Tuesday, May 02, 2017

Debating philosophers: The Lu and Bourrat paper

John Wilkins posted a link on Facebook to a recent paper by his colleagues in Australia. The authors are Qiaoying Lu of the Department of Philosophy at Macquarie University in Sidney Australia and Pierrick Bourat of the Department of Philosophy at The University of Sydney in Sidney Australia.

Lu, Q., and Bourrat, P. (2017) The evolutionary gene and the extended evolutionary synthesis. The British Journal for the Philosophy of Science, (advanced article) April 20, 2017. [doi: 10.1093/bjps/axw035] [PhilSci Archive]

Abstract: Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance.

1 Introduction
2 The Gene-centric Evolutionary Theory and the ‘Evolutionary Gene’
      2.1 The evolutionary gene
      2.2 Genes, phenotypes, and environments
3 Epigenetic Inheritance and the Gene-Centred Framework
      3.1 Treating the gene as the sole heritable material?
      3.2 Epigenetics and phenotypic plasticity
4 Conclusion
The goal of the paper is to make epigenetics compatible with current evolutionary theory. The argument consists of three parts ....
  1. Define "current" evolutionary theory as a gene-centric, adaptationist view of evolution.
  2. Re-define a "gene" as any heritable trait that affects phenotype.
  3. Demonstrate that epigenetic effects (e.g. methylation) are encompassed by the new definition.
The conclusion is that epigenetic inheritance is compatible with current evolutionary theory.

I have often criticized philosophers on two grounds ...
  1. Many of their papers have little of no connection to the real world. Their arguments focus on nitpicky twists of logic and definitions and the conclusions they reach are out-of-touch with the scientific consensus. [Massimo Pigliucci tries to defend accommodationism (again): result is predictable] [Methodological naturalism at Dover] [Philosophy and reality] [John Wilkins discusses the "Demarcation Problem"] [Territorial demarcation and the meaning of science] [Science Doesn't Have All the Answers but Does It Have All the Questions?] [Alvin Plantinga Explains Why Naturalistic Evolution Is a Self-Defeating Proposition] [Boudry vs Plantinga] [John Wilkins Defends Methodological Naturalism] [John Wilkins Defends Philosophy: A Bit of History] [What Kind of Knowledge Does Philosophy Discover?] [The Flying Spaghetti Monster Steals Meatballs (What's the Purpose of Philosophy?)] [What's Wrong with Michael Ruse's View of Accommodationism?] [The Trouble with Scientism?] [The Problem with Philosophy: Elliott Sober] [What Is Knowledge?]
  2. They often fail to represent the current views of science. They frequently get their facts wrong. [When philosophers talk about genomes] [A Philosopher Trashes Junk DNA] [On the Difference Between "Evolutionary Theory" and Scientific Fact] [The Collapse of the "Dawkins Dogma"]
There is room for a diversity of views in molecular biology, genetics, and evolutionary theory. I do not fault Lu & Bourrat for holding views that are different than my own. My criticism will focus on two fronts ....
  1. They do a poor job of defending their view. The reasoning is flawed and sometimes their facts are wrong.
  2. The fail to mention legitimate alternative views that conflict with their own. This omission is a serious error for philosophers since those legitimate alternative views undermine their case.
My criticism is divided into five blog posts.
Pierrick Bourrat responds to the criticism at: Debating philosophers: Pierrick Bourrat responds to my criticism of his paper

4 comments :

  1. Hi Larry. Interested to see how this critique develops, but as both the authors have higher degrees in biology I find the headline a bit misleading :-)

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  2. It is very depressing how much of this discussion and commentary focuses on the low standards of 'amateurs' and 'autodidacts' and 'philosophers'. This is an argument from authority. It is also a bit silly, as both these authors have biology degrees, and one published a number of articles in behavioral ecology in their previous career as a scientist. I say that just to neutralise the argument from authority. Now let's focus on the substance!

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  3. RE: There can be no debates but withdrawal of the flawed Evolutionary Theory in Biology of the 20th century past!?

    In addition to the nice LAM criticisms above, I would like to present a more specific but brief critique of the Lu and Barrett paper, point by point as argued in their Abstract above as follows:

    1) “Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance.” -- This is right; however the standard evolutionary theory (SET) as formalized in the Modern Synthesis (MS) since 1930s-40s, in itself, is flawed beyond repair; therefore any extended theory based on the SET or the MS would be equally flawed to the core.

    Besides the epigenetic inheritance does not invoke the core DNA sequence or genetic inheritance at all; it only involves in certain “on” or “off” switches only to the genetic expressions of the core DNA sequence, depending on its immediate surrounding environmental factors, such as methylations of certain nucleotides in the DNA sequence; and such an epigenetic inheritance is generally non-permanent as demethylation will occur as environmental factors change within the nuclear biochemistry.

    2) “The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient.” -- That is right; this is because the epigenetic inheritance is not permanent nor sufficiently adequate so as to effect the original DNA sequence or the core genetic inheritance (also see explanation 1 above).

    3) “We suggest that the ambiguity surrounding the conception of the gene a background semantic issue in the debate.” -- Wrong! These are the complex and multi-folded cellular background, biochemical, physiological, and genetical issues in the debate!

    4) “Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way that makes them consistent with gene-centric evolutionary theory.” -- On the contrary, this statement is arguing from the faulty anthropomorphic theory of “The Selfish Gene” perspectives; any erudite scholars or philosophers of Science and Biology should know better!

    5) “We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles.” -- Wrong again! This is a neo-darwinist pseudo-scientific statement arguing from ignorance of my arguments as presented in 1 - 4 above; in addition, as the brainiac “meme” pseudo-scientific terminology theory, there is No epialleles has had been defined in genetics or epigenetics at all; the most close scientific term for the epigenetic discovery would be “methylated-alleles” (please see explanations 1 and 2 above)!?

    6) “If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance.” -- Wow! This is a very wishful thinking proclament: Wishing a very flawed evolutionary theory to be broadly understood and accepted by further extending or incorporating even more faulty premises or imaginary epigenetic mechanisms, so as to turn it into a “grand old evolutionary theory” of the 21st century into the future!? Good luck, happy philosophizing!

    Best, Mong 5/6/17usct03:51; practical public science-philosophy critic (since 2006).

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  4. No epi-alleles?
    http://www.sciencedirect.com/science/article/pii/S0169534704001065
    E.g. http://www.nature.com/nature/journal/v401/n6749/abs/401157a0.html

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