Relevant extracts from my posts of August 1999
Re: An irrelevant "abiogenesis" paper
| In other words, under even optimized laboratory conditions even remotely | relevant polymers won't form. | The peptide bonds are thermodynamically unstable, meaning the reversal | to starting amino acid is strongly exothermic. Take a wild guess what | any water, such as the co-product from the condensation reaction, would | do to the amide bond? | | It is not possible, with the best of intentions, to see any relevance of | this experiment to the abiogenesis discussion. I wrote in June on the same subject: A huge discrepancy exists in abiogenesis research between what is actually possible and what is generally reported to be possible. Imagine: the abiotic creation of peptide chains of up to six glycine residues (the simplest amino acid of proteins) under highly artificial conditions (a 100 mM glycine solution dissolved in pure water) is still in 1999 considered such a sensation that this result can be published in _Science_, one of the two most widely read scientific journals!!! Julie Thomas has written an excellent short post on this subject.
Re: The Death of Neo-Darwinism (was: Molecular Sequence Proof of Common Descent) For most gene loci only one or very few alleles exist. That's a fact. Simulations of genetic drift can in principle explain this fact under certain hypotheses. You and your fellow scientists simply ignore the fact that these hypotheses, under which genetic drift predicts correct allele distributions, do not at all agree with reality. The fact that substitution rates depend much stronger on time than on the number of generations is also strong evidence against neo-Darwinism. According to this theory it is expected that substitution rates should rather depend on the number of generations than on time. Assume that the probability for a selectively neutral random mutation in a certain protein is 10^6. If we assume a constant population of 10^9 with one single allele at the respective locus in the first generation, we get 10^3 alleles differing from the original form in the second generation. After a million generations a huge number of different selectively neutral allels have appeared and the frequency of the orginal allele is reduced to around 37 percent. That's simplest probability theory and cannot be denied in a reasonable way. In my (homozygous) example, in the second generation 1000 new alleles have appeared. Every of these alleles would have a theoretical probability of 10^-9 (inverse of the population size) to reach 'fixation' by drift after a huge amount of generations only if no more mutations occured. But in every new generation around 1000 alleles differing from the most frequent allele do appear. My example starts with a population having only a single allele. But if neo-Darwinism were right, it would be almost impossible to get a population with only one allele at a given locus because far more functionally equivalent (DNA) sequences must exist than any species can have individuals.
Re: The Death of Neo-Darwinism (was: Molecular Sequence Proof of Common Descent) My calculation assumes that every new generation reduces the number of the original allele by the factor 1 - 10^-6 After a million generations the allele is reduced to (1 - 10^-6) ^ 10^6 = 1/e = 37% You probably agree with me that in the second generation we have 1000 neutral variants. The probability that any of theses variants will reach fixation is each 10^-9. The probabilily that together they will edge out the original allele is 10^-6. For that to happen it would be necessary that random drift increases their number from 1000 to 1'000'000'000. What happens in the third generation with the variants of the second generation? Several variants may have disappeared, but others may have two or even more copies. On average 1000 alleles differing from the original allele give rise to 1000 differing alleles one generation later. The probability of less than 800 or more than 1250 is rather low. Because 1000 further variants appear by mutation, in the third generation there are on average 2000 variants, in the forth generation 3000 variants, and so on. After thousand generations variants have reached on average a proportion of 0.1%. Extreme bottleneck effects seem to be to the only reasonable explanation within neo-Darwinism for the low number of functionally equivalent alleles. On the one hand neo-Darwinism predicts that macro-evolutionary steps are more likely in small than in large populations. On the other hand however, if we look at the low probability of beneficial mutations, a rather large population is needed for useful adaptive mutations to occur with reasonable likelihood.
