Probability of life: NO FAQ!
Alex Matulich
month, have looked at all the FAQ files on ics.uci.edu that appear
relevant to my question, and haven't found it.
I have seen a couple of threads here, where a person quotes some
research about the probability of a single protein molecule occurring by
chance is 1 in 10^262 years, and that of a single cell is 1 in
10^119841 (this comes from James Coppege, _Evolution:_Possible_or_
Impossible?_, Zondervan Publishing, p. 180).
In these threads, the inevitable response is "This has been beaten to
death hundreds of times in this group! Go away!" -- or some similar
unhelpful non-refuting response.
Well, then, if this has been covered many times, WHERE IS THE DAMN FAQ?!
A few people have attempted to answer this "probability of life"
challenge, and I have captured there replies. One person mentioned a
protein molecule made up of two amino acids (implying a 100% chance of
forming the protein) but didn't say what the protein was.
One would think, for such a supposedly oft-discussed topic, that a FAQ
would exist someplace. Well, does it?
--
Alex Matulich
matul...@seaa.navsea.navy.mil
matu...@oasys.dt.navy.mil
Dan Day
>He has found that none of the published abiogenesis theories
>(inorganic matter -> life theories) can adequately address the self
>organization of the information content found in the genome.
"He has found"... using what assumptions? Unless he claims to fully
understand the origin of life, any calcuations he makes are going
to be based on his assumptions as to what is and is not necessary,
and how it may or may not have occurred. So what are his assumptions?
>While the ardent believer in self organizing abiogenesis may not
>appreciate Yockey, they will continue in their faith because they don't
>question their presupposition.
*snort*. I'm questioning *Yockey*. What are *his* "presuppositions"?
Or are "ardent believers in self organizing abiogenesis" the only
ones who supposedly rest their beliefs on presuppositions?
--
"Don't tread on me"
Dan Day
>: "He has found"... using what assumptions? Unless he claims to fully
>: understand the origin of life, any calcuations he makes are going
>: to be based on his assumptions as to what is and is not necessary,
>: and how it may or may not have occurred. So what are his assumptions?
>
>appropriateness of using Shannon entropy to evaluate information flow
>(this is not Boltzman entropy from statistical mechanics). So it seems
>rather than making assumptions, he is seeking to establish a mathematical
>basis for evaluating biological information (genetic information).
He's still going to have to make assumptions to make any calculations
based on "information flow". Like, how big did the first replicator
have to be? You have to pick a number before you can analyze how
likely it was to have come about by chance. How fast are the
chemical reaction times in question? How many places on the early
Earth were hospitable to such reactions? How large were they, and
what volume of reaction "soup" was there? How many reactions per
second would be taking place simultaneously all around the Earth?
All these things have to be considered before one can even attempt
to put some kind of number on the probability of abiogenesis, regardless
of what metric one is using. Winning the lottery is highly improbable,
but to make any meaningful statement about it you're going to have
to know how many people play it, how many places run lotteries, and
how often they have drawings.
>He certainly doesn't claim full understanding, but rather that current
>self organizing abiogenesis theories are flawed. He examines
>"protein first", RNA first, pyrite, and clay theories and their flaws.
Again, he will have to make assumptions about how large the first
replicator had to be, and the reactions that would go into forming
that *particular* replicator. Once replication began, all calculations
of "information flow" that assume random processes become moot, because
various other processes come into play.
>: *snort*. I'm questioning *Yockey*. What are *his* "presuppositions"?
>
>If you think thats bad, you should try reading Yockey. He doesn't have
>kind words for "unfettered speculation" that continues to pass as
>abiogenesis science.
I believe the main argument in abiogenesis is: It only takes one
replicator to kick off the whole process, and we know that very simple
processes and/or structures are capable of replication, therefore it's
not unreasonable to assume that a single such simple beginning could have
occurred by chance. Abiogenesis studies focus on the various possible
ways in which such early beginnings could take place, ruling out some
possibilities and focussing on others. Part of it is speculation and
part of it is hard science, but that's true of any field in its early
years.
>
>: Or are "ardent believers in self organizing abiogenesis" the only
>: ones who supposedly rest their beliefs on presuppositions?
>
>I think its universal. However, believers in "SOA" risk deceiving
>themselves if they think they have scientific evidence that undergrids
>their beliefs.
