Saturday, October 01, 2016

Extending evolutionary theory? - Paul Brakefield

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Paul Brakefield's talk on Does the way in which development works bias the paths taken by evolution?

Developmental bias was defined in a seminal review some thirty years ago that resulted from an early ‘meeting of minds’ of developmental and evolutionary biologists driven by John Maynard Smith and Lewis Wolpert. Although there has been dramatic progress since then in revealing in exquisite detail how morphologies develop, there are few well-worked case studies of potential developmental bias, as well as little understanding of how important the process has been in shaping the evolution of animal form. Therefore, it is timely to think about what is needed to facilitate the analysis of the extent to which patterns of evolutionary diversification are biased by how development works, and indeed whether it is useful to distinguish this process from that of genetic channeling.
Here are two possible questions for Paul Brakefield ...
Stephen Jay Gould published Ontology and Phylogeny in 1977. He wrote extensively about developmental constraints until his death in 2002. Richard Dawkins also wrote about developmental constraints, most notably in his discussion of whether pigs could fly in The Blind Watchmaker. How do your views differ from those that have been around for decades and why do you think it requires a modification of evolutionary theory today?


In The Structure of Evolutionary Theory, Gould wrote 270 pages on developmental constraints emphasizing their POSITIVE role in evolution as opposed to just their negative effects on limiting natural selection. He said,
The concept of constraint must include theoretically legitimate and factually important positive meanings—i.e., constraints as directing causes of particular evolutionary changes—rather than only the negative connotations of structural limitations that prevent natural selection from crafting an alteration that would otherwise be favored and achieved.
How do your views differ from what Gould wrote about so extensively in 2001?

Extending evolutionary theory? John Dupré

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for John Dupré's talk on The ontology of evolutionary process.

Ontology is the branch of philosophy that considers in the most general way the nature of reality. An ancient and fundamental ontological question is whether reality is ultimately composed of stable things or is everywhere processual, in flux. A number of distinguished 20th century biologists, including, for instance Conrad Waddington, Joseph Needham, and Ludwig von Bertalanffy, thought it important to stress the fundamentally dynamic, processual character of living systems. While evolution is of course a process, it is often implicitly supposed that the entities that evolve or that constitute the evolutionary process, whether genes, organisms, populations, or whatever, are kinds of things. Following the authors mentioned above, I argue that these too are better seen as processes, albeit highly stabilised processes.

In this talk I shall argue that a process ontology is correct and that it has important implications for how we should think about evolution. First, with regard to the constituents of the evolutionary process, process ontology highlights the limitations of atemporal descriptions of organisms, for example in terms of gene sequence, and of populations as atemporal abstractions from evolving lineages. Second, whereas in an ontology of things the primary explanatory task is that of understanding change, in a world of process it is of equal or even greater importance to explain stability. The first step in articulating a fully processual view of evolution is to describe the processes that sustain persisting lineages. Doing so should provide fresh perspectives on the processes that can produce changes in lineages.
John Dupré is a philosopher. He talks like a philosopher. I don't understand what he's talking about and, quite frankly, I don't care. No questions for him.

Friday, September 30, 2016

Extending evolutionary theory? - Tobias Uller

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Tobias Uller's talk on Heredity and evolutionary theory.

Heredity is a central concept in biology and one of the core principles needed for evolution by natural selection. For most of the past century inheritance has been conceptualised and defined in terms of transmission of genes. Emerging developmental perspectives on evolution appear to challenge this perspective in several ways. Here I will explain how evolutionary biologists treat heredity conceptually and mathematically. These perspectives are heuristically useful but they impose a certain structure on evolutionary theory and leave out aspects of heredity that may be important to understand evolution. An alternative representation understands heredity as an outcome of developmental processes. I will suggest that this perspective helps to clarify how different mechanisms of inheritance contributes to evolution.
I have to wait to hear this talk in order to figure out what he means. From reading the abstracts to some of his papers I think he's going to promote plasticity and epigenetics ... or maybe maternal effects.

In any case, the standard understanding of "heredity" is when alleles (genes) are passed from one generation to another. The process usually involves DNA replication and cell division but it encompasses horizontal transmission. I'll be interested in hearing about other mechanisms of heredity.

Extending evolutionary theory? - Russell Lande

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Russell Lande's talk on Evolution of phenotypic plasticity.

