Tuesday, August 28, 2007

Are you incredulous?

In a couple of posts so far I've been analysing some of the logical dodges and tricks that often turn up in popular Darwinist argumentation:

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

  2. What is the "Fine Tuning" argument?
Here's another one today: the "argument from personal incredulity".

EvoWiki defines this logical fallacy this way: "An appeal to ignorance is an argument that absence of proof is evidence of absence." (http://wiki.cotch.net/index.php/Argument_from_incredulity)

In the 80s film "Back to the Future" (part 3), Doc Brown, having lost the love of his life, stays up all night in a 1880s saloon bar. He doesn't actually get round to drinking anything until 8am the next morning. Having loved and lost, he no longer cares enough to keep up the pretence of being a bona fide resident of the 19th century, and starts spilling the beans about the future. He explains to his fellow bar-dwellers about engines and cars - and that in future, people will only run for fun. They, of course, just laugh at him.

After all, nobody runs just for fun. And the idea of mechanical, motorised vehicles - pure nonsense! Unbelievable! The Doc is obviously a crank.

If we look around today, lots of what we take almost for granted would seem like magic to those of previous generations, and if we were able to hold a conversation with them and tell them about it all, they might think we were barking mad. To be able to see a live picture of a person on the other side of the globe and hear their voice in real time? Visiting the moon? An orchestra that fits in your pocket and weighs only 50 grammes? Nonsense, my boy!

That's the appeal to personal incredulity. And it's bogus. Things that we can't explain do exist. An explanation may be forthcoming in future; or maybe already exists now but you just don't know it.

So, there is such a thing as a bogus appeal to personal incredulity. It's arguing that because you can't understand how a thing could be, therefore that thing isn't. (At this point you may like to pause and consider Richard Dawkins' well-worn argument that it is illegitimate to speak of an intelligent designer because we can't explain where that designer came from, or in its briefer form - "Who designed the designer?"...)


This is a logical fallacy which Darwinists are very confident that critics of Darwinism use all the time. EvoWiki in the article above, under the heading "Examples in creationist arguments" offers us a sample of 41 instances covering a vast amount of ground. What strikes me, though, as I look at some of the instances under that list, is the extent to which the authors of the articles linked from it have over-played their hand.

Let's float back to that 1880s saloon, and imagine that a different conversation is taking place. Doc Brown is still at the bar, glass (not yet drunk!) in his hand. He's explaining that in the year 1985, where he comes from, people will be able to travel at faster than the speed of light, and that telegrams will actually travel completely instantaneously - no time at all. The other regulars in the bar are laughing at him - they are incredulous.

Are they laughing because of their personal incredulity? Very likely. But the scientific data which we have actually points to their incredulity being right. Transport the Doc back into the late 20th century, and have him make the same case to a competent group of physicists. They laugh just like the bar-dwellers did. Their laughing, though, is an informed one - and arguably correct. They have some data, and it points in the opposite direction to the Doc's ideas. Of course, they don't know with absolute certainty, because their interpretation of the data might be based upon faulty assumptions at some point. Their may be new data yet to be discovered which may give a different spin on things. But the point is, it's not just personal incredulity which is driving their skepticism.

That's enough to begin with. Next time, God-willing (or, for the atheists out there, should the molecules favour us by bouncing into the right positions), I'll develop this line of thought a bit more, and identify some particular and telling ways in which the argument from personal incredulity is being abused in order to shore up the troubled foundations of the materialist world view. If you want something to chew over and see where it leads, start pondering these questions. What is the relationship between skepticism and the scientific method? When is incredulity good? 'Til next time...

David Anderson


Monday, August 27, 2007

Clues About Gene Expression from Mice

The following paragraph appears at the linked article entitled Scientists Find Clue To Mechanisms Of Gene Signaling And Regulation, from Science Daily.

"Scientists have discovered a pattern in the DNA sequence of the mouse genome that may play a fundamental part in the way DNA molecules regulate gene expression. The research, led by Emory University scientists along with colleagues at Jacobs University, Bremen, Germany, will be published in the August 22 Advance Online publication of the journal Nature."

The article then focuses on epigenetics; a phenomenon involving the regulation of gene expression. An epigenetic process called methylation is a means by which genes are silenced. Methylation involves the addition of a methyl group to DNA. Histone proteins, in the vicinity of DNA, can also undergo methylation. This is another means of gene regulation.

