Biology – our incomplete fundamental science – A journey, a library, and a blog parsing through the theoretical disarray within the life sciences in pursuit of a hoped-for paradigm breakthrough

Biology? And your relation to it?

By Jake K on Sunday, November 27, 2022

INSTRUCTIONS for evaluation of biology and your relation to it:
Do each of the 8 statements below reflect contemporary views among biologists?
To what degree do you agree with each statement?
The larger question is what does any dissonance between your two answers for each statement say about the state of biology or your relation to it. I have placed my own partial reflection on each statement down below.

1 The key feature of life is organisms or living things,
2 The path from chemistry to the first cell is either highly improbable or, if a deterministic event, then beyond current science to explicate,
3 life is a collection of species where multicellular animals are the main event,

General

Life? – after physics, before biology, and fallen through the cracks

By Jake K on Sunday, December 20, 2020

After not having written throughout this year, I will take the chance for a quick summary of my own path in the philosophy of biology as a condensation of what this blog aims for. A core issue that I see is that our current paradigm has a naive view of the nature of life. Whatever life is has been reduced to a living thing or better, the collection of living things. But what is a living thing? No such concept comes out of physics in its terms of mass, length, time, and forces. But biology is just as clueless; so evolutionary theory conveniently begins with the first living thing, presumably a first cell, or maybe a collection of protocells in what amounts to undefined almost living things. This is astounding when put in context. Many people today get excited about the “mysteries” at the edge of physics such as dark matter or string theory, but why is life not a much more important mystery as we are of it and it is all around us? While science has generally been considered to be mature and to have done a formidable job of

B - Human major transition in evolution

How Big is the Human Evolutionary Turn?

By Jake K on Friday, May 10, 2019

Are humans just another species in a long evolutionary line? Or, are humans part of an unknown and unfolding large change in the nature of evolution itself – something beyond the species? Common opinion, I think, holds to neither of these; instead, humans are considered to be a very special species, which has somehow surmounted and escaped evolution-as-usual. Evolution led up to us; today we ride airplanes. Sure, we might go extinct, possibly in some sci-fi version of apocalypse or some primitive version of evolution after an ecological collapse. But in general, we are assumed to be somehow post-evolutionary.

A - Evolutionary theory General

Two strong voices moving against neo-Darwinism

By Jake K on Saturday, February 16, 2019

In 2017 two books by renowned biologists came out strongly against the neo-Darwinist synthesis. They both share the positive message of moving towards homeostasis, physiology, and systems biology as complementary to the role of genes. The times they are a changing in evolutionary theory.

The books are Purpose and Desire by Scott Turner (of SUNY Syracuse) and Dance to the Tune of Life by Denis Noble (of Oxford). Both are clear and easy reading. Scott Turner comes down hard: “I have come to believe that there is

C - Evolutionary theology

Back to Process Theology

By Jake K on Monday, February 11, 2019

In a post from two days ago entitled “How beliefs about life influenced Darwinism” I described some trends in theology that led up to the Scientific Revolution. My claim was that the assumptions from theology just before the birth of biology shaped assumptions that are still part of our view of life. These include assumptions that: 1) god was an active agent rather than a generalized, creative process; 2) organisms tell us all about life without having to understand any deeper questions about the nature of life; and 3) humans too are best understood as individuals (organisms) rather than as facets of any larger or smaller constellations (seen in the bottom left group of blue circles in chart below).

But biology is changing. Themes (A) and (B) are discussions about these changes and the potential for further changes. In my own posts I have come out strongly to forecast significant changes in evolutionary theory. These include our conception of civilization’s place within evolution as being radically changed and improved. This would mean understanding modern human life – all of it including skyscrapers and the internet – as integrated into the theory of evolving life. If this is true, then these will have momentous implications for theology. If the forecast for theme (A) and evolutionary

