Transapient Musings of an S6 Archailect Hey there, my name is Bryan Bishop. Here's to trying to keep up with yourself. RSS.
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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.
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.
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.
The model cell uses as the cytoplasm a solution of two different polymers, PEG and dextran (Panel A). The image in Panel B is the image in Panel A highlighted with fluorescent dyes. The blue region is PEG, which is concentrated in the outer polymer solution; the green area is the portion of the membrane that contains PEG groups, which interact with the contents of the cell; and the red area is the portion of the membrane with fewer PEG groups, which interact with the contents of the cell to a lesser extent. After exposure to a concentrated solution of sugar, the cell converted to a budded form (Panel C). A dextran-rich mixture filled the bud, while a PEG-rich mixture remained inside the body of the cell. Panel D shows the image in Panel C highlighted with fluorescent dyes. The blue area is the PEG-rich region. This new structure exhibits polarity both in the membrane and in the aqueous interior of the model cell. (Credit: Christine Keating, Penn State)
The team's next step is to create a cascade in polarity. "By creating a model cytoplasm with different compositions, we demonstrated that we can control the behavior of cell membranes," said Keating. "Now we want to find out what will happen if, for example, we add an enzyme whose activity depends on the compositions of the cytoplasm and cell membrane."
Although Keating and her colleagues plan to continue adding components to their model cell, they don't expect to make a real cell. "We aren't trying to generate life here. Rather, we want to understand the physical principles that govern biological systems," said Keating. "For me the big picture is trying to understand how the staggering complexity observed in biological systems might have arisen from seemingly simple chemical and physical principles."
Evolutionary biologist Paul Ewald drags us into the sewer to discuss germs. Why are some more harmful than others? How could we make the harmful ones benign? Searching for answers, he examines a disgusting, fascinating case: diarrhoea.
...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?
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
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.
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'.
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. . .
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.
Following is an email that I received from the EngineerLive.com newsletter. Just wanna spread it out loud...
Weimar, Germany, June 10-12: Petroleum and Chemical Conference
Can you afford to miss a conference that could affect the way you use electrical and automation solutions for years to come?
At PCIC Europe 2008, you can learn from the experience of engineers like yourself who have installed, implemented and used electrical and automation equipment in real applications in your industry. Register now at:
With the emphasis on the practical, a number of papers will be presented at the conference, by experts from end user companies, engineering companies, manufacturers, regulators, certifying bodies and international standardization organizations. See the latest agenda at
Speakers will be available for questioning, making PCIC Europe a place for end users to air their views and influence the way your industry implements and uses electrical and automation equipment, now and in the future.
As well as the programme speakers, there will also be a guest appearance by Dr Bernard Bulkin, a leading expert on climate change who will give a presentation entitled, 'What do Engineers need to know about Sustainable Development?'-go to http://www.pcic-europe.eu for more information on this.
His presentation will examine the core issues of sustainable development and how they can be applied to engineering design, the importance of systems thinking and the education of the next generation of engineers.
Join us in Weimar, Germany, from June 10 -12, Register now at:
Following is an invitation by email that my university friend, Dr. Manal from UKM has sent to potential participants. This round the 15th Regional Symposium on Chemical Engineering (RSCE) will be carried out together with 22nd Symposium of Malaysian Chemical Engineering (SOMChE), which is Malaysia level symposium. Check out the adopted email below:
Dear Potential Participants of RSCE-SOMChE 2008,
We are inviting you all to participate in the 15th Regional Symposium on Chemical Engineering that will
be held in conjunction with the 22nd Symposium of Malaysian
Chemical Engineering on the 2nd - 3rd December '08, Impiana KLCC Hotel & Spa, Kuala Lumpur, Malaysia.
You are welcome to KL and enjoy your stay here while attending the conference
Updates of RSCE-SOMCHE08 :
The conference date: 2nd - 3rd December 2008
The venue of the conference: Impiana KLCC Hotel & Spa
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NASA’s Phoenix Mars lander will drop onto the Red Planet’s surface on May 25. JPL has put together a very cool video with animations and interviews with engineers about what this portable lab will go through on its way down. This is very well done (even if one guy talks about friction with the atmosphere, when really it’s compression of the air on Mars that slows the probe down), and gives you a real sense of why landing on Mars is hard. They even high a High Def version (but it’s 187Mb!).
I think it’s fantastic that folks at NASA (or at least JPL) understand that it’s stuff like this that gets people excited, and kudos for them on putting it online. But now if they would just allow embedding it! I couldn’t figure out how to do it. If someone else can, let me know, and I’ll plop it in here. But I can embed the one on YouTube!
