Autopoietic Systems and the Order of Life

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Rob
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Autopoietic Systems and the Order of Life

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de Duve wrote:I have quoted Monod's declaration "The Universe was not pregnant with life," to which he added "nor the biosphere with man." I have made it clear that I disagree with his first statement. Life belongs to the very fabric of the universe. Were it not an obligatory manifestation of the combinatorial properties of matter, it could not possibly have arisen naturally. By ascribing to chance an event of such unimaginable complexity and improbability--remember Hoyle's allegory of the Boeing 747 emerging from a junk yard--Monod does, in fact, invoke a miracle. Much as he would have refused this description, he sides with the creationists. (217)

-- de Duve, Christian (Nobel Laureate) Blueprint for a Cell: The Nature and Origin of Life. Neil Patterson Publishers. 1991.
At heart, de Duve's assumption that "life belongs to the very fabric of the universe" is based on his blind faith in the "combinatorial properties of matter," which is little more, quantitatively (scientifically) speaking, than numerology, for Prior Probabilities Have No Probative Force. Imagine that, a scientist who is a Nobel Laureate basing such a fundamental assumption upon the ignorant superstition of "numerology"! Such a blind faith exists even in the face of growing evidence that the whole is greater than its parts with regards to Emergence of realities which are not merely reducible to their aggregate parts. Such is the nature of the blinders placed upon human reason and imagination when one subscribes to a mechanistic materialist philosophy which a priori reaches certain assumptions despite the growing body of evidence to the contrary.

The fact is that de Duve makes this assumption based upon philosophical materialism, not science, and to claim that such an assumption is science or scientific is nothing less than the pseudo-science, or to be more specific, the false science of scientism: a philosophical viewpoint attempting to mask its a priori philosophical assumptions with appeals to the authority of science. Consider the irony of these two world renowned scientists, both materialists, one of whom reaches the conclusion that life must be extremely rare in the universe because it is caused by a "chance ... event of such unimaginable complexity and improbability," and the other who reaches the conclusion that "life belongs to the very fabric of the universe" because it is an "obligatory manifestation of the combinatorial properties of matter, [or] it could not possibly have arisen naturally," a conclusion he reaches because he cannot accept the argument that an "event of such unimaginable complexity and improbability" can be ascribed to mere chance. Hence, he opts therefore to ascribe it to necessity, but unfortunately, there is no scientific factual basis upon which to base such a claim, leaving him only to resort to a pseudo-scientific claim that life is an "obligatory manifestation" based upon superstition: the numerological belief in the "combinatorial properties of matter."
Harold wrote:In the beginning was the Word; so says the gospel of Saint John. Goethe's Faust, the prototypic modern man and scientist, thought otherwise: in the beginning was the Deed. Rephrased just a little, scholars still divide into those who seek the origin of life in information and those who look to energetics. Those who believe, a I do, that living organisms are autopoietic systems capable of evolution by variation and natural selection, must keep a foot in both camps and risk being scorned by both. But the definition really sharpens the issue: the question is not only how life arose on earth, but how nature generates organized material systems to which terms such as adaptation, function and purpose can be applied. Readers will have noted that this is still a free-wheeling inquiry, in which the few solid facts need not seriously impede the imagination; let me take advantage of what, sadly, become a very rare privilege. (Harold 2001: 249-250)

Granted that, as de Duve says, we are compelled by our calling to insist at all times on strictly naturalistic explanations; life must, therefore, have emerged from chemistry. [See above.] Granted also that simple organic molecules were present at the beginning, in uncertain locations, diversity and abundance. Leave room for contingency, some rare chemical fluctuation that may have played a seminal role in the inception of living systems; and remember that you may be mistaken. With all that, I still cannot bring myself to believe that rudimentary organisms of any kind came about by the association of prefabricated organic molecules, born of purely chemical processes in their environment. Did life begin as a molecular collage? To my taste, that idea smacks of the reconstitution of life as we know it rather than its genesis ab initio. It overestimates what Harold Morowitz called the munificence of nature, her generosity in providing building blocks for free. It makes cellular organization an afterthought to molecular structure, and offers no foothold to autopoiesis. And it largely omits what I believe to be the ultimate wellspring of life, the thermodynamic drive of energy dissipation, creating mounting levels of structural order for natural selection to winnow. If it is true that life resides in organization rather than in substance, than what is left out of account is the heart of the mystery: the origin of biological order. (Harold 2001: 250)

Scientists formulate hypotheses, not just at the conclusion of an inquiry but from its very outset. Karl Popper and Thomus Kuhn both taught that, absent a preconception of some sort, we do not know what questions to ask or even what facts to observe. The downside is that we will cling to an outworn hypothesis, well aware of its shortcomings, until a more credible alternative comes to hand. This, I suspect, is where the study of biopoiesis now stands: the past unburied, the future not yet born. I will also venture an opinion about where we should look. The hurdle is to understand, not the origin of organic molecules, but of systems that progressively come to display the characteristics of organisms: boundaries, metabolism, energy transduction, growth, heredity and evolution. This is hardly a startling or even original proposition, but its unapologetic holism makes it a minority view. (Harold 2001: 250-251)

I hold, then that cellular organization was not a codicil to the true origin of life, but part and parcel of it. That implies compartmentation of some kind (not necessarily lipid membranes) from the beginning. Biological order is dynamic, created and sustained by a continuous stream of energy, and that also must have been true all along. Therefore, a credible biopoietic theory will be one that generates mounting levels of complexity naturally, by providing the means to convert the flux of energy into organization. But energy dissipation can only carry life over the first jump; evolution is hamstrung until the emerging "functions" within the developing system have been codified in a "text" of some kind that can be transmitted, executed, altered, and put to the test of utility again and again. Nucleic acids or their precursors must have come on stage early, if not when the curtain rose. No satisfying scheme of this kind is presently on the books, and I have none to offer, I have only the strong hunch that there is much more to this mystery than is dreamt of in molecular philosophy. (Harold 2001: 251)

