Good Math, Bad Math, and David Berlinkski

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David Berlinski is the Disco Institute’s ex-pat math jester (vying with Dembski for the lead in that role). He apparently regards himself as a polymath, taking on evolutionary biology from his vantage point in Paris. He’s been taken down on the Thumb a number of times – see, for example, here and here – and Jason Rosenhouse has also nailed Berlinski for his misrepresentations of evolutionary biology, concluding

So, once again, we have caught Berlinski making stuff up. There is almost no intersection at all between Berlinski’s points and those made by Dawkins and Coyne, and where there is overlap the latter had a far different points in mind than the former. But then, if they didn’t resort to total fiction the anti-evolutionists would have nothing to say at all.

Recently the Disco Institute put up Berlinski’s analysis of the probability of the naturalistic origin of life. Math is allegedly Berlinski’s field of expertise, so it seems reasonable to imagine that he’d do a better job in it. But Mark Chu-Carroll at Good Math, Bad Math gives it a look, concluding

This is what mathematicians call “slop”, also known as “crap”. Bad reasoning, fake numbers pulled out of thin air, assertions based on big numbers, deliberately using wrong numbers, invalid combinatorics, and misapplication of models. It’s hard to imagine what else he could have gotten wrong.

That’s pretty much the same conclusion that Rosenhouse reached regarding Berlinski’s work. Give Chu-Carroll’s full post a read.

RBH

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Richard:

Why thank you very much for posting this dull and uninformative reply to Berlinski’s essay. I say dull because it presents painfully tired objections that Berlinski himself understands and addresses in his article; and I say uninformative because it *seems* that the author has very little knowledge of prebiotic chemistry, and thus his post is less than illumninating. Berlinski builds upon what Joyce and Orgel and the entire metabolism first camp have been saying for some time–it is highly improbable that self replicating RNA arose from a pool of activated nucleotides.

And I quote…

“The fact that it’s damned unlikely that we’ll see new simple self-replicators showing up today is irrelevant to discussing the odds of them showing up billions of years ago. Why? Because the environment is different. In the days when a first self-replicator developed, there was no competition for resources. Today, any time you have the set of precursors to a replicator, they’re part of a highly active, competitive biological system.”

Um…yeah. I don’t really know what he means by this. The whole premise of the work of Szostak and Bartel is that we can artificially create an environment not only akin to, but much more condusive to the production of self-replicators than the actual primordial ocean. In the real primordial oceans there would not have been selection-amplification techniques (using nifty proteins unavailable in prebiotic times)thus allowing for Darwinian selection before selection was available. And even in the laboratory they haven’t created a ribozyme capable of sustaining self-replication and darwinian evolution. The best so far is just a ribozyme 180 nt in length that can ligate pieces of nucleotides up to 14 nt long. NO ONE KNOWS HOW COMPLEX AN ACTUAL RIBOZYME REPLICASE MAY NEED TO BE TO SUSTAIN INDEPENDENT SELF-REPLICATION CYCLES. No one knows how big or small the area (if any ata all) of RNA sequence space that viable replicases occupy. And, once more, whatever it is, matters are made much more complicated since ANY sequence must have a nearly exact compliment to replicate.

“Only that product formulation for combining probabilities only works if the two events are completely independent. They aren’t. If you’ve got a soup of nucleotides and polymers, and you get a self-replicating polymer, it’s in an environment where the “target template” is quite likely to occur. So the odds are not independent - and so you can’t use the product rule.”

Come again? Why is the target template likely to occur? And the probability of formation for the template and its compliment are independent. One has nothing to do with the other. One is a folded ribozyme, and the other is a linear RNA molecule. That’s the only way copying can proceed. The formation of one has nothing to do with the formation of the other.

I would say in conclusion that the general point of Berlinski’s essay is *NOT* to present an exact probability; indeed, he says as to the actual proability he hasn’t a clue. Instead it is to get a grasp of how unlikely it *probably* was. Joyce and Orgel BOTH argue it was unlikely. I refer anyone to “The RNA World” 1st, 2nd, and 3rd editions. If anyone is interested, they might read this http://web.wi.mit.edu/bartel/pub/pu[…]cience01.pdf

where David Bartel concludes:

“Our shortest construct retaining activity was 165 nt…Ribozymes with the efficiency, accuracy, and other attributes of an RNA replicase might have to be even larger than this one. However, current understanding of prebiotic chemistry argues against the emmergence of RNA molecules at even a tenth of this length.”

In all reality it IS unlikely that a pool of nucleotides, including cytosine, formed in significant concentration, that some clay catalyzed the formation of chains of nucleotides, and that two complimentary chains were in close enough vicinity to react and stick to each other for the correct amount of time, and that these complimentary chains were catalytic replicases, and that their products were viable enough to avoid error catastrophe.

There may have been an era of evolution BEFORE RNA. Berlinski is just trying to open up the floor to discussion. One cannot dismiss Berlinski’s criticisms without as well dismissing a great many similar criticisms from other prominent scientists–Gerald Joyce, Leslie Orgel, Robert Shapiro, Harold Morowitz, Christian de Duve, etc.

Berlinski may be a cynical crazy old man, but he isn’t stupid.

There may have been an era of evolution BEFORE RNA. Berlinski is just trying to open up the floor to discussion. One cannot dismiss Berlinski’s criticisms without as well dismissing a great many similar criticisms from other prominent scientists—Gerald Joyce, Leslie Orgel, Robert Shapiro, Harold Morowitz, Christian de Duve, etc.

Why not? Garbage in garbage out. Let’s not confuse Berlinski’s simplistic assumptions with the work by scientists such as you mention above.

Could you elaborate as to examples of these scientists, which are similar to Berlinski’s? I exclude Orgel since his work on probabilities seems to suffer from similar follies.

Yes, it’s easy to reject strawman pathways, it’s much harder to come up with plausible pathways.

