Saturday, March 29, 2008

A Teleological Coping Strategy

It is not unusual for me to come across written articles that strike me as important or impacting current modes of thought while others yawn when seeing the same. This may be one of those times. Stochastic switching as a survival strategy in fluctuating environments by Murat Acar, Jerome T Mettetal and Alexander van Oudenaarden (Nature Genetics 40, 471 - 475 (2008) might be a diamond in the rough. How is population fitness maximized in environments that are fluctuating? The answer might entail stochastic transitions among multiple phenotypes according to the cited paper. This could have the effect of enhancing fitness with a strategy that makes it possible for there to always be some cells ready for the vissicitudes of unanticipated environmental flux. This looks like a teleological approach to biological 911s or a means of lending guidance to the famed blind watchmaker.

The related study focused on Saccharomyces cerevisiae. What struck me was the suggestion that rates at which phenotypic switching occurs are tied to the frequency of environmental changes. Fast switching populations were found to outgrow slow switchers in rapidly fluctuating environments whereas slow switchers have the growth edge in environments where changes are rare.


Wednesday, March 26, 2008

The DNA Damage Response: the Enabling E2F Family

The E2F transcription factor family has been found to be important in determining the outcome of certain cancers. The abstract of a paper titled DNA-damage response control of E2F7 and E2F8 which is authored by L Panagiotis Zalmas, Xiujie Zhao, Anne L Graham, Rebecca Fisher, Carmel Reilly, Amanda S Coutts and Nicholas B La Thangue, correlates to EMBO reports 9, 3, 252–259 (2008). Quoting:

Here, we report that the two recently identified E2F subunits, E2F7 and E2F8, are induced in cells treated with DNA-damaging agents where they have an important role in dictating the outcome of the DNA-damage response. The DNA-damage-dependent induction coincides with the binding of E2F7 and E2F8 to the promoters of certain E2F-responsive genes, most notably that of the E2F1 gene, in which E2F7 and E2F8 coexist in a DNA-binding complex. As a consequence, E2F7 and E2F8 repress E2F target genes, such as E2F1, and reducing the level of each subunit results in an increase in E2F1 expression and activity. Importantly, depletion of either E2F7 or E2F8 prevents the cell-cycle effects that occur in response to DNA damage. Thus, E2F7 and E2F8 act upstream of E2F1, and influence the ability of cells to undergo a DNA-damage response. E2F7 and E2F8, therefore, underpin the DNA-damage response.


Sunday, March 23, 2008

Blogging at the Discovery Institute

The Discovery Institute's Discovery Blog discusses issues unrelated to Intelligent Design. That's noteworthy because ID critics accuse the DI of being in the forefront of an "ID movement" which is said to be characterized by misusing science to support political and social causes. The blog is direct about its views and makes no attempt to link science to non-scientific matters. Since science blogs contain an abundance of social commentary, most of it at odds with the DI's views, it is hypocritical to denounce the DI for straying into the realm of politics and social issues without at the same time criticizing science blogs for doing the same.

The following blog entry illustrates the point. The Appeal and Folly of Anti-Business Politics discusses business and politics. PZ Myers and other anti-IDists have been known to dabble in non-scientific matters at their respective blogs. Are they criticized for using mainstream evolution to promote their social agenda?

Carping over the ID movement looks like whining over nothing. Or to put it more precisely whining because the the DI's positions are not slanted to the left of center.

Friday, March 21, 2008

Antibiotic Resistence

Dr. Michael Egnor authored the blog entry titled Dr. Larry Moran, Darwinism, and Vicious Personal Invective at Evolution News and Views. Some personal invective from biochemistry professor Larry Moran is the focal point. The initial barrage was aimed at Dr. Jonathan Wells, who dared to suggest that recent research, related to bacterial resistence to antibiotics, was made independently of Darwin's theory. Egnor was also a target. The rhetoric can be viewed at the link. The insults were laced with predictable but unimaginative verbiage like "Idiots" and "lying for Jesus." So what else is new?

What do Moran, Myers and other wannabe tough guys get out of their poddy mouth antics? The approval of their readers? Promotion of the jackbooted image? And why is it so important to them to liken design to ignorance when ignorance is the byword aptly describing empirical supporting evidence for a non-design origin of life theory?

