Genes in Context

My conversation with Jason Hoskins, a molecular geneticist and systems biologist at the National Cancer Institute, explored the convergence between contemporary systems biology and process-relational philosophy. Jason studies how inherited genetic variation becomes effective through gene-regulatory systems to influence pancreatic cancer risk. His research begins with genome-wide association studies, but his experience has increasingly convinced him of the limits of trying to trace simple molecular chains from a genetic variant to a disease phenotype.

The strongest biological point of contact with process thought was Jason’s commitment to radically contextualizing everything. When I contrasted his relatively bottom-up genetic work with Michael Levin’s tissue-level bioelectric approach to cancer and suggested that the two might need to meet in the middle, Jason replied that this was absolutely the direction biology needs to go. He described systems biology explicitly as a reaction against reductionism informed by complexity science. His own experience provided a concrete example: after identifying a pancreatic-cancer-associated regulatory region and tracing its influence to a distant gene through three-dimensional chromatin folding, he found that isolating the gene in cultured tumor cells could not adequately reveal its function. The cells had been removed from the pancreas, its signaling environment, morphogenetic gradients, and potentially its bioelectric context. For Jason, molecular effects become intelligible only within such wider contexts.

This leads to a picture of genes quite different from simple genetic determinism. Jason emphasized that alternative splicing, epigenetic regulation, transcriptional dynamics, cellular stress, inflammation, and environmental conditions continually affect what a gene actually does. His refrain was “context, context, context”: one cannot isolate a gene in a single cellular system and expect thereby to grasp the life systems in which it participates. I suggested that DNA is therefore not adequately understood as a linear program running from gene to RNA to protein but is something analogous to another organ system participating in organismic development. Causal influence loops across scales, with the spatial position of chromosomes, cells, and tissues helping determine which genetic potentials become actualized.

This opened onto a broader historical and methodological question about the relation between biology and process philosophy. I suggested that the mid-twentieth-century ascendancy of molecular biology and genetic reductionism represented something of an interruption in an earlier organicist trajectory in biology. Once DNA was identified as the hereditary molecule, it became easy to treat it as the privileged causal key to life. Yet systems biology, developmental biology, epigenetics, and multiscale approaches are now recovering a more process-relational picture, not because philosophers persuaded scientists to adopt it, but because empirical scientific research itself forced the issue.

For me, this illustrates Whitehead’s understanding of speculative philosophy, wherein metaphysics should remain downstream of the natural sciences. Its task is not to tell scientists what they ought to discover or prescribe experimental programs in advance. It should learn from scientific discoveries, generalize from them, and ask what picture of nature they collectively suggest. That said, speculative philosophers also have a legitimate role as critics of abstraction whenever scientists themselves begin extrapolating from specialized findings to broader claims about the nature of life, mind, evolution, or humanity’s place in the universe. At that point scientific interpretation has already crossed into cosmology, and philosophical dialogue becomes unavoidable. But as regards the concrete work of identifying regulatory mechanisms in the laboratory, Jason and I agreed that process metaphysics need not supply an alternative experimental vocabulary. His relation to Whitehead remains, in his words, more “aspirational than operational.”

The conversation became more explicitly Whiteheadian when Jason wondered whether familiar molecular entities such as proteins, RNA, and DNA are really as sharply definite as scientific models often make them appear. He resisted identifying Whitehead’s actual occasions with a privileged microscopic scale. I emphasized that concrescence is scale-free. An actual occasion should not be imagined as a tiny quantum event. Concrescence is Whitehead’s most generic description of how a past world becomes immanent in a novel present which then gives itself to a future. That pattern may be relevant at atomic, molecular, cellular, psychological, or even much larger scales.

This has a specific implication for scientific abstraction. Within a successful model, the differences between two hydrogen atoms may be negligible enough that we properly treat them as identical. Similarly, molecular biology may often treat every instance of a given protein as functionally equivalent. But Whitehead’s process ontology reminds us that no concrete actuality literally repeats another. Every occurrence of a protein is embedded in a unique historical nexus and has never existed before in precisely that context. Scientific abstraction isolates repeatable characteristics from this historical becoming, and rightly so, but we should not confuse the invariants identified by our models with the concrete actualities from which they are abstracted.

Jason picked up this point beautifully by describing science as seeking invariants emerging from an “improvisational becoming.” This brought us to what I take to be one of the central philosophical problems of process ontology. Science is extraordinarily successful at discovering what does not vary. But if becoming, novelty, and historical creativity are basic to life and, indeed, all physical processes, then invariance itself becomes something requiring explanation. Whitehead’s achievement was to insist on both poles simultaneously: variation is ontologically basic, yet the recurrence of definite potential characteristics is equally indispensable if scientific explanation is to have any purchase on the real. The challenge is to track invariance as rigorously as possible without reifying it into a static world behind the flux. Scientific models gain their predictive power precisely by isolating recurrent patterns, but these patterns remain abstractions from actualities undergoing continual creative advance.

That polarity led naturally to our deepest philosophical disagreement concerning eternal objects. Jason accepts Whitehead’s conception of familiar enduring entities as achievements of process, but asks whether Whitehead stops one step too soon with his category of definite potentials. Why begin with definite eternal objects in order to explain how recurring patterns arise? Jason identifies himself as a relational realist rather than a nominalist, but suspects that definiteness itself might emerge from relation. He wonders whether mathematical resources unavailable to Whitehead, particularly category theory and sheaf theory, might allow potentiality itself to be conceived more relationally.

I defended Whitehead while also welcoming the pressure Jason is placing on the concept. Eternal objects should not be confused with enduring objects such as proteins, cells, organisms, planets, or stars. All such entities are historically emergent societies of actual occasions. Eternal objects are instead abstract characteristics or definite potentials. Whitehead is not straightforwardly claiming that they exist beforehand as a warehouse of Ideas waiting in Platonic heaven to enter actuality. Rather, whenever we describe a concrete actuality at all, we necessarily refer to definite characteristics: this color rather than another, this shape, this quantitative relation, this possible manner of organization. Eternal objects are meant to name that abstract definiteness.

Still, Jason’s challenge is a serious one. Is this appeal to definite potentiality genuinely indispensable to a process-relational ontology, or is it partly an inheritance from the mathematical and physical milieu in which Whitehead worked? I have found eternal objects difficult to dispense with because they perform crucial work in explaining recurrence, abstraction, and scientific knowledge of invariances. But precisely for that reason the concept deserves to be stress-tested. Any alternative account must explain how determinate possibilities arise without covertly presupposing the very definiteness it seeks to derive.