Sunday, April 29, 2007

There are Reasonable People in Kansas

I found this blog as a result of a post at Uncommon Descent. It is amazing how many weak and easily led people are out there. Threaten someone with an intolerance accusation or homophobia and you might end up with a legal ban on saying mom or dad. And why not gender neutral bathrooms for those who are "confused." Oh please.

Here is a post at the same blog about a Telic Thoughts exchange. And another about Michael Egnor.

Saturday, April 28, 2007


This is worth a look. Not only for the information. There is a video too. Different types of mutations (point mutations, silent mutations, missense mutations, nonsense mutations, insertions and deletions) are described as are the causes of mutations.

BioSolutions is an excellent internet resource.


Friday, April 27, 2007

A DNA Repair Disorder

An article at the website of the National Institute of General Medical Sciences shows a link between faulty DNA repair and Huntington's Disease. As the article entitled 'Study Links Faulty DNA Repair to Huntington’s Disease Onset' reveals oxidative lesions can damage DNA although particular DNA repair enzymes exist enabling organisms to remove such lesions. The process can break down. The following article quote is instructive.

"To see if the oxidative lesions played a role in expansion of the extra DNA segment, the researchers next deleted OGG1, a key enzyme in oxidative lesion repair. Without OGG1, the bulk of the DNA’s oxidative lesions remained untouched, and the inserted segment did not grow at all or it grew far less than in mice carrying a working version of OGG1.

These findings show that while doing its part in removing oxidative lesions, OGG1 triggers a far more damaging effect—the DNA expansion associated with Huntington’s disease."

A DNA segment in those having Huntington's Disease expands. A protein encoded by the relevant gene becomes corrupted and has toxic effects on the brain.

Some of the most revealing experimental results are ones induced by nature. Diseases show what occurs when a biological part malfunctions. Faulty DNA repair engenders genetic disorders that are all too often fatal.


Thursday, April 26, 2007

Around the Blogosphere 4/26/07

This post of Mike Gene's also contains Gene's elegant comment:

"This is what conventional theory taught. But in come new data that “now reveal that the vertebrate nervous system is probably much older than expected.” This is the type of thing FLE predicts and the type of thing we see with many molecules/systems. “Older than expected” means closer to the design event. That the last common ancestor of vertebrates, insects and worms already had a centralised nervous system resembling that of vertebrates today is something that is quite friendly to FLE. Yet the original view could have turned out to be correct."

A discerning comment from gpuccio; a commenter with obvious good taste and sound judgement. Thanks gpuccio.

It may take awhile but it has been said that science is self-correcting.

Photosynthesis. A topic that merits greater coverage.

Stephen Jones on Hoyle and intelligent design.

Denyse O'Leary's blog about free will.

The ID issue from a Sci Fi perspective.

Wednesday, April 25, 2007

Wolfgang Pauli

Wolfgang Pauli, a noted 20th century physicist, was born on this date in 1900 in Vienna. Early in his career he worked with two other prominent physicists of his era- Max Born and Niels Bohr.

As indicated at the linked article:

"Pauli was outstanding among the brilliant mid-twentieth century school of physicists. He was recognized as one of the leaders when, barely out of his teens and still a student, he published a masterly exposition of the theory of relativity. His exclusion principle, which is often quoted bearing his name, crystallized the existing knowledge of atomic structure at the time it was postulated and it led to the recognition of the two-valued variable required to characterize the state of an electron. Pauli was the first to recognize the existence of the neutrino, an uncharged and massless particle which carries off energy in radioactive ß-disintegration; this came at the beginning of a great decade, prior to World War II, for his centre of research in theoretical physics at Zurich."

The colorful comment by Pauli: "This isn't right. This isn't even wrong." has often been quoted.


Tuesday, April 24, 2007

What is the Significance of Sequence Similarity?

