PART 9 OF 10

Response on the issues to:
"Science or science?" and "Darwin on Trial"

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(SECTION #4, CONTINUED)

The way the analogy works with respect to genetic copying errors is as
follows. Normally, when mutations occur in genes, they are either quickly
eliminated (if they have a detrimental impact on survival and
reproduction), so that no errors are retained. Or else the mutations are
beneficial, in which case they contribute to survival and are retained
_because_ they are beneficial. However, there is a separate class of
copying errors that can occur in what are called "pseudogenes" (extra
copies of genes within portions of an organism's genome that are themselves
nonfunctional), so that the errors in the pseudogenes continue to be
reproduced from parent to child _even_
_though_they_have_no_survival_effect_ on the organism.

What these errors amount to, then, is "plagiaristic errors" that persist
from one generation to the next. Thus, when exact copies of these
pseudogenes are found in differing organisms--and in identical locations in
the gene sequences of each organism--it is considered nigh onto airtight
evidence that the two organisms had a common ancestor that had that same
pseudogene. And there have now been many examples found of these so-called
"plagiarized" genetic copying errors in pseudogenes, that when analyzed,
have confirmed the same pattern of genealogical relationships suggested by
both the fossil evidence and "genetic distance" studies.

For a list of the examples and a far more in-depth discussion of
pseudogenes and exactly why and how telltale plagiaristic copying errors
demonstrate genealogical relationship, see
http://www.talkorigins.org/faqs/molecular-genetics.html - Plagiarized
Errors and Molecular Genetics, by Edward Max, MD, Ph.D.
<[log in to unmask]>, a molecular geneticist doing current research on
pseudogenes.

Again, the only way to argue around what the copying of plagiaristic errors
in pseudogenes indicates is to argue that God in his/her/its infinite
wisdom inadvertently let errors creep into the genetic apparatus of human
beings and all other creatures. That hardly paints a picture of an
intelligent God. Or perhaps God decided to stick them in just to fool us in
our scientific research. But what kind of God would do that? It paints God
as a malicious being just having misanthropic fun that no one in their
right mind would want to put their trust in. You either have a God who is
an inept klutz at designing things or a God who is malicious. Or if God
_is_ in direct control, then he/she's fallen asleep at the wheel.

To make this point clearer and perhaps closer to home for creationists:

Terry Gray, a former elder in the Presbyterian church, points out in his
review of "Darwin on Trial" (at
http://mcgraytx.calvin.edu/gray/evolution_trial/dotreview.html) that
creationists themselves use this same type of inferential logic all the
time to reveal the threads of genealogy in biblical lines of authorship
when they are trying to determine the source of ancient manuscripts. Says
Gray:

     Take for example New Testament manuscripts. When we find extant
     manuscripts that have inserted sentences or paragraphs (e.g., the
     concluding sentence in the Lord's Prayer) and compare them with other
     extant manuscripts that are otherwise identical, we do not conclude
     that these two manuscripts are completely independent in origin. We
     re-create the scenario that at some point in the manuscript history, a
     scribe either added or deleted the inserted text. All manuscripts
     deriving from that errant copy would also contain the error.

The point of the analogy here is that the similarity between imputing a
line of ancient authorship by using the presence or absence of inserted
text by scribes that gets handed down to further copied manuscripts is
*exactly* the same logic used to infer common genealogical ancestry between
organisms and species by noting the mutations and certain identifying gene
sequences they hold in common. That creationists are so conveniently
willing to dismiss the same logic when used by evolutionists shows just how
arbitrary their program of denial really is. They aren't really objecting
on scientific grounds, they are objecting on religious grounds. Which is
fine if they want to cop to the fact their objections _are_ from religious
grounds. But to then claim their grounds are _scientific_ is plainly
dishonest--wanting to have the veneer of scientific respectability without
the price of consistently abiding by the logic required to be scientific.


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SECTION #5

EVOLUTION IS SUPPOSEDLY NOT FACT, ONLY A THEORY.

Perhaps the best summaries of the above point come from the scientists
themselves (Gould, Ernst Mayr, Dobzhansky, Futuyma, etc.). To quote from
talk.origins.org site (these three following quotes come from the passages
at http://www.talkorigins.org/faqs/evolution-fact.html (put together by
Lawrence Moran <[log in to unmask]>:

>From Stephen Jay Gould:

     In the American vernacular, "theory" often means "imperfect fact"--
     part of a hierarchy of confidence running downhill from fact to theory
     to hypothesis to guess. Thus the power of the creationist argument:
     evolution is "only" a theory and intense debate now rages about many
     aspects of the theory. If evolution is worse than a fact, and
     scientists can't even make up their minds about the theory, then what
     confidence can we have in it?...

