Category Archives: Evolution

Universal Common Descent Dilemma

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  1. Despite lack of observational basis, Darwin proposed Universal Common Descent (UCD) saying: “Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed“. He also said elsewhere (referring to UCD): “…the littlest creature (or four or five of them)…” With his remarks, Darwin left the door open to creation (“life was first breathed”), but since then, Neo-Darwinists have rejected creation and replaced it with belief in undirected abiogenesis while maintaining belief in UCD.

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

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

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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

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ICC 2018, mtDNA hetero and homoplasmy

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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).
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Does embryo development process require ID?

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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.

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How much Adam could an uneducated evangelical Adam if an uneducated evangelical could Adam Adam?

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For those interested in discussions of evolutionism, creationism, Intelligent Design as they impact science, philosophy and theology/worldview in society and education today, please find below a small piece of news.

In short, IDism isn’t really all that hard to counter. Most of you have done it here already countless times against IDists. As for me, I’m batting 100% against IDists in person and 99.5% against IDists online. Only Cameron Wybrow in Canada is the lone holdout. I have questions for every IDist that CSC’s John West would (not) ‘expel’ me for!

The DI is afraid of me because I saw it on the inside. But who could ever see the inside of quality, rigorous, ‘good science’ that is done ‘peacefully’, when there is no institutional centre currently available to hold such an abstract utopia, even better than IDism?

No, what is really difficult is to counter IDists who are actually TEists & ECists also at the same time. This combination is much more difficult than just arguing here with lowbrow IDists or mainly heterodox theists. And this, folks, is where you will find them: https://discourse.peacefulscience.org

Vincent J. Torley is already there and he has an offer to co-author his first scientific publication since his PhD with the site host. So it can’t be too hard to handle for TSZers since Vincent is now officially (yet?) a moderator at TSZ. So that’s a perfect introduction for you to show Peaceful Science what you think about their “Science of Adam.”

When the California-born & accented Dr. Swamidass gets the money, as he is already asking for at Peaceful Science, then let me assure the vast majority atheists here they had better be ready to buckle their belts in the North American “creation war” as Swamidass repeatedly calls it. Why? A recycled neologism known as “Genealogical Adam” is coming to a theatre near you & guess what: if your worldview doesn’t like it, then Swamidass cares. http://peacefulscience.org

Swamidass openly welcomes atheists at Peaceful Science. He even prefers them over thoughtful religious critics that don’t play ball his way, displaying why he was not long ago banned by Deborah Haarsma at BioLogos for refusing to bow to former BioLogos biology-lead and Haarsma’s current darling, Dennis Venema, who has blindly followed his Canadian counterpart Denis Lamoureux into becoming what Swamidass calls “no Adam Christians.” Let’s just say the evangelicals at BioLogos and Peaceful Science aren’t getting along right now and with the ASA meeting about to come up with “The Science of Adam” on the agenda, fireworks could result.

It’s almost as if ‘ideologically self-contradictory’ is something evangelical Protestants of the Swamidass, Venema, Lamoureux, BioLogos-variety deny they ever could be accused of themselves.

BioLogos banned Swamidass for claiming what IDist Ann Gauger did: “We could have come from two … A bottleneck of two [A&E] that is older than 500,000 years ago is possible … based on analysis of the genetic data”. What do the biological scientists here say about that?

So, Swamidass is busy preparing either a noble or an ignoble (depending on who you are) place in history by intentionally relativising Adam and Eve with Genealogical Adam. Will anyone ask him what his qualifications for becoming, finally in these previous @18 months, a ‘scientific genealogist’ as he is now claiming to be?

Go to this site, but ask him nicely. Atheists can be nice, good people about Adam and Eve most times too.

https://discourse.peacefulscience.org

Help the gliding snake grow wings

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Evolution “…is as much a fact as the heat of the sun…”– Richard Dawkins

Unfortunately, what evolution no doubt is missing to be such a fact is the actual proof that evolution can do what its supporters claim it has done and can do…
Simply pointing to a fully developed organism and saying – “evolution did” – is just as good a claim as saying – “God did it, or ID must have done it”- unless there is some kind of falsifiability for the claims…Otherwise, such claims remain in the realm of optimism bias, blind faith, or simply science-fiction…and give science bad name at the same time…

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The Death Evolution

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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…

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Does gpuccio’s argument that 500 bits of Functional Information implies Design work?

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On Uncommon Descent, poster gpuccio has been discussing “functional information”. Most of gpuccio’s argument is a conventional “islands of function” argument. Not being very knowledgeable about biochemistry, I’ll happily leave that argument to others.

But I have been intrigued by gpuccio’s use of Functional Information, in particular gpuccio’s assertion that if we observe 500 bits of it, that this is a reliable indicator of Design, as here, about at the 11th sentence of point (a):

… the idea is that if we observe any object that exhibits complex functional information (for example, more than 500 bits of functional information ) for an explicitly defined function (whatever it is) we can safely infer design.

