Massimo Pigliucci tries to defend accommodationism (again): result is predictable

Massimo Pigliucci is an atheist who thinks that science and religion are compatible because they rule in different domains. He takes a very narrow view of "science"— one that excludes the work of historians and philosophers who are presumably using some other way of knowing. (He doesn't tell us what that is.)

I prefer the broad view of science as a way of knowing that relies on evidence, rational thinking, and healthy skepticism. This broad view of science is not universal—but it's not uncommon. In fact, Alan Sokel has defended this view of Massimo Pigiucci's own blog: [What is science and why should we care? — Part III]. According to this view, any attempt to gain knowledge should employ the scientific worldview. Historian and philosophers should follow this path if they hope to be successful. Pigliucci should know that there are different definitions and any discussion of the compatibility of science and religion must take these differences into account.

Answering two questions from Vincent Torley

Vincent Torley read a post by Jerry Coyne where Jerry wondered if Intelligent Design Creationism was in trouble because the Discovery Institute has lost Bill Dembski and Casey Luskin [Is the Discovery Institute falling apart?].

Torley disagrees, obviously, but he focuses on a couple of the scientific statements in Jerry Coyne's post and comes up with Two quick questions for Professor Coyne.

I hope Professor Coyne won't mind if I answer.

Before answering, let's take note of the fact that Vincent Torley has been convinced by the evidence that most of our genome is junk. I wonder how that will go over in the ID community?

Here's question #1 ...

Quotations

I'm creating a post where I can store quotations so I can link to them from other posts. Enjoy.

The great fear of many leading creationists and the misunderstanding of many creationist students is that accepting MN [methodological naturalism] rules for doing science will necesarily lead to a supernaturalless/Godless worldview.
Brian Alters (2005) p. 77

Persons in this faction [of theists] basically accept evolutionary theory with the proviso that the God of the Bible, not chance, decided the human outcome by directly guiding the process. Such theists are most commonly referred to as theistic evolutionists.
Brian Alters (2005) p. 62

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...
Peter Atkins

The defective design of organisms could be attributed to the gods of the ancient Greeks, Romans, and Egyptians, who fought with one another, made blunders, and were clumsy in their endeavors. But, in my view, it is not compatible with special action by the omniscient and omnipotent God of Judaism, Christianlity, and Islam.
Francisco J. Ayala (2004) p. 71

In conclusion, then, macroevolutionary processes are underlain by microevolutionary phenomena and are compatible with microevolutionary theories, but macroevolutionary studies require the formulation of autonomous hypotheses and models (which must be tested using macroevolutionary evidence). In this (epistemologically) very important sense, macroevolution is decoupled from microevolution: macroevolution is an autonomous field of evolutionary study.
Francisco J. Ayala (1983) p. 131

Science is not committed to the nonexistence of God, as it would be if it were based on metaphysical naturalism. Science is committed to naturalistic explanations. Science does not count any explanation that appeals to God or to supernatural phenomena as a scientific explanation (thus it is committed to methodological naturalism).
Lynn Rudder Baker (2000)

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.
Sydney Brenner (2000)

There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.
Sydney Brenner

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.
Francis Crick

The Astonishing Hypothesis is that "You," your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behavior of a vast assembly of nerve cell and their associated molecules.
Francis Crick (1994)

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.
Jerry Coyne (2009)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.
Charles Darwin (1859)

The old argument of design in nature, as given by Paley, which formerly
seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.
Charles Darwin (c1880)

An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.
Richard Dawkins

Theologians, if they want to remain honest, should make a choice. You can claim your own magisterium, separate from science's but still deserving of respect. But in that case you have to renounce miracles. Or, you can keep your Lourdes and your miracles ... But then you must kiss goodbye to separate magisteria and your high-minded aspiration to converge on science. The desire to have it both ways is not surprising in a good propagandist. What is surprising is the readiness of liberal agnostics to go along with it; and their readiness to write off, as simplistic, insensitive extremists, those of us with the temerity to blow the whistle.
Richard Dawkins (2003) p.150

It is absolutely safe to say that if you meet someone who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I'd rather not consider that).
Richard Dawkins (1989)

... those evolutionists who see no conflict between evolution and their religious beliefs have been careful not to look as closely as we have been looking, or else hold a religious view that gives God what we might call a merely ceremonial role to play.
Daniel C. Dennett (1995) p.310

Operational science takes no position about the existence or non-existence of the supernatural; it only requires that this factor is not to be invoked in scientific explanations. Calling down special-purpose miracles as explanations constitutes a form of intellectual "cheating."
Richard E. Dickerson (1992) p.119

Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science. Without that light it becomes a pile of sundry facts—some of them interesting or curious but making no meaningful picture as a whole.
Theodosius Dobbzhansky (Dobzhansky 1973)

It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God's, or Nature's method of creation. Creation is not an event that happened in 4004 BC; it is a process that began some 10 billion years ago and is still under way.
Theodosius Dobbzhansky (Dobzhansky 1973)

Under the conditions described [for Hardy-Weinberg equilibrium], there is a genetic inertia in mendelian populations. Unless mutation, selection, differential migration, certain changes in the mating pattern, or a drop in population size disturbs the equilibrium, there is no change in the genetic structure of the population. To a very large degree, overcoming this inertia (especially changing of the gene frequency) is what is described as "evolution."
Paul R. Ehrlich and Richard W. Holm (1963) p.95

Speciation is critical to conserving the results of both natural selection and genetic drift. Speciation is obviously central to the fate of genetic variation, and a major shaper of patterns of evolutionary change through evolutionary time. It is as if Darwinians—neo- and ulra- most certainly included—care only for the process generating change, and not about its ultimate fate in geological time.
Niles Eldredge (1995) p.106

Macroevolution is more than repeated rounds of microevolution.
Douglas H. Erwin (2000)

Just as mutation and drift introduce a strong random component into the process of adaptation, mass extinctions introduce chance into the process of diversification. This is because mass extinctions are a sampling process analogous to genetic drift. Instead of sampling allele frequenceis, mass extinctions samples species and lineages. ... The punchline? Chance plays a large role in the processes responsible for adaptation and diversity.
Freeman and Herron (1998) p.520

It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations.
Douglas Futuyma

There is no justification for teaching creationism in the science classroom. But if it were taught, would it be subjected to the same critical analysis as the creationists insist should be brought to bear on evolution?
Douglas J. Futuyma (1982) p.217