The scope and relative rates of adaptive phenotypic change from plasticity versus standard Darwinian evolution adaptive genetic changes depend on the time scale and the range of phenotypic alteration being considered. This distinction becomes blurred when plasticity itself evolves. Using standard methods from neo-Darwinian population genetic theory, I review recent models on the evolution of phenotypic plasticity in changing environments, emphasising the roles of environmental predictability and costs of plasticity in constant and labile characters. Adaptation to a novel environment may often occur by rapid evolution of increased plasticity followed by slow genetic assimilation of the new phenotype. I elucidate the connection between environmental tolerance and plasticity. The theory of evolution of phenotypic plasticity is an important extension to neo-Darwinism, but does not necessitate a major revision of its foundations. The same conclusion applies to epigenetic mechanisms including interactions between genes or tissues in development, and to transgenerational phenotypic effects such as somatic inheritance, maternal effects and DNA methylation.
I could ask this question ...
Imagine a small group of organisms that find themselves in a new environment. Let's assume they have a genome containing 10,000 genes. How do they select for increased phenotypic plasticity in order to better adapt to the new environment? Are all genes affected or just a small number that might increase fitness? Which genes acquire additional potentially beneficial alleles that were not present in the small population before it encountered the new environment and how does that mechanism work?

Extending evolutionary theory? - Sonia Sultan

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Sonia Sultan's talk on Developmental plasticity: re-conceiving the genotype.

For several decades, the phenotype of an organism (i.e, its traits and behaviour) has been studied as the outcome of developmental ‘instructions’ coded in its DNA. According to this model, each genotype is expressed as a specific phenotype; individual differences in fitness-related traits are seen to arise from this stably inherited internal information. This simplified view of development provides the foundation for a Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. As developmental biologists are aware, however, an organism’s phenotype is not strictly pre-determined by its genotype, but rather takes shape through the interplay of genetic factors with the organism’s environmental conditions. By means of this developmental plasticity, a given genotype may express different phenotypes under different environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction.

Re-conceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical insights, as illustrated by norm of reaction data from Polygonum plants. Plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Environmental responses can extend across generations via effects on progeny growth and fitness, a form of inherited yet non-genetic adaptation. Finally, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent.
Here's a possible question ...
Back in the 1960s we learned that transcription of the lac operon in E. coli was regulated by the environment. This regulation, activation or repression, was passed on to daughter cells as the cells divided. Why didn't this discovery lead to a major revision of evolutionary theory?

Extending evolutionary theory? - Douglas Futuyma

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Douglas Futuyma's talk on The evolutionary synthesis today: extend or amend?

Evolutionary theory has been extended almost continually since the Evolutionary Synthesis, but the principal tenets of the Synthesis have been strongly supported, the single most important exception being the greater importance accorded genetic drift, especially in molecular evolution. The calls for an extended synthesis today are largely a continuation of this process. Some elements of the EES movement, such as the role of niche construction, are welcome emphases on long recognised but perhaps under-studied processes. The union of population genetic theory with mechanistic understanding of molecular and developmental processes is a potentially productive conjunction of ultimate and proximal causation; but the latter does not replace or invalidate the former. Newly discovered molecular genetic phenomena have been easily accommodated by orthodox evolutionary theory in the past, and this appears to hold also for phenomena such as epigenetic inheritance today. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation. Evolutionary theory today will continue to be extended, but there is no sign that it requires emendation.
Here are two possible questions for Futuyma.
Why do you think that most participants at this meeting seem to be unaware of random genetic drift and the evolution of structures and phenotypes by nonadaptive processes? Doesn't this strike you as bizarre for a group that's so concerned about evolutionary theory?

As you explain in your textbook, describing the pathways to modern species contributes to the FACT of evolution and the FACT of descent with modification but how those genetic changes actually occur and become fixed is part of evolutionary theory. Do you distinguish between evolutionary theory and the actual history of life?

Extending evolutionary theory? - Gerd B. Müller

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Gerd B. Müller's talk on The extended evolutionary synthesis.

