About
Transapient Musings of an S6 Archailect

Metacognitive trivialities over smooth topologies and Julian knots of subgeometric spaces; a.k.a mastermind Singularitarian, node of the Larger Submind and Clone of the Ineffable Original.

Bryan Bishop
http://heybryan.org/
email: kanzure@gmail.com
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phone: #1-512-203-0507


Archives

• 2008 (720)
  • April (370)
  • May (257)
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Wed, 28 May 2008

Innovation Transfusion
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NASA Solicitation: Request for Information for NASA Innovation Transfusion Developmental Assignments

"The NASA Innovative Partnerships Program (IPP) is hereby requesting information from organizations interested in hosting NASA employees participating in the NASA Innovation Transfusion project. The goal of the Innovation Transfusion project is to increase the flow of new ideas into NASA by increasing connections between NASA employees and outside organizations that are creative leaders in areas that could benefit NASA missions.

The Innovation Transfusion project has two elements: Innovation Ambassadors and Innovation Scouts. The Innovation Ambassadors program will provide a temporary developmental assignment for select members of NASA's technical workforce. The Innovation Scouts program will provide for small teams of NASA employees to participate in focused workshops with a host external organization to exchange information on specific technical innovations."

TARC Today
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Today is the Team America Rocketry Challenge held in The Plains, Virginia. Spaceref has a press release about the Jacksonville Florida Challenger Learning Center participation in the event with 1 of the 100 finalist teams. In addition, they will be

providing astronaut training activities for all event guests and participating students from across the United States. Students will be able to take a ride in the Barany chair, a spinning chair used to help pilots and astronauts adjust to disorientation, and to try their hand at tossing a ball using special glasses that simulates what it might be like to work on the space station.

Update (May 17 evening): Here are the 2008 contest final results. Currently on the main TARC page:

A team from Enloe High School in Raleigh, North Carolina, won the national Sixth Annual Team America Rocketry Challenge Saturday, beating out 99 rivals for the title. The 10-member team rose to the top of squads of middle and high school-aged students facing off in the final round of the world's largest rocket competition held today outside of Washington, D.C.

"We saw it go up and it looked perfect and it was ideal," Enloe team Captain Levon Keusseyan said.

posted at: 11:49 | path: /sci/astro | permanent link to this entry

Aztreonam - The lonely monobactam from a purple bacterium
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I'm on a bit of an obscure antibiotic kick right now, so prepare for lots of awesome microbiological content in the next couple of posts.

In 1928, a Scotsman named Fleming discovered that a contaminant mould growing in one of his petri plate-based bacterial cultures was dissolving the bacterial colonies around it as it grew. He fiddled around with this mould for a bit and managed to extract an antibacterial substance that he boringly named penicillin, after the genus of mould that produced it. It was subsequently shown to be effective at treating bacterial infections in humans. World War II came along, spurring the development of a means of mass-production of the drug and ultimately saving the lives of a huge number of infected Allied soldiers. Penicillin went on to revolutionize the treatment of bacterial infections worldwide. The functional group in penicillin that enables it to smite bacteria is the beta-lactam ring. This ring is only four-sided, making it relatively unstable and permitting it to bind to and inactivate an enzyme necessary to make a strong bacterial cell wall. Affected bacteria with wussed-out walls are killed by the uncontrolled buildup of osmotic pressure, which generally causes them to pop/burst/rupture.

A zillion derivatives of penicillin have since been made, in an attempt to increase the range of bacteria that it can fight and improve its pharmacokinetics (ability to get to the site of infection) and safety. Further research in the realm of microbe-produced antibiotics has yielded a slew of other beta-lactam ring-containing classes of drugs. These include cephalosporins (original compound is produced by fungi of the genus Acremonium), cephamycins (produced by bacteria of the genus Streptomyces), cephabacins (produced by several bacteria of the family Xanthomonadaceae), carbapenems (based on thienamycin, a product of the bacterium Streptomyces cattleya), nocardicins (produced by the bacterium Nocardia uniformis), and monobactams (produced by the bacteria Chromobacterium violaceum).

The monobactams are neat because a) only one of them (aztreonam) has actually been developed into a commerically-available drug and b) their beta-lactam ring is not fused to another ring, as it is in all of the other classes except the nocardicins. The natural synthesizer of aztreonam (Azactam), Chromobacterium violaceum, is a Gram-negative rod-shaped bacteria found in water and soil in the tropics and subtropics that occasionally infects humans. When grown in culture, it produces distinctive smooth metallic dark violet colonies, reflecting the production of a pigment called violacein, which is capable of killing amoebae and trypanosomes. C. violaceum also produces other antibiotics, including aerocyanidine and aerocavin. Unlike the penicillins, aztreonam is lousy at binding to and destroying gram-positive and anaerobic bacteria. However, it has good activity against most aerobic gram-negative bacteria, including those belonging to the genus Pseudomonas. In the clinic, aztreonam must be injected. An inhaled form has been developed (based on the use of an ultrasonic nebulizer to render a solution of the drug airborne as a mist) and is currently in trials.

- Aoki H, Sakai H, Kohsaka M, Konomi T, Hosoda J. Nocardicin A, a new monocyclic beta-lactam antibiotic. I. Discovery, isolation and characterization. J Antibiot (Tokyo). 1976 May;29(5):492-500.
- Durán N, Menck CF. Chromobacterium violaceum: a review of pharmacological and industiral perspectives. Crit Rev Microbiol. 2001;27(3):201-22. Review.
- Hellinger WC, Brewer NS. Carbapenems and monobactams: imipenem, meropenem, and aztreonam. Mayo Clin Proc. 1999 Apr;74(4):420-34. Review.
- Ono H, Nozaki Y, Katayama N, Okazaki H. Cephabacins, new cephem antibiotics of bacterial origin. I. Discovery and taxonomy of the producing organisms and fermentation. J Antibiot (Tokyo). 1984 Dec;37(12):1528-35.

How neurotech will change the world, one brain at a time
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High end business magazine Condé Nast Portfolio has a feature article on the latest developments in the 120 billion dollar neurotech industry that aims to develop drugs and devices to cure diseases and optimise our brains.

The article takes a broad view of the industry, but also highlights a few areas which are looking hot and gives a guide to the sort of business thinking that motivates both the neurotech giants and the fledgling startups.

