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So now the argument against abiogenesis must be reformulated into a third version. In this third version the word "complexity" in the earlier formulation is now capitalized and, largely through the use of mathematical reasoning, it is deemed either highly improbable or nearly impossible that, even though the chemical foundations for the creation of life may be demonstrated, the genesis of life will be of such a complex nature that it can never be proven. And I expect that eventually scientists will get beyond this objection as well, though I think they will have to get a much better handle on discerning what the constraints of the atmosphere of the early earth were before they are able to move to the next step. But they are working to do just that, so the process and progress continues.

I am very happy to hear it, StJacques – especially about the innovation in capitalization! As already indicated, I await developments on this front with great interest. But I have to tell you: I’m not holding my breath until such time as the expected confirming “breakthrough” occurs.

Frankly, I strongly suspect that the so-called theory (or is it hypothesis?) of abiogenesis is a myth (and you can’t “prove” a myth). The myth relies on statements like this:

“The very fact that life sprang up on earth constitutes conclusive proof of a primary reducing environment since the latter is a necessary prerequisite for chemical evolution and spontaneous origin of life.” [Manfred Schidlowsky, quoted in Robert Shapiro, Origins: A Skeptic’s Guide to the Creation of Life on Earth, 1986]

This is a great example of circular reasoning: It turns out its conclusion is already actually implicit in its premise.

But for the sake of argument, let’s assume I’m wrong about this, and abiogenesis – the spontaneous emergence of life from inorganic matter by sheer random processes – is a viable theory. Still, it would have a very steep hill to climb, and would have to overcome or explain away the following objections (a partial list):

(1) Both the above quote and your own remarks point to a main difficulty. You wrote, “[Science] will have to get a much better handle on discerning what the constraints of the atmosphere of the early earth were before they are able to move to the next step.”

As Dean Overman points out [in The Case Against Accident and Self-Organization 1997), “A methane rich reducing atmosphere [i.e., an atmosphere that has no oxygen] is essential to the Oparin-Haldane hypothesis and the Miller and Uray experiment. Miller based his experiment on the cosmic abundance of hydrogen and the ingredients in the solar nebulae which he believed produced the earth’s early atmosphere. The current geological consensus, however, maintains the view that the interior earth, rather than the solar nebulae, produced the primitive atmosphere and that methane and ammonia were not present. Today geologists understand that chemical reactions from sunlight would have destroyed methane and ammonia within a few thousand years. The sun’s ultraviolet radiation would have converted the methane to hydrocarbons with higher molecular weight and formed an oil slick up to a depth of ten meters. Ammonia is destroyed by ultraviolet radiation, dissociating into nitrogen gas and hydrogen. This presents a stumbling block for anyone building his or her theory of the origin of life on the Oparin-Haldane foundation. As Miller himself admitted, ‘If it is assumed that amino acids more complex than glycine were required for the origin of life, then these results indicate a need for CH₄ (methane) in the atmosphere.’”

Yet many scientists today are of the opinion that the earth’s primitive atmosphere was not so strongly reducing and probably contained significant amounts of oxygen. Overman notes, “The presence of even a small amount of oxygen, assiduously avoided in the laboratories of the [Miller-Urey] experiments, would prevent the formation of amino acids and nucleotides, because atoms and molecules would bond with the oxygen atoms rather than hydrogen atoms. Even if amino acids could be formed, oxygen would cause them to decompose quickly and terminate any further random processes which could eventually produce life. If the early earth’s atmosphere had oxidizing conditions, abiogenesis would have been impossible.”

Later he adds another important consideration, “Even if oxygen was not present in the early earth’s atmosphere, the absence of oxygen would present obstacles to the formation of life. Oxygen is required for the ozone layer which protects the surface of the earth from deadly ultraviolet radiation. Without oxygen this radiation would break down organic compounds as soon as they formed.” This is Michael Denton’s “Catch 22” of abiogenesis: “If we have oxygen we have no organic compounds, but if we don’t we have none either.”

