Explaining the Cancer Information Calculation

There’s a lot of wiggle room in there, no? How do you define it? Does a cell need to be involved?

I think that the fact that the ribosome is a ribozyme is a very strong indication that the first biological catalysts were RNAs, not proteins. How do you integrate that evidence into your conclusion?

How much of OOL research have you reviewed? A global negative requires a lot of supporting evidence.

The data? How much of the actual data have you examined for yourself?

But is your inference based on any data at all?

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I’m assuming you are referring to RNA-world?

RNA-world theory suggests that the first life may have been a self-replicating RNA molecule. The problem is, as far as I know, scientists have only been able to get an RNA molecule to copy 10% of itself. The physical mechanisms involved prevent a single molecule from copying itself in it’s entirety. You would need two identical RNA molecules that could copy each other, compounding the starting information requirements.

Stephen Meyer does a full exploration of the RNA-world hypothesis in his book Signature in the Cell. He covers the history, arguments for, and arguments against.

He cites 5 major problems for the theory:

1.) RNA Building Blocks Are Hard to Synthesize and Easy to Destroy.
2.) Ribozymes Are Poor Substitutes for Proteins.
3.) An RNA-based Translation and Coding System Is Implausible.
4.) The RNA World Doesn’t Explain the Origin of Genetic Information.
5.) Ribozyme Engineering Does Not Simulate Undirected Chemical Evolution.

How are you defining genetic information?

That’s wrong. The RNA World is simply (hypothetically) a world in which RNA is the main replicating and catalyzing macromolecule, before DNA and proteins. No one has ever claimed that an RNA molecule was “life.”

It seems you have read a single book by an author with low credibility. Have you read any scientists’ writing about the RNA World?

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That’s how RNA world is described on wikipedia, and many other places I have seen it…

You say “RNA is the main replicating and catalyzing macromolecule”. Replicating what? You seem to be saying the same thing as me?

From the dictionary:
rep·li·cate

verb

gerund or present participle: replicating

/ˈrepləˌkāt/

  1. make an exact copy of; reproduce.
  • (of genetic material or a living organism) reproduce or give rise to a copy of itself.

Ok, I know you don’t think Meyer is credible. But others such as Tour have raised similar criticisms of RNA world models. Perhaps you have an equally low opinion of Tour, I don’t know Do you think they are mistaken on all accounts?

No I have not read a book that is specially about RNA world, though I have read about it in biology textbooks, seen it presented on educational programs, and watched college lectures about it. They included lots of creative story telling, and did not address any of the issues raised by skeptics. If you have any suggestions I’d be happy to hear, though my book queue is about 50 deep at this point…

No, it’s not. No one refers to RNA as “life.”

Replicating genetic information, and itself. DNA is the main replicating macromolecule in current life.

Please don’t waste my time with the dictionary. Please spend that time reading credible science about the RNA World.

Do you think that “mistaken on all counts” is somehow a reasonable standard here?

But you are comfortable typing claims about it. That’s where your conduct is inappropriate. You don’t understand it enough to know that it never claimed that RNA is “life” but you are comfortable typing objections from a philosopher who works at a propaganda firm. If you want to learn about the RNA World, there are lots of things you can read but first you have to decide if learning is your goal. That’s not the impression you give. Instead, it seems you are intent on copy-pasting the words of apologists.

So, if you want some recommendations of reading with the goal of learning, let me know.

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So I take it Tour didn’t say anything of relevance to the point I was quoted stating?

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I am no expert, but I have seen some debates. I have heard him say on different occasions that experiments that attempt to replicate the chemical conditions for producing life are invalid because they are not occurring naturally, they are being replicated. I think Tour’s argument is more that there is no lab condition that would suffice, once the lab is brought into play, it is no longer naturally occurring.

Wrong right off the bat. It’s just a hypothesis, not a theory.

Nope.

…is that you are pontificating based on hearsay without knowing very much.

Everything you’ve written here suggests that you never looked at a single datum before making grand pronouncements that cite “the data.”

I’ll ask again: how much of the actual data have you examined for yourself?

That is objectively false. A full exploration would have necessarily included addressing the strongest evidence for it: the fact that peptidyltransferase, the core of the ribosome, is a ribozyme.

No reader of Meyer’s book is informed of this Nobel Prize-winning fact.

So, on what evidentiary basis did you judge the exploration to be a full one?

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Those are the questions. We don’t know which sequences and maybe not even what machines, but we know their chemical building blocks. Can we even realistically get the building blocks to form naturally?

Ok, you seem to have a problem with my choice of words, and I can see why.

How about “the RNA world hypothesis suggests that RNA was the original precursor to the formation of life, before DNA and Proteins evolved.”

