idnet.com.au

http://www.nature.com/nrm/journal/v9/n9/pdf/nrm2472.pdf “MicroRNAs (miRNAs) are known to regulate gene expression at the level of translation, but how does this affect what proteins are produced? Two recent papers have shown that individual miRNAs can affect the expression of hundreds of proteins. One known as miR-223 seems to function as a rheostat to finely adjust protein output. Another miRNA let-7b is can fine-tune protein production from thousands of genes. Individual miRNAs can have an effect on global protein expression, and protein repression is likely to be mediated by a specific complementary sequence target region in the corresponding messenger RNA. The emerging picture is that miRNAs do not have just a small number of mRNA targets — they function at the transcriptional and translational level Read More ›

Where is ID on this scale? Bruce G. Charlton Editor-in-Chief, Medical Hypotheses “An old joke about the response to revolutionary new scientific theories states that there are three phases on the road to acceptance: 1. The theory is not true; 2. The theory is true, but it is unimportant; 3. The theory is true, and it is important – but we knew it all along. The point of this joke is that (according to scientific theorists) new theories are never properly appreciated. The ‘false’ phase happens because a defining feature of a revolutionary theory is that it contradicts the assumptions of already-existing mainstream theory. The second ‘trivial’ phase follows from a preliminary analysis which suggests that the new idea is Read More ›

In his excellent paper, Jeffrey Koperski argues very well that ID has been unjustifiably excluded from rational scientific consideration. He says that motives imputed to ID proponents should not color consideration of the validity of the theory, and that excluding a theory on definitional grounds is not historically or logically valid. He argues not so well that ID goes further than the data demands. He says there are other competing theories that require less radical movement by consensus science, and evolutionary theology. What do you think? “ID arguments about the limited explanatory power of mutation and natural selection fit comfortably within Conway Morris’s picture. Both agree that new kinds of explanations are needed that would lead to a more general theory of biology. Read More ›

This paper will be quoted for many years as the basis for faith in the de novo origin by evolution of useful proteins. How good is the evidence? De Novo Origination of a New Protein-Coding Gene in a yeast species by Wen Wang et al “THE total number of different proteins in all organisms on earth is estimated to be 10exp10 to 10exp12. How the protein repertoire evolved the giant diversity that underlies the evolution of the complexity of life is attracting many evolutionary biologists to the field. Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes creating new genes using pre-existing genes as the raw materials are well characterized, such Read More ›

In an essay that is ten times the length of the following extracts, Jeff Schloss, a Christian College professor, weighs in on Expelled. He says Expelled misses the central issues. Unfortunately his essay also missed the central issue. His own personal religious views have led him to write the way he does.

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Youtube has a series of monotonous lectures by Barbara Forrest. They call Barbara the woman creationists don’t want you to listen to. Dear Barbara, after listening to you, I know who is really deceiving people, and who is really afraid (or is it paranoid?), and it is not those who support ID. ID is about following the evidence where it leads. It is not about America, or the US Constitution or undermining the rest of science. There is no one ready to steal away your power and supress your rights. ID is a theory that doesn’t automatically Expell evidence for intelligent causation, but considers it along side other explanations for physical phenomena. If Barbara is the best they offer, there is not much on offer. Read More ›

Before the ink is dry on the revision of the tree of life, giving comb jellies pride of place near the base , we now need to redraw the tree again. “ScienceDaily (Apr. 14, 2008) — Darwin’s tree of life represents the path and estimates the time evolution took to get to the current diversity of life. Now, new findings suggest that this tree, an icon of evolution, may need to be redrawn. In research to be published in the April 13 advance online issue of Nature, researchers at Rockefeller University and the University of Tokyo have joined forces to reveal that insects have adopted a strategy to detect odors that is radically different from those of other organisms — an Read More ›