Re: The Death of Neo-Darwinism (was: Molecular Sequence Proof of Common Descent)
Re: The Death of Neo-Darwinism (was: Molecular Sequence Proof of Common Descent) | From paleontological evidence, chimps and humans diverged approx. | 5 million years ago. Given a generation time of ~15 years (probably | and underestimate), you only get about 300,000 generations. To the tremendous progress over about 300,000 generations corresponds a rather small change in the genome. We cannot explain the evolution of humans after their separation from chimps by the same means as the evolution of bacteria. As I have already stated in another post, it is not very likely that natural selection could have acted on more than five births per couple per generation, because many deaths are unrelated to Darwinian fitness. Neo-Darwinism states that random mutations are the primary cause of human evolution. So almost all deleterious mutations must be so harmful that concerned gametes do not lead to pregnancy (or result in early spontanous abortion), and the remaining (slightly) harmful mutations in new-borns must not be substantially more frequent than (slightly) beneficial mutations. Two beneficial point mutations per generation affect 4 bits and after 300'000 generations 150'000 bytes have been beneficially changed. Can this account for all the differences between chimps and child prodigies (e.g. chess, piano)? I don't think so. In addition to that, the two beneficial mutations per generation must spread over the whole population by selection whereas at the same time deleterious mutations must disappear by selection. Is this a realistic scenario? I don't think so. My statement that "all possible DNA sequences coding for a given amino acid sequence are equivalent" does not exclude the possibility that they may behave differently in special situations (e.g. in the presence of restriction enzymes). And I would argue that codon bias is no prediction of neo-Darwinism. (It can be explained by the relative abundances of the tRNA molecules assigned to each codon.) Nevertheless, if muations are random then the disappearance of certain codons must be explained by selection. This poses no problem in the case of bacteria evolution because of their short replication cycles. | I showed that >10^49 DNA sequences can code for the exact same cytochrome c | protein sequence in humans and chimps. If we further assume that 99.99 % of | these sequences are actually less fit, due to such factors as suboptimal | codon usage, there are still >10^45 genuinely functionally and phenotypically | equivalent DNA coding sequences that could have been used to specify this | cytochrome c protein. I don't think that your assumption is consistent with human evolution. There is already the problem of the missing 'functionally equivalent alleles' which must be attributed to selection. Now you assume that in addition to that even 99.99% of silent mutations are so deleterious that they disappear by selection. Remember, all biological innovations of human evolution are said to derive from random mutations. The proportion of beneficial to deleterious mutations is therefore a crucial factor. If "there are still >10^45 genuinely functionally and phenotypically equivalent DNA coding sequences" then one must not take it for granted that the common acestors of chimps and humans used only one single version of more than 10^40 possiblities. There is also no obvious reason within neo-Darwinism why most (all?) humans share one version and most (all?) chimps share another one. NEO-DARWINISM DOES REMAIN DEAD because it predicts either huge numbers of functionally equivalent alleles and coding sequences or so many constraints on non-deleterious mutations that evolution becomes impossible (at least in the case of species having long replication cycles).
Re: Bottlenecks and biochemical novelties (was: The Curtain's Falling)
A simple question: How probable are horizontal transfers of complex biochemical systems involving several genes under purely neo-Darwinian premises?
Re: Implications of Intelligent Design "The reductionist scientific world view as many religious world views is based on the premise that we humans are outside nature." Human intelligence is part of nature. It can be seen as a manifestation of the 'intelligence aspect' of nature. It would be presumptous not to admit that the intelligence of nature is much higher than purely human intelligence. The most complex systems we know have not been constructed by humans but by nature. (The assumption that natural laws have by chance exactly the form needed for random errors and selection to be able to give rise to complex ecosystems without any kind of intelligence is untenable for several reasons.) The evolution-creation-debate is rooted in many false dichotomies such as: Either human languages were designed or they evolved by purely materialistic means excluding any form of intelligence. Either bee languages were designed or they evolved only by genetic trial and error. Either human tools such as hammer and sickle were designed or they evolved indirectly by random mutations in humans. Either animal housing such as bird's nests or termites' mounds were designed or they evolved indirectly by selection of random mutations leading to animal behaviour resulting in the housing. A living cell can be compared with a huge spacespip. Maybe humans will construct in the future such autotroph spaceships which will replicate in our galaxy by building up copies of themselves. There may be lots of different dangers for such spaceships in the same way there are lots of dangers for bacteria. Situations can be imagined where the best strategy for a spaceship could be something analogous to bacterial spore development.
Re: The Death of Neo-Darwinism (was: Molecular Sequence Proof of Common Descent) | Assuming that each mutation generates a new allele (the infinite allele | assumption), the expected heterozygosity is given by: | | h = 4Neu/(1+4Neu) This formula predicts heterozygosity values of almost 100% for the many species whose population size lies in the order of 10^10 or more. Have e.g. mice such a high heterozygosity? I don't think so. And is it true that most insects have heterozygosity rates of almost 100%? | Humans have a polymorphism of about 0.28 (that is, 28 % of the loci | examined have more than one allele) But 72% of the loci have only one allele despite the fact that an incredibly high number of functionally equivalent alleles are possible.
