These are posts in the thread "Phillip E. Johnson now on the WWCW!"

9-Mar-1999

Hello (Dr.) Gavin (Tabor)

>> Philip E. Johnson seems to me a great logician and epistemologist,
>> much better indeed than most neo-Darwinist high priests
>> (e.g. Richard Dawkins) and believers.

> Do you really think that he is so wonderful? On what is your
> judgement based? I suppose that it is based on orthodoxy,
> dogmatism, authority and prejudices!

I'm not a theist (at the most a pantheist), but an evolutionist even
more consequent than Darwinists, because I do not accept such
a discontinuity in evolution as the magical appearence of
consciousness some billions years after 'big bang'.

So I do not think that all of Johnson's opinions are wonderful. My
judgement on Johnson is primarily based on his texts about AIDS,
which I really do appreciate. In my opinion the AIDS hysteria
(comparable with the medieval witch-hunting) shows better than
anything else that modern science is only quantitatively better than
medieval theology.

I proved my unprejudiced attitude by the fact that I have changed
my mind about evolution and many other things over the last
12 years. My own ideas cannot be based on orthodoxy, dogmatism
and authority, because they are too different from all prevailing ideas.
see: http://members.lol.li/twostone/E/psychon.html


> Where have I heard that before? Whenever I read
> stuff that Johnson writes I am strongly of the opinion that he is
> attempting to communicate the least possible ammount in the
> maximum number of words. I am reminded of Dawkin's comment
> about those who are educated beyond their capacity for coherent
> thought. All of his material is opinion : very rarely does he resort
> to a consideration of facts.

In my opinion Johnson (contrary to Dawkins) is able to recognize
the real (philosphical) problems and to discriminate between what
is important and what not.

It is quite normal that material in agreement with one's own
prejudices seems to be facts whereas the rest seems to be opinion!


It is my, Johnson's and many others' right to find it disquieting (or
even absurd) that "the mind is merely what the brain does" and
that "our thoughts and theories are products of mindless forces".

see for instance: http://members.lol.li/twostone/E/reductionism.html


> This is just a recycling of the usual claim that NS selects
> pre-existing genetic information, and evolution cannot generate
> new information. This can be shown not to be the case.
> Consider the work presented at
http://www.newscientist.com/ns/971115/features.html
> This describes the use of genetic algorithm techniques to evolve
> a circuit that not only does a particular job, but does it in a way
> not previously thought possible by humans.

It is not difficult to make computer games or AI programs where
also chance influences the result. It may even happen that the result
is one not expected by the programmers, but I do not believe in results
which are in principle different from what could have thought possible
by the programmers.

In any case, such algorithms are rather evidence for a guided (there
are engineers and programmers) evolution than for a purely random.

J>" There are many excellent reasons for doubting the adequacy of
J>" this kind of explanation. Random changes (such as copying errors
J>" in the DNA) do not generate increases in information, whether
J>" they are small or large.

> Yes they can.

They can in principle under special conditions, but it is much more
probable that random mutations have negative effects. At least
point mutations do not increase the information size (as measured
in bytes).

J>" To illustrate the point with an analogy: It is hard enough to
J>" earn one million dollars by winning the grand prize in a lottery,
J>" but it is no easier to achieve that feat by winning a $100 prize
J>" 10,000 times.

> This is only true if the events are random and uncorrelated. In
> evolution the events are not random and they are correlated :
> NS sees to that.

My opinion is quite similar to Johnson's:

"If it cannot be denied that the probability for random emergence
of a system (e.g. a living organism) is unrealistically low, the system
is taken apart to smaller and smaller sub-systems until random
emergence gets realistic. But it is ignored that the probability for
the whole system is calculated by multiplying the probabilities for
the emergence of all systems from their respective sub-systems.
Reductionist causal laws do not explain why sub-systems which are
useful for the whole reproduce themselves instead of disappearing
after having appeared by chance."
( http://members.lol.li/twostone/E/psychon.html#a03 )


Wolfgang

9-Mar-1999

Hello Jamie Schrumpf!

J>" As we have seen, Darwinian evolution is by definition unguided
J>" and purposeless, and such evolution cannot in any meaningful
J>" sense be theistic.

> It is neither totally unguided, as natural selection is indeed
> guided by the environmental pressures with which an organism
> is faced, nor purposeless, as its function is to make populations
> more fit within their environments. It certainly is not designed
> to result in human beings, or to move toward "higher" life forms.
> If he had said, "intelligently guided" and "apparently purposeless,"
> then he would have been more accurate.

Nothing is 'guided', 'unguided', 'random' or 'determined' in every
respect. One should always choose the most consistent
interpretation of a text. So the meanings of 'unguided' and
'purposeless' as used by Johnson are clear, at least for me.

You think Johnson would have been more accurate if he had said
"apparently purposeless". This shows that you do not understand
what Johnson wants to say: according to neo-Darwininism the
apparent purposefulness of nature (which cannot be denied) is
based on an (ontological) purposelessness.

> Sure, and He could personally be holding atoms together as well,
> but the strong and weak nuclear forces are well-accepted in the
> world at large.

That "the strong and weak nuclear forces" as conceived by modern
physics are holding atoms together, seems to me not much better
(maybe even worse in some respects) than an explanation by God.

-----------------------------------------
An excerpt from a correspondence with a physician:

>> Electrostatic attraction cannot even be explained qualitatively in this
>> way because under momentum conservation two bodies can only
>> drift apart by exchanging photons, and momentum conservation
>> of photons has been experimentally confirmed!

> It's not that simple. If it were, don't you think
> somebody would have noticed by now?

That's really an interesting answer!
-----------------------------------------

> One has to follow the evidence in the earth itself, and the evidence
> indicates that the biodiversity of life on earth didn't just "poof"
> appear, nor did it _require_ intelligence to design.

The evidence in the earth can inform us that there has been a
continuous evolution of live, but this evidence certainly can
not inform us whether reductionist causal laws are enough to
explain the actual biodiversity on earth! And the very basis of
at least neo-Darwinism is the rejection of any teleological
principle.

see: http://members.lol.li/twostone/E/psychon.html#a04
or: http://members.lol.li/twostone/E/reductionism.html

Wolfgang

9-Mar-1999

Hello Bonz!

J>" Everybody with even a cursory knowledge of the literature knows
J>" that the textbook examples (Kettlewell's peppered moths,
J>" Grant's finch beaks) describe relatively trivial changes that involve
J>" no innovation or increase in genetic information.

> I have somewhat more than a cursory knowledge, and I think this
> statement is pure bull shit.

It is a fact that all experimentally produced changes are relatively small.
Do you know an exception?

I know an 'exception', but this exception refutes reductionist
Darwinism: the instinctive behaviour of rats could be substantially
changed by breeding and training rats over a few generations.
See: http://members.lol.li/twostone/E/aa1.html

J>" But when materialism is assumed as the very basis of science,
J>" they can re-emerge a few logical steps later in triumph. Something
J>" had to guide evolution, to produce those wonders of apparent
J>" design, and natural selection is just about the only materialist
J>" contender.

> This makes no sense at all.

This makes no sense for you because you lack knowledge in
epistemology! This makes a lot of sense and your reasoning
even elegantly shows how much sense it makes.

Wolfgang

9-Mar-1999

Hi Mike!

J>" There are many excellent reasons for doubting the adequacy of
J>" this kind of explanation. Random changes (such as copying errors
J>" in the DNA) do not generate increases in information, whether
J>" they are small or large. It is not necessarily easier to provide the
J>" same amount of information in multitudinous small doses, rather
J>" than a single large one. Each increment is less unlikely, but the
J>" price one pays is that one has to have a great many increments,
J>" each of which must supply the precise kind of new information
J>" required. To illustrate the point with an analogy: It is hard enough
J>" to earn one million dollars by winning the grand prize in a lottery,
J>" but it is no easier to achieve that feat by winning a $100 prize
J>" 10,000 times.

> When I walk to the shops at lunchtime (they are a kilometre away
> approximately), I get there through 1,000 steps, not one huge leap.
> Also, if instead of buying a lottery ticket each week I deposit that
> money in a bank account I will definitely be a millionaire in the long
> run.
> I suggest that Mr Johnson should walk to the shops and put some
> money in his bank account. He may learn something.

If for a first organism with the power of reproduction to apppear
only twenty different conditions with a probability of each 0.001
were necessary, then the probability of such an organism to appear
would be only 10^60. Even if 19 of the 20 conditions were fulfilled,
the organism could not replicate and evolution of life could not
start. In realty certainly more conditions with lower probabilties
are necessary for such a self-replicating system with the additional
capacity to undergo further improvement by mutation and selection.

Probabilities must be multiplied!
See: http://members.lol.li/twostone/E/psychon.html#a03

Here a quotation from a genuine orthodox believer:

"But no one knows what that first organism was, for it naturally had
no bones and thus left no fossils, and it certainly would have been
vastly overpowered and driven to extinction by its more advanced
children who were born after successive mutation and selection."
( http://www.columbia.edu/~rcc20/foster9.html )

Within neo-Darwinian framework one must not take it for granted
that the "first organism" "certainly would have been vastly
overpowered and driven to extinction by its more advanced
children who were born after successive mutation and selection."


Wolfgang

10-Mar-1999

Hi Bonz!

>> If for a first organism with the power of reproduction to apppear
>> only twenty different conditions with a probability of each 0.001
>> were necessary, then the probability of such an organism to appear
>> would be only 10^60.

> Not true. Show your math.

You are right!

0.001^20 = (10^-3)^20 = 10^-60


>> Even if 19 of the 20 conditions were fulfilled, the organism
>> could not replicate and evolution of life could not start.

> Not true, Show your math.

No math is necessary, because my argument is based on the
premise that all 20 (independent from each other) conditions
must be fulfilled for replication to start.


>> In realty certainly more conditions with lower probabilties
>> are necessary for such a self-replicating system with the additional
>> capacity to undergo further improvement by mutation and selection.

> Probably not true. Show your math.

No math is necessary. A look at the complexity of living systems should
be enough.

Regards
Wolfgang

10-Mar-1999

Hello Mike!