Still, let’s try to answer the question whether the early-earth atmosphere was strongly reducing (methane-rich, no oxygen), or one in which oxygen was present. I guess all we’ve basically got to go on is the geological record. But this would seem to lend little support to the doctrine of abiogenesis. Here’s the problem:

“If there ever was a primitive soup, then we would expect to find at least somewhere on this planet either massive sediments containing enormous amounts of the various nitrogenous organic compounds, amino acids, purines, pyrimidines, and the like, or alternatively in much-metamorphosed sediments we should find vast amounts of nitrogenous cokes (graphite-like nitrogen-containing minerals). In fact, no such materials have been found anywhere on earth.” [J. Brooks and G. Shaw, Origin and Development of Living Systems, 1973]

Michael Denton gets the next-to-the-last word on “objection (1)” as follows, and then we must move on:

“The existence of a prebiotic soup is crucial to the whole scheme [of abiogenesis]. Without an abiotic accumulation of the building blocks of the cell no life could ever evolve. If the traditional story [i.e., myth] is true, therefore, there must have existed for many millions of years a rich mixture of organic compounds in the ancient oceans and some of this material would very likely have been trapped in the sedimentary rocks lain down in the seas of those remote times. Yet rocks of great antiquity have been examined over the past two decades and in none of them has any trace of abiotically produced organic compounds been found. Most notable of these rocks are the ‘dawn rocks’ of Western Greenland, the earliest dated rocks on Earth, considered to be approaching 3,900 million years old. So ancient are these rocks that they must have been lain down not long after the formation of the oceans themselves…. Sediments from many other parts of the world dated variously between 3,900 million years old and 3,500 million years old also show no sign of any abiotically formed organic compounds…. Considering the way the prebiotic soup is referred to in so many discussions of the origins of life as an already established reality, it comes as something of a shock to realize that there is absolutely no positive evidence for its existence.” [Evolution: A Theory in Crisis, 1985]

And Hubert Yockey gets the last word:

“Although the Oparin-Haldane paradigm is now just a relic of the cosmology of the time when it was invented, it certainly deserved extensive research and much has been learned in investigating it. The same can be said for many other failed paradigms. Nevertheless, like the luminiferous ether, one has to conclude that there is no evidence that a ‘hot dilute soup’ ever existed. In spite of this fact adherents of this paradigm think it ought to have existed for philosophical or ideological reasons…. I have emphasized that in science one must follow the results of experiments and mathematics and not one’s faith, religion, philosophy, or ideology. The primeval soup is unobservable because, by the paradigm, it was destroyed by the organisms from which it presumably emerged. It is most unsatisfactory in science to explain what is observable by what cannot be observed. Since creative skepticism and not faith is the cardinal virtue in science one would expect that proponents of the primeval soup paradigm would be actively searching for direct geological evidence of such a condition of the early ocean. The power of ideology to interpose a fact-proof screen is so great that this has not been done (perhaps for fear that its failure might be exposed).” [Information Theory and Molecular Biology]

(2) Abiogenesis must explain how inorganic matter, by purely random or accidental processes, can give rise to a fully living system, which George Gaylord Simpson, distinguished professor of paleontology at Harvard, defines as follows:

“A fully living system must be capable of energy conversion in such a way as to accumulate negentropy, that is, it must produce a less probable, less random organization of matter and must cause the increase of available energy in the local system rather than the decrease demanded in closed systems by the second law of thermodynamics. It must also be capable of storing and replicating information, and the replicated information must eventually enter into the development of a new individual system like that from which it came. The living system must further be enclosed in such a way as to prevent dispersal of the interacting molecular structures and to permit negentropy accumulation. At the same time selective transfer of materials and energy in both directions between organism and environment must be possible. Systems evolving toward life must become cellular individuals bounded by membranes.” [“The Nonprevalence of Humanoids,” Science 143, 1964]

Some issues arise here: (a) How does matter, which is wholly subject to the second law, get the idea to “go against the law?” That is, how can stuff wholly subject to entropy generate other stuff that is able to counter that law, which that other stuff must do in order to be alive [e.g., as seen in Simpson’s requirement of negentropy production and accumulation]? (b) What is the impulse directing random matter to give rise to something that must be much less random than it is in order to be alive? In other words, by what principle does randomness – accident -- produce less-randomness? It seems an accident of an accident is still an accident, ad infinitum. (c) The information contained in the genetic code is not material. All forms of information are not made of matter. How did matter create this “non-matter” so essential to the life, self-maintenance, and reproductive capabilities of even the simplest organism? Consider these lines from Michael Denton:

“Molecular biology has shown that even the simplest of all living systems on earth today, bacterial cells, are exceedingly complex objects. Although the tiniest bacterial cells are incredibly small, weighing less than 10^-12 gms, each is in effect a veritable micro-miniaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world…. The recently revealed world of molecular machinery, of coding systems, of informational molecules, of catalytic devices and feedback control, is in its design and complexity quite unique to living systems and without parallel in the non-living world.” [Ibid.]

