Rand and Darwin - Conflict or Not?

Doug Bandler's picture
Submitted by Doug Bandler on Fri, 2011-01-14 09:06

A common critique of the Objectivist ethics from evolutionary theorists is that it is in violation of the facts of biological reality. These critics say that Rand based her ethics on an Aristotelian meta-biology and not a Darwinian one. Thus for Aristotle, the teleology of an oak tree, the essence of the tree's existence, is the full grown tree itself. But Aristotle's biology has been replaced by Darwin's, in which an oak tree is an acorn's way of making more acorns.

The criticism is that Rand is wrong in one of her basic statements about life. She says that every function of a living organism is directed toward a single goal: the organism's survival. But this isn't true. Living organisms have reproductive organs, and the functioning of those organs is not directed to the organism's survival. Most living organisms spend a significant part of their lives living for the sake of something that will happen when they are no longer there to care about it, that something being the survival and reproduction of their descendants.

Thus the characteristics of living organisms are best explained by reproduction, not by survival. It is argued that this fact seriously undermines if not destroys the Objectivist ethics.

What are some opinions on this. I understand that Binswanger weighed in on this subject. Does anyone know what his answer was?


Holy cherry-picking batman...

Robert's picture

And here ladies and gentlemen is yet another example of how Darren operates.

This is what I wrote:

"Do you realize that regressing one step in the logical chain will now expose you to an examination of your knowledge of basic chemistry and geology?

Are you sure that you want that? Because I suspect that your knowledge of these is as bad as your knowledge of protein biochemistry.

In your defense, I myself have to concede that I will need to refresh my memory of these principles by referring to a few textbooks that I have lying around. "

Here is what Darren quotes:

"I myself have to concede that I will need to refresh my memory of these principles"

That fragment is not self supporting and Darren has deliberately made it so in order to bend my words to his meaning. Not only is he a Kantian, he is dishonest too. But I repeat myself.

Now I'll admit this. I mistakenly assumed that someone as smart as Darren would realize that "Basic chemistry" refers to a larger field of which protein biochemistry is merely a subset. For instance it involves the characteristic reactions seen with small molecules which later become amino-acids. It deals with these reactions as they would occur in the environment (hence the need to consider geology).

I am guilty of not being exact enough with my language and I let Darren in through this crack.

I mistakenly assumed that Darren appreciated that there was more than one flavor of chemistry (organic, physical, inorganic, biochemical, geological) on account of the size of the field and the absolute need to specialize in one area of it. Moreover, I mistakenly assumed that someone as learned as Darren would appreciate the difficulty in remaining familiar with all aspects of the field at all times - hence my need to 'refresh' my memory.

My cardinal sin was to assume that the man could be honest.

So yes, I wasn't clear in this one sentence. But the post that accompanies the one that Darren mauled makes it abundantly clear that there is more to the Chemistry than is admitted by this single poorly conceived sentence. And you will note how Darren ignores it all.

See how quickly he seized on the error in order to drop context? It's amazing isn't it. The entire body of biochemical knowledge directly contradictory to his notions is cast aside.

In a heartbeat, the is subject changed from the deficiencies in his ideas to the deficiencies in my intellect.

Have I not already plead no contest to the charge of being a mere chrome polishing mechanic? Why then does he not bury my objections under a mound of facts?

Obviously if he were more familiar with basic chemistry and geology then all of us, he would illuminate some of the facts that we have forgotten. After all, he used to be very quick to post papers supporting his thesis when previously we were pottering around the fringes of the issue.

But now we are at the nub of it he has replaced his attempt at a fact-based argument with bizarre non sequitur dressed up as insults punctuated with context dropping straw-men.

But even here he is inadequate.

---------------------------

First up the insults:

"because yours is a Ph.D's arse with expensive new biochem textbooks in it"

This is just poor. What would be the difference between an Ph.D's arse and a standard one?

And if the Ph.D's arse issues forth expensive new Biochemistry textbooks rather than turds, how is this bad again? He's admitted that the textbooks are an expensive commodity. So a Ph.D's arse should logically be to value. Perhaps it would be more valuable than a Financial Analyst's arse? This is hardly what he was striving for.

Clearly Darren needs fortifying with some more communion wine. This isn't offensive, it's just silly.

-----------------------------

Next up, the context dropping straw-men:

"What you're too uneducated and natively too stupid to understand, Leo, is that design played a starring role in the founding of modern science by luminaries such as Kepler, Boyle, and Newton. Only later on was it made verboten."

Verboten? This must be a reference to the mythical "Protocols of the elders of Zion's Department of Science" because I've never come across any dictum or law or rule or edict that forbids religion in science. And I should know! As discussed above, I read too many textbooks to the point where I have to pass one with every bowel movement.

As for Newton, he was a highly religious man by nature, a follower of Descarte (not going to find a philosophical argument against god there) and he worked at a University where the teachers HAD to be ordained Anglican clergy in order to hold office. Newton avoided this by direct appeal to King Charles II - the nominal head of the Anglican Church.

Does this not suggest to you that the cards were somewhat stacked against athiestic ideas in Newton's day?

Robert Boyle was cut from similar cloth being Newton's contemporary. He too studied at Oxford. Oxford, you will remember was one of the focal points during the English civil war; a war notable for its religious intemperance. That is, it ended the monopoly (in England) on Christian worship held by the Church of England and led to the ascendancy of Prodestant factions in Ireland - an earthquake whose after-shocks are still being felt in Ulster to this day.

Boyle and Newton arrive on the scene just after the demise of Cromwellian rule and the crowning of Charles II, whose father had his head removed on the orders of a Parliament engaged in the task of proving that Charles I did not -- in spite of the Charles I's protestations to the contrary -- have a 'divine' (there's God again) right to do whatever the fuck he wanted.

And you are to have us believe that such tumultuous times - charged as they were with religious tension - had no effect on the scientific objectivity of either Newton or Boyle? That probably is your most audacious piece of context dropping yet.

It isn't scientific history that you need to read. It is the history of Europe in general. But that would require a trip to the library and the opening of a book. So I don't expect anything will come of this.

As for Keppler, he was a mathematics teacher at a seminary school in Graz FFS! I'm sure he was a devout follower of whatever Christian sect was chosen for him by accident of his birth place.

Has it escaped your notice totally that there has been a sea change in European Geo-politics since the 17th Century? That in today's world one can be a professional intellectual/scientist on one's own terms. That one can do this based on merit and drive alone without having to court the patronage of some aristocratic block-head or the church?

Why?

Because the American and Industrial revolutions blasted the old geo-political landscape, caste system and all, from the landscape of the Western world.

No longer do men with a passion for science have to seek refuge in the clergy or an 'enlightened' Prince in order to find a way to pay for their food and board and still leave enough time in the day to do their work.

The modern scientist in the 21st Century is more free. If he does pray thrice daily it is no longer out of a fear that some robed sadist from the Church/Mosque/Temple will have him tortured for the 'sin' of not prostrating himself before the unknowable, invisible super-beings worshiped in the area he finds himself in.

Call me stupid if you like, but I think that this sort of arm-twisting might have influenced the 'public' ideas of 17th Century scientists somewhat.

I would bet that in a proper, open market place of ideas that the God-based influence would have been driven from the work of Boyle, Keppler and Newton for the same reason it was driven from Pierre-Simon Laplace's work: "je n'avais pas besoin de cette hypothèse-là"

In fact, I don't have to bet. It has already come true. God hasn't been forbidden from modern science. He's been set aside. And it is because he isn't needed to explain the workings of nature.

Indeed, the idea that the majority of modern scientists are avowed atheists like me is as absurd as your notions on the origin of life.

Most scientists I know compartmentalize the lives into the scientific and spiritual and never mix them. Why? Because to add God to their work complicates it mightily, requiring the conscious acceptance of an unknowable super-reality superseding the one they are investigating. Requiring, in other words, the denial of the primacy of existence and the law of identity. In other words, the denial of the basis of science itself.

This is what Darren is finding and that is why his panties are in a such a bunch.

Meanwhile...

Frediano's picture

Gravity stratification in the Freetown Basic Igneous Layered Complex, Sierra Leone, West Africa

A. C. Umeji

Article first published online: 30 APR 2007

DOI: 10.1002/gj.3350100202

Copyright © 1975 John Wiley & Sons, Ltd

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Geological Journal
Geological Journal

Volume 10, Issue 2, pages 107–130, 1975

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Abstract

An area of 78 sq. km in the vicinity of Freetown is mapped for the first time. By systematic mapping and study of about 1,500 thin sections, nine macro layered units have been recognized in this lowest exposed part of the intrusion. Each unit grades upward from magnetite or olivine-rich layers, through pyroxene-rich to plagioclase-rich rock. Field data of fine-scale layering, ‘false-bedded’ layers and slumping are given. These and other sedimentary structures and features indicate that the Freetown magma was convective. It is suggested that rhythmic layering in the Freetown basic intrusion originated from slow accumulation of density-sorted crystals which precipitated simultaneously from the magna-pulses.

I guess, in financial analyst world, those 'density-sorted crystals' arranged themselves without gravity.

By rolling the dice, I would imagine.

No, wait a minute: "because they must," As in, they had 'no choice' among the gazillion of other purely spatially possible configurations.

As in, gravity acted as a filter to rule out most of the other randomly possible configurations of those crystals.

But wait... 3 billion years go by, and then the world is treated to 'financial analysis' by 'financial engineers' -- the kind of disconnected mental geniuses that gave us 'mortgage backed securities' -- as in, virtually near total physics illiterates, parroting via ctrl-C and Ctrl-V the mashed exponents of others, impressing mostly himself with his vice-like grasp of Feynman's Cargo Cult Science.

The gravity of the situation seems to be ruining everything.

darren's picture

You mean, the already human ordered brickwall. But that is about a gazillion steps after the events under discussion.

You asserted that gravity was an ordering filter. In the case of something that already had order, it had the opposite effect: it added randomness. So much for your filter.

Of all the gazillions of places in space that those bricks could possibly end up...

They can't end up anywhere except where they, in fact, do end up. There are no gazillions of places. There is only one place. The only way to test your statement, fraudster, is by removing gravity from the scenario, and then seeing if, in fact, they end up somewhere else. Unfortunately, you can't remove gravity from the scenario, because gravity . . . like physical matter, of which it is a property . . . is everywhere; so gravity is a "condition of existence." There are no "choices" or "options" or "different paths" those bricks could have taken in the absence of gravity because there is no absence of gravity.

There are apparently plenty of your upside down brethren who have no problem at all grasping the concept of gravity as a gradient producing filter candidate.

Yes, gravity as a "gradient filter" that organizes and orders matter is a very profound, idea, fraudster. I urge you to develop it, publish, and see where you get. A good place to lecture on it might be in front of the various ruins in Athens.

By the way, it seems that English is not your first language. Just wondering: what is?

Gee, should I fire even if I can't see the whites of your eyes?

darren's picture

I myself have to concede that I will need to refresh my memory of these principles

LOL! Talk about a white flag!

So you publicly admit that "steric hindrance" and "this stuff is basically just charge-repulsion - fundamental atomic physics" were fetid, hot-air, not even pulled out of your own arse -- because yours is a Ph.D's arse with expensive new biochem textbooks in it -- but pulled out of gregster's arse, which has nothing in it but some old Sennheiser headphones?

You're lucky that I'm such a polite, diplomatic, and humane opponent. I politely, diplomatically, and humanely accept your waving the proverbial White Flag of Surrender.

I can't wait for you to do some reading on this subject, so that you understand what the hell is going on in it.

Prayers won't help you. You're damned as eternally goofy.

darren's picture

Proteins emerged as a result of spontaneous self-organization of amino-acids.

Non-starter. (1) Amino acids don't form in the absence of a reducing atmosphere. Since the prebiotic earth didn't have a reducing atmosphere, there was no "primordial soup" of free-floating amino acids eager to polymerize. (2) Spontaneous self-organization of functional proteins from contemporary amino acids has never been observed.

This process doesn't require any codes,

That must be very convenient for a process that never occurred.

This is obviously that codes emerged later on in order to code existent proteins,

It's only obvious to those still stuck in the rut of a "proteins-first" scenario. Almost no one accepts that hypothesis anymore. Congratuations, Leo; you're 50 years behind the times.

no other way around.

Alas, most current research accepts just that "other way around." It's called the RNA World hypothesis, first tentatively suggested by Carl Woese and then greatly elaborated by Walter Gilbert. Unfortunately, no one believes them, either, since there are unsolvable, logical, chicken-and-egg dilemmas throughout that scenario. So "code-first" scenario is also a non-starter.

Obviously, you double-espresso-drinking jackass, codes and amino acids had to develop together -- separately in space, but together in time, and then brought together, as a separate step.

The reason they had to develop separately in space is that the prebiotic chemistry needed to create the sugar backbone of RNA -- called the "formose reaction", and which makes use of formaldehyde -- does not function in the presence of nitrogenous compounds such as the nucleotide bases employed by the very same RNA. It's like trying to make an ice-cream cake in a single step -- can't be done. The step needed to create the cake (baking) prevents the ice-cream from appearing; conversely, the step needed for the ice-cream (freezing) prevents the cake from appearing. Clearly, the cake (the ribose backbone) has to be done in a separate step, while the ice-cream (the nitrogenous bases: adenine, guanine, cytosine, and uracil) has to be done in its own separate step, and then a third would be required to bring the two together.

If I ask you, where the fucking codes came from your only possible answer will be-“Leprechaun moves in mysterious ways”. So much for you commitment for the science and mind.

Nothing mysterious about the way intelligence moves. Whether God, martian, or Leprechaun, it can choose a goal out of many possible ones.

What you're too uneducated and natively too stupid to understand, Leo, is that design played a starring role in the founding of modern science by luminaries such as Kepler, Boyle, and Newton. Only later on was it made verboten. Read some history of science books.

At least my premises could be scientifically proved or disproved;

True. And since they have been disproved, you ought to drop them. Zero evidence in favor of spontaneous self-organization is valid falsification of the theory.

Your premise is out of the field of any scientific inquiry.

Not at all. All you have to do is demonstrate chance or necessity creating a code. It's completely falsifiable. To date, nothing has created a code except intelligence. No amount of chance events will create a code; no amount of strictly determined events will create a code; no amount of chance events plus determined events will create a code. You might try inventing a simple code yourself, Leo, and then try to come up with any plausible scenario in which chance, determinism, or a combination of those two, could reproduce your code without you.

The Gravity Meister

Frediano's picture

Try telling that to someone whose orderly brickwall just fell down. Gravity also creates disorder from order.

You mean, the already human ordered brickwall. But that is about a gazillion steps after the events under discussion.

I wonder. In financial analyst world, when the brickwall collapses. Of all the gazillions of places in space that those bricks could possibly end up(we should get out our exponents and mash them together to figure this one out), what is the likelihood that they should all end up on the ground at the base of the once wall, given that there are no natural ordering filters to be found? An artithmeticians miracle, akin to all the O2 molecules spontaneously aligning themselves on the right side of the room...

Or, is what you are saying, they end up there, and not in the millions of other mathematically possible(but not physically possible)states 'because they must?' Because there are alternative states where all that brick dust is simply floating randomly through the air, once again waiting for your lottery to miraculously result in a (relatively)ordered pile just on the ground.

It's as if, when a volcano erupts into the atmosphere, we'd expect a Magic Jinni to come along and arrange for all those dust particles to end up, over time, deposited only on the ground, in a layer.

But, there is no ordering filter about, so what is the arithmetician's mathematical probability that, of all the possible states in the atmosphere, much if not all of those volcanic particles would soon end up self organized as a thin layer on the ground, waiting for geologists in the future to come along and examine all that evidence of non-filtering order from disorder? And look at that! New gradient. What are the resulting rates, plural, of change of concentration of whatever that volcano spewed out, w.r.t. whatever else you care to examine, as a result of that gradient producing gradient? Can you find a use for one or more of those new order producing gradient/filters?

I know it's not simply antipodal thing. There are apparently plenty of your upside down brethren who have no problem at all grasping the concept of gravity as a gradient producing filter candidate.

Pray, Darren

Leonid's picture

"Where the fuck did the proteins come from in the first place, you little prion shit!"

Proteins emerged as a result of spontaneous self-organization of amino-acids. This process doesn't require any codes, as emergence of water molecule from the hydrogen and oxygen doesn't require any codes. Moreover, such a process is thermodynamically inevitable. This is obviously that codes emerged later on in order to code existent proteins, no other way around. If I ask you, where the fucking codes came from your only possible answer will be-“Leprechaun moves in mysterious ways”. So much for you commitment for the science and mind.

"Because the ones you mentioned are not plausible and don't pertain to reality."

And your intelligent leprechaun does?
At least my premises could be scientifically proved or disproved; they pertain to reality in the positive or negative way. Your premise is out of the field of any scientific inquiry. The only argument you presented is: I don't know (don’t understand, don't bother to learn) X, ergo-there is god. This is an argument from the ignorance, as any other religious argument. You think that by substitution of unknown X by unknown Y you can solve the equation of life. The only thing you'll achieve is a substitution of mind by faith. In this setting there is no place for an application of any epistemic tools, no place for science or logic. The only thing which you premise permits as a tool of inquiry is a prayer. Pray, then.

BTW, I never drink decaf, but I wonder what stuff you’re smoking?

"Where did the proteins come from in the first place"

Robert's picture

Is that a white flag on the issue of protein evolution?

Do you realize that regressing one step in the logical chain will now expose you to an examination of your knowledge of basic chemistry and geology?

Are you sure that you want that? Because I suspect that your knowledge of these is as bad as your knowledge of protein biochemistry.

In your defense, I myself have to concede that I will need to refresh my memory of these principles by referring to a few textbooks that I have lying around.

You see I want to be sure of my facts here. However, I know that isn't a major concern of yours.

No intelligent lab technicians...

Robert's picture

"I asserted that the prebiotic environment was missing intelligently designing lab technicians to add and subtract possibly existing denaturing agents at just the right critical moments for critical reactions to occur"

So if not in the prebiotic stage, just when does your intelligent designer arrive?

And who is he? What is he like? How does he influence the natural physical laws that govern our universe?

As for misunderstanding: that would be you. I'm not the one attempting to constrain the various micro-environments within the prebiotic environment so as to derive an unassailable and completely arbitrary probability number to solidify my case for invisible dieties.