Gerald Joyce Joyce did make some minable quotes:

The most reasonable assumption is that life did not start with RNA .… The transition to an RNA world, like the origins of life in general, is fraught with uncertainty and is plagued by a lack of experimental data. [2] (http://www.ncbi.nlm.nih.gov/entrez/[…]opt=Abstract)

Others may have raised criticisms of particular scenarios or argued that science lacks the data or knowledge to answer many of these questions but I somehow doubt that these people reject abiogenesis based on the simplistic calculations by Berlinski.

One cannot dismiss Berlinski’s criticisms without as well dismissing a great many similar criticisms from other prominent scientists—Gerald Joyce, Leslie Orgel, Robert Shapiro, Harold Morowitz, Christian de Duve, etc.

All of whom think Berlinski (and ID) are full of crap. (shrug)

it is highly improbable that self replicating RNA arose from a pool of activated nucleotides.

How dreadful.

What, again, did you say the scientific theory offered by ID on this matter is . … ?

Since you like Bartel

The RNA World is a hypothetical ancient evolutionary era during which RNA was both genome and catalyst. During that time, RNA was the only kind of enzyme yet in existence, and one of its chief duties was the replication of RNA. This scenario presupposes that among all possible RNA sequences, there exist RNA replicase ribozymes, capable of synthesizing RNA using the information in an RNA template. The goal of the present work is to provide experimental evidence in support of this conjecture, by isolating such ribozymes in the laboratory. We created a large pool of RNA molecules each containing a previously isolated RNA ligase ribozyme and a large stretch of random RNA. Applying in vitro evolution to select for molecules that could extend a tethered RNA primer using nucleoside triphosphates, we isolated nine distinct classes of polymerase ribozymes. Two of these rudimentary polymerases were further evolved to the point that they each could add 14 nucleotides to an untethered primer-template. One of them was subjected to a detailed further characterization. The polymerization it catalyzes was shown to be accurate, with an average fidelity of nearly 97%. It was shown to be general, with primer-templates of all sequences and lengths being accepted as substrates. Finally, it was shown to be partially processive, with the polymerase achieving processivity as high as 90% in a few instances. The polymerase is currently limited by its low affinity for the primer-template. Future work will focus on improving primer-template binding, in order to produce a polymerase that can synthesize longer RNA.

by Lawrence, Michael S., Ph.D., Massachusetts Institute of Technology, 2005; Advisor: Bartel, David P.

or

On the path to RNA self-replication? Each of these nine rudimentary polymerases is a potentially promising evolutionary intermediate between ligase and replicase. In the case of Pol 1, the promise has already borne fruit: After eight rounds of optimizing selection and a little site-directed tinkering, it gave rise to Evolved Pol 1, the strongest polymerase ribozyme yet reported. Evolved Pol 1 can add 14 nt to one particular PT, but more typically it adds 4—8 nt (Fig. 4Go). Previous work demonstrated its sensitivity to PT sequence: A change as slight as adding or subtracting a single nucleotide from the starting primer altered the observed extension rate by as much as an order of magnitude (Lawrence and Bartel 2003Go). Such sequence-specific variation is not surprising, having been observed as well with proteinaceous polymerases (Echols and Goodman 1991Go; Kunkel 1992Go). Nonetheless, without exception, Evolved Pol 1 has extended every PT tested: It is truly a general RNA polymerase.

New ligase-derived RNA polymerase ribozymes MICHAEL S. LAWRENCE and DAVID P. BARTEL RNA (2005), 11:1173-1180.

I’ve only given the Berlinski paper a quick scan, and on a hunch, did a search for the words “volcanic vent”, “smoker”, and “deep sea” because the last theory I heard about abiogenesis involved deep sea volcanic vents called black smokers.

Berlinski made no note of that theory my search says.

I’m not aware of all the details of the black smoker theory but around the black smokers they’ve found “chemolithoautotrophic hyperthermophilic archaebacteria.”

And archaebacteria are believed to be the most similar of today’s organisms to the ancestral organism from which all life is descended.

Maybe something like a Miller-Urey experiment should be performed based on our knowledge of what a 4 billion year old black smoker’s chemistry would be like?

idon’treallycare:

You sure do have a lot to say, though.

Here’s a bit of math for you:

(un)clever username + self defeating argument* ————————— Troll

*

NO ONE KNOWS HOW COMPLEX AN ACTUAL RIBOZYME REPLICASE MAY NEED TO BE TO SUSTAIN INDEPENDENT SELF-REPLICATION CYCLES

exactly, so how can Berlinski say that it is so astronomically improbable?

What is it with Berlinski anyway? He mystifies me. I’ve been reading A Tour of the Calculus, something he wrote a dozen years ago, in the expectation that a mathematician should do a better job writing about math than he does with biology. His math exposition is mostly okay, if you can tease it out of the heavy-handed metaphors and rhetorical twists that he loves so much. But he recounts one incident in which he allegedly lectured some Hungarian mathematicians on elementary calculus and they were stunned by his insights. Yeah, right. Pompous to the nth degree.

I tried reading some book of his once. A few pages in, he was mocking the other elementary school kids in Gauss’s class for being dumb. I realized I was reading a book by an a55hole, and stopped.

“Berlinski is just trying to open up the floor to discussion.”

Berlinskis purpose seems to fit with “critical analysis” in DI’s main drive to redefine science.

He’s telling us that this is the second paper in a series on “origins” of mind, life and matter (the universe). And he concludes “let us suppose that questions about the origins of the mind and the origins of life do lie beyond the grasp of “the model for what science should be.” In that case, we must either content ourselves with its limitations or revise the model. If a revision also lies beyond our powers, then we may well have to say that the mind and life have appeared in the universe for no very good reason that we can discern.”

So he’s attacking some remaining gaps in knowledge and threatens us with either redefining science (to specifically let a useless creationism in) or let creationism be an alternative ‘explanation’. In the process he doesn’t mention that “I don’t know (yet)” are two perfectly good answers, who don’t necessarily depend on limitations of science.

Unfortunately for creationists, science by it’s very nature doesn’t respond to blackmail.

BTW, I look forward to the “matter” paper, it will both be a laugh and terribly misguided.