It would be agreeable to conclude this book with a cheery fanfare about science closing in, slowly but surely, on the ultimate mystery; but the time for rosy rhetoric is not yet at hand. The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication. Even the principles of biopoiesis still elude us, for reasons that are as much conceptual as technical. The physical sciences have been exceedingly successful in formulating universal laws on the basis of reproducible experiments, accurate measurements, and theories explicitly designed to be falsifiable. These commendable practices cannot be fully extrapolated to any historical subject, in which general laws constrain what is possible but do not determine the outcome. Here knowledge must be drawn from observation of what actually happened, and seldom can theory be directly confronted with reality. The origin of life is where these two ways of knowing collide. The approach from hard science starts with the supposition that physical laws exercise strong constraints on what was historically possible; therefore, even though one can never exclude the intervention of some unlikely but crucial happenstance, one should be able to arrive at a plausible account of how it could have happened. This, however, is not how matters have turned out. The range of permissible options is to broad, the constraints so loose, that few scenarios can be firmly rejected; and when neither theory nor experiment set effective boundaries, hard science is stymied. The tools of "soft," historical science unfortunately offer no recourse: the trail is too cold, the traces too faint. (Harold 2001: 251-252)

They tell a story of Max Delbrück, one of the pioneers of molecular genetics and the ironic inventor of DNA, whom I was privileged to meet during his later years at the California Institute of Technology. He had stopped reading papers on the origin of life, Max once observed; he would wait for someone to produce a recipe for the fabrication of life. So are we all waiting, not necessarily for a recipe but for new techniques of apprehending the utterly remote past. Without such a breakthrough, we can continue to reason, speculate and argue, but we cannot know. Unless we acquire novel and powerful methods of historical inquiry, science will effectively have reached a limit. (Harold 2001: 252)

[Franklin M. Harold is Emeritus Professor of Biochemistry and Molecular Biology at Colorado State Univeristy.]

-- Harold, Franklin M. The Way of the Cell: Molecules, Organisms and the Order of Life. New York: Oxford University Press; 2001; pp. 249-252.
Sarkar wrote:Many influential contemporary discussions of the origin of life have concentrated on the origin of information, in which information is construed simply to be nucleic acid sequences (e.g., Eigen 1992). Implicit in these discussions is the assumption that nucleic acid sequences ultimately encode all that is necessary for the genesis of living forms and, therefore, that a solution to the problem of the initial generation of these sequences will solve the problem of the origin of life. The move away from sequences [reductionism] would put these efforts in proper perspective: to explain the possible origin of persistent segments of DNA [which we can only speculate about at this time] does not suffice as an explanation of the origin of living cells. However, I do not wish to harp on this point since, quite justifiably, most molecular biologists think that such discussions of the origin of life are little other than idle speculation. (Sahotra 2005: 246)

-- Sarkar, Sahotra (2005) Molecular Models of Life. The MIT Press.

[Sahotra Sarkar is Professor of Integrative Biology and Philosophy at the University of Texas, Austin.]
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Rob
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3.5 Billion Year Old Fossil Evidence

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Dates are open to critical evalution:
de Duve wrote:Fossilized remnants of typical bacteria (microfossils) and, even, of complex bacterial colonies, called strometolites, astonishingly similar to extant living formations, have been found in a number of ancient rocks, including some Australian cherts estimated to be almost 3.5 billion years old.

According to their discoverer, the American microfossil expert William Schopf, the Australian traces originate from highly evolved bacteria, closely related to present-day cynobacteria, that is, bacteria that carry out a sophisticated kind of oxygen-generating photosynthesis. This claim, which, as we shall see, raises some difficulties, has recently been seriously questioned.[3]

[3] In The Cradle of Life (Princeton, NJ: Princeton University Press, 1999) J.W. Schopf has documented in detail the evidence supporting his claim that the traces he has discovered in some ancient Australian rocks believed to be almost 3.5 billion years old are the fossilized remnants of microorganisms related to present-day cynobacteria, that is, organisms that carry out an advanced form of oxygen-producing photosynthesis. As we shall see in chapter 8, this claim conflicts to some extent, though not irreconcilably, with the observation that the atmosphere levels of oxygen began to rise only some two billion years ago. The question has recently been revived by two articles published side by side in the March 7, 2002, issue of Nature. One article, by Schopf's group (vol. 416, pp. 73-76), offers additional evidence reinforcing his claim. The other article, by M.D. Brasier et al., follows immediately (pp. 76-81) under the title "Questioning the Evidence for Earth's Oldest Fossils." In it, a number of data are presented that raise serious doubts on the cynobacterial origin of the traces and, even, on their biological origin. (fn. 3, p. 314)

-- de Duve, Christian. Life Evolving: Molecules, Mind, and Meaning. Oxford: Oxford University Press; 2002: 314.

[Winner of the Nobel Prize in Physiology or Medicine]
Klein wrote:Banded iron-formations (BIFs) occur in the Precambrian geologic record over a wide time span. Beginning at 3.8 Ga (Isua, West Greenland), they are part of Archean cratons and range in age from about 3.5 until 2.5 Ga. Their overall volume reaches a maximum at about 2.5 Ga (iron-formations in the Hamersley Basin of Western Australia) and they disappear from the geologic record at about 1.8 Ga, only to reappear between 0.8 and 0.6 Ga.

