Richard B. Hoppe posted Entry 2160 on April 1, 2006 07:09 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2155

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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Comment #92797

Posted by idon'treallycare on April 1, 2006 8:03 PM (e)

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/publication_rep…

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.

Comment #92831

Posted by PvM on April 1, 2006 9:15 PM (e)

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/query.fcgi?cm…)

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.

Comment #92836

Posted by 'Rev Dr' Lenny Flank on April 1, 2006 9:19 PM (e)

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)

Comment #92839

Posted by 'Rev Dr' Lenny Flank on April 1, 2006 9:20 PM (e)

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 …. ?

Comment #92873

Posted by PvM on April 1, 2006 10:26 PM (e)

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.

Comment #92882

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.

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?

Comment #92887

Posted by John Marley on April 1, 2006 11:01 PM (e)

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?

Comment #92938

Posted by Zeno on April 2, 2006 1:56 AM (e)

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.

Comment #92947

Posted by steve s on April 2, 2006 2:18 AM (e)

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.

Comment #92957

Posted by Torbjorn Larsson on April 2, 2006 2:39 AM (e)

“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.

Comment #93056

Posted by Markus on April 2, 2006 6:26 AM (e)

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?

Comment #93061

Posted by KC on April 2, 2006 6:35 AM (e)

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.

Comment #93064

Posted by Jaime Headden on April 2, 2006 6:58 AM (e)

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!”

Comment #93131

Posted by MrKAT on April 2, 2006 10:02 AM (e)

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?)

Comment #93139

Posted by Corkscrew on April 2, 2006 10:10 AM (e)

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.

Comment #93149

Posted by Anon on April 2, 2006 10:29 AM (e)

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

Comment #93156

Posted by k.e. on April 2, 2006 10:46 AM (e)

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 ***

Comment #93230

Posted by David B. Benson on April 2, 2006 2:49 PM (e)

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.”

Comment #93236

Posted by normdoering on April 2, 2006 3:07 PM (e)

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 ©. 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.

Comment #93292

Posted by Russell on April 2, 2006 5:49 PM (e)

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.

Comment #93296

Posted by 'Rev Dr' Lenny Flank on April 2, 2006 5:54 PM (e)

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.

Comment #93329

Posted by normdoering on April 2, 2006 7:16 PM (e)

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?

Comment #93348

Posted by Zeno on April 2, 2006 7:46 PM (e)

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

Comment #93380

Posted by 'Rev Dr' Lenny Flank on April 2, 2006 8:51 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #93381

Posted by 'Rev Dr' Lenny Flank on April 2, 2006 8:53 PM (e)

Here’s something interesting:

From:
http://www.brightsurf.com/news/headlines/view.ar…?
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.”

Comment #93414

Posted by David Berlinski on April 2, 2006 10:53 PM (e)

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.

Comment #93434

Posted by Anton Mates on April 3, 2006 12:17 AM (e)

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.

Comment #93562

Posted by Torbjörn Larsson on April 3, 2006 6:15 AM (e)

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/2006/04/so-much-sm… 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/2005_12_11_evo… . It takes a crank to not recognise another crank.”

Comment #93570

Posted by Torbjörn Larsson on April 3, 2006 6:25 AM (e)

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/2006/03/david-berl… 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.”

Comment #93575

Posted by Torbjörn Larsson on April 3, 2006 6:37 AM (e)

A clarification:

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

Comment #93589

Posted by Torbjörn Larsson on April 3, 2006 6:55 AM (e)

Sigh! And a correction:

The excerpts of analysis are from a brief attempt at analysis of Berlinskis paper “On the Origins of the Mind”, preceding “On the Origins of Life”.

Comment #93618

Posted by idon'treallycare on April 3, 2006 7:49 AM (e)

Okay, a few observations…

The first is that most (though not all) of you are morons. It is quite clear that almost all of you have never read a single technical paper dealing with the origin of the RNA world. At very best you puke up some abstracts from pubmed without bothering to read them in their entirety. I especially like PvM’s abstract that linked to Bartels work with a ribozyme that can ligate up to 14 nt, since I myself mentioned it in my original post. I mean, seriously guys. Think about what you write before you write it. This is especially apparent since none of you realize how *replication* must proceed in an RNA world. An RNA polymerase could *only* act to join free floating nucleotides or chunks of nucleotides to a prexisting template. This is a point made by David Bartel in his section of “The RNA World.” An RNA polymerase would act the same way a *PROTEIN* polymerase would today–joining nucleotides to an RNA template. Two RNAs are needed, both in close vicinity, and both capable of recognizing the other. But since almost NONE of you have read a paper about prebiotic RNA formation, I guess you wouldn’t know.

And the RNA sequence has to be a compliment, Mr. Anton Mates, because if it isn’t THERE IS NO HEREDITY! Idiot. Yes, theoretically polymerase RNAs could join and break other RNAs at random. The only problem is that if by chance a viable replicase sequence was ever hit upon it would be randomized and garbled very soon due to the fact that the polymerase that joined it the first time would be unable to recognize it as a viable template to make more polymerases, since by definition the folded polymerase is joining at random. If you don’t believe me go read a paper by Gerald Joyce. The RNA World second edition would be nice. Joyce and Orgel have a lovely section dealing with just this point. Joyce also has a recent paper in Nature talking about this.

So before an army of you beign lighting the fireworks and starting the parade, just remember that the work of Berlinski which you are so very eager to discredit is squarely based upon what the major scientists in the field of the origin of life have been saying for some time.

Comment #93631

Posted by idon'treallycare on April 3, 2006 8:22 AM (e)

And one last thing…

Mr. Mates–

Since you linked to Szostak I must ask you if you have read the paper in question, and whether or not you can put it into context. Since you seem to be the type that likes lay instead of technical scientific reads, refer to this section by Carl Zimmer at http://www.carlzimmer.com/articles/2004/articles… about just the paper you linked:

“In 1991 he (Szostak) and graduate students Jennifer Doudna and Rachel Green succeeded in making a crude prototype. They created a molecule that could grab shorter chunks of RNA and make copies of them. It was a remarkable achievement, but Szostak knew it was only a small step toward something that could accurately be called alive.

Enzymes in living cells can make duplicate RNA sequences one nucleotide at a time. Szostak’s ribozyme could only piece together chains of RNA, each of which was several nucleotides long. And his new molecule was grievously sloppy, making regular copying errors. In a single generation, it could turn a life sustaining genetic code into sheer gibberish.”

Of course, this is what Gerald Joyce has said about many experiments thus far in several reviews. The consensus so far is that ribozyme replicases *probably* exist in sequence space of RNAs somewhere, though many would argue that it would take 200 + nucleotides to do the trick (as I said and quoted in my first post). It would be highly improbable for such a ribozyme to arise de novo, or at least it would *seem* highly improbable, as Szostak himself admits. This is why he proposes an era of evolution before RNA (although this era faces its own hurdles.)

I’m done posting here. But in conclusion, I will quote Berlinski above:

“Posted by David Berlinski on April 2, 2006 10:53 PM (e)

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.”

Would someone please address this?

Comment #93645

Posted by Torbjörn Larsson on April 3, 2006 9:10 AM (e)

“Would someone please address this?”

Hasn’t PvM done that? “I exclude Orgel since his work on probabilities seems to suffer from similar follies.”

Comment #93667

Posted by normdoering on April 3, 2006 10:08 AM (e)

idon’treallycare wrote:

… most (though not all) of you are morons.

At which point Lenny and I look at each other and half agree with you.

You’re right about one thing – I’m not reading the technical papers (at least not in biology, computer science is another story) – I’m not even bothering to read Berlinski.

I’m waiting to see what someone like PvM can teach me.

I suspect, however, one error in your thinking will be here:
“… *replication* must proceed in an RNA world. An RNA polymerase could *only* act to join free floating nucleotides or chunks of nucleotides to a preexisting template… Two RNAs are needed, both in close vicinity, and both capable of recognizing the other.”

That mentalistic concept of “recognizing” something is not a black and white, either/or, concept. Primitive forms could half recognize and 1/3rd recognize I’m betting.

I, for one, only partly recognize your errors.

Comment #93673

Posted by PvM on April 3, 2006 10:22 AM (e)

So before an army of you beign lighting the fireworks and starting the parade, just remember that the work of Berlinski which you are so very eager to discredit is squarely based upon what the major scientists in the field of the origin of life have been saying for some time.

Berlinski’s arguments may be inspired by some of the research in this area but his calculations seems to be simplistic. As I said, it is easy to find small numbers, it is much harder to find plausible pathways. Berlinski has taken the easy route to inflate numbers based on a strawman scenario. Scientists in the mean time are addressing how RNA world and possible predecessors to it may have played a role.

You yourself argue quite well that ‘no one knows how complex an actual ribozyme replicase may need to be to sustain independent self-replication cycles’ and yet this ignorance has not stopped Berlinski from inflating the numbers?

In addition to the design of novel DNA catalysts, we have been interested in the origin of the first simple self replicating systems. Simple replicators based on short oligonucleotides as well as peptides have been demonstrated. We have designed a cross-catalytic system based on a well characterized peptide-RNA aptamer interaction, in which the peptide serves as a template for the ligation of RNA aptamer half-molecules. Our results demonstrate that the peptide could specifically enhance the rate of RNA ligation, and suggest the possibility for increased diversity of early replicators.

Design and evolution of functional nucleic acids
by Levy, Matthew, Ph.D., The University of Texas at Austin, 2003, 197 pages;

Also

Short oligonucleotide and peptide replicators have been described. To determine whether cross-replication could have occurred between such systems, we have attempted to show that peptides can specifically template the ligation of nucleic acids. A complex between a 35-mer anti-Rev RNA aptamer and a 17-mer arginine-rich motif (ARM) peptide from the HIV-1 Rev protein served as a model system. Aptamer half-molecules were activated for ligation via two activation chemistries, representing two distinct kinetic possibilities for early replicators. Cyanogen bromide activation was transient relative to oligonucleotides that terminated with a 5’-iodine and a 3’phosphorothioate, respectively. The Rev ARM specifically enhanced the degree or rate of ligation by both methods: there was a 10-fold increase in the production of full-length aptamer in the presence of cyanogen bromide and a 5.9- to 7.6-fold enhancement in the rate of ligation for stably activated aptamer half-molecules. These results support the possibility that life could have originated with peptide replicators and transitioned to nucleic acid replicators or that peptide and nucleic acid replicators could have been interdependent.

Peptide-Templated Nucleic Acid Ligation, Matthew Levy and Andrew D. Ellington

So what is your best explanation as to how life arose?

Comment #93699

Posted by normdoering on April 3, 2006 12:04 PM (e)

idon’treallycare wrote:

And his new molecule was grievously sloppy, making regular copying errors. In a single generation, it could turn a life sustaining genetic code into sheer gibberish.

I believe that’s called descent with modification. Yes it could produce gibberish and most of the time it will – but sometimes it won’t. Sometimes it will produce a better self-replicator and that pattern will survive while the gibberish pattern dies.

Do you actually not understand the Darwinian concept of evolution – or am I missing something? Excuse me for being a moron. But I don’t get idon’treallycare’s argument.

Comment #93702

Posted by k.e. on April 3, 2006 12:09 PM (e)

Indeed PvM

So what is your?[idon’treallycare’s]? best explanation as to how life arose?

Apart from sliding ‘Blastfromthepast like’ along the bleeding edge of frontier reports and then clutching at a straw ‘see you are all wrong about everything, my personal fantasy is better than your science’
idon’treallycare’s genius does not extend to doing any actual science such as ‘here is a hypothesis try and break it’ ….he’s just another god-bothering coward.

Has this happened in the past ?

Lets look through the annals of human stupidity.

Hog Mythology.

hey idon’treallycare this is really basic stuff.
Are you suggesting that science is NOT going to find a NON-natural explanation for abiogenesis? ….Of course you’re not that would be crazy.

So which cynical gap do you choose..oh yes the “I’ll use the latest research to debunk …er the latest research”.
What theory is that? The “idon’treallycare knows goddidit everytime a new natural explanation removes our ignorance?But produces another question”

You said
Um…yeah. I don’t really know what he means by this.
in reply to
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.”

means ….something ate it.
Simple deduction my dear idon’treallycare …..alimentary really.

Ah but….. your not crazy, cynical (according to you) or stupid idon’treallycare are you? You add the additional rider that EVEN IF a chemical soup in a lab manages to produce a prebiotic replicator it will not satisfy your vision of how the earth existed at the time of the big G’s miracle. Sort of having a bet each way. Can’t lose really…except it’s not science…dang you lost again.

But hey I don’t have a problem with your miracle you can have as many as you want, in any order you want, mix and match creation or plain vanilla with matching cuff links.

Just explain to me how that first replicator wrote the old testament and you’ve won me over.

Comment #93737

Posted by Anton Mates on April 3, 2006 1:46 PM (e)

idon'treallycare wrote:

The first is that most (though not all) of you are morons. It is quite clear that almost all of you have never read a single technical paper dealing with the origin of the RNA world. At very best you puke up some abstracts from pubmed without bothering to read them in their entirety……This is especially apparent since none of you realize how *replication* must proceed in an RNA world. An RNA polymerase could *only* act to join free floating nucleotides or chunks of nucleotides to a prexisting template.

It’s funny you should say that, especially after mentioning Orgel, since I was reading his 2004 paper Prebiotic Chemistry and the Origin of the RNA World, and he has a nice section on experiments concerning template-directed synthesis without the help of RNA polymerases. What was that you were saying about not reading papers in their entirety?

And the RNA sequence has to be a compliment, Mr. Anton Mates, because if it isn’t THERE IS NO HEREDITY! Idiot.

Unless a template isn’t necessary, as you yourself mention below, because the polymerase replicates itself by ligation of pre-existing subsequences rather than by facilitating template synthesis.

And of course even if a complementary template is required, if the RNA sequence is self-complementary, or if the complement is generated from the original through non-enzymatic template synthesis, then Berlinski remains incorrect (as do you) in arguing that the production of the sequence and of its complement are independent of one another.

Yes, theoretically polymerase RNAs could join and break other RNAs at random. The only problem is that if by chance a viable replicase sequence was ever hit upon it would be randomized and garbled very soon due to the fact that the polymerase that joined it the first time would be unable to recognize it as a viable template to make more polymerases, since by definition the folded polymerase is joining at random.

…unless the polymerase isn’t joining things at random, but due to its own action or the sequence distribution of the RNAs in its environment, is preferentially producing copies of itself. As in Joyce & Paul’s 2002 paper A self-replicating ligase ribozyme.

So before an army of you beign lighting the fireworks and starting the parade, just remember that the work of Berlinski which you are so very eager to discredit is squarely based upon what the major scientists in the field of the origin of life have been saying for some time.

I think you may not have read Berlinski’s whole essay. No one’s arguing that there aren’t promising alternatives to RNA-first models. (I’m hardly an expert, but the Orgel paper I cited above makes a very convincing case for pre-RNA abiogenesis.) But Berlinski’s criticism of the latter is based on bad math, and again, he’s arguing that natural science cannot explain abiogenesis, period. I’ll repost part of his conclusion, bolding for emphasis:

“It is now more than 175 years since Friedrich Wöhler announced the synthesis of urea. It would be the height of folly to doubt that our understanding of life’s origins has been immeasurably improved. But whether it has been immeasurably improved in a way that vigorously confirms the daring idea that living systems are chemical in their origin and so physical in their nature—that is another question entirely.

In “On the Origins of the Mind,” I tried to show that much can be learned by studying the issue from a computational perspective. 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.”

Do you really think the above follows from the work of Joyce or Orgel, or that they would agree with this?

Mr. Mates—

Since you linked to Szostak I must ask you if you have read the paper in question, and whether or not you can put it into context.

I’m afraid I haven’t read it; I only had access to the abstract. As for context…

Since you seem to be the type that likes lay instead of technical scientific reads, refer to this section by Carl Zimmer at http://www.carlzimmer.com/articles/2004/articles…… about just the paper you linked:

“In 1991 he (Szostak) and graduate students Jennifer Doudna and Rachel Green succeeded in making a crude prototype. They created a molecule that could grab shorter chunks of RNA and make copies of them. It was a remarkable achievement, but Szostak knew it was only a small step toward something that could accurately be called alive.

Enzymes in living cells can make duplicate RNA sequences one nucleotide at a time. Szostak’s ribozyme could only piece together chains of RNA, each of which was several nucleotides long. And his new molecule was grievously sloppy, making regular copying errors. In a single generation, it could turn a life sustaining genetic code into sheer gibberish.”

This doesn’t seem to be relevant to the point I was making, namely that (contrary to your claim) an RNA replicator need not require a pre-existing complementary strand to operate. It seems I got the context right after all.

Comment #93740

Posted by Anton Mates on April 3, 2006 1:53 PM (e)

By the way, I recommend Carrier’s The argument from biogenesis: Probabilities against a natural origin of life as a very lucid review of probability estimates in this area, along with the reasons why they’re pretty much all invalid. And yes, I have actually read it!

Comment #93746

Posted by Anton Mates on April 3, 2006 2:02 PM (e)

Zeno wrote:

What is it with Berlinski anyway?
[snipped]…he recounts one incident in which he allegedly lectured some Hungarian mathematicians on elementary calculus and they were stunned by his insights. Yeah, right.

Oh, my. I hope you don’t mind, but this is just so incredible that I had to swipe it from your blog. Berlinski’s explaining limits–of the function f(x)=x^2, no less–to an audience of mathematicians:

“I mean,” I say, “what happens to the values of f as its arguments approach 3?”
I look out toward my audience. Swoboda and Schweik are looking at me intently, their faces serene, without irony. It is plain to me that they do not know the answer yet.
“They approach, those values, the number 9, so that the function is now seen as running up against a limit, a boundary beyond which it does not go.”
Swoboda leans back and sighs audibly, as if for the first time he had grasped a difficult principle. The room, with its wooden pews and narrow blackboard, is getting close.
I say, “The concept of a limit, as it is applied to functions, is forged in the fire of these remarks.”

Wow. And he even throws in a bonus error by (incorrectly) implying that a function can’t surpass its limit at a point as it approaches that point. No wonder the poor mathematician was sighing.

Comment #93809

Posted by idon'treallycare on April 3, 2006 5:48 PM (e)

Anton Mates, and the rest of the board:

Anton, I’m going to commend you for at least *attempting* to read an actual peer-reviewed paper. That is more than I can say for most all of the rest. And I will retract my comment that you are an idiot.

Now with the preliminaries aside, let’s get to that paper by Orgel. I read that paper some time ago and struck my interest that this paper, which you hold in very high regard, IN NEARLY EVERY RESPECT PARALLELS BERLINSKI’S PAPER. From Abiotic synthesis all the way to RNA formation. I will quote the concluding paragrah from Orgel’s paper:

“Although tentative solutions to most of the problems that arise in attempting to achieve a prebiotic synthesis of RNA have been offered, nearly every one of them, as we have seen, is problematic. The synthesis of ribose leads to a complex mixture of sugars, with ribose as only a minor constituent under most conditions. The synthesis of purines nucleosides directly from ribose and a base is inefficient, while the only available prebiotic synthesis of the pyrimidine nucleosides starts from arabinose-3-phosphate, a marginally prebiotic molecule. Phosphorylation of nucleosides leads to a complex mixture of isomeric mono- and polyphosphates, while polymerization even of pure nucleoside-5’-phosphates leads to a product with mixed phosphodiester linkages. The phosphorimidazolides used in most studies of both template-directed and of template-independent synthesis are unlikely to be prebiotic molecules. It is possible that all of these, and many other difficulties will one day be overcome and that a convincing prebiotic synthesis of RNA will become available. However, many researchers in the field, myself included, think that this is unlikely and that there must be a different kind of solution to the problem of the origin of the RNA World.”

Compare this to Berlinski’s concluding paragraph:

“At the conclusion of a long essay, it is customary to summarize what has been learned. In the present case, I suspect it would be more prudent to recall how much has been assumed: First, that the pre-biotic atmosphere was chemically reductive; second, that nature found a way to synthesize cytosine; third, that nature also found a way to synthesize ribose; fourth, that nature found the means to assemble nucleotides into polynucleotides; fifth, that nature discovered a self-replicating molecule; and sixth, that having done all that, nature promoted a self-replicating molecule into a full system of coded chemistry. These assumptions are not only vexing but progressively so, ending in a serious impediment to thought….This view of things—metabolism first, as it is often called—is not only intriguing in itself but is enhanced by a firm commitment to chemistry and to “the model for what science should be.” It has been argued with great vigor by Morowitz and others. It represents an alternative to the RNA world. It 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…. Worse things have happened. In the end, these are matters that can only be resolved in the way that all such questions are resolved. We must wait and see.”

Anton, and the rest of the Pandas Thumb, can you see no parallels? Why are you jumping on to Berlinski again?

Now, on to the meat of the discussion–self-replicating RNA. Berlinski’s calculation *IS* incomplete in that he is highlighting the idea that it is NAIVE TO THINK ABOUT RIBOZYME REPLICASES EMMERGING FROM POPULATIONS OF RANDOM SEQUENCE RNA. In this view there is a folded ribozyme to do the work of copying, and a template to join nucleotides to, one-by-one, to get another RNA. This is how most pseudointellecutal internet jockies think it is done, and they are wrong. Not just in Berlinski’s view, but in Joyce and Orgels as well.

There IS another way to think about the problem, though, and that is non-enzymatic synthesis cycles of templated and untemplated reactions. This is what is mentioned in Orgels paper. THE PROBLEM IS, HOWEVER, IT HAS NEVER BEEN DEMONSTRATED THAT ANYTHING LIKE THIS IS POSSIBLE UNDER PREBIOTIC CONDITIONS. I refer to Orgel’s own paper for the quotes, each followed by some comments:

Orgel: “Whenever a complementary complex is formed, the template influences the ligation reaction, but the devil is in the details. The ligation reaction may be more or less efficient and may lead to a greater or lesser excess of 3’-5’-phosphodiester linkages over 2’-5’-linkages. The objective of most research programs in this field has been to find conditions that lead to the efficient synthesis of predominantly 3’-5’- linked oligonucleotides for as broad a range of template sequences as possible.”

COMMENT: The problem, as I stated in my last post, is finding a cycle of reactions that will NOT garble either the message or the medium. In this context, the chemical linkages (3’-5’-linked oligonucleotides) need to be specific if there is to be a prayer of hope for an RNA-first model. However, as Orgel expands on, this is not quite so easy.

ORGEL: “ was found, surprisingly, that when 2-methyl imidazole replaced imidazole in the activated nucleotide (IX; to give 2-MeImpG) the synthesis of long oligo(G)s on a poly© template no longer required the presence of any metal ion other than Mg++. In this context, 2-Me-imidazole seems unique since neither imidazole nor its 2-ethyl derivative can substitute for it. Furthermore, the product oligomers formed from 2-MeImpG are almost exclusively 3’-5’-linked (Inoue & Orgel, 1981). One further advantage of using the 2-methyl imidazolides is that it allows the copying of heteropolymers containing all four bases, but only if the template contains at least 60% of C residues (Joyce, 1987). This latter restriction rules out the possibility of repeated rounds of replication, since the product of a successful template-directed oligomerization contains at most 40% of C residues and cannot, therefore, act efficiently as a template.”

COMMENT: Please notice that in this reaction a premdominance of cytosine must be present. It must be dryly noted that Orgel in the same paper previously attacked abiotic cytosine synthesis, deeming it highly improbable, and saying that modest amounts (~5%) are by far the best honest yields in any prebiotic experiment thus far. So if templates in THIS scenario were to replicate, a large excess of cytosine was available (enough to account for over half of the nucleotides in any growing RNA structure), yet as far as we know it appears in nature in only minute traces, not nearly enough to power replication. Not only this, BUT THE REACTION CAN ONLY PROCEED FOR ONE CYCLE AND NO MORE, SINCE +60% C IS NEEDED AND IN THE NEXT CYCLE THERE IS ONLY 40% AVAILABLE DUE TO WATSON-CRICK BASE PAIRING!

“Incorporation of G opposite C in the template is most efficient, while incorporation of U opposite A is least efficient. Incorporation of A opposite U or of C opposite G is of intermediate efficiency. A pair of adjacent A residues in the template is an almost complete barrier to further synthesis. The fidelity of these reactions is usually very good, but with one notable exception: wobble pairing of G opposite U leads to extensive misincorporation of G, particularly on some RNA templates. The results of a long series of detailed studies show, therefore, that a wide variety of DNA or RNA sequences can be copied, but replication is not possible in this system.”

COMMENT: The last sequence speaks for itself. In additon, note the necessity of Cytosine.

“Any prebiotic synthesis that yields ribonucleotides would produce racemates. Unfortunately, the L-enantiomers of activated nucleotides are efficient inhibitors of template-directed synthesis using the naturally occuring D-enantiomers (Joyce et al., 1984). This difficulty, often described as enantiomeric cross-inhibition, is not easily overcome without making substantial changes to the nature of the backbone of the template (Kozlov et al., 1999a). This is a major obstacle to any scheme for polynucleotide replication from plausibly prebiotic, monomeric substrates”

COMMENT: This is perhaps the largest objection to the model. This model REQUIRES a pure homochiral template and chunks of nucleotides that will attach to the template, and Orgel himself admits that the solution to the problem has not presented itself.

