THE EVOLUTION DEBATES
Tuesday, March 13, 2001
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- Mr. Sobral begins
- Reopen with math: combinations: Lafferty would have loved it.
- Patricia Lanca
This began as letters about micro and macro evolution. I'll reprint those and add all new ones on the subject in here. This all took place between about 4 and 8 April, 2000; in future I'll try to remember to time-stamp mail that gets transferred here.
Here is how it started: I put this up in view:
Greg Cochran has a very defensible theory that many problems we think are hereditary are in fact caused by infectious agents (as ulcers turned out to be). I'm in correspondence with him. One of these days we'll have a large presentation, but until then
http://www.theatlantic.com/issues/99feb/germs.htm.
will give a summary. May be one of the most important inferences from the theory of evolution we have ever made.
And came the reply:
You have a terrific site! Thanks for all the thought provoking discourse, and the helpful tips and advice you give. I have to have my "fix" of your site about the same as my "Rush" fix.
I read the very interesting article about the new germ theory. On the surface it made a lot of sense. The problem that I had with it is that it assumes that Darwin was right. "As far as Ewald is concerned, Darwin's legacy is the most interesting thing on the planet. The appeal of evolutionary theory is that it is a grand unifying principle, linking all organisms, from protozoa to Presidents, and yet its essence is simple and transparent. "Darwin only had a couple of basic tenets," Ewald observed recently in his office. "You have heritable variation, and you've got differences in survival and reproduction among the variants. "That's the beauty of it. It has to be true -- it's like arithmetic." It makes assumptions and great leaps of faith without any real proof of evolution. The next paragraph talks about "These Darwinian laws ...". I guess I missed the article about Darwin's theory being proved and upgraded to a Law.
Regards Leroy Ortiz
I suppose it is flattering to be compared to the very popular Rush, but I am not sure what he says lately. I only listen to him when I am in a car in the mornings and that is not very often. Anyway, thanks.
Regarding evolution, there seems to be little to no question about micro-evolution, which is what Cochran assumes. Macro evolution or the Origin of Species is a bit more controversial, at least in its extreme form as pretty well asserted by The Blind Watchmaker. There are some mathematical problems with macro-evolution: some species to get from one to another must have passed through intermediate forms that do not seem very viable. In any event one may postulate that conditions were just right for those intermediate forms to have thrived for the time it took to get from one (surviving or found in fossil form) form to another, then those intermediates vanished along with the conditions that made them viable.
This is certainly plausible, but it is as much an Act of Faith as any religions statement that says there must have been Divine Intervention in the process. After all, the Divine Intervention people have some science on their side too: Schlieman and Schwann, omnia cellula e cellula, etc. Every farmer can tell you about micro evolution, and it is not hard to postulate "survival of the fittest" which is what Cochran is counting on.
Note that I don't say macro evolution is impossible, or has been proven right or wrong, or whether or not I "believe" in it; nor do I find it incompatible with revealed religion. St. Augustine himself speculated that God might have created the universe in "germinal causes" and allowed things to work out from there; religion only requires that you believe God does intervene in the affairs of nature through miracles, not that He does so in the ordinary course of events. A miracle is by definition NOT part of the natural order but in direct contravention of it. Miracles are also rare, and again by definition beyond the scope of science, which looks for repeatable experiments.
I don't find it takes any leap of faith at all to accept micro evolution. And see below.
Note: Sir Fred Hoyle has several works on the statistical probabilities of macro evolution. Of course my friend Adrian Berry says "Sir Fred is off his head, don't you agree?" I don't have to say: I have not myself been satisfied that all of Hoyle's questions have been answered.
===
Occam's Razor points to macro-evolution, given the available data; like yourself, St. Augustine, and the Pope, I see absolutely no conflict between religion and science in this arena.
After all, doesn't Genesis fit quite nicely as a handy parable describing our current thesis of how lower forms came first, followed by higher forms?
I think the fundamental problem most everyone at one time or another has with the concept of macro-evolution, including even such an eminence as Sir Fred Hoyle, is that the sheer span of geological time is very, very difficult for we short-lived humans to grasp.
When we state that the Earth is approximately 4 billion years old, we tend to think about the '4', and not the 'billion'.
If we write it out thusly - 4,000,000,000 years - it becomes a bit easier to accept that in such a vast span of time, micro-evolution may cumulatively equate with macro-evolution. If we think of all the solitary events (activity at the cellular and bacteriological levels; meteor strikes; gamma rays passing through; etc.) which transpire all over the world in any given day, and then write out our 4 billion years as approximately 1,460,000,000,000 24-hour days, the premise becomes more plausible, no?
>From my perspective, acceptance of macro-evolution does not by definition insist upon acceptance of a Blind Watchmker - a Master Craftsman fits the bill just as well.
Roland Dobbins <mordant@gothik.org>
===
From: Stephen M. St. Onge saintonge@hotmail.com
Subject: Evolution
Dear Jerry:
The letter from Mr. Dobbins, replying to you and Leroy Ortiz, inadvertently reveals what's wrong with evolution as a scientific theory.
No, I can't emotionally grasp 4,000,000,000 years, or 1, 461,000,000,000 days, or 126,230,400,000,000,000,000,000 microseconds, and neither can Mr. Dobbins. We can work with them mathematically, and when we do, the answer that comes up is that the chance of one organism evolving into a second in the time period available is too low to bother with. The 'sheer span of geologic time' is a red herring invoked by those who resolutely refuse to do the math.
Evolutionists assume that if you don't believe in their story, you must believe in some other story. My favorite example of this is in "Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution," the transcript of a symposium held at the Wistar Insitute in Philadelphia in April of 1966. The mathematicians point out the reasons for believing that random search could not attain the results we see about us in the time period available, and the believers insist that the math must be wrong, because they know evolution as then conceived is true. Finally, one of them loses his cool and angrily accuses a speaker of belief in Divine Creation ('shouts of "No!" from the audience.')
Every culture on earth has a creation story, one that it made up to fill a psychological need (my favorite is HOW THE WORLD WAS MADE by Dorothy Straight, the then four your old daughter of ex-KGB agent and New Republic publisher Michael Straight). When science-the-discipline-for learning-about-nature became Science-The-Oracle-With-All-The-Answers, it needed a creation story, and some version of Evolution is it. If I had to choose, I'd prefer Dorothy's. Her pictures are prettier, and she doesn't try to b.s. me. But I rathered not choose on faith.
Without faith, you have to face the awful truth that we do not know how life began or why it is so diverse. Rather than look in that abyss, most people fantasize.
For what's wrong with evolution as science, I'd recommend starting with the symposium, and looking at Michael Denton's "Evolution, a Theory in Crisis," and Michael Behe's "Darwin's Black Box." But I doubt very many will have the courage to admit ignorance to themselves.
Thanks for the pointer to the picture of Mrs. Pournelle and your new granddaughter. Don't know how I missed it last week, but I did.
Best, St. Onge
Behe is certainly worth your attention. And the abyss does stare back... For that matter, I am unconvinced that Sir Fred is off his head.
====
Jerry,
Roland correctly points out the fact that it is hard for us to imagine how long 4 billion years is. 4 billion is a very large number (except to Uncle Sam). In your reply you stated that there were mathematical problems to macro evolution. You are correct. For example, human hemoglobin is a string of 574 amino acids of 20 varieties. There are 10E 654, different ways to combine these amino acids. That is kind of meaningless all by itself, but consider this: It is thought by evolutionary proponents that life began 2,500 million years ago, which is still a very long time. However, the number of seconds since life began is 10e 17. The number of seconds since the big bang 5000 million years ago is 10E 18. The number of stars in the universe is 10E 22. The number of atoms in the universe 10E 80. The improbability of hemoglobin occurring by random selection is 10E -654. I'm not a math major, but that looks like 0 to me.
The problem I have with macro evolution is that it has gone from an idea that "kind of makes sense" to "This is the way it is" in the scientific community. There is absolutely no credible evidence of macro evolution, yet it is accepted without question. Just because something makes a good story doesn't mean it's true.
>From my perspective, belief of macro evolution takes more faith than belief in God.
Leroy Ortiz leroyortiz@netscape.net
Subject Evolution
Dear Jerry,
There is a beautiful chapter in Arthur Clarke´s 25 year old book „Profiles of the Future“, titled „Failure of Nerve“. In it Clarke quotes one example after another, where famous scientists were unable to recognize something even if all the facts were starring into their faces. Macro evolution is another example.
The results of a mathematical analysis are clear: 4 billion years or 126,230,400,000,000,000,000,000 microseconds are just not long enough to explain macro evolution as outlined in the Origin of Species. As a matter of fact, the mathematical reasoning is not that difficult to understand.
Assume, you are trying to open a numeric lock in a bank vault. Assume, the lock has 1024 positions. There are 2 ways to open the lock. You can try all combinations, succeeding on the average after 512 tries. Or you receive the key (exactly 10 bits long) from some source, opening the lock with a single try. If you did it by trial and error, you can remember the 10 bits and succeed in the future after 1 try.
