Jump to content

Episode 0/13: Reasons // A Course on Abiogenesis by Dr. James Tour


Recommended Posts

Feb. 14 2021

In this prologue episode, Dr. James Tour explains why he is addressing abiogenesis and common misconceptions in this series of lectures. After providing the outline for the course, Dr. Tour provides a sneak peak of the upcoming critique.

Video Index:

00:00 - Introduction & Dr. Tour's Background

02:52 - Some Background on the Series

07:01 - Reasons & Intent of this Abiogenesis Series

12:22 - Unskilled & Unaware

14:29 - "Biochemistry"? And what's in a name?

17:29 - Abiogenesis Series Outline

19:53 - Thermodynamics Addendum

22:12 - Origin of Life: Low Entropy & High Energy

25:03 - Closing Remarks & What's

Link to interview with Dr. Brian Miller: https://youtu.be/RJeUH7IhQHo

(Snip)

Link to Professor Dave's video: https://youtu.be/SixyZ7DkSjA

Link to post
Share on other sites

Feb. 15 2021

In this episode, Dr. James Tour defines abiogenesis and describes the characteristics for life, including a discussion on early Earth's conditions and challenges for prebiotic chemistry. After reviewing the four classes of molecules needed for life, Dr. Tour elaborates on the synthesis problems currently facing today's origin of life researchers.

Video Index:

00:00 - Introduction

00:44 - Reasons & Intent of this Abiogenesis Series

02:34 - Abiogenesis Defined 04:39 - Life's Characteristics

06:40 - Early Earth Conditions

11:01 - Prebiotic Chemistry Defined

12:23 - Four Classes of Molecules and their Building Blocks

14:37 - Car Parts: Assembly, Collection, Degradation

17:30 - The Synthesis Problem

22:54 - Closing Remarks: "Molecules Don't Care About Life" and What's Next

in this Series | Addressing Abiogenesis & Common Misconceptions

======

(Snip)

Link to post
Share on other sites

Feb. 16 2021

In this brief episode, groundwork is still being laid, as Dr. James Tour explains the early Earth primordial soup concept and enlightens the listener on the layperson's understanding. Dr. Tour then shows what the contemporary belief is, what levels of education it is held, and where it is taught.

Video Index:

00:00 - Introduction

00:42 - Reasons & Intent of this Abiogenesis Series

02:54 - Primordial Soup, Laypersons, and Talking Points

05:12 - Education Confirmation: "Not too bad at all" (and sans correction)

08:31 - A Survey on Primordial Soup

11:52 - Summary and What's Next

(Snip)

Link to post
Share on other sites

Feb. 17 2021

In this episode, Dr. James Tour examines hyperbole surrounding origin of life claims. Beyond a mere attribution to the press for creating hype, Dr. Tour looks into the published works by researchers themselves, discovering a more proper attribution of the source. He then elaborates how this snowballs further by the press into confusion by professors and laypersons. Finally, some agreement on prebiotic relevance is revealed.

Video Index:

00:00 - Introduction

00:36 - Reasons & Intent of this Abiogenesis Series

02:24 - To be clear: Not just press. Researchers too.

04:32 - Example: This is common chemistry?

24:19 - Example: How close are we?

28:14 - Example: OOL reproduced in the lab?

32:55 - Example: This is self-replication?

34:44 - Example: Simple Extant Imaginations

38:07 - Example: Fair Representation?

39:19 - Example: Deck Stacking, No Resemblance, Misappropriation

45:42 - Prototurkey for Thanksgiving 47:15 - Agreement on Prebiotic Relevance Requirement

48:18 - Summary and What's Next

(Snip)

Link to post
Share on other sites

Feb 18 2021

Diving into the science on homochirality, Dr. James Tour teaches the core chemistry concepts of enantiomers and chirality, exposing enormous challenges in the prebiotic synthesis and resolution of the molecules needed for life. By digging into the cited video's only provided reference, Dr. Tour puts ink on paper and shows how the devil is in the details when it comes to proper interpretation of the data. Finally, Dr. Tour touches on the stereoisomeric challenges facing synthetic chemists doing origin-of-life, prebiotic research.