"Evidence" in the sense of inarguable support? No, but the field
is still young. However, their beliefs are based on the position
I state above, about how "it is not unreasonable that..." In the
absence of anything more plausible, it's all we've got at the moment,
but it's better than any of the alternatives, and it's not at all
out of the question. Given the nature of the earliest known life,
it also seems clear that we came from quite simple humble beginnings,
so the extrapolating backwards just a bit farther leads one almost
inevitably to the standard abiogenesis view.
>This is basically an "arguement from authority". Yockey has been doing
>serious study of information theory and molecular biology for a long
>time. (He was publishing in 1958.)
Could you give a quick overview of his method? Using "information
flow" sounds like empty hand-waving. I'd like to see a few specifics.
At the very least, does he take into account the fact that some
chemical processes are more likely to occur than others? If he
treats them all as equally likely transfers of information, he's
wrong from the start. Chemicals and molecular arrangements are not
bit patterns which can take any arbitrary pattern without preference.
If he *does* take such things adequately into account, he deserves
the Nobel Prize, because such a feat would be astounding (and unlikely).
Gallagher - Sean J.
:Sean, you still don't get it, do you? People working on the origin of
:life (of whom I am not one) will be the _first_ to tell you that
current
:theories (if any of them are even fleshed out sufficiently to deserve
:that name) are all seriously flawed. Maybe we will _never_ have
^^^ ^^^^^^^^^ ^^^^^^
:a really satisfying scientific theory- who knows, as even the most
:optimistic would admit that this is a peculiarly intractable field.
^^^^^^^^^^ ^^^^^^^^^^^
Nice to talk with you again Steve. I am glad we are in agreement. I
don't think I have seen you put it so pessimisticly though. Some how
our view hasn't made it to many of the folks who develop the popular
portrayals of the origin of life.
:But what, in your opinion, is the alternative- postulating that God
:simply stuck out her finger and said, "Let life begin"? That is
:simply to give up any attempt to do science on the origin of life. Why
:should people do that?
I think you may be jumping to conclusions. I appreciate the work
science has done in this area. It has illuminated the wonder and
complexity of even the simplest life forms. However, this has served to
show how difficult it is even to conceptualize self organizing
abiogenesis.
: And who are you to tell God how the thing
:ought to have been done- seeing that it was God (yes, though a
Unitarian
:I'm not afraid to use the G-word!) who created the laws of chemistry
:and physics?
Er, could you remind me when I did this. If I did, which I can not
remember an occasion of, I would have certainly been wrong.
: Why should God not have worked through these laws, rather
:than by "magic" as you seem to wish? This is something about your
position
:that you have never attempted to explain, and I really wish you would.
Again, I can not ever remember wishing for God do use magic. Far be it,
as a matter of fact. God does what ever he pleases. I agree with
Darwin's sentiments when he said something like, tis far grander that
creation would unfold so eloquently [if in fact that is how it
happened]. My desire is for the truth, for knowledge about reality, and
the principles that govern reality.
However, I consider it an appeal to magic when people believe the
goddess Fortuna (borrowed from Yockey) created life out of mythical
organic soup. My complaint is when this is passed off as "science" to
the unsuspecting. As you probably will agree, this happens in many of
the popular depictions of the "origin of life".
I believe this springs from a philosophy of scientific materialism
because when the flaws are pointed out in these depictions, true
believers rush to their defense with religious zeal, even grilling the
critic concerning his religious beliefs. The skeptic is then accused of
allowing religion to motivate his criticism.
I admit there are creationists who muck up the waters. Will you admit
there are materialists that likewise permit their faith to interfere
with their perception of science?
--
Steve LaBonne *********************** (labo...@csc.albany.edu)
"It can never be satisfied, the mind, never." - Wallace Stevens
BTW, if you haven't already, I think you would find of interest the
book: "Informational Theory and Molecular Biology" by Hubert Yockey
(1992, Cambridge).
-- Sean Gallagher -- sea...@umd5.umd.edu
The more I learn, || All views expressed
the more I realize I don't know. || are mine alone.
Gallagher - Sean J.
In article <3ivs5a$p...@hecate.umd.edu> sea...@hamlet.umd.edu (Gallagher - Sean J.) writes:
[Please bear with me as I messed up the symbols to indicate who is speaking]
In article <3ivs5a$p...@hecate.umd.edu> sea...@hamlet.umd.edu (Gallagher
- Sean J.) writes:
>: "He has found"... using what assumptions? Unless he claims to fully
>: understand the origin of life, any calcuations he makes are going
>: to be based on his assumptions as to what is and is not necessary,
>: and how it may or may not have occurred. So what are his
assumptions?