     Well evolution is a theory. It is also a fact. And facts and theories
     are different things, not rungs in a hierarchy of increasing
     certainty. Facts are the world's data. Theories are structures of
     ideas that explain and interpret facts. Facts don't go away when
     scientists debate rival theories to explain them. Einstein's theory of
     gravitation replaced Newton's in this century, but apples didn't
     suspend themselves in midair, pending the outcome. And humans evolved
     from ape-like ancestors whether they did so by Darwin's proposed
     mechanism or by some other yet to be discovered.

     Moreover, "fact" doesn't mean "absolute certainty"; there ain't no
     such animal in an exciting and complex world. The final proofs of
     logic and mathematics flow deductively from stated premises and
     achieve certainty only because they are NOT about the empirical world.
     Evolutionists make no claim for perpetual truth, though creationists
     often do (and then attack us falsely for a style of argument that they
     themselves favor). In science "fact" can only mean "confirmed to such
     a degree that it would be perverse to withhold provisional consent." I
     suppose that apples might start to rise tomorrow, but the possibility
     does not merit equal time in physics classrooms.

     Evolutionists have been very clear about this distinction of fact and
     theory from the very beginning, if only because we have always
     acknowledged how far we are from completely understanding the
     mechanisms (theory) by which evolution (fact) occurred...

--Stephen J. Gould, "Evolution as Fact and Theory"; Discover, May 1981

And this from Theodosius Dobzhansky:

     Let me try to make crystal clear what is established beyond reasonable
     doubt, and what needs further study, about evolution. Evolution as a
     process that has always gone on in the history of the earth can be
     doubted only by those who are ignorant of the evidence or are
     resistant to evidence, owing to emotional blocks or to plain bigotry.
     By contrast, the mechanisms that bring evolution about certainly need
     study and clarification. There are no alternatives to evolution as
     history that can withstand critical examination. Yet we are constantly
     learning new and important facts about evolutionary mechanisms.

--Theodosius Dobzhansky "Nothing in Biology Makes Sense Except in the Light
of Evolution", American Biology Teacher vol.35 (March 1973) reprinted in
Evolution versus Creationism, J. Peter Zetterberg ed., ORYX Press, Phoenix
AZ 1983

And this from R.C. Lewontin:

     It is time for students of the evolutionary process, especially those
     who have been misquoted and used by the creationists, to state clearly
     that evolution is a FACT, not theory, and that what is at issue within
     biology are questions of details of the process and the relative
     importance of different mechanisms of evolution. It is a FACT that the
     earth with liquid water, is more than 3.6 billion years old. It is a
     FACT that cellular life has been around for at least half of that
     period and that organized multicellular life is at least 800 million
     years old. It is a FACT that major life forms now on earth were not at
     all represented in the past. There were no birds or mammals 250
     million years ago. It is a FACT that major life forms of the past are
     no longer living. There used to be dinosaurs and Pithecanthropus, and
     there are none now. It is a FACT that all living forms come from
     previous living forms. Therefore, all present forms of life arose from
     ancestral forms that were different. Birds arose from nonbirds and
     humans from nonhumans. No person who pretends to any understanding of
     the natural world can deny these facts any more than she or he can
     deny that the earth is round, rotates on its axis, and revolves around
     the sun.

     The controversies about evolution lie in the realm of the relative
     importance of various forces in molding evolution.

--R.C. Lewontin "Evolution/Creation Debate: A Time for Truth" Bioscience
31, 559 (1981) reprinted in Evolution versus Creationism, op cit.

This difference between "fact" and "theory" is an important one because the
creationist arguments rarely fail to confuse the forest for the trees--to
be so myopic in their objection to the _details_ of evolutionary mechanisms
and the fault-finding they engage in--that they slyly divert attention away
from what is the real issue. Which is that there is no other logical
explanation for the fossil evidence we see without invoking supernatural
explanations.