The stratigraphic sequences in which BIFs occur are highly variable. Most Archean iron-formations are part of greenstone belts that have been deformed, metamorphosed, and dismembered. This makes reconstruction of the basinal setting of such BIFs very difficult. The general lack of metamorphism and deformation of extensive BIFs of the Hamersley Range of Western Australia and the Transvaal Supergroup of South Africa allow for much better evaluations of original basinal settings. Most Archean iron-formations show fine laminations and/or microbanding. Such microbanding is especially well developed in the Brockman Iron Formation of Western Australia, where it has been interpreted as chemical varves, or annual layers of sedimentation. BIFs ranging in age from 2.2 Ga to about 1.8 Ga (e.g., those of the Lake Superior region, U.S.A., Labrador Trough, Canada, and the Nabberu Basin of Western Australia) commonly exhibit granular textures and lack microbanding.

The mineralogy of the least metamorphosed BIFs consists of combinations of the following minerals: chert, magnetite, hematite, carbonates (most commonly siderite and members of the dolomite-ankerite series), greenalite, stilpnomelane, and riebeckite, and locally pyrite. Minnesotaite is a common, very low-grade metamorphic reaction product. The Eh-pH stability fields of the above minerals (and/or their precursors) indicate anoxic conditions for the original depositional environment.

The average bulk chemistry of BIFs, from 3.8 through 1.8 Ga in age, is very similar. They are rich in total Fe (ranging from about 20 to 40 wt%) and Si[O.sub.2] (ranging from 43 to 56 wt%). CaO and MgO contents range from 1.75 to 9.0 and from 1.20 to 6.7 wt%, respectively. A[l.sub.2][O.sub.3] contents are very low, ranging from 0.09 to 1.8 wt%. These chemical values show that they are clean chemical sediments devoid of detrital input. Only the Neoproterozoic iron-formations (of 0.8 to 0.6 Ga in age) have very different mineralogical and chemical make-ups. They consist mainly of chert and hematite, with minor carbonates.

The rare-earth element profiles of almost all BIFs,with generally pronounced positive Eu anomalies, indicate that the source of Fe and Si was the result of deep ocean hydrothermal activity admixed with sea water.

The prograde metamorphism of iron-formations produces sequentially Fe-amphiboles, then Fe-pyroxenes, and finally (at highest grade) Fe-olivine-containing assemblages. Such metamorphic reactions are isochemical except for decarbonation and dehydration.

The common fine lamination (and/or microbanding) as well as the lack of detrital components in most BIFs suggest that such are the result of deposition, below wave base, in the deeper parts of ocean basins. Those with granular textures are regarded as the result of deposition in shallow water, platformal areas. Carbon isotope data suggest that for a long period of time (from Archean to Early Proterozoic) the ocean basins were stratified with respect to [delta][sup.13C] (in carbonates) as well as organic carbon content. In Middle Proterozoic time (when granular BIFs appear) this stratification diminishes and is lost.

The Neoproterozoic BIFs occur in stratigraphic sequences with glaciomarine deposits. These BIFs are the result of anoxic conditions that resulted from the stagnation in the oceans beneath a near-global ice cover, referred to as "Snowball Earth."

All of the most "primary" mineral assemblages appear to be the result of chemical precipitation under anoxic conditions. There are, as yet, no data to support that BIF precipitation was linked directly to microbial activity. The relative abundance of BIF throughout the Precambrian record is correlated with a possible curve for the evolution of the [O.sub.2] content in the Precambrian atmosphere.

-- Klein, Cornelis. Some Precambrian banded iron-formations (BIFs) from around the world: their age, geologic setting, mineralogy, metamorphism, geochemistry, and origin. American Mineralogist. 2005 Oct; 90(10):1473(27).
Sapp wrote:Oxygen became abundant in the atmosphere by around 2.5 billion years ago. This is evidenced by the occurrence of massive deposits of Fe2O3, in the context of "banded iron formations" (BIFs), beds of alternating reduced (black Fe2+) and oxidized (red, Fe3+) sediments of that age.[31] Oxygen production must have been going on for a long time before that, however, to bring the atmosphere to the oxic state required the precipitation of iron oxide. For instance, the oxygen concentration in the oceans alone must have accumulated to about 50 mM, the amount required for production of the ambient marine sulfate concentration (by oxidation of sulfide).

When, then, did oxygen-forming photosynthesis begin? Biologically, it is presumably began with the emergence of cyanobacteria, because only cyanobacteria carry out that form of metabolism. This must have been early in evolution, at the time of the radiation of the main bacterial lines, soon after the appearance of cellular life. The early BIFs indicate that this could have been as early as 3.8 billion years ago.[32] If the oxygen in those ancient BIFs is of biological origin, which is by no means certain, then oxygenic photosynthesis must have been in place at that time. A biological origin of the oxygen is consistent with the carbon isotope fractionation, in the same rocks, which indicates biological processing.

31 N. Sleep, "Oxygenating the Atmosphere," Nature 410 (2002): 317-319.
32 S.J. Mojzsis, G. Arrhenius, K.D. McKeegen, T.M. Harrison, A.P. Nutman, and C.R.L. Friend, "Evidence for Life on Earth Before 3.800 Million Years ago," Nature 384 (1996): 55-59.

