Felsenstein presents the 37th Fisher Memorial Lecture

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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

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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

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

Biological Information

  1. ‘Information’, ‘data’ and ‘media’ are distinct concepts. Media is the mechanical support for data and can be any material including DNA and RNA in biology. Data is the symbols that carry information and are stored and transmitted on the media. ACGT nucleotides forming strands of DNA are biologic data. Information is an entity that answers a question and is represented by data encoded on a particular media. Information is always created by an intelligent agent and used by the same or another intelligent agent. Interpreting the data to extract information requires a deciphering key such as a language. For example, proteins are made of amino acids selected based on a translation table (the deciphering key) from nucleotides.
  2. Continue reading

Human Evolution debunked

 

  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

The Joe G Memorial Math Problem

Regular readers of TSZ will remember the hilarity that ensued when former commenter JoeG grappled unsuccessfully with the cardinality (loosely, the size) of various infinite sets. In honor of that amusing episode, I’m posing a new problem involving an infinite set.

Here’s the problem:

Consider the set containing every real number that can be described using a finite number of English words. For example, “thirty-three” and “two point eight” obviously qualify as members of the set, but also “pi minus six”, “the cube root of e”, and “Zero Mostel’s age in years on July seventh, nineteen sixty-three”, all of which designate specific real numbers. The set is infinite, of course.

Prove that the set of all such numbers takes up exactly zero percent of the real number line.

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.

A dubious argument for panpsychism

At Aeon, philosopher Philip Goff argues for panpsychism:

Panpsychism is crazy, but it’s also most probably true

It’s a short essay that only takes a couple of minutes to read.

Goff’s argument is pretty weak, in my opinion, and it boils down to an appeal to Occam’s Razor:

I maintain that there is a powerful simplicity argument in favour of panpsychism…

In fact, the only thing we know about the intrinsic nature of matter is that some of it – the stuff in brains – involves experience… The theoretical imperative to form as simple and unified a view as is consistent with the data leads us quite straightforwardly in the direction of panpsychism.

…the brains of organisms are coloured in with experience. How to colour in the rest? The most elegant, simple, sensible option is to colour in the rest of the world with the same pen.

Panpsychism is crazy. But it is also highly likely to be true.

I think Goff is misapplying Occam’s Razor here, but I’ll save my detailed criticisms for the comment thread.

NAS admits it, evolution was a good joke

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.

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.

Testing the claim that intentional mutations can be differentiated from nonintentional mutations

fifthmonarchyman has helpfully explained how we can detect intention for specific mutations:

No, I have suggested that humans are hardwired to infer that intentional things are non-random and non-algorithmic.

Therefore directly intentional mutations would be differentiated from those that would be categorized as nonintentional by this property.

Given that statement, I hope that fifthmonarchyman can give a demonstration of how to determine if specific mutations are directed or not.

So, fifthmonarchyman, can you walk us through the process of how you perform that differentiation? Or will you admit that this claim cannot be grounded in reality and that you nor anyone else cannot perform any such differentiation?

I can give some examples of fully sequenced mutations in human populations if that would be useful fifth? Or pick your own, it really does not matter as it’s more about the process then the specific mutation.

 

Feser’s fourth proof and the mystery of existence

If the Aristotelian argument for a purely actual Being (which I critiqued in my previous post) is the backbone of Feser’s five proofs of God’s existence, the Thomistic proof is the beating heart, as it gets to the very core of what God is: Pure Existence itself, according to philosophy Professor Edward Feser. Today, I’m going to argue that this notion of God is utterly nonsensical. But it is not merely the argument’s conclusion which is flawed: the Thomistic proof also rests on shaky foundations, as the real distinction it posits between a finite thing’s essence and its existence is a highly dubious one: the main argument cited in support of it actually points to a matter-form distinction, instead. The second argument for a real distinction between a thing’s essence and its existence establishes nothing of the sort: all it shows is that whatever causes a thing to have existence also causes the nature or essence of that thing. A third argument for the essence-existence distinction illicitly assumes that the term “existence” names a single perfection, which is inherently simple and unlimited.

In addition, Feser’s Thomistic proof trades on an equivocation between the notion of a Being whose essence is identical to its own existence and that of a Being whose essence is Pure Existence – an equivocation which is grounded in the background metaphysical assumption that the concept of “existence” is a simple and unlimited one. In reality, as I shall explain below, the concept of “existence” is neither simple nor complex, neither limited nor unlimited, but rather, indefinite – which is one reason why the attempt to characterize God as Pure Existence, or Being itself, is doomed at the outset. Finally, any attempt to construe God as some sort of activity – whether it be Pure Existence, Pure Actuality, or Thought thinking Itself, or Love loving Himself – is radically mistaken, either because it reifies an abstraction (Existence exists, Actuality acts) or because it generates an infinite regress (Love loves love loves love…). In plain English: We need to think of God first and foremost as a noun, and not merely as a verb – in other words, as an Agent, rather than simply as an unlimited act of thought or love or “be-ing.”

Despite its flawed conception of God, Feser’s Thomistic proof is not without its merits: Continue reading

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.

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

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

Moral Judgment and Moral Standards

Consider the following argument:

1. One would be rationally entitled to make moral judgments about the institutions and practices of cultures distant from us in space or time only if one had reliable epistemic access to some transcendent (culture-independent) moral standard against which such institutions and practices could be evaluated.
2. But no one has reliable epistemic access to a transcendent, culture-independent moral standard.
3. Therefore, no one is rationally entitled to make moral judgments about the institutions and practices of cultures distant from us in space or time.


Continue reading

Dark DNA and the New Mechanism of Evolution?

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…

Continue reading

Why do Christians get banned at UD?

It looks like I just got banned at UD, which to me it means I have been noticed by “true Christians”, like Barry Arrington, who has proven, time and time again, that he deserves what he stands for…

I know that Sal got banned there too and he is a Christian..

What should we do? Should  we abandon uncommondescent.com all together?

Many have…  Who is left other then the few and the same style of comments appearing regularly?