Saturday, June 30, 2007

Around the Blogosphere 6/30/07

The bafflement centers around life's origins and Mike Gene writes this in his blog entry:

"Koonin recently authored a paper entitled, The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life."

An excellent post that highlights both the problems and metaphysical concerns surrounding the matter of life's origins. It also featured a stellar comment in response to it by David Heddle:

A You Tube wow moment.

A post on efforts to legislatively gag conservative radio talk shows. Freedom of speech is a basic and paramount issue that impacts science as well as discussions of evolution and intelligent design. Politicians need to respect the First Amendment.

The molecular clock...

The design of complex systems.

Gradualism, fossils and stasis.

The search for earth like planets.

Heterochromatin and its many essential functions.

History and biological validity: when Darwinian thinking leads to foolish conclusions.

Thursday, June 28, 2007

Is "God of the gaps" always a fallacious argument?

In contemporary materialist apologetics, much is made of the alleged "God of the gaps" fallacy. It goes a little something like this:

  • X argues that Y cannot be explained by purely natural processes. Therefore X infers that a creative super-intelligence has been involved.

  • X, though, is invoking "God of the gaps". X's God lives only in the gaps that cannot be explained by naturalism; his God must shrink every time science advances. His God must be very small by now.

  • Therefore, X's arguments can be dismissed.

At worst, naturalists resort just to wheeling out the phrase "God of the gaps" whenever their paradigm is challenged, in order to avoid argument.

The Gaps Are Real!

Actually, "God of the gaps" can be a perfectly valid argument; in fact, a required argument. If phenomena Y cannot be explained satisfactorily within naturalism, then we might say we have a "gap". We grant, for the sake of argument, that naturalism could cover a certain amount of space - but then we show that there is space that it doesn't and can't cover. That space is a "gap". The logical complement to naturalism is super-naturalism; if a naturalistic explanation can't cover the gap, then a supernatural one is required. That's not "God of the gaps"; that's simple logic. The gap is evidence of the supernatural. For the naturalist to merely trot out the retort "you're using a God-of-the-gaps argument!" is no kind of rebuttal - in some cases, it is merely identification of problem which he has no solution for within his world-view. To identify the problem is not the same as solving it!

Over the last decades, science has made tremendous progress in analysing and describing the universe that we live in. As it has done so, it has revealed a number of staggering "gaps". Complexity has appeared at lower and lower levels - levels at which, according to naturalism, we ought to be finding simplicity, not complexity.

In physics, the simplicity of Newtonian mechanics has given way to the greater complexity of Einsteinian relativity and quantum mechanics. As physicists have got to lower levels, they have discovered that the structure of the physical universe has more gaps than they thought: it is not the simple machine that Newtonian mechanics posited. Wave-particle duality is another instance: lower-level explanation has shown not that complex things are the result of the amalgamation of simple things, but that when we take apart the complex things we find more complex things.

In biology, the idea that life could arise out of the bringing together of a few simple chemicals in primitive conditions is now acknowledged as a non-starter. And as biologists have gained the ability to examine the macro-structure of the "simplest" cells, they've discovered that they're not simple at all. The most "primitive" organisms turn out to have just as much complexity as the most "advanced" - contrary to the predictions of naturalism. The building blocks of life, the DNA code, turns out to be the most intricate and complicated code known to man; its origin is a total mystery to naturalism, because there is nothing intrinsic in the nature of amino acids that requires them to construct themselves into codes. The DNA code reveals deliberate, detailed, fine-tuned complexity. The complexity of life is not reducible to simplicity, but is fundamental to it.

This is a pattern being repeated over and over. Naturalism predicts that as we get "lower down", we will find more simplicity; in fact, as we get lower down, we discover fundamental complexity. There is an enormous reality gap between naturalism's possibilities, and the universe which actually exists. These reality gaps are clear testimonies of the supernatural.

There are such things as invalid "God of the gaps" arguments. Those arguments have this structure:
  • We don't understand X.

