Tuesday, December 09, 2008

Consciousness (2): Introducing the garden-variety biologist

This is the second of my ongoing discussion of biological approaches to consciousness and creationists' recent attacks on such approaches. In this post I sketch a portrait of a fictional character, a garden-variety biologist we'll call 'Mr B.'

Let's assume Mr B doesn't understand how neurons fire action potentials. In the rest of this post we'll examine his general approach to the problem. In a future post we'll consider how he approaches the problem of consciousness.

He believes that neuronal excitability is likely complex, but that it will ultimately be explained in terms of individually innocuous mechanisms, a complicated orchestra of proteins, lipids, carbohydrates, and other ingredients standardly found in cells. The mechanisms should all conform to physical principles, even if many of them cannot strictly be derived from the laws of physics. For instance, if there are untethered chemicals in a neuron, he expects their diffusion to follow the rules laid out in physical chemistry.

Mr B takes an empirical approach to his subject matter. He is likely to sit down at the lab bench with an example of what he is studying (a model system), and poke and prod at it to see how it behaves.

For instance, to get a bead on how neurons are activated, he may prepare a single neuron in a dish and treat it with various chemicals (e.g., sodium, potassium, neurotoxins), expose it to different temperatures, different light and oxygen levels, etc while measuring the voltage across its membrane. Such experiments will reveal how the behavior of the neuron depends on different variables in the preparation.

The experiments, guided by his best guess at how neurons work, will help him form new ideas or refine his old ideas. For instance, when he removes sodium from a neuron's bath, he finds that the neuron stops firing action potentials. This suggests to him that the action potential is caused by an influx of sodium into the neuron.

Mr B will usually write out equations to summarize what he has observed. However, he doesn't just want to describe his observations. He will attmpt to come up with new experiments to test his ideas about the action potential (e.g., if his sodium-based theory is true, then increasing the concentration of sodium in the neuron's bath should result in a larger action potential). The desire to turn his ideas into predictions often involves translating his words into mathematics so the concepts can be more clearly expressed, make his assumptions explicit, and provide a basis for precise predictions.

So far, Mr B is not much different than a physicist or chemist. All take an empirical approach to their subject matter, prefer mathematical to word-based models, and value empirical tests of their theories.

I've been painting Mr B as a bit myopic, focusing exclusively on how this little mechanism works. This leaves out his broader uniquely biological perspective. By focusing in on mechanisms, Mr B might be able to explain how a sperm locomotes, but that will tell him nothing about its function, about its role in the biological system in which it is embedded. This biofunctional orientation is what tends to distinguish Mr B from his colleagues in physics and chemistry.

Focusing in our our example, Mr B wants to know why neurons fire action potentials. What do action potentials contribute to the nervous system's higher-order goal of controlling behavior? Are action potentials involved in signalling from neuron to neuron? Could he be studying an epiphenomenon? It could be that the mechanisms he found in the dish are not even used in vivo. For instance, is there enough extracellular sodium in the nervous system for his sodium-based theory to work? Such questions will haunt Mr B and suggest new experiments.

Some might be tempted to insist that another facet of Mr B's approach is that he takes an evolutionary perspective on what he is studying. This is certainly possible, but not essential. Mr B realizes that brains are organs that evolved to help organisms navigate the world. But this doesn't necessarily help him understand how individual neurons work, or even their functional role in an intact animal. Evolution will indirectly color his perspective on the system he is studying, and certainly he has no patience with creationists who would say that the mechanism of action potential generation could not have evolved without divine intervention. Mr B realizes he doesn't even understand the mechanisms involved yet, and that is an important prerequisite to constructing a phylogenetic history.

Before taking leave of Mr B, we should note that he believes his ignorance of neural excitability is a relatively boring psychological fact about himself, not a deep fact with profound metaphysical implications (this is a point Patricia Churchland likes to make about consciousness, but right now we're leaving aside consciousness). He knows, as he approaches the problem of neuronal excitability, that he might be like the biologists in 1900 trying to understand the mechanisms of inheritance, that it might be a long time before he succeeds. A novel conceptual and empirical infrastructure might be required before the problem can be solved, or even posed in a way that yields results. His ignorance spurs his curiosity and creativity, it doesn't make him think there is something fundamentally wrong with biology. He stubbornly resists creativity sinks such as claims that neuronal excitability is forever beyond our understanding, or that supernatural beings are required to explain the strange animal electricity observed in nervous systems.