Nanotechnology—inspired by biology—can use catalytic motors to convert chemical to mechanical energy, using fuels that are chemically simpler than ATP—the energy currency of biology—and catalysts that are simpler than enzymes. In a Nanowerk Spotlight, Michael Berger describes nanotech catalytic motors for transporting micron-scale cargo. Excerpts from “Catalytic nanotransporters for nanotechnology applications outside biological systems“:
The catalytic conversion of chemical to mechanical energy is ubiquitous in biology, powering such important and diverse processes as cell division, skeletal muscle movement, protein synthesis, and transport of cargo within cells. Catalytic ‘engines’ will be key components of active micron- and sub-micron scale systems for controlled movement, particle assembly, and separations. …we show an example where catalytic nanomotors can, in principle, be tethered or coupled to other objects to act as the engines of nanoscale assemblies. Additionally, an object that moves by generating a continuous surface force in a fluid can, in principle, be used to pump the fluid by the same catalytic mechanism. Thus, by immobilizing these nanomotors, a group of scientists have developed micro/nanofluidic pumps that transduce energy catalytically.
“Until recently, catalytic micro- and nanomotors have been more or less unknown outside biology” Dr. Ayusman Sen explains to Nanowerk. “For nanotechnology researchers, catalyzed movement on the nanoscale is a fairly new phenomenon and there is much to be learned from nature’s motor systems. There is a good possibility that unexpected applications will arise from exploratory research.”
…”By analogy to biological systems” he says, “we can project some obvious applications of catalytic nanomotors, including: (a) engines for micro/nanoscopic machines, (b) chemotactic roving sensors, (c) delivery vehicles for molecules and nanoparticles, and (d) formation of patterns or arrays by autonomous local deposition of materials.”
Sen’s group has demonstrated that one can build nanomotors ‘from scratch’ that mimic biological motors by using catalytic reactions to create forces based on chemical gradients. These motors are autonomous in that they do not require external electric, magnetic, or optical fields as energy sources. Instead, the input energy is supplied locally and chemically.
…The motor function is not disrupted due to the presence of passive cargo although a decrease in speed was observed. In addition, motors with nickel segments can overcome both Brownian orientational fluctuations and biased rotation of the rod-sphere doublet to enable persistent steerable uniaxial motion in an external magnetic field. The scientists are thus able to control even Brownian motion, at the microscopic level.
…Sen’s work, which is the first examples of nano/microscale objects outside biological systems that move through catalysis, also reveals that chemotaxis (i.e. the movement by a cell or organism in reaction to a chemical stimulus) does not require a sophisticated ‘temporal sensing’ mechanism commonly attributed to bacteria. Rather, the nanoparticles move up a fuel gradient through catalysis; a straightforward extension is movement towards or away from a signaling molecule — a promoter or an inhibitor of the catalytic reaction.
This behavior provides a novel way to direct particle movement towards specific targets, even while allowing them to sample a large region of fluid by apparently diffusive motion. Sen says this discovery is potentially important in the design of ’smart’ autonomous nano-robots, which could move independently in the direction they are needed, perhaps by harvesting energy from glucose or other abundant fuels in biological or organic systems.
I'm not sure if this is new or not, but the X PRIZE Foundation has a lot more information on their future X PRIZE plans than I've seen before on their web site. I've posted on some of this already based on XPF lectures and articles, but without nearly as much detail. I don't know how many of these will ultimately become actual competitions; some of them clearly at least have initial funding for prize development.
Exploration - No new space prizes are listed here, but they have
received a grant to explore an Ocean X PRIZE Suite. The suite will likely focus on any or all of four target areas:
oceanographic research, exploration, conservation, and healing. Some of these sound like they belong in the energy/environment suite as much as the exploration one, but there's nothing wrong with addressing 2 areas at the same time. In fact I'd like to see some space prizes that overlap with these other areas.
Life Sciences - This mentions a Human Longevity X PRIZE, but most of the section covers the Cancer X PRIZE Suite, which I'll discuss in a separate post.
Education - They are investigating education prizes that might involve learning technologies or city competitions. Their inspirations range from the FIRST Robotics Competition to Expeditionary Learning. One approach I might take, instead of something like an educational software tool prize, is an X PRIZE (or numerous smaller prizes) that students can try to win like FIRST, TARC, Cansat, and so on. The prizes of course would be designed to require the competitor students to learn a lot.
The X PRIZE Foundation has secured grants to explore a Village Utility X PRIZE. ... The global competition would leverage technology-based innovation to develop more effective ways to deliver power, water and connectivity to communities in need in the developing world.
