Eddie and ID books

[sfmatheson]

@Eddie

The Mendelssohn review refuted every single point made in the book?

This is just not a reasonable way to counter the critique of the book. I am just one of many (most? nearly all?) here in this conversation who believes that an author can discredit themselves with dishonesty or oblivious ignorance (just two examples of how to do that) and who believes that a book can become worthless by revealing itself to be riddled with falsehood. Your rebuttals now look like pleas for critics to acknowledge the inclusion of complete sentences, and unfortunately your rebuttals lack any content of their own.

Even if Puck is–as I suspect–overstating the degree of awfulness of The Design of Life, he has dealt it a crippling if not fatal blow by quoting a passage that illustrates falsehood so egregious that critics on this thread are struggling to describe how it even came to be. @Eddie, this is really important: falsehoods like that do discredit books, and their authors, and at some point, they discredit people who defend the work. If The Design of Life includes more examples of shit like that, then it is a book that should be exposed as worse than worthless.

Your plea by itself–to give credit where it is due–is not unreasonable. My reviews of ID books have always pointed out things that the authors did well and got right. Maybe there are some good sections in The Design of Life, and maybe there are even some pages that contain interesting explanation or theorizing. That doesn’t mean the book is redeemable. And no one should have to explain that to you.

[Mercer (John Mercer)]

@Puck_Mendelssohn

Nobody who would like to know anything about the CE would be well advised to read Meyer, when other works are available.

The same goes for knowing anything about the RNA World hypothesis, when both books are false on the strongest evidence favoring it.

@Puck_Mendelssohn

One could sort of reverse-nit-pick a book like The Design of Life, isolating small portions of it which are not wholly false.

I’m sure that there are a few passages that we would not find to be misleading! The question is, can Eddie find any?

@Puck_Mendelssohn

But what would be the point?

For Meyer (which I’ve read, @Eddie), we’d find that those parts are sophomoric at best. I’d bet that The Design of Life would be more of the same.

[Eddie (Edward Robinson)]

@Mercer

Wrong. This enzyme is a ribozyme, not a protein. That’s the whole point, man.

I stand corrected on that point. Enzymes have generally been classed as proteins, but the ribozyme would be an exception to that. And yes, I do understand that the whole point of the RNA world hypothesis is that RNA can in some cases have some catalytic ability.

But it’s my understanding that peptidyl transferase is essentially a stretch of RNA within the ribosome. Is that correct? And RNA is considered a macromolecule. So it’s not wrong to call it a molecule, and that’s what I was originally defending – my use of the term “molecule.” Of course, if you want to go pedantic again, and say that within the ribosome it’s not called a “molecule” but a “moiety”, well, have it your way.

@Mercer

The ribosome is not a molecule.

I didn’t say that it was. I understand it to be an organelle, composed of more than one kind of molecule.

@Mercer

Are you saying that the anonymous EN&V author who described it as an error was lying?

I read that column, long ago. Give me the link to it again. The author did admit that Meyer made a slip, but did the author agree that the slip invalidated Meyer’s entire book? Or even the entire chapter? I have my doubts. But give me the link, and I’ll review it.

[Mercer (John Mercer)]

@Eddie

I stand corrected on that point.

My additional point is that reading those books completely misinformed you about a fact that is so important that it won the Nobel Prize.

@Eddie

And yes, I do understand that the whole point of the RNA world hypothesis is that RNA can in some cases have some catalytic ability.

No, you don’t understand the point in the slightest.

The whole point of the hypothesis is that life was entirely based on RNA catalysis before any protein catalysis arose. That’s why it predicts that we will find incredibly important functions, like the meat of protein synthesis, will still be handled by ribozymes. There’s no reason why an Intelligent Designer would choose a ribozyme for something so important, but evolution can’t replace it. That’s why there is nothing pedantic about my point.

Another question: why are the adapters in protein synthesis RNAs (tRNAs) and not proteins?

