Baloney. There’s no misunderstanding Tour’s false claim. Your paraphrasing is totally false and misleading.
More baloney. This was not in the peer-reviewed part of Nature.
How did YOU determine that it is not a ribonucleotide? And Tour did not allow for an oversight, assuming it isn’t one, did he?
This is pathetic.
Szostak did not lie.
Tour lied, repeatedly.
Period.
There is no other way to interpret that video.
There is no other way to take it, because why else would he mention it? He goes on to say that he himself could not get away with saying these things, and really hammers on the fact that this is in nature. His point clearly is that in the origin of life field nonsense you couldn’t get away with anywhere else, can be published in the primary literature, even in a journal as prestigious as nature.
This isn’t a willful misunderstanding, that seems to be his main point.
44:23 the pimary objection here is the word “nudge” which is ill-defined. Allowing this word in the journal Nature was a major oversight.
First of all, again with the journal nature. Why can’t the word “nudge” be used in a pop-sci article that ISN’T part of the primary literature? Speaking colloquially as one is bound to do in an article intended for a lay audience, to say that certain chemical reactions were “nudged” along is really just to say that some environmental factor drove them, as in catalyzed them or made them thermodynamically favorable. That could be UV light, other chemicals in solution, mineral surfaces, and many other things. There’s nothing unusual or problematic going on here that isn’t in some sense a problem with ALL scientific writings intended for a lay audience.
Tour’s claim seems to be that this is a particularly big problem in the origin of life field in a way or to an extend it is not a problem in other fields such as his own (synthetic organic chemistry), that things are published in the primary literature that is unusually egregious, but he doesn’t actually show this is the case.
44:47 “some stages of RNA production are still not well understood” This is misleading insofar as this is not
No, it isn’t. It’s completely correct in every way that sentence could be plausibly understood.
and there is not a disclaimer about combinatorial complexity.
There are a million things there are no disclaimers about, which is to be expected from a pop-sci article intended for a lay audience, as opposed to a 400 page doctoral dissertation in the philosophy and history of science on the origin of life. It simply can’t be expected to fully discuss every imaginable caveat, alternative, speculation, or assumption. Again, there is nothing unusual about this that makes this article stand out compared to millions of other types of science articles on other subjects, of a limited scope intended for a lay audience.
Here the “some stages” is basically all stages, and “not well understood” is not understood at all.
But that’s just wrong. RNA has in fact been synthesized in the lab, and the steps in those syntheses are understood to varying extends. It would be more correct to say that it isn’t actually known whether these synthetic pathways produced in the lab is how RNA actually first originated, but the article is actually totally upfront about the fact that there are origin of life researchers who disagree with the RNA-first proposals. The premise for the graphic is that IF RNA was involved already from the beginning, then these synthetic pathways may have been how it first came about.
In order for a process to get from stage x to stage x+1 some purification of the reaction products is an absolute requirement.
Is it? How do you know?
Without purification the individual reactions do not form a comprehensive chain
What is that, a “comprehensive chain”?
and thus calling them stages is 100% misleading.
Not really. Whether the process is continuous, or broken up into bits, the fact is that any one of these molecules is synthesized by multiple consecutive reactions, each of which can be considered a step. In the same way that the growth of a salt crystal atom by atom could be considered a long chain of “steps” by each atom added to the crystal.
The audience understands this, and that’s why they are laughing.
The audience is clueless and they’re laughing because James Tour is pushing their buttons by in part with body language and his tone of voice, and by tossing dog whistles at them they’ve been indoctrinated to expect by conservative religious upbringing for decades. Among them this rather insidious insinuation that there’s some academic conspiracy by “Darwinists” and atheists at universities engaged in some delusional pursuit of naturalistic explanations out of some combination of fear and hate of God, a final judgement, and because they’re self-deluding liberals who just want to sin bla bla bla bla look at what they’re publishing hahahah.
Don’t ask me to pretend to not understand what the hell is going on here.
45:19 By the time we get to the infamous slide there are already three major objections to the article.
Objections which are egregiously wrong and misleading.
45:59 So, basically, this could be a misunderstanding on dr. Tour’s part, being colorblind. Come to think of it, the graph does resemble the Ishihara test, so I wouldn’t exclude the possibility dr. Tour misunderstanding the graph, in which case YOU’re railing against Him because of a disability he has.
No, we are railing against him because the things he say are wrong and unreasonable. If Tour has a disability that causes him to make these mistakes, then Tour can simply admit that and retract his poor objections and accusations of lying, and all can be forgiven. We all make mistakes. But no, Tour isn’t being railed against merely for having a disability. He’s being railed against for putting on a circus of public confirmation bias and playing to an audience with egregious accusations of lying by origin of life researchers.
How charitable of you. He even says “maybe” a couple of times, which means that he is not 100% sure about this graph.
He’s sure enough to scream HE’S LYING TO YOU, apparently.
46:10 So already, the “he’s lying to you” has been taken out of context, and is irrelevant to the objection dr. Tour actually has with this graph.
Not even forking remotely, buddy.
The graph says that the reaction product is an RNA nucleotide, but the picture shown is not an RNA nucleotide. Could’ve been an oversight on the part of the illustrator.
