On Plato, the Early Church, and Modern Science: An Eclectic Meditation

November 30, 2004 | Jean F. Drew

[StJacques]

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.

[PatrickHenry]

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.

An excellent post! I'm frequently faced with the proposition that life's initial appearance was either a divinely caused miracle, or else it had to be a "random" event; and when that alternative is presented by those objecting to even the possibility of a natural cause, the word "random" is often expressed with genuine horror. I've previously attempted to deal with the issue, and to alleviate what seems to be some kind of revulsion to the possibility of a natural process, but I never came close to the quality you've just given us.

I suspect that the issue here isn't, as one might assume, with the details of biochemistry; it's the false dichotomy of "either divinely ordained miracle or random event." My response is that the alternative to a miracle is not -- as creationists often claim -- a case of unconnected atoms from all over the universe just happening to fly together (at random) and then -- kaboomo! -- a fully-formed living organism appears. Rather, at each step of the process, the laws of physics and chemistry apply, and the process therefore isn't random at all, but is determined by natural law, and is therefore predictable, at least in principle. Given the laws of nature, one might even say that the appearance of life is inevitable. It's just that there are so many variables involved that we cannot, in practice, deal with them all to make such predictions. Your lightning strike example is along the same lines.

Anyway, thanks for a great post.

[Alamo-Girl]

Thank you so much for your thorough and engaging post, StJacques!

I have a reply - not surprisingly focused on Yockey and the subject of "information theory and molecular biology" - but it is related both to this subject of abiogenesis and also to the complexity discussion on the other thread.

To post it in both places would be "spamming", so because it contains information to help define the "information theory/complexity" issues, I've posted it to the other thread.

For anyone interested, please follow this link to post 150.

[StJacques]

". . . 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. . . ."

I forgot to respond to this point in my last post. Actually, I was NOT suggesting that you were one of those looking to science to validate your faith. I was speaking to Patrick Henry in response to his comments on posts #258 and #261, in which he addressed the issue as a larger problem with these kinds of debates, and he did not attach his criticism to anyone in particular either.

I've reviewed the language I used to see if my remarks could have been interpreted in the way you took them and, in a moment of self-criticism I believe I would have been better advised to have included a dependent clause along the lines of "a mistake that does not apply to those present in this discussion" or something similar. I pinged you and others because I had earlier discussed the primacy of Morality and Ethics as substantiating belief in God, and it is this to which Patrick responded, so I wanted to keep you in the loop. I apologize if I have given any offense as a result.

[StJacques]

Let me correct something I just posted. I wrote about pinging you on my response to Patrick, which I had assumed was what led you to believe that I attached the charge to you. I just reviewed that post and I notice that I did not ping you. It's been a few days since then and I'm hoping I was trying to be careful by just responding to Patrick. But once again, I meant no offense.

[StJacques]

I just did a quick read of that post Alamo-Girl and I'm coming back here to let you know that I'm aware it is there, but I also recognize that we are heading into a discussion about "randomness" and I am hoping Doctor Stochastic, who I am pinging here, may help out as a "moderator" on this subject, since we want to be careful to keep the friendly tone of the discussion intact. And I think we may need to get our discussion of "randomness" in and of itself well in hand before we apply probability theory to molecular biology, as Yockey's work will bring us to do. I want to repeat what I posted above, that I do take Yockey seriously and I want our discussion of him to reflect that fact.

So Doctor Stochastic, if you get a free moment, could you comment on what I posted above in #281 on randomness? And if you, or anyone else for that matter, can think of others whose opinions may be useful please ping them as well.

And Alamo-Girl, I'm still pretty busy, but I want to get back on the "Atheist" thread and catch up to you. I'm just stopping by now for a minute while I'm between work tasks.

[Doctor Stochastic]

I'll look at this tonight. The term, "randomness" is often misused. I've got some comments, naturally.

[StJacques]

Thanks Doc. I do have a pretty good background in mathematics myself. I did quite a bit of work in Quantitative Analysis in grad school, primarily in analyses using Partial Correlation, Simple and Multiple Regression, and especially Ecological Regression Analysis. I've used the techniques in everything from voter analysis to charting Demographic trends, the latter of which formed the brunt of my "real world" work as a Research Analyst, before I migrated into software development in the late 1990s.

