A most excellent piece of work: Ryan Gregory is featured in this article on the ubiquity of junk DNA. Good explanations all around.
Darwin was certainly ignorant about genomes, as scientists would continue to be for decades after his death. But Gregory argues that genomes embody the very mix of adaptation and arbitrariness that Darwin had in mind. Over millions of years, the human genome has spontaneously gotten bigger, swelling with useless copies of genes and new transposable elements. Our ancestors tolerated all that extra baggage because it wasn’t actually all that heavy. It didn’t make them inordinately sick. Copying all that extra DNA didn’t require them to draw off energy required for other tasks. They couldn’t add an infinite amount of junk to the genome, but they could accept an awful lot. To subtract junk, meanwhile, would require swarms of proteins to chop out every single dead gene or transposable element — without chopping out an essential gene. A genome evolving away its junk would lose the race to sloppier genomes, which left more resources for fighting diseases or having children.
The blood-drenched slides that pack Gregory’s lab with their giant genomes only make sense, he argues, if we give up thinking about life as always evolving to perfection. To him, junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.
Exactly! If evolution works, this is what we expect, whereas a human genome that was 3 billion nucleotides worth of perfectly optimized functional DNA is what creationists want…and why they’re so adamant in denying the evidence.
That excerpt is a great explanation. PZ, I’m sure you don’t remember, but that was the very question I asked you when you gave a presentation at Stanford University.
ENCODE zealots responding in 3…2…1….
Cool to hear.
Obviously, as your excerpt points out, the junk DNA does not cause any serious problems. Does it, though, cause any minor problems? If there was a technique created (I know, we’re *DEEP* into sci-fi here, and if such a technique existed there are many, many better ways to use it) that could alter the DNA in every cell of a human being, would that human benefit from the junk DNA being removed?
As I was typing that out, @2 posted that “ENCODE zealots” would be responding.
I’m unfamiliar with that term – care to explain?
I’m also really, really hoping that my question (which I promise is asked as an honest question, with an intent to learn, not as a leading one or to draw someone into a false position) doesn’t paint me with that brush.
I always describe an organisms evolution by saying that it does not involve evolution towards perfection, just the idea that “An organism just has to be more successful in a given environment than it’s nearest competitor for resources and reproductive output”
It’s as if they don’t see that the total genomic entropy has been increasing even though some areas of the genome have had a decrease in entropy…why does that sound so familiar:-/
#7
Intended as a follow-up to the Human Genome Project, the ENCODE project aims to identify all functional elements in the human genome.
But they used a super-liberal interpretation of “functional”, basically denying that much (or any) of our genome is “junk”. This was like catnip to ID doofuses, because a perfect god should not fill us full of junk DNA, and here was “scientific proof” that he/she/it didn’t.
Sorry, I meant that comment to respond to #4, not #7.
“An organism just has to be more successful in a given environment than it’s nearest competitor for resources and reproductive output”
In other words, “I don’t have to outrun the bear; I just have to outrun YOU.”
Kaintukee Bob #3,4
moarscienceplz#6 explains why ENCODE thinks that 80% of the human genome is “functional”
PZ on why only a small part of the human genome is truly functional, and if at the 80% functional, we wouldn’t be here.
https://proxy.freethought.online/pharyngula/2015/01/06/the-genetic-load-problem/
As a follow-up thought on #3:
Wouldn’t it actually be beneficial if you had junk DNA? My line of reasoning would be that there is a somewhat constant rate of errors in the DNA (through incorrect copying, outside influences (radiation etc.)), so by having more DNA (i.e. more base pairs than the organism actually needed) the chances of those errors affecting ‘functional’ DNA would actually decrease. I’m familiar with molecular biology only on a layperson’s level, so could anyone tell my if I’m (slightly) right, wrong, or not even wrong.
And then Nerd of Redhead swoops in and points to the answer of my question. Thank you very much :-)
“slow and slovenly” — such a great description. I’m going to use that.
Kaintukee Bob #3
Eliminating junk DNA would have some benefits to an organism. The simple fact that fewer nucleotides need be copied would mean that cell division could happen faster and with lower energy cost.