@Eddie

And RNA is considered a macromolecule. So it’s not wrong to call it a molecule, and that’s what I was originally defending – my use of the term “molecule.”

You’re moving the goalposts. You are also claiming that this is not important and that peptidyl transferase is a protein. You’ve only retracted one of those false claims.

Neither they nor Meyer put out this falsehood in passing. They base arguments on the false claim.

So, back to the OP, here is the argument they make:

“It follows that without some catalyst that promotes peptide bonds (for amino-acid sequences) or 3-5 phosphodiester linkages (for nucleotide sequences), there can be no materialistic route to proteins, DNA, and RNA.”

The current catalyst does precisely that. It is a ribozyme. Therefore, that “materialistic” route clearly exists.

“But the only catalysts we know capable of handling this task are enzymes and other protein-based products (e.g., the ribosome)”

This was known to be false 7 years before this was published.

You have now admitted that the ribosome is a ribozyme, so this challenge has been met in spades. Will they admit it? Will YOU admit it?

Calling the ribosome “protein-based” is like calling the Mona Lisa “wood-based” because it has a wood frame, while claiming that no one has shown that it is an oil painting. It also suggests deliberate deception to me.

“… and these in turn presuppose the entire DNA-RNA-protein machinery. This machinery, however, is precisely what origin-of-life research may not presuppose but rather must explain.”

And the fact that the ribosome is a ribozyme, with proteins as mere decorations around TWO rRNA cores (one for each subunit), explains that very well. That’s why it’s so important.

So, what’s your ID explanation for this relic?

@Eddie

I read that column, long ago. Give me the link to it again.

No, let’s discuss the book whose flaws you said you were more than willing to address instead.

@Eddie

The author did admit that Meyer made a slip, but did the author agree that the slip invalidated Meyer’s entire book?

Nice try, but I’m not saying that. I’m saying that it is representative of ID scholarship–when you can’t explain the facts, hide them or blatantly misrepresent them.

@Eddie

Or even the entire chapter?

Yes, I would say that ignoring the most important evidence necessarily invalidates any chapter claiming to address the RNA World hypothesis.

But then, unlike you, I’ve known that the ribosome is a ribozyme for 20 years, and we suspected it many years before that:
https://science.sciencemag.org/content/256/5062/1416

[Eddie (Edward Robinson)]

@Mercer

No, you don’t understand the point in the slightest.

Yes, I understand it exactly.

@Mercer

The whole point of the hypothesis is that life was entirely based on RNA catalysis before any protein catalysis arose.

Which is exactly the understanding of the RNA world theory that I have, and which I understood from reading Meyer and many other ID writers, as well as non-ID writers.

@Mercer

There’s no reason why an Intelligent Designer would choose a ribozyme for something so important,

So you know how such a being would think? Another example of evolutionary thought being based on tacit theological premises.

@Mercer

The current catalyst does precisely that. It is a ribozyme. Therefore, that “materialistic” route clearly exists.

Only a limited catalytic capacity has been demonstrated for RNA. It’s a long, long way from being established that RNA catalysis explains origins. But then, speculation beyond the data has been evolutionary theory’s stock-in-trade since Darwin, who didn’t even know what the insides of a cell looked like or how inheritance worked, but was certain of his conclusions.

@Mercer

No, let’s discuss the book whose flaws you said you were more than willing to address instead.

So, you won’t provide the reference that would enable me to answer your question whether the writer of the Discovery column was “lying”?

@Mercer

Nice try, but I’m not saying that.

Interesting. So if you weren’t saying that, why didn’t you clarify that you weren’t saying that when you were asked the question (whether Meyer’s error invalidated more than a few pages of the book) about ten times over about a three-year period on BioLogos? Just being difficult for the sake of being difficult?

[Mercer (John Mercer)]

@Eddie

Which is exactly the understanding of the RNA world theory that I have, and which I understood from reading Meyer and many other ID writers, as well as non-ID writers.