Now look at a particular example of macro evolution, where we do not have to guess at the numbers too much. The example I use is the evolution of australopithecus to homo sapiens. This is a back of the envelope calculation using rather round numbers.
The evolution took 4 million years, or roughly 400 000 generations. It is assumed, the average worldwide population at any time was around 100 000 - 1 million humans, neglecting the last 20 000 years. Let us assume 1 million. So there were a total of 400 billion humans reaching sexual maturity, or 400 billion tries in the survival of the fittest game.
We know of a few intermediate steps between australopithecus and homo sapiens: e.g. homo erectus, homo habilis, homo neanderthalensis. Let us be generous and assume 10 steps. Let us assume, after each step, the improved model was capable to surplant his successor, like homo sapiens did it with homo neanderthalensis.
Thus there were 40 billion tries in each step. This is the equivalent of a bank vault numeric lock with 40 billion positions. It represents a key of 35 bits.
Therefore 35 bits added (or changed) to the human chromosomes should be sufficient to improve the capability of the race to better hunt saber tooth tigers and to supplant the predecessor race worldwide.
Repeat this 10 times, and the homo sapiens genome differs from the australopithecus genome by only 350 bits.
This is difficult to believe. The human chromosomes represent some 3 billion bits of information. The difference between a human and a chimpanzee is only about 100 million bits. Many scientists wonder whether this is the full story, but let us assume, it is. Even assuming a lot of redundancy, the gap to 350 bits is so huge as to exclude any survival of the fittest explanation.
Remember, NT 2000 has some 40 million instructions, or maybe a total of 4 billion bits.
Thus the question is: Where do the missing 100 million bits come from? This of course we do not know. However, assume they arrive at a constant rate: 100 million bits in 4 million years results in 25 bits/year, or about 1 bit every 1 million seconds.
Regards, Wil Spruth, spruth@sps-partner.de
See Will Boatright's answer below.
I would not go so far as to say there is no evidence for macro evolution. I would say there is not enough to make the case proven, and many think there had to be interventions. Note that the interventions need not have been supernatural. And once evolution is Lamarkian instead of Mendelian things can go VERY quickly.
===
I'm going to move all this thread to its own page when I get a chance.
Jerry,
Leroy Ortiz writes:
"...human hemoglobin is a string of 574 amino acids of 20 varieties. There are 10E 654, different ways to combine these amino acids. That is kind of meaningless all by itself, but consider this: It is thought by evolutionary proponents that life began 2,500 million years ago, which is still a very long time. However, the number of seconds since life began is 10e 17. The number of seconds since the big bang 5000 million years ago is 10E 18. The number of stars in the universe is 10E 22. The number of atoms in the universe 10E 80. The improbability of hemoglobin occurring by random selection is 10E -654."
Short answer from a molecular biologist (me).
It can't have happened by random selection, but that's not what those of us in the molecular biology community think had to happen.
First, life arose quickly after the earth's crust cooled, but still a very long time ago. Cooling of the crust was 4e9 years ago; convincing microbial fossils in Australia are 3.5e9 years old. Schopf has given a good popular account of his work on this (_Cradle of Life: The Discovery of Earth's Earliest Fossils_, by J. William Schopf. Princeton Univ. Press, 1999).
We have some partial answers about how this could have happened naturally. Our understanding of the very first steps is still quite poor -- i.e., how you get from dead mud to *some* very primitive cell. But we do know the following things that make that cell somewhat easier to imagine than formerly.
You don't need to jump immediately from nothing to proteins plus RNA plus DNA. Having RNA alone is a viable basis for early life, because it turns out that RNA can be both hereditary and an enzyme. Specifically, it appears very probable that the core of the ribosome (the anvil on which modern proteins are forged) is actually, even in you and me now, an RNA enzyme and not a protein one. Other natural RNA enzymes are found in splicing of messenger RNA and in an E. coli enzyme called "RNAse P". More generally, it is reasonably easy to create RNA catalysts and binding sites in the laboratory for a great variety of purposes. For details, see: _The RNA World_, 2cd. ed., ed. Gesteland et al., Cold Spring Harbor Press, 1999.
Once you have RNA, you don't immediately need to construct hemoglobin; you probably need to build up a shell of proteins to gradually replace preexisting RNA catalysts and extend their functions. Even today, the total number of proteins required for minimal cellular function is less than or equal to 350 (Hutchison et al. [1999], Science vol. 286, pp. 2089-2090). If you have preexisting RNA catalysts you can build that slowly.
>From 350 proteins to the 14,000 of a fly or the perhaps 70,000 of a human is much easier to do than it sounds, because protein-encoding genes can duplicate and the duplicate copies can then diverge in function. It has been known for many years that the alpha and beta subunits of hemoglobin are similar (both in amino acid sequence, and in three-dimensional structure) to both one another and to the simpler protein myoglobin. Extensive phylogenies have been reconstructed for these proteins from many species on the basis of protein parsimony (constructing an evolutionary tree in which modern proteins are given branch lengths to one another than minimize mutations between them, following Occam's Razor). Trees constructed in this fashion closely resemble, in their organismal clustering, the phylogenies previously devised for organisms on the basis of classical taxonomy. More importantly, such trees show the subunits of hemoglobin diverging from one another after splitting off from myoglobin but well before the emergence of modern animals. A fine, though slightly dated, treatment of this remains Dickerson and Geis' _Hemoglobin: Structure, Function, Evolution, and Pathology_, by Dickerson and Geis.
While it *is* necessary for a protein to be constrained in its sequence, it is not true that (say) modern alpha-hemoglobin in a human being must have exactly one sequence to be functional at all. We know from comparisons of well-characterized protein families that very large divergences in amino acid sequence (up to 50% dissimilarity) are entirely consistent with conserved structure and function. At the same time, while mutation is random, selection is not: bad mutations are "destroyed" immediately (with the deaths of their carriers), neutral ones are statistically likely to be lost through drift alone, and rare good mutations may or may not end up being fixed in a future species. The "motion" of a protein through "sequence space" via evolution is therefore neither an infinitely narrow track nor a purely random one. Again, Dickerson's work is a good review of this applied to the protein Ortiz cites. A more recent and general treatment is Graur and Li's _Fundamentals of Molecular Evolution_, 2cd. ed., Sinauer Press, 1999.
Most proteins are to some degree replaceable by other proteins. Recently a team of computational biologists in Bethesda, MD did a study of some two-dozen microbial genomes to try finding what proteins were *absolutely* conserved in all of them, without a single species exception. The final number was 81 proteins:
http://www.ncbi.nlm.nih.gov/cgi-bin/COG/palog?phy=amtkyqvcebrhujgpolinx
Most of these are involved in protein translation, and some of them could well have been duplicates of one another very early on (e.g., two different GTPases involved in protein translation).
So the task of explaining very early life really involves explaining how a primitive RNA life arose and then how it acquired a set of 80-350 proteins -- but with the caveat that the proteins could be acquired incrementally, and that it was not at all necessary that their sequences be "perfect" or "exact". It is a hard problem, but it is not a problem that actually involves explaining the *random* occurrence of *one* configuration out of 1e654. It is also a problem that we have made real progress on: absolutely nothing that I have described was known, or even accessible to science, a mere century ago, and much of it was not known until a few decades ago at most.
--Erich Schwarz
Well, yes; but as we find out more, we also see more problems. From the outside it looks as if every new discovery posits at least three more stumbling blocks while clearing out one or two old one; the clearing out raises the level of faith that the new ones will also go away. Perhaps I read it wrong, but I have been watching this for about fifty years now.
Jerry,
Having some knowledge of the theory and with some experience modeling evolutionary systems, I can provide my perspective on the problem.
Question: How fast is evolution? Answer: Very, very fast. Suppose you have a wild-type gene and an alternative allele with 1% selective advantage in a specific environment. The alternative will evolve to fixation in a few hundred generations. For prokaryotes, this could be a few days; for humans, 2500-10000 years. And that isn't much of a selective advantage. The only thing that keeps this process from going to completion globally is geographic or very rapid temporal variability.
Question: What about Lamarckian evolution? Answer: Actually, cultural coevolution is Lamarckian. Darwinian evolution goes to fixation very quickly, even when there is no selectively advantageous allele, simply because the strongest selection gradient is associated with mutation rate--low mutation rate alleles waste less zygotes on monster mutations. Lamarckian evolution is dynamic. Mutation is not random, and the system can evolve chaotically. The evolutionary game underlying territoriality happens to be chaotic (expressed in bluffing strategies) when allowed to evolve culturally. So humans have been evolving chaotically for a long time. Given that mammals learn, first from their parents and later from their social group, I suspect some aspects of mammal behavior have been evolving 'culturally' for a long time. Most people are unaware of the sophistication of basic mammalian intelligence.
Question: What about macroevolution? Answer: There's evidence that life started up very rapidly--within 400 MYr of the end of the era of bombardment. There is fossil evidence in the genome and in basic cellular metabolism that suggest life emerged around a set of chemical hypercycles that may have been driven by elevated levels of carbon dioxide in the environment in a direction reverse to that seen now. That is, the metabolic cycle originally went in reverse and was associated with efficient chemical breakdown of more complex carbon compounds to carbon dioxide and water. Also, interestingly, the genetic code maps in a very natural way to the metabolic cycle, with amino acids being produced in similar ways corresponding to similar codons. Hence, life is probably not a random phenomenon, either in origin or in history. This universe may have properties that encourage the emergence of simple life in many common environments. I believe Harold Morowitz may have written something on this.
