Friday, September 28, 2007

How Does Ateleology Generate Foresight?

At times a comment at Telic Thoughts brings up a broader issue than the subject matter of the comment itself. This occurred recently with respect to this comment. Quotes from the linked comment follow (appearing in red letters). My responses are in blue.

Genetic hotspots may evolve due to inherent advantages in rapidly changing and stressful environments. Any mutations still appear to be random with respect to fitness. There have been a few results that suggest directed mutations may occur in some situations, but these results are ambiguous at best. Research continues.

Results are not "ambiguous at best." I posted a comment in the same thread citing one of several studies indicating discernable genomic patterns evident with respect to mutations. Genomes are not equal opportunity mutation sites. Not only is a genomic region relevant, so too is the mutation rate which is known to vary. All of this affects the phenotype that might result from a mutation\selection process.

The insistence on randomness with respect to fitness despite data indicating a contrary conclusion is not surprising. Old habits and entrenched viewpoints die hard. The issue of randomness does not challenge a process. However, it does affect teleological considerations which ID critics are loathe to allow. More from the cited Telic Thoughts comment:

Keep in mind that even if directed mutations were shown to exist, this would not falsify evolution generally, but only the Central Dogma of Molecular Biology. Furthermore, Intelligent Design, as normally construed, will be supported only if there is evidence of foresight due to an outside agency. Genomes can be very "intelligent" and still have spontaneously evolved by incremental adaptation.

Evidence of foresight due to an outside agency? Foresight has qualities that are intrinsically intelligent in nature but how would one determine that foresight is generated by incremental adaptation? If adaptation is linked to environmental pressures and foresight entails the perception of events that have not yet occurred then what is the external event that generated foresight? Intelligent design fits foresight enabling mechanisms like the proverbial glove. But how does an ateleological process lead to an intrinsically teleological property like foresight?

If a bias toward non-randomness or teleology was present at the origin of life then an inferential bias toward intelligent design would exist. All the more so since alternative non-design explanations lack a natural selection criteria. Genomes indeed do appear "intelligent." But that only suggests that there may be something to intelligent design after all.


Sunday, September 23, 2007

Around the Blogosphere 9/23/07

Baylor President Stays Mum on University's Suppression of Intelligent Design

Scientific Journals Promoting Evolution alongside Materialism

Is It Really Intelligent Design that has the Great Derb Worried?

The Incorrigible Dr. Berlinski Exposes a Whale of Tale

UK Columnist Spots Dawkins' Arrogance in Argument against Intelligent Design

Eukaryotic Complexity

Another Perspective on Origins

Post details: Useful guidance for avoiding adaptationist fantasies

Post details: Molecular recognition within the cell

Tuesday, September 18, 2007

Evidence for the Evolution of the Brain?

Michael Egnor posted a blog piece covering a claim that links the evolution of amylase enzymes, which are found in saliva, to the evolution of the human brain. It is titled Spit-Brain Research. The following two paragraphs are quoted (in blue):

"Much of recent evolutionary self-satire involves the origin of the human brain. How did an organ of such staggering complexity and biological novelty arise? For evolutionary biologists, no speculation (except design) is too outlandish. Evidence: a paper in Nature Genetics offers a new theory to account for the human brain: spit.

According to the authors, evolution of the human brain was helped along by the evolution of spit, or more precisely, by evolution of the genes that code for the amylase enzymes in spit. Our brains needed a lot of energy, so evolution favored hominids with more effective carbohydrate-dissolving spit."

Worthy of note, from my persective, is the flimsy linkage of a moderate enhancement in the efficiency in carbohydrate metabolism to the evolution of what may be nature's most complex and extraordinary biological feature. While the brain may be an energy hog it is much more. Human intelligence is quite unique and I would be interested in more analysis of the physical pathways said to be associated with a biologically revolutionay adapatation within a time frame that is small by geologic standards. Another quote of Dr. Egnor follows:

"The spit-brain paper no doubt contributes to the literature on salivary amylase. A study of the comparative biology of salivary enzymes- genuine science but with limited (to say the least) popular appeal- would have languished on dusty shelves were it not for the authors’ utterly unwarranted inference that their research is relevant to the origin of the human brain. It seems to be a contemporary maxim in evolutionary biology- ‘attach preposterous speculation about the origin of the human brain to your arcane research, and you’re famous’, at least for a day or two.

Nature recently published an editorial asserting that the inference to design has no place in our effort to understand the origin of the genetic code or the origin of the intricate nanotechnology in living cells. Now, a few months later, Nature lauds a research paper that asserts that groundbreaking insight into the origin of the human brain can be gained by extrapolating from the comparative biology of spit.

Egnor makes a laudable note of Nature's capricious standards of evidence. The saliva inference is generous extrapolation indeed. Yet the obvious design inherent to the genetic code is given short shrift in a petulant Nature editorial. A good example of a mindset influencing the clarity of one's outlook.