  • Therefore X is supernatural.
I do not believe that God inhabits only the gaps, or that the "natural" exists separately from him. That would be another "God of the gaps" fallacy. I believe that the "natural" is God's ordinary way of working, and the "supernatural" is God's extraordinary way of working. Such arguments deserve to be rejected. To point out, though, that reality contains fundamental complexity which cannot be explained within naturalism's paradigm, is not only valid, but essential. By definition, the only way to point to the supernatural is to point to that which is beyond the natural. When materialists deny this as a valid argument, they are trying to win the argument by default. If pointing to the gaps is disallowed, then no discussion is possible, because it is the only thing that can be discussed. When materialists have to resort to that, it's becoming clearer that their world-view has some severe problems.

David Anderson


Introduction: David Anderson

The guys at "Intelligently Sequenced" have kindly invited me to join their blog - so, let me introduce myself.

My name's David Anderson. I haven't reached 30 quite yet and am married with a lovely wife and three delightful tiddlers. My academic qualifications are in Mathematics (Oxford) and Theology (Glamorgan), in the UK. I've been blogging for the last 8 months or so at "BCSE Revealed", an investigative blog whose aim is to expose the so-called "British Centre for Science Education". This group have been lobbying MPs, newspapers and the public, presenting themselves as an authoritative voice on science education debate. But: they're an absolute and shameless fraud. Read about it at "BCSE Revealed" if you want to know more.

In my day job, I'm a trainee pastor of a church in Derbyshire, United Kingdom (here). My aim is to be pleasing to Jesus Christ, who I worship as Creator and Saviour. I make no bones about the fact that I think that science, philosophy, religion and all the rest are part of a single, seamless whole: the universe that he created. I expect science to be a profitable and fruitful field of human activity, because I don't believe that the universe is random or accidental. I believe that materialists, imposing their philosophy upon science, are subverting it and suppressing many clear evidences of design - and shutting off whole avenues of fruitful inquiry by refusing to think outside of their materialistic paradigm.

My posts on "Intelligently Sequenced" will likely focus on popular-level discussion of some of the philosophical issues surrounding design and intelligence. I am told, though, to "post at will", so who knows what I'll end up coming out with!

Finally, something fun in case you haven't seen it before. Here's my response to Richard Dawkins. You can read this as a parable on Dawkins' brand of hyper-skepticism; it's amazing what you can deny if you're perverse enough.

I look forward to talking with you!


Wednesday, June 27, 2007

Transcription and DNA Repair

This linked news article, from the National Institutes of Health, Scientists Discover Role of Enzyme in DNA Repair, notes a mechanism involved in DNA repair and the transcription function. From the linked article (in green) (I added the link which helps to explain ataxia telangiectasia):

Scientists from the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Cancer Institute (NCI), and Integrative Bioinformatics Inc. have made an important discovery about the role of an enzyme called ataxia telangiectasia mutated protein (ATM) in the body’s ability to repair damaged DNA. NIAMS and NCI are part of the National Institutes of Health (NIH).

When DNA within a cell is damaged, the cell’s protective mechanism must do one of two things: repair the defect or “commit suicide,” says Rafael Casellas, Ph.D., an investigator in NIAMS’ Molecular Immunology and Inflammation Branch and leading author of a new paper describing the discovery. But the way in which the cell performs these protective functions has been largely a mystery, says Casellas, whose research is beginning to unravel this mystery.

Casellas’ research focuses largely on certain genes that are deliberately broken and repaired as part of the immune response. Through a tightly controlled process of breaking and rejoining DNA segments, immune system cells called B lymphocytes are able to produce tens of millions of different types of antibodies to fight almost limitless types of invaders. This process of genetic recombination requires the activity of repair enzymes, which must be able to recognize and repair breaks in tightly wrapped and inaccessible DNA. During immunoglobulin gene recombination, DNA is rendered accessible by the process of transcription, which unzips double-stranded DNA as part of the conversion of genetic information into functional proteins.

When DNA is transcribed and damaged DNA is present what happens? Effective repair entails shutting down transcription; specifically interfering with the function of RNA polymerase. Shutting down transcription is accomplished by specified proteins recruited to the site of the DNA damage. Three repair protein factors, ATM, Nbs1 and MDC1, are probably involved in the regulatory shut down function.

