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

November 30, 2004 | Jean F. Drew

[betty boop]

...natural laws are inherent in the very fact of existence (a photon is a photon and thus behaves as a photon behaves), then things are merely doing what they do, and not as some external Determiner directs that they should do.

I think you're not seeing the issue I raise, PH: What is the reason for the photon to behave as a photon, and not as an electron? Far be it from me to allege that a great Determiner is pulling on the strings in order to make things happen. But if a photon is a photon and not an electron, this is due to its having the nature of a photon, and not the nature of an electron. Moreover, if nature works towards an end or goal in the production of things living and non-living, then it seems exceedingly important that the photon should act like a photon and not like an electron, and vice versa. I guess my question boils down to: What is the reason these particles have the nature they have? They must be different natures, or we wouldn't need both.

Or to put the matter still another way, if there is no goal in view, the question of whether we need both photons and electrons, etc., wouldn't matter. Absent a purpose to be achieved, anything could be just anything at all.

[PatrickHenry]

What is the reason for the photon to behave as a photon, and not as an electron?

Ah ... the Great Differentiator makes his debut in our discussions.

(Just kidding, BB. My real answer is: I don't know. Nobody does.)

[BMCDA]

Excellent post!!
Worth a bookmark ;^)

[betty boop]

My real answer is: I don't know. Nobody does.

And yet logic lets us see the problem involved with this "unknowable." An infinite chain of (accidental) causes produces nothing but a piling up of accidents; therefore, in order for anything to exist -- to be the way it is and not some other way -- there must be a first cause. And if there is a first cause, it seems clear that it is acting towards a final cause, a goal or a purpose. Otherwise, why bother to do anything at all?

Of course, it can be said that this is an example of anthropocentric reasoning. Which raises another question: Is logic "anthropocentric?" Does it depend on the human mind, or rather, is it an independent something that the human mind just "naturally" resonates to? If the latter, and if everything that we see in nature is a purely "natural" product of nature's "laws," what in nature generates these laws, or the principles of logic?

[betty boop]

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."

I think your guess is right, A-G. I doubt that Yockey has a hidden agenda of some sort. It seems plain from his statement that what he's pointing out to us is that Marxism actually takes the form of a religion, a religion that is premised on metaphysical naturalism, which is the ultimate core and touchstone of its faith. The faith is consciously and deliberately intended to be a-theist. It is an attempt to explain the universe from purely natural causes. To the extent that proponents of abiogenesis tend to share this particular faith, they have something strongly in common with Marxists.

When you come right down to it, it seems that abiogenesis invokes the miraculous every bit as much as divine creation ex nihilo. Yockey's point may be that science isn't supposed to be in the miracle business....

[PatrickHenry]

An infinite chain of (accidental) causes produces nothing but a piling up of accidents ...

Not "accidental." That word introduces a bit of bias into the situation. The events are a chain of causes and effects which are "determined" by natural laws. And one of those piled up "accidents" is something as wonderous as you.

... therefore, in order for anything to exist -- to be the way it is and not some other way -- there must be a first cause.

Well, there cartainly needs to be a universe, however it came to be. First Cause is a possibility, I agree. I'm not certain it's a necessity. Could be. This is something I'm still thinking about. Again, we're talking science here, not religion.

And if there is a first cause, it seems clear that it is acting towards a final cause, a goal or a purpose. Otherwise, why bother to do anything at all?

It's not clear to me. As I said earlier (and here I shall quote myself, post 320): "Sometimes, when we look back on a long sequence of natural cause-and-effect events, teleology may seem to have been involved, but this may be an illusion of the retrospective viewpoint."

Finally, as to "why bother to do anything at all?" that's what our free will is all about. It's our decision. Ain't life grand?

[betty boop]

The events are a chain of causes and effects which are "determined" by natural laws. And one of those piled up "accidents" is something as wonderous as you.... as to "why bother to do anything at all?" that's what our free will is all about. It's our decision. Ain't life grand?

Yes it certainly is, PH! But I think you need to explain to me how "something as wondrous" as me reduces to a pile-up of "a chain of causes and effects," and yet this wondrous "me" at the very same time is said to have free will; that is, is capable of making free decisions and implementing them. What wondrous Maxwell's Demon intervened to reconcile these two mutually inconsistent claims, and when (figuratively speaking, of course)?

Plus remember, we exercise our free will in pursuit and furtherance of our own goals and purposes. If your theory is true, this would mean that human beings chronically suffer from baseless illusions; e.g., that we can actually control anything by deciding, making choices. (Notwithstanding, if I am not mistaken, this sort of thing is fundamental to scientific experimentation generally speaking.)

For if everything that is, is constituted from "a chain of causes and effects which are 'determined' by natural laws," then surely, willing anything other than the inevitable set-up being shaped by nature (which we cannot know in advance in any case) is an exercise in futility. Life is futility. Knowledge, science itself, is impossible. And we are delusionary to think otherwise.

