Rummaging About in the Genetic Junkyard
Hi all. I often have the urge to post videos of lectures or presentations that are scientifically educational in nature, but I rarely do so because of their length (usually 45-120 minutes), which severely limits interest and discussion. So, today I thought I'd try something new. I've produced a written companion for this one, to save people the time of watching the video if they don't want to, in the hope of fostering more discussion than would likely otherwise be the case.
The video is a talk from Skepticon 4, in 2011. According to Wikipedia, Skepticon is...
one of the largest skeptic and secular conventions held in the United States. It was co-founded by Missouri State University students Lauren Lane and JT Eberhard. Guest speakers are invited to discuss skepticism, science, education, activism, and other related topics. This free event is in part sponsored by organizations including American Atheists and the American Humanist Association, among others.
And when it started in 2008...
The event was considered particularly controversial because Springfield, Missouri, is also the home to the Assemblies of God national headquarters and the campuses of several religious universities such as Evangel University.
Good place for an atheist conference, I suppose. It looks like it's going to be held in St. Louis this year, though.
At any rate, the speaker is PZ Myers, an American biologist who founded and writes the Pharyngula science-blog. He is associate-professor of biology at the University of Minnesota Morris (UMM) where he works in the field of developmental biology. He is a critic of intelligent design (ID), the creationist movement, and other pseudoscientific concepts.
This talk is his refutation of the popular ID claim that non-functional, useless, so-called "junk" DNA cannot, and does not exist, because it was intelligently designed by God, and therefore it must have a useful purpose.
Persons not interested in the over-arching topic of evolution vs. ID might still enjoy my written companion. It contains some excellent information about the human genome from PZ's talk.
I begin the companion with a transcript of the first few minutes, and then I switch to notes. The bracketed time at the beginning of each item shows from where in the video it was taken, allowing anyone who wants to hear a particular part in PZ's own words to find it quickly.
So, without further ado, here's the 43 minute video. My written companion follows.
Introductory comment:
[02:50] "What I'm basically going to be doing here is I'm going to be taking one creationist point and pounding it to death. So, one way to visualize this -- this is a spoiler alert -- imagine creationist mouse in my left hand, sledge hammer in my right, and wham! And then I do it 20 more times, and at that point the mouse is pulp, but as you know, this is a zombie mouse, so it will rise from the dead and keep pestering us. I'm sorry about that. I cannot get rid of it completely. The other bad thing about these zombie mice is that they're brainless, so the shooting them in the head thing doesn't work. Don't even try. They just keep coming and coming."
Presentation begins:
[04:17] "OK, so what I want to talk about is genomic junk. And I want to talk about it because, as was mentioned earlier in a talk, the creationists have made a mistake: They have made a prediction, a testable prediction, and I'll just give you some examples of the kinds of things they say. This is good old Bill Dembski, and what he's said here [referring to screen] is, a distinction, that... "Intelligent Design", he says, "is not a science stopper." He says real science is a science stopper. I know..."
"Anyway, he's saying that it's not, because it can, "foster inquiry where traditional evolutionary approaches obstruct it." And he specifically mentions the idea of junk DNA. And he says that there's -- an evolutionary view would say that we "expect a lot of useless DNA", which is really peculiar because no evolutionist predicted this ahead of time... [If] "on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function." A prediction. We can test this."
"If most of the genome is entirely functional, if there's no wasted space, if it's really efficient, then that proves that [...] adaptationist evolution is true? No... They say it proves that creationism is true. The other way it can go is that if there's lots of junk, that says that -- well, that's falsifying a prediction by creationists, and we're done, they've been disproven. This is our goal."
"Stephen Meyer says much the same thing, so he says [referring to screen], "Thus, far from being dispersed sparsely, haphazardly, and inefficiently within a sea of nonfunctional sequences" ... "genetic information is densely concentrated on the DNA molecule." He says this. Information "densely concentrated on the DNA molecule." Now, some of you here are biologists, and you know you can go onto the NIH website, and there's, the full human genome is right there, and you can go browsing through it, and the one thing we know is, no, it's not densely packed with information. He says, OK [referring to screen], "Far from containing a preponderance of junk -- non-protein-coding regions that supposedly perform no function -- the genome is dominated by sequences rich in functional information." Prediction again."
