No, not a tale, rather a reflection.
Recently, we learned that biochemist emeritus and (at one time) Uncommon Descent commenter Larry Moran is writing a book (2022) arguing that human DNA is 90% junk. Non-functional junk.
Our physics commentator Rob Sheldon writes to reflect on the many meanings of the word “function” in biology:
If I recall correctly, the original definition of “functional” was whether that piece of DNA was turned into a protein, which depended on finding a “start” and a “stop” codon. The Human Genome Project reported that some 90% of the human genome didn’t have these “start/stop” features, and hence was “non-functional”.
a) However, there was extensive editing of RNA in the “spliceosome” with the removal of introns and customization of proteins such that one “start/stop” strand of DNA could make 100 distinct proteins. So the first piece of news is that the mapping is “one to many”.
b) Since the function of start/stop was to tell the DNA polymerase where to start/stop reading, then the fact that the “spliceosome” is spitting out chunks of RNA totally indiscriminately of start/stop codons, means that start/stop is not a good way to characterize functional DNA. Some pieces were still being transcribed into protein without these markers.
So that led to the second method of defining “functional”. Let’s cut out that piece of DNA using CRISPR (or more likely, blocking it with a small anti-sense RNA fragment). Is the edited critter still viable after that DNA is rendered inoperable?
c) Again, a person is “still viable” without legs, just not very competitive. So what exactly does viable mean? If a bacterium lives for 2 weeks but doesn’t reproduce, is it viable? If a bacterium lives indefinitely in a Petri dish but dies when injected into a host, is that viable? If a bacterium lives in a host but dies when the host runs a fever, is that viable?
So we are back to not really knowing when something is functional or not.
So that led to a third method of defining “functional”. Let’s see if there are any protein strands in the organism that are derived from that piece of DNA.
d) But then we discovered that RNA does a million other things — it builds the ribosome, it brings in marked amino acids, it regulates transcription, it carries information outside the cell. Just because a piece of DNA isn’t converted to protein doesn’t mean that it has no function.
So we are up to our fourth method of defining “functional”. If that DNA is turned into RNA then it is functional.
e) That’s where ENCODE comes in and says that 80% and more of the DNA is converted to RNA, which is where Dan Graur loses it and starts ranting about creationists and TV sets. He builds a toy population genetics model and says that 80% destroys his model, and therefore the data is wrong. (No, he isn’t unique, all theorists harbor dark thoughts about experimentalists.)
f) But as experimentalists showed all the new things RNA does, Dan’s model gets less and less compelling. For one example, a piece of “junk DNA” was found to regulate cancer. When that junk DNA was removed, the organism died early of cancer. It was viable, just not competitive.
My analogy is that DNA is like a tool box. Just because we don’t have a hammer in our hand all day, doesn’t mean that the hammer is junk. When you need a hammer, a screwdriver just won’t do. I’ve used pipe wrenches as a hammer in a pinch, but I’ll tell you, it was ugly. My brother spent ten years as a truck mechanic, and as he would gladly tell you, he was often hired because of his toolbox.
So why should the genome be any different? Shouldn’t the default be that if some item is found in his toolbox, it has a function? Why is Dan Graur so adamant to tell my brother that his toolbox is full of junk? Whose reputation is he spitting on anyway?
Dan Graur had announced in 2014 that he didn’t “do politeness” on this topic so maybe forewarned is forearmed.
Rob Sheldon is the author of Genesis: The Long Ascent and The Long Ascent, Volume II.
See also: Larry Moran to write new book: Claims genome is 90% junk If he wants to pick a fight with ENCODE, grab a seat.
With all due respect to physicist Robert Sheldon, given that we have just been discussing how much weight should be given to the opinions of experts on matters outside their own field of expertise, might it not be more appropriate to consider the reflections of biochemist Laurence Moran on the meaning of the word “function” in the context of the human genome? He has after all written a sequence of lengthy posts on this very subject on his blog Sandwalk under the heading of “The Function Wars”. For example:
Of note to ‘functionality, and as I cited on the other thread this morning,
On the spliceosome, does anyone have a link explaining how the spliceosome knows how to cut a pre-mRNA strand into mRNA? Presumably, it needs some sort of marker on the pre-mRNA, but I don’t haven’t seen anything written about this.