That’s not what you wrote.

@Eddie

So you know how such a being would think?

Because RNA is an inferior catalyst.

@Eddie

Only a limited catalytic capacity has been demonstrated for RNA.

False. It literally assembles every protein in your body!

@Eddie

It’s a long, long way from being established that RNA catalysis explains origins.

Nice straw man! That suggests that you don’t understand the RNA World hypothesis, then.

@Eddie

But then, speculation beyond the data has been evolutionary theory’s stock-in-trade since Darwin

Here, we are discussing how ID proponents, whom you claim to be great thinkers, conceal evidence from their readers. It worked very well on you.

@Eddie

So, you won’t provide the reference that would enable me to answer your question whether the writer of the Discovery column was “lying”?

I prefer to discuss the glaring flaws of the book mentioned in the title. You said that you were “more than willing” to discuss the flaws IIRC. Shall we?

@Eddie

So if you weren’t saying that, why didn’t you clarify that you weren’t saying that when you were asked the question (whether Meyer’s error invalidated more than a few pages of the book)…

How many pages was the RNA World chapter, Eddie?

[Mercer (John Mercer)]

@Eddie

And RNA is considered a macromolecule. So it’s not wrong to call it a molecule, and that’s what I was originally defending – my use of the term “molecule.”

You used the singular article “a” to diminish the significance of the finding. There are two rRNAs within the large subunit of the ribosome and another one in the small subunit. Are you suggesting that they are dispensable for ribosomal function?

The evidence for them strengthens the RNA World hypothesis even more. Shall we go there? I’m more than willing, and when I write that, it is true.

[sfmatheson]

@Eddie

@Mercer

The current catalyst does precisely that. It is a ribozyme. Therefore, that “materialistic” route clearly exists.

Only a limited catalytic capacity has been demonstrated for RNA. It’s a long, long way from being established that RNA catalysis explains origins. But then, speculation beyond the data has been evolutionary theory’s stock-in-trade since Darwin, who didn’t even know what the insides of a cell looked like or how inheritance worked, but was certain of his conclusions.

This is crudely and disgracefully dishonest. @Mercer is offering you the opportunity to learn about the RNA World, after showing you that you were deliberately and systematically misled. You have an opportunity to recover some integrity after yours was eroded, perhaps by your own weakness but maybe because you made the understandable mistake of trusting some like-minded scholars who you assumed would try to deserve that trust.

I think you have failed here, and I think you should reconsider your stance. You admitted to being mistaken, which should earn you praise and respect, that I will offer unconditionally right now. The next step should have been something like “okay, let me find out where I went wrong.” And ideally the next step would have been “I look forward to learning more.” You opted for a pitiful redirection and a blanket insult, aimed at science. Disgraceful. Reconsider.

[Eddie (Edward Robinson)]

@sfmatheson

This is just not a reasonable way to counter the critique of the book.

I didn’t offer it as such. I offered it as a rebuttal to Art Hunt’s claim that the review showed that the book had “no merits.” The review did not establish that the book had no merits.

I am not saying that it is wrong to render a negative judgment on a book that has some merits. For example, I think Darwin’s Origin of Species has some merits, and more than some – it has a lot of merit. But that doesn’t mean that I have to conclude that the argument of the book is correct. (I’m speaking of the argument Darwin puts forward regarding mechanism, not regarding common descent.) It’s possible to believe that a book is intelligent, well-researched, well-argued, yet not finally convincing. And the flip side of this is that one doesn’t have to dogmatically assert that a book has “no merit” just because one finds one or more of its fundamental theses to be flawed. It might have merit regarding a number of subsidiary points. It might have merit in raising certain important questions, even if it does not answer them successfully.