C - Evolutionary philosophy for humans

Philosophy for limited beings

By Jake K on Sunday, February 10, 2019

To speak of humans as “limited beings” is to criticize the current Modernist perspective that has grown up since the Enlightenment of humans as essentially masters of the universe – all knowing with free will to do as we please. It is also a nod to philosopher William Wimsatt and his book with the title Re-Engineering Philosophy for Limited Beings: Piecewise Approximations to Reality (2007). The perspective associated with Modern philosophy has been criticized since at least Nietzsche as a view that separated humans from the world by putting us as merely observers of objective reality (Nagel 1986). It has been lampooned under the notion of a split between body and mind or matter and spirit that have no relation to each other. Language is almost as ethereal as mind when it is considered to be just a reflection of objective reality (Harris 1981). Emotions are merely epiphenomena of no real consequence. The criticisms of these legacy views of

C - Evolutionary philosophy for humans C - Evolutionary theology

How beliefs about life influenced Darwinism

By Jake K on Friday, February 8, 2019

Darwin’s Origin of Species appeared at an auspicious moment in history. The exploration of the whole globe with its strange creatures as in Darwin’s voyage on the Beagle was in full swing, and the hopeful sense of human progress following the Industrial Revolution was in full blossom. But the sciences of mechanics and mathematics as from Descartes and Newton formed a legacy that themselves descended from changing notions of god, humans, and agency. The discussions of evolutionary theory (A) and the evolutionary significance of civilization (B) are inextricably tied to these scientific and theological roots.

Three long term themes in the West are worth tracing. The first is a shifting focus in the life sciences from the general question of the nature of life versus the investigation of specific organisms. The second is the shift in theology over the Middle Ages and into the age of science from a concept-less and name-less view of god to a view of god as having specific powers. The third is

A - Biological self-organization B - Human major transition in evolution General

Evolutionary transitions instead of revolutions

By Jake K on Wednesday, February 6, 2019

Did humans create civilization and discover all its technology? Or, did evolution and life’s patterns provide avenues into which human behavioral adaptability stumbled? In my estimation the former of these is the default answer of most of us and even of evolutionary theorists. However, it is hard to answer with the second option above since it has hardly been explored. My own answer is the second of these, and I want to do as much as possible to investigate this alternative in order to put the two choices above at least on an equal footing.

The upshot of this second option is that recent human evolution signals an incipient and huge pattern change in evolution on the order of the formation of some type of superorganism. The collective dynamics such as the obvious massive coevolution with domesticated species herald an unknown pattern such as a super-society of multiple species. Instead of “revolutions” like the

A - Biological self-organization A - Evolutionary theory A - Origin of life in evolution General

The Chemical Side of Evolution

By Jake K on Monday, February 4, 2019

While the winds of change are stirring across evolutionary theory, there is larger, long-term current of change approaching from chemistry. The chemists have a claim that chemical evolution is the real basis of evolution while species evolution is a secondary process (Williams & Frausto da Silva 2006; Williams & Rickaby 2012). At the same time there are many origin-of-life researchers who are studying how prebiotic chemistry could lead to life, and they are making rapid progress. They are effectively studying a chemical evolution that occurred for hundreds of millions of years before the first cell or before any life as we know it. And some of these same researchers see the species concept as a secondary phenomenon to the biosphere as a whole (Smith & Morowitz 2016).

Most of us assume that chemistry is what living organisms use for their lives. This suite of ideas from chemical evolution, biosphere primacy, and prebiotic chemistry sees evolution as a big, changing current driven by energy that gets its chemical energy organized and partitioned by different forms of life. Chemical evolution is seen to be primary, and the evolution of organisms or

A - Biological self-organization A - Evolutionary theory

Winds of Change

By Jake K on Friday, February 1, 2019

Evolutionary theory is in growing ferment. And few people are paying attention. At least two biologists have shouted from megaphones. Biologist Robert Reid in his 2007 book screamed about the need for a new synthesis. He talked about how many issues across biology at that time that he listed as “[p]ost-Lamarckism, structuralism, complexity theory, the lucky-strike paradigm of neo-catastrophism, evo-devo, and symbiosis studies.” He then went on to warn that: “But their individual adherents, whether modern mutineers or postmodern privateers, lack the resolve to escape the vortex of Darwinism. If they do not all hang together in a new synthesis they will all hang separately, to be scavenged by the Modern Synthesis, stuck in the hold, and forgotten.” (Reid 2007, p. 422).

Another biologist, Scott Turner, in 2017 is equally distraught. He states that: