Sunday, July 28, 2019

James Tour lies again, 3'



More James Tour

Following my chat with Bill Ludlow, and the resulting creationist spams of pain and outrage, I was going to next post on James Tour's lame whine about "homochiral" everything. But, this seems to be a more obvious next step.

In James Tour’s “letter to John West” where he tried to deflect his many lies and slanders, Tour flatteringly wrote;

“The superb work by Professor Sutherland shows the enormous intellectual prowess of some of the top synthetic chemists in the world, restricting themselves to the reagents that might be found on a prebiotic earth, and yet cleverly making some key intermediates and then finally to a racemic nucleotide. That intellectual effort is something that a mindless prebiotic earth would be lacking. Sutherland and his team should be commended for first rate synthetic work. I wish I were as good a synthetic chemist as is John Sutherland.”

We will see this is a 180 degree spin from Tour’s Disco’tute lie fest to 1,000 Baptist preachers.
Just after James Tour lied about, and slandered Nobelist Jack Szostak, he trash talked Cambridge University Professor John Sutherland.

46:54, Slide: Patel, B.H., Percivalle, C., Ritson, D.J., Duffy, C.D. and Sutherland, J.D., 2015. Common origins of RNA, protein and lipid precursors ina cyanosulfidic protometabolism. Nature chemistry, 7(4), p. 301.


Tour's Commentary on his Lie Fest;
47:27
“He makes a little bit of it, and it is a bunch of junk.” “Then he says, we’ll just use synthetic organic techniques – real techniques – to make more – just to simplify handling procedures.”
47:37
“Come on, because you could only make a like a fraction of it and you wanted to carry it on but it was just a bunch of junk. It was just a peak in ah … “
47:46
It’s not real. And even with all your synthetic prowess … And these are just for intermediaries, not even the real compounds. (Next Slide) 

47:54 New Slide
48:54 New Slide
49:07 New slide

Tour posts a slide supposedly with Patel et al quoted on the slide, and follows “Then he (Sutherland) even goes so far as to say, “All the cellular subsystems could have arisen simultaneously through common chemistry.”

49:15
That is crazy! Man! I’ll tell you, if you work in the area of nanotechnology you try to build systems, you take molecules to build into a system that functioned. He (Sutherland) says they, “could have arisen simultaneously through common chemistry?”

49:30
"That is a lie! And it is accepted in the best of journals! This is crazy!"

All he made was a couple of precursors and he is going into the assembly of all substance – Show me! If it could have happened, show me? He’ll never show you.”

So, James Tour keeps on lying even about how he lies. In his effort to save face from lying about Harvard Professor Jack Szostak, he lies about how he similarly treated Cambridge University Professor John Sutherland.



James Tour also has claimed to be an expert on the work of John Sutherland and sugars;  

“A professor of psychiatry from a Canadian university even wrote to me last week saying that I was wrong in my Dallas lecture since Sutherland has shown that those simple compounds can lead to the nucleotides, and accusing me of not being familiar with a 2012 paper by Sutherland.  Little did he know that I had extensively studied Sutherland’s work and critiqued it in 2016: http://inference-review.com/article/animadversions-of-a-synthetic-chemist . And that poor psychiatrist had been misled by Szostak to believe that all this chemistry is worked out and simply heat and light can work this magic. How misled even professors can become from these writings in Nature. The academy is led astray.”

The paper that James Tour linked to was “Animadversions of a Synthetic Chemist, Why is everyone here lying? — Fyodor Dostoevsky “ James Tour, Inference: International Review of Science May 19, 2016 in Volume 2, Issue 2. And, as the editors clearly stated, “Inference is not a peer-reviewed journal.”

And what were the papers co-authored by Sutherland that Tour had “extensively studied … and critiqued?”