Whether intelligence is also inevitable is another issue. I suspect not, based on currently emerging theories about the Cambrian transition.
Harry Erwin, Ph.D., Computational Neuroscientist (Bat Behavior) and Adjunct Professor of Computer Science, George Mason University
I note that while everything about microevolution -- within species -- is pretty well consistent with what's known, when it gets to macroevolution there's a lot more handwaving, and speculation about what might have been (and in the case of hard core evolutionists, what must have been). What we don't have is much in the way of hard evidence. Some species paths are easy enough to see (although even there we don't have much in the way of intermediate forms). Some transitions from one species to another go through stages that hardly seem viable at all, much less viable in a competitive environment; yet we don't see how to get from one to the other without passing through those disadvantaged forms, nor have we any evidence those intermediates ever existed, or ever could have existed. This is a non-trivial problem, one that has driven people like Hoyle to postulate "evolution from space" and the like.
The interesting part is the number of people who insist that this knotty problem is settled one way or another, and who will use political mechanisms to have their particular view taught to the exclusion of others. Me, I'm quite happy to realize there are many thing I don't know and may never know. But that view isn't popular with either camp...
Hi Jerry,
Sorry to keep hammering on this, but, well, I do this stuff for a living and in some sense I'm obliged to make a case for it.
Wil Spruth writes:
"Repeat this 10 times, and the homo sapiens genome differs from the australopithecus genome by only 350 bits."
Actually, that's pretty close to being the scientific view: DNA sequence comparisons of human with *chimp* genes are easy to do now, and the results of my own random checking is that they are routinely 99% identical. Many of the differences are actually likely to be neutral polymorphisms fixed in populations by statistical drift, not phenotypically significant. The mutations required to make a human from a chimp are probably closer to 350 bits than 3500 bits.
Which specific mutations *are* needed should be known once we have the genome sequences of both humans and great apes, and can compare them. Very little work as yet has been done to pin this down, but two cases have been turned up: a luteinizing hormone in chimps has a higher affinity for its receptor than in humans (and thus we humans may have a "tardy" puberty, allowing greater time for parents to teach their offspring), and humans lack a sialic acid present in all other primates. There will be other differences, but they aren't going to be a vast number -- we already know from DNA that they can't be.
Science is scary because the more we know about our world, the more precarious and precious our existence seems. There is a very small gap between us and "brute" apes, and not really much more of a gap between us and lifeless matter. If there were interventions, fine -- but I don't think you need to postulate them to explain the world. I think the world may just be beautiful and terrible, on its own steam.
--Erich Schwarz
We have no argument about that last paragraph. And thanks for the summaries.
I find this discussion interesting precisely because there is not enough evidence to "settle" it and say that those who don't agree fall in the same category as the Flat Earth Society believers (although I gather most members of that outfit don't really believe...) Yet, although smart people can disagree on macroevolution, there are those on BOTH sides who would simply mandate that their view, and only their view, shall be taught and discussed in schools. THAT is what I find interesting. As if the fate of the world depends on choosing the right answer. Well, a day.
==== Here endeth the material copied from mail. New begins below. ===
The hemoglobin example Leroy Ortiz presents is an interesting one. Sure, the probability is very low, but every event of non-zero chance of occurring _happens_, as a study has shown. Also, there is the small matter of paralelism, but some other factors are more relevant here.
First, genetic combination has proven to be a very effective "search" method for problems with huge domain. Well, it just couldn't be otherwise, evidently. :-)
Second, life is built from components. Multi-celular life did not suddenly combine out of the primordial soup. It was composed from smaller, successful, parts. That's why it's multi-cellular, as a matter of fact. You divide hemoglobin in 58 parts of approximately 10 amino-acids, and then combine the successful ones of of these, and you suddenly have in your hands a manageable problem.
Third, and perhaps most important, why would one need to exaust 10e654 possibilities to come up with hemoglobin? Or even half of that on average? What's so special about hemoglobin? There are probably many other efficient ways of transporting O2 and CO2, some even with the same size. Hemoglobin was not _required_ for the task, it was just one of the combinations that _did_ happen, and got used. If you look around and see how many different ways there are of doing the micro and macro processes of life, you'll see that there is plenty abundance of them. And these are just the ones that survived...
-- Daniel C. Sobral (8-DCS) dcs@newsguy.com dcs@freebsd.org capo@zurichgnomes.bsdconspiracy.net
The size of the pizza is inversely proportional to the intensity of the hunger.
====
I should have finished reading the mails before sending mine... <sigh>
I just _have_ to make some comments on Wil Spruth's message, because there are some huge holes in the logic there.
First, the numeric lock. I'd guess Wil has no programming experience, as he seems to have little knowledge of pattern matching and search algorithms. The "genetic" search for a key would go like this: generate a number of random keys, then combine random elements of the two most closer to the unknown key, and replace the worst key with that one. 10 bits? I doubt it would take you more than 30 tries.
As for the "closer to the unknown key", which someone might object to, that is perfectly valid. In nature, there is usually shades of gray instead of right and wrong. Besides, the idea of a single "right" key is preposterous. We are humans because that's how the dice rolled. They could have rolled in a number of other ways, and some of them might even have been much superior. As any science fiction author. :-)
Next... 400 billion humans reaching sexual maturity is NOT the same as 400 billion tries, as anyone who have cats (or has visited some of the poorer places of the world) will readily tell you. Throughout the period mentioned, most humans never reached sexual maturity.
Next, there is the unbelievable proposition that the 35 bits that would be needed to enumerate 400 billion humans somehow translate in the number of "bits" changed in our genetic code! I garantee you that a SINGLE "try" yields an individual that is different by far more than 35 bits. :-)
Finally, there is this idea that evolution _HAD_ to yield us. It didn't. As a matter of fact, if we could see all the possibly beings that could have resulted, we would probably reach the conclusion that, indeed, evolution is just not good enough. It failed, and the result of that failure is called Homo sapiens. :-)
-- Daniel C. Sobral (8-DCS) dcs@newsguy.com dcs@freebsd.org capo@zurichgnomes.bsdconspiracy.net
The size of the pizza is inversely proportional to the intensity of the hunger.
=========
Jerry,
In regards to the letter sent by Mr. Oritz, I'd like to make a few minor corrections. Actually, adult hemoglobin is a tetromer, composed of two alpha (each 141 amino acids) and two beta chains (each 146 aa). Although his total number of amino acids is correct, it should be clear that it isn't simply one long protein. This actually gets to the math of the situation. Were this simply one long protein, the correct number of possible combinations would be 20^574 or about 10e747 by my calculations. Instead, we have two chains, each capable of having changes, making the number of possible combinations (20^141)x(20^146) or only about 10e373 different combinations. (the fact that hemoglobin is a tetromer doesn't change these numbers since only 2 distinct proteins are involved). Despite these quibbles, the main thrust of his argument remains quite valid.
Best regards, >Keith
Keith F. Woeltje MD, PhD
=====
I was interested in macroevolution about 15 years ago, and stumbled across a reference to a guy named (I think) Cairns-Smith. The article was called "The mineral orgins of life" or something like that. In combination with John Hooland's book about evolutionary theory, it at least makes a respectable showing for macroevolution.
Cairns-Smith said that the original life-form would be simple, and be a ubiquitous physical system. His simile was something like, the original life-forms would be closer to a stone knife than a powered lawnmower, i.e. just a naked gene in an environment that can copy it.
He also said that common clays form such a system. It seems that many clays consist of little crystalline plates of mineral salts. A plate has a pattern of charges that it presents to the environment. These encourage identical plates to form on the surface of the plate. If the environment has roughly (not exactly!) similar ratios of salts, the plate will grow long strings of identical plates. This is not speculative; reproductive clay has been observed. I vaguely remember a microphotograph in the article. I think that the tough slimy clays in caves are probably such clays.
His speculative thesis is that if many organics were available, such clays evolved organic adjuvants to help them grow faster. When the organic systems got complex enough, they developed seperate genomes, and clay-based genomes became irrelevant. Finally, clays using organic adjuvants became (mostly?) extinct as pure organic life ate clays' organic parts.
This could easily explain why God said that we were dust. It could be literally true.
About the speed of evolution: John Holland wrote a book about the mathematical theory of evolution. Evolution of dual-chromosome systems is about the only algorithm anywhere that tests and rejects huge numbers of uninstantiated combinations of data by testing relatively few instantiated, random combinations. It evolves to a logarithmic approximation of a perfect solution in linear time. Computer models validate the math. Only about a million individuals are needed to evolve a minimal logic function of 4 variables from a random valid LISP string.
Combined, these two ideas roughly invalidate the big numbers argument against macro-evolution by providing an existence proof of a plausible means of forming complex organic life.
But, there's some positive evidence.
