Critical Analysis of a Paper on Evolution by Frameshift Translation

Ohno’s 1984 Proceedings of the National Academy of Science paper put forward the hypothesis that frameshift mutations can create novel proteins and illustrated his claim with the supposed evolution of nylon eating bacteria. Several researchers cite Ohno’s 1984 paper favorably including Dennis Venema, Ken Miller and our very own Arlin Stoltzfus of TSZ. Unfortunately, Ohno’s 1984 hypothesis, as far as nylon eating bacteria, is dead wrong.

Here is another paper that also cited Ohno’s 1984 hypothesis favorably. This paper may or may not hold promise as it claims to have found 470 frameshift translations in the human genome.

Frequent appearance of novel protein-coding sequences by frameshift translation

Now, just going through the first few examples of framshifts in the paper, when I actually went to the NIH GenBank to look up the exmaples I got messages like this for the very first “example”

NCBI Reference Sequence: NM_207478.1 (click to see this obsolete version)

Record removed. NM_207478.1 was permanently suppressed because currently there is insufficient support for the transcript and the protein.

Continue reading

Promiscuous Domains and Motifs Are Better Explained by Common Design than Common Descent, (Sal’s module Hypothesis)

Dr. Winston Ewert put forward his module hypothesis, but I put forward an alternate module hypothesis at the domain and motif level of proteins. It is based actually on papers by evolutionists who have pointed out that the problem of “Promiscuous Domains” remains an unsolved problem in evolutionary biology.

When I put Promiscuous Domains on the table in the Common Design vs. Common Descent thread, the TSZ Darwinists ignored the problem and then declared victory. I viewed their non-response as evidence they didn’t understand the problem and/or preferred to ignore it.

Perhaps pictures are worth ten thousand words. From the NIH, that great source inspiration for the Intelligent Design community, we have the CDART database viewer.

From the CDART viewer, I provide a few of the thousands of diagrams that show the promiscuity of protein domains. The diagrams below show the classical zinc finger ZF-C2H2 “ZF” domain and the Plextrin Homology “PH” domains. Note how the location of domains is “shuffled” to different locations in different proteins. It’s as if proteins are made by different lego-like parts in different order and position. My preliminary look into small 4-amino acid motifs that are the target of phosphorylating kinases suggests the the problem of promiscuity goes all the way down to small motif levels.

Such promiscuity is more consistent with common design than common descent.
Continue reading

Carter, Lee, Sanford’s ICC 2018 Adam and Eve paper, Congratulations Bill Basener

Bill Basener (a participant here) co-authored a paper with John Sanford. He was given the honor of delivering a KEYNOTE ADDRESS at an international SECULAR biology conference. A video of his presentation is available in a link inside my write up of his presentation below. He alluded to some of the helpful input from his critics at TheSkepticalZone in his talk:

http://crev.info/2018/07/keynote-speech-falsifies-darwinism/

John Sanford is sort of the “Papa John” of creationist genetics. It is customary for the leader of a research group to be listed as the last author in a publication. That convention is seen in a variety of papers and books such as Rupe & Sanford; Basener & Sanford; Carter, Lee & Sanford; Montanyez, Fernandez, Marks & Sanford; and let’s not forget the Legendary High Velocity Team of Klein, Wolf, Wu & Sanford that permanently ensured the infusion of intelligently designed genes into a sizable fraction of Genetically Modified Organisms on planet Earth.

And perhaps one day in the distant future there will be a paper, “Cordova & Sanford”! 🙂

Below is a link of a paper from Papa John’s team about Adam and Eve which will be presented this week, July 29,2018 – August 1, 2018 at the 8th International Conference on Creationism

Continue reading

ICC 2018, mtDNA hetero and homoplasmy

In the link below are the abstracts with links to the papers presented at the International Conference on Creationism 2018 in Pittsburgh, PA July 29-August 1, 2018. Those presenting are professors at Christian colleges, professors already expelled from secular colleges, or professors at secular colleges who (by God’s grace) can’t be expelled. 🙂

http://www.creationicc.org/icc18_abstracts.php

A topic I will raise among the population geneticists there (John C. Sanford, Rob Carter, Nathaniel Jeanson, and others) is the issue of heteroplasmy in mtDNA as they are presenting on these topics.

Mature human cells have 100,000 to 600,000 mitochondrion. So how can a cell be mostly homoplasmic yet have mtDNA mutations that are reflected in lineages whereby an individual has a mostly homoplasmic mtDNA that enable us to identify the 7 daughters of Eve (to quote Oxford Geneticist Bryan Sykes).
Continue reading

Powerful Evidence of Natural Selection on Society

As a card carrying Creationist, the video link below is one of the best arguments for the influence of natural selection on society as argued by Professor Walter Block. It also echoes arguments by Jerry Coyne vs. PZ Myers:
When ideology trumps biology

In my earlier post I pointed out the pervasive biological evidence that in both humans and other species, the conditions for sexual selection hold—a greater variance in male than in female reproductive output—probably explaining why men are bigger and stronger than women, and have beards and other secondary sexual differences. It also explains why male peacocks have showy tails, why male sage grouse do “jumping displays” to attract females, why male insects have weapons and ornaments, and so on. (See my bullet-point list of biological facts in that post.) Further, though Bateman’s experiments were flawed, they have been repeated properly in other species and have shown that, yes, males in general have the potential to have many more offspring than females: a higher variance in offspring number). — Jerry Coyne

It explains why matriarchal societies are unlikely, the 4-sigma smartest people will be men, the number of mentally ill and homeless are men, and why heads of countries and corporations will tend to be men and societies that are not patriarchal will not compete as well as societies that are.