Rather, I'm pointing out -- in a slow and piecemeal way because (1) I'm busy, (2) I'm not getting paid for this and (3) you've already expressed a disdain for reading -- that your impression about how proteins fold is one-dimensional (literally). And I am using this ignorance the principles of protein biophysical and biochemistry (all of which generally known, accepted and extensively proven -- which is why it appears in textbooks for college undergraduates) as an example of how imaginary your theory actually is.

In actual fact, protein folding is a co-operative process whose success or failure is determined by more than just a 1/nth sequence configuration (where n = no of amino acids in the sequence). You have to take the sequence into consideration, but also the sequence of various domains that may be remote from one another. You have to take into account any co-factors or accessory proteins - including dimers, trimers of the same protein - that may enhance the folding beyond what you would expect from the sequence. You then have to take into account the physical environment the protein finds itself in.

Crossing over into the terminology of statistics, your model underestimates the degrees of freedom by which you could arrive at a workable molecule. I used to suspect that it was deliberate (that is, you knew the counter arguments but were attempting to bluff your way by them), but it is becoming more apparent that you are ignorant of the counter-evidence and militantly so if the indignation you display at being corrected is anything to go by.

Back to protein folding:

Note that the volume of the protein folding environment can be as small as a couple of nano-liters of solvent. Purely aqueous environments aren't a necessary requirement either see Alexander Klibanov's work and extrapolate the evolutionary significance of his (multiple) observations of enzymes able to function in the presence of organic/aqueous mixtures of solvent.

You may or may not believe that proteins can fold in such a small amount of solvent, but you yourself are an example of it.

Each one of your cells contain 100s of nano-liters of water (depending on type) and the chemical environment within them is critical to the proper folding & function of the molecules within. Hence my supposition that a change in the chemical environment of the cell was the underlying feature of amyloid-diseases of which the formation of amyloids is most often a symptom and not the cause.

Note here that this (chemistry of the external environment has a profound influence on folding) is an argument founded on basic principles of chemistry and will hold regardless of which biolomecule you invoke: DNA, RNA, Proteins, Peptides, lipids, carbohydrates etc.

This is what Fred and others (I myself made this argument with respect to the evolution of bacteria on another thread) were trying to tell you about the error you committed when you assumed a single homogenous prebiotic environment (i.e. one lottery as opposed to many billions of lotteries run simultaneously).

If you think about the scale required to form proteins or any biomolecule for that matter , the assumption that the entire surface (including water permeable rock) of the primordial earth harbored a single environment is simply ludicrous.

That isn't even the case in today's oceans where (for example) gradients (there's that word again) of salinity, available light, macro nutrients, micro nutrients, temperature pressure, available oxygen combine to control the micro-flora that grows within. This is another concrete example (from oceanic microbial ecology - learned out of a textbook even) of the abstract principle Fred was attempting to explain to you and get you to apply to your problem of primordial synthesis. It is something you could examine by going Scuba diving. Go without an oxygen mask or some manner of telling depth or a dry-suit or all three and you will see even more clearly. You see why shouldn't the chemical and physical laws that govern today's oceans not govern yesterday's primordial Earth (Law of identity)? Your only answer is the invisible hand of your giant unknowable friend that only you can see.

But let us return again to your model of protein evolution to see yet another example of your context dropping/anti-reality philosophic approach:

The other thing you underplay is that there are many many ways to arrive at a protein that does the same task as your favorite ~family~ of enzymes. Don't take my word for it. Go to the Protein Data Bank and run the search yourself. See how many clades of serine proteases there are for instance. See how much of these enzymes is actually at the 'sharp' end of the proteolytic reaction that they carry out (hint: there is a catalytic 'triad' involved).

As an aside: observe that the enzyme that Darren picks (cytochrome C) is a relatively modern one that relies upon a lot of support mechanisms to function properly. That is, it is membrane bound. I suspect that he and others deliberately target this one because it isn't able to function independently like a much more primordially appropriate (to coin a phrase) protein like a protease. Helps build the incredulity factor when their tortuous logic eventually spits out a probability estimate for Godless origin of life.

More over, there are yet more ways then that to arrive at proteins that carry out a structural role as my research into hydrophobins showed me.

For instance, the intellectually curious might wish to look into work done by David Eisenberg (UCLA-DOE institute for Genomics and Proteomics). They have successfully investigated the structure of amyloid fibres related to disease and seen that there are (at present) half a dozen 5-8 residue sequences that are key to the formation of amyloid fibers. They have also shown that the amino-acid Glutamine is a particular culprit because it's longer than average side chain replete with an additional amine group that simultaneously makes it uniquely capable of 'interdigitation' (Eisenberg's terminology) and forming hydrogen bonds that further strengthen the amyloid superstructure to the point where it becomes quite resistant to chemical and proteolytic attack.

This research is relatively recent (2008-2011 vintage) completely independent of my own chrome-polishing mechanic incompetence. And yet it undercuts Darren's idea that all amino-acids contribute an equal amount to the stability of a protein regardless of their position because their side-chain chemistry has nothing to do with anything.

I made suggestions to the contrary and backed it up with graphical evidence illustrating the combined results of 10,000 independent structural determinations of every sort of protein. The man didn't even need to read anything.

Darren's response was to instantly dismiss me as a one-trick pony, chrome-polishing, mechanic, cretin, umber prion shit, twat. Did I miss any of your adjectives Darren? I have such a short attention span and diminished intellectual capacity (compared to yours) that it's hard for me to keep up.

And all this before we've even touched on the evidence given by phylogenetics (the study of gene evolution/relatedness), that regions of genes and proteins evolve at different rates. This would introduce the idea that evolution of genes and proteins is an iterative process, with the selective pressures operating at different rates on different portions of the molecule - to the point where the daughter molecules evolve different capabilities then their parents. I might add that none of the phylogenetics studies were generated by my hands of clay. I remain confident that Darren will dismiss them anyway.

This brings me to the observation that - Darren's protestations to the contrary - that I'm not the problem here. Maybe, just maybe Darren's problem lies with the facts that I'm quoting and the vitriolic ad hominem is a smokescreen used to distract the reader away from the facts being used against his theory.

The problem for Darren et al. is that the facts will remain with or without me. They are independent of him or me or Fred or Leonid or Marcus. So the question dear reader is whom should you believe? Darren or the facts?

I predict that this will lead to another bout of one-trick pony accusations. Let me pre-empt them by pointing out how I stick to something that I know - with certainty through repeated observation- and build from there. I stick to things that are proven, things that are real. My one-trick is to accept the primacy of existence as the bedrock for everything else. So in that sense, I am a one trick pony.

This is in contrast to Darren who seems to arrive at his conclusions by abandoning his senses and withdrawing into the Never-never land of his imagination.

I'm not sure if Darren is fully consistent with this approach through all aspects of his life. But I issue this caution: anyone whose wealth depends on Darren's expertise had better determine whether or not he does apply his philosophy consistently or face the consequences of placing their wealth in the hands of a Kantian/Platonist .

Oh I get it...

Robert's picture

Modern proteins have different properties from primordial ones because both are constructed from amino acids whose nature has been the same since forever...

And if you argue with that logic, you're a "fuckin' moron, chrome polishing cretin, prion shit fraudster."

Now it would seem that you have a problem with the Law of identity. Gee, who would have thought that would be the case.

Not I!

I'm too dumb. I read textbooks.

Hell, I've even denatured

darren's picture

Hell, I've even denatured proteins by shaking them. Come to think of it, I've induced others to polymerize by doing the same thing. What? Primordial Earth didn't have Earthquakes? There's a first.

Where the fuck did the proteins come from in the first place, you little prion shit! That's the topic! Not the fact that you or an earthquake can denature them once they've arrived. Fuckin' moron. You're completely clueless as to what the issue is. No wonder you admire fraudster!

Twatlogic, again.

Prions, again.

darren's picture

For instance: take your assertion that denaturing agents didn't exist in the prebiotic environment.

For instance, take the fact that I never asserted any such thing, twatlogic. I asserted that the prebiotic environment was missing intelligently designing lab technicians to add and subtract possibly existing denaturing agents at just the right critical moments for critical reactions to occur: critical reactions that would be highly implausible (to say the least) if we attribute them to the chance actions of undirected nature. You were too busy trying to formulate a "comeback" before you had read and understood my post.

That's why I put your intellect (and if only I could make the "i" in that word lower than a lower-case one, since even lower-case, it inadvertently dignifies the vacuum inside your head far beyond what it deserves) just slightly below the level of an extruded sliver of thin, umber prion shit.

On 2nd thought, quit your day job -- retire early.

darren's picture

However at some point the oxygen build-up in the ocean from prokaryote photosynthesis . . .

(Ahem) There are no prokaryotes in a prebiotic scenario, genius. There are no living organisms at all. Duh, that's why the scenario is called prebiotic: as in PRE- (meaning "before") and BIOTIC (meaning "life").

Prokaryotes require amino acids in their proteins, fraudster. The point of the exercise is to find a plausible route by which undirected nature could have created those amino acids in the absence of a reducing atmosphere. Obviously, you can't cheat in the exercise by assuming the existence of living organisms that already make use of the very thing you're trying to explain.

Close but no cigar -- not even a cigarette butt

darren's picture

Gravity is one example of a gradient field effect that creates order from disorder

Try telling that to someone whose orderly brickwall just fell down. Gravity also creates disorder from order.

Gravity is everywhere in the universe, Fraudy, and it's effect on a particle of mass "m" can be calculated precisely, whether in space or on earth. Therefore, there are no "possible" paths that a particle of water, or anything else might have taken. The direction water takes under the influence of gravity has a probability of 100% -- that's why it is NOT a filter. For something to be a "filter", in the context of this discussion re homochirality, or peptide bonds, it requires that the probability be less than "1" to move a long a certain path in the absence of the filter. The "less than 1" indicates your "possible" paths (that's what "possible" means in probability, fraudy: it means "a probability of less than 1"). Unfortunately, there are no places in the universe that have no gravity, so particles that indeed respond to gravity, all do so along paths whose probabilities are "1".

Keep trying, though, fraudy. Just don't give up your day job.

No need to answer a rhetorical question, gruntster.

darren's picture

This is because it is way too complex. This is because he makes it so by discarding gradual evolution.

Never said anything about complexity, fuckhalfwit. We've been talking about code. Re gradualism: lots of evolutionists have discarded gradualism and embraced some form of punctuated equilibrium, and mostly for a very good reason: the fossil record is what it is -- "existence exists", right? So does the fossil record. And it mainly shows stasis, followed by geologically sudden appearances of new forms; it doesn't show all those intermediate forms that Darwin, and the early Darwinists, predicted. Unlike you -- trying to "induce" the truth from an incorrect theory -- later Darwinists simply got tired of of denying that "the fossil record is what it is" by carping on about how it is "incomplete."

Did you become this dense from overuse of headphones in your work? Or were you born stupid? Just wondering.

Still drinking decaf, Leonid?

darren's picture

You simply ignored everything I just posted.

I usually do.

Especially the obvious fact that if the process of peptides' formation randomly started from L-amino acid, then only L-amino acids could participate in the further process.

LOL! Nice one. In the absence of a genome and a code, no purely chemical or physical force requires one levo-form to be followed by a second, a third, etc.

The randomness of the beginning of such a process from the L or R amino acid is 50%.

Er, no. One amino acid doesn't cause or bias the next amino acid to have any particular chirality. Therefore, the total probability of just getting levo-amino's is the probability of each amino being levo multiplied together. If you have one amino, it's obviously 1/2, if you're considering two amino's together, the probability that both will be levo is 1/2*1/2, for three, it's 1/2*1/2*1/2. Since an average protein chain is about 300 amino's long, that's 1/2 multiplied by itself 300 times.

You also ignored the possibility that polypeptides formed by R-amino acids could have been eliminated by evolutionary process,

No, I broached the topic in my post to Adrian Hester. Listen up: Darwinian evolution is surmised to work on things that replicate. That's the whole idea: mutation plus natural selection: the entity in question REPLICATES, and by doing so, incorporates a slight variation, mutation, error, mistake -- makes no difference what you call it. Natural selection is then surmised to select that new trait or not. So you need replication. Without a genome already conveniently in place with a genetic code ready to do its work, do proteins replicate? No. Therefore, the Right-handed-protein world you posit is a fantasy. The reason we don't have dextro amino acids comprising proteins is because we don't. No one knows why . . . except Whiney, who claims he read it in an undergraduate textbook but forgot the actual explanation . . . and besides, he would conclude that "it doesn't matter because existence exists." Spoken like an ideologue, but not a scientist.

But why should you bother yourself by looking into any plausible explanation which pertains to reality

Because the ones you mentioned are not plausible and don't pertain to reality.

And that brings me to the sad contemplation about our age and times . . .

Oy. You're philosphizing for us? Why don't you try switching from decaf to the real stuff? It might help sharpen your thinking process.

What next?

gregster's picture

There's still an aspect of this exhibition from Dazzler that I await. What tactic will he use to explain the likelihood of the intelligent designer entity? If we forget for the moment all of the linguistic tricks and false arguments he employs - how will he extricate himself from the hole he is digging? He says that life couldn't have occurred without aid from a designer. This is because it is way too complex. This is because he makes it so by discarding gradual evolution. To many honest people the fact that we're here is self-explanatory and a near non-event. Not something to tie oneself up in knots about. Years of compartmentalised thought has deleterious effects as he well demonstrates. Life too complex - but wait - there's a designer too. An entity who must, by using Dazzling logic, be very complex indeed.

Uh-oh.

Frediano's picture

The Early Earth and the Evolution of the Atmosphere.

Early Earth probably had an atmosphere dominated by carbon dioxide similar to the atmosphere of Venus today.

There are a group of one-celled organisms that can live in an oxygen free environment. These are the bacteria or prokaryotes. They do not have a nucleus and reproduce only by cell division. These creatures are the earliest evidence of life on earth. They were the first organisms to develop photosynthesis. Photosynthesis today is balanced by oxygen using respiration.

Hypothesis: Oxygen was nearly absent in the atmosphere of early Earth so photosynthesis would have created a net gain of oxygen first in the ocean and later in the atmosphere. Eventually with sufficient oxygen in the atmosphere respiration would have balanced photosynthesis except when burial removed the organic material from the oxygenated water or air. Before oxygen could build up in the atmosphere it must have oxidized reduced ions in seawater.

Evidence to support the above hypothesis:

Iron (Fe) is a very abundant element in the earth's crust so much is released by the chemical disintegration of minerals contained in rocks. Fe++ is slightly soluble in seawater while Fe+++ is insoluble (Figure 6). During the time when the earth had a reducing atmosphere Fe++ should have accumulated as dissolved ions in seawater. However at some point the oxygen build-up in the ocean from prokaryote photosynthesis should have oxidized the Fe++ to Fe+++ resulting in the precipitation of insoluble iron compounds. Are such ancient iron rich compounds preserved? Yes there are, in fact the bulk of the iron ore mined to produce steel comes from iron deposits that are about two billion years old (Figure 7). Such deposits are found on all continents and all look much the same (Figure Cool. They are reddish and have clearly visible bands hence they are called Banded Iron Formations. The Messabi range of Minnesota is an example of such a deposit. It was for much of US history the primary source of iron ore for the steel mills of Pittsburg, Pennsylvania and Gary, Indiana. If we know the mass of these banded iron formations and the rate at which we mine them we can calculate their residence time and determine how long they will last, or when we will run out of this kind of iron ore (Figure 9).

A second line of evidence, to suggest that the early earth had a reducing atmosphere like Venus and Mars, is the presence of detrital (formed from the products of erosion of pre-existing rocks) pyrite in sedimentary deposits older than two billion years old. Iron pyrite forms in reducing environment and is quickly chemically decomposed in the presence of oxygen. Today such minerals are only preserved in rocks that formed in reducing environments such as swamps etc. However, in rocks older than two billion years old this mineral (iron pyrite) is found in rocks that were probably formed in streambeds.

Those damned gravity driven streams, creating order from disorder under the influence of natural gradients...

But in financial analysts world, gravity and gradient has nothing to do with anything.

You were asserting something about reducing atmosphere. Boldly, even.

This is just unsightly at this point. It's like watching a public train wreck.

Darren

Leonid's picture

"Uh, yeah, but it's 50/50 multiplied by itself per amino acid. So if there are 100 amino acids to consider, and the odds of choosing a left-handed one are 50%, or 1/2, then the odds of ALL of them being left-handed (and you would need all of them to be left-handed in order for the protein to function) are 1/2^100, or about 1 in 10^30."

You simply ignored everything I just posted. Especially the obvious fact that if the process of peptides' formation randomly started from L-amino acid, then only L-amino acids could participate in the further process. The randomness of the beginning of such a process from the L or R amino acid is 50%. You also ignored the possibility that polypeptides formed by R-amino acids could have been eliminated by evolutionary process, possible because that they unable to fold into functional 3-dimensional proteins suitable for life's purposes.

But why should you bother yourself by looking into any plausible explanation which pertains to reality when you already arbitrary postulated the existence of an intelligent leprechaun who does all the job by moving in mysterious ways? By doing so you substituted one mystery by another and effectively closed the door for any scientific inquiry without to explain anything.

And that brings me to the sad contemplation about our age and times. Just 100 years ago it would be completely impossible to publicly express such a position as yours in any educated company. It would be amount to the flatulence in public, and the offender would be treated accordingly.

Today you do it shamelessly, with impunity and also expected to be taking seriously.

Verily, as Talmud says " The face of generation as the face of dog"

Textbooks.

Robert's picture

True, Linus Pauling probably didn't cling to textbooks. But he did read them once, he would have had to in order to rapidly educate himself about the state of the art prior to his starting as a professional scientist if only to save him the trouble of 'reinventing the wheel.' So I'm sure that some of the time he spent at Oregon State University and Cal-Tech was spent looking at textbooks and old papers.

You on the other hand have never bothered to learn basic physical, chemical and biological principles and so you miss state them and violate them at will. And yet everybody else is a fraud, a cretin, a chrome-polishing poo-poo head who wasted the time he spent at college reading textbooks.

For instance: take your assertion that denaturing agents didn't exist in the prebiotic environment.

In fact, they did. Why? Because damned near anything can denature a given protein.

Depending on the context salt concentration can act as a denaturing agent. As can acidic or basic pH. As can temperature. Reducing agents can have a denaturing effect, oxidizing agents too. Certain chemical interactions with other proteins can denature a protein - for example miss-folded versions of the protein (Prusiner's Prions to name one iteration). The lack of a metal co-factors or the miss incorporation of a metal ion with the same chemical characteristics as the beneficial co-factor can induce a detrimental structural change (e.g. some types of heavy metal poisoning). Hell, I've even denatured proteins by shaking them. Come to think of it, I've induced others to polymerize by doing the same thing. What? Primordial Earth didn't have Earthquakes? There's a first.