The facts are very simple: If you assume the evidence in the fossil record
(not to mention the evidence for, and observable instances of, modern-day
speciation) is explainable at all, the ONLY explanation that makes any
logical sense is evolution. You have to assume, unless creatures and
fossils materialized out of thin air, that parent creatures reproduce child
creatures in an unbroken sequence of genealogy from past to present--just
like we see today. Given that, there is no other factual alternative than
that early fossil forms in the nested and hierarchical succession of
changing fossil forms in the geological record gave rise to later ones via
some physical route of continuity through ancestry, unless you propose some
arbitrary, unexplainable exceptions to physical causation and posit an
external supernatural cause.

Again, it really is that simple: evolution is the only physical, factual,
explanation there is that makes any logical sense of all the evidence. Even
where sufficiently exact explanations for certain phenomena still are
lacking and being investigated (perhaps the primary one still remaining is
the investigation of the complete suite of mechanisms necessary to fully
explain macroevolutionary events), nobody who is interested in logical
physical explanations doubts the general coherence of the evolutionary
explanation--because there *is* no other logical physical explanation.

And while it is certainly true that nothing is ever proven "for certain" in
science, still, that evolution occurred is a "fact" of equal merit with the
"fact" of a spherical earth orbiting the sun. Remember that for a general
acceptance of the most basic outline of evolutionary theory--that later
organisms came from earlier ones somehow--not much more than the evidence
available in Darwin's day, fossil gaps or not, is all that is needed to
show that an evolutionary explanation (whatever the specific mechanisms
might turn out to be) is the only logical physical explanation of the
evidence possible.

For more on "Science as both a fact and a theory," see the following link:
http://www.talkorigins.org/faqs/evolution-fact.html - Evolution is Both a
Fact and a Theory, by Lawerence Moran <[log in to unmask]>.

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SECTION #6

EVOLUTIONARY PRINCIPLES SUCH AS "SURVIVAL OF THE FITTEST" ARE
SUPPOSEDLY
ONLY TAUTOLOGIES--THINGS THAT ARE TRUE BY DEFINITION IN SUCH A WAY
THAT IT
MAKES THEM MEANINGLESS AND UNTESTABLE.

See http://www.talkorigins.org/faqs/evolphil/tautology.html ("Evolution and
Philosophy: A Good Tautology is Hard to Find") for a good refutation of
this idea. While it is true that scientists themselves do sometimes
mistakenly fall into the trap of using the "survival of the fittest"
criterion as a simplistic tautological statement, the strict interpretation
of the statement does not depend on a tautological equation.

Strictly speaking, fitness is the degree of match or "fit" between a
physical trait and how well that function performs in the environment the
organism lives in. Fitness is therefore tied to TRAITS and physical
FUNCTIONS and how well they "do the job" they are designed to do in terms
of their DESIGN--especially in comparison to other variations of that
trait. Fitness is thus a question of "good design," and how well that
design survives is a RESULT (i.e. survival itself is not the entire
definition).

Fitness, however, can also be expressed as a _relative_ mathematical
probability indicating the tendency of a certain trait to survive--i.e., it
is probabilistic, not deterministic. The point in this is that tautologies
are always totally deterministic, such as in saying that the most fit are
always the ones who survive. (That way of stating the equation IS a
tautology.) However, expressing fitness in terms of relative probabilities
of one trait (gene variant) vs. another in a statistical equation
recognizes that survival is not a certain nor determined thing--it depends
on contingencies--yet there are still very strong tendencies for survival
that make the most fit (with the best functional design given the
environmental niche) usually the ones who survive.

The reality of the situation is that instead of deterministic results
(which is what creates the idea of a tautology) there are _tendencies_ to
survival of various traits which can be expressed statistically as
mathematical probabilities for survival against other variations of the
trait. These are _not_ tautological since any given result does not always
give the outcome of survival, as a tautological definition would. It is in
the statistical _aggregate_ that the fitness of any particular trait can be
assessed mathematically. The fittest _ought_ to end up being the ones who
survive most often, and to say otherwise is to deny that survival is a
legitimate criterion for fitness that can be measured, and that make the
fittest (those with the best functional design given the environmental
niche) the ones who survive _on average_. (Otherwise no one would be saying
"survival of the fittest" in the first place.)

As John Wilkins puts it on the above web link:

     'Fitness' to Darwin meant not those that survive, but those that could

     be EXPECTED [emphasis not in original] to survive because of their
     adaptations and functional efficiency, when compared to others in the
     population. This is not a tautology, or, if it is, then so is the
     Newtonian equation F=ma [Sober 1984, chapter 2], which is the basis
     for a lot of ordinary physical explanation.