Somehow, this doesn't make any sense to me. But just show me the source of the error in my thinking, and you might persuade me yet.

Patrick, you wrote: "Sometimes, when we look back on a long sequence of natural cause-and-effect events, teleology may seem to have been involved, but this may be an illusion of the retrospective viewpoint."

I know that, Patrick. But it's a different problem from the one we're discussing here -- the teleology implicit in [Aristotelian] logic itself, not what events look like to me in restrospect, once I've had the chance to "filter them" through my normal set of expectations, desires, and prejudices.

Thank you so much for writing, dear Patrick.

[PatrickHenry]

But I think you need to explain to me how "something as wondrous" as me reduces to a pile-up of "a chain of causes and effects," and yet this wondrous "me" at the very same time is said to have free will; that is, is capable of making free decisions and implementing them.

I really can't explain free will. It may be an attribute of our big brains. We had a thread more than a year ago in which the concept of "emergent characteristic" was considered. It's an attribute of complex systems that gives the whole certain features that the component parts alone don't possess. Some people around here are knowledgable about such things. I'm not. Free will may be that, or it may be more than that. It's difficult to make any kind of scientific test, either way. All we can demonstrate is that when a person's brain dies, we have no more indication that the dead person has any free will. This is, to me, inconclusive, except to demonstrate that the brain is necessary. It it all there is? I don't know. Nor do I know of any way to find out, to anyone's scientific satisfaction

Plus remember, we exercise our free will in pursuit and furtherance of our own goals and purposes.

Yes, we do.

If your theory is true, this would mean that human beings chronically suffer from baseless illusions; e.g., that we can actually control anything by deciding, making choices.

I don't think that's a "baseless illusion." We can excercise a great deal of control over things, and we can certainly make choices. (Example: the American Revolution.) We're not omnipotent, so our free will is limited. Yet it's real. Otherwise, we're just characters in an old movie, the end of which is already determined. Life would be pretty much the same from one generation to the next. For a long time, life was like that. But it isn't like that now, so there's evidence of free will in action. We can't literally prove that we have free will, but I certainly live as if I do. I suspect we all do.

For if everything that is, is constituted from "a chain of causes and effects which are 'determined' by natural laws," then surely, willing anything other than the inevitable set-up being shaped by nature (which we cannot know in advance in any case) is an exercise in futility. Life is futility. Knowledge, science itself, is impossible. And we are delusionary to think otherwise. Somehow, this doesn't make any sense to me. But just show me the source of the error in my thinking, and you might persuade me yet.

But BB ... knowledge certainly is possible; and we do have free will. I've suggested that after the event of creation, everything unfolded naturally -- stars, planets, life itself. If the universe had produced nothing but worlds, rocks, and tundra, then I'd agree with you. Futility. Lotta stuff, no pizzaz. But as part of that process, we came along. Whatever we are is consistent with the laws of the universe. But ...

But we're special because -- perhaps alone in the universe, yet in accordance with natural law -- we have the capacity of free will. That means our lives are the exact opposite of futile! Here we are, at the tail end of an enormously long, perhaps improbable, never-to-be-repeated chain of events, and we've got intelligence and free will. (Consider a sequence of Brownian Motions, to give you the idea I have in mind of a perfectly natural, yet probably unrepeatable sequence.) We're probably unique. Even if we're not the only intelligent life in the universe, we're certainly rare. That means, to me, that we're precious. We're the icing on the cake. We're irreplaceable in the whole cosmos! [Pause, as my hand-waving, red-faced rant cools down.]

How could anyone ponder that and even think about futility? I literally tingle with awe at the magnificence of it all. I can't understand how someone could find it depressing.

[StJacques]

". . . But as Denton indicates, there's a problem regarding the lower-order life, which on the one hand, needs a reducing environment in order to arise, but on the other, needs an oxygen-rich environment in order to survive (i.e., preeminently oxygen's role as constituent of the ozone layer, which protects organisms against the fatal effects of ultraviolet radiation) -- the "Catch-22" of abiogenesis. In other words, absent oxygen -- the presence of which (it is argued) would preclude abiogenesis -- the life rising by means of a methane-rich reducing environment would be wiped out almost immediately after coming into existence, presumably before it had the chance to replicate. . . ."

Denton's so-called "Catch-22 of Abiogenesis" only works if you make four assumptions:

1. That there was no oxygen whatsoever in the early earth's atmosphere.

2. That the origins of an oxygen-rich atmosphere are not related to the presence of life forms acting to enrich the atmosphere with oxygen.

3. That the earliest forms of life required an oxygen rich atmosphere.

4. That the presence of ultraviolet radiation prevented all forms of life from surviving and propagating.

All four of the above assumptions are false.

