Wednesday, July 23, 2008

Comparing and Contrasting Creationism and Evolution

On one of the discussion groups I participate in, the issue of creationism came up. I posted the following to the group as a means of comparing and contrasting between Creationism and Evolution. My argument is that there are a number of core differences between how creationists and scientists deal with their respective ideas. One of the first and most poignant things one notices is that in evolutionary biology, work proceeds apace without any reference to creationism. One could read through journals and never encounter a single reference to creationism. Put more bluntly, evolutionary biology stands on its own as a scientific theory. It explains phenomena based upon its own rules and need not look to creationist literature for definition. On the other hand, Creationism is what I call a negative theory. By this neologism, I mean that creationism can only define itself in reference to evolutionary biology. There are no free-standing creationist ideas, meaning that all of creationism can be encapsulated in the statement: “Evolutionary biology is wrong, therefore creationism is true”. This is stunningly sloppy logic. It is akin to assuming that because I don’t care for eggplant, that I must like okra.

I’ll spare you the discussion group specific run-up and jump right into it:

 I Googled for the exact same terms, changing ONLY the word
creationism or evolution.  I will take a representative sample of text
from *each* result which appears to best demonstrate the respective
positions.  My first search was "Genetic evidence for evolution" and
"Genetic evidence for creationism":
Here is a representative sample from a paper on evolution:
From the Abstract:
Rapid evolution driven by positive Darwinian selection is a recurrent 
theme in male reproductive protein evolution. In contrast, positive 
selection has never been demonstrated for female reproductive 
proteins. Here, we perform phylogeny-based tests on three female 
mammalian fertilization proteins and demonstrate positive selection 
promoting their divergence. Two of these female fertilization 
proteins, the zona pellucida glycoproteins ZP2 and ZP3, are part of 
the mammalian egg coat. Several sites identified in ZP3 as likely to 
be under positive selection are located in a region previously 
demonstrated to be involved in species-specific sperm-egg interaction, 
suggesting the selective pressure is related to male-female 
interaction. The results provide long-sought evidence for two 
evolutionary hypotheses: sperm competition and sexual conflict.
From the Discussion:
We have demonstrated that the female reproductive proteins ZP2, ZP3, 
and OGP are subjected to positive Darwinian selection. These results 
lend support to the models of sperm competition (1, 18, 19), sexual 
conflict (2, 20, 37), and cryptic female choice (15) driving the 
evolution of reproductive proteins, because these models involve male- 
female interactions. It is important for functional as well as 
evolutionary studies to examine the rapid evolution of both female and 
male reproductive proteins. Functional studies can glean important 
information not only from conserved regions of the molecules but also 
from the divergent regions under positive selection, because the 
latter may be functionally important for specificity. Our analysis 
identified several sites in ZP3 under positive selection. These 
include a region previously implicated as functionally important in 
sperm-egg interaction (41–43). Additionally, a region in ZP3 
immediately following the signal sequence was identified (Fig. 1 
Right) for which tests of functional importance have not been reported 
and which our data predict might also play a role in species 
specificity. The sites we identified in ZP2 as likely to be under 
positive selection are candidates to test for functional importance in 
ZP2's role as receptor for acrosome-reacted sperm (21, 27).
It is likely that the evolution of additional female and male 
reproductive proteins also are promoted by positive Darwinian 
selection. For example, many reproductive proteins (including ZP2, 
ZP3, and the sperm protamines analyzed here, but not OGP) are found in 
the 10% most divergent sequences from an aligned set of 2,820 human- 
rodent orthologs (ref. 51 and our unpublished analyses). These 
reproductive molecules are as divergent as many genes involved in 
immune response. Another ZP glycoprotein (ZP1) is also among these 
rapidly evolving proteins, but insufficient phylogenetic sampling to 
date precluded its analysis by using likelihood ratio tests. Future 
sequencing and phylogenetic analyses of these reproductive proteins 
are necessary to determine whether their rapid divergence is promoted 
by positive selection or caused by lack of constraint. It also will be 
important to determine in general what proportion of reproductive 
proteins show signs of selectively driven rapid evolution seen herein.
Our demonstration of positive Darwinian selection in female as well as 
male reproductive proteins lends support for models of sexual conflict 
and sperm competition driving the divergence of reproductive proteins 
(2, 20, 37). Although the nature of the selective pressure remains 
unclear, our observation that selection acts to diversify a region in 
ZP3 previously identified as functionally important for species 
specificity suggests that the selective pressure may be related to 
male-female interaction, in this case sperm-egg interaction.
The entire paper, so that you can read the whole thing (I cut out 
2/3rds of the paper for the sake of length and because it gets VERY 
technical), is located at:
