But this misses Tour’s challenge entirely, which was to start with all the components of an actual cell, assemble it, and have it work. So all the biomolecules were from a cell, and presumably needed or neutral, and describing a process of evolving the interactome does not address the challenge.
Your’re pathetic.
BTW, I actually did correspond with Jack Szostak about another incident where Tour misrepresented his work. He stated that he had better things to do with his time than respond, especially since people like Tour are not actually interested in evidence.
You are more than welcome to contact Szostak himself if you are that interested.
Beyond pathetic.
If someone hits a double, and you say they didn’t hit a home run so they might as well have struck out, you are very stupid.
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The question being considered is if the number of potential interactions (most of which will never occur, typically because they’re thermodynamically unfavored) is at all relevant or informative with respect to the origin of life.
As a purely theoretical exercise in mental masturbation you are of course allowed to calculate anything you want, but what is clear is that the sheer number of potential interactions in some complex system tells us nothing about how the cells first evolved, or how likely it was/is.
Tour invoking Levinthal’s paradox (and other similarly useless estimates) simply betrays his vast confusions. Remember, Levinthal’s paradox is a thought-experiment that is supposed to tell us that protein’s can’t fold by exhaustively searching the total conformational space of amino acid sequences. In conclusion: they must fold some other way.
Similarly, the number of potential interactions is a meaningless number. They never occur and don’t have to occur, and it isn’t a physically real quantity that has to be designed, evolved, searched, or otherwise. It’s a useless number.
It looks like just another attempt to try to use big number technobabble to leave the impression for gullible laypeople that “the odds are low.” But when we look close at the calculation we see it is completely uninformative to the processes that are hypothesized to give rise to the first cells.
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ATP provides energy when it is hydrolyzed to AMP + PPi (ATP + H2O → AMP + PPi). The phosphoanhydride bond being broken is a hydrolysis reaction, in that it consumes a molecule of water.
This is true for RNA polymerase catalyzing the elongation reaction just as it is true for other enzymes that depend on ATP (such as ATP synthetase). Either way, it’s a hydrolysis reaction of a phosphoanhydride bond.
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Who gives a crap about this meaningless challenge that has nothing to do with how anyone thinks the fist cells might have arisen?
Nobody postulates that the individual components of a cell were individually synthesized and then later assembled in some big assembly event. No matter how difficult such a process might appear for human beings it bears no relation to any postulated model of the origin of life.
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They are basically unavoidable.
Here’s how we know that functional “interactomes” aren’t unlikely at all. We can move genes around from different species and show they function perfectly well, and even in cases where they have deleterious effects they’re often small and can easily be alleviated by mutation.
Take the example of Green Fluorescent Protein (GFP), a protein that first evolved in bioluminescent jellyfish on the bottom of the ocean. Prior to their first isolation by human biochemists, these proteins have never encountered the internal biochemistry of mammals such as humans. Their potential molecule-to-molecule interactions are staggering. Yet researchers have found they are ubiquitously well-tolerated in innumerable species, from bacteria, through yeast and other fungi, to countless cell lines and even several model organisms and pets, such as mice, zebrafish, fruit flies, nematodes, rats, pigs, primates, even genetically modified aquarium “glowfish” you can buy and have them swim around and look pretty as they glow green under a blue light.
That’s just GFP. Many thousands of other proteins (and genes functioning in ways other than as protein coding) are routinely used and inserted in countless other organisms in both medical, genetic, and molecular biology laboratories all over the world.
Now consider the reality that innumerable organisms have mechanisms explicitly functioning to facilitate horizontal gene transfer. Bacteria will routinely attempt to take up foreign genetic material and either express it from plasmids, or some times even incorporate it into their own chromosomes. If foreign, never before encountered genes were overwhelmingly likely to cause disruption this could not be a viable survival strategy for bacteria.
Heck, you could meaningfully argue that this includes the very mechanisms responsible for fertilization, and the ensuing meiosis, during sexual reproduction. When two gametes fuse, the genetic material is transferred from one cell into another, and since this new genetic material is different from that already present (it would have to be or there would be no reason to bother with sex in the first place), the tolerance to novel genetic architecture must be likely enough for this to be a viable strategy. That is not to say there is never any compatibility problems, just that the frequency of it being tolerated simply isn’t a vanishingly small probability at all.
Basically all of cell and molecular biology testifies to the falsity of your intuition. It is not only baseless, everything we know tells us it is false and the diametrically opposite. It is rather highly likely that novel molecules have little to no effect, and might even frequently be beneficial.
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Yes, you were. The context is your utter failure to defend Axe’s use of a binary assay.
No, you weren’t:
There.
Your use of “know” here is conclusive. You claimed that they used a binary variable to make a binary decision. The challenge you are running away from is to provide a case of that.
Why didn’t Axe do that?
We all know that you don’t understand basic molecular biology or biochemistry, yet you repeatedly make false claims about both.
Wherever ATP provides energy.
No, it’s not “like a nucleotide.” It’s a nucleoside TRIPHOSPHATE. They’re often called nucleotide triphosphates, but that’s like saying “ATM machine” or “HIV virus.”
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Which is just plain silly. Here’s an example of real OOL research:
I’ll take that as a “no”.
Well, Tour reads their papers, and points out problems. So he examining evidence. A response to his challenge, that would also be evidence, no response was given, that also is evidence that they can’t meet the challenge. And all you people here need to do, is show how OOL research has advanced substantially! That would be evidence, and then let’s inform Tour, he even responds to YouTube “Professor Dave”, so he’s not withdrawing, and no doubt would be interested in real evidence that his claims are false.