It’s also April 1 today.

NOTES:
Prof. Walter Block is a professor of economics. He currently holds the Harold E. Wirth Chair in Economics at the J. A. Butt School of Business at Loyola University New Orleans. He is a senior fellow of the Ludwig von Mises Institute in Auburn, Alabama.

Kondrashov’s Paper, Synergistic Epistasis, Soft Selection

Regarding Kondrashov’s paper Why have we not died 100 times over?, an internet “pupil” of mine who goes by the handle of “nomenmeum” asked what is synergistic epistasis and soft selection. The definition of synergistic epistasis seems to be the major issue as I don’t see the term much in literature. I don’t know exactly what it means. Does synergistic epistasis entail a change in S-coefficients?

For example in Brenda Andrews’ double and triple knockout experiments with yeast, the corresponding single knockout experiments had little-to-no noticeable effects, but several double and triple knockouts would clearly have deleterious effect when their component individual single knockouts did not in isolation.

Below is Brenda Andrews’ description of her experiment which I mentioned at Sandwalk in connection with the ENCODE 2015 planning meeting (Larry Moran knew Dr. Andrews as a graduate student at his school):
Continue reading

Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Continue reading

Invited responses to my nylonase research and the question of “New Proteins Without God’s Help”

Susumo Ohno (who coined the term “junkDNA”) published a paper in 1984 through the National Academy of Sciences that was used by the NCSE, Ken Miller and Dennis Venema to claim “proteins can evolve without God’s help”. At the request of John Sanford, a courtesy associate research professor at Cornell, I was recruited to write a paper to refute Ohno’s evolutionary hypothesis on nylonases. I wrote it under John’s guidance based on his intuitions about genetics, his life-long specialty of 40 years and for which he became famous as attested by the fact he is one of the few geneticists who had their work featured in the Smithsonian National Museum of American History.

The actual paper is now in review, but it is not intended to be published in any journal, but will be released in a variety of channels shortly. It is hoped the material can be used by others to actually create papers that enter peer review. The motivation for releasing the paper in this way is to counter Venema’s book while it is still hot off the press.
Continue reading

Working out a gentleman’s agreement between TSZ and my publishing activities

As much as the TSZ regulars may have sharp disagreement with many of my views, I actually have a vested interest in seeing TSZ survive and prosper and attract participation with talent and brains. TSZ is valuable because of the quality of the participants, namely, professors (like Joe Felsenstein, Jeff Shallit), textbook authors (like Larry Moran), specialists (Tom English, John Harshman, Mark Frank, Mike Elzinga, etc.), academics, practicing scientists, etc. I suspect JohnnyB and VJTorley might have comparable reasons for their participation at TSZ.

The purpose of me posting here is to see what sort of INFORMAL gentleman’s agreement can be worked out to the mutual benefit of TSZ and my publishing efforts.
Continue reading

For VJ Torley: Christianity’s consistency with Evolutionary Theory, JB Peterson’s Interview

Various creationists and ID proponents, myself included, have raved about the work of elite scholar and clinical psychologist Jordan B. Peterson who connected the rise of Christianity with concepts in evolutionary theory. His recent 2.5-hour interview was profound on many levels. I provide a link to the interview below.

Even though Peterson is an die-hard evolutionist, many ID proponents and creationists have said they were blessed to hear what he had to say. I know I was. Since I know VJ studied the topic of animal intelligence, I thought Peterson’s work might be of interest to him since Peterson ties the rise of Christianity to behavioral and neurological traits he sees deeply conserved in the mammalian kingdom.
Continue reading

My presentation at Lipscomb University in front of faculty and deans of several universities available for free online (expense for live attendance is $390)

Below is a link to a 22.5-minute video which is a rehearsed version of a speech (with power point and video and animation) to be delivered before several faculty and deans of various Christian Universities at the Christian Scholar’s Conference at Lipscomb University June 7, 2017.

My talk addresses the design of chromatin and the problem of evil.


Continue reading

When did nylon-eating proteins actually evolve the ability to eat nylon?

