I am doing well physically. So pardon the cut and pasting, my writing skills and the long read.
It is difficult to explain how Ribose occurred in any origin of life scenario. For instance, it reacts almost instantaneously with amino acids. So the make RNA you have to make the amino acids and ribose separately and later combine them to make RNA. Having them created in the same time in same place creates problems. I also found this interview I found interesting.
At the Jet Propulsion Laboratory Nov. 5, a world-renowned origin-of-life researcher spoke to a packed auditorium on the status of his field, chemical evolution and the origin of life. Dr. Steven Benner (U. of Florida) trains graduate students in the subject, knows all the big names in the field personally, and has published and worked on this subject for over 20 years. His outline dealt with 4 approaches to probing the black box of lifeÃ¢â‚¬â„¢s origin: (1) working forward in time from stars and planets, (2) working backward in time from existing life to its ancestors, (3) experimenting with synthetic life, and (4) searching suitable habitats in space.
More interesting, though, were his candid admissions about the problems facing anyone in this field, and his joking references a couple of times that if these problems remain unsolveable, he might have to become a creationist. He didnÃ¢â‚¬â„¢t mean it, of course. These were chuckle-garnering hyperboles to express the frustration he has felt for decades over problems that are still far from a solution. For instance:
1. DNA: as good as it gets? Benner spent some time discussing how perfect DNA and RNA are for information storage. The upshot: donÃ¢â‚¬â„¢t expect to find non-DNA-based life elsewhere. Alien life might have more than 4 base pairs in its genetic code, but the physical chemistry of DNA and RNA are hard to beat. Part of the reason is that the electrochemical charges on the backbone keep the molecule rigid so it doesnÃ¢â‚¬â„¢t fold up on itself, and keep the base pairs facing each other. The entire molecule maximizes the potential for hydrogen bonding, which is counter-intuitive, since it would seem to a chemist that the worst environment to exploit hydrogen bonding would be in water. Yet DNA twists into its double helix in water just fine, keeping its base pairs optimized for hydrogen bonds, because of the particular structures of its sugars, phosphates and nucleotides. The oft-touted substitute named PNA falls apart with more than 20 bases. Other proposed alternatives have their own serious failings.
2. Sugar substitute: Ribose sugar is the molecule of choice for nucleic acids, yet because it is difficult to imagine forming under plausible prebiotic conditions and has a short lifetime, origin-of-life researchers have searched diligently for alternatives, like glycerol, that might have served as scaffolding for prebiotic chemicals prior to the emergence of DNA. Unfortunately, they donÃ¢â‚¬â„¢t work. He was emphatic: over 280 alternative molecules have been tested, and they just do not work at all; those that might be better than ribose are implausible under prebiotic conditions. Ã¢â‚¬Å“Ribose is actually quite good Ã¢â‚¬â€œ uniquely good,Ã¢â‚¬Â he said. Deal with it: oneÃ¢â‚¬â„¢s chemical evolution model is going to have to include ribose. That means figuring out how it can form, how it can avoid destruction in water, and how it can avoid clumping into useless globs of tar. (RNA, the main player in the leading Ã¢â‚¬Å“RNA WorldÃ¢â‚¬Â scenario for the origin of life, uses ribose; DNA uses a closely-related sugar, deoxyribose.)
3. Genetic takeovers: Benner chided those whose models invoke genetic takeovers: i.e., starting with another sugar then switching to ribose, starting with another informational macromolecule then switching to DNA, etc. For instance, some flippantly suggest to get DNAÃ¢â‚¬â„¢s sugar, Ã¢â‚¬Å“just add an OH to ribose....Ã¢â‚¬Â The professor got animated. That adds a charge to the molecule, he exclaimed, and what is more important to the behavior of a molecule than its electrostatic charge? You canÃ¢â‚¬â„¢t just add a charge to a molecule and expect it to keep behaving like it did before.