How does “dumb matter” – ubiquitous and uniform – accidentally give rise to even such a comparatively “simple” life form as a bacterium, a creature able to transact the most sophisticated information processing upon which not only its life, but also the global governance of its extraordinarily complex system, its sensitive responsiveness, its mobility, its ability to “communicate” with its constituent subsystems and to its external environment, etc., depends? Matter itself does NONE of these things as far as we know. So, how does its “progeny” acquire these skills?

Other questions present themselves; but these three very basic ones will suffice for now. I’m interested in how you propose to answer them.

(3) You refer to James Ferris’ experiment involving the catalyzation of RNA aqueous solutions in mineral clays, seeming to regard it as a harbinger of the next great breakthrough that will validate abiogenesis. But I have a question: Since RNA in natural systems is a sort of “slave” to DNA; and since it is a human experimenter who has, in effect, taken on DNA’s role with respect to an “artificially derived” RNA under laboratory or controlled conditions; and since the entire enterprise may spring from a (perhaps) faulty initial premise (see above) – in what way can we expect this to reliably tell us anything about what’s actually going on in (untampered with) natural systems? Especially when we still have so much to learn about DNA itself – which does not even enter the purview of this experiment?

* * * * *

Must close, have run on too long. But I must add just one more thing, unrelated to the above discussion. And that is the idea that people (I gather you’re suggesting I’m one of them) come to science to validate their faith in God. From my perspective, nothing could be further from the truth; on the contrary, the truth of the matter goes the other way around. My faith in God is not in the least dependent on scientific discoveries. I believed in God long before I “believed” in science; you might say I came to science because I believe in God. I study it because I realize that the “book of nature,” of the living universe, is also a “book” sacred to God; and that being so, that I might profitably study it and find in it the glory of the Lord, as I do in the pages of the Holy Scriptures. So far, this has proven to have been a well-rewarded endeavor – and if I might add, a spiritually rewarding one especially.

Oh, one last thing that might be useful to you, StJacques, PH, and many of my other friends out there in FreeperLand: It might be profitable if you could begin to draw distinctions between such words as: religion, theology, Spirit, metaphysics, transcendence, while seeing that they all point in a direction needful for man individually, and for the human race. I think some of you guys just toss them all into a single category, the category of irrelevancy. You just flush them all away, it seems to me, without understanding what it means to do that. But FWIW, your own essential humanity goes down the dumper with them, if you do that. JMHO. But then again, nobody listens to an ersatz-Cassandra….

Thanks so much for writing, StJacques, PatrickHenry, All – this has been a marvelous discussion so far. I look forward to your replies, as ever.

Ok, it looks like I've finally got some time to come in and give you a response to your post #268 betty, so let me get to it.

". . . I await developments on this front with great interest. But I have to tell you: I’m not holding my breath until such time as the expected confirming “breakthrough” occurs. . . ."

I expect it will take decades personally. It was forty plus years between Stanley Miller's generation of amino acids from inorganic material and the catalyzation of RNA in mineral clays. And not all scientists working upon pre-biotic synthesis agree upon the best strategy to pursue.

". . . 'The very fact that life sprang up on earth constitutes conclusive proof of a primary reducing environment since the latter is a necessary prerequisite for chemical evolution and spontaneous origin of life.' [Manfred Schidlowsky, quoted in Robert Shapiro, Origins: A Skeptic’s Guide to the Creation of Life on Earth, 1986]

This is a great example of circular reasoning: It turns out its conclusion is already actually implicit in its premise. . . ."

That is not circular reasoning at all, since science must account for the oxygen-rich atmosphere present here on earth, which it is theorized was not present in the "Primary Reducing Environment" in sufficient quanities to sustain large ecosystems and higher-order life forms, but had to be manufactured by lower-order life before more complex types could emerge. That line of reasoning is in fact linear:

Primary Reducing Environment -> Abiogenesis -> Lower-Order Life -> Non-Reducing Environment Containing Sufficient Oxygen -> Higher-Order Life

As a scientific explanation the above model is plausible because it proposes a cause and effect sequence of events to explain both the oxygen-rich atmosphere and the development of higher-order life forms. It does not prove abiogenesis, which I think you take the statement to imply, but it does propose a plausible theory into which abiogenesis fits as a necessary step in the evolution of life on earth.

