talk.origins probability-abiogenesis FAQ criticized

Ian Musgrave & Peta O'Donohue e21092_insert at minyos.its.rmit.edu.au
Wed Jan 10 21:21:18 EST 2001


G'Day All
Address altered to avoid spam, delete RemoveInsert

This is the second last of my posts before I dissapear due to family
and work pressures.

On 4 Jan 2001 11:57:32 -0500, zOz <wissenschaftskritik at my-deja.com>
wrote:

>[ Extended version of my previous critique ]
>
>Extracts from http://www.talkorigins.org/faqs/abioprob.html :
>
>
>| Problems with the creationist "it's so improbable" calculations:
>
>The genuine problems are rather on the neo-Darwinian side. BTW,
>I'm an uncompromising evolutionist (i.e. I'm convinced of a
>continuous emergence of the world and of life).

Now that's a weird twist on neo-Lamarkianism.

>| 1) They calculate the probability of the formation of a "modern"
>| protein, or even a complete bacterium with all "modern" proteins,
>| by random events. This is not the abiogenesis theory at all.
>
>A probability of 10^-100 is enough to refute abiogensis, so
>it doesn't help to criticize calculations resulting in e.g.
>10^-1000000.

This still shows you don't understand, you are trying to calculate a
cumulative probability for a structure that is the end result of a
series of parallel events, that do NOT occur at random, and assuming
that that and only that structure is the one required.

>For comparison: in the order of 10^20 milliseconds have passed
>since the birth of the earth, a planet consisting of in the
>order of 10^50 atoms. This results in 10^70 "atom-milliseconds".
>It is obvious that the number of any reasonably defined
>"abiogenesis events" is by many orders of magnitude lower than
>the number of "atom-milliseconds".

Again, irrelevant. The process of abiogenisis (eitiobiology) is not
about random events, but about chemical and physical processes.

>Even if we assume that 1) around 10^20 planets could have given
>rise to us, and that 2) one single successful abiogenesis event
>leads inevitably to higher forms of life, a probability of
>10^-100 would still make our existence very improbable.

Again, it's a nonsense calculation. The processes are NOT random.

>Because neo-Darwinism is not even consistent with the evolution
>of the upright gait in humans, assumption 2) is obviously
>untenable. See http://www.deja.com/=dnc/getdoc.xp?AN=698302471

Cute, but irrelevant. You really have to look up the roles of
developmental genes, where you get a lot of co-ordinated structure in
one go. An interesting example is the axolotl, where a single point
mutation results in a large change in morphology.

>| 2) They assume that there is a fixed number of proteins, with
>| fixed sequences for each protein, that are required for life.
>
>This assumption is not necessary in order to refute (purely
>materialistic) abiogenesis, because the improbabilty lies
>already in functional constraints which are a prerequisite
>for any form of self-replication.

Definitely not, take for example Kaufmann's catalytic closure system,
where any system of protoenzymes become self replicating, or Eigens
hypercycles (and variants thereof), a hypercycle based on lyine-rich
proteinoid would be very likely. Or look at the metabolism first
systems of Wachterhauser (none of the above three systems are mutually
exclusive by the way). All of which develop stable, self-replicating
systems with high probability (1 in Kaufmanns case).

>If six protoenzymes with each a probability of at most 10^-10
>are necessary for self-replication to start, we get already a
>probability lower than 10^-60.

Heck, in a mole of polypeptides you'd have at least 10^11 high
efficacy enzymes (see below) let alone 6 "protoenzymes", you are
falling into the "sequentiallist" trap again.

>The probability of random emergence of a proto-enzyme cannot
>be higher than 10^-10 even if it consists of only 10 rather
>widespread building blocks.

In fact, the figure is likely to be much less than that. For example,
lysine rich proteinoid is formed with a probability of exactly 1 from
drying of a mixture of amino acids containing lysine, it both a
peptidyl synthetase AND a polynucleotide synthetase. the probability
of _high_eficency_ enzymes is around 1 in 10^12 from work with
catalytic antibodies and ribozyme, the frequency of protoenzymes is
much higher.

>Such a value must include both the probability that a
>correctly bonded system of 10 building blocks arises and the
>"combinatorial probability". (0.5 * 0.2)^10 results in 10^-10,
>where 0.5 is the probability of correct bonds per building
>block and 0.2 the combinatorial probability per building block.

And these figures are nonsense, polypeptide condensation doesn't work
that way.