Regarding No. 1: "Free oxygen" or O2, was present in the early reducing earth's atmosphere in what geologists refer to as "oxygen sinks" or reservoirs of oxygen, primarily present as a result of the cooling of both rocks within the mantle and surface igneous rocks, as well as some that may have been produced as a result of "hydrogen escape" from photodecomposition of methane and ammonia. There were also oxygen-containing compounds, especially carbon dioxide and sulfates produced by vulcanism. And water was also present in the early Archaean Age as well. And these propositions are argued from geologic evidence. I recommend you read the following article:

Kump, Kasting, & Barley: Rise of Atmospheric Oxygen and the "Upside Down" Archaean Mantle

See also the MIT article cited below, page 5, for evidence from Uraninite (UO2) which establishes the presence of oxygen, it's in the composition of the mineral itself, within an "anoxic environment" (no free oxygen) since the elements become unstable in the presence of "free oxygen."

Regarding No. 2: The Geologic evidence that the development of our oxygen-rich atmosphere was created by a combination of photosynthesis and hydrogen escape is extremely large. I refer you to the following two sources, the first of which I cited earlier:

MIT Article - Photosynthesis and the Rise of Atmospheric Oxygen

Catling, Zahnle, & McKay: Biogenic Methane, Hydrogen Escape, and the Irreversible Oxidation of Early Earth

3. The proposition that the earliest forms of life required an oxygen-rich atmosphere is defeated at two levels. The first is that there are numerous life forms, such as cyanobacteria and eukaryotes that do not require an oxygen-rich environment and which both produce oxygen as a result of their metabolic processes. See the MIT article for more on this. Second; there may have been bacteria that used very low amounts of oxygen extracted from sulphates. The following quote is from Norman H. Sleep's "Oxygenating the Atmosphere" article on the Nature web site:

". . . But it is possible that these bacteria were part of a global microbial ecology that used sulphate as the main oxygen carrier and so would consume only trace amounts of oxygen . . ."

You can read more about sulfurous environments and microbial ecology in the article "Biochemical Keys to the Emergence Of Complex Life" by Kenneth M. Towe of the Smithsonian Institution, especially within paragraphs eleven and twelve. And in addition to all of this there is more I could find on how CO2 environments may not be defeating of life as well, but I'll skip that for now.

Regarding No. 4 there are at least three direct points to make about ultraviolet light. The first is that higher emissions of ultraviolet rays enhance the catalyzation of RNA solutions and break down inorganic molecules, which makes UV rays an important agent in explaining a possible RNA world transition to life within that particular model of abiogenesis. Two; not all life dies in the presence of ultraviolet radiation, whether you speak of today -- GFP strains of e. coli bacteria need UV ray emissions to survive in fact -- much less in the Archaean Age. Three; the "Faint Sun Paradox," which is the most important. There is solid astronomical evidence that 3.5 Billion Years ago the Sun was not as luminescent as it is now. Carl Sagan and Christopher Chyba jointly developed the so-called "paradox" of the faint sun and its impact on the origins of life because one of the real objections raised by scientists against abiogenesis was that the sun was not warm enough to sustain life at the period when we date its origin, not that ultraviolet rays were an insurmountable problem preventing it because there is evidence in the geological record of life existing before the oxygen-rich atmosphere developed which has always restricted scientific inquiry to explaining how and why life existed under higher levels of UV photolysis (see the references under explanations for #s 2 and 3 above), not whether or not it was possible. But as Chyba pointed out in a response to a critique of the theory by Stanley Miller:

". . . a high-altitude organic aerosol on early Earth would make the persistence of a reducing atmosphere more likely, and that such an atmosphere favors organic synthesis, making the origin of life easier to envision. As we stated, atmospheres rich in CO2 have been considered more likely candidates for early terrestrial atmospheres for two reasons. One is the rapid UV photodissociation of methane and ammonia. Our article suggests that a reducing "Miller-Urey" atmosphere, when treated self-consistently, avoids this difficulty because such an atmosphere would become self-shielding against UV photolysis. . . ."

And to add to my earlier statement that "I question [Overman's] credentials to describe the state of scientific opinion on the early earth's atmosphere" I must now add that "I question whether Overman has done any adequate reading in scientific scholarship useful to explaining the origins of life on this planet."

The mesh on Overman's "Catch-22" net is so large that it catches nothing at all.

[StJacques]

Patrick and Alamo-Girl, I meant to ping both of you on my preceding post #329 but I forgot. Sorry.

PING!!!!

[PatrickHenry]

Don't worry. I'm following the thread. Ping or no ping, I'll comment when I can make a contribution.

[cornelis]

Don't worry. I'm following the thread. Ping or no ping, I'll comment when I can make a contribution.

Same here. Good discussion.

[StJacques]

This is a followup to my post #329 above. I think there is something I need to add.