The problem with anti-ID bloggers is that they have the compulsive need to assert that Page 1 of the book is crap, Page 2 of the book shows scientific ignorance, Page 3 shows deliberate dishonesty … up to Page 500. This renders their judgments suspect, even when those judgments are probably reasonable on some points. Nobody trusts a review that is obviously extremely partisan and written out of animus or indignation. (Indeed, ID garnered much sympathy for itself among “neutral” folks merely because of the extreme hostility with which it was met.)

[Mercer (John Mercer)]

@Eddie

I offered it as a rebuttal to Art Hunt’s claim that the review showed that the book had “no merits.” The review did not establish that the book had no merits.

A actual rebuttal would point out the points YOU think have merit, Eddie.

I can’t help but notice that Steve described your response to me as dishonest, but you did not even attempt to rebut him, just launching into a page-long rant of whataboutism.

@Eddie

The problem with anti-ID bloggers…

I’m not a blogger, Eddie.

Why are you ranting about bloggers instead of thinking about why your heroes either don’t know or can’t tell (the choices are equally bad) the truth about an enzyme at the very center of all life?

[Mercer (John Mercer)]

@Eddie

But it’s my understanding that peptidyl transferase is essentially a stretch of RNA within the ribosome.

That doesn’t even come close to doing it justice. Here is a much more accurate description, including a better art simile than my Mona Lisa one:

"Viewing the three-dimensional structure of the bacterial ribosome (Cate et al. 1999; Ban et al. 2000; Schluenzen et al. 2000; Wimberly et al. 2000) makes a profound impact on the viewer that has a variety of manifestations. First, there is a level of detail in the structure that the brain is simply not equipped to grok. The soft and gentle curves from the models constructed by Jim Lake are now familiar and somehow pleasantly sufficient to represent the ribosome in our minds (Lake 1976). Second, there is a strangeness in seeing how all of the RNA that we knew in an abstract way was at the core of ribosome function, really is there at the core of the ribosome after all. It is as if the artist Christo was commissioned to drape the stately RNA core with a set of absurd protein festoons. Finally, as if the intricacy of the RNA fold in the ribosome was not overwhelming enough, we are left to grapple with the question ‘‘By Jove, how does this thing get put together?’’

After the ribosome structures: How are the subunits assembled?

And how it gets put together tells us a lot about its design, whether it was a Designer or evolution.

Showing that the active site was only partly RNA would still have supported the RNA World hypothesis strongly. The astounding thing about the structure is that evolution has been unable to insert even a tiny finger of protein into the catalytic site in billions of years. None. No one expected it to be that segregated. The RNA is the guts of the other ribosomal functions in protein synthesis too, all combining to scream that RNA came long before protein. [That should in no way be taken to mean that RNA was necessarily the very beginning of life.]

It’s incredibly constrained in a way that could not possibly constrain any conceivable intelligent designer, especially an omnipotent one.

[sfmatheson]

@Mercer

instead of thinking about why your heroes either don’t know or can’t tell (the choices are equally bad) the truth about an enzyme at the very center of all life?

I’ll bow out by asking everyone but especially @Eddie to think about this and to aim to understand it. It’s worse than @Mercer writes here, actually. Not only did this author miss or misrepresent the truth about this epic and central enzyme, but he did it while writing about the RNA World in an attempt to discredit it. To portray this as a little mistake in the midst of an otherwise sound treatise is to butcher truth and knowledge grotesquely.

The next step is to admit that the author is not credible and that writings by him and his collaborators are suspect. And the immediate step after that is to ask whether and how to learn from credible sources. Basic intellectual integrity.

[Eddie (Edward Robinson)]

@Mercer

False. It literally assembles every protein in your body!

Misleading. RNA is involved in the assembly, but not by itself. The ribosome, though you have contrived all through this discussion to avoid mentioning it, is not composed solely of RNA. It also has a protein component. The whole machine, not just the RNA in it, is necessary to generate the amino acid chain that folds into the protein.

@Mercer

How many pages was the RNA World chapter, Eddie?