There is a practical effect of denigration that is worth noting- it tends to freeze fence sitters. Humans possess a herd instinct. Most of us do not like to buck popular opinion particularly when its spokesperson is an authority figure. Who is likely to say of another: "He raises a good point."- if the he is being demonized by one's college professor? Few have that kind of moral courage.

Here is Egnor's description of what Wells said from the linked blog entry:

…Darwinian evolution had nothing to do with [the research]…some bacteria happen to have a very complex enzyme (acetyltransferase), the origin of which Darwinism hasn’t really explained…And although an understanding of genetics is important when dealing with antibiotic resistance, Darwin’s theory of the origin of species by natural selection is not…they were not guided by Darwinian evolutionary theory [Emphasis mine] Dr. Wells pointed out that research on antibiotic resistance wasn’t guided by Darwinian evolutionary theory. That evolution occurred — that is, that the population of bacteria changed over time — is obviously true, and obviously was relevant to the antibiotic resistance research. Dr. Wells made the observation that the research owed little to Darwin’s theory that all biological complexity arose by natural selection without teleology.


Monday, March 17, 2008

Damaged DNA Ages Caenorhabditis Elegans

The linked paper titled Longevity and resistance to stress correlate with DNA repair capacity in Caenorhabditis elegans (Nucleic Acids Research, 2008, Vol. 36, No. 4 1380-1389) which is authored by Moonjung Hyun, Jihyun Lee, Kyungjin Lee, Alfred May, Vilhelm A. Bohr and Byungchan Ahn, argues that a correlation exists between DNA repair capacity and the aging process. The paper notes that effects of the aging process have been associated with diseases caused by an accumulation of damage in cells and tissues. Since DNA encodes structural components and functions found in cells and tissues, the authors thought DNA to be connected with the damage leading to aging. DNA repair of course can prevent damage to DNA. Consequently the aging process linkage was natural. Quoting from the concluding paragraph:

In conclusion, the data presented here demonstrate for the first time that longevity correlates with DNA repair capacity in C. elegans. The results strongly support the hypothesis that DNA damage plays a direct role in the process of aging. In addition, this study demonstrates that C. elegans has an NER-like DNA repair pathway that repairs UV-induced pyrimidine dimers. However, additional studies are needed to determine the exact relationship between specific factors that influence life span, stress resistance and DNA repair capacity in C. elegans.


Sunday, March 16, 2008

A Study of Transfer RNA

A PLOS Computational Biology paper titled Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses and authored by Feng-Jie Sun and Gustavo Caetano-Anollés, reported findings the authors state implies the following relationships between Archaea, viruses, Eukarya and Bacteria:

Archaea was said to be the most ancient followed by viruses which were linked to Archaea. Following in order were Eukarya and Bacteria. Transfer RNA (tRNA) was the object of study. The linked paper had this to say:

Transfer RNA (tRNA) molecules are central to the entire translation process. They interact with the ribosomal RNA (rRNA) subunits as they are being ratcheted through the center of the ribosome [1],[2]. Their acceptor arms charge specific amino acids through the activity of cognate aminoacyl-tRNA synthetases, while triplets of bases on their ‘anticodon’ arms recognize complementary ‘codon’ sequences in messenger RNA. These and many other molecular interactions define the identities and functions of these tRNA adaptors and establish a genetic code that translates nucleic acid into protein information in the cell. The structural make-up of tRNA is therefore fundamental to our understanding of how the biosynthetic machinery was set up into place in an emerging protein and organismal world. tRNAs are clearly ancient molecules [3] and they have been used profusely to study the evolution of ancient life [4]–[8]. The identity and function of tRNAs are fundamentally delimited by the structure of the molecules, and structure is more conserved than sequence. In fact, we recently showed that tRNA structure carries deep phylogenetic signal and can be used directly to reconstruct evolutionary history [9]. However, understanding phylogenetic trees is challenging because tRNA evolution embeds a history of recruitment in which structures gain or co-opt new identities and functions or takeover established ones.

The authors utilized an established cladistic method, embedding structure into phylogenetic analysis, to explore phylogenetic signatures in tRNA. The phylogenetic analysis entailed treating molecular structural features as phylogenetic multi-state characters. The multi-state characters have transforming character states. The assumption of an evolutionary tendency towards molecular order was made in polarizing character state transformations.


