Monday, November 27, 2006

Around the Blogosphere

Some links to information from other sites on the net:

Is SETI Science?
by Mike Gene

Gene notes some reasons why SETI is not a scientific endeavor. He noted that SETI does not explain what is about us but rather is searching for something which, if found, would need explaining. Gene also questioons whether SETI generates testable hypotheses and whether it can be falsified.

This short post links to another site with an article about that relates to the anthropic principle.

Dembski's post on Granville Sewell's "Why Are They So Angry?" Does the real cause of the rage correlate to the reasons given?

A website (Week in Science) with an article containing a half dozen references to science articles from the previous week.

Thursday, November 23, 2006

Dinosaur Soft Tissue?

A velvet dinosaur visted this blog recently but a discovery in Montana may yield information about fossilized skin belonging to a well preserved duckbilled dinosaur.

A linked article describing the find: Dino Skin Preserved in Rare Fossil Find indicates that a technique, previously used to recover what looked like blood cells of tyrannosaurus rex, may be useful in recovering soft tissue in this recent find.

A snippet from the article in bold print indicates how rare and important this find may be.

Julia Clarke, a North Carolina State University assistant professor of paleontology, worked on the dig. She told Discovery News that the skin is preserved in three dimensions, which is extremely rare.

"The skin appears to have internal structures inside of the scales," Clarke said. "These could be some kind of ligament attachments."

The world of paleontology expectantly awaits further analyses related to this discovery.

Wednesday, November 22, 2006

The Design of Life

I'm going to conduct a dissection of the first two paragraphs of an essay titled Life's Grand Design. It was authored by Kenneth R. Miller, Professor of Biology at Brown University. The essay is linked here.

A concept known as "intelligent design" (ID) has been used as an argument against Darwinism from the publication of On the Origin of Species in 1859 right up to the present day. Quite simply, ID states that living organisms must be the product of careful and conscious design, so perfectly formed that they cannot be explained by the random workings of evolution alone. Modern ID theorists contend that this is a new and novel scientific alternative to evolution.

ID, however, has been rejected by the modern scientific community for the same reasons that it failed in the 19th century. When closely examined, the living world is filled with evidence that complex organisms not only could have evolved through evolution's trial-and-error mechanism, but must have done so, because their structure, their physiology, and even their genetic makeup are all inconsistent with the demands of intelligent design.

Let's examine the claim of inconsistency. Presumably Miller has a good idea as to what would be consistent with intelligent design since examples abound. Cells function by virtue of a complex of interacting molecular structures that are regulated to perfom timely functions. A genetic blueprint contains the information needed to synthesize cellular components and allow cellular replication. Moreover there are self-correcting mechanisms that compensate for copy errors and environmental damage to DNA. If the existence of the foregoing appears to you to be inconsistent with intelligence then so must every man made object and many encoded systems for they are clearly inferior in design to these examples which are alleged to be stochastically generated.

On the other hand we've witnessed this strategy before. What Miller and others are up to is a theological ploy. Point to sub-optimal design (all organisms are imperfectly designed for death and disease is their destiny) and argue that any intelligent designer would either be stupid, wicked or both. Miller, a theistic evolutionist, would argue that God is good but that evolution is his mechanism of choice. In a logically tortured way Miller views this choice as excusing both sub-optimal design and ill-motives, which deliberate design would not do. One would think that scientific arguments would be the weapon of choice against ID but alas this type of critique is not an uncommon strategy. More dissection in future posts.

Monday, November 20, 2006

Chemical Codes

This is the second of a multi-part series related to David Berlinski's essay entitled 'On the Origins of Life.'