Each of the things I've been pointing out here and elsewhere are basic physics and chemistry. They were as true in Pauling's day as they are today. That is why they are taught to budding biochemists. It saves them kind of time you've been wasting building castles in mid-air.

And they add up to one thing that violates a primary tenet of all of your algebra:

"a primary structure of 100 amino acids can exist in any of 10^130 combinations, each of them of equal probability."

No. They can't exist in any of 10^130 combinations because when you link them together with a peptide bond they interact with one another.

That increases the likelihood that certain combinations will result in something soluble and with other combinations of amino acids the opposite change occurs. This is basic chemistry.

I believe you dismissed it as bull-shit in a prime example of you ignoring facts because they don't fit your theory.

The probability equations you are building are based on the assumption of independence when (due to the physical and chemical interactions summarized in textbooks and exhaustively tested by chrome polishing cretins like myself) the proper model should be based on conditional probability.

But the only way you'll ever figure out how to assign realistic conditional probabilities to these equations of yours is to learn the basics. The fastest way is to read the textbooks that I told you about.

But that's right you don't like to read do you? Such things are beneath you - it would be akin to being a mechanic. Science to you is something you do exclusively in an office with a white-board without ever having to degrade yourself by stepping into a laboratory or even a library.

But suppose you did read one relevant textbook. You'd learn about research describing a whole bunch of additional factors that lower the probabilities in your equations.

(1) The manner in which proteins fold (hint: it doesn't happen sequentially from left to right in your primary sequence).
(2) The fact that accessory molecules (co-factors) and chaperones will assist with folding by lowering the energy landscape to make a difficult fold energetically possible (or the opposite).
(3) The fact that interfaces such as the phase boundary between oil and water or water and air or water and stone or water and clay can also influence folding. There's three, there are more.

There are three. There are more, but I'm done with lunch and so that's all the time I've got to waste on you.

And waste it I have because all of the above is rendered moot by your not having acknowledged the primacy of existence. Of course if you did, then there wouldn't be anyway you could avoid having to prove the existence of your hitherto unseen intelligent designer.

You've come a long way ...

Frediano's picture

...from "Gravity acts uniformly -- '1G' on everything/has nothing to do with anything" or whatever you were sputtering about before.

Gravity is one example of a gradient field effect that creates order from disorder (using your words ..."because it must") ...and not only that, but results in a cascade of other ordering gradients.

What is the probability that all of the O2 molecules in the room are going to self align on the left side of the room, and all the N2 molecules on the right? That is your analysis, without gradient.

Then, what of molecules of oil, in water? Not in free fall, but as a result of buoyant forces, ie, the effect of gravity on solutions that have different densities ("because they must.")

That results in an ordering of the molecules of oil in water, as a direct influence of that gravity which you claim does not act as a filter. If there are ten species with 10 different densities in solution, then there will be an ordering of the ten species. ("because they must.")

But, we're not close to being done yet with gradient, because now the effect of gravity is to have cascaded brand new gradient. What is the spatial concentration of these species? Now, we have gradients, plural, in the concentration of these several species, brought about by the gradient of gravity.

Are we done with the cascading gradient yet? We'll let you tell us all when all that order producing/noise filtering/state eliminating comes to a stop.

In the meanwhile, how many random discarded states have been eliminated...("because they must") ?

Seriously. Did I ask for your help?

Go back to sleep, fraudiano

darren's picture

When water runs downhill, it doesn't throw dice to choose the resulting path.

That's one good reason why it has zero to do with this discussion, fraudiano. It's because water responds in a predictable, deterministic way to a physical force called gravity, while protein synthesis responds to a set of coded instructions from RNA, that the two examples are not analogous. Obviously, you're clueless about this entire thread.

It responds to gradient.

Because it must respond to the gradient. There are no degrees of freedom involved . . .

. . . unlike protein synthesis -- prebiotically, outside of the environment of a cell -- in which the odds of getting certain outcomes are, indeed, precisely similar to tossing dice. Even inside the modern cell, the situation is completely different from water flowing downhill in response to gravity. Water is a physical thing; gravity is a physical force that acts on physical things; the two things "recognize" each other. Not so with amino acids and nucleic acids in the cell. According to Harold Morowitz (George Mason University) and other biochemists and molecular biologists, there is no physical property connecting amino acids and nucleic acids: the two things -- unlike water and gravity -- do not directly interact or recognize each other. They interact by means of a code. Something completely different from either one of them, and certainly completely different from the way water interacts with gravity.

Of all the millions of possible paths that water could randomly take from state A to state B,

What millions of paths? You mean in outer space? There's gravity there, too, so your water would deterministically flow to the nearest large mass -- a star, perhaps. So, what millions of possible paths are you talking about?

millions are ruled out by the filter of gradient and water rolls where it must, under the influence of gradient.

Nothing is ruled out, fraudiano, because everything was pre-determined from the get-go. Water doesn't have millions of "possible" flow-paths that it might have taken in the absence of gravity, because gravity is ubiquitous. Every move of water is deterministically pre-determined, and there are no "possible paths it might otherwise have taken"

. . . with the possible exception of a form of water that routinely does NOT constrain itself to your gradient, which is steam. I can't help noticing that it doesn't flow downhill, fraudiano. Steam acts in a very indeterminate, stochastic way. Now find a way to filter steam with a gradient so that only certain molecules go in one direction while the rest go in another.

Not over millions of other possible paths. Else there would never be rivers and streams (ordered water/dirt), just randomly moist earth waiting for your lottery results to result in order.

Ah, I get it. You believe that gravity must be a "filter" because it rules out water flowing uphill -- one of its possible flow-paths. Very good, fraudiano. You're a fucking genius.

Non-intuitive arithmetician's view of statistics

Frediano's picture

365 days in the year.

Birthdates are randomly distributed.

You want to discover the odds of any two people in a random group of people 'miraculously' having the same birthdate.

In financial analyst world, it is necessary to "cover" 365 samples before he can say it is likely to happen.

In everyone else's world, it is -highly unlikely- that it would be necessary to make 365 samples before reaching that match. In fact, such an occurrence would represent an amazing act of luck, akin to hiding a mine somewhere on a checkerboard with 365 squares and randomly choosing it last.

But, keep mashing those blind-to-all-field-effect-gradients exponents together. It's wowing them in the churches. Folks are rolling their eyes back from the back of their heads long enough to stare in wonder.

@ Leonid

darren's picture

After all, unlike coffee's brands, there were only two possibilities-left or right and the chance is 50%, not bad for any bet.

Uh, yeah, but it's 50/50 multiplied by itself per amino acid. So if there are 100 amino acids to consider, and the odds of choosing a left-handed one are 50%, or 1/2, then the odds of ALL of them being left-handed (and you would need all of them to be left-handed in order for the protein to function) are 1/2^100, or about 1 in 10^30. That number then has to be multiplied into the odds of each bond between each amino acid being the right kind of bind -- a peptide bond -- which is another 1 in 10^30. So, as just a rough estimate, whatever number you get for the odds of an amino acid sequence appearing by chance, add "60" to the exponent to get an idea of the overall odds of the structure being a chance one.

In the case of nucleic acids, if you're just considering chance alone, you have to multiply the odds of each nucleotide base being right-handed. You also have to factor in the odds of getting a right-handed ribose molecule for the backbone.

However, it was quite easy to come up with the conclusion that you like double espressos, because it wasn't chance at all but, rather, determinism: you're a dweeb, a twit, a nerd, and a spleef. All dweebs, twits, nerds, and spleefs drink double espressos. No randomness there.

@ Whiney

darren's picture

For instance: those who refold proteins in vitro using gradients of denaturing agents... This is something I do myself on occasion.

And I'm sure nature, including the environment of prebiotic earth, was full of "those who refold proteins in vitro using gradients of denaturing agents", thus biasing amino acid polymerization in certain directions and away from others . . . er, however, in the absence of those intelligent designers, and left to nothing but its own devices, a primary structure of 100 amino acids can exist in any of 10^130 combinations, each of them of equal probability. Lab techs like you can bias the process in one direction or another; but the laws of chemistry by themselves don't care which amino acid they choose; which bond gets chosen; or what chirality ends up where. Only the lab techs and the researchers care.

As for your touching recommendation of yet another textbook, I can tell you're a wet-behind-the-ears, newly-minted Ph.D. twit: you still cling to textbooks the way Linus clung to his security blanket (that would be Linus of the "Peanuts" cartoon; not Linus Pauling, who -- if you hadn't noticed -- didn't cling to his textbooks but actually started to think for himself at some point. Hey, why don't you try doing that, too?).

@ TalkOrigins and Darwinist Shills

darren's picture

The basic error mentioned there is intact in Darren's post--assuming that what must be calculated is the probability of just one protein, with the implication that all other sequences are complete misses.

They don't have to be complete misses; they just have to be "not-cytochrome-c." The letters "Sarah Palin" can also be rearranged to spell "Sharp Nail." Nevertheless, only the first combination serves as functional in a voting booth.

there are 3.8*10^61 distinct cytochrome c proteins, not 1 or the handful Darren implies.

Yockey also claimed, in another paper, that there were actually 10^93 cytochrome-c combinations, so his figures appear to vary with time. However, even assuming Yockey is correct about the total number of possible functional cytochrome c's -- using his 10^61 number -- that would leave a search space of:

10^130/10^61 = 10^69.

That's equal to the number of atoms in the Milky Way galaxy. Do you personally believe that chance alone searched through a space of 10^69 combinations in order to find one that functions as cytochrome-c?

Let's see the rest of the calculation:

Freddy-boo estimated 1000 x 10^18 earthlike planets in the universe. That's 10^21 total.

10^21 planets * 10^17 amino acid molecules you pretend exist in each planet's ancient oceans (more on that fantasy later). That equals 10^38. Assuming 1 polymerization trial per second, with 10^17 seconds since the Big Bang, we have:

10^38 * 10^17 = 10^55.

The search space is 10^69 combinations and you've covered 10^55 of them. So far, you're short by a cool 14 orders of magnitude. That's a cool 100 trillion.

However, I'll grant that if you can catalytically bump up the number of polymerizations by a factor of 100 trillion, you have a chance of finding any one of those 10^61 combinations somewhere in the universe.

And you find this plausible?

In any case, you miss the point about cytochrome-c. Since there are about 100 million species on planet earth, there cannot, in fact, be more than 100 million different kinds of cytochrome-c's in actual use. Actually, there are fewer, since man and chimp have identical cytochrome-c's, and several other species might, too. However, the important thing is function: human cytochrome-c works just great inside of a yeast cell, and many different cytochrome-c's work fine in the cells of other species. What this points to is not lots of independently evolved cytochrome-c's, but one ancient, master cytochrome-c molecule -- an archetype molecule -- that morphed into all the other forms over time. Though some cytochrome-c's have as many as 600 residues, the average is about 107 -- I chose the sunflower at 111; it won't make any difference if we choose a lower number like 100. As you can see, it didn't even make much difference if we assumed that there were already a pre-existing library of possibly functional combinations of 10^61.

However, more about your fantasized oceans with all those rich soups of amino acids just waiting around to polymerize into something interesting.

there will be 6*10^17 molecules of each amino acid, all free to polymerize with each other,

First of all, I don't buy a "proteins-first" scenario because of the existence of the genetic code: the code has a library of 64 characters (4 bases in 3 different combinations each, so 4*4*4), while the aminos necessary for life only equal a library of 20 characters. It isn't possible, mathematically, to go from a library of 20 and map it to a library of 64. You can never generate a code that way. You can only go the other way around: from 64 to 20, which now allows for some 3-nucleotide combinations to map onto the same amino acid -- i.e., redundancy, an aspect of all well-designed codes. The only reason I chose to do a calculation with a protein, was to show the high improbability, in some cases impossibility, of assuming that chance alone could successfully search through large combinations over time, test each one for functionality, and then "select" it. Instead of the protein for cytochrome-c, I could have chosen the nucleic-acid code for cytochrome-c -- which it obviously would have required to come into existence -- and arrived at similar numbers, as far as chance is concerned.

But assuming a "proteins first" scenario just as an exercise, here are the problems with your comfortably convenient fantasies:

Vast oceans of all the essential amino acids did not exist, ever, on the prebiotic earth; and since they did not exist on this earth, they did not exist -- by definition -- on the rest of the 10^38 earthlike planets through the universe.

The reason we know these amino acids did not exist on prebiotic earth is because of the famous Miller-Urey experiment in 1953. They created a few amino acids using a spark discharge device in a chamber with a mixture of gases presumed to represent the atmosphere of prebiotic earth. Unfortunately, they were wrong. They used an atmosphere that was rich in hydrogen, which "reduced" its own electrons to the surrounding environment and made polymerizing reactions possible. This is called a "reducing atmosphere." It turns out that the early earth atmosphere was completely different: far more stable, with lots of carbon dioxide, some methane, and no reducing hydrogen. Ergo: no polymerizing reactions possible, and therefore, no production of amino acids.

When Miller, et al., later repeated his experiment with a mixture of gases more closely resembling what actually existed on the prebiotic earth, he got tar.

Miller himself said the following:

"Either you have a reducing atmosphere, or you're not going to have the organic compounds required for life."

So much for your concentration of amino acids conveniently lying in wait to polymerize in just the ways you'd like them to. First show us how those amino acids got there without a reducing atmosphere.

that's a *lot* of trials per second given common chemical reaction rates,

I showed above that, even given Yockey's number of 10^61 useful combinations out of a possible 10^130, you'd need trials occurring at the rate of 10^14 per second to find one of those 10^61 cytochrome c's in the time available . . . and we haven't even factored in the odds of (1) only getting peptide bonds between each amino acid (about 50/50, so for 100 residue polymer, that's 1/2^100, or about 1 in 10^30 to get peptide bonds between each amino acid); and (2) of only getting left-handed forms (also 1/2^100 = 1 chance in 10^30). So, to the Yockey-revised search space of 10^69 combinations, we factor in 10^30 for peptide bonds only, and 10^30 for left-hand chirality = 69+33+33=135, or one chance in 10^135 possible combinations. And -- as if it that weren't enough -- how do you protect the polymer after it has formed, assuming one has formed? Invoke one of freddy-boo's magic filters?

Your whole set of convenient assumptions is goofy.

a figure is given of about a million years to get cytochrome c on Earth.

LOL! See what I mean. Make goofy assumptions, arrive at goofy conclusions.

(Note too that independent trials of RNA are occurring simultaneously.)

What do you mean "trials of RNA" are occurring? You have no idea what the fuck you're talking about. RNA is a nucleic acid, with a ribose backbone and 4 bases, all of which have to have right-handed chirality. Where did the bases come from? In nature, solutions are racemic -- mixed right-and left handedness. How did your "independent trials" of RNA manage to resolve (i.e., segregate) the left-handed molecules from the right-handed ones and make use of only the right-handed ones? And at the same time that the same vast oceans were apparently resolving the amino acids into only the left-handed ones?

Additionally: one of the nucleotide bases required by RNA is called cytosine. Where did it come from? It exists nowhere in nature except where we find it: in the RNA of an actual cell. In 1995, a biochemical pathway was discovered for the production of cytosine -- oddly enough, by the same Stanley Miller as above -- that involved using concentrated urea -- essentially, concentrated pee. I hope you see that the need for concentrated pee in your presumed "vast ocean" won't wash: if you haven't noticed, vast oceans tend to dilute things, especially pee. So your "independent trials of RNA" are going to have to occur out of those vast oceans, preferably in an environment conveniently hypothesized to create vast amounts of concentrated urea: e.g., drying lagoons.

So now, your myriad planets require (1) vast oceans for amino polymerization, essential for proteins, and (2) vast lagoons to create urea for cytodine synthesis, an essential component of RNA.

Molecular biologist Robert Shapiro of NYU wrote a review of Miller's research which appeared in the Proceedings of the Nat'l Academy of Science, and said, among other things, the following, about what would be required for the hypothesis of "drying lagoons":

"It would further be necessary that the residual liquid be held in an impermeable vessel [in order to prevent cross-reactions]."

"The concentration process would have to be uninterrupted for some decades . . . to allow the reaction to occur."

"At this point, the reaction would require quenching (perhaps by evaporation to dryness) to prevent loss by deamination."

"At the end, one would have a batch of urea in solid form, containing some cytosine (and urea)."

Then he added that such an occurrence "cannot be excluded as a rare event on early earth, but it cannot be termed plausible."

Combined with the fact that, as Shapiro also showed, the reaction that Miller, et al. used to produce cytosine very quickly morphed into uracil through "deamination", and this deamination occurs at a faster rate than the original production of cytosine! That's why he wrote that you would have find a plausible route by which what little cytosine was produced could be preserved, away from the original process that was actively producing it.

So the problem here, laddy, is that the very environment you believe would be just great for polymerizing pre-existing amino acids (vast oceans) is exactly the wrong environment for producing an essential component of RNA (cytosine).

Your problems aren't over yet.

Regarding RNA, where are you going to get the sugar "ribose" from? Ribose is difficult to synthesize in the laboratory using prebiotic means, so it most likely appeared by means of an enzyme (a kind of protein); but, then, how did the enzyme appear? I'll tell you how it appeared: by means of RNA! So you've nicely posited another chicken-and-egg dilemma.

The reason I didn't link to anything at TalkOrigins is that the site has a bad reputation -- even Darwinists don't like it. It's populated by a bunch of know-nothing cranks who do nothing except shill for the extreme neo-Darwinist explanation of things. The article you linked to is full of many errors such as:

Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

Straw man. No one's questioning known laws of chemistry, and no one's claiming protein synthesis ever violated them. We're talking about the odds of just those laws of chemistry having produced a functional protein of 100 residues, given (i) freedom to choose any amino acid it pleases; (i) freedom to choose one of several kinds of bonds, and (iii) freedom to use any left-or-right optical isomer.

Secondly, the entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long.

Any evidence these protobionts ever actually existed? No, none. They are fantasized into existence in order to justify retaining the theory behind them: neo-Darwinism.

These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below.

