Abiogenesis: Is the RNA hypothesis dead?

Minerva

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Wow, that's a r e a l l y long article...but the intro gave a very smooth exaplanation...I'll have to read it later...
 

bob b

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Here is the creationsafari commentary on the Scientific American article by Dr. Robert Shapiro:

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OOL on the Rocks 02/15/2007
An important survey of the origin-of-life (OOL) field has been published in Scientific American. Robert Shapiro, a senior prize-winning chemist, cancer researcher, emeritus professor and author of books in the field, debunks the Miller experiment, the RNA World and other popular experiments as unrealistic dead ends. Describing the wishful thinking of some researchers, he said, “In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry.”
Shapiro had been explaining that millions of organic molecules can form that are not RNA nucleotides. These are not only useless to life, they get in the way and clog up the beneficial reactions. He went on to describe how extrapolation from the Miller Experiment produced an unearned sense of euphoria among researchers: “By extrapolation of these results, some writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case,” he warned in a section entitled, “The Soup Kettle Is Empty.” He said that no experiment has produced amino acids with more than three carbons (life uses some with six), and no Miller-type experiment has ever produced nucleotides or nucleosides, essential for DNA and RNA.
Shapiro described in some detail the difficult steps that organic chemists employ to synthesize the building blocks of RNA, using conditions highly unrealistic on the primitive earth. “The point was the demonstration that humans could produce, however inefficiently, substances found in nature,” he said. “Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA.” Here, for instance, is how scientists had to work to create cytosine, one of the DNA bases:

"I will cite one example of prebiotic synthesis, published in 1995 by Nature and featured in the New York Times. The RNA base cytosine was prepared in high yield by heating two purified chemicals in a sealed glass tube at 100 degrees Celsius for about a day. One of the reagents, cyanoacetaldehyde, is a reactive substance capable of combining with a number of common chemicals that may have been present on the early Earth. These competitors were excluded. An extremely high concentration was needed to coax the other participant, urea, to react at a sufficient rate for the reaction to succeed. The product, cytosine, can self-destruct by simple reaction with water. When the urea concentration was lowered, or the reaction allowed to continue too long, any cytosine that was produced was subsequently destroyed. This destructive reaction had been discovered in my laboratory, as part of my continuing research on environmental damage to DNA. Our own cells deal with it by maintaining a suite of enzymes that specialize in DNA repair."

There seems to be a stark difference between the Real World and the imaginary RNA World. Despite this disconnect, Shapiro describes some of the hype the RNA World scenario generated when Gilbert first suggested it in 1986. “The hypothesis that life began with RNA was presented as a likely reality, rather than a speculation, in journals, textbooks and the media,” he said. He also described the intellectual hoops researchers have envisioned to get the scenario to work: freezing oceans, drying lagoons, dry deserts and other unlikely environments in specific sequences to keep the molecules from destroying themselves. This amounts to attributing wish-fulfillment and goal-directed behavior to inanimate objects, as Shapiro makes clear with this colorful analogy:

"The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck."

Realistically, unfavorable molecules are just as likely to form. These would act like terminators for any hopeful molecules, he says. Shapiro uses another analogy. He pictures a gorilla pounding on a huge keyboard containing not only the English alphabet, but every letter of every language and all the symbol sets in a typical computer. “The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne.” That’s why Gerald Joyce, Mr. RNA-World himself, and Leslie Orgel, a veteran OOL researcher with Stanley Miller, concluded that the spontaneous appearance of chains of RNA on the early earth “would have been a near miracle.”

Boy, and all this bad news is only halfway through the article. Does he have any good news? Not yet; we must first agree with a ground rule stated by Nobel laureate Christian de Duve, who called for “a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry.” That rules out starting with complex molecules like DNA, RNA, and proteins (see online book).

