Biology

[From a colleague:] The species problem is real, but I think that (a) it is way overblown in importance in the phil. biol. literature as a result of our fixation on metazoans; and (b) it may already have a pretty good answer (Paterson’s “recognition” concept). Briefly, on (b): the idea is just that the “glue” holding species together is the fact that members recognize each other as members, which is a fact about their cognitive systems analyzable in terms of pheromones or whatever. Of course, there is also the fact that recognition has to be correlated with reproductive viability, which raises all the usual design issues. But I don’t see that there are any deep problems here that are not Read More ›

http://www.junkdna.com/fractogem/

http://www.fractogene.com/

On the subject of “junk DNA” Dr. Pellionisz believes these sections are caused by DNA being a “FractoGene” (Fractal DNA generating Fractal Organelles). I wouldn’t be surprised if DNA uses recursive mathematics for generating its complexity (plants do this for their structure at a macro level). As he explains it:

“[The] FractoGene approach to DNA, indeed, does not do away with “design”. While “genes” provide the “materials” (“building blocks” of nucleic acids for proteins, much like a building is built by bricks, concrete, steel, glass, wood, tiles, marble, etc.), the “architecture” of a building is *not* in its materials. THE ARCHITECTURE IS IN THE DESIGN. In case of the DNA and organs and organelles, FractoGene provides an *explanation* for the design; that “Junk DNA” provides auxiliary information for each (fractal) recursion how to build a hierarchy of protein structures. The explanation is algorithmic, i.e. it is given in hard terms of mathematics (fractal geometry), that is inherently “software and nanotechnology friendly”. Besides, FractoGene also put forward (quantitative) predictions that are experimentally verifiable or refutable. (Experimental support of the “Fugu prediction of FractoGene” was published in peer-reviewed science journal; see http://www.junkdna.com/fractogene/05_simons_pellionisz.html).”

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http://news.yahoo.com/s/afp/20060714/sc_afp/swedenspainscience_060714171218

STOCKHOLM (AFP) – A Swedish-led team of scientists has discovered 400,000-year-old DNA in bear teeth, the Uppsala University in Sweden said.
The team, made up of Swedish, Spanish and German researchers, discovered the remains of the bear in a cave in Atapuerca, northern Spain.

“It is usually hard to find DNA that is older than 100,000 years, and work on fossilized DNA mostly focuses on material that is a few tens of thousands of years old, at most,” team leader Anders Goetherstroem said in a statement.

He said the find “pushed back the frontier” concerning the age of DNA that scientists could work with. “It means that it will be possible to subject a large number of extinct animals to DNA analysis,” he said.

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As some of you may recall I wrote that I was experimenting with laboratory propagation of volvariella volvacea (Chinese Straw Mushrooms). Recently, among several other lines of R&D, I was experimenting with hydrogels as a nutrient media. So far I’ve been using them as an agar replacement with mixed results. I think the mixed results are due to uneven moisture distribution in the fine powder form I was using but that’s neither here nor there. Since the hydrogels can be loaded with nutrients at room temperature (the big advantage over agar) I decided to play around with another sterilant that would decompose at temperatures required to melt agar. I’ve been extremely successful using ampicillin at 1mg/20ml to prevent bacterial contamination in agar cultures – haven’t had a single bacterial infection in hundreds of agar plates. Ampicillin however breaks down quickly at temperatures over 60C so it must be added to agar at a critical stage after it’s cooled down (agar melts at 95C) some but before it solidifies (about 40C). This requires pouring fast and keeping a 60C water bath on the bench. However, ampicillin is so inexpensive it can be considered free of cost compared to wide spectrum antibiotics that survive pasteurization and autoclave temperatures. Once poured, ampicillin plates must be refrigerated until use as ampicillin in solution breaks down quickly at room temperature (a matter of days).

