Philosophy of Genetics

What is Life?

What is life?  Life is simply “a form that can replicate itself”.  What then is a form? 

A form is a configuration of matter that exists at a particular time, in a particular region of space, that exhibits substantially less randomness (entropy) than the surrounding space, and is stable over time.  Having low entropy means that the form couldn’t have appeared in that time or place by chance alone.

Since life must replicate itself, it must be able to grow, by aggregating other matter from its space/time neighborhood.  In other words, it must transport other matter (within a reasonable amount of time) to a higher concentration, and then configure that matter as needed to build the form being replicated.

Transporting matter takes energy, especially when it's being concentrated into one small region.  So life replication requires an external energy source, like the sun.  Life must capture that energy and redirect it to the transportation function.

Not all matter is the same.  So life must identify the specific materials it needs, by elemental or molecular type (sulfur, carbon, water), prior to transportation. Thus life acts as an “attractor” just like any other force of nature (gravity, etc).

According to quantum physics, the concepts of identification, measurement, and transportation have no meaning, except as examples of matter interacting with other matter at the subatomic level.  So the life form must perform its functions as a set of interactions with the environment that remain stable over time.

Life is thus a “stable configuration of interactions” between matter within a specific space/time region, that consume energy, and decrease entropy.  This "stability through time" transports knowledge from the past into the present.

Thus, life is knowledge (of the environment) from the past, transported to the present, through the stable interactions of physical form.

Life on a chip

According to an article in the journal Cell, scientists have devised a computer simulation of single-celled organisms named "Halobacterium salinarum NRC-1". The model accurately predicts the activity of Halobacterium's 2,400 genes, in silico.

In all living cells, genes are constantly switched on and off by so-called "transcription factors" (the Halobacterium has 72 of them). When a gene is active, it acts as a micro-scale protein factory. The resulting proteins are then used by the cell as building materials, signaling devices, and new transcription factors.

The computer model accurately simulated the behavior of roughly 80 percent of the Halobacterium's gene regulatory and functional interrelationships (called "networks" or "pathways"). The Halobacterium cell is genetically hard-wired to respond to 9 external environmental factors (EFs).

Gene activity in the Halobacterium cell is highly interconnected. (Like pressing a bag of marbles with your finger, you don't know where it will bulge out, since all the pieces are connected.) By perturbing one or more genes (perhaps by a change in the environment), scientists can test how well their computer simulation of the cell is working.

Yet, 38 percent of the Halobacterium's genes seem to do little or nothing.  That may be because scientists have yet to explore other gene regulatory mechanisms (small RNAs, epigenetic modifications, post-translational modifications, metabolite-based feedback) in their computer simulation.

Quantum physics and genetics

When you observe very tiny things, strange things begin to happen.  At a fine grain, beneath what you can see at a microscopic level, even smaller than individual genes and molecules, there lies a world of subatomic particles.  At that level, there is no longer a meaningful distinction between an observer and the thing being observed.

What does that mean?  When you measure something, you are using a probe, which is made of matter.  (Or, when you measure the amount of light reflected from the object you use a light meter.)  But according to quantum physics, at the subatomic level, matter and light both consist of waves which don't fully exist (as particles) until they are measured.  And this works both ways.  The surface of the measurement device (or light meter), and the thing being measured, both consist of discrete waves.  And so neither the surface of the measurement device nor the "observed entity" fully exist until the measurement event occurs.

Yet the word "measurement" is itself misleading.  At the subatomic level, the observed and the observer are both simply wave phenomena, waiting for an interaction to make them "real".  You can't say one party has the privilege of being called the "observer" or "measurer", since they mutually cause the other to exist!

To explain this, I like the analogy of soap bubbles.  Two soap bubbles can interact, but you can't call one the "observer" and the other one the "observed".  They are both changed by the interaction with each other.  At some level, there is no separate observer performing a measurement on something else.  There is no observation, nor any measurement at all.  There is simply "interaction".

Still, I worry about this... Perhaps one entity has more experience encapsulated in its form, and therefore has a more privileged position.  For example, a drug (ligand) binds with protein targets (receptors) in the body.  Once this so-called receptor-ligand complex occurs, the protein undergoes a contortion, or change in shape.  The interaction is what leads to the effect. But it took millions of years for the protein to evolve, therefore it encapsulates more time and experience.  Got to think about this one some more!

Genes and time travel

If time travel were possible, how much energy would be required to transport something back in time?  In my opinion, the amount of energy would be related to the amount of knowledge manifest in the matter being transported.

For example, imagine transporting a mechanical clock back in time to ancient Egypt (1500 BC) when the first sundials were being invented.  People were clearly ready for the concept of tracking time, so they would probably understand the purpose of the clock.  By having the clock in their hands to explore and decipher, it would shorten (by millenia) the time to invent such a clock.