No, it’s not a reasonable standard. But that’s not what I’m asking. I’m asking if you are willing to admit that any of the challenges to RNA world have merit? Tour claims biologists are collectively clueless on OOL. I’m curious how you respond to that. Here is an article written by Dr. Tour where he brings up numerous challenges to OOL research: Time Out | Articles | Inference: International Review of Science

Yes, please. Ideally something available on audiobook.

Ok, my mistake.

I’m trying to learn. Hook me up with some good recommendations.

I don’t know how much data there is, so I can’t really say how much I have examined. I have already stated where I have learned about RNA world.

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I don’t know what sequences are required. But again, a random string of bases is unlikely to be constructive. I suspect you know what RNA is made of.

From Tour:
FOUR MOLECULES are needed for life: nucleotides, carbohydrates, proteins, and lipids. Nucleotides are composed of a trimeric nucleobase-carbohydrate-phosphate combination, and once polymerized, constitute DNA and RNA. Five different nucleobases comprise the entire alphabet for DNA and RNA. The nucleotides and their subsequent DNA and RNA structures are homochiral, yielding one of two possible enantiomers. Amino acids are most often homochiral. When amino acids are polymerized, they form proteins and enzymes. Proteins and enzymes also display a tertiary homochirality. Lipids are dipolar molecules with a polar water-soluble head and a nonpolar water-insoluble tail. They, too, are most often homochiral. Cells use carbohydrates for energy, and carbohydrates, along with proteins, are identification receptors. Carbohydrates are also homochiral, and their polymeric forms take on tertiary homochiral shapes. OOL researchers have spent a great deal of time trying to make these four classes of molecules, but with scant success.

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I must agree with Rumraket here.

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You have to start somewhere. Can you expand on this?

Tour brings experiments like this up here at ~28 minutes: James Tour: The Mystery of the Origin of Life - YouTube

and here under the “Synthetic Hyperbole” section: Time Out | Articles | Inference: International Review of Science

I’m curious how you would respond to Tour on this.

By the way, thank you for the respectful responses!

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The point I first responded to was whether “we have a decent idea of some of the basic hardware a self-replicating cell will require.”. And I am giving an example of how we could get transport across a primitive cell membrane to work without requiring complex protein machinery to do it. That is the whole point here, that those complex machines aren’t required at these simpler stages. The kinds of molecules that would get in and out are small ions and monomers, and the internal and external concentrations are driven by primitive physical mechanisms instead.

But at the time you gave me (28 minutes) Tour is talking about whether the kinds of chemistry some have proposed to form nucleotides could plausibly occur on magnitudes large enough to yield high concentrations of nucleotides. I’m going to skip that because it’s just not relevant to what I was saying.

At about 30:00 Tour goes on to give various complaints about work in primitive cell membranes, many of which are highly dubious and might simply not be of any relevance to the origin of life, and I couldn’t possibly be bothered to go through them all here. But what can be said about most of them is that they in effect all constitute red herrings.

Tour is taking it as a given that, since modern cells HAVE those structures, these MUST be spontaneously formed at the origin of life somehow, otherwise he appears to basically consider the research irrelevant.

To see an example of how he does this, he says at 30:46: “Every experiment uses just homogeneity throughout the whole thing, and so it isn’t, isn’t really a protocell, it’s not reminiscent of a cell”.

Disregarding that the assertion is flat out false(many experiments have been done with complex lipid mixtures), I have to ask, why not? Why is it not a protocell just because it doesn’t fully resemble a modern cell in all aspects? Why does it HAVE to be reminiscent of an extant cell? Isn’t that the whole goddamn point of a proto-cell? Something that came BEFORE the modern cell, that evolved into modern cells as we see them? Cells that began simpler and then became more complex over time?

Once you notice this, you see he does it everywhere. He appears to dismiss all the research being done as not relevant(he calls it “garbage”) in his mind because the kinds of things researchers are producing don’t look like cells with 4 billion year evolutionary histories. No shirt?

He gets away with dismissing lots of research out of hand because it doesn’t produce modern cells. But it’s not supposed to produce modern cells. The questions researchers are seeking to address is if simpler cells than modern cells are possible, and if they are, how could these simpler come about and how would they work? Cells that don’t have thousands of lipids and membrane transport machineries, don’t have complex chains of carbohydrates extending from their membranes, etc. etc.

Modern cells are the results of approximately 4 billion years of evolution by natural selection. Is it really any surprise that these are different and more complex from what researchers are trying to determine how could have emerged and function at the origin of life? Many of these systems we are all deeply fascinated by, evolved subsequently to the origin of cellular life. Some later than others. But obviously it makes more sense to explore a hypothesis that life began at a state of cellular complexity much simpler than we currently see. That is basically the hypothesis being explored in this research.

At 30:23 he gives a list of things modern cells use lipids for, and mentions for example subcellular organelles such as the eukaryotic nucleus and mitochondria.

