‘Junk DNA’

There are many “Neutral Theorists” who maintain that there is a lot of “junk-DNA,” among which long, non-coding DNA=lncDNA is some of the “junkiest.” But now consider this from Wikipedia: Nevertheless, despite low conservation of long ncRNAs in general, it should be noted that many long ncRNAs still contain strongly conserved elements. For example, 19% of highly conserved phastCons elements occur in known introns, and another 32% in unannotated regions (Siepel 2005). Furthermore, a representative set of human long ncRNAs exhibit small, yet significant, reductions in substitution and insertion/deletion rates indicative of purifying selection that conserve the integrity of the transcript at the levels of sequence, promoter and splicing (Ponjavic 2007). If lncDNA is ‘junk’, then according to ‘neutral theory’ Read More ›

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 ›

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 ›

Jean Claude Perez is a self-organizational theorist, he is not a creationist. He has also published papers with an occasional visitor to UD, Andras Pellionisz. If the mathematical/musical patterns Perez has found in DNA are improbable relative to laws of physics and chemistry, then he may have found yet another design feature of DNA, and this feature is found by combining coding DNA with non-coding DNA and viewing it holistically. Here is the simplest explanation I found of his work: When cells replicate, they count the total number of letters in the DNA strand of the daughter cell. If the letter counts don’t match certain exact ratios, the cell knows that an error has been made. So it abandons the Read More ›

Can designs be selectively neutral and even deleterious but still functional? Yes. As Allen Orr said: selection can wreck their exquisite engineering just as surely as it built it. An optic nerve with little or no eye is most assuredly not the sort of design one expects on an engineer’s blueprint, but we find it in Gammarus minus. Whether or not this kind of evolution is common, it betrays the fundamental error in thinking of selection as trading in the currency of Design. Actually, Orr made a mistake, selection can’t build exquisite engineering design, but it can wreck it! In a rare moment of honesty, from the most recent Wiki version of Genetic Redundancy, we read how genes can be Read More ›