It seems the industry is currently a high stakes, high risk investment prospect as the majority of companies do not make money, so investors are betting long-term or hoping they're backing a blockbuster.

The piece also mentions the work of Zack Lynch of the neurotech industry group NIO, who in partnership with his co-director and wife Casey Lynch, seems to have been lobbying the US government for significant support for the sector:

The couple’s new push is to get more federal dollars channeled toward the industry. Zack has been traveling back and forth to Washington, sometimes taking along neurotech C.E.O.’s, to promote a $1 billion “national neurotechnology initiative” that Representative Patrick Kennedy, a Rhode Island Democrat, recently announced he will introduce in Congress. The legislation asks the federal government to spend $200 million a year for five years on neurotech, including $30 million for the Food and Drug Administration to train more experts, $80 million for the National Institutes of Health to coordinate the neuroresearch efforts that are now run by 16 different institutes, and $75 million to increase small-business grants for neurotech companies.

One issue the article touches on is the deregulation of the industry so they can develop pharmaceuticals for cognitive enhancement of healthy people without having to get their medication licensed for a specific medical disorder.

While some remain suitably demure about the possibilities (at least in public), this is obviously the neurotech holy grail and is undoubtedly high on the long-term goals of the industry.

The article also has a couple of fantastic interactive features accompanying it - one on drugs and the other on implants. Also check the right-hand column for a series of related articles from the same publication.

Link to Condé Nast Portfolio article 'The Ultimate Cure' (via BrainWaves).

Brain Blogging, Thirty-Third Edition
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Welcome to the thirty-third edition of Brain Blogging. In this round, we cover a range of topics from personality disorders, crying men, mastering self-control, total body detoxification, and working out your brain to Martian invasions.

If you were left out, just leave a comment with your blog entry. Don’t worry, we’ll format it to match the blog carnival (or even include it in the main post).

Remember, we review the latest blogs related to the brain and mind that go beyond the basic sciences into a more human and multidimensional perspective. You can check our Brain Blogging archive for all editions.

For future editions, please remember to submit your blog entries using the online submission form. We will do our best to review and include your entry! Enjoy your readings…

Psychology

Phil for Humanity asks Why People Interrupt?:

Some conversations are very boring, and some people feel an immediate need to make the conversation more interesting. For example, they may try being humorous.

Improved Lives asks Is Happiness Contagious?:

Happiness spreads in networks. If your friend’s friend becomes happy, it ripples through the network and can make you happy.

Providentia reports on When the Martians Invaded:

Grover’s Mill was largely deserted when the broadcast began but this changed rapidly as people rushed to the area. Police needed to be called in to control the crowds and reinforced the impression that something catastrophic was happening. In the town of Concrete, Washington, there was a power failure that occurred during the broadcast plunging almost all of the town’s 1,000 residents into darkness.

Nutrition & Food

eDetoxify reports on Body Detoxification - Simple Ways To Detoxify Your Body:

The first thing you should do is to reduce and eliminate the intake of alcohol, coffee, and how the harmful toxins you usually take in. You should also reduce the use of chemical products like toothpaste and shampoo. You should use substitute natural alternatives.

Mind, Soul, and Body reports Grapes of Wrath:

I remember often as a pediatric resident warning parents about unsafe foods. It did cross my mind, “are hot dogs and grapes really that off limits for toddlers? How many really have the food lodged immobile in their windpipe? Is it enough to justify a major health campaign?” Every well child visit was just one of a long list of continuous warnings we provided the parents.

Personal Development

Conservatives and Normals asks How Personal Development Effects Us All?:

Think about something that you would like to start or stop doing or change in your life. One of my biggest crutches in the past was smoking cigarettes. I’m told that quitting smoking is one of the most difficult things in the world to give up. I challenge those people and say that giving up eating is FAR more difficult than giving up smoking.

BlogMotivation reports How To Do Anything Properly:

Be proud of what you are doing. Every action has a reason for existing, no matter how uninteresting or insignificant it might seem. When you do something with pride, you bring it to a whole new level of importance.

Memory & Cognition

Diary From England reports Modern Brits Out of Memory:

According to recent research, it seems that more and more Britons have come to rely on Blackberrys, Ipods and mobile phones to store information. Many people have come to rely on them as a “memory substitute”.

Sharp Brains reports Exercise your brain in the Cognitive Age:

The brain fitness market is growing fast and this trend will continue. This is not just a Nintendo-fueled fad. The article reflects this point best. Part of the market confusion lies in the disconnect between what computerized brain fitness programs can do (the ones with more science behind them than Nintendo Brain Age) and what people seem to want them to do.

Stigmatization

Dr. Deb reports on Crying Men:

In my work, being vulnerable, being sad, and crying are hard things to do. Even harder for men. When this exhibition was turned into a book, I had to buy it. It now rests on the bookcase in my office for anyone to view.

Mental Health Disorders

SystemsThinker reports on Borderline Personality Disorder Awareness Month: Discussing, Understanding & Publicizing an Under-Recognized Epidemic:

I have gone so far as to say that Borderline, along with perhaps Narcissistic Personality Disorder (NPD), is the core disorder of our culture. In this assessment I seem to be in agreement with the eminent pioneer in the treatment of Personality Disorders, James F. Masterson, M.D., whose book, Search For The Real Self, focuses almost exclusively on these two disorders and, in its subtitle, identifies them as “The Personality Disorders Of Our Age.”

Dr Shock reports Genes Predict Response to Lithium Addition for Treatment Resistant Depression:

I am convinced that especially lithium addition is a very effective treatment strategy if an antidepressant fails and should be preferred above more experimental addition strategies such as atypical antipsychotics.

Parenting Teens Blog reports on Teens and sexual addiction:

Sexual addiction is not limited to “having sex” with the opposite gender, it can also involve pornography, masturbation and obsession about the act and the participants.

State of Mind

Learn This reports Beliefs: They’re Entirely Yours to Control:

Some people feel that you can develop beliefs by choosing them (I certainly agree with that) and others feel that beliefs come about only through experiences that train you to think about things a certain way, which eventually becomes a belief. Looking at both of these options, there are obvious arguments for both side as to which happens most often, but I look from the perspective of which I want to happen more often and that is certainly creating or choosing my own belief.

