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Stephen L. Talbott’s Home > From Mechanism to a Science of Qualities > Biology Worthy of Life

Biology Worthy of Life

What’s New in This Project?

(May 17, 2016:) Can Darwinian Evolutionary Theory Be Taken Seriously? — you won’t hear an answer quite like this from any of those occupying entrenched positions in the culture wars.

(November 10, 2015:) Genes and Organisms: Improvising the Dance of Life — The organism is a living, intentional activity coordinating its parts in relation to the needs of the whole. This truth is made extraordinarily vivid in the regulation of gene expression.

(April 29, 2015:) Where Do Intelligence and Wisdom Reside? — Part 3 of “From Bodily Wisdom to the Knowing Self”. We see nothing but an almost unsurveyable wisdom in the organism. Does that wisdom need explaining, or is it what explains?

(March 26, 2015:) How to Unthink Epigenetics — If you’re confused about epigenetics, you’re in good company.

What’s Most Popular?

(April 24, 2014:) Biology’s Shameful Refusal to Disown the Machine-Organism

(November 11, 2014:) How Does an Organism Get Its Shape? The Causal Role of Biological Form

(September 9, 2014:) Let’s Loosen Up Biological Thinking!

(November 14, 2013:) The Unexpected Phases of Life

(February 11, 2014:) RNA: Dancing with a Thousand Partners — Or, the Problem of Biological Explanation

(August 1, 2014:) Vladimir Solovyov on Sexual Love and Evolution

Index and search box List of articles     RSS feed: RSS feed for “Biology Worthy of Life”
image of bird singing

[Photo © Ernst Vikne (CC)]  

What Is This Project About?

After Crick and Watson unraveled the structure of DNA, molecular biologists were destined, so they thought, to understand organisms as physical mechanisms and nothing more. Instead, ever more sophisticated experimental techniques have been revealing organisms whose wisdom and subtlety, whose powers of development and adaptation, whose embodied insight and effective communication, and whose evolutionary ingenuity far outstrip our current capacities for comprehension. Yes, new molecular “mechanisms”, isolated from the organism as a whole, continue to be proclaimed daily. But when we restore these products of our one-sided methods to their living contexts, allowing them to speak their own meanings, what they actually show us is this: every organism is intent upon telling the eloquent story of its own life. Its living intentions govern and coordinate the lawful physical performance of its body, not the other way around.

No, you have probably not heard about these developments; they don’t make the pages of the New York Times or even Scientific American. Indeed, many biologists themselves lament that their unavoidable focus on the minutia of their own narrow research topics prevents their paying adequate attention to wider fields of discovery. But the reality now being proclaimed from the pages of every technical journal could hardly be more dramatic. Perhaps the central truth is this: we human beings discover our conscious, inner capacities — our capacities to think and mean, to plan and strive — unconsciously and objectively reflected back to us from every metabolic process, every signaling pathway, every gene expression pattern in all the organisms we study. We are akin to these organisms in ways we have long forgotten. This matters in a world whose future has been placed in our hands. No form of life is alien to us.

You deserve to know what is going on — not via the heated and fruitless rhetoric of the science–religion wars, and not through vague references to vibrations, energy fields and quantum mysteries, but rather directly from molecular biologists themselves. That’s what this project is about.

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Letting the Organism Speak for Itself

Stephen L. Talbott

My aim here is to bring some of the current and unexpected trends in biology to a wider audience. I will piece together a broader picture that shows us what the biology of the future may look like, particularly as we can glimpse it through the work of molecular biologists wrestling with the problems of genetics, organismal development, and evolution. The literature today, despite the powerful and still-dominant inertia of old thought-habits, is rife with hints of creative thinking and new directions that would have sounded revolutionary and unthinkable a few decades ago.

What we can no longer doubt is this: every organism pursues its own purposes by means of its active capacities — capacities for developing and shaping its own body, sensing and responding to stimuli, repairing and healing, signaling and communicating. At every level of observation — and all the way down to its molecular structures and processes — the organism displays a plastic, adaptive power responsive to context. The essential elements of the organism are activities and dynamically maintained relationships, not static things.

Through its living activity, the organism speaks. That’s why biologists use terms such as “information”, “code”, “message”, “signal”, “program”, “response”, “communication”, and so on — all in order to express the language-like activity they can’t help trying to describe (even if they prefer to think in terms of computerized rather than living speech). And just as words and gestures carry many meanings, even opposite meanings, depending on their context, so it is with all the structures and processes of our cells, including our genes. The language of the organism is turning out to be vastly more complex, expressive, and nuanced than our old, mechanistic heritage ever led us to expect.

It’s time we let organisms speak for themselves. That is the opportunity and responsibility of the new science of biology.


This project is a work in progress, and all parts of it are subject to ongoing revision. You can peruse the available texts in any of several ways:

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Photo courtesy of Peter Kindlmann. All rights reserved.

