Saturday, July 24, 2010

Everything I Know About RNA I Learned From Bill Murray


I love metaphor, analogy, and Bill Murray (oh my gosh Dr. Leo -- you're the greatest!).  So, I gotta love this quote embedded inside a serious science article:

"It's a molecular groundhog day".  (Shouldn't that be "molecular Groundhog Day"?

Why Evolution is True:

"Short of positing celestial design, the only way to explain optimization is via the workings of selection. If so, the code of life must have evolved."

This is the circularity of darwinian assumptions applied to origins of life. "If it wasn't created, it must have evolved. Created is not a scientific explanation. Since science is the only way of eliciting reality, evolution must true. Evolution-is-true proves creationism false!"

But, there are disturbances in the force. Another metaphor:

"Effectively, RNA can't see past its own nose and is never going to generate complexity in a solution."

Ha! O faithless one. This one is simple. The RNA first evolves a Pinnochio-sized nose.

Next?  "This is a chicken-and-egg situation just as ineluctable as the DNA-protein loop, albeit less celebrated. (p. 54)"

I'm gonna let noted evolutionist Paul McCartney take this one. "There will be an answer. Let it be."

The answer comes "...in a fluke of fortune bordering on the unbelievable, it might be that both the bacteria and archaea emerged from the very same hydrothermal mound."

This is the state-of-the-evolutionary-assumpted-science. A scientific description which resorts to using the words fluke and unbelievable.

An unbelievable fluke (i.e., the scientific approach) or intelligent design (i.e., the unscientific, superstitious, bone-headed creationist approach).

There will be an answer. Let it be.

PS - Jonathan. I couldn't dig out the quote I was thinking of on RNA world problems, but this article will do.

25 comments:

xn--hrfn-woa said...

"This is the circularity of darwinian assumptions applied to origins of life."

Ah, the standard creationist whine.

This is NOT a "darwinian assumption", it is part of the basic assumptions necessary to do ANY meaningful science. This is because:

1) You cannot test the hypothesis of "celestial design".

2) "Posit[ing] celestial design" leads to no useful predictions.

3) It is impossible to distinguish between the effects of "celestial design" and some unknown natural agency, or some unanticipated combination of known natural agencies.

4) It is impossible to distinguish between the effects of "celestial design" and the effects of some other supernatural agency (demiurgic design, diabolical design, the actions of the Tao, etc, etc).

As "posit[ing] celestial design" serves no scientific purpose, it is ruled out as allowing no concrete answers, merely a lot of answerless philosophical musing. If you want the latter, then you're welcome to read a book on philosophy, rather than one on science.

xn--hrfn-woa said...

Likewise science refuses to entertain the hypothesis that the world was created last Tuesday, with a false history, false memories, etc (a hypothesis known as 'Last Tuesdayism', created as an argumentum ad absurdum extension of the Omphalos hypothesis), because such a hypothesis is untestable (and impossible in practice to distinguish from either Last Thursdayism and "celestial design").

RkBall said...

Nothing you have said dispenses with the circularity of reasoning that I caricaturized.

RkBall said...

1) You cannot test the hypothesis of "celestial design".

Then why do darwinists say that they have produced evidence which falsifies it?

xn--hrfn-woa said...

"Nothing you have said dispenses with the circularity of reasoning that I caricaturized."

Given that you simply assert, WITHOUT ANY EVIDENCE WHATSOEVER that "circularity of reasoning" exists, I see no point in addressing it.

I would further point out that you likewise don't "posit "demiurgic design, diabolical design, the actions of the Tao, etc, etc", so your own logic is very closely as purportedly 'circular' as Lane's own.

"Then why do darwinists say that they have produced evidence which falsifies it?"

Given that you neither specify (i) exactly what they said & (ii) in what context they said it, HOW THE HADES DO YOU EXPECT ME TO SAY "WHY" THEY SAID WHATEVER THEY ACTUALLY SAID?

I actually very much doubt if they said any such thing. Most design claims are unfalsifiable. It's only where you get into YEC claims, such as the age of the Earth, the Genesis flood, etc, that creationism makes falsifiable (and centuries-falisfied) claims.

More likely they stated such things as that the design claims were unsubstantiated, unscientific, based upon flawed logic, etc. This is not the same as stating that they're unfalsfiable.

xn--hrfn-woa said...

Correction, final sentence should read "This is not the same as stating that they're falsfied."

xn--hrfn-woa said...

"Then why do darwinists say that they have produced evidence which falsifies it?" is what is known as a "loaded question", as it assumes a claim (that "darwinists say that they have produced evidence which falsifies it") that the questionee (i.e. me) disputes.

The most commonly cited version of such a question is "have you stopped beating your wife yet?"

