Archive for June, 2010
Phylogenetically, it looks like the ancestral proteasome subunit diverged into alpha- and beta-subunits, whereas E. coli contains only one beta-type subunit, termed HslV, which each harbors a proteolytically active site. HslV is a homomer composed of 12 identical subunits made by one gene. The 20s proteasome is a heteromer composed of 28 non-identical subunits. Those 28 proteins can be made from anywhere from 2 to 14 different genes, but they will all have the same fold. The 20s proteasome is the result of a duplication of a homomer. When the 28mer came up, a new intermolecular interface had to be formed to attach the alpha to the beta ring. If alpha and beta would be identical, then there would have been the possibility to make a long fiber like an actin or myosin fiber. Therefore alpha and beta need to be different. Thus, the gene duplication that lead to alpha, beta was necessary to allow for the 28 mer. A neat animation below the fold
Intelligent Design is ___________. A Trojan horse, a wedge strategy, stealth creationism… Place your favorite cliche into the blank. In doing so ignore the real world. In that world Venter recognizes what was already plain to see. Instructions within cellular genomes reveal what life is. Venter:
This is as much a philosophical as a technological advance. The notion that this is possible means bacterial cells are software-driven biological machines. If you change the software, you build a new machine. I'm still amazed by it.
Not unrelated to the film ‘Expelled -no intelligence allowed’-I submit for your thoughts and comments:
‘Dawkins is prepared to acknowledge the facts while denying their significance. Neither the Nazis nor the Communists, he affirms, acted because of their atheism. They were simply keen to kill a great many people. Atheism had nothing to do with it. They might well have been Christian Scientists.
In the early days of the German advance into Eastern Europe, before the possibility of Soviet retribution even entered their untroubled imagination, Nazi extermination squads would sweep into villages, and after forcing the villagers to dig their own graves, murder their victims with machine guns. On one such occasion somewhere in eastern Europe , an SS officer watched languidly, his machine gun cradled, as an elderly and bearded Hasidic Jew laboriously dug what he knew to be his grave.
Standing up straight, he addressed his executioner. “God is watching what you are doing,” he said.
And then he was shot dead.
What Hitler did not believe and what Stalin did not believe and what Mao did not believe and what the SS did not believe and what the Gestapo did not believe and what the NKVD did not believe and what the commissars, functionaries, swaggering executioners, Nazi doctors, Communist Party theoreticians, intellectuals,Brown shirts, Black shirts,gauleiters, and a thousand party hacks did not believe was that God was watching what they were doing.
And as far as we can tell, very few of those carrying out the horrors of the twentieth century worried overmuch that God was watching what they were doing either.
That is, after all, the meaning of a secular society.”
(taken from David Berlinski’s book ‘The Devils delusion Atheism and its scientific pretensions’)
I observed an interesting exchange among IDists which was sparked by the antics of Moran and Matheson who have criticized Stephen Meyer in a manner that is all too familiar. The following remarks are my own and reflect my own views but insights supplied come from others. Matheson and Moran continue a tradition of nastiness which characterizes most ID critics. But the nastiness is not without cause. After all these people are defending science; a noble endeavor which allows for little discretion and even less valor. For them it is not about politics or religion. Oh no. This is a righteous cause pitting science defenders against the unwashed masses represented by a handful of IDist luminaries- knaves to the bone. When you are up against unprincipled ignorant attackers of science what are you to do? See that's the beauty of it. When you are up against a despised foe anything goes. And remember- it's all for science.
Matheson and Moran have done us all a favor. Their arrogance, drawn from over confidence, has inspired some questionable statements as Salvador Cordova has drawn attention to in the comment section in another thread devoted in large part to silly analogies made by Matheson. The M&M boys may strut like they are 10 feet tall but their statements make them look small. They look more like peevish juveniles than infallible experts.