From that principle, Shapiro advocated a return to scenarios with environmental cycles involving simple molecules. These thermodynamic or “metabolism first” scenarios are only popular among about a third of OOL researchers at this time. Notable subscribers include Harold Morowitz, Gunter Wachtershauser, Christian de Duve, Freeman Dyson and Shapiro himself. Their hypotheses, too, have certain requirements that must be met: an energy source, boundaries, ways to couple the energy to the organization, and a chemical network or cycle able to grow and reproduce. (The problems of genetics and heredity are shuffled into the future in these theories.)

How are they doing? “Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them,” Shapiro admits. “In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle.” In addition, “An understanding of the initial steps leading to life would not reveal the specific events that led to the familiar DNA-RNA-protein-based organisms of today.” Nor would plausible prebiotic cycles prove that’s what happened on the early earth. Success in the metabolism-first experiments would only contribute to hope that prebiotic cycles are plausible in principle, not that they actually happened.

Nevertheless, Shapiro himself needed to return to the miracles he earlier rejected. “Some chance event or circumstance may have led to the connection of nucleotides to form RNA,” he speculates. Where did the nucleotides come from? Didn’t he say their formation was impossibly unlikely? How did they escape rapid destruction by water? Those concerns aside, maybe nucleotides initially served some other purpose and got co-opted, by chance, in the developing network of life. Showing that such thoughts represent little more than a pipe dream, though, he admits: “Many further steps in evolution would be needed to ‘invent’ the elaborate mechanisms for replication and specific protein synthesis that we observe in life today.”

Time for Shapiro’s grand finale. For an article predominantly discouraging and critical, his final paragraph is surprisingly upbeat. Recounting that the highly-implausible big-molecule scenarios imply a lonely universe, he offers hope with the small-molecule alternative. Quoting Stuart Kauffman, “If this is all true, life is vastly more probable than we have supposed. Not only are we at home in the universe, but we are far more likely to share it with unknown companions.”

Update Letters to the editor appeared in Science1 the next day, debating the two leading theories of OOL. The signers included most of the big names: Stanley Miller, Jeffrey Bada, Robert Hazen and others debating Gunter Wachtershauser and Claudia Huber. After sifting through the technical jargon, the reader is left with the strong impression that both camps have essentially falsified each other. On the primordial soup side, the signees picked apart details in a paper by the metabolism-first side. Concentrations of reagants and conditions specified were called “implausible” and “exceedingly improbable.”

Wachtershauser and Huber countered that the “prebiotic soup theory” requires a “protracted, mechanistically obscure self-organization in a cold, primitive ocean,” which they claim is more improbable than the volcanic environment of their own “pioneer organism” theory (metabolism-first). It’s foolish to expect prebiotic soup products to survive in the ocean, of all places, “wherein after some thousand or million years, and under all manner of diverse influences, the magic of self-organization is believed to have somehow generated an unspecified first form of life.” That’s some nasty jabbing between the two leading camps.
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1Letters, “Debating Evidence for the Origin of Life on Earth,” Science, 16 February 2007: Vol. 315. no. 5814, pp. 937 - 939, DOI: 10.1126/science.315.5814.937c.
 

Skeptic

New member
bob b said:
From the article:
Yet the clues I have cited only support the weaker conclusion that RNA preceded DNA and proteins; they provide no information about the origin of life, which may have involved stages prior to the RNA world in which other living entities ruled supreme.

... Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them. In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle.

... A success might demonstrate the initial steps on the road to life. These steps need not duplicate those that took place on the early Earth. It is more important that the general principle be demonstrated and made available for further investigation. Many potential paths to life may exist, with the choice dictated by the local environment.

An understanding of the initial steps leading to life would not reveal the specific events that led to the familiar DNA-RNA-protein-based organisms of today. However, because we know that evolution does not anticipate future events, we can presume that nucleotides first appeared in metabolism to serve some other purpose, perhaps as catalysts or as containers for the storage of chemical energy (the nucleotide ATP still serves this function today). Some chance event or circumstance may have led to the connection of nucleotides to form RNA. The most obvious function of RNA today is to serve as a structural element that assists in the formation of bonds between amino acids in the synthesis of proteins. The first RNAs may have served the same purpose, but without any preference for specific amino acids. Many further steps in evolution would be needed to "invent" the elaborate mechanisms for replication and specific protein synthesis that we observe in life today.