Chapters
Part 1. Organisms and Their Genes: Molecules, Mysticism, and Meaning
Research in molecular biology is leading us far, far away from the simplistic view that the “secret of life” was revealed with the discovery of the structure of DNA, and from the equally simplistic view that the Human Genome Project would enable us to read the “book of life”. Organisms are revealing themselves as intentional wholes not governed by any particular parts.
Getting Over the Code Delusion: Biology's Awakening
Epigenetics and the organism’s almost unfathomably complex and intricate skill in managing its genes are finally ridding biology of the notion that DNA embodies a linear code that spells our destiny.
*** Summary        *** Full Text
Associated Articles:
The Unbearable Wholeness of Beings
If you want to understand living beings, then listen to how biologists describe them and ignore how they try to explain them. Descriptions, based on observation, show organisms to be full of meaning and purpose, intention and agency. By contrast, explanations based on philosophical inclination pretend that the organism is really a kind of machine.
*** Summary        *** Full Text
Associated Articles:
From Physical Causes to Organisms of Meaning
The choice between organisms as biologists describe them (see previous chapter) and organisms as biologists would like to explain them is often misunderstood as a choice between physical lawfulness and a “spooky” sort of vitalism. It’s a false choice — as false when brought to bear upon molecular biology as it would be if applied to the physically and chemically lawful, but not physically and chemically explainable, brushstrokes of a Raphael or Picasso. (This chapter was formerly published as “What Do Organisms Mean?”)
*** Summary        *** Full Text
Part 2. Key Themes: Looking More Deeply
This section picks up some of the topics touched upon in the previous chapters — topics that prove problematic for biologists — and takes a more focused and sustained look at them. These are the problems of meaning, of the supposed DNA “program”, of unconscious purpose (teleology), and of the nature of biological understanding.
How Biologists Lost Sight of the Meaning of Life — And Are Now Staring It in the Face
You don’t hear biologists speaking about meaning — not in their professional work, anyway. Yet the distaste for meaning is a historical aberration that can only distort a science that is awash in meaning.
*** Summary        *** Full Text
The Poverty of the Instructed Organism
Are You and Your Cells Programmed?
Understanding organisms on the model of the computer was supposed to save biologists from facing up to the discomfort of dealing with well-directed lives. That’s because computers can give the appearance of thoughtful intention while remaining strictly mechanical. But it turns out that information-processing machines miss just about everything we have been learning about organisms in this era of molecular biology.
*** Summary        *** Full Text
Associated Articles:
From Bodily Wisdom to the Knowing Self
What is the relation between the purpose, meaning, and agency to which we humans give conscious expression, and the analogous features we observe in cells and organisms that surely do not have our sort of consciousness? The answer seems inseparable from various imponderables such as: Where does consciousness or intelligence occur? What is the relation between the intelligence, such as it may be, of the individual bacterium and that of the bacterial colony? Is there such a thing as a pure individual, as distinct from a larger community, whether we are speaking of schooling fish or humans? Might our own reasoning powers be a raising to consciousness and a bringing to individual freedom of the intelligence we witness in the fashioning of our own bodies? It is important to acknowledge both the centrality of such questions for biology, and how little we are currently able to penetrate them.
*** Part 1: The Problematic Effectiveness of Reason in Biology
*** Part 2: Psyche, Soma, and the Unity of Gesture
*** Part 3: Where Do Intelligence and Wisdom Reside?
Biological Truth as Character Portrayal Rather Than Causal Explanation
Alien as it may seem to many biologists, their primary task is not to explain each organism in physical and chemical terms, but to form an accurate, observation-based picture of its unique way of being, different from other organisms. When we look closely, we see that this is always the direction in which the science of biology is being nudged, despite the strong will to gain so-called “mechanistic explanations”.
*** This chapter has not yet been written. However, this earlier paper touches some of the relevant themes.
Part 3. Bringing Life to Evolution
To reconceive the organism more faithfully is to transform our understanding of evolution in a way that seems far beyond the imagination of most conventional biologists as well as their opponents in the “religious wars”. Evolution can be no less a coherent and meaningful story than are the lives of the individual organisms and the myriad, diverse communities of organisms whose stories actually compose the larger, historical drama.
Evolution and the Illusion of Randomness
The modern version of evolution is commonly said to be founded upon mindless, blind processes, and this claim is rooted in the belief that mutations are random with respect to fitness. The claim, it turns out, is the subject of remarkably groundless faith among biologists.
*** Summary        *** Full Text
Associated Article: Natural Genome Remodeling
The organism has powers to transform its own genome, involving a wide range of highly directed molecular processes.
*** Summary        *** Full Text
The Truth and Triviality of Molecular Biology’s “Central Dogma”
The so-called “central dogma of molecular biology”, first promulgated by Francis Crick in 1958, holds most importantly that information moves from the sequence of nucleotide bases (or “letters”) in DNA to those of RNA, and from RNA to the sequence of amino acids in protein, but cannot move from protein back to DNA. Not as sequence, anyway. But this truth, significant as it may be, misses almost the entire literature of molecular biology during the past few decades, which has laid bare endless processes of meaningful exchange that are not based on mere sequence, and also processes that make something structural, three-dimensional, mobile, and living out of the otherwise inert DNA sequence. In other words, so far as it is true, the dogma is hardly central, and the truth it misses points us toward an entirely new understanding of the organism and its evolution.