This is known as a "Just So" story. I guess you can invent any scenario you want and then fantasize to your heart's content. Molecules don't "evolve" at least not in the Darwinian sense of "mutation followed by natural selection." Natural selection acts on things that reproduce; so first you have to plausibly get to a self-replicating molecule, and that hasn't been done yet. It has been done implausibly, by means of intelligent-designer lab technicians helping the transitions along at every step of the way; but it has never been shown that in the absence of intelligent-designer lab technicians, in a plausible pre-biotic environment, that any of this molecular evolution can occur.

Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle.

Impossible under real-world conditions, as opposed to fantasizing about conditions that never existed (or have never been shown to exist outside of the fever-addled brain of Darwinist shills). For example, take the last part of the above quote: either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle. This is handwaving bullshit. "Protein enzymes" -- a redundancy, by the way -- are CODED FOR in a nucleotide sequence, either DNA or RNA; so you need the code to create the enzyme -- unfortunately, you also need the enzyme to create the coding mechanism. So you have a chicken-and-egg paradox, as already explained above. The case is not so different for ribozymal RNA: though it can autocatalyze, the backbone of the RNA molecule is a difficult-to-synthesize sugar molecule called ribose. So how can ribose actually form under physically plausible conditions? It requires an enzyme. And where would the enzyme come from? From RNA! So ribozymal RNA, in a putative, never-proven-to-exist RNA World, merely creates another chicken-and-egg dilemma. As an explanation of origins, it's a non-starter.

An example is the SunY three subunit self-replicator [24]. These catalytic cycles could be limited in a small pond or lagoon, or be a catalytic complex adsorbed to either clay or lipid material on clay. Given that there are many catalytic sequences in a group of random peptides or polynucleotides (see below) it's not unlikely that a small catalytic complex could be formed.

These two models are not mutually exclusive. The Ghadiri peptide can mutate and form catalytic cycles [9].

The subunit replicators you copy/pasted from TalkOrigins are ribozymes that suffer from the same explanatory weakness as any ribozyme: chicken and egg dilemma. Since we know that vast oceans are not good places for polymerization to take place, origin of life (OOL) researchers of the Darwinist ilk fantasize about huge, drying lagoons in the prebiotic world. Same for the Ghadiri peptide. Another flaw in your fantasy is that both of these peptides were engineered in laboratories under conditions that would never have appeared on the real prebiotic earth. You're confusing "engineering" with "origins-of-life research."

No matter whether the first self-replicators were single molecules, or complexes of small molecules, this model is nothing like Hoyle's "tornado in a junkyard making a 747".

LOL! That's very true! But the "tornado in a junkyard making a 747" was meant to show the absurdity of chance --- the leading force in the Darwinian paradigm -- having put disparate elements into a meaningful order. It wasn't meant to show or ridicule the idea that putting elements into a meaningful order could be done with the help of intelligent-designer lab technicians engineering the thing at each step! If your goal is actually to construct a 747 from parts in a junkyard, Hoyle would obviously approve of the path the lab technicians above took regarding subunit self-replicators: send some intelligent designer lab technicians into a junkyard, have them intelligently select which pieces of junk they find relevant to constructing their pre-ordained end-product, and let them engineer the thing together. That's what the lab technicians did in the SunY and Ghadiri replicators.

Aside from linking to site known both for both its misinformation and its disinformation, your entire post rests on two mistakes:

1. You've mistaken the kinds of engineering researchers have done in the lab creating some fragile self-replicating molecules (Ghadiri, for example) with research about the prebiotic earth and plausible pathways by which abiogenesis could have occurred. The former shows what can be done with intelligent designers helping the process along at each step; the latter has yet to be demonstrated.

2. Aside from misunderstanding the relevance of the cytochrome-c example, your handwaving, nonsensical assumptions about "vast oceans" on many earthlike planets missed some of that basic chemistry your author on TalkOrigins bragged about: (1) to get those amino acids, you need a reducing atmosphere; conversely, without a reducing atmosphere, you'd better have another way of getting those amino acids (since the early earth did not have a reducing atmosphere, this scenario is a non-starter). (2) to get ribose for the RNA backbone, you need an enzyme -- but to get the enzyme, you need RNA (non-starter). (3) to get cytosine for RNA coding -- assuming one uses Stanley Miller's pathway -- you need to get out of the "vast oceans" and into some "vast lagoons" on land, and start making some very implausible assumptions -- and in any case, the pathway Miller specified quickly deaminates cytosine into uracil -- as explained above by Robert Shapiro of NYU, the main problem with Miller's pathway is that the deamination reaction occurs faster than the synthesis of cytosine. So you're short cytosine for your RNA (non-starter).

Nice try, but your scenarios hover between the impossible and the highly implausible. There's no reason to accept them just because they're naturalist scenarios, and there's every reason to reject them.

"The odds of a functional

Robert's picture

"The odds of a functional protein aggregating by chance alone are the same as the odds of an insoluble useless aggregate aggregating by chance alone."

And here we come again to another arbitrary assumption made by you that has been invalidated many times by those involved in actually researching proteins.

For instance: those who refold proteins in vitro using gradients of denaturing agents... This is something I do myself on occasion.

Here's an idea: how about you actually read that book on protein structure and Robert Weaver's textbook on Molecular Biology

That way you'll be immunized against making such arbitrary statements unworthy of even a freshman biochemistry student.

Functional combos of AAs = functional combos of letters

darren's picture

Ah, presuming that you want a functional protein and not an insoluble useless aggregate

Exactly. Thank you for waking up and restating a point I've made fifty times in this thread.

The odds of a functional protein aggregating by chance alone are the same as the odds of an insoluble useless aggregate aggregating by chance alone. The difference is that there are many more combinations of useless aggregates than there are functional combinations. And what I showed below was that it could not have been chance alone that "sifted" through all of the possible combinations and then "selected" the one or two combinations that function.

The letter combination Who is John Galt (16 characters in a certain order) has the same probability of appearing by chance as any other 16-character combination like uqcp zinqw zxcvb. The difference is that the former is functional (i.e., intelligible in English) and the other is a useless aggregate. The total number of 16-character combinations is 27^16 (assuming 26 letters and a space) = 16xlog[27]=10^23.

So we have a huge number possible aggregates (i.e., letter combinations) and only one that functions ("Who is John Galt"). Obviously, then, chance alone could not have searched through this combination space, test each one for functionality, and then select the one that works. Language acquisition can't work that way; neither could the origin of proteins have occurred that way.

Incompetent or dishonest statistics

Adrian Hester's picture

Darren's basic argument was dispatched many long years ago; the basic response to his sort of calculation can be found here:

http://www.talkorigins.org/faq...

The basic error mentioned there is intact in Darren's post--assuming that what must be calculated is the probability of just one protein, with the implication that all other sequences are complete misses. (I'll note parenthetically that Darren also chose a particularly long cytochrome sequence to further skew his figures; the smallest sequence listed at the site Darren linked to has 103 amino acids, which is probaby closer to the minimal cytochrome structure you'd need to take into account, giving him an extra factor of 2.6*10^10 in his favor for right-handed amino acids and the same factor for left-handed ones, or about 5*10^20.) In fact, what needs calculated is the probability of *any* cytochrome c sequence, and as the page above points out, there are 3.8*10^61 distinct cytochrome c proteins, not 1 or the handful Darren implies. (Note that the very fact that Darren links to a page comparing different cytochrome sequences shows that he's aware on some level of this objection; the fact that he doesn't link to other essays at that selfsame site about creationist fallacies dependent on misunderstanding cytochrome strongly suggests less than total scientific objectivity on his part. Curiously, one such essay starts with a quote involving sunflower cytochrome c, of all things--one wonders how much Darren is simply cribbing from his superiors:

http://members.cox.net/ardipit... )

Second, his figure for number of independent trials per earthlike planet is grotesquely small. Again using the figures linked to above: Each of these planets has an ocean of around 10^24 liters of water, and within each liter, assuming amino acids at 10^-6 M concentration, there will be 6*10^17 molecules of each amino acid, all free to polymerize with each other, and each polymerizing reaction is a separate trial (though not an independent one) for purposes of probability calculations, and even if we don't assume Darren's maximum figure of 10^45 for the number of trials per second, that's a *lot* of trials per second given common chemical reaction rates, certainly far greater than 10^41; including the actual models of biochemical evolution taken into account on that page, a figure is given of about a million years to get cytochrome c on Earth. (Note too that independent trials of RNA are occurring simultaneously.) This is all in addition to the problems Darren dismisses of the freedom with which amino acids can be added in sequence.

"I said that in order to know what to observe..."

Robert's picture

"you first have to have ideas as to what is interesting, relevant, and worth observing -- that's one of the purposes of hypothesis and theory."

So theories trump observation...

That's a short skip away from "theories guide the observations and if necessary observations are discarded or distorted to fit the theory." You seem to have already made that leap and haven't stopped running. I mean, observations that don't fit your theories just aren't that interesting are they?

Like the 10,000 observations that invalidate the statement that opened your last little algebraic tantrum.

(Post 96975 if you can't remember)

"Like beads on a string, there is no physical restriction on the order of amino acids: physically, any amino acid has the capability of appearing on any place in the string (just as letters on a piece of paper, or a computer screen, have no physical restriction as to their order)."

Ah, presuming that you want a functional protein and not an insoluble useless aggregate - yes there are some restrictions.

But we've been over this ground already. The conclusions drawn from observations found in 10,000 protein crystal structures isn't pertinent or interesting to you because it opposes your theory.

Basically we're at an impasse.

I'm not ready to abandon my senses for your noumenal world and your only concern seems to be the novel combination of insults in order to mask your disdain for inconvenient facts.

So I shall retire and leave the field to you. There isn't any point to arguing with someone who doesn't believe in the primacy of existence.

Prions and Prusiner?

Robert's picture

No. I was working with hydrophobins and not transmissible spongiform encephalopathies. Though I'm not surprised that you don't know and don't care about the difference.

The difference is great nonetheless. You eat probably about a half a gram of hydrophobins per serving of mushrooms. A similar dose of prions would be predicted to be lethal if you subscribe to Prusiner's initial hypothesis that naked prions constitute an infectious agent.

So yes, I have read Prusiner. I remain unconvinced of the conclusions he drew initially, and last time I checked he himself appeared to be down-playing the more out-landish of his claims.

I find the work of Chris Dobson to be more convincing. That is Dobson has demonstrated that with the right conditions any protein can be induced to form the cross-beta sheet structure familiar to amyloid and prion researchers.

Dobson is one of those that explains his findings with energy landscapes. So if you'd like to email him and call him a cretin, you'll be able to track him down through the Royal Society (of which he is a fellow). Last I heard he was a professor at St John's College at the University of Cambridge. But I don't keep close tabs on the man so you'll probably have to use those Google skills of yours to track down his close associates and abuse them for no apparent reason. I know you get off on that.

Dobson's work and that of others leads me to suspect that rather than being an 'infectious' disease, amyloids/prions are more likely indicative of an underlying fault in the protein processing machinery or the immune system of the patient. A fault the becomes exacerbated by the presence of a prion which - somehow - nucleates a cascade of mis-folding.

That is my own opinion on the matter and not something that either Dobson or Prusiner would necessarily subscribe to.

I predict that this will set off yet another bout of meaningless verbiage about my inferior intellect. Anything to disguise the fact that you do not believe in the primacy of existence.

A chestnut

Frediano's picture

There is a kind of meant to be funny chestnut that many engineers and scientists are exposed to at some point in their academic career, and it is the line:

"gradients drive everything."

It is meant to be funny, but it is funny because it is true.

I have yet to find an exception.

Not even 'love.' Love is one of the most intense gradients known to man. The rate of change of love w.r.t. others varies intensely.

Even 'identity.' The rate of change of 'you' varies intensely at the boundary that is your skin. 'You' are not uniformly distributed throughout the universe, as an identity.

This universe appears to be on a historical trend of consuming all gradient, on its way to a dim 3 deg K future. From order to complete disorder.

But we're not there yet, by far. The Universe is jam packed with gradient. Along the way, there is plenty of opportunity for miraculously ordered streams.

A more interesting question is, where did the initial intense gradient come from?

But maybe that isn't the right question, because it assumes something not known. Maybe the correct question is, where did the initial intense gradeint come from in the current cycle of gradient consumption?

Look! A stream!

Frediano's picture

If I imagine all those water molecules at the top of the hill and an infinite number of paths for each of them to reach the bottom of the hill, I should calculate the odds that, randomly, without the influence of a filtering gradient, they would all choose the path that results in a stream. And not just 'any stream', mind you, but this very stream. (Why? I have no idea. One stream is as good as another, when it comes to miraculaously creating 'streams' out of the noise.)

That is an exceedingly small probability! Look at the size of those exponents! And yet, look, I see the stream.

The only conclusion I, being a physics illiterate, can reach is, the water molecules were deliberately path ordered by a stream designer.

I mean, how else is it possible to come up with 'this stream', by pure chance.

Hammer?

Frediano's picture

Ho, ho!!! So, because you used "energy landscape" in your dissertation, it must be useful everywhere, including the mystery of amino-acid and nucleic-acid chirality!

You really, really don't begin to grasp the concept of 'gradient', do you?

Not with gravity, not with energy, not with any of the many fields produced by nature.

When water runs downhill, it doesn't throw dice to choose the resulting path. It responds to gradient. Of all the millions of possible paths that water could randomly take from state A to state B, millions are ruled out by the filter of gradient and water rolls where it must, under the influence of gradient. Not over millions of other possible paths. Else there would never be rivers and streams (ordered water/dirt), just randomly moist earth waiting for your lottery results to result in order.

Darren

Leonid's picture

A double espresso is my favorite. How did you know that? Should I invoke some supernatural being as an explanation, or assume the pure chance like in case of chirality? After all, unlike coffee's brands, there were only two possibilities-left or right and the chance is 50%, not bad for any bet. In your cytochrome's example you ignore the fact that complex proteins are result of long evolution of the simple short polypeptides and such an evolution could have started from the connection of two L-amino acids purely by chance. The other possibility is that polypeptides based on R-amino acids couldn't undergo proper folding and create functional 3 dimensional proteins. Therefore they have been eliminated by natural selection. The same could apply to nucleotides. Apparently only R-nucleotides have an affinity to L-amino acids.

"Anyway, your stuff on the Murchison meteorite, etc., is old news and irrelevant"

Am I to assume that your idea of god (intelligent designer) is brand new, relevant and exiting?

In any case I quoted this stuff as an example of scientific data which could be submitted to the proper epistimic analysis versus arbitrary premise like god, intelligent designer or leprechaun.

What you call a code is not code at all. The simple common sense tells that properties has to exist before "codes", otherwise what they can code? The mapping you refer to is a result of an affinity of certain nucleotides' triplets to certain amino acids which requires no more coding than affinity of hydrogen to oxygen. Proteins emerged as result of self-organization of amino acids; nucleotides, which initially were only vehicles of energy's transfer (like in AMF-ATF cycle) became vehicles of further protein synthesis as result of that affinity, and emerged RNA-DNA system simply reflected and preserved evolutionary successful proteins. In other words your "code" is a result of the long selective process of constant interaction between amino acids and nucleotides. Such a process doesn't require any arbitrary assumed entity like god or big codifier.

Not to mention the fact that the most important biochemical event-3 dimensional folding of proteins which defines their functions and in fact all properties of the organism, is spontaneous event and doesn't require any " code". Many other crucial biological events also do very well without codes-for example the building of the cell's membrane, or the process of cell's division.

And finally, I have to mention that all these I already explained in my two previous posts which you missed. Maybe you need cup of coffee. Which one you prefer?

God's moron

gregster's picture

"No arbitrary premises in coding theory or what it implies: codes are mappings between two data sets -- mappings; not the data sets themselves. Mappings require intelligence. You might, perhaps, generate the data sets by purely material means; you can't generate the mapping between the two sets."

Hey fuckface - you're the one saying these ancient existent realities require an intelligent coder. So prove it, or go back to bedwetting. You are seriously no longer funny.

A double espresso for Leonid

darren's picture

Well, you've finally awakened, Leonid. Congratulations. Smell the coffee.

One doesn't treat arbitrary premise as scientific theory.

No arbitrary premises in coding theory or what it implies: codes are mappings between two data sets -- mappings; not the data sets themselves. Mappings require intelligence. You might, perhaps, generate the data sets by purely material means; you can't generate the mapping between the two sets.

Anyway, your stuff on the Murchison meteorite, etc., is old news and irrelevant. The Murchison meteorite was found in 1969; though it had some amino acids (possibly contamination from terrestrial amino acids) and a nucleotide, the important handedness or chirality of the amino acids was not 100% of the L-form, there being only a slight "enantiomer excess" ("e.e.") of a few percent. Hardly enough to get excited about.

You're still in the dark about all this, I can tell. You think the problem is "Where did chemicals called amino acids come from?" That's not the issue. I don't care where they came from; they could have come from thermal vents in the ocean or from meteorites (though I think both explanations are pretty implausible). The issue is (1) why are they all left-handed in living organisms, and why are nucleic acids all right-handed in living organisms; and (2) how did a precise mapping between a suite of 64 3-letter nucleotide sequences and a suite of 20 amino acids occur? Nature doesn't "map" data sets, even if we grant that it could have created the data sets.

Have another cup of coffee, Leonid.

Re:falsifiability

Leonid's picture

"Re falsifiability: it's easy to falsify my claim that, e.g., codes require intelligence to create the mapping between the two character libraries: just show plausibly how it could be done by chance and necessity alone."

One doesn't treat an arbitrary premise as scientific theory. Any explanation based on observable fact is more plausible than pure fantasy. And as a matter of fact amino acids and nucleotides present in meteorites.

"Summary: A new study shows that meteorites may contain concentrations of amino acids that are ten times higher than levels previously measured. This means the early Solar System was quite rich in the organic building blocks of life, and that fallout from space may have played a role in life's origin on Earth."

http://www.astrobio.net/pressr...

"Carbon-rich meteorites, carbonaceous chondrites, contain many biologically relevant organic molecules and delivered prebiotic material to the young Earth. We present compound-specific carbon isotope data indicating that measured purine and pyrimidine compounds are indigenous components of the Murchison meteorite. Carbon isotope ratios for uracil and xanthine ofδ13C=+44.5‰ and +37.7‰, respectively, indicate a non-terrestrial origin for these compounds. These new results demonstrate that organic compounds, which are components of the genetic code in modern biochemistry, were already present in the early solar system and may have played a key role in life's origin."

http://www.scribd.com/doc/3358...

Now, this data could be scientifically scrutinized. We may discuss its plausibility and falsifiability, not your arbitrary assumptions which are outside the field of epistimic inquiry and belong to the field of faith.