Learn This also reports A Guide to Mastering Your State of Mind:

The best thing to do with the ability to follow these visualization steps to get into a state of mind is to next, associate that state of mind with something instant. This allows you to activate that state and learn to call upon it whenever you want.

Highlight Health reports Remembering Lunch Can Help Reduce the Desire to Snack:

Mind over matter may really work when it comes to managing appetite. Researchers at the University of Birmingham, U.K. have found that recalling foods eaten at lunch has an inhibitory effect on subsequent snacking later the same day.

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Related Articles at Brain Blogger:

• Brain Blogging, Thirty-First Edition
• Brain Blogging, Thirty-Second Edition
• Blog Carnivals
• Brain Blogging, Fourth Edition
• Encephalon, Thirty-Third Edition

13 Ways to Quickly Improve Your Decision-Making
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1. Whenever possible, consider alternatives
Our brains are not good at evaluating evidence dispassionately. Force yourself to generate alternatives. Research has demonstrated the value of counter-factual thinking: thinking about the opposite helps us make better decisions.

2. Reframe the question
Our memories are highly contextual so the background to any issue we consider has a huge impact on how we view it. Politicians, advertisers and other influencers use framing extensively to persuade us of their point of view. You can fight back by reframing their propositions.

3. Correlation doesn't equal causation
An oldie but a goldie. There's a clear correlation between foot size and being richer, owning your own house and having a better education. On the other hand people with smaller feet are often still struggling with potty training. Guessed it yet? People with small feet are usually children, so of course they have less money, don't own their own houses and, haven't been to school yet. Correlation doesn't equal causation.

4. Never forget the sample size
When we think about someone and a few seconds later they call us, is that evidence of ESP? Consider the sample size. How many times have you thought about that person in the past year? How many times have they called you in the last year? What first seems like a freak occurrence soon starts to look inevitable. Sample sizes are easy to forget.

5. Anticipate your impulsivity
The best of intentions often break down in the face of vicious temptation. People find it difficult to predict just how far off course their emotions can pull them (e.g. the projection bias). Use any method you can to counter your impulsivity: cancel the credit card, join a Christmas Club, avoid the confectionary store. It's all about planning ahead.

6. Make contingency plans
Humans are better at concrete goals; abstract goals like 'read more' or 'lose weight' get lost in the mix. Substitute these with: 'read this book by next Tuesday' and 'don't buy any junk food on the weekly shop'.

7. Make important decisions when relaxed and rested
What, I need to explain this?

8. Weigh costs against benefits
Common advice but actually quite tricky to do. Research shows that our minds prefer to consider either costs or benefits; taking both into account takes considerable effort. Professor Marcus points out that one factor we often forget is the 'opportunity cost': when we do one thing, we can't be doing something else. When I watch TV the benefit might be relaxation and enjoyment but the cost is that I can't be reading that mind-improving book that's being lying around for weeks.

9. Imagine your decision will be spot-checked
When we think someone will check up on us we make more cognitive effort, leading to better decision-making. Even if no-one is checking up on you, imagine their reaction if they did: would you be proud of your decision?

10. Distance yourself
When making decisions we are influenced by whatever thoughts and emotions are swirling around in our heads at that moment. Help distance yourself by thinking about how this decision will affect you in the future. Big decisions are always better made after a night's sleep. Again, it's common advice but it can be surprisingly difficult to distance yourself.

11. Beware the vivid, personal and anecdotal
It's so easy for us to be swayed by vivid or personal stories that we may ignore more considered, scientific evidence. Remember that our minds are naturally fascinated and influenced by the sensational at the cost of quotidian. Look carefully at the information source - are you being manipulated?

12. All decisions are not equal
Some decisions are more important than others. Not all decisions warrant effortful deliberation: sometimes it's better just to choose and be done with it. The trick is knowing which is which - experience should provide strong clues.

13. Be rational!
Sounds vacuous, right? But Professor Marcus argues that research suggests just reminding ourselves to think rationally could help us make better decisions. Consciously trying to think rationally will also help activate all the other techniques described here. Our memories being what they are, this is no bad thing.

» Find out more about the 'klugey' nature of our minds in Professor Marcus' new book. 'Kluge' provides a useful, readable guide to how the mind falls short in language, decision-making, memory and happiness.

» Buy it now from Amazon.com.

» Kluge is released in the UK on the 5 June, you can pre-order from Amazon.co.uk.

One more chunk of SUSY parameter space ticked off
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I am preparing the slides for the PPC08 conference, which will be held in Albuquerque next week, and I thought I would post here two slides that show how present Tevatron data is increasingly wiping off the board one Supersymmetric model after another - yes, I regard a choice of parameters as a single “model”, since the phenomenological implications of varying the >100 SUSY parameters are just too varied to call it a single model: instead, SUSY is a framework, and points in the parameter space are models.

The models we kill today belong to a version of the minimal supersymmetric extension of the Standard Model which has “minimal SO(10) soft-SUSY breaking boundary conditions“. No, I am not going to tell you what this is: you will have to read it on hep-ph/0506233 if you really must. Instead, I will show the present limit that CDF has obtained on a particular decay of the meson, which is heavily suppressed in the standard model, but which could be enhanced by up to three orders of magnitude in SUSY models. Because of this enhancement, and because we could be sensitive to it, the matter is intriguing: by measuring the decay, one would instantly achieve two things: 1) prove the SM is wrong; 2) favor some SUSY models among the various possible interpretations of the effect.

mesons are hadrons composed of a b and a s quark. They are electrically neutral, and have a long lifetime because the b-quark is unwilling to turn into a 2nd generation charm quark (decays across generations are suppressed). But they do, in about a picosecond. Blitzing fast for our senses, but quite slow for 5 GeV unstable subatomic bodies. What happens is that the b-quark emits a W boson, changing into the charm quark. The W boson is virtual, because it has a mass way below its nominal one of 80.4 GeV, and it immediately turns into a pair of light quarks or a lepton-neutrino pair.

What is described above is the rule, but there are exceptions. In an exceedingly rare combination of circumstances, the standard model predicts that a meson will instead decay by emitting two W bosons, with a box diagram (see below, top) or a penguin diagram (bottom) whose end product may be a pair of charged muons: a striking signature of the decay! This, however, is calculated to happen only four times in a billion decays. That means we have to study several billion decays to observe it!