Video Index:

00:00 - Introduction

00:37 - Recall Dunning-Kruger

01:06 - Reasons & Intent of this Abiogenesis Series

03:01 - Enantiomers, Diastereomers, and Chirality

07:36 - Resolution of Enantiomers, Methods, and Requirements

09:26 - Quoting the Only Reference Cited 11:20 - Homochirality Explained

14:17 - Digging into the Misread of that Reference

23:26 - Summary and What's Next

(Snip)

Link to post
Share on other sites

Feb 20 2021

n this episode on carbohydrates, Dr. James Tour comes right out of the gate refuting the claimed triviality of biomolecular synthesis. Rather than agree with the claim on the ease of polysaccharide synthesis, Dr. Tour explains the difficulty of their creation, including homochirality and the prebiotic problems facing multiple isomers, blind pathways, and polymerization and positioning. Also, Dr. Tour points out the fallacy of borrowing products from biology in prebiotic syntheses, and the challenge of early Earth blindly working through unfathomable procedures.

Video Index:

00:00 - Introduction

00:48 - Reasons & Intent of this Abiogenesis Series

02:45 - Correcting the Record on Polysaccharide & Biomolecular Synthesis

07:28 - Before Nucleotides, Ribose

09:48 - Cannizzaro vs Formose

13:01 - Eschenmoser's attempt

19:47 - Time & Equilibrium 22:18 - "homo-DNA" instead

23:36 - Real world difficulties

25:53 - Polymerization - Hooking the Sugars

42:36 - Summary and What's Next

(Snip)

Link to post
Share on other sites

Feb. 22 2021

n this episode, Dr. James Tour pauses and goes back to the basics, in a most literal sense. The matter at hand is not merely synthesizing the four classes of compounds needed for life – polysaccharides/carbohydrates, proteins, nucleic acids, and lipids – but rather their respective building blocks – monomeric sugars; amino acids; nucleotides; and fatty acids and glycerol. When restricted to prebiotic chemicals and methods, and with no store from which to purchase these building blocks while remembering homochirality, is biomolecular synthesis easy?

Video Index:

00:00 - Introduction

00:39 - Reasons & Intent of this Abiogenesis Series

03:25 - Car Parts' Building Blocks

07:16 - "Easy" Misconception Regarding Building Block Syntheses

11:56 - Cellular Building Blocks & their origin

14:01 - Convenience vs Prebiotic Rocks & Atmosphere

15:59 - Summary and What's Next

(Snip)

Link to post
Share on other sites

Feb. 24 2021

In this episode, Dr. James Tour identifies gross speculatory language and refers to published literature stating the implausibility of the sudden emergence of peptides from amino acids. Without careful activation, side chain protection, and water-free conditions, amino acids do not polymerize into peptides. Dr. Tour also dispels the view that human-made synthesizers, which were not present on prebiotic earth, somehow render polypeptide synthesis as trivial, let alone the fact that amino acids themselves have never been prepared in homochiral fashion using a prebiotically relevant route. Finally, with no solution to the amino acid sequence that comprises functional proteins, Dr. Tour then shows how some ignore the sequence specificity question necessary for the informational code, and how this dilemma is being pushed to the extraterrestrial in a plea to the heavens.

Video Index:

00:00 - Introduction

00:47 - Reasons & Intent of this Abiogenesis Series

02:58 - On Speculatory Fallacies

06:26 - Synthetic Chemists: "Inconceivable"

10:36 - Interesting Proposal Still Falls Short

12:45 - Basics: Amino Acids, Peptides, Proteins

16:47 - Separating Amino Acids and Peptides

18:29 - Solid-Phase Peptide Synthesis

22:53 - Peptide Structures Explained

26:03 - Protein Synthesizer Machine Prebiotically Relevant?

30:57 - Peptide Synthesis: Requirements and Efficiency 38:23 - Pushing the Amino Acid Sequence to the Celestial

48:13 - Summary, Equilibrium Memo, and What's Next

(Snip)

Link to post
Share on other sites

Feb. 26 2021

In this episode, Dr. James Tour educates us on nucleotides, comprised of a sugar (carbohydrate), a nucleobase, and a phosphate. With the reminder how manufacturers extract nucleotides from biological sources and how the oligomer synthesis cycle in solid phase DNA synthesis must use synthetically-prepared protective mechanisms, prebiotic nucleotide synthesis remains a mystery. Furthermore, it is revealed that the problem of sequence specific biological information—a world where order matters—remains unaddressed, with RNA World still looking incredibly unstable and bleak. Finally, with the secret of relay synthesis exposed, origin of life research faces a real challenge in the quest for prebiotic relevance, especially when these syntheses only provide nucleotides in racemic form and gross mixtures of diastereomers on the ribose.