I believe it's the same way with genes.  Evolution is a process of trial and error, whereby genes change in response to the environment.  Genes gain knowledge of the environment.  For example, genes responsible for the formation of eyes have knowledge of the three-dimensional nature of the world.

The amount of intelligence (i.e. knowledge of the environment) contained in a gene is related to the experience manifest over millions of years of evolution.  So the energy required to transport a gene back in time would be equivalent to the time spent manifesting that knowledge into its form.

What is the meaning of life (at a molecular level)?

What is the meaning of life at the level of individual molecules?  At what point does an individual molecule attain a purpose that allows it to contribute to living beings?

My favorite example of a “purposeful molecule” is a catalyst.  A catalyst simply helps two reactant chemicals bond more quickly, by reducing the barriers to their pairing, like a matchmaker who gets a couple married more quickly than if they were left alone.  After all is done, the catalyst is left unchanged by the reaction.

Because there are around 1,670,000,000,000,000,000,000 molecules in every drop of water, you can see that there is plenty of opportunity for reactant chemicals to bond on their own (just by accidentally bumping into each other), if they are already predisposed to do so.  The predisposition exists when the product of a reaction is more stable (having less energy) than the individual reactants themselves (i.e. if the married couple is happier together than as separate individuals). 

However, adding a pinch of the right catalyst greatly increases the rate of a chemical reaction, by reducing the barriers for the formation of a bond between the reactants.  Life relies heavily on such catalysts in the body, called “enzymes”, which are made from proteins as specified by our genes.

Still, a catalyst molecule by itself has no meaning, especially when we enclose it in a small box without potential reactants.  Or, more precisely, the catalyst has no meaning in that place and time.  The catalyst is simply a three-dimensional form, without a purpose.

Only when the catalyst exists in the same box as a sufficient number of reactant chemicals does its purpose become clear to an observer.  Its purpose is then defined by the increased rate of chemical reaction, a purpose which is necessary (but not sufficient) for life.  You might say the purpose of the catalyst "emerges" in that context -- or “is discovered” -- where previously there was no purpose.  But unless an external observer makes a record of the event, the catalyst's purpose is lost once the context -- the spacetime box -- goes away.

Genes and donut holes

When studying genes, we must not forget what they really are: embodied experience from the distant past, manifest in the present as physical form.  An axe, as an analogy, is a physical form defined by its history.  Many humans, over thousands of generations, perfected the axe's form.  What we see today is an axe that is well designed to perform a function, stripped of all superflous matter.  What we don't always see is its history or its true purpose.

Genes are like time machines, bringing knowledge from the past into the present.  Like axes, they are elegant works of art.  They are all they need to be, and no more.

Genes are often defined by what can't be seen (think "donut holes").  A gene may be active in very specific situations, sometimes only for a few hours in utero.  Unless you know its complete history (which is impossible), it's difficult to understand its purpose.

Genes can only be affected by the environment only to the degree to which they were designed to be affected by the environment.  The hooks provided by the genes are often quite subtle.  Sometimes you can't see what a gene's purpose really is, unless you already know what to look for, and can devise the conditions for the gene to express itself.

Experience and Form

Humans have natural variation (for example, some people are introverted, some are extroverted, etc). The process of evolution "selects" certain "fitter" variants over others -- which is the same thing as saying that some people (with a specific set of gene variants) are able to survive longer than others, and so can pass on more of those gene variants to their children.

Thus, evolution is the process of converting knowledge about the environment (i.e. how to better "fit") into our physical form. The form of our genes, body and brain is the result of evolution, which is itself the action of selection of one form over another (against the environment) over time.

This turns the debate of nature vs. nurture on its head. We humans are the physical manifestation of millions of years of experience. Our form manifests an intimate knowledge of the environment, including knowledge of the other forms (people, animals, plants) around us.

Thus, the experience of mankind (over millions of years) creates our nature (the physical manifestation of experience), as our genes and form.  Our form is designed to respond to the (expected) experiences in our lifetime, by bringing past experience (through the configuration of matter) to the present.

Form and Knowledge

In the recent movie War of the Worlds, invading aliens were eventually overcome by Earth-bound diseases for which they had no immunity.  The only possible conclusion is that the aliens must have lived and evolved on Earth for millions of years before returning, since if they hadn't, the diseases would have no knowledge of how to infect them!

This illustrates of the critically important concept of form, which is needed to understand the philosophy of genetics.  In order for one organism (bacteria, virus) to affect another organism (man, alien) in any way, it must have an intimate knowledge of the other.  Knowledge must ultimately be represented as three-dimensional form (e.g. the shape of the organism down to the cell-level and DNA-level, as well as the shape of neuronal connections in higher organisms).

