Biology is Messy, Because Physicists Failed
I came across an interesting blog post titled Biology is Messy. The main argument is that biology is not built on top of reductionist theories, and the current push to collect large amount of data and use “AI” to “solve” biology is not likely to lead to finding reductionist theories either. Instead we will get a bunch of overfitted models hyped up as “solutions” by corporate entities.
I agree with the key argument in the article with one exception (will discuss later). First let us look at how we arrived at the current juncture, because knowing the history may better guide us forward. My understanding is strongly influenced by “A new biology for a new century” and Translation: in retrospect and prospect by Carl Woese and Erwin Chargaff’s Heraclitean Fire: Sketches from a Life Before Nature.
“Biology” discussed in the mentioned blog post is primarily molecular biology, or biology of the physicists. Therefore, its failure to find reductionist theories can be blamed on the physicists. More specifically, their early claim to victory left the most important shortcoming unaddressed. This is addressed by both Woese and Chargaff, who came to similar conclusions from different angles.
I went over the history of genetics since 1950 in an earlier post. Prior to 1950s, biologists were mostly interested in cataloging and classifying living organisms. This tradition started with Linnaeus in 1750s, and Darwin’s theory (1858) made the process more systematic. In parallel, doctors learned a great deal about anatomy and physiology by cutting corpses. I will skip over the foundational work done by biochemists, developmental biologists and geneticists before 1940s to get to the main point.
Schrodinger’s book titled “What is Life?” (1944) could not have been written in 1870 or 1910, because the book had the implied question - “What is life in terms of the wonderful theories we physicists developed?”. Quantum theory was not full developed until 1930s, and many physicists came to biology with their tools, techniques and intellect to make amazing contributions. Unfortunately they claimed victory too early. Also, they missed some of the implications of quantum theory clarified in 1960s. Let me explain.
The Dark Side of Molecular Biology
Title of this section is from “Translation: in retrospect and prospect” by Woese. He argued correctly that, in the rush to claim victory, the molecular biologists (physicists) left the translation problem unaddressed.
As familiarity with the ribosome and the process of translation grew in the 1960s, a need arose for a theory of how the process worked. That need was fulfilled by the A-site–P-site model (Watson, 1964, 1976), which quickly became the most powerful shaping influence of all on the developing paradigm. The theory’s power stems largely from its being pictorial, a cartoon that has appeared in all biology texts for the last several decades. Such a cartoon is easy to remember, almost impossible to forget—and, most importantly, it is impossible to think around. Virtually all of the many new findings concerning translation over the last several decades have been interpreted in terms of this model. And through what amounts to circular reasoning, we have come to see A-site–P-site as a powerful theory that explains almost everything about translation— with the result that the model has been accorded a sacrosanct status within the translation paradigm. There seems no reason to question or test it; no need to conceptualize translation in any other than this simplistic pictorial way.
Translation is like black body problem with respect to classical physics of the early 1900s. The failure to address it is what makes molecular biology “messy”. This point is argued in detail in Woese’s paper.
Reductionism versus Reductionism
This is another title from Woese’s second paper - “A New Biology for a New Century”. It is a must read for anyone trying to derive reductionist theories for biology.
“Reductionism” is a confused and cathected issue at the moment, in large measure because biologists use the term in two senses, usually without distinguishing them. This we now have to do. We need to distinguish what can be called “empirical reductionism” from “fundamentalist reductionism.” Empirical reductionism is in essence methodological; it is simply a mode of analysis, the dissection of a biological entity or system into its constituent parts in order better to understand it. Empirical reductionism makes no assumptions about the fundamental nature, an ultimate understanding, of living things.
The main point here is that reductionist physics died in the 1950 and 60s with the development of theory of superconductivity. This is a problem Feynman worked unsuccessfully on for many years. The solution introduced the idea of emergent properties in physics. Quoting Woese -
Fundamentalist reductionism (the reductionism of 19th century classical physics), on the other hand, is in essence metaphysical. It is ipso facto a statement about the nature of the world: living systems (like all else) can be completely understood in terms of the properties of their constituent parts. This is a view that flies in the face of what classically trained biologists tended to take for granted, the notion of emergent properties. Whereas emergence seems to be required to explain numerous biological phenomena, fundamentalist reductionism flatly denies its existence: in all cases the whole is no more than the sum of its parts. Thus, biology of the 20th century was in the strange position of having to contort itself to conform to a world view (fundamentalist reductionism) that 20th century physics was simultaneously in the process of rejecting. In a metaphysical sense, molecular biology was outdated from the onset!
Chargaff, who was trained as chemist, noticed this right from the start. In the 50s and 60s, he noticed many pronouncements from reductionist physicists as “life is nothing but”, but none of them could really explain what life is. Incidentally, around the same time, biology was rebranded as “life science” through a NIH-sponsored marketing campaign, and Chargaff found that as amusing.
Why is life nothing but DNA, RNA, protein, transcription, translation, signaling, etc.? The answer is “emergent properties”. Chargaff argued that music could be presented by reductionist scientists as “nothing but wood and strings and drums and so on”, but music is more than a collection of those parts. So, Schrodinger’s original question remains unanswered.
Exception
Earlier I said that I agreed with the mentioned blog post but with one exception. That exception is regarding where we set the level of abstraction. I will be borrowing from Sydney Brenner’s Sequences and consequences here.
If the level of abstraction is set at the cell level instead of molecular level, it will be feasible to derive a description of the system from massive data. Please check “Gene regulatory networks” and linked posts for more detail.
What is the benefit of abstracting at the cell level? It avoids the “what is life” question, and instead goes into how to morph one form of life into another. More specifically, the cells in the body are all in different states based on the genes expressed within them, and the purpose of data is to identify the key genes directing their state changes. Surely, this will bring up emergent properties of higher order (e.g. consciousness), but we are nowhere close to address them.