-- Sapp, Jan, Editor. Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Norton; 2005: 66-67.
de Duve wrote:Since this historical [Miller-Urey] experiment, the field has veritably exploded. In the last three decades, the origin of life has been the subject of dozens of books, scores of essays, thousands of articles, relating an enormous amount of experimental and theoretical work. Periodicals devoted exclusively to the subject have been founded. Textbooks dedicate whole chapters to it. The reason for this upsurge of interest is simple. As I have attempted to show ..., we have come to know enough about life to draw the basic blueprint according to which all extant living organisms are constructed. Scientists faced with the blueprint (or, rather, with their own version of the blueprint, because they tend to see life through different glasses, depending on their fields of specialization) find the problem of how the plan materialized almost inescapable. This turned out to be my case as well. (110)

But I must add a warning. If not considered totally outlandish any more, the field still remains largely confined to speculation. When it comes to events that happened several billion years ago, hard data are scarce and, perforce, are supplemented by reasoning and imagination, if not blind faith. Yet, life did start somewhere, sometime, somehow. Trying to reconstruct the events that led to its birth holds almost irresistable fascination, especially now that we have available so much new knowledge on the nature of life and so many new tools for digging into the past and approaching the problem. (110)

The tale is told in simple historical style, without any of the probability weighings, plausibility assessments, and other precautionary periphrases that it requires.[2] These will come in due course. According to my reconstruction, emerging life went through four main successive stages--or "worlds," to use a popular expression: the primeval prebiotic world, the thioester world, the RNA world, and the DNA world. This version of the script differs from the current favorite mainly by the insertion of a thioester world. I consider this insertion essential because I cannot accept the view of an RNA world arising through purely random chemistry. (112-113)

[2] The readers' attention is called to this point, lest they be misled by the apparently dogmatic style of the script. All statements should be read as conditional and hypothetical. (112)

I have quoted Monod's declaration "The Universe was not pregnant with life," to which he added "nor the biosphere with man." I have made it clear that I disagree with his first statement. Life belongs to the very fabric of the universe. Were it not an obligatory manifestation of the combinatorial properties of matter, it could not possibly have arisen naturally. By ascribing to chance an event of such unimaginable complexity and improbability--remember Hoyle's allegory of the Boeing 747 emerging from a junk yard--Monod does, in fact, invoke a miracle. Much as he would have refused this description, he sides with the creationists. (217)

-- de Duve, Christian (Nobel Laureate) Blueprint for a Cell: The Nature and Origin of Life. Neil Patterson Publishers. 1991.
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Rob
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Probability Arguments Euphemism for Ignorance

Post #3

Post by Rob »

Fitelson wrote:In Chapter 12 of Warrant and Proper Function, Alvin Plantinga constructs two arguments against evolutionary naturalism, which he construes as a conjunction of E&N. The hypothesis E says that "human cognitive faculties arose by way of the mechanisms to which contemporary evolutionary thought directs our attention" (p. 220). With respect to proposition N, Plantinga (p. 270) says "it isn't easy to say precisely what naturalism is," but then adds that "crucial to metaphysical naturalism, of course, is the view that there is no such person as the God of traditional theism."

[Of course, Plantinga is overlooking the fact that their is a difference between methodological naturalism and philosophical naturalism, and that science is based upon methodological naturalism, and it is mistaken to conflate the two. (See Pennock, p. 57)

Platinga goes on to assign subjective propabilities to his propostions, upon which there is no "objective basis for such probability assignments." (Pennock, p. 412)]

Plantinga says (p. 220, footnote 7) that his probabilities can be interpreted either "epistemically" or "objectively," but that he prefers the objective interpretation. However, Bayesians have never been able to make sense of the idea that prior probabilities have an objective basis. The siren song of the Principle of Indifference has tempted many to think that hypotheses can be assigned probabilities without the need of empirical evidence, but no consistent version of this principle has ever been articulated. The alternative to which Bayesians typically retreat is to construe probabilities as indicating an agent's subjective degree of belief. The problem with this approach is that it deprives prior probabilities (and the posterior probabilities that depend on them) of probative force. If one agent assigns similar prior probabilities to evolutionary naturalism and to traditional theism, this is entirely consistent with another agent's assigning very unequal probabilities to them, if probabilities merely reflect intensities of belief. (Fitelson et al. 2002: 411; cited in Pennock)

Although Plantinga's arguments don't work, he has raised a question that needs to be answered by people who believe evolutionary theory and who also believe that this theory says that our cognitive abilities are in various ways imperfect. Evolutionary theory does say that a device that is reliable in the environment in which it evolved may be highly unreliable when used in a novel environment. [Evo-devo is revealing new levels of plasticity in the development and adaptation of the organism.] It is perfectly possible that our mental machinery should work well on simple perceptual tasks, but be much less reliable when applied to theoretical matters. We hasten to add that this is possible, not inevitable. It may be that the cognitive procedures that work well in one domain also work well in another; Modus Ponens may be useful for avoiding tigers and for doing quantum physics. (Fitelson et al. 2002: 424-425; cited in Pennock)

Anyhow, if evolutionary theory does say that our ability to theorize about the world is apt to be rather unreliable, how are evolutionists to apply this point to their own theoretical beliefs, including their belief in evolution? One lesson that should be extracted is a certain humility--an admission of fallibility. This will not be news to evolutionists who have absorbed the fact that science in general is a fallible enterprise. Evolutionary theory just provides an important part of the explanation of why our reasoning about theoretical matters is fallible. (Fitelson et al. 2002: 425; cited in Pennock)

Far from showing that evolutionary theory is self-defeating, this consideration should lead who believe the theory to admit that the best they can do in theorizing is to do the best they can. We are stuck with the cognitive equipment that we have. We should try to be as scrupulous and circumspect about how we use this equipment as we can. When we claim that evolutionary theory is a very well confirmed theory, we are judging this theory by using the fallible cognitive resources we have at our disposal. We can do no other. (Fitelson et al. 2002: 425; cited in Pennock)

Plantinga suggests that evolutionary naturalism is self-defeating, but that traditional theism is not. However, what is true is that neither position has an answer to hyperbolic doubt. Evolutionists have no way to justify the theory they believe other than by critically assessing the evidence that has been amassed and employing rules of inference that seem on reflection to be sound. If someone challenges all the observations and rules of inference that are used in science and in everyday life, demanding that they be justified from the ground up, the challenge cannot be met. A similar problem arises for theists who think that their confidence in the reliability of their own reasoning powers is shored up by the fact that the human mind was designed by a God who is no deceiver. The theist, like the evolutionary naturalist, is unable to construct a non-question-begging argument that refutes global skepticism. (Fitelson et al. 2002: 425; cited in Pennock)

-- Fitelson, Branden and Sober Elliott. Plantinga's Probability Arguments against Evolutionary Naturalism. In Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives (Robert T. Pennock, ed.). Cambridge: MIT Press; 2002; p. 411; 424-425.
Fox wrote:The steps that have been identified by experiment are:

1. Formation of amino acids from primordial reactants.
2. Formation of proteinoids by polymerization of sets of amino acid.
3. Formation of microstructures by contact of polymers with water.
4. Origin of the genetic apparatus within such microstructures.