Posted by normdoering on April 1, 2006 10:47 PM (e) I’ve only given the Berlinski paper a quick scan, and on a hunch, did a search for the words “volcanic vent”, “smoker”, and “deep sea” because the last theory I heard about abiogenesis involved deep sea volcanic vents called black smokers. Well, in all fairness the January-February issue of American Scientist covered alkaline springs instead of black smokers as the beginnings of life.. Did he at least mention those?

Zeno writes:

But he recounts one incident in which he allegedly lectured some Hungarian mathematicians on elementary calculus and they were stunned by his insights. Yeah, right. Pompous to the nth degree.

Just a geographical nit pick. I read your link, and wonder if Berlinski specifically said the mathematicians were Hungarian. The reason I bring it up is, the lecture occurred at Prague University, which is in the Czech Republic.

Torbjorn wrote:

He’s telling us that this is the second paper in a series on “origins” of mind, life and matter (the universe). And he concludes “let us suppose that questions about the origins of the mind and the origins of life do lie beyond the grasp of “the model for what science should be.” In that case, we must either content ourselves with its limitations or revise the model. If a revision also lies beyond our powers, then we may well have to say that the mind and life have appeared in the universe for no very good reason that we can discern.” [emphasis added– JAH]

It also seems like he’s trying to lead us away from that purpose- and pointless conclusion to the other idea he offered: “revis[ing] the model [for what science should be.]” If he is really into this ID trip, then he’s gonna want to make “science” a field where you can throw in any unmeasurable quality, any untestable idea, and use it as basis for reasoning by pretending you can develop a model to conceptualize it. Now, in tying this with the Templeton Grant and the fellow who decided he’s gonna prove God’s existence scientifically, I’d like to know, if there is a designer, what is it, how is it, how does it affect the universe? Is this effect measurable? Is the force of God’s will measured in amens? “It’s 300 amens on the deometer! Oh, wait, that’s just a dog mating. Must be a miracle!”

Excuse me but with this kind of t.o-evo-cre slang.. ”..Disco Institute’s ex-pat math jester (vying..” - ..on the Thumb.. ..we foreigners have harder times to follow You. Especially if someone visits here only occasionally. (What “ex-pat” means? “vying” means?)

MrKAT:

“Ex-pat” = “expatriate” - someone not living in their own country. For example, a British guy living in France, or a French guy living in Britain.

“vying” = “competing”

Neither of these terms are exclusive to Panda’s Thumb folk.

Is some poster in this discussion writing about himself in the third person and under a pseudonym?

Yes well.…. until he is Peon Reviewed by Dave Scott Springer he will have to wait in line with all the other hopeless cases at the DI Asylum.

Heck Herr DSS seems to know just about as much of that evolution stuff as Berlinski.

I mean what does that guy do anyway? Cry into his Dom Perignon about how bored he is on the right back, Une vie de merde. He should get the DI to pay him in Prozac.

What are the chances that life started from nothing ? One, 100%, a slam dunk, with or without mans imaginary friends.

Berlinski needs to take his head out of his ***

Abiogenesis — In hopes of encouraging rationality on the subject, I hope more of you will read “Into the Cool” and inform me about whether their arguments are worthy of further thought.

I did read/skim a conference proceedings concerning early life and abiogenesis. The most important point I came away with was “we don’t know enough about conditions on/near the surface or in the proto-ocean to really be able to say much of anything.”

Markus wrote:

Well, in all fairness the January-February issue of American Scientist covered alkaline springs instead of black smokers as the beginnings of life.. Did he at least mention those?

I searched for both the words “alkaline” and “springs” and my word searcher didn’t find them.

I tried reading some more of Berlinski’s paper, but it makes me doze off to sleep. Most of what he’s talking about, and more, I found covered in an old booklet I bought at the Chicago planetarium on the subject of “xenobiology” – whether there is life in outer space. Abiogenesis was given a lot of attention.

I did, of course, find “panspermia” here:

Summarizing his own perplexity in retrospect, Crick would later observe that “an honest man, armed with all the knowledge available to us now, could only state that, in some sense, the origin of life appears at the moment to be almost a miracle.” Very wisely, Crick would thereupon determine never to write another paper on the subject—although he did affirm his commitment to the theory of “directed panspermia,” according to which life originated in some other portion of the universe and, for reasons that Crick could never specify, was simply sent here.

I do think the statement there about Crick affirming “his commitment to the theory of ‘directed panspermia,’” is a lie of sorts. Crick did write about panspermia, but I don’t think he committed himself to that idea.

The word “comet” shows up here:

Among the questions is one concerning the nitrogenous base cytosine (C). Not a trace of the stuff has been found in any meteor. Nothing in comets, either, so far as anyone can tell. It is not buried in the Antarctic. Nor can it be produced by any of the common experiments in pre-biotic chemistry. Beyond the living cell, it has not been found at all.

Since when did we search inside comets? How can we be sure there is no nitrogenous base cytosine in comets when there are still scientists speculating we may find nanobacteria in comets?

David Berlinski certainly does seem to be cherry-picking his abiogenesis theories and data.

normdoering Wrote:

I do think the statement there about Crick affirming “his commitment to the theory of ‘directed panspermia,’” is a lie of sorts. Crick did write about panspermia, but I don’t think he committed himself to that idea.

If you read Crick’s book, “Life Itself”, I think you’ll see that normdoering is right and, surprise!, Berlinski’s not.

Crick did write about panspermia, but I don’t think he committed himself to that idea.

As I recall, it was just a semi-jocular method on Crick’s part for discussing the limitations of the various abiogenesis models.

idon’treallycare wrote:

One has nothing to do with the other. One is a folded ribozyme, and the other is a linear RNA molecule. That’s the only way copying can proceed. The formation of one has nothing to do with the formation of the other.

Are you saying RNA cannot code for the making of a ribozyme?

If RNA codes for a ribozyme then their formation is easily tied together in a co-evolutionary spiral. If RNA codes for the structuring of a ribozyme then the RNA that produces more and better ribozymes might easily begin falling into a Darwinian spiral of natural selection.