I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p. 1339

The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1980)

Progress is a noxious, culturally embedded, untestable, nonoperational, intractable idea that must be replaced if we wish to understand the patterns of history.
Stephen Jay Gould (1988)

The shift of gene frequencies in local populations is an adequate model for all evolutionary processes—or so the current orthodoxy states.
Stephen Jay Gould (1980) p. 187

Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)

Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p. 335

The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p. 84

[My diagram] accepts the Darwinian contention that microevolutionary modes and principles can build grand patterns by cumulation through geological immensity, but rejects the argument that such extrapolations can render the entire panoply of phenomena in life's history without adding explicitly macroevolutionary modes for distinctive expression of these processes at higher tiers of time ...
Stephen Jay Gould (2002) p. 21

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)

We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm.
S.J. Gould & R.C. Lewontin (1979) p. 584

We welcome the richness that a pluralist approach, so akin to Darwin's spirit, can provide.
S.J. Gould & R.C. Lewontin (1979) p. 584

My practise as a scientist is atheistic. That is to say, when I set up an experiment I assume that no god, angel, or devil is going to interfere with its course; and this assumption has been justified by such success as I have achieved in my professional career. I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world. And I should be a coward if I did not state my theoretical views in public.
J.B.S. Haldane

Since religion ... stands or falls with the question of cosmic purpose, the Darwinian debunking of design—and with it the apparent undoing of cosmic teleology as well—strikes right at the heart of the most prized religious intuition of humans, now and always.
John F. Haught (2004) p. 230

Whatever the God implied by evolutionary theory may be like, He is not the Protestant God of waste not, want not. He is also not a loving God who cares about his productions. He is not even the awful God portrayed in the book of Job. The God of the Galapagos is careless, wasteful, indifferent, almost diabolical. He is certainly not the sort of God to whom anyone would be inclined to pray.
David I. Hull (1991) p. 486

Johnson finds the commitment of scientists to totally naturalistic explanations dogmatic and close-minded, but scientists have no choice. Once they allow reference to God or miraculous forces to explain the first origin of life or the evoluton of the human species, they have no way of limiting this sort of explanation.
David I. Hull (1991) p. 486

This evolutionary procedure —the formation of a dominant neocortex coupled with the persistence of a nervous and hormonal system partially, but not totally, under the rule of the neocortex—strongly resembles the tinkerer's procedure. It is somewhat like adding a jet engine to an old horse cart. It is not surprising ... that accidents, difficulties, and conflicts can occur.
François Jacob (1977) p.1166
Jacob, F. (1977) Evolution and Tinkering Sci. 196:1161-1166.

Natural selection has no analogy with any aspect of human behavior. However, if one wanted to play with a comparison, one would have to say that natural selection does not work as an engineer works. It works like a tinkerer—a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him whether it be pieces of string, fragments of wood, or old cardboards; in short it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.
François Jacob (1977) p.1163

It is hard to realize that the living world as we know it is just one among many possibilities; that its actual structure results from the history of the earth. Yet living organisms are historical structures: literally creations of history. They represent, not a perfect product of engineering, but a patchwork of odd sets pieced together when and where opportunities arose. For the opportunism of natural selection is not simply a matter of indifference to the structure and operation of its products. It reflects the very nature of a historical process full of contingency.
François Jacob (1977) p.1166

Ecologists and microevolutionists are beginning to appreciate the importance of events over larger time scales than the decades or centuries that are their usual bounds, and a new effort is needed from both neontological and paleontological sides to get beyond a simple extrapolation of ecological phenomena into macroevolutionary time scales.
Jablonski, D. et al (1997)

Many biochemists find it easy to accept the concept that large portions of protein molecules serve mainly to bring the molecule up to suitable size and shape and have very little specific function as compared with small specialized active sites. Most of a protein molecule, according to this concept, can evolve freely by random drift
Thomas H. Jukes (1980) p.204

In conclusion, I would like to emphasize the importance of random genetic drift as a major cause of evolution. We must be liberated, so to speak, from the selective constraint posed by the neo-Darwinian (or the synthetic) theory of evolution.
Motoo Kimura (1991)

In contrast to the Darwinian theory of evolution by natural selection, the neutral theory emphasizes the great importance of random genetic drift (due to finite population size) and mutation pressure as the main causes of molecular evolution.
Motoo Kimura (1991)

According to the neutral mutation–random drift hypothesis of molecular evolution and polymorphism1,2, most mutant substitutions detected through comparative studies of homologous proteins (and the nucleotide sequences) are the results of random fixation of selectively neutral or nearly neutral mutations. This is in sharp contrast to the orthodox neo-Darwinian view that practically all mutant substitutions occurring within species in the course of evolution are caused by positive Darwinian selection.
Motoo Kimura (1977)

Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so
high that many of the mutations involved must be neutral ones
Motoo Kimura 1968

Selective elimination of definitely deleterious mutants and random fixation of selectively neutral or very slightly deleterious mutants occur far more frequently in evolution than positive Darwinian selection of definitely advantageous mutants.
Motoo Kimura and Tomoko Ohta (1974)

The main tenet of the neutral theory is that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random fixation of selectively neutral (or very nearly neutral) alleles through random sampling drift under continued mutation pressure.
Motoo Kimura (1989)

There appears to be considerable latitude at the molecular level for random genetic changes that have no effect upon the fitness of the organism. Selectively neutral mutations, if they occur, become passively fixed as evolutionary changes through the action of random genetic drift.
J.L King and T.H. Jukes (1969) p.789

The idea of selectively neutral change at the molecular level has not been readily accepted by many classical evolutionists, perhaps because of the pervassiveness of Darwinian thought.
J.L King and T.H. Jukes (1969) p.788

The suggestion that macroevolution should be divorced from microevolution provides Creationists only with a debating point. It allows Creationists to say that there are some evolutonary theorists who distinguish the mechanisms studied in classical population genetics from those they take to be involved in large-scale evolutionary change ... But this is not to suppose that the distinction drawn by heterodox evolutionists is that favored by the Creationists.
Philip Kitcher (1982) p.150

Overheard at breakfast on the final day of a recent scientific meeting: "Do you believe in macroevolution?" Came the reply: "Well, it depends on how you define it.".
Roger Lewin (1980) p.884.

The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the positions of some of the people at the meeting, the answer can be given as a clear, No.
Roger Lewin (1980) p.884.