Searching in 2 inverse femtobarns of data, CDF has seen no signal, and a limit on the fraction of these rare decays has been set at 5.8E-8: no more than 58 in a billion. The search was done by looking for pairs of muons with an invariant mass compatible with that of the meson, and by training a neural network on the dimuon kinematics and purity to distinguish true decays from other backgrounds.

In the slide below you can see the neural network discriminator output for signal and backgrounds, in the top right graph. The scatterplot in the lower right instead shows the NN output versus the reconstructed dimuon mass: the two small boxes are the regions where the signal for and mesons were sought.

The result on the branching fraction has implications on the models of SUSY with SO(10) soft susy breaking, as was said at the beginning. In the slide below you can see that indeed, for a particular choice of the parameters describing the space of these theories, the area not yet painted with any color - indicating it was still not disproven by searches of Higgs bosons, charginos, or other constraints - has been fully excluded by the CDF limit.

In the graph, the green band is the one most favoured by cosmological bounds on the relic density of dark matter. The full black line is the lower limit on charginos found by LEP. That bound has also been updated by CDF, and from 104 GeV the lower limit has been brought up to 140 GeV.

As Veltman puts it, “SUSY is hiding just around the corner… It has been hiding there for a while” (I am quoting by heart… but the meaning is unaltered). So, as we continue turning corners and finding nothing but good-old standard model physics, one starts to wonder whether we are fooling ourselves.

Federal Government Taps NC State Experts To Explain Nanotech Risks
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The arm of the federal government responsible for coordinating nanotechnology research and regulations across the country has called on experts from North Carolina State University to craft a white paper that will lay out how government and industry officials should communicate potential risks associated with nanotechnology to the media and the public.

Hm. Maybe NC State Experts aren't the people to be talking to -- what about CRnano and other nanotech institutes? Foresight Institute? etc.

posted at: 11:44 | path: /nanotech | permanent link to this entry

Wire EDM Machine
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Wire EDM is a method to cut conductive materials using a thin wire electrode that follows a programmed path.

posted at: 11:42 | path: /tech | permanent link to this entry

Congress Pushes Participatory Exploration
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National Aeronautics and Space Administration Authorization Act of 2008 (Introduced in House) H.R.6063

"SEC. 407. PARTICIPATORY EXPLORATION. (a) In General- The Administrator shall develop a technology plan to enable dissemination of information to the public to allow the public to experience missions to the Moon, Mars, or other bodies within our solar system by leveraging advanced exploration technologies.

1. Rep. Mark Udall [D-CO] (www) (contact)
2. Rep. Tom Feeney [R-FL] (www) (contact)
3. Rep. Barton Gordon [D-TN] (www) (contact)
4. Rep. Ralph Hall [R-TX] (www) (contact (email))

Giant Ravenous Ants Threaten JSC
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This one is hitting a little too close to home.

NASA moves to save computers from swarming ants, ComputerWorld

"A flood of voracious ants is heading straight for Houston, taking out computers, radios and even vehicles in their path. Even the Johnson Space Center has called in extermination experts to keep the pests out of their sensitive and critical systems. The ants have been causing all kinds of trouble in five Texas counties in the Gulf Coast area.

Because of their sheer numbers, the ants are short-circuiting computers in homes and offices, and knocking systems offline in major businesses. When IT personnel pry the affected computers open, they find the machines loaded with thousands of ant bodies."

InsideNASA, NASAWatch, and NASAsphere
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Editor's note: I got a Twitter note an hour or so ago from someone@arc.nasa.gov: "reference to nasawatch at the all-hands - how folks use that more than insidenasa." Interesting. I am curious to see how the new inside-the-firewall NASAsphere system works. Does anyone have a screen grab they can send me of NASAsphere that they can share? This is what InsideNASA looks like today.

Editor's update: this is a screen grab from NASAsphere. I have learned that this is not a permanent NASA feature - at least not yet. It is undergoing an evaluation period for the next month or so. At that point a decision will be made whether to go ahead - and what software platform to use.

classic papers of the week -- 68
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Light Pulses from the Night Sky associated with Cosmic Rays

• W. Galbraith & J. V. Jelley (Atomic Energy Research Establishment, Harwell, Didcot, Berks.)

Visible Radiation Produced by Electrons Moving in a Medium with Velocities Exceeding that of Light

• Čerenkov, P. A. (The Physical Institute of the Academy of Sciences of U.S.S.R., Moscow)

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

• J. D. Watson & F. H. C. Crick

First LASER
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Aargon lite: full screen game... (click)
Nobel LASERs: full screen game... (click)

X PRIZE Foundation Cancer X PRIZE Suite
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Quick, somebody get John Kanzius and his do-it-yourself radiotumor destruction system.

In the Future X PRIZE content from the X PRIZE Foundation I just posted on is a link to a 15-page Cancer X PRIZE Suite Strategic Plan document. It describes initial prize definition work funded by the Lance Armstrong Foundation and the Goldhirsh Foundation, and goes into details on why we're seemingly "stuck" in the goal of better patient outcomes even though much progress has been made in cancer science. As with space, many of the problems are economic, regulatory, and institutional. It also describes the approach that would be taken by the XPF - not duplicating cancer drug research which is already well-funded, but instead covering the whole range of prevention, diagnosis, and therapy, in areas where current incentives aren't sufficient. The emphasis will be on prevention and diagnosis.

They propose (realize they probably need to convince someone to fund the prizes) 3 prizes, and 3 backups:

1. Smoking Cessation X PRIZE - an X PRIZE to the team getting the largest number of people to quit smoking for at least 2 years. It seems like they'd like to launch this one in 2009. Note that Elon Musk produced Thak You for Smoking; I wonder if he'd be interested in this one.

2. Imaging X PRIZE - for a technology that allows for the detection and localization at a very early stage ... The resulting invention would allow physicians to non-invasively explore the body and detect and characterize disease as small as a few hundred cells. I suspect there would be some uses for it outside the cancer field, too.

3. The third proposed prize would be for the ability to selectively and specifically destroy tumors anywhere in the body.