Your chain of reasoning is a pure non-sequitur, like your claim: L-amino acids dominate D-amino acids-ergo: there is god ( big codifier, intelligent designer etc...)

Prions, eh?

darren's picture

(Yawn) a prion guy, eh? Read Prusiner's work?

The concepts of energy landscapes help to visualize the process but they are a difficult thing to explain to a layperson

Ho, ho!!! So, because you used "energy landscape" in your dissertation, it must be useful everywhere, including the mystery of amino-acid and nucleic-acid chirality!

In other words, when you're a fucking hammer, everything else looks like a fucking nail.

Got it.

Do you make housecalls, Dr?

darren's picture

Twat-for-brains, I never claimed that one should place theory above observations. I said that in order to know what to observe, you first have to have ideas as to what is interesting, relevant, and worth observing -- that's one of the purposes of hypothesis and theory.

Re falsifiability: it's easy to falsify my claim that, e.g., codes require intelligence to create the mapping between the two character libraries: just show plausibly how it could be done by chance and necessity alone. This has never been done. I admit that lots of implausible scenarios have been fantasized about -- "RNA Worlds richly populated with never-before-seen mini-helices", or "Free-floating amino acids in interstellar space struck by never-discovered Synchronically Pulsed Circularly-Polarized Ultraviolet Light from convenient nearby neutron stars, thus creating the chiral form we see today" -- but try disproving those scenarios! Can't be done. As Hubert Yockey wrote in "Information Theory, Evolution, and the Origin of Life" (Cambridge University Press), origin-of-life scenarios, similar to Rudyard Kipling's famous "Just So" stories for children, are a cottage industry in biochemistry today.

Regarding Popper: Start with "Conjectures and Refutations" (Routledge).

I suppose you've read Thomas Kuhn, "Structure of Scientific Revolutions"?

10,000 observations...

Robert's picture

Thrown aside because they invalidate one of the suppositions that underpinned your math.

That's what you get when you place theory above observation.

I may or may not have the opposite tendency but at least I'm not left attempting to turn false statements into truthful ones by the pungency of my vitriol.

I haven't read Popper, but someone did tell me once that he reckoned that for a statement to be true, it must be falsifiable. Seems like you've gotten that one backwards.

May I suggest in future that you read from left to right instead of the other way round. It should help.

Bull shyte

darren's picture

You curse all you like, but this stuff is basically just charge-repulsion - fundamental atomic physics in other words.

Old news. Slight bias to electron spin in laevo forms can account for very slight e.e. but not enough to make a difference or lead to pure chiral forms we see in amino acids; nor does it explain the opposite chirality in nucleic acids.

Been there, done that. Never been shown. Non-starter. Not surprised you believe "it's all been explained . . . by the bright physics boys down the hall." They haven't a clue, either.

You curse all you like...

Moi? When have I ever cursed?

Theory first.

Robert's picture

No.

The observation that existence exists comes first.

Theories (or at least those worth a damn) come after that light bulb has been lit.

Or as Isaac Azimov put it: "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...'"

And here again we arrive at your point of departure with both your opponents and reality.

Clouds, Shmouds

darren's picture

Next time you look at an amino acid remember that it is a three dimensional assortment of linked atoms surrounded by electron clouds.

That's also literally true of plastic beads. So what.

We can stick with primary structure for explaining the idea of amino acid sequence as being very much like beads -- different colored beads -- on a necklace string. The important concepts to get across are (i) discreteness and (ii) sequence. If it was good enough for Christian B. Anfinsen, who discovered this property of proteins and won a Nobel for it -- it's good enough for me. You have higher standards? or are you just incorrigibly stupid?

(Rhetorical question. No need to answer.)

Steric hindrances

Robert's picture

Next time you look at an amino acid remember that it is a three dimensional assortment of linked atoms surrounded by electron clouds.

Being covalently linked to each other means that an amino-acids freedom of movement in space is constricted not just by the bond but by the repulsive charges present on neighboring amino acids.

Observe that the 26 amino acids you list are distinguished by their side-chains - the assortment of atoms covalently bonded to the amino acid's 'alpha carbon.'

Now observe that some of those chains are quite large and that the geometry of their bonds will restrict their ability to move out of the way should a side chain from an adjacent amino acid come into close proximity to it.

The result of these constraints on the freedom of amino-acids to rotate about one another mean that amino acids cannot be considered to be beads on a string. Not if you wish the string to assume a particular super-structural configuration (such as a helix or beta pleated sheet) in order for it to be functional and soluble in water as opposed to an insoluble aggregated mess.

The graphical manifestation of this concept is the Ramachandran plot (derived in ~1966 by GN Ramachandran using principles of chemistry and physics). It is described in the links I gave above. His work has been validated independently at least 10,000 times since then - with every protein crystal structure yet derived.

As I stated this partly contributes to the supramolecular chirality idea that Fred was trying to get through to you. Throw a R- and L- amino acids together and soon you will find that you will not be physically able to form helices and beta-sheets.

You curse all you like, but this stuff is basically just charge-repulsion - fundamental atomic physics in other words.

Something that proto chrome polishing cretins in minute NZ colleges are made aware of in their freshmen courses.

I gather you missed that lecture.

Say, you didn't miss it because you were too busy looking up the meaning of 'fecund' did ya? You know, just in case you had the opportunity to drop it in a debate and show everybody how brainy you are?

Genomically Enhanced Love Potion Number 9

darren's picture

Hint: in science, the fundamentals are identification and observation.

Except first you need a theory or hypothesis to direct your gaze into a direction that is defined as "relevant"; otherwise, you're just staring blankly out the window.

Theory or hypothesis (or even "hunch") first; then observation.

Herr Professor Veinfield -- Ja!

darren's picture

Probably because I'm a cretin mechanic and not a financial analyst.

Seems to me you struggle mightily with a lot of things on that account -- like simple logic, clear sentence structure, elegant vocabulary, and a vigorous style.

You mean they didn't teach that stuff at that little 2-year community college you went to in NZ?

Demand your money back. YOU WUZ ROBBED!

Phone call for Dr. Whinefield!

darren's picture

Nice.
Of course you could have used "fertile" in it's place but that would be too low rent for someone as legendary as you imagine yourself to be.

Smiling

Don't tell anyone, Dr. Whiney, but "fecund" is one of my favorite $5.00 words, especially since most people (1) aren't expecting it when they hear it, and (2) momentarily think it means something dirty.

Next time you're at a party, try using it instead of "fertile" or "rich" and watch people's reaction.

Guaranteed, you'll get laid that same evening.

@ Fraudiano

darren's picture

How does one manage to get a PHd, and never hear the word 'gradient?'

Uh, freddy-boy. You were speaking of "filters."

A "filter" is something that filters OUT certain things, letting others pass. Right?

So do tell, fred. What things does gravity filter out?

Fecund.

Robert's picture

Nice.

Of course you could have used "fertile" in it's place but that would be too low rent for someone as legendary as you imagine yourself to be.

You might like to ponder the fact that fertility is actually the handmaiden of preparation, which is why most fertile minds spend time as apprentices - you would call them mechanics - learning the fundamentals of their craft so that they don't end up creating castles in the air.

Hint: in science, the fundamentals are identification and observation.

I've already explained the reason why my apprenticeship has been longer than the norm for scientists bound for an academic-career.

Strangely that reason only elicited derision from someone who "likes to see entrepreneurship flourish wherever it can."

PolitSci?

Robert's picture

No. The PhD was for elucidating the solution structure of a protein believed at the core of a fungal pathogen's ability to attack plants.

My work led to the elucidation of the solution structure assumed by the monomeric form of the protein. The polymeric form assumes a structure broadly similar to the amyloid fibrils found in patients with diseases such as Alzheimer's and Huntington's. In these diseases the proteins 'miss-fold' into an insoluble, non-functional but hyper-stable form. Yet the fungi I was examining deliberately expressed proteins with this structure.

Why proteins can assume multiple stable conformations of which only one may be of any use and the others toxic. How is this possible? The concepts of energy landscapes help to visualize the process but they are a difficult thing to explain to a layperson - someone like a venture capitalist for instance.

In that sense, your summary of energy gradients and such as being 'filters' is a helpful, if linguistically inexact metaphor that I can use.

It is for that reason that I thanked you. Grant/business plan writing is something that I struggle mightily with. Probably because I'm a cretin mechanic and not a financial analyst.

C'est la vie.

what about it?

darren's picture

what about causally specific compounds, period?

I assume by this you mean "purely physical, materialist explanations"? Right?

Already posted. Noise, filters, and gradients, don't map one set of symbols onto another set of symbols in precise ways to get a precise result. Show otherwise, if you have evidence. Try to be specific instead of vague and general.

Whine and Dyne

darren's picture

So critical thinking skills and creative insight are superior to the devices that allow me to perceive nature?

As tools of scientific research and inquiry? Yes. Better to have great critical thinking skills and a fecund imagination with inferior devices, than to have great devices with shitty critical thinking skills and stick-in-the-mud imagination. Read Karl Popper. Then ask your former boss and current boss which are more important.

@ Ellen Stuttle

darren's picture

The logic of your case for an Intelligent Designer rests on 3 premises, one of which is separable from the other two, although you entwine the three as if they were all required parts of a unified case.

The first, and separable, premise is a variant on the old argument for design regarding the eye. The eye, this argument goes, has to come together as a functional whole all at once or it would be useless; no intermediate stages would confer any selective advantage. But the eye is so complicated and intricate an organ, the probability of its appearing all at once as a functional whole is impossibly small. Ergo, it must have been designed.

That was old William Paley's argument in his classic work "Natural Theology."

You employ a modern variant of this with your probability calculations.

You mean, the mere fact that one compares probabilities of various scenarious to decide which is more plausible marks one as a devotee of Paley and the Argument-From-Design (AFD)? I don't think so. And that's a biased, ideological way of looking at science. The fact is, Ellen, the first people to employ real probability calculations were a bunch of mathematicians and computer scientists -- all atheists -- who confronted their biologist and evolutionist colleagues at a meeting on the campus of University of Pennsylvania in the 1960s at a research facility called The Wistar Institute. The reason for the conference was that the math and engineering people -- after reading up on biology, genetics, and evolution soon after the exciting discoveries by Watson and Crick -- were absolutely shocked at the flimsy, sloppy, assumptions made by their biological colleagues regarding the likelihood of certain events happening, or having happened.

Adopting the premise that the DNA molecule has to appear all at once as a functional whole in order to have had any usefulness,

First, I never said that, and to my knowledge, neither did anyone else. Second, you're conflating two things. You're conflating the classic AFD with Behe's idea of "irreducible complexity." In some ways, they mutually support each other, but they're not the same argument. Additionally, I've never heard that DNA is irreducibly complex. The gist of Behe's argument is that: some things are irreducibly complex (e.g., a mousetrap), and some things are not. Biologically, regarding the eye, he never said the eye is irreducibly complex; what he wrote is that the biochemical cascade causing vision to occur is irreducibly complex; that it has no function unless every step is there, and that, in the entire biochem literature, despite brash assertions to the contrary, there are no detailed descriptions of actual biochemical pathways a simpler cascade could have taken in order to arrive at the end result of vision. If a single link in the vision-cascade is missing, you don't get impaired vision; you get no vision.

Regarding DNA, the problem is not that it's "irreducibly complex" -- again, I've never used that argument -- the problem is the classic "chicken-and-egg" one: DNA requires other proteins in order to replicate; but these other proteins are themselves the result of DNA encoding. That's the problem. The approach that modern Darwinists have taken is to look for something in the genome that can be both chicken and egg at the same time, under the assumption that the "chicken function" and the "egg function" eventually split up. They found it in certain kinds of RNA, which they discovered (to their delight) could be both an encoder of amino acids (and, hence, proteins) AND behave like a kind of enzyme (which is a kind of protein). They called such a creature a "ribozyme." Then they invented the scenario of a world populated by nothing but a primordial soup of ribozymal RNA, replicating itself and encoding its own amino acids, which scenario is now called the "RNA World Hypothesis." It's fraught with many problems and implausibilities, not least of which is the geological embarrassment that there is no evidence that such a condition ever existed on planet earth. However, non-existence of evidence never stopped committed Darwinists from publishing. Inventing fantastic, non-existing prebiotic scenarios is a cottage industry amongst Darwinist origin-of-life researchers.

you then argue that there hasn't been time in the whole hypothesized span of the universe since the "Big Bang" for the chances of an all-at-once appearance of DNA happening to be other than impossibly small.

A quick lesson in probability:

If you throw one die and get "5", the odds of that happening were one in six, or 1/6. If you then throw the same die and get "2", the odds of getting that were also one in six, or 1/6. The odds of throwing a "5" followed by a "2" were 1/6*1/6 = 1/36. So far, so good?

Now, if you have two dice, and you throw them simultaneously, the odds of coming up with the simultaneous combination "5, 2" are exactly the same: 1/6 * 1/6 = 1/36. So, incremental odds, or simultaneous odds -- they're the same.

And the same is true of a biological structure like cytochrome-c, which -- from a purely probabilitist standpoint -- you can think of as rolling 111 dice (each die-face represents an amino acid in the primary-structure of the protein), except that instead of 6 possible choices (which correspond to the 6 faces of die), you have 20 possible choices (corresponding to the 20 possible amino acids required by living organisms). So think of it as tossing 111 dice, each die with 20 sides on it, and on each die-face is printed the name of one of the amino acids needed by life. As in the dice example above, it makes no difference for the probability of coming up with the "winning" combination of cytochrome-c whether you roll one die, or whether you roll 111 of them simultaneously. The odds stay exactly the same. The reason they stay the same is that each die, and each die-roll, is independent from the rest, so each has its own probability that it must contend with, and -- like all probabilities -- the probabilities have to multiply. So whether we hypothesize that the amino acids slowly accrued together, or that they came together simultaneously into cytochrome-c, the odds of that particular SEQUENCE of amino acids being just what it is is very, very, very small compared to the overall number of other possible sequences. To claim that chance created that molecule, you would at least have to hypothesize enough time in the universe to plausibly search through most of those possible sequences to arrive at the right one. What I showed is that there are far more possible combinations than there is time available to search through them.

I'm afraid the only hope for you materialist, gradualist viewpoint is to assume -- and then prove, please -- that the biological die-rolls are NOT independent of one another; that the very appearance of a certain amino acid (in our cytochrome-c example) somehow biases the structure toward selecting the next correct amino acid: you would have to show that the first appearance of amino acid (A) somehow biases the whole evolving structure toward excluding amino acids (B) and (C) and favoring (D), so that when we look at an actual cytochrome-c molecule we see that there is indeed (D) at the second position in the chain, and never (B) or (C). Conversely, if we do find (A) consistently followed by (D), but no evidence of biochemical or physical bias, then you can't assume that the bias is there but hidden; if there's no bias, then there's no bias; and you now have to ask how that particular sequence came into being without the help of physical biases "nudging" the right elements into the right order. Fred's handwaving answer is "what works, works." I hope you realize, that's not an answer.

Unfortunately for materialism and gradualism, no chemical bias has ever been observed: as far as the brute chemical facts are concerned, any amino acid can be a neighbor to any other amino acid in a chain. IT'S JUST LIKE LETTERS. As far as chemistry is concerned, any letter can be a neighbor to any other letter. The only question is: do the letters form meaningful chains that function (in this case, function in our minds as having meaning), such as "Who is John Galt", or is the chain functionless, such as "wnueomq wo fgtwq". Replace the letters and spaces with amino acids and you'll get the idea. "Proteins" are the biochemical analog to sentences.

That argument can be addressed on the basis that, no, it isn't necessary for the DNA molecule to have appeared as a functional whole all at once. The DNA molecule could have developed by cumulative retained increments.

As I showed above, you can pretend and assume any scenario you want. Probability is what it is.

The second premise is the one point on which I think you're entirely right. (I partly but not entirely agree with you on a few other points which I'll leave aside for now.)
This is the premise that a literal code requires a codER -- i.e., that to say something is a literal code does entail that it was designed.

So far, good.

On the issue of the genetic code literally qualifying as a code, however, you rely on "information theory" ideas of its supposed isometry to, quoting you (#96771), "all other known codes." You explain, "i.e., it has all of the same formal characteristics as Morse Code, ASCII, and languages. So calling the arbitrary-yet-meaningful sequence of bases a 'code' is far more than metaphor."
ASCII you can almost get away with in seeing close similarity. Morse is more of a stretch. By pulling natural languages in (I'm assuming you mean natural languages), you both go afield from isometry -- you have to stretch very thin to argue for isometry there -- and you equivocate, whether intentionally or not, on a literal code having *meaning*, on the elements of that code being symbols which *reference*. But only according to an ambiguous definition of "meaning" can the codons, as they're called, of the DNA molecule be thought of as referencing anything.

That last sentence is completely untrue. The codon triplet in DNA (which gets transcribed into a similar codon-triplet in messenger RNA) is a free, chemically undetermined, symbol-set for a specific amino acid. Since there are 4 nucleotide bases, there are 64 possible codon-triple symbols; there are 20 possible amino acids necessary for life -- the genome MAPS the first set of 64 symbols onto the second set of 20 symbols, and by doing so, correctly specifies which proteins ought to be constructed. Locationally, the mapping physically occurs at the ribosome, where the codon-triplet from messenger RNA (mRNA) meets its code complement -- the anti-codon triplet from transfer RNA (tRNA) which accompanies the amino acids in the body of the cell. The entire process is formally identical to mapping Morse Code (2 symbols -- "dot" and "dash", -- but with freedom to repeat any of them as needed) onto the 26 symbols of the English alphabet. No chemical force or physical law determines that the letter "S" has to be represented by the code symbols "dot-dot-dot." That was freely chosen and completely optional.

This is all structurally identical to the genetic code. Nothing chemically or physically pre-ordained the codon-triplet CGT (CGU after RNA transcription) to represent, or specify, the amino acid "arginine." Physically, it could have been anything, just as the letter "S" could have been anything in Morse Code. The important thing in a code is not what symbols are chosen to represent other symbols; the important thing is (i) the first set of symbols has to be at least as large, if not larger, than the second set (in Morse Code, the first set of dots and dashes is as long as needed. Morse obviously had the freedom to repeat whatever symbols he wanted to represent each letter of the alphabet. In the genetic code, since there are 4 bases arrayed in groups of 3, each triplet called a "codon", there are 4x4x4 triplets in total = 64 codons, which is a bigger number than the 20 amino acids that are being coded for). As pointed out earlier, the larger number of codons allows many of the proteins to be coded for by several slightly different codons -- think of these additional codons as "synonyms" for the same amino acid), but there cannot be any ambiguity: you cannot have a functional code system if at one time "dot-dot-dot" referred to the letter "S", but at another time it changed its meaning and referred to the letter "A". This would be an example of ambiguity. However, you can have synonymity: it's perfectly all right to have "dot-dot-dot" refer to "S" AND to have another set of symbols -- e.g., "dash-dash-dot-dot-dot-dash-dash" refer to "S" also. As long as each set of code symbols is unambiguous, you can have a functional code.

