Re: Random origin of biological information

Date: Wed Sep 27 2000 - 18:27:03 EDT

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    Hi Peter,

    On Wed Sep 27 14:03:58 2000, wrote:

    > You keep misunderstanding what I argued.

    Well, I don't mean to do that. Sorry.

     There are (at least) five
    > different types of search processes that have surfaced in our
    > discussion:
    > (a) search for a meaningful letter sequence among random ones,

    I started with this one.

    > (b) artificial selection of a functional ribozyme from a collection of
    > random RNA sequences,

    I did mention this one.

    > (c) evolution of a functional ribozyme in RNA world organisms,

    This one, I haven't discussed and keep trying to say that I am not discussing
    that one but you keep wanting to discuss it.

    > (d) evolution of a protein by mutation of the DNA and natural selection
    > of the protein,

    I raised that only as a response to your contention that proteins wouldn't
    behave as does an RNA. I think the evidence says that they do.

    > (e) a random DNA mutational walk finding a minimally active protein.

    I don't remember this one at all. But I will take your word for it.
    > I fully agree with you that both (a) and (b) are relatively easy, and
    > certainly successfully doable (although you may be overestimating the
    > fraction of letter sequences representing a recognizable meaning - but I
    > don't know). These are the only two types you have been dealing with up
    > to now. As we don't know anything about the feasibility of an RNA
    > world, it is too uncertain to speculate about the chances for success of
    > (c).

    As I have said at least twice before, I am not discussing the RNA world. I am
    merely pointing out that the classical anti-evolutionary position which claims
    (erroneously) that randomness is incompatible with meaning or specificity is
    clearly false. We can sit in our homes and say that airplanes can't fly
    ignoring the crowded airways full of planes carrying the busy throngs on their
    way to their meetings or we can acknowledge that they fly. This is what is
    wrong with the classical anti-evolutionary argument. It is very, very weak.


    > Where we part company, for the moment, is with case (e), which you have
    > never considered in our discussion,

    Thanks for confirming that my memory is still in tact. At my age sometimes one
    wonders. Senior moments become more and more common. :-)

     although my argument focussed on
    > this case alone, from the beginning, with the calculated model of the
    > probability of a random walk leading to a minimal enzyme activity within
    > the geologically available time. What's so different about case (e)? As
    > the activity wanted does not yet exist, not even to a minimal degree,
    > there is nothing to select, and natural selection of intermediates in
    > the mutational random walk just is not possible - by definition. Both in
    > (a) and (b), and presumably in (c), some activity or meaning is present
    > in the sample collection from the beginning, or can be generated
    > relatively easily by mutagenization. In (d), it is present by
    > definition, because (e) is its precursor.

    First off, there is no enzymatic activity if one doesn't allow selection and
    comparison. Isolated proteins, created by random mutation won't do anything to
    anybody unless one allows them to be tested against another protein for a given
    function. Now, here is how I view that the probability argument will
    eventually be defeated. A protein that engages in Function X has this broad

    variable amino acids-invariant amino acids-variable amino acids.

    (and no I don't believe that they have to be segregated but use that as a
    diagram). Now. I think eventually for function X we will find

    variable amino acids-invariant amino acids A-variable amino acids

    variable amino acids-invariant amino acids B-variable amino acids


    This is exactly as the case of the two sentences:

    Picking noses begets warts

    fingers in the nares creates hypertrophy of the corim

    skin protuberances come from pulling bugers from one's nostril.

    All these sentences convey the same idea without using any of the same
    invariant sequences. They consist of a separate family of solutions for
    conveying this idea. One family has the invariant word warts. Another has the
    invariant word corium, a third has the invariant bugers. I can create hundreds
    of thousands of sequences for EACH of these families. I think eventually we
    will find the same thing in proteins, and we have found it in RNAs. The
    solution that life uses, which seems so limiting, is merely the solution that
    life chose early in its evolution.
    > A question which remains, of course, is the amount of semantic
    > information at the transition point between (e) and (d). If this is just
    > a few bits, my problem doesn't exist. What we can do is to try to define
    > an upper and a lower limit for this transition point. Presumably, the
    > two limits are very far from each other, but this is the best we can do
    > for the moment. For the upper limit we may look at the amount of
    > semantic information required for a modern (i.e. a known) enzyme.

