The Genetic Code: Expected Before it was Found

IDists often act as though there is something surprising about the DNA code. A recent post at UD highlights a letter from Crick containing the line “Now we believe that the D.N.A. is a code.” The typical implication is that somehow it came as a surprise that DNA would involve a code.

But there was nothing new about such an idea. Indeed, what is difficult is to imagine how genetic information could be held without being coded. In 1943, a decade before DNA’s structure was revealed, Erwin Schrodinger explained how a code would work in life, writing:

THE VARIETY OF CONTENTS COMPRESSED IN THE MINIATURE CODE

It has often been asked how this tiny speck of material, nucleus of the fertilized egg, could contain an elaborate code-script involving all the future development of the organism. A well ordered association of atoms, endowed with sufficient resistivity to keep its order permanently, appears to be the only conceivable material structure that offers a variety of possible (‘isomeric’) arrangements, sufficiently large to embody a complicated system of ‘determinations’ within a small spatial boundary

Page 21 of the pdf What is Life?

Indeed, and DNA fits quite well with that description. In addition, the linear nature of the DNA code allows for a straightforward geometry for producing transcripts and eventual translation of DNA information. The fact that Crick underscores “is” before “a code” appears to be nothing but recognition that what had been predicted is what was actually discovered, a genetic code.

Of course Schrodinger, like Crick and Watson, had no doubt that life had evolved. To be sure, this does nothing to demonstrate that DNA did evolve or any such thing, just that while the IDists simply assume that a code must be designed, people who lacked their biases merely considered how a genetic code was functional within life. The DNA code is just something that well fits the requirement for compact information storage and provides for a straightforward output of that information into proteins, RNA, and other needed molecules.

The evolution of the genetic code may well involve certain affinities between RNA and amino acids, and thus may not be entirely arbitrary in its origins, but that is a subject beyond the scope of this short post. The point at present is merely that one should not be hung up on the word “code” as if that means anything about its origins, for the fact is simply that it stores and puts out information in a manner that functions well for life. The term “code” denotes something important about DNA’s function, but not about its origin.

Evolutionary Informatics catches modelers doing modeling

As Tom English and others have discussed previously, there was a book published last year called Introduction to Evolutionary Informatics, the authors of which are Marks, Dembski, and Ewert.

The main point of the book is stated as:

Indeed, all current models of evolution require information from an external designer to work.

(The “external designer” they are talking about is the modeler who created the model.)

Another way they state their position:

We show repeatedly that the proposed models all require inclusion of significant knowledge about the problem being solved.

Somehow, they think it needs to be shown that modelers put information and knowledge into their models. This displays a fundamental misunderstanding of models and modeling.

It is a simple fact that a model of any kind, in its entirety, comes from a modeler. Any information in the model, however one defines information, is put in the model by the modeler. All structures and behaviors of any model are results of modeling decisions made by the modeler. Models are the modelers’ conceptions of reality. It is expected that modelers will add the best information they think they have in order to make their models realistic. Why wouldn’t they? For people who actually build and use models, like engineers and scientists, the main issue is realism.

To see a good presentation on the fundamentals of modeling, I recommend the videos and handbooks available free online from the Society for Industrial and Applied Mathematics (SIAM.) “[Link]”.

For a good discussion on what it really means for a model to “work,” I recommend a paper called “Concepts of Model Verification and Validation”, which was put out by the Los Alamos Laboratories.

Ubiquitin: a challenge for evolutionary theory?

Glancing at Uncommon Descent (I still do as Denyse O’Leary often reports on interesting science articles, as here*, and the odd comment thread can still provide entertainment), I see an OP authored by gpuccio (an Italian medical doctor) entitled The Ubiquitin System: Functional Complexity and Semiosis joined together, telling the story of the ubiquitin protein and its central role in eukaryote biochemistry in some considerable detail. 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.