Pardon me, but eukaryotes and mitochondria came roughly 2 billion years after the origin of life, why even mention these? They’re the product of evolution. By the way, mitochondria are derived from bacteria, they have bacterial cell membrane lipids. Tour goes on to insist nobody knows how mitochondria or the nucleus obtained their lipid compositions. This is extremely misleading, and really just reveals Tours vast ignorance on research into evolutionary history and the origin of eukaryotes. I still have to wonder why he even brings these things up, they’re eukaryotic characters. Life did not begin with eukaryotes.

It’s like complaining that prebiotic chemistry doesn’t produce lungfish, and then acting all surprised and dismissive since now the origin of life doesn’t explain lungfish. Come on dude!

Finally at 31:30 tour comes to talk about the transport machines and how these are required in modern cells, because in modern cells the phospholipids yield an impermeable membrane that does not allow anything to leave or enter the cell. I know, that’s the whole point. If the cell is NOT made of modern phospholipids, but a dirtier mix of simpler, more prebiotically plausible amphiphilic molecules like fatty acids and fatty alchols, the sort of membrane these can form DOES allow passive ion and small molecule transport across the membrane. One could go on and on with Tour being dissatisfied that work on protocells and primitive cell membranes do not produce modern cells that can do all the things modern cells can do. And I just have to ask, why should we think it has to? The point of the research is to explore whether simpler systems can function in principle, and if so, how they could emerge. The work isn’t over by any stretch of the imagination, but many of Tours theatrically delivered concerns make zero logical sense.

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Of course. Scientists who study topics related to the RNA World are constantly discussing the challenges. There are competing views, ranging from different “versions” of the RNA World to views that reject the premise of the RNA World. This is apparent even from the Wikipedia entry. I don’t quite understand why you would think that my rejection of the unqualified Meyer would somehow imply blanket endorsement of the hypotheses that make up the RNA World.

If he claimed that, then he’s begging you to stop paying attention to him. No informed person, with or without technical expertise, would say that. I haven’t read Tour and I doubt I will, since he seems to raise only arguments from personal incredulity, and has made indefensible comments about fellow scientists.

May I suggest that you ask yourself why you are drawn to Christians who bash OOL theories?

My suggestions would be review articles from the primary literature. With a single exception, I don’t read books on OOL since I prefer the primary lit but there are some good recommendations here. I own and have read this book and it’s very good but it’s strongly technical and is a series of review articles. It might be hard to find and it certainly won’t be on audio.

Two ideas for reading:

This one is a somewhat lay level piece that is very good:
How life can arise from chemistry

This is more technical but a broad overview and also very good:
The RNA World as a Model System to Study the Origin of Life

I hope you will notice that in both of these articles, the caveats and difficult unanswered questions are emphasized. Perhaps you will reconsider listening to any “expert” who attacks this area of science on the basis of a claim that OOL researchers overstate what we know. My experience is that OOL researchers are more conscientious than most scientists are, when it comes to identifying challenges and caveats.

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How does he know that they are? Are they required for life? Could something we recognize as living not function without these? How do you know?

Try to question the fundamental premise, and then ponder what basis there is for it in the first place? I’ll give you a hint: Tour thinks it’s required because he hasn’t seen life without it, and he can’t envision how it could work without it. Are those good reasons to think they are required for life? Nope.

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10 posts were split to a new topic: Regarding James Tour

Let me make sure I understand you. Are you basically saying that becasue we don’t know for sure what is required for the most basic life, we can’t really make a judgement about what it must be comprised of?

Perhaps I can pose the question another way: Is there any known life that does not consist of these elements (nuceotides, carbohydrates, proteins, and lipids)? If not, wouldn’t it be pure speculation to say that possibly they aren’t required?

Nope. How about reading this paper(not data):

https://www.nature.com/articles/319618a0.pdf
“RNA is then relegated to the intermediate role that it has today - no longer the centre of the stage, displaced by DNA and the more effective protein enzymes. But a few RNA enzymic activities still exist, the two described recently, and possibly others in the role of ribosomal RNA or in the splicing of eukaryotic messenger RNA.”

That “possibly” is now “definitely.” Meyer grossly misleads his readers about this.

That’s not how science works, you know.

People who are truly trying to learn don’t start by making sweeping, global claims based on hearsay. People trying to learn look at evidence. I don’t see any evidence that you’ve looked at any evidence.

Let’s make this simpler. Have you examined any at all?

And there was not a speck of data cited in anything you stated. Let’s look at the peptidyl transferase data:


(not just the abstract–free full text with registration)

Lay summaries that explain the significance:


“Our structure shows that these proteins are deeply embedded in the RNA and are essential for its folding. And it shows unambiguously that the ribosome is a ribozyme because we can see where the substrate binds and there’s no protein atom near enough to that site to produce any catalytic activity.

The catalytic activity is peptidyl transferase. So, what does Meyer say specifically about peptidyl transferase in the chapter you so confidently and unequivocally claimed to be “a full exploration”?

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