Extending evolutionary theory? - Karola Stotz

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 Karola Stotz's talk on
Developmental niche construction.

In the last decade niche construction has been heralded as the neglected process in evolution. But niche construction is just one way in which the organism’s interaction with, and construction of the environment, can have potential evolutionary significance. This constructed environment not just selects for, it also produces new variation. Nearly three decades ago, and in parallel with Odling-Smee’s book chapter ‘Niche-constructing phenotypes’, West and King introduced the ‘Ontogenetic Niche’ to give the phenomena of exogenetic inheritance a formal name. Since then a range of fields in the life sciences and medicine has amassed evidence that parents influence their offspring by means other than DNA (parental effects). Diverse scientists use different theoretical constructs for overlapping sets of processes, all of which show one way or another how heritable variation can be environmentally induced and developmentally regulated. Here I propose the concept of ‘developmental niche construction’ as a framework to integrate findings from fields ranging from molecular biology to developmental psychology. It elucidates how a diverse range of mechanisms contributes to the transgenerational transfer of developmental resources. This talk will explore the overall significance of these developments in the life sciences, and particularly how they advance the ongoing integration of development, heredity, ecology, and evolution.

Karola Stotz is a philosopher at Macquarie University in Sydney, Australia.

Organisms interact with, and change, their environment. This is hardly news but it's being promoted as one of the "new trends in evolutionary biology." Why?

I think I'll ask her what's "new" about this?

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Scientists at the Lawrence Berkeley National Laboratory do not understand basic molecular biology

The Lawrence Berkeley National Laboratory employs a number of scientists who work on genes and gene expression. Here's part of a press release published two days ago [For Normal Heart Function, Look Beyond the Genes: Loss of noncoding elements of genome results in heart abnormalities, finds Berkeley Lab study]. It demonstrates that the workers at this National Laboratory don't understand anything about mammalian genomes.

The only other possibility is that the person who wrote the press release doesn't understand molecular biology¹ and the scientists who work there just don't care what their institution publishes.

Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered “junk” because they do not code for specific proteins.

Regular readers of this blog know that ...

1. No knowledgeable scientist ever said that all noncoding DNA was junk.
2. We've known about regulatory sequences for half a century. We've known about enhancers—just another kind of regulatory sequence—for thirty-five years. Nobody ever thought they were junk. Nobody ever thought they were unimportant.

When scientists sequenced the human genome, they discovered that less than 5 percent of our DNA were genes that actually coded for protein sequences. The biological functions of the noncoding portions of the genome were unclear.

Over the past fifteen years, however, there has been a growing appreciation for the importance of these noncoding regions, thanks in large part to the efforts of individual labs and, more recently, large international efforts such as the Encyclopedia of DNA Elements (ENCODE) project.

What became clear from this work is that there are many elements of the genome, including enhancers, that are involved in regulating gene expression, even though they do not encode for proteins directly.

At some point this flagrant misrepresentation of facts must be stopped. It's hurting science.

How can you believe anything in the press release once you read this? Do you think this represents the views of the scientists who published the paper? Is so, shame on them. If not, shame on the Lawrence Berkeley National Laboratory.

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1. I sent her a link to this post.

Extending evolutionary theory? - Patrick Bateson

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 Patrick Bateson's talk on Adaptability and evolution.

The capacity of organisms to respond in their own lifetimes to new challenges in their environments probably appeared early in biological evolution. At present few studies have shown how such adaptability could influence the inherited characteristics of an organism’s descendants. Nevertheless such effects on biological evolution are likely to have been important and when they occurred accelerated the pace of evolution. Ways in which this might have happened have been suggested many times since the 1870s. I shall review these proposals and discuss their relevance to modern thought.

I don't get it. A key example of organisms responding to their environment is transcription of the lac operon in E. cloi. How does regulation of the lac operon accelerate evolution?

Part of the confusion here is that Bateson is using "adaptability" in two different senses. I'm curious to see if he makes this distinction clear in his talk.

I don't see anything new or revolutionary here. Apparently his motive isn't to overthrow or extend evolutionary theory but to introduce evolution to nonscientists. Here's what he said in an interview with Suzan Mazur [Sir Patrick Bateson: Zoologists Should Not ‘Hog’ Upcoming Royal Society Evolution Meeting ...

Patrick Bateson: It may be a mistake not to have anybody talking about that specifically at the meeting. But I want to repeat that in organizing the meeting we are focused on a discussion about evolution with our colleagues in the social sciences and the humanities, and we don’t want to blind them with all the details of the sciences.