Is there something I don’t understand about the molecular mechanisms here or is that a logical flaw?

Duh! No, Berlinski did not say they’re Hungarian. It was my oversight entirely. Thanks for the correction, KC.

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Here’s something interesting:

From: http://www.brightsurf.com/news/head[…].article.php? ArticleID=23629

‘Accelerated evolution’ converts RNA enzyme to DNA enzyme in vitro (Scripps Research Institute, 3/28/2006)

Experiment offers fresh insights into the origins of life on Earth

This “evolutionary conversion” provides a modern-day snapshot of how life as we understand it may have first evolved out of the earliest primordial mix of RNA-like molecules-sometimes referred to as the “pre-RNA world”-into a more complex form of RNA-based life (or the “RNA world”) and eventually to cellular life based on DNA and proteins. Nucleic acids are large complex molecules that store and convey genetic information, but can also function as enzymes.

While the transfer of sequence information between two different classes of nucleic acid-like molecules-between RNA and DNA, for example-is straightforward because it relies on the one-to-one correspondence of the double helix pairing, transferring catalytic function is significantly more difficult because function cannot be conveyed sequentially. The present study demonstrates that the “evolutionary conversion” of an RNA enzyme to a DNA enzyme with the same function is possible, however, through the acquisition of a few critical mutations.

The study was released in an advance online version of the journal Chemistry & Biology.

Scripps Research Professor Gerald F. Joyce, a member of the Skaggs Institute for Chemical Biology whose laboratory conducted the study, said, “During early life on earth both genetic information and catalytic function were thought to reside only in RNA. In our study, the evolutionary transition from an RNA to a DNA enzyme represents a genuine change, rather than a simple expansion, of the chemical basis for catalytic function. This means that similar evolutionary pathways may exist between other classes of nucleic acid-like molecules. These findings could help answer some fundamental questions concerning the basic structure of life and how it evolved over time.”

As Francis Crick, the Nobel laureate who, along with James Watson uncovered the double helix structure of DNA, articulated in 1970, all known organisms operate according to the central dogma of molecular biology-that the transfer of sequential genetic information proceeds from nucleic acid to nucleic acid, and from nucleic acid to protein. But a far different situation exists with regard to the transfer of catalytic function, which does not occur sequentially in contemporary biology. The new study shows that catalytic function can be transmitted sequentially between two different nucleic acid-like molecules, suggesting how it might have been conveyed from pre-RNA molecules to RNA during the simpler pre- RNA world period.

There are several candidates for the initial pre-RNA molecule, all of which have the ability to form base-paired structures with themselves and with RNA. Cross-pairing would allow genetic information to be transferred from these pre-RNA molecules to RNA. The catalytic function of these early enzymes might have been transferred to a corresponding RNA enzyme following the acquisition of a few critical mutations, the study said, just as the evolutionary change of a ribozyme to a deoxyribozyme with the same or similar catalytic functions might also have occurred through random mutation and selection.

For the study, an RNA ribozyme was converted to a corresponding deoxyribozyme through in vitro evolution. The ribozyme was first prepared as a DNA molecule of the same RNA sequence but with no detectable catalytic activity. A large number of randomized variations of this DNA were prepared, and repeated cycles of in vitro evolution were carried out. The result was a deoxyribozyme with about the same level of catalytic activity as the original ribozyme.

“The use of in vitro evolution provides the means to convert a ribozyme to a corresponding deoxyribozyme rapidly,” Joyce said. “In the laboratory these procedures allow us to carry out many generations of test tube evolution. The resulting molecules have interesting catalytic properties, they teach us something new about evolution, and they have potential application as therapeutic and diagnostic agents.”

I must observe that the probabilistic arguments in question are not mine, although I certainly endorse them. They were made originally by Gustave Arrhenius, Leslie Orgel and Gerald Joyce (Arrhenius, G., ‘Life out of Chaos,’ in Fundamentals of Life, G. Palyi, Ed., Paris, 2002, 203-210 and Joyce, G.F., & Orgel, L.E., ‘Prospects for Understanding the Origin of the RNA World,’ in The RNA World, 2nd edition, Eds. R. Gesteland, T. Cech, J. Atkins, Cold Spring Harbor Laboratory Press, 1999, 48-77), a point clearly indicated in my essay. In repeating these arguments, I have corrected a trivial error in Arrhenius’ paper, and I have done so with Professor Arrhenius’ permission.

idon'treallycare Wrote:

“The fact that it’s damned unlikely that we’ll see new simple self-replicators showing up today is irrelevant to discussing the odds of them showing up billions of years ago. Why? Because the environment is different. In the days when a first self-replicator developed, there was no competition for resources. Today, any time you have the set of precursors to a replicator, they’re part of a highly active, competitive biological system.”

Um…yeah. I don’t really know what he means by this. The whole premise of the work of Szostak and Bartel is that we can artificially create an environment not only akin to, but much more condusive to the production of self-replicators than the actual primordial ocean. In the real primordial oceans there would not have been selection-amplification techniques (using nifty proteins unavailable in prebiotic times)thus allowing for Darwinian selection before selection was available.

But that’s not what Chu-Carroll is talking about. He’s talking about why we don’t see RNA self-replicators in nature, in response to Berlinski’s statement that “no one has ever seen anything like it.” And his answer is that in modern natural environments, the molecular precursors to a replicator are likely to get eaten by something before the replicator can actually appear (or else the replicator doesn’t last long before it gets eaten.)

You’re asking why, if they’re possible, we haven’t seen them in the lab. That isn’t hard to explain, since lab environments are many orders of magnitude smaller-scale and shorter-lived than the primordial oceans. Amplification techniques can’t fully make up that difference.

NO ONE KNOWS HOW COMPLEX AN ACTUAL RIBOZYME REPLICASE MAY NEED TO BE TO SUSTAIN INDEPENDENT SELF-REPLICATION CYCLES. No one knows how big or small the area (if any ata all) of RNA sequence space that viable replicases occupy.

