Relevant extracts from my posts of May 1999

Re: Phillip Johnson interview (Communiqué, Spring 1999)

> People attach all sorts of weird baggage to the word "evolution" too, even though all it means is a change in allele frequencies.

Until know did not know that Charles Darwin explained the existence of life by "a change in allele frequencies".

That your definition is logical nonsense one can see more easily if one transfers it to 'technological progress'. An analogue definition of this progress would be:

All it means is a change in data of computers.

Re: Common Descent is a Fact?

If you are right, such "common ancestors" had to have the following properties:

  1. They had to be able to build up copies of themselves more efficiently and quickly than they disintegrated or were distroyed by the environment.
  2. They had to be based on principles which allowed a further improvement by random errors in constructing the copies.
  3. If evolution is defined by "changes in allele frequencies", then they had to include at least a predecessor of the genetic code.
  4. If a continuous transition from a two-nucleotide-based to a three-nucleotide-based code is impossible (too improbable), then the common ancestor(s) had to include a three-nucleotide-based genetic code.

There are the two possibilities:

  1. All life on Earth derives from one common ancestor.
  2. Life derives from a group of common ancestors.

The probability that one single self-replicating system using a complex genetic code emerged by chance from non- replicating sub-systems is virtually zero.

The probability that a group of common ancestors using similar mechanisms (genetic code) emerged by chance from non-replicating sub-systems is even lower.

So we must conclude that essential parts of the common ancestor(s) must have been self-replicating systems themselves, i.e. they must have been able to construct somehow copies of themselves.

If evolution means a continuous transition from simple atoms to modern species, than common descent is rather a piece of Darwinism than of evolution itself.

Re: Does life violate second law of thermodynamics?

That's really embarrassing for me: I post to "alk.orgins" and accuse "talk.orgins" of censorship!

This episode has shown me how difficult it is not to draw a conclusion in agreement with one's own prejudices if there are some conincidences suggesting the conclusion. Apart from the two answers to you, I never have had posting problems.

If the HIV-AIDS-thesis is an error, as I assume, then even more and stronger coincidences must have led to its emergence and general acceptance.

Re: Phillip Johnson interview (Communiqué, Spring 1999)

In that case, Darwin is erroneously considered to have resolved the problem of the origin of species. Even for explaining frequency distributions of simple traits such as the colour of peppered moths by "a change in allele frequencies", additional premises are needed. But in the case of complex organs such as the eye or capacities such as the human ability of language, all what is relevant must be derived from such additional premises.

To reduce the very very obvious increase in complexity and consciousness during evolution of life to "a change in allele frequencies" is even worse than to reduce the development of literature to a change in word frequencies.

... do you know the difference between real science and a belief system? The supporters of a belief system will deny the obvious if necessary.

Incredible! Are you really convinced that there is no analogy between technological progress and evolution of life?

A few billion years ago only relatively simple molecules existed on earth. And now? Look around! Several thousands years ago only very simple tools existed. And now? Look around!

Re: Common Descent is a Fact?

> I think the idea of a common ancestor, of a naked replicator, so to speak, is wrong. There is no such thing now and likely there never was such a thing. There are now, and likely were then, sets of systems and chemicals that, in toto, have the property of replicating themselves with some reasonable degree of fidelity.

Do you admit here that the distinction between abiogenesis and evolution, introduced in order to remove some serious problems from Darwinism, is arbitrary? According to the prevailing view, abiogenesis ended and evolution started with the first common ancestor(s).

The probability that "sets of systems and chemicals" able to build up copies of themselves in toto, appeared by chance from non-replicating systems and chemicals is also extremely low.

Re: Does life violate second law of thermodynamics?

The development of macroscopic life depends on the capacity of innumerable enzymes to efficiently move to different sites in living cells.

A typical diameter of a living cell is around 10'000 nanometers and there are around 1'000'000'000'000 cubes of a side length of 1 nanometer in it.

If the recognition of the correct DNA position depends on direct contact of an active site of the transcription factor with the DNA, then this active site must come very near to the corresponding DNA position, maybe even nearer than 1 nanometer. A nanometer is three times the length of a water molecule, and the major groove of DNA is about 2 nanometers large.

The fact that enzymes move very efficiently in living cells clearly refutes the second law, and your statement "every macroscopic observation regarding the 2nd law of thermo is derivable from statistical mechanics" is simply wrong.

Re: Theory of Natural Selection VS Reality

There are 20^393 = 10^511 different 393-aa-long sequences. So even if there were as many as 10^300 functional p53 proteins, the ratio of functional p53 proteins to all possible sequences would still be as low as 1 to 10^211.

Re: Common Descent is a Fact?