The backup prize ideas are for making an expensive cancer fighting technology cheaper so more people have access to it, a smoking prevention vaccine, and the cancer center with the best patient outcomes.

posted at: 11:18 | path: /competitions | permanent link to this entry

Maurizio Gasperini & cosmological constant
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Besides Tony Zee's cute musings about the mysteries of gravity, one of the most inspiring (or at least entertaining) papers today is

Gasperini's prediction of SUSY at a TeV from his solution to the cosmological constant problem.

L^-2 = 8πG TeV⁴ = millielectronVolt²

ρ = millielectronVolt⁴

Pomerantz on Lunar X PRIZE Guidelines 2.0
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Will Pomerantz has 2 blog posts today related to the Google Lunar X PRIZE. From the posts, you can expect a lot more in the next few days from an upcoming GLXP event and the ISDC.

Je suis arrivée! - Will arrives at the ISU, where the first Google Lunar X PRIZE Team Summit is going to take place May 20-21.

New Google Lunar X PRIZE Guidelines Released - I'm skimming through the guidelines now; I'm not sure if I ever had a look at the "official" first draft of the rules. Will shows you where you can get a copy, and also posts a cover letter that highlights changes in the rules. One major change deals with payload mass: payload can be split in a lander/rover scenario, and very lightweight systems don't need to carry as much payload. Another big change deals with media rights. The Foundation plans to hire a media agency of some sort to deal with TV and other media. Resulting income helps cover XPF expenses to run the competition. However,

The XPF will share and distribute the revenue from these media sales with the teams. The Grand Prize winner will be entitled to the largest single share of any net revenue. If there is a Second Place winner, that Team will also earn a significant share of the revenues. A portion of the remaining funds will be split between the other registered Teams, who, though they haven’t won, will have added to the overall value and quality of the competition. The media revenue share formula is still being developed and will be released soon.

Here are a couple snippets from the Guidelines themselves. It's 24 pages, so please download them and check them out if you want to know about them. This is just a tiny peek. Both snippets involve possible, do-not-count-on-it additional revenue for teams. First:

Purse values and Mooncast Requirements shall be assigned to each Bonus Prize no later than January 1, 2009, though new Bonuses may be subsequently offered.

Second (this could be cool if it involves milestones that are useful as products in and of themselves, and/or involve public demos at venues like the X PRIZE Cup):

XPF is seeking to develop an investment pool from which TEAMs could earn small cash payments by participating in or completing XPF-designated Demonstrations or Milestones.

posted at: 11:11 | path: /competitions | permanent link to this entry

NASA Authorization Act of 2008 Introduced
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Subcommittee Chairman Udall's Statement on the NASA Authorization Act of 2008

"Finally, the NASA Authorization Act of 2008 recognizes that America's human space flight activities are not, and should not, be an end in themselves. We need a results-oriented human space flight program that serves the nation's geopolitical goals in addition to advancing America's exploration of outer space. I believe that we provide the foundation for such a results-oriented approach in the bill I am introducing today. Thus, the bill includes provisions to ensure that the International Space Station--a unique orbiting R&D facility that represents a significant investment of resources by both American citizens and those of a host of other nations--will be utilized in as productive manner as possible."

Full Bill Text

Satellite Navigation Challenges
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From Jim Volp Blog comes news of the European Satellite Navigation Competition and UK SatNav Challenge. The competitions aim

to identify and stimulate new GNSS applications and technologies throughout Europe. It will also encourage a support network to nurture emerging ideas from concept to commercial reality.

There are a number of prize categories.

The European Space Agency’s Technology Transfer Programme is seeking innovative and creative business ideas, aiming at a quick market implementation and a high value capture The field of application is not relevant for this innovation prize as long as it is based on the utilisation of satellite navigation in a non-space business environment.

posted at: 11:07 | path: /competitions | permanent link to this entry

TARC Approaches
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Here's more on TARC (Team America Rocketry Challenge). The finals are scheduled for this Saturday:

Future astronaut 'A-Ok' on ACT - Cincinnati.com

It is rocket science for this Oktoc homeschooler - Commercial Dispatch Online

posted at: 11:07 | path: /competitions | permanent link to this entry

Space Business Plan Competition
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So. This is interesting. I'm going to go out on a limb here and suggest a free / open source business plan for space 'business'. It's not about trade, it's about donations. ( http://heybryan.org/mediawiki/index.php/Space_Business_Plan_competition). I suggest looking into OpenVirgle, OSAEROSPACE, Interplanetary Ventures, Team FREDNET, and the GLXP forums for starters. Anyway, the business plan should be a business selling to philanthropists: converting 'scarcity' into post-scarcity. Try that one on for size.

This one is from Space for All: The 8th Continent Project at the Colorado School of Mines is going to have a Space Business Plan competition in 2009. In past years this was called the "Lunar Ventures" competition.

8th Continent Project Announces Business Plan Competition - Space 2.0 Blog

As with Lunar Ventures:

the competition focuses on developing viable space-related business plans for technologies that have real-world potential. The 8th Continent Project Business Plan Competition challenges students in business, engineering and science to collaborate in creating business ventures related to space, but with immediate application on Earth. Teams should consist primarily of graduate students, although undergraduate participation is welcome. Prizes for the winner include up to $50,000 in cash and in-kind services.

2009 Business Plan Competition Video

posted at: 10:23 | path: /competitions | permanent link to this entry

When We Left Earth: The NASA Missions
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Reader note: "In conjunction with the NASA 50th anniversary show When We Left Earth: The NASA Missions, which airs on Discovery Channel beginning next month, we'd love to hear any short stories you may wish to share about missions from the agency's early days or from the shuttle program. Here's a link:
http://dsc.discovery.com/tv/nasa/audio-messages/audio-messages.html

1) for the early missions- Mercury, Gemini, Apollo 866-947-6272
2) for crews and anyone involved with the space program 866-948-6272
3) for Shuttle stories 866-949-6272"

Microsoft WorldWide Telescope
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Google and Microsoft should not be our only options for 3D mapmaking of the world and galaxies. It would be useful if amateurs would automate their telescopes to point to the sky at specific positions, have servers that broadcast position requests, and then compile the photographic information into an online virtual observatory, free for anybody to download (no matter the (unfortunate) bandwidth costs). See the virtual observatory project..



I think that Microsoft has just surpassed Google in one discipline. WorldWide Telescope is better than Google Sky. The latter is included in Google Earth.