>> If for a first organism with the power of reproduction to apppear
>> only twenty different conditions with a probability of each 0.001
>> were necessary, then the probability of such an organism to appear
>> would be only 10^-60. Even if 19 of the 20 conditions were fulfilled,
>> the organism could not replicate and evolution of life could not
>> start. In realty certainly more conditions with lower probabilties
>> are necessary for such a self-replicating system with the additional
>> capacity to undergo further improvement by mutation and selection.
>>
>> Probabilities must be multiplied!

> Only if the events are independent you nitwit. If not, then the
> calculations get MUCH more complicated. Every prob. of life
> calculation I have seen assumes this and ignores the effects
> of chemistry. Thus all such calculations are useless.

Certainly at least 20 (independent) conditions with a probability
of at most 0.001 are necessary for a self-replicating system to
appear. If it were less, it should be possible to show how such a
system could appear and work or even to produce one in the
laboratory.

I agree with you that it useless to calculate exactly such probabilites!
However, it is possible to estimate upper limits. It is my opinion that
everybody who deals with this problem in a logically correct and
unprejudiced way must recognize that reductionist causal laws
cannot explain the appearence of such a self-replicating organism.

Regards
Wolfgang

10-Mar-1999

Hello Jamie Schrumpf!

>> You think Johnson would have been more accurate if he had said
>> "apparently purposeless". This shows that you do not understand
>> what Johnson wants to say: according to neo-Darwininism the
>> apparent purposefulness of nature (which cannot be denied) is
>> based on an (ontological) purposelessness.

> "What Johnson wants to say" is more or less the problem here.
> He is not reaching for truth, but -- in his lawyerly way -- is merely
> arguing the point in which _he_ wants to believe. If he has, as
> most lawyers have, ever defended someone whom he believes is
> guilty, then we can certainly imply that the truth is incidental to any
> position he may take.

Are you sure that what you are insinuating here, is not relevant for
you yourself? My personal impression is that Johnson is reaching
for truth, in the same way as you do. There are many things where I
do not agree with Johnson or with you, but I respect both your and
Johnson's opinions, even if I'm convinced that they are false.

I'm sure that Johnson is or was a much more unbiased lawyer than
the average.

> Not to put too fine a point on it, he doesn't _care_ what the truth
> may be. He has an agenda to push and if he can twist words to
> advance it, that is what he'll do.

Why do you know that? Are you sure that you are not pushing an
agenda which will seem absurd to future generations?

>> The evidence in the earth can inform us that there has been a
>> continuous evolution of live, but this evidence certainly can
>> not inform us whether reductionist causal laws are enough to
>> explain the actual biodiversity on earth! And the very basis of
>> at least neo-Darwinism is the rejection of any teleological
>> principle.

> Well, thank you for admitting that the evidence indicates constant
> evolution of life on earth. And you do understand that one of the
> basic principles of science in general -- not just evolution -- is to
> "assume no unnecessary entities"? You can't ignore the proven
> explanatory and predictive powers of the theory of evolution just
> because it doesn't require a god to work.

If reductionist causal laws cannot explain life, neo-Darwinism is
refuted and it is necessary to look for new entities or principles
which can explain life. I'm sure that neo-Darwinism will seem to
future generations a completely absurd theory, because it denies
the most obvious.

Whereas Johnson suggests God for what cannot be explained
by causal laws, I suggest final laws of nature and immaterial
unities undergoing evolution which I call psychons or souls.

Cheers
Wolfgang

http://members.lol.li/twostone/E/psychon.html

10-Mar-1999

!! An excerpt from a correspondence with a physician:
!!
!! >>> Electrostatic attraction cannot even be explained qualitatively
!! >>> in this way because under momentum conservation two bodies
!! >>> can only drift apart by exchanging photons, and momentum
!! >>> conservation of photons has been experimentally confirmed!
!!
!! >> It's not that simple. If it were, don't you think
!! >> somebody would have noticed by now?
!!
!! >That's really an interesting answer!


> I can only hope it *was* a physician and not a physicist! ;-)

I'm sorry, it was a physicist (Sverker Johanson).

>> Especially as I don't see the relevance. How do you think that
>> "electrostatic attraction" is related to the conservation of
>> momentum?

> The explanation must have been that electrostatic attraction/repulsion,
> as a specific case of electromagnetic interactions, is mediated by the
> exchange of virtual photons.

> While this may be an rough and intuitive way of describing the
> underlying mathematics (Feynman diagrams etc.), for many
> questions it is "too rough". If one has an over-realistic picture of
> virtual photons as ping-pong balls going back and forth, I can
> imagine how one might think that only repulsion could be achieved
> in that manner.

One must never abstain from correct logical reasoning! This must
be valid also for theoretical physics, which in several respects plays
nowadays the same role theology played in the past.

The empirical evidence for most elementary particles is no better
than for angels and demons.

> The question why opposite charges attract while similar charges
> repel is actually quite subtle and has to do with the vector nature
> (i.e. photons are particles of spin one) of electromagnetism.

Here another quotation from my correspondence (Darwinism refuted
by adverse selection experiments) with Sverker Johansson:

"There are physical theories with no predictive value at all. The
explanation of the simple Coulomb law by obscure mathematical
formulas in QED is a good example. Photons as postulated by
Einstein are concrete, measurable things with frequency, energy
and momentum. Can you tell me how much photons of what kind
are active in a concrete situation of electrostatic attraction?"

There is an infinity of possible explanations of the fact that opposite
charges attract! However, only the simplest explanations should be
taken seriously according to sound epistemology.

Wolfgang

10-Mar-1999

Hello Loren!

I have seen that you have published some online texts on the
subject we are discussing. As far as I have read in them, they
give me a positive impression of you.

But I think that you overestimate science and scientists.
Representative of modern science is Galilei. At a time when
the Copernican theory was already spreading he usurped
this theory and fought the theories of Johannes Kepler.
Kepler had been the first to surpass substantially the
astronomy of Aristarchus by smashing the whole epicycle
theory and by introducing modern physical laws.

Also Kepler's explanation of life which was quite similar to
mine was ridiculed and fought.

>> Certainly at least 20 (independent) conditions with a probability
>> of at most 0.001 are necessary for a self-replicating system to
>> appear.

> Why is this certain? If we don't understand the details of the process
> (or even the generalities), then how could we estimate how many
> conditions are involved, whether they are independent, and what their
> respective probabilities are?

For a self-replicating system at least 20 molecules which are at least
as complex as nucleotids or amino acids are necessary. According
to neo-Darwinism the movements of molecules depend on random
thermal collisions (apart from chemical and physical laws).

Now I assume that 20 molecules are enough for a self-replicating
system to appear, if every molecule has the right position in space.

A further simplification is needed. I assume that all 20 molecules
are in a cube which is subdivided into 1000 mini-cubes, and for the
right position nothing more is required than the center of gravity of
the molecule being located within the right mini-cube.

In this simpified case the probability for the self-replicating system
to appear is 10^-60. Common sense is enough to show that for a
self-replicating system to appear in nature, the probability is even
much much lower.

Here a quotation of my text 'Arguments against Reductionism':

"How impossible it is that random thermal motions determine the
happenings in living cells would become obvious, if one created an
enlarged model of the DNA helix with a helix diameter of 50 cm,
and if persons had to take over the functions of the many enzymes
which are involved in the DNA replication. The whole human DNA
(of one single cell), which normally is tightly packed, would be at
such an enlargement about 500'000 km long. This model would
also show how improbable it is that transcription factors could find
a given DNA position, if there were only random motions and if
recognition of the position were possible only by direct contact.
Because of the enzyme size, this improbability cannot be hidden
behind the Heisenberg uncertainty relations."
( http://members.lol.li/twostone/E/psychon.html#a06 )


>> I agree with you that it useless to calculate exactly such probabilites!
>> However, it is possible to estimate upper limits.

> How, precisely? If you know little or nothing about the generating
> mechanisms or the resultant distributions, how could you possibly
> infer anything about the distributions?

It is possible to calculate upper limits of such probabilities, because
we can recognize conditions which must be fulfilled in any case.


>> It is my opinion that everybody who deals with this problem in a
>> logically correct and unprejudiced way must recognize that
>> reductionist causal laws cannot explain the appearence of such a
>> self-replicating organism.

> What, precisely, is the basis of your opinion?

The basis of my opinion you can find in 'The End of Reductionism':
http://members.lol.li/twostone/E/reductionism.html

> In my view, anyone who approaches this question in an unprejudiced
> and scientific way should recognize that: (a) "reductionist causal laws"
> is a vague statement, open to several plausible interpretations; and (b)
> scientists have not yet explained the appearance of self-replicating
> organisms.

(a) For me "reductionist causal laws" is not vague, see:
http://members.lol.li/twostone/E/psychon.html#a04

(b) I think I have explained at least in principle the appearance
of self-replicating systems.

> It appears to me that you believe the following: some interpretation
> of the phrase "reductionist causal laws" gives force to the claim that
> existing scientific methods and theories are critically insufficient for
> the task of explaining the appearance of self-replicating organisms.
> But I'm not at all clear why you believe this; it certainly isn't an
> obvious point.

If after having read 'the psychon theory' you are still unclear why I
believe this, I'll willingly explain you.

Cheers
Wolfgang

10-Mar-1999

Hello Mike!

>> Certainly at least 20 (independent) conditions with a probability
>> of at most 0.001 are necessary for a self-replicating system to
>> appear. If it were less, it should be possible to show how such a
>> system could appear and work or even to produce one in the
>> laboratory.

> You realize, of course that they have discovered replicating molecules
> around 32 molecules long? And furthermore that molecules do not
> form randomly? What independent events are you proposing need
> to happen? Can you use the above ideas to predict the yield of
> Miller's experiements?

That's actually new for me: the existence of "replicating molecules
around 32 molecules long". The only possibility I see is the following:
there are RNA enzymes 32 bases long which replicate by base
pairing. Are you sure that such molecules actually have been
discovered, molecules replicating independently? However, even if
they actually exist, they are not enough to start evolution.

Do you know the results of Miller's experiment? A mixture of simple
organic molecules. This result is almost irrelevant to the explanation
of life and evolution.