"Now, what I wanted to talk about today is whether this is actually true, and I'm going to show you that no, it's not. The first thing I have to do, though -- and this is where I have a little trepidation, because you've had all these exciting talks today -- I'm going to teach you some molecular biology. [crowd cheers loudly] Yeah. OK. Isn't that exciting? [laughs] Man, I wish my students would respond that way. OK. So, here we go..."
Notes from the presentation:
- [07:10] Gene layout (in humans) - Promoter, utr regions, exons (coding), and introns (non-coding).
- [07:10 - 12:20] Gene expression - An enzyme begins at the promoter and copies the gene into messenger RNA. The non-coding intron regions are cut from the copy, thrown away, and the coding exon regions are spliced together and go on to be translated into a protein. Only a small portion of the information contained in a sequence is usable information, much does nothing and is actually discarded. Genes in certain other organisms do not share this wasteful characteristic. Examples given are E. coli and yeast.
- [15:38] An average human gene contains about 8 introns. The average exon size is 170 base pairs (bp). The average intron size is 5,400 bp. The human genome contains about 20,000 genes, while the total genome length is about 3,300,000,000 bp. An average gene is about 1,500 bp broken up into 8 fragments scattered over 43,000 bp in a sea of bases about 165,000 bp long. Translation - Only about 1.5% of your genome is protein-coding information.
- [18:26] There is a fair amount of regulatory information contained in the non-coding parts of DNA, pertaining to growth and development of the organism, and it's been known about for 50 years. Best estimates for quantities of regulatory DNA is about 3% of the genome.
- [25:10] Other known categories of functional DNA are ribosomal RNA genes, transfer RNA genes, and micro RNA genes. These may be numerous (4,400 copies of tRNA for instance), but small (tRNA is less than 100 bases long), thus they account for only around half of one percent of the total genome.
- [25:41] So far... 1.5% protein coding info + 3% regulatory + 0.5% other = 5% of the genome.
- [26:00] In addition to that 5%, huge lengths of repeating code are known to exist in telomeres, and for a very non-intelligent reason -- the enzyme responsible for copying DNA is "buggy". It doesn't work very well. It gets near the end of a chromosome and fails to finish copying. To get around this dilemma, there is an instruction in DNA that tells another enzyme to add lots and lots of repeats of useless code at the end of chromosomes to provide extra length, assuring that the first enzyme will copy well past the necessary information before shutting down prematurely. This can be counted as a function, a stupid function says PZ, but a function nonetheless. These repeats of useless code in telomeres make up about 10% of the genome (including centromeres, which act as a "handle" for manipulating chromosomes during mitosis and meiosis), so now we've accounted for 15%.
- [29:58 -35:18] Of the remaining 85%, there are enormous regions of parasitic DNA called LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), ERVs (endogenous retroviruses), and DNA transposons.
- [29:58] LINEs are relic viral fragments that are read just like a gene, transcribed into mRNA, and translated into a protein called a reverse transcriptase, which performs the opposite function of transcription and causes a copy of the LINE to be written back into DNA during replication. That's all they do, hijack our DNA to make copies of themselves. PZ likens this to a guy in an office who does nothing but sit on the copy machine making photocopies of his butt all day. We have 20,000 to 40,000 copies of LINEs in our DNA, accounting for about 21% of the genome.
- [32:21] SINEs are also viral relics, but they don't produce a protein for copying themselves, they get recognized by the LINEs' reverse transcriptase protein and trick it into writing a copy the SINE back into the new DNA. They hijack the LINEs' hijack. They're a parasite of a parasite. We have about 1,500,000 copies of SINEs in our DNA, accounting for about 13% of the genome.
- [33:37] ERVs are whole pieces of viruses, complete with genes for assembly and replication, that have also hijacked our DNA. We have about 450,000 copies of ERVs in our DNA, accounting for about 8% of the genome.