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

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

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

– 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

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

The Search Problem of William Dembski, Winston Ewert, and Robert Marks

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.1

Search is a central term in the work of Dr. Dr. William Dembski jr, Dr. Winston Ewert, and Dr. Robert Marks II (DEM): it appears in the title of a couple of papers written by at least two of the authors, and it is mentioned hundreds of times in their textbook “Introduction to Evolutionary Informatics“. Strangely – and in difference from the other central term information, it is not defined in this textbook, and neither is search problem or search algorithm. Luckily, dozens of examples of searches are given. I took a closer look to find out what DEM see as the search problem in the “Introduction to Evolutionary Informatics” and how their model differs from those used by other mathematicians and scientists.
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To Basener and Sanford: This is the 21st Century

What is The Skeptical Zone, William Basener and John Sanford? Why should you care?

The Skeptical Zone is where a couple of distinguished biologists, Joe Felsenstein and Michael Lynch, have dignified a recently published article of yours with a response. That is all you need to know. If they had responded on the back of a cereal box instead, providing you with a form to clip, then it would have behooved you to clip the form, fill it out, and send it, along with a self-addressed, stamped envelope, to their post office box in Battle Creek, Michigan.

Of course, I am dating myself — and also you. That is just the point. You ought to know that, even as the computer enables studies that were impossible when Ronald Fisher dubbed a not-so-fundamental result of his the Fundamental Theorem of Natural Selection, it enables interaction with domain experts in ways that were impossible in Fisher’s time. We are well into the 21st Century, and no one under the age of 50 will find credible any reason you might offer for declining to engage Joe in this forum. You can ignore all of the riff-raff, myself included, and interact with the scientist who happened, about the time that your paper addressing Fisher’s theorem was published, to address the theorem in the 37th Fisher Memorial Lecture (via video link, I might add).

The prospects for resolving some points, and arriving at a degree of agreement, are much better in a modern exchange of comments than in an old-fashioned exchange of essays. One aspect of The Skeptical Zone makes it particularly appealing in discussion of mathematical models: you can enter stuff like \LaTeX between two dollar signs, and cause readers to see stuff like \LaTeX. It’s a miracle!

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.
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The Mystery of Evolution: 10. Falsifying the Evolution-The Experiment #1

I have promised that I will try to falsify the evolutionary theory by performing some simple experiments, as many of Darwin’s faithful on this blog have been really reluctant to do or even to suggest such an experiment…

However, one video was posted on TSZ suggesting that such an experiment has already been performed by Biologist Ken Dial in a study of how young birds use their developing wings that is supposed shed light on the evolution of flight in birds.

The Origin of Flight–What Use is Half a Wing? | HHMI BioInteractive Video


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A Problem to Solve

Evolution is often presented as problem-solving. Genetic algorithms are often offered as proofs of evolution’s ability to solve problems. Genetic algorithms are as search algorithms.

As one book says:

Fundamentally, all evolutionary algorithms can be viewed as search algorithms which search through a set of possible solutions looking for the best – or “fittest” – solution.

Tom has asked me to specify a problem independently from the evolutionary process. Now I have to admit that I don’t really understand what that means. But I like Tom and I have a lot of respect for him, so I want to give it my best shot and see where it takes us. I’m also hoping this will shed some light on claims about how problem-solving genetic algorithms are designed to solve a particular problem.

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The Mystery of Evolution: 9. I Origins by Richard Dawkins

Bumping around for millions of years without sight is not a problems for Richard Dawkins…Why would it be for evolution?

Question: Do not  ALL (systems involved in seeing and processing image) have to be working (fully functional) for the eye to receive and process vision? (or something like that)

Answer Richard Dawkins: It is a bit a fallacy because 1/4 of an eye or a100th of an eye is better than nothing…

Please watch the video as my keyboard can’t handle the rest of this Dawkins’ nonsense…

 

!8 mysteries to go…

The Mystery of Evolution: 8. Common Descent-The Tree of Life or a Bush? An Orchard?

Special Update!!!

It turns out that professor Larry Moran of the University of Toronto agrees with Craig Venter. Thanks to Allan Miller, I discovered a blog on a similar theme at sandawalk link here 

This is what professor Moran says about the video (his video is 42 min long):

” Everything that Ventor says is correct. He didn’t need to quibble about the universality of the genetic code but it’s true that there are variants.”

