Creation Bits

I found Pharyngula's most recent blog entry amusing, since, he starts out by saying:

These enzymes are not smart or guided in any way

and later in the essay says:

Even more impressive is a truly maximal pairing that allows all of the homologous portions to be in register, a structure called an octavalent that brings all 4 pairs of chromosomes together in a very specific tangle. This is an optimal arrangement for pairing, but is less likely to have occurred simply because getting that many chromosomes into an ideal arrangement is difficult.

Apparently they are guided. This is precisely the property of created systems. They have backup systems that try to mitigate damage. It is a "very specific" tangle. It is an "optimal arrangement". How many undesigned systems are fault tolerant through modulating themselves into "very specific" or "optimal" arrangements?

I suggest everyone read the article -- it is very fascinating. I imagine that repetitive elements are used by the chromosomes for alignment purposes. So much for "junk" DNA! This paper is going on my Inter-library loan request list!

I just finished Malcom Gordon's The Concept of Monophyly: A Speculative Essay.

For those of you not up on terminology, monophyly is a fancy way of saying "Universal Common Ancestry". This means that the variety of life can be viewed as one giant family tree. Polyphyly means that organisms had more than one root. Creationists believe in a polyphyletic system -- each "created kind" represents a uniquely rooted tree. Non-creationists can also believe in a polyphyletic system in two ways. (1) There were multiple starts to life, each resulting in a different branch of life today. This is usually thought of in terms of the three domains of life -- archaea, eukaryota, and bacteria. Another view is that there were numerous starts to life, but that in the past, horizontal transfer was the rule instead of the exception. Life started in many different ways according to many different paradigms, and then merged in different ways to establish the higher levels of taxonomy. The latter approach is the one examined by Gordon in this paper.

First of all, it was nice to see that my previous comments about common ancestry being the result of specific origin-of-life scenarios, not evoolutionary theory itself is backed up in the scientific literature. Even more so, when you remove the requirement that the origin of life must be naturalistic, you remove even the reasons for assuming that certain groups had ancestors in the first place.

Gordon shows the diverse functioning in the genome as essentially being built up from multiple ancestral lines which came together through lateral transfer. He argues his point by showing that very diverse organisms have very interesting patterns of gene sharing that aren't explainable by a monophyletic common descent, but are explainable in a very high lateral transfer scenario. However, this requires that (a) such degrees of lateral transfer is even possible, and (b) that it would have been so widespread. Another way of looking at the data, however, is in terms of design patterns. If you allow an intelligent designer, then I think that common design patterns is the most natural result of following this data. There are no direct evidences of ancestry, the monophyletic view isn't tenable, and the degree of lateral transfer required for Gordon's polyphyletic view has never been observed. However, design patterns are indeed exactly how designing intelligences go about the act of creating.

He distinguishes three levels of evolutionary differentiation:

• Micro-evolutionary differentiation (populational changes)


• Meso-evolutionary differentiation (genera and families)


• Macro-evolutionary differentiation (kingdoms, phyla, and classes)

He points out that monophyly works best for micro- and mesa- levels of evolutionary differentiation. Interestingly, this is exactly what creationists claim! Also note that interbreeding among species can adversely affect monophyletic assumptions in even these cases.

Another interesting thing about the paper is that he notes that the monophyly/polyphyly question affects the "perception of how many different kinds of organisms there are and have been". I hadn't thought of that, but indeed assuming monophyly would require a massive number of unseen transitionals, while for polyphyly these would not be necessary.

Also, he points out to a number of known cases of gene transfer, and that it occurs even between highly diverse groups of organisms -- even between kingdoms. This includes plasmid transfers, viruses incorporating their genomes into hosts, and host DNA into their genomes, and transposons which can be experimentally transferred between organisms in different lineages.

Personally, I think the ability for organisms to be able to incorporate DNA from other sources indicates (a) that life is based on a common, unified plan, and (b) that organisms can transfer DNA as a mechanism to help other organisms in the environment adapt to each other. However, these claims have not been investigated to my knowledge.

Anyway, here are some good quotes from the paper:

There is, however, no doubt that strong circumstantial cases have been made, based largely upon morphological evidence, for polyphyletic origins of a number of major groups of organisms.