This is a portion of the quote from betty's description of Denton's "Catch 22":

". . . In other words, absent oxygen -- the presence of which (it is argued) would preclude abiogenesis -- . . ."

It occurs to me that I left something out, since it is mentioned that the presence of oxygen would "preclude abiogenesis." This means that I must now add a fifth assumption to the four I listed in my post #329:

5. That the process of abiogenesis requires either the simultaneous absence and presence of oxygen to be completed successfully or the absence of oxygen initially quickly followed by the presence of oxygen.

This is also false.

Let me repost the image I displayed in my post #281 on the previous page:





Now first of all, there is more than one theory of abiogenesis which fits the overall model described in the above image, but I believe that Denton may have been following the Miller-Urey model in which amino acids are produced from inorganic materials within an environment in which free oxygen was absent and, by the laws of chemistry, in which the presence of free oxygen would prevent the formation of those amino acids. That is step 1, the transition from "simple chemicals" to "polymers." For anyone who needs to brush up on their chemistry, proteins are "polymers" of numerous amino acids. The Miller-Urey model will not work if oxygen is present, in fact, if you replicate the Miller experiment in the lab and add free oxygen you get an explosion. In some models free oxygen is not necessary at all throughout this process, but in others it may only be desirable or necessary only in the later stages.

What is important here is that the model is not:

simple chemicals -> bacteria

which is what would be required for Denton's model to make any sense. There could in fact be millions of years between the realization of a transition between some of the steps outlined in the image posted above.

[StJacques]

I need to make a quick edit to something I just posted in number 323 above.

I wrote:

". . . That is step 1, the transition from 'simple chemicals' to 'polymers.' . . . "

That should have been written, with my edit underlined for emphasis:

". . . That is part of step 1, the transition from 'simple chemicals' to 'polymers.' . . . "

Sorry about that.

[StJacques]

DARN!

I meant post number "333" not "323."

I think I need a break. Or maybe better yet, a beer.

[Alamo-Girl]

Thank you so much for all of these interesting links!

From the first two or three links it became apparent that the date for free oxygen in the environment was settled to be between 2.4 and 2.2 gya – with photosynthesis hacontributions from 3.5-2.7 gya. The NASA link was particularly informative (Biochemical keys to the emergence of complex life). An important excerpt:

If the first 2.5 billion years of Earth history were dominated by an environment in which free oxygen was generally unavailable to the biosphere because of primitive reduced inorganic acceptors or "sinks," then one of the principal strategies of life would have been to adapt to this environment Neither collagen nor extensin would have been possible in the absence of free oxygen, and the fossil record shows that during this period few significant increases in body size were made. After the exhaustion of most primordial inorganic oxygen sinks about 2 billion years ago (Cloud, 1976; Schopf, 1978) and the development of the eucaryotic cell and oxygenic photosynthesis, the major environments of the world began to turn from predominantly reducing to predominantly oxidizing conditions. Multicellularity would have been a priority development and collagen one of its certain prerequisites. The geologic evidence shows that the transition to an oxygenic world did not take place rapidly; if it had, there would be major deposits of reduced carbon in the sediments of the period, and none is found. The buildup of free oxygen is more likely to have been rather slow. With some limited free oxygen present in the environment, limited collagen (and extensin) could have evolved in some organisms where the wide-open ecological niches available and the adaptive advantages being conveyed outweighed the complexities and expense involved in its manufacture. I have already discussed how this may have affected the fossil record (Towe, 1970), but it is worth repeating that in this initially low-oxygen environment, the competition for the low levels of free oxygen by oxidative metabolisms would have restricted most collagen use to small, thin, diffusion-limited organisms unlikely to be found preserved as fossils. As Boaden (1977) has emphasized, the world at this time may have been like the modern thiobios-a sulfide-rich habitat dominated by mostly microscopic, interstitial meiofaunal elements.

The biochemistry of collagens from modern near-anaerobic nematodes is instructive in making further comparisons with the Late Precambrian fossil record. Both the cuticle and body wall of Ascaris lumbricoides contain collagen. The body-wall collagen has large amounts of hydroxyproline and hydroxylysine. Adapted to low oxygen tensions, their formation through the [301] hydroxylating enzymes is actually inhibited by too much oxygen (>1%) in the environment (Fujimoto and Prockop, 1969). The cuticle collagen lacks hydroxylysine, contains little hydroxyproline, and appears to be strengthened by disulfide crosslinks (McBride and Harrington, 1967), another adaptation to low-oxygen tensions.