"It is revealing that the chemosynthesis of urea of the year 1828
symbolizes the victory of the reductionist view on life. Whereas
an urea molecule consists only of eight atoms, enzymes consist
of thousands of atoms and behave in an astonishingly versatile
and purposeful way. Enzymes construct and modify cells and
macroscopic organisms in a similar way termites construct
and modify their mounds. That enzymes also work in vitro (e.g.
polymerase chain reaction) does not prove the reductionist view.
For such a proof it would be necessary to explain roughly how
complex behaviour of enzymes (e.g. the ability of orientating
themselves in cells) could emerge from physical and chemical
laws, if probabilities are estimated in a reasonable way."
( http://members.lol.li/twostone/E/reductionism.html )

Further answers you can find in my last message to Loren King.

Wolfgang

11-Mar-1999

Hi Gavin!

>> >> If for a first organism with the power of reproduction to apppear
>> >> only twenty different conditions with a probability of each 0.001
>> >> were necessary, then the probability of such an organism to
>> >> appear would be only 10^-60.
. . .
>> >> Even if 19 of the 20 conditions were fulfilled, the organism
>> >> could not replicate and evolution of life could not start.
>>
>> > Not true, Show your math.
>>
>> No math is necessary, because my argument is based on the
>> premise that all 20 (independent from each other) conditions
>> must be fulfilled for replication to start.

> Where did you get the figure of 20 independent conditions, all
> with such low probabilities from? I think that thats the real question.

Look at the complexity of living cells!

I have answered this question in my last message to Loren King.
Here an excerpt:

"For a self-replicating system at least 20 molecules which are at least
as complex as nucleotids or amino acids are necessary. According
to neo-Darwinism the movements of molecules depend on random
thermal collisions (apart from chemical and physical laws).

Now I assume that 20 molecules are enough for a self-replicating
system to appear, if every molecule has the right position in space.

A further simplification is needed. I assume that all 20 molecules
are in a cube which is subdivided into 1000 mini-cubes, and for the
right position nothing more is required than the center of gravity of
the molecule being located within the right mini-cube.

In this simpified case the probability for the self-replicating system
to appear is 10^-60. Common sense is enough to show that for a
self-replicating system to appear in nature, the probability is even
much much lower."

> My understanding is that the smallest self-replicating protein
> has 32 base units in it. If there are say 10 different amino
> acid choices for each block, that implies there are 10^32
> such proteins which can form - ignoring any issues of
> chemistry. In a liquid molecules interact at a rate of around
> 10^14 interactions/sec : lets say new arrangements are formed
> at that rate. In 1 mole of amino acids that means there are
> 10^22 32-element proteins, and in 1 second, there are
> thus 10^36 proteins being tried. Thus in 1 second, 10^4
> of these self-replicating proteins will be formed.
> Sounds like pretty good odds to me.

Are you telling a joke?

What is a self-replicating protein? To assume that every collision
between molecules corresponds to a new arrangement of a
sequence of 32 amino acids seems absurd to me. Incorrect
chemical bonds between amino acids are possible. Bonds with
other molecules cannot be excluded. Where could a soup with
such a high proportion of amino acids have existed?

Regards
Wolfgang

12-Mar-1999

Hello Loren!

It actually were your texts concerning Naturalism and Creationism
which gave me a good impression of you. Your summaries of
my convictions show me that you also tried to understand at least
parts of my texts.

I think we have a problem of communication, and that's quite normal.
Therefore it will be necessary for mankind to create efficient artificial
languages with clear words and linguistic structures!

The problem of unclear words and expressions unfortunately cannot
be resolved by definitions, because they themselves depend on
other words. The best way is to give concrete examples.

However, to explain every word or expression is somewhat tiring.
The concepts 'causality' and 'finality' are very old philosophical
concepts. Maybe until the time of Descartes (1596-1650) they had
equal rights in philosophy and science. There is, however, no
apriori reason why 'causality' should be more scientific than 'finality'.

Johnson's concept 'naturalistic' is in some respect almost the same
as my concept 'reductionist', but there is also a (maybe only linguistic)
difference: according to my usage of 'natural' there is nothing
supernatural. Final laws or souls are totally natural entities.

In this context it may be interesting to look at the history of
'naturalism'. A certainly questionable and maybe subjective
simplification is the assumption that there was an evolution from
animism to polytheism, to monotheism with God outside the world,
to monotheism with God inside the world, to pantheism and finally
to atheism. The difference between atheism and pantheism is not
big, because in pantheism 'God' is only a synomym for 'world' and
'nature', or means a special aspect of the world.

The basis of modern science was build in the 17th century. One of
the first consequent naturalists was Baruch Spinoza (1632-1677),
who explained the world in a panpsychist and panmaterialist way:
space or matter is one aspect of the world (or of God or of nature),
and thinking or consciousness a second. Johannes Kepler (1571-
1630) had explained the world in a quite similar way, based on a
monotheism with God inside the world.

Both Kepler and Spinoza were fought and ridiculed especially by
theologians but also by scientists. The alternative was the philosophy
of Descartes: on the one hand was the material world and on the
other human souls and God. Animals were considered pure
machines without consciousness. The current scientific world view
is based on the philosophy of Descartes. The big inconsistency of
Cartesianism (animals as pure machines, humans having souls)
was removed by removing the concept 'soul' (and 'God').

So why do you consider panpsychism as something supernatural?
One main reason for its defeat was that it was a naturalistic
explanation of the world not in agreement with theology.

According to my usage of the word 'reductionist', Descartes'
philosophy is reductionist with the exception of the concepts
'human soul' (and 'God'), whereas all explanations involving final or
teleological principles, or based on vitalism or panpsychism are not.

I have put together some further extracts on this subject in:
http://members.lol.li/twostone/E/evidence.html#epistemology

Many enzymes work at defined places in a cell. If we create an
enlarged model, where enzymes are like little balls, then the volume
of the whole cell is about 1000 cubic metres. Imagine concretely
this situation: a little ball must come very near to a substrat and the
substrat recognition even depends on the correct alignment of the
little ball. In addition to that, enzymes often have to pass cell
membranes in order to reach their destination. What is the moving
force of enzymes? It cannot be electromagnetic attraction or
repulsion. So the moving force must primarily depend on random
thermal motions (as Brownian movements do).

You certainly will object that we do not know well enough the
chemistry of enzymes in order to conclude that: there may always
be the needed chemical forces responsible for the 'apparently'
very purposeful motions of enzymes. This implies that the information
for these motions to desired destinations is somehow stored in
the amino acid sequence of an enzyme, in addition to to the
information for folding, substrat specifity and so on, because even
similar enzymes can have very different destinations. A mutation
could change a description factor in such a way that the protein
would search its usual substrate in a wrong chromosome.

The voyage of transcription factors to their destiny can be compared
with the voyages of migratory birds and other migratory animals.

You ask me, how can I "be certain that 'at least 20' independent
and mutually improbable conditions all have to be satisfied, in one
particular sequence". I have the same right to ask you, how can you
be certain that not at least 20 different conditions with low probablilty
must be at the same time satisfied for a replicating system to appear.
Within the reductionist framework there is no sound reason to
assume that stages which could give rise to a self-replicating system
are rather conserved than other stages, or that steps in the right
direction have somehow a higher probability than steps in a wrong
direction.

The present-day scientific ignorance is no better evidence for
reductionism than for panpsychism! But is it really a necessary
ignorance? Ignorance is often the result of false premises.

I'm convinced that physical laws as described by classical physics
or by QM cannot be responsible for the fact that living organisms
evolved and survive. The often cited 'complex dynamic systems' as
e.g. the appearance of ordered vortices, waves or similar things
doesn't affect evolution much more than the appearance of solar
systems does. And the appearance of crystals (carefully studied
by Kepler) is rather evidence for panpsychism than for reductionism.

One must not confuse logical reasoning with empirical facts.
Calculations of probability must be based on clear and sound
assumptions, but the calculations themselves must not be
influenced by empirical facts. From the fact that evolution has
occured we cannot conclude that it can be explained on the basis
of the generally accepted metaphysical principles of current science.

Philip E. Johnson:

"But when materialism is assumed as the very basis of science, they
can re-emerge a few logical steps later in triumph. Something had
to guide evolution, to produce those wonders of apparent design,
and natural selection is just about the only materialist contender."

Cheers
Wolfgang

14-Mar-1999

Loren, this time your post gives me a rather bad impression of you.

Didn't you intentially try to twist what I have said in order to portray
my position absurd? I use the word 'reductionism' very frequently
and always in the same way (I'm very conscious with linguistic
problems). 'Methodological reductionism' is nothing more than the
only sound scientific method and in the main it is almost the same
as 'Occam's razor'.

My use of 'reductionism' is: to reduce all phenomena of nature to
a purely material basis.

> Defining such [final] ends has always been a problem, since we
> generally have to infer such ends (consciously or inadvertently)
> from the observation and interpretation of causes. But if final
> ends in natural systems are inferred from causes, it isn't clear
> why the concept of cause alone isn't sufficient to explain
> natural phenomena.

What you write here is a very elegant example of a well-known
philosophical fallacy: circular reasoning!

If you actually are "familiar with the philosophical history of the
concepts", then what I have written in 'Causal and Final Laws'
should be enough to understand my meanings of 'causality' and
'finality'. It is not enough to know something primarily from the
perspective of modern Darwinism.

> Johnson's naturalism is a blending of a bare materialist
> ontology (i.e. everything is ultimately material) with a
> rationalist epistemology (i.e. everything real is knowable
> through experience and cognition) ... is this analogous to
> what you mean by reductionism?

Yes.

I am a friend of a rationalist epistemology. But I am aware that
the theories by which we explain the world cannot be explained
themselves in the same way. The rationalist epistemology is
sometimes used to explain the simple (gravitation) by something
complicated (material gravitons).

> I think it's a bit simplistic to say that "the current scientific
> world-view" (whatever that is) is based on Cartesian ideas.
> A lot of water has gone under the bridge since Descartes.

But the way was pointed at that time for our current materialist
reductionism and against panpsychism. Leibniz was the last
well-known panpsychist, but the many inconsistencies of his
'monadology' (a compromise between panpsychism and christian
theology) were rather harmful.

