I have been delighted to watch the rapid progress of understanding of DNA over my lifetime.    I am amazed by the number of different directions for progress: improved technologies for rapid reading DNA sequences, improved understanding how DNA is copied, transferred toward proteins, replicated across generations, etc.   Each of these areas have seen increases far too rapid for me to keep up.   Even if it were slower, I would be handicapped from limited knowledge about the subject.    I generally get the point for most of popular (general audience) descriptions of findings.    However, there is one area in particular that doesn’t make sense to me.  That area is to say that behaviors are programmed in DNA.

For background, my understanding of DNA is very limited with most of the learning from a backward high-school from 40 years ago.   I understand DNA to be a molecule consisting of two mirror image strands that can replicate by splitting the strands and reconstructing the dual strand by matching the individual bases.  In other words, except for occasional transcription errors (that have their own mechanisms for repair), the DNA replication is a perfect copy of the original DNA.  From DNA, the cell creates matching RNA that eventually provides a template for producing proteins.   At the point the world of proteins take over in terms of refining and combining proteins to eventually settle into something useful.     But overall, information flows only in the direction of DNA to proteins and the only information DNA provides is information about proteins.

On the other hand, I recall early on when people described DNA as a kind of computer language language.  Internally I objected to the notion of comparing it to a computer software language, preferring instead an analogy of a cook book: DNA provides recipes for building proteins when they are needed.

When I think of software languages, I think of logical decision points or conditional statements exemplified by if-then-else.   The code is repeatedly executed for new iteration.  Each execution follows its own path through the conditionals to accomplish things.   I realize software languages do more than conditional statements, but it is set of instructions meant to be followed repeatedly for each new set of inputs.   I don’t see DNA working that way.  It creates proteins.   When the cell encounters a new piece of information, all of the logical work is done by proteins and none of it by the DNA.

While it is easy to conceive of DNA as a kind of language providing instructions, it is very hard (at least for me) to see proteins as encoding a language.   Proteins appear to be actors with self-contained instructions.   Proteins are miniature (and very specialized) analogs of people who do their assigned duties for a job.   They may have been trained by memorizing some instructions, but the success of their actions depends on what they are rather than rehearsing some instructions.

With this admittedly limited understanding of DNA, proteins, and genetics, I find myself perplexed at the real observation that animal behaviors are inherited.     In particular, I’m talking about behaviors an animal is fully capable of performing but does not perform unless it has inherited the right genes.    A good example is illustrated in this article describing burrowing behaviors of two closely related mice.   This article includes a video that describes the convincing theory that the choice to build an escape tunnel is inheritable.

The mouse is fully capable of building burrows into the ground, but the burrows for a particular population always follows the same basic design and dimensions (such as depth).   The distinction between different populations is whether the burrowing continues to provide an escape tunnel stopping just short of breaking through to the surface.     The article describes that the difference between building or not building an escape tunnel can be isolated to a very small set of genes.    I only watched the video so I’m granting that the video-maker is accurately describing sound research.    I see no reason to doubt that the behavior is inherited.

I suppose my problem is how this inheritance is described in human language.    The video reinforces the human language description by depicting the mice as rigid mechanical robots that agitate their limbs according to some instructions.   The video clearly implies the mice are robots following computer-like software programs.   While I object that this is misleading, I think the animator is faithfully depicting the way the process is described in human language.

Non-human animals are identical to robots following instructions passed to them through their inherited DNA.   The conclusion is that DNA is providing computer-language instructions to not only build the robot but to provide the robot its instructions for operation.

Imagine the mouse encountering different soil conditions or obstacles and thus having to make decisions.   It takes a different number of limb-strokes with differing amounts of effort to proceed to accomplish the inevitable structure that must be built.   In order to proceed, the robot must consult exception handling instructions.   All of this instruction is in a very limited amount of DNA that appears insufficient to capture these instructions.    Their conclusion is that the instructions are exceptionally simple and that complex behaviors are nothing more than a combination of very simple behaviors that could conceivably be encoded in DNA.

At this point, we are left with experimental evidence that a complex behavior only occurs when it is inherited.    Lacking this inheritance, the animal will not exhibit this behavior even though it has all the mechanical capabilities to do so.     There is also something apparently beneficial about this optional behavior, again emphasized in our language by calling it an escape tunnel.   The implication is that mouse lacking this ability essentially lacks the ability to escape.    Both the description and animation presents a case that takes for granted that the optional behavior is beneficial.

From the point of view of the narrator and animator, what makes the behavior is complex is because it appears smart.  The difference between complex behaviors and simple behaviors is that complex behaviors appear smart while simple behaviors appear robotic.    The conclusion that this complex behaviors is a combination of simple behaviors says that this apparently smart behavior is really just robotic simple behaviors.   The depiction of the mouse as a mechanical robot is fully justified by the scientific explanation.

I encounter animals of various sizes.   I encounter even very small tiny-brained animals.   As I mentioned in earlier posts, I marvel at invertebrates.   As I watch these creatures, it never occurs to me to describe or animate them as robots.   They may have limited faculties with behavior that is not hard to predict, but this does not suggest to me that they are mindless robots.