This kind of post is long overdue in that it addresses some points that Darwinists take for granted. Logan Gage posted 'What Exactly Does Genetic Similarity Demonstrate?' at Evolution News & Views. From the article:

"My hope is that one day thinking about Darwinian Theory will become clearer in the public square. Recall that Darwin made two claims: (1) all living beings descend from one or a few original ancestors, and (2) the mechanism driving the changes among species is the blind, unguided mechanism of natural selection."

The second claim unites all IDists although the first one is not uniquely supported by the descent paradigm. The second claim rests heavily on unwarrented extrapolations of adaptive changes observed largely in unicellular organisms.

"As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities, “This evidence alone does not, of course, prove a common ancestor” because an intelligent cause can reuse successful design principles. We know this because we are intelligent agents ourselves, and we do this all the time. We take instructions we have written for one thing and use them for another. The similarity is not the result of a blind mechanism but rather the result of our intelligent activity."

The author makes a good point. The reuse of successful design strategies is practiced by known intelligent designers. It is logical and therefore something one would expect in an intelligently traced causal trail. The trail, in this case, began with the origin of life which, evolutionists frequently go to pains to point out, is distinct from the evolutionary process itself. A genetic code itself and the coming into existence of encoding sequences strongly suggests intelligent causality. Particularly since the chemical bonds, identified in nucleic acids, would not favor either random development of a code or the alignment of sequences linked to the synthesis of basic universal enzymes thought to exist in initial cells. Symbolic codes however, are an indicator of intelligence. There is a reasonable and, I would argue, compelling link between the two.


Monday, April 23, 2007

Haldane's Dilemna

Recently a post at Uncommon Descent detailed Walter ReMine's difficulties in obtaining alleged evidence in favor of a solution for Haldane's Dilemna. In a prior post I had written:

"Is a recessive mutation, causing a deleterious phenotype, selected against? Of course if the mutation is not expressed because of a dominant allele there is no basis for selection. But if there are two recessive alleles and a deleterious trait is expressed, will the reproductive fitness of the effected organism be compromised? Probably not."

The analysis of Haldane's Dilemna has not kept pace with developments in molecular biology. There have been some admirable attempts to precisely define the problem and there have been efforts directed at a solution. A formula intended to address both is the following:

P = 1-e^-4Nsq/1-e^-4Ns


N = the population size
e = the natural logarithms base
P = the fixation probability
The fitness of different genotypes is represented 1, 1+s, 1+2s... s being positive when advantagous and negative when deleterious.
q = initial frequency

The problem with the foregoing lies with an inability to assess all relevant variables within a genome. Genes can be identified in isolation for the purpose of assessing their impact- be it advantagous or deleterious. However we are unlikely to know with precision both the number of genes contributing to the genetic load and their collective impact on reproductive fitness for both an organism and the relevant population.

I'm not, of course, the only one who has observed an intrinsic uncertainty to analyses of Haldane's Dilemna. But this only affords further credence to suspicions about the credibility of computer programmed solutions; particularly those whose code is unavailable.


Sunday, April 22, 2007

Nonhomologous End Joining

'DNA-Repair Machine Maintains Genomic Stability' is a good introductory article for DNA repair in general and, more specifically, for a type of repair known as nonhomologous end joining; often represented by the acronym NHEJ. There are two well known mechanisms by which the repair of DNA double-strand breaks are made. The already mentioned nonhomologous end joining being one and homologous recombination the other. As the article states:

"The fidelity of the genome is under constant threat — toxic chemicals, ionizing radiation, even the byproducts of normal cellular metabolism can wreak havoc on DNA. In some instances, DNA damage is severe enough to chop the double helix in two. When this happens, a group of proteins that fixes double-stranded DNA breaks mobilizes to make repairs. If a break goes unfixed, the consequences to the cell can be disastrous, ranging from wholesale gene rearrangements to massive chromosomal breakdown."