Given this information, one can speculate that the early use of collagen in Late Precambrian low-oxygen environments may have eventually produced "worms" with similarly adapted collagen metabolism, which permitted some of them to attain much larger sizes than the remaining interstitial faunal elements. Perhaps the enigmatic coiled fossils from the billion-year-old Greyson Shale (Walter et al., 1976) or from the Little Dal Group (Hofmann and Aitken, 1979) are rare body fossils of such worms. Or perhaps some of the Late Precambrian burrows were produced by similar worms who had become adapted to the low-oxygen environment and were, like their modern thiobiotic descendants, burrowing to avoid the increasing oxygen tensions that must inevitably have taken place. Burrowing to avoid oxygen at the sediment-water interface in this very early stage of metazoan history seems more likely than burrowing to avoid predators, the types of which are unknown and the fossil evidence for which is otherwise nonexistent.

Ultimately, the further increase in availability of free oxygen as the result of increasing oxygenic photosynthesis would have brought an end to such adaptations, and therefore any experiments toward developing collagens completely free of an oxygen requirement were terminated. At the same time, the high competitive priority of respiratory events for oxygen would have been moderated, allowing many more morphological experiments with collagen to take place in other previously limited metazoan phyla. Even the sclerotization of the arthropod cuticle, which is also inhibited by lack of atmospheric oxygen (Richards, 1951), would have been improved All this would have caused a dramatic worldwide increase in the size and hence ready preservability of numerous organisms. The Late Precambrian-Early Cambrian fossil record can then be interpreted as an explosion of fossils rather than as a sudden eruption of metazoan phylogenesis with highly evolved, diverse, and morphogenetically advanced forms appearing suddenly side by side around the world, few of which have any plausible immediate ancestors as fossils.

All of the above “goes to” the likelihood that the complexity of biological life was due to self-organizing complexity and not happenstance. Also from another link:

Armen Y Mulkidjanian, Dmitry A Cherepanov, and Michael Y Galperin (emphasis mine)

In modern concepts of the origin of life, there is an glaring gap between the abiogenic formation of the first building blocks and the origin of the "RNA world" i.e. of the first RNA-like polynucleotides that could undergo a Darwinian-type evolution. Indeed, there is a wealth of experimental evidence for the abiogenic formation of amino acids, nitrogenous bases and carbohydrates from inorganic compounds like cyanide, thiocyanate, and carbon monoxide under reducing and/or neutral conditions (reviewed in ref.). On the other hand, the documented catalytic activity of RNA molecules allows to suggest that primordial ribonucleotides could have initially evolved on their own, without assistance from proteins. What is missing is a physically plausible mechanism for the thermodynamically unfeasible event of formation and accumulation of long oligonucleotide-like polymers.

This problem can be focused even further. Aluminosilicate clays have been shown to catalyze the formation of oligonucleotides of up to 50 units long, when supplied by preformed and pre-activated mononucleotides under optimized laboratory conditions. However, no oligonucleotide formation from pentose phosphates and nitrogenous bases has been reported so far under the supposedly primordial conditions where the formation of amino acids, nitrogenous bases and carbohydrates took place. Furthermore, the current understanding implies that the environmental conditions on the primeval Earth were unfavorable for the survival of oligonucleotide-like polymers. A particularly important factor is that, due to the absence of the ozone layer, the UV flux at the Earth surface must have been approximately 100 times larger than it is now, causing deterioration of most organic molecules. The existing theories consider the high UV level as a major obstacle and offer several different strategies for hiding the first life forms from it (see e.g. ref.). Here we invoke an alternative possibility, i.e. that the UV irradiation played a positive role in the origin of life by serving as a principal selective factor in the formation of pre-biological structures. Moreover, the influx of energy into the system in the form of the UV irradiation could be seen as the driving force required for the gradual complication of the system. These considerations prompted us to analyze the possible effects of the UV irradiation on oligonucleotide formation in primordial conditions.

continuing in the discussion…

Thus, the results of our Monte-Carlo simulation indicate that a mechanism of natural selection, similar to the one that has driven the subsequent biological evolution, could have been responsible for the primordial polymerization. It seems quite unlikely that the extremely effective UV-quenching by all five major nucleobases is just incidental. Accordingly, one can assume that these bases had been selected to perform the UV-protecting function before they became involved in the maintenance and transfer of genetic information. This assumption provides a physically plausible rationale for the primordial enrichment in oligonucleotide-like compounds and also sheds new light on the earliest steps of evolution….

The suggested mechanism turns the high UV levels on primordial Earth from a perceived obstacle to the origin of life (see e.g. ref. [19]) into the selective factor that, in fact, might drive the whole process. Indeed, biochemical condensation reactions proceed with release of water, so that the presence of latter favors hydrolysis of biological polymers. Because of this feature, Bernal [27] and many researchers after him (as reviewed in ref. [10]) advanced the view that life has begun in tidal regions, so that condensation of primordial monomers proceeded under "fluctuating" conditions where the wet periods, enabling the exchange of reagents, alternated with dry ones, favoring the condensation reactions. The awareness of the potential danger of the UV damage, however, prompted other scientists to invoke a UV-protecting water layer (see e.g. ref. [19]), which apparently would impede the condensation reactions. More recently, several authors even moved the point of the life origin to the bottom of the ocean, where the reducing power of minerals and/or of hydrothermal vents was considered to be the energy source for the first condensation events [28,29]. It remained unexplained, though, how inorganic reductants could drive primordial condensation reactions in water in the absence of enzymes (see the discussion in refs. [30,31]).