You can count as well as I can, and you can presumably divide as well as I can, so you should be able to compute what % of the book is affected by Meyer’s error, even on the questionable assumption that the error invalidates everything in the chapter.

Speaking of which, I notice that you dodged my question above. Repeatedly, on BioLogos, and I think even once or twice here, in past months, you were asked whether the error Meyer made was such that it invalidated the argument of his whole book. You never would answer, even though you could not possibly have missed a question that was asked so many times. And now, you say that you never claimed that his error in one chapter invalidated the whole book. So why didn’t you offer that clarification earlier, like, maybe, the very first time the question was posed to you, years ago? Or on any of the subsequent times it was posed?

[Eddie (Edward Robinson)]

@sfmatheson

You opted for a pitiful redirection and a blanket insult, aimed at science.

The insult was not aimed at “science.” You biologists have a most irritating and inaccurate habit of equating acceptance of the currently popular flavor of evolutionary theory with “science” itself. And even worse, some of your number (not necessarily yourself) seem to think that speculations about the origin of life are very rigorous examples of science.

@sfmatheson

And ideally the next step would have been “I look forward to learning more.”

If I were to learn more about origin of life hypotheses, it wouldn’t be from Mercer. He’s nothing more than a layman in that field – it’s nothing to do with any of his published research. In fact, I don’t believe anyone here has any special research track record in that area. So this is not a place that I would choose as a place to get a reliable picture of current thought on that subject.

That is not to say that I regard Meyer as an expert on origin of life theory, either. His book is merely a general-level introduction to the history of the notion and some of the general theoretical problems involved. I don’t take it as anything more than that. I don’t regard it as the final word.

It remains true that much more work needs to be done to show exactly what kind of “life” could have existed in an RNA-only world, and to show a plausible, stepwise transition from the RNA-only world to the DNA-RNA-protein world of today. However clumsy Meyer’s own account may have been, there is still a very high speculation-to-fact ratio in RNA world theorizing – and in all chemical origin of life theorizing. And I don’t fault scientists for that, as long as they don’t overclaim about what is known, and as long as speculation is clearly labelled as such, and as long as verbs in the indicative aren’t employed in cases where the subjunctive would be more appropriate.

[John_Harshman]

@Eddie

The whole machine, not just the RNA in it, is necessary to generate the amino acid chain that folds into the protein.

Oh, dear. I think we’ve been over this claim before, and you should remember that. In fact, there are experiments in which all the protein was carefully digested away, and the naked RNA ribosome was still able to make protein. I swear we’ve done this before.

[Mercer (John Mercer)]

@Eddie

The ribosome, though you have contrived all through this discussion to avoid mentioning it, is not composed solely of RNA.

Yet another false claim. I even offered a simile: the proteins are merely a frame around the RNA machine.

@Mercer

Calling the ribosome “protein-based” is like calling the Mona Lisa “wood-based” because it has a wood frame, while claiming that no one has shown that it is an oil painting.

@Mercer

And the fact that the ribosome is a ribozyme, with proteins as mere decorations around TWO rRNA cores (one for each subunit), explains that very well.

@Mercer

The astounding thing about the structure is that evolution has been unable to insert even a tiny finger of protein into the catalytic site in billions of years.

@Eddie

It also has a protein component. The whole machine, not just the RNA in it, is necessary to generate the amino acid chain that folds into the protein.

That’s objectively false. I even linked to a paper that demonstrated that, and you didn’t even have to go beyond the abstract–even the title alone tells you!

https://science.sciencemag.org/content/256/5062/1416
“Ribosomes from the thermophilic eubacterium Thermus aquaticus remained more than 80 percent active after treatment with proteinase K and SDS, which was followed by vigorous extraction with phenol [i.e., protein is being removed]. This activity is attributable to peptidyl transferase, as judged by specific inhibition by the peptidyl transferase-specific antibiotics chloramphenicol and carbomycin. In contrast, activity is abolished by treatment with ribonuclease T1.”

