Tuesday, January 8, 2008


"Gerald Joyce and Leslie Orgel-two scientists who have worked long and hard on the origin of life problem - call RNA `the prebiotic chemist's nightmare.' They are brutally frank: `Scientists interested in the origins of life seem to divide neatly into two classes. The first, usually but not always molecular biologists, believe that RNA must have been the first replicating molecule and that chemists are exaggerating the difficulties of nucleotide synthesis.... The second group of scientists are much more pessimistic. They believe that the de novo appearance of oligonucleotides on the primitive earth would have been a near miracle. (The authors subscribe to this latter view). Time will tell which is correct. [Joyce G.F. & Orgel L.E., "Prospects for Understanding the Origin of the RNA World," in "The RNA World," Gesteland R.F. & Atkins J.F., eds. Cold Spring Harbor Laboratory Press, Cold Spring Harbor NY, 1993, p.19] Even if the miracle-like coincidence should occur and RNA be produced, however, Joyce and Orgel see nothing but obstacles ahead. In an article section entitled "Another Chicken-and-Egg Paradox" they write the following: `This discussion ... has, in a sense, focused on a straw man: the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNAs catalytic potential.... Without evolution it appears unlikely that a self-replicating ribozyme could arise, but without some form of self-replication there is no way to conduct an evolutionary search for the first, primitive self-replicating ribozyme.' [Joyce & Orgel, 1993, p.13] In other words, the miracle that produced chemically intact RNA would not be enough. Since the vast majority of RNAs do not have useful catalytic properties, a second miraculous coincidence would be needed to get just the right chemically intact RNA." (Behe M.J., "Darwin's Black Box: The Biochemical Challenge to Evolution," Free Press: New York NY, 1996, pp.171-172)


Daikazu said...

Here is some recent information on the subjent of RNA which contradicts some of the statements that you have quoted.

A team led by Purdue structural biologist Barbara Golden crystallized a fungus molecule that has allowed researchers to visualize a stage of evolution. Researchers from Purdue and the University of Texas at Austin collaborated to study the change from a world of RNA to one of RNA and proteins and DNA.


Jeff said...

Thanks for the news link. Here's a review of it:

"Missing Links or Linking Misses? The Case of the Fungus Crystal 01/03/2008

Another evolutionary missing-link claim showed up in the news recently. The suggestive phrase “missing link” implies a chain with just one piece missing. It also implies that the chain is visible from one end to the other. Maybe a magic crystal from a fungus can help us visualize the chain.

A “critical missing step” has been filled in by a fungus crystal, claimed a press release from Purdue University. This crystal has magical powers: “The crystal structure of a molecule from a primitive fungus has served as a time machine to show researchers more about the evolution of life from the simple to the complex.” How did this fungus achieve such power? By helping evolutionary biologists “visualize how life progressed from an early self-replicating molecule that also performed chemical reactions to one in which proteins assumed some of the work.”

What really happened? Barbara Golden and Alan Lambowitz isolated a protein-RNA complex from the fungus Neurospora crassa and crystallized it to analyze its properties. They did not really take a trip in a time machine. “Obviously, we can’t see the process of moving from RNA to RNA and proteins and then to DNA, without a time machine,” Golden confessed. “But by using this fungus protein, we can see this process occurring in modern life.”

All they really did, though, is observe a modern complex molecule and its analogue in related species – some of which lack certain of the adaptations seen in Neurospora. The story of how the molecule acquired more complexity through an evolutionary process, from a hypothetical “RNA World” of primitive molecules, was all conjecture:

“It’s thought that RNA, or a molecule like it, may have been among the first molecules of life, both carrying genetic code that can be transmitted from generation to generation and folding into structures so these molecules could work inside cells,” said Purdue structural biologist Barbara Golden. “At some point, RNA evolved and became capable of making proteins. At that point, proteins started taking over roles that RNA played previously – acting as catalysts and building structures in cells.”

The language in this paragraph suggests purposeful behavior in molecules: role-playing, building, and making things. This is disallowed in Darwin’s universe.