In a sense, the absence of a consensus on a plausible mechanism for the origin and accumulation of the first RNA-like molecules has significantly hurt the development in the whole field and stimulated proliferation of the Panspermia hypothesis, not to mention various kinds of creationist ideas. It appears that our consideration of the UV irradiation as a positive, selective factor in primordial evolution may suggest a way out of the dead end. This view allows to place the cradle of life onto the sun-illuminated (semi) dry surface of the ancient Earth, as originally considered by Bernal [27]. Indeed, no other known energy source could compete with the UV component of the solar irradiation either in ability to serve simultaneously as both selective and driving force, or in continuity, strength, and access to the whole surface of Earth...

IOW - here, the investigators are turning the UV objection into a positive and suggesting that it is the energy source which (vaguely) drives biological complexity. However, they also indicate that the UV protection “function” must have existed before the UV irradiation actually occurred to protect some. This is what I would call a "just so" story until it is backed up with some empirical investigation.

Here are a few more for the discussion: Abiogenesis

[speaking of the Urey-Miller experiments being repeated with success] But the Earth's early atmosphere is nowadays thought to be neutral, consisting mostly of nitrogen and carbon dioxide, instead of hydrogen, ammonia, and methane (reducing), as had been suggested from cosmochemical grounds. Urey-Miller experiments performed with a neutral mixture are much less successful than those with a reducing mixture; however, the early Earth could easily have had reducing microenvironments, like hot springs and hydrothermal vents.

There is also the conundrum that bodies of water are poor places for the formation of biomolecules like proteins and nucleic acids, since the "primordial soup" is inevitably very dilute, making it difficult for molecules to "find" each other. This conundrum has led to the "primordial pizza" hypothesis of the origin of life on mineral surfaces like clay surfaces, which organic molecules can easily stick to, and which have catalytic properties that can easily assist in the formation of complex molecules. Günter Wächtershäuser has proposed that the Krebs Cycle (a.k.a. citric acid cycle, tricarboxylic acid cycle) had originated on such mineral surfaces, powered by iron-sulfur chemistry.

And while some biological molecules, like the smaller amino acids and nucleic-acid bases, are readily produced in Urey-Miller experiments, others, like sugars, are not. This means that nucleic acids are difficult to produce, since they contain the sugar ribose and its derivatives; this is a major difficulty with the otherwise-very-attractive "RNA world" hypothesis.

Thus, how to get from there to a complete self-reproducing system is still an unsolved problem, but this question is being actively researched.

Concerning the “primordial pizza” on such mineral surfaces, here’s more on Wächtershäuser. BTW, Intelligent Design theorists ought to get a kick out of this after all the abuse they have taken over lawyers (LOL!)

Günter Wächtershäuser

Günter Wächtershäuser, a chemist turned patent lawyer, is mainly known for his groundbreaking and influential work on the origin of life, and in particular his "iron-sulphur world theory", a theory that life on Earth had hydrothermal origins. The theory is consistent with the hypothesis that life originated near submerged hydrothermal vents.

Dr Wächtershäuser, a chemist by training, has been an international patent lawer in Munich since 1970. He has published numerous articles in organic chemistry, genetic engineering and patent law, and has made at least two significant contributions to evolutionary theory: the origins of perception and cognition, and the origin of life.

One of the key ideas advanced by Wächtershäuser is that an early form of metabolism predated genetics. Metabolism here means a cycle of chemical reactions that produce energy in a form that can be harnessed by other processes. The idea is that once a primitive metabolic cycle was established, it began to produce ever more complex compounds.

Wächtershäuser has hypothesized a special role for acetic acid, a simple combination of carbon, hydrogen, and oxygen found in vinegar. Acetic acid is part of the citric acid cycle that is fundamental to metabolism in cells.

And here’s the model for Wächtershäuser’s theory et al (emphasis mine):

Multi-Phase Artificial Chemistry

Phase equilibria and the segregation of molecules into different phases probably were of utmost importance in prebiotic evolution. The presence of different phases allows certain species to concentrate to a level necessary for reaction, of which the products can subsequently switch phases to encounter reaction partners which would have before rendered impossible its synthesis. Concentration gradients, in particular pH gradients, between different phases might also have provided the driving force for chemical reactions. Hydrogen cyanide, for example, has been proposed to have polymerized first in an ice phase before its polymerization products continued to react further under warmer conditions [14]. This would avoid the problem possed by its tendency to react with formaldehyde [2]. Allamandola et al. [1] and Trinks et al [15] have also proposed models including different ice mantels in comets or ice phases in the sea.