> ... given my (provisional) commitment to methodological
> naturalism (namely that the external world exists independent
> of our experiencing and thinking about it, and our senses and
> reasonings are roughly accurate in conveying to us basic facts
> about this world, and explaining causal relations).

What you describe as methodological naturalism, I would rather
call 'naive realism'. Do you know the ideas of Immanual Kant?

> there are no glaring and persistent anomalies that lead me to
> radically revise my assumptions about the basic reality and
> comprehensibility of the world.

There are a lot of glaring and persistent anomalies, but in order
to recognize them, an unprejudiced attitude is a prerequisite.

>> You ask me, how can I "be certain that 'at least 20' independent
>> and mutually improbable conditions all have to be satisfied, in one
>> particular sequence". I have the same right to ask you, how can you
>> be certain that not at least 20 different conditions with low probablilty
>> must be at the same time satisfied for a replicating system to appear.

> The burden of proof isn't on my shoulders: after all, you're the one
> making claims about the certainty of your probability estimates.
> I'm just asking you how you can meaningfully make such estimates,
> given that you and no one else yet understands very much about
> the mechanisms and processes involved.

That's a reasoning based on authority and dogmatism. The fact
that we do not understand very much about the mechanisms and
processes involved, is unconsciously taken as evidence for God,
neo-Darwinism or any other world view we believe in.

When Pythagoras said, the earth is not flat, the burden of proof
seemed to be only on his shoulders. Despite a lot of evidence
most people continued to believe in a flat earth for many centuries.
Kepler has provided much empirical evidence for his three laws,
but not even Galilei did accept the evidence!

I repeat myself: "The present-day scientific ignorance is no better
evidence for reductionism than for panpsychism!"

>> Within the reductionist framework there is no sound reason to
>> assume that stages which could give rise to a self-replicating system
>> are rather conserved than other stages, or that steps in the right
>> direction have somehow a higher probability than steps in a wrong
>> direction.

> Why not? I see nothing preventing such incrementalist processes
> in standard evolutionary theory.

I agree that such incrementalist processes are necessary for
evolution to occur.

Let us assume that there are two stages of the same appearance
probability. One stage could be part of a self-replicating system,
whereas the other could not. Within the reductionist causal
framework there is really no reason at all to assume that the first
stage is rather conserved than the second, only because it could
be part of a self-replication system in future.

That's exactly one of the reasons why I have introduced final laws
of nature: steps in the right direction can have a higher probability
than steps in a wrong direction. There is some kind of 'causal
effect' from the future. You know, in relativity theory the present,
past and future are given in some respect 'at the same time'.
That events of different times are correlated in a non-causal way,
is in principle similar to actions at a distance, where events of
different places (e.g. motions of the earth and of the sun) are
correlated without mediating material causes such as gravitons.

>> I'm convinced that physical laws as described by classical physics
>> or by QM cannot be responsible for the fact that living organisms
>> evolved and survive.

> What, specifically, convinces you of this?

The fact that the behaviour of matter or particles is explained
only by relatively simple mathematical relations.

>> The often cited 'complex dynamic systems' as e.g. the appearance
>> of ordered vortices, waves or similar things doesn't affect evolution
>> much more than the appearance of solar systems does.

> Do you have specific evidence to support this strong claim?

Yes. Waves and vortices are incomparably less complex than
simple living cells. They really can be understood on the basis of
simple physical principles. They appear under certain conditions
and disappear with these conditions.

>> And the appearance of crystals (carefully studied by Kepler) is
>> rather evidence for panpsychism than for reductionism.

> I don't see this at all.

Do you understand at least in principle the appearance of very
elaborate snow crystals? I understand the emergence of the
highly ordered planetary movements (described by Kepler's laws)
from two simple hypothesis (law of inertia, reciprocal attraction),
but I do not understand the formation of crystals. If a sound
(and therefore simple and elegant) explanation existed, this
explanation should be more widespread.

For me it is not enough that a problem is declared to have
been resolved. The fact that computer simulations of crystal
formation are possible, explains not very much.


Cheers
Wolfgang

http://members.lol.li/twostone/E/psychon.html

14-Mar-1999

Hello George Acton!

>> Many enzymes work at defined places in a cell. If we create an
>> enlarged model, where enzymes are like little balls, then the volume
>> of the whole cell is about 1000 cubic metres. Imagine concretely
>> this situation: a little ball must come very near to a substrat and the
>> substrat recognition even depends on the correct alignment of the
>> little ball. In addition to that, enzymes often have to pass cell
>> membranes in order to reach their destination. What is the moving
>> force of enzymes? It cannot be electromagnetic attraction or
>> repulsion. So the moving force must primarily depend on random
>> thermal motions (as Brownian movements do).

> I'm sorry to contradict you, because I enjoyed your account of the
> history of ideas in this area, and looking at some of these issues
> from your perspective. But I'm afraid your description of the
> cellular localization of enzymes misses the point. The cellular
> "traffic control" that directs enzymes and other substances to
> their destination is entirely mechanical. Not only does the enzyme
> have the information to assume its shape and form the active site,
> but it has portions that tag it as destined for different destinations.
> The transport systems that move the enzymes recognize these "bar
> codes" and move the enzyme to the appropriate site. The obvious
> experiment is to alter that portion of the enzyme without changing
> the active site. And the result is an active enzyme located in
> the wrong place. And you are correct that a mutation could change
> the protein so it would wind up in the wrong place, although
> "Search" is more anthropomorphic than most people in science
> would prefer.

Now it's me who is afraid that the explanation of the purposeful
movements of enzymes by an entirely mechanical "traffic control"
misses the point. How do you explain such a "transport system"?
Are there some kind of currents in the cell or even some kind of
taxis which transport the enzymes to their needed destinations?

When I wrote "the information for these motions to desired
destinations is somehow stored in the amino acid sequence
of an enzyme" I did not mean some kind of "bar code" on the
enzyme, which is interpreted by a cellular transport system being
responsible for the motions of the enzyme. It seems to me even
much more difficult to explain how such a "traffic control" could
transport all the enzymes to their very different destinations
depending on such a "bar code".

That enzymes may consist of several parts or domains and that
one such domain can be resonsible for the destination of the
whole enzyme is obvious. There is no clear transition line between
simple proteins and protein complexes. But my explanation goes
rather in a different direction:

"Also relations analogous to the one between horse and rider or between
shepherd, dog and herd are possible on different complexity levels. An RNA
nucleotide consists of three parts which are evolutionarily older than the
whole nucleotide: 1) RNA base, 2) ribose and 3) chain of phosphate groups."
( http://members.lol.li/twostone/E/psychon.html#a09 )


> More generally, all theories that impute knowledge or purpose
> to subcellular or cellular structures have been discarded. One of
> the classic instances was discovered by Monod. When the bacterium
> E. coli is placed in an enviroment with a high concentration of
> the sugar lactose, it makes more of the tramsporter protein in the
> cell membrane, which imports more of the compound. The naive
> explanation is that the transporter "knows" how much of itself is
> needed by sensing how much sugar it contacts. It turns out that
> the sensor is an entirely separate mechanism, with a different
> protein, and that it doesn't sense exactly the same shape of
> sugar at all. One can use chemically modified sugars recognized
> by the sensor, which cannot be transported or provide nutrition.
> And the systems can be mutated separately to have different
> specificities for different sugars. So what appeared to be
> an intelligent, purposive response by the cell turns out to be
> totally mechanical. The story is told in The Eigth Day of
> Creation, by Jodson.

It is actually a fact that "all theories that impute knowledge or
purpose to subcellular or cellular structures have been discarded"
by mainstream science. But my suspicion is that reductionist
(materialist) prejudices have been the main reason. In physics,
actions at a distance have been discarded despite the fact that
experiments (electrostatic attraction and repulsion) showed and
show their existence.

Normally the first who detects a new mechanism has the
possibility to provide a philosophical interpretation. I do not
agree with Monod's interpretation, because it is not based on
facts. The same facts can be interpreted in very different ways.

According to Monod's interpretation, every system we have
examined carefully enough can be called mechanical.


> (A small pedagogic point. Your model is correct in size, but
> the thermal motion at the molecular level is much faster than
> we would guess from everyday objects. Some enzymes can catalyze
> thousands of reactions per second, and the calculations show that
> random encounters will indeed expose them to that many substrate
> molecules in a second.)

In my model, little proteins have diameters of few millimetres, e.g.
myoglobin with 153 amino acids about 4.5mm x 3.5mm x 2.5mm.
The major groove of DNA is about 2mm large. The whole human
DNA (both chromosome sets) is about 2000 km long. The major
groove is even longer. If the recognition by transcription factors
depends on direct contact, then a transcription factor must
come very near (maybe 1mm or 2mm) to its destination and
should even have the correct alignment. A normal living cell
with a diameter of about 10m would consists of 10^12 different
cubes of 1mm length.


> The general doctrine of purpose or intelligence at the
> cellular level is known in the Twentieth Century as "vitalism".
> This is confusing, since the term has had several contradictory
> meanings in philosophy and biology. Some people consider that
> the "death of vitalism" was in the explanation of antibody
> diversity. Our blood contains perhaps a million different kinds
> of antibody proteins, out of billions of possibilities. The
> intuitively obvious explanation is that the immune system "sees"
> a foreign antigen and somehow molds the shape of the appropriate
> antibody. This is the "instructive theory". But the immune
> system doesn't work that way. It assembles a random sample of
> the billions of possibilities, each on a separage cell, then kills
> or inacivates those that react to "self" and allows the cells that
> encounter antigens to proliferate to make large quantities of
> antibody. This is the "clonal selection" theory, and the Nobel
> prizes for it were give out 40-50 years ago. Any immunology text
> will give an account.

There is an essential difference between panpsychism and vitalism.
Vitalism starts with dead matter and introduces some kind of 'vital
forces' or souls. In panpsychism, however, there is no dead matter,
because even elementary particles have two aspects, a 'materialist'
and a 'vitalist'.

In a similar way a human soul influences the behaviour of a
human body, some kind of primitive soul is responsible for the
astonishingly complex behaviour of photons.

The immun system has turned out to be more complex than
assumed by the "instructive theory". To kill or inactivate those
cells whose antibodies react to "self" is not so easy.

There was once the following problem:
How can the immune system distinguish between "self"
and "foreign"?

