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David Christopher LaneDavid Christopher Lane, Ph.D. Professor of Philosophy, Mt. San Antonio College Lecturer in Religious Studies, California State University, Long Beach Author of Exposing Cults: When the Skeptical Mind Confronts the Mystical (New York and London: Garland Publishers, 1994) and The Radhasoami Tradition: A Critical History of Guru Succession (New York and London: Garland Publishers, 1992).


Epistemological Soap

Naturalistic Methodologies and Evolution

Resisting the ‘Transcendental Temptation’

David Lane

Almost every month, if not weekly, a new discovery is made in molecular biology that advances our understanding of how evolution works.

I remember hearing a very illuminating off the cuff remark from one of my history professors during my undergraduate days. He said of the four most influential thinkers in the last two centuries three of them were Jewish and one of them was Christian: Sigmund Freud in Psychology; Karl Marx in Sociology; Albert Einstein in Physics--all three of whom had a Jewish background. The only Christian in the bunch, at least in terms of his family background and upbringing, was Charles Darwin. But, as my professor sarcastically mumbled, "But the Christians don't want him."

Of course, my Professor's comment is a bit of an exaggeration, but it does underline the controversial work of Charles Darwin, especially as outlined in his most famous book, On the Origin of Species (1859). However, I think even the most strident Creationist will be hard pressed not find Darwin a very likeable and agreeable personality. Indeed, given the radicalness of his thought (even if couched in understated terms), Darwin lived a relatively conservative life and was morally above reproach.

My old mentor, the late Dr. Bennett Berger, Professor of Sociology at UCSD, often said that the key to understanding any thinker is to discover precisely what was bugging him or her--what he called their "metaphysical" pathos. In reading Darwin's short but exquisite autobiography it isn't very difficult to discern what was troubling him. He wanted to understand how nature worked, without unnecessarily resorting to a religious explanation.

This, I believe, is the key to understanding Darwin's agenda in grappling with the world at large. Can we understand the evolution of life without resorting to “trans” or “meta” physical concepts that appear, at least on the surface, recalcitrant to empirical verification? Darwin's colleague, Alfred Russel Wallace didn't think so particularly when it came to the human mind. As Stephen Montgomery explains,

“Darwin and Wallace also disagreed on human evolution. For Darwin, all aspects of humans, including the emotions, conscious mind and intelligence could be explained by natural or sexual selection. By the late 1860s Wallace had become a Spiritualist, and perhaps linked to this, began to reject evolutionary explanations of human intelligence and abilities invoking 'the unseen universe of Spirit'. This, he claimed, had intervened in the normal run of natural selection three times; at the creation of life, the introduction of consciousness, and the generation of man's mental capacities. Later in his life Wallace also believed in teleology; the idea that the development of the universe has had a direction and that direction is towards the perfection of man. There are suggestions that Wallace also applied his teleology to evolution. Darwin was clearly a bit perplexed by his former ally's new views and at one point wrote to Wallace pleading with him not to kill 'our baby'.”

I think it is important to distinguish methodological naturalism from a philosophically absolutist position, since trying to ground all things down to the empirical realm and testable realm is a practical process and doesn't necessarily mean that nothing else exists beyond what we can scientifically discern.

Too often the practicality of the scientific method gets conflated with ontology, and because of this religionists and others resist the very real benefit of what hard core reductionism has to offer. Simply put, wielding Occam's Razor or Hume's Maxim or Laplace's Dictum doesn't then mean that only “simple things” exist, but rather that before building any future scaffolding we make certain not to leave the ground floor wanting because of our hurried inspection.

Thus while I enjoyed Joe Corbett's latest essay, Trans-Darwinian Evolution, and can appreciate that one can indeed speculate about “non-local” influences and how such could play a role in morphology, I don't think we have fully exhausted all of the (“here and now”) physical influences that have shaped evolution's past, present, and future. For instance, it is only in the past three decades or so that Darwin's theory of sexual selection has been properly reconsidered and is now regarded as elemental along with natural selection in determining the genotype/phenotype of future replicators.