Video Index:

00:00 - Introduction

00:40 - Reasons & Intent of this Abiogenesis Series

02:17 - Nucleosides & Nucleotides

05:49 - Structure and Composition of DNA/RNA

08:58 - What was said about synthesis

11:40 - Solid Phase DNA Synthesis explained

17:19 - Prebiotic Relevance & Invoking Relay Synthesis

26:57 - "small molecules" to RNA - Never Been Shown

29:57 - Random Information vs Life's Functional Information

32:57 - Prebiotic Sequence Selection

35:18 - RNA Self-Replication

38:18 - Time & Molecular Degradation

48:48 - Summary and What's Next

(Snip)

 

Link to post
Share on other sites

FYI Comment

Elucidating the Agenda of James Tour: A Defense of Abiogenesis

 

Hi Professor Dave, I have a doctorate in chemical engineering with an emphasis in the biotechnology area. I have never seen any published literature where the problems with homochirality without any human intervention has been solved. For example in 1995, at the conference in Los Angeles on the origin of homochirality (Science Vol. 267, March 3, 1995) William Bonner (PhD Organic Chemistry from Stanford) states in this paper, "There's a huge intellectual gap between the origin of homochirality and the origin of life--a huge gap. Bonner said that he spent 25 years looking for a mechanism and never found any. I had no idea that issue has been solved. Could you send some publications that verify that this issue has been solved with some plausible recipe that involves no intelligence involved. I would be excited to see a published paper where this issue has been solved. I would greatly appreciate it, if I have missed that publication. Please send a link in a return comment.
 

 

 

Yeah, a lot has happened in the past 26 years, my friend. Look up the work of Donna Blackmond, which James pretends doesn’t exist. Or just wait for my response video, because I’ll be personally interviewing her. James is going to wish he kept his mouth shut, he’s about to get exposed ten times worse than this video.
_________________________________________________________________________________________
 
This should be interesting.

 

Link to post
Share on other sites

Feb. 28 2021

In this pause from the series, Dr. James Tour reminds us that confidence in speaking about subject does not necessarily mean mastery of the subject, and welcomes scientific critique. After recapping what has been covered in the series thus far, Dr. Tour provides reasons for seeking clarity in hopes to advance the field on origin of life.

Video Index:

00:00 - Introduction

00:49 - Reasons & Intent of this Abiogenesis Series

02:40 - Confidence ≠ Mastery

04:17 - Scientific Critique - Learn Together

04:59 - Series Recap

07:02 - Reasons for Clarity & Advancing the Field

08:27 - What's Next

(Snip)

Link to post
Share on other sites

Mar. 2 2021

In this episode, Dr. James Tour teaches lipids and phospholipids, including their structures and organizational assemblies. With the thousands of different lipid structures identified in cell membranes, a discussion of whether simple lipid bilayers can be suitable cell membranes is had. Dr. Tour then looks at various syntheses as potential routes to fatty acids, bringing prebiotic relevance into the equation. With relay syntheses, chain swapping, and racemic mixtures amuck, early Earth is still left with enormous supplementary material procedures to follow, with no chemist available. When it comes to the synthesis of lipids, the luxuries of today indeed become "first world problems" for the first years of our world.

Video Index:

00:00 - Introduction

00:34 - Reasons & Intent of this Abiogenesis Series

02:48 - Lipids and Phospholipids

05:26 - Phospholipid Structure & Cellular Membrane

11:26 - Synthesis of Lipids

13:27 - Fatty Acid Proposed Routes

16:27 - Science: "salad dressing" won't suffice for proton gradients

21:01 - Prebiotic Earth's "Waldo": Chasing Relay Synthesis, Stereochemistry, and more

39:47 - Addressing Inaccurate Prebiotic Chemistry Claims

41:12 - Summary, Appeal to Origin of Life Researchers, and What's Next

 

(Snip)

Link to post
Share on other sites

Mar. 4 2021

In this episode, Dr. James Tour analyzes a false claim of molecular homochiral evolution, asking, in one example, how proteins could become homochiral when no prebiotically relevant route has been shown to synthesize, separate, or polymerize homochiral amino acids. Furthermore, a discussion on the possibility of racemic molecules in cells takes place. Finally, the amazing phenomenon of chiral-induced spin selectivity (CISS) is introduced, and Dr. Tour shows us how this enables the cell to be the amazing efficient machine that it is.