ORGEL: “Encouragingly, the ligation of 5’-triphosphates, a close analog of enzymatic ligation, yields almost exclusively 3’-5’-linked products. In the context of prebiotic chemistry, 3’-5’-linked oligonucleotides are superior to mononucleotides as substrates with respect to regiospecificity, and they permit ligation over wider temperature ranges. However, it is not obvious that homochiral, exclusively 3’-5’-linked oligomers are plausible prebiotic molecules (see previous section), and the fidelity of template-directed ligation of oligomers is lower than the fidelity of oligomerization of monomers.”

COMMENT: As stated in both this paragraph and the conclusion, THE MOLECULES NECESSARY FOR A CYCLE OF NONENZYMATIC REPLICATION CYCLES IS CRITICALLY DEPENDENT ON UNLIKELY PREBIOTIC MOLECULES.

So any alternatives to Berlinski’s calculations right now are dead ends.

I hope this discussion ends at this. I can’t see how it can go any further.

Comment #93815

Posted by 'Rev Dr' Lenny Flank on April 3, 2006 6:07 PM (e)

just remember that the work of Berlinski which you are so very eager to discredit is squarely based upon what the major scientists in the field of the origin of life have been saying for some time.

Let’s just remind everyone that the total number of peer-reviewed science journal articles based on ID “theory” published by Berlinski (or any other IDer) regarding abiogenesis (or anything else) is … well … zero.

Zip. Zilch. Nada. None. Not a single one.

I wonder why that is?

Comment #93816

Posted by 'Rev Dr' Lenny Flank on April 3, 2006 6:10 PM (e)

(snip big long God of the Gaps argument)

How dreadful.

What, again, did Berlinski say the alternative explanation offered by ID, uh, “theory” is …. . ?

Ohhhhhh, that’s right— he DIDN’T, did he.

I wonder why that would be?

Comment #93825

Posted by Mike Z on April 3, 2006 6:25 PM (e)

Interesting…Seems like much of that dispute was over who’s an ignoramus and who isn’t. Otherwise, all participants seem to agree that there are many unsolved problems within the origins of life field.

But, there is still the question of whether those problems will ever be solved. If the probability of life forming spontaneously is extremely low–no matter what the environmental conditions–then the episode may be very difficult or impossible to figure out scientifically. That is, if it was some completely unique concurrence of highly improbable events that got things going, then science may never be able to pin down exactly what those events were. Certainly, the creationist camp interprets this as “god did it,” but even some people who are otherwise committed to naturalism may still think that science will never be able to figure it out because there are not enough clues left for us examine.

On the other hand, if the emergence of life is quite likely–given some common general environmental conditions–then scientific investigation is quite capable of figuring it out eventually. Needless to say, this attitude is common among origin researchers.

However, actually calculating the probabilities is extremely problematic because the numbers are based on many controversial assumptions about chemical behavior and the conditions of the early earth, to say nothing of the estimated probability of finding some unknown pathway to fill the gaps. So, when Berlinski (or anyone else) claims to have come up with a probability calculation for the spontaneous formation of something like the RNA world, we should all be very skeptical. It seems that Berlinski is singled out for PT wrath because he uses his results to argue for ID, not because other people have better calculations that show the RNA world to be highly likely.

Comment #93832

Posted by 'Rev Dr' Lenny Flank on April 3, 2006 6:40 PM (e)

But, there is still the question of whether those problems will ever be solved.

No, the real question is HOW they are to be solved.

Science proposes to solve them through experimentation and research.

ID proposes to “solve” them by declaring “You can’t explain it, so Godiddit!!!!”

See the difference?

Can you cite any ID-sponsored peer-reviewed research into the origin of life?

Me neither. (shrug)

Comment #93838

Posted by 'Rev Dr' Lenny Flank on April 3, 2006 7:01 PM (e)

all participants seem to agree that there are many unsolved problems within the origins of life field.

Indeed, there are many unsolved problems within ANY field of science. After all, that is why scientists still have jobs, and haven’t all retired to the Bahamas by now. (shrug)

The fundies, for some oddball reason, seem willing to bet their entire religious faith on the hope that certain problems will NEVER be solved.

Every time they have made that bet before, they have lost. Every time.

I doubt they’ll do much better this time. (shrug)

Comment #93844

Posted by normdoering on April 3, 2006 7:09 PM (e)

…It is possible that all of these, and many other difficulties will one day be overcome and that a convincing prebiotic synthesis of RNA will become available. However, many researchers in the field, myself included, think that this is unlikely and that there must be a different kind of solution to the problem of the origin of the RNA World.”

Compare this to Berlinski’s concluding paragraph:

“…These assumptions are not only vexing but progressively so, ending in a serious impediment to thought….This view of things—metabolism first, as it is often called—is not only intriguing in itself but is enhanced by a firm commitment to chemistry and to “the model for what science should be.” It has been argued with great vigor by Morowitz and others. It represents an alternative to the RNA world. It 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…. Worse things have happened. In the end, these are matters that can only be resolved in the way that all such questions are resolved. We must wait and see.”

I see a major difference between those two views. One has confidence in the scientific method and our human ability to solve problems and the other, Berlinski’s, is defeatist and uninterested in trying to solve the problem (he will merely wait and see rather than engage it). Without explicitly coming out and saying it, Berlinski’s argument endorses a god-of-the-gaps view of the problem.

The critical difference is spin and attitude.

Comment #93860

Posted by Anton Mates on April 3, 2006 8:11 PM (e)

Mike Z wrote:

But, there is still the question of whether those problems will ever be solved. If the probability of life forming spontaneously is extremely low—no matter what the environmental conditions—then the episode may be very difficult or impossible to figure out scientifically. That is, if it was some completely unique concurrence of highly improbable events that got things going, then science may never be able to pin down exactly what those events were. Certainly, the creationist camp interprets this as “god did it,” but even some people who are otherwise committed to naturalism may still think that science will never be able to figure it out because there are not enough clues left for us examine.

I think that’s certainly true. Indeed, even if the formation of life turns out to be particularly probable, we’ll always be left uncertain as to exactly which possible pathway represents its origin. The scientist will admit the uncertainty, the creationist/IDer will say “therefore God.”

Comment #93879

Posted by Mike Z on April 3, 2006 8:50 PM (e)

Lenny–
Yes, I see the difference. That is why I explained the difference in my comment.

I apologize if I was not sufficiently clear, but I was not trying to defend a non-scientific approach. Rather, I was merely trying to clarify the positions on both sides, and also to point out that there are actually some people who claim to follow a completely naturalistic research program yet also believe that research into life origins will never uncover the truth.

Personally, I’m in favor of the “let’s try everything we can think of to figure it out scientifically and never give up” camp.

Comment #93884

Posted by Sir_Toejam on April 3, 2006 9:05 PM (e)

After all, that is why scientists still have jobs, and haven’t all retired to the Bahamas by now.

aside from the fact that not many could afford to, either.

;)

Comment #93889

Posted by Mike Z on April 3, 2006 9:15 PM (e)

Anton–
Excellent point. How to narrow down the options?
Maybe the emergence of life is TOO probable! :)

Comment #93891

Posted by Anton Mates on April 3, 2006 9:21 PM (e)

idon'treallycare wrote:

Anton, I’m going to commend you for at least *attempting* to read an actual peer-reviewed paper. That is more than I can say for most all of the rest. And I will retract my comment that you are an idiot.

Well, I’m very glad to have earned some measure of respect from a random anonymous Internet poster!

Now with the preliminaries aside, let’s get to that paper by Orgel. I read that paper some time ago and struck my interest that this paper, which you hold in very high regard, IN NEARLY EVERY RESPECT PARALLELS BERLINSKI’S PAPER. From Abiotic synthesis all the way to RNA formation. I will quote the concluding paragrah from Orgel’s paper:

In the interest of accuracy, I will point out that your quote is not the concluding paragraph, nor anywhere near the conclusion. It is, rather, the introduction to the section on “RNA-later” scenarios. Moreover, if we actually go to his concluding summary, we see that Orgel’s dissatisfaction with the RNA-first scenarios centers on prebiotic synthesis of nucleotides in the first place; he finds the development of a replicator from a pre-existing RNA library quite plausible:

“The most impressive advances in the past decade or so have come in the field of RNA selection. Enough is already known to suggest that each of the steps neded to evolve from a library of randomly sequenced double-stranded RNAs to a self-sustaining RNA organism can be demonstrated in laboratory experiments.”

Compare this to Berlinski’s concluding paragraph:

This is also not the actual concluding paragraph of Berlinski’s essay. I hope you’re not doing this on purpose. I have my doubts, however, mostly because the bit you omitted was precisely what I posted before–and heck, I’ll do it again now:

“It is now more than 175 years since Friedrich Wöhler announced the synthesis of urea. It would be the height of folly to doubt that our understanding of life’s origins has been immeasurably improved. But whether it has been immeasurably improved in a way that vigorously confirms the daring idea that living systems are chemical in their origin and so physical in their nature—that is another question entirely.

In “On the Origins of the Mind,” I tried to show that much can be learned by studying the issue from a computational perspective. 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 goes without saying that this is a tentative judgment, perhaps only a hunch. But 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.

Worse things have happened. In the end, these are matters that can only be resolved in the way that all such questions are resolved. We must wait and see.”

This makes the difference between the two viewpoints quite clear, just as Lenny reiterated. Orgel is arguing for scientific alternatives to RNA-first abiogenetic models, while Berlinski is arguing that no scientific model will suffice. (Unless science is “revised,” wink wink!)

Moreover, Berlinski’s math is–no matter where he borrowed it from, and after the “limits” debacle I have my doubts that he did so accurately–invalid.

Anton, and the rest of the Pandas Thumb, can you see no parallels? Why are you jumping on to Berlinski again?

Because it’s not enough to just borrow some valid arguments from researchers in the field–if he also employs bad math and comes to an unjustified conclusion, that merits criticism.

Again, nobody here (as far as I know) is championing RNA-first models or criticizing any particular actual researcher of the origins of life. We’re just saying Berlinski wrote a lousy essay. That’s it.

Now, on to the meat of the discussion—self-replicating RNA. Berlinski’s calculation *IS* incomplete in that he is highlighting the idea that it is NAIVE TO THINK ABOUT RIBOZYME REPLICASES EMMERGING FROM POPULATIONS OF RANDOM SEQUENCE RNA. In this view there is a folded ribozyme to do the work of copying, and a template to join nucleotides to, one-by-one, to get another RNA. This is how most pseudointellecutal internet jockies think it is done, and they are wrong. Not just in Berlinski’s view, but in Joyce and Orgels as well.

I’ve already shown that you’re incorrect in attributing the above view to Orgels, but let’s compare this to Berlinski’s own words:

“The odds, then, are daunting; and when considered realistically, they are even worse than this already alarming account might suggest. The discovery of a single molecule with the power to initiate replication would hardly be sufficient to establish replication. What template would it replicate against? We need, in other words, at least two, causing the odds of their joint discovery to increase from 1 in 10^60 to 1 in 10^120.”

It seems clear that “how most pseudointellecutal internet jockies think it is done” is exactly how Berlinski thinks it must have been done, if it were done at all. You’re giving him far too much credit here.

So any alternatives to Berlinski’s calculations right now are dead ends.

I would agree, in the sense that (as amply demonstrated in the Carrier paper I cited above) all probabilistic calculations for the origin of life are pretty much pointless. We simply don’t know enough about the early state of the Earth–let alone all possible chemical reactions–and probably never will to make such a calculation valid.

The alternative which is not a dead end, which is what Orgel and others are actually doing, is to not worry all that much about probabilities and instead focus on possibilities–look for pathways which work, period.

I hope this discussion ends at this. I can’t see how it can go any further.

As I recall, you already said you were “done posting here.” You’re welcome to stay, of course, but don’t feel obligated on our account.

Comment #93895

Posted by Anton Mates on April 3, 2006 9:24 PM (e)

Sir_Toejam wrote:

After all, that is why scientists still have jobs, and haven’t all retired to the Bahamas by now.

aside from the fact that not many could afford to, either.

The clever thing to do is to find a job that requires frequent trips to the Bahamas or someplace similar for “research purposes.” Damn those marine biologists!

Comment #93900

Posted by Sir_Toejam on April 3, 2006 9:34 PM (e)

The clever thing to do is to find a job that requires frequent trips to the Bahamas or someplace similar for “research purposes.” Damn those marine biologists!

heh. been there, done that. Well, i spent more time in Tahiti than in the Caribbean, but there ya go.

studying damselfishes had its advantages, but it certainly didn’t pay enough to retire on.

Comment #93907

Posted by Moses on April 3, 2006 9:49 PM (e)

Comment #93618

Posted by idon’treallycare on April 3, 2006 07:49 AM (e)

Okay, a few observations…

The first is that most (though not all) of you are morons.

Classic case of projection.

On a more serious note, one thing I’ve noticed about life is that while models can be made and people say “such and such can’t/won’t happen,” some of the damndest things do happen. In part, because the models used in biology are, frankly, very often gross simplifications of a very, very complex process.

So, as you’re blathering along about your little RNA world, I get a chuckle because I know it’s not so cut and dried. It’s not so simple. And mostly, it is not nearly as rigid and limited as you pretend in your corrupt arguments. Life, simply, doesn’t fit in this little simple box you pretend exists and is, in fact, capable of over-coming great obstacles. And if you knew that much about biology, you’d realize just what an ass you’ve been.

BTW, are you Jonathan Sarfati of Answers in Genesis? Or are you just aping his criticism of the RNA World Hypothesis. Because it’s not like you’re bringing up a particularly new argument or insights.

And, BTW, why should we give a fig about your bronze-age religious beliefs that were cobbled together from various local superstitions including (but not limited to) Greek, Ugartic, Canaanite, Egyptian, Babylonian and Sumerian?

Comment #93915

Posted by normdoering on April 3, 2006 10:19 PM (e)

Moses wrote:

It’s not so simple. And mostly, it is not nearly as rigid and limited as you pretend in your corrupt arguments. Life, simply, doesn’t fit in this little simple box you pretend exists and is, in fact, capable of over-coming great obstacles. And if you knew that much about biology, you’d realize just what an ass you’ve been.

That reminds me… wasn’t it Orgel who said “Evolution is cleverer than you are,” or something like that? Or was it Crick who said that?

All those scientific models of ours have to get housed in ether the 3 pounds of jello-like gray matter we call our brains or in our best computers. Evolution, life, well, it gets to work with a planet’s surface full of chemicals for billions of years attempting, or randomly branching into, more possibilities than we can ever think of.

The simple ability we have that might beat all that time and matter using an evolutionary algorithm is our ability to learn from our mistakes (something evolution doesn’t seem to do) but in order to do that you first have to see you are making mistakes. If we can’t get past a 2000 year old superstition then maybe things are beyond our human ability.

Comment #93923

Posted by Anton Mates on April 3, 2006 10:45 PM (e)

In “idon’treallycare”’s defense, he hasn’t presented himself as a creationist/IDer, so there’s not much point in complaining about his as-yet-unknown religious beliefs. He seems to be an “RNA-later” advocate under the (erroneous) impression that Berlinski’s also defending that position.

For all I know he could be a closet IDer–wouldn’t be the first time here, and I find it hard to believe that someone as articulate as he is could honestly be that confused about what Berlinski’s saying–but IMO one might as well wait until he makes that explicit to discuss it.

Comment #93943

Posted by Torbjörn Larsson on April 4, 2006 12:13 AM (e)

Anton refers to Berlinski:

“In “On the Origins of the Mind,” I tried to show that much can be learned by studying the issue from a computational perspective. 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.”

If one looks at “On the Origins of the Mind” one sees that Berlinski’s account of what he does is false.

First, Berlinski models the mind as a Turing machine, which I don’t believe many neuroscientists think are realistic. He wants to make a correspondence with his idea that a scientific model must contain differential equations. So he disregard the abstract algorithmic content of the Turing model, realises it with a digital computer, and then tries to make a model of the Turing algorithm by describing the EM fields inside the computer!

We can note that not only is this pitiful as a philosophical model, he would never get a research grant to verify such a preposterous “scientific” model.

Second, Berlinski rejects this model by noting that an abacus is a realisation of Turing machine too, and so the Turing machine hypothesis are not plausible. Who knew!

He ends with noting that our everyday account of our mental life is what remains, and since he already introduced magic as a disjunction of scientific theories, he seems to believe that “an account frankly magical in its nature” is what a model of a mind must rely on.

I think it’s clear that he didn’t learn much, but tried to discount modern research of the mind such as neuroscience by verbiage and handwaving, and reintroduce the “magical” soul. This is very similar to the discussed paper where he tries to discount abiogenesis by handwaving.

Furthermore it’s clear that he holds both mind and abiogenesis science to a ridiculously constrained and outdated standard. Newton’s model of science was from the 17th century, my pet peeve the induction ‘proof’ model is probably from the 19th century, and in the 20th century modern ideas on the method of science were established.

Now I better get started on reading some peer-reviewed papers on abiogenesis, so I can be a full part of the next interesting discussion. ;-)

Comment #93946

Posted by Torbjörn Larsson on April 4, 2006 12:17 AM (e)

“Now I better get started on reading some peer-reviewed papers on abiogenesis, so I can be a full part of the next interesting discussion. ;-)”

Duh, that didn’t come out right. I meant to say a part that was accepted by some of the more critical members of this discussion. I do prefer biologists informed contributions on biology above my own.

Comment #93992

Posted by David Berlinski on April 4, 2006 2:40 AM (e)

1 I did not in my essay on the origins of life for a moment suggest that Joyce & Orgel endorsed or would endorse my own speculative conclusions. The position that they themselves reach is in any event stronger than my own: In writing of scientists “pessimistic” about various origins of life scenarios, they remark that “they believe that the de novo appearance of oligonucleotides on the primitive earth would have been a near miracle.” Joyce and Orgel then add that “they subscribe to this … view,” (Joyce & Orgel, op. cit. p. 68).
2 The concept of a well-posed problem in analysis is due to Jacques Hadamard. There are, of course, ill-posed problems both in analysis and in physics, as a study of Tikhonov & Arsenin’s Solutions of Ill-Posed Problems would reveal. It is a point I mentioned in my essay on the origins of the mind. The idea that Rene Thom – of all people – was indifferent to considerations of stability is absurd. I have written at length about catastrophe theory and its applications, and I spent a year at the Institut des Hautes Etudes talking about catastrophe theory with Thom. Thom considered structural stability a normative principle in the sciences; he regarded both his own classification theorem and the (Malgrange & Mather) preparation theorems as a justification of this point of view. Details may be found in my own Black Mischief: Language, Life, Logic & Luck, or in my monograph, The Rise of Differential Topology, Laboratoire Informatique et Programmation, No. 88-33, Université de Paris, VII, Paris, France, 1980, or in my review of Catastrophe Theory and its Applications, in Behavioral Science, 1978.

Comment #94060

Posted by Torbjörn Larsson on April 4, 2006 5:20 AM (e)

“There are, of course, ill-posed problems both in analysis and in physics, as a study of Tikhonov & Arsenin’s Solutions of Ill-Posed Problems would reveal. It is a point I mentioned in my essay on the origins of the mind.”

Excerpt from “On the Origins of the Mind”:
“With these requirements met, a well-posed differential equation achieves a coordination among coordinates that is determined for every last crack and crevice in the manifold of time. And is this the standard that I am urging on evolutionary psychology? Yes, absolutely.”

This essay not only rejects other scientific models than describable by differential equations, it rejects specifically ill-posed problems and their solutions.

“The idea that Rene Thom – of all people – was indifferent to considerations of stability is absurd.”

Of course, and I didn’t say so.

Comment #94131

Posted by idontreallycare on April 4, 2006 8:13 AM (e)

Anton:

You quote Orgel as saying,

“Enough is already known to suggest that each of the steps needed to evolve from a library of randomly sequenced double-stranded RNAs to a self-sustaining RNA organism can be demonstrated in laboratory experiments.”

Notice first of all that it is *SUGGESTED* that this can happen in a laboratory setting; it has not happened yet, and this with heavy handed experimenters and trillions of purified reagents acting as mightily as they can. This may indeed be true, as Berlinski states in his essay; yet understanding *how* the laboratory methods work as opposed to the prebiotic ocean is a crucial distinction. In Vitro RNA evolution uses selection-amplification techniques (ie RNAs are “assigned” a task and those that perform the task well enough are amplified by reverse transcriptases–in the real ocean their would be no amplification before replication was found) unavailable in the primordial oceans. As I have said before, Orgel is referring to the fact that it *seems* there exists somewhere in the sequence space of RNA a true RNA replicase. Yet it is not a question of whether they exist or not but rather what area of the sequence space they occupy, and how likely their occurence was in the primordial oceans. One can do many more things in a laboratory setting than is realistic in practical settings. Remember the original quote from Bartel–

“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.”

But, you must read *EVEN FURTHER* to find Orgel’s opinions about YOUR impression of how nonenzymatic templated synthesis would proceed. And I quote:

“Nonenzymatic, template-directed copying of single-stranded RNA to generate double strands has been explored in detail. While exponential replication CANNOT be achieved using presently available methods, a wide range of single-stranded RNAs can be converted to double strands.”

Read this in the context of my earlier comments WHICH YOU DID NOT ADDRESS. Orgel says that the probability of an appropriately linked pure homochiral template with oligonucleotides (containing an excess of C) that are equally homochiral beggars even the optomist view of things. This is why he referred to the RNA-first scenario as a near-miracle.

You *can* replace Berlinski’s calculation, but only at the expense of embracing another astronomical improbability. The best alternative is to simply say RNA did not come first.

You are wrong in that Berlinski wrote a terrific essay. The discussion of prebiotic synthesis was on the mark, as Orgel demonstrates; his probabilistic calculations WERE DRAWN DIRECTLY FROM JOYCE AND ORGEL AND ARRENHIAS, although to be more complete he should have discussed nonenzymatic template replication, and his discussion of the genetic code origin was on par as well. I think many of you are just sore because a DI member wrote a decent paper.

What more is there to discuss?

Comment #94140

Posted by harold on April 4, 2006 8:47 AM (e)

Just to make an obvious point here -

Berlinski and Ireallyreallycare are arguing against a strawman version of abiogenesis.

Their motivation is not clear. One might conjecture religious insecurity; inability to maintain faith in God unless critical events in the history of life remain “unexplained”.

On a less noble level, egotistical refusal to back down from a “clever” idea that turned out to be wrong could be playing a role.

Let’s just remember that none of this is really relevant to ID.

That’s right. ID is about denying evolution. The theory of evolution deals with the evolution of cellular life (and post-cellular life like viruses). Even if God did directly poof the original cell into existence, the bacterial flagellum is almost certainly better explained by evolution than by magic.

A good solid hypothesis, or even theory, of abiogenesis, would be nice. But the theory of evolution doesn’t depend on such.

Comment #94142

Posted by wamba on April 4, 2006 8:54 AM (e)

The clever thing to do is to find a job that requires frequent trips to the Bahamas or someplace similar for “research purposes.”

You know, the best place in the world to do fruit fly genetics is in Hawaii.

Comment #94174

Posted by NJ on April 4, 2006 10:09 AM (e)

Anton Mates wrote:

The clever thing to do is to find a job that requires frequent trips to the Bahamas or someplace similar for “research purposes.” Damn those marine biologists!

Modern carbonate sedimentology. Requires skin diving in warm, shallow waters. Paid for by oil companies.

Was I smart enough to choose this as a thesis topic? Nooooooooo. I got to hunt for century-old copper mines in the Piedmont. You ever seen a black widow with a body the size of a golf ball before?

NJ

Comment #94195

Posted by Glen Davidson on April 4, 2006 11:24 AM (e)

“With these requirements met, a well-posed differential equation achieves a coordination among coordinates that is determined for every last crack and crevice in the manifold of time. And is this the standard that I am urging on evolutionary psychology? Yes, absolutely.”

This essay not only rejects other scientific models than describable by differential equations

Good point, even if written in order to make another one.

This brings up the problem that anti-evolutionists (do I care if evolution is accepted by those who deny the scientific understanding of evolution? I mean, without meaningful criticisms or alternatives to our successful current models) often pose not only to origins science, but to all of science altogether. They typically have a narrow view of science and of what it is capable of doing. They level the charge at others that the latter are “closed” to new and different ways of thinking, as if any decent scientist is actually opposed to differential equations or to appropriate design inferences.

I should make one caveat: Of course we should, in principle, be able to reduce everything in our models down to differential equations. However, many subjects are better understood via evolutionary developments (biological or otherwise), contingency, and, naturally, according to empirical intrusions into the pristine mathematics proposed. Galileo substantially contributed to physics sans differential equations, which was possible because of his fine intuitions regarding empirical affairs (to be sure, physics today is not to be done without differential equations).

This brings up one small problem I have with a number of responses to Berlinski’s latest, here on the Panda’s Thumb. Certainly the evolutionary mathematics that Elsberry trumpets (on his own blog) are crucial parts of evolutionary theory, however evolution via natural selection was sound prior to the development of the math of evolution (the latter added quantitative abilities, and persuasiveness). Berlinski has science quite backward, for everything of value rests first and foremost upon empirical data, which are ideally mathematizable, yet do not always reduce down to mathematics nor must they do so in practice. While Elsberry and others have not said otherwise, they have tended to answer Berlinski in line with Berlinski’s faulty understanding of science, as if Berlinski’s narrow views were legitimate.

Science is broad and accepting of various strategies for doing science. The anti-evolutionists impose strictures upon science, then complain when we do not accept their narrow “calculations” of probabilities which are at this time unknown, or when we refuse to accept the standard that science must reduce down to differential equations in practice. The open-endedness of empiricism, and of a wide variety of scientific methods, is generally the enemy in the minds of the anti-evolutionists.

When we do not accede to their blinkered view of science they will often resort to claims of “censorship” and the various supercilious epithets and put-downs that we get from Berlinski. Yet we do not “censor” differential equations, nor probability equations where these rest on proper data. Indeed, we are trying to keep science open as opposed to those who would close it off by using faulty assumptions. The censorious cry “censorship” when their blinkered views are left out of education. And if there is some ambiguity in the meaning of “censorship” (after all, we do wish to exclude anti-evolutionists from promoting their ideas via the schools), the effective and practical meaning of opposing censorship surely must include the prevention of narrow views of science from being taught as legitimate science.

Thus there is little to commend serious consideration of the idea that the mind must be understood according to differential equations, or that probability calculations without knowing the “search space” available to abiogenesis are meaningful. The openness and empiricism of science are what are essential, and neither evolution nor the science of mind should be ruined by the preconceptions held by the antievolutionists.

Glen D
http://tinyurl.com/b8ykm

Comment #94304

Posted by k.e. on April 4, 2006 3:03 PM (e)

Glen said:
The openness and empiricism of science are what are essential, and neither evolution nor the science of mind should be ruined by the preconceptions held by the antievolutionists.

Well yes ……but there are limits(smirk)

For Berlinski science=> Function(science) and as it approaches the limit (of his imagination) beyond which ..in his mind..it cannot go.

For Berlinski that Function is a black box that mechanically processes data.

He dreams he can have his black box process (without irony) his ‘limits’ as he (serenely) turns the handle. Not unlike Marcel Duchamp’s “The Large Glass
complete with chocolate grinders, scissors, peep holes ,(well worth a look at by the way scroll to 1923 The bride stripped bare by her bachelors,even)
One wonders if that was the reason for the scrap heap of wives or if he just needed more room for jouissance…..

Seems a little post modern to me perhaps he is trying to ‘resurrect’ Jacques-Marie-Émile Lacan who famously said about the square root of minus one

Thus the erectile organ comes to symbolize the place of jouissance [ecstasy], not in itself, or even in the form of an image, but as a part lacking in the desired image: that is why it is equivalent to the of the the square root of minus one signification produced above, of the jouissance that it restores by the coefficient of its statement to the function of lack of signifier (-1).

Being a Freudian he should have know all about projection, still no ones perfect.

Anyway crankish pseudoscience is not art and certainly not science but attracting his alter ego idon’treallycare who calls himself (Berlinski)” may be a cynical crazy old man, but he isn’t stupid.”

No of course not, tell that to the men with the white coats when they come to take you away.

Comment #94311

Posted by idon'treallycare on April 4, 2006 3:12 PM (e)

To The Panda’s Thumb Board:

Although I feel that I have already adequately presented and defended my stance on Berlinski’s essay, and that my rebuttals to any dissenters flat and misinformed replies remain for the most unanswered, I will push the envelope even futher. I am going to quote Gerald Joyce from his 2002 paper for Nature entitled “The Antiquity of RNA-Based Evolution.” The analysis presented in this field review almost *exactly* parallels Berlinski’s. And I quote:

////////”The general features of RNA-based life can be inferred by considering
the requirements for darwinian evolution and the biochemical
properties of RNA. The central process of the RNA world was the
replication of RNA, presumably catalysed by RNA. The most
widely studied, but by no means exclusive model for RNA
replication involves template-directed polymerization of activated
mononucleotides. Alternatively, replication may have involved the
joining of oligonucleotides or even larger subunits36, perhaps by
modular assembly rather than organization along a linear template.
The standard model, however, is most congruent with known
biological systems and illustrates the requirements for RNAcatalysed
RNA replication. (p. 216)”

“Although a very large number of RNA polymerase ribozymes
might be possible, collectively they would comprise only a tiny
fraction of the huge number of possible RNA sequences. For RNA
molecules that contain 100 nucleotides, there are 4100 (~1060) possible
sequences. A pool of one copy each of these molecules would have a
mass greater than 1013 times that of the Earth. A pool of one copy each
of all possible 40mers, with a mass of 26 kg, just might be achievable,
but it is not clear if 40 nucleotides are sufficient to provide robust
RNA polymerase activity. The ribozyme would be required not only
to perform the chemistry of polymerization, but also to do so with
sufficient fidelity to maintain the selected sequence information over
successive generations. Occasional mutations are needed to maintain
variability in an evolving population, but too many mutations make
it impossible to retain an advantageous genotype. There is a wellestablished
theoretical framework for assessing the effect of genome
size, replication rate and replication fidelity on the ability to maintain
heritable genetic information52. As a rule of thumb, the error rate of
replication per nucleotide must be no more than about the inverse of
genome length, corresponding to 99% fidelity for replication of a
100mer and 97.5% fidelity for replication of a 40mer. There may be
polymerase ribozymes that meet these requirements, although such
molecules have not yet been demonstrated.

The above discussion ignores other obstacles to RNA-catalysed
RNA replication, such as maintaining a supply of activated
mononucleotides, ensuring that the ribozyme will recognize its
corresponding genomic RNA while ignoring other RNAs in the
environment, overcoming stable self-structure within the template
strand, separating the template and product strands, and operating
in a similar manner on the product strand to generate new copies of
the template. Additional genetic information might be required to
overcome these obstacles, but a longer genome would necessitate an
even higher fidelity of replication. Mitigating against these demands
is the likelihood that RNA polymerase activity first arose in a
pre-RNA world. The earliest RNA polymerases need not have been
responsible for replicating entire RNA genomes, but merely for
generating RNAs that enhanced the fitness of pre-RNA-based life.
Further evolutionary innovation could have occurred by exploring
sequences related to these functional polymerases, rather than a
much broader search of all possible sequences. (p.217)”//////

Now, this passage seems to parrallel almost exactly what Berlinski has said. May I quote Berlinski’s paper:

//////////”For the moment, no one knows how precisely to compute those odds, if only because within the laboratory, no one has conducted an experiment leading to a self-replicating ribozyme. But the minimum length or “sequence” that is needed for a contemporary ribozyme to undertake what the distinguished geochemist Gustaf Arrhenius calls “demonstrated ligase activity” is known. It is roughly 100 nucleotides.

Whereupon, just as one might expect, things blow up very quickly. As Arrhenius notes, there are 4100 or roughly 1060 nucleotide sequences that are 100 nucleotides in length…. “Solace from the tyranny of nucleotide combinatorials,” Arrhenius remarks in discussing this very point, “is sought in the feeling that strict sequence specificity may not be required through all the domains of a functional oligmer, thus making a large number of library items eligible for participation in the construction of the ultimate functional entity.” Allow me to translate: why assume that self-replicating sequences are apt to be rare just because they are long? They might have been quite common.

They might well have been. And yet all experience is against it. Why should self-replicating RNA molecules have been common 3.6 billion years ago when they are impossible to discern under laboratory conditions today? No one, for that matter, has ever seen a ribozyme capable of any form of catalytic action that is not very specific in its sequence and thus unlike even closely related sequences. No one has ever seen a ribozyme able to undertake chemical action without a suite of enzymes in attendance. No one has ever seen anything like it.

The odds, then, are daunting; and when considered realistically, they are even worse than this already alarming account might suggest. The discovery of a single molecule with the power to initiate replication would hardly be sufficient to establish replication. What template would it replicate against? We need, in other words, at least two, causing the odds of their joint discovery to increase from 1 in 1060 to 1 in 10120. Those two sequences would have been needed in roughly the same place. And at the same time. And organized in such a way as to favor base pairing. And somehow held in place. And buffered against competing reactions. And productive enough so that their duplicates would not at once vanish in the soundless sea.

In contemplating the discovery by chance of two RNA sequences a mere 40 nucleotides in length, Joyce and Orgel concluded that the requisite “library” would require 1048 possible sequences. Given the weight of RNA, they observed gloomily, the relevant sample space would exceed the mass of the earth. And this is the same Leslie Orgel, it will be remembered, who observed that “it was almost certain that there once was an RNA world.”

To the accumulating agenda of assumptions, then, let us add two more: that without enzymes, nucleotides were somehow formed into chains, and that by means we cannot duplicate in the laboratory, a pre-biotic molecule discovered how to reproduce itself.”//////

I don’t know about you all, but I can see ALMOST NO DIFFERENCE BETWEEN THESE TWO PASSAGES. Berlinski’s calculations *ARE* incomplete, as was said before; AFTER ALL, IT IS RATHER HARD TO CRAM IN EVERY TECHNICAL DETAIL AND SCENARIO INTO A GENERAL REVIEW FOR THE LAYMAN. He COULD NOT pursue EVERY possible scenario for how RNA can replicate. Instead he chose ONE scenario, noting, as Orgel has, that they are ALL fraught with difficulty. I think almost EVERYONE on this board owes the man an apology for making use of bad numbers and cobbling together a sloppy review. His review of ribose and cytosine formation were excellent; his probabilistic analysis was derived from Joyce, Orgel, and Arrenhias; his discussion of the genetic code origin was well in order; and the history of abiogenesis that he included was on the mark. No sweeping conclusions that “Goddidit”, just a view of open ended research and uncertainty where the future will lead. Most of you are letting your bias dictate the merit of Berlinski’s paper. You are so eager to say, “The origin of life is a field of open research with many problems,”, yet when Berlinski specifies the exact problems researchers are working on the board explodes in anger and stupidity. Just admit it–it was a good lay review. Of course you will not, and that’s okay. But the point is Berlinski was right in that there are many other avenues to pursue outside of an RNA-first view.

Comment #94315

Posted by idon'treallycare on April 4, 2006 3:16 PM (e)

Correction

*’…owes the man an apology for /accusing him falsely of/ making use of bad numbers and cobbling together a sloppy review”*

Comment #94328

Posted by k.e. on April 4, 2006 3:35 PM (e)

hahahahah

Solace from the tyranny

things blow up very quickly

And yet all experience is against it

they observed gloomily

To the accumulating agenda of assumptions

ALL fraught with difficulty
at once vanish in the soundless sea

The odds, then, are daunting; and when considered realistically, they are even worse than this already alarming account might suggest.

oh woe is me

don’t count to 9

Monkey took him up an’ said, “You can fool the others, but you can’t fool me!”

At least this won’t go on your CV …or will it?

Comment #94332

Posted by Glen Davidson on April 4, 2006 3:42 PM (e)

Idon’treallycare (Berlinski?), who obviously cares a great deal about the meaningless question of whether Berlinski was “right”, apparently misses the conclusions of Berlinski’s piece:

But whether it has been immeasurably improved in a way that vigorously confirms the daring idea that living systems are chemical in their origin and so physical in their nature—that is another question entirely.

In “On the Origins of the Mind,” I tried to show that much can be learned by studying the issue from a computational perspective. 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 goes without saying that this is a tentative judgment, perhaps only a hunch. But 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.

I have no idea whether or not people have been beating up on Berlinski unfairly with regard to numbers, but his “conclusions” above are the embodiment of ignorance, a strong propensity toward throwing science overboard after a cursory analysis of one hypothesis, and an inability to even follow the logic of his piece. There is nothing at all that would suggest that life forms are anything other than “physical in their nature”, which means that he simply threw in that non sequitur. Anyone who claims a philosophy background ought to be able to follow logic better than that.

And sure, all of the weasel words are included as he makes his sweeping generalizations from very limited data. I don’t care, his “conclusions” are unsupported even as “hypotheses”, and he simply turns to “non-physicality” because of his own prejudices. We stick with science and “the physical” largely because these are all that are knowable to us, so he makes a frightfully bad epistemological mistake in suggesting either the overthrow of science or its radical revision. I’d like to see if he were so happy to destroy science if he were being tried using pseudoscience of the sort that he spouts (you know, the ‘reality is mathematics’ garbage).

I have never really bothered with the numbers, since it’s all garbage in…. His greatest sins are his approach to “science”, and his preconceptions that the computational perspective actually provides much insight into mind. His logocentric biases are more than a little obvious as he compares mind to computer, and finds (oh the shock!) that they are different, and thus the mind is not explainable as a physical system. His inability to understand biological systems strikes in the area of mind as much as in the area of evolution, and so he is absolutely incapable of making a good “layman’s review”.

If the man were not so arrogant he might learn something, instead of demanding that everyone credit his narrow perspective. Likewise for idon’treallycare, on the off chance that he is not Berlinski.

Glen D
http://tinyurl.com/b8ykm

Comment #94355

Posted by k.e. on April 4, 2006 4:11 PM (e)

I wonder what will be next from the 2 Berlinski’s ?

Reciting gloomy poetry while tap dancing ?

I for one don’t give rats patooei, but dissembling philosophers/theologians? Always fun to watch, as long as they don’t have a gun.

Comment #94450

Posted by William E Emba on April 4, 2006 5:54 PM (e)

Glen Davidson wrote:

His logocentric biases are more than a little obvious as he compares mind to computer, and finds (oh the shock!) that they are different, and thus the mind is not explainable as a physical system.

Let me see if I can comprehend Berlinski’s thinking processes here. My toaster is not a computer, therefore, my toaster is not explainable as a physical system? My stapler is not a computer, therefore, my stapler is not explainable as a physical system? My copy of René Thom Structural Stability and Morphogenesis is not a computer, therefore, my copy of René Thom Structural Stability and Morphogenesis is not explainable as a physical system?

Three for three. I think this Dr. B. fellow is onto something.

Comment #94480

Posted by 'Rev Dr' Lenny Flank on April 4, 2006 6:29 PM (e)

But the point is Berlinski was right in that there are many other avenues to pursue outside of an RNA-first view.

That’s nice.

How does ID “theory” propose we pursue them, again …. ?

(sound of crickets chirping)

Yep, that’s what I thought.

Nothing more to discuss, is there? (shrug)

Comment #94525

Posted by Glen Davidson on April 4, 2006 7:55 PM (e)

Three for three. I think this Dr. B. fellow is onto something.

It certainly makes life easy for him.

Comment #94526

Posted by Glen Davidson on April 4, 2006 7:55 PM (e)

Three for three. I think this Dr. B. fellow is onto something.

It certainly makes life easy for him.

Comment #94576

Posted by Anton Mates on April 4, 2006 9:25 PM (e)

David Berlinski wrote:

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.

This is broadly true in the sense that individual elements of Dr. Berlinski’s arguments are found in these sources. However, there are also elements which are found in neither, or even refuted by at least one.

Berlinski’s claim that
“the minimum length or “sequence” that is needed for a contemporary ribozyme to undertake what the distinguished geochemist Gustaf Arrhenius calls “demonstrated ligase activity” is known. It is roughly 100 nucleotides.”
is, of course, taken from the 2002 Arrhenius paper. However,

a) it’s not Arrhenius’ calculation (a minor point, but the statement that he’s a “distinguished geochemist”–which he is–is somewhat irrelevant in that light),
b) Joyce & Orgel disagree in the very paper Berlinski references above, arguing “A triple stem-loop structure, containing 40-60 nucleotides, offers a reasonable hope of functioning as a replicase ribozyme,” and,
c) the same year as Arrhenius’ paper was published, Joyce together with Natasha Paul disproved his claim by reporting a ligase ribozyme of only 61 nucleotides. (Paul & Joyce, “A self-replicating ligase ribozyme,” PNAS, October 1, 2002.)

Berlinski goes on to say, “Whereupon, just as one might expect, things blow up very quickly. As Arrhenius notes, there are 4^100 or roughly 10^60 nucleotide sequences that are 100 nucleotides in length. This is an unfathomably large number. It exceeds the number of atoms contained in the universe, as well as the age of the universe in seconds. If the odds in favor of self-replication are 1 in 10^60, no betting man would take them, no matter how attractive the payoff, and neither presumably would nature.”

This implied conclusion–that the odds given the premises are 1 in 10^60–is of course erroneous, since there may have been many distinct replicating sequences of the given length, as well as a very large set of candidates over space and time from which to draw. Arrhenius does not make such a claim, nor do Joyce and Orgel (using a different minimum length) make an analogous one. (Indeed, the latter take care to refute it, saying, “there may be many such 40-mers…as a result, even a small fraction of the total library…might be expected to contain at least one self-replicating RNA with the requisite properties.”) Berlinski attempts to deal with this objection, but Chu-Carroll has already shown why he fails.

Lastly, consider Berlinski’s combinatorial claim, “The discovery of a single molecule with the power to initiate replication would hardly be sufficient to establish replication. What template would it replicate against? We need, in other words, at least two, causing the odds of their joint discovery to increase from 1 in 10^60 to 1 in 10^120.”

Arrhenius does not discuss this, and Joyce and Orgel advance an analogous calculation only to raise precisely the same objection Chu-Carroll raised–namely, that the template/complement need not be generated independently of the original replicator. “The above calculations assume that a self-replicating RNA can copy itself (or that a fully complementary sequence is automatically available; see below)….Suppose that the initial ensemble of polymers was not produced by random copolymerization, but rather by a sequence of untemplated and templated reactions, and further suppose that members of the initial ensemble of multiple stem-loop structures could be replicated, albeit inefficiently, by the template-directed process. This would have two important consequences. First, any molecule with replicase function that appeared in the mixture would likely find in its neighborhood similar (and complementary) molecules, related by descent, thus eliminating the requirement for two unrelated replicases to meet.” (The RNA World 2nd ed., pp. 61-63.)

One can see from the above that, although Berlinski did indeed draw on the work of Arrhenius, Joyce and Orgel, the two primary math errors Chu-Carroll criticizes (an incorrectly-defined target space and bad combinatorics) are his and his alone. Moreover, Berlinski seems to have intentionally selected a minimum replicator length estimate that was not only contradicted by one of his two main sources but was also known to be false for the last three years–and given that Joyce was one of the researchers who falsified it, Berlinski could hardly be unaware of this!

On the other hand, Berlinski is quite right to say

In repeating these arguments, I have corrected a trivial error in Arrhenius’ paper, and I have done so with Professor Arrhenius’ permission.

Arrhenius had an erroneously large exponent on his probability calculation, and Berlinski, to his credit, revised it downward as needed.

I did not in my essay on the origins of life for a moment suggest that Joyce & Orgel endorsed or would endorse my own speculative conclusions.

Yes, this is quite clear from the essay. Hopefully “idon’treallycare” will read this, though…he may not really care.

The position that they themselves reach is in any event stronger than my own: In writing of scientists “pessimistic” about various origins of life scenarios, they remark that “they believe that the de novo appearance of oligonucleotides on the primitive earth would have been a near miracle.” Joyce and Orgel then add that “they subscribe to this … view,” (Joyce & Orgel, op. cit. p. 68).

That hardly constitutes a “stronger” position than your own, Dr. Berlinski, if by “stronger” you mean “more critical of the hypothesis of chemically-driven abiogenesis,” since they immediately present alternate scenarios (still within the bounds of science) which don’t require such a de novo appearance.

Comment #94628

Posted by k.e. on April 5, 2006 12:01 AM (e)

Anton; I do suspect you are poking fun here with:
Hopefully “idon’treallycare” will read this, though…he may not really care.

Interestingly “idon’treallycare” has not yet denied he is Berlinski
….pity really an argument with himself would certainly increase the entertainment value of …what is otherwise a trivial arm waving exercise.

Maybe the 2 Dr. B’s could get together and interview each other.

Dr. B –Mr “idon’treallycare” why is it you don’t really care ?

IDRC— Well Dr. B. I’m bored, a brain the size of the universe etc etc Anyway I have the answer but I don’t know the question. Now a question for you–Why is it you don’t really care?

Dr. B–Well Mr.Idon’treallycare I’m bored, a brain the size of the universe etc etc Anyway I have the answer but I don’t know the question. Now a question for you–Why is it you don’t really care?

IDRC—Don’t be a smart arse.

More fun than dissecting frogs though. The voices the voices, the horror the horror.

Comment #94632

Posted by Anton Mates on April 5, 2006 12:09 AM (e)

idontreallycare wrote:

You quote Orgel as saying,

“Enough is already known to suggest that each of the steps needed to evolve from a library of randomly sequenced double-stranded RNAs to a self-sustaining RNA organism can be demonstrated in laboratory experiments.”

Notice first of all that it is *SUGGESTED* that this can happen in a laboratory setting; it has not happened yet, and this with heavy handed experimenters and trillions of purified reagents acting as mightily as they can.

Yes. But it’s Orgel who’s saying it’s suggested, which was my point. You may personally doubt that it’s possible, and you may be right, but that’s irrelevant.

Yet it is not a question of whether they exist or not but rather what area of the sequence space they occupy, and how likely their occurence was in the primordial oceans. One can do many more things in a laboratory setting than is realistic in practical settings.

When the “practical setting” in question is the entire planet, over a space of a few hundred million years? You’ll need to provide evidence for that, I think.

But, you must read *EVEN FURTHER* to find Orgel’s opinions about YOUR impression of how nonenzymatic templated synthesis would proceed. And I quote:

“Nonenzymatic, template-directed copying of single-stranded RNA to generate double strands has been explored in detail. While exponential replication CANNOT be achieved using presently available methods, a wide range of single-stranded RNAs can be converted to double strands.”

Again, Orgel’s opinion is apparently positive. Your opinion is negative, as I’m well aware.

Read this in the context of my earlier comments WHICH YOU DID NOT ADDRESS. Orgel says that the probability of an appropriately linked pure homochiral template with oligonucleotides (containing an excess of C) that are equally homochiral beggars even the optomist view of things. This is why he referred to the RNA-first scenario as a near-miracle.

The above, like your earlier comments, is irrelevant to the question of whether Orgel finds it plausible that evolution “from a library of randomly sequenced double-stranded RNAs to a self-sustaining RNA organism.” I certainly agree that he finds it implausible that such a library could arise de novo in the first place, and the above refers to that problem.

The best alternative is to simply say RNA did not come first.

And I agree, personally (though the fact that my limited knowledge in this area is derived almost entirely from Joyce & Orgel probably biases me.) But Berlinski is not endorsing that alternative, and he actually turned up here to say so:
“I did not in my essay on the origins of life for a moment suggest that Joyce & Orgel endorsed or would endorse my own speculative conclusions.”

Apparently Berlinski disagrees with you. Hopefully that resolves that question.

I think many of you are just sore because a DI member wrote a decent paper.

Hardly. As I understand it, Behe, for instance, has written many worthwhile papers. Just not ones about irreducible complexity. I presume Berlinski did plenty of useful work to earn his Ph.D., even if his anecdote about limits suggests otherwise.

Comment #94636

Posted by Anton Mates on April 5, 2006 12:15 AM (e)

k.e. wrote:

Anton; I do suspect you are poking fun here

Just taking him at his word. After all, he must not care, since he’s declared that the conversation’s over and he intends to leave. More than once, in fact.

Interestingly “idon’treallycare” has not yet denied he is Berlinski

Berlinski’s penchant for self-interviews aside, wouldn’t it would be very odd if they were the same person, since “idon’treallycare” continues to argue that Berlinski’s somehow championing RNA-later abiogenesis models while Berlinski says that he isn’t? And surely a Discovery Institute Fellow wouldn’t be odd.

Comment #94640

Posted by k.e. on April 5, 2006 12:25 AM (e)

Anton said:

And surely a Discovery Institute Fellow wouldn’t be odd.

oh I think Mr Hyde idon’treallycare is just giving Dr Jekyle Berlinski an out… after all Dr B. is only trying “to open up the discussion” and who better to explain it than his buddy/alter ego and they must be reaaly good friends after all idon’treallycare said

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

Yeah ? who says ?

Comment #94777

Posted by idon'treallycare on April 5, 2006 7:43 AM (e)

To the Panda’s Thumb Board:

First of all, k.e., since you seem to be so very interested in my identity, I am NOT (repeat NOT) Berlinski. For those of you out there scratching your heads as to why I enjoy and would even bother talking about the origins of life, ask yourselves why you are right now engaging in the same dialogue I am in.

Now, onto more misunderstandings. Anton, buddy, friend, I appreciate what you are doing. But could you at least read the material AND put it into context before posting? You mention Gerald Joyce’s paper, which I have reviewed some time ago, and upon reading it I at once recognized that you had selectively misrepresented both him and his coauthor Natasha Paul. Did you miss this quote:

///////////////////////”All of the chemical self-replication systems that have been described, including the ribozyme-based system of the present study, are not capable of undergoing Darwinian evolution. These systems usually offer no choice other than to form a particular product molecule. Even in those cases where one template can direct the synthesis of multiple products (13, 31, 35), the products do not “breed true” such that each product species only gives rise to additional copies of itself. Furthermore, product formation typically involves only a single joining reaction. Thus the information content of a particular self-replicating species can be no more than log2(NA•NB ), where NA is the number of different A substrates and N B is the number of different B substrates that can be joined and faithfully replicated. Laboratory systems have been devised for the Darwinian evolution of nucleic acid or protein molecules ( 36-38). These systems use large heterogeneous populations of compounds, each of which is assembled from many subunits….However, all of the laboratory evolution systems that have been described do not involve self-replication; replication is instead carried out by polymerase proteins that are not part of the evolving system.”/////////////////////////////////////

Yep, that’s right. Even the ribozyme engineered in the lab wasn’t TRULY a replicator. Now, on to more pressing matters. You take issue with Berlinski for using a 100mer as an example. Well, Joyce and Orgel think an optimistic guess would be a 40-60mer. However, as Joyce said in the 2002 paper “The Antiquity of RNA-Based Evolution,” it is not clear whether anything this short could replicate /accurately/ enough to avoid error catastrophe. Again, Joyce states:

“The above discussion ignores other obstacles to RNA-catalysed
RNA replication, such as maintaining a supply of activated
mononucleotides, ensuring that the ribozyme will recognize its
corresponding genomic RNA while ignoring other RNAs in the
environment, overcoming stable self-structure within the template
strand, separating the template and product strands, and operating
in a similar manner on the product strand to generate new copies of
the template. Additional genetic information might be required to
overcome these obstacles, but a longer genome would necessitate an
even higher fidelity of replication.”