I don't see the pressing need (at least not yet) for invoking “involution”, “eros”, “morphic resonance”, or “Akashic fields,” particularly when much more mundane mechanisms may be operative. Genetic drift, for example, helps explain how genes that are not fit may be passed on simply by random chance or because they are neutral, neither adding nor detracting from the genome. Cooperation versus competition (co-evolution for mutual assistance and survival) has also shed a clearer light on the field. Neo-Darwinism isn't stuck to a 1930s/1940s synthesis, as any one conversant in the field knows, especially with the advent of advanced computational simulations and our deeper understanding of fossilized DNA.

Almost every month, if not weekly, a new discovery is made in molecular biology that advances our understanding of how evolution works. It is not a static field and thus it is important to keep up to date on the latest findings, lest our critiques lag decades behind.

For example, just recently Science Daily reported one solution to the “chicken and egg dilemma” explaining a pathway how erstwhile genetic parasites can be silenced or turned-on in order to keep the genome's integrity in tact. As the Daily elaborates,

“One important pathway that maintains the genomic integrity of animals is the piRNA pathway. This system is active in germ cells and utilizes small snippets of RNA -- so called piRNAs -- which fit like mirror images onto the transcripts of selfish sequences and thereby initiate silencing with their associated Argonaut proteins. The Brennecke lab at IMBA has been rigorously exploring these RNA-based self-defense mechanisms in fruit flies, using cutting-edge next generation sequencing. The source of piRNAs is within silenced regions containing the selfish elements. This organization established an evolutionary "chicken and egg" dilemma: How could piRNAs be generated from the very regions that they silence? In their current Nature publication, Brennecke's lab not only solve this enigma but also describe a completely new mechanism for gene-expression. The newly discovered pathway is centered around a protein called moonshiner. Moonshiner is related to basal transcription factors, and interacts with Rhino, a protein bound to heterochromatin at the selfish genes. Rhino recruits Moonshiner to the heterochromatic region, and Moonshiner initiates assembly of the RNA polymerase II pre-initiation complex, that catalyzes the transcription. Therefore, gene expression is activated in an otherwise silent region via a different code embedded in histone marks rather than DNA sequence. The findings show that piRNAs are transcribed by bending the classical rules of gene activation, combining elements of standard gene activation with gene silencing.”

In computer terms, what we have here is the mechanism by which “cells hack their own genes” and how this plays a key role in evolution. But we cannot appreciate these developments if we merely read only outdated, popularized books on Darwinian evolution, which has been the habit of some creationists and intelligent design advocates who have not kept abreast of the current studies in the field.

No doubt it is true that reading technical papers found in such journals as Nature can be a daunting task (and this is why we need science “unpackers” who can draw out the implications and the larger meanings embedded in such works), but it is a necessary requirement if wish to appreciate how our knowledge of evolution is (and here is the pun) “evolving.” Here is an excerpt from the original abstract by Peter Refsing Andersen, Laszlo Tirian, Milica Vunjak & Julius Brennecke explaining their findings in Nature (August 23, 2017). It makes for dense reading, no doubt, but is made more understandable in the context of Science Daily's more accessible exposition:

“Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced is not understood. Here we show that, in Drosophila, transcription of PIWI-interacting RNA (piRNA) clusters—small RNA source loci in animal gonads—is enforced through RNA polymerase II pre-initiation complex formation within repressive heterochromatin. This is accomplished through Moonshiner, a paralogue of a basal transcription factor IIA (TFIIA) subunit, which is recruited to piRNA clusters via the heterochromatin protein-1 variant Rhino. Moonshiner triggers transcription initiation within piRNA clusters by recruiting the TATA-box binding protein (TBP)-related factor TRF2, an animal TFIID core variant. Thus, transcription of heterochromatic small RNA source loci relies on direct recruitment of the core transcriptional machinery to DNA via histone marks rather than sequence motifs, a concept that we argue is a recurring theme in evolution.”

Notice that the authors in the first and last sentences explain succinctly why their specific study is important because it shows how “small pathways safeguard genome integrity” and this is “a recurring theme in evolution.”

I don't think we have fully exhausted all of the physical influences that have shaped evolution's past, present, and future.