In the next post Mr B will examine the neural basis of consciousness at an abstract level, considering what types of processes in the brain are most likely to be conscious. He will also see how daunting his task is.


Anonymous said...

I have a couple difficulties with this post-
You say-
“The mechanisms should all conform to physical principles, even if many of them cannot strictly be derived from the laws of physics. For instance, if there are untethered chemicals in a neuron, he expects their diffusion to follow the rules laid out in physical chemistry.”

It is truer to say that what he finds will either fit with the existing theories, or that he will make a discovery for which a modification to the existing theory may need to be made. It is not true that everything we will ever know about physics and chemistry are known, as is implied by your statement.

You say-
“Evolution will indirectly color his perspective on the system he is studying, and certainly he has no patience with creationists who would say that the mechanism of action potential generation could not have evolved without divine intervention.”

Yet Sir John Eccles won the Nobel Prize in medicine for discoveries concerning the ionic mechanisms involved in excitation and inhibition in the peripheral and central portions of the nerve cell membrane. I’m not so sure he wouldn’t have patience and perhaps even agree with the creationist. You seem to imply that creationists are not capable of doing science, yet nearly all the greatest scienctists in history were creationists. I’m thinking of Newton, Maxwell, Planck, Pastuer, for openers. To assume that this scientist isn’t a creationist is to assume too much.

I hope you can make your points without portraying science in a way that is historically and factually inaccurate-

Eric Thomson said...

I am painting a portrait of a contemporary garden-variety biologist, not all biologists. I never said no biologists are creationists, but obviously in a post-1859 world a creationist biologist is a curiousity.

As for your claim about the possible discovery of new physical laws, that's a good point. Generally, Mr B thinks processes in a cell will conform to established laws; if there are undiscovered laws of physics, the processes in a cell should obviously conform to those.

Quantum mechanics is needed to explain light absorption in the retina, so in 1900 retinal function couldn't be fully explained--as I mentioned in the post for a different problem novel conceptual and empirical resources were required to solve the problem--in this case down to the level of physical law.

Mr B knows all this, but he attacks the problem of neuronal excitability using the best methods and conceptual resources available, even though those will likely change.

Luckily for Mr B, he didn't need quantum mechanics to explain neuronal excitability. Classical statistical mechanics is enough to get the predicted equilibrium voltages of ions in neurons (technically, the Nernst equation is derivable from the Boltzmann Distribution, which can be derived from classical assumptions).

Is Mr B confronting consciousness more like the 1900 biologist of retinal transduction/inheritance, or like the 21st-century biologist of retinal transduction/inheritance?

Note that I am not Mr B. He is a character. A handsome and likeable character, to be sure, but just a character.

Anonymous said...

You did say garden-variety. I think I got distracted because the example was so Eccles. Sorry.
If you asked biologists, "Do you believe in God?" I think you would find the answer to be yes more than no. So a creationist (in that sense) would not be an oddity.

Mr. B is cool, I'm thinking about 6 feet tall with slightly curly brown hair- a handsome devil you bet. Knows a few jokes too, right?

Eric Thomson said...

Anon: yes, many biologists believe in God, but qua biologists it doesn't enter into their approach.

As for their personal views outside of the lab, I would predict a majority are either agnostic or atheist, so compared to the general public it is likely a very different demographic.

Mr B definitely wears glasses.

transformation said...

most impressive. thank you for bringing me back here. you are a man of many and obvious talents. whatever you decide, you can do. thank you. warmly, dk

Anibal Monasterio Astobiza said...

What are the necessary conditions for the appearing, within the garden-variety biology, of consciousness?

Eric Thomson said...

Anibal: Later posts are looking at his take on consciousnes, this is just giving a little about his general approach.He thinks he will discover the mechanisms of consciousness, which he doesn't yet understand, so he has to do experiments to find out what is necessary and sufficient for consciousness.