Take note of the last sentence. Also, refer back to my original post. Bartel thinks a replicase ribozyme may take >200 nts to do the job!!! Certainly Berlinski’s numbers were NOT unfair. Bartel says this:

“How could general polymerase activity
have arisen on early Earth? If emergence of the
first RNA replicase ribozyme coincided with
the origin of life, it would have had to arise in
a single step from prebiotically synthesized
RNA, without the benefit of Darwinian evolution.
Our shortest construct retaining activity
was 165 nt, with about 90 nt involved in important
Watson-Crick pairing and at least another
30 critical nucleotides (23). Ribozymes
with the efficiency, accuracy, and other attributes
of an RNA replicase might have to be
even larger than this. However, current understanding
of prebiotic chemistry argues against
the emergence of meaningful amounts of RNA
molecules even a tenth this length (1). This
difficulty is anticipated by those who propose
that life, and Darwinian evolution, began before
RNA.”

Bartel UNDERSTANDS that the kind of in vitro evolution in the lab, with purified reagaents, fast acting proteins, and heavy handed chemists CANNOT reflect what would be happening in the primordial oceans. A 200 nt ribozyme would have to arise all at once, and he recognizes this is just FAR too improbable and thus leans heavily towards a pre-RNA World.

And although Arrenhius’ calculation was not /exactly/ Berlinski’s, it was something akin:

///”Elongation is in itself message- (sequence-) independent; it can proceed with meaningless sequences and produce libraries that consist of mostly meaningless oligomers. The probability of stochastic formation of specific and thus potentially meaningful sequences decreases with increasing length. The size of a ribozyme with demonstrated ligase activity has been shown to be about 100 nucleotide residues (Ekland et al. 1995). If uniqueness of the nucleotide sequence were strictly required the probability for such an oligomer to arise stochastically is approximately 10 exp-158, a highly improbable event. If an additional requirement of regiospecificity of the phospodiester bond would be imposed (Joyce and Orgel, 1999), the probability is further decreased. Reaction of an RNA nucleotide or oligonucleotide with an activated nucleotide normally yields 5’5’-pyrophosphate-, 2’,5’-phosphodiester- and 3’,5’,-linked adducts (Joyce and Orgel, 1999). Without a remedy for this triple complexation, the probability exponent above deteriorates to -614.”////

Joyce and Orgel, made the statement you quote by Joyce and Orgel which is:

““The above calculations assume that a self-replicating RNA can copy itself (or that a fully complementary sequence is automatically available; see below)….Suppose that the initial ensemble of polymers was not produced by random copolymerization, but rather by a sequence of untemplated and templated reactions, and further suppose that members of the initial ensemble of multiple stem-loop structures could be replicated, albeit inefficiently, by the template-directed process. This would have two important consequences. First, any molecule with replicase function that appeared in the mixture would likely find in its neighborhood similar (and complementary) molecules, related by descent, thus eliminating the requirement for two unrelated replicases to meet.”

Only after they disproved the idea that two replicases had to meet, as Berlinski did. AS WE HAVE ALREADY SEEN, HOWEVER, A SERIES OF TEMPLATED AND UNTEMPLATED REACTIONS IS BY FAR VERY UNLIKELY BECAUSE OF THE REACTANTS NEEDED—A PURE HOMOCHIRAL, C DOMINATED TEMPLATE WITH MONOMERS OF THE SAME KIND, AND BOTH APPROPRIATELY LINKED TO ONE ANOTHER. AND EVEN IN THIS SCENARIO, AS I HAVE QUOTED AND EXPANDED ON BEFORE, THE REPLICATION CYCLES DO NOT LAST MORE THAN A GENERATION.

As to suggestions from Orgel, I am totally prepared to accept that there are indeed viable replicases in the sequence space of RNA. BUT AS WE HAVE SEEN FROM THE BARTEL QUOTE, THIS DOES NOT IN ANY WAY MEAN THAT IT IS LIKELY THAT REPLICASES WOULD FORM SPONTANEOULSY FROM A GROUP OF MONOMERS.

You state,
“The above, like your earlier comments, is irrelevant to the question of whether Orgel finds it plausible that evolution “from a library of randomly sequenced double-stranded RNAs to a self-sustaining RNA organism.” I certainly agree that he finds it implausible that such a library could arise de novo in the first place, and the above refers to that problem.”
Actually, what Orgel believes, as Joyce does, is that a pre-RNA world existed and a genetic takeover of replication happened in an evolutionarily seemless manner. That’s what he thinks happens—replication and heredity, controlled by another molecule, was taken over from RNA. It wasn’t so much about RNA luckily finding its way to a viable replicase but rather taking this function from another molecule with the help of natural selection and mutation. If you want, we can calculate the odds of RNA forming DE NOVO to a self-sustaining riboorganism. Let’s see, homochirality considerations, production of cytosine, limited sequence specificity, considerations of information required to specify the rate of template formation, etc.

Alright, for the last time, YES, BERLINSKI’S CALCULATIONS ARE INCOMPLETE. THEY DID NOT TAKE INTO CONSIDERATION TEMPLATED AND UNTEMPLATED REACTION CYCLES, ALTHOUGH THESE ARE UNLIKELY, BASED ON CURRENT EXPERIMENTS, TO HAVE ORIGINATED THE FIRST RNA ORGANISM BY THEMSELVES. REFER TO MY PREVIOUS POSTS.

Berlinski may not agree in an RNA-last position, and that’s well and fine; but his criticisms are not to be taken lightly just because he refuses to create his own scenario for how life originated.

Comment #94788

Posted by Rilke's Granddaughter on April 5, 2006 7:57 AM (e)

doesn't know wrote:

To the Panda’s Thumb Board:

First of all, k.e., since you seem to be so very interested in my identity, I am NOT (repeat NOT) Berlinski. For those of you out there scratching your heads as to why I enjoy and would even bother talking about the origins of life, ask yourselves why you are right now engaging in the same dialogue I am in.

But you’re not talking about the OOL. You’re getting hot and bothered because we’ve pointed out that Berlinski’s article is composed of meaningless calculations, unsupported assertions, and unjustified conclusions. For some reason that bugs you.

[Snip points already addressed by others - be careful, you’re beginning to repeat yourself in caps as though it’s going to change things.]

Berlinski may not agree in an RNA-last position, and that’s well and fine; but his criticisms are not to be taken lightly just because he refuses to create his own scenario for how life originated.

His criticisms are to be ignored because they are bogus. His calculations are meaningless, his conclusion unjustified, and his use of the literature suspiciously close to quote-mining.

Your responses have done nothing to demonstrate otherwise.

Comment #94819

Posted by Anton Mates on April 5, 2006 9:08 AM (e)

Rilke's Granddaughter wrote:

But you’re not talking about the OOL. You’re getting hot and bothered because we’ve pointed out that Berlinski’s article is composed of meaningless calculations, unsupported assertions, and unjustified conclusions. For some reason that bugs you.

More than that, “idon’treallycare” is showing an increasing reliance on that favorite Creationist/IDer tactic, “I can ignore the evidence in support of X if it doesn’t support unrelated Y simultaneously.” (As exemplified most often by “This research only shows microevolution, not macroevolution. Therefore, ignore it.”)

Cases in point from his/her most recent post: After I refuted Berlinski’s assertion that the minimum length for a ligase ribozyme would be 100 nucleotides with

“the same year as Arrhenius’ paper was published, Joyce together with Natasha Paul disproved his claim by reporting a ligase ribozyme of only 61 nucleotides. (Paul & Joyce, “A self-replicating ligase ribozyme,” PNAS, October 1, 2002.)”,

IDRC responds with:

Anton, buddy, friend, I appreciate what you are doing. But could you at least read the material AND put it into context before posting? You mention Gerald Joyce’s paper, which I have reviewed some time ago, and upon reading it I at once recognized that you had selectively misrepresented both him and his coauthor Natasha Paul. Did you miss this quote….Yep, that’s right. Even the ribozyme engineered in the lab wasn’t TRULY a replicator.

I’m not really sure how I could “selectively misrepresent” a paper simply by mentioning its name and the base length of its subject molecule, but regardless, the tactic is clear. Because the ligase in question isn’t the sort of replicator that could be a plausible ancestor to the RNA world (which is perfectly true) we should ignore the fact that its published existence falsified Berlinski’s claim years before he wrote this essay.

Another example:

You take issue with Berlinski for using a 100mer as an example. Well, Joyce and Orgel think an optimistic guess would be a 40-60mer. However, as Joyce said in the 2002 paper “The Antiquity of RNA-Based Evolution,” it is not clear whether anything this short could replicate /accurately/ enough to avoid error catastrophe.

Because Joyce is doubtful that a replicase of the aforementioned length would function well enough to single-handedly kick off the RNA world, we should ignore the fact that he and Orgel think that length to be a “reasonable” (not “optimistic”, as IDRC writes) minimum, again contradicting Berlinski.

Another example:

As to suggestions from Orgel, I am totally prepared to accept that there are indeed viable replicases in the sequence space of RNA. BUT AS WE HAVE SEEN FROM THE BARTEL QUOTE, THIS DOES NOT IN ANY WAY MEAN THAT IT IS LIKELY THAT REPLICASES WOULD FORM SPONTANEOULSY FROM A GROUP OF MONOMERS.

Because Orgel (and Bartel, for an extra dose of irrelevance) are highly skeptical of the total RNA-first scenario, we should ignore the fact that Orgel, unlike Berlinski, does not find the appearance of a replicase in a given RNA library to be in itself wildly implausible.

And so forth. IDRC also employs the standard fallacy that if scientists can’t accomplish X within a given amount of time, natural forces could never have done so. (Often exemplified by “Scientists can’t turn a dog into a cat through evolution, so common descent is false.”):

Bartel UNDERSTANDS that the kind of in vitro evolution in the lab, with purified reagaents, fast acting proteins, and heavy handed chemists CANNOT reflect what would be happening in the primordial oceans.

It does seem pretty clear that, as you say, IDRC isn’t interested in origin-of-life research for its own sake, and from his/her rhetorical style and unrelenting defense of Berlinski, I would guess that s/he’s an IDer putting on a “mainstream science” hat temporarily. Still, I doubt s/he’s Berlinski himself.

Comment #94827

Posted by Rilke's Granddaughter on April 5, 2006 9:28 AM (e)

Anton Mates wrote:

It does seem pretty clear that, as you say, IDRC isn’t interested in origin-of-life research for its own sake, and from his/her rhetorical style and unrelenting defense of Berlinski, I would guess that s/he’s an IDer putting on a “mainstream science” hat temporarily. Still, I doubt s/he’s Berlinski himself.

True. Though I thought that beginning the series of posts by calling us morons was a nice touch. Calculated rhetoric is so rarely displayed by the ID self-support group.

Comment #94829

Posted by David Berlinski on April 5, 2006 9:33 AM (e)

I have never used any name other than my own, although over the years I have dropped my first name (Jerome), which I dislike; I have never posted to any site under a false name or pseudonym. The very idea is repugnant. My e-mail address is available to anyone who wishes to contact me.

Comment #94832

Posted by Rilke's Granddaughter on April 5, 2006 9:37 AM (e)

David Berlinski wrote:

I have never used any name other than my own, although over the years I have dropped my first name (Jerome), which I dislike; I have never posted to any site under a false name or pseudonym. The very idea is repugnant. My e-mail address is available to anyone who wishes to contact me.

I don’t think it was really a serious suggestion on our part. It’s simply that IDRC makes the same errors in support of your article as you do in the article. While you’re here would you care to address any of those criticisms?

Comment #94852

Posted by Glen Davidson on April 5, 2006 10:17 AM (e)

I have never used any name other than my own, although over the years I have dropped my first name (Jerome), which I dislike;

Good call, I’d say.

I have never posted to any site under a false name or pseudonym. The very idea is repugnant.

I hope ol’ idon’treallycare learns something from your rather higher standards in this matter. And anyway, I expect RG is mostly right, we generally care little enough (other than the ape factor in idon’t’s repertoire), but it’s odd how quickly the pseudonymous writer struck, and how he makes does not so much defend ideas as he does one person’s writings. One of the ID sycophants, no doubt, and I like how you fail to support sycophancy.

Otherwise, I’ve probably written as much as is prudent on this issue.

Glen D
http://tinyurl.com/b8ykm

Comment #94862

Posted by k.e. on April 5, 2006 10:47 AM (e)

hahahaha
Dr Jekyll/Mr Hyde Dr Berlinski/Mr. idon’treallycare, me thinketh thou protesteth too much (Repeat TOO MUCH)

The very idea is repugnant

hahahahhaha

…for one so clever you may try varying your self congratulatory flourishes (It must be dryly noted) , conversation style, hyperbole and the same reading interests, Try introducing more radical conflicting views, time zones, street address and ex wives …they tend to color ones choice of adjectives.

Oh and more insults and back patting at the same time BUT please, please make it more convincing don’t let him off the hook so easily.(smirk)

And do try to knock out the Berlinskisms from idon’treallycare writing Dr.B. they stick out like dogs balls.

Take up a creative writing class or something.

I mean really ….we’re not the dunce projecting his (serene and ironic) fantasy in front of an audience of mathematicians…and then boasting about it to the whole world…do you realize how pathetic that is ??No ?

Oh so you’re going to go even further ?

Fire away this should be interesting. Obviously embarrassment or credibility are not issues, this should be another feather in the cap for the DI ignorati.

Here is a tip let Dr B say this tripe below and get the other one to say something a little more pedestrian.(Bwhahhahahah)

For those of you out there scratching your heads as to why I enjoy and would even bother talking about the origins of life, ask yourselves why you are right now engaging in the same dialog I am in.

Comment #94881

Posted by k.e. on April 5, 2006 11:29 AM (e)

Oh Dr. B there’s 2 of you remember?
….ask yourselves why you are right now engaging in the same dialog I am we are in.

Comment #94898

Posted by Anton Mates on April 5, 2006 12:10 PM (e)

David Berlinski wrote:

I have never used any name other than my own, although over the years I have dropped my first name (Jerome), which I dislike

Sounds quite nice to me. Maybe I just like it because it’s the first word in a Pharcyde song.

A question for anyone knowledgeable on the subject, Berlinski and IDRC included: It seems that one of Joyce & Orgel’s chief objections to RNA-first models is based on chirality; they think it unlikely that prebiotic reactions could produce a mostly homochiral pool of nucleotides, and a racemic mixture would be terrible for template-directed synthesis.

Now I know that assorted mechanisms for producing a homochiral population have been proposed, such as amplification of an initially slight chiral excess by autocatalysis, and chirally-biased breakdown (for instance, by polarized light.) Most of these ideas aren’t incredibly new, so I assume RNA-later proponents have considered and refuted them at one time or another. Does anyone know of a good paper on this?

Comment #94906

Posted by normdoering on April 5, 2006 12:47 PM (e)

Anton wrote:

…so I assume RNA-later proponents have considered and refuted them at one time or another. Does anyone know of a good paper on this?

I’m not sure it’s the refutations that are moving some scientists toward a pre-RNA world but rather an emerging vision of what that pre-RNA world could have been like. At least that’s what part of this article suggests to my novice ears:

http://www.eurekalert.org/pub_releases/2006-03/s…

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.

Refutations are generally weaker forms of science than that.

Comment #94907

Posted by harold on April 5, 2006 12:48 PM (e)

If David Berlinski says he’s not “Idon’treallycare” then that should be good enough.

I completely disagree with his flawed logic on the subject of hypothetical RNA self-replication. As far as I can tell, he’s not only arguing that only one single specific RNA sequence could be a replicator, which is bad enough, but also that there would only be one chance in the history of the world for it to form.

Because the probability he gives is not only wrong if multiple possible sequences could be replicators, but also, even if that were the case, if there were many “interactions”, each one of which could produce the said sequence. If you mix a bunch of RNA bases up in conditions that polymers form, then look at polymers that are 100 bases long, the actual odds of finding a specific 100-base polymer, assuming four base pairs, are -

1 minus ((1 minus (1/4^100))^n).

The “^” sign means to the power of. “n” is the number of polymers you sample.

To give a more intuitive number, if you only have a 1/4 chance of achieving something, but you try 3 times, your chances of achieving it at least once are

1 - (3/4)(3/4)(3/4). Which is 37/64.

There are 6.02 X 10^23 molecules in a mole, eg about 100-150 grams of a small amino acid. So interactions in a solute can actually be quite plentiful.

Having said that, I think it’s a bit over the top, even if you have a decent case, to accuse Berlinski of misreprensenting which posts he made. Understandable, yes, but without stronger evidence than style, I’ll give him the benefit of the doubt.

Comment #94917

Posted by David Berlinski on April 5, 2006 1:12 PM (e)

Rilke’s grand-daughter has very thoughtfully asked me to comment on various criticisms directed at my essay. I am not sure I have anything to add to the discussion and certainly nothing to add to what I have already written. Wer jetzt kein Haus hat baut sich keines mehr, Wer jetzt allein ist, wird es lange bleiben … Rilke’s grand-daughter, of all people, will know what I mean.

Comment #94918

Posted by Steviepinhead on April 5, 2006 1:15 PM (e)

David Berlinski wrote:

I have never used any name other than my own, although over the years I have dropped my first name (Jerome), which I dislike…

Try adding on “o” on the end: Jeromeo.

More felicitous all around–more sonorous, rhythmic, lilting, and even that trembling little frisson of romance.

And if you read “zero” for “o,” the “addition” doesn’t even change the outcome of the equation…assuming there’s any real math there in the first place.

Comment #94947

Posted by Rilke's Granddaughter on April 5, 2006 2:11 PM (e)

David Berlinski wrote:

Rilke’s grand-daughter has very thoughtfully asked me to comment on various criticisms directed at my essay.

True. I presumed that someone interested in the integrity or accuracy of his work would be interested in criticism.

I am not sure I have anything to add to the discussion and certainly nothing to add to what I have already written.

Apparently, I was wrong.

Wer jetzt kein Haus hat baut sich keines mehr, Wer jetzt allein ist, wird es lange bleiben … Rilke’s grand-daughter, of all people, will know what I mean.

Personally, I would be embarrassed to cite the Herbsttag in this context; do you really consider your intellectual meandering to be pointless?
But you are demonstrating the two characteristics of which you are often accused: evasion and a penchant for florid, pseudo-intellectual bon-mots. Disappointing, actually.

Comment #94961

Posted by k.e. on April 5, 2006 2:53 PM (e)

Harold
..it’s a bit over the top.etc.
….er its not like I’m accusing him of plagiarism (giggle).
Tad more than style by the way ….either one of them could have quoted Rilke’s “Autumn Day”.

Still things can’t be all that bad, after all who needs friends when you can just make them up…except of course if they share the same gloom, tch …misery loves company….. maybe that’s why he’s hooked up with the DI.

Comment #94996

Posted by idon'treallycare on April 5, 2006 4:32 PM (e)

To the Panda’s Thumb Board Members:

There are a number of points that I wish to address:

1. One of the major topics in this painfully redundant discussion is the question of my identity. As I have said, and will say again, I am NOT David Berlinski, as both Dr. Berlinski and myself have affirmed. To be quite honest, I find this small diversion from the real question at stake rather amusing; after all, NONE of you, except perhaps Anton Mates, are even attempting to keep the discussion of Berlinski’s calculations along with the theme of prebiotic evolution alive. Most attacks have either centered on my own personal convictions about the origin of life or the illusion that Berlinski and myself have a secretly shared identity. This is, of course, absurd. But so, for the most part, is the blog I am posting on.

2. This is specifically for Anton. You are absolutely correct to note that researchers have managed to coax ribozymes capable of ligation that are shorter than 100 nucleotides. Berlinski used a 100mer as a model, it seems to me, because this is the number Arrenhius used. Arrenhius was, of course, describing one of the most famous and widely heralded ligating ribozymes derived by Ekland’s group in 1995. Therefore, Berlinski was using Ekland’s ligating ribozyme as a model for the number of nucleotides needed in a replicase. (Replicases, it goes without saying, are occupy a smaller area of RNA sequence space than ligating ribozymes.) If Berlinski’s number was unfair, then so too the 100mer calculation used by Joyce in “The Antiquity of RNA-Based Evolution” and the 100mer mentioned by Arrenhius in his 2002 paper.

I argue, however, that Berlinski’s number was more than fair, because we are not merely considering sloppy ligases, but high fidelity replicases. Berlinski, if one reads carefully, uses a 100mer as his model for the minimum replicase length, not a minimum ligase length, drawing from the context of this quote:

“For the moment, no one knows how precisely to compute those odds, if only because within the laboratory, no one has conducted an experiment leading to a self-replicating ribozyme…[i]t is roughly 100 nucleotides…As Arrhenius notes, there are 4100 or roughly 1060 nucleotide sequences that are 100 nucleotides in length. This is an unfathomably large number. It exceeds the number of atoms contained in the universe, as well as the age of the universe in seconds. If the odds in favor of SELF-REPLICATION are 1 in 1060, no betting man would take them, no matter how attractive the payoff, and neither presumably would nature.”

As is noted by Bartel, true replicases needed to sustain any riboorganism might have required one hundred more nucleotides than this, thus making the sequence space even larger and the search for viable replicases even more daunting. I think Berlinski’s question was appropriate,

“Why should self-replicating RNA molecules have been common 3.6 billion years ago when they are impossible to discern under laboratory conditions today?”

In this regard, Berlinski is to be counted among the pessimist camp, as per Joyce and Orgel:

“A highly pessimistic view is that because no known polymerase
ribozyme combines all of the properties necessary to sustain its own
replication, no such ribozyme is possible. A more reasonable view, we
believe, is that RNA is clearly capable of greatly accelerating the templatedependent
polymerization of nucleoside 5_-polyphosphates. Such catalytic
RNAs can operate in a sequence-general manner and with reasonable
fidelity. It seems only a matter of time (and likely considerable effort)
before more robust polymerase ribozymes will be obtained. Nature did
not have the opportunity to conduct carefully arranged evolution experiments
using highly purified reagents, but did have the luxury of much
greater reaction volumes and much more time.”

Berlinski’s response would entail, I imagine, I’ll believe it when I see it.

3. Since we all seem to enjoy quoting Joyce and Orgel, how about some more quotes from the third edition of the RNA World.

“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.” (p.21)

This quote, of course, captures the counter-argument that Replicase action could have arisen through a cycle of templated and untemplated reactions. It is simply improbable that a 40mer would have a purely homochiral backbone dominated with cytosine. The substrates would have to be of the same kind, and appropriately linked (remember Arrenhius’ quote: “ Reaction of an RNA nucleotide or oligonucleotide with an activated nucleotide normally yields 5’5’-pyrophosphate-, 2’,5’-phosphodiester- and 3’,5’,-linked adducts.”)

Joyce and Orgel again:

“RNA replicase activity is probably not the only catalytic behavior that was
essential for the existence of the RNA World. Maintaining an adequate
supply of the four activated nucleotides would have been a top priority.
Even if the prebiotic environment contained a large reservoir of these
compounds, the reservoir would eventually become depleted, and some
capacity for nucleotide biosynthesis would have been required….None of these four RNA-catalyzed reactions has precisely the right
format for the corresponding reaction in a hypothetical nucleotide
biosynthesis pathway in the RNA World. However, they demonstrate that
RNA is capable of performing the relevant chemistry with substantial
catalytic rate enhancement. It remains to seen whether ribozymes can be
developed that catalyze the formation of the fundamental building blocks
of RNA, D-ribose and the four nucleotide bases, using starting materials
that would have been abundant on the primitive Earth.” (pp.18-19)

It appears that a replicase may not be the only molecule necessary. Many more ribozymes must be postulated, although they have yet to appear in a lab. Moreover, they must appear in close proximity to a replicase and must develop a coevolutionary relationship with the replicase, all the while working to replicate pure nucleotides from a cluttered prebiotic ocean that forms a harsh environment. Recall Berlinski’s words:

“Those two sequences would have been needed in roughly the same place. And at the same time. And organized in such a way as to favor base pairing. And somehow held in place. And buffered against competing reactions. And productive enough so that their duplicates would not at once vanish in the soundless sea.”

And echoing this fact in point, Joyce’s harsh words in his 2002 paper:

“The above discussion ignores other obstacles to RNA-catalysed
RNA replication, such as maintaining a supply of activated
mononucleotides, ensuring that the ribozyme will recognize its
corresponding genomic RNA while ignoring other RNAs in the
environment, overcoming stable self-structure within the template
strand, separating the template and product strands, and operating
in a similar manner on the product strand to generate new copies of
the template.”

Berlinski’s general point is that this all seems suspicious and highly unlikely. I think you should at least respect his opinion, as it is shared by a great many in the field.