Not sure what value there is in asking someone without a highschool level of understanding about biology to share their opinion about a biological question. Start codons have nothing to do with DNA polymerase, and DNApol isn’t involved in gene expression. It’s also bizarry to imagine people using crispr shortly after the publication of the human genome
Not sure what value there is in asking someone without a highschool level of understanding about biology to share their opinion about a biological question. Start codons have nothing to do with DNA polymerase, and DNApol isn’t involved in gene expression. It’s also bizarry to imagine people using crispr shortly after the publication of the human genome
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Yep, lug nuts don’t have anything to do with tires either. I can spot, all the way across the room, that the writer very likely meant “RNA” polymerase. And no one in biology has ever made that mistake, writing DNA when they meant RNA, or vice versa.
But while you are gracing us with your presence, can you answer a question: when the first ever aaRS was synthesized from memory, how many of the other aaRS had to be in place? Some fellas down at the bar were asking.
Well, even if he meant RNApol (maybe), there is still the issue that start codons aren’t associated with transcription start sites (apart from being relatively nearby). The whole text is full of equally horrible confusions.
I’m not really very interested in the origin of life questions like the first aaRS, and given our last conversation served to be a massive waste of time I’m even less interested in this one.
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Yes, cutting and running seems to be your best move.
cutting and running from what, exactly. You asked a wildly off-topic question about something that doesn’t interest me very much.
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Hi Ortho,
Firstly your opening comment on this thread was opportunistic and unnecessarily condescending. Secondly, this is not the first time you’ve appeared on this board with a razor and an attitude. And when you get called out on the things you say, your pattern is to become suddenly disinterested and far too busy polishing your smugness to respond. I suppose that’s all fine, but you shouldn’t expect a free pass — not when you are being unnecessarily aggressive, nor when you are being unnecessarily aggressive and simultaneously misinformed.
lol “fluxes across time”, that’s a good one.
UBP
Ok, that was brilliant and hilarious … reading that I literally LOL.
You might want to read the actual thread, with non clipped comments: https://uncommondescent.com/intelligent-design/stunning-levels-of-ignorance-regarding-the-genetic-code
The topic was Barry’s ignorance of the genetic code, UB tried to salvage something but never made a clear statement of what he was trying to say or why it matters. Not a very useful way to spend time, so I asked him to make a clear statement instead of asking leading questions.
You might want to read the actual thread, with non clipped comments: https://uncommondescent.com/intelligent-design/stunning-levels-of-ignorance-regarding-the-genetic-code
The topic was Barry’s ignorance of the genetic code, UB tried to salvage something but never made a clear statement of what he was trying to say or why it matters. Not a very useful way to spend time, so I asked him to make a clear statement instead of asking leading questions.
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I second that motion. Read it.
Ortho
Thanks. I read the entire thing. I’m surprised you referred me to it. You and Ed George repeated the single argument (paraphrasing) “the entire process is determined by chemical properties and reactions”. Barry, Upright BiPed and ET attempted to explain why this is not the case. I think every IDist here on UD could see how you had entirely missed the point and had no response to it. To me it is crystal clear and blatantly obvious.
But maybe you don’t understand or see what the argument against you was saying. I find that hard to accept because you didn’t ask any questions about the details of what was presented. Again and again, arguments and evidence were provided, but there was no engagement, no buy-in from you guys. You just fell back on the one argument: “all chemicals”.
After a while, as UBP explained more and more, you stopped asking about what he meant. If you needed clarification, why not explain what you didn’t understand, or how much of it you did understand? But then you and Ed George just became quiet – holding to the same argument “it’s all just chemical properties and reactions”.
Again, being charitable, most the IDists here have seen this argument many times so for us it puts a radiant spotlight on the major problem of the materialist story — but someone new to the concept might not understand the terminology or what, precisely it is pointing to.
The fact that you directed me to read the thread tells me that. So perhaps if you work in the field of biology (as it seems), all of your intellectual work is done from some starting assumptions, and from that you just analyze what is seen, using those rules and concepts. You wouldn’t normally question the rules of your work – you just accept what is there. Plus, you wouldn’t look at the deeper problems that are with regard to the origin of such processes (that’s what ID looks at – how could they evolve). You just accept that “they evolved and here they are”. But we’re asking for some evidence on how a discontinuous process of code-sender-translation-receiver resulting in variable, specified functions can be the product of modifications over time, or even of blind, unintelligent matter and regularities (chemical properties and reactions).