The fact is that almost the entire theoretical apparatus of random genetic drift and directional selection can be derived from a haploid model of the genome and that the introduction of diploidy and sexual recombination makes no qualitative chane and only trivial quantitative changes in the predictions of evolution under these forces.
Richard C. Lewontin (1974) p.83

The [neoclassical] theory does not deny adaptive evolution but only that the vast quantity of molecular variation within populations and, consequently, much of the molecular evolution among species, has anything to do with that adaptive process
Richard C. Lewontin (1974) p.85

The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.
Richard Lewontin

Evolution is a process of change in the genetic makeup of populations, with the most basic component being change in allele frequencies with time.
Wen-Hsiung Li (1997) p.35

... the independence of macroevolution is affirmed not only by species selection but also by other processes such as effect sorting among species.
Bruce S. Lieberman and Elisabeth S. Vrba (2005)

Macroevolution is given expanded meaning by punctuated equilibrium, which is a theory more about species and their reality and individuality (sensu Hull 1980) than about speciation.
Bruce S. Lieberman and Elisabeth S. Vrba (2005)

The universe doesn't seem to me to be like the kind of entity that could have a higher purpose. I literally don't know what it would mean to say that the universe has a higher purpose. But I also have to say just simply as far as my own personal experience is concerned I have not found it a depressing doctrine. I do not find myself in the least depressed by feeling that if there is a purpose it's a purpose in my friends in my people I love and myself and human beings. It's a product of human beings it's not something that's sort of you know comes out the physical universe because the universe was created.
John Maynard Smith (1998)

Molecular genetics has found that mutations frequently occur in which the new allele produces no change in the fitness of the phenotype. Kimura (1983) has called the occurrence of such mutations neutral evolution, and others have referred to it as non-Darwinian evolution. Both terms are misleading. Evolution involves the fitness of individuals and populations, not of genes. When a genotype, favored by selection, carries along as hitchhikers a few newly arisen and strictly neutral alleles, it has no influence on evolution. This may be called evolutionary 'noise' but it is not evolution. However, Kimura is correct in pointing out that much of the molecular variation of the genotype is due to neutral mutations. Having no effect on the phenotype, they are immune to selection.
Ernst Mayr (2001) p.199

... I pointed out more than a decade ago (1977) that 'the reductionist explanation, so widely adopted in recent decades— Evolution is a change in gene frequencies in populations—is not only not explanatory, but is in fact misleading. Far more revealing is the definition: 'Evolution is change in the adaptation *and* in the diversity of populations of organisms.'
Ernst Mayr (2001) p.162

Neither the discovery of numerous new facts relating to evolution nor the development of new concepts of speciation and genetic variation have required any essential revision of the picture of evolution as developed during the evolutionary synthesis. I emphatically deny the claims of various authors that these recent developments have led to an end of Darwinism, or of neo-Darwinism, or of the evolutionary synthesis.
Ernst Mayr (1988) p.191

The attack directed by Gould and Lewontin against unsupported adaptationist explanations in the literature is fully justified. But the most absurd among these claims were made several generations ago, not by modern evolutionists.
Ernst Mayr (1988) p.152

[referring to Tielhard de Chardin] ... it's author can be accused of dishonesty only on the grounds that before deceiving others he has taken great pains to deceive himself.
Peter Medawar (1961) p.1

Although not completely random, chance does affect which mutations, which mistakes, appear in which individuals. ... this inherent unpredictability is not a matter of inadequate scientific knowledge. Rather, it is a reflection that the behavior of matter itself is indeterminate, and therefore unpredictable. It is one of the reasons why we cannot predict, with any detailed certainty, the future path of evolution.
Kenneth R. Miller (1999) p. 233

... evolution is as much a fact as anything we know in science. It is a fact that we humans did not appear suddenly on this planet, de novo creations without ancestors, and it is a fact that the threads of ancestry are clear for us and for hundreds of other species and groups.
Kenneth R. Miller (1999) p. 233

No question about it. Rewind that tape, let it run again, and events might come out differently at every turn. Surely this means that mankind's appearance on this planet was not preordained, that we are here not as the products of an inevitable procession of evolutionary success, but as an afterthought, a minor detail, a happenstance in a history that might just as well have left us out. I agree.
Kenneth R. Miller (1999) p. 233

In any discussion of the question of "Intelligent Design," it is absolutely essential to determine what is meant by the term itself. If, for example, the advocates of design wish to suggest that the intricacies of nature, life, and the universe reveal a world of meaning and purpose consistent with an overarching, possibly Divine, intelligence, then their point is philosophical, not scientific. It is a philosophical point of view, incidentally, that I share, along with many scientists.
Kenneth R. Miller (2004) p. 94

The thesis I shall present in this book is that the biosphere does not contain a predictable class of objects or of events but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles and therefore essentially unpredictable.
Jacques Monod (1971) p.43

All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its own contingency."
Jacques Monod (1971) p.44

Another curious aspect of the theory of evolution is that everybody thinks he understands it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually, as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.
Jacques Monod (1974)

... I must correct a wrong idea that has been spreading for the past three or four years. It was discovered some years ago that in some cases, the transcription of step from DNA to RNA works in the reverse direction. That is nothing surprising. ... it could be predicted that such events could occur. They do occur, indeed, but this must not be taken to mean that information from protein could possibly go back to the genome. ... I am ready to take any bet you like that this is never going to turn out to be the case.
Jacques Monod (1974) p.394

The privilege of living beings is the possession of a structure and of a mechanism which ensures two things: (i) reproduction true to type of the structure itself, and (ii) reproduction equally true to type, of any accident that occurs in the structure. Once you have that, you have evolution, because you have conservation of accidents. Accidents can then be recombined and offered to natural selection to find out if they are of any meaning or not.
Jacques Monod (1974) p.394

The aspect of evolutionary theory that is unacceptable to many enlightened people, either scientists or philosophers, or idelogists of one kind or another, is the completely contingent aspect which the existence of man, societies, and so on, must take if we accept this theory.
Jacques Monod (1974) p.394

We must conclude that the existence of any particular species is a singular event, an event that occurred only once in the whole of the universe and therefore one that is also basically and completely unpredictable, including that one species which we are, namely man.
Jacques Monod (1974) p.395