4. So, in sum, we have a calculation made by Berlinski that is an almost exact copy of a similar calculation made by Joyce in 2002. Berlinski notes that the prebiotic ocean would be a mess and that sequences are not likely to find each other to replicate, as Joyce does. Where is the problem? If Berlinski is pessemisic, so be it. It is, however, no matter how you look at it, no matter how you turn it, completely rational. That Berlinski did not mention every single technical point is of no interest. He was writing a LAY REVIEW. I don’t see anyone ripping Carl Zimmer’s stuff to shreds, although if you were picky, I’m sure you could. I still fail to see the difference between the contents of Berlinski’s paper and the more thorough analysis contained in Joyce (2002) and Joyce and Orgel (1

Comment #94997

Posted by idon'treallycare on April 5, 2006 4:39 PM (e)

And one more point to add:

Look at this quote from Berlinski’s paper:

“At the conclusion of a long essay, it is customary to summarize what has been learned. In the present case, I suspect it would be more prudent to recall how much has been assumed:

First, that the pre-biotic atmosphere was chemically reductive; second, that nature found a way to synthesize cytosine; third, that nature also found a way to synthesize ribose; fourth, that nature found the means to assemble nucleotides into polynucleotides; fifth, that nature discovered a self-replicating molecule; and sixth, that having done all that, nature promoted a self-replicating molecule into a full system of coded chemistry.”

The strange thing is, all of this HAS been assumed. Does this not strike anyone as suspicious, that at every aching step there is something that researchers cannot quite do, whether it is synthesizing cytosine or creating a full-blown replicase? What /has/ been accomplished would never be adequate in real life. This is the point Berlinski is stressing. We have a long way to go to gain any ground on forming a rigorous theory for the origins of life.

Comment #95000

Posted by Steviepinhead on April 5, 2006 5:05 PM (e)

Dude, you’re repeating yourself. You’re becoming tiresome, like the drunk on the next barstool recycling all his grievances.

Show us something new, or enough already…

Comment #95004

Posted by k.e. on April 5, 2006 5:36 PM (e)

Gee Doc you don’t mind stretching credibility do you?
Just go back and look at how many times you spoke about yourself in the third person in your last 2 posts.

Seems like idon’treallycare knows more about what you think than you do and besides he/you is the only one promoting your/his ideas on this thread where earlier you said he did ….I mean you did.(smirk)

You know doc there was a guy who came on here and ticked us all off about how evolution was a tautology except in 3 or 4 sentences he used the word 13 times.

Keep going please, you may be amused but your little charade HAS TO BE the most tragic performance on ever on PT.

Comment #95009

Posted by 'Rev Dr' Lenny Flank on April 5, 2006 5:51 PM (e)

First of all, k.e., since you seem to be so very interested in my identity, I am NOT (repeat NOT) Berlinski.

I don’t care if you’re Jesus Christ himself come down from Heaven. (shrug)

All I want to know is (1) what alternative theories of the origin of life do you have to offer, and (2) how do you propose we go about investigating them.

(sound of crickets chirping)

Nothing more needs to be said, huh.

Comment #95010

Posted by 'Rev Dr' Lenny Flank on April 5, 2006 5:55 PM (e)

I am not sure I have anything to add to the discussion and certainly nothing to add to what I have already written.

I, on the other hand, am quite sure. (shrug)

But since your mouthpiece, whoever he is, won’t answer my simple questions, perhaps you could give it a go yourself:

(1) what alternative hypothesis do you have to offer for the origin of life, and

(2) how can we test it using the scientific method.

Comment #95017

Posted by idon'treallycare on April 5, 2006 6:24 PM (e)

To Anton and the Board:

In reviewing my last comments I found them exceedingly fuzzy and long winded. I will try my best to neatly summarize the points, Anton, and see if at each step we come to an agreement:

1. Berlinski’s 100 nt figure came from observations from Ekland’s ligase. The number in itself was NOT the minimum length of a ribozyme retaining ligase activity, but rather an estimated minimum length of a replicase. Taken in light of Bartel’s observations, this is not a horrible figure.

2. Berlinski’s calculations for a 100mer were almost exactly akin to the calculations Gerald Joyce put forth in his 2002 Nature paper

3. Both Berlinski and Joyce agree that a full blown replicase arising catalyzing complementary sequences is astronomically improbable

4. Both Berlinski and Joyce agree that other scenarios have to face the same hurdles, since:

“Those two sequences would have been needed in roughly the same place. And at the same time. And organized in such a way as to favor base pairing. And somehow held in place. And buffered against competing reactions. And productive enough so that their duplicates would not at once vanish in the soundless sea.” (Berlinski)

“The above discussion ignores other obstacles to RNA-catalysed
RNA replication, such as maintaining a supply of activated
mononucleotides, ensuring that the ribozyme will recognize its
corresponding genomic RNA while ignoring other RNAs in the
environment, overcoming stable self-structure within the template
strand, separating the template and product strands, and operating
in a similar manner on the product strand to generate new copies of
the template.” (Joyce)

5. Berlinski FAILED to discuss templated and untemplated reaction cycles, but this is a trivial point because a. this idea fails in general because conditions are critically contingent on astronomically improbable availability and concentration of unlikely prebiotic molecules, and b. it was a LAY REVIEW. Heck, Joyce didn’t really make mention of templated and untemplated reactions in his Nature review. Why would we expect Berlinski to do this for Commentary?

6. As per Joyce and Orgel, other complex ribozymes would be needed in close vicinity to any replicase, reacting in ways conferring survival advantages, in order to complete nucleotide biosynthesis

7. The existence of ribozymes catalyzing the formation of nucleotides AND ribozymes catalyzing self-reproduction have NEVER been demonstrated in the lab

8. It is suspicious and wildly optimistic to assume the presence of an abundance of homochiral, C abundant, appropriately linked templates (although C, ribose, and phosphate are all unlikely prebiotic molecules)without interfering cross reactions from other vagrant and harmful molecules, along with invaluable mineral catalysts and mild environmental conditions. Add to this the necessity of ribozymes originating that catalyze the reaction of biosynthesis of nucleotides in close vicinity to the replicase, somehow enclosed by a membrane, with more complex ribozyme pumps. Does this not seem a bit improbable? This is the large point made by Berlinski. And it *seems* correct, as I think you yourself agree.

9. There are many possible alternatives to an RNA-first view, but none of them as of now have really caught fire.

Comment #95020

Posted by Steviepinhead on April 5, 2006 6:32 PM (e)

Dude. Catch a clue. The only real internet crime is feloniously boring your audience to death.

Seriously. Whatever you thought your point was, you exhausted it. Long ago.

Comment #95026

Posted by 'Rev Dr' Lenny Flank on April 5, 2006 7:31 PM (e)

There are many possible alternatives to an RNA-first view

Such as intelligent design, huh.

But I’d like to ask Berlinski a simple question —— the DI’ers keep pointing to him as a “non-religious design supporter”.

So I’m a little curious — what does Berlinski think the designer is, if it ain’t a god or gods? Is the designer a space alien? A time-travelling human biochemist? What.

Or is DI just BS’ing us. Again.

Comment #95027

Posted by normdoering on April 5, 2006 7:31 PM (e)

idon’treallycare wrote:

In reviewing my last comments I found them exceedingly fuzzy and long winded.

Just your last comments? I think this is why people suspect you’re really Berlinski.

Does this not strike anyone as suspicious, that at every aching step there is something that researchers cannot quite do, whether it is synthesizing cytosine or creating a full-blown replicase? What /has/ been accomplished would never be adequate in real life. This is the point Berlinski is stressing. We have a long way to go to gain any ground on forming a rigorous theory for the origins of life.

There used to be a lot of people who said “man will never fly” or “if man were meant to fly God would have given him wings.” There is an old video composed of black and white film clips of all sorts of flying machines that failed – weird contraptions, rockets burning people’s asses off, umbrellas pumping up and down, people flapping artificial wings… Today we can understand their absurd mistakes. They had tried since the time Da Vinci to try and fly.

Then one day two brothers who fixed bikes got it right.

There is nothing suspicious about failing to do what has not yet been done. I’m sure the people who said man will never fly had reasons as good as Berlinski’s for not thinking we can solve the origin of life problem.

Comment #95039

Posted by Frank Schmidt on April 5, 2006 8:46 PM (e)

Ah my. I feel a little like Prof. Steve Steve when facing a devotee of Intelligent Bamboo (or is that Bamboozlement). I offer my bona fides:

1. I am posting under my real name.
2. I have recently published a paper that bears on the topic: J.C. STRIGGLES, M.B. MARTIN, and F.J. SCHMIDT
Frequency of RNA–RNA interaction in a model of the RNA World
RNA 2006 12: 353-359.

The RNA World model for prebiotic evolution posits the selection of catalytic/template RNAs from random populations. The mechanisms by which these random populations could be generated de novo are unclear. Non-enzymatic and RNA-catalyzed nucleic acid polymerizations are poorly processive, which means that the resulting short-chain RNA population could contain only limited diversity. Nonreciprocal recombination of smaller RNAs provides an alternative mechanism for the assembly of larger species with concomitantly greater structural diversity; however, the frequency of any specific recombination event in a random RNA population is limited by the low probability of an encounter between any two given molecules. This low probability could be overcome if the molecules capable of productive recombination were redundant, with many nonhomologous but functionally equivalent RNAs being present in a random population. Here we report fluctuation experiments to estimate the redundancy of the set of RNAs in a population of random sequences that are capable of non-Watson-Crick interaction with another RNA. Parallel SELEX experiments showed that at least one in 10(6) random 20-mers binds to the P5.1 stem–loop of Bacillus subtilis RNase P RNA with affinities equal to that of its naturally occurring partner. This high frequency predicts that a single RNA in an RNA World would encounter multiple interacting RNAs within its lifetime, supporting recombination as a plausible mechanism for prebiotic RNA evolution. The large number of equivalent species implies that the selection of any single interacting species in the RNA World would be a contingent event, i.e., one resulting from historical accident.

While there are many questions about the RNA World model, not least of which is the difficulty of prebiotic synthesis of activated nucleotides, RNA remains the only molecule we know of that is likely to have both template and catalytic properties.

Frank

Comment #95043

Posted by idon'treallycare on April 5, 2006 9:11 PM (e)

To Mr. Frank Schmidt:

I thank you and appreciate your post. Before I analyze your paper, may I ask if it is available online in its entirety? If I have read your abstract correctly, you are proposing that there may be many functionally equivalent RNA, and if these oligomers were separated into short chunks they could amply react with one another, thus facilitating templated reactions. I haven’t looked at your references, but I have a feeling your positing something like pools of Landweber’s 29mer ligase forming on the early earth.

My concern with this is the same concern that Joyce expresses, namely that I doubt an RNA replicase’s activity could be specified in such a small base sequence. From the scientists I have privately corresponded with, 300 nts were very good estimates, considering what is needed:
a)the replicase must recognize the complement and primer in a sequence independent so that the system is not too specific and can evolve, b). catalyze with reasonable accuracy, and c). operate in a geometrically close manner that allows the ribozyme to associate closely with the template and primers to allow long sequences of primers to form on the complement.

Of course, a concern is that with RNAs interacting so readily, the template will not time enough to react with the replicase to make an exact duplication. Another worry, of course, is the interfering molecules, as expressed in Robert Shapiro’s 2000 paper, “A replicator was not involved in the origin of life.” Harmful side reactions would take place at many times the frequency that biologically friendly reactions would.

What did you think about my analysis about Joyce and Orgel? Have I missed something?

Finally I might add that no one is saying that RNA was NOT an ideal candidate molecule; Berlinski says this much in his essay. But there are right now many difficulties facing an RNA first scenario. I am inclined to join Szostak, Bartel, Orgel, and Joyce in pursuing an alternative replicating molecule. I am even more excited about Harold Morowitz and Robert Shapiro’s suggestions. But I cannot say that these new ideas will with the passing of times promote themselves to the status of other firmly established scientific theories.

Comment #95045

Posted by Anton Mates on April 5, 2006 9:38 PM (e)

normdoering wrote:

…so I assume RNA-later proponents have considered and refuted them at one time or another. Does anyone know of a good paper on this?

I’m not sure it’s the refutations that are moving some scientists toward a pre-RNA world but rather an emerging vision of what that pre-RNA world could have been like.

You’re no doubt right. Better to explore new avenues of research when they become apparent, than to wait for a rock-solid disproof of the old. Still, I can’t imagine that some of the RNA-later supporters haven’t made, if not refutations, then at least solid criticism of the putative mechanisms for homochirality. Just curious.

Comment #95047

Posted by Anton Mates on April 5, 2006 9:43 PM (e)

Frank Schmidt wrote:

Ah my. I feel a little like Prof. Steve Steve when facing a devotee of Intelligent Bamboo (or is that Bamboozlement). I offer my bona fides:

1. I am posting under my real name.
2. I have recently published a paper that bears on the topic: J.C. STRIGGLES, M.B. MARTIN, and F.J. SCHMIDT
Frequency of RNA–RNA interaction in a model of the RNA World

Thanks for showing up, Frank. It’s great how relevant experts almost always show up on PT if a thread goes for long enough. I look forward to reading your paper as soon as work allows.

Any take on the chirality thing?

Comment #95050

Posted by Anton Mates on April 5, 2006 10:02 PM (e)

idon'treallycare wrote:

The strange thing is, all of this HAS been assumed. Does this not strike anyone as suspicious, that at every aching step there is something that researchers cannot quite do, whether it is synthesizing cytosine or creating a full-blown replicase? What /has/ been accomplished would never be adequate in real life. This is the point Berlinski is stressing. We have a long way to go to gain any ground on forming a rigorous theory for the origins of life.

You can’t seriously post that and expect us not to think you’re an IDer, can you? There’s always something researchers can’t quite do in science. Then, later, they do it and there’s something elsethey can’t quite do. So it goes.

I’m also rather surprised to see you say

9. There are many possible alternatives to an RNA-first view, but none of them as of now have really caught fire.

since it seems to me that research into both metabolism-first models and pre-RNA genetic systems has been quite promising and has moved at a surprisingly fast rate. I thought you’d be even more enthusiastic, given the position you’ve taken in this thread. But, again, it makes a lot of sense coming from an ID advocate.

Other than that, the conversation does seem to be repeating itself, but when I have Joyce’s review in front of me I’ll see if there’s anything more to say re: comparisons between him and Berlinski. Doesn’t really bear on the demonstratedly invalid math in Berlinski’s paper, though, and the conclusions which Berlinski himself showed up to say would not be supported by the relevant experts.

Comment #95051

Posted by idon'treallycare on April 5, 2006 10:04 PM (e)

I thought this paper might help the discussion (Note that Shapiro is suggesting taking new avenues of research, not just repair to God’s masterful design):

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cm…

A replicator was not involved in the origin of life.

Shapiro R.

Department of Chemistry, New York University, NY 10003, USA. [Enable javascript to see this email address.]

Many scientific theories of the origin of life suggest that life began with the spontaneous formation of a replicator (a self-copying organic polymer) within an unorganized chemical mixture, or “soup.” A profound difficulty exists, however, with the idea of RNA, or any other replicator, at the start of life. Existing replicators can serve as templates for the synthesis of additional copies of themselves, but this device cannot be used for the preparation of the very first such molecule, which must arise spontaneously from an unorganized mixture. The formation of an information-bearing homopolymer through undirected chemical synthesis appears very improbable. The difficulties involved in such a synthesis are illustrated by considering the prospects for the assembly of a polypeptide of L-alpha-amino acids, based on the contents of the Murchison meteorite as an example of a mixture of abiotic origin. In that mixture, potential replicator components would be accompanied by a host of interfering substances, which include chain terminators (simple carboxylic acids and amines), branch-formers, D-amino acids, and many classes of substances for which incorporation would disrupt the necessary structural regularity of the replicator. Laboratory experiments dealing with the nonenzymatic synthesis of biopolymers have not addressed the specificity problem. The possibility that formation of the first replicator took place through a very improbable event cannot be excluded, but greater attention should be given to metabolism-first theories, which avoid this difficulty.

Comment #95077

Posted by David Berlinski on April 6, 2006 1:22 AM (e)

To Rilke’s Granddaughter –
Pointless? No. Futile, certainly, especially in context.

Comment #95098

Posted by 'Rev Dr' Lenny Flank on April 6, 2006 7:09 AM (e)

An email to me from Berlinski:

You raised a question on the Panda’s Thumb and since it was specifically addressed to me, I’ll take a moment to answer it specifically. I have NO religious interests or beliefs beyond a curiosity about pre-Humean
arguments in 11th century Arabic theology. I have never endorsed intelligent design in any way, and I have written a long essay in Commentary (‘Has Darwin Met his Match’) taking issue with all of the intelligent design arguments – those of Johnson, Behe, Dembski, and anyone else I could think of. I have been since the publication of ‘The Deniable Darwin’ on record as a critic of intelligent design. Every time I publish a serious piece, I go out of my way to affirm my skepticism.

Hmmmmm. Is Berlinksi BS’ing me, or is DI …. .?

Comment #95099

Posted by Rilke's Granddaughter on April 6, 2006 7:15 AM (e)

David Berlinski wrote:

To Rilke’s Granddaughter —
Pointless? No. Futile, certainly, especially in context.

True. But I would have expected that you, of all people, would recognize the futility of trying to persuade scientists with rhetoric rather than reason.

Shirayuki ni suberi-ochikeri masshigura!

Comment #95111

Posted by k.e. on April 6, 2006 8:33 AM (e)

Indeed RGD

hateshinai mirai hirogaru kono sora atarashii jibun ni umare kawaru
sekaijuu shiawase no yuki o furasete miseru yo

Lenny on Dr. B/Mr Idrc

Just tugging our chains ….jealousy I suppose. But the DI_kh__ds should get a sniff off it and then he can do the same dance all over again in front of them …..pathetic really

Comment #95148

Posted by Anton Mates on April 6, 2006 12:18 PM (e)

'Rev Dr' Lenny Flank wrote:

An email to me from Berlinski:

[snipped]I have never endorsed intelligent design in any way, and I have written a long essay in Commentary (‘Has Darwin Met his Match’) taking issue with all of the intelligent design arguments — those of Johnson, Behe, Dembski, and anyone else I could think of. I have been since the publication of ‘The Deniable Darwin’ on record as a critic of intelligent design. Every time I publish a serious piece, I go out of my way to affirm my skepticism.

Hmmmmm. Is Berlinksi BS’ing me, or is DI …. .?

A little of both. Berlinski, so far as I’ve seen, generally focuses (even more than the average IDer) on criticism of evolutionary theory, while avoiding strong endorsement of any alternative. He used to make statements that sorta kinda supported ID, but generally backpedaled as soon as anyone noticed. For instance, in 1996’s “The Deniable Darwin,” he wrote:

How so? The question has historically been the pivot on which the assumption of religious belief has turned. How so? “God said: ‘Let the waters swarm with swarms of living creatures, and let fowl fly above the earth in the open firmament of heaven.”’ That is how so. And who on the basis of experience would be inclined to disagree? The structures of life are complex, and complex structures get made in this, the purely human world, only by a process of deliberate design. An act of intelligence is required to bring even a thimble into being; why should the artifacts of life be different?

Darwin’s theory of evolution rejects this counsel of experience and intuition. Instead, the theory forges, at least in spirit, a perverse connection with the second law itself, arguing that precisely the same force that explains one turn of the cosmic wheel explains another: sheer dumb luck….Amazing. Sheer dumb luck.

which, you know, kind of sounds like he thinks intelligence is a more likely choice, especially since he goes on to make the usual complaints about how “random” evolutionary processes couldn’t produce X,Y, and Z. But as soon as criticism started coming, he retreated to agnosticism in his responses:

Darwinian theorists accept the first of Paley’s inferences, but reject the second. Biological artifacts are complex, they say, but not designed. Their existence may be explained in terms of random variation and natural selection. I dispute this claim, without endorsing Paley’s theological inference. It is not necessary to choose between doctrines. The rational alternative to Darwin’s theory is intelligent uncertainty.

(emphasis added)

Codes may be designed to remain robust in the face of background noise; what is required is redundancy, and the genetic code is, in point of fact, highly redundant. In communication systems, redundancy appears as a matter of design. It does not arise spontaneously…. I will return to this point in a number of other responses, but let me repeat what I stressed in my essay, that I am not advancing an argument on this issue, only expressing intellectual unease.

So it’s often difficult to work out if he has any positive views at all, or is simply criticizing mainstream science. Of course the DI’s happy to have him, since the latter is what most IDers spend their time doing anyway, and I imagine that his moments of half-hearted support for ID (as shown above) have been mostly for the DI’s benefit.

More recently he’s taken a more firmly agnostic position, criticizing ID more but mainstream biology no less. Since he’s also disputed the Big Bang and supported astrology, calling it a “finely geared tool for the resolution of practical problems,” it seems clear that he’s basically driven to “express intellectual unease” over any popular theory, scientific or not. Maybe the best way to categorize him is “Fortean.”

Comment #95160

Posted by The Ghost of Paley on April 6, 2006 1:34 PM (e)

Anton Mates wrote:

A little of both. Berlinski, so far as I’ve seen, generally focuses (even more than the average IDer) on criticism of evolutionary theory, while avoiding strong endorsement of any alternative.

Again with the obsession about the other guy’s P.O.V. Why don’t evolutionists see criticism (however misguided) as an opportunity to improve their model? Why do Darwinists so often choose to sell their theory as the best among an unsatifying lot, rather than as as something with intrinsic value? You guys should appreciate the special contributions that the Master can provide, if only you would let him:

1) A philosopher’s insight into the unsupported assumptions, circular reasoning, and faulty logic endemic to your cult

2) A mathematician’s magic, that you may quantify said assumptions

3) A broad historical/cultural understanding of the mistakes of past science, so you may avoid them in the present

4) One of the sharpest wits in the literature

5) and finally, boundless patience with evo sniping.

Cast down your bucket where you are.

Comment #95165

Posted by Rilke's Granddaughter on April 6, 2006 2:00 PM (e)

Ghost wrote:

Again with the obsession about the other guy’s P.O.V. Why don’t evolutionists see criticism (however misguided) as an opportunity to improve their model? Why do Darwinists so often choose to sell their theory as the best among an unsatifying lot, rather than as as something with intrinsic value? You guys should appreciate the special contributions that the Master can provide, if only you would let him:

1) A philosopher’s insight into the unsupported assumptions, circular reasoning, and faulty logic endemic to your cult

2) A mathematician’s magic, that you may quantify said assumptions

3) A broad historical/cultural understanding of the mistakes of past science, so you may avoid them in the present

4) One of the sharpest wits in the literature

5) and finally, boundless patience with evo sniping.

Cast down your bucket where you are.

Excellent satire of an ignorant fundie. Dead on! Kudos!

Comment #95174

Posted by k.e. on April 6, 2006 2:42 PM (e)

Gee Ghosty
Point by point projection of your “self”
that has to be the most honest Freudian slip I’ve seen in a while.
Do you not have the slightest bone of self awareness ? (a redundant question I know)

Oh except for point 4 that should be Shining Wit

What with Doc B’s terminal pining and your sycophancy you should make a nice couple, are you thinking of taking up skating?

Comment #95181

Posted by frank schmidt on April 6, 2006 2:59 PM (e)

idon’treallycare asked if the paper I referenced is available. It should be on the RNA Journal website. If not, email the address in the abstract, under your own name, of course, and I’ll be happy to forward a copy.

The point of the paper was that recombinational scenarios likely can generate RNAs long enough to do something, and that having two RNAs able to hang together long enough for recombination to occur is reasonably likely, given the frequency of interaction.

Anton Mates asked about the “chirality thing.” Here are a couple of papers that show some degree of discrimination:

In the first, RNA is inherently able do discriminate between D and L amino acids (of course, this merely sets the question back to the stereospecific synthesis of RNA): Science 27 August 2004:Vol. 305. no. 5688, p. 1253 Chiral-Selective Aminoacylation of an RNA Minihelix, Koji Tamura and Paul Schimmel*

In the second, crystallization procedures may carry out the separation: Shinitzky M. Nudelman F. Barda Y. Haimovitz R. Chen E. Deamer DW. Unexpected differences between D- and L- tyrosine lead to chiral enhancement in racemic mixtures.[erratum appears in Orig Life Evol Biosph. 2002 Dec;32(5-6):following 546]. [Journal Article] Origins of Life & Evolution of the Biosphere. 32(4):285-97; discussion 283, 2002 Aug.

I doubt that these two papers are definitive, but experimental results always show interesting ways to go.

Frank

Comment #95191

Posted by Anton Mates on April 6, 2006 3:42 PM (e)

The Ghost of Paley wrote:

Again with the obsession about the other guy’s P.O.V. Why don’t evolutionists see criticism (however misguided) as an opportunity to improve their model?

We worked out that any useful content of Berlinski’s essay was better extracted from his scientific sources, minus the misinformation. PoV’s all that’s left to talk about now.

Why do Darwinists so often choose to sell their theory as the best among an unsatifying lot, rather than as as something with intrinsic value?

I don’t know. Perhaps you should find an unsatisfied Darwinist and ask them.

You guys should appreciate the special contributions that the Master can provide, if only you would let him:

“Special” is the word…but if the Wizard himself can’t get the math right, what hope does a lowly Master have?

Frank: Thanks much for the paper recommendations.