Well, exactly. So it’s a bad idea of Berlinski’s to arbitrarily decide that the size of that space is 1 sequence, isn’t it?

And, once more, whatever it is, matters are made much more complicated since ANY sequence must have a nearly exact compliment to replicate.

Or it could just make the complement itself, and vice versa. A SunY derivative, for instance, catalyzes the production of the complement of one of its subunits.

“Only that product formulation for combining probabilities only works if the two events are completely independent. They aren’t. If you’ve got a soup of nucleotides and polymers, and you get a self-replicating polymer, it’s in an environment where the “target template” is quite likely to occur. So the odds are not independent - and so you can’t use the product rule.”

Come again? Why is the target template likely to occur? And the probability of formation for the template and its compliment are independent. One has nothing to do with the other. One is a folded ribozyme, and the other is a linear RNA molecule. That’s the only way copying can proceed. The formation of one has nothing to do with the formation of the other.

You’re drawing a fictitious distinction. A single-unit ribozyme is a folded, linear RNA molecule.

I would say in conclusion that the general point of Berlinski’s essay is *NOT* to present an exact probability; indeed, he says as to the actual proability he hasn’t a clue. Instead it is to get a grasp of how unlikely it *probably* was.

So he tried to find a probable probability? I’m not sure how that differs from a probability, except that you get to compute it to fewer decimal places–but whatever his intent, his math is faulty.

There may have been an era of evolution BEFORE RNA. Berlinski is just trying to open up the floor to discussion.

No, he’s not. He’s not interested in discussing pre-RNA abiogenetic models. He mentions them in passing: “[The metabolism-first model] is a work in progress, and it may well be right. Nonetheless, it suffers from one outstanding defect. There is as yet no evidence that it is true.” But he concludes, like any good IDer, that natural science cannot explain the origin of life.

“Analogously, in contemplating the origins of life, much—in fact, more—can be learned by studying the issue from the perspective of coded chemistry. In both cases, however, what seems to lie beyond the reach of “the model for what science should be” is any success beyond the local. All questions about the global origins of these strange and baffling systems seem to demand answers that the model itself cannot by its nature provide.”

It’s certainly true that there are several worthwhile avenues of abiogenetic research that don’t employ an RNA-first model. But Berlinski’s essay isn’t supporting them; it’s arguing that all such research is likely to fail.

It took a while to appear, but now there is a rudimentary analysis of mine on the first paper of Berlinski “On the Origins of Life” at http://austringer.net/wp/?p=252 , where BTW a discussion of the 3rd installment of Berlinski’s “ID the Future” interview are discussed.

Excerpt from the analysis: “Berlinski’s math skills are further looked at on http://zenoferox.blogspot.com/2006/[…]han-you.html which recounts a remarkably naive discussion on limits.

This got me interested in the first paper in Berlinski’s series “On the Origins of the Mind”. I find it remarkable on five accounts.”

“The philosophical treatment goes without further analysis from treating “the idea that human beviour is “the product of evolution”” as “a modest consensus of opinion” to “evolutionary psychology” as a theory of the mind. That seems rather limited for a philosophical study.”

“The mathematical treatment is reminding of the limit treatment. Berlinski, who seems careful when a point that suggest creationism is treated, states that differential equations on one side has “a variable denoting an unknown function; on the other, a description of the rate at which that unknown function is changing at every last moment down to the infinitesimal”. Leaving aside the fact that infinitesimals doesn’t need to be defined to solve such equations (they aren’t real numbers), of course both sides are rates here. … Berlinski finishes off this section with an old description of a “well-posed problem” in analysis as physically useful. The fact that the description is really about partial differential equations goes Berlinski by. Not only are ill-posed problems solvable, by regularization for example, but one of his referents, Thom, uses much more common ill-posed ordinary differential equations in his catastrophe theory. Heck, I’ve used them myself, favourable!”

Excerpt from the discussion: ““There is, in fact, a good deal of heterodoxy on the margins of the scientific world. You look at Tom van Flandern’s web page and the blog that he’s got up and running, it’s just full of attacks on relativity, reports of forgotten experiments, clever little thought experiments, that sort of thing; and oddly enough, a lot of it is quite plausible. Note what I am not saying. I’m not saying it’s true. Just plausible.”

No. it’s not plausible: Jason Rosenhause tears into Tom van Flandern’s claim that special and general relativity aren’t used for GPS (they both are) in http://evolutionblog.blogspot.com/2[…]archive.html . It takes a crank to not recognise another crank.”

I forgot - this excerpt explains the cryptic phrase “the model for what science should be” that Berlinski uses in “On the Origins of Life”:

“The scientific treatment is remarked upon on at http://zenoferox.blogspot.com/2006/[…]goliath.html as “Berlinski is particularly enamored of physics, which is highly mathematized and fraught with numbers.” By way of a *frequently employed phrase*, see below, one can see that it comes from an observation in Hubbard and West textbook on differential equations there they observe that “historically, Newton’s spectacular success in describing mechanics by differential equations was a *model for that science should be*”.

It’s unfortunately a popular philosophical pastime to try to confine the method of science to a specific model. It’s also unclear if it’s doable. After all, we know from Gödel that even rather simple formal systems needs to be indefinitely axiomatised as they are explored. If the result of science is unbounded, the boundedness of the models of it’s methods isn’t immediately obvious. Experience tells us otherwise, different fields use more or less different variants. So far, the method of science is more art than science.

Furthermore, this is an old model. It’s as bad as saying that science is verified by induction, which is also a very old and nonrelevant model that is often and in vain referred to. Differential equations and inductions are sometimes sufficient for establishing and describing hypotheses, but they are not necessary.”

A clarification:

“Excerpt from the discussion: “[Berlinski] “There is, in fact, …”””

Ah, so Berlinski is just a crank.

Got it.