". . . let’s assume I’m wrong about this, and abiogenesis – the spontaneous emergence of life from inorganic matter by sheer random processes – is a viable theory . . . "

I do not in any way accept your definition, perhaps I should say "description," of abiogenesis. From the perspective of the physical sciences there is nothing "spontaneous" or "random" about it and I believe this is the true crux of the debate. Those who attempt to refute the possibility of abiogenesis insist that it is an argument for a spontaneous and/or random occurence, which gives them a "straw man" that is easy to knock down. "Spontaneity" implies the lack of a cause for an effect, and I'll deal with that farther on in this response. As for "randomness," in its simplest form, it is defined (from the dictionary) as "the quality of lacking any predictable order or plan." Now there are separate mathematical definitions which, depending upon which one you use, will present randomness differently, including Chaitin, who denies that randomness can ever be proven, but these definitions are always applicable to a particular systemic construct, and are not suitable to the physical sciences in general -- I'll say more about that in a moment. However the term is used, the concept of "randomness" must always be formulated as "random relative to what?," because it implies a perspective. To take a pertinent example relative to Stanley Miller's experiment which proved that amino acids could be generated from inorganic matter, consider the predictability of when and where lightning will strike. You can take a meteorologist and a physicist schooled in electromagnetism, position them both on the ground while a thunderstorm rages overhead, and ask them to tell you when and where the next lightning bolt will strike. In terms of simple ordinary language they cannot do it, so you might conclude that the timing and positioning of lightning strikes are "random" relative to an explanation you would accept in ordinary language. But those same two scientists could express in the language of Physics an equation that will take into account the variables that go into cloud formation, the density of moisture within clouds, temperature, wind patterns, differentials between the electromagnetic charges of the clouds and the ground beneath, etc. and express to you an equation that will predict where and when lightning will strike and that equation will be accurate, though it will not be understood in ordinary language. Therefore; from the perspective of ordinary language, the lightning strike appears as a "random" event, but from the perspective of the meteorologist and the physicist, it is nothing of the kind, because the location and timing of the strike is governed by the laws of physics as they pertain to meteorological phenomena and electromagnetism.

The same line of reasoning I have just outlined with respect to lightning strikes applies to abiogenesis. Now; there are several theories about just how and why abiogenesis occurred, and I am not qualified to say just which of these theories is the most plausible, because I am not trained sufficiently in the scientific disciplines necessary to explain and differentiate between these theories, though I suspect that James Ferris's "catalyzation of RNA solutions" approach may be the best going at present. But in general form, most theoretical models constructed explain abiogenesis look something like the following:

At each and every one of the above stages listed, and in truth there are many "sub-stages" involved in the transition between those depending upon just which theory you are using, the laws of chemistry, biochemistry, physics (especially concerning energy sources), and in the later stages, microbiology are all applicable. And the ways in which these theories have been constructed is to entertain these transitions as the effects of material causes that occur naturally, which means that from the perspective of the physical sciences, they are in no way "random" or "spontaneous," but the expected result of natural phenomena occurring within a given set of constraints that are plausible in themselves.

Now; for the citations you gave on the implausibility of abiogenesis:

Overman's claim about the state of scientific opinion on the impact of geological opinion on the early earth's atmosphere as defeating the prospects for abiogenesis is flat-out false. I do not like to use Ad Verecundiam arguments, but I must point out that Overman is a lawyer and for that reason I question his credentials to describe the state of scientific opinion on the early earth's atmosphere, because if I have correctly identified the source of his information, and I think I have, then I can say that on one thing I am absolutely certain, the current state of thinking in Geology does not negate the conditions for abiogenesis, which includes the evaluation of the early earth's atmosphere. I will refer you to one online article at the MIT web site that I believe can be held out to contain a much more accurate viewpoint of the current state of Geological thinking on the rise of the oxygen-rich atmosphere we now enjoy. I wanted to present particular evidence from one of the sources they cite at the beginning of the article, J.F. Kasting's work on "Earth's Early Atmosphere," since I found several online articles which cite it, but I cannot find the online source for the article itself. Kasting is a very prominent geologist -- he has co-authored textbooks on the subject -- and he may be the individual Overman refers to because he has been critical of some scientific studies which fail to take into account photodecomposition of methane and ammonia in the early earth's atmosphere, one of the bases for Stanley Miller's theoretical approach, and which Miller has since addressed. The net impact of all of this upon geological thought has not been to discount Miller's, nor Ferris's work, quite the contrary. Geologists find ample geological evidence for the development of several scenarios for the origins of life, as shown within the MIT article, including the transition from an RNA-world to higher orders of life, which Miller and Ferris's combined contributions argue. Overman's statement of the state of geologic opinion does not fit in with what geologists are saying, as the MIT article shows, so I will wait to see if anyone can present geologic scholarship to support Overman's presentation. I can only conclude that Overman did not understand what he was reading.

