The Secret Powers of Time by Philip Zimbardo

Kon-Tiki by Thor Heyerdahl (1950)

Le Monde Du Silence By Louis Malle (1956)

Frankenstein's bacterium

Apprearing in tomorrow's edition of Science, we have news of considerable advances in genomics from the J. Craig Venter Institute. One team of geneticists at the institute led by Daniel Gibson succeeded in creating a synthetic genome capable of reproduction. While the genome is not a Frankenstein-esque monster, it is synthetic in the sense that it is the first ever genome constructed from raw chemicals. The process has been long and daunting, calling on years of previous breakthrough work from the institute in order to materialize the bacteria chromosomes in yeast and then transplant them successfully. Often using the analogy of computer terminology, Venter explains that once a genome has been sequenced and placed in a recipient cell's cytoplasm (devoid of genetic material), the newly inserted genome "boots up like software."

Of course this instance wasn't without some error at the outset. The genome the team attempted to synthesize was switched at one point during the course of the project. Initially using a simpler, smaller genetic sequence, the team found that the cell's phasing took so long to cycle, they needed to switch gears and use another species in order to yield results. In the end, the constructed genome was that of Mycoplasma capricolum, a bacterium containing 1.1 million base pairs. Even so, the initial trial of M. capricolum didn't yield any results as the cell remained completely inactive. The project underwent a delay of three months while software analysis checking the constructed genome indicated a single base pair was a "typo" and the team located and amended the mistake.

This research proved not only the magnitude of possibility the field holds, but also the necessity for complete accuracy in genetic engineering. Venter and his institute have plans, provided no governmental interference, to pursue wholly synthetic creations that could provide effective health, commercial and industrial applications to some of the most pressing world issues of energy, waste, and medicine. Of course, from the pitfalls in the process of this research, it logically follows that the essential components that make nature's "software" work need to be understood before completely fabricated species have their "software" engineered entirely anew.

TED provided video of J. Craig Venter's press release.

Holographic paradigm

I've resurrected some notions regarding unified theories of consciousness and the universe. The holographic paradigm is of particular interest as a perspective to account for anomalies in our material understanding of the known physical realm. In the video below, note Michael Talbot's depiction of entanglement through the prescient analogy of an aquarium. His characterization of a reduction toward some cosmic unity seems to acquiesce with the concepts that begat my introduction to the holographic paradigm. I've always found it a curious notion the manner in which quantum physics portrays the former classical model particles as energy fields. Accounting for the disparate nature of these fields must (one would think) reduce to some uniformity. Albeit a matter of perception, perhaps certain quantitative properties can be manifest in qualitative ones as is such in electromagnetic radiation. Simple adjustments in frequency is the attribute responsible for all types of electromagnetic radiation let alone the colors in the visual spectrum. This holographic hypothesis may be a univocal paradigm for the manner in which energy fields interact and formulate an interface of reality.

Null-i

In previous musings, I questioned the hegemonic notion that all life on Earth has a common ancestor. I expressed this notion as thus: "If conditions on Earth supported one biological genesis, then these conditions were such that a genesis could have been supported on multiple occasions." For whatever independently arriving at this conjecture is worth, I later found this notion to be referred to as the Shadow Life Hypothesis. The ramifications vary based upon how stringent one's claims are therein, yet the foundation of the hypothesis is simply more than one origin of life. However, published in the latest edition of Nature, life's origins were analyzed.

Douglas Theobald, a biochemist at Brandeis University, began his study by selecting 23 proteins ubiquitous across the taxonomic spectrum. Each species represents these proteins via a structure that is particular to that given species. Theobald then ran the gamut of statistical analyses in order to yield the likelihood of any model to derive these protein structures. His computational simulations indicated that the universal common ancestor hypothesis is 10^2,860 times more probable than any concatenation of multiple ancestors. In spite of the fact that many microbiologists may note that microorganisms of disparate species may swap genetic material, the computations accounted for this and still found a single ancestor to be the most efficacious solution.