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Monday, June 25, 2007

Second Thoughts?

This post at Telic Thoughts brought up some disturbing possibilities that could occur in Europe due to existing laws and a Council Of Europe proposal that could adversely impact advocates for intelligent design. There may have been a development that would restrain the institutionalization of Darwinism in Europe and consequent penal action directed at dissenters.

This article has the details. Don't be misled by the opening sentence. The proposed policy went beyond the public school issue and was based on a non-existent threat to science meme.

Friday, June 22, 2007

The Formation of Centrioles

A blog entry from Science Sampler opens with this sentence: "A big question in cell biology has been if centrioles can be formed de novo or they required a template." Centrioles play a key role in cell division. Science Sampler discusses a paper from 'Science' entitled Revisiting the Role of the Mother Centriole in Centriole Biogenesis. The paper notes the following:

"Thus, centriole biogenesis is a template-free self-assembly process triggered and regulated by molecules that ordinarily associate with the existing centriole. The mother centriole is not a bona fide template but a platform for a set of regulatory molecules that catalyzes and regulates daughter centriole assembly."

Tuesday, June 19, 2007

Blaise Pascal

Blaise Pascal was born on this date in Clermont, France in 1623.

"Before Pascal turned 13 he had proven the 32-nd proposition of Euclid and discovered an error in Rene Descartes geometry. At 16, Pascal began preparing to write a study of the entire field of mathematics, but his father required his time to hand total long columns of numbers. Pascal began designing a calculating machine, which he finally perfected when he was thirty, the pascaline, a beautiful handcrafted box about fourteen by five by three inches. The first accurate mechanical calculator was born."1

Pascal was a mathematician of the first order and made major contributions to probability theory. He was also noted for what has come to be known as Pascal's principle which concerns the fact that in a fluid static pressure is exerted on container walls and acts perpendicular to the walls. Pascal's principle indicates that an external pressure applied to the fluid is uniformly transmitted throughout the fluid.2

1. Blaise Pascal;

2. 'Physics;' Jonathan S. Wolf; Barron's Educational Series, Inc; Chapter 13, 'Fluids,' Page 183.


Monday, June 18, 2007

Around the Blogosphere 6/18/07

Bilbo's post on Behe's new book.

News about genomic dynamics and differing perspectives on it.

Are functionally or structurally important genomic sites subject to selective constraints?

Do digital counters, that numerically control protein expression, parallel human-engineered systems?

More on "junk DNA."

Ken Miller embarrassed? Behe vindicated?

Denyse O'Leary cites 'Brains on Purpose;' a blog expressing skepticism about the neuroscience fad.

Michael Egnor setting PZ Meyers straight on altruism.

Saturday, June 16, 2007

On Behe's New Book

There have been posts in the anti-ID part of the blogosphere that have taken note of a surprising (from their perspective) lack of attention given to Behe's latest book (The Edge of Evolution) among ID blogs. Speculation then abounds as to why this is so. There probably is less than expected attention devoted by ID blogs but the reason for this is unlikely to be found in posts authored by anti-IDists. Anti-IDists feel comfortable with one or two individuals they can point to as authority figures for ID. Behe and Dembski fill that niche well. Aiming at those two and thinking they have scored well emboldens anti-IDists.

A brief tour of the two main ID blogs- Uncommon Descent and Telic Thoughts- indicates that the number of commenters with ID viewpoints has risen over the years. Many are knowledgable and some have intriguing ideas to offer that will not be found in books authored by Dembski or Behe. ID has broadened well beyond the literal handful of individuals that initiated things in the 90s. So too have the ideas that proliferate among IDists.

As the number of adherents to a viewpoint increases so too does diversification of concepts. It is simply a reflection of the fact that a greater number of minds are focused on an issue. It happened in the latter part of the 19th century among Darwinists and is a pattern that has been repeated throughout history. It also explains the decreasing reliance of ID on its founding fathers; accounting for Behe's declining influence among IDists. It is not that he is no longer respected. Only that he has now become one voice among many, albeit still a prominent one.