"Randomness" naturally falls within Statistics and Probability Theory and the "lightning" example I posted was drawn directly from what I remember from an "Introduction to Quantification Theory" lecture in and "Advanced Logic/Elemental and Set Theory" seminar in which the professor wanted to introduce us to the idea of using quantification as a means of reducing doubt or, "eliminating randomness" as an acceptable explanation.

[Alamo-Girl]

I very much look forward to your discussion of randomness! I'm pinging tortoise also because of the need to "square" randomness and complexity in its various forms.

[Doctor Stochastic]

I think you posting #281 does get at most of notion of "randomness" in evolutionary theory. I would like to give some illustrations of "randomness" in computation and physics. These are not exhaustive nor deeply explained (if they were, I would just publish them somewhere, like in Erkenntnis, just because it has a nice consonant cluster.)

For this discussion, I'll just "random" to mean processes that satisfy the usual axioms of probability. (Kolmorogov is sufficient, but other interpretations are OK, Fineti for example.) The idea is that probability applies to any system that satisfies these axioms. In one sense, "random" phenomena must (or may) be described by averages.

One example is in the computation of averages or distributions in a game. One has a complete description (example: a die has probablity of 1/6 to show the numbers 1 to 6), and thus one can compute everything. It's sort of randomness through saturation. One assumes a large number of trial games and also assumes that these games will obey the same rules each time.

A second and much more interesting "random" system is given by Brownian motion. Consider a particle (dust, pollen, dust mites, etc.) being bombarded by even smaller particles (molecules) many times per second. Einstein (and others) developed the theory of the motion of such particles. There are some surprises; the velocity of the test particle cannot be defined, but it's position can. A test probe small enough to measure velocities would be subject to Brownian motion of the same size as the test particle and thus would yield no useful information. (Experiments bear this out; by 1900 or so, people knew that velocity could not be defined for Browinian particles.) Even though this system is deterministic in the sense of Laplace, there is no method (even in theory) to measure the exact conditions of the experiment. One must resort to averages. The system can be easily simulated deterministically though.

A third type of randomness would be that implied by quantum mechanics. Single particles act "randomly" and there is no method of resolving such even with simulation. (Exact simulation of quantum systems takes an exponentially large amount of time.) In this case, one must resort to probabilistic descriptions (albeit, not classical probability) to describe such systems even in principle.

The fourth "random" system would just to consider "relative independence" of events. For example, a cosmic ray may be produced on Sirius and strike a germ cell on Earth, causing a mutation. An observer won't see any connection between the local environment of the germ cell and goings on at Sirius. Similarly, a volcano (or a pack of wolves or a piano falling from the 13th floor of a hotel) may wipe out a person (dog, cat, plant) before that person can reproduce and thus kill off the person's genetic contribution. However, nothing in the physics or chemistry of DNA caused the volcano to errupt.

"Random" events (as I'm using the term) are those which may affect the outcome of an observation, but are not themselves (necessarily) implied by the physics of that observation. The lightning example is more like Brownian motion that the other forms. One cannot measure the boundary conditions well enough to exactly predict a lightning bolt, but one can do very well with averages. For example, high points (steeples, trees, golf clubs during a backswing) get struck relatively often.

[tortoise]

Now Hubert Yockey we must take seriously as a mathematician, because he is a genuine expert on information theory.

No disrespect, but what has Yockey contributed to the field? I have copies of essentially every important and vaguely interesting bit of theoretical work in the field and he is cited nowhere. And when I do a search on citations, all the papers I can find with his name on them appear to be theoretically quite shallow and arguably of dubious fitness. Yockey may be genuine in an academic sense, but his work is in the shallow end of the pool as far as I can tell on the mathematics side of things, and certainly with regard to information theory.

From my vantage point, Yockey looks more like a dabbler in information theory than a genuine expert. There are not that many "genuine experts" in the field, and I am acquainted with most of them -- he is not one of their peers.

[Alamo-Girl]

Thank you oh so very much for your discussion of randomness!