The experimental results show that the probability of each step is close to unity .... For purposes of argument let us assume 90%, although the experiments indicate > 90%. The probability of reproductive, infrastructured cell-like entities arising in steps from inorganic matter containing atoms of carbon, hydrogen, oxygen, and nitrogen is then at least (9/10)4 = 65%. (All such "numerology," however, on either side may be considered a quantitative euphemism for ignorance.)

-- Fox, Sidney W. Creationism and Evolutionary Protobiogenesis. In Science and Creationism (Ashley Montagu ed.). Oxford: Oxford University Press; 1984; p. 212.
Kitcher wrote:Throughout his book, Behe repeats the same story. He describes, often charmingly, the complexities of molecular structures and processes. There would be nothing to complain of if he stopped here and said: "Here are some interesting problems for molecularly minded evolutionists to work on, and, in a few decades time, perhaps, in light of increased knowledge of how development works at the molecular level, we may be able to see what the precursors were like.” But he doesn’t. He tries to argue that the precursors and intermediaries required by Darwinian evolutionary theory couldn’t have existed. This strategy has to fail because Behe himself is just as ignorant about the molecular basis of development as his Darwinian opponents. Hence he hasn’t a clue what kinds of precursors and intermediaries the Darwinian account is actually committed to--so it’s impossible to demonstrate that the commitment can’t be honored. However, again and again, Behe disguises his ignorance by suggesting to the reader that the Darwinian story must take a very particular form--that it has to consist in something like the simple addition of components, for example--and on that basis he can manufacture the illusion of giving an impossibility of proof. (Kitcher 2002: 265)

Although this is the main rhetorical trick of the book, there are some important subsidiary bits of legerdemain. Like pre-Reformation creationists, Behe loves to flash probability calculations, offering spurious precision to his criticisms. Here’s his attack on a scenario for the evolution of a blood-clotting mechanism, tentatively proposed by Russell Doolittle:

“… let’s do our own quick calculation. Consider that animals with blood-clotting cascades have roughly 10,000 genes, each of which is divided into an average of three pieces. This gives a total of about 30,000 gene pieces. TPA [Tissue Plasminogen Activator] has four different types of domains. By “variously shuffling,” the odds of getting those four domains together is 30,000 to the fourth power, which is approximately one-tenth to the eighteenth power, and if a million people played the lottery each year, it would take an average of about a thousand billion years before anyone (not just a particular person) won the lottery…. Doolittle apparently needs to shuffle and deal himself a number of perfect bridge hands to win the game.” (DBB 94) (Kitcher 2002: 265-266)

This sounds quite powerful, and Behe drives home the point by noting that Doolittle provides no quantitative estimates, adding that “without numbers, there is no science” (DBB 95)--presumably to emphasize that born-again creationists are better scientists than the distinguished figures they attack. But consider a humdrum phenomenon suggested by Behe’s analogy to bridge. Imagine that you take a standard deck of cards and deal yourself thirteen. What’s the probability that you got exactly those cards in exactly that order? The answer is 1 in 4 x 1021. Suppose you repeat this process ten times. You’ll now have received ten standard bridge hands, ten sets of thirteen cards, each one delivered in a particular order. The chance of getting those cards in just that order is 1 in 410 x 10210. This is approximately 1 in 10222. Notice that the denominator is far larger than that of Behe’s trifling 1018. So it must be really improbable that you (or anyone else) would ever receive just those cards in just that order in the entire history of the universe. But, whatever the cards were, you did. (Kitcher 2002: 266)

What my analogy shows is that, if you describe events that actually occur from a particular perspective, you can make them look improbable. Thus, given a description of the steps in Doolittle’s scenario for the evolution of TPA, the fact that you can make the probability look small doesn’t mean that that isn’t (or couldn’t) have been the way things happened. One possibility is the evolution of blood-clotting was genuinely improbable. But there are others. (Kitcher 2002: 266)

Return to your experiment with the deck of cards. Let’s suppose that all the hands you were dealt were pretty mundane--fairly evenly distributed among the suits, with a scattering of high cards in each. If you calculated the probability of receiving ten mundane hands in succession, it would of course be much higher than then priority of being dealt those very particular mundane hands with the cards arriving in just that sequence (although it wouldn’t be as large as you might expect). There might be an analogue for blood-clotting, depending on how many candidates there are among the 3,000 “gene pieces” to which Behe alludes that would yield a protein able to play the necessary role. Suppose that there are a hundred acceptable candidates for each position. That means that the chance of success on any particular draw is (1/30)4, which is about 1 in 2.5 million. Now, if there were 10,000 tries per year, it would take, on average, two or three centuries to arrive at the right combination, a flicker of an instant in evolutionary time. (Kitcher 2002: 266-267)

Of course, neither Behe nor I know how tolerant the blood-clotting system is, how many different molecular ways it allows to get the job done. Thus we can’t say if the right way to look at the problem is to think of the situation as an analogue to being dealt a very particular sequence of cards in a very particular order, or whether the right comparison is with cases in which a more general type of sequence occurs. But these two suggestions don’t exhaust the relevant cases. (Kitcher 2002: 267)