    Oxytocin has only 8 amino acids. Several others have that also. An enzyme does
    not a priori have to have a long sequence.

    > is what Yockey did. To find a lower limit, we may estimate how much
    > semantic (specified) information can be generated in a random walk and
    > how much time this would take. And that's exactly what I tried to
    > present for discussion in my first post. But you dismissed my
    > (tentative) conclusion out of hand, without discussing it, by referring
    > to cases (a) and (b), which cannot be compared with it at all.

    It ignores the possibility I discuss above about different families of
    solutions. With the RNA experiments, we have already seen the same experiment
    run twice yeilding totally different sequences that perform the same function
    exactly as I illustrated in the sentences above.
    > > [snip]
    > Here you snipped out what explained the sentence following it, referring
    > to a combination of processes (e) and (d), as well as any amount of
    > horizontal gene transfer and exon shuffling you like:
    > " In the evolutionary process, the only possible natural source of
    > information is the environment. But the extraction of this information
    > is extremely slow, probably only a fraction of a bit per generation -
    > when any useful mutants are available at all. And if they are, they must
    > penetrate the entire population before being fixed. For small selective
    > advantages and large populations, the mutation still risks being lost by
    > random drift."

    Having looked at informational flow calculations for the genome, like those
    Spetner published in Nature in 1964, I am not at all impressed with his
    calculations. There is most assuredly more than 1 bit of information generated
    per generation. This is especially true in long sequences in which many
    mutations occur during a generation.

    > All this is just Shannon information. For a string of length L and 4
    > nucleotides, the maximum amount of information corresponds to 4^L
    > possibilities. This may be called information potential. But none of
    > this tell us anything about usable or semantic information or meaning in
    > the sense of specification of biological function. Mutations add nothing
    > to the semantic information until you test them by the environment.

    We agree here. The question is how efficient is nature at finding solutions.
    The experiments with biopolymers that I have cited clearly show that
    functionality occurs at a rate of 10^-13 or so. In the case of one of Joyce's
    RNAs the classical probability argument would say that he had something like a
    1 chance in 10^236 of finding a useful sequence. But Joyce has been showing
    that he can find functionality in a vat of 10^13 ribozymes. Surely that must
    cause the anti-evolutionist pause because at that rate, there are 10^223 or so
    different sequences that will perform a given function. I really fail to see
    how someone can not see the implication of this except for theological reasons.
    > >
    > > Now, because of this fact about copying adding only 1 bit, you get 1 bit of
    > > information for every clone on earth--plus 20 billion for the first species.
    > > This is why the additional one bit of information from each individual
    > > isn't enough to worry about.
    > >
    > > So, if the earth has 10^19 bits of information how rapidly does that have to
    > > develop? 100 bit per second as 10^19 is 100 times the number of seconds in
    > > billion years. This is not a rapid rate.
    > Your calculation omits some very crucial details about how an organism
    > functions and how the biosphere communicates. Before you apply natural
    > selection, you have no semantic or functional information whatever. Your
    > string of a huge amount of Shannon information (which equals amount of
    > randomness or entropy) is nothing but raw material for selection, bit by
    > bit. First you need a functioning organism coded by the string (how do
    > you get that?), then you can start testing each of the other bits
    > against the environment in which this organism lives - a rather slow
    > process.

    I think you keep trying to mix the problem here. I started this thread merely
    by pointing out that randomness isn't incompatible with semantical meaning. I
    think I proved this. Now you want to change it to the origin of life where you
    think you have a better defense for your case. First off, we don't need a
    functioning organism to to have selection. We merely need reproduction. Now I
    will freely admit I don't know how the raw molecules would reproduce and right
    now no one else does either. However, to claim that our lack of knowledge is
    equivalent to a law of nature seems to rest your case on our continued
    ignorance. History has shown over and over again that that is a weak place to
    rest one's case.