Do traceable lines of descent exist that might ultimately permit characterization of the genomes of organisms basal to the clades for the highest categories? The answer to this question increasingly appears to be no. Recent work on genomic structures demonstrate that all living organisms are genetic composites: mosaics and chimeras composed of bits and pieces of multiple genomes derived from multiple sources.

The base of the universal tree of life appears not to have been a single root, but was instead a network of inextricably intertwined branches deriving from many, perhaps 100 or more, genetic sources. The traditional version of the theory of common descent apparently does not apply to kingdoms as presently recognized. It probably does not apply to many, if not all, phyla, and possibly also not to many classes within the phyla.

[about tetrapod evolution] everything we know is circumstantial and indirect, and what actually occurred remains unknown.

[concerning traditional analyses of phylogeny] Possible polyphyletic scenarios were methodologically and philosophically excluded as impossible [emphasis mine]

The crucial role that statistically inadequate sampling of Devonian faunas has played in the development of our perceptions must explicitly be acknowledged...The animals found represent only a small, stochastically selected, possibly quite unrepresentative, sample of the biodiversity that existed in these groups at those times. There is no way of knowing to what extent, if at all, those specific organisms were relevant to later developments, or what their relationships might have been to each other.

Th evidence cited and the arguments made in this essay indicate that the applicability of the concept of monophyly at the macro-scales of evolutionary differentiation increasingly appears to be severely limited. An operational definition of the concept does not seem possible at the macro-level. Indeed, the phenomena of a monophyletic origin for the universal tree of life probably did not occur.

It is also desirable to avoid restricting frameworks for the evaluation of relevant data to only cladistic models.

The author's hope is that this essay may contribute in a small way to the mitigation of the strong trend toward more and more reductionism that pervades much of modern biology. I think biologists should try to avoid what I call "physics envy." The search for the simplest, most inclusive explanations for biological phenomena certainly must continue. However, that search should be tempered with the realization that over-generalization (including efforts to force everything in entire fields of study into single conceptual molds, such as the cladistic mold in evolutionary biology) is also a hazard along the path to understanding of the natural world.

Sorry for the massive quoting. I'm too tired to summarize.

My wife is dialated to 2 centimeters. If posts suddenly stop for a time, that's because I'm busy :)

Creationists often object to evolution because of the lack of transitional forms. Evolutionists often claim that finding a fossil C in between species A and B will just create two gaps - A to C and C to B, and therefore creationists will never be satisfied. In a recent post David Woetzel responded to this objection, and his post is below (reproduced by permission):

Now let's consider the evolutionist's argument that finding "in betweens" will just create two more gaps, so creationists will never be satisfied that something is transitional. This is a wrong-headed argument. We can establish an absolute yardstick based on the evidence from the field and lab experiments. There is a certain range of genetic variability within a species. Be generous and take the extremes of that (akin to a biblical "kind") and we have a credible gap measurement. Then if we find a morphological breach in the panorama of life that is much larger than that, the creationists can rightly assert that there are "missing links." If the evidence, on the other hand, is that the record of life is largely "continuous," then evolution becomes MUCH more credible. We might not know HOW it happened, but it sure LOOKS like common descent happened. Unfortunately for the darwinists, that is not the case. This is not merely the assessment of the creationists. The page I cited above links to hundreds of quotes by leading evolutionists buttressing the claim that the primary characteristic of the fossil record is "discontinuity."

For a simplistic graphical presentation of this idea, go to:
http://www.genesispark.com/genpark/audit/pattern4.htm

Genesis Park has lots of other resources on it for anyone interested, as well as a section on transitional forms.

In the book Ever Since Darwin, Stephen Jay Gould made the following criticism of Vellikovsky:

As startling as specific claims may be, I am more interested in Velikovsky's unorthodox method of inquiry and physical theory. He begins with the working hypothesis that all stories reported has direct observation in the ancient chronicles are strictly true—if the Bible reports that the sun stood still, then it did (as the tug of Venus briefly halted the earth's rotation). He then attempts to find some physical explanation, however bizarre, that would render all these stories both mutually consistent and true. Most scientists would do exactly the opposite in using the limits of physical possibility to judge which of the ancient legends might be literally accurate.