>The FAQ ("Coin tossing for beginners and macromolecular
>assembly") completely ignores the question of the "bonding
>probability". Only the combinatorial probability of a
>(32 amino acid long) sequence is taken into account and the
>experimental fact that correctly chained 32 aa-long sequences
>do not arise abiotically is discarded.

Oh they don't do they? Had a look at any of Ferris's experiments have
you?

>And we must keep in mind that the final product of abiogenesis
>must be able to undergo neo-Darwinian evolution and to survive
>a change in its environment (e.g. drying up of the primordial
>pond).

Na und?

>Also if "not even a protobacteria, or a preprobacteria" is
>necessary for further evolution by replication with mutation
>and selection to start, "but one or more simple molecules
>probably not more than 30-40 subunits long", then we still
>remain with the fact that the average probability of correct
>bonds with viable neighbours is certainly lower than 0.1 per
>subunit. 

Where on earth does this 0.1% figure come from? not chemistry.

>So the probability of the emergence of one "simple
>molecule" of this kind is still lower than 10^-30.

And in a prebiotic ocean with a amino acid concentration of 10^-6M
then we could expect something on the order of 10^9 of these molecules
using the above figures (actually it is somewhat less, but there is
still a hell of a lot of them)

>On abiotic formation of peptide chains:
>http://www.deja.com/=dnc/getdoc.xp?AN=507707704
>
>The abiotic emergence of RNA enzymes is even more questionable
>because it contains ribose. Ribose is not even resistent to
>water of normal temperature.
>http://members.lol.li/twostone/E/deja3.html --> ribose

Uh, your dead wrong, ribose is certainly "resistant to water", and is
made in several plausible abiotic reactions, the main problem is that
it is usually only present in small quantities (although some systems
can produce up to 30% of the sugars from formaldehyde condensation as
ribose). However, ribose is not necessary for RNA-like compounds,
Peptide Nucleic acids, Pyranosyl RNA and Teranosyl Nucleic acids all
have the requisite properties to play roles for a ribozymal world.

>
>| 3) They calculate the probability of sequential trials, rather
>| than simultaneous trials.
>
>This statement can be interpreted either as a strawman
>or as a summary of a central error of the FAQ, namely the
>assumption that whole protoenzymes emerge by simultaneous
>trials, and not by sequential steps (i.e. addition and
>breaking off of building blocks).

You don't understand the concept of simultaneous trials do you, even
given the one vs multiple coin example. Each individual peptide is
grown by the sequential addition of subunits, but as there are
something like between 10^23 and 10^40 growing peptide chains at any
one time, the time it takes to get a specific sequence (or a class of
sequences) is _much_ faster than the one chain at a time approach.

>http://members.lol.li/twostone/E/deja6.html --> 21-Mar-1999
>
>
>| 4) They misunderstand what is meant by a probability calculation.
>
>Those who declare simple and logically correct common-sense
>reasonings wrong in order to save the currently prevailing
>"scientific" dogmas are the ones who "misunderstand what is
>meant by a probability calculation".

In science "common sense" is very often wrong. But this is not the
issue. The issue is correct statistical reasoning (and an appreciation
of frequentist vs Bayesian probability approaches). Doing probability
calculations based on a false hypothesis of randomness is not going to
get you anywhere.

>| 5) They seriously underestimate the number of functional
>| enzymes/ribozymes present in a group of random sequences.
>
>The low actual number of functionally equivalent proteins and
>even DNA-coding sequences is rather evidence against the
>relevance of this argument.

Uh, no. There is a high number of functionally equivalent proteins,
for example the various independent serine proteases with minimal
sequence homology, the swappable PAX_9 eyeless proteins etc.etc.

>See: "The Death of Neo-Darwinism (was: Molecular Sequence Proof of
>Common Descent)" in http://members.lol.li/twostone/E/deja4.html

The above isn't relevant to the issue, but you need to read up on
silent mutations, single nucleotide polymorphisms and neutral drift
(remember that the majority of neutral mutations are lost rapidly to
genetic drift)

>The fact that each of e.g. 90% of the amino acids of a protein
>can be replaced by others without loss of function does not
>entail that the protein would still work if most of these
>replaceable amino acids were replaced at the same time.

Yes, in fact it does, eg in the RNAse enzyme Barnase you can replace
the entire core with random sequences in one go with no effect on the
enzyme activity. However, this is not the issue

>But even if we accept the argument, in this context it does not
>change a lot whether the combinatorial probability of a 100 amino-
>acid long enzyme is 20^-100 or 4^-100 (leading to 5^100 viable
>variants).