    Furthermore, it's no use having all these bits randomly
    > distributed in 10 million bags (species), or even further spread out
    > among the individuals of a species. Biology only works if the right
    > information is in the right place at the right time. Each individual
    > must have all the information it requires. That will slow down the
    > process tremendously. For each bit of information, you must consider
    > that it can be input into the biosphere almost anywhere on earth. One
    > bit improves cytochrome c in a fish on an Australian shelf, the next one
    > improves a kinase in a worm in Canadian soil, the next one improves an
    > ATPase in a heterotrophic bacterium 1 km below the surface in a Siberian
    > rock, etc. This may help if each of the functionalities needed is
    > already in place in each organism and is just made a little bit better.
    > To make use of the improvements, the other organisms of the same species
    > would have to trade their genes among themselves, which is not a matter
    > of seconds, nor even of a few years. And if other species should profit,
    > the trade between species or even higher taxa is much slower.

    First off, bacteria have sex with other bacteria of different species all the
    time. There is a blizzard of genetic ;material that flows through the
    biological world, trading genomes and genes. (see La Ronde, Scientific
    American June 1994 P. 28-29

    But, most
    > importantly, how about the origin of new functionalities by process (e)?

    New functionalities are found exactly as the experiments are showing new
    functionalities to be found with Ribozymes. They appear at a frequency of 10^-
    13. You seem to continue to ignore this frequency that appears over and over in
    biopolymer experiments.

    > This last factor might easily transcend any estimate for process (d) by
    > a transastronomical magnitude.

    Experimental data would say it doesn't.

    > > ...
    > > >
    > > > In my post, I was discussing the evolution of functional proteins in a
    > > > DNA-RNA-protein world, not evolution in an RNA world. I never talked
    > > > about ribozymes (I did mention ribonucleases, but these are protein
    > > > enzymes). I know about the in vitro selection of functional ribozymes,
    > > > but I do not consider these as valid models of evolution at all. They
    > > > just are techniques for finding active ribozymes among as many sequences
    > > > as possible.
    > >
    > > It is always a bit amazing to me how no experiment is every considered to be
    > > good evidence of evolution by those who don't like evolution. Why do you
    > > that is? The claim that useful variants of long biopolymers are too rare
    to be
    > > found is one that is claimed over and over and over again by the anti-
    > > evolutionary crowd, yet when one points them to an example where usefulness
    > > found at a relatively high level of probability, the claim is made that it
    > > isn't evidence at all. It most assuredly is evidence that the rates of
    > > biopolymers has been vastly underestimated by the anti-evolutionary crowd if
    > > nothing else.
    > These objections should be answered by what I wrote above. And if you
    > think I'm one of those (despised? ;-)) anti-evolutionists, you may read
    > what I published with Armin Held in PSCF 51 (Dec. 1999), 231. Mainly for
    > theological reasons, I do believe that God used (and uses) evolution as
    > (one of) his tool(s) of creating and maintaining the biosphere. But that
    > doesn't oblige me to uncritically swallow every belief of the
    > "evolutionary crowd". Are questions about unsolved problems forbidden?

    No, unsolved problems are not forbidden, but reliance on unsolved problems to
    support one's position is a god-of the gaps (small g) type of approach and is
    philosophically, historically and scientifically poor. It postulates that the
    lack of solution for this problem supports my theory. No lack of any solution
    supports any theory.
    > > "Extrapolating to the rest of the protein indicates that there should be
    > > 10^57 different allowed sequences for the entire 92-residue domain.
    > This fits in very nicely with Yockey's cytochrome c estimate. Now, using
    > his "effective number of amino acids" 17.621, we get 17.621^92 = 4.3 x
    > 10^114 possible sequences, and the probability of finding any one of the
    > 10^57 [lambda] repressor sequences is 0.23 x 10^(-57), rather low!

    And once again, it ignores the data found by Szostak and colleagues that a
    repeat of the same selection experiment yields vastly different sequences to
    solve the same biological problem.

    > At least for the last 20 years, this has been taken into consideration
    > by critics of evolution (e.g. in my papers at the 1988 Tacoma, WA,
    > conference about Sources of Information Content in DNA, and in PSCF 44
    > (June 1992), 80). But nevertheless, even with this caveat, asking
    > questions about the feasibility of evolution is not accepted in the
    > established big journals (in the early 80's, I tried J. of theoretical
    > Biology, Nature, Origins of Life, Philosophy of Science, and a German
    > journal, all in vain). It is not politically correct to question the
    > possibility of evolution.