While de Vries' and Goldschmidt's views on the origin of species were extreme and unrealistic, from our current knowledge of genetics, de Vries' ideas led Morgan (1925, 1932) to propose a more resonable theory of evolution. ... In his view, selection plays a less important role than mutation, its chief role being to preserve useful mutations and eliminate unfit genotypes. That is, natural selection is regarded merely as a sieve to choose beneficial mutations. For this reason, his theory is often called mutationism, but a better terminology would be mutation-selection theory or classical theory in Dobzansky's sense, since he did not neglect natural selection.
Masatoshi Nei (1987) p.406

At the DNA level, most new genes seem to have been produced by gene duplication and subsequent nucleotide changes .... In these cases, the mutational change of DNA (duplication and nucleotide substitution) is clearly responsible for creating a new gene of character. Natural selection plays no such role. The role of natural selection is to eliminate less fit genotypes and save a beneficial one when there are many different genotypes in the same environment. Therefore, it seems clear that at the molecular level evolution occurs primarily by mutation pressure, though positive selection certainly speeds up gene substitution in populations.
Masatoshi Nei (1987) p.415

... are all individual differences in morphological and physiological characters adaptive as claimed by extreme neo-Darwinians? More than 4 billion people live on this planet, and all of them except identical twins are different with respect to morphological and physiological characters. Are all these differences adaptive? Is random genetic drift unimportant for generating morphological and physiological diversity among organisms? It seems to me that in some morphological characters a substantial part of genetic variation is nonadaptive.
Masatoshi Nei (1987) p.422

In this book, I have examined various aspects of molecular evolution and concluded that mutation is the driving force of evolution at the molecualr level. I have also extended this view to the level of phenotypic evolution and speciation, though I do not deny the importance of natural selection in evolution. I have challenged the prevailing view that a population of organisms contains virtually all sorts of variation and that the only force necessary for a particular character to evolve is natural selection. I have also emphasized the unpredictability of the evolutionary fate of organisms caused by uncontrolable external factors such as rapid climatic changes, geological catastrophes, or even asteroid impacts.
Masatoshi Nei (1987) p.431

The primary cause of evolution is the mutational change of genes. A mutant gene or DNA sequence caused by nucleotide substitution, insertions/delections, recombination, gene conversion, and so forth may spread through the population by genetic drift and/or natural selection and eventually be fixed in the species.
Masatoshi Nei and Sudhir Kumar (2000) p.4

Most new mutations are deleterious, and most mutations with very small effects are likely to be very slightly deleterious. Such mutations are selected against in large populations, but behave as if neutral in small populations.
Tomoko Ohta (1996) p.96

Mutation is a fundamental process for evolution. Under the orthodox view, mutations are raw materials on which natural selection works and organismal evolution is mainly governed by selection. With the accumulation of molecular data, the importance of random drift is being reevaluated. If the effect of a mutant is very small, random drift rather than selection determines its fate.
Tomoko Ohta (1998) p.83

Are we here because of a natural superiority (opposable thumbs, big brains and so on), or are we just plain lucky? In other words, is the evolution of life a fair game, as the survival-of-the-fittest doctrine so strongly implies?
David Raup (1991) p.xi

Is extinction through bad luck a challenge to Darwin's natural selection? No. Natural selection remains the only viable, naturalistic explanation we have for sophisticated adaptations like eyes and wings. We would not be here without natural selection. Extinction by bad luck merely adds another element to the evolutionary process, operating at the level of species, families, and classes, rather than the level of local breeding populations of single species. Thus, Darwinism is alive and well, but, I submit, it cannot have operated by itself to produce the diversity of life today.
David Raup (1991) p.192

Evolution at the molecular level appeared to have properties that would not have been predicted if it were driven by natural selection; and much of molecular evolution is now widely (if not universally) thought to be non-adaptive.
Mark Ridley (1997) p.4

A habit has grown up among some molecular biologists of using homology to mean similarity, regardless of whether the similarity is due to descent from a common ancestor. They thus talk about the "% homology" between two molecules, meaning the percentage of amino acid, or nucleotide sites that are the same in the two molecules. They are often criticized for their unorthodox usage .
M. Ridley (1997) p.208

The working biologist's reaction on learning that evolutionary theory does not fit some philosophical criterion for what a scientific theory should be like is—so much the worse for philosophy.
M. Ridley (1997) p.368

... Kimura's original radical claim, that most molecular evolution proceeds by drift, not selection, remains intact in the nearly neutral theory. It still contrasts strongly with the view that molecular evolution is powered by Darwinian natural selection.
M. Ridley (1997) p.78

Many universes can exist, with all possible combinations of physical laws and constants. In that sense, we just happen to be in the particular one that was suited for the the evolution of our form of life. When cosmologists refer to the anthropic principle, this is all they usually mean. Since we live in this universe, we can assume it possesses qualities suitable for our existence.
Eugenie C. Scott (2004)

... the thesis that evolution is primarily driven by natural selection is sometimes called Darwinism. Unfortunately, many people misapply the term to refer to the concept of descent with modification itself, which is erroneous. Natural selection is not the same as evolution.
Eugenie C. Scott (2004) p.34

Scientists sometimes colloquially refer to macroevolution as "evolution above the species level," but this term does not do justice to the complexity of topics included within the concept.
Eugenie C. Scott (2004) p.183

Micro- and macroevolution are thus different levels of analysis of the same phenomenon: evolution. Macroevolution cannot solely be reduced to microevolution because it encompasses so many other phenomena: adaptive radiation, for example, cannot be reduced only to natural selection, though natural selection helps bring it about.
Eugenie C. Scott (2004) p.183

If God is intervening into our world, he must be doing so in some measurable way. That's what we do with science. We measure.
Michael Shermer (2006)

If a sect does officially insist that its structure of belief demands that evolution be false, then no compromise is possible. An honest and competent biology teacher can only conclude that the sect's beliefs are wrong and that its religion is a false one.
George Gaylord Simpson (1964)

I do not think that evolution is supremely important because it is my speciality. On the contrary, it is my speciality because it is supremely important.
George Gaylord Simpson (1961)

The extreme view that evolution is basically or over all an orthogenetic process is evidence that some scientists' minds tend to move in straight lines, not that evolution does.
George Gaylord Simpson (1949)

Macroevolution is decoupled from microevolution, and we must envision the process governing its course as being analogous to natural selection but operating at a higher level of organization.
Steven M. Stanley (1975) p.648

