I am glad you all dig me! :) But don't forget you heard it from me first: If
something cannot in principle be measured by means of physical devices, then
that something is not the subject matter of science. Moorad
>===== Original Message From email@example.com =====
><Thus we should not rule out the possibility that many of the older,
>more disrupted lunar craters could have formed supernaturally and are
>not the products of natural causes. (Or, pace Moorad: We never
>saw the impact which produced Bessel crater, so why couldn't it have been
>made by elves? Science can't apply to any crater formed before 10000 BC,
>because there weren't modern humans or instruments to record it. Let it
>forever be an enigma!)>
>.end speculations here...>>
>>I don't know why you threw in the concept of the supernatural in your
>>moon example, which I suppose was meant to address my statement. Did
>>I say anything about the supernatural? No. So why do you?
>That was more of a dig at Moorad than you. However, I do not see why
>the idea of descent with modification becomes more problematic the further
>one goes back in the history of life. Perhaps if one goes very far back,
>say around the eubacterial, archaebacterial, eukaryotic split, that
>question may apply, but not for most of what has happened since then.
>Tim: <Genetic variation is the major change agent. What locks a particular
>change into a population or affects its frequency in a population includes:
>natural selection, neutral drift, and other factors. It is actually a hot
>debate about which of the two, selection or drift, are the most influential
>agents of change. Certainly neutral mutations accumulate in a genome faster
>than selective ones.>
>>While I can understand the mechanism of selection, I find it difficult to
>>understand what drives neutral drift. I'd appreciate it if you would explain
>>it. It seems to me to be a radical departure from natural selection. What is
>>the significance of their "faster accumulation in the genome" that you
>Nothing 'drives' neutral drift. It's simply variation that accumulates
>in the absence of selection. For example, point mutations in the third
>position of many codons are effectively neutral because the changes often
>don't alter the amino acid sequence of proteins made. Similarly, there can
>be changes made to proteins which have little or no effect on the immediate
>viability of the organism. These are changes which can occur "under the
>radar" of selection and pools of such variations can be supported in
>a population with no immediate cost. These variations accumulate in the
>population at approximately the rate of mutation (the majority of mutations
>being neutral or negative), and that average rate is far greater than
>rate of accumulation of positive mutations through selection.
>Where does neutral drift fit in? One necessary factor for evolution
>is the existence of variation within a population. Evolution won't happen
>if species can't "move about in genomic space". Selection can "drive"
>systems to particular locations (optima) in these "spaces", or neutral
>drift can allow systems to "drift" across the landscape in "non-directed"
>steps. One of the questions is: How much of the change which accumulates
>during evolution resulted from neutral mutation and how much can be
>attributed to selection?
>[Note: Sometimes, as conditions change, variations which might once
>started out neutral may actually have some affect on survival.]
>Tim: <<Reversibility is irrelevant and in fact, many of the changes are not
>reversible at the genetic level. Remember that there is a gaping chasm
>between genotype and phenotype. The mapping between the two domains is
>anything but linear in all but the rarest situations. Point mutations
>can confer antibiotic resistance. However, given the odds of hitting that
>exact site again to exactly reverse the point mutation, it's more likely
>that a mutation that eliminates resistance will occur in another
>portion of the genome. Thus a phenotypic reversal (short-term or otherwise)
>does not equate to a genomic "reversal". And we have a recently described
>case where a bacterium acquired streptomycin resistance in a "long-term"
>manner such that loss of the resistance, even in the absence of the
>antibiotic, was selected against (A secondary mutation occurred which
>effectively "locked in" the first one). So, we can say that ratchet-like
>evolutionary progression has been observed even over short timescales.>>
>>One case doth not a theory make.
>But one case doth destroy a blanket refutation...
>(Further, the emergence of second-site suppressors is pretty commonly
>observed. Some examples have become common in bacterial genetics
>> Moreover this is not a ratchet-like
>>evolutionary progression, as you claim. It is step one. Has anything
>>been observed that builds on step one to produce step two? Unless it
>>has you do not have a progression. You have merely a locked-in
>The case I've described involved two-steps. First, the bacterium
>acquired resistance to streptomycin. This is wonderful for such strains
>when there is streptomycin around: All the wild-type strains which would
>otherwise compete for food die. But the resistance carries a slight
>penalty when no streptomycin is around. Strains carrying that mutation
>tend to grow slightly slower and are thus handicapped against their
>wild-type counterpart in an antibiotic-free environment. As a result,
>these streptomycin resistant strains were not expected to persist in
>the "outside" environment, where there is little of the antibiotic
>However, there is a secondary mutation which can occur that eliminates
>the growth handicaps of the resistant strains. This "suppressor" mutation
>allows the bearers to not only grown when streptomycin is around but
>also to grow as fast as the wild-type strains when the antibiotic is
>Interestingly, this second mutation, by itself, also inhibits growth
>rates. Only when teamed with the streptomycin resistance mutation
>do the two mutations persist in the population. Strains missing either
>one of the two mutations tend to be eliminated. This is an example
>of lock-in (or ratcheting).