Re: anthropic principle and probablility; OR, Dembski undermined
| Scientific creationism: a religious dogma combining massive | ignorance with incredible arrogance. | Creationist: (1) One who follows creationism. (2) A moron. (3) A | person incapable of doing math. (4) A liar. (5) A very gullible | true believer. What would you say if I wrote the following: Purely materialist evolution: a pseudo-religious dogma combining massive ignorance with incredible arrogance. Reductionist evolutionist: (1) One who follows neo-Darwinism. (2) A moron. (3) A person incapable of doing math, especially probability calculations. (4) A liar. (5) A very gullible true believer. And take into accout, I would be at least as entitled to write my version as you are entitled to write your version.
Re: Order from Disorder: ID Theory Disconfirmed
| And yet clouds form. Is this then evidence of Intelligent Design? Not necessarily evidence of intelligent design but at least evidence of intelligent behaviour (of water molecules) and hence evidence of panpsychism! Maybe pannaturalism or pantheism would be better notions than panpsychism. The notion 'panpsychism' as I use it makes sense only insofar as materialism is taken for granted. According to Baruch Spinoza (1632-1677), maybe the first consistently naturalistic scientist, the psychic or vital aspect (thinking, consciousness, intelligence) is not the only aspect of Nature (or of God), there is also the material aspect (spacial extension): Pannaturalism (pantheism) = panmaterialism + panpsychism.
Re: The Death of Neo-Darwinism (was: Molecular Sequence Proof of Common Descent) It is a fact that lots of animal (and plant) species consist of much more than 10^10 individuals. If these species have heterozygosity rates of not almost 100% then at least some of the premises leading to the corresponding formulas must be wrong. I do not believe in a 25-fold population increase in the last 1000 years. A 25-fold increase in the number of persons living in not totally illiterate environments may have occured. One must not confuse the increase in the registered populations with real population increase. Is there any evidence of a continous population increase e.g. in black Africa before the introduction of modern health care? Is the human species the only species for which such an incredibly high population increase over the last few thousands years is postulated? How many chimps, gorillas and orang-utans can live within one square kilometer in regions best suited to them? To assume that every primate needs at least e.g. one square kilometer is certainly absurd. One square kilometer consists of 1'000'000 square meters and can contain more than 10'000 huge trees. Why do you not accept the only logically correct conclusion from this thread, namely: neo-Darwinism is inconsistent with the empirical facts concerning genetic polymorphism. You are certainly intelligent enough to understand that drift does not work and that the assumption of regular bottlenecks of only a few individuals per species is untenable. There seems to be a big advantage of chess over science: the possibility of checkmate. For scientists unlike chess players it is possible to simply ignore checkmate!
Re: Info Theory destroys Neo-Darwinism
I'm a programmer, too, so I would like to give some good advice to the programmers using "exactly the same Darwinian random creation / selection process". It is (almost) always possible to increase the effectiveness of such a process by replacing the "random creation" part by a "systematic creation" part. The reason is simple. If a mutation has turned out to be deleterious it makes no sense to try it out several times. If the replacement of an amino acid 1 by an amino acid 2 has extremely negative effects it makes no sense to try out also 3 if 3 is very similar to 2. Furthermore, the "systematic creation / selection" process has been proven very effective for many different problems, e.g. chess. To create a chess program without regular selection of the most interesting positions before calculating further moves would be extremely silly because the number of possible positions grows exponentially with the number of moves (...). Neo-Darwinists believe on the one hand that computer simulations prove neo-Darwinian evolution, and on the other hand they must admit that such a basic prerequisite of evolution as the folding of a simple protein is much too complex to be treated computationally. If it were possible to do the necessary calculations, then it became obvious that it is just an unfounded belief to assume that quantum mechanics (or similar theories) somehow can explain life.
Re: What does "supernatural" mean?