RkBall said...

I'm thinking of the claims that Behe's claims of irreducible complexity have been refuted -- usually by nothing more than, "it could have, conceivably, possibly, happened this way".

BTW, I think Behe is wrong in trying to address Darwin's challenge. All one has to do is come up with something that is not impossible -- no matter how improbably -- and Behe is refuted.

A good example is this post -- "a fluke of fortune bordering on the unbelievable" is not impossible, and therefore, by Darwin's challenge, his theory is not refuted!

RkBall said...

You can test the hypothesis of intelligent design, without speculating further on the name or nature of the intelligent agent.

xn--hrfn-woa said...

Wrong, wrong, WRONG

1) Irreducible complexity, is not identical to intelligent design, merely an argument for it. Therefore that IC has been found to be a logically invalid argument does not falsify ID.

2) Given the level of equivocation involved in IC, it is not clear that even IC is falsifiable -- it may simply be insufficiently precisely defined to be falsifiable. Rather than test it and falsify it, really all scientists can do is present holes in its underlying logic, and demonstrate how specific examples of purportedly IC systems might evolve.

"You can test the hypothesis of intelligent design, without speculating further on the name or nature of the intelligent agent."

Please state what this test of "the hypothesis of intelligent design" (as opposed to the arguments of IC, complexed specified information, etc) is. Please demonstrate that this test is practical (i.e. does not involve doing something impossible to falsify ID). Please specify how this a result of this test would unambiguously falsify the hypothesis (i.e. result A clearly means that ID is false).

Your quoted statement is simply a bare, unsubstantiated, assertion. As such it is worthless, until you substantiate it.

jonathan said...

**WARNING: THIS WILL BE A LONG POST**

I have serious issues with the Discovery Institute articles and authors. The individuals who write for them could not be any more wrong or any more incompetent when it comes to verifying information. It would also behoove them to read up on the latest findings instead of relying on outdated scientific articles, that by the way were not meant to prove anything.

Chapter 1 - The Origin of Life

"However, numerous problems abound for the hydrothermal vent hypothesis for the origin of life, as will be discussed in more detail later in this review. For example, as Stanley Miller has pointed out, the polymers are "too unstable to exist in a hot prebiotic environment." Miller has also noted that the RNA bases are destroyed very quickly in water when the water boils. Intense heating also has the tendency to degrade amino acids such as serine and threonine. A more damning problem lies in the fact that the homochirality of the amino acids is destroyed by heating."

I do hate to say that Stanley Miller was/is wrong because it is due to him, his experiment based off of Alexander Oparins theory, that research into abiogenesis took off, BUT he is wrong about the "polymers are "too unstable to exist in a hot prebiotic environment." In fact, the author of that article in Discovery Institute apparently disregarded in any new scientific findings completely. Here's the abstract of a RECENT peer reviewed article.

"Generation of Long RNA Chains in Water*:
The synthesis of RNA chains from 3 ,5 -cAMP and 3 ,5 -
cGMP was observed. The RNA chains formed in water, at
moderate temperatures (40–90 °C), in the absence of enzymes
or inorganic catalysts. As determined by RNase analyses,
the bonds formed were canonical 3 ,5 -phosphodiester
bonds. The polymerizations are based on two reactions not
previously described: 1) oligomerization of 3 , 5 -cGMP to
25-nucleotide-long RNA molecules, and of 3 ,5 -cAMP to 4-
to 8-nucleotide-long molecules. Oligonucleotide A molecules
were further extended by reciprocal terminal ligation to yield
RNAmolecules up to>120 nucleotides long and 2) chain extension
by terminal ligation of newly polymerized products of 3 ,5 -
cGMP on preformed oligonucleotides. The enzyme- and template-
independent synthesis of long oligomers in water from
prebiotically affordable precursors approaches the concept of
spontaneous generation of (pre)genetic information."

That was done in 40-90 degree C water, which is in the range of 104-194 degree F. So there are the first two major inaccuracies in the Discovery Institues article and I've barely even put my toes in the water, let's see what happens when I put my foot in.

Chapter 2 - The Origin of DNA

"This means that several codons can code for the same amino acid. Such a choice of genetic code is not arbitrary, but seemingly the product of rational scheming, such that the cell would be optimally protected from the detrimental effects of substitution mutations."


This is an illogical assumption. The seemingly 'appearance' of a product of rational scheming is that it is the human brains 'need' to find meaning in unmeaningful patterns and associate them to some sort of unknown. These non-arbitrary genetic codes would have been the results of natural phenomenon that would define how the chemicals acted/reacted. This would not just happen to them one at a time, but to multiples at a time. The result would be the ones that replicated better or faster would have an advantage and with combination to other replicants would eventually lead to the most effecient path. It's about effeciency, not about what seems to be rational scheming; it should also be noted that some chemicals are intrinsically predisposed to other chemicals which would speed up the process of effecient matching.

jonathan said...