A particular type of gene expression known as imprinting entails the expression of only one allele- one of a pair of genes. Normally both copies are expressed. Imprinting occurs when one allele is methylated, and thus silenced, and the other allele is expressed. Areas of the brain where genes are imprinted are called differentially methylated regions. The Emory and Bremen researchers, referred to in the article, believe that there is a biochemical pattern which acts as a signal indicating that a gene should be imprinted by an epigenetic mechanism. So what does the pattern look like? It appears to be a repetitious pattern of eight to ten base pairs between two CG dinucleotides. Researchers believe the message of the signal involves the location wherein differential methylation should occur. Researchers had studied the mouse genome.

The paper's authors include Emory chemistry graduate student Da Jia as well as Emory biochemist Xing Zhang and Renata Jurkowska and Albert Jeltsch from Jacobs University Bremen.


Saturday, August 25, 2007

Nature Suggests Intelligent Design

A post written by Anika Smith, UK Columnist Spots Dawkins' Arrogance in Argument against Intelligent Design, at Evolution News and Views, comments on a piece authored by Melanie Phillips in the UK's Daily Mail. Quotes of Melanie Phillips are in green and my commentary is in blue. Melanie Philipps is quoted as stating:

There is no evidence for this whatever and no logic to it. After all, if people say God could not have created the universe because this gives rise to the question "Who created God?", it follows that if scientists say the universe started with a big bang, this prompts the further question "What created the bang?"

In other words the infinite regress causal chain dilemna is inherent to all explanations.

Moreover, since science essentially takes us wherever the evidence leads, the findings of more than 50 years of DNA research - which have revealed the almost unbelievable complexity of the arrangements which are needed to produce life - have thrown into doubt the theory that life emerged spontaneously in a random universe.

It is not merely a matter of complexity. The uniqueness of nucleic acids lies in the fact that their nucleotides are encoding symbols for amino acids. Symbolic encoding systems are familiar to us of course. You encounter them in the course of reading and their causal source is always intelligence.

These findings have given rise to a school of scientists promoting the theory of Intelligent Design, which suggests that some force embodying purpose and foresight lay behind the origin of the universe.

The suggestion is found in nature. A search for the cause of life consistent with non-telic, non-intelligent causal factors has been sterile since Darwin.


Thursday, August 23, 2007

Gil Dodgen's Music

ID advocate Gil Dodgen, whose posts can be found at Uncommon Descent and the Teleological Blog, has both an interest in and a talent for music. This link provides the details.

Saturday, August 18, 2007

Multiple DNA Repair Articles

DNA Repair is Highly Coordinated, at Creation Evolution Headlines, is a condensed reference source on recent papers related to DNA repair. The linked articles cover a variety of issues including specialized locations where DNA repair occurs, the identification of a gene whose function entails suppressing tumors, a chromatin remodeling pathway, DNA checkpoints and the regulation of a checkpoint pathway by chromatin remodeling.

Two particularly interesting bits of information include mention of the highly specified sensitivity of RNA Polymerase II to DNA damage (possibly the most specified protein with reference to damage recognition) and the efficiency of the zebrafish at detecting and repairing lesions. Sources for the different articles are documented in this concise news item.


Tuesday, August 14, 2007

If Life Is Out There, We're Not Related

Paul Falkowski, a Rutgers professor of biochemistry and biophysics, believes he has proof that life on earth was not seeded from a comet; “The two fundamental questions in science are: where did we come from, and are we along? Almost certainly, any life in our solar system evolved uniquely in this solar system.", Falkowksi said.

Samples of microbes that had been frozen in the Antarctic ice for millions of years had DNA that suffered extensive deterioration. Cosmic radiation was responsible for the deteriorated state of the microbes DNA. The potential for microbes to survive on or in comets as they travel through deep space is dismal. “It’s almost an impossibility for comets to seed other planets with life after they’ve been in space for millions of years”, he stated.

During its travel the comet would be bombarded by cosmic radiation. Any genetic or organic material would become so corrupted and damaged by this radiation that hopes for a successful seeding would be wiped out. The organic material would be destroyed.

These findings may be significant in dispelling the notion of panspermia; the belief that life on earth was seeded from an outside source. The theory involves the possibility of microbes traveling on comets or meteors, the comets striking the earth and the organic contents inhabiting their new home.