Video Index:

coming soon...

(Snip)

Link to post
Share on other sites

Mar. 6 2021

In what is being touted as his best episode yet, Dr. James Tour brings everything taught in the previous episodes into Part 1 of this multipart episode, discussing the construction of the cell and the problems of its assembly. With the surgical lights now shining directly on the subject, Dr. Tour begins his vivisection, exposing the sophistry of the origin-of-life narrative held by many while systematically excising fallacy by fallacy where the storytelling should stop. With the state of the origin-of-life field remaining stagnant post-Miller-Urey, Dr. Tour short circuits with yet another reference—an honest scientist studying the homochirality problem who remains circumspect in conducting autocatalysis toward homochirality with prebiotic relevance. Finally, after the biopsies of dissected specimens like RNA World come back from the pathology lab showing no signs of viability, Dr. Tour lists requirements not addressed by the cited fairy tale, including an unraveling of covalent molecular synthesis that somehow is being hand-waved into existence via a magical, nonsensical force called "spontaneous assembly".

Video Index:

00:00 - Introduction

00:37 - Reasons & Intent of this Abiogenesis Series

03:27 - Miller-Urey Problem and Beyond

10:18 - Flashback: Misunderstanding of Cited Video's Cited Literature

14:26 - Stop No. 1: No Small Misinterpretation

15:00 - Homochirality Advance Still Falls Short, say Authoring Scientists

22:57 - "No Problem" Nucleotides

28:00 - Stop No. 2: Researcher Hype to Layperson Mislead

29:14 - Panspermia: Kick the can to space

30:16 - Code Word: "Spontanous"

31:27 - Sleight of hand: Monomeric sugars

31:48 - Stop No. 3: No Sugars

32:59 - The Polymerization Problem & "some mechanism"

35:43 - Stop No. 4: Skipping Ribose

36:11 - Prebiotic Earth: RNA, "Hot", and "Clay"

44:43 - RNA's "UH-OH", impurity shutdown, & no interference?

49:46 - Stop No. 4: Information and RNA Failures

50:47 - Ribozyme vs Prebiotic Relevance

53:14 - Water break

55:04 - RNA World Problems, Krishnamurthy & more

58:36 - Condensation Reactions in Water

1:01:09 - Stop No 5: In practice, ineffective

1:01:25 - Enantiomeric Amino Acids & Polymerization, Not Shown

1:04:34 - Stop No. 6: Too much not shown

1:06:07 - Fatty acids, not spontaneously

1:08:39 - Stop No. 7: Fatty Acid Failure

1:08:54 - Self-Assembly: "Imagine" the "Hypothetical"

1:10:10 - Hypercycle Magic

1:11:01 - Stop No. 8: No Metabolism in Protocells

1:13:13 - What's Next

Clarification at 35:58: It was stated that "If it's not homochiral, it's not ribose", meaning, if it is not D-ribose, then it is not of general prebiotic relevance, which is what was assumed from the context of the discussion.

 

(Snip)

Link to post
Share on other sites

Mar. 9 2021

This is Episode 12, PART 2. Part 1 is here: https://youtu.be/IaJo5jWs_6k

In Part 2 of this multipart episode, Dr. James Tour transitions into a discussion on the assembly problem. After a flashback to the unaddressed complex cellular membrane, a separate and bewildering discussion on the Levinthal paradox of interactomes ensues. Dr. Tour then cites a mainline scientific journal with authors stating a miracle is the only explanation for a primitive living cell having the information hurdle accomplished within Earth's time frame, followed by an inspection of what the most basic gene set must look like in order to carry out the necessary functions of cellular life. Can RNA do the same? Did meteors deliver the molecules needed? Those questions are evaluated, and something new is presented, as Dr. Tour says that even if one has all the components, the problem of making the simplest living cell with those components remains. Finally, Dr. Tour shifts the conversation to the positive, providing good targets that origin of life research should solve in this desperate race to reach the finish line before the distance is increased yet again. Video Index: coming soon...

(Snip)

Link to post
Share on other sites

Create an account or sign in to comment

You need to be a member in order to leave a comment

Create an account

Sign up for a new account in our community. It's easy!

Register a new account

Sign in

Already have an account? Sign in here.

Sign In Now
  • 1620742884
×
×
  • Create New...