Papers don’t get much clearer than that. Did you not understand that? How can I not infer deliberate dishonesty from your denial?

@Eddie

You can count as well as I can, and you can presumably divide as well as I can, so you should be able to compute what % of the book is affected by Meyer’s error, even on the questionable assumption that the error invalidates everything in the chapter.

It’s not an assumption. If you fudge the most important piece of evidence, you’ve violated the most fundamental principle of scholarship. That’s true whether the reason was incompetence or dishonesty.

However, if you’d like to try to rehabilitate Meyer (or Dembski and Wells) with the silliness of the rest of the chapter, that would still be fun.

[Roy (30-year veteran)]

@Mercer

@Eddie

I offered it as a rebuttal to Art Hunt’s claim that the review showed that the book had “no merits.” The review did not establish that the book had no merits.

A actual rebuttal would point out the points YOU think have merit, Eddie.

That’s clear throughout this thread - Eddie keeps suggesting that The Design of Life has points of merit, but has yet to name a single one.

If Eddie, an ID supporter, can find nothing in this book worth highlighting, then it must be atrocious.

[Eddie (Edward Robinson)]

@John_Harshman

Oh, dear. I think we’ve been over this claim before, and you should remember that.

I have no memory of being involved in any discussion about the components of the ribosome and their roles in its activity. Perhaps the discussion occurred here, but with someone else. I have no recollection of it.

I remember repeatedly asking John Mercer why he was so focused on that one point, out of the 500+ pages in Meyer’s book, and asking him if any error concerning the transferase invalidated the thesis of the whole book. He never answered. He still hasn’t answered now.

@Mercer

That’s objectively false. I even linked to a paper that demonstrated that,

I have not yet looked at it. But for the sake of argument, I will temporarily accept that you are right, and that I made an error in saying the protein part was necessary for the ribosome to perform correct protein synthesis.

Let’s put this purported fact into everyday English, to make sure I understand it. Are you saying that if we went inside any living cell whatsoever, of any creature of any species that has the ribosome (and I assume that all or almost all do have the ribosome), and literally ripped away every single scrap of protein from the ribosome, leaving only the RNA, that the RNA remainder would continue to produce chains of amino acids exactly like the ones the ribosome produces now? That there would be no difference in the cell’s ability to produce correct proteins?

And if that is true, how do you explain this, in evolutionary terms? Why would the ribosomal complex ever have evolved in the first place, if the combination did not serve some function? Are the protein parts the outcome of a mere evolutionary accident? What do you think they are doing there?

[John_Harshman]

@Eddie

Let’s put this purported fact into everyday English

By which you apparently mean let’s produce an extremely exaggerated version in which the proteins of the ribosome do absolutely nothing, holding up an impossible standard of evidence, as is your habit.

@Eddie

Why would the ribosomal complex ever have evolved in the first place, if the combination did not serve some function?

The combination does serve some function. The proteins improve the ribosome’s stability and function. Ribosomes work better with the proteins in place. But you have forgotten a basic pathway in the evolution of IC systems: 1) add a part; 2) make it necessary. The proteins are added parts, and in fact they have not reached the “necessary” condition. A naked RNA ribosome doesn’t function as well as one with its proteins intact, but the point is that it does function, making an ancestral ribosome consisting solely of RNA entirely plausible, and thus suggesting the RNA world, or at least the antiquity of RNA vs. protein.

I will charitably assume that your gross misunderstanding was not intentional, but could it have been influenced by bias?

Mercer is focused on that point because it invalidates an entire chapter of the book, an important chapter, and it shows the dishonesty of the authors.

[RonSewell (RonS)]

@Eddie

If I were to learn more about origin of life hypotheses… I don’t believe anyone here has any special research track record in that area.

We have at least one contributor here with a recent specifically origin of life publication list, with an astronomical chemical focus.