaning. At this point we could say the picture is not just a sign but a symbol.

    Why do I make these distinctions. Well DNA is information in much the sense of the bee’s dance. There is a regular association between the DNA and the amino acids and while there is a physical causal chain between the two it is not obvious simply by inspecting the sign what is signifies. But DNA is not information in the sense of the picture. The bases are not symbols of the corresponding amino acids. There is no need to make assumptions about the creator of the DNA to garner the information.

  89. This whole discussion of information and biology is a joke. It is well known within biology just what is meant by information in the genome and it corresponds to how we use it here at ID. It is not Shannon information though apparently you can apply the Shannon information concept to it. But Shannon information has nothing to do with the information or instructions found in the genome which governs so many biological processes.

    So anybody who feigns confusion is being disingenuous. They are trying to play mind games with the ID people. It is easy to understand and the motives for pretending to not understand are the usual. So dealing with them when they ask for clarification is another example of playing the fools errand.

    One discussion of biological information is at

    http://plato.stanford.edu/entr.....iological/

    And there are others. I recently finished a Teaching Company course on the DNA of humans and it was by an extremely anti ID person who constantly talked about information content of the genome and how it is used in biology. So anyone here who claims not to understand what information is are playing a game and those who want to pursue it with them then you are on the fools errand being led by the anti ID people.

  90. I would like to throw something out here – just because the obfuscation around the topic is often mind-numbing.

    Firstly, you always hear people saying things like…there is information that exist in, say, the structure of an atom, or the frequency at which a substance resonates, etc, etc,.

    This is incorrect because it is a category mistake as to what information is.

    There is no information in the structure of an atom. The structure of an atom is a matter of its existence, but it contains nothing more than its structure. It simply exists. The only time that information is extracted from the structure of an atom is when it is 1) perceived and 2) transmitted.

    Information is the product of perception – and perception cannot happen without transmission. The lowly earthworm does not accidently crawl onto a sidewalk and spend its remaining days desperately trying to dig a hole in the concrete. Instead, it senses its surroundings and transmits those perceptions to its ability to move on. Such is the case in every instance where information is exists, and is used.

    Perception is manifest step in the creation of information, and transmission must then follow. That transmission may be from my fingertips to my brain or from one’s lips to another’s ears, but in every case the transmission can only be accomplished by symbols and their rules (what we term as language in all its various and wonderful forms). All the rummaging over information (its measurement, qualities, value, definitions, usefulness) is completely secondary to its creation in the first place.

    Perception (and its transmission by symbols and rules) is the quality of an agent, and only of an agent. This conclusion is intractably validated by our universal experience with “information”. So when we see information being recorded, transcribed, and used to manipulate the atoms within living tissue, it is a dead give-away that it came about by the act of an agent.

    That’s why Tom Peeler’s challenge is valid, and it’s valid every time it is presented.

  91. jerry:

    So anybody who feigns confusion is being disingenuous. They are trying to play mind games with the ID people.

    Speaking for myself, I can assure you that my confusion is not feigned, and my objective is clarification, not mind games. (Of course, that’s exactly what you would expect a mind game player to say.)

    As I said before, my understanding of the colloquial usage of information doesn’t seem to jibe with tgpeeler’s claims. I don’t know any way to align my understanding to his without asking for clarification.

    But we’re still not on the same page. The lion’s behavior in tgpeeler’s scenario is not a symbol as I understand the term. So I’m left not knowing what tgpeeler means by symbol.

    And while he has at times described rules as syntactic, tgpeeler has recently described them as dictating what combinations of symbols mean. That changes my understanding of his usage of the term rules.

    The Encyclopedia of Philosophy article that you recommended shows that different people take different and contradictory approaches to the concept of information. Interestingly, the authors’ metaphysical position seems to contradict that of tgpeeler, Stephen Meyer, and others in this debate.

    Upright BiPed’s approach is yet another data point. When he says, “There is no information in the structure of an atom,” presumably that applies to DNA molecules also. But we commonly speak of DNA containing information, so Upright BiPed’s usage seems different from the common usage.

    I realize that the call for good definitions seems pedantic, but superficially reasonable arguments sometimes turn out to be specious when the details are fleshed out.

  92. 92

    tgpeeler at 87,

    It will take me a little while to review Thomas Schneider’s work. In the meantime, I wonder what these evolutionary “mechanisms” are and again, I say, how is it possible for the information Schneider says is created by “evolution” to exist apart from some set of symbols that are arranged according to some set of rules?

    This is why the definition of information is so important. Since we’ve agreed to use Shannon Information as the metric, it is possible to compute the amount of information in a particular binding site, as Schneider does. Your questions about symbols and rules aren’t applicable.

    And how did Schneider’s program come into existence? Did it write itself or happen by accident? What if I randomly changed a piece of code? Would you think that would improve his program or crash it? And if I changed it randomly again? And if his code could error correct itself wouldn’t that make it even more obvious that it didn’t arise by accident? Or by any conceivable “evolutionary process”?

    You’re confusing the simulator itself with what is being simulated. Schneider’s thesis discusses molecular binding sites observed in real biological organisms. He found an interesting correspondence between the amount of information required to identify a binding site and the amount of information present in the binding site. His software simulates simple mutation and differential reproductive success based on fitness. It’s quite possible to modify the parameters of his simulation to determine the effects of different random changes. Applying random changes to the simulator itself would be the equivalent of trying to apply random changes to the laws of physics and chemistry — they are the givens, not what is being modeled.