Now, I'm not here to defend Vellikovsky, but there is something in Gould's crticism that is fundamentally wrong. Gould criticized Vellikovsky for his method of inquiry. Here is the question -- how does science operate? Does it not proceed by observations which are then systematized? When conflicting views of physics were developed by electromagnetics and classical physics, finding a physical explanation that rendered both these observations true was the concept of general relativity, which, last I heard, was still enjoying scientific success, even though at the time many thought that it was outside the limits of physical possibility.

Vellikovsky's method is simply to take observations at face value. Since the writers of these histories were there and we were not, they are the best ones to report what it was that they saw and did. Should we rewrite observations because they don't fit in with current theory, or should we rewrite current theory when it conflicts with recorded observations?

Obviously ancient histories will not be error-free. However, that is not the same as unreliable. A modern false dichotomy is that you must either view scriptural history as 100% accurate without even a single mistake, or you must view it as a fairy tale. But we do not hold any other history or account to such a standard. If the existence of an error or even a set of errors would cause a historical work to be considered fantasy, then the whole of Western history should be discarded at once. But we do trust histories to be reliable, and the existence or possibility of the existence of isolated errors does not keep us from viewing historical accounts as being true and reliable.

It is a complete shame that Vellikovsky's primary idea is seen as some bizarre view of planetary motion. What Vellikovsky brought to the table was not a physical theory of space, but a collection of observations that demanded explanation. The specific explanation that Vellikovsky put forth is interesting but ultimately irrelevant. What Vellikovsky pointed out was that, in these periods of time, there were earth-wide events that are testified to from cultures around the world which had no contact.

Now, I haven't read Vellikovsky's books yet (I have a few sitting on my shelf), so these examples may or may not be representative of his. But bear with me.

What's interesting is not just that the Bible reported that the Earth stood still, but that it was corroborated by many other cultures. Now, on the other side of the world, they did not experience a prolonged day. They experienced a prolonged night! And we find stories there of not a long day but a long night.

And then the flood. Richard Dawkins once compared questioning evolution with questioning the existence of the Roman empire. I assume that his thinking was that while we might not have documentation of every day of the Roman empire, the historical evidence overwhelmingly testifies to it. However, while the Roman empire made its mark in history, there were many cultures that had never heard of it. However, what culture in the whole world does not have testimony to the great flood? The flood is the most widely-testified to event in history. (Well, almost. Actually, the most well-attested idea in history is the seven-day week, which is not only present in a huge number of cultures worldwide, but is also present throughout the biological world, including single-celled organisms, in what is called circaseptan cycles -- however this isn't observation so is only tangential to the present conversation).

Now let's get back to Gould. Scientists rely on observation to build models. While we may have circumstantial evidence of what happened in the past, historical documents provide the only first-hand evidence of what occurred. Should not a scientist conform their theories to observations, rather than the other way around? Do not scientists often rely on the observations of others? Why is it then out-of-bounds to consider the observations of the ancients in consideration of physical theory?

The question is one of trust. Scientists tend to trust each other more than those outside their field. They don't trust ancient documents. However, is this not simply an instance of chronological snobbery? How is the decision to trust another scientist's data set not the same as the decision to trust the written observations of the ancients? Why is one data set necessarily scientific and the other one not?

Ultimately, what sets Creationists apart is that we trust the historical writings of the Hebrews. This is not a blind trust, as many before us have shown how it connects with surrounding histories, including Josephus and Ussher. Ultimately, our physical theories must conform to the observations -- if we trust those that gave us the history, then there is no reason to exclude their observations any more than one should exclude non-confirming data from an experimental data set.

UPDATE -- for more on historical dinosaur reports, see this entry.

GRRRR... -- it appears I am unable to spell. It's not stegasaurus it's stegosaurus.

Dinosaurs in Ancient Cambodian Temple

It appears that the ancient cambodians had drawings of many common creatures in their temples. Creatures they probably saw every day. Including monkeys, deer, water buffalo, parrots, lizards, and ...... a stegasaurus.