Well, yes it does. Work with ribozymes and catalytic antibodies shows
that there is roughly 1 high efficiency enzyme per 10^12 random
sequences, in a mole of random polypeptides or polynucleotides (which
is a pretty trivial amount of polywhatevers)  then you would have
10^11 efficient enzymes, by no means inconsiderable. Given that we
don't really need high efficiency enzymes (eg the lysine proteinoid is
an example), the number of potential enzymes is much higher.

>| [T]he formation of biological polymers from monomers is a
>| function of the laws of chemistry and biochemistry, and these
>| are decidedly not random.
>
>The laws of chemistry and biochemistry do indeed lead to the
>needed chemical bonds. (They also lead to undesired bonds and
>to the decay of desired bonds. If peptids are synthesized in
>vitro, special methods are needed in order to prevent undesired
>chemical bonds.)

Name them. Ever done any solid phase peptide synthesis? What do you
think happens on the mineral surfaces in the Ferris type experiments?

>However these laws do not concern the question whether a final
>sequence is able to fold into an enzyme and to carry out complex
>tasks. 

Oh yes they do. We don't fully understand the laws that govern protein
folding, but it is a physicochemical process, and enzyme activity is
likewise a chemical process the activity of serine proteases is
determined largely by the chemistry of serine. similarly, the folding
and enzymic activity of lysine rich proteinoid, derived from heating a
simple mixture of amino acids, is the result of basic chemical and
physical laws.

>So these laws have rather to do with the probability
>of correctly chained sequences long enough to arise at all
>than with the combinatorial probability of such sequences.

Now that is completely wrong.

Cheers! Ian

References:
Nelson KE, Levy M, and Miller SL.  (2000 Apr 11). Peptide nucleic
acids rather than RNA may have been the first genetic molecule. Proc
Natl Acad Sci U S A , 97,  3868-71.

Ferris JP.  (1999 Jun). Prebiotic synthesis on minerals: bridging the
prebiotic and RNA worlds. Biol Bull , 196,  311-4.

Jeffares DC, Poole AM, and Penny D.  (1998 Jan). Relics from the RNA
world. J Mol Evol , 46,  18-36.

Orgel LE.  (1998 Dec). The origin of life--a review of facts and
speculations. Trends Biochem Sci , 23,  491-5.

Miller SL.  (1997 Mar). Peptide nucleic acids and prebiotic chemistry
[news] [see comments] Nat Struct Biol , 4,  167-9.

Di Giulio M.  (1997 Dec). On the RNA world: evidence in favor of an
early ribonucleopeptide world. J Mol Evol , 45,  571-8.

Hager AJ, and Szostak JW.  (1997 Aug). Isolation of novel ribozymes
that ligate AMP-activated RNA substrates. Chem Biol , 4,  607-17.

James KD, and Ellington AD.  (1997 Aug). Surprising fidelity of
template-directed chemical ligation of oligonucleotides [In Process
Citation] Chem Biol , 4,  595-605.

Bolli M, Micura R, and Eschenmoser A.  (1997 Apr). Pyranosyl-RNA:
chiroselective self-assembly of base sequences by ligative
oligomerization of tetranucleotide-2',3'-cyclophosphates (with a
commentary concerning the origin of biomolecular homochirality). Chem
Biol , 4,  309-20.

Ekland EH, and Bartel DP.  (1996 Sep 12). RNA-catalysed RNA
polymerization using nucleoside triphosphates. Nature , 383,  192.

Ferris JP, Hill AR Jr, Liu R, and Orgel LE.  (1996 May 2). Synthesis
of long prebiotic oligomers on mineral surfaces [see comments] Nature
, 381,  59-61.

Ertem G, and Ferris JP.  (1996 Jan 18). Synthesis of RNA oligomers on
heterogeneous templates. Nature , 379,  238-40.

Fox SW.  (1984). Self-sequencing of amino acids and origins of
polyfunctional protocells. Orig Life , 14,  485-8.

Lacey JC Jr, Yuki A, and Fox SW.  (1979 Mar). Coprecipitation of
thermal lysine-rich proteinoids with polyribonucleotides. Biosystems ,
11,  1-7.
=====================================================
Ian Musgrave Peta O'Donohue,Jack Francis and Michael James Musgrave
reynella at werple.mira.net.au http://werple.mira.net.au/~reynella/
a collection of Dawkins inspired weasle programs http://www-personal.monash.edu.au/~ianm/whale.htm
Southern Sky Watch http://www.abc.net.au/science/space/default.htm






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