There’s also a lot of fascinating work going on in population genetics that we’re not going to talk about. Evolutionary biologists will say this is an important part of evolutionary biology, which it is, of course. But it isn’t relevant to this particular meeting.

Suzan Mazur: How will an evolution paradigm shift affect society in general?

Patrick Bateson: I’m not sure we’re going to be talking about a completely new set of ideas, a lot have been around for a while. Frankly, I think some evolutionary biologists have not shed their neo-Darwinist clothing. There are some conservative-minded biologists who still think of the organism as being essentially passive, a view about which I am particularly concerned. However, the overall movement in biology is to integrate different disciplines making it a very lively area at the moment. The molecular biologists are talking to the ethologists, the ecologists to the physiologists, the population geneticists to the paleontologists, and so forth.

I don't know who's going to be at the meeting but I don't see very many molecular biologists or population geneticists among the speakers. It's mostly zoologists and a few philosophers.

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Extending evolutionary theory? - Andy Gardner

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 Andy Gardner's talk on Anthropomorphism in evolutionary biology.

A longstanding tension exists in evolutionary biology between behavioural ecology – in which organisms are treated as having adaptive, fitness-maximising agendas; and population genetics – in which such notions are decried as naïve ‘anthropomorphism’ and are widely rejected. I explore the formal and scientific justification for evolutionary anthropomorphism and consider its application to the understanding of adaptive design at the level of genes, individuals and societies.

Andy Gardner is a biologist at the University of St. Andrews in Scotland (UK). Here's a description of his research interests from his website.

I work on Darwinian adaptation. Natural selection explains the appearance of design in the living world, but at what level is this design expected to manifest – gene, individual, society – and what is its function? Social evolution provides a window on this problem, by pitting the interests of genes, individuals and societies against each other. I develop general theory on the topics of inclusive fitness and multilevel selection, and also tailor general theory to the biology of particular species to facilitate empirical testing. I work on a wide range of biological systems, including viruses, bacteria, protozoa, crustaceans, insects, fish and humans.

I'm not sure how this view differs from Gould's writings on hierarchical theory. I'm looking forward to hearing the answer.

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Extending evolutionary theory? - Denis Noble

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 Denis Noble's talk on Evolution viewed from medicine and physiology.

Medicine and physiology are multi-level disciplines. So is physics. From physics we learn that ordered properties at high levels co-exist with randomness at lower levels. Molecules in organisms must obey the same principles. Stochasticity at low levels does not therefore exclude order at higher levels. Organisms enlist stochasticity in their development of functional behaviour, through restraints exerted by higher over lower levels. The physics of organisms must therefore interact with their genomes to produce the phenotype1,2. Reverse engineering from physiological models is then required to understand genotype-phenotype relations3. There is no privileged level of causality4, nor privileged level of selection5. Evolution involves interaction between several processes at multiple levels, as Charles Darwin also believed5,6. Without understanding these interactions, gene-centred approaches will continue to produce disappointing results in healthcare7,8, including trans-generational disease risks.

I have heard Denis Noble speak and I've read some of his papers [Physiologists fall for the Third Way; A physiologist thinks about evolution]. Denis Noble is a physiologist who worked on hearts and circulation in complex mammals (humans). He's very annoyed at biochemists and molecular biologists for getting so much attention (and money) over the past few decades. He has constructed in his mind a false image of evolution. He thinks it's entirely adaptationist and gene-centric and that's what he rails against. He doesn't like Richard Dawkins. He's a prominent member of The Third Way.

You can see for yourself by watching a video of a talk he gave a few years ago.


I agree completely with Jerry Coyne's analysis of this talk [Famous physiologist embarrasses himself by claiming that the modern theory of evolution is in tatters]. Jerry says ....

I’m writing this post in a bit of anger, as Noble’s attacks on the modern synthesis are both poorly informed and clearly motivated by his ambition to make physiology a central part of evolutionary biology. Although he’s an FRS and famous, he wants more: he wants his field to be central to evolution. But such misguided hubris is not the way science is supposed to be done. And physiology is already important in evolutionary biology. It’s the reason why we look at the effects of a gene substitution, for example, not as a simple one-gene-produces-one-trait issue, but as a the gene’s overall effect on reproductive output through its effects ramifying through the complexities of development. Noble says that evolutionists are guilty of this “one-gene-one-trait” error, but he’s just wrong: I don’t know a single person in my field who holds this simplistic view.