WWT website (nice presentation!)
Download & install (direct link; don't be afraid to install DirectX 9, it won't destroy DirectX 10 on Vista)
My screenshot (there are better things to see)
A tour; how kids react

The selfish smell
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I figure this would be interesting within the context of brain modifications since the olfactory system is pretty easily accessible and has a direct route into the brain. Also, it's better than hacking the optic nerve immediately. We are surrounded by smells. Pleasant ones and not so pleasant ones, hard to distinguish ones, mild ones and strong ones. Smells are not part of our everyday life for the simple sake of pleasure. They are there for a purpose. The perfume of a flower can be used as an attractant for a potential pollinator, for instance. The scent given off by a poisonous mushroom is a way of warding off a predator and, by the same token, can be instantly recognised as toxic by an animal, thereby saving both species. Special scents are also given off by males and females when mating is in the air, and no wine grower will ever argue that a wine’s fragrance is not for the sole purpose of seduction. But what is a smell? More often than not, a scent is made up of a mixture of odorant molecules which, together, will trigger off a complex olfactory system that will ultimately let us perceive it and, if we wish to, put words to it. The very first step in such a system involves an odorant receptor to which an odorant molecule binds. Recently, a new human odorant receptor – OR7D4 – was discovered. OR7D4 is special in that it is the first receptor known to respond to a specific odorant molecule.

posted at: 10:08 | path: /sci/chem | permanent link to this entry

Development of the new JChemPaint
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A quick screenshot, after some work on the JChemPaint code based on CDK trunk/. Nothing much to see, but a rather small code base, which is good. Today, I have set up cdk/cdk/trunk/ and cdk/jchempaint/trunk as Eclipse plugins, allowing the second to depend on the first. So, no more use of svn:externals. This is what it now looks like, and basically formalizes the end result of Niels' work of last year:

A possible spin of is that Bioclipse2 can use these plugins too, instead of defining plugins itself.

To reproduce the above screenshot, just import cdk/cdk/trunk and cdk/jchempaint/trunk into Eclipse, and run the TestEditor from the JChemPaint plugin.

posted at: 09:54 | path: /sci/chem | permanent link to this entry

Chemistry on Mars
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As I live and breath. The space community has gotten serious again about chemical analysis of Martian soil. NASA is very much driven by physicists and engineers, so it is nice to see chemistry get some flight time. Why don’t more chemists elbow these physicists out of the way to put packages on rockets? I guess we are insufferable ground pounders.

The Phoenix Lander which, to NASA’s great credit, has successfully landed in the North polar region of Mars, is equipped with an array of analytical instruments and wet chemical apparatus for on-the-spot analysis of soil samples. Among the devices on board is a Swiss-made Atomic Force Microscope. This device will provide direct microscopic imaging of Martian soil samples. In true Swiss fastidiousness, it has multiple cantilevers for redundancy. I’m sure it keeps good time as well.

The Canadian Space Agency has contributed a meterological station on the lander.

The lander was constructed by contractor Lockheed Martin.

Given that the lander contains hazardous chemcials for the analyses, somebody is going to have to dispose of the hazardous waste after 90 days. I hope it is properly placarded. \

Gut Microbiota Transmission Affects Body Weight Regulation
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For the past almost 20 years my body weight remains constant – no matter what I eat. Bad metabolizer is what most people (and maybe textbooks) would say. Another explanation I once heard from a colleague is that people like him and me would ‘suffer’ from a reduced gut surface to body size ratio, i.e. in comparison to same size, ‘normal’ weighed people, the capacity to absorb the ‘right’ amount of nutrients is reduced in us lean ones.

But there’s more: what happens if you transfer the gut microbiota of a normal weighed mouse to a germ-free mouse? The mouse will develop a normal body weight. And how will a germ-free mouse look like after receiving the gut microbiota of an obese mouse? Overweighed! And this despite the fact that the two mouse models ingested the same amount of food.

If you want to know more about the details of the study (which has been published in Nature in 2006 already), I recommend you take 15 minutes and watch the Nature movie featuring the work of JI Gordan’s group at Washington University.

A special article by DiBaise et al. summarizes the advances in understanding “Gut microbiota and its possible relationship with obesity”, Mayo Clin Proc 2008;83:460-469

Don't Phage Me, Bro
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In the packed back-room of Asgard's Irish Pub in Cambridge, a diverse crowd of 25+ enthusiasts gathered to discuss the next big thing in biology: amateurs. Mackenzie (Mac) Cowell led-off the night with an overview of recent history in biological engineering, and asked the question: Can molecular biology or biotechnology be a hobby? Will advancements in synthetic biology be the tipping point that enables DIYers and garagistas to make meaningful contributions to the biological sciences, outside of traditional institutions? Can DIYbio.org be the Homebrew Computer Club of biology?

Noting that he was a recent expatriate from the institutional setting himself, Mac wondered out loud whether he would ever again be able to wield a pipette. A proliferation of projects and protocols available online make his prospects, and the prospects of the 25 or so individuals attending the first DIYbio meeting, quite good.

Over the noisy background of Thursday night pub chatter, just a few blocks from MIT, attendees around the room took a few moments to introduce themselves and their interests. "I've been a software engineer my whole life and I'm looking for something new," said one attendee, who was accompanied by his enthusiastic teenage son. Also present were a dozen or so graduate students, several software engineers, journalist and her boyfriend, and even a few professors from Harvard and MIT.

Mac flipped through slides indicating that "backyard biology" is alive and well. One illustrated guide found online describes how to isolate DNA using chemicals found in every kitchen cupboard. Need more DNA? A $10 PCR device assembled from basic parts might do the trick. And a recipe from the pages of MAKE magazine provides the know-how for armchair anthropologists to combine a few legos, a source of current, and a cheap enzyme kit to generate DNA fingerprints.

While backyard biology promises to be an avenue for individuals to flex their intellectual muscles and explore the molecular world around them, Jason Bobe argued that the possible impacts of a DIY world go well beyond that. Amateurs and hobbyists are making significant contributions to engineering, environmental sensing, and even medical devices.

A ham-radio hacker, turned reluctant cancer patient, recently combined his expertise about radio waves with spare parts from his home to build a prototype device capable of targeting the destruction of cancer cells. This device is undergoing clinical trials at two major medical research centers, after attracting investments from venture capitalists and the collaboration of a Nobel Laureate who was intrigued by preliminary results generated from the DIYers garage.

