Nature Chemistry | The Sceptical Chymist

More Nobel reflections

In December, we published an editorial called “Questioning chemistry” that discussed the definition of chemistry on the back of the recent awarding of the Nobel prize in chemistry for research into the “structure and function of the ribosome”. It was further discussed here on the Sceptical Chymist.

We have since received a comment from Dr. Paolo Ghigna at the University of Pavia giving his views on the apathy of some chemists to the award. These can be found below and may just spark off a little more debate on the subject.

Gavin Armstrong (Associate Editor, Nature Chemistry)


The Editorial in the December 2009 issue of Nature Chemistry remarked on the apathy of the chemical community for the 2009 Nobel prize.

Of course, such a debate would entail the definition of ‘chemistry’, and the editorial defines chemistry as ‘the study of matter and its transformation’. Although it is true, as the editorial says, that “defining research topics is becoming increasingly difficult”, this definition is really too broad to be effective. On one side, elephants are pieces of matter, and during their lives, they go through transformations; on the other side, neutrinos are also pieces of matter that also transform. But no one would doubt the fact that the study of elephants’ life is pertinent to biology, and that studying neutrino oscillations would be the business of physics.

We are then carried back to the question ‘What is chemistry?’. For sure, chemistry is a way of studying matter but we also have to ask how chemists study what kind of matter. To answer this question, as is implicit in the editorial, we need to think about what is the focal point in chemistry classrooms. The large majority of the chemical community would agree that this is the notion of ‘chemical reaction’: chemists are proud of their chemical intuition, that is the ability of being able to predict how a compound would react even in the absence of detailed kinetic and thermodynamic information.

A further step forward can be made simply by looking at the IUPAC definition of a chemical reaction “a process that results in the interconversion of chemical species” Now, a definition of ‘chemical species’ is required. Looking again at IUPAC one finds that a ‘chemical species’ is “an ensemble of chemically identical molecular entities that can explore the same set of molecular energy levels on the time scale of the experiment. The term is applied equally to a set of chemically identical atomic or molecular structural units in a solid array”. Note how, with this definition, questioning about what is pertinent to chemistry does not involve problems of length scale: any crystal of rock salt belongs to a chemical species, is usually much bigger than a ribosome, and is not a molecular species (this is a point chemists tend to forget. For example, CaF2 was named ‘molecule of the week’ on the ACS website).

Probably, one of the reasons for the debate could be that chemists do not recognize a ribosome as a “chemical species”: a ribosome does not fulfill the IUPAC definition. Or, to look at the flip side of the coin, can we apply our chemical intuition to a ribosome?

Comments

  1. Report this comment

    Preston MacDougall said:

    A crystal of rock salt is a molecule. Who ever said molecules can’t be HUGE? Correspondingly, chemistry is a hugely diverse subject. Let’s just get on with it.

  2. Report this comment

    Paolo Ghigna said:

    A crystal of rock salt is not a molecule. At least, is not a molecule in the sense a water molecule is. If you divide a crystal of rock salt you get two crystals of rock salt: no change in properties. If you divide a water molecule you would get hydrogen and oxygen: huge change in properties. A molecule can indeed be huge (polymers are the most obvious example). But chemistry is not the study of molecules. As you said, chemistry is a hugely diverse subject, and a lot of chemistry currently deals with non-molecular entities.

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    RM said:

    Dr. Ghigna, you are telling me that if I split a multi-megadalton-sized molecule of polyethlene in two, I get a change in properties on the order of splitting water into hydrogen and oxygen, rather than on the order of “If you divide a (molecule) of (multi-megadalton polyethylene) you get two (molecules) of (megadalton polyethylene)”? (Though I agree with you that the molecule/non-molecule distinction is irrelevant to the definition of chemistry.)

    Additionally, and more importantly, I am wondering on what basis you make the claim that “a ribosome does not fulfill the IUPAC definition.” (That is, in what way are ribosomes not “an ensemble of chemically identical molecular entities that can explore the same set of molecular energy levels on the time scale of the experiment”, at least any less so than polyethlene or other polydisperse polymers are?

    At any rate, I believe the modern definition of Chemistry is slightly moot, in context. Given the Nobel committee’s desire to be faithful to the will of Alfred Nobel in not creating new prize categories (e.g. no Biology Nobel or Biochemistry Nobel), the ruling definition of what does or does not warrant a Chemistry Nobel should be a contemporary (to Mr. Nobel’s will) definition, rather than a modern one. To a late-1800s practitioner, “Studies of the structure and function of the ribosome” would most likely be classed as a study in chemistry, rather than (late 1800s) biology, or any other turn-of-the-century scientific field.