    So, if you are an evolutionist as you seemed to imply earlier in this letter,
    why are you taking this position? It seems to me that one who accepts something
    is very unlikely to then turn around and claim persecution for questioning it.
    Don't get me wrong, I think you have a right to question it. What I am
    questioning is the correctness of your assertion that you believe in evolution.
    What you say above and below, sounds so much like the claims of young-earthers
    who can't get their ideas published in reputable journals.

    And before you get mad at me for this claim, there was a time when no one would
    publish a thing I wrote either. I got on internet and fought for my ideas. Now
    I can be published.

    The editors' justifications of refusal were
    > quite evasive. As you see, even the huge numbers of possibly active
    > sequences are by far not sufficiently huge.

    On this we disagree.

    > These artificial mutations were targeted intelligently to specific small
    > sequence regions to be tested, which makes it practical to recover
    > biologically active mutants. Thus, this is not an experimental
    > simulation of darwinian evolution. If you want to use these results for
    > probability estimates, you have to factor this in.

    I would rather see them start with totally randomly generated strings rather
    than try to substitute one at a time. I think they could be surprised as others
    have been at that approach.

    > >
    > > Degeneracy equals lots and lots of different proteins to perform the same
    > > And before you say that there is an invariant region that must be as it is
    > > order to assure protein function, have you ruled out that other sequences in
    > > other protein folded structures can't perform the same thing?
    > The sequences of the same fold are already taken into consideration in
    > the 10^57 sequences. Whether there are sequences of different folds with
    > the same activity is not known. If I remember correctly, cases of
    > different folds having the same activity are extremely rare, if they
    > exist at all.

    You misunderstand. Not the same sequences having different folds--different
    sequences haveing different folds!

    > What I meant with "unknown bias" is this: the starting pool of RNAs was
    > certainly about random (within the limits of biochemical precision), but
    > this was only a minute fraction of all possible sequences.

    This is precisely the point that amazes me. If it is such a small fraction of
    all possible sequences, and yet they still find active sequences, the ONLY
    WRONG, WRONG WRONG! If the functional sequences were so rare as to make it
    impossible for life to evolve, as you have contended throughout this thread,
    then why on earth were they able to find one in a couple of months of work? We
    can't claim that functional sequences are rare when we can find them in a
    couple of months. If Szostak and Joyce can find them that quickly, then so can

    Whatever is
    > contained therein has a greater chance of being selected than sequences
    > not in the starting pool, which just might, but need not, be formed by
    > later mutagenesis. And Lorsch & Szostak (Nature 371 (1994), 31), for
    > instance, indicate that their starting pool already contained the ATP
    > binding site required, "which greatly increased the odds of finding
    > catalytically active sequences". Furthermore, they suggest it would be
    > better to mix, match and modify small functional domains.

    The ATP is irrelevant as far as the frequency of the functionality is

    > The don't-knows are Orgel's! (you clipped out his very relevant comments
    > I quoted.)You don't want to claim he hasn't done anything worth while,
    > during several decades of work, to solve these questions, do you? It's
    > not just one "guy's failure", but the failure of a whole field of
    > research, in ALL research groups having had a try at it. Orgel is one of
    > the leaders in the field.

    So we base our position upon other people's failure. Most scientific theories
    are based upon positive experimental support, not other people's failure. This
    is the wrong approach for Christians to take. If we depend upon failure, what
    happens when they finally succeed?

    > >
    > > I am asking that you cease doing what all antievolutionists do, which is
    > > throwing, and actually propose a workable system that can be verified. Can
    > > do this?
    > Now, Glenn, if you call my arguments "stone throwing", what are YOU
    > doing with your harsh criticism of those who try to build bridges across
    > the awful gulf presently existing between Christians (in the biblical
    > sense) on the theistic evolution side and Christians (in the biblical
    > sense) on the YEC or ID side in this area of trying to understand
    > Creation? Our testimony to the world appears to be severely compromised!
    > Although I agree with most of your criticism of the YEC position and
    > some of that of the ID folk, there is certainly some value in their
    > sincere commitment to biblical doctrins like divine inspiration of the
    > Bible, and the idea of the ID "wedge" fighting the nihilistic
    > degeneration of our society is worth of approval, although some of the
    > intellectual tools used may be questionable.