- [34:37] DNA transposons are genes that don't try to make endless copies of themselves, what they do is jump around the genome. They cut themselves out of one location and reinsert themselves somewhere else. They can be bad for you because they cause mutations (they are like a built-in mutagen). We have 300,000 copies of DNA transposons, accounting for about 3% of the genome.
- [35:18] Final tally... 45% known parasitic DNA + 10% structural DNA + 5% functional DNA = 60% of the genome. PZ drives home the point that almost HALF of our genome (the known parasitic 45%) should indeed be considered "junk", saying it is not functional and not to our advantage to have. The other 40% of the genome remains a mystery for now, but they're working on it. PZ jokes that the unknown 40% is job security for molecular biologists. Based on past experience he expects only a small portion of it to be useful, and most of it to be garbage, including broken pseudo genes, which by themselves should add up to about 1.5% of the genome.
[36:58] PZ winds down the presentation with a couple of open questions for anyone claiming that all DNA must have a useful purpose (the creationist/intelligent design viewpoint).
[37:02] First, the so-called Onion Test from Ryan Gregory. He gives an example of two different onion species, one having twice the amount of DNA as we do, and another having ten times as much, but neither having any more functional genes than us. The difference is in their junk DNA, and the requirement of the test is to explain that peculiarity. If there's no such thing as junk DNA, and every bit of it is useful (because it has been intelligently designed), then why is there such a huge difference in the two, which are otherwise barely distinguishable from each other? They both grow like onions. They both look like onions. They both taste like onions. What is all that extra DNA, especially in the one with ten times the size of the human genome, supposed to be doing?
[38:41] Second, he asks the opposite of the Fugu fish, with a genome of only 390,000,000 base pairs (whereas ours is 3,300,000,000 base pairs). Sequencing shows that Fugu has managed to get rid of most of its junk DNA, but is doing just fine. If the junk is needed and purposeful and intelligently designed, then how can Fugu be surviving perfectly well without it?
[40:36] In closing, PZ reminds us of the Dembski quote from the beginning of the presentation, the one with the testable, falsifiable claim: "Thus, on an evolutionary view we expect a lot of useless DNA." [prediction 1] "If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function." [prediction 2]
[40:55] PZ asks which of the predictions is true, and then says, "One. We're done."
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So what do you think? Not just about the subject of the video, but also about the written companion. Does it help make a topic covered by a video that might not be watched because of its length more accessible and discussable?
I was reading last night that dandelions are apomixus and have done away with sex altogether, they simply produce seed by replicating themselves.
This includes the flowers' useless petals which it no longer needs but cannot stop replicating. Junk DNA
I didn't know that about dandelions. Good one. PZ should have worn one in his lapel.
Interesting. But bees still stop by and collect a little pollen, don't they?
Great video (watched the whole thing).
PZ makes a very compelling point that the designer seems to be sloppy and wasteful. So I agree with his point and his argument.
That said, there is ongoing work (especially with transcription factors) that suggests much of what we have considered junk DNA in the past is quite likely potent. But even if we find that the vast majority of DNA makes good sense, there really is no explanation for things like LINE and SINE sequences other than 'undirected' or 'incompetent design'.
The next time you come across a really good talk or article about that, please let me know. Being directed straight to some really good info beats the hell out of wading through heaps of mediocre stuff looking for it (which is what I usually find myself doing).
According to PZ's accounting, those two alone represent 34% of the genome. So even if all of the remaining DNA were shown to be useful, it would still be true that a full third of the energy and material we use for reproducing DNA is wasted. PZ also includes the ERVs and transposons, though, bringing it up to 45%. That's beyond incompetence. Undirected, natural processes are the only reasonable explanation as far as I'm concerned. Besides, they are apparently obvious viral relics, and that's what viruses do, they use the biological machinery of other organisms to reproduce themselves. Why would anyone even think it makes sense to posit a designer to explain them?
Here is a lecture from one of my all time favorites - Professor Robert Sapolsky:
This is where you might want to start for the DNA content. But I recommend the entire course.
