These numbers are just exercises in navel gazing. We do not know enough about gene regulation, epigentic imprinting, and chromatin dynamics to even say how much of the genome is superfluous.  I would venture to guess that much of the genome is designed to regulate the complex processes of cell-type specific gene expression and embryonic development.  Even the ENCODE project, looked at a relatively small number of cell types.  There are many transient progenitor cell populations whose epigentic marks are not yet described.   So I really would not waste much thought about whether it is 8% or 80% functional.  I would say there is likely to be remnants of DNA from transposons, gene duplications, pseudogenes etc.  but how much of this is truly non-functional remains unknown. 

It doesn't meant that rest of the DNA is totally non-functional. it might be not functional to an extent that we know of or we have capability to measure. Just as previously it was thought that introns are non-coding/non-functional. But now we know introns are also involved in coding. Similarly as the research continues and development of more and more advanced methods continue this may change. Even now we are unaware of thousands may be millions of mutations and other stuff like this. 

These numbers are just exercises in navel gazing. We do not know enough about gene regulation, epigentic imprinting, and chromatin dynamics to even say how much of the genome is superfluous.  I would venture to guess that much of the genome is designed to regulate the complex processes of cell-type specific gene expression and embryonic development.  Even the ENCODE project, looked at a relatively small number of cell types.  There are many transient progenitor cell populations whose epigentic marks are not yet described.   So I really would not waste much thought about whether it is 8% or 80% functional.  I would say there is likely to be remnants of DNA from transposons, gene duplications, pseudogenes etc.  but how much of this is truly non-functional remains unknown. 

This is a fascinating  gap between data collection and understanding.  The converse situation was the model of gene control for both metabolic and viral operons under repressor control with proposal of an RNA messenger intermediate through pure deduction in the virtual absence of any molecular sequence data, as proposed by Jacob and Monod with important input from Sydney Brenner. Is there a qualitative difference in scientists and their ability to stand back and analyse what they are doing, and which are the important questions to be asked, comparing the 50s and now?... or is it just that the data mass paralyses analysis? The Puffer fish doesn't have introns so maybe one could start there asking what else can be eliminated without disturbing things. In a biological system there cannot be too much interdependence of functional units since this would prevent the development of divergence required for evolution at least for organisms such as eukaryotes with relatively limited population sizes (i.e. 10e7 rather than say 10e26) and relatively large genomes ( e.g., 10e9 bp compared to say 10e6). The ability for radiation resistant organisms to survive DNA double-strand breaks by efficient rejoining and repair in cells containing multiple copies of their genome would imply for a start that a lot of mistakes and "junk" can be tolerated. It would seem simple logic to assume that a large fraction is without function. Early in evolution (say 3 milliard years ago) the situation was a lot worse. At the other extreme there is Pelagibacter ubique which has streamlined its functional genome down to apparent perfection. This has been done at the cost of loss of gene regulation, sex, transposition etc, allowed by the luxus of extremely large populations and a very small genome, whereby in the World population point mutations at every position are present as well as enormous number of combinatorial variants. In the latter case predation and growth have reached an equilibrium via the low density of cells in a huge volume and an essentially constant growth rate.

Thanks John,

One of your many points is close to my heart: Big Data and its "use".

Love the Manure Heap theorem. Just think about the probability to find a golden coin in a heap of manure when its size tends to infinity....

So much info will take time to digest!

Thanks all

Hi guys,

I completely agree with Gregory Dressler's comment and would say that the actual percentage is not even the 'right' or 'interesting' question.  And, Jean-Baptiste, I think your point about how the 'difference in opinion would reflect on the general public view of robust, fact-based, science, if it were picked up by the media' is so important!  Do you think the drive to go for the publication angle that stirs the most interest/controversy is or will end up hindering public trust in scientists? 

Thanks Angela,

Let's not forget there is more than publications that counts in the Scientific world:

Visibility, via blogs and discussion such as this one, matters too. The importance of Q&A in the RG score is quite revealing. 

Yep, exactly!  I really hope that a trend focusing less on perceived 'impact' and more on these visibility (and other) sorts of things gets stronger :-)

I think having a sounding board is important, however it must have content  and interchange of ideas and knowledge between participants with different backgrounds. One problem in defining functionality in eukaryotes in particular is genetic redundancy. When deletion mapping was being done in haploid Saccharomyces only about 25 % of mutations in functional genes could be detected because of this type of problem. Having a forum with "like" or "dislike" voting can become trivial.

I would like to venture something that I hope will spark some more conversation. We all know that complexity of an organism does not mean a bigger genome. It is well known that the rice genome is much bigger than the human genome and conversely that the puffer fish is eight times smaller. I would suggest that a great deal of non exonic sequence, as has been mentioned above, contains regulatory sequences involved in controlling environmental insults, as well as all the other functions mentioned above.

Please discuss!

I too raise my voice against such provoking affirmation. I wonder how reviewers didn’t veto it. We all know about the ENCODE consortium project which is still at its very infancy (what would you expect from a child?). As said above the term functionality itself is expanding with new discoveries….How do we define functional from non-functional? Yes, you can rip off somebody’s limb and he will still live. From a blind perspective he will not tell the difference as he can only hear…Does it mean limb is non-functional? Of course it affects the quality of life as defined even by popular standards….we don’t know if we delete those #non-functional part of the genome# how that would affect the organism, ……It is already known that some ethnic groups have several Mb deletions compared to the human genome draft…does that make them more pure than the rest of us….So, we cannot talk about functionality until we understand what we are talking about. Our ignorance of biological systems cannot be translated into crystallized conceptions about the very essence of the genome. We should never forget the Aristotles premise #the whole is greater than the sum of its parts#. That means integrating the parts you don’t obtain the whole.

Having said that, we should not confuse plasticity of the genome with functionality. Even some coding parts are redundant to maximize survival. Where do we stand then? To me this is pure vanity disguised in scientific jargon without any fundament. Even if Synthetic Biology reaches its summit I don’t think it will change that much. I have nothing against Synthetic Biology but I which I will live enough to see how much it can enrich our knowledge.