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So after reading articles like "People Use Just 8.2% of Their DNA" etc., and thinking a bit... I got this idea:

What if DNA is actually like a software source code repository? You know, it has "master" branch - which is most stable and up-to-date version of program but also it has other branches, experimental ones and of course it has huge amount of "junk" - i.e. backed up version of files from previous changes to code that is not used in any way in actual program.

So what if first primitive single-cellar organisms had super primitive and very short DNA, then it got improved, but original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

Theoretically, the more primitive organism is, the shorter DNA it should have. For example, some very old sharks that still survive from Mesozoic era should have shorter DNA than modern sharks... Is this confirmed by actual experiments?

This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

Also this explains why human embryo come though all this steps of been single cell, multi-cell, fish, amphibian, mammal etc.

I'm no expert in biology by any means, and I suspect that this idea was around for long time, but I'm not sure... What do you think?

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    $\begingroup$ Comments are not for extended discussion; this conversation has been moved to chat. $\endgroup$
    – Bryan Krause ♦
    Apr 19, 2019 at 19:10
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    $\begingroup$ @BryanKrause — Let’s make it clear. I have no wish to discuss anything, only to use the comment box for it’s correct purpose to ask the poster for clarification: What is your biological question? $\endgroup$
    – David
    Apr 19, 2019 at 20:01
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    $\begingroup$ that seems to me like a very open-ended "discussion"-type question right now. How is it about biology? $\endgroup$
    – aaaaa says reinstate Monica
    Apr 19, 2019 at 22:48
  • $\begingroup$ @David umm... this hardly seems like the place to discuss it. Please take it to meta if you feel it's important. $\endgroup$
    – rotaredom
    Apr 19, 2019 at 23:02
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    $\begingroup$ @rotaredom — “Discuss”? I’m asking the poster to clarify his question. Poster, are you asking what junk DNA is, whether it’s the decaying remnants of duplicated genes, whether the expansion of the gene repertoire of organisms occurs/ed by duplication, whether duplicated genes can acquire different functions or what? But just one at a time, please. Biology is an experimental science. A lot of genomes have been sequenced and analysed and we can attempt to answer questions on the basis of this analysis. Proposition of theories by people, however much biology they know, is not a question. $\endgroup$
    – David
    Apr 20, 2019 at 17:45

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I think this analogy is not actually that bad, but you are making some incorrect conclusions from it especially regarding 'junk' DNA and which parts of a repository DNA holds (which shows the limits of analogy!). Think instead of the DNA of an organism as a single local copy of a particular commit.

There is no remote to compare to and no list of historical changes, each organism just has its own local copy of the most recent source that can sometimes be merged with other local copies via sexual reproduction or horizontal gene transfer.

What you need to drop from the analogy

Get rid of any thought of a master branch or ideas that the repository contains backups of previous versions. These thoughts will only mislead you.

This statement:

original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

makes little to no sense in biology. There is no backup, except in that each organism is a branch of it's parent(s) source.

Where the analogy could work

Genomes of different species are all branches from some original source code. Therefore, you find a lot of commonality when you compare even very distantly related life, especially in the most key libraries that are involved. There is a ton of conserved sequence in the basic machinery for replicating DNA and producing proteins, for example.

This is why your statement:

This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

is mostly correct.

Length of source

Your analogy has gotten some criticism for your conclusion:

Theoretically, the more primitive organism is, the shorter DNA it should have.

but I would argue this is actually a way in which your analogy works, yet your conclusion from it does not. Software development involves both adding new code and deleting obsolete code. Lines of code is a poor measure of how primitive some code is. Biology shows this well: all life is equally primitive in terms of years of existence, and single-celled organisms are much more advanced in terms of numbers of generations. If organisms contained some log of all the past changes (which they do not), the repository would be way way bigger in bacteria than in animals because of that large number of generations.

Summary

In summary, analogy can be helpful to wrap your head around some information, but be careful in taking it too far. Sometimes analogy is good for generating new hypotheses and for guiding your learning, but you need to verify those hypotheses in the actual biology (see Richland and Simms 2015 for one take on the usefulness of analogy as an educational tool).

I disagree strongly with the comment by @SPr stating "The analogy between the genome and source code repository is unhelpful and poor": even the imperfection in an analogy can be very helpful in that they help you build a relational map of the world by finding where analogies work and where they conflict.

Richland, L. E., & Simms, N. (2015). Analogy, higher order thinking, and education. Wiley Interdisciplinary Reviews: Cognitive Science, 6(2), 177-192.

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Watch out with analogies. Even when they are somewhat helpful, they are only analogies. That being said, unfortunately, your analogy is completely unhelpful!