Because they really, really want that to be true.
I've seen parts of that Stanford course come up a million times in searches, but I've always skipped them because the course is titled Human Behavioral Biology , which always made me think it was about recent anthropological stuff. Not that there's anything wrong with that, I like anthropology, but it never struck me as what I was looking for at the time. I guess I should watch it after all.
You're probably already aware of this, but Yale has one with an evolution-specific title... Yale Evolution Lectures .
The Yale one is from 2009, and the Stanford one is from 2011, so neither are newer than PZ's talk. As fast as genetics is moving, I wish they would put up some new stuff.
Bay Path has a course with videos from 2016 and 2017, which is the most recent I've been able to find on YouTube lately... Genetics Lectures, but I haven't watched all of it yet.
Cal Berkeley used to put fresh course videos up almost in real time, the same day they occurred, every single semester. They had a lot of biology, physics, and astronomy lectures, and it was absolutely FANTASTIC! I loved it, but they stopped doing that a couple of years ago. Huge loss, IMO. I used to consider their YouTube channel one of the the best things on the entire internet.
And end up creating a bubble of false reality for themselves. Which is really kind of sad, when you think about it. If they weren't always trying to push their nonsense into schools and government, they'd be more worthy of pity than scorn. But, unfortunately, that's not the case.
Something occurred to me today. Organisms with lots of mutation-causing jumping genes in their DNA could possibly gain an evolutionary advantage by having lots of extra, non-functional DNA for them to randomly land on. It would reduce the probability of harmful mutations occurring in the really important genes during an organism's lifetime, and could add time to their lives to help raise and nurture offspring, which is important in complex, social organisms like humans (often, parents and grandparents are involved).
So, if you have lots of parasitic elements in your DNA that are potentially mutagenic, maybe it helps to give them plenty of extra, useless junk to tear up, in order to minimize damage to the really important stuff. With the functional parts of our DNA making up only about 5% of the genome, and the protein-coding parts only 1.5%, then that makes it all a pretty small target for the jumpers to hit. Which is not to say that it never gets hit, just that the probability of a hit is lower than it would be if it represented a much larger percentage of our genome.
That could possibly be a way to consider junk DNA useful. Maybe it provides the much smaller, more critical parts of DNA with a bit of cover from jumper attack, helping organisms live longer, and increasing the odds of successful reproduction and rearing of offspring.
Side note -- PZ didn't make this clear, but from what I've read since watching his talk, those LINEs and SINEs are also considered to be transposable elements (not just the DNA transposons). Apparently, they're classified as retrotransposons, but luckily, evolution has managed to render many transposable elements inactive .
Possibly but this is of course a double-edged sword. Reducing the chance for 'bad' mutations to go into effect is beneficial but that very mechanism also reduces the changes for advantageous mutations. Transposons are one or many elements of DNA that are peculiar from a software perspective. DNA seems like an extremely inefficient algorithm that has the ability to modify itself. But the modifications are not directed (intelligent). Some of these new functions are inhibited (modified by undoing) by contra functions at times. It is like taking 1 +/- 2 steps forward and then 1 +/- 1 steps backwards at every single step in the algorithm. Very strange and very odd that, in the end, this seems to actually produce mechanisms that function in aggregate.
True, in germ line mutations. I was thinking more along the lines of lessening harmful mutations in somatic cells as the organism lives out its life, though, since cells (and the DNA in them) are reproduced constantly as the organism develops and grows old.
I was thinking that junk DNA could lower the probability of particular genes in new cells being damaged by random transposon hits, which could prevent them from being properly expressed (as new bone cells, skin cells, blood cells, whatever). A lower rate of somatic cell damage should help the organism live longer, and would thus have a positive effect on reproductive success, no?
In our specific case, it could also have helped by allowing for an older generation of wise elders to function as knowledge sinks, from which the younger generations could learn valuable lessons and skills (part of that whole collective learning thing that made us so successful over time).
None of this would be evidence of a creator, though. Or at least not an intelligent one. An intelligent creator would surely have just left the mutagens out of the equation. Especially if evolution isn't supposed to occur.