Undergraduate participants of iGEM are increasingly capable of engineering biological systems that have the potential to do real work in the world. Banana-scented E. coli might be fun, but arsenic sensing bacteria for identifying contaminated water supplies might actually save lives. If undergraduates are able to design these systems, who else might?

Model organisms like E. coli are still frustratingly difficult to engineer, even for professional biologists. "If amateurs can help make biological engineering more reliable, I certainly would find that of value," a graduate student remarked, half-jokingly. "I would think that amateurs would prefer to experiment with organisms that can be more readily inspected without expensive instruments," said another. "Forget E. coli. They're too microscopic. How about a plant, like moss?"

Jason cautioned that not everyone is ready to embrace a DIY biotech culture. In NYC, a proposal is currently under review that would make possession of environmental sensing devices a potential criminal offense. Tom Knight, an MIT professor and open source biology advocate, reminded the crowd of the recent attempt to prosecute artist Steve Kurtz for his home biology projects. "Is biological engineering fundamentally more dangerous than the risks posed by other fields, such as mechanical engineering?" asked John Cumbers, a graduate student at Brown University.

Mac proposed organizing a Boston-based bio-workshop for sharing equipment, space, and other resources. He flashed a few screenshots of Techshop, a west coast organization that has established nine shared workspaces for amateur technologists. "This same model could work for biotechnology hobbyists," he added.

-Jason Bobe
Report from the 1st DIYbio.org meet-up
Thursday May 1st, 2008
Asgard's Pub (Cambridge, MA)

posted at: 08:47 | path: /sci/bio | permanent link to this entry

Tue, 20 May 2008

UsefulChem Automation Trial with Mettler Toledo
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Kevin Owens and I have been looking into equipment to automate some UsefulChem experiments.

This is something that I feel strongly will become important in Open Science applications, especially as it relates to Open Notebook Science. I think it is one of the paths of least resistance for the automation of the scientific process.

Industry is automated to the gills but it will probably be easier to convince academic practitioners of Open Science to automate their procedures rather than to get industry to open their data. Can you imagine a company allowing crowds to design and analyze experiments run on their machines? That is what we've been proposing and it would be difficult to reconcile that with a business model based on IP protection.

In that NSF proposal, we planned to use ChemSpeed's technology. Kevin and I recently visited ChemSpeed at their Princeton location and we were impressed with the capabilities of their reactors. We're in the process of planning a trial run of the Ugi reaction on their system and we'll post on the progress of that on this UC wiki page. The idea is to couple a digital camera within the robot's workflow to be able to generate results comparable to those manually generated by my students.

ChemSpeed's systems are quite powerful but also expensive (200-400K). In order to take advantage of more funding opportunities, we've also been looking at Mettler-Toledo's MiniMapper/MiniBlock solutions. We're planning this out openly on this wiki page - any feedback is welcome.

I've had a good discussion with Frank Schoenen at the University of Kansas, where they run both systems as part of servicing the NIH Roadmap Program. Based on his feedback I think this trial run should be successful.

Artificial cell created from scratch
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Simple artificial cell created from scratch

A team of Penn State researchers has developed a simple artificial cell with which to investigate the organization and function of two of the most basic cell components: the cell membrane and the cytoplasm--the gelatinous fluid that surrounds the structures in living cells. The work could lead to the creation of new drugs that take advantage of properties of cell organization to prevent the development of diseases.

Saturday Cinema: Can we domesticate germs?
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You've got to know when to hold em...
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...Know when to Fold It. *sigh*, you know the creative juices just aren't flowin' when you're quoting Kenny Roger's music from several decades past.

The protein folding game is going public though and that's great news. The computer game Fold It, where you muck around with strands of amino acids in an attempt to find the best possible protein conformation, is getting more coverage around the net. A few weeks ago it was featured on Slashdot and now there's an article over at Technology Review. A snippet...

Luis von Ahn, a computer scientist at Carnegie Mellon University, agrees that humans bring problem-solving skills to the protein-folding game that computers can't match. "The computer does a brute-force search, where we may know the shortcut," he says. "We live in a 3-D world; we know how to navigate space." Von Ahn has designed games that get people to help label images for Google and digitize books. Computers are bad at some tasks that are trivial for humans, such as recognizing a dog in a photograph or reading a blurry word.

While Fold It might be a bit too challenging to reach escape velocity, the concept of human-machine combined computation for problem solving is quite spectacular. If we can merge the power of silicon and grid computing with the power of millions of human imaginations, we might just be able to have a supercomputer of future centuries in this century, perhaps in the next decade or so granted we can get our shite together and coordinate such an effort.

The question is, what are the grand challenges we need to apply this to? Is it predicting protein structure? Curating the sequence and protein databases? Synthetic molecular engineering? Untangling the proteins networks? Trial and error designs of molecular therapies?

read more

Astrobotic Analysis; Getting Around at GLXP Summit
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Astrobotic has posted 3 more GLXP Pictures. Each comes with a brief description:

Solar Analysis

Structural Analysis

Second Prototype Rover

They're all in the Astrobotic Public Gallery of photos, where you can run a slide show or download them for close-up views.

William Pomerantz has some Quick Summit Notes on things like transportation to the ISU site for those going to the GLXP Team Summit.

posted at: 23:51 | path: /sci/astro | permanent link to this entry

Computational modeling of GPCRs: not too bad
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GPCRs constitute one of the most important family of proteins in our body, both for their innate importance in signal transduction and neurotransmission, and as important targets for drugs. Many of the important drugs on the market today target GPCRs. And yet there is an unusual gap between knowledge and application when it comes to this important family. That's because only two crystal structures of GPCRs are known. And one of them was derived last year, so there's been a real dearth of structural information about GPCRs for a long time.

We do know something about many GPCRs, however. We know that they are 7-TM receptor-spanning proteins. And the two structures we do know about shed valuable insight on GPCR function. One is rhodopsin which has been around for a while. Then there was big news last year about the second important GPCR whose structure was determined- the ß-2 adrenergic receptor.