>
>He has shown the
>appropriateness of using Shannon entropy to evaluate information flow
>(this is not Boltzman entropy from statistical mechanics). So it seems
>rather than making assumptions, he is seeking to establish a
mathematical
>basis for evaluating biological information (genetic information).
Dan:
He's still going to have to make assumptions to make any calculations
based on "information flow". Like, how big did the first replicator
have to be? You have to pick a number before you can analyze how
likely it was to have come about by chance. How fast are the
chemical reaction times in question? How many places on the early
Earth were hospitable to such reactions? How large were they, and
what volume of reaction "soup" was there? How many reactions per
second would be taking place simultaneously all around the Earth?
All these things have to be considered before one can even attempt
to put some kind of number on the probability of abiogenesis, regardless
of what metric one is using. Winning the lottery is highly improbable,
but to make any meaningful statement about it you're going to have
to know how many people play it, how many places run lotteries, and
how often they have drawings.
Sean:
O.K., O.K., He does make assumptions in the examination of scenerios.
You really should go get his book if you are interested in evaluating
it. He usually accepts the assumptions of the proponents of the theory,
unless they are glaringly wrong. I'll give you a sample (from Yockey,
Hubert, Information Theory and Molecular Biology, 1992, Cambridge
Press):
9.2 The probability of generating protein sequences by chance
[9.2.1 was a discussion of other attempts to calculate probability and
their flaws, i.e., failure to account for the differing probabilities of
the various amino acids to match up]
9.2.2 Correct methods of calculating the probability
The biochemical questions of the polymerization of the amino acids in an
aqueous medium to form a sequence that would fold up to make a protein
with biological activity are not discussed in the papers cited in
section 9.2.1 (Previous attempts at calculating the probability). Such
subjects are skipped over with vague statements to the effect that 'the
desired substances will arise spontaneously'. If the scenario is
thought of being carried out with nucleotides the fact that 2',5' linked
isomers predominate in non-biological reactions (Orgel, 1986) is
ignored. The authors of ancient Greek plays used a deus ex machina
(feminine deu ex machina, plural dei ex machina), a god or goddess as a
machine, as a means to release humans from their otherwise inextricable
predicaments. These authors have done the same thing to bypass these
problems. For dramatic effect and to make it quite clear that these
important questions are bypassed by the authors advocating these
scenarios, I shall assign the task of selecting amino acids and of
polymerizing them to form proteins or DNA to the three Fates acting as
dei ex machina.
Let see how the Fates could go about selecting an iso-I-cytochrome c
sequence from a primeval soup. Lachesis, the caster of lots, casts her
110 icosahedral dice, suitably weighted to reflect the probabilities of
each amino acid. Clotho, who spins the thread of life, polymerizes
them, Atropos watches the progress of the spinning of the thread of
iso-I_cytochrome c and cuts it when Lachesis assigns an amino acid to a
site that is not among those that are functionally equivalent.
... whats the probability that Lachesis and Clotho will complete a chain
of 110 amino acids in the iso-1-cytochrome c homologous family without
having it cut by Atropos? The number of iso-1-cytochrome c sequences in
the high probability set obtained from Table 9.1 (Effective number of
amino acids for iso-1-cytochrome c) is 2.316 x 10^93. The total number
of sequences in the high probability set in a sequence of 110 sites if H
= 4.139 is 1.15 x 10^137. Therefore an estimate of the probability
that Clotho will complete her chain and find an iso-1-cytochrome c
molecule in one trial is 2.00 x 10^-44. Using the Poisson distribtion
it is easy to calculate that the Fates must carry out 1.5 x 10^44 trials
to have a probability of .95 of finding one molecular of iso-1-
cytochrome c.
9.2.3 The effect of chirality on the probability
The situation becomes much worse the more realistic one makes the
scenario. I pointed out (Yockey, 1977c) that all references on chemical
evolution that lead to the primeval soup report that many non-proteinous
amino acids and analogues are formed along with the proteinous amino
acids. ...
The estimate of the total number of all sequences in the high
probability set is 1.005 x 10^168. When Atropos recognizes that the
amino acids selected by Lachesis must be all of the same symmetry, the
estimate of the probability of selecting one iso-1-cytochrome c sequence
where all the amino acids are of one optical isomer is 2.316 x
10^93/1.01 x 10^168, which is equal to 2.3 x 10^-75.