This definition of fitness can be used to make predictions about which
organisms will survive (as it was used in the Anolis lizard experiments in
the Caribbean mentioned above in section #2 on macroevolution), thus
meeting the scientific criterion of testability.

Finally, what creationists rarely bother to mention is that the father of
the idea that evolutionary arguments like "survival of the fittest" were
tautologies--Karl Popper--later recanted his views. Again, as John Wilkins
in his series on Evolution and Philosophy on www.talkorigin.org puts it at
http://www.talkorigins.org/faqs/evolphil/notes.html:

     Note 1. The article by Stamos [1996] is by far the best review of
     Popper's views on evolution, and I recommend finding it if you have
     access to an academic library. Popper later 'recanted' his claim that
     Darwinism was unfalsifiable and a tautology (which were related
     arguments in Popper's view), in "Natural Selection and the Emergence
     of Mind", Dialectica 32(1978), pp. 339-355, but it was rather weakly
     done. This recantation is rarely cited by those who interminably argue
     about the tautology argument.

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Lastly we come to Phillip Johnson's biggest beef with science:

SECTION #7

THE "RULES" OF SCIENCE ARE PHILOSOPHICALLY BIASED BY THEIR
"MATERIALISTIC
NATURALISM" AND SUPPOSEDLY RIGGED SO AS TO RULE OUT ANY OTHER
EXPLANATION
THAN EVOLUTION.

As I mentioned in my initial criticism of David Wolfe's earlier essay "On
Form and Actuality," the most telling and damning argument against
creationists is the last one we'll examine here: They have absolutely no
serious, testable scientific explanation to offer for the fossil record.
None. They never have had (other than the old propositions based on a
literalist interpretation of the Genesis creation account, or "Noah's Ark"
Flood theory," and so forth, that haven't long since been falsified). At
best, they carp at the details of evolution itself. But do they have an
alternative themselves? Nope--none that can be fairly tested in any way.
For the same 140 years that David Wolfe alleges evolutionists have not been
able to point to transitional fossils (which we have seen is wholly false),
the creationists have been stymied in even PROPOSING a serious explanation,
other than Noah's Ark and similar biblically-based "young-earth" scenarios
long since shown false, that could stand up to the test of science.

Now the creationists will say that that's just because the scientists won't
let them propose their (untestable-in-principle) metaphysically
supernatural explanations, and that that makes science "biased." (Yes,
Mabel, that really is what they call "philosophical bias"! ;-) ) But the
requirement that things be rigorously explainable AT ALL (i.e., testable)
can't HELP but rule out supernatural explanations--as it should. Why?
Because at root, supernatural explanations are not explanations at
all--they are FAITH. Faith in something that you can't test or demonstrate
is not an explanation, it is the LACK of one! To be an explanation at all
requires that a proposal have some details that can be examined, tested,
and DEMONSTRATED in some kind of concrete fashion.

What this means where agreeing to do science is concerned is that you agree
that you are going to abide by a few rules as your basis for investigation:
(1) That physical things can be explained by physical causes. (2) That to
qualify as a scientific hypothesis, an explanation has to be testable or
verifiable. (Supernatural explanations are by their very nature not--since
they invoke non-physical causes that can't be tested.) (3) That you are
willing to abide by the evidence, or acknowledge the need to change your
theory to better explain the evidence that is observed or that results from
tests.

Phillip Johnson quite rightly points out that these are philosophical
assumptions. But they are certainly not "bias" in the sense of unfairness.
And he has some quite philosophical assumptions of his own. Given Johnson's
absolute silence in proposing any kind of testable alternative, he is
apparently embarrassed to acknowledge that his only alternative is one
based on philosophical irrationality: whenever any "gaps" appear in
explanation, why, let's invoke supernaturalism as the cause! And then he is
indignant and wants to fault scientists for ruling that out in principle as
a NON-explanation because there is nothing in it that can be verified?! I
marvel at his naivete. Which is more reasonable: to assume physical things
can be explained by physical causes, or to assume instead that if certain
things haven't been explained just yet, they in principle CAN'T be, and
never will be?

A scientific theory does not rise or fall depending on the existence of a
few as-yet-unexplained details or facets--it has to work sufficiently as a
wide-ranging logical theory of explanation for many different phenomena; or
it has to fail in explaining a range of important phenomena before it will
be given up as lacking. Science does not proceed by throwing out entire
theories just because one or a few details remain out of place or
unexplained at any point in time; it does not just "give up" at any given
point, throw up its hands in despair, and start resorting to supernatural
explanations. More work proceeds attempting to explain the anomalies with
logical, physical explanations.