Friday, June 15, 2007

Gene Expression Clocks

A EurekAlert article entitled Clocking in and out of gene expression contains the following opening paragraphs (in red).

HOUSTON (June 15, 2007) – A chemical signal acts as time clock in the expression of genes controlled by a master gene called a coactivator, said Baylor College of Medicine researchers in a report that appears in the journal Cell today.

“We have long known that our bodies live by a daily and monthly and even yearly clock and that cells have clocks as well,” said Dr. Bert O’Malley, chair of molecular and cellular biology at BCM and senior author of this report. “We have actually taken this concept to the gene now and said that we are made up of 25,000 genes that have clocks too.” Genes get expressed and carry out their functions through proteins, he said. Gene expression involves the machinery of the cell translating the gene’s code into a protein that carries out function. This process has to have a beginning and an end.

Gene expression is time regulated and O’Malley indicated that master genes or coactivators determine when genes will be expressed. The regulating clock can be triggered by post-translational modifications of steroid receptor proteins. Ubiquitinylation is one such modification strategy. Successive ubiquitins are added correlating to the transcription of gene messages into proteins. A chain of five ubiquitins causes the destruction of the protein. Some more from the article:

“It’s built-in self destruction,” said O’Malley. “It prevents you from activating a potent factor in the cells that just keeps the clock running and the gene continuing to be expressed.” In that scenario, the result could be cancer, too much growth or an abnormal function.

“It means there’s a fixed length of time that the molecule can work. When it’s activated, it’s already preprogrammed to be destroyed. The clock’s running and each time an ubiquitin is added, it is another tick of the clock.” When the clock system fails, problems result.

Tuesday, June 12, 2007

Causes of Genomic Decay are Ubiquitous

Here is a modified version of a prior post whose publication led to some technical glitches.

Radiation is but one of many genomic degradation factors. It is likely the least damaging. More problematic are replication errors and damage to DNA caused by highly reactive oxygen radicals and a phenomenon known as deamination. It is important to bear in mind that all degradation factors would have been present when life first appeared on earth. There are a number of chemicals that would cause damage to nucleic acids in extra-cellular, prebiotic scenarios. But even within a protective cellular environment biochemical reactions within cells, specifically those involved in cellular respiration, cause collateral DNA damage through oxygen radicals.

Cell can't hide from the causes of genomic decay which are everywhere. It is also not helpful to use the "simpler cell" approach. "Simple" cells exist in the imagination. They are not empirical entities. Basic cellular functions like respiration and information storage cannot be dispensed with in the name of simplicity.

From a natural history perspective the question raised by genomic repair functions is: Would new genetic information, required to generate adaptive responses to degradation factors, outpace the loss of information engendered by those same factors?


Monday, June 11, 2007

A Minimal Cell

An article at Science Week entitled ORIGIN OF LIFE: IN SEARCH OF THE SIMPLEST CELL, discusses different approaches to determining the nature of the simplest possible cell. The following paragraph is quoted from the article (in red):

"In investigating the origin of life and the simplest possible life forms, one needs to enquire about the composition and working of a minimal cell that has some form of metabolism, genetic replication from a template, and boundary (membrane) production."

Mechanisms able to maintain the integrity of a genome could be added to the above. Cellular functions with energy requirements need to be accounted for and the alluded to functions and structures are all multi-component in nature. The template would have to be ordered to enable both cellular replication and the synthesis of biomolecules. More from the same source:

"A top-down approach will not take us quite to the bottom, to the minimal possible cells in chemical terms. All putative cells, however small, will have a genetic code and a means of transcribing and translating that code. Given the complexity of this system, it is difficult to believe, either logically or historically, that the simplest living chemical system could have had these components."

It is difficult to believe yet the belief persists that incremental pathways to an initial replicating cell existed in the absence of a teleological cause. If data indicates that the simplest cells require scores of genes, a genetic code by which they function and transcribing and translating mechanisms then there is a biological canyon to traverse without mechanisms that allow for change. Gene duplications require a functional genome which in turn is dependent on the existence of a complex of genes. The theoretical mechanism by which genes are generated calls for preexisting genomic complexity. That does not bode well for opponents of intelligent design.