It was 'resolved' in this way:
Cells or antibodies reacting to "self" are inactivated or killed
by the immune system whereas those reacting to "foreign"
are not.

Once I read somewhere (or I dreamt to have read) that if we put
antigens to one of two glasses with the same fresh blood, also
in the glass without antigens corresponding antibodies appear.
If it is true, it would be very strong evidence for the psychon theory.
(It would be quite similar to the improvement of Agars control line
rats in learning: http://members.lol.li/twostone/E/aa1.html )


> So in general, there are no subcellular or biochemical systems
> that embody purpose in their present-day operation. Reductionism
> has been triumphant for many years, and is embodied on the once-
> controversial slogan "anything organisms can do, cells can do;
> anything cells can do, molecules can do".

I go even further. I assume a continuity from elementary particles
to human souls. The mind body problem, one of the oldest
philosophical problems, has never been resolved by materialist
reductionism, it only has been declared a pseudo problem.

Also the appearance of consciousness some billions years after
big bang is an open question. In addition to that, it is impossible
to localize the memories in the brain. Theories have seriously been
proposed where one memory is somehow stored in the whole
brain (in a holistic way). That seems to me rather evidence that
such memories are not stored in the brain.


Regards
Wolfgang

14-Mar-1999

Hello Jamie Schrumpf!

>> I'm sure that Johnson is or was a much more unbiased lawyer
>> than the average.

> Why would you say that? What is your evidence?

If have read some texts of Johnson about AIDS which I really
do appreciate. These texts have shown me that Johnson
is very conscious of the problem of bias. All his texts I have
read are much sounder than his opponents try to give the
impression.

> You are also overly fond of your own hypotheses, a usually-fatal
> affliction in science.

I don't think that this is necessarily a usually-fatal affliction. Many
great scientific successes would have been impossible if not
at least the scientists themselves had been fond of their
own hypotheses.

Cheers
Wolfgang

http://members.lol.li/twostone/links.html

14-Mar-1999

Hello Ian Musgrave!

Ian, why do call persons with religious, philosophical or scientific
convictions you don't like, damned liars? I think this should
not be the attitude a of scientist, it's rather the attitude of a
fundamentalist.

I am convinced that the HIV AIDS thesis represents maybe
even the biggest medical error of all times. Nevertheless, I do
not call the persons believing in AIDS orthodoxy damned liars,
even if I cannot exclude that some members of the AIDS
establishment are consciously lying.

>> Many enzymes work at defined places in a cell. If we create an
>> enlarged model, where enzymes are like little balls, then the volume
>> of the whole cell is about 1000 cubic metres. Imagine concretely
>> this situation: a little ball must come very near to a substrat and the
>> substrat recognition even depends on the correct alignment of the
>> little ball.

It is necessary to have a concrete imagination of the proportions
between cells, enzymes, molecules and so on. Therefore I have
introduced the enlarged model where 1mm corresponds to 1nm.
The 'diameters' of enzymes are then in the order of a few millimetres
and the 'diameter' of a water molecule is about 0.3 mm (there is
room for 33.3 water molecules in 1 cubic millimetre).

> Sometimes, but sometimes the enzymes are thethered to mebranes
> or other structures (eg some of the respiritory enzymes, signal
> transducing G-protiens etc). As Gavin tTabor pointed out, in aquoes
> solution there are around 10^14 interactions/sec between molecules,
> and the volume involved is nanoliters, which is miniscule compared to
> the free diffusion paths of these molecules, so it is not particularly
> difficult for a substrate to meet it's enzyme in the right orientation
> just by randomly bouncing around in the cell.

One nanolitre gives a cube with a side length of 0.1mm, and in
our model this corresponds to 100 m !!! You even claim that such
lenghts are minuscule compared to the free diffusion paths of the
enzymes. Are you confusing kinetic theory of gases with diffusion
in aqueous solutions, are you telling us a joke, or are you even
telling us a ... ?

It seems that you do not know the theory of Brownian motion.
Einstein calculated in a 1905 paper that a particle with a
diameter of 0.001mm (the size of a bacterium) would result
in an average motion of 0.0008mm in a second and of 0.006mm
(less than the length of normal cell) in a minute (at a temperature
of 17°C). The average motions per time unit of enzymes are
certainly longer because they are much smaller. The bigger
the particles, the slower random thermal motions. The reason
is simple: random collisions with many surrounding molecules
can cancel each other out and the remaining change in
momentum does not increase proportionally to the mass
of the moving particle.

In our model, a normal living cell with a diameter of about
10m consists of 10^12 different cubes of 1mm length. So its
rather difficult for a substrate to meet it's enzyme in the right
orientation "just by randomly bouncing around in the cell".
Don't forget, most of the 10^14 random collisions primarily with
water molecules have no effect at all! Every square millimetre
of the enzyme surface corresponds to about 10 water
molecules.

>> In addition to that, enzymes often have to pass cell
>> membranes in order to reach their destination.

> This happens very rarely, and then the enzymes are usually secreted
> via a specific membrane targeting peptide. (Unless you are talking
> about passage of transcription factors into the nucleus, where they
> pass through the pores in the nuclear membrane)

Only at the most 5 percent of the hundreds of different
mitochondrial proteins are coded by mitochondrial DNA. The
proteins even have to pass a double membrane in order to
reach their destination. According to the very convincing
endosymbiont theory, at least most of these proteins (or their
ancestors) were coded once by the mitochondrial DNA itself.
How do you explain the fact that the proteins could find
even after the transfer of the genetic code to the nucleus
their destinations within the mitochondrion?

>>What is the moving force of enzymes? It cannot be
>> electromagnetic attraction or repulsion.

> Sometimes it is a contributor, many proteins have a small net charge,
> but for untethered proteins, simple random motion works nicely.

>> So the moving force must primarily depend on random
>> thermal motions (as Brownian movements do).

> Okay. Whats the mean free path of a small molecule such as say,
> glycine in free solution. What is the mean free path of a haeomglobin
> molecule

There is no free path at all!

>> You certainly will object that we do not know well enough the
>> chemistry of enzymes in order to conclude that: there may always
>> be the needed chemical forces responsible for the 'apparently'
>> very purposeful motions of enzymes.

> What apparent purposeful motion of proteins?

For instance motions of transcription factors or of ribosomal
proteins. There are many other examples: look for instance at
the many enzymes involved in DNA replication. If there were
only random thermal motions, only a very small percentage of
the enzymes would work (by chance).

>> This implies that the information
>> for these motions to desired destinations is somehow stored in
>> the amino acid sequence of an enzyme, in addition to to the
>> information for folding, substrat specifity and so on, because even
>> similar enzymes can have very different destinations.

> For tethered proteins, certainly yes. As an example, signal
> transducing GTPases (G-proteins) are targeted to the membrane by a
> palmitoyl group attached to the enzyme, for protein kinase B, it the
> plextrin homolgy domain that does the job of targeting. For things
> like the monoamine oxidases, its a combination of structure and local
> production that confines them to the mitochondrial wall.

>> A mutation
>> could change a description factor in such a way that the protein
>> would search its usual substrate in a wrong chromosome.

> Most certainly.

>> The voyage of transcription factors to their destiny can be compared
>> with the voyages of migratory birds and other migratory animals.

> Not really, you're missing the scale of the cell and thermal motions.
> A transcription factor can cross the cell in a nanosceond, the
> observed rates of transcription factor initiation is entirely
> compatible with the enzymes just randomly boncing around in the cell.

If this is true and transcription factors generally reach their
destinations some micrometres away in a nanosecond, than
(materialist) reductionism is dead !!!

>> You ask me, how can I "be certain that 'at least 20' independent
>> and mutually improbable conditions all have to be satisfied, in one
>> particular sequence". I have the same right to ask you, how can you
>> be certain that not at least 20 different conditions with low probablilty
>> must be at the same time satisfied for a replicating system to appear.

> Well, that's a nice way to avoid the question. But from model self
> replicators, and our current knowledge of chemistry, we can say that
> the steps (however many they are) are not independent and at least
> some are not particularly improbable.

I don't speak of steps but of conditions. If in an experiment
the necessary amino acids are are put together in an optimal
concentration, than we have a condition whose probability is
certainly less than 10^-100.

> Where do the "at least 20 steps" come from? is there a mathematical
> analysis? what is the "granularity" of the steps? Are you refering to
> the sequential formation of 20 discrete molecules? or are the steps
> something else for example:

> 1) formation of building blocks
> 2) formation of a self-replicating molecule from bulding blocks
> 3) expansion of the replicator to a catalytic hypercycle
> 4) encapsulation of the hypecycle in a membrane
> 5) compartmentalization of the hypercycle into a genetic and a
> metabolic compartment
> 6) formation of a genome from the genetic hypercycle
> (this is the Eigen style model, a Kaufmann model would replace steps 2
> and 3 with formation of catalysits and catalytic closure respectively)

These are also conditions which must have been satisfied for a
self-replicating cell to appear. And the probabilty for each
condition is very low or almost zero (within the reductionist
causal framework).

>> Within the reductionist framework there is no sound reason to
>> assume that stages which could give rise to a self-replicating system
>> are rather conserved than other stages, or that steps in the right
>> direction have somehow a higher probability than steps in a wrong
>> direction.

> Depend on whether you are using a Eigen style "single replicator"
> hypercycle model, an RNA/ribopeptide world co-operative hypercycle or
> Kaufmanns catalytic closure. In the latter two self replicating
> systems are significantly advantaged in their chemistry.


>> The present-day scientific ignorance is no better evidence for
>> reductionism than for panpsychism! But is it really a necessary
>> ignorance? Ignorance is often the result of false premises.

> How often, example please.

For instance ignorance about a cure for AIDS.

> What is a prediction of panpsycism in chemistry that can be tested.

Unfortunately panpsychism predicts what you think can be
explained by reductionist causal laws.

I ask you: can you imagine anything which would convince you
that neo-Darwinism is not generally correct?

If it would be possible to produce large amounts of rare proteins
such as luminous proteins by biotechnological means, this would
be strong evidence against the psychon theory.

>> I'm convinced that physical laws as described by classical physics
>> or by QM cannot be responsible for the fact that living organisms
>> evolved and survive.