1. Most organisms evolve efficiently, which is powerful (though tail-chasing) evidence that macro evolution produced most organisms: Most failures occur in the womb, spore, egg or seed, before the mother invests more than a tiny amount of material.
2. All organisms distribute most materials by diffusion. Conveyor-belt systems to carry substrates to enzymes are thousands of times faster, and lighter-weight (no solute). They would have a strong payoff. The only conveyor-style system in most cells is the genome and its copies. This proves that conveyors are possible, just not used for some reason... The macroevolutionary answer is that conveyors have complex interfaces that would evolve badly.
Best wishes Ray Van De Walker
=====
From: Stephen M. St. Onge saintonge@hotmail.com
Subject: More about Evolution
Dear Jerry:
The trouble with the evolution story is what gets left out.
Erich Schwarz says there are micro-fossils from 3.9 billion years ago. Maybe, though some of the previous alleged micro-fossils turned out to be mistakes. But assume he's right. How did they get there?
Origins of life: Read most descriptions of the Miller/Urey experiments, and you'd think that the first time anyone tried, life was durn near created in the test tube. Charles Thaxton et. al.’s The Mystery of life’s origins, Robert Shapiro's Origins: A Skeptic's guide to the Creation of Life on Earth , and John L. Casti's Paradigm's Lost discuss this at length. Turns out all current creation of life experiments involve three steps: 1) The "scientist" sets up conditions pre-selected to be favorable, but unlikely to have existed on pre-biotic earth (such as methane and ammonia rich atmosphere with no free oxygen and no UV); 2) An experiment gets run in which mostly junk is produced, as well as a small yield of chemicals that appear in living things (half of them, of course, the wrong stereo isomer); 3) The "scientist" claims a proof of principle, throws away what he's brewed up, goes to a chemical supply house, and buys highly pure mixture of just the chemicals he wants, in the proper stereo-isomers and energy states, mixes them in the right proportions, and performs another experiment. When real scientists come up with natural phenomena that duplicate steps one and three, I'll have some confidence in the results.
Probability cheating: Yes, indeed, you can substitute some amino acids in some proteins for other amino acids of the same type. Some portions of most proteins are structural, and almost anything can go into those slots. Other portions are active sites that catalyze reactions, and are much more restrictive in amino acids. And you may be able to run a cell with only a 350 proteins, and some preexisting RNA, and some a cell membrane to hold it together, and an energy system to make otherwise unfavorable reaction occur (polymerizing proteins and nucleic acids involves the release of water molecules, an energetically unfavorable reaction in a water based environment), and some other stuff -- provided they are the right substances, of the right stereo-isomers, produced in the proper amounts at the right time. What's the probability of the natural occurrence RNA catalysts that reproduce themselves, and gradually build up this library of proteins and energy catchers, and how did they ever get by without them? Ans.: none knows. Mr. Schwarz and other believers simply assert it's likely.
Simple life-forms: all known self-reproducing systems have lots of different, complex, highly specified molecules. The idea that a relatively few, relatively simple chemicals can self-reproduce and gradually grow more complex is interesting, but the people whom work on this always build mathematical models in which components with the properties desired exist by hypothesis, actual chemical nature unspecified. You can't test a hypothesis by assuming it's true.
Evolution of primitive micro-organisms: estimates I've seen say that only one in a thousand mutations is beneficial, and that may be handwaving -- I'm not sure that anyone has ever observed a beneficial mutation in nature. If the mutation rate goes too high, you get 'error catastrophe' -- unfavorable mutations kill off the organisms. Keep it low, it gets hard to get enough favorable mutations is geologic time, especially after error correction appears ( which eliminates one in a hundred thousand mutations before they can do anything) and very especially after sexually induced genetic drift arrives (which kills about 98-99% of all BENEFICIAL mutations). That works out to one or two mutations in ten billion surviving and being beneficial.
Levels of evolution: Evolution works fine for micro-evolution (germs acquire penicillin resistance) and similar species radiation (one species of finch on the Galapagos becomes a dozen species of finches). Once you start trying to go from there to new organs, illogic shows up. For instance, the origin of the eye is 'explained' by ASSUMING that a very primitive eye can evolve from a blind condition, then can evolve into a better eye, then a much better eye. The 'evidence' is the existence of various eyes of varying complexities in currently living creatures, plus the assertion that there was some such 'chain of eyes' in unspecified ancestors that haven't shown up in the fossil record. No evidence is ever offered of how many mutations would be required for each step, or the overall probability of the chain.
When you get to the problem of going from one life form to a completely different one (say, invertebrates to vertebrates), evidence collapses almost completely. Intermediates are assumed to have existed, and assumed to have had reproduction advantages that are hard to even imagine, but somehow they never show up in the fossil record. The Wistar symposium Mathematical Challenges to the neo-Darwinian Interpretation of Evolution had a charming paper by an evolutionist, manipulating his mathematical model with charming naiveté to get the results he wants, but nature is unlikely to be so accommodating. When some of the mathematicians pointed this out, the evolutionists got very angry and accused them of being theistic creationists, but didn't answer the arguments.
Evidence vs. logic: All theories of evolution worked out so far show what Darwin originally assumed: very gradual divergence from one form to several similar forms, gradually getting more diverse. The fossil evidence shows the exact opposite -- the Cambrian Explosion suddenly creates multiple phyla, the phyla soon have multiple species, ect.
Overall circular reasoning: some years back, journalist Tom Bethel pointed out that 'survival of the fittest,' as used by evolutionary theory, is a tautology. 'Fitness' is defined as 'more likely to survive,' and 'survival' used interchangeably with 'staying alive' and 'having lots of offspring in the next generation.' So Stephen Jay Gould wrote an essay in Ever Since Darwin to refute Bethel, saying that the real criterion of fitness was 'good design as an engineer would judge it.' Evolution will produce this, and weed out bad design. As an example of such proper reasoning, he cites another essay in that volume about the extinct Irish Elk -- which he says died out not because of bad design, but because it 'failed to adapt.' In his next book, he introduces the 'panda's thumb' principle, which explains that evolution will sometimes tend to produce cruddy design. So evolution creates good design, except when it doesn't. wow. This is typical of the literature I've seen.
Refusal to consider alternatives: Mr. Schwarz notes the similarities of the alpha and beta chains of hemoglobin, and assumes the similarity is evidence of evolution. But as John Campbell put it, 'Hydrogen isn't Cultural.' To carry Oxygen, release it as required, and come back to the lungs carrying Carbon Dioxide which gets released there means that only certain molecules will do out of a very large universe of possibles. So the similarities of the alpha and beta chains, and the similarities between various species may simply be because they are independent solutions to the same problem. By the way, I've seen some trenchant criticisms of the evolutionary trees constructed by those protein similarity comparisons.
The only really honest conclusion is that we don't know how life arose and diversified, and that believing any of the current "scientific" theories is as much an act of faith as the Genesis literalist. Take your choice -- mine is to refuse to believe without much better evidence.
Best, St. Onge
I'll defer most of this to the biologists in the crowd, but I will discuss levels of evolution.
We are beginning to understand how development is controlled, and the evidence seems to point towards a long period prior to the Cambrian of advanced metazoan evolution. Why so few fossils? Well, there is also some evidence that the early metazoans during the period 1000-600 MYr BP were almost microscopic and that the Earth was in a snowball state prior to 600 MYr BP. What happened in the Cambrian? Quite possibly open seas for the first time in aeons.
Developmental and genetic studies are indicating that most organs go way back. Eyes, for instance are not just analogous; they're homologous. Invertebrates and vertebrates share segmentation, many organs, and developmental pathways. If you evolve backwards to a microscopic ancestor, the basic structure is the same. This has come as a surprise.
The origins of classes and orders in the various phyla are becoming clearer, and intermediates are showing up in the fossil record. Arthropods now appear to share a series of anatomical features that suggest a trilobite relative or primitive crustacean as a common ancestor. The evolution of the vertebrates is becoming much better understood. So far, there have been no 'hopeful monsters'.
The rate of evolution hasn't been as slow as was suggested, either. Given the appearance of species flocks of fruit flies in Hawaii since 800 CE, and of cichlids in Lake Nabunago since 200 CE, we have evidence that evolution can proceed very rapidly under suitable conditions. Both cases were of adaptive radiations into vacant niches, suggesting that the error-correction machinery of the genome might be better described as error-suppression machinery. It's apparently selectively advantageous to maintain enough genetic variation to be able to occupy significant portions of the landscape.
Harry Erwin, Ph.D., Computational Neuroscientist (Bat Behavior) and Adjunct Professor of Computer Science, George Mason University
From: Stephen M. St. Onge saintonge@hotmail.com
Subject: Talking past each other
Dear Jerry:
The other problem with discussion evolution, aside from all the stuff that gets left out, is that people bring so many hidden assumptions to the discussion that you can't communicate. Recall Euclidean geometry, with five axioms, five postulates, and about fifty-five hidden assumptions that no one realized were there before the nineteenth century.
