Uncommon Descent Serving The Intelligent Design Community

Many thanks to Gordon Davisson and Joe Felsenstein for review and criticism of my UD article

I previously highlighted the work of Jean Claude Perez in my Vodka! essay. I had encountered Perez work in my google searches related to the 3-base periodicity pattern in DNA. The 3-base pattern seems widely acknowledged in the literature as On the origin of three base periodicity in genomes. Genomes of almost all organisms have been found to exhibit several periodicities, the most prominent one is the three base periodicity. It is more pronounced in the gene coding regions and has been exploited to identify the segments of a genome that code for a protein. The reason for this three base periodicity in the gene-coding region has been attributed to inhomogeneous nucleotide compositions in the three codon positions. However, this Read More ›

Request for help verifying non-random 3mer pattern in Human Chromosome 1

3-base periodicity is a well-known non-random feature of the DNA. That is to say, a base will sometimes be repeated 3 nucleotides away. This should happen randomly at a frequency of about 25% if all the bases are equally represented, but I got something that was slightly away from random. 3-base periodicity is a well known pattern that seems to identify exonic regions. For lack of a better word, I use the word “3mer” whenever I encountered the same base 3 nucleotides away. 3mer is a term Dr. Sanford’s DNA Skittle uses, but I have to confer with him whether that is what he means. I tried to see how frequently A,T,C,G repeated every 3 bases. It seems the Adenenine Read More ›

No-one Knows the Mind of God . . . Except the Committed Atheist

Fair warning to the regular readership. Typically I like to cover intelligent design and evolution-related issues, but I trust I may be permitted a bit of a detour.  There have been a couple of interesting posts recently by Sal, vjtorley and Barry about issues of a more philosophical bent.  vjtorley’s OP, in particular, quoted parts of an essay from Professor Jerry Coyne.  I would like today to share some thoughts on point. With apologies to those not of the Judeo-Christian tradition, my comments will focus in part on the Bible, given that the Bible and the God of the Bible have been the brunt of many new atheist attacks recently, including Coyne’s.  Similar points, no doubt, could be made with Read More ›

Non Randomness of DNA as a whole

Stretches of DNA that code for proteins are considered non-random, but what about DNA as a whole? DNA Densely Packed without Knots “‘We’ve long known that on a small scale, DNA is a double helix…But if the double helix didn’t fold further, the genome in each cell would be two meters long. Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter…’ “The researchers report two striking findings. First, the human genome is organized into two separate compartments, keeping active genes separate and accessible while sequestering unused DNA in a denser storage compartment. Chromosomes snake in and out of the Read More ›

RNA, the origin of life and the gullibility of the science media

Yesterday, “News” brought readers a fascinating story about a report from Science Daily, titled, Reconstructed ancient ocean reveals secrets about the origin of life (25 April 2014), which was also picked up by Linda Geddes, writing for New Scientist. Reading the Science Daily article, I was struck by the extraordinary naivete of mainstream science reporters covering the origin-of-life issue. Consider the following excerpt, taken from the final two paragraphs: “In the presence of iron and other compounds found in the oceanic sediments, 29 metabolic-like chemical reactions were observed, including those that produce some of the essential chemicals of metabolism, for example precursors of the building blocks of proteins or RNA,” says [Dr. Markus] Ralser, [Group Leader at the Department of Read More ›