> Why, what is it about, say bacterial respiration that can't be
> explained in modern physics and chemistry.

>> The often cited 'complex dynamic systems' as
>> e.g. the appearance of ordered vortices, waves or similar things
>> doesn't affect evolution much more than the appearance of solar
>> systems does. And the appearance of crystals (carefully studied
>> by Kepler) is rather evidence for panpsychism than for reductionism.

> Crystals from by well studied physical laws. Name an aspect of crystal
> formation that is explained by panpsycism and not modern chemisrty and
> physics. Can you predict from panpscism which molecules will
> crystalise to form face centered cubic structures?

In the same way you cannot predict from an evolution theory,
what kind of animals have appeared you cannot predict from
the psychon theory what kind of behaviour molecules have
developed during evolution.

>> One must not confuse logical reasoning with empirical facts.
>> Calculations of probability must be based on clear and sound
>> assumptions, but the calculations themselves must not be
>> influenced by empirical facts.

> Ahh, nice try, but in probability you must always check your empirical
> facts (if you assume you have a normal distribution, when you in fact
> don't have one, your calculations are meaningless).

I think your calculations are meaningless because they are
based on premises which represent themselves very improbable
conditions.

>> From the fact that evolution has
>> occured we cannot conclude that it can be explained on the basis
>> of the generally accepted metaphysical principles of current science.

> z@z meet William of Occam, he has a razor he thinks you should use.

My razor is certainly much better than yours. It has no sense
to cut off not only the hair but also the ears (Mike Tyson would
rather bite them off).

>> Philip E. Johnson:
>>
>> "But when materialism is assumed as the very basis of science, they
>> can re-emerge a few logical steps later in triumph. Something had
>> to guide evolution, to produce those wonders of apparent design,
>> and natural selection is just about the only materialist contender."

> Of course, there is the little problem of all this _evidence_ for
> selection (both natural and sexual) that people keep turning up.

I don't understand what you mean here and probably you don't
understand what Johnson means.

We all make errors, it's almost impossible to avoid them, but we
should try to correct them as soon as possible.


Cheers
Wolfgang

http://members.lol.li/twostone/E/psychon.html

16-Mar-1999

Hello Jim Lippard!

>> I am convinced that the HIV AIDS thesis represents maybe
>> even the biggest medical error of all times. Nevertheless, I do
>> not call the persons believing in AIDS orthodoxy damned liars,
>> even if I cannot exclude that some members of the AIDS
>> establishment are consciously lying.

> Check out Steven Harris's letter in response to Johnson's
> _Reason_ magazine article:

> http://www.reason.com/9504/letterstext.apr.html

I recommend that everybody should study this article, but WITH
the few paragraphs of the reply of Charles Thomas, Kary Mullis,
and Phillip Johnson at the end.

The following quote is representative insofar is it shows
better than anything else that the HIV AIDS thesis is
primarily based on authority and dogmatism:

"I thought the Thomas/Mullis/Johnson article an unusually
bitter one for REASON to be running, since its authors
suggest not only that the U.S. government has failed with
AIDS but that just about everyone else has failed to think
properly as well. The authors essentially suggest that the
scientific method itself failed when it has come to this
problem--that instead, hundreds of independent working
groups in public and private labs in scores of countries are
even now participating in the same shared conspiracy or
mass delusion. Supposedly, every major HIV study lab has
been afraid to acknowledge openly that the emperor has
no clothes. Does this really seem likely to the reader? I am
strongly reminded of the conspiracy theories of creationists
and UFO-coverup enthusiasts when I read this kind of thing."

Karry Mullis is nobel laureate in chemistry of 1993 for discovery
of polymerase chain reaction, and because of the importance
of his discovery he is certainly one of great nobel laureates!
Without his method not even in all HIV antibody positive AIDS
patients the virus could be detected.

(Further condensed information e.g. on the proportion of
HIV to blood cells you can find in in my German text:
http://members.lol.li/twostone/dialog.html )


> as well as Harris's _Skeptic_ magazine article on this subject:
>
> http://www.skeptic.com/03.2.harris-aids.html

I know very well this article, because I myself have written a
critique of it some months ago (unfortunately in German). I
use a lot of quotations from the article, so one can grasp my
objections, even without my German comments:

http://members.lol.li/twostone/aids.html#definition


Here some quotations of Harris' article:

*** Redefining AIDS ***

"Acquired Immune Deficiency Syndrome is the name
historically chosen for a new medical syndrome which is
essentially 100% fatal"

"In the early days of AIDS, before HIV was discovered,
the syndrome was indeed defined using such opportunistic
diseases, and people with these infections are still included
in the federal Centers for Disease Control (C.D.C.) clinical
surveillance definition of AIDS (but now only if they are
also HIV infected). We will not be able to use this C.D.C.
definition. Not only does it assume HIV infection, but for
historical, political, and technical reasons, it also is
constructed in a way which does not assess current
immune status in the best way."

"CD4+ lymphocyte blood counts tell much of the story in
AIDS and other immunodeficiencies involving the
T-lymphocyte immune system. A healthy adult might have
a CD4+ lymphocyte count of 800 to 1000, with a CD8+
count half of this. These are normal values. Under physical
stress, injury, or chronic infection, CD4+ lymphocyte count
might drop to 500 (to even less than the CD8+ count), and
mild, non-fatal opportunistic infections might be the result.
A CD4+ count less than the CD8+ count was once used
as a crude marker for AIDS, but today with progress we
know that this immune state is non-specific."

The important point: "Under physical stress, injury, chronic
infections ... "

"Thus, we must also exclude from our AIDS definition all
those people who have one of the classic reasons for a
very low T-lymphocyte count--reasons which were well-known
before the AIDS era (cancer, malnutrition, tuberculosis,
radiation, chemotherapy, etc)."

The important point: cancer, malnutrition, tuberculosis,
radiation, chemotherapy can lead to "a very low T-lymphocyte
count".

AZT, which had been invented in an attempt to find a
chemotherapy against cancer because it can prevent DNA
replicatation, turned out to be so toxic that it could not even be
used as a temporary treatment against cancer. In the end,
however, it has been prescribed for thousands of healthy
(HIV antibody positive) people!


*** HIV-Free AIDS ***

"This syndrome was named 'ICL' (idiopathic CD4+
lymphocytopenia), meaning 'people with low CD4+
lymphocyte counts without a medically-defined disease.' "

"Why was ICL not simply called 'HIV-free AIDS?' Critics have
darkly suggested that the reason is politics, but in fact there
were problems with considering these people as AIDS cases
which had nothing to do with AIDS politics or the HIV theory.
One difficulty was that people labeled as having "ICL" were
found not to come from the AIDS risk groups."

But poverty related diseases in Africa or elsewhere have been
called 'AIDS' despite the fact, that the patients "were found not
to come from the AIDS risk groups" !!!

*** The Origins of AIDS ***

"In addition, the American homosexual-male community was
apparently many times re-infected by many world-traveling
disease "vectors" from other countries in the 1970s, including
an airline steward named Dugas (described in Shilts as the
C.D.C. 'patient zero') who traveled widely in Europe, Canada,
and the U.S., died of AIDS, and is known to have had sex
with no less than 40 of the first 248 Americans to be
diagnosed with AIDS by April, 1982."

Now we know how difficult it is to transmit HIV (see below).
Hundreds of sexual acts are necessary to transmit the virus
with a high probability from one person to another!

"The rise in total mortality risk in people with hemophilia was
sudden: total mortality in this population, which had been
stable in 1982 and 1983, suddenly increased by a factor of
approximately 900% in the first quarter of 1984. Such an
increase in raw numbers of deaths was consistent with an
epidemic, or ..."

What is the real explanation of this sudden increase "by a factor
of approximately 900%" in mortality in one quarter of a year?

Panic and antiviral drugs !!!

The effects of stress and depression on the immune system
are studied nowadays by psycho-neuro-immunology.

"In the 1980s, total mortality for hemophilia increased in all
age groups above nine years of age, and age at death
shifted markedly to lower ages, decreasing from 57 years
of age in 1979-1981 to 40 years of age in 1987-1989."

The only sound explanation:

The introduction of AZT (see above: chemotherapy).

"About 50% of people with hemophilia in the U.S. had
been HIV infected by early 1986, when screening and
treatment of the clotting factor concentrate stopped HIV
spread. Still, the long latency of the virus (as long as 15
years for 50% progression to AIDS in this group) caused
death rates to rise for long after the window of new HIV
infection closed."

On the one hand a sudden increase "by a factor of
approximately 900%" in one quarter and on the other hand
a latency of the virus as long as 15 years !!! !!! !!!

*** Attacks on Straw Men ***

"It is an unfortunate fact that a great deal of the debate
over AIDS and HIV has been over what rhetoricians call
'straw men'. A straw man is an argument or viewpoint
set up in a debate only for the purpose of being knocked
down, and one which the opposite side never really
defended or held; or one which is not very important to
the central issue of the debate, even if it has been held."

"It is also asserted in a related argument by Root-
Bernstein that the HIV/AIDS hypothesis does not explain
the generally-low measured levels of HIV virus in semen,
the low (but not zero) rate of HIV infection in mates of
HIV-positive men with hemophilia, or the nearly zero rate
of infection in U.S. heterosexual prostitutes (unless they
are drug users). If AIDS is an infectious disease, ask the
skeptics, then why does HIV not infect very well?"

Is this actually "not very important to the central issue of the debate"?

Wolfgang

http://members.lol.li/twostone/links.html

18-Mar-1999

Hello Ian!

[several snips]

I'm sorry that I wrote in another post to you that you call other
persons 'damned liars'. You answered that you do not, so I
believe you. My claim was primarily based on your site "Lies,
Damned lies, Statistics and Probability Abiogenesis Calculations"
http://www-personal.monash.edu.au/~ianm/prob.htm .

I had found this site through a link of Richard C. Carrier and I
thought it was your main page. In the meanwhile I have seen
also your main page giving a much better impression of you.

Nevertheless, you call my convictions and claims "damned lies".
Even if such convictions are wrong, they are no lies! If you
don't want that people can get the impression that you call them
"damned liars", then you should change at least the name of
your site.

