To fully appreciate the intellectual disruption that’s underway in 21^st century biological thinking, you need to go back to April 1953. That’s when the (still) renowned science journal Nature published Watson & Crick’s manuscript describing the helical structure of DNA, and how its ladder-and-wrung assembly of nucleotides might be the long sought biochemical template for transferring genetic information from cell to cell and parent to progeny.

The Second World War had ended just eight years earlier, brought to a grim conclusion by the obliteration of two Japanese cities with nuclear fission bombs – a dark triumph of modern physics.

Allied science and technology had been decisive.  American and European-Jewish physicists had transformed nuclear theory into nuclear weaponry. British and American intelligence agencies had decrypted the radio communication codes of the Axis militaries thanks, in part, to the use of first-generation computers. The war’s lessons couldn’t be clearer: Godlike powers could be mined by decoding nature’s underlying operative principles.

And now, with Watson & Crick’s discovery, here was the biological equivalent of nuclear fission; the hidden code for life; the mythical “gemmules” prophesied by Darwin that provided the deep mechanism for passing traits down through generations.  

Science had conquered the atom, now it would conquer the gene.   

How DNA actually produced proteins – life’s structural and operational modules – was soon revealed by two French scientists, Francois Jacob, who’d been wounded in the war while serving with a French armored division, and Jacques Monod, a highly decorated former member of the French resistance. Every biology undergraduate from the 1960s onward has been expected to memorize Jacob and Monod’s Lac operon model for gene regulation, using RNA for transcribing and translating long strands of DNA nucleic acid code into long strands of protein amino acid code.

And so, here was the complete story: DNA was the working substance of the gene which was the working substance of the genome. The morse-code-like nucleotide sequences in DNA corresponded to the 23 amino acids which living systems strung together to make proteins, which can consist of anywhere from two or three amino acids up to many thousands.

But then came the theoretical leap that fatefully shaped biological thinking (and many other things) for the remainder of the century: The Neo-Darwinist paradigm that conjoined Watson & Crick’s DNA with Darwin’s observations held that all the living complexity we see around us blossoms upwards from genome. The genome’s information is transcribed into a precise matrix of proteins that self-direct and self-organize themselves into the cell’s structural and functional components.  The flow of information, and thus control, was one way: from genome to cell to organism.

Sure, many other things might influence how a cell grows and lives, but they’re peripheral to the central dogma of gene-to-protein translation as the driving force behind life’s defining features of replication and evolution. It gave biologists a mechanistic framework for deconstructing the complex back to the simple. Life’s messy details could be streamlined down to its underlying principles, which could then be mathematized and universalized.

In this sense, biology was like chemistry: The physical properties of any substance can be explained by the properties of its elements, whose properties can be explained by each element’s arrangement of electrons, neutrons, and protons.  

Life could be plugged into the top of this mechanistic schema through the molecular biology of DNA transcription. Nature’s wondrous diversity could be streamlined back to nucleic acid sequences. The operative framework beneath life’s complexity was exposed. How, precisely, this all actually worked at the molecular and cellular levels was mere detail to be worked out later. What was important … vitally, vitally important … was that science finally had a coherent theory with which to smooth away life’s apparent mysteries.

And the protagonist of this new narrative was the gene. The traits that distinguished one organism or species from another were mutable and expendable. The real story was the gene. The gene directed cell operations so as to ensure its own survival and transmission to the next generation of bacteria or plant or sponge or animal or … whatever.  The organism’s phenotype, its collective traits, were a consequence of the genome’s actions. All organisms eventually die, all species eventually evolve into other species, but the universal, eternal-but-ever-changing thread was the gene.

Biologist Richard Dawkins captured the essence of neo-Darwinism in his 1976 book The Selfish Gene, declaring, with nihilistic nonchalance, that all organisms, including humans, should most accurately be seen as “survival machines – robot vehicles that are blindly programmed to preserve the selfish molecules known as genes.”