Then what is it? What are we looking at? It looks to me like the RNA nucleotide Cytosine bound to phosphate through the two 2’ and 3’ -hydroxyl groups of Ribose. What does it look like to you?
But does phosphate ever bind to the 2’ and 3’ hydroxyl groups in that way?
Yes. This particular form of RNA (RNA 2′,3′-cyclic phosphate) has been known about since, apparently, 1952.
Interesting, and it seems that such cyclic ribonucletides are quite relevant in the OOL field. To quote the a 2017 paper:
Cyclic nucleotides have for long been considered as plausible building blocks for the synthesis of the first RNA oligomers.1, 2 Their strained intramolecular phosphodiester linkage accumulates chemical energy which can be utilized to drive transphosphorylation reactions leading to oligonucleotides.3 Recently, various plausible prebiotic pathways have been elaborated for their synthesis,4-6 among which the one based on formamide5, 7, 8 has been found to yield a mixture of both 2’,3’ and 3’,5’-linked cyclic forms.
So it seems that Szostak chose a pretty apt structure for his graphic, while Tour mocks him at 46:04 in the video for supposedly getting the structure wrong.
It’s almost as if Jack Szostak has decades of experience in molecular biology and genetics, is familiar with various nucleotide structures and their properties, and is using that knowledge in his research on the origin of life. ¯_(ツ)_/¯
You need to watch again. As I detailed nearly second by second, James Tour not only slandered Jack Szostak, but he also lied. The most obvious lies are claiming that the 2 1/2 page item was an example of “primary literature,” and that Szostak lied. His other lies could only be excused if James Tour is too senile to read the undergraduate course work.
I cited all this.
So I looked at your blog post one more time.
Here we see two interconnected 5-rings and a 6-ring in the same molecule.
My understanding of chemistry may be rudimentary, but I don’t see the two interconnected 5-rings. I see the 6-ring with the two nitrogen atoms at the right position, but instead of the two interconnected 5-rings I see a structure which I do not understand.
In the bolg post you also say that “It is directly and spontaneously formed in nature from the starting chemistry.” Does it form with the right chirality?
Again, a source of misunderstanding is perhaps at hand here. The sugars shown on the graph are neither monosaccharides, nor disaccharides. So it is a misunderstanding, but it also could be a willful misrepresentation on the part of dr. Tour. Perhaps instead of “simple sugars” the graph should’ve said “sugar precursors”.
Compare the slide to this schematic of cyclic cytidine monophosphate (cytosine plus a phosphate group):
It’s the same as your schematic apart from the additional phosphate structure at the bottom and the associated sodium ion.
Is
an RNA Nucleotide?
No, because only adenine, guanine, cytosine or uracil are legit RNA nucleotides. Cytidine is not cytosine. It’s the wrong structure.
Wrong. Adenine, Cytosine, Uracil, and Guanine are the nitrogenous bases of RNA, they are not nucleotides. A nucleotide is a nucleoside with phosphate attached. A nucleoside is the base attached to ribose on the 1’ carbon of the ribose ring.
Not nucleotides, but purine and pyrimidine bases:
Cytosine is an RNA base, it is not a nucleoTIDE. The whole structure with the base (in red) atached to ribose (together making the part circled in bright blue), with monophosphate attached to the 2’ and ‘3 carbons of the ribose ring(dark blue), is the “legit” RNA nucleotide called Cytidine-2’3’-cyclic monophosphate, and it actually does exist in living cells:
“Nucleotides are the building blocks of nucleic acids; they are composed of three subunit molecules: a nitrogenous base (also known as nucleobase), a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group.”
Cytosine is not a nucleotide, it is a base from which a nucleotide can be formed.
Cytidine is a nucleoside, i.e. a base plus ribose.
Cytidine monophosphate is a nucleotide, because it contains a base, a sugar and a phosphate group. Cytidine monophosphate is one of the nucleotides used in RNA.
Cyclic cytidine monophosphate is also a nucleotide. It is what you get if you break up RNA on the other side of the phosphate link, so that the phosphate group is attached to the 3’ carbon atom of the downstream ribose component rather than the 5’ carbon atom of the upstream ribose group. Molecules of cyclic cytidine monophosphate can combine to form RNA chains as shown below. Thus, while cyclic cytidine monophosphate is not the nucleotide which is usually involved in the formation of RNA, it is still an RNA nucleotide.
So cytosine is not an RNA nucleotide, but cyclic cytidine monophosphate is. The slide is correct, and you are completely wrong.
(Drat! Ninjaed by Rumraket!)
He can. But why should he be excused for not checking before he posted?
When people explain things, many learn. These discussions are public so that others can participate in the learning, even if they do not post. It is most important that people show up here to discuss, rather than showing up correct. And, furthermore, two of you responded simultaneously with the same answer. That’s some nice validation, right?
The second structural image left off the phosphate. The upper ring is cytosine, and the 4 carbon ring at the bottom is ribose. To see this in detail, including reaction steps and kinetics see;
“Prebiotic synthesis of simple sugars by photoredox systems chemistry” (Ritson, D. and Sutherland, J.D., 2012 Nature chemistry, 4(11), p.895).
Nice bit of graphics!
Can I use it with attribution to you?
