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Biochemist: Is RNA world wrong after all?


Remember when RNA world just had to be true, in that multiverse/global warming/Darwinism way? Where the observer soon realizes that evidence is superfluous—is even a threat? According to many origin of life researchers, RNA world (RNA preceded DNA and once did its job) has had that status for some time now among science writers. Well…

From New Scientist:

Why ‘RNA world’ theory on origin of life may be wrong after all

Note: We are told, “Registration is required to view the article.” Not only that, but one can’t now even preview the first two graffs from the article before signing up for something. That said, a friend who did sign up offers the salient point:

At some point, the idea goes, this RNA world ended when life outsourced enzymatic functions to proteins, which are more versatile. The key step in this switch was the evolution of the ribosome, a structure that builds protein molecules from genetic blueprints held in RNA.

But that would mean that RNA would not be acting as enzymes, while proteins would—and that is not said to be a simple model at all.

Williams has further reason to question the RNA world. His detailed study of the ribosome shows that its most ancient part, which is identical in every living thing, acts as an enzyme to link amino acids in a growing protein chain. But this ribosomal core works pretty badly, Williams told the Astrobiology Science Conference in Chicago last week, and so is unlikely to be the product of a long period of evolution by natural selection.More.

Other theories by which life could just somehow have got started randomly were kicked around and contested at the conference.

As noted before, if we really wanted researchers not to find out how life originated, we would urge that they continue with full-bore Darwinism: Natural selection somehow acted on random configurations to produce trillions of sophisticated little machines. In fact, we discourage that approach. But there is no stopping Darwin’s zealots. It is the air they breathe. Hope the food at the venue is good.