    I’m very interested in your views on Schneider’s papers, once you’ve had the time to review them.

  93. “Information” has a couple of common mathematical definitions. Are you willing to use Shannon Information for the rest of this discussion? The colloquial definition of information does not permit measurement, an essential characteristic of the scientific method.

    Could we back up a few steps?

    How does Shannon define information mathematically?

    How do Chaitin-Kolmogorov define information mathematically?

    How does Shannon Information provide us with the means to measure information?

    Is it crucial to the discussion that we be able to “measure” information?

    How much information is in a novel?

    How much information is in a Berlinski essay on the Big Bang theory?

    iirc, Shannon defines “information” as a reduction in uncertainty. I guess by that definition, the more information we have, the more certain we are. more certain about what?

  94. I’m very interested in your views on Schneider’s papers, once you’ve had the time to review them.
    I’m pretty sure both ev and Schneider’s work have been discussed previously in the ID community, maybe over at iscid.

    I’m interetsd in finding out:

    1. how he defines information

    2. how he measures it

    3. how his definition differs from the “colloquial and informal” usage

    4. how he ties it to Shannon information.

  95. Hello R0b,

    There is certainly no need to be confused by the point I am making. It is appropriately narrow.

    There is no information within any atom of matter; there is only information about an atom of matter. And the only way to create that information is for the atom of matter to be perceived and for that perception to be transmitted. And that transmission will necessarily be by the use of symbols – no matter to where or how it is being transmitted. That includes from the sensory organ to the brain (or other organ), or from one entity to another.

    That is my point in a nutshell.

    (Now – I know I will get no traction for my conclusions here, and that is fine. It is unnecessary to me)

  96. (Now – I know I will get no traction for my conclusions here, and that is fine. It is unnecessary to me)

    Sounds like we’re on the same track:

    iirc, Shannon defines “information” as a reduction in uncertainty. I guess by that definition, the more information we have, the more certain we are. more certain about what?

  97. Mustela Nivalis

    For the record, I have observed your participation here on several threads and it is my personal opinion that you lack both a basic understanding of biology and the desire to acquire the required education.

    IOW you can’t answer my questions so you refuse to deal with them.

    You are an intellectual coward and a loser.

    You couldn’t support your position if your life depended on it.

    All you can do is blindly parrot the high priests of evolution.

    And you sure as heck can’t form a coherent argument.

    Oh BTW I will take my knowledge of biology over yours any and every day.

    I am more than willing to put my money where my mouth is.

    That said I will continue to respond to you as people reading this blog need to know how much of a coward you are.

  98. Mustela Nivalis

    As it turns out, an increase in Shannon Information has been demonstrated in a simulation of simple evolutionary mechanisms corresponding to a real world organism.

    Seeing that “evolution” is not being debated saying “evolutionary mechanisms” is useless and misleading.

    Are those mechanisms blind and undirected?

    THAT is what is being debated.

    And for anyone interested:

    The Problem of Information
    for the Theory of Evolution
    Has Tom Schneider Really Solved It?
    :

  99. 99

    Mung at 93,

    How does Shannon define information mathematically?

    His seminal paper is available online. There are many other online resources that discuss and apply Shannon Information.

  100. 100

    Mung at 94,

    I’m interetsd in finding out:

    1. how he defines information

    2. how he measures it

    3. how his definition differs from the “colloquial and informal” usage

    4. how he ties it to Shannon information.

    His PhD thesis is online and very readable. The description of his simulator and a lot of discussion about it is available on the ev homepage.

  101. It is generally agreed that the sense of information isolated by Claude Shannon and used in mathematical information theory is legitimate, useful, and relevant in many parts of biology. In this sense, anything is a source of information if it has a range of possible states, and one variable carries information about another to the extent that their states are physically correlated. But it is also agreed that many uses of informational language in biology seem to make use of a richer and more problematic concept than Shannon’s.
    here

  102. Are those mechanisms blind and undirected?

    THAT is what is being debated.

    Joseph is correct. This is what computer simulations allegedly demonstrate, and why they are claimed to be relevant to the debate over biological information.

  103. 103

    Mung at 102,

    Schneider’s ev program simulates a couple of known evolutionary mechanisms and shows that they are sufficient to generate information in a genome. He then shows that the information generated reflects what is found in real biological systems. You can read his papers and his code to see that this creation of information occurs.

    While his simulation doesn’t show that this is how the information came about in the real biological systems, it does show that it could come about via these known, natural, unintelligent mechanisms. That refutes tgpeeler’s (and others’) claim that information cannot be the result of natural processes.

  104. weasel man:

    Schneider’s ev program simulates a couple of known evolutionary mechanisms and shows that they are sufficient to generate information in a genome.

    Two problems with that:

    1- Shannon Information is nothing more than mere complexity

    2- EV does not correlate to living organisms.

    Also “evolutionary mechanisms” is irrelevant.

    Design is natural.

    Unitelligent mechansims?

    How, exactly, was that determined?

    But anyway keep being a weasel, it suits you very well…

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