Monday, January 29, 2018

Scientific mysteries – the next time someone tells you science has everything under
 control, send him here 
Top 10 scientific mysteries for the 21st century
Solving the toughest problems posed by nature is not just fun and games
8:00AM, JANUARY 28, 2015
The last few centuries have been pretty good for science. In the 17th century, Isaac Newton solved the ancient controversy over the nature of forces and motion with his three laws. In the 18th, Ben Franklin figured out a lot about electricity. In the 19th, Darwin explained the diversity of species, Maxwell revealed the physics of light, Mendeleyev defined the families of chemical elements. In the 20th we had Einstein, who figured out all sorts of stuff, including gravity. No to mention Watson and Crick, who deciphered the molecular foundation for genetics and life. What more do you want?
Well, there are still lots of mysteries left for the 21st century to solve, and it has only 86 years left in which to solve them. So it’s a good idea to put them in a list, just to avoid any danger that everybody will forget to work on them.
Actually there are many more than 10, so this list will have to be restricted to my favorites. To select from all the many possibilities, let’s make a game of it.
10. How did life originate?
It doesn’t seem like this one should be so hard, but it continues to defy solution. There’s plenty of speculation, often related to RNA’s ability to act both as catalyst and bio–hard drive to store information. And new findings turn up all the time about how life’s basic building blocks could have been generated in primordial conditions or delivered to Earth from space. I think this question will end up having something to do with game theory, as biomolecules interact in competitive ways that could be described as strategies, and the math for calculating optimal strategies is what game theory is all about.
9. What is the identity of the dark matter?
It has been eight decades or so since astronomers began to notice that there is more gravity pulling stuff around out in space than there is visible matter able to produce such effects. Attempts to detect the supposedly exotic (as in, unknown) species of subatomic particle responsible for the extra gravity have been frustrating. Hints seen in some experiments have been ruled out by other experiments. I think there’s a missing piece to this puzzle, but it probably has nothing to do with game theory.
8. What is the nature of the dark energy that drives cosmic acceleration?
If you think dark matter is frustrating, try explaining dark energy. Something is driving space to expand at an ever increasing rate. Physicists think that they know what it is — the never-changing density of energy residing throughout all of space, referred to by Einstein as the “cosmical term” and now called the cosmological constant. But when you calculate how strong the cosmological constant should be, the answer is too big by dozens of orders of magnitude — much more than the difference between the size of the entire universe compared with a proton. So dark energy’s identity remains a mystery; if it is the cosmological constant, something else is seriously wrong with what physicists think they know. And so far game theory has been absolutely no help.
7. How to measure evidence
This one is so mysterious that many scientists don’t even know there’s a mystery. But if they paused to think, they’d realize that the standard way of inferring conclusions from experimental data — calculating “statistical significance” — makes about as much sense as punting on fourth and seven when you’re down by 15 with eight minutes to go. One small example: if you do an experiment and get a statistically significant result, and then repeat it and get a statistically significant result again, you’d think you have better evidence than doing the experiment only once. But if the significance level was a little less the second time, the combined “P value” would be less impressive after the second experiment, even though the evidence ought to be regarded as stronger. It’s a mess. Game theory would surely be able to help somehow, possibly by virtue of its relationship to thermodynamics.
6. Genes, cancer and luck
You might have read recently that most cancer is caused by bad luck, as a study published in Sciencesupposedly concluded. (Actually, the study concluded that the disparity in prevalence of cancer of various types was largely due to luck.) A firestorm of protest followed, essentially based on the belief that such a study must be wrong because it would “send the wrong message” to the public. Proving the illogic of that syllogism should be left as an exercise for the reader. Other responses revealed that experts do not agree on how random mutations (bad luck) compare with heredity (parent’s fault) plus lifestyle (your fault) and environmental exposure to bad things (somebody else’s fault) in causing cancer. Sorting all that out, and in the process solving cancer’s other mysteries, should be a high-priority exercise for 21st century science. And yes, there is a considerable amount of research relating game theory to cancer.
5. Are there extra dimensions of space?
I don’t know why people keep thinking this is a mystery, as I have on several occasions pointed out that there are no extra dimensions. However many there are, they are all absolutely necessary. Posed properly, this question should be how many dimensions of space are there? (For that matter, you could also ask about how many time dimensions there are, but that might overlap with No. 4.) Many physicists believe more dimensions than the ordinary three will be needed for physics to make sense of the universe. (Don’t even ask if they’re talking about bosonic or fermionic dimensions.) A key to understanding this issue is the mathematics of Calabi-Yau manifolds, which can curl up in gazillions of different ways to prevent easy detection of the additional dimensions’ existence. And that makes it really hard to figure out which of the gazillion possibilities would correspond to the universe we inhabit (unless there is some sort of fixed point theorem that would choose one, like a Nash equilibrium in game theory). In any event, anyone attempting to solve this riddle should first read Edwin Abbott’s Flatland, in which the protagonist character, A. Square, demonstrates the existence of an extra dimension and is promptly thrown in jail.
4. The nature of time
So many mysteries, so little time in which to solve them, unless solving this one would reveal some clever tricks to play with time. Many submysteries underlie this one, corresponding to almost all of the 44 definitions of time in the dictionary (and that’s just as a noun). What’s the nature of duration and the flow of time — is it illusory or “real” in some elusive way? What about the direction of time — does it always go forward? Why? Is time travel possible, or can messages at least be sent backward in time? (Forward in time is easy — just print this blog post out and read it a year from now.) Perhaps the biggest mystery is whether all these issues about time are related or are completely separate questions. Of course, it would all be simpler if somehow time could be connected to game theory, which it might be, because game theory can be related to cellular automata, which in turn can be related to time.
3. Quantum gravity
Quantum physics and general relativity (aka Einstein’s theory of gravity) both seem to describe the universe and its components with compelling accuracy, yet they seem wholly incompatible with one another. Attempts to combine them into a coherent unified theory have been as successful as brokering compromise in the U.S. Congress. Yet there are clues. In 1930, Einstein tried to refute quantum mechanics (specifically, the Heisenberg uncertainty principle) by suggesting a clock attached to a box hanging on a scale could measure both the mass of a photon and the precise time that it escaped from the box. (Heisenberg said you couldn’t measure both at the same time). But Niels Bohr pointed out that the time on the clock would be uncertain, because as the box moved upward in the gravitational field, Einstein’s relativity required a change in time that would introduce just the amount of uncertainty in the timing that Heisenberg required. So how, you might ask, did the uncertainty principle know about this effect of general relativity? Maybe if the experts posed the question that way they would be able to figure out the quantum gravity mystery. The next best bet would be to undertake the study of quantum game theory, which hasn’t been adequately exploited yet in this regard.   
2. Does intelligent life exist elsewhere?
It’s tempting to delete the “elsewhere,” but given what passes for intelligence on Earth, it makes sense to wonder if anything like it could be blundering about on some distant world. It seems likely, given how many other worlds there are out there. But finding out for sure will probably require receiving an actual message. Projects like SETI have been listening for some such message, so far unsuccessfully. There are two (at least) possible explanations: One, there have been no messages (perhaps the aliens are experts at game theory and calculated that contacting humans would be a bad strategy). Two, the messages are there, but nobody knows how to detect or recognize them. Perhaps enhanced scrutiny is in order on Twitter, where numerous tweets every day seem most plausibly to be the work of aliens. 
1. The meaning of quantum entanglement
All sorts of quantum mysteries remain unsatisfactorily resolved, but maybe the rest would succumb if entanglement does. Entanglement occurs in systems with widely separated parts that share a common history; a measurement of one of the parts reveals what you will find out when you measure its distant relative. Entanglement is a fact of nature, well-established by experiment. It suggests that time and space do not constrain quantum phenomena the way they do ordinary human activity. Among the latest intriguing aspects of entanglement to be studied involves black holes. It seems that black holes can be entangled, which apparently is equivalent to their being connected by a wormhole. Related work suggests that space, time and gravity are all part of a vast quantum entanglement network. Since both the evolution of networks and quantum entanglement fit nicely into game theory, solving all sorts of mysteries might boil down to viewing the world from a game-theoretical perspective. But maybe that will still be too hard for human brains — it might take advanced artificial intelligence, which, as this paper suggests, might be created with the help of some version of quantum game theory.  
Editor’s Note: It might not surprise readers to find out that Tom Siegfried is the author of a book about game theory. But he says the book did not include the sort of wild speculation that is suitable only in blog posts.