The microevolutionary process that adequately describes evolution in a population is an utterly inadaquate account of the evolution of the earth's biota. It is inadequate because the evolution of the biota is more than the mutational origin and subsequent survival or extinction of genes in gene pools. Biotic evolution is also the cladogenetic origin and subsequent survival and extinction of gene pools in the biota.
George C. Williams (1992) p.31

I'm not going to be one of these scientists who keep wafling and saying "oh well, science has it's role, religion has it's role... science has it's own kind of truth and religion has it's own kind of truth... somehow, as we work more and more they will somehow come together." I don't believe that for a minute. I don't think that Darwin would have believed it.
Edward O. Wilson

The fundamantal evolutionary event is a change in the frequency of genes and chromosome configurations in a population. If a population of butterflies shifts through time from 40 percent blue individuals to 60 percent individuals, and if the color blue is hereditary, evolution of a simple kind has occurred.
Edward O. Wilson (1992) p.75

That evolution involves nonadaptive differentiation to a large extent at the subspecies level is indicated by the kinds of differences by which such groups are actually distinguished by systematicists. It is only at the subfamily and family levels that clear-cut adaptive differences become the rule. The principal evolutionary mechanisms in the origin of species must thus be an essentially nonadaptive one.
Sewell Wright (1932) p.38

(concerning more evidence for evolution) Some beating of dead horses may be ethical, where here and there they display unexpected twitches that look like life.
Emile Zuckerkandl and Linus Pauling (1965) p.101

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3,000 new genes discovered in the human genome - dark matter revealed

Let's look a a recent paper published by a large group of medical researchers at the University of California, Los Angeles (USA). The paper was published online a few days ago (Oct. 26, 2015) in Nature Immunology.

The authors clam to have discoverd 3,000 previously unknown genes in the human genome.

The complete reference is ...

Jim Lake and the Eocyte tree

I met James (Jim) Lake for the first time more than 20 years ago but I had a chance to talk to him more recently in Chicago in 2013 [People I Met in Chicago at SMBE2013].

He became famous (infamous?) for challenging the Three Domain Hypothesis of Carl Woese (and friends) and for advocating better methods of constructing gene trees. Jim Lake proposed that eukaryote nuclei arose from within the archaebacterial clade and not as a sister groups of Archaea as the Three Domain Hypothesis claimed. The sister group was the "eocytes," represented at the time by Sulfolobus solfataricus, an archaebacterium that lives in hot springs (~80°C) and uses sulfur as a source of energy.

The origin of eukaryotes and the ring of life

The latest issue of Philosophical Transactions of the Royal Society B (Sept. 26, 2015) is devoted to Eukaryotic origins: progress and challenges. There are 16 articles and anyone interested in this subject has to read all of them.

Many (most) of you aren't going to do that so let me try and summarize the problem and the best current ideas on how to solve it. We begin with the introduction to the issue by the editors, Tom Williams, Martin Embley (Williams and Embly, 2015). Here's the abstract ...

Insulators, junk DNA, and more hype and misconceptions

The folks at Evolution News & Views (sic) can serve a very useful purpose. They are constantly scanning the scientific literature for any hint of evidence to support their claim about junk DNA. Recall that Intelligent Design Creationists have declared that if most of our genome is junk then intelligent design is falsified since one of the main predictions of intelligent design is that most of our genome will be functional.

THEME

Genomes & Junk DNA
They must be getting worried because their most recent posts sounds quite desperate. The last one is: The Un-Junk Industry. It quotes a popular press report on a paper published recently in Procedings of the National Academy of Sciences (USA). The creationists concede that the paper itself doesn't even mention junk DNA but the article in EurekAlert does.

Razib Khan defends old-fashioned evolution theory

Razib Khan writes at Gene Expression. He's a big fan of personal genetics and genome sequencing and, in the past, has been a defender of the Modern Synthesis version of evolutionary theory. In light of the recent Nature discussion on "Does evolutionary theory need a rethink?" (Laland et al. 2014), Razib thought he would re-state his position [Evolution Ever Evolves].

I laid out my position in: Rethinking evolutionary theory. I don't think any of the new ideas like epigenetics, plasticity, facilitated variation etc. are about to change evolutionary theory significantly. However, I do think that the standard version of the 1940s Modern Synthesis was far too rigid and that a modern emphasis on population genetics (including Neutral Theory and more emphasis on random genetic drift) have significantly changed evolutionary theory—something close to a "revolution." The problem is that many scientists, and even many evolutionary biologists, haven't really integrated this change into their way of thinking. This resistance was very well described in a paper by Stephen J. Gould and Richard Lewontin over 45 year ago (Gould and Lewontin, 1978) [What Does San Marco Basilica Have to do with Evolution?]

I think there's already been a "revolution" but most people didn't notice and are still stuck in the 1940s adhering to an old-fashioned version of evolutionary theory that emphasizes adaptation.

Razib Khan doesn't like Gould and doesn't like new-fangled ideas like "neutralism" and "random genetic drift". Let's see what he thinks of the latest kerfluffle.

It seems that rather regularly there is a debate within evolutionary biology, or at least in public about evolutionary biology, where something new and bright and shiny is going to revolutionize the field. In general this does not pan out. I would argue there hasn’t been a true revolution in evolutionary biology since Mendelian genetics and classical Darwinism were fused in the 1920s and 1930s during the period when population genetics as a field was developed, and the famous "synthesis" developed out of the interaction of the geneticists with other domains of evolutionary relevance. This does not mean that there have not been pretenders to the throne. Richard Goldschmidt put forward his "hopeful monsters," neutralism reared its head in the 1970s, and evo-devo was all the rage in the 2000s. Developments that bore scientific fruit, such as neutralism, were integrated seamlessly into evolutionary biology, while those that did not, such as Goldschmidt’s saltationism fell by the wayside. This is how normal science works.

The main point here is whether Neutral Theory and an increased emphasis on random genetic drift "were integrated seamlessly" into the Modern Synthesis view that was popular in the 1960s. Is it true that the way modern population geneticists look at evolution is just a little bit different from the way evolutionary biologists thought about evolution in the 1920s, 1930s, and 1940s? I don't think so. I think there's been a significant shift—so much so that we can no longer refer to the "Modern Synthesis" as the most modern version of evolutionary theory.

Unlike Razib Khan, I am not convinced that most evolutionary biologists have made the shift. At my university, for example, the students must take a first-year course on evolution taught by members of the Dept. of Evolution & Ecology. I see these students in subsequent years and they don't understand the basics of population genetics. Nor do they appreciate the role of neutral alleles and random genetic drift. They are being taught the evolutionary theory of the Modern Synthesis (circa 1960).

