James Tour on carbohydrate synthesis

[TheLurch]

Well eventually you need to get to proteins. But I will grant you that the RNA world need not have proteins.

So, just to be clear on this, your first two suggestions for needs for carbohydrates on early cells, the cell wall and glycoproteins, would not have existed in early life.

Yet you feel confident you understand biology better than actual scientists. What would ever cause you to revisit that conclusion if this sort of thing doesn't?

No, he didn't mention that, but why are OOL researchers attempting to create sugars if there is this easier route available?

Will you admit that not including that information is misleading?

In any case, the results i mentioned are only about five years old. Prior to that, people had thought you needed to synthesize the two separately, and had worked on sugars as a separate challenge. Maybe some people still find it interesting, but there's also an issue of labs not shutting down projects immediately because people have to wrap up their thesis projects, etc., so there are probably still papers on the subject being published.

I'm not plugged in to that field, so i don't know the details.

In any case, Tour posted those in 2021, so he's got no excuse not to know.

How about here?

Source: Wikipedia

Glycolipids are lipids with a carbohydrate attached by a glycosidic (covalent) bond.^[1] Their role is to maintain the stability of the cell membrane and to facilitate cellular recognition, which is crucial to the immune response and in the connections that allow cells to connect to one another to form tissues.

Source

© Copyright Original Source

Maintaining the stability of the membrane would seem to be a critical need.

Not necessarily! But more on that in a moment.

First, i want to note that the wikipedia entry doesn't cite anything on stability, and none of the examples of their function have anything to do with membrane stability. I've also tried to search the literature for this function, but not come up with anything. The only things i find are about the stability of the cell wall of bacteria. So, i'm not sure where that comes from.

Assuming it's accurate, however, this may be a feature and not a bug. The first cells lacked the sophisticated proteins that control which molecules cross the membrane, and lacked the machinery that allows cells to divide. So, to a certain extent, they relied on the membranes being meta-stable. Jack Szostak, who does a lot of origin of life work, has developed systems where membranes spontaneously form (encapsulating RNAs), incorporate more lipids, and then spontaneously divide when the system is jostled a bit.



As a general note: i expect Lee to quote the bit about membrane stability, and ignore the two questions I've asked above, or dismiss them as ad hominem or something similar. But these are precisely the sorts of questions all of us need to be asking constantly. Are the sources i'm using reliable? Might i not understand this subject as well as i thought i did? etc. It's essential that we all constantly take a critical look at our own arguments and beliefs; widespread failure to do so is why we have crazy stuff like Bill Gates putting microchips in vaccines and 5G causing the 'rona circulating everywhere.

Lee has shown no indication that he's capable of that sort of self-evaluation, so i worry about him.

[HMS_Beagle]

Spoiler: it's really hard...

James Tour goes into how hard it is to get just D-ribose synthesized in early earth conditions, a dozen steps or more, and you just get racemic ribose at about 6% yield. Then you need to stop the reaction, otherwise it all degrades in a couple of years (a blink of an eye in abiogenesis). Then you need to purify it, then you need to hook them together (there's a huge number of ways to hook them together, and only one of them is the desired product).

James Tour is a religious fanatic who gave up his scientific integrity to proselytize for his religion. A few years back he hooked up with the professional liars of the Discovery Institute to make his "abiogenesis is impossible so therefore GAWDDIDIT!!" videos. Tour is making a complete laughingstock of himself in the scientific community.

[rogue06]

James Tour is a religious fanatic who gave up his scientific integrity to proselytize for his religion. A few years back he hooked up with the professional liars of the Discovery Institute to make his "abiogenesis is impossible so therefore GAWDDIDIT!!" videos. Tour is making a complete laughingstock of himself in the scientific community.

That Tour is still a credible scientist is attested by the fact that just last year (2020) he was awarded the Royal Society of Chemistry's Centenary Prize^[1] for innovations in materials chemistry with applications in medicine and nanotechnology. I've seen where he was also made a Fellow of the Royal Society of Chemistry but don't see his name mentioned here (although I may be looking in the wrong place).

If nothing else, Tour, who is also a signer of A Scientific Dissent From Darwinism, pretty much serves to repudiate the "Expelled" persecution myth propagated by organizations and people affiliated with the Discovery Institute.

And while he may indeed be a first rate synthetic organic chemist and nanotechnologist, it appears that he is one of those who's brilliance appears to be narrowly focused. The moment he steps outside his niche is when he starts getting himself into trouble.