Sunday, September 16, 2007

Selection Inefficiency

Jerry Bergman, authored 'Darwinism and the Deterioration of the Genome.' Data exists indicating that natural selection is not an efficient means by which deleterious traits are eliminated from genomes. Selection eliminates fatal genomic mistakes. Moderately harmful ones can be retained and passed on to future generations. Examples are abundant in individuals throughout populations. The abstract to the linked article follows (in blue):

An evaluation of DNA/RNA mutations indicates that they cannot
provide significant new levels of information. Instead, mutations will produce degradation of the information in the genome. This is the opposite of the predictions of the neoDarwinian origins model. Such genome degradation is counteracted by natural selection that helps maintain the status quo. Degradation results for many reasons, two of which are reviewed here. 1) there is a tendency for mutations to produce a highly disproportionate number of certain nucleotide bases such as thymine and 2) many mutations occur in only a relatively few places within the gene called "hot spots," and rarely occur in others, known as "cold spots." An intensive review of the literature fails to reveal a single clear example of a beneficial information- gaining mutation. Conversely, thousands of deleterious mutations exist, supporting the hypothesis that very few mutations are beneficial. These findings support the creation origins model.

If harmful mutations can escape the selection filter then on what basis must we assume that slightly advantagous ones, would not only be passed on, but become fixed in populations?


Saturday, September 15, 2007

What Type of Pathway Leads to This?

A Creation Evolution Headlines entry with the title Ant Pedometer Discovered quotes this from a research paper (in red):

"Foraging Saharan desert ants, Cataglyphis fortis, use a mode of dead reckoning known as path integration to monitor their current position relative to the nest and to find their way home. This enables them to return on a direct route, rather than retracing the tortuous outbound journey performed when searching for food items in their flat desert habitat, which is often completely devoid of landmarks. The path integrator requires two kinds of input information: about directions steered, as obtained via the ant’s celestial compass, and about distance traveled, as gauged by the ant’s odometer."1

The author of the piece then makes this comment (in blue):

"There was no mention of evolution in this paper. Only in evolutionary theory would someone attempt to say, with a straight face, that celestial compasses, path integrators and odometers are the result of a blind process lacking a navigation target."

Putting it another way, is there any limit to what can evolve through a non-teleological process? Most evolutionists would not put limits on a random mutation, selection process but neither are those maintaining that persepective able to supply us with a testable step by step approach indicating a pathway. Can "celestial compasses, path integrators and odometers" evolve in incremental fashion? How do we know?

1 Wittlinger, Wehner and Wolf, “The Ant Odometer: Stepping on Stilts and Stumps,” Science, 30 June 2006: Vol. 312. no. 5782, pp. 1965 - 1967, DOI: 10.1126/science.1126912.

Wednesday, September 12, 2007

Minimal Genomes: An Area of Research

One of my Telic Thoughts comments serves as a means to make a point about evidence for intelligent design. Mike Gene had written the following in the blog entry that led to my comment:

"Here Derbyshire expects ID to behave as a form of metaphysics that comes with answers to Ultimate Questions. He fails to realize that ID is focused on proximate causes that best account for the immediate phenomenon under consideration."

That prompted comments including this:

Bradford: If one looks at proximate causes one can construct a case for ID.

Zachriel: What is the proximate cause?

It depends on what you are looking at. One of the focal points I believe to be helpful to ID is the exploration of minimal genomes. It seems to me that IDists would be well advised to consider this an area of research within which varying hypotheses could be constructed and tested much like their counterparts do with respect to abiogenesis. The overarching principle would be the position that a minimal level exists but varies within a range that is linked to the nature of the organism cited. Exploration of proximate causes, that lead to the demise of a specific organism when the threshhold is transgressed because function x is not present, would simultaneously lead us to a better understanding of minimal function. Only then would we be in a good position to assert that gradual, incremental process y leads to (or does not lead to) the minimal function of organism z.

Living organisms contain sets of instructions, encoded in nucleic acids, which dictate what genes are expressed and when. There is a minimal number of genes needed to enable life. What is that minimal level? It will vary with the organism tested but are we able to make reliable predictions about the numerical range and functions of genes found in minimal genomes? Moreover would data reveal anomalies in a mutation/selection process supportive of intelligent design at the expense of abiogenesis? There is a strong likelihood. Our species is entitled to an honest return on its investment of time, money and effort into discovering the truth about earth's natural history.


Tuesday, September 11, 2007

RecA and DNA Repair

This linked EurekAlert article New mechanism discovered for DNA recombination and repair, references two papers related to the RecA protein family; one a PLOS ONE paper and the other appearing in Nucleic Acids Research. The following quote (in blue letters) is taken from the linked article:

"RecA family proteins are the central recombinases for HR. The family includes prokaryotic RecA, archaeal RadA, and eukaryotic Rad51 and Dmc1. They have important roles in cell proliferation, genome maintenance, and genetic diversity, particularly in higher eukaryotes. For example, Rad51-deficient vertebrate cells accumulate chromosomal breaks before death. Rad51 and its meiosis-specific homolog, Dmc1, are also indispensable for meiosis, a specialized cell cycle for production of gametes. Mammalian Rad51 and Dmc1 proteins are known to interact with tumor suppressor proteins such as BRCA2.