    First off, it is the ID group, Phil Johnson in particular who has basically
    excluded the TE's as being 'compromisers' or some such.

    And aren't some TE all too
    > eager to accept without questioning anything "anti-fundamentalists" are
    > saying, hardly stopping short of ideas like those of Dawkins,
    > E.O.Wilson, Gould, Teilhard de Chardin, process theology, deism, liberal
    > theology, destructive Bible criticism, syncretism etc.?

    I will tell you my experience. I believed Christian apologists when I was in
    college. I came out as a YEC and went into the oil business. What I saw there
    horrified me. Eventually, after 20 years of struggling, I finally had to admit
    that everything the YECs had told me about geology was absolutely false. And
    they made arguments just like you do. They said that the other guy couldn't
    prove this or that but I would go look at the data and find out that the other
    guy had shown what had just been claimed to be impossible. This created a
    tremendous scepticism on my part towards what apologists say. They usually are
    behind the times (like you were with Yockey's work). They ignore modern data
    and explain it away rather than incorporate it into a coherent world view (as
    you are doing with the frequency data). In otherwords, data doesn't behave for
    apologists like it does for scientists. Data becomes something to be discounted
    rather than incorportated into a world view. I should start a discounting
    factor measurement for apologists. But that would then be criticized for 'not
    building bridges'. The problem I have is that I want no bridges to falsehood.

    It's not just
    > science against "anti-science", it's also about what we believe
    > concerning God, revelation, the Bible, Creation and God's "maintenance"
    > of everything. It's all too easy to call "myths" and "errors of the
    > ancient near eastern culture" anything in the Bible we don't understand.

    And by using this overriding belief that we have interpreted the Bible
    correctly, we then twist the science, and discount the data as I discussed
    above. The YECs make the same kind of epistemological claim. They KNOW that God
    created the world 6000 years ago and they then discount any data that violates
    that belief, just as you are discounting any data that violates your
    theological system.

    > All this has been dealt with above. I wrote about the RNA world because
    > I thought you considered the artificial ribozyme selections to be valid
    > models of evolution in an RNA world, as I think Szostak and others do.
    > This was before you told me you weren't thinking of the RNA world.

    If I had been discussing the RNA world, I would have used that term. I didn't
    in my original set of notes.
    > > >
    > > > You are right in pointing out that Yockey revised his probability
    > > > estimate for cytochrome c (now iso-1-cytochrome c) in his book
    > > > "Information theory and molecular biology" (Cambridge: Cambridge
    > > > Univ.Press, 1992). On p.254, he gives the probability of accidentally
    > > > finding any one of the presumably active iso-1-cytochromes c as 2 x
    > > > 10^(-44), which is 21 orders of magnitude better than his 1977 estimate
    > > > for cytochrome c.
    > >
    > > The reason I hit you so hard is that I know that you are in the area of
    > > and write as an apologist. I have grown very tired of apologists who
    insist on
    > > using 20, 30 and 40 year old data as if it is dogma and can't be change. It
    > > shows that we are doing sloppy apologetics by not keeping up in the areas
    > > which we write. If you and I were 30 years behind our respective fields of
    > > employment, I can guarentee you that we would both be unemployed. At least I
    > > know I would be in the oil industry. If we keep up with our fields for the
    > > sake of our employment, why don't we keep up when we are working for the
    > You are being unfair. Check what I have written!

    You did cite outdated 1979 Yockey material which was at least 13 years behind
    what I believe to be the last statement on the topic in 1992. If there is a
    more recent one I wish someone would point me to it so I won't be behind the
    > What you find in oil are bits not of primitive, but of highly functional
    > enzymes. The first fossil bacteria found date back 3.5 billion years,
    > and they look like cyanobacteria which are highly complex biochemically.
    > Life had to evolve from a prebiotic world before that, and awfully fast,
    > starting after the big meteorite bombardment.

    So tell me what exactly is your definition of 'primitive' enzymes? How would
    you recognize one? What objective criteria would you use? Is Oxytocin
    primitive because it is short? Or are the enzymes of cyanobacteria primitive
    because cyanobacteria are so old?

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