Mr. Sobral's letters illustrate this (I do NOT mean this as a personal attack; lets get that clear now). Some quotes, with comments:
'every event of non-zero chance of occurring happens, as a study has shown." Yeah, if you have infinite tries. Not if you have finite tries (roll a pair of dice once, I guarantee they won't turn up both snake eyes and seven). Basically, to have a decent chance of event x with probability 1/y occurring, you need y tries. How many tries are available in terrestrial time, or even over the entire history of the universe? "First, genetic combination has proven to be a very effective "search" method for problems with huge domain. Well, it just couldn't be otherwise, evidently. :-)" This assumes that evolution is true. I thought that was what we were discussing? And I have seen professional mathematician flatly disagree with that idea. See the Wistar symposium MATHEMATICAL CHALLENGES TO THE NEO-DARWINIAN INTERPRETATION OF EVOLUTION.
"Second, life is built from components. Multi-celular life did not suddenly combine out of the primordial soup." Periannan Senapathy's INDEPENDENT BIRTH OF ORGANISMS argues precisely that they did.
"It [life] was composed from smaller, successful, parts. ... You divide hemogoblin in 58 parts of approximately 10 amino-acids, and then combine the succesful ones of these," What does it _mean_ to call a sequence of amino acids "successful," what evidence is there that any of the component parts of primitive hemoglobin was "successful," and what combined them, how, and why? We seem to have banished purpose out the front door, and let it back in through the servants' entrance here.
"Third, and perhaps most important, ... There are probably many other efficient ways of transporting O2 and CO2, some even with the same size. Hemogoblin was not _required_ for the task, it was just one of the combinations that _did_ happen, and got used. If you look around and see how many different ways there are of doing the micro and macro processes of life, you'll see that there is plenty abundance of them. And these are just the ones that survived..." Evidence? All I see are two families of molecules that transport oxygen, the hemoglobin family, and the copper based one some marine organisms use. Again, we seem to be assuming the truth of the hypothesis to be tested.
'The 'genetic' search for a key would go like this: generate a number of random keys, then combine random elements of the two most closer to the unknown key, and replace the worst key with that one.' This assumes that you have a criterion for partial success. But what if the only answers you get are "log-in successful" or "access denied?" It's not at all clear what partial success at transporting oxygen would be.
"As for the 'closer to the unknown key', which someone might object to, that is perfectly valid. In nature, there is usually shades of gray instead of right and wrong. Besides, the idea of a single 'right' key is preposterous. We are humans because that's how the dice rolled. They could have rolled in a number of other ways, and some of them might even have been much superior. Ask any science fiction author. :-)" Again, a circular argument. There's not much "gray" between alive and dead, or between reproduced and didn't reproduce. Nor is there any EVIDENCE that the dice rolled, and could have come up with something else. Science FICTION postulates it.
All I can think of when I read these types of argument is the famous S. Harris cartoon, where the blackboard reads "Then, a miracle happens." We do indeed need to be more explicit in the intermediate steps.
Best, St. Onge
The question is the nature of that miracle, no?
I'm surprised that no one here has mentioned the finds in recent years of fossils in Liaoning Province, China, of dinosaurs which had feathers. See the article "Feathers for T. Rex?", National Geographic November 1999. One fossil, Archaeoraptor liaoningensis, appears (letter March 2000 NG by its original discoverer, Prof. Xu Xing) to be a composite of a bird body and a dinosaur tail, but there are other fossils from the area which are decidedly not composites and are agreed by all scientists who have evaluated them to indeed be genuinely from dinosaurs who had feathers. What I find curious is that no one has come straight out and said that the Archaeoraptor is a modern composite. I keep imagining Cretaceous taxidermist Strangeloves, forewarned by therapsid astronomers of the imminent asteroid strike, lobbying a Congress of pterosaurs for funding for a crash program of survival eugenics, proposing to create as engineered high-survival-prospect offspring their equivalent of the modern jackalope...
M. Praeger
Dr. Jane has a song about that... I gather there is considerable interest in these intermediates. Thanks.
I'll address some misunderstandings "St. Onge" had about my comments.
> 'every event of non-zero chance of occurring happens, as a study has > shown." Yeah, if you have infinite tries.
Surprisingly, no. Events with a very low probability seems to happen even in finite series much smaller than one would expect. There seems to be a whole new field studying very low probability events these days. One might be advised to research it before commenting on how such events are "impossible" in such and such conditions.
> Basically, to have a decent chance of event x with probability 1/y > occurring, you need y tries.
It will happen, on average, after y/2 tries. But, as a matter of fact, the above statement turns out to be common sense not backed by experimental results.
> "First, genetic combination has proven to be a very effective > "search" method for problems with huge domain. Well, it just > couldn't be otherwise, evidently. :-)" This assumes that > evolution is true.
Does it? Genetic algorithms are commonly used nowadays to solve "computationally impossible" problems (actually, problems that would take too long to solve using deterministic algorithms) in computer science.
Interestingly, there is a process with many similar properties to genetic algorithms in "nature". Annealing (a process used in metalurgy).
No, I'm not assuming evolution is true. I'm just pointing out that the mechanisms that are supposedly used in evolution have been succesfully applied elsewhere to deal with problems similar in nature.
> What does it _mean_ to call a sequence of amino acids "successful," > what evidence is there that any of the component parts of primitive > hemoglobin was "successful," and what combined them, how, and why? > We seem to have banished purpose out the front door, and let it > back in through the servants' entrance here.
We are talking about life, aren't we? Succesful is anything that gets reproduced.
It's not like our bodies decided they needed an oxygen carrier, and then tried to create something that would do. It's just that something, along the way, happened to "grab" hemogoblin, and survived because of it.
Think of the bacteria in our stomachs. At some point (assuming evolution is true, of course, but right now we are illustrating why would this happen), we didn't have them. They existed, but were not related to us in any way. Then, one ancestor got a bunch of them in his stomach, in a relation that helped both. So, they survived.
> This assumes that you have a criterion for partial success. But > what if the only answers you get are "log-in successful" or "access > denied?"
Then it's chance of happening are much lower. Or, rephrasing that, mechanisms for which success is graded are much more likely to exist.
> It's not at all clear what partial success at transporting > oxygen would be.
For a human being, low efficiency. But that's looking at just one side of the equation. The human being (well, whatever being) did not create the hemoglobin.
The partial success for hemoglobin "ancestors" is getting reproduced. It need not need to have anything to do with oxygen.
Alas, notice that "success" comes in many ways. CO2 is very successful, for instance. Why aren't you questioning the chance of we being able to produce CO2? Producing CO2 is a vital requirement for us. You might just wonder what was the chance of our body "developing" the mechanisms needed to produce CO2.
Of course, the answers are: 1. we didn't "develop" it, we just "adopted" it; 2. we don't _need_ to produce CO2, that's just how we happen to generate energy. There are other ways in use by other living beings.
-- Daniel C. Sobral (8-DCS) dcs@newsguy.com dcs@freebsd.org capo@zurichgnomes.bsdconspiracy.net
The size of the pizza is inversely proportional to the intensity of the hunger.
I don't know if it was intended as a joke but you managed to spell hemoglobin as hemogoblin throughout. I corrected it as grating.
What I see here is a restatement of the theory of macroevolution. If you assume macroevolution, some things must be true. In many cases this seems reasonable; but sometimes the evolution of A to C must, so far as we can see, pass through B which is a nonviable intermediate. Perhaps it was viable at another time under other conditions. We have no evidence that those conditions ever prevailed. "But they must have." "Why?" "Because that's what necessary for A to become C."
Now this isn't as circular as it seems to be. If we have many proofs of a theory, we are justified in using that theory to draw inferences concerning events we never observed and never could observe. I can infer that the sun rose in Addis Ababa this morning although I have not been there and have no easy means of getting a reliable observation. The question here is, is macro-evolution sufficiently confirmed --that is, have enough falsifiable hypotheses been tested without falsification -- that we can rely on the theory in cases where we have an entire absence of observations? That, I would suppose, is the entire question. So far as I can tell, the answer to that one is 'no'. Many have faith that the answer will one day be yes, and there's nothing terrible about that. We relied on Newtonian physics for a century until observations contradicting it piled up and it was clear that it needed corrections.
But suppose Newtonian physics had been taught as The Truth, and evidence contradicting it was suppressed on the grounds that, being in contradiction of the Truth, it could not possibly be real, and must have been made up? Or vice versa: every objection to Newtonian physics was blown up into a full fledged "refutation", so that anyone drawing inferences from Newton would be considered 'unscientific' and in fact an idiot?
As to probability theory, I used to know a lot about that. I am unaware of anything that demonstrates that improbable events are anything other than, well, improbable. The problem with probability models is that they rest on assumptions, some of which are unverifiable. By definition it is not improbable that a watch was made by a watchmaker, and if you find a watch the probability is high that a watchmaker was involved as opposed to the parts happening to wander together and being shaken by an earthquake fell precisely into place. There's no way to make that event probable. Even a little probable. But of course that's not an accurate statement of the model of macroevolution, which says that over time each part of the watch shaped itself, the parts clumped, each clump was more successful than unclumped, and slowly the watch developed.
