Harold Bernhardt outlines the failings of the RNA World Hypothesis, and makes his case for "proteins first".
Some memorable quotes:
"The RNA World scenario is bad as a scientific hypothesis"
-Eugene Koonin
“[The RNA world hypothesis] has been reduced by ritual abuse to something like a creationist mantra”
-Charles Kurland
"I view it as little more than a popular fantasy."
-Charles Carter
Richard Sternberg opens his post with this statement:
I have long questioned the assumption that most genomic DNA sequences are “nonsensical” or “junk.” And given the data that have emerged over the past seven or so years, a functionalist view of genome has robust empirical support. It is for this reason that I think many of the arguments presented by the Biologos Foundation are “wrong on many counts,” to borrow a phrase from Darrel Falk.
Sternberg's attention was drawn to this post by Darrel Falk who in turn was critiquing Stephen Meyer. This may be familiar ground to readers of Telic Thoughts as criticisms of Falk have been previously noted at this blog. The exact comment made by Falk which Sternberg notes is:
Stephen Meyer, author of Signature in the Cell wrote Response to Darrel Falk’s Review of Signature in the Cell. A prior post focused on the first few paragraphs. Continuing with the article:
Falk first cites a scientific study published last spring after my book was in press. The paper, authored by University of Manchester chemist John Sutherland and two colleagues, does partially address one of the many outstanding difficulties associated the RNA world, the most popular current theory about the origin of the first life.
Starting with a 3-carbon sugar (D-gylceraldehyde), and another molecule called 2-aminooxazole, Sutherland successfully synthesized a 5-carbon sugar in association with a base and a phosphate group. In other words, he produced a ribonucleotide. The scientific press justifiably heralded this as a breakthrough in pre-biotic chemistry because previously chemists had thought (as I noted in my book) that the conditions under which ribose and bases could be synthesized were starkly incompatible with each other.
Nevertheless, Sutherland’s work does not refute the central argument of my book, nor does it support the claim that it is premature to conclude that only intelligent agents have demonstrated the power to produce functionally-specified information. If anything, it illustrates the reverse.
Very true. Sutherland's work is causally inadequate as an explanatory model for the issues raised in Meyer's book.
Introducing David Berlinski:
Having with indignation rejected the assumption that the creation of life required an intelligent design, Mr Fletcher has persuaded himself that it has proceeded instead by means of various chemical scenarios.
These scenarios all require intelligent intervention. In his animadversions, Mr Fletcher suggests nothing so much as a man disposed to denounce alcohol while sipping sherry.
Heh, heh. Vintage Berlinski.
I just tried reading the 2008 paper of the late Leslie Orgel, long time origin of life researcher, which assessed the plausibility of existing self-organizations theories of the origin of life. Most of the article was way over my head. But I think I understood the final sentence:
Read the rest of this entry »
On page 344 of Signature in the Cell Meyer makes note of the interdependence of functionality existing in cells. The cellular relationships between DNA, ATP and proteins have sometimes been dubbed as the chicken-egg dilemma for origin of life explanations. Chicken-egg causal pathways are common to designed outcomes. They signal a logical point at which intelligent input can be indentified. But is a chicken-egg scenario compelling either for design or deniers of it? Meyer does more than leave the issue hanging.
The most highlighted approach to resolving the chicken-egg conundrum is probably the RNA world explanation. Its enzymatic and information storage properties are said to have been sufficient by proponents of the RNA world. The RNA world hypothesis has been much explored both at Telic Thoughts and within many other sites, papers and books.
At the end of chapter 5 ("The Molecular Labyrinth") of his book, Signature in the Cell, Stephen Meyer summarizes what he thinks needs to be explained:
…scientists investigating the origin of life must now explain the origin of at least three key features of life.
Agnostic chemist Robert Shapiro has claimed for decades that the RNA world scenario is too implausible, and that origin of life scientists should explore other alternatives. His message has largely fallen on deaf ears. Why?
Read the rest of this entry »
Deep-Sea Rocks Point To Early Oxygen On Earth is a Science Daily article. Quoting:
Red jasper cored from layers 3.46 billion years old suggests that not only did the oceans contain abundant oxygen then, but that the atmosphere was as oxygen rich as it is today, according to geologists.
The article goes on to explain that the amount of oxygen indicated implies that cyanobacteria, or organisms like it which produce oxygen, must have been found on earth at an earlier point in natural history than previously thought. Theories like the RNA world hold that a series of events involving catalytic RNA led to earth's first cells. Aside from findings like hematite which supply time frame limits, is there anything intrinsic to theorized RNA world processes indicating duration from start to the appearance of cyanobacteria like organisms?
There are two other problems with synthesizing RNA. The first is the presence of other substances. As Stephen Meyer points out: Read the rest of this entry »
In Signature in the Cell Stephen Meyer presents five problems for the RNA world. The second part of the first problem involves the production of ribose, one of the constituents of RNA. Read the rest of this entry »
In his book, Signature in the Cell, Stephen Meyer devotes a chapter to the RNA World scenario. He offers five problems that it faces. This thread will be devoted to the first part of the first problem: "RNA Building Blocks are Hard to Synthesize and Easy to Destroy." I'll just quote from his book. Read the rest of this entry »
The question of the plausibility of the RNA world scenario has come up on the Information Content of Proteins thread. So I thought I better start an RNA world thread quick, before it takes over the discussion of proteins. So Gringo Royale and others, bring your discussion over here, please.
From here:
Scientists have shown in literally thousands of studies that the p53 gene deserves its reputation as "the guardian of the genome." It calls to action an army of other genes in the setting of varied cell stresses, permitting repair of damaged DNA or promoting cell death when the cell damage is too great. A key net effect of p53's action is to prevent development of cancerous cells.
Now, University of Michigan Medical School scientists provide the most thorough evidence yet that p53 also regulates a trio of genes from the realm of so-called "junk" genes "” the roughly 97 percent of a cell's genetic material whose function is only beginning to be understood.
The article ENCODE finds the human genome to be an active place, by John Timmer, is provacative. The issue it highlights serves as a useful focal point around which to contrast the predictive utility of a teleological approach with that of standard evolutionary thinking. This is particularly so since more data relevant to the junk DNA question soon will be forthcoming. From the article:
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