PART 2:

"Hubert Yockey, a biophysicist and information theorist, has argued that the number of potential genetic codes is of the order of 1.40 x 1070. Yockey concedes the extremely conservative figure of 6.3 x 1015 seconds for the time available for the genetic code to evolve. Note that this assumes that the genetic code has been evolving since the Big Bang."

Firstly, I would like to know why he thinks the genetic code has been evolving since the Big Bang, which is the beginning of matter but not the beginning of life. This in itself is illogical and is absolutely false. Secondly, if the author of the journal were to do any sort of research he would find that most scientists have ignored his ramblings as many of them are based off of ill conceived or illogical assumptions. If you want to know why you can visit:

http://richardcarrier.blogspot.com/2006/11/yockey-on-biogenesis.html

The authors other musings on mathematical improbabilities are just as illogical as Hubert's so I'm going to go ahead and jump into his misunderstandings of RNA.

"Even conceding that such a system is plausible (and ignoring the lack of an explanation for the transition from an RNA-based system to a DNA-based system), the proposal still fails to account for the origin of the sequential arrangement of the chemical constituents of the RNA molecule."

The explanation is probably more on the path of stability and effeciency, but the 'chemical constituents of the RNA molecule' are exactly that, CHEMICALS. They behave in a certain way based off of the thermodynamic, geothermic, and chemical mechanisms that have governed our universe since its beginning. There is no need for a 'designer' to assemble these pieces into what he thinks may or may not be meaningful code.

"For example, the formation of the first RNA molecule would have required the prior emergence of smaller constituent molecules, including ribose sugar, phosphate molecules, and the four RNA nucleotide bases. However, it turns out that both synthesizing and maintaining these essential RNA building blocks -- especially ribose -- and the nucleotide bases is a very difficult task under origin-of-life conditions."

If he would have just looked around instead of going off of his presupposed notions.

Ribose - An aldol reaction of glycolaldehyde and glyceraldehyde would produce the puranose form of Ribose which can subsequently be turned into the furanose form of Ribose; these two forms can convert back and forth.

Phosphate- This would have already been abundant on a prebiotic earth.

RNA Nucleobases - Cytosine, Uracil, Adenine, Guanine. These four nucleobases are seperated into two groups: pyrimidines and purines. The pyrimidines are Cytosine and Uracil and the purines are Adenine and Guanine. The pyrimidines are chemically attracted to purines as purines are chemically attracted to pyrimidines, which means pyrimidines will only attach to purines. These nucleobases have been synthesized in their own forms in experiments that were based off of a pre-biotic earth.

What I have stated above is what a lot of people have believed when it comes to ribonucleotide formation; that you would combine a ribose, phosphate and nucleobase to get a ribonucleotide. This, NOT being a very difficult task as the author states, but rather produces very low yields of activated ribonucleotides. If the author would have actually done any research, and it wouldn't have been hard to find this one, he would have found that as recently as May 2010 scientists found a more effecient, greater yield producing path to activated ribonucleotide synthesis. This new pathway produces much better yields and would solve both problems of a continous stream of ribonucleotides and the illogical fallacy of mathematical probabilities of nucleotide synthesis. I have the peer reviewed journal that explains all of this in GREAT detail, along with supplemental information on its chemistry if you would like to verify it. Moving on.

jonathan said...

Part 3:

"There also exists the difficulty that naturally occurring RNA molecules possess very few of the specific enzymatic properties of proteins. Ribozymes can perform a small handful of the thousands of functions performed by proteins."

http://www.sciencedaily.com/releases/2010/02/100222162009.htm

That shatters the authors contentions.

"However, as noted previously, problems abound for this hypothesized account. For example, at 100 degrees Centigrade (the boiling point of water), the half lives of the nucleic acids Adenine and Guanine are 1 year. The half life of Uracil and Cytozine is 12 years and 19 days respectively. Remember that in hydrothermal vents the temperatures would be much higher than this. Such short-lived molecules could never be stockpiled in the way in which Lane envisions."

This is if you believe that life formed directly on said vents. If could have easily existed in the 40-90 degree C zone above the thermal vents which would adequately allow it to exist and would allow theromdynamic and geothermic mechanisms to do their work. Also, think about this, if the half life Adenine and Guanine is one year then this is significant time for nucleobases to be incorporated. It will not be the only base made as other bases will be in the middle of being developed as illustrated earlier above. Establishing time frames as evidence of its immposibility is irrational as it implies that these bases will be the only ones made and completely disregards the entire process of abiogenesis.