The most accepted model for the origin of life has been proposed by [13,17] with the primordial ‘soup’. Hot deep sea vents as the birth place of life (the primordial ‘pizza’) were discussed as an interesting alternative [26. However, all these models need a prebiotic chemistry with complicated synthesis. As described in [20] and [21], they cannot occur in single, unpartitioned environment. A sequence of different environments would be important for the orgin of life, just as in the traditional organic synthesis. During such a synthesis a reaction mixture is subjected to certain conditions, then some products are extracted, purified, and/or crystallized, new reagents might be added, and the next step with new conditions begins. We can imagine an analogous situation in prebiotic chemistry, where the different conditions and steps are mimicked by different environments, i.e. phases like hot vents, the atmosphere, and ice, and intermittent evaporation, phase change, crystallization or filtration. This might mitigate the problems of complicated synthesis in prebiotic chemistry.

IMHO, this brings us right back to Luis Rocha

The idea that life may have originated from pure RNA world has been around for a while. In this scenario the first life forms relied on RNA molecules as both symbolic carriers of genetic information, and functional, catalytic molecules. The neutralist hypothesis for the function of RNA editing assumes such a RNA world origin of life. It posits that RNA editing could offer a process by which the dual role of RNA molecules as information carriers and catalysts could more easily co-exist. The key problem for the RNA world origin of life hypothesis is precisely the separation between these two functions of RNA. On the one hand RNA molecules should be stable (non-reactive) to carry information, and on the other hand they should be reactive to perform their catalytic function. RNA editing, could be seen as means to fragment genetic information into several non-reactive molecules, that are later, through RNA editing processes, integrated into reactive molecules. This way, the understanding of this process of mediation between the role of RNA molecules as information carriers and catalytic molecules based on RNA editing, can also offer many clues to the problem of origin of a semiotic code from s dynamic (catalytic) substrate.

IOW, even if one were able to account for the phases necessary to accomplish autonomy and bootstrap a replicating RNA world, in all of this there is not yet proposed a natural origin for the communication (information, Shannon) itself or the semiosis necessary for self-organizing complexity (for those models which eschew happenstance).

Where do we go next?

[StJacques]

I will have to digest some of the earlier information you posted, so I'll hold off, I especially want to think about Wächtershäuser. I've heard of the theory, but never examined it.

I do want to get right to the end of your post. You wrote:

". . . even if one were able to account for the phases necessary to accomplish autonomy and bootstrap a replicating RNA world, in all of this there is not yet proposed a natural origin for the communication (information, Shannon) itself or the semiosis necessary for self-organizing complexity (for those models which eschew happenstance). . . ."

I think I have an answer, maybe I should say "a link," for this one.

Stuart A. Kauffman: The Nature of Autonomous Agents and the Worlds They Mutually Create

The answer, I believe, is that autonomous agents "created" the information.

[StJacques]

Let me add a supplementary comment to my previous post on "autonomous agents" and the creation of information, calling attention to Luis Rocha, whose quote you posted.

I will want to think a bit more about what Luis Rocha had to say about "Disabled Syntactic Autonomy" and "Enabled Syntactic Autonomy" with respect to your question on the "origins" of information. I believe that the two types of autonomy may be what he is leading up to in the quote you posted, I'm not sure about that but I'll want to review. It may be that something along the lines of information contained in "synthesized or catalyzed RNA," such as Ferris has created and which contains at least some "information," though I doubt very much, can be regarded as the type of information sent within "Disabled Syntax" and more complex types of information, such as that from "fully autonomous agents" along the lines of which Kauffman discusses, are sent by "Enabled Syntax." Maybe, I'm just thinking in print here.

I'll have to think about all of this a bit, which means I will have to reread Rocha.

[Alamo-Girl]

This is a superb article. Thank you! Kauffman goes the extra mile to make the concept of autonomy and its importance to abiogenesis very clear Kudos!

betty boop, I suspect the seventh chapter will be of particular interest to you. For Lurkers, here are some of what I see as key points in the article:

The Nature of Autonomous Agents and the Worlds they mutually create

…What properties must a physical system have such that it can be said to be able to "act on its own behalf." A bacterium swimming upstream in a glucose gradient is acting on its own behalf, seeking dinner. Yet the bacterium is "just" a physical system. In attempting to answer this question, I have been led to a tentative definition of an "autonomous agent" making a living in an environment. By this definition, an autonomous agent is a collectively autocatalytic system that performs one or more thermodynamic work cycles.