Matthew Powner, BĂ©atrice Gerland, and John Sutherland, “Synthesis of Activated Pyrimidine Ribonucleotides in Prebiotically Plausible Conditions,” Nature 459 (2009): 239–42.
http://hoffman.cm.utexas.edu/courses/nature_prebiotic_rna.pdf

Patel, B.H., Percivalle, C., Ritson, D.J., Duffy, C.D. and Sutherland, J.D., 2015. Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism. Nature chemistry, 7(4), p.301.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568310/

These had nothing at all to do with “Prebiotic synthesis of simple sugars by photoredox systems chemistry” Ritson, D. and Sutherland, J.D., 2012 Nature chemistry, 4(11), p.895. That paper was the exact citation that Dr. Ali, the poor misled professor of psychiatry, had suggested James Tour should read. And then in Tour’s self adulation, and self excuse, he goes on and on about Patel et al, 2015. Sugars are mentioned, but in the confused reading by James Tour, he is avoiding the real point of that paper. The extensive mapping of the chemical reactions in Patel (2015) was descriptive. It was not prescriptive.

I must conclude that this is a common thread through all of James Tour’s failed reading of Origin of Life research. In his religion driven mania he must see all things as a “Divine Plan,” with a Divine Being needing to interfere periodically. There is nothing merely descriptive “this is just what happened.”


For more of Tour's and John West's supporting lies exposed, see; "Prof. James Tour and the Disco’Tutes: Still Lying, Part 3"

Tuesday, July 16, 2019

Prof. James Tour and the Disco’Tutes: Still Lying, Part 3.



This is the closing section of my reply to John West of the intelligent design creationist "Discovery Institute." I recommend starting with Part 1 if you really want the total range of new lies told by the creationist Disco'tute. There will be more technical reviews to follow about James Tour's failed objections to origin of life research.

Or, see Part II here.

Journalism degree winner John West claims that his 3 remaining lies are directly from James Tour. And James Tour claims these next set of lies are from his telephone call with Jack Szostak. The one where Tour apologized for lying that Nobel winner Jack Szostak was a liar. Tour doubles down implying Szostak too stupid to recognize simple chemistry.*1


 
“Those are not sugars!”

Here is what John West wrote as his point #1;

1. According to Hurd, Tour was lying when he criticized as scientifically inaccurate two figures in Jack Szostak’s article labeled “Simple sugars.” When I asked Tour about this criticism, he responded that Szostak himself conceded to him that these figures were inaccurate! Tour wrote me:

    “As listed, the sugars do not look like sugars. One needs to have the double bond shown to one of the oxygen atoms or they are not sugars. Shown are a diol and a triol. Even Jack, when he and I spoke on the phone, conceded that point. And he blamed the error on a staff artist from Scientific American, and the mistake was transcribed when the article was used by Nature.
So much for this supposed lie by Tour.”


I want to look a little closer at this lie by James Tour. The science lie is that these “stick figure” illustrations were not representative of simple sugars, and that these simple presentations of complex molecules are unusual, or inaccurate. Here is the illustration Tour insisted is a lie. I showed that these were simple sugars. Mostly Tour rants that this is a “lie,” and Jack Szostak is a liar. When he had to apologize, Tour still doubled down that it was still a lie he now called; “mistake,” “an error,” and  “simply incorrect.”



Here is the famous Krebs Cycle in two illustrations. The first is for a popular audience without any professional chemistry background. Note well that the atoms are colored dots, hydrogen atoms are not shown, and the chemical electron bonds are represented by simple lines.





Here is a still simplified, but more detailed example intended as a teaching aid for undergraduates. The different audience and the different details are obvious, and appropriate.




But, the bigger lie is that James Tour didn’t honestly report his conversation with Jack Szostak. I asked Prof. Szostak by email if he “admitted”
to James Tour that the illustration was an error? And, if he had “blamed” illustrators for Scientific American, and Nature magazines? His reply was

Szostak to Hurd (May 17, 2019), “What I did was to explain the use of the simplified diagrams as a means of communicating the chemistry to a general audience (and note, even chemists by convention draw molecular structures without showing most hydrogen atoms).  At the time he appeared to have no problem accepting this explanation, but I guess it did not stick.”