Berlinski noted that two very different structures- information management and chemical activity- must be coordinated and that this is accomplished by the genetic code. Berlinski emphasizes the word code. He goes on to state the following:

"By itself, a code is familiar enough: an arbitrary mapping or a system of linkages between two discrete combinatorial objects."1

This arbitrary property is distinct from a linkage dictated by underlying chemical forces that would make the linkages inevitable under specified conditions. The genetic code operates in conformity to laws of physics and chemistry even as they do not explain its origin. More from Berlinski:

"To note that codes are arbitrary is to note the distinction between a code and a purely physical connection between two objects. To note that codes embody mappings is to embed the concept of a code in mathematical language. To note that codes reflect a linkage of some sort is to return the concept of a code to its human uses."2

The arbitrariness of codes is linked to the question of whether the genetic code was generated by chemical properties of nucleic acids and proteins through which the code is manifested. If the genetic code is not the inevitable outcome of a specified series of reactions or of a stochastic selection process then there is little reason to think the biochemical objects forming the code are not like other objects expressing other codes. The objects in these codes are intelligently linked. An ID hypothesis would infer that shared properties result from the shared cause namely, intelligence. A prominent alternative cites a preponderance of amino acids in tRNA as an explanation for a chemically based origin of the genetic code. RNA molecules have been shown to bind tightly to some amino acids in vitro selection experiments. Note the following comment made about this.

"The nucleotide sequences of these RNAs often contain a disproportionately high frequency of codons for the amino acid that is recognized. For example, RNA molecules that bind selectively to arginine have a preponderance of Arg codons and those that bind tyrosine have a preponderance of Tyr codons. This correlation is not perfect for all the amino acids, and its interpretation is controversial, but it raises the possibility that a limited genetic code could have arisen from the direct association of amino acids with specific sequences of RNA, with RNAs serving as a crude template to direct the non-random polymerization of a few different amino acids."3

How does a "limited genetic code" arise? The direct association alluded to is not a chemically based explanation for an tRNA molecule. A detailed look at tRNAs reveals why. There are invarient properties common to all tRNAs. For example, structually all tRNAs have four tRNA stems, which are sometimes referred to as arms and all acceptor stems contain the sequence "CCA." The sequence is also found in the same location- the 3' end of the RNA chain. Acceptor regions and anti-codon regions are 76 Å apart. No doubt theoretical explanations can be concocted that explain forces leading to both invariance and variations. But where does selection play into this and why are there tRNAs that do not have a preponderance of the amino acid associated with them? How useful are constructs that seek to simultaneously explain both a particular property (tRNAs and an amino acid linkage) and its counterpart (the absence of such linkage) without furnishing the chemical details of how this was accomplished?


1. 'On the Origins of Life.'

2. Ibid

3. Molecular Biology of the Cell; Fourth Edition; Bruce Alberts, Alexander Johnson, Julian Lewis, Martin raff, Keith Roberts and Peter Walter; Garland Science; Chapter 6; Page 372.


Saturday, November 18, 2006

When Undirected Forces Do Not Suffice

An editorial from The People's Cube shows how, for some, natural forces explain everything.


Friday, November 17, 2006

Is it Evolution or Adaptation?

The article 'Short Legs Win Evolution Battle' is a focal point in determining what evidence supports evolution and what would support a design inference.

An environment that favors faster runners and the longer legs that enable faster running is presented as an example of observed evolution. Brown anolis lizards can live both on the ground and in trees. When predators were introduced into an environment containing the lizards, the predators of them reduced their population but survivors were found to have longer legs. The longer legs enabled the lizards to run away faster from the predators. In a following time period shorter legs, associated with easier tree navigation, were observed to correlate with more time spent by these lizards in trees. The tree dwelling avoided predators. In both time periods advantages conferred by limb length corresponded to adaptive behavior aligned with increased survival chances.

Is this evidence for evolution or adaptation? Are they one and the same or does adaptation occur within phenotypic limits? Could this be evidence for design? Answers should be based on the underlying genomic changes that generate changes in phenotype. If, for example, the alleles for the long and short legs existed within the lizard genome at the time the predators were introduced, then what we could be observing is mere allele variation back and forth. If, on the other hand, the changes resulted from new genomic features, made possible through genetic mutations, the analysis would be affected by this. I suspect the former dynamics account for this observation.