Outside of an autonomous agent, or a coevolving community of autonomous agents, the chance occurrence of intricate "Rube Goldberg" machines channeling the constrained release of energy are vastly improbable spontaneously. Nor would such linked systems be likely to sustain themselves. While channeling energy flows, the general Rube Goldberg does not construct itself. Thus, the cyclic life cycles of Autonomous agents coevolving with one another to create ecosystems and finding and incorporating new functionalities in the adjacent possible begin to appear to be the major way that organization arises and proliferates in the Universe. If building order requires degradation of free energy, then autonomous agents ratchetting themselves far from equilibrium, thereby storing energy and "recorded embodied know how" in structure and flow to control their own constrained release of energy, construction of themselves, and exploration of the adjacent possible, appear the paramount way to build up complexity.

Indeed, once such autonomous agents exist and create a world in which they proliferate, the Darwinian categories of "function" come into play. A given molecule is "food" or "poison" to a situated agent. Hence, once Agents exist, a genuine semantics, with a physical interpretation, appears to arise. A coevolving community of non-equilibrium Maxwell Demons is a union of matter-energy-information into an organization that proliferates and constructs hierarchical complexity...

But lecture four emphasizes very puzzling questions partially noted and developed in lecture three, concerning constraints and propagating work in Agents. We appear to have, as yet, no physical theory that comfortably unites matter, energy and information in a single dynamical framework. Yet Maxwell's Demon is one place in physics where matter, energy and information come into intimate contact. A collectively autocatalytic, autonomous Agent performing linked propagating work, however, is characterized by a new and objective property: It is a physical system that achieves a collectively self-consistent functional "closure" in a space of catalytic and work tasks. An autonomous agent, a non-equilibrium Maxwell Demon, coevolving in its community has embodied know-how. It knows how to make a living in the context in which it lives and carries out real construction work in doing so. Its self consistent structure and dynamical logic constitute the embodied "record" of its environment, its reproduction and proliferation carries out linked work cycles and simultaneously, via mutation and selection, updates its record. A growing microbial community constitutes something like "propagating coconstructing organization of propagating constraints - work - record."

...More broadly, they suggest that the biosphere is non-ergodic, as is the Universe as a whole. The three component laws claim that any biosphere will self-organize to three phase transitions: The dynamical "edge of chaos" among a community of agents; a self-organized critical state among those agents considered as a coevolutionarily constructable ever changing system; a system poised on a subcritical-supracritical boundary at which the total chemical and perhaps functional diversity of the biosphere expands, on average, as fast as it can.

Kauffman’s hypotheses are quite engaging, but so far I haven’t read where he has specifically addressed how information itself (communication) and the required symbolization emerge within the autonomous agents – which are the two issues central to Rocha, Yockey, et al. But he does a great job laying out the environment which would be required for such to emerge autonomously.

There is another huge stumbling block to his hypotheses, Maxwell’s demon.

Tom Schneider’s article in Nanotechnology explains on page 14 why Maxwell’s demon is dead. Elsewhere, Peter Corning, Institute for Study of Complex Systems, specifically disputes Kauffman’s appeal to Maxwell’s demon.

[StJacques]

". . . Kauffman’s hypotheses are quite engaging, but so far I haven’t read where he has specifically addressed how information itself (communication) and the required symbolization emerge within the autonomous agents – which are the two issues central to Rocha, Yockey, et al. But he does a great job laying out the environment which would be required for such to emerge autonomously. . . ."

This goes back to my previous post, #338, in which I raised the issue of "what Luis Rocha had to say about 'Disabled Syntactic Autonomy' and 'Enabled Syntactic Autonomy'" and whether this may be related to differing levels of complexity in information. I've now reread portions of that paper and, though I have not come to a final conclusion on this yet, I am leaning towards the conclusion that I am right. The title of the section within Rocha's paper from which you quoted is "RNA Editing: the Origin of Syntactic Autonomy in Biology?," which I am using as a question to keep in mind when looking at Kauffman's work, in which he discusses a "hierarchy of combinatorially complex entities." That hierarchy is preceded by the flow of "matter-energy-information" from the "'Actual' to the 'Adjacent Possible'" in the transition from a mere "agent" in "a fitness landscape" to a point in which that agent "achieves a specific self-organized critical state." Like Rocha, Kauffman appears to see a connection between the way(s) information is transferred and the development of "autonomy" in a biological system, i.e. an "organism."

Now, I repeat, if RNA has been catalyzed in mineral clays (Ferris) then we have a scenario for the origins of at least some degree of information, since by definition RNA is composed of nucleotide sequences and those sequences in and of themselves are information. But that degree of information -- and I am just guessing here, though I doubt you will disagree -- cannot be of such a "complex" nature that it explains how information originates and functions within an "autonomous agent," a term that is still far removed from RNA that was produced by mere chemical reaction, such as occurred within the experiment Ferris conducted. With that in mind I think the real question that must be asked is not "what is the origin of information in biological systems?" but rather "what is the origin of complex information?" or perhaps even "what is the process of complexification by which information rises to a level necessary for the functioning of autnomous agents?"

These are still just thoughts on my part, but I'm putting them up for discussion.