4. Adding Ad Hoc: When a researcher keeps having to multiply ad hoc scenarios to keep his model together, it quickly becomes a target of criticism. The professor spoke of Robert Shapiro, a long time critic of this bad habit among his colleagues. He said one of his requirements for graduate students is to endure ShapiroÃ¢â‚¬â„¢s critique. He spoke as if this is a common, well-known fault in the origin of life community Ã¢â‚¬â€œ invoking a meteor strike here, a clay mineral there, a volcano over yonder, a deep sea vent somewhere else Ã¢â‚¬â€œ all needing to be present at the right time and place to get the scheme to work. He also spoke as if his own model was not immune from that criticism.
The ribose problem appeared so severe to him early in his studies, he felt certain at the time that researchers simply had to find an alternate sugar for chemical evolution. Stanley Miller was similarly emphatic in his writings, stating that ribose sugars were not components of the earliest life. His colleagues (researchers in this field tend to be a sociological society, he quipped) have gone back and forth on this issue for years, but the 280 molecules they have tested are worse than ribose; they donÃ¢â‚¬â„¢t work.
This intractable problem has led him to a novel solution: life didnÃ¢â‚¬â„¢t form in the water, but in a desert. Serendipitously, he found that a mineral Ã¢â‚¬â€œ borate Ã¢â‚¬â€œ can stabilize ribose long enough to make it a contender (see 01/09/2004 headline). Like ribose, borate also decomposes in water and needs a dry environment. If borate is found on Mars, he speculated, maybe ribose will also be found there, he announced to the planetary scientists and engineers in the room. But then, how can the other necessary molecules associate with ribose if it is in a desert? And how would it be shielded from ultraviolet radiation, as a questioner asked about Mars (to which he answered that much more research needs to be done on the effect of sunlight on ribose). And how could ribose on a desert continent survive the impact record on the early earth? Worse, the fact that borate and ribose seem made for each other raises the old specter of the Anthropic Principle: why should two independent substances that are not common in the universe be found together in the same place and time? He admitted this gave him a shrinking feeling; Ã¢â‚¬Å“it was almost a creationist argument,Ã¢â‚¬Â he confessed half seriously.
This reporter had the opportunity to ask follow-up questions to the professor during the Q&A period, and in person after the meeting was adjourned:
5. Information: What is information, and how much would be needed to get a prebiotic chemical to the point of being accessible to Ã¢â‚¬Å“Darwinian evolutionÃ¢â‚¬Â? (assuming, for the moment, that Darwinian evolution would be effective after that point). When he bluffed about ambiguities over the meaning of Ã¢â‚¬Å“information,Ã¢â‚¬Â I pointed to functional information; i.e., the need for replication and metabolism (see 06/12/2003 headline). He estimated that 1000 nucleotides might be sufficient, maybe as low as 200 or 300Ã¢â‚¬â€œ yet he admitted readily that 200 is still an enormous sequence: 4200 permutations, which translates into something like 10120. He shrugged off any consideration of how improbable that was, instead making the problem far worse by intimating that 10,000 nucleotides might be necessary to contain enough information for Darwinian evolution (see online book).
6. Chirality: The professor readily admitted that getting a polymer of all one hand was enormously improbable (see 06/21/2004 headline and online book). He suggested some experiments that showed an excess of one hand, but agreed, when reminded, that even one base of the wrong hand destroys the molecule. It has to be 100% single-handed, he conceded, to be useful for life. How could that come about? He dodged the question, saying he prefers to stay focused on his own research and leave that problem to others.
7. Science or Myth? I saved the hardest question for last: How can chemical evolution theory be distinguished from just-so storytelling? He jovially shrugged the question without getting offended. Ã¢â‚¬Å“Well,Ã¢â‚¬Â he replied, Ã¢â‚¬Å“I think we have made progress,Ã¢â‚¬Â and mentioned one or two things that have been learned in the last 20 years or so. But since there was little to show for it, and in a real sense the problems are worse now, since we have learned so much more about the complexity of life than was known in the Miller Experiment days, how can it be claimed all the activity is not mere oscillation rather than progress? He smiled as if stumped, but was out of time; his escorts had to take him to the airport.
Besides the problems, another thing stood out from his presentation: the exquisite perfection of DNA, RNA and ribose for the jobs they have to do. Maybe this would be a good time to follow the path of former chemical evolution researcher, Dean Kenyon: become a creationist.