“Humans are almost unimaginably complex, but have scarcely more genes than a fruitfly or a worm. The human genome comprises about 99% ‘junk DNA’ — genetic code that is not used to make the protein building blocks of life. Junk DNA accumulates in organisms’ genomes simply because it is good at accumulating.Genes that do code for proteins may recruit some or all of this junk DNA to regulate when, where and how much they are expressed. Something has to instruct genes to team up to produce complex structures such as hearts and kidneys. Regulation is how we can have over 98.5% similarity to chimpanzees in the sequences of our coding genes, yet differ so utterly from them. The huge quantity Read More ›

A new find has shocked scientists who didn’t imagine the earliest critter could be so complex. “This was a complete shocker,” said study team member Casey Dunn of Brown University in Rhode Island. “So shocking that we initially thought something had gone very wrong.”   “Our data reinforce several previously identified clades that split deeply in the animal tree, unambiguously resolving multiple long-standing issues. We find strong support for the placement of ctenophores (comb jellies) as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. A diminishing number of lineages remain recalcitrant to placement on the tree. The spiral cleavage programme, a complex and highly stereotyped mode of early Read More ›

by K.D. Kalinsky “Either biological life required intelligent design or it did not. As with most problems in science, it is difficult to prove one option or another with absolute certainty. Instead, options can be evaluated against each other in an attempt to estimate which option is more likely. Even then, the fact that one option may be more likely than another does not ‘prove’ that it is actually the case. Instead, I will propose a way in which both options can be evaluated against each other. The results indicate that it seems highly likely that intelligent design was required for biological life.” PDF paper available here

An on line appeal for RD and PZ to make sacrifices in the interest of winning the “war on science”. Will they take the advice? “Richard and PZ, when it comes to Expelled, it’s time to let other people be the messengers for science. This is not about censoring your ideas and positions, but rather being smart, strategic, tactical, and ultimately effective in promoting science rather than your own personal ideology, books, or blog.” Go here.

The following is an edited extract from a Nature paper. It is an example of real ID research. Notice that the designers only used evolutionary techniques to very slightly tweak the enzymes scaffold structure that had been designed with “borrowed components” from existing enzymes tacked together.  The novel active site was completely intelligently designed. doi:10.1038/nature06879

Kemp elimination catalysts by computational enzyme design

“We designed eight enzymes with computationally designed active sites. In vitro evolution enhanced the computational designs, demonstrating the power of combining computational protein design with directed evolution for creating new enzymes.

Natural enzymes bind their substrates in a well-defined active site with precisely aligned catalytic residues to form highly active and selective catalysts for a wide range of chemical reactions. The design of stable enzymes with new catalytic activities is of great practical interest, with potential applications in biotechnology, biomedicine and industrial processes.

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Research led by Prof Frank Gannon has uncovered new revelations on possible ways to switch genes on and off and how cells interpret their DNA. Only some genes are expressed in any given tissue. Proteins active in nerve cells are not expressed in the liver. How this is controlled is complex. One fundamental factor is whether the DNA is tagged or modified (methylated) in the region of a gene. This is important in gene expression and balancing the level proteins in different cell lines. Although gene methylation (when a gene is turned on or turned off) was thought to be stable and unchangeable, this is not the case. Things are even more complicated than previously thought. Transient, cyclical and dynamic Read More ›

David Goldston (extensively edited) “Scientists tend to underestimate the public receptivity to science, and the battles ahead. Intelligent-design advocates try to sell their wares as science rather than religion partly as a legal gambit, but also because science and scientists are held in high esteem. Scientists do not face a public inherently hostile to science even among fundamentalists, and should address the public with respect rather than contempt. Although a remarkably high percentage of Americans do not believe that humans evolved from earlier life forms, it’s not clear whether this is just a casual way of saying they viscerally reject the notion of a random Universe. Evolution is largely a symbolic issue to the public, and may be a poor measure of how religious Read More ›

Prof Richard Dawkins is retiring from his position at Oxford. There is a search underway for the next Charles Simonyi Professorship in the Public Understanding of Science. Who would we at UD like to take up this position and why? http://www.admin.ox.ac.uk/fp/wd9-018.shtml