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 →
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 →
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 →
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 →
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:
Alternative splicing of RNA that produces multiple proteins from one gene
Duons – Overlapping sequences that code for both protein expression and transcription factor binding sites simultaneously
Dual coding genes in which one sequence is read in multiple frames to produce completely different protein
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 It’s a miracle!
The blogs of creationists and advocates of ID have been abuzz lately about exciting new work by William Basener and John Sanford. In a peer-reviewed paper at Journal of Mathematical Biology, they have presented a mathematical model of mutation and natural selection in a haploid population, and they find in one realistic case that natural selection is unable to prevent the continual decline of fitness. This is presented as correcting R.A. Fisher’s 1930 “Fundamental Theorem of Natural Selection”, which they argue is the basis for all subsequent theory in population genetics. The blog postings on that will be found here, here, here, here, here, here, and here.
One of us (JF) has argued at The Skeptical Zone that they have misread the literature on population genetics. The theory of mutation and natural selection developed during the 1920s, was relatively fully developed before Fisher’s 1930 book. Fisher’s FTNS has been difficult to understand, and subsequent work has not depended on it. But that still leaves us with the issue of whether the B and S simulations show some startling behavior, with deleterious mutations seemingly unable to be prevented from continually rising in frequency. Let’s take a closer look at their simulations.
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.
Congratulations to our resident theoretical biologist of high renown, Joe Felsenstein, on his presentation, yesterday, of the 37th Fisher Memorial Lecture. [ETA: I’ll post a separate announcement of the video, when it is released.] Following are the details provided by the Fisher Memorial Trust (with a link added by me).
Title: Is there a more fundamental theorem of natural selection?
Abstract. R.A. Fisher’s Fundamental Theorem of Natural Selection has intrigued evolutionary biologists, who wondered whether it could be the basis of a general maximum principle for mean fitness of the population. Subsequent work by Warren Ewens, Anthony Edwards, and George Price showed that a reasonable version of the FTNS is true, but only if the quantity being increased by natural selection is not the mean fitness of the population but a more indirectly defined quantity. That leaves us in an unsatisfactory state. In spite of Fisher’s assertion that the theorem “hold[s] the supreme position among the biological sciences”, the Fundamental Theorem is, alas, not-so-fundamental. There is also the problem that the additive genetic variances involved do not change in an easily predictable way. Nevertheless, the FTNS is an early, and imaginative, attempt at formulating macro-scale laws from population-genetic principles. I will not attempt to revive the FTNS, but instead am trying to extend a 1978 model of mine, put forth in what may be my least-cited paper. This attempts to make a “toy” model of an evolving population in which we can bookkeep energy flows through an evolving population, and derive a long-term prediction for change of the energy content of the system. It may be possible to connect these predictions to the rate of increase of the adaptive information (the “specified information”) embodied in the genetic information in the organisms. The models are somewhat absurdly oversimple, but I argue that models like this at least can give us some results, which decades of more handwavy papers on the general connection between evolution, entropy, and information have not.
Darwinism is incomplete because it only takes account of matter and ignores spirit.
Evolution is a process of matter ascending and spirit descending. It is a process whereby physical substance goes through process that prepares it to accommodate the descending spirit. The continuity of living matter is sustained by hereditary and it takes on various forms due to adaptive radiation. But these forces come from the earth and they tie organisms to the environment and lead only to specialization. They take organisms down ever narrowing paths. The fossil record is a tableau of forms that are frozen in their specializations, evolutionary dead ends. These earthly forces radiate from the centre.
The spiritual forces work in the opposite direction drawing the living substance outwards, emancipating it from the earthly forces. Through these forces organisms separate out from the earth as a plant grows towards the sun. Emancipation is evident in such things as inner temperature control, freeing of the upper limbs to perform creative functions rather than them being used for locomotion or support and taking responsibility for care of offspring.
It is only in the human form that the self-conscious ego can occupy physical substance as a material individual. This is the place on earth where matter and spirit meet. In as much as each of us know ourselves, we know the spirit within. And this is only possible because our form has been prepared in such a way that it can accommodate our ego, the spirit within.
Darwin’s conforming of his theory to the old vera causa ideal shows that the theory of natural selection is probabilistic not because it introduces a probabilistic law or principle, but because it invokes a probabilistic cause, natural selection, definable as nonfortuitous differential reproduction of hereditary variants.
There is a pretty interesting discussion going on in Noyau regarding the many definitions of “fitness” in evolutionary biology. It would be a shame for it to be lost in that particular venue here at TSZ. At the risk of being censored by the admins for posting too many OPs in one month I thought I’d start this thread.
Here’s my take so far:
Allan Miller was charged by phoodoo with resorting to different definitions of fitness. Allan denied the charge and when asked for a definition of fitness Allan provided one. Allan later stated that his definition only properly applied to asexual species.
Others chimed in to say that the definition of fitness depends on the context, which hardly seems to contradict what phoodoo was saying.
My own position is that fitness has its definition within a particular mathematical framework. My position is also that fitness can be defined generically but that such a definition is tautological. Special definitions of fitness are required to make the concept testable.
Here’s hoping we can move the discussion about fitness out of Noyau.
I received my copy of Theistic Evolution today. The book contains three chapters dedicated to skepticism of universal common ancestry. As common descent seems to be a hot topic here lately I thought I’d read those chapters first and offer comments and invite responses.
I’ll start with Chapter 12, authored by Paul Nelson, which carries the title: Five Questions Everyone Should Ask about Common Descent. The five questions are as follows:
1. If species were not connected by common descent, how would we know it?
2. What were the actual transformation pathways, satisfying the continuity rule, which connect all organisms to LUCA?
3. Have we genuinely tested UCD, or merely assumed its truth?
4. When explaining the history of life, have we assumed methodological naturalism only, or have we allowed for the possibility of intelligent design?
5. In the light of intelligent design as a causal possibility, what histories for life on earth might be the case?
As usual, I don’t expect anyone else here to actually read this book because, you know, it just isn’t skeptical enough.
Because evolution proves that God does not exist. Except when it doesn’t.
In June 2004, the science historian Frank Sulloway and I began a month-long expedition to retrace Charles Darwin’s footsteps in the Galápagos Islands. It turned out to be one of the most physically grueling experiences of my life…
– Shermer, Michael. Why Darwin Matters: The Case Against Intelligent Design.
Just like taking a pilgrimage. All hail Darwin.
Any other Darwin worshipers here who have taken the Darwin pilgrimage?
What motivated you to try to retrace the footsteps of your master?
High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory.