Wednesday, January 17, 2018

A “Mathematical Proof of Darwinian Evolution” Is Falsified
January 5, 2018, 1:12 AM

Due to the tradition of professional scientific writing, major developments in scientific literature often arrive muffled in language so bland or technical as to be totally missed by a general reader. This, along with the media’s habit of covering up for evolution, is how large cracks in the foundation of Darwinism spread unnoticed by the public, which goes on assuming that the science is all settled and will ever remain so.
A case in point is a recent article in the Journal of Mathematical Biology, a significant peer-reviewed publication from the influential publisher Springer. The title of the article announces, “The fundamental theorem of natural selection with mutations.”
Including a verb would, presumably, be too much of a concession to populist sensationalism. Yet the conclusion, if not sensational, is certainly noteworthy.
Generations of students of biology and evolution have learned of the pioneering work of Ronald A. Fisher (1890-1962). A founder of modern statistics and population genetics, he published his famous fundamental theorem of natural selection in 1930, laying one of the cornerstones of neo-Darwinism by linking Mendelian genetics with natural selection. Wikipedia summarizes, “[T]his contributed to the revival of Darwinism in the early 20th century revision of the theory of evolution known as the modern synthesis.”
Fisher’s theorem, offered as what amounts to a “mathematical proof that Darwinian evolution is inevitable,” now stands as falsified.
His idea is relatively easy to state. It goes:
The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time.
His proof of this was not a standard mathematical one; fitness is not rigorously defined, and his argument is more intuitive than anything else. The theorem addresses only the effects of natural selection. Fisher did not directly address any other effect (mutation, genetic drift, environmental change, etc.) as he considered them to be insignificant. Later mathematicians took issue with Fisher’s lack of rigor, some at considerable length. But the omission of the effects of mutation got the most attention.
Now along come mathematician William F. Basener and geneticist John C. Sanford who propose an expansion of the fundamental theorem to include mutations. Basener is a professor at the Rochester Institute of Technology and a visiting scholar at the University of Virginia’s Data Science Institute. Sanford is a plant geneticist who was an associate professor at Cornell University for many years. He is an editor of the volume Biological Information: New Perspectives (World Scientific, 2013).  The Journal of Mathematical Biology is the official publication of the European Society for Mathematical and Theoretical Biology.
Basener and Sanford expand the Fisher model to allow both beneficial and deleterious mutations, following and extending earlier work. They use zero mutation levels to test their model’s agreement with Fisher’s. They establish that there is an equilibrium fitness level where selection balances the mutational effects. However, if mutations at biologically plausible levels are used, overall fitness is compromised. In some cases this leads to “mutational meltdown,” where the effect of accumulated mutations overwhelms the population’s ability to reproduce, resulting in extinction.
Extinction is the opposite of evolution. They conclude:
We have re-examined Fisher’s fundamental theorem of natural selection, focusing on the role of new mutations and consequent implications for real biological populations. Fisher’s primary thesis was that genetic variation and natural selection work together in a fundamental way that ensures that natural populations will always increase in fitness. Fisher considered his theorem to essentially be a mathematical proof of Darwinian evolution, and he likened it to a natural law. Our analysis shows that Fisher’s primary thesis (universal and continuous fitness increase) is not correct. This is because he did not include new mutations as part of his mathematical formulation, and because his informal corollary rested upon an assumption that is now known to be false.
We have shown that Fisher’s Theorem, as formally defined by Fisher himself, is actually antithetical to his general thesis. Apart from new mutations, Fisher’s Theorem simply optimizes pre-existing allelic fitness variance leading to stasis. Fisher realized he needed newly arising mutations for his theorem to support his thesis, but he did not incorporate mutations into his mathematical model. Fisher only accounted for new mutations using informal thought experiments. In order to analyze Fisher’s Theorem we found it necessary to define the informal mutational element of his work as Fisher’s Corollary, which was never actually proven. We show that while Fisher’s Theorem is true, his Corollary is false.
In this paper we have derived an improved mutation–selection model that builds upon the foundational model of Fisher, as well as on other post-Fisher models. We have proven a new theorem that is an extension of Fisher’s fundamental theorem of natural selection. This new theorem enables the incorporation of newly arising mutations into Fisher’s Theorem. We refer to this expanded theorem as “The fundamental theorem of natural selection with mutations”.
After we re-formulated Fisher’s model, allowing for dynamical analysis and permitting the incorporation of newly arising mutations, we subsequently did a series of dynamical simulations involving large but finite populations. We tested the following variables over time: (a) populations without new mutations; (b) populations with mutations that have a symmetrical distribution of fitness effects; and (c) populations with mutations that have a more realistic distribution of mutational effects (with most mutations being deleterious). Our simulations show that; (a) apart from new mutations, the population rapidly moves toward stasis; (b) with symmetrical mutations, the population undergoes rapid and continuous fitness increase; and (c) with a more realistic distribution of mutations the population often undergoes perpetual fitness decline.
Is this unfair to a historical figure? What about models developed after Fisher?
In the light of Fisher’s work, and the problems associated with it, we also examined post-Fisher models of the mutation–selection process. In the case of infinite population models, what has commonly been observed is that populations routinely go to equilibrium or a limit set — such as a periodic orbit. They do not show perpetual increase or decline in fitness, but are restricted from either behavior because of the model structure (an infinite population with mutations only occurring between pre-existing genetic varieties). On a practical level, all biological populations are finite. In the case of finite population models, the focus has been upon measuring mutation accumulation, as affected by selection. Finite models clearly show that natural populations can either increase or decrease in fitness, depending on many variables. Not only do other finite mathematical population models show that fitness can decrease — they often show that only a narrow range of parameters can actually prevent fitness decline. This is consistent with very many numerical simulation experiments, numerous mutation accumulation experiments, and observations where biological systems have either a high mutation rate or a small population size. Even when large populations are modeled, very slightly deleterious mutations (VSDMs), can theoretically lead to continuous fitness decline.
The final blow comes wrapped in compliments:
Fisher was unquestionably one of the greatest mathematicians of the twentieth century. His fundamental theorem of natural selection was an enormous step forward, in that for the first time he linked natural selection with Mendelian genetics, which paved the way for the development of the field of population genetics. However, Fisher’s theorem was incomplete in that it did not allow for the incorporation of new mutations. In addition, Fisher’s corollary was seriously flawed in that it assumed that mutations have a net fitness effect that is essentially neutral. Our re-formulation of Fisher’s Theorem has effectively completed and corrected the theorem, such that it can now reflect biological reality.
What they mean to say is stated most bluntly earlier in the article:
Because the premise underlying Fisher’s corollary is now recognized to be entirely wrong, Fisher’s corollary is falsified. Consequently, Fisher’s belief that he had developed a mathematical proof that fitness must always increase is also falsified.
That’s the “biological reality.” Fisher’s work is generally understood to mean that natural selection leads to increased fitness. While this is true taken by itself, mutation and other factors can and do reduce the average fitness of a population. According to Basener and Sanford, at real levels of mutation, Fisher’s original theorem, understood to be a mathematical proof that Darwinian evolution is inevitable, is overthrown.
Kudos to Basener and Sanford for making this important point. Now, will the textbooks and the online encyclopedia articles take note?
Photo: Ronald A. Fisher, via Wikicommons.

Wednesday, January 3, 2018

#8 of Our Top Stories of 2017: Theorist Concedes, Evolution “Avoids” Questions
At this past November’s Royal Society meeting, “New Trends in Evolutionary Biology,” the distinguished Austrian evolutionary theorist Gerd B. Müller gave the first presentation. As we’ve noted before, it was a devastating one for anyone who wants to think that, on the great questions of biological origins, orthodox evolutionary theory has got it all figured out. Instead, Müller pointed to gaping “explanatory deficits” in the theory. Now the Royal Society’s journal Interface Focus offers a special issue collecting articles based on talks from the conference.
Let’s see what Dr. Müller has to say in an article titled, “Why an extended evolutionary synthesis is necessary.” A friend highlights the following paragraph, with his own emphasis added.
As can be noted from the listed principles, current evolutionary theory is predominantly oriented towards a genetic explanation of variation, and, except for some minor semantic modifications, this has not changed over the past seven or eight decades. Whatever lip service is paid to taking into account other factors than those traditionally accepted, we find that the theory, as presented in extant writings, concentrates on a limited set of evolutionary explananda, excluding the majority of those mentioned among the explanatory goals above. The theory performs well with regard to the issues it concentrates on, providing testable and abundantly confirmed predictions on the dynamics of genetic variation in evolving populations, on the gradual variation and adaptation of phenotypic traits, and on certain genetic features of speciation. If the explanation would stop here, no controversy would exist. But it has become habitual in evolutionary biology to take population genetics as the privileged type of explanation of all evolutionary phenomena, thereby negating the fact that, on the one hand, not all of its predictions can be confirmed under all circumstances, and, on the other hand, a wealth of evolutionary phenomena remains excluded. For instance, the theory largely avoids the question of how the complex organizations of organismal structure, physiology, development or behavior — whose variation it describes — actually arise in evolution, and it also provides no adequate means for including factors that are not part of the population genetic framework, such as developmental, systems theoretical, ecological or cultural influences.
Uh, whoa. Or as our friend says, “BOOM.” Read that again. Müller says that “current evolutionary theory…largely avoids the question of how the complex organizations of organismal structure, physiology, development or behavior…actually arise in evolution.” But how stuff “actually arises” is precisely what most people think of when they think of “evolution.”­­­
Says our friend, see Michael Behe in The Edge of Evolution, where Dr. Behe asks, “The big question, however, is not, ‘Who will survive, the more fit or the less fit?’ The big question is, ‘How do organisms become more fit?’” Müller concedes that conventional evolutionary thinking “largely avoids” this “big question.” Though expressed in anodyne terms, that is a damning indictment.
Here are some other gems from the paper (emphasis added throughout):
A rising number of publications argue for a major revision or even a replacement of the standard theory of evolution [2–14], indicating that this cannot be dismissed as a minority view but rather is a widespread feeling among scientists and philosophers alike.
That could have appeared in a work from an intelligent design proponent. But wait, it gets even better:
Indeed, a growing number of challenges to the classical model of evolution have emerged over the past few years, such as from evolutionary developmental biology [16], epigenetics [17], physiology [18], genomics [19], ecology [20], plasticity research [21], population genetics [22], regulatory evolution [23], network approaches [14], novelty research [24], behavioural biology [12], microbiology [7] and systems biology [25], further supported by arguments from the cultural [26] and social sciences [27], as well as by philosophical treatments [28–31]. None of these contentions are unscientific, all rest firmly on evolutionary principles and all are backed by substantial empirical evidence.
“Challenges to the classical model” are “widespread” and “none…are unscientific.” Wow — file that one away for future reference.
Sometimes these challenges are met with dogmatic hostility, decrying any criticism of the traditional theoretical edifice as fatuous [32], but more often the defenders of the traditional conception argue that ‘all is well’ with current evolutionary theory, which they see as having ‘co-evolved’ together with the methodological and empirical advances that already receive their due in current evolutionary biology [33]. But the repeatedly emphasized fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them.
Orthodox Darwinists of the “All Is Well” school meet challenges with “dogmatic hostility”? Yep. We were aware.
Here he obliterates the notion, a truly fatuous extrapolation, that microevolutionary changes can explain macroevolutionary trends:
A subtler version of the this-has-been-said-before argument used to deflect any challenges to the received view is to pull the issue into the never ending micro-versus-macroevolution debate. Whereas ‘microevolution’ is regarded as the continuous change of allele frequencies within a species or population [109], the ill-defined macroevolution concept [36], amalgamates the issue of speciation and the origin of ‘higher taxa’ with so-called ‘major phenotypic change’ or new constructional types. Usually, a cursory acknowledgement of the problem of the origin of phenotypic characters quickly becomes a discussion of population genetic arguments about speciation, often linked to the maligned punctuated equilibria concept [9], in order to finally dismiss any necessity for theory change. The problem of phenotypic complexity thus becomes (in)elegantly bypassed. Inevitably, the conclusion is reached that microevolutionary mechanisms are consistent with macroevolutionary phenomena [36], even though this has very little to do with the structure and predictions of the EES. The real issue is that genetic evolution alone has been found insufficient for an adequate causal explanation of all forms of phenotypic complexity, not only of something vaguely termed ‘macroevolution’. Hence, the micro–macro distinction only serves to obscure the important issues that emerge from the current challenges to the standard theory. It should not be used in discussion of the EES, which rarely makes any allusions to macroevolution, although it is sometimes forced to do so.
This a major concession on the part of a major figure in the world of evolution theory. It’s a huge black eye to the “All Is Well” crowd. Who will tell the media? Who will tell the Darwin enforcers? Who will tell the biology students, in high school or college, kept in the dark by rigid Darwinist pedagogy?
Evolution has only “strengths” and no “weaknesses,” you say? Darwinian theory is as firmly established as “gravity, heliocentrism, and the round shape of the earth“? Really? How can anyone possibly maintain as much given this clear statement, not from any ID advocate or Darwin skeptic, not from a so-called “creationist,” but from a central figure in evolutionary research, writing in a journal published by the august scientific society once presided over by Isaac Newton, for crying out loud?
To maintain at this point that “All Is Well” with evolution you have to be in a state of serious denial.