Well, no. That didn't happen either, and we know that. What happened is that biological parts through small to large increases in the probability of survival of their offspring, eventually made human beings who then, through a more Lamarkian evolutionary process, made a watch. The watch didn't happen by chance at all. It was the WATCHMAKER who happened by chance, partial watchmakers being more survivable than partial watches. And as argued in The Blind Watchmaker, the watchmaker didn't exactly happen by chance, but through the evolutionary model.
Now evolution is appealing as a way of explaining much, and microevolution has proven to be a rich source of hypotheses about about our world; this discussion began with a reference to Greg Cochran's use of the theory of evolution to postulate germ causes for many disorders previously thought to be hereditary. Macroevolution neatens things up, and may turn out to be just as useful as microevolution.
But then there's that conflict with religion. Evolution was forbidden in the schools by law at least until 1950 in Tennessee (Scopes lost his case and paid his fine). Now teaching any alternate to evolution is to be forbidden, and any suggestion that there are problems with the theory are met with derision. The result is not helpful to either science or religion.
So far as I can see, macroevolution is a plausible but unproved theory with some rather implausible elements. It requires some assumptions that are pretty hard to swallow. Proponents of macroevolution naturally try to hide those by armwaving. Opponents naturally try to bring them to the fore and hide the more plausible elements.
When the evidence against Newtonian physics began to pile up, the result was a step outside the theory. Interestingly, Eddington's observational "proof" of relativity turns out to have been highly doctored: a fact which religious opponents of relativity pounced on when known (for some reason I don't fathom there are religious opponents of Einstein). But there have been plenty of other confirmations of the highly implausible implications of relativity.
One suspects that there is a missing piece of the macro-evolution puzzle. Sir Fred Hoyle postulates intelligent intervention through tailored protein molecules from space. Adrian Berry says Sir Fred is off his head. Creationists have their own views; I am insufficiently acquainted with creation science to know, but I am told there are various schools within that camp. My last acquaintance with creation science was a pamphlet that showed a number of implausible implications of macroevolution, but not a lot to take its place. This isn't a bad thing: counter-examples to a theory's predictions are useful.
And we are back where we started: to believe in macroevolution as taught at present requires an act of faith. To believe in interventionism also requires an act of faith. Neither seems to have put forth a set of falsifiable statements crucial to that position, although the macroevolutionists do seem to try.
And I am comfortable with not knowing.
(Hollywood, CA, April 8, 2000)
In the interest of fairness I add this:
Dear Jerry,
St. Onge wrote a great many things about the views of my colleagues, which if taken at face value make them sound either stupid or dishonest. Unfortunately, a number of those things aren't substantively true. May I reply to them?
I recognize that this reply is long, but, then, it's hard to make a serious scientific response fit on a bumper sticker.
I don't mean this as a criticism of your own views, which have struck me as moderate and open to argument. But if somebody doesn't speak up for my colleagues, I am very afraid that the critics of macroevolution reading your alt.mail pages will be left in a fool's paradise. That is no favor to anybody.
Thank you for your consideration.
Mr. St. Onge writes:
> Erich Schwarz says there are micro-fossils from 3.9 billion > years ago. Maybe, though some of the previous alleged > micro-fossils turned out to be mistakes.
Yes, they did, for reasons described in great detail by one of the references I gave (Schopf's _Cradle of Life_). The current criteria are quite stringent; they include independent verification of the fossils based solely on geographic instructions and structural anatomy through thick sections of intact, non-metamorphic rock.
The oldest fossils reside between two volcanic deposits of zircon crystals containing lattice-embedded U-Pb mixes that date to 3.645 and 3.655 billion years, respectively.
> Origins of life: Read most descriptions of the Miller/Urey > experiments, and you'd think that the first time anyone tried, > life was durn near created in the test tube.
That depends partly on how careful the scholarship of the writer was and the *date* of the writing. When Urey did his work, he used a mix of gases that was the closest to primordial which people knew at the time. By the 1980s it had become clear that Urey's mix was too reducing. However, mildly reducing mixes also give amino acids considered "biological." More importantly, external samples of early cosmic carbonaceous material, such as the Murchison meteorite, also contain mixes of amino acids overlapping with those seen in modern life.
It is quite clear from available experimental data that at least some of the monomers required for life can and do arise naturally. What is still a problem is how to provide a complete account of all early monomers and their organisation. Recent work on this is intense. Eschenmoser (Science [1999] 284, 2118-2124) has done experimental work to determine the specific fitness of DNA's actual components, as opposed to several other possibilities. Other work has been done to come up with syntheses for riboses with considerably greater specificity than the (originally postulated) formose reaction (Arrhenius et al. in _The RNA World_, 2cd. ed., Cold Spring Harbor Press). This is not nearly as backward a state of knowledge as St. Onge seems to be implying.
> When real scientists come up with natural phenomena that > duplicate steps one and three, I'll have some confidence in the > results.
The reason why working scientists cannot themselves act this way is that no serious problem in science gets solved all at once. Providing a complete account of the origin of life is one of the most adult and difficult challenges that biologists can tackle. Most don't -- it's hard, financially unrewarding, and not really sexy except to people more interested in the meaning of life than in cloning the hottest, most lucrative biomolecule.
Those who do attack the problem simply cannot provide the complete account at once. In a fantasy land, yes; in the real world of adult, difficult work, no.
So scientists attack the problem piecemeal. It took decades, for instance, merely to show that the peptide-elongating function at the core of the ribosome is probably an RNA catalyst rather than a protein catalyst. This is a huge advance strongly consistent with a naturalistic view of macroevolution, but outside critics complain because it's not the *whole* story. Which leaves me at something of a loss for words.
> Probability cheating: Yes, indeed, you can substitute some amino > acids in some proteins for other amino acids of the same type. Some > portions of most proteins are structural, and almost anything can go > into those slots. Other portions are active sites that catalyze > reactions, and are much more restrictive in amino acids.
Actually, you can totally substitute something like 85% of the residues in a protein chain and retain both three-dimensional structure and function. That is not "cheating", it is strongly established scientific fact, as has been known for decades (see Dickerson's _The Structure and Function of Proteins_ and _Hemoglobin_ for examples going back 20 to 30 years, or any of a number of modern textbooks for more recent fare). It is difficult to make any two proteins *more* than 85% dissimilar because, well, there's only 20 amino acids to play with. There are key residues in the active site of a protein, but they are very few in number -- so hemoglobin is not, by any means, an astronomically improbable molecule.
> And you may be able to run a cell with only a 350 proteins, and > some preexisting RNA, and some a cell membrane to hold it > together, and an energy system to make otherwise unfavorable > reaction occur (polymerizing proteins and nucleic acids involves > the release of water molecules, an energetically unfavorable > reaction in a water based environment), and some other stuff -- > provided they are the right substances, of the right > stereo-isomers, produced in the proper amounts at the right > time.
Not "may", but "very probably can." See: Hutchison et al. [1999], Science vol. 286, pp. 2165-2169.
At least one biochemical pathway (histidine synthesis) has enzymatic components that are visibly duplicates of one another. See: Fani et al. (1995), J. Mol. Evol. 41, 760-774. Another instance where we can trace the elaboration of proteins through intra- and extra-genic duplication is chlorophyll-dependent biosynthesis (Lazcano and Miller [1994], J. Mol. Evol. 39, 546-554).
> What's the probability of the natural occurrence RNA catalysts > that reproduce themselves, and gradually build up this library > of proteins and energy catchers, and how did they ever get by > without them? Ans.: none knows. Mr. Schwarz and other believers > simply assert it's likely.
No: we point out that experimental evidence strongly indicates that the ribosome itself *is* an RNA catalyst at its core. See: Scott, W.G. (1998), Curr. Opin. Struct. Biol. 8, 720-726 (for a recent review); or, for classic experimental work on this, Noller et al. (1992), Science 256, 1416-1419.
> Simple life-forms: all known self-reproducing systems have lots > of different, complex, highly specified molecules. The idea that > a relatively few, relatively simple chemicals can self-reproduce > and gradually grow more complex is interesting, but the people > whom work on this always build mathematical models in which > components with the properties desired exist by hypothesis, > actual chemical nature unspecified. You can't test a hypothesis > by assuming it's true.
You can *only* test a hypothesis if you *first* assume that it is true, then design experiments to test that assumption. Given the great complexity of the problem, that has only been done piecemeal, because it can literally be done no other way.
At this point we have quite a few pieces of evidence that we did not have until quite recently:
The unity of biochemistry and molecular biology, which actually allows genes from organisms as distant as yeast and humans to function biologically in one another. The first instance of such experimental cross-expression goes back 15 years (Kataoka et al. [1985], Cell 1985 Jan;40(1):19-26). There have been a great many instances since then, typically involving complementation of a mutation in nematodes or flies by a human transgene. This is consistent with the assertion, first made by Darwin, that all life has a common root, diverged through macroevolution. It was not at all obvious from other views of evolution.