It has been widely advertised that nylon eating genes evolved after 1940. I have no problem with that claim in principle since new antibiotic and malaria resistances have evolved since 1940. Even though I can easily accept the possibility of post-1940 nylon-eating evolution in principle, where is the slam dunk evidence that this is actually the case? Did a significant portion of the ability for bacteria to digest nylon take place after 1940 (or 1935 when nylon was first created)?
Continue reading

Mind blowing presentation by George Church at the NIH

Last week, George Church talked at the school where I take part-time evening classes. I provide a link to that talk. He talked about re-engineered codons (something I’m grateful to Rumraket for introducing me to), stem cell research, human animal chimeras, aging therapies, human genome re-engineering, and just a little bit about ENCODE. Though I have ethical concerns about human/animal chimeras, and human genome re-engineering (like what happens if you mess up), Church goes into the technologies and raises questions as to what our world may look like in the not too distant future. Not that I’m trying to make a point about ID or God by linking this video, but it shows how rapidly we may be forced to deal with certain issues.

I personally don’t have too much problem with GMO foods. After all, my YEC friend John Sanford created the gene gun through which a large fraction of genetically engineered crops on the planet were made at one time. But one thing that bothers me is genetically engineered bacteria. Church discussed super bacteria created for research applications. I can imagine an accident where germs are created accidentally that become really hard to kill and we basically have an apocalypse. Maybe that will be the fulfillment of prophecy by Jesus, “there will be famines and pestilence”.

Here is the video (with Francis Collins speaking at the start):
https://videocast.nih.gov/summary.asp?Live=21803&bhcp=1

Here is a description of the talk:
Continue reading

Larry Moran’s Exit Exam

Attached is Larry Moran’s exit exam for biochemistry and molecular biology. Exit Exam for Biochemistry.

I probably will not get a lot of these right on the first try, but it is a good learning experience. When I don’t know the answer, I can look it up, so this is a good chance to review important concepts.

I will provide answers I think Professor Moran wants students to give, and then I’ll provide my own answers which I think he might dock points for if he were grading. I always try to give the answer the professor is expecting even if I disagree. It shows that I am trying to understanding of what he was trying to teach. It’s not a confession of belief on my part.

For example:

21.How much of your genome is functional?

Answer I think Larry is expecting:

10%, because of the limits mutational load imposes on a genome the size of a human’s and their reproductive excess. But even the 10% number is likely high since the Muller Limit of 1 mutation/person/generation might allow even less than 10% function for the human genome.

Continue reading

The Glories of Global Warming and the Faint Young Sun Paradox

It is a little known fact that scientists who argue that the paleontological record of life is hundreds of millions of years old, when confronted with astrophysical facts, must eventually rely heavily on the hypothesis of finely tuned, large scale global warming. The problem is known as the Faith Young Sun Paradox. A few claim they have solved the paradox, but many remain skeptical of the solutions. But one fact remains, it is an acknowledged scientific paradox. And beyond this paradox, the question of Solar System evolution on the whole has some theological implications.

Astrophysicists concluded that when the sun was young, it was not as bright as it is now. As the sun ages it creates more and more heat, eventually incinerating the Earth before the sun eventually burns out. This is due to the change in products and reactants in the nuclear fusion process that powers the sun. This nuclear evolution of the sun will drive the evolution of the solar system, unless Jesus returns…
Continue reading

Mouse Utopia, Mutational Meltdown, Extinction by Natural Selection

The National Institute of Mental Health (NIMH) of the National Institutes of Health (NIH) sponsored the work of John Calhoun on social behaviors. Here were the results of one of his experiments:

On July 9th, 1968, eight white mice were placed into a strange box at the National Institute of Health in Bethesda, Maryland. Maybe “box” isn’t the right word for it; the space was more like a room, known as Universe 25, about the size of a small storage unit. The mice themselves were bright and healthy, hand-picked from the institute’s breeding stock. They were given the run of the place, which had everything they might need: food, water, climate control, hundreds of nesting boxes to choose from, and a lush floor of shredded paper and ground corn cob.

This is a far cry from a wild mouse’s life—no cats, no traps, no long winters. It’s even better than your average lab mouse’s, which is constantly interrupted by white-coated humans with scalpels or syringes. The residents of Universe 25 were mostly left alone, save for one man who would peer at them from above, and his team of similarly interested assistants. They must have thought they were the luckiest mice in the world. They couldn’t have known the truth: that within a few years, they and their descendants would all be dead.
Continue reading

How Comfortable is Naturalism with Highly Atypical Events?

There are numerous definitions of naturalism. Here is one definition with some additional observations from infidels.org:

As defined by philosopher Paul Draper, naturalism is “the hypothesis that the natural world is a closed system” in the sense that “nothing that is not a part of the natural world affects it.” More simply, it is the denial of the existence of supernatural causes. In rejecting the reality of supernatural events, forces, or entities, naturalism is the antithesis of supernaturalism.
Continue reading

In Slight Defense of Granville Sewell: A. Lehninger, Larry Moran, L. Boltzmann

The basic biochemistry textbook I study from is Lehninger Prinicples of Biochemistry. It’s a well regarded college textbook. But there’s a minor problem regarding the book’s Granville-Sewell-like description of entropy:

The randomness or disorder of the components of a chemical system is expressed as entropy,

Nelson, David L.; Cox, Michael M.. Lehninger Principles of Biochemistry (Page 23). W.H. Freeman. Kindle Edition.

Gag!

And from the textbook written by our very own Larry Moran:

Continue reading