I don't think I've ever heard creationists trying to get around the potential for germ line mutations from transposons before. You'd think that those PhD YEC'ers (and I can't believe that's actually a thing) would have learned about them while earning (or, lying for) their degrees. Have you ever heard any of them bring the subject up before?
Makes sense. Somatic cell mutation equates to aging so it follows that mitigating mutation leads to a longer life. Longer life yields societal benefits (e.g. the ability of individuals to learn more and thus pass on more to the next generation).
These people are enigmas. My position is that they have a primary lifelong mission to serve their God. They believe the Bible is the word of God and they will force-fit reality (with severe confirmation bias) to that end. What really surprises me though is that they go beyond mere confirmation bias to very clever dishonesty (lies). I just do not know how they can realize they are wrong and resort to lying about it with clever deceptions to keep their minions in check (e.g. Noah had baby dinosaurs on the ark) and still think they are serving their God.
If one must lie to preserve the Bible as divine does that not make a reasonably intelligent person question what they are doing?
I'm almost positive that I came across a video on YouTube that looked like people were being asked if it was OK to lie for Jesus. I didn't bother watching it, but I'll bet most of the replies were yes.
Maybe lying for Jesus is a thing?
You're absolutely right, though. Any reasonably intelligent person should question the motive.
I know that was rhetorical but it sure is or was for Mormons and they're hardly the only ones. There are tons of examples including the so-called "crisis pregnancy centers" which recently won the right in California to lie (or put another way, to not be forced to utter the state's speech despite its factuality and the center's intent to defraud the public).
Ahhhh. Pious fraud. That's a really good article. Thanks for that. I see Lying for Jesus even has its own section.
I've always thought religion was a lot like Santa Claus for adults. Be good boys and girls (or at least whatever we say is being good) or you won't be rewarded with a 'present' at the end of your life.
The excellent sf author Robert J Sawyer blends ideas and action in all his books. In Illegal Alien, he recounts the court case of an alien accused of murdering a popular scientist. The aliens are on Earth for several reasons. The most important, if least public, is to decide if humans are the particular children of God.
One way of deciding is to look at how well the species is designed. (This is essential to the plot, so I won't spoiler it.)
In short, we are NOT well designed. Our key organs are not redundant. Our skeleton is wacky. Our circulatory systems are inadequate.
If God designed us, He's a piss-poor designer!
You sound like you are primed for the Aquatic Ape theory. Many of the very things that are wrong with us on land
have unique advantages for us in the water.....
This is worth reading
alas it is not fiction although many many scientist in love with the Savannah Theory think so, lol
Fifty years ago, I was very impressed with Desmond Morris's The Naked Ape. I'd guess that everything he wrote has since been overruled, but the essential idea remains: we are apes, and a large part of our behavior is innate ape-ness.
Being intelligent apes (ha ha), we can voluntarily override our genetic inheritance to some degree. Or... alternatively... we can be apes in a pack of apes...
Our kidneys, lungs, and tonsils are redundant. Sort of. I really wouldn't want to lose one of my kidneys or lungs but the fact is I could live with only one of each.
And then there are the organs we don't need at all, like the appendix.
I actually disagree on that. That appendix actually takes in a lot of toxins that might otherwise go elsewhere in our bodies.
Some people think tonsils are redundant. I got tonsillitis a lot as a kid but not so much anymore. I think my tonsils kept me getting sicker. I still have my tonsils and they are YUGE!
Relative to the term "creation science" I was looking for a non insulting description of "pig headed".
Alas, that doesn't seem possible.
But I did find this gem.
It seems like I've heard about pig heart valves being transplanted into humans.
The pigs must be genetically altered to eliminate known viruses. Approval and a good supply should be within 2 years...
Oh, man. That CRISPR stuff is amazing. It's also a little terrifying, though.
another CRISPR article
My mother had her mitral valve replaced back in the mid 70's with a pig valve. A few years later they replaced it with plastic and then plastic again. They only used the pig valve once in the 3-4 replacements that she had.