If so then what are the answers to the questions posed? The observations would record evidence for adaptation within limits. This could be evidence for built-in design flexibility. Evidence for evolution would entail data supporting the hypothesis that novel systems, containing multiple proteins, came about through random, selected mutations. That was not the type of evidence provided by this article.

Cellular Garbage Disposal Systems

Cells routinely degrade faulty proteins. There exist proteins whose functions relate to this task. Research at the University of North Carolina at Chapel Hill is focused on a protein known as the cystic fibrosis transmembrane conductance regulator or CFTR for short. The idea being to enable CFTR to form a functional shape and thereby treat the disease cystic fibrosis. Faulty CFTRs end up in a cellular trash bin known by a more scientific term called the ubiquitin proteasome pathway. Ubiquitin ligases and proteasomes are part of the system.

There would have been a point in time when no protein degradation systems existed. However as long as proteins are synthesized some will become faulty with respect to their function. Dysfunctional proteins can become more than simply cellular clutter. The can interfere with needed cellular functions.

IDers do not assume the sufficiency of a selection guided generating process. What type of cells would make the transition to cells with fully functional disposal systems. How would they have been described before and during the transition process?

Darwinism functions as the central cosmological myth of modern culture- as the centerpiece of a quasi-religious system that is known to be true a priori rather than as a scientific hypothesis that must submit to rigorous testing.- Phillip Johnson; Darwin on Trial.

Where is the rigorous testing for an evolved protein degradation system?

Wednesday, November 15, 2006

From: Week in Science

Four recent articles from Week in Science contain useful information. 'New Use for DNA Microarrays' cites newly developed procedures "for using DNA microarrays to rapidly identify mineral catalysts which pair well with abiotic building blocks of important biomolecules."

As the author indicated the multidisciplinary appoach (chemistry, biology and geology) offers promise and may result in an accelerated search for productive pairings.

'Radiation Resistance' cites a cellular repair switch- the "DNA damage checkpoint response"- which is an effective antidote to DNA damage incurred through radiation. I've argued that genomic correction and repair mechanisms are a prerequisite to cellular life and offer possibilities for ID based predictions and testing.

'APOBEC Proteins and Immunology' provides details about a family of proteins that protects primates against viral pathogens as well as "jumping genes." While one can readily envision changes in existing genes associated with viral adaptations, it is not clear how the genes connected with this complex of proteins would have gradually evolved as an adaptive response.

'How Changing are Constants?' deals with physics constants. An allusion to the significance of cosmological phenomenon for teleology is made.

Monday, November 13, 2006

Why are they Enemies?

An article from 'The Guardian' entitled 'Enemies of Science' was critical of Tony Blair's government and detailed some reasons why. It is authored by Alok Jha. I've focused on one paragraph of the article which I've broken into two parts for the purpose of providing commentary. The passage appears in italics.

Furthermore, scientists are becoming concerned at the rise of creationism in the British education system. The geneticist Steve Jones, who has lectured on evolution at schools for 20 years, says that he now regularly meets pupils who claim to believe in creationism.

Shocking huh? One of the difficulties with assessing a statement like this is the use of the term creationism. What does the writer mean by it? He probably conflates this with a belief in young earth creation. However there are non-YEC Bible believers and non-Christians who consider themselves creationists too. What exactly is the objection?

The creationist interpretation of fossil evidence is even encouraged in the new GCSE Gateway to Science curriculum. In August, a survey of British university students found that a third believed in either creationism or intelligent design.

A third believe in creationism or intelligent design. So what? How does this impede their capacity to learn chemistry, physics, mathematics...? Would the author have thought a survey, indicating that a third of the students believed that science supported their atheist beliefs, alarming? I doubt it.

Thursday, November 09, 2006

Darwinism's Central Tenet

'Darwin's Nemesis,' edited by William Dembski and published by Inter-Varsity Press, is a book about Phillip Johnson and intelligent design. The different chapters of the book have different authors. The first chapter is authored by Stephen C. Meyer.