If one accepts the basic dogmas of modern reductionist science (i.e. dead matter governed by reductionist causal laws is enough to explain nature) then naturalism becomes almost a synomym of materialism or (ontological) reductionism. All what defies an explanation by reductionist causal laws, e.g. telepathy (if it exists), can then be called supernatural. On the other hand, if one does not restrict the concept 'natural' to the currently prevailing views of 'natural explanations' then it becomes at least very difficult to distinguish 'supernatural events' from simply unexplained events. (Whether such events are repeatable or not is not the decisive point.) For most monotheists, God is by definition 'supernatural'. But even for them it is difficult (in principle) to distinguish supernatural effects caused by God from simply unexplained or fabricated events. I think that the reductionist premises of current science can be very strong support to believing in a supernatural God, because things or events (e.g. abiogenesis, strange coincidences) which defy the current scientific world view seem to suggest the existence of something which is not accessible to the scientitfic method.
Re: evolution of bat echolocation (Was: Lucy, Tampered evidence)
Based on the genes-fully-determine-phenotype premise, (progressive) saltation implies EITHER the sudden emergence of much new genetic information OR switching on preexistent information. Both consequences seem very unlikely to me. Nevertheless, the "increases in the _sensitivity_ of preexisting features" can even be better explained by a (psycho-)Lamarckian than by a Darwinian mechanism. Simple experiments could easily discriminate between the two.
Re: Reproduction destroys Neo-Darwinism
Do you know how many chemical uphill reactions must occur for a simple bacterium to replicate? Certainly far more than 10^10. Think about it: every structure of the cell must be replicated. Innumerable chemical bonds are involved! The assumption that the only errors worth a mention are correctly bonded DNA changes and that a substantial proportion of these changes has even positive effects is totally unjustified on the basis of random thermal movements. It's an empirical fact that living things preserve characteristics across generations. But how do you explain the emergence of reproduction and inheritance? The only possibility you have: physical and chemical laws and chance. In general, a principle is called finalistic if it is defined not by some kind of mechanism but by a result. And reproduction is without doubt defined by a result: the copy (with minor changes) of the original. It is perfectly natural that you must deny the fact that reproduction is a finalistic principle, because this fact refutes not only neo-Darwinism but modern mainstream biology as well (as far as this principle is used without being itself reduced to causal principles). So in order to explain a continuous evolution of life, reproduction and mutation (i.e. difference of the copy from the original) must be connected in a very special (and therefore apriori in a very improbable) way that entails inheritance of the mutation. Mutation without reproduction and inheritance is a very simple principle which can be compared with random errors in a written text or in a digitally transmitted message, but it is not very helpful for explaining evolution. Mutation with reproduction and inheritance is an extremely complex principle: it entails the whole ontogenesis until fertile age, and therefore even depends on protein folding. Neo-Darwinism as a simple theory needs this ambiguity of 'mutation'. Therefore it is not exaggerated to conclude that neo-Darwinism is founded on a well-known philosophical fallacy. Instead of explaining that a highly complex organism is able to create a very similar copy, it is only postulated that an organism has a certain number of descendents.
Re: Reproduction destroys Neo-Darwinism
My argument does not depend on abiogensis, but on the undeniable fact that without finalistic principles (error correction is a finalistic principle), every replication cycle would introduce lots of errors (remember: in the order of 10^10 apriorily highly improbable chemical bonds must be made for every replication), and these errors would accumulate so that after not too many cycles reproduction would no longer be possible. Furthermore, based only on causal reductionist laws of physics and chemistry, not even one single replication cycle would be possible. It can be shown that the motions of enzymes violate the theory of Brownian motion and therefore the second law. Bacteria florish below hundreds of meters of sediments on the seabed or in other areas where thermal energy is the only durable energy supply. This is very strong evidence that bacteria can replicate without decreasing usable energy. Maybe they even increase usable energy (stored in the chemical bonds). I really do appreciate much of what you write, e.g.: "Proteins are /more/ complex than DNA and RNA. DNA and RNA are both such artificial molecules that it is virtually impossible to imagine them forming the first repicating objects on the planet."