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This might be one of those relatively “simple” systems that could–like the bacterial flagellum–become a primary example used by ID proponents.

http://www.eurekalert.org/pub_releases/2006-05/cp-nro050306.php

By using an electronic ultra-high-speed camera, researchers have characterized the explosive discharge of stinging jellyfish nematocytes and show that this event represents one of the fastest cellular processes in nature. The research is reported by Thomas Holstein of the University of Heidelberg and his colleagues in the May 9th issue of Current Biology. Read More ›

For those looking to see if ID returns false positives (ASSUMING that indeed there is additional CSI involved in this immunity, which is apparently unknown at this time).

http://www.pnas.org/cgi/content/abstract/0602382103v1

Spontaneous regression/complete resistance (SR/CR) mice resist very high doses of cancer cells that are lethal to WT mice even at low doses. In this study, we show that this resistance is mediated by rapid infiltration of leukocytes, mostly of innate immunity, in both primary and repeated challenges. Formation of rosettes with infiltrating natural killer cells, neutrophils, and macrophages was required for the subsequent destruction of cancer cells through rapid cytolysis. Highly purified natural killer cells, macrophages, and neutrophils from the SR/CR mice independently killed cancer cells in vitro. The independent killing activity by each subset of effector cells is consistent with the observation that the resistance was abolished by depleting total infiltrating leukocytes but not by depleting only one or two subsets of leukocytes. The resistance was completely transferable to WT recipient mice through SR/CR splenocytes, bone marrow cells, or enriched peritoneal macrophages, either for prevention against subsequent cancer challenges or eradication of established malignancy at distant sites.

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http://domino.research.ibm.com/comm/pr.nsf/pages/news.20060425_dna.html

IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do.

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,” or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins. Read More ›

While reading about Pianka I noticed one statement related to Intelligent Design that has been overlooked amidst the furor:

“Although [Ebola Zaire] Kills 9 out of 10 people, outbreaks have so far been unable to become epidemics because they are currently spread only by direct physical contact with infected blood. However, a closely-related virus that kills monkeys, Ebola Reston, is airborne, and it is only a matter of time until Ebola Zaire evolves the capacity to be airborne.” – Pianka

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http://www.umich.edu/news/index.html?Releases/2006/Feb06/r021406

Researchers who speculate about human origins have come up with three main scenarios for how we ended up with our unique traits, Zhang said. The first possibility is that we acquired completely new genes that other apes don’t have. Another is that some of our genes have taken on different functions through mutation.

It’s also possible that we humans lost some genes along the way, and those losses provided opportunities for changes that otherwise could not have occurred. Read More ›

http://www.sciencemag.org/cgi/content/short/311/5764/1068b

Mesozoic mammals have been thought to have been small, nocturnal, and confined to a few niches on land until the demise of the dinosaurs 65 million years ago. Most are recorded by isolated jaw fragments or teeth. Ji et al. (p. 1123; see the cover and the Perspective by Martin) now describe a Jurassic mammal from China that breaks this mold. The fossil is well preserved, and impressions of fur can be seen on its body and scales on a broad tail (similar to a beaver overall). The animal was fairly large, approaching not quite half a meter in length, and the shape of its limbs suggest that it was adapted for swimming and burrowing. The combination of both primitive and derived features in this early mammal, and the demonstration that mammals had occupied aquatic habitats by this time, expands the evolutionary innovations of early mammals.

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Go here to read the article.

It has come to my attention that because the genetic code isn’t quite universal some people think that is grounds for calling into question how many more than one common ancestor there might be. Read More ›

http://www.umc.pitt.edu:591/m/FMPro?-db=ma&-lay=a&-format=d.html&id=2297&-Find

Schwartz hearkens back to earlier theories that suggest that the Darwinian model of evolution as continual and gradual adaptation to the environment glosses over gaps in the fossil record by assuming the intervening fossils simply have not been found yet. Rather, Schwartz argues, they have not been found because they don’t exist, since evolution is not necessarily gradual but often sudden, dramatic expressions of change that began on the cellular level because of radical environmental stressors-like extreme heat, cold, or crowding-years earlier. Read More ›

In browsing the New Mexicans for Science and Reason site and the Oynate Man prank (which I’d seen before but since it’s so hilarious enjoyed reading again) I came across this statement in the April Fool article explaining what would constitute real evidence against evolution: Read More ›

By popular demand…

Julian Huxley’s Confession

by John A. Davison

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