You can also see the mathematical reason here for Crick's original formulation of his "Central Dogma": instructions ONLY flow FROM the genetic code TO the end-resulting proteins, and not the other way around. Because mathematically, proteins are composed of an alphabet of 20 amino acids, and there's no way to have a code starting with an alphabet of 20 and mapping them onto a set of 64 codons; the first set has to be as large, or larger, than the second set (otherwise, you run out of symbols). The upshot of this Central Dogma as far as origins-of-life scenarios are concerned, is that it would not be possible to start with the creation of a protein and then have the protein, or proteins, create the genetic code. You can't start with a symbol-set of 20 and map them to a symbol-set of 64.

It's as if one were to say that baking soda added to dough is a symbol for, that it "means," "dough rising."

I can see you simply don't understand what a code is, so you alway find an irrelevant analogy, which then further convinces you of your mistaken position. The relevant code in your baking example would be the recipe, as originally written -- that is, encoded -- by a coder named, e.g., Julia Child. She encoded a desired end-result -- a physical/chemical entity called "bread" -- by putting a chemical thing called "ink" in a physically undetermined series of shapes called "letters" on a physical substrate called "paper". The purpose of this whole thing, as you correctly noted, is to arrive at a physical thing called "bread." Now look BETWEEN the occurrence of physical events of letters on a page and the physical appearance of bread out of the oven, and there's a process of decoding, in this case done by a mind capable of making the correct mapping between the code symbols "A-d-d b-a-k-i-n-g s-o-d-a t-o d-o-u-g-h a-n-d l-e-t r-i-s-e" and the correct physical processes and events (i.e., actually taking a can of baking soda, opening it up, adding the specified amount to the dough, etc.). That was all an example of going from a code, to a decoder, to a physical/chemical event (meaning, the bread out of the oven).

So I don't get your problem. The genetic code is like a recipe, whose end-result is protein-out-of-the-ribosome instead of bread-out-the-oven. Instead of letters on a page in a printed recipe decoded by the cook, it's codons on a molecule (DNA or RNA) decoded by the ribosome. Formally, it's the same process. If you admit that the printed recipe contained information, then there's no problem admitting that codons contain information. The recipe contains information for making bread; the codons contain information for making proteins. Formally and structurally, there's no difference.

I doubt that anyone would be so easily "beguiled," as I put it, into accepting the description of DNA codons as "symbols" if it weren't for prior softening up of by theories of "substrate equivalence." The idea of "substrate equivalence" has been talked about earlier in the thread. I think you've mentioned it yourself.
The idea of "substrate equivalence" has been talked about earlier in the thread. I think you've mentioned it yourself.

I don't remember mentioning "substrate equivalence" though you can certainly search through my posts and try to find an example of it. MInd telling me what you mean by it?

Whether you've explicitly brought in "substrate equivalence" or not, it's the third premise on which your logic rests -- and one of the two premises you require in order to make a case for an "intelligent designer." Without the premise of "substrate equivalence," you'd be stuck in a circular infinite regress on your second premise, that of a literal code entailing a codER.
The reason you'd be stuck is because you're claiming that the DNA molecule, which you accept as the basis of life, has to be designed.

I said that the CODE PART of the DNA molecule could not have arisen by purely material means. Not every part of the DNA molecule is code. The helical backbone of the molecule is simply a kind of sugar. I certainly don't believe that a simple sugar molecule required intelligent input to appear. I was careful in what I wrote: the coded part of the DNA molecule is the sequence of nucleotides. The SEQUENCE, the ORDER. Frankly, it's not a hard concept to grasp; I don't understand your difficulties with it.

But if it has to be designed, then without a premise of substrate equivalence, the designer -- in order to be "intelligent" -- would itself have to be a life form, which in turn would require a literal code for its existence, hence a prior codER, etc., etc. You can only get out of this circular regress by separating "intelligence" from "life" and claiming that something which isn't alive can nonetheless be "intelligent" by virtue of substrate equivalence.

If you're complaining that the idea of an intelligent coder leads to the question "who coded for the design of the coder"? which can then lead to a infinite regress, I agree -- I admitted so early on. As a materialist yourself, you shouldn't complain, since materialist explanations of life must also entail an infinite regress. Materialists wriggle out of it by claiming that at some point in the regress, a certain kind of entity "just was." Good. I do the same with an intelligent coder: if life on earth was coded by intelligent martians, then the intelligent martians were coded by intelligent venusians, who were coded by intelligent jovians, etc., until we get to some point in the regress where we say "this particular intelligent coder just was." It's exactly the same form of argument as the materialist's, Ellen . . . except that it admits that the thing needing explanation -- codes -- i.e., mappings between two sets of symbols in order to create a physical/chemical end result -- are never arrived at by purely physical occurrences of chance and necessity.

That actually was the approach taken by Fred Hoyle and Hubert Yockey, both atheists, both anti-gradualists. For them, life is an axiom. You have to start with the idea of biological entities as already being part of the universe from the get-go, and then you can profitably ask question as to how it got seeded onto earth, or how the various biological elements became built up, like "Leggo" blocks, into larger structures. Not saying I agree with this approach, just saying that a number of people cut short the infinite regress by declaring living organisms to be an axiom of biology . . . you can't prove or demonstrate the axiom itself; you start with the axiom and reason from there.

Thus, whether or not you specifically mentioned "information theory" in your earlier posts (seems to me you did, but I'm not sure), you've been relying on notions which are liberally employed in the mish-mash which currently goes under that rubric.

You haven't shown that there's any "mish mash", only that you don't really seem to understand it. Shannon-Weaver, by the way, is not the only information theory out there; there are others that try to tackle the problem of syntactic meaning, and not just sequential likelihood. So it's not as if people involved in the field are unaware of its various shortcomings. However, "mish-mash" isn't one of them.

"Additional support..."

Robert's picture

Interesting terminology. So critical thinking skills and creative insight are superior to the devices that allow me to perceive nature? Who would have believed that you would have tended towards rationalism?

Has it occurred to you that my first task as a molecular mechanic is to first perceive nature? That is, the things molecular biologists study are difficult to observe unassisted with the five standard senses.

So ability to perceive reality on the atomic level goes hand in hand with critical and creative thinking. They are equals. Separate the two and you start doing things like believing that a God created the universe in 7 days.

causal specifity and 'coding' theory

Frediano's picture

My assertion that codes don't form naturally by adding noise, "filters", or "gradients", and always require intelligence? That's not a religious argument. That's simply a fact of semiotics and coding theory.

"Semiotics?"

How long before 'semiotics' lurches into the Periodic Chart of the Elements to find more 'codes' about? Never mind the building blocks of life, what about causally specific compounds, period? Tell all those collapsing stars to stop whatever the hell they think they are doing immediately...

You can always tell when Derrida is about.

"Semiotics?"

My earlier reference to http://www.elsewhere.org/pomo/ is no longer in jest. {"The essay you have just seen is completely meaningless and was randomly generated by the Postmodernism Generator.")

I'm going to have T-shirts printed up: "My financial analyst is into semiotics."

They will come pre-torn, and ragged.

In a perfect world(as in that much simpler artihmetic world without field effect gradients) you would cough up to the fact that your PhD was somewhere in the vicinity of 'semiotics.'

It's a dirty job, but somebody had to do it.

reed

Frediano's picture

Perhaps it was a philosopher's reaction.

That is easily forgiven. It happens with little warning.

Presumably "it" is a reference to your beliefs about life's origins.

Then we've identified the source of confusion; I only have doubts, not beliefs/certainites, on that subject. There's a rager about filled with certainty on the subject, complete with exponents mashed together, obeying his demands that there be 'a' singular experiment being conducted in the , excuse me for saying this, I'm really not trying to be funny, but it is key to his so called analysis ... entire universe. And not just that 'a', but 'the' goal of this singular experience is not to reach any solution, but to reach the current locally/parochially observed solution, as its goal. Kind of, a vice like grip on 'singular' but squared, as if on singular perseverance steroids.

The entire subject is logically way beyond my pay grade, in terms of my setting rules or conditionals for my own existence. As if I could somehow reason myself out of or into existence. Too late, I'm already here. That's what I meant.

It is fun to watch others try to set conditionals for their own existence. As if it was possible. I would love to see them try to enforce that. I suppose a time machine of some kind would be required... it seems in all liklihood to be a waste of time to try to do that.

Because of my drunken prose, you might be confusing other's certainties/beliefs for my uncertainties on the existential paradox. I'm a devout non-aligned agnostic theist. I accept the defacto existence of at least one form of creator -- the universe, as it is, which emitted us, as we are, in it. Depending on which of my fellow merely here beings you talk to, that is either too God like or not God enough, too creative/not creative enough, too intelligent design, not intelligent design enough. On any given day, I can be accused of really being an athiest, or really being a theist. But on the topic of supernatural beings, I'm not sure what 'really' means.

I never understood any of that, logically. The religious variant is a topic safely locked up forever outside of the natural universe, by definition. If it turns out to be cold process all the way down, intelligence all the way down, or turtles all the way down, it still doesn't have any impact whatsoever on the religionists who forever play the carny hucksters trick and imagine an authority forever safely outside of the natural world that yet remarkably requires those within the natural world to speak for it.

You know, like the carny huckster trick that Rawls pulled.

There's no church in my religion, and no religion. And no need to speak for the universe, as it is. It speaks for itself. It saves alot of time, there's no need for men in funny hats imploring the congregation to sing terribly, and by extension, severely reduced opportunities for pervs in robes to molest choir boys.

@ Frediano Mustachio

darren's picture

Because the religious arguments presented so far are perseverating on 'one' for some reason--

What "religious argument"?

My assertion that codes don't form naturally by adding noise, "filters", or "gradients", and always require intelligence? That's not a religious argument. That's simply a fact of semiotics and coding theory.

Fred- ... I mean, after all,

reed's picture

Fred-
... I mean, after all, we're already here, it is a fait accompli...

Presumably "it" is a reference to your beliefs about life's origins.

That's why I asked "Is this a scientist's reaction or a religionist's reaction?"
Perhaps it was a philosopher's reaction. Smiling

@ Rand & Darwin Cult Member (Lifetime Membership)

darren's picture

To keep doubt away, a system of elastic defences is established.

That describes Objectivists and their naive belief in purely materialist explanations for the origin of life. Congratulations, gruntster. You successfully diagnosed yourself.

My tools are a Gilson

darren's picture

My tools are a Gilson autopipette and a Mass Spectrometer.

Wrong. As a scientist, your tools ought to be your critical thinking skills and creative insight. The physical stuff you polish and maintain is simply supposed to provide additional support.

I sling Jurkat cells

You should be slinging hash at a greasy-spoon diner.

I'll defer.

Frediano's picture

Is this a scientist's reaction or a religionist's reaction?

That is a philosopher's question. And by ohilosophers, I don't mean all, but some. I know of no serious scientists, and few philosphers, who hold significant doubt that we're already here. I can live with that giant leap of faith.

My favorite scientist, Feynman on philosphers: "They need to learn more than anything else to laugh at themselves."

The Yogi And The Commissar

gregster's picture

“Deep-rooted, archetypal beliefs lead only to neurosis when doubt provokes a conflict. To keep doubt away, a system of elastic defences is established. The outer defences are provided by [insert relevant form of mysticism]. They produce a characteristic sectarian intolerance, which, coming as it often does from otherwise good-natured people, manifests itself in surprisingly violent forms.

The inner defences are unconscious. They consist in a kind of magic aura which the mind builds around its cherished belief. Arguments which penetrate into the magic aura are not dealt with rationally but by a specific type of pseudo-reasoning. Absurdities and contradictions which outside the magic aura would be rejected at once are made acceptable by specious rationalizations. The higher developed the mental faculties of the person, the subtler the patterns of pseudo-reasoning which he develops.”

May I suggest you work on your subtlety Dazzler.

Fred - Scientists react with

reed's picture

Fred -
Scientists react with doubt and limited certainty about that which is known in the natural universe.
Religionists react with absolute certainty about that which is unknown in the supernatural universe.

... I mean, after all, we're already here, it is a fait accompli...

Is this a scientist's reaction or a religionist's reaction?

Gravity had little to do with

Frediano's picture

Gravity had little to do with any of it

So, in financial analyst world, those sediments did not form at the bottom of those seas(ie, were ordered), but were distributed randomly throughout space.

The physical world must be a completely baffling thing to you.

How does one manage to get a PHd, and never hear the word 'gradient?'

PolitSci?

Wrong field for field-gradients, I suppose.

When rigging the probabilities game...

Frediano's picture

... I have to wonder.

Has anyone proved what the upper bounds is on the number of states that lead to self-aware animated stardust? Or even, guessed an order of magnitude?

Because the religious arguments presented so far are perseverating on 'one' for some reason-- as if there is any evidence of theory or 'causally specific' argument that declares that 'this' is the only solution.

It is one thing to go all rabid over the probabilites of arriving at 'this' solution.

It is another thing to ponder the probabilities of arriving at 'a' solution.

Assuming 'this' isn't the only solution, then the probabilities of arriving at 'a' solution are likely far greater than the probabilities of arriving at 'this' solution.

After the fact of arriving at any solution ... I mean, after all, we're already here, it is a fait accompli ... to miss-apply statistical analysis by looking backwards and pondering the liklihood only of arriving at 'this' solution and represent it as the liklihood of arriving at any solution is equivalent to comparing the liklihood of an individual winning the lottery compared to the likelihood of any individual anywhere winning the lottery. The former may never happen in your lifetime, the latter is all but guaranteed to happen in your lifetime.

With a lower bounded probability of .7x10^38, a small but finite probability in the visible universe which is likely much larger than even that.

Scientists react with doubt and limited certainty about that which is known in the natural universe.

Religionists react with absolute certainty about that which is unknown in the supernatural universe.

I don't know why religionists so fear scientific doubt, it is of no possible threat to their rolling their eyes into the backs of their heads little moments. In the hypothetical of highly probable evidence that life in this universe was always a small but finite probability, a likelihood even, given the combination of noise and natural filters, it is only necessary for the religionists to claim that the external to this universe/supernatural first designer chose that as his means of creating life. The realm of that which is always safely outside of the natural universe is forever untouchable by science, and the religionists are forever safe to do what carny hucksters forever have done, and that is, safely hypothesize an authority forever outside the known universe and then claim to speak for it.

@ Ellen Stuttle

darren's picture

First, "information" is defined in such a way that it needn't require a living entity conveying "information" or being informed.

But not requiring a living entity is what allows it to be quantified. Obviously, Ellen, what you disapprove of is math and quantification. "HEAVINESS" is a qualitative, subjective, human experience that cannot be quantified or meaningfully spoken about apart from human beings; "WEIGHT" is quantitative and need not have a human being around to be meaningful . . . yet it obviously incorporates the original idea and experience of "heaviness." "COLOR" is a qualitative, subjective, human experience that cannot be quantified or meaningfully spoken about apart from human beings; "WAVELENGTH (or FREQUENCEY)" is quantitative and need not have a human being around to be meaningful . . . yet it obviously incorporates the original idea and experience of "color."

"INFORMATION" (in the sense of "learning some juicy gossip about Frank O'Connor's excessive drinking") is subjective, human, and cannot be quantified or measured. "INFORMATION" (in the sense of a Shannon-measure of the inverse of probability) is a measure of probability (the less probable an occurrence, the more information; the more probable an occurrence, the less information). Shannon not only found a way to make "information" quantifiable" but even made it easy to do so by converting the whole thing to the binary log (log-base-2), because -- as I've been trying to teach freddy -- probabilities have to multiply, but logs can add. So if you want to know the amount of information -- or "information-carrying-capacity" -- in several systems, just add up the number of bits in each. Easy.

It's robbed of its *communicative* sense -- for instance, the sense in which I would describe posts as conveying "information", or you might think of many, many other ways in which we speak of informing each other or being informed by or about.

You're a riot, Ellen. You've been complaining throughout this entire thread that modern science's use of linguistic/syntactic/semiotic terms like "code", "transcription," "translation," "encode," "decode," "read", and "information", in describing cellular processes, is merely metaphorical not literal; now you're complaining that these same terms are literal, thus robbing their meaning of the human experience of "communication".

Shannon, Weaver, Hamming, etc. didn't "rob" any meaning from anything. They more narrowly focused the meaning to one small part of the original concept that permitted quantification, hence more universal applicability to systems other than human ones.

Are you really going to say -- more than ten years into the 21st century -- that you don't accept the idea that a CD, DVD, or computer hard-drive stores information? It's pretty silly.

It's defined as a term which applies to computers as well as to humans, such that "information" becomes bits on computers,

"Bits" are a unit of information, just as "meters" are a unit of distance and "kilograms" a unit of mass. I don't understand your problem.

or, in the original Shannon meaning, capacity for transmitting and reliably receiving "data." Thus computers are said to be doing "information" processing.

Shannon and Weaver understood the limitations of their definition. For them, "information" was an inverse measure of probability: the higher the probability of an occurence -- such as a series of discrete elements like letters -- the lower its information-bearing capacity, and vice-versa. And since probability can be measured, so can information. Information here becomes a kind of measure of "surprise." It, of course, differs from the qualitative, human notion of information by not incorporating any notion of syntax, grammar, or meaning. For Shannon and Weaver, the probability of generating the alphabetic sequence "Who is John Galt" is identical to the probability of generating the alphabetic sequence "robma qpzz awphx". Since their probabilities are the same, they carry the same amount of information -- Shannon Information doesn't distinguish between meaningful sequences and meaningless ones; it distinguishes between likely ones and unlikely ones.

Slowly, the need for a conscious entity is dropped by "substrate equivalence" -- the idea that what a computer does is equivalent to what a brain does, extending from there to speaking of "information" as if it were a property of matter as such.

