The limits of chemical reductionism

“Everything in chemistry turns blue or explodes”, so sayeth a philosophy major roommate years ago.  Chemists are used to being crapped on, because it starts so early and never lets up.  However, knowing a lot of organic chemistry and molecular biology allows you to see very clearly one answer to a serious philosophical question — when and where does scientific reductionism fail?

Early on, physicists said that quantum mechanics explains all of chemistry.  Well it does explain why atoms have orbitals, and it does give a few hints as to the nature of the chemical bond between simple atoms, but no one can solve the equations exactly for systems of chemical interest.  Approximate the solution, yes, but this his hardly a pure reduction of chemistry to physics.  So we’ve failed to reduce chemistry to physics because the equations of quantum mechanics are so hard to solve, but this is hardly a failure of reductionism.

The last post “The death of the synonymous codon – II” puts you exactly at the nidus of the failure of chemical reductionism to bag the biggest prey of all, an understanding of the living cell and with it of life itself.  We know the chemistry of nucleotides, Watson-Crick base pairing, and enzyme kinetics quite well.  We understand why less transfer RNA for a particular codon would mean slower protein synthesis.  Chemists understand what a protein conformation is, although we can’t predict it 100% of the time from the amino acid sequence.  So we do understand exactly why the same amino acid sequence using different codons would result in slower synthesis of gamma actin than beta actin, and why the slower synthesis would allow a more leisurely exploration of conformational space allowing gamma actin to find a conformation which would be modified by linking it to another protein (ubiquitin) leading to its destruction.  Not bad.  Not bad at all.

Now ask yourself, why the cell would want to have less gamma actin around than beta actin.  There is no conceivable explanation for this in terms of chemistry.  A better understanding of protein structure won’t give it to you.  Certainly, beta and gamma actin differ slightly in amino acid sequence (4/375) so their structure won’t be exactly the same.  Studying this till the cows come home won’t answer the question, as it’s on an entirely different level than chemistry.

Cellular and organismal molecular biology is full of questions like that, but gamma and beta actin are the closest chemists have come to explaining the disparity in the abundance of two closely related proteins on a purely chemical basis.

So there you have it.  Physicality has gone as far as it can go in explaining the mechanism of the effect, but has nothing to say whatsoever about why the effect is present.  It’s the Cartesian dualism between physicality and the realm of ideas, and you’ve just seen the junction between the two live and in color, happening right now in just about every cell inside you.  So the effect is not some trivial toy model someone made up.

Whether philosophers have the intellectual cojones to master all this chemistry and molecular biology is unclear.  Probably no one has tried (please correct me if I’m wrong).  They are certainly capable of mounting intellectual effort — they write book after book about Godel’s proof and the mathematical logic behind it. My guess is that they are attracted to such things because logic and math are so definitive, general and nonparticular.

Chemistry and molecular biology aren’t general this way.  We study a very arbitrary collection of molecules, which must simply be learned and dealt with. Amino acids are of one chirality. The alpha helix turns one way and not the other.  Our bodies use 20 particular amino acids not any of the zillions of possible amino acids chemists can make.  This sort of thing may turn off the philosophical mind which has a taste for the abstract and general (at least my roommates majoring in it were this way).

If you’re interested in how far reductionism can take us  have a look at http://wavefunction.fieldofscience.com/2011/04/dirac-bernstein-weinberg-and.html

Were my two philosopher roommates still alive, they might come up with something like “That’s how it works in practice, but how does it work in theory? 

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Comments

  • Wavefunction  On May 14, 2011 at 9:57 am

    There is one first-rate and rather unique philosopher of chemistry whose works you should sample- Eric Scerri of UCLA. Look up his writings on Amazon (he also wrote a piece or two for Nat Chem)

  • MJ  On May 14, 2011 at 11:21 am

    One question to think about – is it really even that the equations are too hard, or is it that we don’t have the mathematical language necessary? The n-body problem is an old one, and predates quantum mechanics. There are a couple of analytical solutions for various restricted three-body problems (I imagine you probably stumbled across the entire confocal elliptical coordinate method for the hydrogen molecular ion in your studies of QM), of course, but they’re hardly generally applicable.

    And people were really trying to rationalize the differences in the amounts of beta and gamma actin based purely on chemical grounds? I admit my brief flirtation with actin and actin-binding proteins in research was a little while ago, but that just sounds rather silly. Then again, I am a woefully corrupt biophysical chemist who is about a moment away from turning into a systems biologist at my current rate. Heh.

    • luysii  On May 14, 2011 at 1:34 pm

      I don’t think people are trying to rationalize the differences in the amounts of beta and gamma actin on chemical grounds. My point is that chemistry can explain nearly exactly why their amounts are different, but that chemical concepts are useless in explaining why cellular physiology requires (wants, if you’re in an anthropomorphic vein) this difference for optimal function.

      • MJ  On May 17, 2011 at 9:24 pm

        I asked since I have occasionally heard such optimistic/naive notions from people, typically those without much if any knowledge/experience with biology and/or biological processes.

        I’ve always felt that physics and chemistry define the boundary conditions for biology, but are not in and of themselves going to provide the whole story. For example, the estimates on the size of microorganisms and their use of pheromones – too small, and the diffusion of any attractants is unlikely to work well. But clearly, those who are interested in these microorganisms are going to want more detail in the end.

  • michael  On May 15, 2011 at 3:12 pm

    It seems to me that even a small difference in the protein structure or even the mRNA sequence of beta- and gamma-actin might mean they have different protein binding partners, different localisations etc. In turn this would mean involvement in different cellular functions, and perhaps knowledge of these would lead to an explanation of the functional reason of their different abundance. I can’t see then why in principle your example poses a problem for reductionist explanations (or indeed why philosophers need to get involved in this problem, and not just the usual chemists/cell and molecular biologists). An evolutionary explanation of the mechanism by which the actin proteins came to behave in this way also seems to me, in principle, possible with a ‘reductionist’ or physical/chemical explanation.

  • luysii  On May 16, 2011 at 3:24 pm

    Certainly there is no problem with 4 amino acids changing what a protein binds to or how it acts — it only takes one amino acid change for hemoglobin to become sickle hemoglobin, or the loss of one amino acid (phenylalanine #508) in the 1480 protein mutated in cystic fibrosis. The actin example was chosen because the chemical mechanisms explaining how the cell does this are so well worked out, unlike many other examples.

    Where chemical reductionism fails to tell us anything is why the cell would find it useful to have different amounts of two such similar proteins. So I chose the actin example because it pushes chemical reductionism as far as it can go, and because it shows why it still comes up short when we’re talking about the workings of a cell.

  • offshore bank accounts  On May 17, 2011 at 9:00 am

    Other areas of biochemistry include the RNA protein synthesis cell membrane and signal transduction.This article only discusses terrestrial biochemistry – and -based as all the life forms we know are on . Previously this area would have been referred to as physiological chemistry.

  • CS  On July 24, 2015 at 12:02 pm

    Reductionism is not as clever as it seems. Better to treat chemicals as chemicals and not forget that life is life, and is operates according to its own drives. Macroscopic events have microscopic consequences all the time. The link below is for a series of articles I found extremely enlightening.

    http://www.thenewatlantis.com/publications/getting-over-the-code-delusion

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