Note that the causes of DNA damage are everywhere and exist at all times. Even normal cellular metabolic activities can engender damage to an organism's genome. Repair mechanisms are not a luxury. They are vital to the ability of organisms to maintain vital functions and stave off cancer. Compromising the effectiveness of DNA repair functions can be fatal to an organism. More from the same article:

"In an experiment designed to assess the role of the NHEJ pathway in repairing general chromosomal damage induced by radiation, the scientists irradiated fibroblast cells that were deficient in both Lig4 and p53, a key DNA damage sensor. Normally, p53 prevents damaged cells from proceeding in the cell division cycle."

Repair mechanisms are irreducibly complex in that they are composed of multiple proteins and their encoding genes. There are also many different types of repairs. Yet we repeatedly witness the disabling of a single protein in one of the repair pathways as sufficient to cause fatal diseases. A viable evolutionary process would require effective repair mechanisms very early in the history of life. In my view this means the very begining of life itself. The problem caused by an absence or incomplete set of repair mechanisms is an inability to retain beneficial encoding information within an organism's DNA. This also makes problematic the capacity to generate increases in genomic information that would accompany any selected changes. If information is lost faster than it can be incremented, the demise of affected organisms is an inevitable result.


Saturday, April 21, 2007

More on Ribosomes

I posted a blog entry about ribosomes at Telic Thoughts this week and since then came across an article entitled 'Protein Factory Reveals Its Secrets' at Chemical & Engineering News. The article is well written and contains some colorful illustrations. I like this quote:

"If genomic DNA is the cell's planning authority, then the ribosome is its factory, churning out the proteins of life.

It's a huge complex of protein and RNA with a practical and life-affirming purpose-catalyzing protein synthesis."

The following tidbit would have been a good fit for the TT blog entry which focused on the origin of ribosomes.

"Bacterial cells typically contain tens of thousands of ribosomes, and eukaryotic cells can contain hundreds of thousands or even a few million of them. The ribosome found in the bacterium Escherichia coli is made up of three RNA components and more than 50 proteins. It weighs about 2.5 million daltons. Eukaryotic versions have four RNAs and about 80 proteins and weigh about 4 MDa."

Not only is one left wondering how protein synthesis would have taken place before the advent of ribosomes, it is also curious how these heavyweights, composed of multiple proteins and RNA, would have evolved incrementally in accordance with natural selection.

Friday, April 20, 2007

Around the Blogosphere 4/20/07

Bilbo's post on Plantinga's views.

A post on the evolution of ribosomes linking to a post of William Dembski which covers the topic too.

A post of Mike Gene which evoked a big response. An update on Miller-Urey.

Scot on the argument from incredulity.

Denyse O'Leary on Duval vs. Wells.

Walter ReMine's comments related to Haldane's Dilemna.

Behe and Matzke agree on something!

Hallmarks of teleology.

Denyse O'Leary's post about recent events related to intelligent design.

Tuesday, April 17, 2007

Sequencing T Rex Collagen

The Nature Newsblog features a blog entry about a follow-up investigative step related to the striking find of a fossilized bone of Tyrannosaurus rex. The blog cites a Nature article- 'Dinosaur protein sequence'- of which the first two paragraphs are quoted:

"Palaeontologists have sequenced some protein from a 68-million-year-old fossilized Tyrannosaurus rex bone.

The protein — a key component of bone and connective tissue called collagen — blasts the record for the oldest protein ever sequenced. Before this, the oldest sequenced protein (also collagen) came from a mammoth fossil that was 100,000-300,000 years old. So the new find, reported this week in the journal Science1, is quite a surprise."

This is a fascinating story that is still unfolding. As the article indicates, collagen samples were located "deep within the fossil's large, dense bones" which is believed to have protected the protein. While some sequence fragments have been found to be similar to that of chickens I'm looking forward to further analyses of the sequence patterns.

Monday, April 16, 2007

The Irreducible Complexity of Photosynthesis

An Uncommon Descent blog entry entitled 'Is Photosynthesis Irreducibly Complex?' references two articles (one from 'Nature' and another from 'Science Daily') and cites information from them. This is from the blog entry (my reactions in blue):

"After decades of research, biochemists now understand that this critical biological process depends on some very elaborate and rapid chemistry involving a series of enormously large and complex molecules a set of complex molecular systems all working together.