10 mysteries that physics can’t answer… yet
From why we travel forwards in time to how bicycles travel forwards at all, we present the questions great and small that our finest minds can't explain
Image: Carlo Giambarresi


Has the universe existed forever? Or was there something before it? To find out, we need a working theory of quantum gravity and a new conception of time

We thought we knew the maths behind cycling. We were wrong – and our efforts to figure it out are leading to some weird and wonderful new bike designs


In the bizarre reality of the quantum world, particles can be in two places at once. Why can’t golf balls or milk do the same?

Time goes by, or so it seems. It could be an illusion, or we might need to rescue the flow of time by meddling with our concept of space


The universe might go awry if not for the familiar three dimensions, but theories of everything say there should be more. What are we missing?

The Casimir effect suggests that the vacuum is fizzling with ephemeral particles. Is it real? And can we harness this energy concealed in empty space?


Things aren’t as clear as you might think. Glass is a weird kind of solid liquid – and how it comes to be like that defies all explanation

Most think it’s down to a liquid layer, but can’t agree on how it forms. One theory insists it’s a “supersolid skin” capable of electrostatic repulsion
Description: Why is ice slippery?


They are the essential heart of every atom, so it’s just as well we’ve never seen a proton fall apart. But they can’t live forever – can they?

The size of the observable universe is easy enough to measure, but what lies beyond the cosmic horizon? We have a long way to go to find out


Tuesday, January 23, 2018

Baloney detection test - Michael Shermer

An excellent presentation of the prejudices that are popularized in the name of science. See how many of his principles falsify his own position, and how many would disqualify the theory of evolution [which he says we know to be true].

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.