The Talk.Origins Archive Post of the Month: August 2004

Subject:    Re: Chuck Colson weighs in against Darwin
Date:       8 August 2004
Message-ID: a766a589.0408080138.25747577@posting.google.com

Wedge Buster wrote in message news:d1abe9ac.0408040759.cfb3d3@posting.google.com...
> Unconvinced Intellectuals
> Putting Darwin on the Witness Stand
> BreakPoint with Charles Colson
> August 4, 2004

[snip]
> Another new name is Edward Sisson, an attorney who used to direct
> avant-garde theater. His chapter sheds some much needed light on the
> Scopes trial. For example, did you know that the very textbook from
> which Scopes taught advocated eugenics and promoted racism? Indeed, it
> divided humanity into five races and ranked them in terms of
> superiority, concluding with "the highest type of all, the Caucasians,
> represented by the civilized white inhabitants of Europe and America."
> This is the book Darwinists insist Scopes had a right to teach?
[snip]

Here Colson and Sisson are lying, there can be no other word for it. The trial was not over the racism and eugenics promoted in the book. The trial was specifically and only over the teaching of evolution in the standard textbook, "Civic Biology" (which expended but two sentences on Darwin, and all of five or six pages on evolution, and even that treatment tepid and Lamarckian rather than Darwinian). The "Darwinists" did not insist that Scopes had a right to teach the racist and eugenic sections of the book; neither did the Creationists demand that they be removed. As point of fact, after Scopes was convicted, for the next edition of "Civic Biology," the author and publisher calmly erased all positive references to evolution and Darwin, while leaving unexpurgated all the racism and eugenics - and the State of Tennessee continued to buy the book and feed it to school kids for many years after. Creationists showed no objections or outrage, nor did they advance censorious legislation. The Creationists cared little about eugenics, and positively advocated racism; what they objected to was evolution.

For however much Creationists thrive on bitter fantasies about their own history, Tennessee schools had been segregated and had taught racism long before Civic Biology went to paper, and remained so long after it ceased to advocate evolution. Indeed, most public and private institutions in Tennessee were segregated and remained legally segregated until in the 1960s, when forced to stop by the Federal government. And so it was and has been the case in every state, evolution-free, dominated politically and socially by white Fundamentalist Protestants.

And Chuck Colson knows this: for thirty-five years ago, he and Harry Dent, a former aid to Strom Thurmond, were assigned by then-President Nixon to develop Nixon's racist "Southern strategy," intended to convert traditionally Democratic white Southerners to Republicans, using racial code words. Colson cannot claim ignorance of Southern political history.

Creationists' revisionist history of the Scopes Affair as a trial against racism is an invention of recent years, possibly only now that white Southern Fundamentalist Protestants have for the most part ceased publicly to advocate racism. It is a fraud, pious and perverse, existing only for Creationists' cynical campaign against science.

"As point of fact, after Scopes was convicted, for the next edition of 'Civic Biology,' the author and publisher calmly erased all positive references to evolution and Darwin, while leaving unexpurgated all the racism and eugenics - and the State of Tennessee continued to buy the book and feed it to school kids for many years after. Creationists showed no objections or outrage, nor did they advance censorious legislation. The Creationists cared little about eugenics, and positively advocated racism; what they objected to was evolution."

My "calmly erased" was inaccurate; there was evidently something of a tizzy between the author, George W. Hunter, and the publisher before a new, expurgated edition could be issued. Meanwhile, a year after the trial, the publisher issued a temporary special edition for sale to Southern states, with all six pages on evolution removed and unreplaced, and all else the same. A year or so later, they issued Hunter's revision, "A New Civic Biology," which is the one I was referring to in my post. The word "evolution" was banished entirely, as were the several illustrations that had upset Bryan so mightily at the trial. Brief and neutral mentions were made of "natural selection" and Darwin.

Most importantly, my comment "The Creationists [...] positively advocated racism" was meant as a general statement about Tennessee Creationists at that time and is untrue in respect to Bryan. Bryan never, to my knowledge, advocated racism. On the other hand, while he does not seem to have been personally racist, by the 'teens and 'twenties his primary constituency was Southern voters, in whose consideration he ignored the segregation and official racism of the entire region.

Summer for the Gods: The Scopes Trial and America's Continuing Debate Over Science and Religion. Edward J. Larson. Basic Books, New York, 1997. p.231.

Under God: Religion and American Politics. Garry Wills. Simon and Schuster, New York, 1990 (paperback). Chpts 8 & 9.