All I can think to add to what you have said is this from Chaitin’s talk on Mathematics in the Third Millennium

Some final words on Stephen Wolfram's fascinating, and unfortunately unpublished, ideas. Wolfram has a very different view of complexity from mine. In my view pi is not at all complex, but to Wolfram it's infinitely complex, because it looks completely random. Wolfram's view is that simple laws, simple combinatorial structures, can produce very complicated unpredictable behavior. pi is a good example. If you didn't know where they come from, its digits would look completely random. In fact, Wolfram says, maybe the universe contains no randomness, maybe everything is actually deterministic, maybe it's only pseudo-randomness! And how could you tell the difference? The illusion of free will is because the future is too hard to predict, but it's not really unpredictable. [To Wolfram's exceedingly bright and sharp mind, the idea of indeterminacy, of randomness, of something irrational, that escapes the power of reason, of simple unifying principles, that happens for no reason—and that he will never be able to understand—is totally abhorrent. The horror of a vacuum of the ancients becomes a modern horror of randomness.

To such a mind, I must appear, because of my belief in randomness, as a muddle-headed mystic!... I'm also reminded of Feynman's fury in a conversation we had near the end of his life when I suggested that there might be wonderful new laws of physics waiting to be discovered. Of course!, I told myself later, how could he bear the thought that he wouldn't live to see it?... Science and magic both share the belief that ordinary reality is not the real reality, that something more fundamental is hidden behind everyday appearances. They share a belief in the fundamental importance of hidden secret knowledge. Physicists are searching for their TOE, theory of everything, and kabbalists search for a secret name of God that is the key that unlocks all understanding. In a way the two are allies, for neither can bear the thought that there is no secret meaning, no final theory, and that things may be arbitrary, random, meaningless, incompressible and incomprehensible. For a dramatization of this idea, see D. Aronofsky's 1998 film pi. See also G. Johnson, Fire in the Mind—Science, Faith, and the Search for Order, and P. Davies, The Mind of God—The Scientific Basis for a Rational World.]

Wolfram also has some fascinating ideas about biology, the origin of life and evolution. One of my big disappointments, the big disappointment in my scientific life, is that I couldn't use my program-size complexity to make a mathematical theory out of Darwin. [I was strongly influenced by von Neumann. For an early report of von Neumann's ideas, see J.G. Kemeny's 1955 article in Scientific American, ``Man viewed as a machine.'' For a statement by von Neumann himself, see ``The general and logical theory of automata'' in volume 4 of J.R. Newman's The World of Mathematics. For a posthumous account assembled by A.W. Burks, see von Neumann's Theory of Self-Reproducing Automata. For samples of contemporary thought on these matters, see P. Davies, The Fifth Miracle—The Search for the Origin of Life, and C. Adami, Introduction to Artificial Life.]

My complexity is conserved, it's impossible to make it increase, which is great if you're doing metamathematical incompleteness results, but hell if you want to get evolution. So I asked Wolfram his thoughts on this matter, and his reply was absolutely fascinating. He has amassed much evidence of the ubiquity of universality. In other words, he's discovered that many, many different kinds of simple combinatorial systems achieve computational universality, and have rich, complicated unpredictable behavior. pi is just one example... So what's so surprising about getting life, about getting clever organisms that exhibit rich, complicated behavior, that need it to survive? That's easy to do!!! And I suspect that Wolfram is right, I just want to get a copy of his 800-page book on the subject and be able to read it and think about it at my leisure. I have held its two volumes in my hands, briefly, once, during a fascinating visit to Wolfram's home...

The point of the foregoing is that randomness may not actually exist in this universe since everything we perceive as random – from lightning bolts to Chaitin’s Omega to Brownian motion – are effects of physical causation.

[tortoise]

"Randomness" means a number of things, and is mostly a convention for "my predictive model is too simple to have utility". In any finite context, it does NOT mean non-deterministic, only means that the relative entropy between the predictor and the actual process has the same complexity as the predictor output itself. Strong pseudo-random number generators work this way, processes with very little complexity but no low-order patterns that can be tractably perceived via induction as a practical matter in our universe (true geometric complexity in time and space puts a damper on that -- O(2^n) is a killer). They will appear "random" by every mathematical measure of their output, even though we know they are not by definition.

This leads to a somewhat interesting situation for physicists in that no apparently "random" process can ever be definitively asserted to be non-deterministic, as even simple deterministic processes are capable of having this apparent property. When you get right down to it, "random" tells you almost nothing about the nature of whatever process you are describing with it. But being able to assert determinism is useful for a few theoretical purposes even if you never figure out how to look inside the box.

It really starts to get interesting when you start considering the fundamental theoretical nature of bias (both intrinsic and apparent) in probability distributions.