In other organisms, RNA performs the work without the help of the protein. The protein in Neurospora makes the reaction more efficient. The presumption is that the simpler RNA came first and the complex RNA-protein later, but both organisms exist today and presumably have not changed for hundreds of millions of years, according to their own time scale. But like Golden said, she could not see the process without a time machine. An alternative hypothesis might be that the simpler organisms appeared at the same time but just got the economy version. How would anyone know?

Press releases from university research labs are often echoed verbatim on science news outlets. That’s what happened with this story on EurekAlert and Science Daily, both of which reiterated the “missing link” theme.

Paper View.
Visions of time machines and magic crystals must have had more popular appeal than the original paper in Nature,1 entitled “Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA.” Does the actual paper support the evolutionary missing-link story?

The molecule they studied appears to be pretty sophisticated. “This RNA binding surface provides an extended scaffold for the phosphodiester backbone of the conserved [i.e., unevolved] catalytic core of the intron RNA, allowing the protein to promote the splicing of a wide variety of group I introns,” the paper states. “The group I intron-binding surface includes three small insertions and additional structural adaptations relative to non-splicing bacterial TyrRSs, indicating a multistep adaptation for splicing function.”

They still claimed that this fits the RNA-World scenario, because purportedly simpler organisms get by without these structural adaptations: “The co-crystal structure provides insight into how CYT-18 promotes group I intron splicing, how it evolved to have this function, and how proteins could have incrementally replaced RNA structures during the transition from an RNA world to an RNP [ribozyme with protein assist] world.”

Yet the evolutionary story appeared tacked onto the end of the actual empirical work. The actual molecule is one of the aminoacyl-tRNA synthetases which are able to translate the genetic code into the protein code (see 12/28/2006, bullet 3, and 06/09/2003). These molecules have little tolerance for error (see 10/31/2007, bullet 3). The particular synthetase examined in this paper actually has another trick up its sleeve. It can also promote the splicing of mitochondrial group I introns, a process that expands the informational content of the genetic code.

In their evolutionary story, they visualized how “an extended scaffold for the group I intron catalytic core developed in multiple steps on a previously unused protein surface in a relatively short period of evolutionary time.” They noted that this ribozyme has a “distinctive genome surveillance mechanism” within this group of fungi, “that effectively prevents functional gene duplications and thereby limits evolutionary options.” This seems like a quality-control mechanism that prevents evolution.

They did not reach back prior to the existence of aminoacyl-tRNA synthetases. They assumed these complex, vital, functional molecular translators already existed. Instead, they imagined how, with further research, evolutionary biologists might be able to imagine how they “can progressively acquire new functions and evolve to bind multiple structurally related RNAs.”

A different press release, this time from Scripps Research Institute, also spoke of the aminoacyl-tRNA synthetase system. They focused on the precision editing of the molecules, which have triple-redundant checkpoints for quality control. Among the talk of instructions and information there was no mention of evolution, except for one inscrutable reference when discussing the importance of accurate protein synthesis: “It is unlikely such a robustly redundant system would have evolved, they say, if this were not the case.” Grab a cup of coffee and think that one over.

1. Paukstelis, Lambowitz, Golden et al, “Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA,” Nature 451, 94-97 (3 January 2008) | doi:10.1038/nature06413.

Here was another example of evolutionists taking a tiny bit of boringly detailed empirical data, irrelevant to the Darwinian tale, and making a snowball out of it. They rolled it down the hill of speculation till it grew into a house-sized story with which to snow the public.

These people did not get into a time machine. They did not perform divination with a magic crystal. As devotees of the Cult of the RNA World, despite all its problems (07/11/2002), they were compelled by the cult ritual to weave their observations into the myth of the watery sipapu from which their race emerged. Some ritual smoke and chanting enhanced the hallucination.

In short, their missing link turned out to be one piece of real data inserted into a chain of imagination and speculation. Would you be impressed if we held up a modern propane camp stove and called it a missing link from space aliens who brought primitive mankind the knowledge of fire?

Suppose we reinforced our claim by showing cheaper models that lacked a flint starter. Q.E.D., we say. Phooey, you reply.

Learn to see through the hype and expose the Darwinist flimflam for what it is. If they aim to shoot down intelligent design, they are making all misses and no hits. Linking misses together doesn’t improve the score."