For instance, he created a kerfuffle a few years ago when he erroneously declared that "there is not a scientist living today that understands macroevolution" (a declaration he made after asking a handful of his chemist colleagues to do so. Given that he was asking fellow chemists rather than biologists, zoologists or geneticists, it isn't surprising he didn't get the answers he sought.

IOW, you don't go to a, say, geologist for an explanation of relativity, you go to a physicist. Likewise if you want to know about the makeup of a range of mountains you wouldn't go to a sociologist, now would be the right time to ask a geologist. And just because your auto mechanic knows a lot about pumps, he shouldn't be your source for cardiac information.

Further, given that his questions revealed that he was actually talking about the origin of life and not macroevolution (which is incredibly easy to explain) it isn't surprising that several of those who he asked just gave him, as he claimed, blank looks and didn't respond.

In any case, evolutionary biologist Dr. Nick Matzke, who played a critical role in the plaintiff's case in the Kitzmiller trial, offered to fly to St. Louis and explain macroevolution to Tour, who initially accepted but later backed out, saying he wanted it to be informal and not recorded. I described what happened in a post from nearly a year ago

In 2013, the website/blog "Uncommon Descent," which describes its purpose as "Serving The Intelligent Design Community" (created by William Dembski who lost interest in it -- though it still serves as his primary platform for making announcements -- and then taken over by Denyse O'Leary) made a big fuss over it: Professor James Tour Accepts Nick Matzke's Offer To Explain Macroevolution.

After going on about it for awhile they finally mention Tour's condition that had not been in the initial offer:

... on one condition!

There's just one condition that Professor Tour attached to the meeting, however. In his email to me, he stated: "It shall not be recorded or extend beyond the three of us as this is not for show but for my edification."

[*bolding and coloring in original*]

O'Leary then takes responsibility for failing to mention "his wish that the meeting be recorded" although she admits that her email to him did contain a link to where this was mentioned. She excused his failure to check it out saying he's "a busy man" so he didn't bother to look at it.

In any case, this was an odd condition given that he has shown that he has no trouble engaging in public debates which are recorded and shown online.

1. annually by the United Kingdom-based Royal Society of Chemistry (RSC) to up to three "outstanding chemists, who are also exceptional communicators, from overseas".

[lee_merrill]

So, just to be clear on this, your first two suggestions for needs for carbohydrates on early cells, the cell wall and glycoproteins, would not have existed in early life.

Yet you feel confident you understand biology better than actual scientists. What would ever cause you to revisit that conclusion if this sort of thing doesn't?

No, I'm learning, and I'm trying out Tour's points here.

Will you admit that not including that information is misleading?

Well, here is an article from 2020 that talks about synthesis of sugars. So it appears that OOL researches still think you need to make them.

First, i want to note that the wikipedia entry doesn't cite anything on stability, and none of the examples of their function have anything to do with membrane stability. I've also tried to search the literature for this function, but not come up with anything. The only things i find are about the stability of the cell wall of bacteria. So, i'm not sure where that comes from.

Here is another reference to stability:

Source: Reference

A glycolipid's carbohydrate structure depends on the glycolsyltransferases that bring in the lipids and glycosylhydrolases which change the glycan after they appear. Glycolipids reach from the phospholipids all the way to the aqueous area outside the membrane of the cell, and at that point, they serve as recognition points for particular chemicals while also maintaining the integrity of the cell membrane and connecting cells in order to create tissues.

Source

© Copyright Original Source

Jack Szostak, who does a lot of origin of life work, has developed systems where membranes spontaneously form (encapsulating RNAs), incorporate more lipids, and then spontaneously divide when the system is jostled a bit.

But those are artificial cells, not live ones. I expect they're talking about stability because cells need more stability than lipids provide.

Lee has shown no indication that he's capable of that sort of self-evaluation, so i worry about him.

As I have said before, I believed Behe had been refuted, by reading Ken Miller's book. I changed my mind about Ken Miller as a source, after reading Behe's book.

Blessings,
Lee

[shunyadragon]

No, I'm learning, and I'm trying out Tour's points here.


Well, here is an article from 2020 that talks about synthesis of sugars. So it appears that OOL researches still think you need to make them.


Here is another reference to stability:

Source: Reference

A glycolipid's carbohydrate structure depends on the glycolsyltransferases that bring in the lipids and glycosylhydrolases which change the glycan after they appear. Glycolipids reach from the phospholipids all the way to the aqueous area outside the membrane of the cell, and at that point, they serve as recognition points for particular chemicals while also maintaining the integrity of the cell membrane and connecting cells in order to create tissues.

Source

© Copyright Original Source

But those are artificial cells, not live ones. I expect they're talking about stability because cells need more stability than lipids provide.