“We know that the process evolved in bacteria, probably before 2.5 billion years ago, but the history of photosynthesis’s development is very hard to trace,” said Blankenship."

Very elaborate chemistry indeed. No wonder the history of photosynthesis development is hard to trace. It's difficult to conceptualize, let alone trace, when explained by a paradigm of purposelessness and mindless direction. One reason for this is the interdependency of different cellular functions. For example, ATP is utilized during photosynthesis. So are by-products of metabolic pathways. If one assumes all related processes (including the Calvin Cycle) evolved prior to photosynthesis, chicken-egg dilemnas arise. They also present themselves if the opposite is assumed. The interdependency of basic universal pathways is strong evidence for design. So too are some points raised in the next comment.

This comment also appeared in that thread:

"There is no question about photosynthesis being IC. But it’s worse than that from an evolutionary perspective. There are 17 enzymes alone involved in the synthesis of chlorophyll. Are we to believe that all intermediates had selective value? Not when some of them form triplet states that have the same effect as free radicals like O2. In addition if chlorophyll evolved before antenna proteins, whose function is to bind chlorophyll, then chlorophyll would be toxic to cells. Yet the binding function explains the selective value of antenana proteins. Why would such proteins evolve prior to chlorophyll and if they did not how would cells survive chlorophyll until they did?"

That comment illustrates another problem for mainstream evolutionists. The evolution of parts can be toxic to the whole. Yet, the selective value of complementary systems is linked to the simultaneous existence of separate and distinct parts. The Darwinian answer is a generous dose of imagination consisting of homologous proteins and speculative "pathways." The purposeful arrangement of parts, suggested by the evidence, is philosophically anethema to mainstreamers.

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Sunday, April 15, 2007

Describing DNA Repair

This blog extensively covers the topic of DNA repair. Its origin has implications for the credibility of intelligent design. Some readers may wish to be more familiar with DNA repair. 'What is DNA Repair?' provides some information and visual aids that could be helpful. The website containing this page has other topics of interest as well.


Saturday, April 14, 2007

Off Topic: Selective Media Frenzy Over Bigotry

Imus is gone after a media frenzy that involved the weighing in of moral stalwarts like Jesse "Heime Town" Jackson and Al "Tawana Brawley" Sharpton before Imus was canned. Don Imus is no favorite of mine. His remarks were as dumb as the rap lyrics containing the term "ho" that are common in the NY area where Imus' famed career was launched. Interestingly another serious incident took place in the same region and was predictably ignored by the drive by media. An e-mail from Mark Earley of Prison Fellowship alerted me to the following.

Anti-terrorist practice drills make sense in the light of 911. It was no surprise that a school district in Burlington Township, New Jersey would conduct one. What was surprising was the identity of possible terrorists. Al Qaeda loyalists were evidently too obvious a choice. So who was the enemy in this drill organized by the local police? None other than conservative Christians! We couldn't have Muslim terrorists could we? That would be politically incorrect. In an effort to make the whole thing more palatable the Christians were described as Fundamentalists. But of course.

Don't make the mistake of calling black women hos unless you are a black rapper but conflating Christians and likely terrorists- now that makes sense to those who would recoil in horror if the mock terrorists were identified as Jewish, Muslim or Buddhist. Having observed the MO of anti-IDists for years this comes as no surprise. Neither does the inattention of the media. Bigotry is not dead. If you are inclined in that direction make sure your target is a believer in Christ. It affords you much greater latitude in the exercise of your hatred.

Friday, April 13, 2007

A Triumph for ID

A post at Uncommon Descent entitled, 'NY Academy of Sciences peer-reviewed paper acknowledges ID proponents,' contains the following remark:

"Most Darwinists erroneously predicted that 98.7% of the DNA was devoid of function (“junk”), while the ID/ET theory correctly predicted some yet to be decoded function of junkDNA."