Saturday, June 09, 2007

Links on Polystrate Fossils

We don't blog much about fossils but I thought this one was more interesting than most on that topic. The linked to blog entry actually links to a second article entitled Polystrate Fossils Require Rapid Deposition. The following is a quote of the summary of that article (in blue):

Polystrate fossils are a strong indication of rapid sedimentation. A number of examples of polystrate fossils were briefly listed. Uniformitarian scientists simply appeal to local rapid deposition to account for polystrate fossils, but they rarely if ever have any evidence for rapid deposition, other than the trees themselves, that is consistent with similar sediments with no polystrate fossils. Thus, polystrate fossils are both positive evidence for rapid deposition and negative evidence for the validity of the uniformitarian paradigm.

Particularly difficult to explain are polystrate fossils found in coal mines. The uniformitarian “swamp” model emphasizes long periods of time. With this in mind, we examined four open-pit coal mines northeast of Anchorage, Alaska. There were about 20 polystrate trees, mainly in two of the mines. The trees were at different levels in the mines, indicating rapid deposition of all the strata, including the coal. The strata were generally evenly bedded in all four coal mines, and the mode of deposition would have been similar over the entire area.

Thursday, June 07, 2007

Explaining Altruism

Michael Egnor's ‘Waiter, My Steak Isn’t Altruistic Enough!’ discusses attempts by neuroscientists to account for altruism. From the article (in green).

The mainstream view among neuroscientists is that the mind, and such things as morality and altruism, are ‘emergent’ properties of the brain, caused entirely by neurons and chemistry. They believe that the brain is a sufficient cause for the mind, and they see human morality as a trait crafted by evolution. I think this view is wrong.

For one process to cause another there must be a point of contact, in the sense that the processes linked in cause and effect must share properties in common. In biology, the liver contains molecules of enzymes and bilirubin and cholesterol, which cause the secretion of molecules of bile. In physics, a moving billiard ball collides with another billiard ball, causing each to change course. Each billiard ball starts with momentum, and momentum is exchanged when they collide. The transfer of momentum mediates the cause and effect. “Cause and effect’ presupposes commonality of at least one property- enzymes or bilirubin or cholesterol or momentum. Without commonality, there is no link through which cause can give rise to effect.

Egnor makes a good point. Is morality and altruism explained by neurons and biochemistry alone? How does the notion that morality and altruism are manifestations of an "emergent property" of the brain indicate cause and effect linkage? What is the shared property? The phrase "emergent property" is a common one but its descriptive value does not enable us to pin down exactly what is the common link between thought and emotions on the one hand and brain matter on the other. We are able to associate biochemicals and reactions among them with brain activity but the predictive utility of such associations is far from a scientifically comprehensive level. Personality profiles give us a much better predictive yardstick than an individual's unique biochemical make-up.

The nature of thought and brain cells differ to such an extent that detailed causality models of altruism are more a dream than reality. Explanations of altruisitc behavoir have an ad hoc appearance. Selfishness reigning over altruism easily lends itself to a survival or pleasure enhancement interpretation but when the reverse occurs then what? A different kind of pleasure that comes with doing good? Group instinct dynamics? Explanations seem more driven by theory than particulars unique to a given situation.

Wednesday, June 06, 2007

Cell Signaling

I like this site. It provides informative descriptions of biological processes with visuals to boot. This one addresses cell signaling. The following quote in blue is taken from the article:

The Notch signaling mechanism is an example of juxtacrine signalling in which two adjacent cells must make physical contact in order to communicate. This requirement for direct contact allows for very precise control of cell differentiation during embryonic development. In the worm Caenorhabditis elegans, two cells of the developing gonad each have an equal chance of terminally differentiating or becoming a uterine precursor cell that continues to divide. The choice of which cell continues to divide is controlled by competition of cell surface signals. One cell will happen to produce more of a cell surface protein that activates the Notch receptor on the adjacent cell. This activates a feedback system that reduces Notch expression in the cell that will differentiate and increases Notch on the surface of the cell that continues as a stem cell.