If the general small-molecule paradigm were confirmed, then our expectations of the place of life in the universe would change. A highly implausible start for life, as in the RNA-first scenario, implies a universe in which we are alone. In the words of the late Jacques Monod, "The universe was not pregnant with life nor the biosphere with man. Our number came up in the Monte Carlo game." The small-molecule alternative, however, is in harmony with the views of biologist Stuart Kauffman: "If this is all true, life is vastly more probable than we have supposed. Not only are we at home in the universe, but we are far more likely to share it with unknown companions."
Ahh, the beauty of science. ..... There will likely be many more paradigm shifts as scientists study the natural origin of life.

Professor Shapiro has not given up on the ability of science to understand the principles that led to the natural origin of life. .... You have, Bob. ... That's one reason you are so anti-science.
 

bob b

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Skeptic said:
From the article: Ahh, the beauty of science. ..... There will likely be many more paradigm shifts as scientists study the natural origin of life.

Professor Shapiro has not given up on the ability of science to understand the principles that led to the natural origin of life. .... You have, Bob. ... That's one reason you are so anti-science.

I am continually being lectured by people that science is tentative and that new evidence may cause one to change one's mind.

All well and good.

Shapiro has devoted his entire professional career to the proposition that life arose naturally.

It is perfectly natural under such circumstances that he would retain his faith in that proposition as long as humanly possible.

I have nothing to lose by placing my faith on the much more favorable hypothesis that life did not arise naturally bur instead was specially created by God.

Let us just say that my tentative conclusion is that life did not arise naturally.

Therefore I will place my faith in God until the very lower probability that life arose naturally is shown to be true by science.
 

Skeptic

New member
bob b said:
Here is the creationsafari commentary on the Scientific American article by Dr. Robert Shapiro:

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"... Didn’t he say their formation was impossibly unlikely?"
No, he did not say that.

Something cannot be both impossible and unlikely. :kookoo:

"... After sifting through the technical jargon, the reader is left with the strong impression that both camps have essentially falsified each other.
:rotfl: ... Hardly.

The author's rhetoric employs a misleading mischaracterization of terms.
 

Skeptic

New member
bob b said:
I am continually being lectured by people that science is tentative and that new evidence may cause one to change one's mind.

All well and good.
Do you admit that new evidence could hypothetically change your mind, meaning that you could someday regard abiogenesis as plausible?

Shapiro has devoted his entire professional career to the proposition that life arose naturally.
Considering the fact that there is no evidence whatsoever that life arose supernaturally, his career choice is much more likely to lead to useful discoveries than the career of those who choose to spend their lives proselytizing unfounded supernaturalistic hypotheses.

It is perfectly natural under such circumstances that he would retain his faith in that proposition as long as humanly possible.
Faith is belief despite the absence of evidence. ... Since there is plenty of evidence suggesting that life could have arisen naturally, and no evidence that life that life could have arisen supernaturally, it is clear that the supernaturalists are the ones who retain faith.

I have nothing to lose by placing my faith on the much more favorable hypothesis that life did not arise naturally bur instead was specially created by God.
What you have to lose is your rationality.

There is no rational empirical support for the claim that your supernatural hypothesis is "more favorable."

Do you think your supernatural hypothesis is "more favorable" because you cannot conceive of any natural processes leading to the origin of life?

Let us just say that my tentative conclusion is that life did not arise naturally.
You're treading on slippery back-sliding ground there, Bob!

Shouldn't you watch it with those unfaithful comments about the tentativeness of your conclusions? .... Do you really think your God appreciates such tentativeness in His Holy Word?

Therefore I will place my faith in God until the very lower probability that life arose naturally is shown to be true by science.
Bob, now that you have declared your view tentative, which means your final conclusion hinges on the evidence, not on the alleged "Word of God", what kind of empirical evidence could lead you to the view that life probably (if not certainly) arose naturally?
 

bob b

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Skeptic,

I composed my prior posting in haste because someone was calling to me to come help them with something.