It is becoming increasingly difficult to find Darwinians who tout the junk DNA position. Not too long ago it was easy as the non-evidence for function was frequently brought to the attention of IDists. Oliver previously covered the junk DNA topic in this post. There is much evidence of function for what was once believed to be junk. I'll add a reference of my own.

The linked article entitled, '“Junk DNA” Creates Novel Proteins,' reports evidence that Alu elements can be incorporated into genes which encode functional proteins. The specific supporting evidence is an enzyme identified as ADAR2 which "contains 40 amino acids in its active site that are derived from an Alu element." A change in enzyme activity is linked to the Alu element.


Thursday, April 12, 2007

The Importance of WIP

The linked article reveals the critical role played by a protein known as WIP in muscle cell fusion. The article entitled, 'Weizmann Institute scientists discover a key player in embryonic muscle development,' also details the related functions of other proteins including actin. Quoting: "The Weizmann Institute team found that the WIP protein is activated by an external signal once myoblasts identify and attach to each other. Only when it receives this signal does WIP hook the actin fibers in the skeleton up to the myoblast recognition protein, allowing cell fusion to proceed."

WIP performs a necessary function within an extensive range of organisms in the biological world. It is found in organisms that include microorganisms, insects and all animals.

Wednesday, April 11, 2007

Genetic Load

What is genetic load? This explanation is found at the linked website:

"Genetic load is a measure of the number of harmful mutations an average member of a population is carrying. Although harmful recessive mutations will be selected against, they will not generally be eliminated from a population because once such mutations are present at a very low frequency, it will be rare for any two individuals carrying them to mate. As a result, most individuals in stable populations carry a number of recessive lethal mutations, termed their "genetic load".

There is a dubious claim made. Is a recessive mutation, causing a deleterious phenotype, selected against? Of course if the mutation is not expressed because of a dominant allele there is no basis for selection. But if there are two recessive alleles and a deleterious trait is expressed, will the reproductive fitness of the effected organism be compromised? Probably not.

Organisms display many thousands of phenotypic effects. Most are functional and benefit the organism. However, some compromise fitness without being lethal. Organisms are composites of mostly functional parts mixed with sub-optimal functions resulting from mutations. The capacity to reproduce despite impaired functions is characteristic of life.

This post is a table setter for another one to come which will focus on assumptions embedded in evolution.


Tuesday, April 10, 2007

Discrediting the Faulty Use of Randomness and Selection

Michael Egnor's 'Pseudo-Darwinism: A Theory for All Seasons' is worth reading. The following quotes are taken from it. Color code: red=Reed Cartwright and blue=Michael Egnor.

"Now the biotech industry is founded on the application of Darwin’s theory of natural selection. Selection is an essential part of the process that creates transgenic organisms, like bacteria that produce human insulin. Humans are unable to create transgenic organisms directly, instead they use recombination DNA technology, which randomly creates transgenic organisms from building blocks provided by the researcher. The result is a population of organisms, in which a small minority contains the desired transgenic trait. The researcher then uses Darwin’s mechanism, selection, to evolve a population that is enriched for the desired trait. And voila [sic], with what to someone like Dr. Egnor must seem like wizardry, a population of bacteria can now produce human insulin, enriching and saving the lives of millions, all thanks to Charles Darwin."

"Dr. Cartwright is mistaken. Darwin asserted that all natural biological complexity arose by random undesigned variation and natural selection. The intentional alteration and intentional selection of microorganisms is a nice example of designed variation and artificial selection. Dr. Cartwright's application of Darwin's theory to intentional design and breeding of bacteria is pseudo-Darwinism."

Excellent response Michael Egnor. You identified the faulty logic behind the exhaltation of Darwinian theory. Kudos.