I know that James Tour lied already about Jack Szostak, and that John West has lied about me. I’ll believe Prof. Jack Szostak over both of them.

To paraphrase John West, “So much for telling the truth by Tour.”

“Is this HCN?”

John West again journalizes,
“2. According to Hurd, Tour was lying when he questioned the scientific accuracy of two figures in Szostak’s article labeled “Cyanide derivatives.” Not so, says Tour, who responded to me:
    Either we fill in the hydrogen atoms or we show the pi bonds. But we cannot omit both. Moreover, the convention is that all heteroatoms should bear the hydrogen atoms. Only carbon can be devoid of hydrogen in the convention. But that is only to fill the valance states. (…blah blah, ... repeat … gh).

Once again, the charge that Tour was lying or incompetent disintegrates.”

What James Tour did say (and he and the Disco’tutes are still repeating to tens of thousands of people on their YouTube) is that the illustrated molecules labeled “cyanide derivatives” were not cyanide. He almost shouts, “That is not HCN! I don’t know that that is!”


The chemical formula for cyanide is HCN. The chemical formula for “cyanide derivatives” is not HCN. I wrote months ago that the simplified molecule sketches are CN2, or cyanonitrene on the left, and C3N, or cyanoethynyl on the right. James Tour failed to even correctly read the illustration title he is attacking. So, is he lying, or incompetent?

In favor of incompetence, Tour wrote in his self-justification about that illustration of cyanonitrne, and cyanoethynyl, "… then the latter of the two “Cyanide derivatives” could be cyanoethene (acrylonitrile) or cyanoethyne. The former could be H2N-C=NH or HN=C=NH or H2N-CN (all hydrogen atoms shown immediately tell us that the last of these three listed here is cyanonitrene)."

Gosh, I had said they were cyanonitrene, and cyanoethynyl. I guess that undergraduate organic chemistry class 48 years ago stuck better than I thought.

We just saw Jack Szostak’s comment about this style of illustration, and I know who I can believe. But, maybe it is incompetence.

“he could have at least used the right structure”

John West’s last try to salvage his "expert witness" is that the simplified illustration of
a nucleotide is utterly mistaken.
“ 3. According to Hurd, Tour was lying as well when he claimed that the diagram labeled “RNA nucleotide” in Szostak’s article was inaccurate. Tour’s response to me: “it is not a nucleotide since it is devoid of any stereochemistry.” Again, the charge that Tour doesn’t understand basic chemistry seems to evaporate.”

As I wrote, and illustrated, “At 46:10 Tour starts to yap that the right most stick drawing is "not a nucleotide." From 46:10 to 46:20 Tour shouts "It is not the right structure, he could have at least used the right structure …" In fact it is cytosine bound to ribose and the phosphate to the ribose. This is RNA's nucleoside cytidine. It is directly and spontaneously formed in nature from the starting chemistry.  It is the “right structure.”

Compare the two side by side. 




I have not anymore to say about John West’s failed attempts to salvage James Tour. But, Jack Szostak does deserve a last word,

As I said in my original email to Jim, I was sad that such an excellent organic chemist was not willing to think about the problems of how life began on the early Earth.  If he would only approach the really interesting problems we are trying to solve with the same energy and creativity with which he approached the synthesis of his molecular race cars, he could actually make real contributions to a scientific understanding of the origin of life.  However, it looks like we will have to solve those interesting chemical problems without his help! 



James Tour makes some new lies in his self-aggrandizement and excuse froth, "Letter to John West" dated May 11, 2019. I took some time to expose them in; James Tour Lies Again, 3'



*1 James Tour wrote in his self defense, "How disingenuous for Szostak to write “in the presence of UV light and phosphate, RNA nucleotides were formed.” Does Szostak himself appreciate the exactness required to conduct these syntheses? Likely not. Most biologists don’t. And they transmit their blissfulness to others."