>Tim: <<I suspect that true reversibility is a relatively uncommon
>phenomenon. Should we be surprised? I think not. In the mind-bogglingly
>huge morphology- or genetic-space available to organisms, it's not
>likely that one could take more than a couple steps in any direction
>and then return to exactly the same starting place.>>
>>I suspect you are overstating your case. Does your "bacterium [that]
>>acquired streptomycin resistance" that you mentioned earlier have
>>"mind-bogglingly huge morphology- or genetic-space available to it"? I
>>doubt it. If so, tell mme what it is.
>E. coli has a genome of about 4.6 megabases. At four possible nucleotides
>per base, that's a genome-space of about 4^(4.6E6) elements. But let's
>start with one particular genome and calculate some odds of exactly
>reversing a single point mutation. That's one in 4.6 million. What are
>the odds of hitting anything else? Those are = 1 - 1/4.6E6 (or ~0.99999978).
>So, long before you've reversed a _single_ mutation, you've probably hit
>millions of other sites in the genome. That is the nature of genetic
>Because most phenotypic traits (such a beak lengths) can be modified by
>more than one gene (comprising thousands of bases/gene), odds are that
>any phenotypic "reversals" aren't going to be genetic reversals.
>Tim; <<Nobody is failing to acknowledge the hierarchical pattern of life and
>discontinuities. These are what led to the conclusion of descent with
>modification in the first place.>>
>>Your first sentence in the above paragraph is simply not true. Read the
>>statement that Dick Fischer presented and see if you can find hierarchical
>>organization and discontinuities in it. Moreover, evolution abhors a
>>discontinuity. Many evolutionary biologists are busy trying to iron them
>From that statement:
>"Nonetheless, no scientific hypothesis other than common descent
>with modification can account for and make predictions about the
>unity, diversity, and properties of living organisms." [...]
>^^^^^ ^^^^^^^^^ ^^^^^^^^^^
>Unity: hierarchical pattern of life
>Diversity and properties: variations = discontinuities. There are
>bears, dogs and cats. They are distinct entities now disconnected
>from each other by breeding barriers.
>Perhaps we are talking about slightly different things when use the word
>"discontinuity". I think of it as the _appearance_ of gaps between related
>species, rather than the _actual existence_ of gaps. True, evolution would
>have problems with actual gaps. But the appearance of gaps (where there
>really are none), is not unexpected, as Keith Miller explains elsewhere.
>Tim: <<Discontinuity is a product of speciation (a mechanism of evolution)
>Keith Miller described why (partially) in a recent post and many times in
>the past. See: http://www.calvin.edu/archive/asa/200112/0080.html
>Reiterated: Speciation reduces genetic exchange between populations
>of organisms. After speciation, the separate populations may travel
>on separate trajectories (i.e. diverge) and the amount of visible
>divergence tends to increase over time. Also "intermediate" species
>become extinct along the way. So while bears and dogs may appear very
>different today, that was not the case for their progenitors. Similarly,
>while extant mammals are clearly distinguishable from reptiles today,
>the earliest mammals where not easy to differentiate from related
>Tim: <<Such discontinuities tend to manifest more in the
>morphological arena than the biochemical one. Also, hierarchical
>organization is a manifestation of the rates of change and the nature
>of speciation and organismal genetics. Understanding the timing and details
>of specific steps behind evolution is real challenge, IMHO.>>
>>Although these words may make sense to you, they don't to me.
>Sorry, I wrote that too fast...
>1) Common descent with modification is a process that generates
> nested hierarchies.
>2) Organisms often (but don't always) differ more on the surface
> (morphology) than they differ from a biochemical viewpoint. E.g.
> Mammals may look different and live in different environments but
> the underlying "hardware" is pretty similar.
>3) The apparent distances between branches of the phylogenetic
> tree of life reflect variations in the rates of change over
> time. As long as the rates of morphological and genetic changes
> are not too great, patterns deduced from morphological comparisons
> can be expected to be consistent with the patterns created on the
> basis of genetic comparisons.
>And finally: Understanding the timing and details of specific steps
>behind evolution is real challenge in the study of evolution.
>>I think our brief discussion illustrates my point that the statement
>>presented by Dick is incomplete, and I add, even misleading. It suggests
>>that evolutionary theory is a done deal. I continue to hold that descent
>>with modification needs a robustly supported mechanism (which in my view it
>>doesn't have) and in addition, an unambiguous refutation of intelligent
>>design, to substantiate its claim to be the all encompassing theory it wants
>Descent with modification has an extremely robust mechanism and can be
>paraphrased as follows: "If your parents didn't have children, neither
>How the variations accumulated and what mechanisms fixed a particular
>variation in a population are definitely open questions.
>Regarding the unambiguous refutation of intelligent design: That is
>simply impossible. One may as well ask: "What could an intelligent
>designer not do?"
>Tim Ikeda (firstname.lastname@example.org)
>mail2web - Check your email from the web at
This archive was generated by hypermail 2b29 : Tue Dec 11 2001 - 20:16:20 EST