Since the last major conceptual integration in evolutionary biology – the Modern Synthesis of the 1940s – the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and of multiple inheritance systems, the -omics revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge regarding the mechanisms of evolutionary change. Some of these results are in agreement with the classical Synthetic Theory and others reveal different properties of evolutionary change. A renewed and extended evolutionary synthesis unites pertinent concepts emerging from these novel fields with elements from the standard theory, but it differs from the latter in its core logic and predictive capacities. Whereas the classical theory had concentrated on genes and adaptive variation in populations, the extended framework emphasises the role of constructive processes, environmental induction, and systems dynamics in the evolution of organismal complexity. Single level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, this entails a revised understanding of the role of natural selection in the evolutionary process. The extended evolutionary synthesis complements the traditional gene centric perspective and stimulates research into new areas of evolutionary biology.
There are so many things I could ask. I'm tempted to ask the following question,
Many of us believe that the role of adaptation in evolutionary theory was considerably revised by the development of Neutral Theory and Nearly-Neutral Theory almost 50 years ago. These concepts, and the importance of random genetic drift, have been integrated into the standard textbooks for many decades. Why don't you ever talk about those challenges to the old 1940s version of the Modern Synthesis? Is it because you don't think they were significant additions to the old theory?

Friday, September 23, 2016

A philosopher's view of random genetic drift

Random genetic drift is a process that alters allele frequencies within a population. The change is due to "random" events. It differs from natural selection where the change is due to selection for alleles that confer selective advantage on the reproductive success of an individual. Here's one description,

If a population is finite in size (as all populations are) and if a given pair of parents have only a small number of offspring, then even in the absence of all selective forces, the frequency of a gene will not be exactly reproduced in the next generation because of sampling error. If in a population of 1000 individuals the frequency of "a" is 0.5 in one generation, then it may by chance be 0.493 or 0.505 in the next generation because of the chance production of a few more or less progeny of each genotype. In the second generation, there is another sampling error based on the new gene frequency, so the frequency of "a" may go from 0.505 to 0.501 or back to 0.498. This process of random fluctuation continues generation after generation, with no force pushing the frequency back to its initial state because the population has no "genetic memory" of its state many generations ago. Each generation is an independent event. The final result of this random change in allele frequency is that the population eventually drifts to p=1 or p=0. After this point, no further change is possible; the population has become homozygous. A different population, isolated from the first, also undergoes this random genetic drift, but it may become homozygous for allele "A", whereas the first population has become homozygous for allele "a". As time goes on, isolated populations diverge from each other, each losing heterozygosity. The variation originally present within populations now appears as variation between populations.

Suzuki, D.T., Griffiths, A.J.F., Miller, J.H. and Lewontin, R.C.
in An Introduction to Genetic Analysis 4th ed. W.H. Freeman (1989 p.704)

A theology student doesn't like Jerry Coyne's book Faith vs. Fact

A theology student named Derrick has written a review of Jerry Coyne's book Faith vs. Fact. He didn't like it very much. (Duh!) You can read his review at: Jerry Coyne, Faith Vs. Fact: Why Science and Religion Are Incompatible.

Before reading that review, let's make sure we understand Jerry's position. Here's what he says on page xx of his book.
My main thesis is narrower and, I think, more defensible: understanding reality, in the sense of being able to use what we know to predict what we don't, is best achieved using the tools of science, and is never achieved using the methods of faith. That is attested by the acknowledged success of science in telling us everything from the smallest bits of matter to the origin of the universe itself—compared with the abject failure of religion to tell us anything about gods, including whether they exist.

Can we ever know if god exists?

A recent issue of New Scientist (Sept. 3-9) is billed as "The Metaphysics Issue: How science answers philosophy's deepest questions." This is probably not going to make philosophers happy.

Several of the articles are devoted to the "big questions." According to New Scientist these questions are normally left to philosophers but the editors go on to say, "Now, though, scientists are increasingly claiming them as their own ..." Let's look at one of the questions: Can we ever know if God exists?. Here's the part I want to discuss ...
No one has proved that God exists, but then no one has proved there is no God. Is working out the truth a supernatural feat?

... Gallons of ink and blood have been spilled over this question but have largely got us nowhere. Belief in a god or several gods is a leap of faith. So is disbelief. The only coherent and rational position is agnosticism.
Really? Disbelief in Thor, Zeus, Quetzalcoatl, and Gitchi Manitou is a "leap of faith"? I have not been convinced by any evidence that these gods exist. Is that irrational and incoherent?

Thursday, September 22, 2016

Ten adaptationist stories about recent human evolution

Does this video contribute to the general understanding and appreciation of science?