>>> ... As Gavin Tabor pointed out, in [aqueos]
>>> solution there are around 10^14 interactions/sec between molecules,
>>> and the volume involved is nanoliters, which is miniscule compared to
>>> the free diffusion paths of these molecules, so it is not particularly
>>> difficult for a substrate to meet it's enzyme in the right orientation
>>> just by randomly bouncing around in the cell.

>> One nanolitre gives a cube with a side length of 0.1mm, and in
>> our model this corresponds to 100 m !!! You even claim that such
>> lenghts are minuscule compared to the free diffusion paths of the
>> enzymes. Are you confusing kinetic theory of gases with diffusion
>> in aqueous solutions, are you telling us a joke, or are you even
>> telling us a ... ?

> No, free diffusion of molecules in solution is very rapid. Have you
> actually had anything to do with diffusion in solutions. ...

>> It seems that you do not know the theory of Brownian motion.
>> Einstein calculated in a 1905 paper that a particle with a
>> diameter of 0.001mm (the size of a bacterium) would result
>> in an average motion of 0.0008mm in a second and of 0.006mm
>> (less than the length of normal cell) in a minute (at a temperature
>> of 17°C). The average motions per time unit of enzymes are
>> certainly longer because they are much smaller.

> Good heavens, just look at your own calculations, a bacteria sized
> particle travels 800 micrometers a second, thats roughly 8 times
> the diameter of an average mamalian cell!!! And that's at 17 degrees,
> whereas mammalian cells are at 37 deg C! Protein sized particles
> travel much faster as you say. Your _own_ calculations show you
> are wrong. Now add in diffusion down a chemical gradient, and you
> are way out of field.

I don't understand: according to Einstein's calculation a bacteria
sized particle travels 0.8 and not 800 micrometers in a second. The
mean path is proportional to the square root of both the absolute
temperature and the time, and inversely proportional to the square
root of the diameter (of a spherical particle). The mean path of a
spherical enzyme with a diameter of 10 nanometers is roughly
10 micrometers in a second and roughly 10 nanometers in a
microsecond. For a mean path of 1 nanometer (about three times
the lenght of a water molecule) ten nanoseconds are needed!
The mean path of a little protein such a trypsin in 10 nanoseconds
is about 2 nanometers.

Why is a 100-fold increase in time needed for 10-fold increase in
the mean path? Because the movements are purely random and
the particle will come back to the starting point over and over
again (in infinite time).

>> In our model, a normal living cell with a diameter of about
>> 10m consists of 10^12 different cubes of 1mm length. So its
>> rather difficult for a substrate to meet it's enzyme in the right
>> orientation "just by randomly bouncing around in the cell".

> On the contrary, it can visit all 10^12 cubes nearly 100 times
> via a random walk.

(That this is impossible, you have recognized yourself.)

Here you assume that collisions of the enzyme result in
movements substantially longer than 1 millimeter and that
the enzymes are regularly reflected in the cell walls.

"The 'diameters' of enzymes are then in the order of a few
millimetres and the 'diameter' of a water molecule is about
0.3 mm (there is room for 33.3 water molecules in 1 cubic
millimetre)."

"The bigger the particles, the slower random thermal motions.
The reason is simple: random collisions with many surrounding
molecules can cancel each other out and the remaining
change in momentum does not increase proportionally to
the mass of the moving particle."

Please imagine very concretely the many water molecules
(0.3 millimeters) colliding with the enzyme (e.g. a diameter of
some millimeters). Think about the effect of such a collision on
a protein whose mass is thousands of times bigger than the
the mass of the water molecule.

>> Don't forget, most of the 10^14 random collisions primarily with
>> water molecules have no effect at all! Every square millimetre
>> of the enzyme surface corresponds to about 10 water
>> molecules.

> But not all of that surface is water, there are also ions, substrate
> molecules and other proteins.

The objection seems not relevant to me.

> Acording to you, enzyme reactions can't take place at all, even in a test
> tube. However, they take place in test tubes at rates that are entirely
> consistent with substrates and enzymes meeting randomly in a diffusion
> limited way (with the exception of enzymes with lipid soluble substrates).
> This is all elementary enzyme kinetics.

On the contrary, according to your reductionist Darwinism enzyme
reactions can't take place at all. The main principle of this modern
word view is the hypothesis that biology can be reduced to chemistry
and chemistry to physics. But if we explain chemistry by physics we
should do it in a careful and consistent way. It has no sense to put
forward some formulas which are in agreement with the experiments,
and to simply assume or claim that they are consistent with physics.

> If your theroy was right, you might expect substantial differences
> between hormone/receptor interactions in broken cell preparations,
> and in intact cells.

I suppose that in the meanwhile you know that this is not true.
It would be true for at least some forms of vitalism.

>> Only at the most 5 percent of the hundreds of different
>> mitochondrial proteins are coded by mitochondrial DNA. The
>> proteins even have to pass a double membrane in order to
>> reach their destination. According to the very convincing
>> endosymbiont theory, at least most of these proteins (or their
>> ancestors) were coded once by the mitochondrial DNA itself.
>> How do you explain the fact that the proteins could find
>> even after the transfer of the genetic code to the nucleus
>> their destinations within the mitochondrion?

> Specific targeting peptide sequences. These can be tailored to
> particular phospholipid ratio's in differnt membranes, or bind to
> a peptide receptor.

How probable is it that hundreds of mitochondrial genes received
during or after their transfer into the nucleus by random mutations
(blind chance) exactly such specific sequences which direct their
corresponding enzymes back to the mitochondria?

>> I ask you: can you imagine anything which would convince you
>> that neo-Darwinism is not generally correct?

> I can imagine several things, including showing that that DNA
> relationships between organisms do not form patterns of descent
> (they do, but that is one potential test).

The assumption that DNA relationships between organisms form
patterns of descent is valid for most sound evolution theories. It can
not even discriminate between Darwinism and the psychon theory.

>> If it would be possible to produce large amounts of rare proteins
>> such as luminous proteins by biotechnological means, this would
>> be strong evidence against the psychon theory.

> Bad news, the rare jelly fish fluorescent protein Aequorin can be
> made in large quantitites by biotechnology see
> http://www.probes.com/handbook/ch22-5.html#Recombinant
> as can things like luciferase. There are receptors that occur in
> only one or two copies per cell (like the Beta receptors) which
> can made in large copy number by biotechnology, you can even
> artifically synthesise some (smallish) peptide hormones that have
> the full biological activity of their natural counterparts.

Have you actually read the Aequorin site? How do you define
"large amounts"? I define it in the following way: at least bigger
amounts than there are in nature.

The biological activity of small peptide hormones depends rather
on the enzymes reacting to them than on them themselves.

Ian, it will be necessary to clarify why our figures are so different.
I hope that the error is on your side you probably hope that it is
on my side.


Cheers
Wolfgang

21-Mar-1999

Hello (Dr.) Gavin (Tabor)

> Hi.
>>
>>>>>> If for a first organism with the power of reproduction to apppear
>>>>>> only twenty different conditions with a probability of each 0.001
>>>>>> were necessary, then the probability of such an organism to
>>>>>> appear would be only 10^-60.
>> . . .
>>>>> Even if 19 of the 20 conditions were fulfilled, the organism
>>>>> could not replicate and evolution of life could not start.
>>>>
>>>>> Not true, Show your math.
>>>>
>>>> No math is necessary, because my argument is based on the
>>>> premise that all 20 (independent from each other) conditions
>>>> must be fulfilled for replication to start.
>>
>>> Where did you get the figure of 20 independent conditions, all
>>> with such low probabilities from? I think that thats the real question.
>>
>> Look at the complexity of living cells!
>
> Noone (to my knowledge) thinks that currently-living cells were
> the first reproducing entities. This is the area of abiogenesis
> (not evolution) which is admittedly speculative : but it seems
> likely that much simpler protein molecules which were able to
> construct copies of themselves from simple amino acids were
> first (see below).

Simple replicating proteins are not enough to start evolution,
because they cannot continuously evolve to proteins which
are coded by RNA or DNA. Take for instance a folded protein
with an amino acid length of 32. Can you imagine some
mechanism by which the sequence information is transfered
to a 96 (or 64 in a genetic precursor code) nucleodid long
RNA or DNA molecule?

How big is the probability that DNA or RNA sequences which
correspond to the yet evolved proteins could have appeared
by chance? How probable is it that proteins being nothing
more than dead matter could invent the genetic code?
"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."
http://members.lol.li/twostone/E/psychon.html#a09

According to the psychon theory, enzymes are like primitive
animals. At least proteins and RNA enzymes should have
evolved at first indepentently. Self replicating proteins learned
sometime to use short RNA templates in order to accelerate
the production of new proteins. This technique was
continuously improved not only by pure chance but also by
final laws of nature (one could call it God).

The emergence of the genetic code can be compared with
the emergence of human languages, and the emergence of
the highly complex living cell with the emergence of modern
cities. All species and evolutionary innovations were designed
in a similar way houses, cars or ships have been designed.
But at the same time they have evolved by chance in a similar
way houses, cars and ships have evolved.

If it is true that living cells using the modern genetic code
appeared very early on the earth, then it is highly improbable that
this very complex code evolved the first time on earth. Such an
information transfer from 'cosmic ancestors' to the earth is
possible, because an essential part of the information of
living systems is stored in the immaterial psychons.

We cannot reproduce the behaviour of enzymes of the early
earth because their behaviour depends on psychons which have
further evolved. So amino acid sequences which would have
folded millions or billions of years ago, today do not fold any more.
In the same way, sequences which fold today did not fold on the
early earth.

>> I have answered this question in my last message to Loren King.
>> Here an excerpt:
>>
>> "For a self-replicating system at least 20 molecules which are at least
>> as complex as nucleotids or amino acids are necessary. According
>> to neo-Darwinism the movements of molecules depend on random
>> thermal collisions (apart from chemical and physical laws).
>
> Excuse me? Since when has neo-Darwinism had anything to do with
> kinetic theory? (I really thought I'd seen it all by now).

Do you really think that Neo-Darwinism is independent from other
disciplines such as mathematics, physics and chemistry?