*Blue dotted line represents swapped genetic material

Theobald qualifies that his study does not in any way suggest the number of times life on Earth emerged. Nonetheless, it does suggests that only one strain would ultimately reign supreme. In any case, while we may concede that this statistical analysis is perfectly cogent, it may be begging the question with regard to our taxonomic categorization. Further, Theobald's statistical analysis as a formal study is questionable; our notion of nature as a pinnacle manifestation of logical eloquence does not always prevail. Considering what we know of the human genome (and genomics writ large), the retention of archaic sequences from genetic ancestors that no longer code for active traits serves as a case in point where the precedent of logical eloquence and simplicity in nature breaks down in biology. (**EDIT** - in light of my critique, I just happened upon this article.)

Why Cecco Beppe Does Not Die

Troglodyte

Today's edition of Science includes the article, "A Draft Sequence of the Neandertal Genome." The aptly titled article not only describes this rough sequence of the neandertal genome, but offers particularly intriguing commentary on the difficulties of ancient DNA retrieval. Yet, most importantly, the article compares the genome of Homo neanderthalensis with that of five modern humans.

Only recent advances have permitted ancient DNA retrieval. In spite of this, problems persist as remains are replete with microbial colonization. The natural process of putrefaction introduces the DNA of microbes which begin to interfere. Roughly 95-99% of the samples were comprised of microbe DNA, which had to be treated with enzymes to "enrich" the samples such that the ratio of neandertal DNA was accessible. Further, a close genetic "relative" must serve as a basis of comparison to ensure the research is on track. It then logically follows that sequencing the neandertal genome would imply an analysis with respect to modern humans.

Insodoing, DNA samples were collected from 21 late Pleistocene (±38,000 year-old) bones of three neandertal women discovered in Croatia's Vindija Cave and compared to samples from five individuals from China, France, Papua New Guinea, Southern Africa, and Western Africa. The genome was analyzed across genetic "hotspots" derived from known deviations between chimpanzee and human DNA. The results suggested that neandertals fall within the degree of genetic variation found in modern humans. There were only five genes found to be distinctly modern human. Interestingly, there was greater variation amongst the neandertal genome when compared to those of the modern human genomes from both African individuals than all non-African samplings.

Considerable speculation on the potential for human and neandertal cross-breeding has circulated academia with regard to hominid evolution for some time. Nonetheless, the hope that this study could formulate a conclusive posit on the notion is unfulfilled. The article suggests that based upon the research, neandertal and human divergence from a common ancestor is too recent to confirm or deny any definitive understanding for the genomic overlap.

How Much Wood Would a Woodchuck Chuck by Werner Herzog (1976)

New findings on AIDS non-progression

I wrote on AIDS non-progressors some time ago, yet today new information was published in Nature pertaining to the genetics behind individuals whose immune systems are seemingly miraculously able to maintain HIV from developing into full-blown AIDS.

The article explains that for some time there has been a known link between these AIDS non-progressors and the expression of the distinctive HLA B57 gene. A team of researchers led by MIT Professor Arup Chakraborty and Harvard Professor Bruce Walker observed that this gene is responsible for immune systems producing an abundance of CD8+ T cells, the killer T cells that destroy infections such as HIV. All T cells bind to foreign proteins on the surface of infected cells; they then seek out all other cells with this same particular foreign protein. The unique CD8+ T cells have the ability to not only bind to one specific protein, but seek multiple proteins and thus destroy any infections that have mutated.

The key to the function of these T cells is their interaction with self-peptides in the thymus. The variety of self-peptides in the thymus dictate the number and type of T cells that can be produced. The variety of self-peptides is a consequence of the HLA genes, including the aforementioned HLA B57.

Based on these findings that illuminate the workings of the immune system, the researchers are optimistic that this may lead to a potential "vaccine." Since all individuals possess the CD8+ T cells, the difference only being in number, they reckon they may find a way to provoke the same production of CD8+ T cells in all individuals as that of those with the HLA B57 gene. There is however one negative repercussion noted about individuals with this gene. The unique ability of these abundant T cells to bind with many proteins means it often does so with healthy cells. Individuals with the HLA B57 gene, therefore, have a high prevalence of autoimmune disease.

Om from India

Located in the West Village, Om from India is a unique shop that specializes in original lithographs of traditional Hindu religious imagery. The collection largely represents the primitive technique of limestone block prints used from the late 19th century until the 1940s. Prints can only be purchased in person and by appointment. Nonetheless, the website offers a great sampling of their compendium.

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