Meyer told how Johnson's doubts about Darwinism were sparked by an incident that occurred at the British Natural History Museum (pp33-35) where a display had described Darwin's theory as one possible explanation for origins. In an ensuing controversy pressure was exerted to get the display removed. Having been denounced by the editors of Nature Magazine, among others, for not being clear that Darwin's theory was the only explanation for origins, the museum took down the display.

Meyers wrote of Johnson explaining that although change (evolution) and common descent were argued, the real substance of Darwinian claims was that change was caused by purely natural mechanisms i.e. without design or intelligent direction. While Johnson acknowledged the operation of science according to methodological naturalism he also pointed out that if Darwinists were to insist on the sufficiency of natural explanations then they could not simultaneously assume the outcome. ID can be denied by definition but at the expense of making it impossible to tell if causality by natural mechanisms is true.

Nowhere is this more evident than the origin of life itself. Beliefs as to how life arose are marked by their speculative nature. There is little evidence of prebiotic pathways to anything other than cellular biochemicals and no understanding as to how a cell would result. Yet rules are rules. Correlating encoding nucleic acids and the code by which they enable the synthesis of proteins to anything other than a chemically determined process, devoid of intelligent influence, is outside the rules.

The rules would allow an admission that a phenomenon lies outside the boundaries of science; an empirical discipline. This avoids having to assume a consequent while at the same time fending off ID. However, it may be philosophically too unappealing. Uappealing too is Darwinian insistence on exclusivity in the matter of origins. They don't have the goods. Those contemplating cellular functions and the specified order of genomes, making both function and inheritance possible, are not about to be deterred by a definition of reality not supported by the empirical discipline to which it is linked.

Wednesday, November 08, 2006


Three separate links follow. The first from Biology News Net, 'Comprehensive model is first to map protein folding at atomic level,' refers to scientists who developed a computer model predicting how small proteins fold. Protein folding is important because the shape of proteins is related to their function. It is also of critical importance to the study of certain diseases caused by impaired protein folding. Finally, protein folding is of importance to discussions of intelligent design and evolution.

A second article from 'Week in Science' is about atavisms. Atavisms are a frequently misunderstood concept and have, at times, been misused as evidence for common descent.

The third article is also from 'Week in Science' and refers to three other articles on the web. One is an amusing story about elephants and mirrors, another is about Saturn's geologically active moon Enceladus and the third, which is the most relevant to the topic of this blog, is about the sequencing of the western honeybee genome. Mentioned in a 'Science News' article was the fact that royal jelly, which is essential to the development of the queen, is associated with nine genes that code for the proteins enabling the synthesis of royal jelly. That raises the interesting question of how royal jelly synthesis capacity evolved in incremental steps as well as how this process would impact the queen's development.

Tuesday, November 07, 2006

An Idea Whose Time Has Come

An article authored by Jonathan Bartlett which appeared in 'Tulsa Today' took the CEO of the American Association for the Advancement of Science, Alan Leshner, to task for his arguments against proposed Oklahoma legislation which related to teaching science. Leshner's views appeared in 'The Oklahoman.'

Bartlett showed that Leshner referred to a legislative intention to encourage critical thinking and expose students to the debate over evolution. He quoted Leshner as stating:

"But this is the sort of code language that supporters of intelligent design doctrine have tried to inject into science education standards in other communities and states nationwide -- not to promote science, but to promote a narrow religious agenda."

It is not just a religious agenda but incredibly, according to Leshner, "a narrow religious agenda." How narrow can it be when no particular religion or religious doctrine is endorsed and intelligent causality points to a likely divine source only as a secondary inference? And who is Leshner to judge what will promote religion? While there are advocates of intelligent design, there are also opponents of the concept and the arguments and data fought over reference actual scientific research. What Leshner and others like him want is to control how science is defined; an endeavor that philosophers of science have differed over for quite some time. Ironically, in my view, it is intelligent design opponents like Leshner who fuel the growth of the movement which has developed roots throughout the world. What began as an American phenomenon now has spread to other parts of the globe including the non-Christian world. Who was it who said there is nothing more powerful than an idea whose time has come?