Comment #95205

Posted by idon'treallycare on April 6, 2006 4:59 PM (e)

Frank and Anton:

Thank you both for your comments. I must draw Frank’s attention to concerns I have expressed previously, and that is the practical problems facing your imaginary scenario. Take Joyce and Orgel in “The RNA World, 3rd Edition (2006)”:

“Random copolymers containing an excess of C residues can be used
to direct the synthesis of products containing G and the complements of
the other bases present in the template (Inoue and Orgel 1983). The
reaction with a poly(C,G) template is especially interesting because the
products, like the template, are composed entirely of C and G residues.
If these products in turn could be used as templates, it might allow the
emergence of a self-replicating sequence. Self-replication, however, is unlikely,
mainly because poly(C,G) molecules that do not contain an excess
of C residues tend to form stable self-structures that prevent them from
acting as templates (Joyce and Orgel 1986). The self-structures are of two
types: (1) the standard Watson-Crick variety based on C_G pairs and
(2) a quadrahelix structure that results from the association of four G-rich
sequences (Fig. 2). As a consequence, any C-rich oligonucleotide that can
serve as a good template will give rise to G-rich complementary products
that tend to be locked in self-structure and so cannot act as
templates. Overcoming the self-structure problem using the standard
C and G nucleotides is very difficult because it requires the discovery of
conditions that favor the binding of mononucleotides to allow templatedirected
synthesis to occur but suppress the formation of long duplex
regions that would exclude activated monomers from the template.
Some progress has been made in discovering defined-sequence templates
that are copied faithfully to yield complementary products (Inoue
et al. 1984; Acevedo and Orgel 1987; Wu and Orgel 1992a). Successful
templates typically contain an excess of C residues, with A and U residues
isolated from each other by at least three C residues. Runs of G residues
are copied into runs of C residues, so long as the formation of selfstructures
by G residues can be avoided (Wu and Orgel 1992b). In light
of the available evidence, it seems unlikely that a pair of complementary
sequences can be found, each of which facilitates the synthesis of the
other using nucleoside 5_-phospho-2-methylimidazolides as substrates.
Some of the obstacles to self-replication may be attributable to the choice
of reagents and reaction conditions, but others seem to be intrinsic to the template-directed condensation of activated mononucleotides.
A related nonenzymatic replication scheme involves synthesis by the
ligation of short 3_,5_-linked oligomers. This is certainly an attractive
possibility, made more plausible by the discovery of analogous ribozymecatalyzed
reactions (Bartel and Szostak 1993; James and Ellington 1999),
but it faces two major obstacles. The first is the difficulty of obtaining
the substrates in the first place. The second is concerned with fidelity.
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.”

The problems are numerous: would short oligomers be able to replicate with the fidelity needed to maintain the genetic integrity of the population? would these short oligomers tend to form stable self-structures? would they would they tend to contain an excess of cytosine, one of the most notoriously difficult nucleotides to synthesize?

But more than this, as Robert Shapiro has demonstrated in his 2000 paper, molecules causing branched molecular structures, and thus molecules mitigating against a fully blown RNA world, would have outnumbered any organic molecules many times to one. Add to this the unliklihood of the presence pools purely of phosphate, ribose, and four D-nucleotides, and the improbability escalates. Not only this, but ribozymes replentishing pools of nucleotides need to be kept in close proximity, and need to be interacting with the replicating molecules in an advantageous manner. Many minerals need to be present as well. I suggest, as Shapiro does, that this is unlikely.

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.”

More recently, in the 2006 3rd edition of “The RNA World” Joyce and Orgel state:

“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.”

As for Schimmel’s paper, it is concerned with amino acids only. Apparently D-nucleotides can select for homochiral amino acids, which is interesting. What is even more interesting is where the original homopolymeric nucleic acid came from in the first place.

Comment #95217

Posted by idon'treallycare on April 6, 2006 5:30 PM (e)

I would also like to as Mr. Frank Schmidt, in addition to answering my concerns above, to state his opinion of David Berlinski’s essay as well as the sharp criticisms made by researchers in the field, such as Gerlad Joyce, Robert Shapiro, and Harold Morowitz. Just exactly where does Berlinski’s concerns wildly and stupidly deviate from mainstream criticism?

Comment #95226

Posted by frank schmidt on April 6, 2006 6:14 PM (e)

Joyce and Orgel wrote:

“We conclude that despite significant recent progress, [emphasis added] 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….

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.”

Well, duh. That’s why they call it research. The thing to do in this situation is get off our collective gluteals and do more science. Even Bob Shapiro (whose private comments about the RNA world model are even more vehement) would probably agree that experimental results are a good thing.

The reason why the RNA world is such a popular model is simple: related RNAs in all extant organisms are responsible for some essential biochemical reactions. The logical conclusion is that these functions arose from a common ancestor for all extant life, whether that was a proto-cell, a population of proto-cells, or something we wouldn’t even call living today.

idon'treallycare wrote:

As for Schimmel’s paper, it is concerned with amino acids only. Apparently D-nucleotides can select for homochiral amino acids, which is interesting. What is even more interesting is where the original homopolymeric nucleic acid came from in the first place.

As I said in my post.

Comment #95242

Posted by 'Rev Dr' Lenny Flank on April 6, 2006 6:47 PM (e)

Hmmmmm. Is Berlinksi BS’ing me, or is DI …. .?

A little of both. Berlinski, so far as I’ve seen, generally focuses (even more than the average IDer) on criticism of evolutionary theory, while avoiding strong endorsement of any alternative. He used to make statements that sorta kinda supported ID, but generally backpedaled as soon as anyone noticed.

I replied to Berlinksi asking him, flat-out, if DI is lying to us when it claims him as an ID supporter.

I very much doubt I’ll get an answer.

Which would, of course, be a quite eloquent answer.

Comment #95244

Posted by 'Rev Dr' Lenny Flank on April 6, 2006 6:51 PM (e)

Again with the obsession about the other guy’s P.O.V. Why don’t evolutionists see criticism (however misguided) as an opportunity to improve their model?

Because ID/creationists don’t ever OFFER anything that might help improve the model. (shrug)

Disagree? Then please, please, pretty please with sugar on it, go ahead and (1) offer an alternative view and (2) show us how to go about investigating it.

Berlinski doesn’t seem to want to answer that.

Neither does idontreallycare (assuming he’s not just Berlinski in yet another schizoid episode).

How about you? Care to give it a go?

Comment #95273

Posted by Anton Mates on April 6, 2006 10:26 PM (e)

idon'treallycare wrote:

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.)

Not that that paper wasn’t extremely valuable, but inasmuch as a) it’s over 20 years old, and b) its subject is why racemic nucleotide mixtures are a problem for template-directed synthesis in particular, from a modern perspective it hardly constitutes a “thorough discussion” of either the necessity of or possible mechanisms for homochirality.

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.”

You’ve got an odd definition of “gloomy!” Orgel begins and ends by pointing out that a racemic environment is not always quite as horrible for template-directed synthesis as previously thought. This can only be considered a step forward for RNA-first models, albeit a small one.

And surely Frank’s own paper is another step forward? If recombination rather than polymerization played a significant role in creating large RNAs in ancient environments, that would both improve the probability of finding replicases within the RNA search space, and possibly allow a temporary sidestep of the enantiomeric cross-inhibition.

More recently, in the 2006 3rd edition of “The RNA World” Joyce and Orgel state:
[snipped]

The above is simply a slightly (as in, about eight words were changed) edited version of the same text from the 2nd edition, in 1999, so I have my doubts concerning its comprehensiveness at the present time. Regardless, as Frank says, it’s an invitation to do more research, not an expression of despair.

As for Schimmel’s paper, it is concerned with amino acids only. Apparently D-nucleotides can select for homochiral amino acids, which is interesting. What is even more interesting is where the original homopolymeric nucleic acid came from in the first place.

Did you read the Shinitzky et al. paper Frank cited? It provides a very interesting putative mechanism for homochirality, though until its results are replicated by other groups it may still be due to some experimental fault.

Also in Origins of Life and Evolution of Biospheres (which is a fascinating journal the existence of which I had no idea–thanks, Frank! I’m going to be a doing a lot of reading now…) is a review article on the topic: Avalos et al. 2004, Symmetry Breaking by Spontaneous Crystallization – Is it the Most Plausible Source of Terrestrial Handedness we have Long Been Looking for? – A Reappraisal. Long name, but a very thought-provoking review, I think.

(In case anyone cares, this hasn’t actually made me into a RNA-first convert! Just seems like both RNA-first and RNA-later scenarios involve many promising sub-avenues of research. My personal and utterly inexpert suspicion is that we’ll end up with about a jillion possible-but-individually-improbable pathways for the origin of life, and scientists can spend the rest of eternity happily arguing over exactly which one we came down. Which is more or less what seems to happen with analysis of any historical event.)

Comment #95335

Posted by idon'treallycare on April 7, 2006 8:05 AM (e)

To Frank and Anton:

First to Frank. I think you and I, at least at this juncture in thought, completely agree as to the future hope of an RNA-World paradigm. Get out there and experiment! We know much more than we did 50 years ago, and there is no reason to assume that the next 50 years will not bring with it some wonderful insight about the origin of life. My comments, however, were pertinent to the limitations we face /now/. So was Berlinski’s.

And to Anton. Yes, Joyce’s paper is 20 years old, but a paper’s age doesn’t /necessarily/ reflect its value; after all, Orgel has cited it favorably in many publications. I don’t really think I have another point I would like to make about this paper, so I will move on.

Yes, there are quite literally scores of models for the origin of homochirality. And there are with them scores of critics blasting each model. Did you read Robert Shapiro’s paper? Not only does he blast chirality speculations, but he as well casts doubt on James Ferris’ work with minerals forming long chains of nucleic acids.

At any rate, take Hazen’s 2003 review in Nature (Chiral selection on inorganic crystalline surfaces), where he states:

“The demonstrated ability of minerals to select and
adsorb organic molecules has long been recognized as a
possible mechanism for one of life’s most distinctive
biochemical signatures — its strong selectivity for Lamino
acids and D-sugars.Almost all prebiotic synthesis
reactions yield essentially equal amounts of L- and Denantiomers3,74.
Thus, to explain life’s chiral excess,two
broad categories of symmetry-breaking phenomena
have been invoked4,75–77.On the one hand,some
researchers favour nebular-scale processes,such as
chirally selective photolysis by circularly polarized
synchrotron radiation from a rapidly rotating neutron
star78–80,magnetochiral photochemistry81 or parityviolating
weak interactions of nuclear particles82.
These processes are consistent with the small but
significant excess of L-amino acids reported from
some carbonaceous chondrite meteorites83–85.
On the other hand,many investigators2,86–88 have
focused on more local ‘asymmetric agents’.Some
mechanisms rely on local amplification of slight chiral
excesses, for example by Bose–Einstein condensation89
or by chiral self-assembly of polymers90–92 or crystals7,93.
These and other chiral selection mechanisms75 require
further investigation, but the conceptually simpler and
geochemically relevant chiral selection mechanism of
adsorption on chiral crystal growth surfaces of
minerals, described above, has been largely overlooked.
According to Lahav3,“if a selective adsorption of chiral
amino acids … on certain crystal faces were observed,
then the problem of biological homochirality would be
possible to comprehend.”
We should note that some authors argue that quartz
and other minerals cannot contribute to the origins of
biochemical homochirality77 because left- and righthanded
surfaces are present on Earth in equal
abundance94,95.This argument is based on the
questionable assumption that multiple origin events
occurred at different geographical locations on Earth;
the preponderance of L-amino acids in biology is taken
as evidence for a global prebiotic excess of L-amino acids
rather than an excess of L-adsorbing environments.
WE HOLD A DIFFERENT VIEW:we assume that the
nucleation of self-replicating molecular systems is
INFREQUENT,whereas the growth of such systems once
nucleated is relatively rapid and efficient. In this
scenario,a single successful self-replicating chiral
synthesis (for example,on one chiral crystal face of one
calcite crystal) PURELY BY CHANCE became the dominant
biochemical overprint IN SPITE of initially racemic
mixtures both of MOLECULES and SURFACES.”

He seems, to my lights, unconvinced by the VERY speculative ideas dominating the field today. Hazen relies on sheer dumb luck for the origin of the first homochiral oligomer. Robert Shapiro, in his paper, shows just how unlikely this is. I ask you to consult that paper.

I believe it is worthwhile to quote Joyce and Orgel (2006) once again:

“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.”

Of course, they could be incorrect, or not savvy as to the recent hypotheses of homochirality origin. They could be ignorant as to the whole mess of it. But why assume this? Why not assume that, to their minds, no new research has really convinced them?

It seems to me no further conversation is necessary or even wanted. I’m beating a dead horse, I’m afraid. Templated and untemplated reactions, length of replicase, relevant Joyce and Orgel calculations, unlikely prebiotic molecules and minerals–I’ve said it all before. And we converge at the point that there is great uncertainty right now, but we SHOULD NOT throw up our hands. Let us see how far new research can take us. This is, to my mind, the best way to end our discussion. It has been nice.

Comment #95341

Posted by k.e. on April 7, 2006 8:45 AM (e)

idon’treallycare said:
My comments, however, were pertinent to the limitations we face /now/. So was Berlinski’s.

Is that so.

–er Doc. B limitations there goes that ‘limit’ again…and it should be “So were Berlinski’s”

Then idon’treallycare ends on a more optimistic note

This is, to my mind, the best way to end our discussion. It has been nice.

but…. but…..but… what about Berlinski? (smirk)

Not interested in the paper offered by Frank Schmidt ?

idon’treallycare asked if the paper I referenced is available. It should be on the RNA Journal website. If not, email the address in the abstract, under your own name, of course, and I’ll be happy to forward a copy.

I didn’t think so.

BTW you misrepresented Shapiro when you said, he said:
A replicator was not involved in the origin of life.

go back a re-read his piece.

and how does Hazen’s view that

….
WE HOLD A DIFFERENT VIEW:we assume that the
nucleation of self-replicating molecular systems is
INFREQUENT,whereas the growth of such systems once
nucleated is relatively rapid and efficient. In this
scenario,a single successful self-replicating chiral
synthesis (for example,on one chiral crystal face of one
calcite crystal) PURELY BY CHANCE became the dominant
biochemical overprint IN SPITE of initially racemic
mixtures both of MOLECULES and SURFACES.”

match your view

He seems, to my lights, unconvinced by the VERY speculative ideas dominating the field today. Hazen relies on sheer dumb luck for the origin of the first homochiral oligomer

Indeed it has been a delight, goodbye.

Comment #95347

Posted by idon'treallycare on April 7, 2006 9:50 AM (e)

Ah, k.e–

I had nearly forgot to address your moronic rants before I left. Aside from the fact that I am NOT Berlinski, I would have to say that your incorrect comments betray a very conspicuous tendency on your part to grab at anything except my technical criticisms.

1. Robert Shapiro’s paper is indeed entitled “A replicator was not involved in the origin of life,” in which he argued, and I know this is a big surprise, that a replicator was not involved in the origin of life.

2. I expressed my concerns about Frank Schmidt’s scenario several times above. It is not a question of the ability of short RNA motifs to combine readily with one another.

3. In regard to the chirality question, I hold with Bonner( Bonner, W. A. Chirality and life. Origins Life Evol. Biosphere 1995, 25, 175-190.”
, who states,

“[T]he scrupulously anhydrous conditions required to enable the occurrence of measurable asymmetric adsorption [of homochiral molecules] on quartz render the mechanism totally implausible in any realistic prebiotic environment.”

I as well hold with Joyce and Orgel’s distinguished opinion.

I think that is all.

Comment #95363

Posted by frank schmidt on April 7, 2006 10:58 AM (e)

idon'treallycare wrote:

Hazen relies on sheer dumb luck for the origin of the first homochiral oligomer

Actually, no. He regards the formation of prebiotic chemicals that are on the pathway to life as inevitable, given (1) the nature of fitness landscapes, and (2)the strength of selection.

All of these “improbability arguments” (including the ones quoted or in Berlinski’s article) that describe difficulties with the RNA world, Miller-Urey, the evolution of complex structures, macroevolution, etc. discount selection.

I propose in contrast to Dembski’s so-called Law of Improbability, the Law of Selection. And I will argue that the Universe is inherently under selection, and that therefore complex life is inevitable {bio}chemically. Now if I could only prove it, the King of Sweden would probably nod approvingly at my speech, too. :)

Comment #95370

Posted by idon'treallycare on April 7, 2006 11:57 AM (e)

Frank:

Interesting idea. Akin to Paul Davies thoughts on the subject. I don’t see how exactly selection (presumably natural selection?) can operate before the invention of self-replication. If you are talking about general bio-friendly principles, like those posited by Christian de Duve, where each step is chemically highly probable, then I admire your passion for pursuing them–those elusive, elegant principles, that is. But until I see that Nature has a propensity, as many a molecular biologist hopes, for organizing a messy prebiotic broth into pure pools of organic molecules, I must remain skeptical.

May I take it that Berlinski’s calculation is correct insofar as selection is not involved? Like Robert Shapiro, I would have to say that selection can only operate after replicating a template. The formation of the very first template is by itself a matter of chance.

Comment #95371

Posted by frank schmidt on April 7, 2006 12:22 PM (e)

The question is almost Clintonian, “It depends on what replication is.” Some possibilities: replication started off with fewer nucleotides (cf Eigen), therefore a smaller probability of making fatal mistakes. Or, replication could have been a template-driven process but didn’t involve a nucleic acid replicator. Remember that the RNA World model says that the earliest RNAs were catalysts and templates only. Thus, replication could come about by other means, e.g., surface catalysis, or solvent-facilitated base pairing. This expands the number of plausible scenarios without trashing the overall model.

Personally, I find it intriguing that the ribosome may work primarily by surface catalysis. If an ancestral rRNA were to find a way to synthesize a small set of amino acid sequences, and if the resulting peptides were able to facilitate replication of the RNA, then we’re off to the (evolutionary) races, and it’s downhill from there, ending with us. Or whatever. (Actually, given our ability to trash the planet, downhill ending with us may be close to the truth - cf what Pianka really said.)

Comment #95374

Posted by normdoering on April 7, 2006 12:57 PM (e)

frank schmidt wrote:

The question is almost Clintonian, “It depends on what replication is.”

That question hit me in a profound way. (No doubt due to me being a complete molecular biology novice).

Can we say that all growing polymers self-replicate? Or is that just the rules of physics and chemistry without self-replication?

Comment #95377

Posted by k.e. on April 7, 2006 2:02 PM (e)

idon’treallycare

Yeah yeah fallen into my trap again, well its here for posterity beginning with the very first line in the very first post stick that on your posterior.

Why thank you very much for posting this dull and uninformative reply to my essay. I say dull because it presents painfully tired objections that I myself understand and address in my 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 illuminating. I build 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.

You do have a reading problem don’t you


From Robert Shapiro’s paper is indeed entitled “A replicator was not involved in the origin of life,” in which he argued, and I know this is a big surprise, that a replicator was not involved in the origin of life.

would that be the same article that said

The possibility that formation of the first replicator took place through a very improbable event cannot be excluded, ….

The title is no surprise considering Shapiro’s public position on his religious stand and the DI almost succeeding in hijacking him for the cause.

And now that religion is just a branch of physics Templeton prize winner Paul Davies gets his mention, I’m sure he would be thrilled.

Now back to the technicalities (ho hum whatever you say) of really big numbers and fanciful language.

Of which there is an awful lot, 15 pages in total just on this thread it won’t take much to do an arrogant flourish matched with arrogant flourish…do you want me to address those ‘technicalities’?…oh and in one long continuous blurb don’t worry they ARE moranic.

Comment #95378

Posted by k.e. on April 7, 2006 2:22 PM (e)

Oh and Dr B. stop begging for tips to ‘fix’ your idiotic ramblings

Comment #95416

Posted by 'Rev Dr' Lenny Flank on April 7, 2006 6:09 PM (e)

goodbye.

So you keep saying.

Is your name “Columbo”?

Comment #95426

Posted by idon'treallycare on April 7, 2006 7:15 PM (e)

Some comments to make:

1. Frank (may I call you Frank, or more respectfully Dr. Schmidt?), I agree that there are a large number of possibilities to consider in regard to how exactly things happened. Perhaps some fortuitous minerals were in place that could preferrentially absorb homochiral nucleotides, organize these nucleotides into long strands, and thereafter these strands could recombine, eventually forming a dynamic RNA ribozyme library. Perhaps fewer than four nucleotides were needed. And, as you note, “replication could have been a template-driven process but didn’t involve a nucleic acid replicator. Remember that the RNA World model says that the earliest RNAs were catalysts and templates only. Thus, replication could come about by other means, e.g., surface catalysis, or solvent-facilitated base pairing. This expands the number of plausible scenarios without trashing the overall model.”

The problem is, of course, that this is what Joyce and Orgel call a molecular biologists dream. In nearly all experiments mentioned above a large excess of cytosine was necessary, yet cytosine is one of the most notoriously difficult nucleotides to assemble. There is no plausible route to the synthesis of ribose. It remains to be seen whether minerals can preferentially absorb exclusively homochiral molecules without relying on a number of implausible circumstances. There is the question of lack of phosphate. Many branch formers and chain terminators were in the prebiotic ocean and outnumbered the organic molecules many times to one. As for replication, observe Stuart Kauffman’s comments athttp://www.santafe.edu/sfi/People/kauffman/sak-p…

“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.”

It still remains to be seen that an RNA replicase can exist, as well as RNA ribozymes catalyzing abiotic synthesis of nucleotides. These are problems that cannot be ignored or simply shoveled off to the side. You are right that there are many speculative scenarios potentially circumventing some (but not all) of these problems. The trouble is that these scenarios are in themselves implausible or rely on a number of happy circumstances. In all reality, the best option is to look for an alternative to the RNA world.

2. You go on: “Personally, I find it intriguing that the ribosome may work primarily by surface catalysis. If an ancestral rRNA were to find a way to synthesize a small set of amino acid sequences, and if the resulting peptides were able to facilitate replication of the RNA, then we’re off to the (evolutionary) races, and it’s downhill from there, ending with us. Or whatever. (Actually, given our ability to trash the planet, downhill ending with us may be close to the truth - cf what Pianka really said.)”

This is, of course, not nearly as simple as what you say. The origin of coded chemistry represents a great paradox to current thought. There are the thoughts of Schimmel, Di Guilio, Szathmary, Knight, Landweber, Orgel, Woese, Crick, Freeland, etc. to consider. The main trouble is linking the data. If there were stereochemical interactions between RNA and amino acids, then why, a priori, should any stereochemical shaping of the code result in the eventual esterfication of the amino acid on the CCA end of the tRNA? To my mind there is no explanation for the separation. The coevolutionary model doesn’t neatly fit with all the data. And the argument that the code is a product of evolution–Freeland’s hypothesis–suffers from the recent studies made that ambiguous genetic codes for the most part cause massive numbers of mutations. The mutations in the studies are, of course, not fatal, because the structure of the genetic code is itself reslient in the face of mutational noise. Still yet though, no plausible path has been achieved in connecting a system of coded chemistry to a pool of interacting nucleotides and amino acids by an evolutionary pathway. Things are especially complicated by the presence of not one, but two genetic codes–they are linked to each other, but no one knows quite how.

An interesting discussion took place a few years back between Di Guilio and Szathmary. Both have opposing views on how the genetic code arose. Di Giulio made the point that a ribonucleoprotein (RNA and peptides interacting) world was necessary from the beginning, because if not the RNA-only world could not have evolved into the RNP world, since its function would so pure future evolution would be impossible. Szathmary responded saying that since evolution is myopic the RNA world could not have been missed, since it was much simpler than the RNP world. He also said Di Giulio’s scenario couldn’t work since it requires a great deal of specificity (and impossibly high catalytic activity) in short peptides before the origin of the code. Both make devastating points, and I would imagine both are correct.

So, no, I would have to say that it is not all downhill from the point of replicating RNAs. Refer to Berlinski’s essay for some interesting experiments by Suga and a deeper discussion of the genetic code origin. It is far from clear how the code arose, how and why we have the number of amino acids we do, and how the two genetic codes are linked.

3. k.e., my persistent, dense, baffled friend, Berlinski never said it was impossible for life to originate, just improbable. Just as Shapiro has stated.They both look for alternatives to the RNA world.

4. Lenny is right–I feel like I know the field well and have a lot to say and just can’t shut up.

Comment #95441

Posted by k.e. on April 7, 2006 9:39 PM (e)

Delicious Doc B. almost Humbertian. complete with another one.
And what have you done with Berlinski Doc B. he can’t defend himself? Or are we going for a structural death here ?

I feel like I know the field well and have a lot to say and just can’t shut up.

Well all those lonely late nights in Paris, I suppose. Haven’t you got anything better to do? Leggy young women to chase or something? Oh that’s right they’re “inaccessible”.

All you creationist types project the most banal reality.

But don’t let me stop you, the more the better.

Redefine Truth away, the DI won’t object although they may want you to remove the sock puppet while you publicly push their case.

The improbability escalates.

Of what? The FSM using his noodly appendage or not?

Oh he was a chemist playing with his chemistry set, makes a change from a little boy with an ant farm. Did you run that by Davies ? He thinks G_D is a physicist looking for the equation to start the universe and when he finds it he can get started making it.

Well actually the improbability doesn’t escalate because as we all know the probability(s) was(were) 1. (Past tense singular/plural)(Not future tense imperfect, but I’ll get to that later)

Time is something most of you twits forget about.

Comment #95455

Posted by 'Rev Dr' Lenny Flank on April 7, 2006 10:17 PM (e)

4. Lenny is right—I feel like I know the field well and have a lot to say and just can’t shut up.

Well, since you’re the expert and all, perhaps you’d be so kind as to give us your alternative hypothesis and explain how we can go about testing it using the scientific method … ?

And for Mr Berlinksi, you’ve not answered my simple question about whether DI is lying to us when it claims you as an ID supporter.

Is there some sort of problem with your answering that simple question for me …. . ?

Comment #95467

Posted by Anton Mates on April 7, 2006 11:00 PM (e)

idon'treallycare wrote:

And to Anton. Yes, Joyce’s paper is 20 years old, but a paper’s age doesn’t /necessarily/ reflect its value; after all, Orgel has cited it favorably in many publications. I don’t really think I have another point I would like to make about this paper, so I will move on.