Monday, January 1, 2018

Five scientific mysteries - D.G.

Ask Ethan: Which Fundamental Science Question Is The Most Important?
Out of five vital questions, which one should we most desire the answer to?

Despite all we’ve learned about physics, science, and the Universe before us, there are still some incredibly fundamental questions whose answers are still elusive. Each one is a challenge to humanity, and the answers are thoroughly uncertain, with tremendous implications depending on what the answer actually is. From our cosmic birth to the fundamental laws governing everything, and from the origin of life to what actually makes up the Universe, there is so much left to discover. If we could only know the answer to one, which one should we choose? That’s what our Patreon supporter Chris Shaw wants to know, as he asks:
If you could have a complete answer to one of these 5 questions what would it be?
* Did cosmic inflation happen or was there another process?
* Is earth the only place in the cosmos with life?
* How [can we] merge general relativity and quantum mechanics?
* What is dark energy and dark matter?
* How did life begin on Earth?
These are all incredible questions, and they’re all open questions that probe our deepest mysteries about the Universe. Here’s why each one matters.

1.) Cosmic inflation: We know that the Big Bang happened, and that the hot Big Bang wasn’t the very beginning of the Universe. There are a number of finely-tuned, unexplained phenomena that need to be set up as initial conditions to give us the Universe we have today, or the Universe wouldn’t exist as-is. Cosmic inflation is the theory that provided the first accurate explanation for these conditions, reproduced the Big Bang, plus made a slew of other predictions, many of which have been confirmed to great precision. It would be great to know exactly what occurred before the hot Big Bang, and whether it was a particular variant of cosmic inflation, or something inflation-like that turns out to be quite different.

2.) Life beyond Earth: Surely, we can all agree that life exists on Earth. But is there any place beyond Earth that also has life? And what would be a good definition of life, anyway? Do other worlds in our Solar System, which certainly have the building blocks of life, have either past or present life on them? What about worlds around other stars? How likely are they or aren’t they to have life, and how advanced, by comparison to us, have they gotten? These are questions that we truly don’t know the answers to, even though we have extremely strong suspicions that all the same conditions that occurred here on Earth have occurred many trillions of times elsewhere in our Universe.

describing the Universe, with General Relativity accounting for gravitation and Quantum Field Theory accounting for the properties of the Universe’s particles and their interactions. But if you passed an electron through a double slit, what would happen to its gravitational field? What happens at the singularity inside a black hole? And is spacetime fundamental, or is itself composed of discrete quanta? Without a quantum theory of gravity, and a theoretical merging of General Relativity and Quantum Field Theory, we may never know. Is it possible? We think so. Does our Universe actually have a theory of everything? Is gravity truly quantum in nature? That we don’t know.