“Programmed” was the crucial concept of Dawkin’s vision. It analogized biology with digital technology (a curse we’re still dealing with). The gene was the brilliant master program, conditioned by three billion years of evolution. Humans, with their delusional self-importance were, in truth, just programmable meat puppets.

Warning signs about this new theory’s myopia started popping up right from the beginning.  

Jacob and Monod had shown how RNA translates DNA’s code, but they had also shown that genes are influenced by the cell’s internal and external environmental. Plant geneticist Barbara McClintock showed that cells could transpose genes from one region of the genome to another. If the gene was the master controller of the cell, why was it so easily moved around or switched off?

Could nature’s complexity really be organized around a one-way information stream of gene to whole organism to environment?  Other sources of “information” seemed to be just as important.

Nevertheless, the gene-centric paradigm had cultural and institutional momentum that carried it forward until the mid-1990s or so – no one can really say – when the totality of molecular biological evidence showed that the paradigm was overly simplistic to the point of being obstructive.

The Grand Yet Unsurprisingly Disappointing Human Genome Project

Some authors suggest that the Human Genome Project that got underway in 1993 as the tipping point in neo-Darwinism’s demise.  Popular media had hyped the Project as biology’s moon shot; a triumph of science and reason.  The “blueprint” for human life would be revealed. Cancer would be cured, and other diseases conquered.  A new era would dawn. Etc., etc.

But based on what was already known about genes and genomes, most people in the “biological community” saw the Project as more of a stunt than a serious research endeavor.  But they were so used to the privileging that governments and bio-pharma companies give to human-centric research, that they kept a bemused silence.  And, lo and behold, the project delivered exactly what they’d suspected: Decoding the human genome delivered a giant bolus of molecular biological mush that would take years to sort out.  

When the decoding was finished in 2003, it revealed that of the three billion or so base pairs in the human genome, only about 20 percent coded for proteins. The remaining 80 percent (often referred to as “junk” or biological dark matter) appeared to be involved in a multitude of “epigenetic” (beyond the gene) interactions with what molecular biologist James Shapiro calls the cell’s “natural genetic engineering machinery.” And, as anticipated, 20 years later we’re still trying to figure out how it all works. In other words, only 20 percent of the human genome functioned in the way that the gene-centric paradigm of inheritance envisioned. Most of the genome was used by the cell (not the other way around) to do what it needed to do.

What we’ve come to understand is that the genome is part of the cell’s genetic engineering machinery. It’s a key part, for sure, but it’s not the dominant part. Computer analogies don’t work here. The genome is not like a program that tells the cell what to do. It’s quite the other way around, if anything. Neither is the genome like a central processing unit. Computers don’t manipulate their CPUs; trim them, rearrange them, suppress them. The cell’s genetic engineering biochemistry is too complex and, at this point, too superficially known to make comparisons to human technologies.

Twenty years later, the genome project helped reinforce the idea that from a systems information view, the flow of information is not just bottom-up, from gene to organism, but also top-down, from organism to gene. The two-way flow of information is rapid and continuous. The cell’s epigenetic machinery is highly responsive, flexible, and sophisticated.  The “genetic code” is malleable and discretional; the cell can actively switch portions of the genome on or off in response to environmental inputs and changes. This bi-directional flow works all the way up to the ecosystem level. Environmental “information” can cause organisms to rearrange genes or turn them off and on. Instead of the mechanistic-robotic model of inheritance and evolution envisioned by “selfish gene” theorists, the living universe turns out to be profoundly more entangled and interactive than anticipated by 20^th century science.

As Shapiro puts it, the old neo-Darwinian theory saw the genome as a “read only” set of instructions dictating which proteins the cell must make. The new paradigm sees the genome as a flexible “read-write” apparatus that provides the cell an interactive framework of possibilities.

The old paradigm was mechanistically simple and, in terms of information processing, completely implausible.  It presumed that once the genome got plugged into the cell’s replication system, it told the cell which proteins to make and when. And then, somehow, in the process of self-organizing and self-arranging themselves the proteins provided all the additional information and structure necessary for the cell to perform all the complex biophysical tasks required to adapt to its environment and be “alive.” In other words, simply by the arrangement of its DNA, the genome communicated all the essential information required for life.