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    Paolo Ghigna said:

    First, let me say that I’m quite happy about the fact that this discussion is going towards the definition of Chemistry, which, as chemists, we should know quite precisely and, indeed, as you wrote is “slightly moot”.

    To answer to your question:

    1) My argument was about rock salt, and a crystal of rock salt can be split into parts without any change in properties. There is no doubt about that. This is because rock salt is an ionic substance, and what is called “ionic bond” is isotropic: NaCl molecules do exist in the gas phase, but this has nothing to do with the fact that a solid rock salt crystal has nothing to do with a molecule. Now, we can go to your point, about splitting in two a molecule of polyethylene. For doing that, you have to break a C-C bond: a covalent, highly anisotropic bond. What would you get, then? Two radicals? A carbocation and a carbanion? In any case, the change in reactivity is huge.

    2) There are several reasons for which ribosomes do not fulfill the IUPAC definition, the most obvious one being that ribosomes from different species have different structures and different reactivity (this is the reasons for which antibiotics can kill bacteria without killing you).

    3) Your last point is fully agreeable. But if you are right, it follows that the major part of modern chemical research would not warrant a Nobel prize!

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    Richard said:

    In my opinion the definition of chemistry as ‘the study of matter and its transformation’ is missing a crucial point, which is that of scale. Chemists focus on objects on the scale of atoms. That is why the ribosome feels slightly fuzzy (unless one concentrates on a smaller part of it, elucidating mechanism) and the elephant and the neutrino are both out of bounds.

    Paolo, re your point (2) – but each particular ribosome from a particular species can be called a chemical species, can’t it? “Ribosome” as a word is a bit like “free radical”, it covers a number of molecular species drawing attention to their similar function.

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    Paolo Ghigna said:

    Richard, it took me a while to reply to your question. I think we are facing a big problem of definition here, and I really hope that someone from IUPAC could read this thread. The point is that a question such as “Can a particular ribosome from a particular species be called a chemical species?” is epistemologically not trivial, and this difficulty extends to all the “nucleic” stuff (ribosomes contain rRNA).

    The IUPAC definition of chemical species requires to have an ensemble of identical entities. As far as I know, ribosomes coming from different individuals of the same species can be non-identical. Polymorphism and mutations are sources of differences. Now, it is also true that polymorphism and mutations are in the largest part of circumstances neutral and/or silent and/or synonymous. In a sense, we have something that can fulfill the second part of the IUPAC definition, i.e. “can explore the same set of molecular energy levels on the time scale of the experiment”, for the sequence of amino acid in the protein that is expressed is unaltered, but does not accomplish with the first one! As a chemist, I have to say that I’m really shocked about that!

    One point is that as chemists, we are educated within a “molecular” paradigm, and this paradigm eventually fails when we are dealing with such complex systems (well, it fails also for ionic solids such as rock salt). On the other hand, if we want chemistry to embrace ribosomes, I think we have to create a new definition (i.e. we have to loosen our “molecular” paradigm, or may be, even find a new one) for such kind of complex stuffs that, without being composed of strictly identical molecular entities, can exploit the same reactivity under the same set of thermodynamic circumstances. May be “chemical quasi-species” would do the job.

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    chiz said:

    Ribosomes from different species may have slightly different sequences and structures but so what? Think of ‘ribosome’, in this context, as a term denoting a class of similar molecules, rather than a specific molecule, a la ‘lactone’ or ‘very long chain fatty acid’.

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    Richard said:

    chiz, that was what I was trying to say and you said it better, thanks. You don’t even have to go to different species, Paolo makes the point that thanks to various local mutations even ribosomes from the same species are not ‘an ensemble of chemically identical molecular entities" as IUPAC defines a chemical species. But, I agree with you, I don’t see this as a big problem, I would see ‘ribosome’ as denoting a class of similar molecules (grouping them together by function, rather than by structure).

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    Paolo said:

    chiz and Richard, as I tried to point out, the IUPAC definition is composed of two parts. This is because both the two parts are required to define an unique chemical potential. Now, I can understand your point. For sure, we can group the substances by considering their function. But in this way, it would be impossible to calculate a chemical potential. On the other hand it should be highly desirable to be able to do that, as ribosomes have (to the pertinent extent) the same reactivity under the same thermodynamic circumstances. That is why I think the molecular paradigm fails with the nucleic stuff.