And to make further discussion easier, I would suggest we be careful with using the phrase "many scientists."

As for the comments/quotes on Overman/Denton and the availability of oxygen, there are early pre-biotic sources of oxygen detectable in the geologic record. See the MIT and Miller articles again, sources of pre-biotic oxygen are directly discussed there.

The objections posed by Brooks and Shaw are also flawed in terms of modern knowledge, because of the timeline involved. Now in part, this may not be their fault, because they were writing in 1973, a year in which the oldest sedimentary rocks may have been dated much later [more recent] in time than those we know today, I don't know for certain. As you quoted them:

". . . we would expect to find at least somewhere on this planet either massive sediments containing enormous amounts of the various nitrogenous organic compounds, amino acids, purines, pyrimidines, and the like, or alternatively in much-metamorphosed sediments we should find vast amounts of nitrogenous cokes (graphite-like nitrogen-containing minerals). In fact, no such materials have been found anywhere on earth."

That may have been true in 1973, but it is not true today. Go back to the MIT article I linked above and scroll down to pages 26 and 27. The evidence in the geological record is for a backwards-revision [to an earlier date in time] of the presence of Carbon isotopes at the dawn of the Archaean Age, which permits extrapolation of its origins (page 26) and the presence of carbon-depleted graphite by 3.8 billion years ago (page 27). You can read more about this evidence by viewing the information on the Isua metasediments of Greenland. Again, I don't think Brooks and Shaw can be blamed for this, because they did describe the evidence, especially graphites, which has been found for the period, and I think, but do not know, that the discovery was after their publication.

Now; Michael Denton again:

". . . Yet rocks of great antiquity have been examined over the past two decades and in none of them has any trace of abiotically produced organic compounds been found. Most notable of these rocks are the ‘dawn rocks’ of Western Greenland, the earliest dated rocks on Earth, considered to be approaching 3,900 million years old. . . ."

Nope. Here's a quote from the preceding article linked on the Isua Metasediments: (note: "Ga"=Billions of years ago, 3.86 Ga = 3.86 Billion years ago)

". . . Akilia (3.86 Ga) and Isua (3.8 Ga) metasediments in southern West Greenland, evidences the existence of liquid water, the prerequisite for life's origin, at the Earth surface at this early stage. It is believed that high-grade metamorphic overprint would not allow the preservation of morphological fossils, permitting tracing of life in these metasediments only from chemical data. Graphitic carbon, isotopically indicative of constituting the remains of primitive organisms, has been identified in both Akilia and Isua rocks (Schidlowski, 1988; Mojzsis et al., 1996, Rosing, 1999). The association of isotopically light graphite with sedimentary apatite crystals has indicated the applicability of such apatite as indirect biomarker in old metasediments. . . ."

Now one may make the argument that the rocks show evidence of the presence of life itself at this stage, rather than just the pre-biotic evidence Denton is commenting upon, but if that was his intent then it is a deliberate deception on his part, which I doubt, because I am convinced that he does not understand what the rocks reveal.

Now Hubert Yockey we must take seriously as a mathematician, because he is a genuine expert on information theory. But he has misapplied the concept of "randomness" to the origins of life, in treating it as a problem in mathematical probability, since probability theory is designed to bring order out of randomness. Abiogenesis is no more the result of random processes than the timing and location of a lightning strike, as I discussed earlier. All steps in the process of abiogenesis function according to the laws of chemistry, molecular biology, physics, and other branches of the physical sciences. Of everything you have posted betty, there is only Hubert Yockey to discuss seriously, but this post has gone on long enough. We will return to Yockey at a later date, but you already know the major issues I have with his theoretical approach as I have just stated them. Since I recognize Yockey as a legitimate scholar -- I did not say "scientist" -- I will give him a much closer look.

And finally, on your question about RNA being a "slave" to DNA, I think the answer is that you may have missed the point that, in addition to being a storehouse for genetic information, RNA acts as a "catalyzing agent" in certain types of biochemical reactions.

I still owe Alamo-Girl a response on the "Atheist" thread, but I won't have time to get there until tomorrow.