Sunday, August 31, 2008

The Versatile Sea Urchin Genome

Sea Urchins' Genetics Add To Knowledge Of Cancer, Alzheimer's And Infertility is a Science Daily article addressing the potential medical benefits that might acrue from the study of the sea urchin. Sea urchins have been mentioned in connection with front loading at Telic Thoughts and elsewhere. Mike Gene did much to advance the case for front loading there and elsewhere. Frankly I did not give the idea much thought prior to frequenting Telic Thoughts.

Mike's influence on me and others is certainly traceable in part to his knowledge and persuasive arguments. But there is another less discussed factor. Mike's temperment and mannerisms make him ideally suited to impact others. He's not insulting or combative as all too many of those involved in discussions of Intelligent Design are. Most of the hostility is traced to ID critics although you would never know it based on alarm bells continually sounded about the ID movement.

The remainder of this blog entry is an apologetic so if you're an atheist you might as well find another use for your time. God sometimes has multiple purposes in mind which, in this case, could center around the genome of the sea urchin. The unexpected number of similar genes to those found in humans might have evidentiary value for Intelligent Design and, as the linked article indicates, for medical uses as well. Humanity is given charge over the earth's resources. We are to use them responsibly. We are also to take advantage of that which is given to us and use it for good. Sea urchin genes look to have been designed with more than the sea urchin in mind. That's consistent with the character of a loving creator.

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Saturday, August 30, 2008

Est Proteins and Telomeres

Keeping Cells Youthful: How Telomere-building Proteins Get Drawn Into The Fold is a Science Daily article providing information about findings made by researchers from the Salk Institute for Biological Studies. A protein aids in the elongation of chromosome ends (telomeres) and in so doing prolongs cellular function as reported in the journal Nature Structure and Molecular Biology. The integrity of telomeres is maintained by a complex of proteins, which from an origins vantage point, makes irreducible complexity a natural perspective.

What is it about telomeres that is associated with problematic cell function? As the article explains cell division tends to result in telomeres becoming progressively shorter. If the progression continues unchecked, affected cells eventually lose their capacity to divide. The solution to this dilemna is an enzyme known as telomerase whose function is to restore the needed length to telomeres following cell division. Telomerase is not a solo performer however. Another protein known as Est1 has been found to help to bring telomerase to telomeres in yeast cells.

Researchers discovered that a protein known as Est3 is similar to a protein found in mammals which is labeled TPP1. TPP1 binds to telomeres and protects them from cellular repair enzymes which might interpret the chromosome ends as damaged DNA. A protein fold common to Est3 and TPP1 facilitates their function.

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Monday, August 25, 2008

Flagellar Pathways

I get ideas about blog topics from many sources for blog entries here and at Telic Thoughts. I'm particularly grateful to an individual named Clare for the news stories she provides. Here is a link to a paper about a familiar topic and a quote from it:

The Evolution of the Flagellar Assembly Pathway in Endosymbiotic Bacterial Genomes (Molecular Biology and Evolution 2008 25(9):2069-2076; doi:10.1093/molbev/msn153; authored by Christina Toft and Mario A. Fares)

Genome shrinkage is a common feature of most intracellular pathogens and symbionts. Reduction of genome sizes is among the best-characterized evolutionary ways of intracellular organisms to save and avoid maintaining expensive redundant biological processes. Endosymbiotic bacteria of insects are examples of biological economy taken to completion because their genomes are dramatically reduced. These bacteria are nonmotile, and their biochemical processes are intimately related to those of their host. Because of this relationship, many of the processes in these bacteria have been either lost or have suffered massive remodeling to adapt to the intracellular symbiotic lifestyle. An example of such changes is the flagellum structure that is essential for bacterial motility and infectivity. Our analysis indicates that genes responsible for flagellar assembly have been partially or totally lost in most intracellular symbionts of gamma-Proteobacteria. Comparative genomic analyses show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal body) have been kept in most of the endosymbionts, whereas those involved in building the filament and hook of flagella have only in few instances been kept, indicating a change in the functional purpose of this pathway. In some endosymbionts, genes controlling protein-export switch and hook length have undergone functional divergence as shown through an analysis of their evolutionary dynamics. Based on our results, we suggest that genes of flagellum have diverged functionally as to specialize in the export of proteins from the bacterium to the host.


