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The final frontier of Biological Sciences could be considered understanding the effects of variation in the DNA (and RNA).

If after fertilization the DNA of the zygote could be genetically engineered to prevent complications occurring later in the life of that human being, it could become the ultimate medicine.

Also, we know that (in humans) only 2% of the genome encodes genes that are translated into proteins; is the rest required for function?

Can DNA & RNA be considered the ultimate blueprint of all living organisms?

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  • $\begingroup$ Answers to your main question (the bold part at the end) will to a large extent "primarily opinion-based" (and speculative). The relationship between DNA/RNA and the functioning of organism is also a very broad topic. I think you should try to ask several narrowed down questions instead. $\endgroup$ – fileunderwater Feb 18 '15 at 12:54
  • $\begingroup$ Will you answer my title as an yes or a no? $\endgroup$ – elvarox Feb 18 '15 at 13:02
  • $\begingroup$ "...all other fields in Biology is just beating around the bush" - tsss... $\endgroup$ – AliceD Feb 18 '15 at 13:21
  • $\begingroup$ Was literally just writing an answer :/ in my eyes there is nothing opinion-based about this (although the question could be phrased better): classical molecular biologay says DNA makes RNA makes Protein. Whilst this is true, less than 2% of the genome is protein-coding, with the rest coding for regulatory regions and non-coding RNA molecules (often with important functions of their own). So whilst in some respects DNA could be considered the 'code' for organisms, it is much more complicated than this: each cell of an organisms has the same genetics but different phenotypes, so clearly ... $\endgroup$ – Luke Feb 18 '15 at 13:37
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    $\begingroup$ ... there is more at work than simply the DNA. This field of regulation and differentiation concerns epigenetics, which are modifications to the DNA that do not change the genetic sequence, and is to some degree hertiable. Therefore it is incorrect to say that DNA alone makes an organism, and it is incorrect to say that other fields of biology are just beating around the bush - there are many more factors at play than just the genetic code. $\endgroup$ – Luke Feb 18 '15 at 13:38
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This question can't be answered with a simple yes/no, but I would say that the analogy of DNA being the "code" used by cells is a reasonable one, if taken with a number of other considerations.

DNA function

When Watson and Crick first described the structure of DNA (being a double-stranded sequence of the nucleotides Adenine, Cytosine, Guanine and Thymine) this led to what is known as the Central Dogma of Molecular Biology [1], which posits that DNA makes RNA makes Protein (figure from [2], as originally produced by Watson).

http://sandwalk.blogspot.co.uk/2007/01/central-dogma-of-molecular-biology.html

As you correctly point out, less than 2% of the genome is protein-coding, however our understanding of the rest of the genome is increasing manifold due to projects like ENCODE [3], which are discovering not only the "regulatory" regions that control the expression of protein-coding genes, but also the discovery of non-coding RNA's, many of which are totally uncharacterised [4].

The point of this section is to clarify that although only 2% of the genome codes for protein, it is incorrect to say the rest is "junk" or non-functional. The Central Dogma described above is now an outdated model - certainly some DNA makes RNA makes Protein, but not all; many RNA molecules are functional in their own right.

You could argue that proteins and non-coding RNA molecules are the product of "scripts" in the DNA that are run or performed by cells, although you are unlikely to find any genomic scientists talking in these terms.

Epigenetic control

Where the analogy breaks down is that all* the cells in an organism have the same genome, yet they are vastly different to one another. These differences are due to epigenetic processes, which are described as non-coding modifications to the DNA that affect expression of transcripts. A basic overview can be found here [5].

These modifications come in several forms and include:

  1. DNA methylation
    • the addition of a methyl-group to cytosine nucleotides that can affect binding of transcription factors etc,
  2. Histone modifications
    • DNA is actually a 3-dimensional structure, and is wrapped around proteins called histones, which wrap together to form chromatin and the characteristic chromosomal structure.

The availability of DNA to transcription factors is completely dependent on these modifications to the DNA, which are specific to individual cell types and prevent retinal cells, for instance, expressing liver enzymes. (Below figure from [6])

http://www.eusem.com/main/CH/epi

Overview

In short, genetics and the DNA sequence can certainly be thought of as the blueprint for an organism - changes to this sequence can profoundly affect phenotype - however it is too simplistic to imagine that the sequence alone provides all the information needed.

Not only are there many non-coding molecules essential for functioning in cells, there is exquisite control over expression by DNA modifications that do not affect the sequence of nucleotides and are essential for cellular differentiation.

The ENCODE (Encyclopedia of DNA elements) project [7] is making headway into the interpretation of the non-protein-coding elements of the DNA, but there is still a long way to go.


* not quite all, for instance B-cells have a hypervariable region to enrich antibodies for variation [8]

  1. http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/central_dogma.html
  2. http://sandwalk.blogspot.co.uk/2007/01/central-dogma-of-molecular-biology.html
  3. ENCODE Project Consortium, “The ENCODE (ENCyclopedia Of DNA Elements) Project.,” Science, vol. 306, pp. 636–640, 2004. PMID: 15499007
  4. http://www.nature.com/encode/threads/non-coding-rna-characterization
  5. http://www.whatisepigenetics.com/fundamentals/
  6. http://www.eusem.com/main/CH/epi
  7. http://www.genome.gov/encode/
  8. http://www.anaptysbio.com/technology/somatic-hypermutation/
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  • $\begingroup$ Quite a comprehensive answer :) $\endgroup$ – WYSIWYG Mar 4 '15 at 13:38
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    $\begingroup$ This is an excellent answer from the biology side (which is appropriate since this is a biology site), but perhaps more could be said from a CS perspective. In particular, I think it's important to distinguish between DNA's self-regulatory mechanisms (e.g. TATA boxes) and fully Turing-complete coding languages. There's a strong distinction, I think, between the epigenetic mechanisms necessary within organisms and the hardware capabilities used to run computer code, and this is probably most clear once it's recognized that DNA is very unlike Turing-complete computer languages. $\endgroup$ – Kyle Strand Mar 4 '15 at 17:15
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    $\begingroup$ I was somewhat busy all these days, and I didn't even imagine this question of mine would get such an elaborate answer. Thanks for answering my question. $\endgroup$ – elvarox Mar 4 '15 at 20:47

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