The pervasive pattern of genetic duplication and divergence as a mechanism for creating elaborate genomes from simple ones. A full list of the cases where such duplication and divergence is visible from primary protein sequence would include a great deal of the proteins studied in molecular biology. Myoglobin versus the alpha and beta subunits of hemoglobin remains the earliest instance; elements of the histidine biosynthetic pathway (cited above) a more recent one. Again, this was not at *all* obvious before the experimental data came in. After those data became available, it was retrospectively obvious that something like this was really the only convincing way to get complex organisms from simple ones. Non-macroevolutionists contributed exactly zero to this finding.
The ability of living cells to function with quite simple protein complements (350 or less). Anti-macroevolutionists have repeatedly argued that cells are irreducibly complicated, and the numbers I've seen used in such arguments have typically been something like 2000 proteins. Again, data trump philosophy.
The very probable existence of a living fossil, ribozyme activity in the core function of all living ribosomes. Consistent with materialistic macroevolution, not predicted by anti-macro. folks, experimentally validated eight years ago.
The exceedingly small genomic differences between humans and the great apes. Experimentally validated, consistent with macroevolution, not particularly expected from anti-macro.
In other words: macroevolutionist scientists do the work, and their critics do the complaining. The critics have the easy job.
> Evolution of primitive micro-organisms: estimates I've seen say > that only one in a thousand mutations is beneficial, and that > may be handwaving -- I'm not sure that anyone has ever observed > a beneficial mutation in nature.
Yes, they have.
In humans, the best-documented instances are sickle-cell anemia (Dickerson, _Hemoglobin_) and cystic fibrosis (specifically, the deletion of phenylalaline-508 from the cystic fibrosis gene product: Morral et al. [1994], Nat. Genet. 7, 169-175; Gabriel et al. [1994], Science 266, 107-109). Both of these mutations are highly unfavorable to homozygotes yet found in heterozygous form in quantities far above that consistent with a purely deleterious form. It turns out that both of those mutations confer resistance to endemic diseases (malaria and cholera).
A less dramatic instance of favorable mutation is the persistence of intestinal lactase in adults of northern European origin (see Online Mendelian Inheritance in Man at http://www.ncbi.nlm.nih.gov/omim, OMIM number 223100). Few, if any, normal adult mammals (and not anything like a majority of humans!) have this capability. The most prevalent allele in Caucasians is geographically linked with a region of Europe in which swozzling down cow's milk was a useful (if rather weird) way to survive the winters. It is clear from mammalian biology and human genetics that adult milk drinking is a mutant trait -- but a useful one.
In microbes, evolution of an entirely new metabolic capability (to assimilate organophosphates) in only 40 years has been documented. This ability appears to have arisen from preexisting enzymes by duplication and mutational divergence (Scanlan and Reid [1995], Chemistry and Biology 2, 71-75).
Generally, the mutation rate need not be high; a low mutation rate coupled with significant positive selection is adequate to spread a new allele through an entire population. The mathematics of this was worked out by Haldane, Dobzhansky, and others by the 1940s.
> Keep [the mutation rate] low, it gets hard to get enough > favorable mutations is geologic time, especially after error > correction appears ( which eliminates one in a hundred thousand > mutations before they can do anything) and very especially after > sexually induced genetic drift arrives (which kills about 98-99% > of all BENEFICIAL mutations). That works out to one or two > mutations in ten billion surviving and being beneficial.
And yet humans do have three obvious cases of beneficial mutation that I have cited. Ergo, this argument is simply contrafactual.
> Levels of evolution: Evolution works fine for micro-evolution > (germs acquire penicillin resistance) and similar species > radiation (one species of finch on the Galapagos becomes a dozen > species of finches). Once you start trying to go from there to > new organs, illogic shows up. For instance, the origin of the > eye is 'explained' by ASSUMING that a very primitive eye can > evolve from a blind condition, then can evolve into a better > eye, then a much better eye. The 'evidence' is the existence of > various eyes of varying complexities in currently living > creatures, plus the assertion that there was some such 'chain of > eyes' in unspecified ancestors that haven't shown up in the > fossil record. No evidence is ever offered of how many mutations > would be required for each step, or the overall probability of > the chain.
The existence of an extremely wide range of functional eyes, from the very simple to the very complex, *is* evidence: it proves that the argument "the eye must be perfect to work at all" is empirically wrong. Which critics of macroevolution have not, to put it mildly, grasped readily. Half a loaf is *not* the same as no bread, in organ evolution or anywhere else.
Mathematically, the evidence has already been obtained: you don't need more than a few hundred thousand years given known rates of mutation (and consistently pessimistic assumptions). See Nillson and Pelger (1994), Proc. R. Soc. Lond. B Biol. Sci. 256, 53-58.
Genetically, we are still deciphering how eyes are built in humans and Drosophila, and any reconstruction of how eyes evolved will have to wait on that. But we already know that a gene required for eye formation in mammals can also generate eye formation in Drosophila: see Halder et al. (1995), Science 267, 1788-1792. These and other data are consistent with the hypothesis that vertebrate and invertebrate body plans descended from a common ancestor which already possessed, among other things, a genetic module for eye formation.
> When you get to the problem of going from one life form to a > completely different one (say, invertebrates to vertebrates), > evidence collapses almost completely.
Wrong. We have a good deal of evidence, it's just not yet *complete* evidence. Specifically, we have a lot of evidence for conserved genetic pathways of animal development -- which makes no sense whatsoever if all animal phyla evolved separately, but a good deal of sense if they arose from a common (perhaps flatworm-like) ancestor which already had eyes and other organ systems. For one recent (and careful) review of the evidence of this, see: Conway Morris, S. (2000), Cell 100, 1-11. For a good counterargument to Conway Morris' arguments against the molecular clock, see Feng et al. (1997), Proc. Natl. Acad. Sci. USA 94, 13028-13033. For one recent argument for the last common ancestor of animals having been acoelate flatworms, see Ruiz-Trillo (1999), Science 283, 1919-1923.
> Evidence vs. logic: All theories of evolution worked out so far show > what Darwin originally assumed: very gradual divergence from one > form to several similar forms, gradually getting more diverse.
A counterexample to this, punctuated equilibrium, has existed for decades (Gould and Eldredge [1993], Nature 366, 223-227). In general there is no good reason to believe that evolution must proceed at a rate which is uniform on *all* time scales, given that the selective pressures which organisms undergo are themselves unlikely to be utterly uniform.
> Overall circular reasoning: some years back, journalist Tom > Bethel pointed out that 'survival of the fittest,' as used by > evolutionary theory, is a tautology. 'Fitness' is defined as > 'more likely to survive,' and 'survival' used interchangeably > with 'staying alive' and 'having lots of offspring in the next > generation.'
No, it's not a tautology. For several reasons.
First, there existed simple progressionist views of organismal change in which all organisms were simply doomed to go on in one direction *regardless* of the environment. Darwinian evolution nontrivially differs from this view.
Second, there existed the famous Lamarckian view, in which the environment actively shaped the content of the genome. Darwin instead argued that the genome varied randomly, and that what the environment did was prune specific varieties of random change. Existing data from genetics and molecular biology very strongly favor the Darwin view. The difference is nontrivial.
Third, "survival of the fittest" is nontautological because "survival" does not occur in a philosophical void, but in a real world, in which events such as the colonization of the land by plants and animals have real consequences. In other words, survival is nontautological because *ecology* is nontautological.
> Stephen Jay Gould wrote an essay in Ever Since Darwin to refute > Bethel, saying that the real criterion of fitness was 'good > design as an engineer would judge it.'
Gould is a famous biologist, and an eloquent popularizer, but he is not the Pope of Evolution speaking ex cathedra. One needn't cite him, or even *know* about him, to see why somebody as intelligent as Darwin didn't consider natural selection tautological.
> Refusal to consider alternatives: Mr. Schwarz notes the > similarities of the alpha and beta chains of hemoglobin, and > assumes the similarity is evidence of evolution. But as John > Campbell put it, 'Hydrogen isn't Cultural.'
But genetic material *is* hereditary. One need not postulate culture. One need only be aware that DNA has an informational content as well as a structural background, and that the existing contents of genomes comprise an extremely small subset of the total possible set of random DNA sequences.
Therefore, speaking of common informational content is meaningful. Statistical assertions of extremely nonrandom similarity are feasible. In the case of the globins, and of a great many other protein families, similarities at the primary sequence level are vastly higher than levels consistent with random similarity. A solid statistical basis for such comparisons has been known for most of the last decade: see Altschul et al. [1994], Nat. Genet. 6, 119-129.
> To carry Oxygen, release it as required, and come back to the > lungs carrying Carbon Dioxide which gets released there means > that only certain molecules will do out of a very large universe > of possibles. So the similarities of the alpha and beta chains, > and the similarities between various species may simply be > because they are independent solutions to the same problem.
But we in fact know that not one but *two* independent solutions are possible; see Terwilliger (1998), J. Exp. Biol. 201, 1085-98. Both hemerythins and hemocyanins carry oxygen, and yet are dissimilar both to hemoglobin and to one another. More generally, Galperin et al. ([1998], Genome Res. 8, 779-790) have documented 34 clear cases where enzymatic activities have arisen twice from independent sources, with the criterion of independence being totally different three-dimensional protein structure.