Suppose you know the exact order of cards in the deck prior to each deal. The probability that the particular sequence would occur would be extremely high (barring fumbling or sleight of hand, the probability would be 1). The sequence only looks improbable because we don’t know the order. Perhaps that’s true for the Doolittle shuffling process as well. Given the initial distribution of pieces of DNA, plus the details of the biochemical milieu, principles of chemical recombination might actually make it very probable that the cascade Doolittle hypothesizes would ensue. Once again, nobody knows whether this is so. Behe simply assumes that it isn’t. (Kitcher 2002: 267)

Let me sum up. There are two questions to pose: What is the probability that the Doolittle sequence would occur? What is the significance of a low value for that probability? The answer to the first question is that we haven’t a clue: it might be close to 1, it might be small but significant enough to make it likely that the sequence would occur in a flicker of evolutionary time, or it might be truly tiny (as Behe suggests). The answer to the second question is that genuinely improbable things sometimes happen, and one shouldn’t confuse improbability with impossibility. Once these points are recognized, it’s clear that, for all its rhetorical force, Behe’s appeal to numbers smacks more of numerology than of science. As with his main line of argument, it turns out to be an attempt to parlay ignorance of molecular details into an impossibility proof. (Kitcher 2002: 267)

-- Kitcher, Philip. Born-Again Creationism. In Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives (Robert T. Pennock, ed.). Cambridge: MIT Press; 2002; pp. 265-267.
Kitcher's argument cuts both ways for both scientists and religionists; one shouldn't confuse so-called probability with certainty, nor should one attempt to parlay ignorance of the true origin of life based upon "pure speculation" into the possibility of proof, such as Wald attempts below:
Wald wrote:About a century ago the question, How did life begin?, which has interested men throughout their history, reached an impasse. Up to that time two answers had been offered: one that life had been created supernaturally, the other that it arises continually from the nonliving. The first explanation lay outside science, the second was now shown to be untenable. For some time scientists felt some discomfort in having no answer at all. Then they stopped asking. Recently ways have been found again to consider the origin of life as a scientific problem--as an event within the order of nature. In part this is the result of new information. But a theory never rises of itself, however rich and secure the facts. It is an act of creation. Our present ideas in this realm were first brought together in a clear and defensible argument by the Russian biochemist A. I. Oparin in a book called The Origin of Life, published in 1936. Much can be added now to Oparin's discussion, yet it provides the foundation upon which all of us who are interested in this subject have built. (Wald 1968: 337)

(....) At the center of the enterprise lies the hope not only of explaining a great past event--important as that should be--but of showing that the explanation is workable. If we can indeed come to understand how a living organism arises from the nonliving, we should be able to construct one. (...) This is so remote a possibility now that one scarcely dares to acknowledge it; but it is there nevertheless. (Wald 1968: 337)

One answer to the problem of how life originated is that it was created. This is an understandable confusion of nature with technology. Men are used to making things; it is a ready thought that those things not made by men were made by a superhuman being. (Wald 1968: 337)

(....) The reasonable view was to believe in spontaneous generation; the only alternative, to believe in a single, primary act of supernatural creation. There is no third position. For this reason many scientists a century ago chose to regard the belief in spontaneous generation as a "philosophical necessity." It is a symptom of the philosophical poverty of our time that this necessity is no longer appreciated. Most modern biologists, having reviewed with satisfaction the downfall of the spontaneous generation hypothesis, yet unwilling to accept the alternative belief in special creation, are left with nothing. (Wald 1968: 339)

I think a scientist has no choice but to approach the origin of life through a hypothesis of spontaneous generation. What the controversy ... showed to be untenable is only the belief that living organisms arise spontaneously under present conditions. We have now to face a somewhat different problem: how organisms may have arisen spontaneously under different conditions in some former period, granted that they do so no longer. (Wald 1968: 339)

The Task

To make an organism demands the right substance in the right proportions and in the right arrangement. We do not think that anything more is needed. (....) (Wald 1968: 340)

The Possible and Impossible

One has only to contemplate the magnitude of this task to concede that the spontaneous generation of a living organism is impossible. Yet here we are--as a result, I believe, of spontaneous generation. [a priori 'philosophical' position taken on belief and faith.] It will help to digress for a moment to ask what one means by "impossible." (Wald 1968: 339-40)

With every event one can associate a probability--the chance that it will occur. This is always a fraction, the proportion of times the event occurs in a large number of trials. Sometimes the probability is apparent even without trial. A coin has two faces; the probability of tossing a head is therefore ½. A die has six faces; the probability of throwing a deuce is 1/6. When one has no means of estimating the probability beforehand, it must be determined by counting the fraction of successes in a large number of trials. (Wald 1968: 340)

Our everyday concept of what is impossible, possible or certain derives from our experience: the number of trials that may be encompassed within the space of a human lifetime, or at most within recorded human history. In this colloquial, practical sense I concede the spontaneous origin of life to be “impossible.” It is impossible as we judge events in the scale of human experience. (Wald 1968: 340)

We shall see that this is not a very meaningful concession. For one thing, the time with which our problem is concerned is geological time, and the whole extent of human history is trivial in the balance. We shall have more to say of this later. (Wald 1968: 340)

But even within the bounds of our own time there is a serious flaw in our judgment of what is possible. It sounds impressive to say that an event has never been observed in the whole of human history. We should tend to regard such an event as at least “practically” impossible, whatever probability is assigned to it on abstract grounds. [a priori grounds] When we look further into such a statement, however, it proves to be almost meaningless. For men are apt to reject reports of very improbable occurrences. Persons of good judgment think it safer to distrust the alleged observer of such an event than to believe him. The result is that events which are merely very extraordinary acquire the reputation of never having occurred at all. Thus the highly improbable is made to appear impossible. (Wald 1968: 340)

