Thursday, July 28, 2011

Mendelian Inheritance: Basic Genetics or Basic Mistake? Part IV

So, if we are right that 'Mendelian' inheritance is fundamentally mistaken--or, at best, generally inaccurate and misleading--then what kinds of conclusions can we draw and how can some of the basic attributes of life be accounted for?  We have to assume that life evolved and that to a great extent means genes, broadly defined.  Indeed, we may be worse off than we think if, as we tried to show in an earlier post, even what a gene is, is elusive with current knowledge.

Waterhouse, A Mermaid
In our book after which this blog is eponymously named, we argued that there has been too much attention placed on evolution (and a competition-centered view of life at that), relative to the more ubiquitous properties found at life's other time scales--of development and maintenance of an organism, and of the interaction of factors on the ecological scale.

The idea of Mendelian inheritance, which is widely extended to the vast majority of gene-trait relationships that clearly are not following the monk's principles, is of discrete states one of which dominates in their various combinations.  This was (and is) extended to evolution, with our grossly inadequate 'winner take all', 'survival of the fittest' notion of one best -- fitness-wise dominant -- variant that natural selection favored into success just as surely as a dominant allele was favored ineluctably into manifestation in the organism.

But if you think of the other properties of life, which we center our book around and will briefly name here, you might ask how Mendelian thinking, which only by deep contortions can be related to those principles, could ever have taken hold, unless it's by what amounts to an ideology, a takeover of a certain highly deterministic, simplistic view of the living world--a view that simply, for decades, wrote off into alleged irrelevance the actual way in which organisms work.

Sequestration and modularity
From DNA on up, life is organized as hierarchically nested partially sequestered units.  DNA has functional sequence elements arranged  together along chromosomes, but partially isolated in that they can serve their individual functions.  The units (such as amino acid codons) are repeated many times.  Proteins have partly separated functional units, too.  Cells are packaged units that have many different partially isolated subunits within them, such as organelles like mitochodria, isolated areas like the nucleus, and local differences in what is present in the cell membrane (e.g., a cell may have a front and back end, so to speak).

An organism (or even collections of organisms as in bacterial biofilms) is made of large numbers of cells.  These are repeated units that communicate with each other via combinations of signaling and other molecules, and this is what leads them to express particular, context-dependent sets of genes.  So that they are repeated, but different.  This process occurs hierarchically during development, and in response to environmental changes during life.  An organism is divided into organs and organ systems, like brain, heart and vessels, digestive organs, and so on.

Organs are made of nested, repeated units.  Intestines are segmented along their length, and their surface is littered with repeated structures called 'villi'.  Skeletons are made of repeated, partially different but interaction bones.  Trees are made of leaves and so on.  Plants and animals alike are constructed by repetition and branching.

Yet, importantly, each organism has only the one genome that it inherited from its parents!  So the same genome makes brains and braincases, that are as different from each other as any two things in all of life.

These processes are both qualitative: each leaf or bone is a separate structure; and quantitative: each such structure is somewhat different.  This is the natural variation that is the material on which evolution can work.

If you just think about this, you would have to wonder how it could be brought about by Mendelian inheritance.  How could just two states at a single gene be responsible for such complexity and quantitative internal organization?

It is perhaps easier to see how breaking a gene could cause a major state change, and thus a normal and dead alternative at a gene could be manifest in Mendelian inheritance terms.  Or if the trait is very close to a protein coded by a single gene, two major alleles (variants) at that gene could have big differences (yellow vs green peas, for example).  But as a rule, Mendelian inheritance makes little sense.  Partly that's because, as mentioned in earlier parts of this series, we confuse inheritance of traits with inheritance of genes.  Genes--specific stretches of DNA--are clearly inherited in a Mendelian way (with some exceptions that don't matter in this context here).  But traits generally are not.

The reason for all of this is that the basic principles of life, that include the above descriptions (see our book for detailed discussion in this context), involve cooperation--that is, co-operation or contemporary interaction--among many different elements, each of them variable in a population.  What an individual inherits are sets of genomic variants from its parents.  The traits an individual manifests are the net results of these variants acting in the particular environments in which they find themselves.


Anonymous said...

As part of your audience and a middle school science educator (CA 7th grade with genetics and evolution as standards to be taught) what impact or changes would you like to see in science education for including concepts of "genomic variants?" But as you indicated in your first post that these ideas did set the stage for discovery as a way of testing and tracking results.

Part of a move toward "common core" standards will preclude any of this history and thinking from making it into our secondary classrooms as teachers are handcuffed more and more as to what experts (not secondary teachers of course) think should be taught and when.

Thank you for the thought provoking posts.

Ken Weiss said...

It's hard to give a quick answer to your question that is not just a superficial one. If history of science an't be taught, or a rigid history must be taught, there's a problem.

