The following essay was written by Wonders for Oyarsa and the views/arguments contained within do not necessarily reflect the views of Mike Gene. Mike Gene hosts such essays simply to provoke thought and promote discussion and communication.
As a Computer Scientist, I never was terribly impressed by the notion of "junk DNA". The idea that 90% of our DNA has no function is counter-intuitive at best. The human genome already seems to be surprisingly small to specify all the information required to describe how to build a human being from a single cell (implying to me some pretty good compression), and further reducing this to the information content of Microsoft Office is not what I would expect. But then again, life isn't always intuitive. Stranger truths have been found in nature, so I suppose we need to keep an open mind.
Then I remembered that we have around 96% genetic similarity to the chimpanzee – meaning large chunks of our genome can be matched up with chunks of the chimp genome almost exactly. These things seem completely at odds to me. If a portion of the genome is junk, than there should be no selective pressure to keep this portion the same. In fact, there may be a functional advantage in removing it altogether (the organism can get by with less nucleotides in its cells). Over 5 million years, it certainly feels like these junk sections would become completely scrambled, rather than maintaining almost total similarity.
So, what better way to demonstrate this than with the clear irrefutable scientific proof of a toxic asexual bunny mutation simulator?
Toxic asexual bunnies are, well, toxic. As such, they are dangerous to everyone, including each other. A mere touch by one toxic bunny to another may be enough to kill it, though some have been known to evolve greater toxin tolerances (which in turn make them more deadly to other toxic bunnies).
- Each bunny has a DNA string of 30 English characters.
- The toxin defense gene is located in the first three characters, which must spell an English word.
- Furthermore, the organism has evolved such that only an English word starting with "BU" is sufficient to defend it under these conditions (we are simulating only a small evolutionary change).
- Each sample starts with the same bunny with the first three letters as "BUN". The rest of its genome is junk, designated by dashes for the sake of easy reading.
- As the bunnies reproduce, random mutations take place. Most of these mutations will do nothing since it occurs in the junk, but some will occur in the first three letters.
- If the mutation occurs in the first two letters, it is a harmful mutation.
- If it occurs in the third letter, there is a 1/4 chance of a new word generated, indicating a functional advantage.
- Once new bunny species dominate both groups, the new genomes are compared.
As I expected, getting a positive change in a single character to a new spices garbles the junk DNA to near oblivion. I'm getting a statistical average of about 35% similarity – a far cry from 96%, and not to far from the 9% or so that would indicate total scrambling.
Obviously the mutations are sped up in my simulation, and I am not including many of the different types of mutations that actually occur (reversals, additions, deletions, splitting, moving, etc). The sample sizes of human and chimp populations are much larger than the ten or so that I show. But I think this easily offset by the sheer size of the genome, as well as the improbability of getting a truly helpful mutation that would provide a serious functional advantage.
I think the simulation sufficient to illustrate the principle – that getting a good mutation in a small area requires a large number of neutral mutations across the board (in the case of junk DNA).
Folks, the bunnies don't lie. We might not know what this stuff does, but it sure ain't junk.
Wonders for Oyarsa is a programmer somewhere in the United States. When he's not working full-time, pursuing his M.S. in Computer Science part-time, and raising two kids, he likes to investigate the notion that intelligent design was involved in the writing of the Bible on his blog.