No different from what Newton did to, and with, the concept of "gravity" which, in his day, meant something completely different. "Gravity", in his day, was analogous to your idea of "information" today: something that required human experience to grasp. In Newton's day, "Gravity" -- in Latin, "gravitas" -- meant "heaviness." Newton focused the concept -- reinvented it, really -- by asserting that gravity is an invisible force emanating from material bodies but acting centripetally, and that the older meaning of gravity -- heaviness -- was the resultant of this invisible force with something else called "mass." We take it for granted today, but there were Ellen Stuttle's in Newton's day who didn't like him redefining things that way.

So you're in good company with the other Ellen Stuttles of history.

@ Earth, Wind, and Fire

darren's picture

So to be clear, gravity does not result in any gradient, and is not an order producing filter. (Eaons of sedimentary evfidence to the contrary.)

You're a moron, fred. "Aeons" of sedimentation are almost exclusively the result of aeons of weathering and erosion. Gravity had little to do with any of it. I wish I could say "nice try", but it was actually pretty lame.

Check your damn spelling, too.

I just want to gauge who I am talking with, so to speak.

I'll tell you WHOM (not "who") you're talking with. I am your biggest fan, freddy, and (needless to say) your most humble servant.

Go back to your +, -, x, /, and %, because by the time you get to 'del' you are so in over your arithmetician head that you are beyond help.

I've learned all I'm going to learn from Mr. Gravity Does Not Produce Gradient in the Universe. I've been fishing a dry hole.

Too stupid to multiply big numbers with exponents together? Just as I thought. (Hint: As long as they're the same base, just add the exponents, Fred. It'll put some "meat" on your origin-of-life fantasies, allowing you to gauge how plausible or implausible they are.)

And what's really funny about all this is that a cretin with a Ph.D. from a little college in New Zealand thanks you for inspiring him!

@ Chief Lab Equipment Polisher Whinefield

darren's picture

http://www.fasebj.org/content/...
THE TWENTY OR SO amino acids found in living organisms occur almost exclusively as L-enantiomers. The origins of this pervasive homochirality have never been explained satisfactorily. Because there is no obvious biochemical reason for choosing L-amino acids over the D-forms, numerous physical and biochemical mechanisms have been invoked to explain the phenomenon

[True. And all of the numerous physical and biochemical mechanisms thus invoked involve inventing convenient "prebiotic" environments that never existed, or for which there is zero evidence of having existed; or performing experiments in laboratories with constructed molecules like "RNA mini-helices" that accomplish the chiral selection, but which require intelligent lab assistants to construct in the first place (no evidence existing of a naturally occurring RNA mini-helix). So invoking these mechanisms amounts to nothing more than story-telling -- like the fun "Just So" stories of Rudyard Kipling -- in which the science is provided after-the-fact to show that no physical laws are being broken. Biochemist Robert Shapiro of New York University -- no relation to James A. Shapiro of Chicago University -- likens this to a golfer, who, after playing several rounds of golf, proceeds to "plausibly explain" how a little white golf ball could seek out holes on a green of its own accord without the intervention of a golfer -- and do so without breaking any physical laws -- simply by invoking whatever naturalistic cause is convenient at each step of the explanation: an earthquake, a flood, a hurricane, etc. See link below for his article in Scientific American.]

http://labquimica.files.wordpr...
The biological system is mostly composed of homochiral
molecules. The most well known examples of homochirality
is the fact that natural proteins are composed of l-amino acids,
whereas nucleic acids (RNAorDNA) are composed of d-sugars.
The reason for this phenomenon continues to be a mystery,
although more than 50 years have passed since the DNA double
helix model was proposed (Watson and Crick, 1953), which led
to the completion of human genome sequencing (International
Human Genome Sequencing Consortium, 2004). No satisfactory
explanations have been provided regarding the origin of the
homochirality of the biological system
.

From the Twit's Mouth:
You could say that the steric hindrances (and adverse chemical interactions) . . . exerts a filtering effect on how amino acids may be combined

Uh, yeah, I guess you could say that. You could also say "Steric hindrances" of WHAT, dummy? Of RNA? Of DNA? Of ribose? Of deoxyribose? Can you be specific, or is that too much of someone like you who likes to "play scientist"?

A handwaving, bullshit argument, based on having pulled a college textbook out of your ass. (Query: can you still sell it back to the campus bookstore as "used" after doing that? Just wondering.)

Anyway, handsome, there are precisely zero theories claiming that steric hindrance of RNA or DNA or anything else, caused living organisms to selectively prefer only left-hand molecules for their amino acids and right-handed ones for their nucleic acids.

That the best you can do?

Now get back to polishing that lab equipment!

http://www.scientificamerican....
Robert Shapiro on Origin of Life Theories, Scientific American

Thanks, Fred - me too, Robert

Ellen Stuttle's picture

Robert: (BTW, thanks Fred for introducing me to an alternate way of explaining energy landscapes).

Fred's discussion of energy landscapes, though I wouldn't call it an "alternate way of explaining" those from my perspective, since I hadn't properly focused on those earlier, was a way which connected with my thoughts on volition and physics to provide what I think/hope is a "missing link" for which I was seeking.

Much pondering to do before I'm sure. But if the thoughts more or less cascading like a fireworks display which Fred's comments have triggered pan out.......YIPPEE!

Fred, you will get a mega thanks in the book I'm trying to write if the clue you provided for me connects as I'm anticipating it will.

Ellen

Doug - "slight of [language]"

Ellen Stuttle's picture

Doug, you ask:

How does substrate equivalence allow something that is not alive to possess "intelligence"? This seems to be slight of hand...

I signed on for two reasons. For one of those, see the next post.

The other was because I realized that I hadn't actually stated in my summary re Darren's thesis why "substrate equivalence" is the key in "allow[ing] something that is not alive to possess 'intelligence.'" I think you asked just the right question.

The connection is the equivocation on "information."

First, "information" is defined in such a way that it needn't require a living entity conveying "information" or being informed. It's robbed of its *communicative* sense -- for instance, the sense in which I would describe posts as conveying "information", or you might think of many, many other ways in which we speak of informing each other or being informed by or about.

It's defined as a term which applies to computers as well as to humans, such that "information" becomes bits on computers, or, in the original Shannon meaning, capacity for transmitting and reliably receiving "data." Thus computers are said to be doing "information" processing.

Slowly, the need for a conscious entity is dropped by "substrate equivalence" -- the idea that what a computer does is equivalent to what a brain does, extending from there to speaking of "information" as if it were a property of matter as such.

I should maybe add, since I've referenced Gibson's theories of perception in earlier posts: Gibson talks about the "information in light." He meant the structural features of light which enable an organism perceiving light to navigate in an environment. He died before "information theory" got well underway as a kind of "theory of everything," but he was aware of Shannon's usage and differentiated his usage from Shannon's. So please don't take my cautions against the term "information" as used in "information theory" as applying to Gibson's theory of perception.

Ellen

Nice Summary Ellen

Doug Bandler's picture

Nice summary Ellen of what has in essence become a thread dedicated to a debate on Intelligent Design. Who would of thought that this is where this post would have lead? Darren is making the ID case. I am actually glad he is because I have never actually read the ID arguments. They are science heavy and as such need to be refuted by those who know the science, although ID really is a sophisticated form of the Design Argument.

A question though. What exactly is 'substrate equivalence'? Its not an easy term to do a Google search on although I see that it is related to information science. How does substrate equivalence allow something that is not alive to possess "intelligence"? This seems to be slight of hand...

Darren - "information theory" and your logic

Ellen Stuttle's picture

#96944: The term "information" hasn't been used that often in this thread, Ellen. The string I've been harping on has been the concept of "code", not "information." Why don't you point out precisely where I (or anyone else) equivocated on the term "information."

I'm not sure if you've specifically used the term "information" in your earlier posts (I haven't time for searching right now). However, the concept of "code" you're using comes from "information theory" notions, whether you've explicitly referred to that framework or not.

 

The logic of your case for an Intelligent Designer rests on 3 premises, one of which is separable from the other two, although you entwine the three as if they were all required parts of a unified case.

The first, and separable, premise is a variant on the old argument for design regarding the eye. The eye, this argument goes, has to come together as a functional whole all at once or it would be useless; no intermediate stages would confer any selective advantage. But the eye is so complicated and intricate an organ, the probability of its appearing all at once as a functional whole is impossibly small. Ergo, it must have been designed.

You employ a modern variant of this with your probability calculations. Adopting the premise that the DNA molecule has to appear all at once as a functional whole in order to have had any usefulness, you then argue that there hasn't been time in the whole hypothesized span of the universe since the "Big Bang" for the chances of an all-at-once appearance of DNA happening to be other than impossibly small.

That argument can be addressed on the basis that, no, it isn't necessary for the DNA molecule to have appeared as a functional whole all at once. The DNA molecule could have developed by cumulative retained increments.

--

The second premise is the one point on which I think you're entirely right. (I partly but not entirely agree with you on a few other points which I'll leave aside for now.)

This is the premise that a literal code requires a codER -- i.e., that to say something is a literal code does entail that it was designed.

On the issue of the genetic code literally qualifying as a code, however, you rely on "information theory" ideas of its supposed isometry to, quoting you (#96771), "all other known codes." You explain, "i.e., it has all of the same formal characteristics as Morse Code, ASCII, and languages. So calling the arbitrary-yet-meaningful sequence of bases a 'code' is far more than metaphor."

ASCII you can almost get away with in seeing close similarity. Morse is more of a stretch. By pulling natural languages in (I'm assuming you mean natural languages), you both go afield from isometry -- you have to stretch very thin to argue for isometry there -- and you equivocate, whether intentionally or not, on a literal code having *meaning*, on the elements of that code being symbols which *reference*. But only according to an ambiguous definition of "meaning" can the codons, as they're called, of the DNA molecule be thought of as referencing anything. The meaning of "meaning" employed has to classify as a "symbol" what's actually just a chemical compound which produces chemical results. It's as if one were to say that baking soda added to dough is a symbol for, that it "means," "dough rising."

I doubt that anyone would be so easily "beguiled," as I put it, into accepting the description of DNA codons as "symbols" if it weren't for prior softening up of by theories of "substrate equivalence." The idea of "substrate equivalence" has been talked about earlier in the thread. I think you've mentioned it yourself.

--

Whether you've explicitly brought in "substrate equivalence" or not, it's the third premise on which your logic rests -- and one of the two premises you require in order to make a case for an "intelligent designer." Without the premise of "substrate equivalence," you'd be stuck in a circular infinite regress on your second premise, that of a literal code entailing a codER.

The reason you'd be stuck is because you're claiming that the DNA molecule, which you accept as the basis of life, has to be designed. But if it has to be designed, then without a premise of substrate equivalence, the designer -- in order to be "intelligent" -- would itself have to be a life form, which in turn would require a literal code for its existence, hence a prior codER, etc., etc. You can only get out of this circular regress by separating "intelligence" from "life" and claiming that something which isn't alive can nonetheless be "intelligent" by virtue of substrate equivalence.

Thus, whether or not you specifically mentioned "information theory" in your earlier posts (seems to me you did, but I'm not sure), you've been relying on notions which are liberally employed in the mish-mash which currently goes under that rubric.

Ellen

Oh! As in ... almost but not quite 0.000000000000000...

Frediano's picture

I never claimed that intelligence is behind all phenomena. Just those that are specific enough that odds of generating it by chance are effectively zero

Would you say that 0.7x10-38 in the visible/known universe is ...what is the weasel word I'm looking for ..."effectively" zero?

Nobody (except filter denying you) is talking about purely 'chance', by itself. The concept of natural filters(including gravity, which you claim is not a filter/does not result in gradient, ie, result in order from disorder)was injected into this discussion many posts ago.

As in, way back when. Noise and box full of coins -- pure chance. Noise and box full of coins + filter: exactly what goes on in bank lobby machines to create order out of disorder.

You've been into your gravity/field producing natural forces denial phase of the religious festivities. The denial --complete with caps and childish obscenities-- of handedness as a physical effect that acts as a natural filter. That is, actual examples of natural filters. I doubt we currently have discovered all such filters, but there is a hell of a serious start.

...against which we can weigh the probability of the boogeyman folks, who have yet to produce even a single verifiable example of an external to this universe 'initial designer.'

And yet, curiously, are willing to throw 'causal specificity' at all things scientific, just... not at their own boogeyman alternative.

I get it. "If we arithmeticians who deny gravity and handedness and so on don't understand how it might be possible, then because of 'causal specificity,' the only conclusion possible is, the replacement of scientific doubt with the certainty that it is... turtles all the way down."

When last I randomly fact checked Darren's fables

Robert's picture

I came across these gems:

"Like beads on a string, there is no physical restriction on the order of amino acids: physically, any amino acid has the capability of appearing on any place in the string (just as letters on a piece of paper, or a computer screen, have no physical restriction as to their order). "

and

"[expletives and gratuitous abuse deleted]...there's nothing filtering out the left-handed molecules from the right-handed ones."

Wrong.

To explain why you are wrong would take up too much time. You could get a ~very~ brief introduction here or you could read the excellent introductory textbook Introduction to Protein Structure by Branden & Tooze.

You could say that the steric hindrances (and adverse chemical interactions) introduced when the bulky amino-acids side-groups are brought into close proximity as their parent amino acids are covalently linked via a peptide bond, exerts a filtering effect on how amino acids may be combined in order to produce useful proteins. (BTW, thanks Fred for introducing me to an alternate way of explaining energy landscapes).

This partly intersects with what Fred was trying to tell you about supramolecular chirality (the handedness of duplex deoxyribose nucleic acid polymers, helical domains within a protein - especially those that interact with chiral duplex DNA polymers for the purpose of regulating gene expression...)

But I'm sure you knew all of this and you don't need a mere mechanic pointing this out.

Handedness

Frediano's picture

HANDEDNESS IS NOT A "FILTER" YOU DUMB FUCKALL!

More caps please, I can't actually see your impotence and incompetence.

Feynman disagreed with you, and described the experiments which demonstrate that handedness is indeed a filter(synthetic/natural sugar,bacteria, polarized light.)

How do those little bacteria tell the difference between the rh and lh handedness of those otherwise identical chemical compounds? They must wait for The Designer to come by, and tell them. Or else, handedness is a filter.

A lot of these organic compounds you claim are impossible without a boogeyman exhibit a handedness (a directional ordering to the helical winding and/or arrangment of the molecular structure.)

Just like threads on a nut and bolt, a rh helix won't easily interact with a lk helix...the handedness acts as a filter.

OK, so you've never worked on cars in your life. Or read any of Feynman's work, either.

And, you are calling others around here 'Nancy Boys.'

Displace much?

THere were almost enough caps in your last post. You seem to be breaking a sweat of some kind. If some of those sweat drops end up 'randomly after all'' rolling up your forehead, and not down, then get back to me on that whole gravity is not a filter thing. It could be an antipode thing.

Gravity does not produce gradient?

Frediano's picture

Darren:

So to be clear, gravity does not result in any gradient, and is not an order producing filter. (Eaons of sedimentary evfidence to the contrary.)

I just want to gauge who I am talking with, so to speak.

OK. If that is what you believe, then I know I'm on the right track when you regard me as an uneducated idiot.

See, this is exactly why I stopped going to church.

Go back to your +, -, x, /, and %, because by the time you get to 'del' you are so in over your arithmetician head that you are beyond help.

I've learned all I'm going to learn from Mr. Gravity Does Not Produce Gradient in the Universe. I've been fishing a dry hole.

Numbers...

Frediano's picture

...are not calculations, and calculations are not algorithms, and algorithms are not logic and logic is not proof and proof is not experimental validation...and all of that is still subject to scientific doubt.

You are so far away from where you self-congradulatory think you are -- except maybe in church, where such arguments might sway the true believers, that you might as well be upside down, on the other side of the world.

I'm still wondering: why isn't the calculus of 'causal specificity' aimable at the concept of a first designer? You IDers aim it everything except your own illogical boogeyman alternatives.

You claim that it slices and dices the impossibility of a self-ordering organic compound in a natural universe jam packed with natural gradient producing filters, but the concept of a self-ordered First Designer is ... what? Not causally specific enough to fall down under this same 'logic', under which some find the relative probability of a 'self-ordering first designer' to be greater than the probability of a 'self-ordered organic compound necessary for life?'

That life that makes up about 0.7^10-38 of the visible universe?

@ Fraudiano

darren's picture

You mean, in the absence of any known filter. Like handedness, gravity, any of the field effects.

HANDEDNESS IS NOT A "FILTER" YOU DUMB FUCKALL! "HANDEDNESS" IS A FUCKING REQUIREMENT. There's nothing filtering out the left-handed molecules from the right-handed ones. Outside of living organisms, they're always found mixed -- such mixtures are called "racemic." Look it up. "Gravity" pulls on everything with the same force, twit-brain: one G. It doesn't "filter" -- and if you claim otherwise, then you can fucking well show it. Prove it. Link to it. An article, An editorial. An interview. Anything. Stop inventing data to convince yourself that your deeply held materialist desires are a real scientific hypothesis. They're not. They're just wishful thinking.

Provide evidence of a filter. Don't assume that "there must have been a filter because after all, we're here!" That's a dumbshit argument.

@ Freddie-boo-boo

darren's picture

You never went to Princeton, you dumb shit, you're too fucking stupid. You can't follow an argument, you can't multiply two numbers together, and you can't put simple sentences together in English. You're useless.

(In other words, freddie-boo, you're a model Objectivist.)

Like beads on a string, there

Frediano's picture

Like beads on a string, there is no physical restriction on the order of amino acids: physically, any amino acid has the capability of appearing on any place in the string (just as letters on a piece of paper, or a computer screen, have no physical restriction as to their order).

You mean, in the absence of any known filter. Like handedness, gravity, any of the field effects.

The can has been kicked, from amino acids to 'specificity of order of amino acids.' And when that can is inevitably kicked, let's guess, the can will be safely kicked to 'the human genome' ... in the absence of any known natural filter.

As opposed to, in the absence of any known designer.

Again, your faith in what has never been proven even once, over what has been demonstrated several times(natural filters)is admirable. In church. Where authoritarian 'Rules for God' are curiously -- even in that religious context -- formulated all the time.

But outside of church, it leads to scientific doubt, not certainty.

And, sport, I wasn't the child who totally inappropriately tried to start a pissant shit fight on Ms. Coddington's post about her grandchild by calling some stranger a 'twit.'