I would think kids would have no problem understanding that new ideas come along for a good reason, but they are almost always incomplete or partly wrong. That's because we don't know everything, but only that new facts (or generalizations) seem to suggest explanations for things we had no good prior explanation for.

The new ideas are almost always more simple than the truth turns out to be, because the new idea leads us to explore things and we learn more, and understand more than we did before.

Sometimes an idea or theory gives a basic understanding of underlying principles, but often we need to be careful that we don't mistake that illustration for the whole truth. However, all of us at any age yearn for simple and easy answers, so dealing with complex things that we know in our hearts we don't fully understand is unsettling. Even scientists like to cling to the 'teddy bears' of easy answers rather than frustrating difficult at finding major answers (like the cure for important diseases) that may take many people more than their lifetimes to be found.

My own kids are long gone from the nest. But kids at 7th grade might understand that Santa Claus and the Tooth Fairy, and even teddy bears, provide very young kids comforting simple explanations for things in life. But later on, they surely can understand that those first things weren't literally true but reflected the deeper truth--that their parents loved them, but couldn't explain everything in adult terms. By the 7th grade kids can surely realize that as they got older they were able to understanding things more closely to the truth, and didn't need false but simplified explanations. And that Christmas and so on are more complicated than a magic gift-giver and elves, and that comfort isn't as easy as hugging a teddy bear.

I'm groping here, because society needs frameworks, and even teaching to test standards represents some agreed-on cultural tenets and a way to (try to) ensure that children get properly acculturated.

On a national basis, maybe it's true that most teachers aren't capable of teaching more nuanced views of the world. They themselves may not have been exposed to them (many if not most scientists aren't). But until the scientists, experts, politicians, and so on themselves are more willing to face the complexity of reality, it may be too much to hope that on a standardized basis, nuance is likely to prevail.

I personally think that understanding the nature of complexity and the fact that we don't understand everything, can be understood by kids. And that if they do, they're more likely to be better citizens (and a few of them, better scientists) as a result. After all, they have the same IQ as their parents and teachers, just less experience!

I hope this responds to your comment, and we certainly appreciate viewers of MT, and hope we can help inform them to things, at least as we see them.

Anne Buchanan said...

When we teach at the college level, our fundamental approach is to try to help students think about how they know what they know. We hope to teach them to critique what they learn, in classes or by reading, about science, to understand what's assumption, what's accepted without a solid foundation, what's probably believable, and how to tell the difference. In a nutshell, I guess, we try to teach critical thinking. I think 7th graders are open to learning this way, too. Some will find it difficult, but some college students resist, too.

Anonymous said...

"After all, they have the same IQ as their parents and teachers, just less experience!"

"I guess, we try to teach critical thinking. I think 7th graders are open to learning this way, too. Some will find it difficult, but some college students resist, too."

Thank you. I know there must be many others who feel as both of you have stated here. But it is nice for me to see someone actually gets it. The idea that children and teachers are more than the sum of their test scores.

Both of your points are given nothing but lip service when it comes to the education legislation (NCLB) and common core standards movement.

What reading your entries on Mendel have done for me is to help look a little deeper and plan to do more with my teaching of genetics this year.

By the way if you are interested I came to your blogg via Pharyngula-Sandwalk (Larry Moran) Carnival of Evolution-The Mermaids Tale.

You both confirm and remind me to do what I "feel" is the most beneficial for my students 1) they are 12 so my number one goal is to build a relationship with them as individuals (not be their friend) but trust is an issue; 2) help them to think critically and be skeptical of what they read and what I teach and if that carries over to other places so be it but they can safely practice by learning to ask questions in their science class 3) see writing as a way to communicate thinking. That is a beginning.

One last thing that I liked about reading the Mendel posts was the idea of uniqueness also stated here in forward to Hermann Hesse's Demian:

But every man is more than just himself; he also represents the unique, the very special and always significant and remarkable point at which the world’s phenomena intersect, only once in this way and never again.

This may be another way to help my students grasp how they can integrate what we are learning in science with other interests they may have such as a interest in literature (ok my interest in literature).

Ken Weiss said...

The country desperately needs more of you! Critical thinking involves synthesis--even across science and literature--and less haste and less immediate material gain.

Teaching dogma rather than at least reasonable levels of critical thinking leads to illusions and then to other ideologies. People as a whole may want simple truths to live by, but at least being aware of the subtleties is an important tempering factor.

Of course all scientists are wrong to some extent, because Nature is complex and we are puny by comparison. Knowing that, it should not be beyond students' grasp simply to know that scientists use current ideas as a framework, and the best scientists are humbly aware of that.

If we lose all of our nuances, we may have huge 3D TV sets, but we'll have fewer dimensions inside ourselves.

Anne Buchanan said...

We appreciate your comments, thanks. And of course, it's not just science teachers that should be teaching critical thinking!

Holly Dunsworth said...

Of course I love the parallel between winner-take-all evolutionary theory and dominant alleles. Awesome.