Also the debates we are having over junk DNA suggests strongly that most scientists are not familiar with modern population genetics and Neutral Theory.

But every now and then you have a self-declared tribune of the plebs declaring that the revolution is nigh. For decades the late Stephen Jay Gould played this role to the hilt, decrying "ultra-Darwinism," and frankly misrepresenting the state of evolutionary theory to the masses from his perch as a great popularizer. More recently you have had more muted and conventional revisionists, such as Sean Carroll, who promote a variant of evo-devo that acclimates rather well to the climes of conventional evolutionary biology.

I do not believe that Gould misrepresented evolutionary theory to the masses. I believe that Richard Dawkins misrepresented evolutionary theory to the masses.

Like Razib, I'm not a big fan of evo-devo and I don't think it contributes much to fundamental evolutionary theory.

Nature now has a piece out which seems to herald the launching of another salvo in this forever war, Does evolutionary theory need a rethink? It’s written in the form of opposing dialogues. I’m very much in the camp of those believe that there’s no reason to overturn old terms and expectations. Evolutionary biology is advancing slowly but surely into new territory. There’s no problem to solve. The one major issue where I might have to make a stand is that it focusing on genetics is critical to understanding evolution, and dethroning inheritance from the center of the story would eviscerate the major thread driving the plot. The fact that evolutionary biologists have the conceptual and concrete gene as a discrete unit of information and inheritance which they can inspect is the critical fact which distinguishes them from fields which employ similar formalisms but have never made comparable advances (such as economics).

I agree with Razib Khan that genetics (population genetics) is the key to understanding evolutionary theory at the population level. I think we disagree on exactly what version of population genetics we support and on the importance of adaptation.

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Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 205, No. 1161, The Evolution of Adaptation by Natural Selection (Sep. 21, 1979), pp. 581-598. [AAAS reprint] [printable version]

Laland, K., Uller, T., Feldman, M., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G. A., Hoekstra, H. E., Futuyma, D. J., Lenski, R. E., Mackay, T. F. C., Schluter, D. and Strassmann, J. E. (2014) Does evolutionary theory need a rethink? Nature 514, 163-165. [PDF]

Fixing CO2 fixation

How biochemistry students can become multi-millionaires by making plants more efficient. Has someone finally succeeded?

Living organisms need carbon to grow and divide. Many get their carbon atoms from organic molecules such as glucose or acetate that have been synthesized in other species.

Most organisms can fix carbon directly from carbon dioxide by a variety of different reactions but this isn't necessarily the primary source of carbon atoms. (We can fix carbon using pyruvate dehydrogenase, isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and phosphoenolpyruvate carboxykinase (PEPCK) among others.)

What are lncRNAs?

Many genes encode proteins and many other genes specify functional RNAs that do not encode proteins. The "RNA genes" include the classic genes for ribosomal RNAs and tRNAs as well as genes for very well-studied RNAs that carry out catalytic roles in the cell. There are a myriad of small RNAs required for things like splicing and regulation. All species, both prokaryotes and eukaryotes, contain genes for a wide variety or functional RNAs.

Eukaryotes seem to have an abundance of genes for small RNAs that perform a number of specific roles in regulation etc. They also have a lot of DNA regions complementary to long noncoding RNAs or lncRNAs (also lincRNA). The definition of long noncoding RNAs seems arbitrary and ambiguous [see Long Noncoding RNA]. Some of them might even encode proteins!

As a general rule, these RNAs are longer than 200 bp and some scientists put the cutoff at 1000 bp. Simple eukaryotes, such as yeast, don't have a lot of lncRNAs but eukaryotes with large complex genomes that are full of junk DNA seem to have a lot of different lncRNAs. The DNA regions¹ that specify these lncRNAs ar not conserved. This strongly suggest that many of the lncRNAs are spurious nonfunctional transcripts even though some of them have well-characteized functions [see On the function of lincRNAs].

As usual, we have a definition problem. Are "lncRNAs" just a generic class of long noncoding RNAs that include thousands of nonfunctional molecules that are nothing more than junk RNA? Or, does the term "lncRNA" refer only to the subset that has a function? If it's the latter, then we should probably be referring to "putative" lncRNAs most of the time since the vast majority have not been shown to have a function. (There are about 10,000 of these RNAs in humans.)

I don't see how you can avoid the elephant in the room whenever you talk about lncRNAs. The most important question in NOT whether some of them have a function—that was demonstrated 30 years ago. The important question is whether the majority, or even a substantial minority, have a function.

That's why I was eager to read a short review by Rinn and Guttman in a recent issue of Science (Rinn and Guttman, 2014). They describe two lncRNAs that probably play a role in organizing chromatin within the nucleus (Xist and Neat1, both fram mammals). That's cool.

Then they say,

Collectively, these studies suggest that lncRNAs may shape nuclear organization by using the spatial proximity of their transcription locus as a means to target preexisting local neighborhoods. lncRNAs can in turn modify and reshape the organization of these local neighborhoods to establish new nuclear domains by interacting with various protein complexes, including chromatin regulators. Once established, a lncRNA can act to maintain these nuclear domains through active transcription and recruitment of interacting proteins to these domains. While the mechanism for how lncRNAs establish these domains is not fully understood, it is becoming increasingly clear that lncRNAs are important at all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization.

It sure sounds like they are describing a particular function (nuclear organization) to the majority of lncRNAs. But what if 90% of all 10,000 lncRNAs have no function and what if only 100 of the remaining functional lncRNAs are involved in nuclear organization? That means there are 900 functional lncRNAs that play a different role in the cell?

If that were true, you would write that last paragraph very differently. If you recognize the elephant, you might say something like this ....

Very few lncRNAs have been shown to have a function and there's a very good chance that most of them are spurious transcripts that have no function. However, a small percentage do seem to have a function. In this review we have identified some long noncoding RNAs that appear to be involved in nuclear organization. We propose to call these RNAs "noRNAs" for "nuclear organizer RNAs" on the grounds that once a function has been identified we should stop referring to them as lncRNAs.

But that doesn't sound nearly as exciting as the subtitle of the article, "Long noncoding RNAs may function as organizing factors that shape the cell nucleus" or the quotation that's prominently displayed in a box in the center of the page, "... it is becoming increasingly clear that IncRNAs are important in all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization." When did science become so dedicated to hype over substance? I must have missed the memo.

