Chemistry Nobel for “directed evolution” (2018)

  1. Very nice. Congratulations! But where is the “directed evolution” oxymoron in this story? The process used is simple organism breeding as done by mankind for thousands of years, in this case sped up by advanced technologies. “Random mutations” are not entirely random as the mutations desired had to converge towards a clear, specified target. Random generator devices also generate within specific ranges, say 0 to 9, rejecting outright any “randomness” outside that range (‘a’, ‘#’, ‘21’ will all be rejected). “Natural selection” is also missing as the selection has been clearly done by qualified researches pursuing a specific goal. At best this would be called “artificial selection”, but even that is misleading since organism breeding is a human activity that goes well beyond simple ‘selection’.
  2. Continue reading

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

Does embryo development process require ID?

Jonathan Wells, who is an embryologist and an ID advocate, has a very interesting paper and video on the issue of ontogeny (embryo development)  and  the origins of information needed in the process of cell differentiation…

Wells thinks that a major piece of information needed in the process of embryo development can’t be explained by DNA,  and therefore may require an intervention of an outside source of information, such as ID/God…

If you don’t want to watch the whole video, starting at about 40 min mark is just as good but especially at 43 min.

Continue reading

The Death Evolution

Death has been on everyone’s mind at one time or another… It’s unavoidable…
Some are fascinated by death; mainly  the possibility of better afterlife. Some, or the great majority of people, are frightened by it. It seems the unknown of after-death is one of the main factors causing many to tremble…

However, it turns out that Craig Venter, the pioneer of  the human genome project and the supposed creator of artificial life, turned his attention and efforts toward decoding death… here

It seems obvious Venter believes that death is be caused by genetics; some genetic mutations that could be fixed and we could live forever, otherwise he wouldn’t be digging in the genome looking to fix the death code…

Continue reading

2. Earth is the Center of the Universe? Full Movie

This is a follow up to Earth is the Center of the Universe? OP with the link to the full documentary entitled The Principle. It is really worth to watch it in its entirety just to get the sense of how cosmologist, like Lawrence Krauss, and many other scientists deliberately resist the data  (verified by 3 different probes) that Axis of Evil are pointing to the special location of the Earth in the Universe…

Continue reading

Felsenstein presents the 37th Fisher Memorial Lecture

Joe Felsenstein, who posts and comments in The Skeptical Zone, presented the 37th Fisher Memorial Lecture on January 4, 2018. The video recording of his lecture is now available. I’d say that the cover frame, at the very least, was well worth the wait.

Rooting out confusion is much harder than sowing it

Excuse me for attaching to this post a brief rejoinder to a pathetic response to the lecture. Andrew Jones’s “The Law of Zero Magic” appeared in the flagship publication of the intelligent design (ID) movement, Evolution News & Science Today. The title is hugely ironic, inasmuch as the movement conceives of intelligent design as violation of a law of nature, and struggles to devise the law that is violated. Continue reading

Rejoinder to Basener and Sanford’s reply, part I

William Basener and John Sanford have responded here to my post concerning whether R.A. Fisher’s Fundamental Theorem of Natural Selection is critical to work on the theoretical population genetics of the interaction between mutation and natural selection. (This reply by Basener and Sanford is also reposted here.) Continue reading

What is the evidence for “purposeful intervention”?

FMM: Purposeful intervention is pretty much the opposite of random mutation.

FMM notes in the same comment:

 If there in nothing about an idea that distinguishes it from it’s alternative it seems to be superfluous.

So the idea is “non designed mutations” and the alternative is “purposeful intervention”.

Give that, and given FMM has not discarded the idea of purposeful intervention there must be something that distinguishes it from non designed mutations.

What is that distinguishing factor? What is the actual evidence for “purposeful intervention” regarding mutations?

And, more broadly, what is the evidence for “purposeful intervention” in any area of biology? Apart from, of course, wishful thinking.

1. Evolution or Design? Duons

Have you ever tried writing palindromes? How about writing phrases that can be read the same way in either direction? Here are some examples:
A man, a plan, a canal: Panama
Live not on evil
Was it a car or a cat I saw
These sentences were no doubt designed…
Can you imagine writing a book that can be read forwards and backwards containing 2 different stories that made sense? Not an easy task…

Watch the video and pay special attention to the following examples:

  1. Alternative splicing of RNA that produces multiple proteins from one gene
  2. Duons – Overlapping sequences that code for both protein expression and transcription factor binding sites simultaneously
  3. Dual coding genes in which one sequence is read in multiple frames to produce completely different protein

Continue reading

Does all of evolutionary theory rest on Fisher’s Fundamental Theorem?

The blogs of creationists and ID advocates have been buzzing with the news that a new paper by William Basener and John Sanford, in Journal of Mathematical Biology, shows that natural selection will not lead to the increase of fitness. Some of the blog reports will be found here, here, here, here, here, and here. Sal Cordova has been quoting the paper at length in a comment here.

