UFO's appear every day. Any object that appears to be flying but is not readily identifiable is a UFO to the observer.

Some people are happy to accept these aparitions as alien, some, me included, simply accept that the observer was not sufficiently qualified to identify the object/phenomenon.

"A UFO is the reported sighting of an object or light seen in the sky or on land, whose appearance, trajectory, motions, lights and colors do not have an obvious conventional or natural explanation, and which cannot be explained, not only by the original witness, but by scientists or technical experts who try to make a common sense identification after examining the evidence." -- Center for UFO Studies

"How does the human proteome folding project (HPF) on the world community grid (WCG) relate to Rosetta@home?

[CASP6 Target T281] It is important to differentiate Rosetta@home from the HPF project (the one currently running on the WCG and grid.org), so I'll take a few lines to explain each from the perspective of motivation. The two grids HPF and Rosetta@home are not competing grids and we would like to see them both thrive.

Rosetta@home is run by the bakerlab as a way to accelerate development of the Rosetta code. With the focus on all-atom refinement and protein design even their benchmarks (to see if they broke the code or improved the code) are taking a large amount of time. Thus, Rosetta@home is primarily for testing/developing new versions of the Rosetta code and making Rosetta better. Also the robetta server could be hooked up to this project. This grid meets the spikes in the compute demands of the robetta server and the bakerlab. Rosetta@home does not aim to produce databases that will in turn be used by biologists but it helps to make the code better, which in turn helps efforts, like HPF, that use the code to give biologists usable fold and function predictions. In that way it is an essential part of the field-wide effort to fold proteomes.

Conversely, our project, HPF on the WCG, aims to use stable versions of Rosetta to make predictions that can be presented to biologists and biomedical researchers in comprehensive databases with intuitive front ends. HPF on the WCG can be thought of as the production phase of the project, where we produce function annotation for many genomes and then distribute this product to biologists. Due to the large number of proteins we're folding (comprehension is essential) we need a great deal of computer time if we want to make our databases comprehensive and availiable to biologists.

We are working with the bakerlab on HPF on the WCG and think of the two grids as very different parts of the solution of getting function out of fold prediction: one using Rosetta and one improving Rosetta (D Baker is involved in both projects)."

UFO have recently landed in the UK

Protein engineering: OK Computer (pp 656-659)

One of the great remaining problems in computational protein design involves the redesign of a DNA-modifying protein so that it recognizes, and alters, a new DNA sequence. For example, changing the specificity of a nuclease a protein that cuts DNA at a specific site could be beneficial for a range of biotechnological and medical applications.
In this week's Nature, David Baker and colleagues have shown that it is possible to modify the sequence specificity of a "homing endonuclease" called I-MsoI. They used a computational approach to screen a virtual library of mutant proteins and predicted which amino acids needed to be changed to re-engineer this enzyme so that it recognized, and cleaved, a new DNA sequence. The mutant protein was highly active and was able to cleave the new DNA sequence, but did not modify the original sequence. The authors hope to redesign this and other DNA-modifying enzymes to alter a range of DNA sequences, so that they could specifically target almost any sequence in the genome. These computationally designed proteins may be useful in a range of medical and biotechnological applications, including gene therapeutic and other targeted genomics applications.

Nature Editor's Summary

1 June 2006
Design for living

Altering the specificity of DNA-cleaving enzymes could be useful in many medical or biotechnological applications, but it is quite a challenge in terms of computational protein design. Ashwell et al. have used computational redesign to alter the target-site specificity of the I-MsoI homing endonuclease, while maintaining wild-type binding affinity. The redesigned enzyme binds and cleaves the new DNA recognition site about 10,000 times more effectively than the wild-type enzyme, with target discrimination comparable to the original endonuclease. These results suggest that computational protein design methods can be used to create novel and highly specific endonucleases for gene therapy and other applications.
Letter: Computational redesign of endonuclease DNA binding and cleavage specificity

Justin Ashworth, James J. Havranek, Carlos M. Duarte, Django Sussman, Raymond J. Monnat, Jr, Barry L. Stoddard and David Baker

‘‘Leon Hess, whose oil company made more than $200 million by trading oil futures during the Persian Gulf crisis ... said he longs for the days when oil company barons could get together and decide prices and supply levels largely among themselves, rather than depending on the violent price swings created by traders who react to rumors and headlines.
‘‘‘I’m an old man, but I’d bet my life that if the Merc [New York Mercantile Exchange] was not in operation there would be ample oil and reasonable prices all over the world, without this volatility,’ Hess said at a hearing the Senate Committee on Governmental Affairs held on the role of futures markets in oil pricing.’’ —‘‘Oil Baron Longs for Past, Not Futures,’’ Newsday, November 2, 1990

"As mentioned before, because of the lack of good information on production, stocks and demand, what rules the market is the consensus view about these numbers rather than the actual situation. This has an important implication for OPEC. When OPEC has to decide on a production policy in order to reverse a price fall as in 1998 and March 1999, it is obliged to reduce production by the volume demanded by traders and not by the amount required to restore the supply/demand balance. And the market has a tendency to believe in myths, such as the myth of the `missing barrels' in 1998. In that year OPEC, together with Mexico and Norway, reduced oil production twice (in March and June) to no avail. The oil price continued to fall. The market did not believe that the reductions were large enough. In March 1999 OPEC cut production by the large amount demanded by the market. This turned out to be too much as evidenced by the relentless price increase that followed throughout that year.

It is nice to say that markets should rule. The statement is however meaningless and indeed dangerous in its implications if one does not specify which market, and the conditions that qualify a market to rule. The oil futures markets as they exist today and for the reasons mentioned earlier on do not qualify. Yet, OPEC has to follow their whims to influence the course of oil prices and this seems to be an important cause of high volatility."

PWR-SAUDI-SCPMA-OIL
Saudi Arabia attributes oil prices hike to lack of advanced refining capacities

RIYADH, July 2 (KUNA) -- Saudi Arabia attributed on Sunday the current hike in oil prices to the lack of advanced refining capacities, not shortage in supplies of crude oil.

According to Saudi Press Agency (SPA), Secretary-General of Saudi Arabia's Supreme Council for Petroleum and Mineral Affairs (SCPMA) Dr. Mutalib Al-Nafisa said the council held a meeting today that included reviewing the oil market's current status in light of the fluctuation in prices that do not serve oil producing or consuming nations.

The council expressed comfort with the current balance between supply and demand with the availability of surpluses that are the highest for quite few years, he added.

The meeting, headed by Saudi King Abdullah bin Abdul-Aziz, approved a national petroleum strategy for 2006 to ensure the market's stability on the short and long terms.

The strategy includes increasing Saudi Arabia's production capacity to meet anticipated international supply and demand, as well as boosting refining capacity by establishing refineries capable of refining heavy crude oils, boosting the oil market's transparency and encouraging the development of international oil industries. (end)