I should have worded it somewhat differently.

I have been following the abiogenesis subject for quite a while, even before I got interested in the Bible and Christianity again.

My first brush with it was the book, The Origin of Life by Operin. I felt that his case was weak.

Later I obtained books by Shapiro and others. Their case was equally weak, actually weaker than Operin's because by this time more had been learned about cells.

In the past 7 years research into cells has accelerated. Some of it is presented in the thread "Cell Trends Too". At the same time research into abiogenesis has shown that some once popular theories like "RNA first" are not as feasible as once thought.

The net effect is that the goal of demonstrating abiogenesis has become a receding target.

I was kind of joshing you by suggesting that I think that there is even a very remote possibility that life arose naturally.

Sorry for my weak attempt at humor. If you knew me better you would realize that I have a strange sense of humor which many people do not "get". I should listen to my wife who tells me not to act like I am serious when telling somebody something outrageous (like there is a possibility that abiogenesis might be true).
 

Skeptic

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bob b said:
My first brush with it was the book, The Origin of Life by Operin. I felt that his case was weak.

Later I obtained books by Shapiro and others. Their case was equally weak, actually weaker than Operin's because by this time more had been learned about cells.
Does the existence of weak cases imply the impossibility of strong cases?

In the past 7 years research into cells has accelerated. Some of it is presented in the thread "Cell Trends Too". At the same time research into abiogenesis has shown that some once popular theories like "RNA first" are not as feasible as once thought.
Scientific abiogenesis research is in its infancy. The next few hundred years of research in this area could be very interesting.

The net effect is that the goal of demonstrating abiogenesis has become a receding target.
Hardly. :rotfl:

I was kind of joshing you by suggesting that I think that there is even a very remote possibility that life arose naturally.
What is your empirical basis for claiming that there is not even a remote possibility that life could have arisen naturally?

In order to make such a bold claim, you must have an air-tight body of scientific research that confirms beyond any shadow of a doubt that the natural origin of life is impossible. Please cite those studies that confirms with 100% certainty that life could never have arisen naturally.

It's too bad you abandoned your tentativeness so quickly with regard to future evidence, Bob. ... Now, no one should have any serious doubts about how anti-science you really are.
 

bob b

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I really wonder sometimes why a person like skeptic who believes that when we die that's the end of it, would waste his short precious time on this Earth arguing with Christians that they should not believe anything unless it has been proven to be true by science.

Which of course would automatically rule out ever believing in God, because he admits that science cannot deal with the question of God.

Go figure.
 

Skeptic

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bob b said:
I really wonder sometimes why a person like skeptic who believes that when we die that's the end of it, would waste his short precious time on this Earth arguing with Christians that they should not believe anything unless it has been proven to be true by science.

Which of course would automatically rule out ever believing in God, because he admits that science cannot deal with the question of God.

Go figure.
I really wonder sometimes why a person like Bob, who believes that, when we die, our alleged soul spends eternity with an alleged supernatural entity with a personality, would waste his short precious time on this Earth arguing with evolutionists that they should not believe that life evolved naturally, because the Genesis story is literally true, even though he has no evidence that this is the case.

Which of course would automatically prevent him from allowing for the possibility that his Biblical fairy tales and superstitions are just that.

Go figure.
 

writer

New member
14

14

14 ...life evolved naturally,
Evolution's not natural.
Evolution isn't.

...the Genesis story is literally true, even though he has no evidence that this is the case.
you're evidence.
You're a wonderful being.
Made in your Creator's image.
For to contain Him,
should you be willing

...allowing for the possibility that his Biblical fairy tales and superstitions are just that.
Evolution and Abiogenesis spontaneous generation,
accidental creation of life and accidental, spontaneous, self-division into species on its part: r both fairy-tales, superstitions, forms of religion,
in the guise of science
 

Skeptic

New member
Since Bob is either unwilling or unable to answer my questions, perhaps other Biblical-literalist supernaturalists would like to give them a try.