We must give the scenario credit for the number of amino acids in the
primeval soup. Let us suppose that the Fates use all the amino acids in
the primeval soup at each trial. Let us accept the concentration of the
amino acids in the primeval soup from those who believe in it.
Shklovskii & Sagan (1966) and Eigen (1971) estimate the primeval soup to
have contained ~ 5.4 x 10^44 amino acid moleculars. ... Using Poisson
probability distribution, it is easy to calculate that Lachesis must
throw her icosahedral dice selecting one from all ~ 10^44 amino acids in
the primeval soup once each second for 10^23 years to have a probability
of 0.95 that her nimble fingered sister Clotho will complete one iso-1-
cytochrome c molecule. If this were the correct scenario, the fatal
sisters would be just beginning since the universe is only about 1.5 x
10^10 years old.
I had already type this excerpt since this orginal thread was about the
probability of chance assembly of a protein molecule. Also of interest
is his conclusion. This comes after an comprehesive examination of all
the mainstream abiogenesis theories, a comprehesive lesson in the
differing probabilities of the various amino acid substitutions at
various sites in proteins, the definition of terms, a mathematical
foundation for examining "information content" in biological context,
and much more. For this, you will have to get his book. But here is a
portion of his conclusion:
10.9 Evalutation of the chemical evolution paradigm
...
That path to 'The broad goal [which] is to arrive at an intellectually
satisfying theory of how living forms could have emeged step by step
from inanimate matter on the primitive Earth' (Dickerson 1978) *is not
in sight*, contrary to Dickerson's optimistic statement. The
considerable work on the orgin of life in the last decades has resulted
in many facts, most of them inconvenient. What is needed is creative
skepticism, fettered by facts, however inconvenient, rather than endless
unfettered speculation. There is no justification today for believing
that life is about to be created *in flagrante delicto* in the
laboratory as was proposed by Jacques Loeb (1912).
Although it was justified when the work started, chemical evolution, a
latter-day alchemism, is still-born and no amount of work on that
paradigm, however religiously it may be carried out, will tell us how
life originated. However, this will not shake the faith of the true
believers. A true beleiver confronted with evidence contrary to his
doctrine regards this as merely a test of his faith. He views the world
behind a fact-proof screen that protects his infallible doctrine from
heretics and unbelievers (Jukes, 1987a; Hoffer, 1951).
Science often finds itself attempting an explanation that is far beyond
its capability at the time. ... The currently accepted scenarios are
untenable and the solution to the problem will not be found by
continuing to flagellate these scenarios.
Again, the above is from Yockey, Hubert, "Information Theory and Molecular
Biology", 1992, Cambridge Press.
Sean:
>He certainly doesn't claim full understanding, but rather that current
>self organizing abiogenesis theories are flawed. He examines
>"protein first", RNA first, pyrite, and clay theories and their flaws.
[snip]
Dan:
"Evidence" in the sense of inarguable support? No, but the field
is still young. However, their beliefs are based on the position
I state above, about how "it is not unreasonable that..." In the
absence of anything more plausible, it's all we've got at the moment,
but it's better than any of the alternatives, and it's not at all
out of the question. Given the nature of the earliest known life,
it also seems clear that we came from quite simple humble beginnings,
so the extrapolating backwards just a bit farther leads one almost
^^^^^^^^^^^^^
inevitably to the standard abiogenesis view.
Sean:
While extrapolating may be appealing, there is no scientific basis for
it.
Sean:
>This is basically an "arguement from authority". Yockey has been doing
>serious study of information theory and molecular biology for a long
>time. (He was publishing in 1958.)
Dan:
Could you give a quick overview of his method? Using "information
flow" sounds like empty hand-waving. I'd like to see a few specifics.
At the very least, does he take into account the fact that some
chemical processes are more likely to occur than others? If he
treats them all as equally likely transfers of information, he's
wrong from the start. Chemicals and molecular arrangements are not
bit patterns which can take any arbitrary pattern without preference.
If he *does* take such things adequately into account, he deserves
the Nobel Prize, because such a feat would be astounding (and unlikely).
Sean:
Maybe you should lobby for his nomination. :-) Half of his book is
about establishing the mathematical basis for the varing probabilities
of amino acid subsititutions and the "information content" of genentic
messages and their translation into proteins.
--
"Don't tread on me"
-- Sean Gallagher -- sea...@umd5.umd.edu