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1. I use "DNA regions" instead of "genes" because the definition of a gene requires that the gene product be functional. You can't call them genes unless you have demonstrated that the RNA has a function.

Rinn, J. and Guttman, M. (2014) RNA and dynamic nuclear organization. Science 345"1240-1241 [doi: 10.1126/science.1252966]

Michael Behe's final thoughts on the edge of evolution

We've been having an interesting discussion about chloroquine resistance and the Edge of Evolution. It began last month when Michael Behe started bragging that his "prediction" had been confirmed by a recent paper [A Key Inference of The Edge of Evolution Has Now Been Experimentally Confirmed]. It didn't take long for Casey Luskin to jump on the bandwagon [So, Michael Behe Was Right After All; What Will the Critics Say Now?]. Luskin demanded an apology from Behe;s critics.

It turns out that Behe and Luskin are wrong and the recent results published by Summers et al. (2014) actually refute most of Micheal Behe's calculations. PZ Myers pointed out that Behe's critics were mostly¹ right when they criticized the original calculations in The Edge of Evolution [Quote-mined by Casey Luskin!].

How many genes do we have and what happened to the orphans?

How many genes in the human genome? There's only one correct answer to that question and that's "we don't know."

The main problem is counting the number of genes that produce functional RNA molecules. The latest Ensembl results are based on build CRch37 from February 2009 and the GENCODE annotation from last year (GENCODE 19) [see Human assembly and gene annotation and Harrow et al., 2014]

The most recent estimates are 20,807 protein-encoding genes, 9,096 genes for short RNAs, and 13,870 genes for long RNAs. This gives 43,773 genes. Nobody knows for sure how many of the putative genes for RNAs actually exist. They may only be a few thousand functional genes in this category.

It's a lot easier to figure out whether a gene really encodes a functional protein so most of the annotation effort is focused on those genes. I want to draw your attention to a recent paper by Ezkurdia et al. (2014) that discusses this issue. The authors begin with a bit of history ...

ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function

Theme

Better BiochemistryThe American Society for Biochemistry and Molecular Biology (ASBMB) has decided that the best way to teach undergraduate biochemistry is to concentrate on fundamental principles rather than facts and details. This is an admirable goal—one that I strongly support.

Over the past few months, I've been discussing the core concepts proposed by Tansey et al. (2013) [see Fundamental Concepts in Biochemistry and Molecular Biology]. The five concepts are:

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]

Alan Sokal explains the scientific worldview

As most of you know, I prefer a broad definition of science as a way of knowing. I usually refer to it as a way of knowing based on rational thinking, evidence, and healthy skepticism but there are many other ways of expressing the same idea.

However you say it, the broad definition of the scientific way of knowing covers everything, not just physics, biology, chemistry and geology. Not only that, it appears to be the only way of knowing that has proven to be successful. Thus, I can tentatively conclude that it is the only way of knowing until someone provides an example of knowledge obtained by another way of knowing.

Alan Sokel has posted three articles on Massimo Pigliucci new blog, Scientia Salon [What is science and why should we care? — Part III].

Here's how he describes science in Part III.

We have now travelled a long way from “science,” understood narrowly as physics, chemistry, biology and the like. But the whole point is that any such narrow definition of science is misguided. We live in a single real world; the administrative divisions used for convenience in our universities do not in fact correspond to any natural philosophical boundaries. It makes no sense to use one set of standards of evidence in physics, chemistry and biology, and then suddenly relax your standards when it comes to medicine, religion or politics. Lest this sound to you like a scientist’s imperialism, I want to stress that it is exactly the contrary. As the philosopher Susan Haack lucidly observes:

“Our standards of what constitutes good, honest, thorough inquiry and what constitutes good, strong, supportive evidence are not internal to science. In judging where science has succeeded and where it has failed, in what areas and at what times it has done better and in what worse, we are appealing to the standards by which we judge the solidity of empirical beliefs, or the rigor and thoroughness of empirical inquiry, generally.” [21]

The bottom line is that science is not merely a bag of clever tricks that turn out to be useful in investigating some arcane questions about the inanimate and biological worlds. Rather, the natural sciences are nothing more or less than one particular application — albeit an unusually successful one — of a more general rationalist worldview, centered on the modest insistence that empirical claims must be substantiated by empirical evidence.

Conversely, the philosophical lessons learned from four centuries of work in the natural sciences can be of real value — if properly understood — in other domains of human life. Of course, I am not suggesting that historians or policy-makers should use exactly the same methods as physicists — that would be absurd. But neither do biologists use precisely the same methods as physicists; nor, for that matter, do biochemists use the same methods as ecologists, or solid-state physicists as elementary-particle physicists. The detailed methods of inquiry must of course be adapted to the subject matter at hand. What remains unchanged in all areas of life, however, is the underlying philosophy: namely, to constrain our theories as strongly as possible by empirical evidence, and to modify or reject those theories that fail to conform to the evidence. That is what I mean by the scientific worldview.

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Hat Tip: Jerry Coyne: Alan Sokal highlights the incompatibility of science and religion

Why does Stephen H. Webb use the word "Darwinism"?

We know why the IDiots use the words "Darwinist" and "Darwinism" to describe evolutionary biologists and modern evolutionary theory. There are three main reasons.

1. They want their flocks to believe that modern scientists worship Charles Darwin and his 150 year-old theory so that when they discredit him—as they are constantly trying to do—it reflects on evolution.
2. They want to link modern evolutionary biology to social Darwinism and it's easier to do so if they refer to evolutionary biologists as Darwinists.
3. They are too stupid to realize that there's a lot more to modern evolutionary biology than natural selection.

Every time you challenge creationists on this point they find some way to defend their use of Darwinism rather than just say "evolutionary biology" or "modern evolutionary theory." There's a reason for this (see above).

Stephen H. Webb is the latest example. Apparently his use of "Darwinism" was challenged so he wrote a blog post on Evolution News & Views (sic) defending it The Strange Mental World of Darwinian Fundamentalists. I hope you appreciate the irony in the title.

The crystal structure of E. coli RNA polymearse σ70 holoenzyme

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The Journal of Biological Chemistry (JBC) publishes a little booklet of the "best of jbc." The latest copy arrived in the mail a few days ago and it alerted me to a paper published one year ago on the structure of Escherichia coli RNA polymerase σ⁷⁰ holoenzyme (Murikami, 2013).¹

The control of transcription initiation is a very important topic in biochemistry and molecular biology and the events in E. coli are the model for transcription initiation in all other species. We know more about RNA polymerase and promoter sites in E. coli than in any other species.