Astronomer Kevin Conod believes that there still may exist the possibility for panspermia. Conod state, “Radiation might be a problem for microbes, but not for very basic organic material”. However, the idea that radiation would not have an adverse effect on basic organic molecules is not well supported. Exposed to radiation, even these basic constituents of life would suffer deterioration. The radiation would initiate a radical reaction; the bumping of one electron out of its orbit or the homolytic cleavage of a covalent bond would create a free radical. The propagation step would then follow; these highly reactive free radicals would bond with some other molecule causing it to lose one of its original constituents in the form of another free radical. This process would continue until termination, the uniting of two free radicals. Because the concentration of free radicals in relation to non-free radical organic molecules is always minute, the propagation step can and will carry on for some time.

Regardless of whether microbes or basic organic molecules are the ones catching a ride on the comet, neither would be exempt from the deteriorative effects of cosmic radiation. Unless it can be shown that the interior of a comet can provide a suitable bivouac protected from cosmic radiation, it would appear that panspermia is conceptually flawed as a theory for how life arrived and subsequently developed on earth.

Monday, August 13, 2007

Ultimate Explanations

I have just finished reading Richard Dawkins' The God Delusion. I wasn't going to read this book initially. First, I'm not entirely interested in what a polemist has to say about a topic as historically rich as the philosophical issues regarding the existence of God; and then see him wave it all away with handy soundbites. Second, I felt that I had read enough reviews of his book and debates pertaining to issues addressed in the book to solidify my initial contention.

About a week ago I had finished reading J.P. Moreland's Scaling the Secular City. Prior to reading this book I was wondering about how applicable it would be today. The book was published in 1987 and quite a bit has happened in the 10 years that have passed; relating to the inquiry of the rationality of theism and the existence of God. Would the topics still be relevant or would he be arguing points that have either been fully addressed and found incorrect or off target from the issues of today. Surprisingly I found the book to be very relevant.
Moreland not only handled the positive arguments for the existence of God and the rationality of theistic belief in a manner that gave it a timeless feel, but the arguments were also carefully drafted and the objections to his conclusions were treated with much respect.

So I became curious as to how Richard Dawkins would present his arguments. Would they be thoughtful (in and of themselves) as well as considerate to the main objections to his conclusion? Or would they be myopic and ignorant of arguments to the contrary?

His crown jewel: Who designed the designer. To capture the thrust of his argument I'll quote from Dawkins, "however statistically improbably the entity you seek to explain by invoking a designer, the designer himself has got to be at least as improbable". So why increase the explanatory regress? Why push it back further and then settle on postulating the existence of something that is more complex than what you were intending on explaining initially?

First, why assume that God is complex? Dawkins assumes that God is complex in the absence of any argument presented for the fact that God is indeed complex. Second, regardless of this assumed complexity of God, Dawkins appears to be unaware of what an ultimate explanation should look like. Nor does he seem to be strongly aware of the differences between a contingent and a necessary. Dawkins believes that God should have an explanation, outside of Himself, that further elucidates the existence of God. He is faulting a necessary for not having characteristics of a contingent. When looking for an ultimate explanation one will have to submit to the fact that it will not have a further explanation in terms distinct from it; if it does then it is not longer an ultimate explanation. Either accept that an ultimate explanation, a necessary, exists that has characteristics that are different from a contingent; or accept the non-existence of any necessary postulating only contingents and deal with the paradoxes that surface when dealing with an actual infinite.

Can God be used as an explanation if we don't have an explanation for His existence? This assumes that for any explanation G ever given for U we would need a complete account of G in terms external to G. Explanations can be (and have been) advanced despite our ignorance towards the nature of that particular explanation.

His inability to consider the objections to his conclusions, along with the handling of his own arguments leads me to wonder how applicable and relevant this book is even today. It might be fun for pep rallies and 'preaching to the choir' sermons, but I feel its usefulness ends there.

Around the Blogosphere 8/13/07


A Viewpoint take on Darwinian extrapolation


Dave Scot on 'Karl Popper's White Swans'


Life and Nano-Machines


Where do genes like this come from?


Bertrand Russell's view


Is Darwinism predictive?