Science is historical and needs time to proceed--theories do not rise whole
and complete all at once. They are hammered out over decades and sometimes
centuries. But creationists want their certainty and salvation *now*, and
are not willing to wait for logical explanation of things. There are always
going to be things on the horizon of science that may remain unexplained
for some time, simply because you can't discover some things until others
have been discovered first, which of course takes time. Creationism springs
from a psychological impulse that feels insecure without absolute emotional
certainty (this is not so different, incidentally, from the search for "the
perfect diet"). And emotional certainty of this sort can only come by
a-priori faith.

Science, on the other hand, works with "bulk of evidence," in the midst of
whatever amount of remaining uncertainty, as its criterion for giving
credence to hypothesis and theories--some amount of which (uncertainty) may
always remain no matter how massive the evidence, but which is not cause
for rejecting explanations that can adequately account for all but a few
still-being-worked-on details. (If everything were totally explained all at
once, there would be nothing for science to do, and it would not exist in
the first place.)

Science and creationism part ways in their preferences and methodology at
the very beginning--not somewhere along the way among the details. When
details still remain to be explained, the creationist preference is--as it
is at the beginning of their program--to fill in the gaps with supernatural
speculation to satisfy longings for emotional security at any cost. The
scientific preference is to assume that a physical explanation will
eventually be found, even if it is not yet known.

Both are based on underlying philosophical assumptions. But this does not
mean the assumptions underneath science are irrational ones. On the
contrary, the assumption that physical events have physical explanations is
the rational assumption. The assumption that physical events are explained
by supernatural mechanisms whenever physical ones aren't yet known is the
irrational one. Despite the fact there is no other logical, testable
explanation for how the sequence of fossils in the record could be the way
it is other than through earlier ones giving rise to later ones through
common ancestry--despite gaps in the fossil record that may be currently
unexplained--the creationist impulse is to prefer a supernatural
explanation for those gaps. Is that logical? Is it reasonable? Is the
belief even testable? Do the creationists even have an explanation
resulting from their belief that *could* conceivably be tested? No.

Now Johnson likes to throw up a red flag at this point and contend that
just because one doesn't have a _better_ explanation doesn't mean we
shouldn't accept a bad one (he thinks evolution is a "bad" explanation),
and we ought to recognize the possibility there could be other ones and
seriously search them out--but this is just a lawyer's trick. Why?
Because--again--he doesn't have ANY explanation at all--other than
supernatural ones, which he won't even divulge in the first place. (Indeed,
when biologist Kenneth Miller challenged him to do so in their on-line
debate at http://www.pbs.org/wgbh/nova/odyssey/debate/ sponsored by PBS's
Nova program, Johnson could not do so, and merely evasively skated away
from the question.) Because evolution is the *only* physical
explanation--given the evidence that we have--that makes any sense of it.
It's not the "rules of science," as Johnson maintains, that rule out any
other explanation than evolution. It's the EVIDENCE that does! And Johnson
doesn't like that evidence, so he decides he doesn't like the "rules of
science" and blames them for eliminating his option of invoking
supernatural cause where none is needed to explain what we see.

The situation we have with evolution is not that the explanations are not
good ones or are not supported by the evidence, but instead that no matter
how fine-grained the explanation gets (in terms of the steps from one
connecting point in the explanation to the next logical step), the
creationists prefer to keep their eyes focused on the ever-finer
interstices between the "grains" in the explanation, so they can invoke
their "God of the gaps," as it is called. Since the gaps keep getting
smaller and smaller, this of course makes a mockery of not only their idea
of God as omni-potent "cause," but also of their refusal to be reasonable.
At some point you either assent to the logic of the explanation or paint
yourself as someone who is in principle predisposed to reject reasonable
explanations in preference to your a-priori beliefs in supernaturalism.

David Wolfe for instance, even makes the facetious claim at one point that
"he doesn't know how" the fossil evidence can be accounted for--in a
supposed show of open-mindedness (but that he does somehow "know" Darwinism
can't). But what that really is, is pure denial of the evidence in favor of
an what is nothing more than an untestable hope, a last-straw bet.

END PART 9

--Ward Nicholson <[log in to unmask]