New research into the deep ocean floor yields promising results for microbiologists is a EurekAlert article. If there is a biological frontier where might that be? Beneath the floor of the ocean deep perhaps. A huge biological reservoir could be located there. Post-doctoral fellow at Aarhus University in Denmark and the University of Southern California, Beth Orcutt, is quoted as saying:
There may be new species of life and new types of metabolism that we haven't discovered yet. The seafloor and sub-seafloor are exciting environments where microbes rule. We have to develop sophisticated experiments to try to learn more about these microbial habitats, experiments which will reveal new information about how life survives and thrives on Earth and maybe about how life may exist on other planets.
Orcutt has good cause for enthusiasm. It sounds as if there are exciting times awaiting her but I'm dubious that much will be learned about life on other planets. Wouldn't it be more likely that if life arose somewhere else in the universe it would occur in conditions that are similar to non-extreme as opposed to extreme earthly conditions?
Bryan Appleyard wrote On Experts and Truth. He notes an article in New Scientist, by Debora MacKenzie, which raised the issue of denialism. Appleyard then delves into the notion of expertise:
"So why don’t we make ourselves the last generation on earth? If we would all agree to have ourselves sterilized then no sacrifices would be required — we could party our way into extinction!"
What do babies know about right and wrong? Perhaps more than is realized. Results of Paul Bloom's study may challenge some ingrained secular assumptions. From the source:
Dr. Bloom's study was carefully designed to challenge one very persistent and pernicious modern belief about childhood, the belief that children are moral blank slates upon which anything can be written. On this view, morality is entirely unnatural—something imposed upon children by "socialization." The most famous advocate of this view was the 18th century philosopher Jean-Jacques Rousseau. Rousseau's view was not the result of careful observation of children, but of his own desire to overthrow the Christian notion that there is a God who defines the moral contours of human nature. Rousseau wanted natural man to be amoral, and so he taught that babies enter the world carrying no moral "baggage." The dual, contradictory result of Rousseau's philosophy was the spread of the notion that children were at once entirely innocent and it was society that made them bad, and the notion that since children were entirely morally unformed it was only society that could make them good. Rousseau's "children" are simultaneously those who are allowed to do anything they want because that is most natural, and those who are taken to be formless clay ready for molding social manipulators.
Steve Matheson has been skirmishing with Stephen Meyer during recent weeks and recently he has had a tiff with Richard Sternberg who posted Matheson’s Intron Fairy Tale. Matheson labeled Sternberg's piece a "nasty rebuttal."
Matheson wrote In rage deaf as the sea, hasty as fire at his blog Quintessence of Dust. From that blog entry:
Clues for intelligently designed objects can be found in their constructive linkages. Whereas basic forces of nature can generate complex designs whose causal genesis can be traced in steps from simpler beginnings to evolving complexity, intelligently designed objects proceed from a blueprint existing first in a mind. The constructive effort seeks to direct or counter forces of nature so as to realize the designed object. Since forces of nature are manipulated by a designer to effect an outcome, evidence for directed forces would constitute evidence for design.
That brings me to The Minimal Cell.
Prokaryotes are far simpler then eukaryotes, and M. pneumoniae has one of the smallest genomes of the prokaryotes. Such small prokaryotes are a good starting point in the search for the minimal cell.
If initial cells resulted from directed forces evidence for this might be found in cellular constructive design. One such indicator would be a level of complexity needed for function which exceeds the capacity of basic forces of nature to generate- the minimal genome concept. M. pneumoniae is a poster organism for this concept.
A recent paper from the lab of Nobel Laureate Jack Szostak describes some of the best current solutions to some big problems.
HT: Mike Gene
In my not so humble opinion, (IMNSHO?) J. Craig Venter just conceded the game to ID:
Venter also points to what the cells–powered by genomes made in a lab from four bottles of chemicals, based on instructions stored on a computer–reveal about what life is. "This is as much a philosophical as a technological advance," he says. "The notion that this is possible means bacterial cells are software-driven biological machines. If you change the software, you build a new machine. I'm still amazed by it." (my emphasis)