[This article is authored by Biologic research scientist Ann Gauger, whose work uses molecular genetics and genomic engineering to study the origin, organization and operation of metabolic pathways. She received a BS in biology from MIT, and a PhD in developmental biology from the University of Washington, where she studied cell adhesion molecules involved in Drosophila embryogenesis. As a post-doctoral fellow at Harvard she cloned and characterized the Drosophila kinesin light chain. Her research has been published in Nature, Development, and the Journal of Biological Chemistry. Dr. Gauger also appears in the upcoming film Metamorphosis.]
Over the last decade I’ve become convinced that in spite of our overflowing databases we don’t understand much about biology. We’re like students who have learned the Bohr model of the atom, and think we have grasped atomic structure. As a beginning, it’s a decent approximation. But atomic structure goes way beyond this simple model.
In the same way, we’re accustomed to talking and thinking about the cell as made up of machines (hardware), with DNA as the software program that somehow determines the hardware. This is an advance over imagining the cell as a few simple chemical reactions. But it’s still radically inadequate, if not obsolete, when trying to capture the reality of what we’re discovering in the biological world. We’re in search of more adequate conceptual categories. And the outcome will make our current descriptions look utterly inadequate. What we want to do is to catch up to the evidence, and get beyond our own, quite limited ways of speaking of these realities.
In a recent essay Steve Talbott highlights the inadequacies of our current way of thinking and speaking about biology. He points out that organisms are more than the sum of their mechanisms. In fact, he rejects the machine metaphor as completely inadequate to describe living things. Living beings are adaptable and responsive to their environments, changing their behavior based on external cues and their own requirements. They are transformative, existing as entities that are much more than the molecules that compose them. They are not what they eat — they make what they eat into themselves. Living beings are integrated wholes that come from other living things. And they are more than their DNA. DNA requires a functional cellular environment to be properly read and interpreted, just as a cell requires DNA to be able to sustain itself. In order to understand the whole picture you have to look at the cell from many points of view, not just a gene-centric one.
Everything in organisms is interconnected causally. Everywhere in biological systems, chicken and egg problems abound. For example, amino acid biosynthesis pathways are composed of enzymes that require the amino acids they make, ATP biosynthesis pathways must have ATP to make ATP, DNA is needed to make proteins, but proteins are needed to make DNA, and the list goes on. Indeed, the scope of the problem is difficult even to grasp.
Ultimately, cellular systems can be made only by — wait for it — cells. We can isolate ribosomes or nuclei or mitochondria or Golgi, and study their parts, but we can’t build them, even though we know what they are made of. It takes a whole cell to make them. For example, ribosomes and spliceosomes, the large ribonucleoprotein particles that are essential for the processing and translation of messenger RNAs into protein, must be synthesized, modified, and partially assembled in particular regions of the nucleus, and then be exported to the cytoplasm for further modification and assembly. Literally hundreds of other proteins and RNAs are involved in these dynamic processes, enabling the many RNA-RNA, RNA-protein, and protein-protein interactions and rearrangements that are required, all the while proof-reading and removing stalled assemblages that may occur along the way.¹
What kind of processes can produce such interconnected, self-reproducing systems? Can a bottom-up process like neo-Darwinism boot-strap its way to such causally circular beings?
Many biologists would answer yes, because after all, what else is there besides neo-Darwinism? Their prior commitment to mechanistic, reductionist thinking and materialist presuppositions prevents them from seeing the problem. In fact, this insistence on purely materialistic, bottom-up explanations goes back a long way.
I have a book of lectures given at MIT by the famous developmental biologist and geneticist, Edmund Wilson, in 1923. The book is called The Physical Basis of Life. Wilson acknowledged that we knew nothing about the origin or functioning of cells or the development of body plans, but insisted as an article of faith that there would be a purely physical explanation, based in chemistry.
Up until now, the materialist, reductionist method has been very successful, because cells can be ground up, probed, measured and tested in a way that life forces or agency can’t be. But now molecular, cellular, and developmental biologists are drowning in a flood of data that we don’t know how to interpret. We do not know, for example, how to read a genome from an unknown new species to say what kind of organism it will produce. We can only determine what other genomes it most closely resembles. In order to predict the nature and appearance of the organism with that genome, we would need to know — just for starters — the maternal and paternal contributions to the egg and sperm, the whole of the developmental path from egg to adult, plus the particular effects of any mutations within that genome on its phenotype, not to mention its environmental history.
When we rely only on a reductionist approach, we cannot see the organism as a whole. An extremely simple analogy, drawn from a human artifact, might help to see why. Imagine an elaborately knit sweater, maybe an Irish fisherman’s. Someone who wants to understand the sweater finds a loose end and starts to pull. He keeps pulling and pulling, expecting to arrive at some causal knot, until the whole thing comes apart and is unraveled on the floor. The sweater as a functional whole depends on the way the wool twines together. To understand the sweater you have to look at the patterns in the whole, not just what it was made of. Pulling it apart destroys its essential nature. Now this is a very poor analogy, but scientists are often like that poor fellow tugging on the string.
I like to show a video to illustrate why we need to look top down as well as bottom up. It’s a real-time visualization of a living cell, with various structures (organelles) highlighted one by one. Go here to see it.
These cellular components, and many others, function in a very crowded cellular milieu, somehow recognizing the molecules and structures with which they are supposed to interact. They send and receive signals, correct errors, and adjust their activity in a dynamic way according to the needs of the whole organism.
Notice the language of intentionality in the last paragraph: ‘function’, ‘recognize’, interact’, ‘signal’, ‘correct’, ‘adjust’. Such language is common in biological writing. Talbott points this out also, and explains why (emphasis added):

[Because] there is no possible way to make global sense of genes and their myriad companion molecules by remaining at their level, researchers have “simply bestowed upon the gene the faculty of spontaneity, the power of ‘dictating,’ ‘informing,’ ‘regulating,’ ‘controlling,’ etc.” And today, one could add, there is at least an equal emphasis on how other molecules “regulate” and “control” the genes! Clearly something isn’t working in this picture of mechanistic control. And the proof lies in the covert, inconsistent, and perhaps unconscious invocation of higher coordinating powers through the use of these loaded words — words that owe their meaning ultimately to the mind, with its power to understand information, to contextualize it, to regulate on the basis of it, and to act in service of an overall goal.

Recognizing the implied intentionality in such language, several authors have called for biologists to abolish these words from their writing. According to them, anything that implies either teleology (being directed toward a goal or purpose) or agency (intelligence acting to produce an effect) is to be eschewed. After all, both teleology and agency have been discarded by modern biologists, along with vitalism. Yet teleological language persists. Maybe the reason such language is so common in biology research is because living things are directed toward a purpose. Maybe biological systems do reflect intelligent agency, because intelligent agents are the only known source capable of designing, assembling, and then coordinating so many interrelated sub-systems into a functional whole. And maybe, by acknowledging this, we can come to understand biology better.
Notes
¹Staley JP, Woolford JL (2009) “Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines.” Curr Opin Cell Biol. 21: 109-118. doi:10.1016/j.ceb.2009.01.003.