[StJacques]

tortoise, thank you for your post. I'm going to respond to you before I reply to Doctor Stochastic's discussion of randomness above, which I want to chew on a bit. And I see no implied disrespect in your taking issue with my portrayal of Yockey as "a genuine expert on information theory" because I am beginning to question the very notion myself. In fact, I may have been dead wrong on that one, though I am trying to get some more information to make up my mind. But I do want to explain what prompted me to write that assessment.

I posted that appraisal of Yockey after learning that he has a Ph.D. in Mathematics from Cal-Berkeley and that he worked on the Manhattan Project, which I regard as pretty good credentials right off the bat. But I also noticed on a web page I visited on a Christian discussion site that he stated his belief that we may be surprised to find out "how many scientists are really talking religion and how many theologians are talking science" when speaking of a need to bridge the gap, which I took to be a decidedly "unscientific" statement, which is why I also posted my qualifying comment "I recognize Yockey as a legitimate scholar -- I did not say 'scientist' . . ." in my post #281. I also noticed somewhere else, and I can't seem to find this reference right away, that he was asked to explain why he quoted the Bible in his book Information Theory and Molecular Biology, which got me to wondering as to whether he had an agenda, a doubt that has since been enhanced by my reading of his appraisal of those arguing for abiogenesis as "Dialectical Materialists," i.e. "Marxists," which frankly leaves me dumbfounded. And I believe I took that Christian discussion site's page at its word when I posted my comment that he was an "expert on information theory." Finally; I'll add in two more quick points. One of the web sites that does a lot of work debunking "creationist myths" posted something to the effect that Yockey's work, though flawed in their opinion, had to be taken seriously and even a couple of pages I visited that were supportive of abiogenesis dealt with some of Yockey's arguments in a serious fashion.

You may in fact be right on this one tortoise. I still want to learn more about what Yockey is actually arguing -- I find so much information from people using his arguments and so little from the man himself -- before I form any final judgements about how it should be treated. But, as I also said in my post #281, I cannot accept his definition of "randomness" as applied to abiogenesis, which is a problem I have with him from the start.

I will be genuinely interested to read any comments you may wish to post about Yockey and/or his work tortoise. Please feel free to fire away. Something tells me you may be quite helpful.

[Alamo-Girl]

Truly, I am amazed that you hold Hubert P. Yockey in such contempt. He is probably twice your age (if not more) - worked with Oppenheimer on the first atomic bomb, is a physicist who studied the effects of radiation on living systems and has studied and published for decades the application of information theory to molecular biology.

I'm sure he was alive at the same time Claude Shannon developed his ground breaking theory which began the field of information theory. The second edition of his book is available: Information Theory, Evolution and the Origin of Life

Here are some of his other publications from the “Chowder Society” website of other scientists who work in the field of information theory and molecular biology:

Yockey, Hubert P. Information Theory and Molecular Biology, Cambridge UK: Cambridge University Press (1992)

When is random random? Nature 344 (1990) p823, Hubert P. Yockey

Yockey, Hubert P. (1981). Self-organization origin of life scenarios and information theory. Journal of Theoretical Biology, 91, 13-31.

Yockey, Hubert P. (1979). Do overlapping genes violate molecular biology and the theory of evolution? Journal of Theoretical Biology, 80, 21-26.

Yockey, Hubert P. (1978). Can the Central Dogma be derived from information theory? Journal of Theoretical Biology, 74, 149-152.

Yockey, Hubert P. (1977a). A prescription which predicts functionally equivalent residues at given sites in protein sequences. 67, 337-343.

Yockey, Hubert P. (1977b). On the information content of cytochrome c. Journal of Theoretical Biology, 67, 345-376.

Yockey, Hubert P. (1977c). A calculation of the probability of spontaneous biogenesis by information theory. Journal of Theoretical Biology, 67, 377-398.

Yockey, Hubert P (1974). An application of information theory to the Central Dogma and the sequence hypothesis. Journal of Theoretical Biology,.46, 369-406.

Yockey, Hubert P. (1960) The Use of Information Theory in Aging and Radiation Damage In The Biology of Aging American Institute of Biological Sciences Symposium No. 6 (160) pp338-347.

Yockey, Hubert P., Platzman, Robert P. & Quastler, Henry, eds. (1958a). Symposium on Information Theory in Biology, New York, London: Pergamon Press.