That’s probably wise, since your position is clearly indefensible. The question’s not whether Joyce’s paper has any value–obviously it does–but whether a 20-year-old paper could remotely be considered a “thorough” discussion of modern research into the origins of and necessity for homochirality. Particularly when said paper did not even claim to be a comprehensive review of such research in its own time, but rather discussed a single study of template-directed synthesis.

But this is yet another rhetorical tool characteristic of the ID advocate–they’re quite happy to pull now-outdated negative statements from older works and use them to attack modern biology. Heck, they still quote Darwin on things like the difficulty of understanding the eye’s evolution.

Yes, there are quite literally scores of models for the origin of homochirality. And there are with them scores of critics blasting each model. Did you read Robert Shapiro’s paper? Not only does he blast chirality speculations, but he as well casts doubt on James Ferris’ work with minerals forming long chains of nucleic acids.

Well, let’s see. Shapiro’s supposed “blasting of chirality speculations” consists of:

a -amino acids, with the notable exception of glycine, will be present as racemates (I set aside the unresolved question of possible enantiomeric excess).

Yeah, that’s a vicious takedown right there. I might add that he doesn’t even mention the issue in reference to nucleotides, making this completely irrelevant to the current discussion.

As for “casting doubt” on Ferris’ work, he does nothing of the sort. 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.

which says nothing Ferris himself wouldn’t say.

Of course, they [Joyce & Orgel] could be incorrect, or not savvy as to the recent hypotheses of homochirality origin. They could be ignorant as to the whole mess of it. But why assume this? Why not assume that, to their minds, no new research has really convinced them?

You’re not seriously arguing that new scientific research should be discounted on the grounds that senior scientist X has not publicly endorsed it, are you?

3. In regard to the chirality question, I hold with Bonner( Bonner, W. A. Chirality and life. Origins Life Evol. Biosphere 1995, 25, 175-190.”
, who states,

“[T]he scrupulously anhydrous conditions required to enable the occurrence of measurable asymmetric adsorption [of homochiral molecules] on quartz render the mechanism totally implausible in any realistic prebiotic environment.”

Great. Of course, that says nothing about other mechanisms, such as crystallization and selective degradation, which are AFAIK more favored by current researchers.

Comment #95472

Posted by Anton Mates on April 7, 2006 11:29 PM (e)

The following was such an appalling example of quote-distortion that I felt it deserved its own post.

idon'treallycare wrote:

At any rate, take Hazen’s 2003 review in Nature (Chiral selection on inorganic crystalline surfaces), where he states:

“The demonstrated ability of minerals to select and
adsorb organic molecules has long been recognized as a
possible mechanism for one of life’s most distinctive
biochemical signatures — its strong selectivity for Lamino
acids and D-sugars.Almost all prebiotic synthesis
reactions yield essentially equal amounts of L- and Denantiomers3,74.
Thus, to explain life’s chiral excess,two
broad categories of symmetry-breaking phenomena
have been invoked4,75–77.On the one hand,some
researchers favour nebular-scale processes,such as
chirally selective photolysis by circularly polarized
synchrotron radiation from a rapidly rotating neutron
star78–80,magnetochiral photochemistry81 or parityviolating
weak interactions of nuclear particles82.
These processes are consistent with the small but
significant excess of L-amino acids reported from
some carbonaceous chondrite meteorites83–85.
On the other hand,many investigators2,86–88 have
focused on more local ‘asymmetric agents’.Some
mechanisms rely on local amplification of slight chiral
excesses, for example by Bose–Einstein condensation89
or by chiral self-assembly of polymers90–92 or crystals7,93.
These and other chiral selection mechanisms75 require
further investigation, but the conceptually simpler and
geochemically relevant chiral selection mechanism of
adsorption on chiral crystal growth surfaces of
minerals, described above, has been largely overlooked.
According to Lahav3,“if a selective adsorption of chiral
amino acids … on certain crystal faces were observed,
then the problem of biological homochirality would be
possible to comprehend.”
We should note that some authors argue that quartz
and other minerals cannot contribute to the origins of
biochemical homochirality77 because left- and righthanded
surfaces are present on Earth in equal
abundance94,95.This argument is based on the
questionable assumption that multiple origin events
occurred at different geographical locations on Earth;
the preponderance of L-amino acids in biology is taken
as evidence for a global prebiotic excess of L-amino acids
rather than an excess of L-adsorbing environments.
WE HOLD A DIFFERENT VIEW:we assume that the
nucleation of self-replicating molecular systems is
INFREQUENT,whereas the growth of such systems once
nucleated is relatively rapid and efficient. In this
scenario,a single successful self-replicating chiral
synthesis (for example,on one chiral crystal face of one
calcite crystal) PURELY BY CHANCE became the dominant
biochemical overprint IN SPITE of initially racemic
mixtures both of MOLECULES and SURFACES.”

He seems, to my lights, unconvinced by the VERY speculative ideas dominating the field today.

I’m sorry? He’s openly supporting those ideas, and complaining that one in particular, mineral adsorption. hasn’t received enough attention!

“These and other chiral selection mechanisms require further investigation, but the conceptually simpler and geochemically relevant chiral selection mechanism of adsorption on chiral crystal growth surfaces of minerals, described above, has been largely overlooked.”

The entire rest of your quote consists of arguments for the value and plausibility of this mechanism! To claim that Hazen is here criticizing models for prebiotic homochirality is blatantly dishonest.

Hazen relies on sheer dumb luck for the origin of the first homochiral oligomer.

Also a clear distortion of his meaning. Hazen writes,

“…we assume that the nucleation of self-replicating molecular systems is infrequent, whereas the growth of such systems once nucleated is relatively rapid and efficient. In this scenario,a single successful self-replicating chiral synthesis (for example, on one chiral crystal face of one calcite crystal) purely by chance became the dominant biochemical overprint in spite of initially racemic mixtures both of molecules and surfaces.”

Hazen is not saying that the appearance of homochiral molecule pools is due to “sheer dumb luck”, but rather that it’s a matter of chance which handedness a given pool would have. L-enantiomers accrete on this crystal face, D-enantiomers on that one. Only one of them happens to host the appearance of a replicator (or if more than one does, only one eventually “wins out” and gives rise to cellular life.)

Your interpretation is equivalent to interpreting the statement “purely by chance, a flipped coin comes down as heads or tails” as saying it’s sheer dumb luck the coin comes down at all.

Robert Shapiro, in his paper, shows just how unlikely this is. I ask you to consult that paper.

And as I just said in the post above, Shapiro explicitly states that he doesn’t intend to even discuss the matter, so this is blatantly false. I don’t think there can be any doubt at this point that you aren’t honestly interested in prebiotic research.

Comment #95473

Posted by Sir_Toejam on April 7, 2006 11:32 PM (e)

In related developments; anybody else see this yet:

http://www.physorg.com/news63628216.html

The core of the debate, Kong said, relates to the behavior of the nucleic acid bases – adenine, thymine, guanine and cytosine - that as A-T and G-C base pairs form DNA and ultimately become the blueprint for all living things. One of the most basic premises of biochemistry is that these nucleic acid bases are very stable, as they would have to be to prevent rampant mutations and make an organized genetic structure possible.

But studies at OSU, which were done with highly sophisticated electron spectroscopy, showed that the alleged stability of the nucleic acid bases in DNA is largely a myth.

The findings suggest, Kong said, how water could have been an absolutely essential compound to allow early DNA bases to remain stable, resist mutation, and ultimately allow for the evolution of life.

OSU researchers were the first to propose the “dark state” model and prove its existence.

“What this is really telling us is that life is a unified process,” Kong said. “It’s not just a group of DNA bases, but it’s also the physical environment in which they exist. Later on, as life became more evolved, there were other ways to achieve genetic stability. But at first, it simply may not have been possible without water.”

Comment #95474

Posted by Anton Mates on April 7, 2006 11:34 PM (e)

On another note, there’s a new Good Math, Bad Math post with Berlinski’s reply to Chu-Carroll’s critique. The exchange continues into the comments there, if you want to see Berlinski saying more silly things about math.

Comment #95475

Posted by frank schmidt on April 7, 2006 11:40 PM (e)

IDRC: The origin of the code is an interesting question. 1. Undoubtedly you are familiar with Mike Yarus’ result that at least some RNAs bind amino acids with motifs that include their codon sequences. 2.I’m not at all sure what the separation question is: are you saying that there is some paradox involved in contemporary tRNAs ending in CCA? Possible, I suppose, but I’m not aware of this being an issue in the contemporary literature (although the CCA-synthesizing enzyme does appear to be sort of weird; see Alan Weiner’s work). 3. Read Eigen for an idea of what the original code might have looked like. I find it fascinating that the G-row codons specify amino acids that are the most common in Miller-Urey experiments. Could this mean that the original code was based on GN dinucleotides with a third nucleotide as a spacer? Dunno, I wasn’t there, but it’s certainly intriguing…

The difficulty with Berlinski, Shapiro and others is that their objections, while reasonable and consistent with the evidence, don’t really lead to an alternative model. Excuse me, I meant alternative testable model. They can carp to their heart’s content about various objections, and most of us in the field will agree that these are difficulties, but we really need some experiments based on testable predictions in order to evaluate their objections. The RNA world model provides that, which is more useful than worrying whether it is right or wrong based on incomplete information.

Frank

Comment #95482

Posted by idon'treallycare on April 8, 2006 12:34 AM (e)

To Anton:

I do thank you for your sharp criticisms. My main focus for the 3 years I have been reviewing mainstream literature has been on the genetic code origin and on various scenarios for the first replicating entity. I have not read up much on chirality, much like you and the rest of the board have not read up on the origin of life. I was very polite in correcting various misunderstandings you had about Joyce and Orgel’s work, so I ask the same amount of patience for me.

1. My errors or trivial tangents–As for the Joyce paper 20 years ago, that was pretty much the paper that set the standard that, yes, we need an abundance of one specifically handed molecule. I threw it in the mix just for interest’s sake. As for Shapiro’s paper, which I haven’t read in nearly a year (and papers tend to get jumbled after reading so many of them), I was going on memory that he had discussed something about chirality in his paper. Other than a passing sentence, he DID NOT. And I was wrong. What struck me about Hazen’s comments was the fact that he said, “… initially racemic
mixtures both of MOLECULES and SURFACES.” I must have misunderstood the quote in question. It happens. I most certainly was not trying to be dishonest. I read it quickly and misunderstood, much like you have for Orgel’s papers. Sorry.

2. Your errors–One error is that Shapiro only weakly criticized Ferris’ mineral polymerization. Since I dug up the paper, allow me to quote freely, and let the board be the judge:

“Those studies were addressed to the question of whether oligomerization in aqueous solution could compete with hydrolysis; they answered it in an elegant manner. They did not, however, deal with the specificity problem discussed here, potentially interfering substances having been excluded by the investigators. In the absence of any competintion studies, there is no reason to believe that a give mineral might preferentially adsorb and combine the monomers that would be useful in construction a particular replicator, while excluding the much greater number that would disrupt such a function.

Apart from this, the experiments were conducted in ways that appear unlikely to take place outside a laboratory. The monomers were specifically activated by procedures involving either the multistep preparation of nucleoside 5’-phosphorimidazolides or the prior treatment of monomers with synthetic reagents such as carbodiimides or carbonyl diimidazole. Fresh batchs of activated monomers were added to the given mineral according to a well-defined feeding schedule. The relevance of these results to events on the prebiotc Earth is therefore questionable. [I]t would be interesting to learn whether they actually do so outside the laboratory.”

But then again, since “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.

which says nothing Ferris himself wouldn’t say.”

I might just be making that all up. What were you saying about quote mining and being dishonest again?

I mentioned the Bonner paper because it is cited by Hazen when he refers to “authors [who] argue that quartz
and other minerals cannot contribute to the origins of
biochemical homochirality77 because left- and righthanded
surfaces are present on Earth in equal
abundance.” I was just offering the idea that there is no consensus thus far, and that much remains to be seen when considering models for homochiral origin, instead of blindly accepting any fringe idea that pops up. Are you suggesting that the puzzle of chirality has been completely solved by these papers? That is a tactic that I have seen many on this board use. When paper x gives a speculation, and you need an answer to the critic, then cite x as if it is a fact and with an air of supremacy as if you have sampled all of the literature and criticisms. There are many promising avenues of research, but none so far, at least to my knowledge, have presented undeniable, irrefutable, prebiotically relevant results. That is why Hazen is urging more research. One question you must consider is how much can one of these mechanisms bias the appearance of handedness of molecules in realtion to how much they would have had to in order to maintain a hope of life. In this context, I follow Joyce and Orgel’s opinion that not even minerals could achieve the level of bias needed to promote self replication. I take their word for it. YOU DO NOT HAVE TO BELIEVE THEM. Feel free to believe whatever you want. But you cannot say that my skepticism is unwarranted when I am repeating only what two of the leading researchers in the field have said. More research is needed. That is Hazen’s position. And mine as well. (By the way, just curious, how many papers HAVE you read about chirality–more than me I’m certain–but still weren’t you the one not to long ago asking for some help searching the field?)

3. Since my criticisms are so easily dismissed–I am a crank scientist, after all–will you be so kind as to answer the relevant questions and issues:

a. abiotic synthesis of nucleotides, especially cytosine

b. Molecules causing chain termination being presumably in abundance in the prebiotic ocean

c. the presence of molecules interupting backbone regularity

d. an abundance of molecules causing branching structures and thus disruption of regularity in a polymer backbone

e. plausible prebiotic synthesis of ribose

f. an abundant source of phosphate

g. a scenario to bring together ribose and nucleotides since their synthesis is mutually exculsive

h. addressing the fragility of nucleotides, especially if you endorse a hot origin of life

i. addressing the my criticisms of replication above (and the quote by Kauffman: “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.” If we instead look to a replicase ribozyme to solve the matter, well, then we are right back at the odds Joyce and Orgel calculated to start out with)

j. showing that ribozymes even have the capacity to synthesize nucleotides abiotically, and that their occurrence is very probable so that they were abundant in the prebiotic ocean

4. Perhaps I am an idiot. But I am not insincere. I hate when RNA first supporters give with the one hand that there are many difficulties with their scenario and take back with the other, saying, yes of course there are dilemmas, but we have pretty much solved them all. The fact is, as Berlinski presented in his essay, these /assumptions/ are enough to make one very uneasy about the whole thing all together. I will conclude with a few of the concluding sentences from Shapiro:

“Arguments of the type presented here cannot disprove the replicator hypothesis, but only render it improbable. Despite the difficulties discussed above, circumstances in particular locations may have improved the chances of replicator formation. A more restricted set of componetnes than that present in the Murchison meterorite may have been generated at certain sites, and by chance, a few of them may have had enriched concentrations of replicator subunits. Aslo by chance, sucha site may have contained a mineral or other natural catalyst that foavored polymerization of those same components. Afater a large number of trials, a replicator may have arisen in such an environment….On the early Earth, the production of an information-bearing homopolymer within a complex misture by chance cannot be excluded, but if such an event was required to start life, then the origin would have been an extremely improbable accident, and prospects for life elsewhere would be diminished.”

Comment #95483

Posted by idon'treallycare on April 8, 2006 1:04 AM (e)

Frank:

I appreciate your comments. Yes, I am very familiar with Mike Yarus’ research. It is very intriguing that certain amino acids *seem* to have affinities for nucleic acid polymers containing an abundance of their representative codons. (Note that there is NO evidence of binding amino acids directly to trinucleotides, but instead long stretches of repeated codons). Similar results were, of course, disputed by Ellington in the past, who imagines that the evolution of the genetic code would have erased its relics. In my opinion they are real, not a result of methodological error–at least for some. The problem is there is no plausible reason why or scheme as to why evolution has placed the codon and the amino acid on opposite ends of the tRNA. Why remove the amino acid from directly interacting with the codons? There are of course, ideas, but most of them are far fetched, as the main researchers will admit. In addition, if codons did indeed bind to amino acids, what in the world are we to make of the code that synthetases use to discriminate amino acids and tRNAs during charging? They must be connected somehow. Its just that we do not know how exactly they were connected yet. Finally, there are the concerns against the model of stereochemistry as rasied by Di Guilio.

I appreciate that you are honest in admitting the RNA World has long way to go (and that critics aren’t just making this stuff up) and that future research is very promising. I agree. Anton take note.

Comment #95506

Posted by Anton Mates on April 8, 2006 7:21 AM (e)

idon'treallycare wrote:

I was very polite in correcting various misunderstandings you had about Joyce and Orgel’s work, so I ask the same amount of patience for me.

And as you’ve demonstrated your patience and politeness with such gems as:

idon'treallycare wrote:

The first is that most (though not all) of you are morons. It is quite clear that almost all of you have never read a single technical paper dealing with the origin of the RNA world. At very best you puke up some abstracts from pubmed without bothering to read them in their entirety.

idon'treallycare wrote:

And the RNA sequence has to be a compliment, Mr. Anton Mates, because if it isn’t THERE IS NO HEREDITY! Idiot.

idon'treallycare wrote:

Since you seem to be the type that likes lay instead of technical scientific reads, refer to this section by Carl Zimmer at http://www.carlzimmer.com/articles/2004/articles…… about just the paper you linked:

idon'treallycare wrote:

Anton, I’m going to commend you for at least *attempting* to read an actual peer-reviewed paper. That is more than I can say for most all of the rest. And I will retract my comment that you are an idiot.

I don’t think it will be difficult to match that standard of etiquette.

(FWIW, reading back I don’t see that I’ve been particularly impolite. I’ve said that I think you’ve been dishonest, which is true, and that I think you’re probably actually an ID supporter feigning support for the RNA-first model to defend Berlinski, which is true. But I’m not sure how to put either of those more tactfully than that.)

Comment #95516

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 8:23 AM (e)

Once again, I ask:

To idontreallycare; What is your alternative hypothesis, and how do you propose we go about investigating it?

To Berlinksi: Is DI just lying to us when they claim you as an ID supporter?

Why oh why why why don’t IDers ever answer my simple questions?

Comment #95521

Posted by idon'treallycare on April 8, 2006 9:20 AM (e)

Anton:

First of all, feel free at any time to address section three of my last post.

Secondly, you state:

“I’ve said that I think you’ve been dishonest, which is true, and that I think you’re probably actually an ID supporter feigning support for the RNA-first model to defend Berlinski, which is true. But I’m not sure how to put either of those more tactfully than that.”

Of course, this is simply nonsense. Deliberately dishonest? Nothing of the sort. I told you what happened. I misread the darn paper. It happens. I admitted my mistake. Though it never should have been made in the first place, I acted appropriately in responding to your semi-truthful allegations. I was wrong.

It therefore strikes me as peculiar that upon making a mistake, somehow it follows that all of my research and criticisms are invalid? This is absurd. Even Frank says that my criticisms, along with Berlinski’s and Shapiro’s, are reasonable. But your tactic is not to admit that most of my criticisms, the ones expressed in my last post as well as the various ones (other than chirality–I was wrong on that one, as you will be quick to express) mentioned above, are correct or even plausible, even if I quote extensively from every source on which I am relying. No, not at all. And the painful fact is that for most of the criticisms leveled above there is no current answer. This is unsettling to you, I believe. Your tactic, it seems, is instead to accuse me of being a dishonest IDer. I presume this is because you see me and the criticisms I make as a threat to science. This is how it *seems* to me, I must stress again. I could be wrong though. I have been before.

Well, like it or not, there are a great deal of problems and research avenues associated with the RNA World. Many of them I have expressed on this thread. Perhaps in time these will resolve themselves, and perhaps not. Is this not a fair conclusion? Time will ulimtately tell. Until then though, I must stress, there are a great number of scientists who are commited to methodological naturalism who yet see the invention of a de novo RNA World as a near miracle.

I will leave you with Shapiro’s letter to a section of “Arts and Letters Daily”:

“We shall understand the origin of life within the next 5 years

Two very different groups will find this development dangerous, and for different reasons, but this outcome is best explained at the end of my discussion.

Just over a half century ago, in the spring of 1953, a famous experiment brought enthusiasm and renewed interest to this field. Stanley Miller, mentored by Harold Urey, demonstrated that a mixture of small organic molecules (monomers) could readily be prepared by exposing a mixture of simple gases to an electrical spark. Similar mixtures were found in meteorites, which suggested that organic monomers may be widely distributed in the universe. If the ingredients of life could be made so readily, then why could they not just as easily assort themselves to form cells?

In that same spring, however, another famous paper was published by James Watson and Francis Crick. They demonstrated that the heredity of living organisms was stored in a very large large molecule called DNA. DNA is a polymer, a substance made by stringing many smaller units together, as links are joined to form a long chain.

The clear connection between the structure of DNA and its biological function, and the geometrical beauty of the DNA double helix led many scientists to consider it to be the essence of life itself. One flaw remained, however, to spoil this picture. DNA could store information, but it could not reproduce itself without the assistance of proteins, a different type of polymer. Proteins are also adept at increasing the rate of (catalyzing) many other chemical reactions that are considered necessary for life. The origin of life field became mired in the “chicken-or-the egg” question. Which came first: DNA or proteins? An apparent answer emerged when it was found that another polymer, RNA (a cousin of DNA) could manage both heredity and catalysis. In 1986, Walter Gilbert proposed that life began with an “RNA World.” Life started when an RNA molecule that could copy itself was formed, by chance, in a pool of its own building blocks.

Unfortunately, a half century of chemical experiments have demonstrated that nature has no inclination to prepare RNA, or even the building blocks (nucleotides) that must be linked together to form RNA. Nucleotides are not formed in Miller-type spark discharges, nor are they found in meteorites. Skilled chemists have prepared nucleotides in well-equipped laboratories, and linked them to form RNA, but neither chemists nor laboratories were present when life began on the early Earth. The Watson-Crick theory sparked a revolution in molecular biology, but it left the origin-of-life question at an impasse.

Fortunately, an alternative solution to this dilemma has gradually emerged: neither DNA nor RNA nor protein were necessary for the origin of life. Large molecules dominate the processes of life today, but they were not needed to get it started. Monomers themselves have the ability to support heredity and catalysis. The key requirement is that a suitable energy source be available to assist them in the processes of self-organization. A demonstration of the principle involved in the origin of life would require only that a suitable monomer mixture be exposed to an appropriate energy source in a simple apparatus. We could then observe the very first steps in evolution.

Some mixtures will work, but many others will fail, for technical reasons. Some dedicated effort will be needed in the laboratory to prove this point. Why have I specified five years for this discovery? The unproductive polymer-based paradigm is far from dead, and continues to consume the efforts of the majority of workers in the field. A few years will be needed to entice some of them to explore the other solution. I estimate that several years more (the time for a PhD thesis) might be required to identify a suitable monomer-energy combination, and perform a convincing demonstration.

Who would be disturbed if such efforts should succeed? Many scientists have been attracted by the RNA World theory because of its elegance and simplicity. Some of them have devoted decades of their career in efforts to prove it. They would not be pleased if Freeman Dyson’s description proved to be correct: “life began with little bags, the precursors of cells, enclosing small volumes of dirty water containing miscellaneous garbage.”

A very different group would find this development as dangerous as the theory of evolution. Those who advocate creationism and intelligent design would feel that another pillar of their belief system was under attack. They have understood the flaws in the RNA World theory, and used them to support their supernatural explanation for life’s origin. A successful scientific theory in this area would leave one less task less for God to accomplish: the origin of life would be a natural (and perhaps frequent) result of the physical laws that govern this universe. This latter thought falls directly in line with the idea of Cosmic Evolution, which asserts that events since the Big Bang have moved almost inevitably in the direction of life. No miracle or immense stroke of luck was needed to get it started. If this should be the case, then we should expect to be successful when we search for life beyond this planet. We are not the only life that inhabits this universe.”

Comment #95522

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 9:24 AM (e)

I will leave you

So you keep saying.

But, YET AGAIN, I ask:

To idontreallycare; What is your alternative hypothesis, and how do you propose we go about investigating it?

To Berlinksi: Is DI just lying to us when they claim you as an ID supporter?

Why oh why why why don’t IDers ever answer my simple questions?

Comment #95524

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 9:37 AM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #95525

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 9:49 AM (e)

To idontreallycare:

You seem awfully determiend to talk for a very very long time about SOMETHING, but for the life of me I simply don’t see your point. Perhaps you could summarize it for me in thirty words or less?

Is your point simply that science doesn’t yet know everything? That there are unanswered questions and things we don’t understand? No kidding. That, after all, is why scientists still have jobs. In EVERY area of science, there are unanswered questions, things we don’t understand, and new research that needs to be done. Does that come as some sort of surprise to you?

(Or are you just looking to point out “gaps” as part of some other agenda that you don’t want to make explicit … ?)

I’m also a little curious as to why on earth you would presume that your rantings, whatever their point, constitute a “threat to science”. Huh? Let’s assume that the “RNA World” hypothesis is indeed absolutely totally unalterably one-thousand percent wrong. So what? How is that a “threat to science”, any more than the fact that phlogiston theory is wrong, or caloric theory, or the luminiferous ether theory? Is it your silly understanding that if we don’t understand any PART of science, that means ALL of it is wrong? Let’s assume that the RNA World is wrong, and that life arose through some other pathway – perhaps Cairns-Smith’s clay particles, or perhaps through some process that we haven’t even thought of or discovered yet. So what? How does that constitute any sort of “threat to science”? How is it a BFD?