Sunday, August 24, 2008

Sequencing Metazoan Genomes

It is not uncommon in my life for some matter to come to my attention and I then note related information which I might otherwise have glossed over. Must be hightened awareness. Anyway there are discussions at Telic Thoughts about a paper authored by Michael Sherman. Then there was a paper published in Nature Reviews Genetics (9, 689-698 (September 2008) | doi:10.1038/nrg2413) entitled The functional repertoires of metazoan genomes. Chris P. Ponting is the author. The sequencing of genomes and identification of protein coding genes and functional genomic sequences are touched on. The abstract:

Metazoan genomes are being sequenced at an increasingly rapid rate. For each new genome, the number of protein-coding genes it encodes and the amount of functional DNA it contains are known only inaccurately. Nevertheless, there have been considerable recent advances in identifying protein-coding and non-coding sequences that have remained constrained in diverse species. However, these approaches struggle to pinpoint genomic sequences that are functional in some species but that are absent or not functional in others. Yet it is here, encoded in lineage-specific and functional sequence, that we expect physiological differences between species to be most concentrated.


Thursday, August 21, 2008

It's About Right and Wrong

Absolutes, Moral Clarity, and the Great Political Divide is an article authored by Michael Medved who those interested in Intelligent Design might know as a member of the Discovery Institute. The article is not about Intelligent Design but does raise some important points of interest to those of us living on this planet. So it will be filed under the off-topic heading. In the article Medved wrote:

Those who take their inspiration from Ronald Reagan enthusiastically embrace moral absolutes; those who admire Jimmy Carter, Bill Clinton or Barack Obama feel uncomfortable with terms like good and evil when applied to politics and world affairs. Republicans relish crisp black-and-white when drawing distinctions; “progressives” feel an incurable fondness for shades of gray. On foreign policy, social issues, even the economy, the right wants to take sides and to make sure the good guys win. The left, on the other hand, seeks to split the difference among warring interests in behalf of a “can’t-we-all-get-along” vision of moral equivalency.

There is much truth to this observation but there are unmistakable push-button issues for which Medved's conclusion does not apply. Recall Senator Trent Lott's speech at the 100th birthday party of Strom Thurmond when he said:

I want to say this about my state: When Strom Thurmond ran for president, we voted for him. We're proud of it. And if the rest of the country had followed our lead, we wouldn't have had all these problems over all these years, either...

The occasion was televised and I watched it. Lott, like everyone else present, was eager to say something nice about Thurmond, a former segregationist. He was not making a policy statement about racial politics. It was not on the radar screen. But you would not have known this based on the ensuing political storm which eventually resulted in severe political punishment for Lott.

For liberals this was good versus evil. At least on the surface. We can't forget that the Democratic Party, dominated by liberalism, included among its ranks Senator Byrd, a one time member of the Ku Klux Klan. Yes, he had forsaken everything associated with the Klan and was forgiven that blot on his record. After all he was now working with the good guys. Lott never was a member of the Klan. He was not even accused of being a segregationist. His sin was saying something at a birthday party. The point is good and evil do exist for liberals and no shades of gray are allowed when PC issues are broached. More from Medved's article:

When John McCain responded to the invasion of Georgia with a full-throated, unequivocal denunciation of Russian bullying, Barack Obama’s top foreign policy advisor, Susan Rice, condemned the Republican nominee for “shooting from the hip” and “complicating” the situation. Her criticism echoed the sentiments of nervous 1980’s liberals who slammed President Reagan’s “simple-minded” and “destabilizing” characterization of the Soviet Union as an “Evil Empire.”

