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 ›

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 ›

Vodka! Jean Claude Perez, the golden ratio, dragon curve fractals and musical design in “junk DNA”

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 ›

Self-study science programs for IDists, organic chemistry

At the school where I received my Master of Science degree in Applied Physics, the basic undergraduate cost was $61,000 per year. Thankfully I wasn’t an undergrad there! I remember during commencement, I thought to myself as each undergrad crossed the stage to receive their diploma, “another quarter million dollars for academia.” I could go back and take formal classes to learn more science, but at this point it would only be for indulging in the joys of science, not advancing my occupation in financial management. To me, science is the study of God’s work. If I thought the universe and life were accidents, the product of a random number generator, I’d probably not be interested in studying it any Read More ›

Evolutionary convergence saves creationist hypothesis over GULO

When similarities cannot be explained by common descent, evolutionists will plead “convergence” (some mysterious coincidental occurrence to explain similarity). Well what is good for the goose is good for the gander. Creationists are now realizing if evolutionists can claim convergence, so can creationists! Evidence of Evolutionary Discontinuity and Genetic Entropy AbstractModern genomics provides the ability to screen the DNA of a wide variety of organisms to scrutinize broken metabolic pathways. This wealth of data has revealed wide-spread genetic entropy in human and other genomes. Loss of the vitamin C pathway due to deletions in the GULO (L-gulonolactone oxidase) gene has been detected in humans, apes, guinea pigs, bats, mice, rats, pigs, and passerine birds. Contrary to the popularized claims of Read More ›

Professor goes Ape at UConn over sign “Evolution is a Lie”, then preaches a pantheist revival

[youtube UpYDaCS0G94#t=136] Christian evangelist Don Karns of Hampton, Virginia, said Boster approached him as he was holding a sign about evolution, mocked him, and then became confrontational. “He asked me if I had accepted Darwin as my lord and savior,” Karns said. “He was very agitated, very demonstrative… it was very unbecoming of a professor.” Within minutes, Boster, who began teaching at UConn in 1997, also began to openly mock campus tour coordinator Scott Smith of Schoolmaster Ministries of Raleigh, North Carolina, as he preached. “As I was pointing to Christ—I was talking about the sin nature—I said, ‘There’s probably some people out there—maybe even professors—who think they descended from monkeys,’” Smith stated. “[Boster] jumped off the ground and came Read More ›

Can designs be functional but selectively neutral or deleterious?

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 ›

AP GfK poll, more non-Darwinists than Darwinists

Here are the numbers for extremely or very confident in the following positions from March 2014 poll by AP GfK Darwinism: 31% non-Darwinism: 42% Earth 4.5 billion: 27% Earth NOT 4.5 billion years old: 36% Anthropogenic global warming: 33% non-Anthropogenic global warming: 37% Big Bang: 21% non-Big Bang: 51% Universe so Complex there must be a creator: 54% Not (Universe so Complex there must be a creator): 25% HT JoeCoder reddit.com/r/creation

If most molecular evolution is non-Darwinian, how can codon bias and duon codes evolve?

Most molecular evolution is neutral. Done. PZ Myers From wiki: Codon usage bias Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (triplets) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons). There are 64 different codons (61 codons encoding for amino acids plus 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. Different organisms often show particular preferences for one Read More ›

Cost of maintenance and construction of design, neutral theory supports ID and/or creation

Most of biological ID literature is focused on Irreducible Complexity and Specified Complexity (Specified Improbability) and information theory, no free lunch, critique of OOL, the Cambrian explosion, etc, But there is another line of argument that is devastating to the claims of mindless evolution that has been underappreciated partly because it is highly technical, and in many cases most biologists will not even learn it in detail, namely that most molecular evolution is non-Darwinian. Here is the simplest way to understand why evolution is mostly non-Darwinian. The ability to select for or against a trait involves the cost of sacrificing individual lives. When we spend money we have a limited budget to buy things. From our budget we can select Read More ›

Why fixation in gigantic but widely separated human populations doesn’t happen

If there was any time the human population was very small, fixation was likely inevitable as discussed in Neutral Evolution for Newbies, Part 2. The time for required for fixation in a population according to standard population genetics is approximately 4 Ne, where Ne is the effective population size.

For example, for an Ne of six individuals, the approximate time to fixation using this approximation is:

4 x 6 = 24 generations

In 24 generations, assuming they don’t die from inbreeding depression, everyone will be pretty much genetically identical according to standard theory. Even if their differences were huge (maybe millions of nucleotides), they should fix in 24 generations using this approximation.

In contrast consider the current human population of 7 Billion, and suppose the effective reproductively viable population is 1.5 billion. Using the approximation, the time to fixation with Ne = 1.5 billion is

4 x 1,500,000,000 = 6 billion generations
Read More ›

A prediction I made in 2006 is coming to fruition

I wrote here in 2006 that the Designer of life has put steganography (hidden messages in DNA) to help scientists understand DNA. The steganography cannot have emerged via selection or neutral evolution, it is just there, it is a design feature. We typically call them “conserved” sequences, but I’ve argued that “conserved” is the wrong term on empirical and theoretical grounds in Larry almost get’s it right. The prediction I made was at some point biotechnology industry will make money studying the steganography, they could care less about the phylogeny. They have done this unwittingly, but done it they have. Who is making money off of the Designer’s steganography? The ENCODE consortium, they’ve made 288 million dollars because of the Read More ›