None of the arguments that Noble makes are new: they’re virtual tropes among those people, like James Shapiro and Lynn Margulis, who embarked, at the end of their careers, on a misguided crusade to topple the modern theory of evolution.

However famous Noble may be in physiology, he’s a blundering tyro when it comes to evolutionary biology. He might try discussing his ideas with other evolutionists and listening to their responses. He obviously hasn’t done that, and yet travels the world trading on his expertise in physiology to show that the edifice of modern evolutionary biology is rotten. And he writes papers to that effect, including the dreadful piece referenced below.

But what’s really rotten is Noble’s knowledge of the field and his claim that virtually every assumption of neo-Darwinian evolution is wrong. In fact, his arguments are so rotten that they stink like old herring.

They’re not even wrong.

I'm not going to ask any questions after this talk. I'll report back on how many people seem to agree with him.

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Extending evolutionary theory? - Eva Jablonka

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 Eva Jablonka's talk on
The role of epigenetic inheritance in evolution.

The construction of the ‘Modern Evolutionary Synthesis’ in the mid-twentieth century involved the exclusion of soft inheritance – the inheritance of the effects of developmental modifications – and, by implication, the possibility of any form of ‘Lamarckian’ evolution. However, in later decades, discoveries of molecular mechanisms that can support such inheritance led to a broadening of the notion of biological heredity. After discussing the historical context in which this change occurred, I present an extended notion of inheritance, focusing on epigenetic inheritance and its underlying mechanisms. I examine the evidence for the ubiquity of epigenetic inheritance, present models of population epigenetics, and discuss the involvement of epigenetic inheritance in adaptive evolutionary change and macro-evolution. I argue that considering the many evolutionary consequences of epigenetic inheritance requires an extension of the evolutionary synthesis beyond the current neo-Darwinian model.

Eva Jablonka has been pushing the importance of epigenetics for many years. Here's a video where she explains why epigenetic inheritance needs to be incorporated into evolutionary theory.


I think she's exaggerating the importance of epigenetic inheritance in evolution. I'd like to ask her how she defines "epigenetics" and how much of it is heritable over enough generations to seriously affect the evolution of a population. I'm particularly interested in her claim that epigenetic inheritance affects macro-evolution.

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Extending evolutionary theory? - Paul E. Griffiths

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 Griffiths's talk on Genetic, epigenetic and exogenetic information in development and evolution.

I outline an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognised. The term ‘epigenetic’ is ambiguous, and I introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in development and evolution.

Paul Griffiths is a philosopher of biology from Australia. He has been interested in genes for many years. I don't know what he's going to say about epigenetics. I suspect he can make a case for information in the sense that a naked DNA sequence differs in information from a methylated DNA sequence. (Restriction/modification is a good example.)

The problem with this kind of hair splitting is that ultimately the extra information (e.g. methylation) is provided by enzymes (methylases) encoded by genes in the genome. Epigenetics, per se, doesn't add any new information. It's just a consequence, or outcome, of the information already in the DNA.

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Extending evolutionary theory? - James Shapiro

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 James Shapiro's talk on Biological action in Read-Write genome evolution.

Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included: (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes; (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes; and (iii) interspecific hybridisations and genome doublings that have generated adaptive radiations and new species of higher plants and animals. Adaptive variations have also arisen by horizontal DNA transfers (frequently involving infectious agents), by natural genetic engineering of coding sequence DNA in protein evolution (e.g. exon shuffling), and by mobile DNA rewiring of transcriptional regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, we now know that biological complexity scales with ‘non-coding’ DNA content rather than with protein-coding capacity in the genome. Coincidentally, we have come to recognise that ‘non-coding’ RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell activities and Read-Write genome modifications provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

I have dozens of questions for Jim Shapiro but here are two possibilities.

Most of the events you describe are one-off events in the history of life. They are mostly accidents. They were unpredictable. How does the occurrence of unique events such as endosymbiosis or genome doubling fit into evolutionary theory as opposed to just historical facts in the history of life.

OR

Michael Lynch and others say that the amount of junk DNA in a genome correlates with the population size of the species. This view is perfectly consistent with modern population genetics. There is plenty of evidence that 90% of our genome is junk. You seem to be implying that this extra DNA is not junk but serves some adaptive purpose. What evidence do you have that supports this claim and why do you disagree with Michael Lynch?