Yockey, Hubert P. (1958b). A study of aging, thermal killing and radiation damage by information theory. In Symposium on Information Theory in Biology. eds. Hubert P. Yockey, Robert Platzman & Henry Quastler, pp297-316. New York,London: Pergamon Press.

Yockey, Hubert P. (1956). An application of information theory to the physics of tissue damage. Radiation.Research, 5, 146-155.

Information in bits and bytes; Reply to Lifson's Review of "Information Theory and Molecular" Biology BioEssays v17 p85-88 (1995)

Comments on "Let there be life; Thermodynamic Reflections on Biogenesis and Evolution by Avshalom C. Elitzur Journal of Theoretical Biology in press (1995).

I assert that Yockey - with his formidable credentials – is an authoritative source for our purposes in exploring complexity in biological systems (including information theory, biosemiosis and randomness).

From my vantage point, Yockey looks more like a dabbler in information theory than a genuine expert. There are not that many "genuine experts" in the field, and I am acquainted with most of them -- he is not one of their peers.

AFAIK, your expertise lies more specifically with strong artificial intelligence than the application of information theory of biological systems. But I could be wrong. If you are in Yockey's arena, then Tom Schneider would be one of your peers.

[StJacques]

This is a response to your #293, which you were evidently writing when I was replying to your previous post.

I love your first sentence:

"'Randomness' means a number of things, and is mostly a convention for 'my predictive model is too simple to have utility.' . . ."

I think this gets to the truth in a big hurry. Chaitin said something similar, but I'll hold off on that now.

Some of what you have in what I'll refer to as the "middle" of your post I will probably want to return to after I go over Doctor Stochastic's earlier discussion, especially your comment "the relative entropy between the predictor and the actual process has the same complexity as the predictor output itself." I may want to return to that, because the use of "entropy" as equivalent to "randomness" can become confusing when other definitions of entropy, as a law of thermodynamics e.g., will probably become part of the discussion as well.

I also loved your final comment about bias and probability distributions, though I tend to doubt that "frequencies" will form part of the discussion. What a shame!

[StJacques]

Alamo-Girl, I am wondering about Yockey. Can you explain why he would use the term "Dialectical Materialists" to describe proponents of abiogenesis? (Go to that review post you put up.) This is waaaaayyyyyyy out of step.

And I am prepared to describe a Dialectical Materialist if the need arises.

[Alamo-Girl]

Thank you for your reply and question!

Can you explain why he would use the term "Dialectical Materialists" to describe proponents of abiogenesis?

Naturally, I cannot read Hubert Yockey’s mind. But I will venture a guess based on the context of what he said, as follows:

Dialectical materialists are atheists. Their belief in a primeval soup without evidence puts them in bed with theologians. In science the "Absence of evidence IS evidence of absence."

Dialectical materialism is the philosophical basis for Marxism: Wikipedia. Considering that he was speaking of nature, Yockey might have been thinking of Friedrich Engels views on the dialectics of nature.

Basically, socialism in extreme (communism) requires a metaphysically naturalistic explanation for physical reality (which must be the sum of “all that there is” in that philosophy). We see the same dogma in far left politics - leading to such initiatives as equal rights for animals, the right to terminate a child within a few months of birth, euthenasia, etc. – all based on metaphysical naturalism.

Based on his wording above, I suspect he said what he did because it is true. If there is no evidence for a primeval soup and yet Marxists believe it exists, then they are like religionists – standing on faith. He continues with the important remark that “In science, the ‘Absence of evidence IS evidence of absence.”

[Alamo-Girl]

Rats, I should have continued by pointing out his position on the Manhattan project and at Aberdeen. That would put him in the heat of wrap up of WWII - very much anti-communist.

Also, if you are willing to give Yockey a fair hearing and read both the criticisms and his responses - I strongly suggest googling with the phrase "From: hpyockey@aol.com (HPYockey)" - that will get all of the contentions and his responses (and the messages to which he is responding on the Chowder Society) concerning complexity, probabilities, randomness, entropy, etc.

[StJacques]

Well, one of the reasons I am such an avid Republican is that I was trained by Marxists in college, so no one needs to explain "Dialectical Materialism" to me, I had it rammed down my throat by my commissars, oops! . . . ahem! . . . professors. But even the quote you offered equates supporters of abiogenesis with atheists, which still seems to indicate an agenda on Yockey's part.