Re: Reproduction destroys Neo-Darwinism
A bird constructing a nest knows how such a nest must look like. Therefore the nest can even be finished if the construction process is obstructed in a way completely unknown to the bird (or its ancestors). That's what I call finalism. Error correction by purely causal principles needs redundancy. Finalistic error correction needs no (material) redundancy. Whether finalistic principles are involved in biochemistry can therefore be decided by experiments. But maybe there is already enough data concerning e.g. post- transcriptional and post-translational editing to decide this question. How probable is the emergence of such an error correction by pure chance? The appearance of a DNA error must coincide with the appearance of other mutations leading to the correction of the error by some form of editing or even by ribosomes ignoring the error. Think about the monks of the past who copied texts by writing them again and again. They were certainly able to recognize and correct most errors of original texts. If a cook reads in a recipe that 3 kg salt must be used and 3 gram seem to be a reasonable quantity, then the cook will probably use 3 gram and not 3 kg. Maybe he will not even notice that there is an error. That atoms prefer more energetically favourable sites is self- evident. But error correction in living cells often leads to less energetically favourable states! Have you an idea of how snow crystals can emerge by purely causal laws? There are many cases where simple causal laws (gravity) result in highly ordered systems (Kepler's laws). But in such cases, simple computer simulations can reproduce the results. Do you know a simple computer simulation (without hidden finalistic principles) showing the formation of snow crystals? If we could follow directly the movements of enzymes in cells (in slow motion), it would become obvious how absurd it is to assume that enzymes are just randomly bouncing around as a result of molecular thermal motions.
Re: Reproduction destroys Neo-Darwinism
My arguments are founded on panpsychism and Kepler was a panpsychist! Neo-Darwinism is based on the philosophy of Descartes, with the main exception that Descartes assumed the existence of God and of human souls (animals however, were considered as machines without consciousness). "Staples" do not move themselves but are moved around. In the same way, there are lots of molecules inside living cells which do not move themselves (apart from constrained motions such as the ones resulting from random thermal collisions or from flows inside the cell) but are moved around by enzymes. If we observe under the microscope a bacterium-sized particle which does not obey the laws of Brownian motion, we simply conclude that it is living. You assume that dead enzymes based on not-goal-directed movements can lead to living systems (bacteria) and goal- directed motions, whereas I assume in the way of Kepler that goal-directed motions of the parts lead to goal-directed motions of the whole. Life without motion is impossible. But why should thermal energy not qualify as an energy source? The second law was derived from experiments with thermal machines involving huge numbers of atoms and molecules and not from experiments with life or single biological molecules. Philosophy and science have always been full of unjustified generalizations. Some hundred meters of sediments and very high pressures should be a rather good insulator against chemical energy from within the earth's crust. For some hundred meters of sediments to accumulate, certainly many thousand years are needed. How can entropy-increasing bacteria live so long on the sediments? The whole universe is perpetual motion machine, isn't it? A simple wall allowing a gas to go through in only one direction would be enough for a perpetual motion machine (of the second kind).
Re: Reproduction destroys Neo-Darwinism
To assume that enzymes are not able to perform goal-directed movements is no better than to assume that workers in a factory are randomly walking around until they find by chance some work to do. In any case, it would be rather simple to definitively decide this question. But unfortunately scientists are interested in truth only if the truth is no threat to their dogmas. | The thing is no one ASSUMES that one or two point mutations can produce | new properties, it has been _experimentally_ _determined_ that even one | mutation can produce a new property. Are you not able or not willing to understand? I do not deny empirical facts, I only challenge an absurdly materialistic interpretation of such facts. It is not astonishing that a single point mutation can switch on a different behaviour if the information comes from elsewhere. Also in computer programs point mutations (switches, parameters) can lead to a very different behaviour. However, somewhere in the program there must be the information (the computer code) corresponding to the new behaviour. According to the psychon theory, the existence of two enzymes differing in only one amino acid and with different behaviour leads to the following conclusions: o Essential parts of the information corresponding to the protein behaviour are not stored in the amino acid sequence but in (empirically relevant) psychons. o Both enzyme types are animated by a different psychon species which very probably evolved from one common ancestor species. Even the same amino acid sequence can be animated by different psychon species with very different behaviour. Maybe in some cases of multifunctional enzymes, there are in fact different psychon species for different tasks. For resistance to a new antibiotic or pesticide to emerge more is needed than some lucky mutations. Enzymes and cells must at first learn to defend themselves. That leads to the prediction that mutations leading to antibiotic resistance in bacteria appear more likely after an antibiotic has been used frequently for a long time. If one starts with a single antibiotic sensitive bacterium one gets regularly antibiotic restistant bacteria after some generations. I would say that normal genetic variability corresponding to the whole bacterium species can reemerge from one single bacterium. But if there are no or almost no bacteria resistant to a new antibiotic then also no mutations can occur leading to antibiotic resistance. After long and intensive application of the new antibiotic, the same experiment gives a different result. Resistant bacteria do emerge from sensitive individuals after some generations. Nowadays, mutations transforming sensitive strains into resistant strains appear with such a high probability that these antibiotics would not have been considered effective enough, if such mutations had had the same frequency when the antibiotics were introduced. THAT'S A FURTHER REFUTATION OF PURE MATERIALISM. THE SAME EXPERIMENT GIVES DIFFERENT RESULTS, BECAUSE A NEW BEHAVIOUR (ANTIBIOTIC-RESISTANCE) HAS EVOLVED.
