While I will at some point get back to more of the warnings about here is a health danger or this looks like a problem or isn’t this truly awful, for the moment I want to continue to just discuss basic science.  Partly because I find this stuff very interesting and partly because if we put the groundwork in place now there are a lot of interesting improvisations that can be riffed off that bass line or baseline.  It also makes it easier to see more clearly and evaluate more thoroughly where people are coming from when they bring up certain health risks.  I am not changing my tune that now everyone should only look to conventional medicine, it is only that science also has its place even if science is quite often presented falsely by the media.  For some this will be all old hat and I ask you to bear with me and there may be some interesting points thrown in as well.  For those outside medical/scientific circles it is probably worth reading this series of posts starting at the beginning to be able to make sense of each new section.  While many of the ideas may be a bit abstract I will try to keep the subject from being too dry.  Actually if its like many of my posts it may likely be for the most part an off topic tangent to what I thought I was going to write about.  In fact, I think I’ll just start off with a tangent and get it out of the way early.

So in the last post we started discussing DNA and how it is replicated (I just added in some pictures today to the last post to illustrate what I was trying to talk about).  An alert reader commented how strange it is that most of the DNA is what is called junk DNA.  That is to say, I know we are still getting to the definition of a gene, but most of human DNA doesn’t code for anything, other parts of it code for things that look to never be used.  In fact over 90% of the genome is so-called junk.

It is possible that there is just a lot of genetic baggage accumulated over the years but it also worth remembering that prior to Oswald Avery’s experiments and the realization that DNA was the most important biological discovery of the past century all of DNA was considered junk.  Moreover, there are thousands of sections within the non-coding “junk” DNA that are evolutionarily conserved, meaning their sequence doesn’t change across different species.  This stability and lack of variability strongly implies that these sections of “junk” are doing something extremely important, we just don’t know what.  So it is a bit revealing that much of the DNA is called junk a more accurate description might be “the 90% of the genome that we don’t understand at all versus the 10% that we have a little bit of understanding of,” pshaw, I’ll stop with the all high and mighty now, let’s just call it junk.

Another reason to speculate that all of DNA, not just the part we understand, actually has an important role is to consider the degree of compression of information in DNA.  By this I mean it is often pointed out with amazement that each of the trillions of cells in a human body contains the whole genetic blueprint for the whole body.  However, even this doesn’t fully express the whole picture.  The DNA doesn’t take up the whole cell, rather within each human cell is a small sphere, the cell nucleus, sort of like the brain for the cell, which takes up maybe one tenth of the volume of the cell.  And within the cell nucleus, among other things, one finds the genetic material neatly folded into chromosomes.  It is these small chromosomes within each of maybe 50 trillion human cells that have enough information to code for an entire human.

Now the information that is stored there is very contextual, it only makes sense within the context of a particular environment.  DNA will only remain DNA on the moon.  So if the temperature is 150 degrees warmer or cooler the information is not expressed, if there is less oxygen or more radiation it is not expressed, if parents choose not to have a child it is not expressed, if it is a war zone it is likely not expressed, etc.  When it is expressed, if a cell is forming in an area that is part of the liver, somehow it knows to use those parts of the blueprint in the correct proportions to lead to a liver cell, if it is in the big toe it somehow knows to form a cell that says, “I’m a big toe cell”.  When the physical, social, political, etc. context is there, something that is far less than a tenth of a part of one of 50 trillion cells has the necessary seed of information to create an organism complex enough to reflect back on the process with awe.

Either that or I belong in a Cheech and Chong movie.

Having said all that, let’s get back to how information is actually encoded into DNA, or at least what we understand through science at present.  In the last post we got so far as to note how DNA’s structure allows for it to be copied and that the base pairs that make up the steps on a twisting ladder of DNA are composed of 4 different molecules, adenosine (A), guanine (G) cytosine (C) and thymidine (T).  And how DNA can be copied because an A only fits with a T and a C with a G so each strand when divided can reproduce the other complimentary half.

There is a lot of discussion and argument on the internet about various types of diet (bear with me), is a high protein diet good or high fat low carbohydrate?  No one ever argues though that one needs a high DNA or low DNA or high DNA low RNA diet.  This is because the actual business of living for an organism is mediated primarily through proteins, the proteins in turn create the fat based compartments (cell membranes), shepard the energy stores of fats and carbohydrates shuttle the energy currency of glucose and ATP around the cell, etc, etc.  So somehow the information that is stored in DNA needs to be translated into the language of proteins for the organism to live and grow.  How this occurs is fairly well understood and quite fascinating.

One strand of the two strands of DNA holds the code for making proteins, the other is there to allow the coding strand to be reproduced generation to generation.  When the genetic information is read, it is done by reading three bases at a time, three steps on the ladder at a time.  Note that we are not concerned about the whole base pair now, just the half of a base pair on the strand that contains the genetic information, so the four letters, A,T,C and G can show up in any combination.  So one might see ATA then GCA, then AAG and so on.

Note in the second picture when we are looking at RNA, the letter T is replaced by the letter U (will touch on it in the next post in the series) but the idea is the same.  If you have four letters and you read them in groups of three you have a total of 64 different possible combinations or words.  These words are referred to in genetics as codons, so there are 64 different types of codons.  Each codon represents a particular amino acid.  The human body actually only uses 20 amino acids so a number of the different codons represent the same amino acid.  When you string a bunch of amino acids together you end up with … a protein.

The last thing you need is a codon which says to start reading and a codon to say stop reading so that everything in between makes up a particular protein. In the chart below, methionine, Met serves as the start codon.

So this is what people are talking about when they say a gene.

For those versed in genetics yes, I know there are nuances that weren’t discussed, introns and exons, alternative splicing and post-translational modifications, regulatory regions outside the coding regions, patterns of glycosylation and so on and so forth, but the idea of a gene as a region of DNA corresponding to a protein is basically correct if not complete.

And so these genes are the heritable traits that Mendel noticed in his pea plants.  While we have discussed how it is that the information stored in DNA corresponds to particular proteins we haven’t said anything about the actual process by which the translation takes place.  That will be the third and likely final part in the series and once we have that down there is really a lot that can be said both about genetics and medicine in general by playing off that base of knowledge.  Again, if you enjoy this let me know, or if it seems like a rather bad episode of lost in space you can let me know as well as perhaps I shouldn’t waste my effort and your time.

Ciao for Now