The battle over Junk

Back in the very early days of molecular genetics, it was assumed that the genome was almost exclusively made up of genes.  However, once we started to sequence genomes, it soon became very clear that a large part of most genomes did not consist of genes at all, but instead consisted of 'junk'.

Junk DNA is a fairly loose term which includes all the parts of the DNA that don't seem to have a function in the species.  Junk DNA is just there, it doesn't seem to have a function.

Recently however, a debate has started about how much 'Junk' DNA there is and what should be included in our definition of 'Junk'.  The ENCODE project is a project which is attempting to build a catalogue of all the 'functional' elements (an element can be thought of as a specific sequences of DNA) in the human genome.  This includes all elements that do something, bind to a protein for example, but it does not take into account whether this function goes on to have an effect on the species (humans in this case).

The Encode project gave some fairly high profile press conferences stating that Junk DNA basically didn't exist, because from a biochemical point of view, most of the DNA 'did something'.  The evolutionary geneticists took a stand against this, their point being that it didn't matter whether the DNA did anything biochemically, if it didn't have an effect on the organism, it was still junk.  It's important at this stage to think about the difference between 'Junk' and 'Rubbish'

Here's a quote from Sydney Brenner explaining it.

‘Some years ago I noticed that there are two kinds of rubbish in the world and that most languages have different words to distinguish them. There is the rubbish we keep, which is junk, and the rubbish we throw away, which is garbage. The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it. Were the extra DNA to become disadvantageous, it would become subject to selection, just as junk that takes up too much space, or is beginning to smell, is instantly converted to garbage . . . ”.

Lots of the evolutionary geneticists have pointed out that we would expect this junk DNA to 'do things' because lots of it is there as a result of it being useful DNA in a past ancestor species, just as the junk in your garage does stuff, it's just not necessarily useful stuff, and because it wasn't doing anything harmful once it lost it's purpose, it was just left there.

It's a really interesting debate, I might talk some more about it in the future as junk DNA is one of the subjects I research.  In the meantime, if you're interested in the arguments, there are a lot of other blogs and articles which go into greater detail than I have here.

Apologies

Apologies for the lack of a new post in the last few weeks.  I should be back to posting regularly next week.

Research & Real Life kind of got in the way.

Positive Selection

Positive selection is one of the great driving forces in evolution.  It is probably the thing we think of most when we're talking about natural selection and survival of the fittest.

Positive selection is a force that acts on a beneficial mutation and causes it to occur more often in the population.

Let's say that an individual in a population has a mutation that gives it some advantage over others.  Maybe it gives it slightly better eye sight so that it can see predators coming more easily, or maybe it helps it survive harsh conditions, or improves fertility.  There are all sort of reasons that a mutation could be beneficial.

In each of these cases, the new mutation helps the individual survive to pass on its DNA to more offspring.  That's basically the point of life from a genetic point of view.  The fitter you are, the more you pass on your DNA.

So, if the individual manages to pass on their DNA more because of a new mutation that they have, this mutation will enter the population more times in the next generation that a non-beneficial mutation would have (because they have more offspring).  And then their children who have this mutation, will pass on their DNA more often as well.

The mechanism causes the mutation to rapidly increase in frequency in a population.  This is called a sweep (and is researched in great depth in the lab I work in).  The speed at which the mutation sweeps through a population depends on how beneficial it is compared to other alleles.  If it is only slightly better, it will take a long time to increase in frequency, if it is much better this process will occur much faster.

If a mutation is particularly beneficial it will probably reach fixation in the population.  This means that all individuals in the population now have the beneficial mutation and there are no other versions.  It is through this process that new species can evolve.