As I have said before, I believed Behe had been refuted, by reading Ken Miller's book. I changed my mind about Ken Miller as a source, after reading Behe's book.

Blessings,
Lee

Tour needs to devote research on 'how things are done' in nature like in real science, and not convoluted Creationist arguments on speculation as to how things cannot be done, which in Methodological Naturalism is trying to prove the negative.

The Lurch addressed this and it went over your head.

[TheLurch]

No, I'm learning, and I'm trying out Tour's points here.

But why can't you think instead of just trying it out? These things shouldn't be hard to reason through, but you don't seem to bother, instead you wait for someone else to tell you they make no sense whatsoever.

Why are you so averse to thinking first? Because by making us do all the thinking for you, it sends us the message that you are incapable of thinking for yourself.

Well, here is an article from 2020 that talks about synthesis of sugars. So it appears that OOL researches still think you need to make them.

One, i just explained why you'd expect to still see some papers coming out on that. Do you even read?
Two, even if that weren't the explanation here, there's a huge difference between "it would be interesting to see if we could make these" and "these need to be made". You've leapt straight to the second without any justification whatsoever.

Here is another reference to stability:

Source: Reference

A glycolipid's carbohydrate structure depends on the glycolsyltransferases that bring in the lipids and glycosylhydrolases which change the glycan after they appear. Glycolipids reach from the phospholipids all the way to the aqueous area outside the membrane of the cell, and at that point, they serve as recognition points for particular chemicals while also maintaining the integrity of the cell membrane and connecting cells in order to create tissues.

Source

© Copyright Original Source

Again, it's a reference without any indication of why they're needed, and no call back to the actual literature showing they are.

They very well may help with stability. It's not at all clear how strong or extensive the evidence for that is, and whether it means necessary or helpful. And, until we know that, it's hard to make any definitive arguments here.

But those are artificial cells, not live ones. I expect they're talking about stability because cells need more stability than lipids provide.

Why do you expect that other than it's convenient for what you want to believe?

In any case, you've completely ignored my explanation of why a degree of instability is probably necessary. Reading: try it.

[lee_merrill]

But why can't you think instead of just trying it out?

I do think about these themes, and it strengthens my faith.

Again, it's a reference without any indication of why they're needed, and no call back to the actual literature showing they are.

Here is a quote which appears to have a reference:

Source: Physics

Glycolipids are components of cellular membranes comprised of a hydrophobic lipid tail and one or more hydrophilic sugar groups linked by a glycosidic bond. Generally, glycolipids are found on the outer leaflet of cellular membranes where it plays not only a structural role to maintain membrane stability but also facilitates cell-cell communication acting as receptors, anchors for proteins and regulators of signal transduction [1].

[1] "Glycolipids". Nature. Nature Publishing Group. Retrieved May 2016

Source

© Copyright Original Source

In any case, you've completely ignored my explanation of why a degree of instability is probably necessary. Reading: try it.

No, I said these are non-living cells, living cells may require more stability, to be able to resist shaking.

Blessings,
Lee

[TheLurch]

I do think about these themes, and it strengthens my faith.

I meant thinking about the science, so you avoid things like suggesting that glycoproteins are needed in an RNA world.

Why do you not think enough to avoid basic scientific mistakes?

Here is a quote which appears to have a reference:

Source: Physics

Glycolipids are components of cellular membranes comprised of a hydrophobic lipid tail and one or more hydrophilic sugar groups linked by a glycosidic bond. Generally, glycolipids are found on the outer leaflet of cellular membranes where it plays not only a structural role to maintain membrane stability but also facilitates cell-cell communication acting as receptors, anchors for proteins and regulators of signal transduction [1].

[1] "Glycolipids". Nature. Nature Publishing Group. Retrieved May 2016

Source

© Copyright Original Source

It might be, if it were a reference that made any sense. But it looks like it's referring to a book, except it assigns the publisher to Nature Publishing Group, which publishes scientific journals and not (as far as I'm aware) books. Searching for it brings up nothing.

I do note that the article that cites it has an entire section on glycolipid functions, and none of them include membrane stabilization.

No, I said these are non-living cells, living cells may require more stability, to be able to resist shaking.

No, you're talking about the example i provided. I said "explanation", which is the part where i described why you might need membranes to be less stable than they are in present day living things. The part that you haven't addressed at all.

[shunyadragon]

I meant thinking about the science, so you avoid things like suggesting that glycoproteins are needed in an RNA world.

Why do you not think enough to avoid basic scientific mistakes?