However, for a human being, the benefit would be irrelevant. Our bottleneck simply isn’t in the area of individual cell divisions. That’s not our niche.
Moreover, as PZ mentions, to preserve this perfect state, you’d need a machinery to maintain it and weed out new mutations. That cost could well outweight whatever small benefits you might get.
Manu of Deche #10
Simply increasing the genome won’t help with mutations, since a larger genome also means more chances for mutations. Mutation rate is calculated as per nucleotide, so you gain nothing.
But the longest and most extensive record of evolutionary success is found in bacteria, which have far, far less junk DNA.
Perhaps junk DNA is a niche advantage.
Randomfactor@8
Not quite, since that would be an individual event between individuals. Evolution occurs at the population level. Individuals can have differences, but it is the frequency of those differences at the population level that matters. So when I talk about the “organisms” I am talking about their populations. It wasn’t clear in my statement above, but I do mention it when I talk about evolution to other people.
llewelly@14
Bacteria have less total DNA. There is an issue of cell size and complexity that needs to be taken into account. With that said I don’t know off hand of what percentage of DNA is junk DNA in bacteria.
@llewelly
That would make some sense. In a fast-reproducing organism, the benefits of a small genome would be most obvious, since speed of cell division is a relevant point of competition.
However, in larger organisms, like ourselves, it simply doesn’t matter as much how fast your cells divide. It’s K- vs r-strategy.
LykeX@13
We do have enzymes to check and correct replicating DNA and newly replicated DNA for mutations, but if they are not noticed in time (after the DNA is methylated) the mutations will stay in the sequence.
These fix point mutations or one base pair of DNA. I don’t know if there is a molecular mechanism to correct large amounts of DNA like transposons. Even if there is to much correction may be detrimental in the end as these unused portions of DNA give organisms the raw material for evolution to work.
Zimmer violates Betteridge’s Law of Headlines.
PZ’s explanation of this topic made perfect sense to me (essentially, our mutation rate requires a buffer to harmlessly absorb many mutations), and then I saw some articles about the bladderwort thing. Some googling led me to Evolution News, who have a long post basically explaining that the results in that paper are actually a giant mess that isn’t really well understood or explained (as far as I understood it without intensive research into the specifics they discuss).
But then that post suggested a book called The Myth of Junk DNA as an explainer for this topic, which seems to directly contradict the whole premise. This is very confusing for a non-biologist; the best I have atm is just, “we really don’t get bladderwort’s genome.”
I mean, that’s fine, we find weird outliers in science all the time that have somehow defied the general rule, and just require more study to understand. Is that basically where we’re at right now?
What? Bacteria are alive today, and have 3+ billion years of evolution behind them. The same can be said for mammals, birds, trees, protists, etc.
Note: just noticed that site is affiliated with the Discovery Institute, so that explains the link to the Myth book. Should have looked more carefully before considering them credible.
LykeX@16
Fast is a relative term (relative to your nearest competitor) and it may not always be a genome size issue that speeds up or slows down the replication.
For example, Under optimal conditions E. coli can reproduce every 20 minutes, whereas some species of Mycobacteria can take hours to reproduce, even under optimal conditions. This slow growth is thought to be due to the increased complexity of their cell walls compared to other bacteria, like E. coli, and not due to their genome sizes which are comparable, ~4.4-4.5 for Mycobacteria species and 4.6 Mb for E. coli.
Since, AFAIK, E. coli and Mycobacteria don’t occupy the same niches very often, and thus don’t compete very often if at all, the difference in reproduction rate doesn’t matter between these two species.
@moarscienceplz:6
If you’re referring to God, shouldn’t it be she/he/it (pronounced quickly)?
Makes sense to me, anyway. People are always saying “Holy she/he/it!”
You need more practice in thinking like a True Creationist. The Fall resulted in the beginning of imperfections in our genome, so things are just steadily getting worse. Which explains why Fugu is god’s favorite [vertebrate].
Of course! It’s puffed up, toxic, and foolish people eat it up….
You’re thinking of Takifugu rubripes. :-) There’s no escape from the splitters!!!1!1!