Tuesday, June 05, 2007

DNA Damaged by Sodium Benzoate

Soft drink preservatives could damage children's DNA, is an article from Tajikistan News reporting of research indicating that the preservative sodium benzoate, which is used in drinks and certain foods, can cause damage to DNA found in the mitochondria. Children appear to be particularly vulnerable. When combined with vitamin C the mix can form a carcinogenic substance known as benzene. Yet sodium benzoate is naturally found in foods like cranberries, prunes, greengages, cinnamon, ripe cloves and apples; some of which are known to contain plenty of vitamin C.

Mitochondrial DNA reportedly can be damaged to the point of inactivation. Given the identification of particular diseases with malfunction of the mitochondria and the association of the ageing process with damaged mitochondrial DNA, concerns about effects of sodium benzoate consumption need to be taken seriously. Retesting of the preservative may be in order.


Monday, June 04, 2007

New Species in Suriname

A Yahoo news article appearing today entitled Purple frog among 24 new species found in Suriname by Deborah Zabarenko, reports of new species that have been located in the nation of Suriname which includes a purple fluorescent frog. The discovery is unusual in that so many of the species are not insects. Many were frogs and fish and other species of larger organisms that include panthers and pumas, monkeys, reptiles, and bats. In addition new species of dung beetles were found as well as a new ant species. Thirteen scientists were engaged in the exploration.

Saturday, June 02, 2007

Detecting Conditions Favorable to Life on Other Planets

While some may want to believe that detecting planets, with environments that are hospitable to life, is something beyond our technological capacities, NASA would disagree. The Terrestrial Planet Finder evidences a belief that not only can conditions favorable to life be detected, but the effort to do so is also worthwhile. This from the linked article:

"The search for habitable planets and life is founded upon the premise that the effects of even the most basic forms of life on a planet are global, and that evidence for life, or biosignatures, from the planet's atmosphere or surface will be recognizable in the spectrum of the planet's light. Observations across as broad a wavelength range as possible are needed to fully characterize a planet's habitability and to detect signs of life.

Direct imaging detection and spectroscopic characterization of nearby Earthlike planets will be undertaken by the Terrestrial Planet Finder missions. The TPF Coronagraph (TPF-C), planned for launch in 2014, will operate at visible wavelengths. It will suppress the light of the central star to unprecedented levels, allowing it to search for terrestrial planets in ~150 nearby planetary systems. TPF-C will be followed about five years later by the TPF Interferometer (TPF-I). TPF-I will operate in the mid-IR and will survey a larger volume of our solar neighborhood, searching for terrestrial planets around as many as 500 nearby stars."

While plans for future missions are already underway NASA is not without existing data to support its views. This link discusses data about planets already discovered. From that article:

"Astronomers have captured enough light from two planets far beyond our own solar system to reveal details of their chemical make-up, marking a new phase in the search for extraterrestrial life.

By analysing the faint glow of one of these alien worlds they have found tentative evidence that suggests the presence of chemicals which play a role in one theory of how life began on Earth.

The chemicals, polycyclic aromatic hydrocarbons, may have helped the formation of RNA, the ancestral genetic material of DNA, the building-blocks of life on our own planet.

Although this planet seems to lack water and is at a searing 800 C - which is thought to be much too hot for life - three teams announce today they have successfully carried out the feat on this and one other alien world, marking a breakthrough in the development of techniques capable of scouring the cosmos for signs of life."

NASA efforts offer opportunities to gather data that either confirm or caste doubt on the belief that life exists elsewhere in the cosmos.


Friday, June 01, 2007

Around the Blogosphere 6/1/07

Mike Gene's post on Neil deGrasse Tyson's criticism of intelligent design.

A post marking the death of Stanley Miller and the research that made him famous.

A blog entry about a soft research project attempting to explain the causes for the beliefs of some.

Denyse O'Leary's list of links that relate to the writings of British physicist David Tyler.

A post about the behavoir of fruit flies and hornets.

The irrelevance of Darwinism to productive research.

More from Granville Sewell on the Second Law of Thermodynamics.