"Pseudo-Darwinism—in this case, the attribution of Darwin's theory to design and artificial selection—is the antithesis of Darwin's theory. Crick and colleagues chose variants to study and artificially selected them. Their work was carefully planned. It wasn’t random and it wasn’t natural. The biotech industry breeds bacteria, combining molecular biology with ancient principles of breeding. Darwin learned from breeding; he didn't invent it or any of its principles. Darwin's theory is not a theory of design by artificial selection. It's a theory about biological change without design and without intentional selection. It has nothing to do with Crick's experiments or with the biotech industry."

No wonder Darwinists are upset by Egnor. This guy has a knack for concisely knocking down faulty arguments. The other side presents examples of intelligent design and tries to sell them as evidence for selection and randomness. Michael Egnor deftly delivers the knock out blow.


Monday, April 09, 2007

The Darwin vs. Design Conference

From April 13-14 there will be a conference held at SMU. Speakers will include Michael Behe, Stephen Meyer and Jay Richards. For more detailed information about tickets and more go here.

Sunday, April 08, 2007

Around the Blogosphere 4/8/07

Playing the theocracy card.

Atheist Fundamentalists

A macho man trashing of Francis Collins.

A contrasting approach to Francis Collins: Denyse O'Leary's book review of Francis Collins's 'The Language of God.'

Mainstream evolutionary theory is an unintelligently guided process that is more ingenius than the best human minds or so this would lead you to believe: "Consciousness seems mysterious because it has evolved to seem mysterious. Fascination and elusiveness are its primary functions." Presumably because fascination and elusiveness conferred enhanced reproductive fitness. Falsify that.

When 'there must be no evidence of design in the universe' becomes a mindset.

Attempting to identify the cause of irrational hatred.

Is the highly specified behavior referred to beyond the reach of undirected mechanisms?

Intellgent design theory based on Reverse Engineering Assumptions.

Saturday, April 07, 2007

Delusional Claims

Michael Egnor posted 'Hitchin’ a Ride: Darwinism is indispensable to Darwinists' in Evolution News and Views. The first two paragraphs follow:

"Philip Skell, a member of the National Academy of Sciences and a pioneer in antibiotic research, said it best: Darwinism is a "narrative gloss" on biology. Darwinists expropriate the work of other fields of science, then claim the credit for Darwin's theory. Nowhere in science is the truth of Skell’s observation more apparent than in the Darwinist claim that Darwin’s theory — the assertion that random variation and natural selection is the source of all biological complexity — is indispensable to modern medicine. It is a claim that, upon inspection, is almost delusional.

I’ve examined this claim in detail in a series of posts: here, here, and here. Darwinists claim that comparative medicine and biology, which is the study of the similarities between non-human organisms and humans, arose from Darwin’s theory. That’s nonsense. Comparative biology has been the been the basis for biological science for thousands of years, and many of the greatest medical advances, such as Galen’s and Vesalius’ studies of anatomy and Harvey’s discovery of the circulation of the blood, were the fruit of comparative biological research that antedated Darwin by centuries. The father of modern comparative biology was Carolus Linnaeus, who worked a century before Darwin was born."

I've also encountered weakly supported claims to the indispensibility evolutionary theory to scientific progress. Egnor sets the record straight. More from the linked article:

"There’s a reason for this almost delusional attribution of scientific progress to Darwin’s theory. Darwinism is based on the radical and unsubstantiated assertion that all natural biological complexity arose from random heritable variation and natural selection. It is the creation myth of contemporary philosophical materialism, which is the view that the material world (matter and energy) are the only things that exist. The materialist worldview depends critically on Darwin’s theory. We can do science just fine without Darwin’s theory, using molecular biology, biological statistics, and other well established fields of biology."

The attachment of ID critics to materialism is evident at Telic Thoughts where many commenters openly defend both materialism and mainstream evolutionary theory as if one logically follows the other. Some materialists foster fear mongering in an attempt to persuade the uncommitted that a theocracy would accompany acceptance of an intelligent inference. It's a propaganda ploy that will grow old and increasingly ineffective with the passage of time. In the interim the focus needs to be on pointing out the inadaquacy of randomness and selection as a sole explanation for both the origin and subsequent diversity of biological complexity.