I don't believe that there are RNA ribozymes capable of reproducing themselves from spare nucleotides without the help of other enzymes.

The last time you made a similar claim (about the Lee peptide) it turned out that what is called a self-replicating protein is nothing more than a peptide able to ligate the halves of its own amino acid chain.

The peptide only replicates in an extremely artificial environment: it puts together two(!) prefabricated molecules. This example shows very well that one must treat 'evolutionist' claims that something has been confirmed experimentally with great caution.

Normally the one who proposes a mechanism must show that it works. For doing that, it would be necessary to show that chemical and physical laws together with pure chance explain that ribozymes are able to build up copies of themselves.

In the case of neo-Darwinism however, instead of explaining 'reproduction', this finalistic principle is taken for granted. If it is explained, then only in a circular way: if reproduction appears by chance, it necessarily spreads (because of reproduction).

For a molecule consisting of a great number of atoms or building blocks it is a very very complex task to construct copies of itself. But there are an infinite number of other tasks which complex molecules could carry out. But why should they carry out complex tasks altogether? And why should they even develop a determination to construct copies of themselves? Why?

> Whereas the evidence suggests that there was one, or at most two, common ancestors.

What evidence? Your statement is at most a correct consequence of a complex theory or belief system.

To assume that exactly two (probably a male and a female) related common ancestors appeared once by chance seems completely absurd to me.

Re: Common Descent is a Fact?

If common descent were such a simple fact as you suggest, then it should be easy to describe exactly the bottleneck all life stems from. All the many genes for which common ancestor genes are assumed must have been in the bottleneck or even part the one single common ancestor. The very complex genetic code (or at least a very similar precursor) also must have been part of the small (how small?) group of common ancestors.

The many examples of independent convergent evolution and the fact that horizontal gene transfer is very frequent show that common descent is not the only possible explanation of the 'facts'.

Re: Phillip Johnson interview (Communiqué, Spring 1999)

Evolution is ambiguous:

  1. Continuous creation of life from simple molecules (or a common ancestor)
  2. A change in allele frequencies

The interesting question is 1) and not 2). Whether 1) has been observed is a different question from whether 2) has been observed, especially if one considers the following points:

1. One can not conclude from genetic variability to phenotypic variability.

2. Whereas genetic variation occurs rather continuously in time, the fossil record shows that species did not evolve in such a continuous way. Times of anatomical conservativism are followed by rapid changes. (Probably these changes are not the consequence of the accumulated genetic mutations but rather the result of environmental pressures, of the spreading of new biological inventions or of other reasons such as species extinction).

Speciation is ambiguous:

  1. Emergence of new phenotypes from (simpler) predecessors (e.g. elephants from trunk-less animals)
  2. Formation of (otherwise more or less identical) populations that can no longer interbreed

The important question is 1) and not 2). That 2) has been observed has not much relevance to 1). One does not even know whether the species which can no more interbreed are really new or whether there exist or existed somewhere species which can interbreed with the so-called 'new species'.

> As you should be able to see, this is completely covered by "a change in allele frequencies". No additional premises needed.

No (essential) additional premises would be needed if you said: "This is completely covered by a change in frequencies of hereditable traits".

It is not usually known to what extent a trait is genetically fixed and to what extent it reflects a reaction to the environment.

In most cases traits are determined by a combination of genes, and the effect of genes on traits is very indirect (this can also mean that one did not succeed in determining the assumed genetic influence).

Furthermore it is not possible to give a clear and simple definition of 'gene'. Are introns part of genes? Transcription factors, which bind to the DNA at a great distance from a gene, can strongly influence the transcription rate. Are such locations also part of the gene? Because alleles are gene variants all the conceptual problems of the notion 'gene' become conceptual problems of the definition of evolution ('a change in allele frequencies').

Re: On the difference between logic and rhetoric

Reasoning by analogy is the most fundamental and probably the oldest way of reasoning. (Even the enzyme-substrate-recognition is somehow analogy based). It's by analogy that animals decide whether something is a danger for them or not. Analogy is also the most fundamental principle of concept forming. Most concepts (e.g. 'inedible', 'danger', 'fish') emerged by analogy.

One should not confuse fundamental common-sense-logic (logic means reason) with special formalized logic systems. Whereas formal logic cannot lead to essentially new knowlegde, reasoning by analogy can.

Re: Does life violate second law of thermodynamics?

> Also, the collision radius is 4 times the particle radius, partly due to water cage effects.

If that's true, then it is very strong evidence for my claim that enzymes are able to perceive their surroundings.

Imagine a spherical enzyme with a radius of 2 nanometers, a volume of around 34 cubic nanometers and a surface of around 50 square nanometers. The active site may have a surface of 4 square nanometers.