Ms. Coddington, I hope you accepted the sentiments expressed in my post in full, and apologize only for illiciting the childish response of this sad little child sullying your thread with his 'twit' hurling. It was best ignored, as is all such immature nonsense, and I did.

He's clearly compensating for something missing in his life with his childish rages. A telethon of some sort might be in order.

Amino acids are created in

darren's picture

Amino acids are created in laboratory
1953

And I assumed the ready-made existence of amino acids in your scenario. Anyway, you're wrong about the importance of the Miller-Urey experiment from the 1950s. They mistakenly assumed a kind of atmosphere that would make it easy to create amino acids with lightning. Turns out that such an atmosphere never existed on the early earth. When they repeated their experiment with the actual sort of atmosphere the geochemists told them had actually existed, they got sludge, not amino acids.

You're a twit, frediano; you make me wince.

I gave you a detailed calculation based on numbers that YOU gave me. If you can't respond to the calculation, then go back to sleep. You're as dumb as a bag of primordial rocks.

@ Marcus

darren's picture

You mean just like a rain forest, diamonds, atoms or the solar system?

Whatever required code, required intelligence. Do diamonds require code? No.

If intelligence is behind the creation and process of life, why not all processes of complexity?

Because not all processes of complexity exhibit the sort precise specificity that life processes do. Lots of complex phenomena can be generated by random events. But nothing highly specific -- such as a specific sequence of letters on a page, or a specific sequence of musical notes, or a specific sequence of amino acids, or a specific sequence nucleotides -- can be generated by randomness. The concept of "specificity" implies that elements in the sequence being studied are unlikely, i.e., occupy positions within the overall sequence that have low probability. Adding noise -- a high-probability occurrence -- to a system in order to perform an experiment in randomness only moves an element that might be occupying a low probability to a position with higher probability -- it makes the system itself noisier and more random; it doesn't impart order and hierarchy.

And if your intelligence is behind them all, how can we be sure of it?

I never claimed that intelligence is behind all phenomena. Just those that are specific enough that odds of generating it by chance are effectively zero.

You admit, I suppose, that to get from a rock to a jet plane requires intelligent input; adding noise to a bunch of rocks will never "evolve" a jet plane, no matter how long we continue to add noise. (Fred Hoyle used the analogy of a tornado in a junkyard creating a Boeing 747.) Well, the gap between mere chemicals and the simplest cell is far greater than the gap between the rock and the jet plane. Francis Crick said so. I believe him. Later in life, Crick advocated panspermia as a better explanation for the origin of life on earth, though he seriously claimed that space aliens invented it. Intelligent input. He understood the limitations of materialism and empirical data collection.

ID was always a zero controversial concept because it was simply an attempt to shoehorn reintroduce the presence of God intelligence, goal-directedness, and teleology into natural material processes that thus far relied on empirical data collected interpreted in such a way as to support natural yet more materialist theories that did not require the presence of a supernatural deity in order that intelligence, goal-directedness, teleology, and Aristotle's old notion of "Final Cause" be expunged from consideration in science altogether - which in of itself is counterproductive to understanding the natural world and impossible unwise to measure ignore or adequately define given the fact that each of us experiences intelligent, goal-directed action all the time and we have no problem recognizing it in other humans when we see it.

There. Fixed it.

Other than documenting...

Frediano's picture

... the unlikelihood of the 'causal specificity'required to emit an 'unknown' First Designer, you claim that the effect of the known(as well as currently unknown)filters are insufficient to guide those experiments.

Your faith in some unknowns -- the existence of miraculously causal specific first Designers -- is greater than your faith in other unknowns -- natural filters -- in the face of evidence of known natural order producing -- gradient producing -- filters -- gravity, electric field magnetic field, handedness and the big one --'What works works.'

What is especially damning --given your very assertive 'Rules for God' claims, is that experiments very similar to what you claim are impossible have long already been demonstrated.

http://www.pbs.org/wgbh/aso/da...

Amino acids are created in laboratory
1953

That's just embarrassing.

So much for the demonstrably flawed analytical skills of fanatical analcysts. Again...did I ask for your help?

You really need to use more caps in your arguments.

You're an existentially terrified child in a rage, abusing science, long ago nailed to the wall by Feynman in his '74 Cal Tech commencement address.

Does your employer know about this public train wreck of logic?

I guess not all crib sheet vendors really care so much.

You wouldn't have liked MIT. They pull the wings off of frauds there just for fun.

Here's me, holding my breath, waiting for you to ever find that out.

As well, I can't wait to hear how your tribe of nuts dreams up their illogical 'Rules for God' to dismiss the Miller-Urey experiments, as well as the subsequent findings. I guess that folks half a century ago didn't have the advantage of 'financial analysis' to tell them what is impossible, as opposed to likely.

Jesus. All those finatical analcyst zeros, shattered by experiments over half a century old.

You really don't want to causally specifically read this.

http://en.wikipedia.org/wiki/M...

'Causal specificity' ... turned into a damn near certainty. Whoda thunk it? Certainly not any TV Evangelists and their crazed flocks of true believers. "Folks, I want you to all to dig deep now, and reach around the back of the Tee-Vee, and I wan't you to FEEEEEEEEEEEEEEL the power! Can you feel it? CAN YOU FEEL IT?"

See how the caps help us all feel the power?

Hallelujah. Sing it, brother.

Where's your dictionary when you really need it, gruntster?

darren's picture

we induce that everything was designed.

LOFL! Fuckhalfwit! The correct word is deduce, not induce.

Man, you really are fucking dumber than a bag of hammers.

"Duh, 2 billion earthlike planets!" (Makes no difference.)

darren's picture

What is a reasonable number for the number of possible earth-like laboratories in the Universe?
2 billion earth like planets, just in our single Milky Way galaxy?
Then, which estimate do we use for the total number of galaxies in the Universe? They range from Hubble's 125 billion to the German simulation's 500 billion.
We readily come to an estimated number like 250 to 1000 x 10^18 earth like planets.
We need to consider what is going on on any one of those singular planets. Is it 'a' experiment? Or like on earth, is it thousands of miles of coastline on myriad seas, billions of tiny crevices in which these serial experiments are being run, subject to what appears to be universally existing filters/bias in the local shake and bake?

Baloney. Here are your numbers you innumerate, illiterate fraud:

10^9 earthlike planets in our galaxy alone (based on nothing but wishful thinking, but let's go with it just to see how it makes zero difference to the end result).

10^11 galaxies in the "known" universe. Assuming 10^9 earthlike planets per galaxy, the total = 10^11*10^9 = 10^20.

Assume each earthlike planet has about the same amount of coastline and "myriad seas" with its "billions of crevices." How many billions of crevices would make you happy, shithead? How about 1,000 billion -- uh, that's a trillion -- per planet, OK? So we have 10^12 crevices per planet, for a total of:

10^20*10^12 = 10^32.

Now, punk, instead of performing mental bukkake on all of us by shouting "Myriad Seas! Myriad Seas! Anything can happen 'cause we got Myriad Seas" why don't you try to attach an actual concrete number to that word "myriad"? You don't have to worry about being too precise, because Sagan makes up his numbers, too.

Let's assume for the sake of calculation that there are 1 billion seas on planet earth -- the more seas, the merrier, right? Because the more seas, the more "experiments" and "filters" there are to make your dumbshit "experiments" and "filters" cough up the kind of answer that will appear to support your "randomist" position. OK? Good.

So 10^9 seas per earthlike planet = 10^32*10^9 = 10^41. That's a nice number, fred. You think 10^41 "experiments" and "filters" are enough to create a highly specific sequence of events necessary for life? Yeah? Ya think? Let's see:

One of the things life as we know it requires is a protein called cytochrome-c. It's "highly conserved" -- found in very similar or even identical sequences across many species in many different kingdoms (single-cell; plant; animal). Like all proteins, it's a sequence -- a "string of beads" -- in which each bead is an amino acid. Like most proteins, the order of the beads on the string is important. (Oh, uh, fred, another way of saying the same thing is "the specificity of the amino acid sequence -- um, to put it into simpleminded Randian terms -- the IDENTITY OF THE SEQUENCE -- is extremely important: without the correct SEQUENCE IDENTITY, there is no functional cytochrome-c and life as we know it wouldn't appear.

Like beads on a string, there is no physical restriction on the order of amino acids: physically, any amino acid has the capability of appearing on any place in the string (just as letters on a piece of paper, or a computer screen, have no physical restriction as to their order).

Below is the amino acid sequence for cytochrome-c of the sunflower. You can check this site for other cytochrome c sequences to get an idea of how similar they are across species:

http://members.cox.net/ardipit...

asfaeapagd / pttgakifkt / kcaqchtvek / gaghkqgpnl / nglfgrqsgt / tagysysaan / knmaviween / tlydyllnpk / kyipgtkmvf / pglkkpqera / dliaylktst / a

Each one of these letters stands for the name of an essential amino acid -- "a" stands for "alanine"; "s" stands for "serine"; "f" stands for "phenylalanine; etc. This cytochrome c chain is 111 amino acids long. (The spaces with the forward-slash are simply for the purpose of dividing up the sequence into easily-seen units of 10.)

For notating long amino acid sequences, it's common to use single-letter abbreviations. See link below for table of abbreviations giving full names of the amino acids:

http://www.buzzle.com/articles...

In your scenario, freddie-boo, we estimated that there would be about 10^41 "experiments" occurring in the universe. Review the calculation if you're unsure how I helped you arrive at a concrete number (and remember, please, that I was especially generous in my assumptions). I'll be more generous still: I'll throw in the existence of all 20 amino acids -- free of charge! You don't have to worry about "evolving" them; let's just assume that they're already in all 10^41 "experiments" in about equal proportions. They're in all those "myriad seas" and "billions of crevices" you sang about.

So now the question is this:

Given 10^41 "experiments", is it likely that chance alone can string 111 beads on a string in the order specified above, given the fact that chemically, there is complete freedom for any bead (that is, amino acid) to occupy any place on the string?

Since any one of 20 amino acids can be in the first position on the string, the odds of an "a" appearing are, of course, 1/20. The odds of an "s" appearing in the second position are also 1/20, making the odds of getting an "a" followed by an "s" 1/20*1/20 = 1/400. Continuing for all 111 amino acids, the odds of obtaining that particular configuration of amino acids are 1/20^111 =

1/20^111 = 1/10^144

In other words, freddie-boop, given 111 beads in a sequence, and a choice of 20 kinds of beads, there are a total of about 10^144 different combinations possible on the string -- and only ONE that matches the sequence for cytochrome c above.

So far, it's not looking good for you. The likelihood of getting that combination of beads on a string are many, many, MANY orders of magnitude smaller than you have laboratories. Just look at the exponents, freddie-boo: ^41 vs. ^144. Forget it.

You have 10^41 farmhands looking through a haystack that has 10^144 strands of hay -- searching for that ONE strand that has significance. Yeah, you have lots of farmhands . . . but not compared to the size of the haystack.

However, it's actually even much, much worse, at least for the case of cytochrome c being found by 10^41 random experiment and filters.

Each bead is not perfectly symmetrical; each one has a "right-handed" form and a "left-handed" form -- called "enantiomers". No physical law prevents a left-handed bead and a right-handed bead from sitting next to each other on the string. The only problem is this: to function properly, the completed necklace must have all left-handed beads -- the right-handed ones can't be used. Since right-handed and left-handed amino acids exist in equal numbers, there is a 50/50 chance (1/2) that only a left-handed amino acid will randomly get chosen to be on the string; and since there are 111 amino acids in all, the odds of each amino acid being a left-handed one are 1/2^111 = 1/10^33.

So the total odds, roughly calculated, of randomly stringing together 111 amino acids to form the cytochrome c we find in sunflowers (and which is very similar to the cytochrome c found in all other species of plant and animal) are about 1/10^144 x 1/10^33 = 1/10^177.

There are about 10^177 different combinations possible with 111 beads sequenced on a string, with 20 different kinds of beads, each having a left-handed and a right-handed variety.

If 10^41 laboratories sprinkled through the universe did nothing but experiment continuously since time began -- 10^10 years ago, or 10^17 seconds ago -- with a random experiment being performed every second, then, to date, you'd only have performed 10^41*10^17 experiments, or 10^58 experiments. Still way, way, WAY too few to plausibly find that one IDENTITY of sequence, out of a possible 10^177 total number of sequences.

And actually, freddie-boo, it's worse than that, since I forgot to add that between one bead and another, a certain "glue" or BOND must exist for the entire protein necklace to work. That bond is a "peptide" bond, and there is no physical necessity for a peptide bond to form just because two amino acids sit next to each other; other kinds of bonds can form, too. So to the final figure, we have to factor in the odds of a peptide bond serendipitously forming between each amino acid in the chain . . . making the odds less than 1 in 10^200. But to make things easy on you, we can stick with the 1/10^177 number.

Finally, even if we assume that each one of your 10^58 experiments was performing not one experiment per second, but 10^45 experiments per second -- the highest number of experiments allowed by quantum physics per second (known as "Planck Time"), your total would only be:

10^58*10^45 = 10^103

177-103=74, or SEVENTY-FOUR ORDERS OF MAGNITUDE LESS PROBABLE THAN ALL OF YOUR FUCKING STUPID "EXPERIMENTS" AND "FILTERS" SPREAD OUT OVER ALL THE EARTH-LIKE PLANETS YOUR DRUG-ADDLED BRAIN CAN FANTASIZE.

You STILL don't have enough resources to find that ONE combination for that ONE enzyme absolutely essential for life.

And we haven't even gotten to DNA CODE or RNA CODE yet! We're just talking about one medium sized protein!

Your "experiments" are failures. You had better hope that those mysterious "filters" you keep harping on are INTELLIGENTLY DESIGNED in a such a way as to purposely seek out specific sequences of beads so that the RIGHT BEAD, with the CORRECT "HANDEDNESS", in the RIGHT ORDER is chosen in each "experiment". Because that's the only way you're going to find that combination.

That was the polite, diplomatic part of my post to you, freddie-boo. Now comes the rest.

You have committed two unpardonable sins:

1. You've bored me. Tsk, tsk. For shame. Inexcusable.

2. Not having many wits to begin with, you unwittingly brought a knife to a gun fight and now -- being a very good shot -- I'm quite simply going to have to blow your mustache off. You see, I've never forgiven you for the execrable -- and ungentlemanly -- way in which you treated Ms. Coddington over the death of her grandchild. She opened herself up to posters on this board, and instead of simply keeping your fat mouth shut, you opened it, removed both of your feet, and made some sort of comment about her mathematics.

So you know what I'm going to do, fuckwit? I'm going to do what you should have done a few weeks ago but were too fucking stupid, socially oafish, and self-involved to have thought of doing:

I'm going to apologize to Ms. Coddington, right here and right now, ON YOUR BEHALF.

And if you object, you know what you can do after I apologize? YOU CAN POST A RETRACTION ON YOUR BEHALF. Go ahead, shit-for-brains; I'd love to see that; retract the apology I'm making for you.

Buy new cartridges for your printer, you miserly son-of-a-bitch, and print this out and stick it on your fridge.

* * * * * * * * * * * * * * * * * *
Dear Ms. Coddington,

On behalf of a ghastly and disgraceful lapse of judgment on the part of a senile poster calling himself, at times, "Fred", at other times, "Frediano", I offer not only sincerest apologies for his unconscionable lack of courtesy toward you during what must have been -- and continues to be -- an extremely painful experience for you, your daughter, and your family, but I offer my own apologies for not having done this sooner, as well as my own deepest condolences.

Cordially,

Darren Q. Wrede

* * * * * * * * * * * * * * * * * *

Go ahead, freddie-boo. Retract it. You should have made this apology yourself.

And you can take this entire post, chop it up on your mirror, and snort it, you foolish old coke-head.

Darren

Leonid's picture

"Not without employing the stolen concept fallacy. I agree that something exists independently of consciousness but we can't call them "objects."

This is pure Kant. You basically postulate two realities. But there is no dichotomy between object and its perception. Validity of senses and perception is axiomatic. Deny it, and any further discussion about anything would be meaningless. We experience object as it is in accordance to law of identity and causality. Puffs of meta-energy which constitute tomato IS tomato and nothing else.

Incidentally you didn't answer my original question:how the premise of god, intelligent designer or big codifier in heaven could have any explanatory power when we in principle cannot know anything about this entity, nor we can learn its modus operandi. The only thing one can say about it that it moves in mysterious ways.

" the fossil record overwhelmingly shows stasis punctuated by sudden change;"

Here is another proof that properties emerged not in the process of slow cumulative changes but as result of self-organization during the critical phase of organism's existence.

"It was intelligence."

Marcus's picture

You mean just like a rain forest, diamonds, atoms or the solar system?

If intelligence is behind the creation and process of life, why not all processes of complexity?

And if your intelligence is behind them all, how can we be sure of it?

In the absence of intervention we effectively have no null hypothesis.

It becomes an article of faith. You have to believe it is everywhere because you can't find its absence.

It then becomes a zero concept.

ID was always a zero concept because it was simply an attempt to shoehorn the presence of God into natural processes that thus far relied on empirical data collected to support natural theories that did not require the presence of a supernatural deity - which in of itself is counterproductive to understanding the natural world and impossible to measure or adequately define.

The concept of a supernatural deity or intelligence will always occupy that space it has always done throughout the ages where it can thrive. That is the space of human ignorance. Yesterday the origin of man, today the origin of life, tomorrow the origin of the universe.

Intelligent design = Ignorant evasion.

No surprise here

Frediano's picture

Ah I see. 'Specificity,'... not 'complexity.'

Damn. I thought we randoms had the existential paradox nailed, until you unleashed the verbal might that is 'specificity.'

This magic talisman must sell well at the 'financial analysts' conventions along with 'synchronicity,' 'synergism' and 'kick ass ninja costumes.'

Remember when 'Six Sigma' was the rage?

Move over 'Six Sigma.' 'Specificity' has arrived to wow the wowable.

Thank you for the mirth. It's been.

Back to your voodoo arithmetic.

And, I think you meant to parrot 'causal specificity.' As in, that which IDers demand of science, but not of their own boogeyman alternatives.

For a glaring hint at where this 'causal specificity' ID argument comes from, compare any article mentioning same to this soure. http://www.elsewhere.org/pomo/ and the can't miss it similarities to the 'argument.'

The 'causal specificity' in this instance is a few lines of code...

I'm converted

gregster's picture

I get it now. Because cars and boats were designed by us intelligent humans - we induce that everything was designed. Fuck me. It's taken me all this time. Thank you Dazzler.

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