Subject:    Re: Evilution's Unanswerable Problems
Date:       16 August 2004
Message-ID: slrnci1g2j.hlb.lamoran@bioinfo.med.utoronto.ca

> In talk.origins Lilith wrote:
> [snip]
>> Only undergraduates with a rudimentary biology education think there
>> are only four nucleotides in DNA. 5-methylcytosine is a minor but
>> important base in DNA, which is chemically different than cytosine. If
>> the bible was trying to tell you that there are only four nucleotides
>> in DNA, where do they mention the fifth one, and how is it described?
>
> Can I have some more simple details please? Google was not really
> helpful on these questions.
>
> (1) Roughly what proportion of the human genome is this fifth base?

5-methylcytosine is the only significant modified nucleotide in the human genome. Up to 5% of all cytosine residues can be methylated in some tissues under some conditions. Typically, in an average human genome about 3% of the C's are methylated. Since cytosine makes up about 25% of the total nucleotides, this means that 0.75% of the total nucleotides contain methylated bases.

Flowering plants also have a high percentage of methylated cytosines in their genomes but most other eukaryotes have very little of this modified base. In addition to 5-methylcytosine, there are about a dozen other modified bases in DNA from various species. The most common ones are N6-methyladenosine, N2-methylguanosine, N4-methylcytidine, and 5-hydroxymethylcytidine. None of these are present in the human genome.

No. The way DNA sequencing is done it isn't possible to distinguish between 5-methylcytosine and unmodified cytosine. However, we know that the methylated version is created by an enzyme that recognizes the dinucleotide -CG- and methylates the C. The vast majority of methylated C's are at -CG- dinucleotides. These dinucleotides can be located in the human genome sequence where they tend to occur in clusters called CG islands. We can predict regions of the genome that are likely to contain a high proportion of 5-methylcytosine by mapping the location of the CG islands. These CG islands tend to be located near the promoters of genes, which is consistent with the idea that methylation of C plays a role in the regulation of gene expression in mammals.

During DNA replication 5-methylcytosine is recognized as C and a G is inserted in the opposite strand. 5-methylcytosine base pairs with G and when the G is copied during DNA replication a normal C is inserted in the opposite strand. This normal C can then be modified to 5-methylcytosine once DNA replication is complete.

If you start with 5-methylcytosine in the two C's of a double-stranded -CG- sequence, you will end up with daughter DNA strands that have a 5-methylcytosine in one strand and a normal C in the other strand.

     m               m
    -CG-    ---->   -CG-   +    -CG-
    -GC-            -GC-        -GC-
      m                           m

This is because DNA replication is semi-conservative. Each new daughter molecule contains one parental strand and one newly replicated strand.

Now, here's the neat part. Notice that the two new daughter strands are "hemimethylated." In other words only one strand contains a methylated C residue. The methylation enzyme specifically recognizes the hemimethylated DNA and not DNA where neither C is methylated. Thus, the methylation enzyme will scan newly replicated DNA looking for -CG- sites where one the the strands has a 5-methycytosine and the other strand does not. When it finds these sites it methylates the normal C on the opposite strand.

In this way the original methylated site is preserved after DNA has been replicated. This is the basis of many epigenetic effects where specific base modification is preserved from one generation to the next. If a gene is regulated in one cell by methylating -CG- islands, then this will be preserved when the cell divides. If, on the other hand, the gene has been regulated by removing the 5-methylcytosine (by a demethylase enzyme) then this pattern will also be preserved when the cell divides because neither of the daughter strands will have a 5-methylcytosine.

5-methylcytosine does not seem to affect RNA polymerase so the DNA is copied as though it had C instead of 5-methylcytosine. The messenger RNA (mRNA) is normal and protein synthesis is normal. The presence of 5-methylcytosine in DNA mostly affects the binding of regulatory proteins to DNA itself. This can have an effect on whether a nearby gene is transcribed or not transcribed and that's why 5-methylcytosine is often found at -CG- rich sequences near transcription start sites (promoters). (The role of methylation in regulating transcription is controversial. It's also possible that methylation affects transcription indirectly by altering the packaging of DNA into chromatin.)

The presence of 5-methylcytosine in coding regions is probably irrelevant. It's an accidental by-product of the methylation reactions.