McCain's reaction was spot-on. Russian aggression was and continues to be abhorent. This is a much clearer example of right and wrong than the birthday speech. So, apart from the political campaigning, why the criticism of McCain's condemnation of Russia? This has much to do with managing our approach to events impacting foreign policy. To criticize the obvious- Russia's indefensible aggression- to some, also encourages a turn toward the despised "interventionism" associated with the Bush administration. To restrain a turn in that direction you manage how news is presented. De-emphasize the unsavory murder of Georgian civilians. Downplay Georgia's attempt at democratization. Play along with timid Europeans who offer the obligatory criticisms while making sure they do nothing to provoke genuine Russian ire. After all western economies run on oil and the west has succeeeded in making itself a whore to Russian and Middle Eastern sources of oil. More from Medved:

Instead, he seemed to suggest that the United States should feel guilty about its own evil deeds, committed on behalf of good intentions, saying it’s “very important for us to have some humility in how we approach the issue of confronting evil, because of a lot of evil’s been perpetrated based on the claim that we were trying to confront evil.” In other words, Obama takes us back to the tired old moral equivalency arguments of thirty years ago, recycling a familiar plot from any number of acclaimed gangster movies – with the crusading cop becoming just as compromised and vicious as the criminal he’s determined to bust.

It is false humility to refrain from taking on evil because of one's own shortcomings. Much evil also has been perpetrated in the name of restraint. In the wake of WWII it was observed that for evil to succeed what is necessary is that good people do nothing. That continues to be true. Ignoring powerful perpetrators of wrongdoing, while swatting the relatively weak Serbians or an individual like Trent Lott, is not heroic. It's not even moral.


Monday, August 18, 2008

Tracing a Pathway to DNA

Yesterday's post on supercoiling identified a constraint inherent to the topological structure of DNA which supports a front loading perspective. It also makes a gradual evolutionary approach to DNA dubious based on properties of DNA. Imagination is a wonderful thing but unconstrained imagination, applied to the solution of scientific dilemnas, is not.

A selection perspective of pathways to DNA should be guided by considerations that go beyond supercoiling. Enzymes enabling deoxyribose metabolism have obvious selection value. But that does not explain their origin. Enzymes are needed prior to the biosynthesis of deoxyribose. Yet what selection value would they confer prior to the point in time when DNA was a repository for genomic information?

Which brings me to a more substantial point. DNA enables cellular functions because it comes loaded with genetic information, mechanisms that enable gene expression and a genetic code already in place. These would have to be accounted for by any viable origins theory. Fitting theory within a selection framework is confounded by the very nature of genes and mechanisms needed to allow for their expression. Step by step approaches are not suggested by the biological systems discussed.

A designer faced with the task of incorporating DNA within a cellular environment would front load genetic information and the means of accessing and expressing it. It would be good design. Yet we are to expect unidentified forces on nature to have accomplished the same. But of what biological use is a gradual encoding process when minimally functional genomes number in the dozens of genes? How do transcription and translation functions gradually evolve? If the structures discussed were anything but biological, a front loaded origin would seem obvious based on the nature of the structures themselves.

Fear of designer implications ought not guide rational considerations of origin matters. That includes irreducibly complex DNA.

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Sunday, August 17, 2008

Supercoiling and DNA

What's notty about DNA? discusses an important property of DNA i.e. supercoiling. The twisting of the DNA helix around what could be envisioned as a central line can be described by the mathematical formula: Lk = Tw+Wr where the sum of the twist about the central line and the writhe (the amount of resistance to straightening the curve) equals the number of times one of the strands winds around the other one.

The linked article contains these quotes identifying supercoiling properties which enable the described functions.

Supercoiling is a very smart form of compact storage that allows for easy manipulation.

Supercoiling allows for easy manipulation and so easy access to the information coded in the DNA. When a cell is copying a DNA strand it will uncoil a strand, copy it and then recoil it.

The compact storage of genetic information and facilitated access to that information can be attributed to topological properties of DNA. We see design features that enhance the function of cells. But let's look at the other side of this coin namely, design constraints

Behavior of Supercoiled DNA, Biophys J, April 1998, p. 2016-2028, Vol. 74, No. 4 and authored by T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette, states this:

Vinograd first understood in 1965 (Vinograd et al., 1965) that the double-helical nature of DNA allows it to be overwound and underwound from its natural state. Today we know that DNA is topologically polymorphic. The overwound or underwound double helix can assume exotic forms known as plectonemes (like the braided structures of a tangled telephone cord) or solenoids (similar to the winding of a magnetic coil) (Marko and Siggia, 1995). These tertiary structures have an important effect on the molecule's secondary structure and eventually its function. For example, supercoiling-induced destabilization of certain DNA sequences can allow the extrusion of cruciforms (Palacek, 1991) or even the transciptional activation of eukaryotic promoters (Dunaway and Ostrander, 1993).

