Monthly Archives: August 2018

Critical Analysis of a Paper on Evolution by Frameshift Translation

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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.

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Peaceful Science has eclipsed Uncommon Descent. How will that impact TSZ’s reason to be?

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The original mission of TSZ, as intended by the U.K.’s Dr. Elizabeth Liddle, who promoted the site to apostate peers & ‘skeptics,’ often at anti-religious online forums, lists & discussion boards, has passed its due date. She & they (many of the early people who joined) shared the experience in common of being ‘expelled’ (banned) from the IDist blog Uncommon Descent (UD) & to have their own sandbox to critique UD was the main mission of TSZ. There was no ‘inspirational’ core that Liddle offered upon departure from her own site, but returning to it in November to talk mainly about UD again could only be a fool’s errand.

My argument here is that UD is by now pretty much outdated. UD is generally seen as oddball &/or gutter-level IDist discussion, far adrift from serious conversation on the topic. It is shrinking in relevance now year on year. It thus isn’t really worth ‘reporting’ on or ‘opposing’ UD at TSZ anymore, though that IDist site was the early focus of TSZ & what brought many (most) of the early participants together. Is UD really worth time for ‘skeptics’ nowadays?

More importantly, the new blog Peaceful Science (PS) has recently surpassed BioLogos in terms of daily & hourly regular traffic & far outreaches the topics that UD used to breach. It has actual scientists, elderly or retired ‘science & religion/worldview’ people who contribute often a LOT, woolly protestants & ‘unitarian’ (or maybe just one who posts as much as 5 people), pedantic ‘natural theologians’, & S. Joshua Swamidass actually just called one person a ‘prophet’ as a welcome greeting. PS even ‘welcomes’ atheists (Swamidass has made it a point to defend Freedom From Religion Foundation proponent who is a self-described ‘militant atheist’ against multiple Christians) & agnostics & patiently fields all legitimate ‘scientific’ questions. Are you skeptical of ‘Peaceful Science’ and a ‘Science of Adam’ as proclaimed by quasi-creationists, ideology-starved geneticists & fence-sitting ‘reformers’?

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Adam, Eve and Nephilim bottleneck-The theistic solution

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Most readers of TSZ are probably familiar with the ongoing debate about the supposed genomic evidence that makes it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals, Adam and Eve, as per Abrahamic beliefs…

The population genetics assumption is that Adam and Eve could NOT have been the only two contributors to the human pool of genes. The supporters of evolution and experts in population genetics say that the evidence points to at least 10 000 individuals  and therefore the biblical description of the act of creation of a pair of two humans must be wrong and therefore the theory of evolution must be right… something like that…

Most of readers are probably familiar with population genetics pros and cons. I could contribute a few of my own, such as: What is the evidence that mutation rate observed in humans today equals the mutation rate (if any) of Adam and Eve after they sinned or after the bottleneck of Noah +7 people? It is obviously assumed… This is  a typical example how ideology drives so-called science or how it pollutes it. However, this is not the main point of my OP.

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Forbidden Archaeology

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Many years ago Michael Cremo and Richard L. Thompson wrote a book entitled Forbidden Archaeology. Cremo discusses it here

They claim that humans in their modern anatomical form have existed for millions of years and that “knowledge filtration” occurs where the evidence supporting the dominant theories of the time pass through with ease whereas contradictory evidence is filtered out.

An NBC broadcast narrated by Charlton Heston based on the book can be viewed here

At the end of an interview given in the making of the film, Thompson had this to say:

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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.

    2. Continue reading →

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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What has TSZ accomplished? 7 years and counting

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I have recently realized that The Skeptical Zone blog has had its 7th year anniversary…
Since Dr. Liddle has return, at least temporarily, I thought it could be a great opportunity to evaluate what the goal of TSZ was, when it opened for business over 7 years ago, and whether such goal(s) have been accomplished, if any…

Here is what Dr. Liddle’s mission statement was in the introductory web page:

” My name is Elizabeth Liddle, and I started this site to be a place where people could discuss controversial positions about life, the universe and everything with minimal tribal rancour (pay no attention to the penguins….) Continue reading →

Is Peaceful Science carefully (enough) scripting its politicking with the Freedom From Religion Foundation?

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What role does the Freedom from Religion Foundation play in the evolution, creation and intelligent design conversation?

I ask for feedback on this here because it would seem that one of the main ‘partnerships’ at what Dr. S. Joshua Swamidass calls ‘Peaceful Science’ (his description is scientistically utopian, but let’s leave that aside), appears to be mainly a politically convenient one between Dr. Swamidass and an atheist named Patrick, who is a representative for the Freedom From Religion Foundation. If was difficult to figure this out because as a non-USAmerican citizen, that organisation is off my national radar. Continue reading →

Squawk box

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I sense a disturbance in the force.

This thread is for people to tell me what they think is going on, going wrong, and what they think we should do about it.  I’m listening.

Lizzie

[Edit added 18.40 pm CET 20/08/2018 by Alan Fox]

As the comments have ballooned, Lizzie would very much like members to summarize their thoughts and suggestions into one statement and there is now a dedicated thread, “Summaries”, where they can be posted. Please just post one summary and please do not add other comments. You are welcome to comment on other people’s summaries in this thread. The idea of the “Summaries” thread is to make it easier for Lizzie to get your input. Comments judged by admins not to be summaries will move to guano.

Members who would rather keep their thoughts confidential are invited to use the private messaging system. Lizzie’s address is Elizabeth.

This post violates site rules

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Statement from administrator team:  This post is in violation of site rules, that we should discuss the message, not the poster of the message.

In the interest of transparency, we are making the post public.  We want to be clear that the administrator team does not agree with the accusations made in the post.  Our initial reaction was to make the post private, to give us time to review the situation.  We are now making it public again, but comments are closed for this topic.  If the original author of this post requests that we make it private once again, that will be considered.

We have kept Elizabeth informed of what we are doing.  And she has given one brief email response, which I am taking as tacit approval of our initial reaction.

Neil Rickert.

Original title: Swamidass caught lying at PeacefulScience.org

If you need some entertainment, here’s a story that follows a familiar Uncommon Descent plot line:

Charlatan lies; charlatan gets caught; charlatan digs the hole deeper; gets caught some more; and charlatan, in desperation, finally bans the messenger.

In this case the charlatan is Joshua Swamidass, the blog is PeacefulScience.org, and the ban is for a week, not permanent. But it’s basically the same old UD story.

It starts here. I hope the comments don’t get deleted. Given the recent censorship kerfuffle there, Swamidass will be feeling pressure not to delete them. But the evidence is pretty damning, and it will be painful for him to leave them in place. We’ll see what happens.