“I’m pretty sure that Dawkins doesn’t agree (in reference to video) with those who question whether there’s a tree of life. One of the most profound implications of the net of life is that it’s consistent with several independent origins of life that preceded the rise of a modern genetic code and contributed to existing species. In other words, there may not be a single LUCA (Last Universal Common Ancestor). Dawkins does not like that. It’s not what he says on the lecture circuit.” (my emphasis)


There is probably no one in the world of biology today as respected as Craig Venter.

Why?

Well, his achievements are indeed great including being involved with sequencing the human genome and assembled the first team to transfect a cell with a synthetic chromosome, which some even went as far as calling the creation of artificial life…

Now apparently, he is involved in the anti-aging research…no surprise here…he is 70 and would like reach immortality like the jellyfish…Who can blame him…He is an atheist…

However, his also known for what some would call radical statements such as denying the common descent which is the very foundation of evolutionary theory…

“Common descent describes how, in evolutionary biology, a group of organisms share a most recent common ancestor. Common ancestry between organisms of different species apparently arises during speciation, in which new species are established from a single ancestral population. Organisms which share a more recent common ancestor are apparently closely related.” –Wiki

The apparent common descent of all organisms on earth doesn’t agree with Craig Venter’s research… Continue reading

Arrival of the Fittest – keiths style

I tire of keiths and his revisionist history. In a recent thread…

Glen: The real question is if Mung has read and comprehended Losos’ book.

keiths: Yes, which brings to mind what happened with Andreas Wagner’s book, Arrival of the Fittest. Mung was blathering about how it was an ID-friendly book, which is nonsense.

keiths:

I challenged him:

Mung,

Alan’s review barely touches on what I think are the most important ideas in the book: those concerning the “libraries”, the “networks”, and the extent to which the networks extend across the libraries.

How about summarizing those ideas for us in your own words? That will serve the dual purpose of 1) filling a gap in Alan’s review and 2) demonstrating that you actually understand what Wagner is saying.

Having summarized those ideas, if you still don’t (or pretend not to) understand the implications for ID, I’ll help you out.

And:

Think of it as being similar to an ideological Turing test. I’d like to see if you even bothered, or were able, to understand the book before dismissing it as no threat to ID.

keiths: To no one’s surprise, Mung squirmed, stalled, and then skedaddled.

Here’s what actually happened:

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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?

The Mystery of Evolution: 7. Falsifying the Evolution-The Prelude to Something Greater

UPDATE: So far NO IDEAS as to how the theory of evolution can be falsified have been proposed…To make things worst, nobody so far picked up any of MY SUGGESTED IDEAS how to falsify evolution – now clearly numbered from 1-4. 

It makes one wonder what the bases are for believing in the theory of evolution if no one seems to even want to at least try to falsify it…

Please keep in mind that by falsifying evolution you can refute many claims by the proponents of ID!!! Isn’t it what Darwin’s faithful want to do?

This OP is just a prelude to hopefully many future ones, where I would like to focus on the specific examples of how to falsify the theory of evolution…

This OP gives everyone an opportunity for the input on no doubt the many available ways how to experimentally falsify evolution…

As most of you know, Darwinists and post-Darwinists, for unknown reasons, are reluctant to experimentally prove their beliefs, so by the series of the OPs on the many possible ways of falsifying evolution, we can hopefully encourage Darwinists and the like, to do so for their own good… I could definitely help with that…

Here are some ideas on how to falsify evolution that I have come across so far:

How a walking mammal can evolve into an aquatic one?

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The Mysteries of Evolution: 6. Endosymbiosis-The second miracle of life after the origin of life

This is one of the most fundamental mysteries of evolution and the origins of multicellular life often called endosymbiosis, which is supposed to explain the origin of eukaryotic cell.

It doesn’t!  Here is why…

What I found perplexing, or even disturbing, is that although it is presented as scientific fact of evolution, as evolution itself often is, there is absolutely not one fact to support that endosybiosis happened or could have happened…

And this the fact…

How could that be?

First of all, the difference between prokaryotic and eukaryotic cell is so staggering that even proposing such quantum leap in evolutionary change goes beyond macroevolutionary claim…

Here are some facts: Continue reading