To Anton: It is becoming comical how quickly your level of irritated indignation is rising with each new post. And this is traced to what? A mistake in citing Hazen? An ill cited reference to a paper by Joyce? Yea, that’s enough to dismiss me as a crank. Never mind that /you/ cited Szostak earlier in this exchange without reading his paper. But that’s all right. Let’s look at your criticisms, point by point: “Ah, so when you said, “as for chirality, it was thoroughly discussed by Joyce et al.,” you meant it wasn’t, but it was still interesting. Gotcha.”

Right—well, if you put the entire quote in context:

“As for chirality, it was thoroughly discussed by Joyce et al at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?ho… (Chiral selection in poly©-directed synthesis of oligo(G). (1984) Joyce GF, Visser GM, van Boeckel CA, van Boom JH, Orgel LE, van Westrenen J.) A SIMILAR DISCUSSION WAS TAKEN UP BY ORGEL IN 1998 (L.E. Orgel, PNAS Oligomerization of activated D- and L-guanosine mononucleotides on templates containing D- and L-deoxycytidylate residues) Where he gloomily conlcudes: “It is striking, and possibly relevant to the origin of the RNA world, that primer elongation with D-2MeImpG continues, even if at a somewhat slower rate, past one or two L-dC residues in the template. If the RNA world was the first organized biological world, as often has been proposed, it must have arisen in an environment containing racemic nucleotides. Our findings do not overcome the problems presented by enantiomeric cross inhibition because none of our templates are copied efficiently when the monomeric substrate is racemic. However, our results do suggest that once a “predominantly D-metabolism” was in place, a small proportion of L-monomers in the template or the substrate would not lead to the termination of replication. Nonenzymatic replication may be more resistant to poisoning by the incorrect enantiomer than previously seemed likely.” So, actually, putting the whole thing into a correct context I was referring to how Joyce and Orgel, in two separate papers, were arguing how *nearly* 100% homochiral synthesis is needed. There is a little latitude in incorporating incorrect enantiomers, which is promising as per Orgel, but not enough to write off enantiomeric cross inhibition as a problem in general. So yes, chirality was discussed in its relation to replication, not its original purification. If I was NOT talking about enantiomeric cross inhibition experiments at this point, WHY would I have cited and quoted Orgel? The whole point of the discussion was to set up for the quote by Joyce and Orgel in their 2006 paper: “We conclude that despite significant recent progress, the direct synthesis of the nucleosides and nucleotides from prebiotic precursors in reasonable yield and unaccompanied by large amounts of related molecules could not be achieved by presently known chemical reactions. The only remotely plausible routes to a prebiotic pool of pure _-D-nucleotides would involve a series of reactions catalyzed by minerals or metal ions, coupled with a series of subtle fractionations of nucleotide-like materials based on adsorption on minerals, selective complex formation, crystallization, etc. Even minerals could not achieve on a macroscopic scale one desirable separation, the resolution of D-ribonucleotides from their L-enantiomers. This is a serious problem because experiments on template-directed synthesis using poly© and the imidazolides of G suggest that the polymerization of the D-enantiomer is often strongly inhibited by the L-enantiomer (Joyce et al. 1984). This difficulty may not be insuperable; perhaps with a different mode of phosphate activation, the inhibition would be less severe. However, enantiomeric cross-inhibition is certainly a serious problem.” The quote speaks for itself. The explicitly state minerals COULD NOT achieve the scale of separation needed to avoid cross-inhibition. This is not to say that the papers you read, all three of them or whatever, could not be right in that there is *some* preferential adsorption and separation. It’s just that it is not nearly enough. Or so it seems to Orgel and Joyce and virtually everyone else in the field. That’s why they still research it. The Bonner quote speaks for itself. It was cited by Hazen as an article critical of certain chirality scenarios, and I cited it as such. On to the next quote: “Actually, I think we’ve established that you’ve misread Orgel too, but the board can judge.”

Okay, this is absurd. YOU, Anton, claimed that Orgel’s paper pretty much refuted the fact that a replicase is needed AND YOU promoted the idea that there is somehow a ready alternative with replicase-free templating reactions. I showed in numerous Orgel quotes (I think I quoted the entire Orgel section to which you referred) that he recognized this was contingent upon a number of unlikely prebiotic molecules. More pressing is that this process is slow and error prone, easily succumbing to error catastrophe. Observe Joyce and Orgel, 2006: “Pairs of oligonucleotides containing a single base mismatch, particularly if the mismatch forms a G_U wobble pair, still hybridize as efficiently as fully complementary oligomers, except in a temperature range very close to the melting point of the perfectly paired structure.Maintaining fidelity would therefore be difficult under any plausible temperature regime.” And Kauffman 1996: “The dominant view of life assumes that self-replication must be based on something akin to Watson-Crick base pairing. The ‘RNA world’ model of the origins of life conforms to this view. But years of careful effort to find an enzyme-free polynucleotide system able to undergo replication cycles by sequentially and correctly adding the proper nucleotide to the newly synthesized strand have not yet succeeded [5,6].” Where he thereafter states: “A polynucleotide system based on a ribozyme polymerase able sequentially to add the correct nucleotides (and thus copy itself) might work.” Of course, if this is the only scenario that WILL work, this is exactly the scenario that Berlinski critiqued, along with Joyce and Orgel.

Next quote:

“Why, that you were doing it, and here we go again. The quote above doesn’t conflict with what I said, unless you think that the specificity objection is more strongly negative than the objection that the experimental setting used is unlikely to reflect nature. Which wouldn’t really make sense since the former is a special case of the latter. And it’s certainly evident that Shapiro is not “casting doubt” on the actual work done by Ferris, as you claimed. But, as you say, we can let the board decide.”

Alright, this is just a stupid post. You *suggested* that Shapiro’s criticisms were passive and weak, saying: “As for “casting doubt” on Ferris’ work, he does nothing of the sort.” Really, nothing of the sort? I must be reading the wrong Shapiro. You continue:

“The most negative thing he says is Apart from this, the experiments were conducted in ways that appear unlikely to take place outside a laboratory.…The relevance of these results to events on the prebiotic Earth is therefore questionable.”