*** This chapter has not yet been written.
Genes and the Central Fallacy of Evolutionary Theory
Is DNA the Decisive Heritable Material?
Perhaps the decisive misstep of conventional evolutionists has been to posit evolutionary change while ignoring the organism that, as an agent of change, is the central figure in the story. The idea that genes, not the integral activities of a living cell, are the essential elements of heredity has greatly supported this disregard of the organism. Yet the idea dissolves under close examination. Once we free our thinking from gene-centered habits, not only does much of contemporary Darwinism lose its explanatory force, but we begin to glimpse evolutionary vistas that are both more dynamic and more in harmony with the life and development of the organisms we observe today.
*** Summary        *** Full Text
Associated Articles:
Natural Selection — or Nature’s Intentions?
It goes without saying that any organism extant at a given time must, throughout its evolutionary history, have been fit enough to survive up to that time. But while this core principle of “natural selection” may be a truism, it is not a creative principle. It does not help us understand the distinct, characterizable ways of any particular organism — its form and physiology, its goal-driven behavior, the aesthetic unity wherein every feature is expressed “just like a fox” or “just like a cat”. Natural selection enables us to say only that whatever features we do observe must have been consistent with survival. And if it does not explain the characteristic weave of intention in particular organisms, even less does it explain generally why organisms are purposive agents, although it is routinely cited as doing so. Natural selection presupposes all the complex interactions among purposive agents — agents seeking their individual and collective ends in environments partly of their own making — and therefore cannot explain the purposive character of those interactions.
*** This chapter has not yet been written.
Part 4. The Missing Foundation of Science: How Do We Know the World?
The problematic aspects of the foregoing chapters, for most biologists, are rooted in misunderstandings about the relation between humans and their cognitive activity on one hand, and the world on the other — misunderstandings that go all the way back to Descartes and his dualism.
This entire section remains to be written. Meanwhile, however, you can look at the two articles listed below. While not written so as to relate explicitly to the content of this current project, they deal with themes I will be presenting in this section.
A Modest Epistemological Exercise
We must begin thinking about the crucial epistemological questions of our day — questions that will, in the end, determine the sort of world we live in. This paper looks at two worlds, the one given through direct, familiar experience and the other through scientific explanation, and concludes that one of these worlds is laced with massive confusions. And it may not be the one you think.
*** Full Text
Reframing the Mind-Body Problem: An Exercise in Letting Go of Dualist Assumptions
Our ways of imagining our relation to the world as knowers are confused and contradictory. All scientists believe they can know the world to one degree or another, but nearly all have failed to reckon with what immediately follows: the universe must be commensurable with the thought, will, and feeling through which we know it. It is neither a blind and mindless, nor a cold and heartless, place. An analysis of our own process of knowing points us toward the truth of the matter, and enables us to overcome the Cartesian dualism that has distorted science and culture for nearly four hundred years.
*** Full Text
Supporting Materials
A (Mostly) Nontechnical Glossary for “Biology Worthy of Life”
Focusing on genetics, gene regulation, and evolution (and also, as much as possible, on the human being), this glossary is being expanded as new material is written. The glossary entries are accessible by clicking on technical terms in several of the articles listed above, as explained at the beginning of the articles. But you can also call up the alphabetized glossary directly and browse it at your leisure.
*** Full Text of Glossary
How the Organism Decides What to Make of Its Genes
This is a rather massive collection of personal notes taken from the technical literature. It’s rough, informal, and unreviewed — strictly "buyer beware". Be sure to read the “caveats” in the introduction. The real value of the collection is that it brings to awareness what has probably escaped even the attention of most working molecular biologists: namely, how extraordinarily varied and complex are the processes by which the organism makes use of its DNA (as also its other constituents). It is the organism that makes use of its genes, not the other way around.

The brief introduction linked to below is entitled “A Thousand-Stranded Tapestry: How Organisms Employ Their Genes”.

*** Brief introduction to the notes        *** Full Text
Selected Excerpts
Place your cursor on any bulleted line below to click on its link.
Chasing the genetic code
The living chromosome
The insufficiency of DNA
Are organisms mechanical devices?
Are organisms information-processing machines?
The meaning of meaning
Contextuality, plasticity, and wholeness
The language and wisdom of the organism
Rhythm and harmony
Meaning and causation: Is biology merely physics and chemistry?
Beyond vitalism: organisms in a mind-shaped world
Transformation of the genome (mutation)
When is an organism fit to survive?
DNA and living developmental processes
Evolution, inheritance, and the organism’s agency
Meaning and evolution

This document: BiologyWorthyofLife.org

Steve Talbott :: Biology Worthy of Life

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