If the collision radius is 4 times the particle radius, we must conclude that the active site can perceive a substrate over a distance of at least 6 nanometers. But these 6 nanometers are filled with other molecules such as water. The diameter of a water molecule is around 0.3 nanometers and there is room for around 33 water molecules in one square nanometer.

If our enzyme were only surrounded by water, than within the 'collision radius' there would be as many as 70 thousand water molecules.

Re: Thermodynamics and Evolutionary Mechanism Theory Challenge 19990511

Every unprejudiced person having common sense must admit that the emergence of life goes against what is predicted by statistical mechanics.

I believe in a continuous self-creation of nature! Whether I'm a SciCre-ist or only a consequent evolutionist depends on how these terms are defined.

What you do not see (as most creationists) is that extant life refutes the second law.

The question is:

  1. does a developing chick produce waste heat or
  2. does it rely on an energy input from outside?

There is a similar question:

  1. does all life without photosynthesis grow by producing waste heat or
  2. are there some forms with a positive energy balance (i.e. the organic material produced by them has more chemical energy than the 'raw material').

Re: Does life violate second law of thermodynamics?

According to neo-Darwinism, enzymes are inanimate macromolecules governed in the same way by physical laws as normal molecules. Why should Einstein's formula, derived from the most fundamental principles of thermodynamics, be valid for simple molecules and for bacteria sized particles, but not for enzymes?

That the formula is not valid for living bacteria poses no problem, because everybody will agree that bacteria are able to perform goal-directed movements.

I agree with you that proteins are not inert particles. They are able to perceive their surroundings and are able to change their shape in order to use the energy of thermal collisions in a goal-directed way.

Re: Common Descent is a Fact?

> The SunY self replicator.

If it really worked as you suggest, the SunY would be much more famous and all the necessary details could be easily found on the net. So I'm quite sure it is only 'replicating' a in similar way the Lee peptide is 'replicating'.

It [the Lee peptide] can mutate? How? It puts only together two prefabricated halves of its own amino acid chain. So it must be a matter of prefabricated mutations.

Also the creation of 'self-replicating' hyper cyclic systems of two, three or even more components becomes easy:

Examine little peptide ligases. Look for an aa-sequence in peptide X which ressembles the site peptide Y normally puts together. If peptide Y has aa-sequence similar to the one peptide X normally puts together, we can try to produce a two-component hyper cycle. In order to do that we must produce the left and the right aa-sequences of both X and Y. If we put many chains of the four sequences in a test tube and add X ligases, then the X ligases will put together left and right halves of Y ligases, which afterwards put together left and right halves of X ligases.

If we succeed, then we have proven once more that abiogenesis has been observed in the lab!

Re: Thermodynamics and Evolutionary Mechanism Theory Challenge 19990511

I must admit that sometimes I like to be a little bit provocative.

Sometimes it happens that a really careful study confirms the common-sense-judgements of half-educated persons (e.g. in the case of relativity theory). Such common-sense-judgements have been declared wrong only because of logical necessity resulting from unquestionable premises (e.g. impossibility of actions at a distance).

Do you really think that the development of a chick in an egg confirms what is predicted by statistical mechanics? Imagine the two following closed systems:

  1. We create a closed system with a fertilized egg in the center and enough surrounding material of the temperature which is optimal for a developing chick.
  2. Instead of a fertilized egg we use an unfertilized.

What happens in these closed systems is quite different. In the first more and more complex macromolecules and structures emerge. In the second however, more and more macromolecules decay to simpler molecules producing heat.

I would say that the two cases are almost diametrically opposed to each other. The second case certainly does not conflict with what is predicted by statistical mechanics, but the first?

Re: Theory of Natural Selection VS Reality

These facts entail that for most genes there are only one or very few alleles. The discrepancy between the huge number of possible alleles and the low number of actual alleles is known (Lexikon der Biochemie, Herder, 1991, -> Allel) but has remained essentially unexplained.

For instance there is only one allele of cytochrome-c, a protein around 100 amino acids long, in humans. Even chimpanzees have the same allele, despite the fact that our species separated millions of years ago.

In any case, if the six-substitution-rule or a similar conclusion were right, random mutations would lead to a huge number of alleles for all genes, and that's obviously not the case. So at least some premises of orthodox neo-Darwinism must be wrong.

Re: Theory of Natural Selection VS Reality

"Regarding the necessity of a mutation to occur at the right time _and_ the right place _and_ in coordination with fellow mutations that themselves occurred at the right times and right places, Grasse says Darwinism relies upon the regular occurrence of 'miracles'."

Re: Theory of Natural Selection VS Reality

A more or less valid principle states that the less one understands and knows the more seems to be possible. So it is good luck for neo-Darwinism that there is only very rudimentary knowledge of how genetic information is used to construct living organisms.

