Thursday, August 20, 2009

Semantic Strait-Jackets in Science

While working on an earlier post, I ran into an annoying issue:  in synapses, the result of a surge of GABA or Glycine is called and IPSP, meaning Inhibitory Post Synaptic Potential.  This remains true even when the effect is actually excitatory.  This is annoying, but easy enough to live with (for me) as I tend to think in historic terms, especially with regard to words.

But it brought to mind an interesting point:  science is full of terms and definitions that are obsolete, with research subsequent to naming and definition having rendered the specific names, and/or some of the assumptions that went into them, invalid.

The case in point makes a good illustration:  the assumption that a particular synaptic action in response to an action potential is inhibitory is built into the name, and it takes an effort of will and memory to keep track of the various times that it might be (or is known to be) excitatory.

But wait! There's more...

Not only does this semantic confusion result in lost time and errors when somebody forgets to allow for all the naming exceptions, but it also tends to channel everybody's thoughts into an assumption that the result of an action potential at a synapse is either one or the other, and that's it. 

The reality, especially with chloride currents, is much more complex.  ... Even if a burst of GABA causes the membrane to depolarize, the equilibrium voltage (also called the "reversal potential") may be somewhere between the resting voltage and the action potential threshold.

Figure 1:  Effect of Cl- current with Equilibrium voltage at ~-62mV as an example.  (Original.  You may link to, copy, and or modify this image.)

In figure 1, we see just this situation.  Compare with those from Axons and Chloride Currents, where the illustrated equilibrium voltages are either below the resting voltage (figure 2), or above the action potential threshold (figure 3).

Figure 2:  Effect of Cl- current with Equilibrium voltage at ~-73mV as typical for a pyramidal cell soma.  (From Axons and Chloride Currents.  You may link to, copy, and or modify this image.)

Figure 3:  Effect of Cl- current with Equilibrium voltage at ~-54mV as typical for a pyramidal cell AIS.  (From Axons and Chloride Currents. ; You may link to, copy, and or modify this image.)

In figure 1, a strong Cl- current will tend to depolarize the membrane, but only so far.  If an EPSP based on sodium or calcium attempts to depolarize it further, the Cl- current will have a shunting action that will tend to resist this depolarization.  How the membrane responds, and whether an action potential is fired, will be a very complex problem.

The very name IPSP, then, tends to prejudice our minds, hiding the complexity of what's going on.  Ideally, IMO, this current should be renamed "CPSP" for "Chloride Post Synaptic Potential".  This name is neutral with respect to whether it will tend to depolarize or hyperpolarize the membrane, as well as calling attention to the fact that the result is more complex than simply that binary choice.

Of course, I doubt it's going to change soon.  Big Science has become as institutionalized as the Roman Catholic Church was in Galileo's day, if not as centralized in its power, and pushing such a change through would probably take as much effort as redefining Pluto as not a planet.  Rather, this particular semantic strait-jacket will continue to inconvenience and distract people who haven't learned to live with it, along with all the other obsolete terms and definitions of this type.

The biggest problem I have with this isn't the distraction and tendency to hide important details.  Rather, there are two ways to approach names, in science and anywhere else:  you can remember them in functional terms, linking the words of the name to their everyday meanings, or you can remember them as arbitrary symbols, strings of words that represent a particular thing completely independently of their everyday meanings.  When the string of words that makes up a scientific name doesn't represent the same thing as what the name is used for, only the latter way of remembering is available (unless you want to load up your brain with a bunch of the history of science).  Thus, IPSP doesn't stand for an actual hyperpolarization of the membrane (which is what the words actually mean), but for a current carried by chloride or potassium ions, regardless of its effect on membrane voltage.

This turns learning about science into a process of memorizing pointless and arbitrary names, that can't be deciphered in terms of the everyday meanings of the words that make them up.  Not only does this interfere with the education and development of people who would make good scientists, but it makes the field more attractive to the sort of people who don't do creative thinking:  all they want to do is memorize formulas and rituals, and spend their career following the rituals they learned in college.  Such people don't, IMO, really have much to contribute to science.


  1. My pet peeve: terms like Dorsal and Ventral that have different meanings depending on whether you're talking human biology or animal. Extra great fun is had when you read a paper written by a medical scientist reporting on neuro findings in a rat model and you have no idea if they are using the human terminology or the animal one. At least once I'm pretty sure they had no idea either (or the coathours used different standards) and just mixed them randomly.

  2. And especially anterior/posterior. AFAIK "Dorsal" and "Ventral" have the same meaning relative to the backbone in all vertebrates, although they're different relative to the direction of motion. When I learned the terms (a long time ago), I was told that all such terms should be in terms of the body of a fish: anterior/posterior refers to the front and back of a swimming fish, and if humans have changed their orientation, the definitions changed with them. A better way can be found at Knowledgerush:  "The terms anterior and posterior should not be used when refering[sic] to most animals however, and are particularly incorrect for quadrupeds. "

    "Dorsal" and "Ventral" become a little confused when talking of invertebrates, especially cephalopods. AFAIK the terms were defined functionally for insects, which like tetrapod vertebrates walk with a definite "belly" towards the surface they're walking on and definite "back" facing the open space/sky. Then they were extended based on development for other invertebrates.

    There are genes that are expressed according to the same dorsal/ventral pattern in almost all bilaterians, then there are genes that are expressed in opposite configurations between vertebrates and "protostomes" (with, IIRC, a different mixture of expressions in hemichordates). And as for Coelenterates!...

    At some point, we'll probably have a pretty good idea what the sequence of evolutionary changes was in various branches of the bilaterians, and that would be the time to standardize terms based on development and evolution. But, just as with IPSP/EPSPs, it probably won't happen.