Territorial demarcation and the meaning of science

Massimo Pigliucci doesn't get enough respect. He's upset by the "New Atheists" who place a great deal of emphasis on the scientific way of knowing and demand evidence that any other way of knowing is successful. These mean New Atheists (I count myself as one of them) use a very broad definition of science that includes most of the admirable activities of philosophers. Pigliucci is mostly a philosopher and he doesn't think that philosophy is getting enough respect from the New Atheists.

Here's the cartoon he published on his blog to illustrate the problem [see Rationally Speaking cartoon: Sam Harris].

What do they mean when they say they want to extend the Modern Synthesis?

As far as I'm concerned, the "Modern Synthesis" has been replaced by modern evolutionary theory that incorporates Nearly-Neutral Theory and random genetic drift as an important mechanism of evolution [see Is the "Modern Synthesis" effectively dead? ]. This extension, and replacement, of the 1940s version of evolutionary theory took place in mainly in the 1970s.

If I'm correct, then why all the fuss in the 21st century about extending the Modern Synthesis?

I think there are two things going on here. First, there are a bunch of biologists who want to incorporate their favorite fad into modern evolutionary theory. They think that their ideas are so revolutionary that this requires an extensive revision of evolutionary theory. Second, those biologists seem to have been asleep during the 1970s when the Modern Synthesis died so they are fighting a strawman.

Vertebrate Complexity Is Explained by the Evolution of Long-Range Interactions that Regulate Transcription?

The Deflated Ego Problem is a very serious problem in molecular biology. It refers to the fact that many molecular biologists were puzzled and upset to learn that humans have about the same number of genes as all other multicellular eukaryotes. The "problem" is often introduced by stating that the experts working on the human genome project expected at least 100,000 genes but were "shocked' when the first draft of the human genome showed only 30,000 genes (now down to about 25,000). This story is a myth as I document in: Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome. Truth is, most knowledgeable experts expected that humans would have about the same number of genes as other animals. They realized that the differences between fruit flies and humans, for example, didn't depend on a host of new human genes but on the timing and expression of a mostly common set of genes.

This isn't good enough for many human chauvinists. They are still looking for something special that sets human apart from all other animals. I listed seven possibilities in my post on the deflated ego problem:

Science Doesn't Have All the Answers but Does It Have All the Questions?

Jerry Coyne has been following the debate between Steven Pinker and Leon Wieseltier on the topic of scientism [see The final round: Pinker vs. Wieseltier on scientism]. Jerry seems to agree with both Pinker and Wieseltier that there are "two magisteria" (science and humanities) ...

[Wieseltier] calls for a “two magisteria” solution, with science and humanities kept separate, but with “porous boundaries.” But that is exactly what Pinker called for, too! Wieseltier claims that Pinker and other advocates of scientism advocate “totalistic aspirations,” i.e., the complete takeover of humanities by the sciences (“unified field theories,” Wieseltier calls them), but Pinker explicitly said that he wasn’t calling for that.

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As you can see above, Steve never argued that science is, or should be, supreme in all the contexts. Indeed, in his earlier piece he noted that art and literature, while they might be informed in some ways by science, nevertheless have benefits independent of science. To me, those benefits include affirming our common humanity, being moved by the plight of others, even if fictional, and luxuriating in the sheer beauty of music, words, or painting. (Note, though, that one day science might at least explain why we apprehend that beauty.)

I'm not sure how Pinker, Wieseltier, and Coyne are defining science but it's clear that they aren't using the same definition I use.

I think that science is a way of knowing based on evidence and logic and healthy skepticism. I think that all disciplines seeking knowledge use the scientific approach. This is the broad definition of science used by many philosophers and scientists.

Maarten Boudry discusses, and accepts, this definition in his chapter on "Loki's Wager and Lauden's Error" in Philosophy of Pseudescience: Reconsidering the Demarcation Problem. Boudry says that the distinction between the ways of knowing used by biologists, philosophers, and historians are meaningless and there's no easy way to distinguish them (territorial demarcation). On the other hand, there is a way to distinguish between good scientific reasoning and bad scientific reasoning like Holocaust denial.

I have expressed little confidence in the viability of the territorial demarcation problem, and even less interest in solving it. Not only is there no clear-cut way to disentangle epistemic domains like science and philosophy, but such a distinction carries little epistemic weight. The demarcation problem that deserves our attention is the one between science and pseudoscience (and the analogous ones between philosophy and pseudophilosophy and between history and pseudohistory).

Sven Ove Hanson is more specific because he actually defines "science in a broad sense" in a way that I have been using it for several decades. This is from his chapter on "Defining Pseudoscience and Science" in Philosophy of Pseudescience: Reconsidering the Demarcation Problem.

Unfortunately neither "science" nor any other established term in the English language covers all the disciplines that are parts of this community of knowledge disciplines. For lack of a better term, I will call them "science(s) in the broad sense." (The German word "Wissenschaft," the closest translation of "science" into that language, has this wider meaning; that is, it includes all the academic specialties, including the humanities. So does the Latin "scientia.") Science in a broad sense seeks knowledge about nature (natural science), about ourselves (psychology and medicine), about our societies (social science and history), about our physical constructions (technological science), and about our thought construction (linguistics, literary studies, mathematics, and philosophy). (Philosophy, of course, is a science in this broad sense of the word.)

If this is what we mean by science" then there's no difference between the ways we try to acquire knowledge in the humanities or the natural sciences and the debate between Pinker and Wieseltier takes on an entirely different meaning.

There aren't "two magisteria" but only one. Unless, of course, someone is willing to propose a successful non-scientific way of knowing. I have asked repeatedly for examples of knowledge ("truth") that have been successfully acquired by any other way of knowing. So far, nobody has come up with an answer so we can tentatively conclude that science (in the broad sense) is the only valid way of acquiring true knowledge.

Clearly we don't have all the answers to everything so it's clear that neither science nor anything else has all the answers. What about the questions? Are there any knowledge questions that science (in the broad sense) can't address? I don't think there are. I think "science" covers all the questions even though it doesn't (yet) have all the answers.

If this is "scientism" then I'm guilty. What is the alternative? Is it revelation (revealed truth)? Or is there some other way of knowing that I haven't heard about?

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