As an aside, I recall my experience yesterday when I spotted a jumping spider wandering the walls of my kitchen.   I wanted to remove it to the outside without killing it or even injuring it.    I did not approach this as a computer scientist trying to hack the spider’s software.   For one thing, I admire free-roaming jumping spiders because they appear so intelligent.   My approach was to negotiate with it, to coax it to jump into a container that I intended to carry outside.    It finally got the message and did go into the container but halfway across the kitchen it jumped out again.   I tried a second time and convinced it to try again.   The second time was successful.   I had to shake it loose so that I can come back in with an empty container.

There are two ways to interpret this encounter.   As someone immersed in computing technologies, I could consider my efforts as being similar to hacking the programmed code, forcing the spider to follow a logic path I knew it had to follow and that path would be consistent with my goals.   As someone who presumes an intelligent world, I could consider my efforts as a dialog with the spider using a shared symbolic language of surfaces and motion.    The second approach makes more sense to me.

The intelligence hypothesis makes more sense to me because I see the animal being more like me than like a computer or a mechanical robot.    I know of nothing in the inner mechanics of a spider that corresponds to storing and executing software instructions.   I see an autonomous being engaging with its world based on its available senses and motion capabilities.

In the earlier mentioned article, it would not have been hard to depict the mouse organically.  Instead, they chose a depiction of mechanical and hinged limbs.    The mechanical behavior is programmed in its inherited DNA.

I suggest an alternative interpretation.    Both populations of mice are sentient beings engaging with their worlds.   They are equally smart and capable.   One chooses to build an escape tunnel, and another chooses not to bother.   Both options may be smart.   The choice not to build an escape tunnel may be that it is not worth the effort, that either the need to escape is rare or that the mouse would still be caught while in the escape tunnel.    Alternatively, it may not find the prospect of needing an escape as something worth its worry.

DNA provides templates to produce proteins.   Proteins don’t provide instructions.  They facilitate certain types of chemical or mechanical properties.   I suggest that the identified small portion of DNA encodes for a protein that heightens the sense of worry in the mouse.   The escape-tunnel burrowing mouse is more anxious, more paranoid, or simply more diligent in its planning.    The additional protein either excites or suppresses this mental temperament.    The complex behavior is truly complex because the anxious mouse implements the escape tunnel intelligently both in terms of providing a distant escape route and not exposing it to be discovered from the surface.     DNA doesn’t say anything about this strategy.   It only provided the additional worry-provoking protein to encourage the additional effort.

A big problem with the software-following robot interpretation is that it makes the finding irrelevant to humans.   Humans are all about complex (intelligent) behaviors.   If we build an escape tunnel it is because we decided it would be a good idea.

In human populations, some people will immediately include backup plans in their endeavors.   Other people will not do it unless coerced by authorities.   For example, earlier in automotive history, the use of seat belts were optional.   Some people chose to use them and some chose not to.   It would be interesting to see if that choice may have an inheritable biochemical basis.   The person who chose not to wear a seat belt wasn’t ignorant of the implications, instead he rationally wasn’t worried about it.   Conversely, the person who did wear it was more inclined to worry or to being diligent in planning.

Even after seat belts became mandatory and nearly universally used, there is still a difference in the population.   Some will drive in a more aggressive manner in order to feel the restraint of the seat belt during high accelerations, braking, or sharp turns.  Others drive in a smooth manner so as to avoid any such sensation of restraint.     There appears to be different dispositions involved.   There are two almost contradictory options where both have some rational basis.   The difference is the considerations used in the decision making.   One is motivated by a sense of worry (may be of injury or of being judged unfavorably).   The other either lacks this sense or has a difference sense of need for excitement or opportunity to prove his ability to get out of dangerous conditions by allowing them to occur.

I think about the recent phenomena of increasingly dangerous sports, called extreme sports.   Often the extremeness is enabled by the availability of protective technologies developed for less extreme variations.   The same technology serves two populations.   One population wants more protection for more mundane activities.   The others welcome the opportunity to push the limits even further, thus experiencing the same danger but in a more extreme way.

We recognize within the human population that there are variations in caution and in diligent planning.   Although we can police behavior to enforce certain cautious behaviors, we acknowledge that some people need more policing than others.  This may be an inheritable kind of trait.   We don’t think of a dare devil trying some new stunt as a stunt that is programmed in DNA.    Instead we recognize that some people are inclined to do such stunts due to a combination of inclination of taking risks, exercising one’s confidence in being able to get through the danger, and and having the attention of the crowds.

In my last post, I used the word absurd to describe hypothesis discovered in patterns observed from big data queries.  I described it that way to emphasize that discovered hypotheses are clever stories where the cleverness is an alert to the need for follow-up analysis.   A default presumption is that there is an element of absurdity to novel clever explanations.

I see DNA and genetic studies as a form of big data analysis where the data is the large information available in DNA sequences and in observations of the associated organism.   The querying of DNA takes the form of a scientific experiment that seemingly giving the impression of a test.   In this case, the experiment suggested a new story of a robotic programmed explanation of a behavior previously assumed to be complex.    That story is interesting and compelling but it appears to be the same thing as a discovered hypothesis.   Breeding experiments to decipher DNA is a biological analog to a database query.   The result is a discovered hypothesis, a new story.  In this case that story is that a complex (code for intelligent) behavior is equal to the sum of simple (code for programmed) behaviors.    That makes an entertaining story.  However, that doesn’t convince me that it is fair to depict living mice at the equivalent of mechanical robots.