What actually happens is that the proteins become integrated into the cell’s higher-level functionality which operates the genome as it needs to. As Ladislav Kovac, professor of biochemistry at Comenius University in Slovenia explains, this cellular “teleonomy” (purposeful behavior) arises from biochemical “vectoriality.”

“This intrinsic goal-directed plasticity of the protein molecule can be dubbed ‘molecular sentience’, and it is this sentience that makes a protein a ‘living’ molecule,” says Kovac.

(Life, chemistry and cognition, Ladislav Kovác, 2006,  EMBO reports VOL 7 | NO 6 | pp.562-566)

Sentience Blossoms Throughout Biological levels

Sentience at the cellular level radiates upward through all levels of biological organization. “Sentience” is emerging as a defining feature of life. Plants, animals, bees, bacteria – all possess a capacity to … “anticipate predictable changes in their environment with a clear sense of both time and space,” say Anthony J. Trewavas and František Baluška, molecular botanists at, respectively, the Institute of Molecular Plant Science, University of Edinburgh, UK and the Institute of Cellular and Molecular Botany, University of Bonn, Germany. (The ubiquity of consciousness, Anthony J. Trewavas and František Baluška, EMBO reports VOL 12 | NO 12 | 201, pp. 1221-1225)

The 21^st century paradigm of inheritance and evolution presumes the cell to be a cognitive, sentient, teleonomic (purpose-driven) complex system which uses the genome as a source of information for making proteins in response to ongoing, real-time environmental signals and stresses.

I may be indulging my own biases, but from my reading of the leading edge work of specialists across the spectrum of biological research, I think there’s a growing belief that “sentience” on the cellular level turns out to be the event horizon threshold between life and non-life. It emerges synergistically from the collective interactions of cellular proteins because of their complex structures that reflexively change conformations to balance energy-entropy forces. 

It’s important to keep in mind that cells typically produce millions of proteins per second. Cells are also continuously processing and responding to subtle movements of ions in and out of the cell and through biochemical cycles. When we consider how dynamic and exquisitely complex and integrated all these protein-mediated operations are, we get a sense of how a synergistic ‘sentience’ arises from it. 

Biologists also once and for all need to get past the reluctance to use words like “consciousness,” “sentience,” and “intelligence” because they imply bias or anthropomorphism. Humans are not the only conscious, sentient, and intelligent beings on the planet. Our conscious self-awareness is profoundly higher level than any other creature, but that doesn’t mean nature is populated with unthinking, lifeless automatons.  

As Trewavas and Baluška explain: “…it is not too much to say that a plant is capable of cognition in the same way that a human being is. The plant gathers and continually updates diverse information about its surroundings, combines this with internal information about its internal state and makes decisions that reconcile its wellbeing with the environment.”

I’ll stress that we’re not talking about the new-age mystical version of plant intelligence that had people back in the 20^th century playing Mozart to their Ficus.  As Zoë Schlanger said in her wonderful 2019 book The Light Eaters (Harper Collins) about current theory of plant sentience, only after carefully and patiently studying the astonishingly sophisticated ways plants interact with their environments does the true nature of their “intelligence” undeniably emerge.

Schlanger makes the point that science still has no clear, universally agreed upon definition of life. Is it about complexity? Reproduction? Metabolism? Astrobiologists like to remind us that if we’re to seek life beyond earth (seems like a waste of resources to me, but that’s a future blog), then we must open our minds to all sorts of chemically ethereal life forms. Or what if some distant organic-based life form died off but left behind a race of self-replicating robots? Would we say that they’re alive?   

I’d like to wrap up this particular post with a not so bold suggestion (because it’s been made by many others) that life is a complexity-gaining process, but also a sentience-gaining process if not a consciousness-gaining process. I think that’s the hidden message that’s going to slowly rise to the surface over the coming decades. Life can’t be reduced to underlying principles, nor can consciousness. People outside the life sciences might not like it, but there it is.