Friday, April 06, 2007


Macht of Telic Thoughts wrote an insightful comment which analyzes the tendency of atheist fundamentalists to incorrectly define faith. His comment and reactions to it follow. (macht = red; Bradford = blue)

According to him, what the Christian means when he or she says "I have faith in God" is "I have insufficient evidence that God exists."

This is an indication that the atheistic assertion about faith lacks intellectual integrity. The term faith is in no need of a definition. It was defined in ancient times. If atheists wish to argue the point laid out by macht then let them do so legitimately.

No matter how many times you say "keiths, you are wrong, that's not what Christians mean" he (and Dawkins and Harris and everybody like them) will ignore you. I guarantee it. Their whole worldview of pitting science or reason against religion relies on that definition and it is about as dogmatic a belief as you will find. I'm sure some of you think I'm exaggerating this point, too, but I assure you I'm not.

Macht's observation accords with my experience. Atheists do rely on their contrived definition to further their science/reason meme.

A frequent Telic Thoughts commenter, John_A_Designer, gave a more accurate description of faith. From his comment:

Jesus himself always linked faith with moral action and good deeds. That is what he was talking about when he talked about the mustard seed: “If you had the faith of a mustard seed you could move a mountain.” He wasn’t talking about mere intellectual assent, believing in Gods existence, for example, he was talking about doing something, performing some great deed or act. It could be a miracle, or it could be some great act of love and compassion. The implication is that more faith one has then greater the resulting act or deed, and the greater the good. Most Christians and theologians I know, or know about, I believe would define faith this way.

Thursday, April 05, 2007

T Cell Maturation

A Physorg article entitled Scientists identify new regulatory mechanism for critical protein signaling domain reveals the potential impact of a small molecule known as IP4 which is involved in the binding of particular proteins to membranes and in the maturation of T cells. From the linked article:

"In findings the authors called "unexpected and striking," the study found that a new regulating messenger IP4, a small soluble molecule, augments the binding of three different PH domain proteins to one of the most commonly recognized membrane lipids, PIP3. The study also showed that inhibiting production of IP4 can result in reduced protein binding to membranes and reduced activation of key signaling molecules in developing T cells, leading to a block of T cell maturation and to severe immunodeficiency in animal models."

Aside from advances in medical treatment that could result from the study, the development of the irreducibly complex signaling pathway connected with T cell maturation is of interest from an ID perspective. The enzyme ItpkB is needed to produce IP4 in mice. The normal development of T cells is disrupted when that enzyme is disabled. T cell development is regulated through signaling. Impaired signaling can lead to the death of T cells. Quoting again from the article:

"Itk is a key activator of another enzyme, PLC g1, in T- cells. PLC g1 is important for signaling in many cells, because it generates the secondary messenger molecules IP3 and DAG (diacylglycerol). We found that ItpkB deficient double positive cells have reduced PLCg1 activity and cannot make normal amounts of DAG. Without the IP4 or DAG messengers, which are essential for positive selection of T cells, these ItpkB-deficient T cells cannot develop into mature, functional cells."

Observe the linkage between biomolecules involved in the T cell maturation function. A study of the origin of pathways to this biochemical complex would be challenging.


Wednesday, April 04, 2007

A Balance Enabled by Sub-Optimal Design?

Joy of Telic Thoughts authored a blog entry entitled Bees in my Easter Bonnet which brought up a disturbing and important phenomenon. From Joy's post:

"So it has been quite alarming to me over the past month to read incoming reports of what they're calling "The Great Bee Die-Off of 2007." Something really, really bad is happening, and no one's quite sure what it is. They call it Colony Collapse Disorder [CCD], and some are likening it to Bee AIDS. The Congress is holding hearings, and the situation is characterized as "Catastrophic".