Re: Who is Phillip E. Johnson
Future will show who really are the specialists in rhetoric and manipulation. Johnson is able to recognize that the emergence of life without any form of creative intelligence is logical nonsense. It is perfectly natural in the case of a convinced Christian that God becomes the fallback position for explaining this obvious creative intelligence. I myself am no Christian and find the idea of an entity outside nature not very appealing (for philosophical reasons). So I have worked out a more naturalistic explanation of the obvious creative intelligence of nature which is based on evolving units (psychons) and finalistic laws of nature.
Re: Reproduction destroys Neo-Darwinism
I do not believe that from an infinite number of disassembled bicycles an infinte number of assembled bicycles may emerge by pure chance. Think about the probability of only one nut and one bolt joining together in the right way. And compare the complexity of life with the complexity of a bicycle. Think about the probabilty of such a genetic takeover from crystal-genomes. You conclude from the impossibilty of life- started-with-RNA to the possiblity of life-started-with-clays. There is another solution: "During evolution, psychon animated molecules have been joining together in always bigger units. Animated molecules such as amino acids and nucleotides began sometime to form chains. By specialization psychons emerged which dominated such chains. Proteins are conceivable which replicate by adding corresponding amino acids to one chain end, until an identical protein can split off. Reproduction by base pairing of two complementary strands is even more efficient. The invention of translation, a complex symbiosis of various ribosomal psychons, was certainly one of the most essential steps during the evolution of life." Some quotes from your posts of this thread: "Clays may synthesize all manner of thermodynamically-unlikely molecules in their struggle for life." (23-Aug-99) "If organic life can form spontaneously (...), it can /certainly/ form more easily in an environment where clay organisms compete with one another, and use organic molecules as their weapons." (24-Aug-99) "Really, once life has got off the ground, that is the /main/ question of our ultimate origins solved - the rest can be happily attributed to the action of natural selection." (23-Aug-99) Here you sound rather like a vitalist and not like a reductionist: a new force (you call natural selection) appears which makes further progress much easier. Without the teleological properties you ascribe to "natural selection" the only effective forces are physical and chemical forces. Selection is only a secondary effect. And clay complexes will not develop a tendency to outcompete their rivals by constructing organic molecules as their weapons. You also have written in this thread: "To me it appears that the first living organisms are likely to be 'naked genomes'". The concept of 'naked genomes' seems rather problematic to me. Genomes represent information and information is no end in itself. Information needs some form of interpretation. Why should "naked crystal genomes" which have outcompeted their rivals represent information transcending its original purpose (which is: being able to efficiently reproduce). The same question arises also in the case of an RNA-world. Why should RNA-molecules which replicate better in a given environment represent information concerning proteins?
Re: Can life evolve?
| Amino acids don't "evolve" into proteins, any more than hydrogen | and oxygen "evolve" into water. It's a chemical reaction. And what you write is nothing more than the (only apparently not totally unreasonable) result of chemical reactions.
For the sake of future generations
| If you really are interested in maintaining the genetic make up of | future populations then you should advocate scrapping all technology and | having us return to hunter gatherer days. There is an even better solution: a nuclear world war. Only the fittest will survive and lots of radioactivity induced mutations will be an invaluable source for further evolutionary progress of our species. * Materialistic evolution theories are essentially * SUPER-CREATION or HYPER-DESIGN theories: the universe * was hyper-designed and super-created in such a complex * way that blind downhill processes can design and * create whole ecosystems.
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