Category Archives: Life Sciences

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 →

What is the evidence for “purposeful intervention”?

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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

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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

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

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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.

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Purpose and Desire

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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.”

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The Mystery of Evolution: One Down

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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

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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 →

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

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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 →

Invited responses to my nylonase research and the question of “New Proteins Without God’s Help”

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Susumo Ohno (who coined the term “junkDNA”) published a paper in 1984 through the National Academy of Sciences that was used by the NCSE, Ken Miller and Dennis Venema to claim “proteins can evolve without God’s help”. At the request of John Sanford, a courtesy associate research professor at Cornell, I was recruited to write a paper to refute Ohno’s evolutionary hypothesis on nylonases. I wrote it under John’s guidance based on his intuitions about genetics, his life-long specialty of 40 years and for which he became famous as attested by the fact he is one of the few geneticists who had their work featured in the Smithsonian National Museum of American History.

The actual paper is now in review, but it is not intended to be published in any journal, but will be released in a variety of channels shortly. It is hoped the material can be used by others to actually create papers that enter peer review. The motivation for releasing the paper in this way is to counter Venema’s book while it is still hot off the press.
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The embarrassing “science” of the origins of life: The missing piece of evidence that persuaded scientists to believe in abiogenesis

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What comes to your mind when you hear or read the word science? To most the word science correlates with fact, proof or  even truth.

In my countless debates over the years with scientist and supporters of the origins of life (OOL) or evolution, I’ve often asked the question what convinced them so strongly about something, like abiogenesis. The answers I often got would be:

“…I believe it,  because I believe in science…”

Is it really science? 

No doubt to many, whether scientists or not, the word science is often paralleled with trustworthiness, credibility, reliability, soundness and even authority and influence.

”If something is dubbed as “science”, you’d better believe!” – many would say.

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When did nylon-eating proteins actually evolve the ability to eat nylon?

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It has been widely advertised that nylon eating genes evolved after 1940. I have no problem with that claim in principle since new antibiotic and malaria resistances have evolved since 1940. Even though I can easily accept the possibility of post-1940 nylon-eating evolution in principle, where is the slam dunk evidence that this is actually the case? Did a significant portion of the ability for bacteria to digest nylon take place after 1940 (or 1935 when nylon was first created)?
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The Arrival of the Fittest: a book review

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Andreas Wagner’s book,The Arrival of the Fittest has been mentioned many times (just try a site search as I’ve just done) since it was published. Petrushka pointed it out in a comment

For anyone interested in whether RMNS can create stuff, I recommend a relatively new book, Arrival of the Fittest. I just bought the Kindle version an haven’t finished, but it has a lot to say about how goldilocks mutations occur.

Much later Mung writes:

Reminds me of petrushka, who is always plugging Andreas Wagner’s Arrival of the Fittest, but will never post an OP on it for discussion.

So I’ve taken the hint and bought the book at last. I can see why people have recommended it. Continue reading →

Mind blowing presentation by George Church at the NIH

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Last week, George Church talked at the school where I take part-time evening classes. I provide a link to that talk. He talked about re-engineered codons (something I’m grateful to Rumraket for introducing me to), stem cell research, human animal chimeras, aging therapies, human genome re-engineering, and just a little bit about ENCODE. Though I have ethical concerns about human/animal chimeras, and human genome re-engineering (like what happens if you mess up), Church goes into the technologies and raises questions as to what our world may look like in the not too distant future. Not that I’m trying to make a point about ID or God by linking this video, but it shows how rapidly we may be forced to deal with certain issues.

I personally don’t have too much problem with GMO foods. After all, my YEC friend John Sanford created the gene gun through which a large fraction of genetically engineered crops on the planet were made at one time. But one thing that bothers me is genetically engineered bacteria. Church discussed super bacteria created for research applications. I can imagine an accident where germs are created accidentally that become really hard to kill and we basically have an apocalypse. Maybe that will be the fulfillment of prophecy by Jesus, “there will be famines and pestilence”.

Here is the video (with Francis Collins speaking at the start):
https://videocast.nih.gov/summary.asp?Live=21803&bhcp=1

Here is a description of the talk:
Continue reading →

Larry Moran’s Exit Exam

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Attached is Larry Moran’s exit exam for biochemistry and molecular biology. Exit Exam for Biochemistry.

I probably will not get a lot of these right on the first try, but it is a good learning experience. When I don’t know the answer, I can look it up, so this is a good chance to review important concepts.

I will provide answers I think Professor Moran wants students to give, and then I’ll provide my own answers which I think he might dock points for if he were grading. I always try to give the answer the professor is expecting even if I disagree. It shows that I am trying to understanding of what he was trying to teach. It’s not a confession of belief on my part.

For example:

21.How much of your genome is functional?

Answer I think Larry is expecting:

10%, because of the limits mutational load imposes on a genome the size of a human’s and their reproductive excess. But even the 10% number is likely high since the Muller Limit of 1 mutation/person/generation might allow even less than 10% function for the human genome.

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The Glories of Global Warming and the Faint Young Sun Paradox

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It is a little known fact that scientists who argue that the paleontological record of life is hundreds of millions of years old, when confronted with astrophysical facts, must eventually rely heavily on the hypothesis of finely tuned, large scale global warming. The problem is known as the Faith Young Sun Paradox. A few claim they have solved the paradox, but many remain skeptical of the solutions. But one fact remains, it is an acknowledged scientific paradox. And beyond this paradox, the question of Solar System evolution on the whole has some theological implications.

Astrophysicists concluded that when the sun was young, it was not as bright as it is now. As the sun ages it creates more and more heat, eventually incinerating the Earth before the sun eventually burns out. This is due to the change in products and reactants in the nuclear fusion process that powers the sun. This nuclear evolution of the sun will drive the evolution of the solar system, unless Jesus returns…
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Mouse Utopia, Mutational Meltdown, Extinction by Natural Selection

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The National Institute of Mental Health (NIMH) of the National Institutes of Health (NIH) sponsored the work of John Calhoun on social behaviors. Here were the results of one of his experiments:

On July 9th, 1968, eight white mice were placed into a strange box at the National Institute of Health in Bethesda, Maryland. Maybe “box” isn’t the right word for it; the space was more like a room, known as Universe 25, about the size of a small storage unit. The mice themselves were bright and healthy, hand-picked from the institute’s breeding stock. They were given the run of the place, which had everything they might need: food, water, climate control, hundreds of nesting boxes to choose from, and a lush floor of shredded paper and ground corn cob.

This is a far cry from a wild mouse’s life—no cats, no traps, no long winters. It’s even better than your average lab mouse’s, which is constantly interrupted by white-coated humans with scalpels or syringes. The residents of Universe 25 were mostly left alone, save for one man who would peer at them from above, and his team of similarly interested assistants. They must have thought they were the luckiest mice in the world. They couldn’t have known the truth: that within a few years, they and their descendants would all be dead.
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