But the claim was that the home run was done! Can you not see this?
We’ll get to that …
It’s generally not possible to predict everything that might happen. That’s why experiements are conducted to observe what happens.
I’m assuming the “parts” inserted function more or less as they are intended to. Tour seems to think the parts will somehow interfere with each other, and so require further regulation (an Interactome). You agree? (Yes, I think?) According to the usual ID claim that such interactions are very rare, so Tour’s objection is unlikely to be a problem.
About the contradiction: My position is that interactions are relatively common but the effects are usually weak, not needing immediate regulation. Even if we limit the number of alleles that can interact to some reasonable number *N, there are 2^N potential interactions, and that still a very big number. Even if such function is rare, it’s mathematically unavoidable that some interactions will occur, creating potential new functions. This is the source material for natural selection.
So I ask again, is new function so very rare that new function cannot arise, or is Tour correct and new function is so common that it will prevent new cells from being assemble from “parts”?
I understand you position on “rare”, but not “diseased”, which just seems off-topic. Disease implies some impairment to normal function, which is irrelevant to the question of creating a functional cell. You are again saying there might be some harmful interaction. Yes this is possible, but by your own beliefs this ought to be rare.
Also, if I assemble a parts from assorted bicycles and produce a 3-speed cruiser instead of an 18-speed touring bike, have I produced a “diseased” bicycle? Back on-topic …
Who says they aren’t? I work in a building that is full of researchers working to understand cell function and protein interactions, and they publish. This is a common activity at any institution doing basic research. So my answer is “yes”. I don’t understand why Tour says this, do you?
You might read up about about “Translational” research. Briefly, it’s an effort to streamline the pathway from basic “bench” science to new medical treatments. It’s barely credible that Tour is unaware of these efforts, even if he is retired from research.
How has this been accomplished?
Here’s an idea; let’s ask a biochemist!
A fine example. Scientists inserted a new gene and it produced the expected function, no additional fiddling about with an “Interactome” required. Were there other effect? Probably, but not so strong that the modified organism could not survive, or that the experiments were considered a failure.
Such examples are fast becoming ubiquitous. There are even approved medical treatments for “gene therapy” that are showing great promise. There is real potential here for negative side effects, which is why these efforts are carefully regulated, but this hasn’t brought progress to a screeching halt. Tour’s “Interactome” challenge seems to be a non-issue.
So Tour’s 5th challenge has easily been met. Shall we direct you to further examples?
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Please quote where someone claimed to have hit a home run. Metaphorically, of course.
NB: Some nutjob religious fanatic saying he heard someone somewhere say they had hit a home run does not count. Neither does the absence of someone denying that they had said they hit a home run.
TIA
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Oh, right. So, remind me: Exactly when did Doug Axe respond to this challenge, that was directed at him specifically?
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Man there are so many flat Earthers out there having trounched the globe conspiracy then. Gonna make your way to the icewall soon?
I already explained to Lee what Axe should have done if he had really wanted to do this experiment properly. Lee’s response basically amounted to “but that work would be more difficult.”
Consider that as an excuse for not doing the science properly. What, you expect me to cross all my t’s and dot all my i’s? But it would be hard you guys. C’mon.
I know. It’s worth mentioning that Axe did enzyme assays in his previous papers, but they had coauthors. I’m going to go out on a limb and speculate that Lee hasn’t even looked at them.
Who, precisely, constitutes “they,” and how would you possibly know if Tour has read their papers?
Hi everyone. I’ve been following this topic for its current 200-post life span and I’ve noticed we’ve hit a wall… one that, in my view, was reached almost immediately.
While the surface level has been a back-and-forth about biological facts and processes (with varying levels of graciousness), there appears to be a meta-level dynamic going on that renders all of that moot. Surely I can’t be the only one seeing this.
@lee_merrill , correct me if I’m wrong, but my impression is that biology is a field you have a lot of interest in. Throughout this thread, several users who are experts in various aspects of that field have clarified concepts you hadn’t previously fully understood. Given that, do you think it’s possible you might be mistaken in your assessment of James Tour or your own understanding of OoL research?
@ everyone else, your current responses don’t appear to be gaining any ground. I’m curious—what is the expected outcome of continuing to interact in this same pattern?
Edit: sorry, I did not mean to tag literally everyone 
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I enjoy the discussion. I have no expected outcome beyond that.
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And it’s not just this thread, it has been ongoing for ~20 years, and that’s just since I got involved. I first encountered Lee Merrill about 20 years ago too. 
I can say with some confidence that everyone participating enjoys this kind of exchange at some level. People keep coming back to these same discussions no matter how many times it has been done before. There are new developments on the science side, and learning about that science from others is interesting, even exciting. Explaining it to others is a good way to improve one’s own understanding too.
On the other side of things, there has been remarkable success in the dumbing-down of our culture and promoting a general distrust in science. The culture wars that started with debates over evolution have blossomed into widespread science denialism, with spillover into nationalism. The debate over evolution has never been about science; it’s about control and what people can be made to believe.
The dynamics of the discussion here reflect what is happing in the culture at large. People are disputing facts, even disputing (gaslighting) what were claimed to be challenges to the facts (ie: Tour’s challenges). The skills we have developed for these smaller debates have some trouble translating to the larger debates, but there are useful parallels. What I find most helpful is the ability to recognize when someone is baiting others into a fact-based discussion of a subjective topic.
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