I bring this up because I don't see why we need to succumb to the “transcendental temptation” quite yet, especially when breakthroughs (as the one mentioned above) are continually occurring in molecular and evolutionary biology. Take as another example the contentious issue surrounding morphology where some New Age thinkers believe that something “supra” natural is necessary to explain how certain physical shapes and forms develop over time. Recently, scientists at Nagoya University, who have focused their attention on “positional diversity of the hindlimb in tetrapod evolution”, discovered the gene and protein that are necessary for “determining the hindlegs in tetrapods.” Their findings were published in Nature: ecology and evolution (July 31, 2017) and explains [that] “Elucidating how body parts from different primordia are integrated during development is essential for understanding the nature of morphological evolution.” What they uncovered is worth reading, even in its technical details,

“In tetrapod evolution, while the position of the hindlimb has diversified along with the vertebral formula, the mechanism responsible for this coordination has not been well understood. However, this synchronization suggests the presence of an evolutionarily conserved developmental mechanism that coordinates the positioning of the hindlimb skeleton derived from the lateral plate mesoderm with that of the sacral vertebrae derived from the somites. Here we show that GDF11 secreted from the posterior axial mesoderm is a key factor in the integration of sacral vertebrae and hindlimb positioning by inducing Hox gene expression in two different primordia. Manipulating the onset of GDF11 activity altered the position of the hindlimb in chicken embryos, indicating that the onset of Gdf11 expression is responsible for the coordinated positioning of the sacral vertebrae and hindlimbs. Through comparative analysis with other vertebrate embryos, we also show that each tetrapod species has a unique onset timing of Gdf11 expression, which is tightly correlated with the anteroposterior levels of the hindlimb bud. We conclude that the evolutionary diversity of hindlimb positioning resulted from heterochronic shifts in Gdf11 expression, which led to coordinated shifts in the sacral—hindlimb unit along the anteroposterior axis.”

What this study and others like it point out is that we are still in the adolescent stages in explaining the various micro-physical processes behind evolution and its varied pathways. No need to rush in “Eros” or “Angels” or “God” into the proceedings quite yet.

In the upper division Science and Religion classes I used to teach at California State University, Long Beach, I often made use of a silly but useful analogy. Whenever my old 36 foot Roughwater boat breaks down (which is more often than not, given that it is 40 years old and looks like a stand-in for the boat on the old television series, Gilligan's Island), I always look at the engine first. Now it could well be that the boat has been taken over by Neptune's neglected wife, Salacia, who in her rage has taken possession of my boat and its navigation. But, practically speaking, I tend never to invoke Sea-faring gods when trying to get my boat back on track to Catalina. Likewise, it may well be that there are superluminal forces at play in evolution, but before we rush in where angels fear to tread, I think we are better off focusing on the empirical arena before prematurely jumping across the bow in search of mermaids.

If Integral theory has any potential merit, then it rests on how well we have fully examined the specifics of each and every particular level. Thus, contrary to what some may believe about science, naturalistic methodologies and intertheoretic reductionism do not in themselves preclude the transcendent or potential metaphysical explanations. Rather they should be likened to “epistemological cleansers”, which wipe away unqualified candidates that cannot withstand rational scrutiny. They are, in a metaphorical way, the tools of science for not jumping “nature's” ship too quickly.

Yes, it may well be that there is “more than meets the empirical or rational eye” (to invoke Wilber's parlance), but before we invoke our “third” eye, we better make really sure that we have fully used our senses (both physical and mental) to the very best of their ability. Otherwise, we will inevitably commit that most egregious of Wilberian fallacies: confusing the pre with the trans.


“False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for everyone takes a salutary pleasure in proving their falseness; and when this is done, one path towards error is closed and the road to truth is often at the same time opened.”
--Charles Darwin, The Descent of Man


Peter Refsing Andersen, Laszlo Tirian, Milica Vunjak & Julius Brennecke, "A heterochromatin-dependent transcription machinery drives piRNA expression", Nature, Published online 23 August 2017.
See also: Institute of Molecular Biotechnology (IMBA). "How cells hack their own genes." ScienceDaily, 23 August 2017.

Yoshiyuki Matsubara, Tatsuya Hirasawa, Shiro Egawa, Ayumi Hattori, Takaya Suganuma, Yuhei Kohara, Tatsuya Nagai, Koji Tamura, Shigeru Kuratani, Atsushi Kuroiwa & Takayuki Suzuki, "Anatomical integration of the sacral–hindlimb unit coordinated by GDF11 underlies variation in hindlimb positioning in tetrapods", Nature Ecology & Evolution 1, 1392–1399 (2017).
See also: Nagoya University, "Mechanisms explaining positional diversity of the hindlimb in tetrapod evolution", ScienceDaily, August 18, 2017.

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