One will note that in neither the abstract OR the discussion is ANY 
reference made to creationism.  (You will not find it in the technical 
text that I omitted either)  You will also notice, in the conclusion, 
that the authors make a positive argument FOR evolution not a negative 
argument *against* creationism.  This is what we would expect from a 
proper scientific paper.
Here is what the search for creationism pulled up:
32.   Genetic Distances
Similarities between different forms of life can now be measured with 
sophisticated genetic techniques.
Proteins. “Genetic distances” can be calculated by taking a specific 
protein and examining the sequence of its components. The fewer 
changes needed to convert a protein of one organism into the 
corresponding protein of another organism, supposedly the closer their 
relationship. These studies seriously contradict the theory of 
An early computer-based study of cytochrome c, a protein used in 
energy production, compared 47 different forms of life. This study 
found many contradictions with evolution based on this one protein. 
For example, according to evolution, the rattlesnake should have been 
most closely related to other reptiles. Instead, of these 47 forms 
(all that were sequenced at that time), the one most similar to the 
rattlesnake was man.b Since this study, experts have discovered 
hundreds of similar contradictions.c
DNA and RNA. Comparisons can also be made between the genetic material 
of different organisms. The list of organisms that have had all their 
genes sequenced and entered in databases, such as “GenBank,” is 
doubling each year. Computer comparisons of each gene with all other 
genes in the database show too many genes that are completely 
unrelated to any others.d Therefore, an evolutionary relationship 
between genes is highly unlikely. Furthermore, there is no trace at 
the molecular level for the traditional evolutionary series: simple 
sea life   fish   amphibians  reptiles  mammals.e Each category of 
organism appears to be almost equally isolated.f
Humans vs. Chimpanzees. Evolutionists say that the chimpanzee is the 
closest living relative to humans. For two decades (1984–2004), 
evolutionists and the media claimed that human DNA is about 99% 
similar to chimpanzee DNA. These statements had little scientific 
justification, because they were made before anyone had completed the 
sequencing of human DNA and long before the sequencing of chimpanzee 
DNA had begun.
Chimpanzee and human DNA have now been completely sequenced and 
rigorously compared. The differences, which total about 4%, are far 
greater and more complicated than evolutionists suspected.g Those 
differences include about “thirty-five million single-nucleotide 
changes, five million insertions/deletions, and various chromosomal 
rearrangements.”h Although it’s only 4%, a huge DNA chasm separates 
humans from chimpanzees.
Finally, evolutionary trees, based on the outward appearance of 
organisms, can now be compared with the organisms’ genetic 
information.  They conflict in major ways.i
A couple of things you will otice.  Firstly, there is hardly a 
sentence that doesn't talk about evolutionists or evolution.  If 
creationism is such a strong scientific position why is it that it 
cannot stand on its own?  (And in this instance, I quoted the page in 
its entirety).  Secondly, you will notice that not a *single* argument 
in favor of creationism is made.   This was from In the Beginning: 
Compelling Evidence for Creation and the Flood  which is a book put 
out by the Center for Scientific Creation (which is why I favored this 
over the ICR although a page came up for them which, upon reading, had 
the same kinds of flaws).  The letters standing on their own all 
represent footnotes which I ran down and found that those quoting 
evolutionary biologists or other scientists were all misquotations (in 
fact, one such quotation is such a flagrant and obvious one that I 
merely had to put in the name of the scientist quoted and the first 
several hits were ALL about the misquotation which makes one wonder 
why a purportedly scientific organization would put it in their book 
and on their website).
One last comment before moving on.  I have been FAR more generous with 
creationism than with evolution.  After I had found my representative 
sample for creationism and genetics, I kept looking for results, 
following some 25 links in the hopes of finding ONE paper that had the 
kind of scientific gravitas that my representative evolutionary 
biology sample did.  I could not find one.  EVERY web page I found was 
similar in that it did not make a case FOR creationism, it made a case 
AGAINST evolution.  I took the *third* result from my search on 
evolution (third on the first page of results) purposely eschewing 
TalkOrigins pages.
In other words, while taking pretty much the first thing I could find for evolutionary biology I looked for the BEST thing I could find for creationism and the most solidly academic thing I could find still didn’t stand on its own.

Monday, July 7, 2008

I feel like Mr. Peabody

This morning, I was mucking about with Entourage and then switched back, deleting the Entourage calendar in iCal. I managed to do this before switching my To-Do list back, thus all of my To-Do items went away. This was the second time since I’ve owned this machine that I have done something so entirely clueless. However, thanks to Time Machine I have managed to get them back and it just looks so cool. I need not worry about deleting things as long as I do so after I’ve been home from work or elsewhere that I’m disconnected from the Time Capsule (see below). (The actual Tardis on top of my TC (also named Tardis) is a USB hub)