Aliens would not be affected by Earth-bound diseases unless those disease organisms (e.g. bacteria) had co-evolved with the aliens for millions of years.  Evolution is the process of translating experience (of one’s environment, including other organisms) into one’s form (DNA, etc).

As another example, consider the HIV virus.  It’s very simple, essentially just a cartridge with DNA inside.  Yet its very form (the specific sequence of DNA, the docking mechanism that allows it to attach to human cells) is intimately aware of human biology, and how to exploit it for its own purposes.  It’s ironic, then, that we may one day harness a non-virulent form of the the HIV virus itself to inject new DNA (of our own choosing) into our cells, to direct our own evolution.

Matter can retain Knowledge through its Form

Form is simply the shape of matter, when that shape has an observable, measurable purpose or effect. The philosopher Aristotle first put forth a notion of form similar to this over 2,000 years ago. The most basic example of form exists at the atomic level, in the shape of certain molecules called catalysts.

A form has the following characteristics:

• Creates a measurable effect by setting up a probability or  tendency, over time or in great quantity, in the right environment
• Requires an observer
• Manifests knowledge from the past in the shape of matter, which can then be applied in the present

We have seen what the first two points mean. A catalyst, for example, is defined by its purpose to the observer (e.g. to catalyse), otherwise it would be just another molecule.

But what about the last point? Once again, a catalyst is a good example. Its form must represent (i.e. "know") something about the chemical reactants it helps to bring together, otherwise it would have no effect. Knowledge is thus manifest in the shape of matter. The catalyst "knows" only what it needs to know, and knows no more, about specific chemical reactants, in the same way that a frog knows only about shadows and not about flies.

This point may be expressed more clearly using a different example of form: an axe. An axe is a tool which has been perfected over thousands of years, to achieve the most efficient shape. Its blade is "designed" just so for its purpose. Any slight change in its shape would make it less effective. Its metal is hardened steel, and its handle is made just right for the human hand. Thousands of years of trial and error were required to identify just the right materials and shape for the axe. That time of trial and error (and the wisdom gained) is manifest in its form.

The Human Brain as Form

Another example of form is the human brain. The connections between neurones in our brain change over our lifetime, manifesting our experience in the their shape. As we learn, we encapsulate that knowledge as our form, literally in the shape and interconnections of the neurons in our brain.

A doctor, for example, may go through years of medical school, but he needs to retain his knowledge in his form, otherwise it is left in his past. His brain is literally changed from his education. Thus his time is more valuable in the present, because he can diagnose problems more quickly, as a catalyst can speed chemical reactions. In the same way that Einstein said that matter and energy are equivalent using the equation e = mc², matter and knowledge are also equivalent through form.

The concept of form is important in answering the mind/body problem as well as questions about our own mortality. Because we employ form in every part of our being, the millions of innate daily reactions the inner eye has with the world need only be impressionistic and probabilistic to have the effect of creating our emergent personality. And because we as individuals are form, we create that emergent effect called society.

What's the value of an Idea?

What’s the value of an idea? If someone creates a better mousetrap, how much of a premium can they charge for it? If someone develops an entirely new process (for example, the first caveman to invent a reliable means to start a fire), what’s the value of that process?

We can learn from Economics. Certainly entrepreneurs are constantly trying to devise new products and processes that replace the old ones.  Joseph Schumpeter called this “creative destruction”. Desirable products can be sold for higher prices, and this is how the entrepreneur makes a profit.  Such products and processes can enhance our productivity. The invention of fire made human life better in many ways. The same with the invention of the light bulb, the computer, the automobile…

So is the value of an idea measurable by its price in the marketplace? Certainly the value of an idea decreases over time, as it is increasingly commoditized, and replaced by other ideas. A new and innovative drug, for example, will become less desirable over time, as alternative treatments (with fewer side-effects) are discovered by other entrepreneurs.

The invention of fire was a revolution in its day.  Prior to that, many people spent their lives trying to uncover its secret (or eating raw meat). Perhaps the person who first discovered fire was paid a rich reward in prestige, power, animals, land and a prized mate. But once the secret was discovered, it was easily conveyed to others in an afternoon’s training session, with the trainers receiving only a minimum wage.

The value of an idea is time-dependent. Imagine if people in the 19^th century woke up one morning and discovered a laptop computer in their office.  Would they even be able to maintain it, charge its batteries, understand it, support it?  What sort of energy would it take to propel such ideas backward in time?

Economics can provide valuable lessons for understanding the process of evolution and intelligent design. Each evolved component of a human being - ability to acquire language, ability to see and hear, etc - is a discovery.  (A catalyst is the most basic idea of all - an idea manifest in the very shape of matter).  Perhaps the process of evolution has its investment bankers, willing to risk capital on a new idea in our form. Perhaps genetic ideas are granted “patents” to protect them from “price competition” for a period of time. Perhaps there is an innate currency used by the process of evolutionto reward winning ideas.