Those nice little dots cut out every potent criticism that he leveled against Ferris. If indeed the monomers used were activated by unlikely prebiotic processes, and fresh batches of these prepared monomers were added to the minerals by a well-defined feeding schedule (unlike it would on the prebiotic earth), and we don’t know if this has ever been done in nature, ever, because thus far it has never been observed, well, then yeah, that most certainly challenges Ferris’ results, at least in relation to what was going on 4 billion years ago. That is what I meant when I originally referred to Shapiro and it appears you agree with me.

“Prior to this thread, I hadn’t read any such papers (well, I’d read Orgel 2004 and the occasional layperson’s review article like “Chirality, Magnetism & Light” (Nature 405, 895 - 896 (22 June 2000), but that’s about it.) Hence my request. I’ve since read as many of your citations as I could easily track down and had time for, plus Frank Schmidt’s paper and the two papers he cited, and I’ve poked around a bit in the Nature and “Origins of Life & Evolution of the Biosphere.” That’s it. I wasn’t kidding when I said I was utterly inexpert in this stuff. But one of the nice things about Panda’s Thumb is that it motivates you to actually do some reading when people say strange things and cite the literature in defense.”

Wow. I like how you are so presumptuous as to quickly discredit any fine sense of skepticism I maintain in regard to various origin scenarios as creationism stealth, yet it is clear you don’t have a firm enough grasp of the field to know exactly what is probable and what isn’t. Not that I do either. But it is, like I said before, humorous when someone who has read less than ten papers on the matter criticizes me, a person who has read hundreds. And the criticisms leveled are, what? I misunderstood Hazen’s quote? One error about chirality in a discussion that is over 20 pages long? Nest quote: “Um, ok. Perhaps you should find a bunch of fervent, ultra-orthodox RNA-first supporters and argue with them? Since nobody on this thread meets that description. Indeed, I think the majority of people here have no particular opinion on the RNA-first vs. RNA-later question, and the only one who seems to be strongly in favor of RNA-first is Frank Schmidt, the guy who happens to be doing relevant research. Most everyone else is here to talk about Berlinski.” Which is what I did, and you agreed that Berlinski’s calculation is nearly identical to the one used in Joyce’s 2002 Nature article (and if you don’t believe me I quoted it above). Your objection was that Berlinski didn’t take into consideration other replication scenarios. I showed that these scenarios were seriously flawed. And the disagreement is where? Quote: “A poster, under the pseudonym “idon’treallycare,” who still hasn’t given a real name, immmediately pops up to fiercely defend Berlinski and to claim, incorrectly, that all the claims identified as problematic in his essay are actually endorsed by leading researchers in the field. As noted, for at least the conclusion, this is refuted by Berlinski.” Well, this is a bait-and-switch of sorts. I NEVER argued that Joyce and Orgel, or Bartel and Arrenhius endorse Berlinski’s tentative conclusion that the problem may never be solved. I NEVER said all the CLAIMS were endorsed by leading researchers. I DID SAY THE RELEVANT CALCULATIONS HAVE BEEN ENDORSED BY LEADING RESEARCHERS. By confusing the conclusions with the calculations, you have put words in my mouth.

“This poster quotes large chunks of the literature and presents it as self-evidently supporting their position. Upon review of said quotes and associated citations, it becomes clear that they do not say what the poster claimed they said.” Hahahaha. That’s funny. Outside of chirality, what long quotation have I distorted? You cite a snip of Orgel, and I put the whole Orgel quote up just to let you see where you have misinterpreted and misrepresented him. You cite Joyce, and I put whatever section you are referring to up on the board to again let you see where you are going wrong. This is pathetic. You attempt to discredit me by a misquote from Hazen and an incorrectly placed reference to Shapiro. This is just nuts. And is this the same Anton Mates who said: “There’s no real point in repeating a laundry list of criticisms of the RNA-first model ad nauseam, since I’ve already said several times that I agree with you on that count. I still believe—again, this is just my layman’s opinion, shaped more by who I’ve happened to read than anything—that RNA-later models seem more likely to be correct than RNA-first models, although my recent chirality readings and Frank’s paper have weakened that belief. So yeah, that’s my answer—I like most of the questions you listed (although i) may be less of an issue given Frank’s work.)” Guess where I got those nice questions that you like so much? From the primary literature that I referenced on this board.

So what are we still arguing about again? You accept my criticisms, and I accept my mistake in misciting Hazen. Berlinski was right insofar as calculating the probability for a 100mer replicase. He mentioned we do not know the sequence space of RNA, so we can’t readily determine probabilities. Where is the problem?

Hey idontreallycare, are you gonna answer my simple questions, or aren’t you?

'Rev Dr' Lenny Flank Wrote:

And if Berlinski is still here, I am STILL waiting to hear an answer to my question; Is DI just lying to us when they claim you as an ID supporter?

Maybe you can provide us with a citation of the DI doing that.

idon'treallycare Wrote:

It is becoming comical how quickly your level of irritated indignation is rising with each new post.

Hey, I readily admit that Berlinski and Dembski irritate me. As a math guy myself, I don’t like to see them make the field look bad. ID advocates like yourself, on the other hand, about whom I know next to nothing, don’t really do much other than depress me.

Anyway, since you seem to be repeating your earlier errors, and Berlinski is busy sabotaging himself on the Good Math, Bad Math blog, and my students expect me to actually do some grading on the weekend instead of just arguing with random strangers on the Internet, I’ll probably have to call it quits here.

Anton:

I respect your decision to leave. But what struck me was your comment:

“ID advocates like yourself, on the other hand, about whom I know next to nothing, don’t really do much other than depress me…Anyway, since you seem to be repeating your earlier errors… I’ll probably have to call it quits here.”

First of all, I am highly skeptical of all intelligent design theories thus far. Dembski, as far as I can tell, hasn’t presented anything close to a coherent biological theory of intelligent design. I think the questions they raise are interesting, though, and if they can ever come up with a biological theory of design, good for them. But they have failed thus far, and until they succeed, there is no reason to suspect that they eventually will.