To give an example: Every physicist knows that there is a very small probability, which is easily computed, that the table upon which I am writing will suddenly and spontaneously rise into the air. The event requires no more than that the molecules of which the table is composed, ordinarily in random motion in all directions, should happen by chance to move in the same direction. Every physicist concedes this possibility; but try telling one that you have seen it happen. Recently I asked a friend, a Nobel laureate in physics, what he would say if I told him that. He laughed and said that he would regard it as more probable that I was mistaken than that the event had actually occurred. (Wald 1968: 340)

We see therefore that it does not mean much to say that a very high improbable event has never been observed. There is a conspiracy to suppress such observations, not among scientists alone, but among all judicious persons, who have learned to be skeptical even of what they see, let alone of what they are told. If one group is more skeptical than others, it is perhaps lawyers, who have the harshest experience of the unreliability of human evidence. Least skeptical of all are the scientists, who, cautious as they are, know very well what strange things are possible. (Wald 1968: 340)

A final aspect of our problem is very important. When we consider the spontaneous origin of a living organism, this is not an event that need happen again and again. It is perhaps enough for it to happen once. The probability with which we are concerned is of a special kind; it is the probability that an event occur at least once. To this type of probability a fundamentally important thing happens as one increases the number of trials. However improbable the event in a single trial, it becomes increasingly probable as the trials are multiplied. Eventually the event becomes virtually inevitable. (Wald 1968: 340)

For instance, the chance that a coin will not fall head up in a single toss is 1/2. The chance that no head will appear in a series of tosses is 1/2 x 1/2 x 1/2 … as many times over the number of tosses. In 10 tosses the chance that no head will appear is therefore 1/2 multiplied by itself 10 times, or 1/1,000. Consequently the chance that a head will appear at least once in 10 tosses is 999/1,000. Ten trials have converted what started as a modest probability to a near certainty. (Wald 1968: 340)

The same effect can be achieved with any probability, however small, by multiplying sufficiently the number of trials. Consider a reasonably improbable event, the chance of which is 1/1,000. The chance that this will not occur in one trial is 999/1,000. The chance that it won’t occur in 1,000 trials is 999/1,000 multiplied together 1,000 times. This fraction comes out to be 37/100. The chance that it will happen at least once in 1,000 trials is therefore one minus this number--63/100--a little better than three chances out of five. One thousand trials have transformed this from a highly improbable to a highly probable event. In 10,000 trials the chance that this event will occur at least once comes out to be 19,999/20,000. It is now almost inevitable. (Wald 1968: 340)

It makes no important change in the argument if we assess the probability that an event occur at least two, three, four or some other small number of times rather than at least once. It simply means that more trials are needed to achieve any degree of certainty we wish. Otherwise everything is the same. (Wald 1968: 340-341)

In such a problem as the spontaneous origin of life we have no way of assessing the probabilities beforehand or even of deciding what we mean by a trial. The origin of a living organism is undoubtedly a stepwise phenomenon, each step with its own probability and its own conditions of trial. Of one thing we can be sure, however: whatever constitutes a trial, more such trials occur the long the interval of time. (Wald 1968: 341)

The important point is that since the origin of life belongs in the category of at-least-once phenomena, time is on its side. However improbable we regard this event, or any other steps which it involves, given enough time it will almost certainly happen at least once. And for life as we know it, with its capacity for growth and reproduction, once may be enough. (Wald 1968: 341)

Time is in fact the hero of the plot. The time with which we have to deal is of the order of two billion years. What we regard as impossible on the basis of human experience is meaningless here. Given so much time, the “impossible” becomes possible, the possible probable, and the probable virtually certain. One has only to wait: time itself performs the miracles. (Wald 1968: 341)

-- Wald, George. The Origin of Life. In The Molecular Basis of Life: An Introduction to Molecular Biology. (Readings From Scientific American, ed.).: Freeman; 1968; pp. 337-341.
As Fox notes, "All such 'numerology,' however, on either side may be considered a quantitative euphemism for ignorance."
Last edited by Rob on Thu Mar 23, 2006 2:58 pm, edited 2 times in total.

Rob
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Origin of Life vs. Evolutionary Theory

Post #4

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Scott wrote:The origin of life is a complex but active research area with many interesting avenues being investigated, though there is not yet consensus on the sequence of events that led to living things. But at some point in Earth's early history, perhaps as early as 3.8 billion years ago, life in the form of simple single-celled organisms appeared. Once life evolved, biological evolution became possible.

Although some people confuse the origin of life itself with evolution, the two are conceptually separate. Biological evolution is defined as decent of living things from ancestors from which they differ. Life had to precede evolution! Regardless of how the first replicating molecule appeared, we see in the subsequent historical record the gradual appearance of more complex living things, and many variations on the many themes of life. We know much more about evolution than about the origin of life.

-- Scott, Eugenie C. Evolution vs. Creationism: And Introdution. California: University of California Press; 2004; pp. 26-27.
Pigliucci wrote:Now there are a couple of important things that evolution is not, misleading claims by creationists [and scientists] notwithstanding. For example, evolution is not a theory of the origin of life, for the simple reason that evolution deals with changes in living organisms induced by a combination of random (mutation) and nonrandom (natural selection) forces. [These assumptions are now being questioned; see Rudolf A. Raff in "The Shape of Life: Genes, Development, and the Evolution of Animal Form," chapter 9 and 10] By definition, before life originated there were no mutations, there therefore there was no variation; hence, natural selection could not possibly have acted. This means that the origin of life is a (rather tough) problem for physics and chemistry to deal with, but not a proper area of inquiry for evolutionary biology. It would be like asking a geologist to explain the origin of planets: The geologist's work starts after planets come into existence, and it is the cosmologist who deals with the question of planetary origins.