Since scientists discovered RecA family proteins, it has been assumed that RecA (and other homologs) forms only 61 right-handed filaments (six protein monomers per helical turn), and then hydrolyzes ATP to promote HR and recombinational DNA repair. Whereas a controversial puzzle came out, how the energy of ATP facilitating DNA rotation during the strand exchange reaction."

Mike Gene has blogged about RecA at Telic Thoughts. RecA has an important role in DNA recombination and repair. DNA repair, in turn, is an important consideration for intelligent design.


Sunday, September 09, 2007

The Mind, the Brain and Intelligent Design

An Evolution News and Views blog entry entitled The Spiritual Brain: An Argument Against Materialism brings up an area of research that impacts consideration of Intelligent Design. Quotes from the linked article appear in red. My comments are in blue type.

"Canadian neuroscientist Mario Beauregard notes at the beginning of his book The Spiritual Brain, co-authored with journalist Denyse O’Leary, that he belongs to a small minority of nonmaterialist neuroscientists. He is upfront about the fact that he “went into neuroscience in part because [he] knew experientially that such things [religious, spiritual, and mystical experiences (RSME)] can indeed happen.” Driven by his curiosity about what is happening to the brain during RSME, Beauregard and his colleague studied the spiritual experiences of Carmelite nuns, coming to the conclusion that it is more likely that these mystics are directly experiencing a reality outside of themselves."

If Beauregard's view is correct then how is the case for Intelligent Design affected? One effect would be to strengthen the position that life itself resulted from an intelligently directed process. While science may not be able to empirically document a source of intelligence that pre-existed the advent of life on earth, empirical evidence favoring the view that the mind is not something reducible to brain matter makes increasingly plausible the view that advanced intelligence is not unique to humans.

"This response of taking the nuns and their spiritual experiences seriously is not the norm in neuroscience, to put it mildly. Here Dr. Beauregard, aided by O’Leary, offers a unique perspective. Unlike his materialist counterparts, his philosophy does not force him to reject, deny, explain away, or treat these religious experiences as problems simply because they deny materialism. The book contains an entertaining if disturbing look at the ridiculous explanation materialists must resort to when confronted with the Numinous, a serious problem for their monistic philosophy. Taking the reader through uninspired arguments such as the “God gene,” the “God spot” in the brain,” and the eminently mockable “God helmet,” The Spiritual Brain reviews current evolutionary explanations for RSMEs and finds them severely lacking."

The author correctly identifies a materialist bias in neuroscience that leads some to couch explanations strictly in terms of genes and evolution. Intelligent Design advocates likewise fight a materialist bias that discounts non-human intelligently directed processes a priori. But chinks to a materialist bias in one area would provide an expectation that similar phenomenon could be found outside neuroscience.

"The power of nonmaterialist neuroscience is not that it has answered these questions already, but that it frees the scientist to study the question at hand, opening doors for new investigations into how the mind works. The Spiritual Brain has the opposite effect of the many materialist screeds which attempt to explain religion. Rather than dulling curiosity with useless theories about God spots and God genes, Beauregard and O’Leary incite a hunger for more knowledge and excitement for the future of neuroscience research."

This is an ironic twist to an anti-ID cliche. It is sometimes said that ID is a science stopper. But that appears to be the role of explanations attributing complex neural activities to an evolutionary process. No doubt, specific genes are involved in particular neural phenomenon. However, existing studies pointing to genes and an evolutionary process tend to oversimplfy matters rather than aid our understanding.


Thursday, September 06, 2007

Ugliness at Baylor

A blog entry entitled Academic Freedom Expelled from Baylor University at Evolution News and Views contains this paragraph:

"What a difference a year or two makes. Or not. The ugly specter of academic suppression seems incapable of being dispelled at Baylor University. It first ghosted across the campus a number of years ago when leading ID theorist William Dembksi undertook the task of heading up an intelligent design research program at the Michael Polanyi Research Center. Anti-ID bigots amongst Baylor’s faculty and staff moved quickly and decisively to stifle any such research on their campus, claiming that they were concerned that “people will make us guilty by association and assume that we are associated with or linked to this organization that is very well established as a pseudo-science.” It was clear then that intelligent design was not a subject that could be freely researched, studied, or discussed at Baylor University. Academic freedom be damned."

Of course it is annoying to IDists and secretly gratifying to the anti-ID movement to observe Baylor's harassment of Robert Marks at the behest of anonymous complaints but there are broader issues that illustrate how destructive anti-IDism can be. Marks is engaged in research at this time and the research encompasses computational intelligence, fuzzy systems and neural networks. But it is his project known as the Evolutionary Informatics Group, which has the potential to produce data favorable to intelligent design, that has motivated Baylor to take the most unusual step of returning a grant received from an outside organization which had been previously approved by the President of Baylor University.

This incident exposes the anti-ID movement as the anti-science, anti-academic freedom, anti-intellectual movement that it is. Anti-IDists like to finger the Wedge document as symbolizing an ID movement. Yet what harmful effects can be attributed to this so called ID movement? On the other hand the list of incidents linked to anti-IDism is unfortunately growing. More ammo for Ben Stein. Good luck with your up coming movie Ben.