Second, you accuse me of making the same errors. WHAT SAME ERRORS? This is what I asked you in my last post, and you did not address it. The way I see it:

1. I presented a critique of the RNA World scenario. On several points–abioitic nucleotide synthesis, RNA replicase length, the relevance of minerals to the RNA world, and more–you seem to agree that there is no answer as of yet. This is my point and Berlinski’s as well. Where is the error? 2. I said Berlinski’s calculations WERE relevant and can to be found several places in the literature. Of course, you *did* find these calculations in Joyce and Orgel (1999), however you said that there were other ways to go about it than forming an RNA replicase and its template. Berlinski and I have both objected to these alternate schemes, citing Kauffmann and Orgel. You, my friend, have not addressed these criticisms.

3. There was my misreading of Hazen. I was wrong. But that still does not take away the force of Joyce and Orgel’s comments in their 2006 RNA World essay about chirality.

So, in all this, what were my errors again? Where, exactly, am I going wrong? What errors am I repeating. How can you say my criticisms are for the most correct, and then say I am making the same bad arguments. What?

Hmmm. In light of the amount of verbiage s/he’s spilled on this, maybe “idon’treallycare” should change his/her moniker to “igetoffonmysmugconfidencethatberlinskiandiarehigherlevelintellectsthanyoudumbgruntswhoactuallyworkinthefield”

So, in all this, what were my errors again? Where, exactly, am I going wrong? What errors am I repeating. How can you say my criticisms are for the most correct, and then say I am making the same bad arguments. What?

ahhh cmon Anton, don’t cold deck him; you’re a better man than that.

idon’treallycare asked:

So, in all this, what were my errors again?

1) Showing up on Panda’s thumb to show support for a writer for the Discovery Institute.

2) Trying to refute an ongoing area of scientific investigation on a light weight forum like Panda’s Thumb or on a Discovery Institute website instead of in a scientific journal. Here we don’t even have to read you or know what you’re talking about because if your arguments had any weight you’d take them to a more productive audience.

So, idontreallycare, that looks like a “No, I’m not gonna answer your simple questions.”

Right?

Well, I’m now pretty sure that idontreallycare is just Berlinksi.

Which, I suppose, explains why he doesn’t want to answer the question about why, since Berlinski has never done a single piece of original scientific research into the origin of life, anyone should give a rat’s ass what he thinks about it. (shrug)

'Rev Dr' Lenny Wrote:

Well, I’m now pretty sure that idontreallycare is just Berlinksi.

It’s possible—they stopped posting here and at the Good Math, Bad Math blog at about the same time—but it still seems to me unlikely, since they don’t seem to agree on the point of Berlinski’s essay.

Of course “idon’treallycare” could, if s/he’s still reading this, settle the question entirely by posting his/her real name and credentials. Which would also help with arguments from authority such as–

“But it is, like I said before, humorous when someone who has read less than ten papers on the matter criticizes me, a person who has read hundreds.”

–which don’t really work well when you’re anonymous.

Berlinski’s bowed out of the GMBM discussion of his last response, but he said a few amusing things before he left. He responded to Chu-Carroll’s criticism of his assumption of independence with:

The thesis that before probabilities can be applied, dependence must be eliminated resembles the thesis that before a man may be engaged he must be married. It has things backwards. Independence is the crucial assumption of probability theory: it is what distinguishes probability from measure theory.

Of course probability theory doesn’t assume independence at all—that’s why the term “conditional probability” exists. What distinguishes probability theory as a subset of measure theory is something entirely different, namely that the measure of the entire sample space is 1.

And probabilistic models always begin with the assumption of independence. Such models are used precisely because we lack a full and complete picture of the facts. We must thus make some assumption about events, and the standard assumption, absent evidence to the contrary, is that they are independent. Imagine rejecting statistical mechanics on the grounds that, who knows?, some forces might be acting mysteriously to segregate randomly interacting molecules.

Berlinski doesn’t seem to realize that we accept statistical mechanics because it’s experimentally verified, not because we automatically assume independence. Sometimes forces are acting mysteriously to segregate molecules. That’s why, for instance, the composition of our atmosphere varies with height. It’s perfectly valid to suggest models with lots of independence assumptions—independence makes a model simpler, and it’s always good to start simple—but probability calculations (and any other predictions/retrodictions) based on such models are useless until they’ve been tested.

Berlinski also continued to defend his minimum RNA length estimate “of the 100 base pairs required for what Arrhenius calls “demonstrable ligase activity.” He responded to my counter-example of the 61-nucleotide ribozyme of Paul & Joyce with “the demonstration reported…was enzymatically driven; and so not properly speaking relevant to pre-biotic chemistry,” and proceeded to clarify that the enzyme he was referring to was the ribozyme in question!

a) A ribozyme by definition has catalytic powers: hence its name: a ribonucleic ENZYME.

Of course a ligase is also a type of enzyme, so for Berlinski to make a claim about ligases while excluding enzymes is nonsensical. For that matter any RNA replicase would be an enzyme (ribozyme) by definition, so if all enzymes are dismissed as “irrelevant to pre-biotic chemistry,” we don’t have much left to talk about.

b) The R3C ligase ribozyme that Paul & Joyce re-designed is roughly 200 nucleotides (or 68, 600 daltons).

This is irrelevant, since their demonstration didn’t use the original ribozyme but their much shorter, redesigned version.

c) The experiment reported in Paul & Joyce was not only enzyme driven-but RNA-template dependent.

The ribozyme was the template, and was self-complementary.

d) Limitations of this approach are discussed candidly in Paul & Joyce.

This is certainly true.

Ironically, he ended with his rejoinder with:

e) There is a threshold of technical incompetence below which discussion is not profitable.

Someone who I assume was identical with “idon’treallycare” also replied with assorted points as to the fact that Paul & Joyce’s ligase isn’t an evolution-capable replicator, and the difficulty of finding an effective evolution-capable RNA replicator in a random sample. None of these really resolved Berlinski’s own errors.

About this Entry

This page contains a single entry by Richard B. Hoppe published on April 1, 2006 7:09 PM.

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