So supercoiling also can lead to overwinding, causing destabilization of function. Another quote:

DNA replication poses a similar but topologically enhanced problem. Once replication is completed, the newly synthesized molecule must be disentangled from its parent. The replication of circular DNA molecules gives rise to two linked circular molecules, but the replication of whole chromosomes leaves the cell with highly entangled chromatids. If the cell does not disentangle the freshly replicated pairs of sister chromatids, they will fragment under the pull of the mitotic spindle. Disentanglement is achieved thanks to topoisomerases (Jannink et al., 1996). Topoisomerases are the cell's tools for managing the topologies of their genomes (Wang, 1996). Type I topoisomerases act by transiently breaking one of the strands of duplex DNA, allowing the intact strand to pass through and thereby changing the number of times the two strands wrap. Type II topoisomerases transiently break both strands of duplex DNA, allowing another segment of duplex DNA to pass through. Type II topoisomerases thus have an unknotting activity, which is required to disentangle linked circles or replicated chromosomes.

The DNA replication process brings about molecular entaglements. Disentanglement is needed to retain DNA function. Enzymes known as topoisomerases enable the disentangling. The entanglement problem is inherent to DNA topology. A design enhancement is also a design flaw whether the designer is viewed as a force of nature, culled by selection, or a more directing cause. This type of flaw calls for a remedy built into the design itself. That's what we witness. The remedy (topoisomerases) are coded for by genes found in DNA. This is a logical indicator of a front loaded option. If not front loaded how would the entanglement dilemna be resolved. Gradual evolution is not helpful when an affliction is immediate and universal. Neither is extinction.

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Monday, August 11, 2008

Irreducible Complexity and Functional Intermediates

William Brookfield wrote a comment at Telic Thoughts, within a thread discussing irreducible complexity, which I think merits some attention. The quote:

It seem to me that if a (mouse) trap is functioning within a biological system not — as a "trap" — but as "a blunt instrument" then NS will be selecting for the optimum "blunt instrument" and RM will just be scrambling in no specific direction (randomly). The result is that the function of this "(Mouse) trap" has no causal anticedent and its appearance by RM&NS or any other such material agents must be taken on faith. It seems to me that NS optimizes for existing function not future function and that these are two divergent directions.

Attempts to refute intelligent design inferences, drawn from Behe's irreducible complexity, are based to a great extent on homology arguments and the cooption concept. Brookfield correctly points out that functional discontinuity is associated with a selection perspective. Although he does not explicitly state it, the discontinuity is linked to cooption and homology based explanations. The explanations lack the detail needed to establish a functional trail. Precusor function is evident when the coopted entity is identified and the function of the relevant IC system is also clear. However, intermediate functions are unclear. If precursor and IC functions are disparate then the lack of clarity becomes problematic for theoretical applications. How predictive are theoretical models lacking identifiable functional intermediates?


Saturday, August 02, 2008

Academic Freedom

Hypocrisy at University of Minnesota; Self-Exposed, a Discovery Blog entry, illustrates what has gone wrong with academic freedom. When appropriately applied academic freedom can secure the right to pursue a line of academic inquiry without concern that popular passions might short circuit the effort. One would not want to see a professor of biology or physics dissuaded from looking into a scientific matter because of political pressure for example.

The linked blog entry contains this comment from the Catholic League:

The Chancellor of the University of Minnesota, Morris (UMN) released a statement today regarding the intentional desecration of the Eucharist by Professor Paul Z. Myers. “I believe that behaviors that discriminate against or harass individuals or groups on the basis of their religious beliefs are reprehensible,” said Jacqueline Johnson. Importantly, she added that the school’s Code of Conduct prohibits such behavior. However, she also stressed that academic freedom allows faculty members “to speak or write as a public citizen without institutional discipline or restraint….” Nowhere did she say Myers would be disciplined.

PZ Myers' action was not about academic freedom. What he did with the Eucharist had nothing to do with freedom to pursue an academic issue within biology- his field.. His action was meant to portray his hostility towards Catholicism. Catholic League president Bill Donohue's analysis nails it.