The situation is the same in Canada, Central and South America, Britain, South Africa, Europe, Australia and even China. Beekeepers checking on their hives after the winter are finding them empty. There aren't many clues, the untended larvae left behind to die show no infestation or disease. Several researchers suggest that it looks like bee immune systems have just collapsed, making them susceptible to problems they could normally tolerate. Bees are disappearing everywhere and nobody's sure why. Though there is one bizarre symptom that has turned up in the few carcasses found in California, Texas and Florida. But nobody knows what it is…"

While the subject matter itself is of interest based on its daunting implications, from an ID perspective it suggests an approach that has the potential to be supportive of intelligent design. Some critics have used a "sub-optimal design argument" to debunk ID. Find a feature of some organism that is imperfectly designed and then claim that its designer would either have to be incompetent or cruel to so design a creature this way. Obviously this is intended to discredit the possibility of divine design.

But is sub-optimal design indicative of incompetence or a brilliant strategy? If perfect design means that predators would become too efficient at catching prey or if the escape mechanisms of the hunted became so efficient that predators starved, there would be good reasons to avoid this type of optimal design. Optimal design has the potential to upset the balance of nature. The scary bee epidemic is a reminder of how things can go radically wrong when nature's balance is upended.

I have not thought about this enough to suggest guidelines that point to intelligent design rather than a non-telic process but believe there are possibilites worth looking into. If nothing else, if a sub-optimal design argument and evidence for it can count against ID, then surely substantive reasons explaining the intelligence behind sub-optimal design, should be counted in favor of ID.


Tuesday, April 03, 2007

Replication Checkpoints

Mechanisms involved with cellular replication include checkpoints intended to allow for repair of damaged DNA prior to cell division. This of course limits the possibility that daughter cells will suffer from the effects of prior deleterious mutations. The function of one checkpoint, identified as S-phase, is associated with a protein known as HCLK2 as well as others such as ATR, ATRIP, claspin and Chk1. The checkpoint function itself could be viewed as irreducibly complex. A shortage of HCLK2 in cells leads to the degradation of the critical protein chk1 and a compromise of repair functions.1

In the words of the authors: "We conclude that HCLK2 promotes activation of the S-phase checkpoint and downstream repair responses by preventing unscheduled Chk1 degradation by the proteasome."2

1. HCLK2 is essential for the mammalian S-phase checkpoint and impacts on Chk1 stability; Nature Cell Biology - 9, 391 - 401 (2007); Spencer J. Collis, Louise J. Barber, Allison J. Clark, Julie S. Martin, Jordan D. Ward & Simon J. Boulton

2. Ibid


Sunday, April 01, 2007


An article entitled At Home in ‘Rocco’s Lab’ focuses on robust life forms that survive harsh conditions in an attempt to "the broad question of life in the universe." The following paragraph is from the linked site. My comment follows it.

"Astrobiologists, those cross disciplinary scientists dedicated to investigating the broad question of life in the universe, often study extremophiles, organisms that live at the edges of what life is known to tolerate. Bubbling acidic hotsprings, deep ocean blacksmokers, and deep dark caves are the sources of some researchers' extremophiles-those that love high temperatures, great pressures or live without light, but Dr. Mancinelli gets his microbes wherever there is lots of salt. Halophiles are salt lovers and thrive where salt abounds in concentrations that would kill most ordinary organisms. Halophiles are incredibly robust creatures."

While the study of extremophiles can be easily linked to many harsh environments existing in the universe, it is unlikely to yield much insight into the origin of life itself. To gain insight into origins, studies of the least complex genomes known to exist would be a better means of discovering what the real obstacles to abiogenesis are. Before cells can function they must be able to perform some basic tasks like storing the instructions needed to sustain life, providing for energy needs, having a capacity to generate needed biochemicals and a capacity to replicate and repair their genomes. Viewing the problem from this perspective makes sense. Unicellular organisms able to tolerate extreme conditions may already possess, not only basic cellular requirements but, some extras that go well beyond this and are not of an origins nature.