4.) Dark energy and dark matter: Do they exist? The evidence certainly strongly suggests it. What, exactly, are they? Those are big, open questions that we don’t know the answer to. Dark energy appears to be a constant form of energy uniformly distributed throughout space; dark matter appears to behave like a particle, clumping and clustering under the influence of gravitation. But is dark matter actually particle-based? Does dark matter interact with either itself or normal matter through any force other than gravitation? How did it come to be? And what about dark energy? Is it a property inherent to space itself? Is it a separate field? And why does it have the numerical value that it has? The answers to all of these have so far proved elusive.

5.) The origin of life: How did life on Earth begin? We know that the building blocks of life can be found throughout the galaxy, in interstellar space, and even in the Solar System. Complex, carbon-based molecules are found all over, from cyanide to sugars to ethyl formate, the last of which is the molecule that gives raspberries their characteristic smell. We’ve found meteorites originating from the asteroid belt with amino acids inside, including more than 60 that aren’t involved in life processes here on Earth. And finally, we’ve found circumstantial evidence supporting the idea that Earth-based life originated prior to our planet’s formation. Yet, we haven’t managed to create life from non-life to this point. And thus, we still don’t know how life on Earth began.

If we can magically snap our fingers and know the answer to one of these, which one should we pick? There are two important considerations:
1.      Which one is the “hardest problem” in terms of knowing how to find the answer, and
2.      Which one would be the most revolutionary and beneficial to our society?
We can throw out cosmic inflation, since we already have many strong lines of evidence that not only support inflation, but also tightly constrain which models of inflation are still valid. We’re too close, and if the next 20–30 years are kind to us, we may even learn how inflation occurred. For the same reason, we should throw out the questions of life beyond Earth, or how it arose. These are active questions we’re making huge progress on, and as much as I want to know that we’re not alone, the amount that we’re learning, both in terrestrial biology and astrobiology, is too important. When you learn the answer, you miss out on all the lessons of finding things out, and over the rest of our lifetimes, we’re likely to see the answers to these questions slowly revealed.

Which leaves the merger of General Relativity with the quantum Universe, and the origin/nature of dark matter and dark energy. These are both incredibly hard problems that have many ideas behind them, but realistically, have seen very little progress. It’s not even a certainty that our Universe has a quantum theory of gravity, or that dark matter and dark energy truly exist, although there are many good reasons to believe all of these are so. All would be revolutionary, and as with all fundamental physical discoveries, the societal benefits are hard to envision.

The cosmic web is driven by dark matter, with the largest-scale structure set by the expansion rate and dark energy. The small structures along the filaments form by the collapse of normal, electromagnetically-interacting matter.
But if we had to choose one, I’d pick the knowledge of dark energy/dark matter. If dark matter turns out to be a particle, it’s possible that we’ll be able to manipulate it in a new way that could be tremendously beneficial to society. It could lead to free, abundant energy, not just here on Earth but anywhere we travel to in the galaxy. It may be as efficient as matter-antimatter annihilation, and if we can harness it, it’ll be there no matter where we go. It’s the majority of the Universe, and our attempts to detect it have all come up empty thus far. It may turn out that we’re looking in all the wrong ways, but until we look in the right way, we have no way of knowing.

Even though the majority of dark matter in the galaxy exists in a vast halo engulfing us, each individual dark matter particle makes an elliptical orbit under the influence of gravity. If dark matter is its own antiparticle, and we learn how to harness it, it may be the ultimate source of free energy. Image credit: ESO / L. Calçada.
There aren’t right and wrong answers here, just choices. The important thing is to realize what we know, what we’re wondering about, what the possibilities are, and what we’re doing to try to learn the definitive answers. If we could simply know something that’s far out of reach today, it could guide us down the correct path. But don’t underestimate the value of the investigative process, or the power of the lessons learned as we make these discoveries. The pleasure lies not just in knowing, but in the act of finding things out!