> By the way, I've seen some trenchant criticisms of the > evolutionary trees constructed by those protein similarity > comparisons.
So have I, mainly because the methods have had to be worked out pretty much by intellectual bootstrapping: first you do it *some* way, then your peers flame you for not doing it a *better* way.
Nevertheless, substantive tools for rigorously computing serious phylogenetic trees do exist for protein and DNA sequences. The best reviews I've seen have been by Hillis et al. ([1993], Methods in Enzymology 224, 456-487; [1994] Science 264, 671-677) and Felsenstein ([1988], Annu. Rev. Genet. 22, 521-565). Again, this is a problem that has been seriously addressed by working biologists for some time.
> The only really honest conclusion is that we don't know how life > arose and diversified, and that believing any of the current > "scientific" theories is as much an act of faith as the Genesis > literalist.
No, it's not.
And before anybody else equates serious molecular evolution with the Bible, please take the time to state the condition of molecular evolution accurately. Thank you.
--Erich Schwarz
I fear I cannot accept your last statement entirely. Yes, certainly, if one takes "Genesis literalist" literally, as did Bishop Usher who used the genealogical tables to determine that Creation happened in 6006 BC on, I believe, an October day; but the entirely of macroevolution still requires leaps of faith, perhaps well-grounded, perhaps not. I recall in Miller's "Fiat Lux" the old theologian, upon hearing that a scientist was attempting top create life using only six elements, asked "And is he also doing so on horseback while playing two trombones?" For which he was disciplined by the Abbot with the cheers of his colleagues...
I had intended to close this, but I find this letter irresistable:
Subject: Macro evolution and genetic search algorithms
Jerry,
I am answering comments made by Daniel C. Sobral. He proposes genetic search algorithms and pattern matching as a solution how macroevolution could succeed despite the limited available time.
Assume a horde of australopithecus sitting in front of a numeric combination lock with 1 billion or 2E30 combinations. The survival value of opening the lock (e.g. because there is some food behind it) is 30 bit. One happy successful individual capable to open the lock has to have the 30 bit key embedded in some form in his genetic structure. The 30 bits are supposed to have been generated by random mutations.
This takes on the average 0.5 billion trials. No known approach of genetic search algorithms or pattern matching approaches is going to change this. If it would, I would use the technology to travel to Las Vegas making a fortune playing roulette. The mathematical foundation for this can be found in an article by J. L. Kelly: “A new interpretation of Information Rate“; Bell System Technical Journal, Vol. 35 (July 1956), pp. 917-926. It studies the case of a gambler placing bets at original odds. The article also outlines the concept of „value of information“ as opposed to random sequences of bit strings.
A related, very readable and easy to understand text has been published by Nobel prize winner Herbert A. Simon: „The Architecture of Complexity“; Proceedings of the American Philosophical Society, Vol. 106, No. 6 (December 1962), p. 467-482. It has been reprinted in Herbert Simons Book: "The Sciences of the Artificial"; The MIT Press, 1969, Mass. Inst. of Techn., pp. 85-117.
I love the debate and would appreciate to receive comments.
Regards, Wil Spruth, spruth@sps-partner.de
Fascinating. And of course this theme has been in SF stories. Ray Lafferty loved to play games with that. Forty million monkeys trying to do Shakespeare...
And I met Patricia Lanca in Seoul at an international symposium on marriage and the family: we were both speakers as was Mrs. Pournelle. We spent a delightful week at the conference (they had me talk about computers as well as marriage laws) investigating Seoul, a city I hadn't seen in 50 years. She recently discovered this web site and contributes this insightful piece:
Evolution and Consciousness.
As Michael Behe says in his preface to Darwin's Black Box "…understanding how something works is not the same as understanding how it came to be." Now, with consciousness we know neither.
1. How it works
Brain science can tell us a great deal about how various components of consciousness work through perception and the neural networks. Smells, colours, spacial dimensions, etc. as the brain interprets them, both in human beings and many other animals: neurology has provided a great deal of knowledge in these areas and there can be no doubt that the advances in brain-mapping will do a great deal for medicine.
However, that essential part of human consciousness, the self, the "knowing that we know", the "knowing that it is I who does the knowing" has not been scientifically explained. Indeed cognitive scientists seem to disregard or at least marginalize the problem. Raymond Tallis, whose main philosophical concern is human consciousness finds his own specialism (he is a practising neurologist) singularly deficient.. Those who do deal with the problem have a physicalist approach, believing that while they cannot explain it now, that it will eventually be explained in materialistic terms precisely how mind can be reduced to events in the brain. This problem of how consciousness works is, of course, also the big problem for Artificial Intelligence theorists. Nevertheless, whatever the pretensions of brain scientists or AI theorists, they all admit they do not know how consciousness works.
2. How it came to be About how human consciousness evolved, or how consciousness in animals came to be we know even less. Evolutionary psychologists, because they work within the framework of neo-Darwinism, see consciousness pragmatically: it emerged in some organisms because it has survival value. But even from the neo-Darwinian optic, does consciousness really have survival value? Evolution has produced a multitude of organisms with exquisitely tuned mechanisms which enable their survival. We humans also have them, and often consciousness interferes with disastrous results in their functioning. If we start thinking step by step of what we are doing as we ride a bike we are likely to fall off. It might well have been a more successful development if evolution had gone in the direction of "advanced mechanism" to "very advanced mechanism".
Some neo-Darwinists such as Humphreys see consciousness as ensuring social cohesiveness. However it has been pointed out (Weiskrantz) that the contrary is more likely to be the case:
"Man is the only creature that perversely gets into social difficulties of any really serious kind, and one reason for this is that he is conscious and thinks about all the social complications he might confront or deviously try to exploit for gain or for protection."
Tallis adds: "Consciousness-and consciousness of others' consciousness-is the necessary precondition of paranoia and other abnormal and maladaptive psychological states.".
Another big problem for an evolutionary explanation of consciousness (and indeed of any other organ) is that it is of the essence of neo-Darwinism that development was gradual. Even if the pace of gradualness were to be speeded up along the lines of Dawkins's contention that while mutation is random, natural selection is very non-random, this still leaves us with an incommensurate rate of gradualness, and here is the nub. How can an incipient development towards a doubtlessly useful organ necessarily be useful in its early stages? In other words, what ensures the survival value of the early steps towards something useful? Dawkins answered Hitchings' example of the eye (which functions whole or not at all) by claiming that even a single photosensitive spot would confer advantage on its owner and thus would begin the evolutionary process ending in eye-hood.
Tallis believes that there are huge difficulties in applying Dawkins's eye argument to consciousness (the mind) whose nature (which we do not really understand) is quite unlike that of physical organs. "Consciousness," he says, "is either there or not: you can't be a little bit conscious any more than you can be a teeny-weeny bit pregnant." How could an organism benefit by having a tiny bit of mind? From one point of view it would be a positive handicap, as we see with those humans now who are in just that position.
Tallis has many subtle arguments in this connection and the foregoing is necessarily schematic. But I believe that discussion about evolutionary theories of consciousness can shed considerable light and indicate some of the basic difficulties with the neo-Darwinist account of the origins and development of life. After all, the latter is a product of our consciousness.
>Assume a horde of australopithecus sitting in front of a numeric combination >lock with 1 billion or 2E30 combinations. The survival value of opening the >lock (e.g. because there is some food behind it) is 30 bit. One happy >successful individual capable to open the lock has to have the 30 bit key >embedded in some form in his genetic structure. The 30 bits are supposed to >have been generated by random mutations.
>This takes on the average 0.5 billion trials.
Arrrrggggghhh
No, the analogy is flawed.
Imagine the same group of australopithicus sitting in front of a cascade of safes, each one with some food, and another safe in it.
The first safe differs by only 2 bits from the second, the australopithicines who get the right two bits, get the food, and have kids. The other Aussy's starve. The successful ones kids have already SOLVED this safe, and may now start working on the NEXT two bits...
That's the presumption of the genetic search algorythm Without it, the search for the correct mutation doesn't take 1/2 billion trials, it takes 2^30 billion trials. The genetic search algorythm saves LOTS of time. Now, most "trials" are useless, and disappear, they cause the reultant sperm or eg simply to be non-functional as a cell. That's why there are a Bazillion sperms... Lots of simultanious trials, sorted quickly leaving only the mostly functional ones. Then we get the next layer of sorta ok when se select if the sygote will implant etc. LOTS of trials for each live birth. Then we get live birth selection, but MANY MANY MANY of those 1/2 billion trials he was talking about were rejected sperms....
Rick Boatright
And really, this is enough: there is little more to be said, and few will be educated further. There is a large literature on this subject, and it need not all be summarized here...
Lamarkian evolution: offspring can inherit characteristics acquired by their parents. Cut off the tails of mice for enough generations and you'll get short-tailed mice. Wear spectacles for enough generations and you'll be born knowing how to make them. Robots can in theory have Lamarkian evolution. Civilizations allow 'inheritance' of intellectual concepts and thus change the daylights out of "natural selection": if we know how to make insulin and what diabetes is, then juvenile onset diabetes isn't going to be bred out of the race.