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Extending evolutionary theory? - Kevin Laland

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 Kevin Laland's talk on The middle ground between artificial and natural selection: niche construction as developmental bias.

Organisms modify and choose components of their local environments. This ‘niche construction’ is subject to extensive research across several academic fields. It is well appreciated that niche construction can alter ecological processes, modify natural selection, and contribute to inheritance through ecological legacies. However, niche construction is not usually regarded as an evolutionary process, probably because traditional evolutionary accounts restrict evolutionary processes to phenomena that directly change gene frequencies (e.g. selection, mutation, drift).

Alternative perspectives can be of value if they generate novel predictions, open up new lines of enquiry, or generate new insights. The niche-construction perspective within evolutionary biology provides an alternative account of the causal relations underlying adaptation, a stance that has already led to a number of valuable insights. Here I suggest that there is heuristic value in regarding niche construction as an evolutionary process, on the grounds that it initiates and modifies the selection acting back on the constructor (and other species) in an orderly and directional manner. As a consequence, niche construction co-directs adaptive evolution by imposing a statistical bias on selection (an externally expressed form of developmental bias).

I illustrate how niche construction can generate developmental bias by comparing it with artificial selection, where I suggest it occupies the middle ground between artificial and natural selection. This perspective has heuristic value for the evolutionary biologist, leading to testable predictions related to: (i) trait evolution, including the evolution of sequences of traits and parallel evolution; (ii) responses to natural selection in the wild; and (iii) biodiversity.

I don't get this emphasis on niche construction. Biologists have been talking about how organisms modify the environment for one hundred years or more. I can see how an understanding of particular examples, such as the increase in oxygen levels due to the evolution of water splitting reactions, can provide insight into the history of life but how does that fit into evolutionary theory?

I don't have any questions for Kevin Laland. I'm anxious to see how the people at this meeting view niche construction.

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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?

OR

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?

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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.

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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.

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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?

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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?

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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?

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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?

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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?

Ten adaptationist stories about recent human evolution

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

1. Blond hair: PROBABLY FALSE ADAPTATION
2. Lactose tolerance: PROBABLY A TRUE ADAPTATION
3. Eating wheat: PROBABLY FALSE 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
9. Male extroverts: PROBABLY FALSE ADAPTATION
10. Having kids earlier: ALMOST CERTAINLY FALSE ADAPTATION

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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

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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.

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."

Chemistry
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

Physics
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

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"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.

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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.

Splice variants of the human triose phosphate isomerase gene: is alternative splicing real?

Triose phosphate isomerase (TIM) is one of the enzymes in the gluconeogenesis pathway leading to the synthesis of glucose from simple precursors. It also plays a role in the degradation of glucose (glycolysis). The enzyme catalyzes the following reaction ....

Triose phosphate isomerase is found in almost all species. The structure and sequence of the enzyme is well-conserved. It is a classic β-barrel enzyme that usually forms a dimer. The overall structure of a single subunit is classic example of an αβ-barrel known as a TIM-barrel in reference to this enzyme.

To the best of my knowledge, no significant variants of this enzyme due to alternative promoters, alternative splicing, or proteolytic cleavage are known.¹ The enzyme has been actively studied in biochemistry laboratories for at least eighty years.

Understanding Michael Behe's edge of evolution

It's been about twenty years since Intelligent Design Creationism rose to prominence. Just last week the Center for Science and Culture celebrated it's 20th birthday [Twenty Years Ago Today, Did This Change the Evolution Debate Forever?]. In all that time, the best that ID proponents can come up with is some work by Michael Behe that attempts to discredit evolution.

The first book by Behe was Darwin's Black Box where he developed the notion of irreducible complexity. The definition of irreducible complexity has changed over the years but the basic idea is that some biological structures are very complex and the removal of any one part will render the complex nonfunctional. This presents an enormous problem for evolution, according to Behe, because all the presumptive intermediates will be nonfunctional.

The conclusion is that it's impossible to evolve an irreducibly complex structure. Evolutionary biologists have no problem accepting the existence of irreducibly complex structures. They see them all the time. What they object to is the idea that irreducibly complex structures cannot have arisen by evolution. Behe's conclusion has been shown to be false and he has admitted on multiple occasions that irreducibly complex structures can arise by purely natural means (evolution).

Do you believe what's written in the introduction to this paper?

I came across this paper while doing research on alternative splicing. The introduction annoyed me. It illustrates what to my mind are some serious problems with modern scholarship.