"But there is a further, and even more damning, problem with Lane's proposed solution. If the origin of life took place in an aqueous solution of pre-biotic monomers (as Lane's proposal maintains), then -- according to Le Chateliers Principle -- the presence of a product (water, in this case) will slow the reaction. It is not possible to polymerize an appreciable amount of monomers into polymers in an aqueous solution (where water acts as the solvent). Thus, the necessary polymerization step in the reaction could not take place in water."

Once again, the authors inability to research leaves him completely ignorant on the topic. I refer you to the already pointed out article: Generation of Long RNA Chains in Water*. You can google it, or if you want the peer reviewed journal I have it as well, but notice that its title 100% contradicts what the author is saying.

I'm going to stop here. The rest of the authors article is littered with false hoods and misunderstandings while at the same time using out dated information and information that is predisposed to his bias. So in summary, he is wrong. (insert Dr. Cox from Scrubs singing his wrong song). If you have any questions on anything specific feel free to ask, but please be skeptical when you read Discovery Institutes articles as they are usually, incredibly, awfully wrong.

RkBall said...

Jonathan:

1. I appreciate you taking the time to post.
2. You know a lot more and a lot deeper science than I do -- I cannot refute or argue with a single thing you say.

When you talk about the "author" are you referring to the poster of the blog item --DI's Jonathan Latchie, or to Nick Lane, the author whose book is being reviewed?

If Nick Lane:

1. He is.... Aw, let me do a fresh post on this. If you're right, and I have no reason to believe you are not, you should be the one writing books.

(this is a compliment.)

I'm going to do a new post on this.

xn--hrfn-woa said...

It's perfectly clear that Jonathan is referring to Jonathan Latchie, who is the only author at issue who is associated with the DI.

jonathan said...

Xn is correct. I have no issues with Nick Lane as I have the book in discussion at home. It is really a good book and for anyone who feels vexed about evolution, or biology for that matter, would definately learn a lot from it. Nick's statements about the beginnings of life are pretty spot on, it's just that he did not have the ability to incorporate the newest findings into a book that he wrote prior to them coming out; which is a pox for everything. Now Jonathan Latchie from the DI did pick and choose from those certain chapters and when he did that he made it seem that Nick was wrong, so it was Jonathan Latchie being disengenous. 10 Greatest Inventions is a good book, go read it.

RkBall said...

"These non-arbitrary genetic codes would have been the results of natural phenomenon "

Would have or could have?

RkBall said...

"Firstly, I would like to know why he thinks the genetic code has been evolving since the Big Bang, "

The article indicates he did so not because he believes the genetic code has been evolving since the Big Bang but to be generously conservative in his calculation.

RkBall said...

I read the Carrier article. Found it philosophically slanted, which is fine since everyone has philosophical assumptions they employ, even in science.

"than the necessary outcome of physical conditions, since the probability of the latter is always high, no matter how complex it appears. Certain aspects of protein structure fall into this category."

"The necessary outcome of physical conditions". Soon as a person moves to the "necessity" side of the equation, rather than chance, they are moving onto ground that is at least amenable to the theist. Science may describe, but cannot explain.

I.e., why are the laws of physics, chemistry, biology the way the are? They themselves require a sufficient cause.

RkBall said...

"They behave in a certain way based off of the thermodynamic, geothermic, and chemical mechanisms that have governed our universe since its beginning. There is no need for a 'designer' to assemble these pieces into what he thinks may or may not be meaningful code."

I'm not going to disagree with you. I don't think ID is necessary (for theism). But the laws themselves which you have so eloquently said have governed our universe since its beginning themselves require explanation.

I think I'll post on this too, so you might want to wait before commenting.

RkBall said...

http://www.sciencedaily.com/releases/2010/02/100222162009.htm

A great article. Thanks for the reference.

I will note the article assumes "directed" evolution.

" the chances are much greater that RNA could direct and accelerate biochemical reactions under primitive conditions."

As always, the language of intention, direction, design!

RkBall said...

J. I think the Discovery Institute should hire you on as a "Devil's Advocate" (if you will excuse the term!).

xn--hrfn-woa said...

Rick:

Why would they hire a devil's advocate, when they ignore so assiduously the many (and often very knowledgeable) ones they have long gotten for free?

RkBall said...

One reason, it's hard to separate out the smears and jeers and philosophical biases of typical DI criticisms from legitimate critiques.

xn--hrfn-woa said...

Rick:

It's the "legitimate critiques" that they try hardest to ignore. The "smears and jeers" they can at least spin as "help, help, I'm being repressed" whinges of faux-persecution.

"... nothing intellectually compelling or challenging.. bald assertions coupled to superstition... woefully pathetic"