> The movement of molecules in a gas or liquid is the result of
> collisions which are usually modelled using classical Newtonian
> mechanics. In something like a cell they are likely to be attached
> to each other electrostatically if in no other way, and will
> vibrate. These _are_ chemical and physical laws :nothing to
> do with biology.

That chemical and physical laws have nothing to do with biology,
is certainly wrong!

>> Now I assume that 20 molecules are enough for a self-replicating
>> system to appear, if every molecule has the right position in space.
>>
>> A further simplification is needed. I assume that all 20 molecules
>> are in a cube which is subdivided into 1000 mini-cubes, and for the
>> right position nothing more is required than the center of gravity of
>> the molecule being located within the right mini-cube.
>
> Actually, all you want is the right topology for the interconnections.
> Distances will be irrelevant : since these will be determined by the
> physics of the situation, not by the probabilities. IE you are
> estimating the wrong things here.

With this example I intend only to show how few conditions give
such a low probabilty of 10^-60. If for a self-replicating system only
60 building blocks were needed and the probability of the correct
chemical bonds with the others is 10% for each of the 60 blocks,
then the final probability of the system also results in 10^-60.

>> In this simpified case the probability for the self-replicating system
>> to appear is 10^-60. Common sense is enough to show that for a
>> self-replicating system to appear in nature, the probability is even
>> much much lower."
>>
>>> My understanding is that the smallest self-replicating protein
>>> has 32 base units in it. If there are say 10 different amino
>>> acid choices for each block, that implies there are 10^32
>>> such proteins which can form - ignoring any issues of
>>> chemistry. In a liquid molecules interact at a rate of around
>>> 10^14 interactions/sec : lets say new arrangements are formed
>>> at that rate. In 1 mole of amino acids that means there are
>>> 10^22 32-element proteins, and in 1 second, there are
>>> thus 10^36 proteins being tried. Thus in 1 second, 10^4
>>> of these self-replicating proteins will be formed.
>>> Sounds like pretty good odds to me.
>>
>> Are you telling a joke?
>
> Do I look like I'm joking? I'm providing you with an example
> of how to go about estimating the likelyhood of generating the
> simplest self-replicating entity given a flask of amino acids.
> This seems much more useful for the discussion than the probability
> of 20 marbles forming a pretty pattern in space (which is what
> you have worked out).

If you have not been joking, then you have been making
catastrophic errors!

I assume that the 10^14 interactions/sec are meant in the
following way: two neighbouring molecules collide with a
frequency of 10^-14 Hertz.

You assume that at this rate new arrangements of 32-element
proteins and only of 32-element proteins are formed! But why
only elements of a length of 32 amino acids?

The hypothesis that correct 32-element proteins are formed in
one step represents a condition whose probability is almost
zero both in nature and in laboratory!

But even if we take for granted this hypothesis, and the correct
sequence could be found by random trials, the folding of the
protein would be impossible because 10-^14 seconds are far
from being enough.

See for instance: http://www.snafu.de/~nolting/pnas97.html
So your calculation is further based on the hypothesis that
if the correct sequence is found, the sequence remains
unchanged for at least microseconds or maybe even
milliseconds so that the protein can fold. But already in one
microsecond all the other amino acids are each part of 10^-8
different 32-element sequences.

This hypothesis represents a condition whose probability is
virtually zero!

That not every thermal collision between two molecules results
in a new chemical bond is self-evident. And far the most
collisions occur between amino acids and water molecules.
Such 32-element sequences can only form by continuously
adding new amino acids. If sequences only grew and never
decayed, then after a short period there woud be no more
spare amino acids and the whole process would stop long
before the correct sequence could have appeared.

If the sequences decay easily, a sequence of 32 elements
can not be reached (this is what occurs naturally). So one
must include in the probability calculations also the probability
that a sequence of 32 correctly chained amino acids can
appear. If we assume that the probability of the correct
addition of a further amino acid is 0.5 (in reality the
probability is even lower) than the probability that a correct
32-element long chain can form is below 10^- 9 and not
10^0 as you assume.

If peptids are synthesized in vitro, special methods are
needed in order to prevent undesired chemical bonds.

And don't forget: Miller-Urey-style experiments result
predominantly in tar. Only the simple amino acids glycin and
alanin appear in substantial quantities. Most amino acids
do not appear in measurable quantities.

In addition to that there is the problem that not only the
needed forms of amino acids appear in such experiments,
but also their mirror-image isomers.

This problem is very well described in the excellent site:
http://www.yfiles.com/origin.html

Gavin, your calculations are representative for all neo-Darwinist
calculations which have 'shown' that evolution is possible
within materialist reductionism. You all seriously misunderstand
what is meant by probability calculation !!!

>> What is a self-replicating protein?
>
> One capable of reproducing itself from spare amino acids.

I agree. But the Lee peptide is not capable of reproducing
itself from spare amino acids! To call a simple peptide ligase
a 'self-replicating protein', even if it is able to ligate two halves
of its own amino acid sequence, is not only misleading but
maybe even dishonest!
see: http://www.scripps.edu/pub/ghadiri/

The Lee peptide is made of 32 building blocks. There are 20
different building blocks, and it is normal to attribute the
probability 20^-32 to the special sequence of the Lee protein.

20^-32 = 2.33 * 10^-42 = 0.000'000'000'000'000'000'000'...

The self-ligating Lee protein is made of 2 building blocks and
there are only 2 building blocks. So instead of
20^-32 = 2.33 * 10^-41
we have a probability of only
2^-2 = 0.25 !!!

Seid ihr Neodarwinisten denn von allen guten Geistern
verlassen !!! ??? !!!

>> To assume that every collision
>> between molecules corresponds to a new arrangement of a
>> sequence of 32 amino acids seems absurd to me.
>
> What I am doing is assuming that every time two molecules
> collide they are going to react to create a new molecule. This
> is rather dubious : but even if only 1% of collisions result in
> a reaction, I'm still ahead of the game.
>
>> Incorrect
>> chemical bonds between amino acids are possible. Bonds with
>> other molecules cannot be excluded.
>
> And I am taking account of these effects.
>
>> Where could a soup with
>> such a high proportion of amino acids have existed?
>
> Didn't say it did in this concentration. The concentration
> would be lower, and the rate of formation of new molecules
> lower (if the biochemists in the audience would like to provide
> some figures, we can factor these effects in). OTOH, there
> would have been far more than 1 mole of amino acids around,
> and its quite likely that the process of abiogenesis
> took O(100myr) - thats 10^15 seconds.
>
> I'd say this (which is definitely a back-of-envelope calculation)
> still holds up pretty well.
>
> Gavin

Cheers
Wolfgang

23-Mar-1999

Hello Gavin!


> Ian has already answered most of your points much better than
> I could, but there are just a couple of minor details I'd add

What Ian has answered is not convincing at all. Here an excerpt:

-----------------------

>But even if we take for granted this hypothesis, and the correct
>sequence could be found by random trials, the folding of the
>protein would be impossible because 10-^14 seconds are far
>from being enough.

This is not relevant, the protein can fold into it's structure later,
it doesn't have to do so during syntheis.

>See for instance: http://www.snafu.de/~nolting/pnas97.html

Which has nothing to do with this argument, it's about the folding
rate of a fully formed protein going from denatured to native states
for goodness sakes.

>So your calculation is further based on the hypothesis that
>if the correct sequence is found, the sequence remains
>unchanged for at least microseconds or maybe even
>milliseconds so that the protein can fold. But already in one
>microsecond all the other amino acids are each part of 10^-8
>different 32-element sequences.

Huh? what does this mean?

>This hypothesis represents a condition whose probability is
>virtually zero!

-----------------------

Do you think that such a reasoning is great? Ian is rather
inconsistent in his posts. And it is not possible to impress me by
scientific papers which presuppose what should be explained.

It is clear that every obstacle to forming a correct chain of amino
acids can be removed by some techniques or by some special
assumptions. But they represent conditions to which we also
must ascribe a probability.

"Mineral catalized or assisted peptide formation" is not available
everywhere. Each of 20 amino acids must then be available in
high proportions exactly in places, where "mineral catalized or
assisted peptide formation" is possible.


The following statements cannot be denied:

"According to neo-Darwinism the movements of molecules
depend on random thermal collisions (apart from chemical
and physical laws)."

According to the psychon theory the movements of molecules
depend not only on random thermal collisions!
http://members.lol.li/twostone/E/psychon.html#a08


>> I assume that the 10^14 interactions/sec are meant in the
>> following way: two neighbouring molecules collide with a
>> frequency of 10^-14 Hertz.

> No. A given molecule will interact with a new molecule
> every 10^-14 s. If you like, the `pack of cards' of each
> molecule is being reshuffled every 10^-14 secs.

The velocity of molecules in the air is around 10^2 or 10^3 m/s.
This gives a distance of 10^-11m or 10^-12 m every 10^-14 s.
(Einstein's formula for Brownian molecular motions gives similar
results in water, but for a x-time increase in distance, a x^2-time
increase in time is necessary.)

The length of simple molecules is 10^-9 or 10^-10, this is
around two orders of magnitude bigger than the distance
molecules move in 10^-14 s. How is it possible that a "given
molecule will interact with a new molecule every 10^-14 s",
if the given molecule moves only a small fraction of the
length of a molecule?

You should study the theory of Brownian motion!


> Within this distribution there are probably a large number
> of possible self-replicating molecules, but still a small fraction
> of all possibilities. So I need data on the distribution and on
> the number of possible self-replicators. Which I don't have.

The existence of real self-replicating (the Lee protein is only
self-ligating) proteins would be strong evidence for the
psychon theory (in the same way as prions and inteins are
strong evidence for this theory). There are proteins with very
different behaviours.

Even if we take for granted that a 32-element protein creates
correct amino acid sequences of the needed length, a big
problem remains. There are 20^32 different sequences.

So general chemical and physical laws must lead to:

1) The sequence of 32 amino acids folds correctly.
2) The folded protein recognizes many different amino acids
and is able to chain them in the correct way.
3) Always the same sequence is created.
4) This sequence corresponds by chance (no base pairing is
possible) to the amino acid sequence of the protein itself.

I garantee you, Gavin, that's completely absurd.


Cheers
Wolfgang

Further posts to talk.origins:
Darwinism refuted by adverse selection experiments
Aids: have we been misled?

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