Scotti, M.M. and Swanson, M.S. (2016) RNA mis-splicing in disease. Nature Reviews Genetics 17:19–3 [doi: 10.1038/nrg.2015.3]

Here's part of the first paragraph in the paper.

Recent analysis from the Encyclopedia of DNA Elements (ENCODE) project (GRCh38, Ensembl79) indicates that most of the human genome is transcribed and consists of ~60,000 genes (~20,000 protein-coding genes, ~16,000 long non-coding RNAs (lncRNAs), ~10,000 small non-coding RNA and 14,000 pseudogenes). Although this gene inventory will change with further analysis, the number of protein-coding genes is surprisingly low given the proteomic complexity that is evident in many tissues, particularly the central nervous system (CNS). High resolution mass spectrometry studies have identified peptides encoded by most of these annotated genes, but the number of isoforms expressed from this gene set has been estimated to be at least 5–10-fold higher. For example, long-read sequence analysis of adult mouse prefrontal cortex neurexin (Nrxn) mRNAs indicates that only three Nrxn genes produce thousands of isoform variants. This diversity is primarily generated by alternative splicing, with >90% of human protein-coding genes producing multiple mRNA isoforms.

Here are some of the problems I have with this introduction. My opinions on these issues differ from those of the authors.

1. I think that pseudogenes are not genes.
2. I think there are NOT ~16,000 lncRNAs and ~10,000 small-noncoding RNA genes. Instead, there are approximately this many putative or predicted genes, many of which will undoubtedly turn out not to be genes. Some of them will be pseudogenes.
3. I don't think there's a discrepancy between the known number of protein-coding genes and proteomic complexity; therefore, it is misleading to say that the number of protein-coding genes is "surprisingly low."
4. I'm pretty sure that nobody has ever proposed a truly scientific "estimate" of isoforms showing that the number should be 5-10-fold higher than the number of genes. This is all speculation and guesswork based mostly on deflated egos.
5. It is not true that >90% of human genes produce multiple mRNA isoforms by alternative splicing. What IS true is that for every human gene researchers have detected low levels of non-canonical splice events upon careful analysis of the transcriptome. We do not know whether these represent true biologically relevant alternative splicing or simply splicing errors. All available evidence suggests that the vast majority are splicing errors.

The authors are certainly entitled to their opinion ... even if it differs from mine!

But surely there has to be a better way of expressing this opinion to make it clear that they aren't stating facts but just their own personal views based on their own interpretation of the literature? This becomes very important if there's widespread scientific controversy over some of these opinions. (It's not so important if there's widespread agreement, or consensus, in the scientific community. In those cases, you aren't obliged to mentions alternative views held by kooks.)

I believe that scientists have an ethical obligation to distinguish between fact and opinion and to make it very clear in their writings which is which. I don't know whether Scotti and Swanson know about the controversial aspect of their statements and are deliberately avoiding any mention of them, or whether they actually believe that their statements are factual. Either way, we have a problem.

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Twenty "sciencey" questions for Trump and Clinton

ScienceDebate.org is a group that wants a "science" debate between Presidential candidates in the upcoming American election. That's not going to happen so the next best thing is to demand that the candidates answer their 20 questions about Science, Engineering, Technology, Health, and the Environment. I would not answer these questions if I were a candidate. Many of them require extraordinarily complex answers. Some of them are based on false premises. Several are loaded. Some of the problems can't be dealt with in any realistic way by a President of the United States. Quite a few cannot be answered in any meaningful way without writing a book.

I'm not sure what this group expects. This seems to be a colossal waste of time. It also seems to be very low on the priority list given all the other problems with Trump and Clinton. The questions don't inspire confidence in ScienceDebate, in my opinion. Here are the questions from: 20 Questions.