See also: Welcome to “RNA world,” the five-star hotel of origin-of-life theories


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'Where the observer soon realizes that evidence is superfluous—is even a threat?' More surreal reality easily mistaken for withering satire. Axel
But this ribosomal core works pretty badly, Williams told the Astrobiology Science Conference in Chicago last week,...
Says the guy who has designed how many molecular factories himself? EDTA
As to their claim that the,,,
"ribosomal core works pretty badly"
Actually the Ribosome, which makes the myriad of different types of proteins found in life, is found to be, contrary to 'working pretty badly', an 'editorial perfectionist' that is found to be severely intolerant to any random mutations occurring to proteins.
The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm
In fact the ribosome's actions have, contrary to 'working pretty badly', been compared to a 'grand ballet':
Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.” http://creationsafaris.com/crev200910.htm#20091010a
Moreover, the way in which ribosomes are arranged in the cell is in such a way that it 'optimizes the dense packing of ER sheets, and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell'.
Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules (ribosome machines) that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell. "The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,, ,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm
Of related interest, the Ribosome of the cell is also found to be very similar to a CPU in a electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf
As to:
"The key step in this switch was the evolution of the ribosome,,,
Yes that would be a key step that evolutionists 'got some serious splaining' to do on:
Imagine How It Happened! "Evolution Presents" the Ribosome, "Nature's Masterpiece" - July 9, 2014 Excerpt: There are even more reasons to reject the evolutionary hypothesis in the PNAS paper on which the film was based. The authors provide no evidence that the "common core" (Phase 1 in the film) of the large ribosomal subunit (LSU) was able to do anything on its own. There is a small ribosomal subunit (SSU) that has to match it. Even more important, a ribosome is useless without a genome! How do they handle that? "In our model, the LSU has evolved in distinct phases," the paper speculates. "This process started with the formation of the P site, possibly in an RNA world, and continues today in eukaryotes." So they lean on the RNA world scenario, which we have shown many times is untenable. This is recognized even by evolutionists, such as Niles Lehman, whom Casey Luskin quoted as saying, "The odds of suddenly having a self-replicating RNA pop out of a prebiotic soup are vanishingly low." This stops the tale before it even starts. The authors try to make the "common core" look small and simple, but the LSU of the simplest bacterium contains on the order of 3,000 nucleotides. The small rRNA subunit (SSU) contains another 1,500 more. These are much larger (and more complex) than anything that origin-of-life researchers could ever hope for in an RNA world. Even more problematic for evolution, both ribosomal subunits for the simplest bacterium contain dozens of protein parts integrated with the RNA parts. But the proteins had to be translated by the very ribosome the evolutionists are trying to explain! It's a profound chicken-and-egg problem that Williams and his co-authors gloss over,,, http://www.evolutionnews.org/2014/07/imagine_how_it2087611.html
George Church, whose team successfully encoded an enormous amount of information on DNA, (And who also endorsed Stephen Meyer's book 'Darwin's Doubt'),,,
Harvard cracks DNA storage, crams 700 terabytes of data into a single gram - Sebastian Anthony - August 17, 2012 Excerpt: A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times.,,, Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored. http://www.extremetech.com/extreme/134672-harvard-cracks-dna-storage-crams-700-terabytes-of-data-into-a-single-gram Information Storage in DNA by Wyss Institute – video https://vimeo.com/47615970 Quote from preceding video: “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.” Sriram Kosuri PhD. – Wyss Institute What George Church, Famed Harvard Geneticist, Says About Darwin's Doubt and Intelligent Design - May 2013 http://www.evolutionnews.org/2013/05/george_church_p072741.html
In regards to the ribosome, George Church stated:
LIFE: WHAT A CONCEPT! Excerpt: The ribosome,,,, it's the most complicated thing that is present in all organisms.,,, you find that almost the only thing that's in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be? - George Church http://www.edge.org/documents/life/church_index.html
Of note, although the ribosome is present, (i.e. 'common'), in all life, the Ribosome's size, sequence, and structure is not uniform (i.e. conserved) across all life:
Ribosome Excerpt: Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth) differ in their size, sequence, structure, and the ratio of protein to RNA. http://en.wikipedia.org/wiki/Ribosome Information Processing Differences Between Archaea and Eukarya—Implications for Homologs and the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 18, 2015 Excerpt: In this article, we,, show how the key molecular features surrounding DNA replication, transcription, and translation are fundamentally distinct in eukarya despite superficial similarities to prokaryotes, particularly archaea. These selected discontinuous molecular chasms highlight the impossibility for eukarya having evolved from archaea. In a separate paper, we will address alleged similarities between eukarya and bacteria. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-archaea-and-eukarya/ Information Processing Differences Between Bacteria and Eukarya—Implications for the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 25, 2015 Excerpt: In a previous report, we showed that a vast chasm exists between archaea and eukarya in regard to basic molecular machines involved in DNA replication, RNA transcription, and protein translation. The differences in information processing mechanisms and systems are even greater between bacteria and eukarya, which we elaborate upon in this report. Based on differences in lineage-specific essential gene sets and in the vital molecular machines between bacteria and eukarya, we continue to demonstrate that the same unbridgeable evolutionary chasms exist—further invalidating the myth of eukaryogenesis. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/
The problems with the "RNA World" hypothesis are too many to mention. But we could try. Mung
Bob O'H:
So how should researchers continue if they do want to find out how life originated?
1- Get rid of materialism 2- Adopt Intelligent Design Virgil Cain
Bob O'H at 1 (but really this is addressed mainly to anyone who may actually be able to hear what is said): One can't get anywhere with information-based problems like life unless one is prepared to take information and how it is generated seriously. Cults in science that attribute magical qualities to randomness - such as natural selection acting on random mutations (Darwinism) - will provide some with a tax-funded living, publications, pop sci attention, etc. in pursuit of the speculation of the month. But will provide no answers. Randomness simply does not generate the information level required. We've always known that. But so much now depends on not accepting it. And why - come to think of it - should I suppose they are really looking for answers? The speculation-of-the-month racket isn't that bad, as long as no one goes and pulls the plug or something. News
As noted before, if we really wanted researchers not to find out how life originated, we would urge that they continue with full-bore Darwinism
So how should researchers continue if they do want to find out how life originated? Bob O'H

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