What if DNA is actually like a software source code repository? You know, it has "master" branch - which is most stable and up-to-date version of program but also it has other branches, experimental ones and of course it has huge amount of "junk" - i.e. backed up version of files from previous changes to code that is not used in any way in actual program.

It is unclear what you would call "junk" here. Typically, if you include regulatory sequences in "junk" as it is often done by lay people (see @iayork comments below for more information), clearly they are being used and are essential. But anyway, seeing non-coding, non-regulatory sequences (such as the ALU sequences) as experiments would be very misleading. Large amount of repetitive DNA usually comes to existence through the work of transposons and retrotransposons. They are not attempts (clearly not with an intuition but even without intuition in mind) to make something "better"

So what if first primitive single-cellar organisms had super primitive and very short DNA, then it got improved, but original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

DNA get lost all the time. A mutation can alter the code, it can also duplicate sequences (or even whole chromosome or whole genome) and it can "remove" sequences (even "remove" whole chromosomes). Genome reduction is indeed not that uncommon.

Theoretically, the more primitive organism is, the shorter DNA it should have. For example, some very old sharks that still survive from Mesozoic era should have shorter DNA than modern sharks... Is this confirmed by actual experiments?

"Old sharks that still survived from the Mesozoic era" are not more primitive than humans, E.coli or than the European green lizard. At least not in any way that "primitive" is easy or intuitive to define. Please have a look at the post Are we “more evolved” than present-day bacteria? for more information.

This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

I am not sure I understand what you have in mind here.

Any two extant lineage share a common ancestor at some point in the past. Depending upon how recent is their Most Recent Common Ancestor (usually abbreviated MRCA), they are more or less likely to have similar genome.

Also this explains why human embryo come though all this steps of been single cell, multi-cell, fish, amphibian, mammal etc.

I am not sure I understand what you have in mind here.

There is MRCA of all living creatures on earth is called LUCA (Last Unversal Common Ancestor). We don't know much about LUCA but it was pretty clearly single celled and had a relatively short genome. Note btw that LUCA itself is not the very first cell though but that does not matter much for our discussion.

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  • $\begingroup$ Typically, if you include regulatory sequences in "junk" (as it is generally done, I think) Not so. Although there are a lot of people who attack the concept of junk DNA with this as a straw man, regulatory sequences are not and never have been considered part of junk DNA. Doesn't change the rest of the argument, just a caution $\endgroup$
    – iayork
    Apr 19, 2019 at 18:27
  • $\begingroup$ I don't know what meant the first people who coined this term but my first 5 google results for "junk DNA" define it as "non-coding DNA". But yes, let's be cautious that it might not be what everyone mean at least. Answer edited. Thanks $\endgroup$
    – Remi.b
    Apr 19, 2019 at 18:42
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    $\begingroup$ The original definition did not use that - I agree it's often used that way, but actual researchers on the field are much more strict. See The Case for Junk DNA, especially the section The origin of “junk DNA” $\endgroup$
    – iayork
    Apr 19, 2019 at 19:19
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I would compare DNA to a computer filesystem rather than a source code repository. Coding sections are "programs" that can be run to produce a protein product. An important difference, however, is alternative splicing, where a gene can code for multiple products. This serves as a form of "compression on disk", where repeated regions can be represented by a copy and pointers wherever the region is required.

The vast majority of what was previously called "junk" DNA instead turned out to be important for other purposes. For example, some serve as regulators or recombination faciliators (source - https://www.scientificamerican.com/article/what-is-junk-dna-and-what/), some serve important structural purposes (source - https://www.sciencedaily.com/releases/2018/04/180411131659.htm), and others serve as important binding sites for transcription control (source - https://ghr.nlm.nih.gov/primer/basics/noncodingdna)

Think of noncoding DNA as filesystem metadata - stuff like file allocation tables, master file tables, journaling, and the master boot record that doesn't represent actual data - although your computer will probably break if this data disappears. Again, the analogy doesn't fit too well considering only about 1.2% of the human genome is coding regions (source - https://www.bing.com/search?q=what+percentage+of+the+human+genome+is+noncoding&pc=MOZI&form=MOZSBR ). On the other hand, computer filesystems are generally designed to minimize the amount of metadata overhead since that costs you an extra storage space that could otherwise be used for files.

Further reading on "junk" DNA that really isn't garbage:

https://www.scientificamerican.com/article/what-is-junk-dna-and-what/

https://www.sciencedaily.com/releases/2018/04/180411131659.htm

https://ghr.nlm.nih.gov/primer/basics/noncodingdna

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