  2. Lactose tolerance: PROBABLY A TRUE ADAPTATION
  4. Losing wisdom teeth: PROBABLY FALSE ADAPTATION
  5. Smaller brains: LIKELY FALSE ADAPATION
  6. Getting shorter: ALMOST CERTAINLY FALSE
  7. Malaria resistance: CERTAINLY TRUE
  8. HIV Resistance: TRUE BUT TRIVIAL

Wednesday, September 21, 2016

An Anglican says that science and religion don't conflict

Are you surprised to hear a religious person say that science and religion are not in conflict? Of course you aren't. That's just what you expect religious people to say.

Why in the world would Nature publish an article where an Anglican makes such a claim? [See Religion and science can have a true dialogue] And why in the world should its readers pay any attention at all to the nonsensical first paragraphs ...
I work for the Archbishops’ Council in the Church of England, and this summer I did something that many people would think is impossible. I sat in a dark lecture theatre engrossed in a computationally generated 3D journey through the Universe. Virtual stars whizzed past and seemed narrowly to miss colliding with my head as we accelerated through galaxies and past exploding stars. I listened to cosmologists speak on research into dark matter, particle physics, the rate at which the growth of the Universe is accelerating and the possibi­lity of multi­verses. I asked questions and they responded.

According to the popular narrative on the relationship between science and religion, this event should not have happened. The entire audience was made up of bishops and church leaders. Science and faith, we are constantly told, are in conflict and have little in common.
Really? What "popular narrative" says that Anglican church leaders can't learn about science? What "popular narrative" says that Anglicans cannot accept the findings of physics and cosmology? Who says that?

The problem here is not the ridiculous false claim but the fact that it's published in a leading science journal. I'm not aware of any Nature articles on the conflict between science and religion and the claim that belief in god(s) is not compatible with a scientific way of knowing. Why is Nature getting involved in this debate and why is it taking sides?

Read Jerry Coyne's take on this article at: Fulsome accommodationism in the journal Nature.1

1. Keep in mind that Jerry uses the word "accommodationist" to mean anyone, atheist or theist, who thinks that science and religion are compatible. In its original sense, the word "accommodationist" referred only to those people who Dawkins referred to as "Neville Chamberlain evolutionists." These appeasers were atheists who argued that science and religion are compatible. Only atheists can be accomodationists according to this original definition—they one I still adhere to. I don't think it's noteworthy that religious people try to make science and religion compatible.

Tuesday, September 20, 2016

Atheism is a catastrophe for science according to Michael Egnor

Michael Egnor doesn't like atheists. He got a bit upset about a recent post by PZ Myers so he responded on Evolution News & Views (sic) with: Atheism Is a Catastrophe for Science.

Modern theoretical science arose only in the Christian milieu. Roger Bacon, Copernicus, Galileo, Newton, Kepler, Faraday, Pasteur, Maxwell and countless other pioneers of the Scientific Enlightenment were fervent Christians who explicitly attributed the intelligibility in nature to God's agency, and even 20th-century scientists like Einstein and Heisenberg and Schrodinger and Rutherford and Planck attributed nature to intelligent agency. Einstein famously explained his quest: "I want to know God's thoughts..."

Vanishingly few great scientists have attributed the world to "undirected processes." Atheism, in fact, has a dismal record in science. For much of the 20th century, a third of humanity lived under the boot of atheist ideology. What was the great science produced by atheist scientists in the Soviet Union? What are the scientific contributions of Communist China and Cuba and Vietnam and Albania? Compare the scientific output of East Germany (atheist) to that of West Germany (Lutheran and Catholic). Compare the scientific output of North Korea (atheist) to that of South Korea (Christian and Buddhist).

The fact is that during the 20th century atheist ideological systems that "assum[ed] that the world is a product of natural, undirected processes" governed a third of humanity. What's the scientific "track record" of atheism? Atheism had its run: it heralded a scientific dark age in any nation unfortunate enough to fall under its heel. Atheism is as much a catastrophe for science as it is a catastrophe for humanity. The only thing atheist systems produced reliably (and still produce reliably) is corpses.
Google is my friend. I found a Wikipedia article on List of nonreligious Nobel Laureates. Here are the Nobel Laureates in science who didn't believe in any gods. This is part of the "scientific track record of atheism."