Whereas it is logically IMPOSSIBLE to understand that random mutations CAN lead to the very purposeful adaptations of animals and plants, it is POSSIBLE to understand that such purposeful adaptations CANNOT be caused by random mutations.

Current-date scientific ignorance is a prerequisite for the survival of reductionist neo-Darwinism.

The actual terrestrial ecosystem may be aquivalent to innumerable possible terrestrial ecosystems (with totally different species or even different biochemistry). It is, however, certainly not equivalent to an earth without a complex ecosystem.

One should really create something like a well-structured FAQ with efficent refutations of false or improbable claims of neo-Darwinism!

Have you an idea of how recombination could create elephants from trunkless animals or could lead to the ability of hibernation? Recombination can only act on already existing genetic material. Every programmer knows that modular programming which allows something similar to recombination imposes much more constraints on conception and programming than simple trial-and-error-programming.

What's the problem with bad design? Most things (e.g. computer programs and keyboards) are in a bad or at least not on the best way designed. The same can be valid in the case of bird's nests, termites' mounds and similar animal housing.

The assumption that creative and goal-directed design, which is an undeniable fact at least in humans, is based ontologically only on blind chance is logically absurd.

Re: Common Descent is a Fact?

Is there possibly a correlation between reproaching others with dishonesty and one's own dishonesty?

Re: Supernatural Causes, Revisited

"As it is, I've had to renounce my long-standing atheism because I've realized that I no longer know what the entity is I supposedly don't believe in."

Re: Theory of Natural Selection VS Reality

Why "too much heterozygosity"? If innumerous equivalent alleles are possible, why should there be a convergence to one or very few in a species. Maybe the main purpose of the too-much-heterozygosity-question was to divert suspicion from the real problem: why do only single alleles exist for the majority of the genes of a species?

Take the case of ubiquitin, a little protein with 76 amino acids and a rather simple behaviour. Human ubiquitin is identical to the one of animals and differs in only 3 amino acids from ubiquitin of saccharomyces cerevisae (yeast). According to Ian's six-substitution- rule (I do not agree with) there should be 6^76 = 10^59 "possible selectively neutral" alleles. It is impossible to explain the disappearce of all but one by random genetic drift as shown in ... because there are too many animals.

So we must conclude that either 1) mutations are very unlikely in the case of ubiquitin or 2) every mutation in ubiquitin is lethal (or at least harmful enough to disappear by selection). Both conclusions are evidence against neo-Darwinism. The ubiquitin gene is only one of tens of thousands of genes influencing the phenopype.

A lot of evidence in favour of Kimura's Neutral theory can easily be interpreted as evidence for the thesis that adaptations are not dependent on mutations.

Re: Does life violate second law of thermodynamics?

It is generally acknowledged that enzyme-substrate-interactions are normally based on the lock-and-key-principle. If we take into account that an average eucaryotic cell consists of 10^12 cubic nanometers and that the diameter of a water molecule (relevant to van der Waal's forces) is a around 0.3 nanometers, we must conclude that enzymes are just randomly bouncing around most time.

One should really create a computer-simulation of the enzyme- substrate-recognition based only on fundamental physical and chemical principles.

A computer simulation based on ad-hoc-hypotheses would be almost worthless.

Re: Thermodynamics and Evolutionary Mechanism Theory Challenge 19990511

The happenings in living cells are a prerequiste for evolution. Furthermore, there are innumerous possible errors in cell replications. Think about it: every structure of the cell must be replicated. Innumerous 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.

The second law has been subject to UNJUSTIFIED GENERALIZATION!!!

It hardly can be denied that the theory of Brownian motion is in the same way a direct consequence of the kinetic theory of heat as the second law is. Whereas bacteria sized inanimate particles do agree with the predictions of the theory of Brownian motion, not all living bacteria do. It follows that at least some living bacteria do not conform to the law.

If living bacteria do not conform to the kinetic theory of heat, why should subcellular organelles, macromolecular complexes, enzymes and all other biomolecules conform to this theory, derived from facts and experiments on dead matter?

Enzymes are very flexible molecules. In order to carry out a task, they must be able to change ('allosterically') their shapes. There are even lots of multifunctional enzymes.

A further possible example [defying the second law]: 5) Transport of water in trees.

Re: Thermodynamics and Evolutionary Mechanism Theory Challenge 19990511

It's rather normal, however, that persons not agreeing with the prevailing evolutionist views are called (dishonest) creationists irrespective of the arguments they present. That's interesting insofar as in former times critical theologians and scientists were called (dishonest) atheists irrespective of their belief in God.

Re: Theory of Natural Selection VS Reality

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