Wednesday, March 12, 2008

Spaceflight and Pathogens

This from the linked EurekAlert article:

Spaceflight not only altered bacterial gene expression but also increased the ability of these organisms to cause disease, or virulence, and did so in novel ways. Compared to identical bacteria that remained on earth, the space-traveling Salmonella, a leading cause of food-borne illness, had changed expression of 167 genes. In addition, bacteria that were flown in space were almost three times as likely to cause disease when compared with control bacteria grown on the ground.

For reasons not yet understood space flight appears to make some pathogens more infectious. Is it because of changes only in the pathogens or a combination of both pathogenic changes and immunological changes in humans? What is the link between a space environment and the result? Studies will occur intended to provide answers. The problem could impair longer flight missions. It's an interesting development.

Friday, March 07, 2008


Go With Your Gut -- Intuition Is More Than Just A Hunch, Says New Research- the title of an article from Science Daily addresses a topic that a commenter at Telic Thoughts brought up yesterday. An ID critic alleged that ID inferences were drawn from intuition. As the linked article points out there are some in the science community who have ridiculed intuition and likened it to pseudoscientific practices like parapsychology and phrenology. Of course that's all the incentive needed for an ID critic to utilize the term in lieu of point by point discussions.

Research results published in the British Journal of Psychology indicate that intuitions are real and hunches should be taken seriously. Why? Because intuition is said to result from the manner by which brains subconsciously process, store and retrieve information. More specifically, researchers believe that a feeling that something is right or wrong occurs very quickly as the brain combines cues from past experiences and external circumstances and uses this as a basis for a decision. Rather than being irrational or emotionally based there appears to be a very logical and sound basis for hunches whose compressed time frame and unconscious level of decision making are distinguishing characteristics. Time pressure and information overload are associated with intuition according to researcher and Professor Hodgkinson.

A specific example involving a race car driver was used to illustrate how the driver saved his life with an instantaneous decision later analyzed to have resulted from his awareness of out of sync crowd behavior.

Both conscious and non-conscious thought are needed by humans if good decision making is the desired result.


Thursday, March 06, 2008

The Krebs Cycle

Here is a good blog entry about the Krebs Cycle. From the blog:

The citric acid cycle, also known as the tricarboxylic acid cycle (TCA cycle) or the Krebs cycle, (or rarely, the Szent-Györgyi-Krebs cycle) is a series of enzyme-catalysed chemical reactions of central importance in all living cells that use oxygen as part of cellular respiration. In eukaryotes, the citric acid cycle occurs in the matrix of the mitochondrion. The components and reactions of the citric acid cycle were established by seminal work from both Albert Szent-Györgyi and Hans Krebs.

In aerobic organisms, the citric acid cycle is part of a metabolic pathway involved in the chemical conversion of carbohydrates, fats and proteins into carbon dioxide and water to generate a form of usable energy. Other relevant reactions in the pathway include those in glycolysis and pyruvate oxidation before the citric acid cycle, and oxidative phosphorylation after it. In addition, it provides precursors for many compounds including some amino acids and is therefore functional even in cells performing fermentation.

A simplified view of the process

The citric acid cycle begins with acetyl-CoA transferring its two-carbon acetyl group to the four-carbon acceptor compound (oxaloacetate) to form a six-carbon compound (citrate).

The citrate then goes through a series of chemical transformations, losing first one, then a second carboxyl group as CO2. The carbons lost as CO2 originate from what was oxaloacetate, not directly from acetyl-CoA. The carbons donated by acetyl-CoA become part of the oxaloacetate carbon backbone after the first turn of the citric acid cycle. Loss of the acetyl-CoA-donated carbons as CO2 requires several turns of the citric acid cycle. However, because of the role of the citric acid cycle in anabolism, they may not be lost since many TCA cycle intermediates are also used as precursors for the biosynthesis of other molecules.

(Follow the link for the rest.)

Monday, March 03, 2008

Information and 2LT

"No process can result in a net gain of information” underlies 2LoT is the title of a blog entry at Uncommon Descent. Frankly I have not yet read the linked articles cited at the blog and will not comment on them. However, the topic is a fascinating one and offers ID friendly possibilities. DNA repair has long been a major theme at Intelligently Sequenced. Living organisms of all types are equipped with sophisticated mechanisms which keep genomic decay in check. Nevertheless despite the mechanisms the ageing process is accelerated by deleterious mutations which are lethal all too often. Life without DNA repair functions is difficult to imagine and imagine we must for DNA repair is ubiquitous in the biological world. Undoubtedly there will be more said about this topic in months to come.