Svante Arrhenius
Paul D. Boyer
Frédéric Joliot-Curie
Irène Joliot-Curie
Richard R. Ernst
Herbert A. Hauptman
Roald Hoffmann
Harold W. Kroto
Jean-Marie Lehn
Peter D. Mitchell
George Andrew Olah
Wilhelm Ostwald
Linus Pauling
Max Perutz
Frederick Sanger
Michael Smith
Harold Urey

Zhores Alferov
Hannes Alfvén
Philip Warren Anderson
John Bardeen
Hans Bethe
Patrick Blackett
Nicolaas Bloembergen
Niels Bohr
Percy Williams Bridgman
Louis de Broglie
James Chadwick
Subrahmanyan Chandrasekhar
Marie Curie
Pierre Curie
Paul Dirac
Albert Einstein
Enrico Fermi
Richard Feynman
Val Logsdon Fitch
James Franck
Dennis Gabor
Murray Gell-Mann
Vitaly Ginzburg
Roy J. Glauber
Peter Higgs
Gerard 't Hooft
Herbert Kroemer
Lev Landau
Leon M. Lederman
Albert A. Michelson
Konstantin Novoselov
Jean Baptiste Perrin
Isidor Isaac Rabi
C. V. Raman
William Shockley
Erwin Schrödinger
Jack Steinberger
Igor Tamm
Johannes Diderik van der Waals
Eugene Wigner
Steven Weinberg
Chen-Ning Yang

Physiology and Medicine
Julius Axelrod
Robert Bárány
J. Michael Bishop
Francis Crick
Max Delbrück
Christian de Duve
Howard Florey
Camillo Golgi
Frederick Gowland Hopkins
Andrew Huxley
François Jacob
Sir Peter Medawar
Jacques Monod
Thomas Hunt Morgan
Herbert J. Muller
Élie Metchnikoff
Rita Levi-Montalcini
Hermann Joseph Muller
Paul Nurse
Ivan Pavlov
Richard J. Roberts
John Sulston
Albert Szent-Györgyi
Nikolaas Tinbergen
James Watson

Saturday, September 17, 2016

"The Soul of the Matter"

Meet Bruce Buff. He's a big fan of the Discovery Institute as he explains in this video.

Bruce Buff has written a novel (fiction) called The Soul of the Matter. The Intelligent Design Creationists are all over it. So far they've put up two posts advertising the novel: Excerpt: The Soul of the Matter, Chapter 3; Excerpt: The Soul of the Matter, Chapter 4.

Here's the description from the publisher's website ...
A scientist’s claim that he’s found the secrets of the universe's origin encoded in DNA sparks a race against time to uncover the truth in this fast-paced thriller of science and faith, power and murder, loss and redemption.

Dan Lawson, a former government cyber-intelligence analyst, is surprised to be contacted by his estranged friend Stephen Bishop, a renowned geneticist. Stephen says that he’s discovered amazing information within DNA, including evidence of a creator, and needs Dan’s help to protect his findings. Dan is skeptical and wonders whether he is being manipulated, or if the recent illness of Stephen’s only child, Ava, has caused his childhood friend to fall back on religion for answers to questions best left to science. Spurred by his desire for proof that life has meaning, however, Dan puts aside his doubts and agrees to help.
I haven't read the book but there may be a clue on the cover. I think the amazing information might be that the DNA helix is left-handed instead of right-handed [On the handedness of DNA ]. It's a little hard to tell from the image on the cover.

Monday, September 05, 2016

How many lncRNAs are functional: can sequence comparisons tell us the answer?

A large percentage of the human genome is transcribed at some time or another during development. The vast majority of those transcripts are very rare transcripts that look very much like spurious products of accidental transcription initiation at sequences resembling true promoters. They have been rejected by genome annotators. They do not define genes. They are junk RNA. Pervasive transcription does not mean that most of the genome is functional.

Among the transcripts is a class called long non-coding RNAs or lncRNAs. These are usually defined as capped and polyadenylated transcripts longer than 200 nucleotides. Many of them are processed by splicing. They look a lot like mRNA except they don't encode any polypeptides.1

We don't know how many of these RNAs exist because different labs use different criteria to describe them. Some databases exclude low abundance lncRNAs and some include non-polyadenylated RNAs. There is general agreement that they number in the tens of thousands. A common number in the scientific literature is 60,000 lncRNAs.