If you claim there is not even a remote possibility that life could have arisen naturally, what is your empirical basis for this claim?

In order to make such a bold claim, you must have an air-tight body of scientific research that confirms beyond any shadow of a doubt that the natural origin of life is impossible.

Please cite those studies that confirms with 100% certainty that life could never have arisen naturally.

If you claim that you do not have 100% certainty, then why do you allow for the possibility that life could have arisen naturally?
 

writer

New member
Life

Life

If you claim there is not even a remote possibility that life could have arisen naturally, what is your empirical basis for this claim?
Life makes life.
Inanimacy doesn't make life. Hasn't. Won't. Couldn't.
Even if it tried.
But then it can't try

In order to make such a bold claim, you must have an air-tight body of scientific research that confirms beyond any shadow of a doubt that the natural origin of life is impossible.
More non-sense.
I think the gentleman's askin to prove a negative.
But the greater nonsense's these phrases: "natural origin of life/life arisen naturally."
Life's the origin of life. God is Life.
Not in a pantheistic sense.
God has His own life.
The Bible calls His "eternal life" (cf Jn 11:25; 14:6).

Nonlife/inanimacy is not the mother of life. It's not even a mother. Becuz a "mother" requires life. Life is the mother, the father, the source, the origin of created life.
Life, in the Bible, doesn't just happen.
In the Bible: "I Am" (cf Jn 8:58).
I am who I am (Ex 3:14). God is. Life is first. And was always (that is, capital "L" Life, God's life). Not inanimacy. Inanimacy didn't make life. It couldn't. It's the other way around

Please cite those studies that confirms with 100% certainty that life could never have arisen naturally.
Since that's a negative, please cite the Frankenstein movies, or whatever you have, to show that life spontaneously generated.

"Life arisen naturally." There's that ridiculous phrase again. What life is not natural?
The Terminator robots? That's not life. That's a movie. That, like Evolution and Abiogenesis,
is fiction. It's not real. It's unreal. I think Louis Pasteur disproved that maggots spontaneously arose naturally. They come from other life. And their own kind of life.
Not from monkeys or nonflies. Humans come from humans. Someone might let the gentleman attend a hospital birth ward sometime. Humans are coming out. Not monkeys, doggies, kitties, ape-men, homo-nonexisticus, flies, plants, or trees.
Would that qualify as a "study" for the gentleman. Or's that over-obvious?

"Life arisen naturally." Translation: life arisen accidentally?
Life spontaneously-generating?
Putting rocks and light and water in a blender and life happening?
"Naturally." U mean w/ no artificial ingredients?
What's artificial? Other life?
God's not artificial. He's eternal Life. And Artist. Artificer. He's not a robot and not dead.
Life uses water and minerals and light (especially plants photosynthesize.)
But inanimacy doesn't "happen" life
 

Skeptic

New member
writer said:
Inanimacy doesn't make life. Hasn't. Won't. Couldn't.
And your empirical evidence for this is .... ?

Life's the origin of life.
And your empirical evidence for this is .... ?

Inanimacy didn't make life. It couldn't.
And your empirical evidence for this is .... ?

Since that's a negative, ...
He who claims that something is physically impossible should provide some empirical evidence that this is the case. ... Don't you think?

I think Louis Pasteur disproved that maggots spontaneously arose naturally.
Did he prove that the first living entities could not have arisen through natural processes?
 

DoogieTalons

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Skeptic said:
He who claims that something is physically impossible should provide some empirical evidence that this is the case. ... Don't you think?
Indeed that's why Atheist never say God is impossible, just improbable.
 

Mr Jack

New member
13.7 billion years ago there was no life in the universe.
4.6 billion years ago there was no life on earth.
3.5 billion years ago there was life on earth.

Somewhere in that first 10 billion years of the universe, or first billion years of the earth something happened that meant life emerged. We don't know how, but we know it did. This is why I find Creationists harping on about abiogenesis so uninteresting; we know it happened, just not how.
 
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