Maybe it’s just the level of study in a field making it hard to see outside of those assumptions.
It’s like a guy who works a printing press – all day long, analyzing the quality, improving flow, darkness of print, duration of paper, speed, cost.
Then someone says “you know, I really wonder how Shakespeare could produce such beautiful poetry and incredible literature”.
The guy says “Duh. He had a good pen, ink and some paper. What do you think?”
No, we’re talking about what he wrote. The vocabulary, rhythm, diction, clarity of images, his influences, surprising plot twists, unity of theme, characterization, historical accuracy, how he connected one theme to another, sub-texts, hidden references.
The guy: “Like I said! When the ink goes on the paper, it makes very dark marks and it stays there. The paper is light, the ink is dark. The pen distributes the ink. His hand moved it. 100% of what he did is just that. What do you think it’s some kind of non-ink and paper magic?”
If you’re looking just at one thing all the time – if that’s your work, I can understand how you would see the answer to those questions in that light. The idea that it’s the creative intelligence that generates the work would be lost to a person in that situation.
I don’t know – again, I’m trying to be charitable. You think your view was vindicated on that thread so both sides are talking past each other.
I can only repeat my first comment in that thread, do you understand what is meant by “genetic code”?
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(My earlier comment somehow appeared on the wrong thread. I repeat it here)
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Ortho is certainly not the first person on UD to state explicitly (or imply) that the gene system is the product of pure chemistry. My issue with Ortho on that particular thread (which originated from a heated exchange between two other participants) is that he claimed, more than once, that the next amino acid bound to a nascent polypeptide is determined by dynamic forces of base pair complementarity. That is flatly incorrect (i.e. it is determined by the physical properties of the aaRS). He begrudgingly conceded that point, then quickly punted away any value to the observation. He asked me why I thought it was important and I gave him the answer – among other things, it helped confirm (along with many other observations) the prediction of a symbol system as the fundamental requirement of the gene system.
He had no further comments.
It appears to me that ortho is making the case that how a car functions is entirely determined by the physical properties of the car, and UB is arguing that the functional qualities of the car cannot be reduced to the properties of the materials of the car.
ortho
I wouldn’t call that a substantive response to questions posed to you on that entire thread as well as the discussion here. But that you “can only repeat” – yes, we have discovered that.
The thread is about (Barry’s ignorance of) the genetic code. Your post isn’t about the genetic code and UB took tens of posts to present a distinction without a difference about one detail of the code.
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As the genuine semiotic system that the gene system was predicted (and experimentally confirmed) to be, each object specified by the system requires one material object to serve as a rate-independent symbol vehicle, and second object (a non-integrable constraint) to establish what is being specified … correct?
This is the point where you get to deny recorded science and history. Let us watch.
The genetic code is a set of rules involved in the transcription of DNA into mRNA (via RNA polymerase) and the subsequent translation of the processed mRNA into a polypeptide, ie a sequence of amino acids. mRNAs REPRESENT amino acids. That is what makes it a code- the symbolic representation of of one thing for another.
There isn’t anything in physics or chemistry that determined the pairings. Just because purely physical and chemical processes are used to carry it out doesn’t mean the genetic code is reducible to those processes.
What are you talking about? What “level” of biology when scientists thought that coding proteins (2 -3 % of total) DNA are functional and enough for life . They tought ink and paper is enough to appear a Shakespeare ‘s book or bricks and cement are enough for building a Cathedral. On the contrary without the mind of the playwright or the mind of the architect ink ,paper and bricks will remain unchanged. What level and quantity of information do you need to make paper or ink ? Not to much compared with “magical” combination of ink and paper made by Shackespeare. And no Shakespeare didn’t put a piece of paper and ink in a box and then shaked de box to obtain a book .
Hi UB
I sent you an email, not sure if you still monitor that inbox. It didn’t bounce back so it seems to be functioning.
Eugene S
As to this thread, what the ID critics here need to see is the Dunning-Krueger curve of how confidence depends on experience. Currently they are sitting on top of Mt Stupid that zero experience coupled with highest confidence is characteristic of. If they really want to engage though, what follows is a dramatic drop of confidence as real experience gets accumulated (the so called Valley of Dispair), and finally the long and steady ascent on the Slope of Enlightenment, as an internet critic painfully turns into a real expert. It takes one years to undergo all these changes. As of now though, they are looking down on us off the top of Mt Stupid.