Given the paucity of structural information and the availability of two structures, a logical question is whether computational modeling can teach us something new about GPCRs whose structure is unknown. To this end, Stefano Costanzi at the NIH did a nice set of experiments which he published in J. Med. Chem. He attempted to build a homology model of the adrenergic receptor based on the sequence and structure of rhodopsin. Since we now have a crystal structure of the adrenergic GPCR, we have something concrete to compare modeled structures and ligand orientations to.

Costanzi was particularly interested in knowing how a small molecule-carazolol- binds to the modeled GPCR. This is important both from a structural and functional drug-discovery point of view. His results indicate that we can do pretty well. In essence, he built two models of the receptor, one of them de novo. While the models were similar to rhodopsin in the conserved regions, the important differences were with respect to a loop that flaps on top of the protein. In one model the loop was buried inside the binding pocket, and in the other one it was open. Docking of carazolol into the buriled-loop model using the Glide program from Schrodinger gave a binding pose in which the ligand was, not surprisingly, buried deeper into the cavity compared to the crystal structure. This was naturally the effect of the loop blocking part of the pocket. The other model in which the loop was not buried gave much better results. Curiously, the ligand was buried a little deep in the pocket even in this model, even though it was much less buried compared to the previous one. It still misaligned considerably with the experimental pose. Inspection revealed that there was a Phe in the pocket which was anti in the model but +gauche in the crystal structure. Since the corresponding residue in rhodopsin was Ala, there was no way this unusual conformation could have been predicted ab initio. Fixing the conformation of this residue to +gauche suddenly gave excellent alignment with the ligand orientation in the crystal structure.

An instructive piece of work that shows that homology modeling and docking of ligands into GPCRs of unknown structure can be fruitful. However, it also indicates caveats like the Phe conformation which are hard to account for de novo. However, since structures of members in this important family of proteins are unavailable anyway, even some predictive ability might be welcome in this area.

Costanzi, S. (2008). On the Applicability of GPCR Homology Models to Computer-Aided Drug Discovery: A Comparison between In Silico and Crystal Structures of the ß2-Adrenergic Receptor. Journal of Medicinal Chemistry DOI: 10.1021/jm800044k

posted at: 23:46 | path: /sci/bio | permanent link to this entry

NASA Authorization Act of 2008 - Innovation Prizes
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Space Politics covers HR 6063, the NASA Authorization Act of 2008. Let the dissection of the bill begin! In my first skim through it, I saw quite a bit that would be interest to commercial space, Earth science, space science, and aeronautic advocates. Innovative-sounding provisions were also added to the NASA lunar plan. It didn't strike me as a "NASA business as usual" bill. There might be some sticker shock along the way, though.

NASA authorization bill introduced in House

NASA authorization bill text available

Here's the prize section (and for your reference, here's Section 314 that's mentioned). Although it would increase the potential size of NASA prizes, I didn't see any request for actual funding for prizes.

SEC. 1106. INNOVATION PRIZES.

(a) In General- Prizes can play a useful role in encouraging innovation in the development of technologies and products that can assist NASA in its aeronautics and space activities, and the use of such prizes by NASA should be encouraged.

(b) Amendments- Section 314 of the National Aeronautics and Space Act of 1958 is amended--

(1) by amending subsection (b) to read as follows:

`(b) Topics- In selecting topics for prize competitions, the Administrator shall consult widely both within and outside the Federal Government, and may empanel advisory committees. The Administrator shall give consideration to prize goals such as the demonstration of the ability to provide energy to the lunar surface from space-based solar power systems, demonstration of innovative near-Earth object survey and deflection strategies, and innovative approaches to improving the safety and efficiency of aviation systems.'; and

(2) in subsection (i)(4) by striking `$10,000,000' and inserting `$50,000,000'.

posted at: 23:40 | path: /sci/astro | permanent link to this entry

Geoengineering Debated
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This is from the website of the Bulletin of the Atomic Scientists:

Has the time come for geoengineering?

Scientists have long studied and debated the promises and perils of deliberately influencing Earth's weather and climate systems. But today, faced with ever more pessimistic predictions about the pace of global warming and the irrevocable damage it could do to the planet, some are talking seriously about implementing theoretical geoengineering schemes such as blocking the sun as an emergency response.

In "20 Reasons Why Geoengineering May Be a Bad Idea" ^PDF (from the May/June 2008 Bulletin), Alan Robock raises a host of scientific, social, and ethical issues posed by geoengineering. Now, Robock and four fellow discussants debate how to weigh geoengineering’s potential benefits against its negative consequences. . .

The site then offers the first two installments of the debate, namely "Climate engineering: Not a panacea, but necessary nonetheless?" by Ken Caldeira, and "Geoengineering could buy the time needed to develop a sustainable energy economy" by Dan Whaley and Margaret S. Leinen.

We'd also encourage you to read a short essay by Martin Bunzl titled "An Ethical Assessment of Geoengineering," which is included as a sidebar in the PDF article referenced above.

There are  no easy answers to the challenges of dangerous climate change and the invariably problematic solutions on offer.  But it's high time that we begin learning about and debating what we can do, and what we should do.

Mike Treder

tipa -- 5/16/2008
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From Shock Breakout to Peak and Beyond: Extensive Panchromatic Observations of the Aspherical Type Ib Supernova 2008D associated with Swift X-ray Transient 080109

• Authors: Maryam Modjaz, W. Li, N. Butler, R. Chornock, D. Perley, S. Blondin, J. S. Bloom, A. V. Filippenko, R. P. Kirshner, D. Kocevski, D. Poznanski, M. Hicken, R. J. Foley, G. S. Stringfellow, P. Berlind, D. Barrado y Navascues, C. H. Blake, H. Bouy, W. Brown, P. Challis, H. Chen, W. H. de Vries, P. Dufour, E. Falco, A. Friedman, M. Ganeshalingam, P. Garnavich, B. Holden, G. Illingworth, J. Liebert, G. H. Marion, N. Lee, S. S. Olivier, E. Olszewski, J. X. Prochaska, J. M. Silverman, N. Smith, D. Starr, T. N. Steele, A. Stockton, G. G. Williams, W. M. Wood-Vasey

Effect of energy deposited by cosmic-ray particles on interferometric gravitational wave detectors

• Authors: Kazuhiro Yamamoto, Hideaki Hayakawa, Atsushi Okada, Takashi Uchiyama, Shinji Miyoki, Masatake Ohashi, Kazuaki Kuroda, Nobuyuki Kanda,