Basener and Sanford argue that the Fundamental Theorem of Natural Selection, put forward by R.A. Fisher in his book The Genetical Theory of Natural Selection in 1930, was the main foundation of the Modern Evolutionary Synthesis of the 1930s and 1940s. And that when mutation is added to the evolutionary forces modeled by that theorem, it can be shown that fitnesses typically decline rather than increase. They argue that Fisher expected increase of fitness to be typical (they call this Fisher’s Theorem”).

I’m going to argue here that this is a wrong reading of the history of theoretical population genetics and of the history of the Modern Synthesis. In a separate post, in a few days at Panda’s Thumb, I will argue that Basener and Sanford’s computer simulation has a fatal flaw that makes its behavior quite atypical of evolutionary processes.

Continue reading

Purpose and Desire

Purpose and Desire: What Makes Something “Alive” and Why Modern Darwinism Has Failed to Explain It is the new book by physiologist J. Scott Turner, author of The Tinkerer’s Accomplice: How Design Emerges from Life Itself.

The book may make some “skeptics” uncomfortable, but maybe they should read it anyways.

From the book:

I have come to believe that there is something presently wrong with how we scientists think about life, its existence, its origins, and its evolution.

Without a coherent theory of life, whatever we think about life doesn’t hold water. This applies to the major contribution we claim that the modern science of life offers to the popular culture: Darwinism.

… there sits at the heart of modern Darwinism an unresolved tautology that undermines its validity.

… do we have a coherent theory of evolution? The firmly settled answer to this question is supposed to be “yes” …

I intend to argue in this book that the answer to my question might actually be “no.”

Continue reading

The Mystery of Evolution: One Down

My kids just informed me that they have seen an okapi evolving, or transitioning into a zebra

Okapi’s stripes appear to be no doubt the same as zebra’s…

Zebra, Equus quagga, Masai Mara Reserve, Kenya : Stock Photo

Well, at least we have one example of species transitioning into another…out of 10 billion and this one looks like a stunner….

I have to run!

I’ll fill in the rest when I get back…

Update!

It turns out that okapi is considered to be more closely related to giraffe than to zebra…if at all…That is surprising…because okapi and zebra do look alike just okapi is missing some stripes…No wonder my kids fell for it…as did some experts…

“…The okapi and the giraffe were assigned to the same order (Artiodactyla) because they both have cloven hooves, and to the same family (Giraffidae) because they share certain distinctive features: Both have large eyes and ears, thin lips and a long, extensible tongue that allows them to lick their entire face (even the ears); their backs slope upward from rump to withers; they also share the same dental formula: ( i 0/3, c 0/1, pm 3/3, m 3/3) × 3 = 32. Both, unlike any other mammal, have molars with rugose enamel and bony horns that remain covered with skin throughout life (Nowak 1999, vol. 2, p. 1085).

Yet the rump and legs of an okapi are covered with black-and-white stripes exactly like those of a zebra. Perhaps, then, if okapis had solid hooves instead of cloven ones, they would be classified as perissodactyls (Order Perissodactyla) and would be considered more closely related to zebras than to giraffes. An okapi is about the same size as a Burchell’s zebra.

The chromosome count of an okapi is also like that of a zebra, to which it is not supposed to be related, and unlike that of a giraffe. Giraffes have 30 chromosomes (Taylor et al. 1967; Hösli and Lang 1970; Koulisher et al. 1971), whereas okapis have a variable chromosome number of 44-46, depending on the animal in question; most seem to have 2n = 45 (Ulbrich and Schmitt 1969; Hösli and Lang 1970; Koulisher 1978). The chromosome number of Grevy’s zebra is 2n = 46 and plains zebras have 2n = 44 (Benirschke and Malouf 1967). Variation in chromosome count is itself unusual among mammals, but common in hybrids…”

The 14-16 chromosome difference between giraffe and okapi is striking isn’t it?

Improbable Destinies

Improbable Destinies: Fate, Chance, and the Future of Evolution

I love books like this. Pure wonder about the living world. The beauty. The mystery. Shattering the myths of Darwinism while still clinging desperately to them.

We learn that Darwinism has retarded evolutionary thought for at least a century because the picture that Darwin gave us (which his disciples followed for over a hundred years) was false. Evolution can be tested. It can be observed within human lifetimes. It doesn’t require the infinitesimal insensible aggregations over millenia previously thought. Evolution can be really really fast. Which ought to be good news for young earth creationists.

We also learn that the oft-heard claim that degree of similarity implies degree of relatedness is false. That some species A looks very much like some species B doesn’t at all mean that they are more closely related than some other species which is visibly different.

Another nail in the coffin.

Continue reading