(....) Evolution is also most definitely not a theory of the origin of the universe. As interesting as this question is, it is rather the realm of physics and cosmology. Mutation and natural selection, the mechanisms of evolution, do not have anything to do with stars and galaxies. It is true that some people, even astronomers, refer to the "evolution" of the universe, but this is meant in the general sense of change through time, not the technical sense of the Darwinian theory.

-- Pigliucci, Massimo (2002) Denying Evolution: Creationism, Scientism, and the Nature of Science. Sinauer Press. pp. 76-77.
Pigliucci on Scientific Fallacies wrote:Millers classic experiments -- as historically important for the field as they are -- are not the solution (or even a valuable starting point) to understanding the origin of life on Earth. An intellectually honest and well-informed science educator (they are usually the former but only more rarely the latter) should therefore point to the amount of [so-called] progress that has been in this field, describe some of the ongoing research, and stop far short of saying that the promblem has been solved.... [D]ismissal of creationist [or honest critical questions] is ... common. But it is wrong, both ethically and educationally.

-- Pigliucci, Massimo (2002) Denying Evolution: Creationism, Scientism, and the Nature of Science. Sinauer Press. p. 242.
Grumpy wrote:For close to 2.5 billion years single celled organisms were all there were. They rose from simple chemical selfcopiers to modern types of DNA based bacteria in that long period of the beginning of life on Earth, created the oxygen atmosphere we all breath and provided the raw materials from which all the more complicated lifeforms(including the beef)arose from that have existed for the last 800 million years.
UB, p. 1138 - §5 wrote:What both developing science and religion need is more searching and fearless self-criticism, a greater awareness of incompleteness in evolutionary status. The teachers of both science and religion are often altogether too self-confident and dogmatic. Science and religion can only be self-critical of their facts. The moment departure is made from the stage of facts, reason abdicates or else rapidly degenerates into a consort of false logic.

Rob
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Schrodinger's Riddle: What is Life?

Post #5

Post by Rob »

Only those of a pseudoscientific mindset on either side of the extreem of the creationist-materialist spectrum are unable to recognize the limits of science; creationists error in that they set limits where there are none; materialists error in that they fail to recognize any limits whatsoever:
Harold wrote:Fifty years after Schrodinger wrote his little book, his challenge still hangs in the air. What is lif? Having learned so much about molecules and mechanisms, structures and functions, physiology and ecology and ontogeny and phylogeny, why are we still at a loss for a satisfying answer? Schrodinger himself posed the riddle with a flourish, but wisely refrained from offering a solution; today we are quick to deflect the mystery with a wry smile, a parable, or a joke. The reason has much to do with the difference between explanation and understanding. We are quickly learning to explain the workings of the biological machinery and even how organisms came to be as we find them, but we have no persuasive answer to the question why life exists in the first place. Loren Eiseley, thirty years ago, was baffled by "the hunger of the elements to become life," and we are not much wiser today. There is nothing in the textbooks of physics and chemistry to forbid a world that teems with bacteria and butterflies, but there is also nothing that would lead one to expect the world to be of this nature. The crux of the matter is that living organisms cannot be rationally and systematically deduced from the principles that generally do account for the properties of inanimate matter. (Harold 2003: 217-218)

We biologists claim for our science a high degree of autonomy from chemistry and physics, and rightly so. Organisms are historical creatures, the products of evolution; we should not expect to deduce all their properties from universal laws. The antics of a troop of monkeys in the forest canopy are doubtless consistent with all of physics and chemistry, but this knowledge supplies no insights that will be useful to a student of animal behavior. All the same, the autonomy of biology must ultimately trouble those who, with late Jacob Bronowski, "seek to find nature one, a coherent unity". The reason that many thoughtful persons continue to find life perplexing, even mysterious, is that sharp division between the organic and inorganic spheres. The distinction turns on those characteristics that are universally associated with entities we designate as living, but essentially absent from nonliving ones: intricate organization and purposeful behavior that unfold over time, both on the individual level and that of the total assemblage. Here yawns a great chasm that all biological scientists recognize, but many are deeply reluctant to acknowledge. (Harold 2003: 218)

There is clearly something special about living things that has not declared itself from beneath our vast heap of knowledge, and that seems to stand outside the circle of light that contemporary research strives to enlarge. What we lack is an understanding of the principles that ultimately make living organisms living, and in their absence we cannot hope to integrate the phenomenon of life into the familiar framework of physical law. I am not here to advocate a veiled vitalism, nor to sneak in a creator by the back door. But I do insist that until we have forged rational links between the several domains of science, our understanding of life will remain incomplete and even superficial. Until that impasse is overcome, we cannot refute philosophers, skeptics, religious believers and mystics who suspect that science is sweeping out of sight [by the fiat of science by re-definition!] the very mystery that it purports to elucidate. (Harold 2003: 218)

I do not have the answer to Schrodinger's riddle; no one does. It is even conceivable that we stand here at one of the limits of science, but it would be quite premature to concede defeat. We are gravely hampered by having but a single kind of life to ponder, and it may turn out that we cannot fully grasp the general phenomenon until we have either found additional versions of life or produced one in the laboratory. Neither prospect seems bright at present. (Harold 2003: 218-219)

-- Harold, Franklin M. wip. The Way of the Cell: Molecules, Organisms and the Order of Life. New York: Oxford University Press; 2003; c2001 pp. 217-219.
Nobel laureate Sir Peter Medawar said,
wrote:Catastrophe apart, I believe it to be science's greatest glory that there is no limit upon the power of science to answer questions of the kind science can answer.

-- Medawar, Peter. The Limits of Science. New York: HarperCollins; 1984: 87.

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