Subject:    Re: Did Homo erectus live in the Americas?
Date:       18 August 2004
Message-ID: 1gir621.df17b33yoi2yN%johnSPAM@wilkins.id.au

> Uytkownik "John Wilkins" napisa" w wiadomoci
> news:1giphok.e9ad1d112b70N%johnSPAM@wilkins.id.au...
> > Uncle Davey wrote:
> >
> > > That the earth looks old is beyond question, and that natural selection
> > > appears to lead given enough time to speciation is also beyond question, but
> > > these two propositions do not destroy the argument that the earth was
> > > created about 10,000 years ago looking mature.
> >
> > And, as Maynard Smith once noted, it does not also destroy the argument
> > that the earth was created at 9am this morning, looking mature. Nor that
> > it was created 1 million years ago, looking mature. Nor that it was
> > created 1 billion years ago, looking somewhat more youthful than today.
> > In fact, nothing is ruled out or in, as a logical possibility.
>
> Exactly.
>
> So we are able to believe what we wish to on the matter without devaluing
> anything in science. All we are saying is that science is not the be all and
> end all in understanding the world. Science is not religion. Science makes
> observations, turns them into theories, and how that impacts on philosophy
> is then not necessarily such a direct process of mapping.

Science is the process of learning definite things about the world by taking data as reliable [lemma 1]

Anything that is logically possible is not in contradiction to science, even if it claims that all data are created as they hit our retinas. [lemma 2]

So, the Davey dilemma is that science is at the same time founded on reliable data that are unreliable.

> > But science cannot deal with logical possibilities. It can only deal
> > with evidence and actualities. Science says that the evidence is that
> > the earth is around 4byo, and the universe around 13.5byo. To claim that
> > it is, in fact, only 6000 years old because despite all the physical
> > evidence and the ways we employ successfully the techniques of science
> > that deliver that result in other aspects of our lives, the
> > interpretation you have of a 2500 year old religious book is to be
> > preferred is to argue what I call epistemic nihilism, the claim that we
> > really know nothing.
> >
> > Well if we know nothing, then I will rely on ersatz knowledge, as it
> > works much better than your "truth". You are doing a fine job of pushing
> > folk away from acceptance of your own version of God.
>
> If you say so, John. The poet Burns say 'something something giftie gie us,
> to see ourselves as others see us', and I'm sure you are able to gauge how

> unpleasant I am looking at me from the outside than I can tell looking out
> from my own head and not really being able to view myself as objectively as
> I could if I had, like eyes on stalks like a snail. However, I am sure that
> if I had a more amenable to evolutionists view of God, or no God at all,
> then I could be as unpleasant as I felt inclined and still people would not
> be in the least put off my views. As it is I walk around on eggshells and
> still manage to offend half the people.

This is a non sequitur. I am not talking about you personally. I am talking about the fact that you make religion deny what science is, and attempt to insert a religious view in its place. Science is the single most successful epistemology ever invented. It actually works. It does not involve revelations, intuitions, mystical visions or the operations of deities. This is to say it is emphatically not a religion. So, when you say:

> You don't have to reject science entirely at all. You can accept science
> in full, but just not make a religion out of it.

and yet you equally say that you will ignore scientific results when they contradict your interpretation of religion, you contradict yourself at the base. Either you think science is a way of knowing, in which case when science tells you the earth is 4.5by old you should accept that until science (good science!) tells you otherwise, or you reject the idea that science is a way of knowing. You cannot pick and choose truth here. If science tells you what is true, even allowing that it is a fallible way to find this out, then you are not at liberty to say "Oh, yes, all that is true except for the bits I think contradict my sacred texts". As soon as you do that, you adopt an epistemic nihilism about science. Since we know pretty well all we know through science, you have in effect declared the world to be unknowable.

Equivocate how you like, soften the blow and give whatever ground you can, this is the logical implication of your views, and it means that in the end the entirety of knowledge in your opinion comes down to people trading doctrinal blows. I think this is purely false. The world is known by the employment of empirical science, and any other claims to knowledge, such as through revelation, etc., have to not contradict science. As I said elsewhere once, if religion contradicts science, so much the worse for religion. The religion either has to realise it made a mistake, or abandon all claims to the ability to know anything, replacing all knowledge with pure faith.

The orthodox catholic (both lowercased to indicate the broad traditions rather than the denominations) Christian tradition has been that faith and reason cannot conflict as two truths cannot be in conflict. The way you set it up, if faith and reason conflict, you will hold fast to the prejudices of your faith ("prejudice" means, literally, "judging before"). In short, you abandon one truth on the basis that you judged before the facts were in, and you were correct from the start. Even the various churches do not take such a nihilistic stance.

Racism and the Scopes Trial

Post of the Month: August 2004

The Fifth Nucleotide

Post of the Month Runner-Up: August 2004

Omphalism and Epistemic Nihilism

Post of the Month Honorable Mention: August 2004