The precision of cell division


Another perspective on gene duplication

Saturday, August 11, 2007

Design, Teleology and Magic

TP posted this comment at Telic Thoughts which contains the following remark (in red):

The Magic of Intelligent Design

"Any sufficiently advanced technology is indistinguishable from magic."
Arthur C. Clarke, Profiles of The Future

One of the biggest obstacles to accepting ID hypotheses as scientific endeavors is their appeal to magic-like mechanisms. But what if a magic-like aspect in nature has been around so long that we don't see it for the magic it is? I suggest what we think of as randomness is, for all practical purposes, magic.

TP is onto something. I'm an optimistic IDist with respect to the amount of supporting evidence I believe exists in its favor. Clearly my view is far from universal so an analysis as to what are the real obstacles to its acceptance intrigue me. Obviously ID needs testable hypotheses that support a sound theoretical framework. But there is more.

ID critics and IDists cannot even agree on what would constitute acceptable supporting evidence. For some critics there is no possible evidence short of a personal encounter with the creator. Enough said about them.

However, there are others who TP alluded to when he mentioned magic. These critics are conflicted by a conceptual clash between how they view science and the nature of possible causal scenarios involving a divine designer. For these critics even if cellular structures like DNA admittedly provide evidence of having properties consistent with known products of intelligent causality, the methodology of a designer signifies a process more akin to magic than known, observable generating mechanisms. Since science and magic appear to be polar opposites so too would science and any scenario invoking causal mechanisms reminiscent of magic.

Is that magician causing the contained fluid to flow up the container sides or is that a superfluid? And look at that! One substance passess right through another. Don't spoil the illusion by telling me the holes are measured by the widths of a few atoms. So what's the point? Simply that what appears magical to one generation can yield to a scientific explanation for the next one. There's no limit to this trend and no telling what the future holds in terms of present day counterintuitive concepts that lose their "magical" hold on the imagination.

One does not have to cite an abstruse quantum physics example either. The ancients knew that rain falls from the direction of the clouds toward earth. But there was a time when the statement that rocks fall from the sky led to the view that the holder of such an idea had rocks in the head. The discovery of meteortites and increased knowledge of the cosmos turned an absurd idea into an accepted scientific norm.

While it is true that metaphysical views predominant in western societies made the advent of science possible it is also true that scientific developments can change metaphysical views. Einstein did that with respect to space and time. That aging rates could be linked to velocity or that space itself could be warped by gravitational fields ran counter to ingrained views of such concepts in prior eras. The more recent multi-universe concept is relevant to an ancient theological concept that God is independent of time and able to operate outside our universe. That position was once debunked as contrary to physical reality.

Intelligent design could be linked to a triad of issues. The observation that the universe is fine-tuned to support life supports teleology. The realization that nucleic acid polymers are ordered symbolic sequences is consistent with both teleology and intelligent causality. There is no "poofing" or magic entailed in these assessments. A rational approach yields the obvious parallels. The third part of the triad is consciousness and it is this one that is likely to be influenced by scientific progress relevant to what we now view as properties of matter; specifically particular types of brain cells. Materialists assert that intelligence is nothing more than an "emergent property" of matter. That metaphysical position is set in stone exposed to to empirical erosion.

When ID critics conflate magic with ID they are providing their personal, subjective view of reality. It is one based on a metaphysical perspective likely to be influenced by the course of scientific progress. History indicates that the metaphysical anchors of one generation will give way to empirical results of the next. Present day wisdom may equate to a future anachronism.


Wednesday, August 08, 2007

DNA Repair through Cohesion

The Biocompare article 'Chromosome Glue Repairs Damaged DNA' shows that DNA repair operates with respect to chromatids. The repair mechanism involves a phenomenon known as cohesion. As indicated by the meaning of the word itself, cohesion holds two chromosome copies together until the right time and is an important function during cell division. The "glue" cohesion is actually a protein complex. It is believed that malfunction of DNA repair mechanisms like cohesion can result in cancer.

A somewhat surprising find was that, aside from chromosome segregation occuring during cellular division, DNA damage can activate cohesion. Cohesion then, has both a vital cell division function as well as a DNA repair function. Researchers at the Karolinska Institutet, a Swedish medical university are credited with the research findings.