1. Science and engineering have been responsible for over half of the growth of the U.S. economy since WWII. But some reports question America’s continued leadership in these areas. What policies will best ensure that America remains at the forefront of innovation?
2. Many scientific advances require long-term investment to fund research over a period of longer than the two, four, or six year terms that govern political cycles. In the current climate of budgetary constraints, what are your science and engineering research priorities and how will you balance short-term versus long-term funding?
3. The Earth’s climate is changing and political discussion has become divided over both the science and the best response. What are your views on climate change, and how would your administration act on those views?
4. Biological diversity provides food, fiber, medicines, clean water and many other products and services on which we depend every day. Scientists are finding that the variety and variability of life is diminishing at an alarming rate as a result of human activity. What steps will you take to protect biological diversity?
5. The Internet has become a foundation of economic, social, law enforcement, and military activity. What steps will you take to protect vulnerable infrastructure and institutions from cyber attack, and to provide for national security while protecting personal privacy on electronic devices and the internet?
6. Mental illness is among the most painful and stigmatized diseases, and the National Institute of Mental Health estimates it costs America more than $300 billion per year. What will you do to reduce the human and economic costs of mental illness?
7. Strategic management of the US energy portfolio can have powerful economic, environmental, and foreign policy impacts. How do you see the energy landscape evolving over the next 4 to 8 years, and, as President, what will your energy strategy be?
8. American students have fallen in many international rankings of science and math performance, and the public in general is being faced with an expanding array of major policy challenges that are heavily influenced by complex science. How would your administration work to ensure all students including women and minorities are prepared to address 21st century challenges and, further, that the public has an adequate level of STEM literacy in an age dominated by complex science and technology?
9. Public health efforts like smoking cessation, drunk driving laws, vaccination, and water fluoridation have improved health and productivity and save millions of lives. How would you improve federal research and our public health system to better protect Americans from emerging diseases and other public health threats, such as antibiotic resistant superbugs?
10. The long-term security of fresh water supplies is threatened by a dizzying array of aging infrastructure, aquifer depletion, pollution, and climate variability. Some American communities have lost access to water, affecting their viability and destroying home values. If you are elected, what steps will you take to ensure access to clean water for all Americans?
11. Nuclear power can meet electricity demand without producing greenhouse gases, but it raises national security and environmental concerns. What is your plan for the use, expansion, or phasing out of nuclear power, and what steps will you take to monitor, manage and secure nuclear materials over their life cycle?
12. Agriculture involves a complex balance of land and energy use, worker health and safety, water use and quality, and access to healthy and affordable food, all of which have inputs of objective knowledge from science. How would you manage the US agricultural enterprise to our highest benefit in the most sustainable way?
13. We now live in a global economy with a large and growing human population. These factors create economic, public health, and environmental challenges that do not respect national borders. How would your administration balance national interests with global cooperation when tackling threats made clear by science, such as pandemic diseases and climate change, that cross national borders?
14. Science is essential to many of the laws and policies that keep Americans safe and secure. How would science inform your administration's decisions to add, modify, or remove federal regulations, and how would you encourage a thriving business sector while protecting Americans vulnerable to public health and environmental threats?
15. Public health officials warn that we need to take more steps to prevent international epidemics from viruses such as Ebola and Zika. Meanwhile, measles is resurgent due to decreasing vaccination rates. How will your administration support vaccine science?
16. There is a political debate over America’s national approach to space exploration and use. What should America's national goals be for space exploration and earth observation from space, and what steps would your administration take to achieve them?
17. There is a growing opioid problem in the United States, with tragic costs to lives, families and society. How would your administration enlist researchers, medical doctors and pharmaceutical companies in addressing this issue?
18. There is growing concern over the decline of fisheries and the overall health of the ocean: scientists estimate that 90% of stocks are fished at or beyond sustainable limits, habitats like coral reefs are threatened by ocean acidification, and large areas of ocean and coastlines are polluted. What efforts would your administration make to improve the health of our ocean and coastlines and increase the long-term sustainability of ocean fisheries?
19. There is much current political discussion about immigration policy and border controls. Would you support any changes in immigration policy regarding scientists and engineers who receive their graduate degree at an American university? Conversely, what is your opinion of recent controversy over employment and the H1-B Visa program?
20. Evidence from science is the surest basis for fair and just public policy, but that is predicated on the integrity of that evidence and of the scientific process used to produce it, which must be both transparent and free from political bias and pressure. How will you foster a culture of scientific transparency and accountability in government, while protecting scientists and federal agencies from political interference in their work?

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A refreshing admission on Uncommon Descent

Some of us have been debating Intelligent Design Creationists for many years. Some of us have even visited the creationist blogs like Uncommon Descent where we discover that no facts and no logic will ever shake their obsession with proving evolution wrong and promoting their gods. That's why it was refreshing to read the following comment by William J. Murray in his post on "The Benefit of Arguments at UD." I only had time to read the first few lines but you get the gist ...

Probably one of the most daunting aspects of carrying on debates either about proper critical thinking, theism vs atheism, or intelligent design and its implications is the seeming implacable nature of those we debate here and elsewhere. It most often seems that no amount of logic, evidence or even reasonable discourse makes one iota of difference ...

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