Finally, as to the “creationism and intelligent design advocates” mentioned in your big long quote — why on earth should science give a rat’s ass what THEY think? Why should anyone pay any attention at all to THEIR religious opinions? What scientific data and evidence do THEY have to offer? What testable scientific hypotheses have THEY put forth? What peer-reviewed contributions have THEY made to the scientific debate? Why should scientists (or anyone else) pay any more attention to what ID/creationists say about the matter than they should to my next door neighbor or my car mechanic or my veterinarian or the kid who served be a Big Mac and fries for lunch yesterday?

Comment #95539

Posted by idon'treallycare on April 8, 2006 10:38 AM (e)

To Lenny:

The main point of my conversation here may be traced back to the original post: Berlinski wrote a fine essay about difficulties addressing the main research program in the field of the origins of life. His calculations were not “slop” mathematics. I have shown that the same calculations have appeared in Joyce (2002), Arrenhius (2002), and Joyce and Orge (2006). I have shown, as Berlinski has more recently on Mark’s website, that 100 nucleotides is a very conservative estimate for the length of a replicating ribozyme. I have shown, through various quotes from Orgel and Kauffman, that alternatives to a scenario involving an RNA replicase and a complementary template face a host of difficulties. (They are slow, inaccurate, and require the presence and concentration of fantastically improbable prebiotic molecules.) My point–Berlinski’s paper was a fair assessment of the field, from nucleotide synthesis all the way through genetic code origin. Even Frank admitted that Berlinski’s objections were reasonable, although he stressed that Berlinski provided no countermodel and hence his contribution to the matter was trivial.

Much of the rest was devoted to showing just exactly how bad the situation was. Branch formers, chain terminators in the prebiotic broth at many times the frequency of organic molecules. Cytosine probably was not present. No plausible scheme exists to link the nucleotides together. Nucleic acids are exceedingly fragile. There is no clean route to ribose synthesis. Etc. The collective improbabilities, as Berlinski notes, are overwhelming.

A small error I made was in discussing chirality. I say small because, while I was wrong, the point I was making remained the same. Following Joyce and Orgel, I believe that not even minerals could have provided the amount of bias in chirality concentration and adsorption needed to promote the formation of a homopolymer template. The studies mentioned by Anton do indeed suggest a bias, but, like Joyce and Orgel note, I suggest the bias included is not nearly the ~100% needed to jump start life. The field is promising though, a point Hazen makes. I wish researchers the best as they try to demonstrate that minerals can indeed provide the level of bias necessary. I wish them even more luck in showing anything like this can happen outside a laboratory setting, just as Shapiro criticized Ferris’ minerals.

I did not suggest for a moment my criticism will end science. Rather, I said I thought Anton was under the impression that I was trying to smuggle supernaturalism into the mix, and thus he was trying to discredit me with whatever he could get his hands on. This, of course, did not address the pressing criticsims of Shapiro, Joyce, Orgel, and Berlinski, which are of course the criticisms of interest.

Comment #95540

Posted by idon'treallycare on April 8, 2006 10:41 AM (e)

I urge the board to appeal to Berlinski’s own comments on Mark Chu-Carroll’s website. He devastatingly responds to Mark’s critique.

Comment #95541

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 10:50 AM (e)

That’s, uh, more than 30 words.

Try again.

Here, I’ll try to make it multiple choice for you. The point you are trying to make is (check one):

( ) Berlinski is a genius
( ) “idon’treallycare” is a genius
( ) Science doesn’t know everything
( ) Science will never ever ever understand how life appeared
( ) Goiddidit

Comment #95542

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 10:52 AM (e)

Much of the rest was devoted to showing just exactly how bad the situation was. Branch formers, chain terminators in the prebiotic broth at many times the frequency of organic molecules. Cytosine probably was not present. No plausible scheme exists to link the nucleotides together. Nucleic acids are exceedingly fragile. There is no clean route to ribose synthesis. Etc. The collective improbabilities, as Berlinski notes, are overwhelming.

So science doesn’t know everything, and lots of areas need to be researched.

Gee, thanks for telling us that.

Once again I ask — so f’ing what?

Comment #95543

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 10:57 AM (e)

This, of course, did not address the pressing criticsims of Shapiro, Joyce, Orgel, and Berlinski, which are of course the criticisms of interest.

Berlinski, of course, has an agenda not shared by the rest of them. Berlinski, of course, has also not published a single whit of original scientific research on any area of life sciences, unlike the rest of them.

So I’m a little curious as to why you think anyone should give a rat’s ass what Berlinski says about the matter?

Comment #95545

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 11:09 AM (e)

My question to Mr Berlinski still remains unanswered:

Is DI just lying to us when it claims you as an ID supporter?

Here, let me remind everyone what you wrote to me:

You raised a question on the Panda’s Thumb and since it was specifically addressed to me, I’ll take a moment to answer it specifically. I have NO religious interests or beliefs beyond a curiosity about pre-Humean
arguments in 11th century Arabic theology. I have never endorsed intelligent design in any way, and I have written a long essay in Commentary (‘Has Darwin Met his Match’) taking issue with all of the intelligent design arguments — those of Johnson, Behe, Dembski, and anyone else I could think of. I have been since the publication of ‘The Deniable Darwin’ on record as a critic of intelligent design. Every time I publish a serious piece, I go out of my way to affirm my skepticism.

And, my dear Mr Berlinksi, if you disagree with DI and reject its conclusions and agenda, why, uh, are you writing articles for them about the origin of life?

I think you are just BS’ing me, Mr Berlinski. Can you offer any reasons why I should not contin ue to think so?

Comment #95549

Posted by Sir_Toejam on April 8, 2006 11:23 AM (e)

He devastatingly responds to Mark’s critique.

LOL.

Yeah, i read that.

your usage of “devastatingly” can only imply some sort of weird sycophantic devotion to Berlinski on your part.

That’s the difference between scientists and sycophants, we look at evidence, rather than people.

You should compare yourself to Slaveador Cordova. He is a classic case of a Dembski sycophant. You two have a lot in common.

Comment #95555

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 11:53 AM (e)

your usage of “devastatingly” can only imply some sort of weird sycophantic devotion to Berlinski on your part.

As does his lumping Berlinski together with Shapiro and Orgel, who (unlike Berlinski) have done actual live research on biological sciences and who (also unlike Berlinski) have published their research in peer-reviewed science journals.

Berlinski, on the other hand, is a crank who publishes in ID religious tracts and who serves as a Senior Fellow at the Discovery Institute, a political activist organization with the aim of imposing their religious opinions onto everyone else, where he serves as their pet “agnostic”. (shrug)

Comment #95562

Posted by normdoering on April 8, 2006 1:01 PM (e)

idon’treallycare wrote:

The origin of life field became mired in the “chicken-or-the egg” question. Which came first: DNA or proteins?

As a matter of rhetorical tactics I wouldn’t talk about “chicken-or-the egg” questions on an evolutionary forum if I were you because we Darwinian evolutionists know that eggs came first – dinosaurs were laying eggs long before they evolved into chickens.

Comment #95590

Posted by The Ghost of Paley on April 8, 2006 3:30 PM (e)

Everybody really needs to see the Master’s response to this essay. I especially like the part where he elegantly disposes of “A Self-Replicating Ligase Rybozyme”:

The Master wrote:

It is perfectly true that no one knows the minimum ribozyme length for demonstrable replicator activity. I said as much in my essay. But the figure of the 100 base pairs required for what Arrhenius calls “demonstrable ligase activity,” is known; it is current in the literature; and it is, all evidence suggests, an under-estimate. In this regard, see Arrhenius’ own source: Ekland, E.H., Szotak, J.W., Bartel, D.P. ‘Structurally complex and highly active RNA ligases derived from random RNA sequences,’ Science 269, 364-370, 1995. No one has successfully demonstrated a markedly lower length for independent ligase activity under laboratory conditions. In this regard, I encourage you to consider Natasha Paul & Gerald Joyce’s ‘A self-replicating ligase ribozyme (Paul, N., Joyce, G., PNAS, Volume 99, No. 20, 2002). The demonstration reported, as Paul & Joyce make clear, was enzymatically driven; and so not properly speaking relevant to pre-biotic chemistry. More to the point, Paul & Joyce comment on the possibility of an in vitro demonstration of a “nucleic acid (or protein) enzyme that catalyses the replication of many different nucleic acid (or protein) molecules, including copies of itself.” They report “substantial progress … along these lines,” – true enough, as their references indicate – but at once add with respect to the laboratory ribozyme in question that “it contains 200 nt, so it is not nearly capable of catalyzing the synthesis of additional copies of itself.” My estimate of one hundred nucleotides as the minimum needed for demonstrable ligase activity was a gross under-estimate of the length required of a true self-replicating ribozyme. It might well serve as a lower bound; this would, of course, strengthen and not weaken my argument.

….and then Mr. Mates replies:

Berlinski says: The figure of the 100 base pairs required for what Arrhenius calls “demonstrable ligase activity,” is known.

That figure was disproved the same year (2002) Arrhenius wrote the above. Paul & Joyce designed a ligase ribozyme of only 61 bases (“A self-replicating ligase ribozyme,” PNAS 99(20) 12733-12740). (Not that Arrhenius should have seen that coming.)

…..proving that he never bothered to read Dr. B’s response. Guys - give it up. The Master’s too much. No - keep going! You can’t buy better entertainment than this!

Comment #95592

Posted by Sir_Toejam on April 8, 2006 3:45 PM (e)

no, what’s entertaining is sycophants like yourself who refer to these folks as “the master” and “the wizard”.

now THAT’S funny, at least at the level of pathetic behavior.

Comment #95602

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 4:36 PM (e)

“The Master”?

“The ***MASTER***” ???????

Let me repeat for all the ID dolts out there what “The Master” told me about ID “theory”:

I have never endorsed intelligent design in any way, and I have written a long essay in Commentary (‘Has Darwin Met his Match’) taking issue with all of the intelligent design arguments — those of Johnson, Behe, Dembski, and anyone else I could think of. I have been since the publication of ‘The Deniable Darwin’ on record as a critic of intelligent design.

It seems as if “The Master” thinks you’re a lunatic, Ghost.

What do you think about that …. . ?

Comment #95603

Posted by The Ghost of Paley on April 8, 2006 4:36 PM (e)

no, what’s entertaining is sycophants like yourself who refer to these folks as “the master” and “the wizard”.

now THAT’S funny, at least at the level of pathetic behavior.

Nah - just appreciate true artistry when I see it. Here’s a relation for ya:

David Berlinski : Panda’s Thumb

Fedor Emelianenko : Mr. Whipple

But to stay on topic, I would like to see a serious reply to the Master’s rebuttal. Overall, I think he did a good job with the original essay. It’s not easy to write about organic chemistry in an accurate and entertaining way, yet he knocked it out of the park. Pop science is a tough field.

Comment #95604

Posted by Anton Mates on April 8, 2006 4:41 PM (e)

The Ghost of Paley wrote:

Everybody really needs to see the Master’s response to this essay. I especially like the part where he elegantly disposes of “A Self-Replicating Ligase Rybozyme”:

The Master wrote:

It is perfectly true that no one knows the minimum ribozyme length for demonstrable replicator activity. I said as much in my essay. But the figure of the 100 base pairs required for what Arrhenius calls “demonstrable ligase activity,” is known; it is current in the literature; and it is, all evidence suggests, an under-estimate. In this regard, see Arrhenius’ own source: Ekland, E.H., Szotak, J.W., Bartel, D.P. ‘Structurally complex and highly active RNA ligases derived from random RNA sequences,’ Science 269, 364-370, 1995. No one has successfully demonstrated a markedly lower length for independent ligase activity under laboratory conditions. In this regard, I encourage you to consider Natasha Paul & Gerald Joyce’s ‘A self-replicating ligase ribozyme (Paul, N., Joyce, G., PNAS, Volume 99, No. 20, 2002). The demonstration reported, as Paul & Joyce make clear, was enzymatically driven; and so not properly speaking relevant to pre-biotic chemistry. More to the point, Paul & Joyce comment on the possibility of an in vitro demonstration of a “nucleic acid (or protein) enzyme that catalyses the replication of many different nucleic acid (or protein) molecules, including copies of itself.” They report “substantial progress … along these lines,” – true enough, as their references indicate – but at once add with respect to the laboratory ribozyme in question that “it contains 200 nt, so it is not nearly capable of catalyzing the synthesis of additional copies of itself.” My estimate of one hundred nucleotides as the minimum needed for demonstrable ligase activity was a gross under-estimate of the length required of a true self-replicating ribozyme. It might well serve as a lower bound; this would, of course, strengthen and not weaken my argument.

….and then Mr. Mates replies:

Berlinski says: The figure of the 100 base pairs required for what Arrhenius calls “demonstrable ligase activity,” is known.

That figure was disproved the same year (2002) Arrhenius wrote the above. Paul & Joyce designed a ligase ribozyme of only 61 bases (“A self-replicating ligase ribozyme,” PNAS 99(20) 12733-12740). (Not that Arrhenius should have seen that coming.)

…..proving that he never bothered to read Dr. B’s response. Guys - give it up. The Master’s too much. No - keep going! You can’t buy better entertainment than this!

Mea culpa–I didn’t read his response as closely as I should have, as I didn’t believe he could possibly persist in his claim while simultaneously mentioning Joyce and Paul, given the obvious contradiction. But he exceeded my expectations, “elegantly disposing” of their paper by the rhetorical device commonly known as “a lie.”

He says,

“The demonstration reported, as Paul & Joyce make clear, was enzymatically driven; and so not properly speaking relevant to pre-biotic chemistry.”

This is, again, simply a lie. The only enzyme driving the reaction was the ribozyme itself. The reaction was performed as follows.

“Ligation assays were carried out in the presence of 25 mM MgCl2 and 50 mM EPPS (pH 8.5) at 23°C. Before initiating the reaction, B plus or minus T were preincubated in reaction buffer at 23°C for 10 min. The reactions were initiated by the addition of 5’-32P-labeled A, which had been preincubated at four times the final concentration in reaction buffer at 23°C for 10 min.”

No enzymes. Well done, Dr. Berlinski! Don’t debate, prevaricate!

The rest of his quote above is, of course, simply irrelevant to the accuracy of his original claim. The ligase in question would not be a good candidate for a pre-biotic self-replicator, and no one has claimed that it would be. But it does exist, and thereby falsifies his claim.

Comment #95607

Posted by Steviepinhead on April 8, 2006 4:43 PM (e)

Hey, Ghost, aren’t you supposed to be off doing deep research on tetrapod sutures or something?

Get back to work!

Comment #95648

Posted by 'Rev Dr' Lenny Flank on April 8, 2006 8:54 PM (e)

I would like to see a serious reply to the Master’s rebuttal.

And I would like to know why Berlinski thinks all the ID arguments are nutty.

Comment #95672

Posted by Anton Mates on April 9, 2006 12:07 AM (e)

idon'treallycare wrote:

1. My errors or trivial tangents—As for the Joyce paper 20 years ago, that was pretty much the paper that set the standard that, yes, we need an abundance of one specifically handed molecule. I threw it in the mix just for interest’s sake.

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.

As for Shapiro’s paper, which I haven’t read in nearly a year (and papers tend to get jumbled after reading so many of them), I was going on memory that he had discussed something about chirality in his paper. Other than a passing sentence, he DID NOT. And I was wrong. What struck me about Hazen’s comments was the fact that he said, “… initially racemic mixtures both of MOLECULES and SURFACES.” I must have misunderstood the quote in question. It happens. I most certainly was not trying to be dishonest. I read it quickly and misunderstood, much like you have for Orgel’s papers. Sorry.

Actually, I think we’ve established that you’ve misread Orgel too, but the board can judge.

2. Your errors—One error is that Shapiro only weakly criticized Ferris’ mineral polymerization. Since I dug up the paper, allow me to quote freely, and let the board be the judge:

“Those studies were addressed to the question of whether oligomerization in aqueous solution could compete with hydrolysis; they answered it in an elegant manner. They did not, however, deal with the specificity problem discussed here, potentially interfering substances having been excluded by the investigators. In the absence of any competintion studies, there is no reason to believe that a give mineral might preferentially adsorb and combine the monomers that would be useful in construction a particular replicator, while excluding the much greater number that would disrupt such a function.

Apart from this, the experiments were conducted in ways that appear unlikely to take place outside a laboratory. The monomers were specifically activated by procedures involving either the multistep preparation of nucleoside 5’-phosphorimidazolides or the prior treatment of monomers with synthetic reagents such as carbodiimides or carbonyl diimidazole. Fresh batchs of activated monomers were added to the given mineral according to a well-defined feeding schedule. The relevance of these results to events on the prebiotc Earth is therefore questionable. [I]t would be interesting to learn whether they actually do so outside the laboratory.”

But then again, since “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.

which says nothing Ferris himself wouldn’t say.”

I might just be making that all up. What were you saying about quote mining and being dishonest again?

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.

(By the way, just curious, how many papers HAVE you read about chirality—more than me I’m certain—but still weren’t you the one not to long ago asking for some help searching the field?)

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.

3. Since my criticisms are so easily dismissed—I am a crank scientist, after all—will you be so kind as to answer the relevant questions and issues:
[list snipped]

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.)

But, as several people have pointed out, the existence of good arguments against the RNA-first model does not imply that you can’t make a bad one, nor that you can’t draw an invalid conclusion. This is what Berlinski did, which is what this entire thread is about, and it’s what he’s still doing in his replies to Chu-Carroll.

Likewise, there’s not much point in posting the criticisms made by Shapiro (except of course as interesting and informative writings in their own right). Berlinski is not Shapiro. Shapiro is an accomplished researcher in the field and his arguments are so far as I can determine entirely grounded in fact (though I personally think he has a tendency toward hyperbole when writing for a lay audience, as was illustrated by his review of Darwin’s Black Box, and by his claim that the laboratory creation of life through a metabolism-first system would actually make RNA-world researchers unhappy!) Berlinski, not.

Comment #95675

Posted by Sir_Toejam on April 9, 2006 12:16 AM (e)

but the board can judge…

that’s an interesting idea.

a board to judge the outcome of debates on PT.

I wonder who would like the responsibility?

Comment #95676

Posted by Anton Mates on April 9, 2006 12:46 AM (e)

And on the subject of “idon’treallycare”’s true position:

idon'treallycare wrote:

Perhaps I am an idiot. But I am not insincere. I hate when RNA first supporters give with the one hand that there are many difficulties with their scenario and take back with the other, saying, yes of course there are dilemmas, but we have pretty much solved them all.

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.

3. Since my criticisms are so easily dismissed—I am a crank scientist, after all

Of course, this is simply nonsense. Deliberately dishonest? Nothing of the sort. I told you what happened. I misread the darn paper. It happens. I admitted my mistake. Though it never should have been made in the first place, I acted appropriately in responding to your semi-truthful allegations. I was wrong.

And the painful fact is that for most of the criticisms leveled above there is no current answer. This is unsettling to you, I believe. Your tactic, it seems, is instead to accuse me of being a dishonest IDer. I presume this is because you see me and the criticisms I make as a threat to science.

Other people have already pointed out why you seem to be a dishonest IDer, and this is probably be an exercise in futility, but let’s recap.

•Panda’s Thumb, an evolution/creationism/ID discussion site, posts an article about mathematical problems in an essay by David Berlinski, an ID advocate Discovery Institute fellow who likes to attack evolution and sort of half-heartedly plug ID into the bargain. This essay concludes with criticism of naturalistic models of the origin of life in general, and Berlinski himself later shows up to say, yes, the researchers in that field. whom he cited would not endorse that conclusion.

•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.

•This poster shows a fairly typical rhetorical style for IDers, saying things like “most (though not all) of you are morons” and “Idiot.”

•This poster routinely overstates the problems associated with the scientific theory they’re criticizing, as well as mindreading the researchers involved. “So any alternatives to Berlinski’s calculations right now are dead ends,” “Where he gloomily concludes,” “Why not assume that, to their minds, no new research has really convinced them?” and so forth. Again, typical of ID writing (and creationist writing for that matter.)

•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.

Given all this, what’s the probability that you’re actually a passing scientist who happens to really like RNA-later models? Well, it’s not exactly zero, but low enough that I’m comfortable invoking Dembski’s cutoff. The likelihood that you’re an IDer, on the other hand, seems awfully high.

I might add that it took a while to convince me of this. Initially I figured you’d just honestly misread Berlinski–or what the hell, maybe you had found respected researchers who’d said everything he said, though obviously that wouldn’t make his arguments correct. Upon further conversation, though, I have to regretfully side with the other posters on this count.

Comment #95677

Posted by Anton Mates on April 9, 2006 12:50 AM (e)

Sir_Toejam wrote:

that’s an interesting idea.

a board to judge the outcome of debates on PT.

I wonder who would like the responsibility?

That would be me. Rules will be as follows

1) I win
2) If I am not involved in the debate, victory will be determined by a Tiktaalik impersonation (costumes must be home-made) and a swimsuit segment. The two may be combined if the swimsuit has sufficient room in the back.

Comment #95678

Posted by Sir_Toejam on April 9, 2006 12:52 AM (e)

LOL.

embrace your inner fish, dude!

Comment #95679

Posted by 'Rev Dr' Lenny Flank on April 9, 2006 1:25 AM (e)

Most everyone else is here to talk about Berlinski.

Well, Idon’treallycare’s entire point seems to be “Berlinski is a genius”.

Alas, he has still not answered my simple questions about Berlinksi: Given that Berlinski has never, ever, not even once, ever done a single shred of original scientific research into any of the life sciences, and has never had a single peer-reviewed publication on the topic of origin-of-life, why on earth should anyone give a flying fig what Berlinski has to say about the subject?

Comment #95680

Posted by 'Rev Dr' Lenny Flank on April 9, 2006 1:30 AM (e)

The likelihood that you’re an IDer, on the other hand, seems awfully high.

I noticed that too. Particularly the way he dodged my simple questions about IDers:

Finally, as to the “creationism and intelligent design advocates” mentioned in your big long quote —- why on earth should science give a rat’s ass what THEY think? Why should anyone pay any attention at all to THEIR religious opinions? What scientific data and evidence do THEY have to offer? What testable scientific hypotheses have THEY put forth? What peer-reviewed contributions have THEY made to the scientific debate? Why should scientists (or anyone else) pay any more attention to what ID/creationists say about the matter than they should to my next door neighbor or my car mechanic or my veterinarian or the kid who served be a Big Mac and fries for lunch yesterday?

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? And if you reject ID and its arguments, why are you a Senior Fellow at the DI?

Why oh why why why don’t fundies EVER answer any of my simple questions …… ?

Comment #95684

Posted by Anton Mates on April 9, 2006 2:20 AM (e)

'Rev Dr' Lenny Flank wrote:

Alas, he has still not answered my simple questions about Berlinksi: Given that Berlinski has never, ever, not even once, ever done a single shred of original scientific research into any of the life sciences, and has never had a single peer-reviewed publication on the topic of origin-of-life, why on earth should anyone give a flying fig what Berlinski has to say about the subject?

Because he’s elegant! And Masterful (if not Wizardly)! And he explains intro calculus facts to mathematicians! And he interviews himself so that he can casually drop common words and then inexplicably fail to recognize them so that he can explain their meaning and etymology to poor uneducated himself!

… But you are on record as someone who does not support intelligent design – or any creation arguments for that matter …

I agree with some things that my buddies over there at the DI advocate – giving Darwinism a remarkably swift kick in the pants, for example, and I disagree with other things. Why not? The DI is a think tank – the only private institution in the world, I suspect, that has had the nerve to take on the entire Darwinian establishment. Why shouldn’t members of a think tank be allowed to think, especially for themselves? Nobody over there is telling me what to write or say. Why should they? I don’t give them much advice either. Why should I? In any case, I am always exhilarated by the David and Goliath impression that the DI has so wonderfully cultivated. The sheer chutzpah of the thing …

…Chutzpah? …

… Sorry, it’s from the New Testament Greek chuspaidaon, it means nervy or provocative …

… I see …

says Berlinski to Berlinski. I mean, that’s just sad.

Comment #95696

Posted by 'Rev Dr' Lenny Flank on April 9, 2006 8:42 AM (e)

Ah, so Berlinski is just a crank.

Got it.

Comment #95704

Posted by idon'treallycare on April 9, 2006 10:57 AM (e)

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?

Comment #95716

Posted by 'Rev Dr' Lenny Flank on April 9, 2006 12:56 PM (e)

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

Comment #95719

Posted by Roger Rabbitt on April 9, 2006 1:17 PM (e)

'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.

Comment #95720

Posted by Anton Mates on April 9, 2006 1:45 PM (e)

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.

Comment #95727

Posted by idon'treallycare on April 9, 2006 2:34 PM (e)

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?

Comment #95729

Posted by Russell on April 9, 2006 3:05 PM (e)

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

Comment #95743

Posted by The Ghost of Paley on April 9, 2006 4:48 PM (e)

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.

Comment #95750

Posted by normdoering on April 9, 2006 5:35 PM (e)

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.

Comment #95761

Posted by Sir_Toejam on April 9, 2006 6:22 PM (e)

hey Paley:

http://home.earthlink.net/~tjneal/hyenas.au

Comment #95793

Posted by 'Rev Dr' Lenny Flank on April 9, 2006 10:11 PM (e)

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

Right?

Comment #95794

Posted by 'Rev Dr' Lenny Flank on April 9, 2006 10:13 PM (e)

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)

Comment #96031

Posted by Anton Mates on April 11, 2006 11:19 AM (e)

'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.