It might be, if it were a reference that made any sense. But it looks like it's referring to a book, except it assigns the publisher to Nature Publishing Group, which publishes scientific journals and not (as far as I'm aware) books. Searching for it brings up nothing.

I do note that the article that cites it has an entire section on glycolipid functions, and none of them include membrane stabilization.


No, you're talking about the example i provided. I said "explanation", which is the part where i described why you might need membranes to be less stable than they are in present day living things. The part that you haven't addressed at all.

I believe the problem is 'Lee's shotgun approach' of quote mining without context to the issue at hand, nor knowledge of hat he is citing.

[lee_merrill]

I meant thinking about the science, so you avoid things like suggesting that glycoproteins are needed in an RNA world.

Well, when you can convince me that you have a living cell in the RNA world, I will believe you.

I do note that the article that cites it has an entire section on glycolipid functions, and none of them include membrane stabilization.

But I find source after source that does mention membrane stability, I would think that would be sufficient.

I said "explanation", which is the part where i described why you might need membranes to be less stable than they are in present day living things. The part that you haven't addressed at all.

I did address this, saying that real cells might need more stability to not divide on Szostak's shaking.

Blessings,
Lee

[TheLurch]

Well, when you can convince me that you have a living cell in the RNA world, I will believe you.

Are you trying to suggest that living cells didn't get started until after we had DNA and proteins as well?

But I find source after source that does mention membrane stability, I would think that would be sufficient.

Sufficient for what? We're trying to understand what happens to membranes without them. We know membranes can form and be stable for extended periods of time without them, so it's not a matter of "can membranes exist without glycolipods?" We know they can. The question is one of what glycolipids actually do for stability, and whether that would be advantageous or disadvantageous for early cells.

So, linking to vague statements like this more than once doesn't advance the discussion at all.

I did address this, saying that real cells might need more stability to not divide on Szostak's shaking.

Nope. That doesn't actually address the main point at all.

The main point was that a certain amount of instability is probably necessary when you lack the elaborate systems needed for nutrient import and cell division. Szostak's demos are just an example of what lower stability membranes can accomplish. But it is illustrative of just one aspect of the larger issue, which you're not seemingly even registered.

[lee_merrill]

Are you trying to suggest that living cells didn't get started until after we had DNA and proteins as well?

No, I said in the RNA world.

The main point was that a certain amount of instability is probably necessary when you lack the elaborate systems needed for nutrient import and cell division.

Well, here, what we know exist are modern cells, if you're going to base an argument on protocells, then they need to be more plausible. Are you proposing that cell rupture is good for nutrient import?

Blessings,
Lee

[TheLurch]

No, I said in the RNA world.

I'm not following this. I think the RNA world hypothesis is a bit agnostic about whether it overlapped with the existence of cells or not. I'm struggling to understand what point you're trying to make regarding it.

Well, here, what we know exist are modern cells, if you're going to base an argument on protocells, then they need to be more plausible. Are you proposing that cell rupture is good for nutrient import?

More plausible than what? I haven't specified anything about the proto cells, other than that they likely lacked sophisticated modern functionalities.

[lee_merrill]

I'm not following this. I think the RNA world hypothesis is a bit agnostic about whether it overlapped with the existence of cells or not. I'm struggling to understand what point you're trying to make regarding it.

Well, I'm focused on what I believe James Tour is focused on, the first living cell. It seems you were taking this tack too, in your mention of Szostak's experiment.

More plausible than what? I haven't specified anything about the proto cells, other than that they likely lacked sophisticated modern functionalities.

More plausible that Szostak's protocells, for instance. How do you deduce that protocells probably lacked modern functionality? An alternative must be given for getting nutrients (carbohydrates?) into the cell, for example.

Blessings,
Lee

[TheLurch]

Well, I'm focused on what I believe James Tour is focused on, the first living cell. It seems you were taking this tack too, in your mention of Szostak's experiment.

Go up to the top of the page, and read the title of your own thread. And tell me again what Tour is focused on.

It's disappointing that you don't pay attention to my arguments. But it's absolutely mystifying how often you fail to pay attention to your own.

More plausible that Szostak's protocells, for instance. How do you deduce that protocells probably lacked modern functionality? An alternative must be given for getting nutrients (carbohydrates?) into the cell, for example.

Exactly the issue. Without a membrane, there's no selection for transporters, so you wouldn't evolve them. Form a robust, modern membrane, and not a lot gets across it unless it's very hydrophobic.

The obvious alternative is a less robust membrane that provides some separation from the outside world, but isn't so rigid that no materials get in and out unless they're very hydrophobic. Is this sort of thing plausible? Szostak's work shows that it most definitely is.