I wonder how this general method works. As far as I can see, it doesn’t work. There would be seem to be three possible ways of arguing for it, and in the end; two don’t work and one is just plain silly. Which of these is the basis for gpuccio’s statement? Let’s investigate …

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Human Evolution debunked

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  1. What separates humans from other organisms, and by how much? Dexterity (opposable thumb), Lifespan, Sociability, Speech, Bipedalism, Hairlessness, Body Size, and Diet, all separate humans from others, but none is more important and more off the chart than our Intelligence. And from these gifts, humans developed even more abilities; some natural like thick fur on demand, flight, excellent sensors, and powerful actuators; while others completely new like handling fire, writing, and life in the outer space. Continue reading →

NAS admits it, evolution was a good joke

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NAS president, April Furst, said today that evolution was a very good joke, but it’s gone on long enough. She stated, “It was an incredible setup, over a century and a half of teaching and ‘research’ into evolutionary theory, but we were waiting until people began to catch on to finally admit the joke. But with UD, and stellar minds like Kairosfocus, blowing our cover, we thought it was time to have a good laugh at the idea of Darwinism.”

There were some protests. Gull Able asked, well, what of the tree of life, why do organisms group into clades as they do? April responded, it’s a clear case of design for the sake of our ability to categorize and understand organisms. What order would you expect from the Designer, anyway? Something like the periodic table?”

Charl Atan tweeted April Furst, asking, “So who made the apparent transitionals, like Archaeopteryx and the various hominin fossils like Homo erctus?” Furst responded, “Haven’t you heard of prototypes?” Cen Sor said, “You were paid not to admit this secret. And anyway, why are later organisms made of strangely modified earlier parts and organs, like bat wings made out of mammalian hands?” April Furst was not abashed in the least, saying, “We were always going to admit the evolution hoax someday. And the Designer just happens to be a strong traditionalist, reworking organs incessantly while making little entirely new. The Designer wants kinds to be recognizable, after all.”

So there you have it, the evolutionary hoax is entirely exposed now. Have a good laugh, and get over it.

Kondrashov’s Paper, Synergistic Epistasis, Soft Selection

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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):
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Rejoinder to Basener and Sanford’s reply, part I

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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 →

Dark DNA and the New Mechanism of Evolution?

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Here is an article on the issue of Dark DNA.

Dark DNA got its name from the cosmological phenomenon called Dark Matter – the undetectable 25% of the mass of the universe that scientists know exists because they can detect its effects…

Similarly Dark DNA has eluded the sequencing of the genomes and yet scientists know it must exist because they see its effects, such as in case of the sand rat…

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Defending the validity and significance of the new theorem “Fundamental Theorem of Natural Selection With Mutations, Part II: Our Mutation-Selection Model

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Defending the validity and significance of the new theorem “Fundamental Theorem of Natural Selection With Mutations, Part II: Our Mutation-Selection Model

– Bill Basener and John Sanford

Joe Felsenstein and Michael Lynch (JF and ML) wrote a blog post, “Does Basener and Sanford’s model of mutation vs selection show that deleterious mutations are unstoppable?”  Their post is thoughtful and we are glad to continue the dialogue. We previously wrote a first part of a response to their post, focusing on the impact of R. A. Fisher’s work.  This is the second part of our response, focusing on the modelling and mathematics.  Our paper can be found at: https://link.springer.com/article/10.1007/s00285-017-1190-x Continue reading →

Natural Selection – Evolution Magic

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Natural Selection is described as “the differential survival and reproduction of individuals due to differences in phenotype”. To this, some add “blind, mindless, and purposeless environmental process” that nonetheless is imagined turning random genetic mutations into superior new features enhancing descendants’ survivability (fitness). Accumulation of these features supposedly turns one lifeform into another over time. Natural Selection seeks to explain the appearance of design in nature without appealing to a designer. Continue reading →

Defending the validity and significance of the new theorem “Fundamental Theorem of Natural Selection With Mutations, Part I: Fisher’s Impact

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– Bill Basener and John Sanford

 

Joe Felsenstein and Michael Lynch (JF and ML) wrote a blog post, “Does Basener and Sanford’s model of mutation vs selection show that deleterious mutations are unstoppable?”  Their post is thoughtful and we are glad to continue the dialogue. This is the first part of a response to their post, focusing on the impact of R. A. Fisher’s work.  Our paper can be found at: https://link.springer.com/article/10.1007/s00285-017-1190-x

First, a short background on our paper:

The primary thesis of our paper is that Fisher was wrong, in a fundamental way, in his belief that his theorem (“The Fundamental Theorem of Natural Selection”), implied the certainty of ongoing fitness increase. His claim was that mutations continually provide variance, and selection turns the variance into fitness increase.  Central to his logic was that collectively; mutations have a net zero effect on fitness.  While Fisher assumed mutations are collectively fitness-neutral, it is now known that the vast majority of mutations are deleterious. So mutations can potentially push fitness down – even in the presence of selection. Continue reading →