Sunday, August 05, 2007

Off Topic: A Double Standard Conceived in Fear

A One News Now article entitled Muslims benefiting from double standard, says Christian law firm, reveals a disturbing, but not not very surprising, trend in America. Muslims are being accomodated by public school and university officials who have agreed to policies facilitating Islamic prayers and other religious practices. This has happened despite multiple U.S. Supreme Court rulings forbidding schools from adopting these same policies toward Christian groups asking for similar accomodations.

Before proceeding further I want to note that this post is not an attempt to align Christians with the victim mentality operating within the United States. I have reservations about legal interpretations of the establishment clause. I also think misinterpretations of that clause have led to unwise public policies toward religion- particularly Christianity. However there are substantive problems with institutionalizing a legal double standard. It makes a mockery of equal protection for one. It is not in the interest of any society to foster policies that favor one group at the expense of others.

Motives are of particular interest. Liberalism rejoices in diversity. Nothing wrong with that in isolation but if it is truly a constitutional violation for Christians to use public school facilities for religious purposes, then how could it also not be a constitutional violation for Muslims to do the same? The logic of the dual policy approach is so flawed it begs for an explanation.

There are many in America, and Europe too for that matter, who fear Islam. Their fear motivates them to push for policies of accomodation even at the expense of violating their own legal and moral principles. The type of accomodation depicted in the linked article is not a demonstration of understanding or tolerance. Rather it flows from cowardice and nothing good will come of that.

Friday, August 03, 2007

The Glycolytic Pathway

There were some exchanges at Telic Thoughts this week, involving Bradford and others, which were focused, to a large extent, on biochemical pathways. The glycolytic pathway was mentioned specifically. This is an opportunity to link to a website that is packed with information about a number of pathways. This one contains information about glycolysis.

Note the ten enzymes involved in this multi-step pathway. As the author noted, this is a highly conserved pathway and has been studied for quite some time. The fact that glycolysis is so common throughout the biological world makes it an ideal pathway upon which to focus for the purpose of evaluating evolutionary claims.

In converting glucose to two molecules of pyruvate, cells are able to draw upon energy to form molecules of ATP. The end product of the pathway- pyruvate- can yield further ATP through another important pathway; the Krebs cycle.


Wednesday, August 01, 2007

Detecting Natural Disasters

The linked article entitled Earthquake Predictors has some intriguing comments about natural disasters and the possibility that animals and insects are able to detect them. Earthquakes and tsunamis are mentioned and there are speculations about how animals have been able to avoid injury and death by anticipating them. Accounts include disasters of antiquity as well as modern day ones but the means by which animals would detect such natural disasters are not yet established.

Identifying how earthquakes and tsunamis are detected raises the issue of how such capabilities initially came about. What biochemicals are involved in the detection process and what are their coding genes? From the article (in blue):

So why do dogs become agitated when they hear rocks scraping underground? Do they understand its meaning? Do they know danger is imminent? Dr. Coren says no. It’s more likely that the sound to them is like nails on a chalkboard and they want to get away from it.

This could at least partially explain why animals survived the Tsunami, which was caused by an earthquake in the Indian Ocean. Although it’s likely there was also other sensory input that caused the animal exodus, it’s possible that those able to pick up on the initial high-frequency sounds fled from the ocean, and those that couldn’t, took their cues from the ones fleeing.

A logical explanation is put forth indicating that detection sensations could agitate affected organisms and induce them to want to escape from the source. A secondary explanation theorizes that animals, unable to detect the oncoming disasters, would take their cues from animals that could. The real question though is whether such musings are accurate. In the case of earthquakes how could animals flee from the sensation itself. If the sensory stimulus is irritating then to where does an animal flee to escape it when the source comes from beneath the ground?

The escape route from a tsunami is clear but it is also more difficult to envision a sensation from it being an irritant. If it is not an irritant then why would an animal react to a tsunami sensation as a danger? What would trigger a danger response and how could it have evolved when the events themselves are rare and too brief in duration to allow for a selection effect. Wouldn't one have to assume that sensory capabilities evolved in response to a separate environmental stimulus and that the natural disaster response was a by-product of this?

It is too soon to evaluate data related to a natural history hypothesis when we are not yet in a position to identify genes essential to disaster responses. Nevertheless the uniqueness of the events correlated to animal behavoir makes it possible to conceive of evidentiary outcomes that could counter mainstream theories.