Analogies For Biochemical Events

[Travis]

Often you hear biochemists make analogies for certain biochemical structures and events such as the membrane ion "pump", and the "crossbridge" theory of muscle contraction. Ray Peat has written about this.

This bothers me too, as it gives biologists permission to think about life below the cell level in mechanistic and silly terms. Besides the unrealism of the analogies, Gilbert Ling has shown there are no "pumps" and Harold Hillman has shown there to be no "crossbridges" (in muscle).

I was reading an article about AMP kinase—from the journal Nature: Cell Biology mind you— and came across this passage:

Thus AMPK controls mitochondrial homeostasis in a situation resembling “Cash for Clunkers” in which existing defective mitochondria are replaced by new fuel-efficient mitochondria (Fig. 3).

Exactly! Adenosine monophosphate kinase phosphorylates mitochondrial proteins in a way that resembles how struggling used-car dealers drum-up business by offering cash (or a trade-in rebate!) for used cars.

All is clear now.

Culture, it seems, starts to make us stupid long before the metabolic problems appear. –Ray Peat

Academic authoritarians, language, metaphor, animals, & science

 

[Ideonaut]

Often you hear biochemists make analogies for certain biochemical structures and events such as the membrane ion "pump", and the "crossbridge" theory of muscle contraction. Ray Peat has written about this.

This bothers me too, as it gives biologists permission to think about life below the cell level in mechanistic and silly terms. Besides the unrealism of the analogies, Gilbert Ling has shown there are no "pumps" and Harold Hillman has shown there to be no "crossbridges" (in muscle).

I was reading an article about AMP kinase—from the journal Nature: Cell Biology mind you— and came across this passage:Exactly! Adenosine monophosphate kinase phosphorylates mitochondrial proteins in a way that resembles how struggling used-car dealers drum-up business by offering cash (or a trade-in rebate!) for used cars.

All is clear now.

Yes, but how to understand what is happening on the biochemical level without relying on some metaphors?


Academic authoritarians, language, metaphor, animals, & science

 

[Travis]

Yes, but how to understand what is happening on the biochemical level without relying on some metaphors?

I guess if they are appropriate enough they can be useful. I just read that ATPK acts like a "metabolic master switch", and that didn't really bother me.

3.6. Berberine activated AMPK Adenosine monophosphate–activated protein kinase is emerging as a metabolic master switch. Changes in AMPK activity have been shown to regulate glucose transport in muscle and adipocytes. Acetyl-coenzyme A carboxylase is phosphorylated by AMPK and is inactivated [20].

Berberine stimulates glucose transport through a mechanism distinct from insulin

I guess it's a matter of taste and accuracy. Likening a biological event to "Cash for Clunkers" goes a bit too far tor my taste. Just imagine reading this about AMP kinase in a prestigious journal:

Thus AMPK controls mitochondrial homeostasis in a situation resembling “Auschwitz” in which existing defective mitochondria are tagged with a "Star of David" (phosphate) to be removed by cytosomal proteases (fig 4).

Although this may help people understand AMP kinase, it goes a bit too far. Perhaps better would be?:

Thus AMP kinase functions to control mitochondrial homeostasis in a manner resembling a University librarian: Existing defective mitochondrial proteins are earmarked for replacement and then "pulled from the shelf" only to be replaced by newer editions of mitochondrial proteins.