Energy and Environment - Again from the site (I hope they find a synonym for "develop"):
The X PRIZE foundation received a grant to develop a prize to develop and promote widespread adoption of clean aviation fuel. We’re also developing a partnership for second generation small scale distributed biofuel production technologies.
Some people go fishing on their day off. Yves Rossy likes to jump out of a small plane with a pair of jet-powered wings and perform figure eights above the Swiss Alps. The revolutionary human flying machine comes after five years of training and many more years of dreaming.
In this week’s Chemistry World business news round-up, we cover a vaccine for hayfever, the quest for cellulosic biofuels, and a potential end to dribbling after visits to the dentist.
Chemical Industry
Scrubbing up: Belgium-based Solvay has launched a new product to treat sulfur dioxide in flue gases. The company is investing $40 million (£21 million) at a site in Wyoming, US, to make the sodium bicarbonate based product, called SOLVAir Select 300, with initial production capacity of 125,000 tonnes per year.
Nitric acid flow: BASF has started operating a new nitric acid plant at its Antwerp site, with a 500,000 tonne per year capacity. The acid will mainly be used in polyurethane manufacture. The German firm says the nitric acid plant is the first built entirely with the company’s own technology - a cost-saving measure, BASF says.
Have a drink: Unilever has opened a global R&D centre of excellence for its drinks business - to develop plant-based products with health angle, ‘from weight management teas to cholesterol-lowering milk drinks’. The centre will employ 90 product developers, and be funded from Unilever’s near €50 million annual drinks R&D budget.
Pharmaceuticals
Hayfever vaccine edges closer: UK-based allergy treatment company Allergy Therapeutics has announced the successful completion of its Phase III clinical trial for its experimental hayfever vaccine. Patients who suffer from hayfever from grass pollen - the most common cause of the allergy - experienced a 13 per cent improvement in symptoms when given the vaccine rather than a placebo. The company says it will file for European approval for the vaccine in early 2009 - and estimated the worldwide market for allergy treatments is over $10 billion.
Further Pfizer closure: US pharmaceuticals giant Pfizer has announced it will close its Indiana plant, formerly used to manufacture Exubera, the inhaled insulin product the firm scrapped in October 2007 due to poor sales. The closure, to be completed by mid-2009, means the plant’s remaining 140 jobs will be cut - adding to the 660 workers made redundant at the plant in January. Pfizer has already announced the closure of several other manufacturing plants - including the UK plant at Sandwich.
Risk of death: AstraZeneca’s beta blocker drug Toprol, frequently given to patients before non-heart-related surgery to reduce the risk of heart attack, more than doubles the risk of stroke and increases the likelihood of death by 33 per cent, researchers report in The Lancet. This increased risk may outweigh the reduced chance of heart attack, the researchers conclude, and further large trials are urgently needed.
Danger downplayed: GlaxoSmithKline has been downplaying the heart attack risk associated with HIV drug abacavir (Ziagen), reports The Independent. The company was officially told about the risk in 2005 - but stronger data published in The Lancet in April prompted the firm to issue a statement to investors that the findings are ‘unexpected’ and ‘unconfirmed’. Independent scientists say the Lancet study doesn’t prove a causal link between the drug and heart attack - but that GSK’s studies do not disprove the link either. The FDA and EMEA are currently reviewing safety data on the drug.
Dentist leaves you numb?: A drug that counteracts the effects of local anaesthetics used by dentists could soon be helping people to avoid dribbling or accidentally biting their numbed tongue after dental work. On 9 May the US Food and Drug Administration (FDA) gave approval to Novalar Pharmaceuticals to start marketing a drug which cuts by more than half the time taken to recover full sensation.
Merck outsources to India: US drugmaker Merck has signed a five year deal with Ranbaxy to develop anti-infective drugs. The Indian firm will discover and develop drugs through to Phase IIa clinical trials, with Merck to carry out later stage clinical trials and bring the drug to market. Ranbaxy will receive an initial payment - and estimates it could eventually receive over $100 million, depending on the drugs developed reaching certain milestones.
Lilly biotech complex complete: Eli Lilly has completed the final phase of its $1 billion new biotechnology research and development facility. The US pharmaceutical firm says 500 scientists and support staff will develop new biotech-based drugs at the site. Two earlier phases - a pilot plant and a research support facility - were completed in 2006.
Trial confirms Trasylol risk of death: Final results of a clinical trial stopped prematurely in October 2007 due to high numbers of patient deaths have confirmed that Bayer drug Trasylol (aprotinin) is associated with a 53 per cent higher risk of death than alternative treatments. Aprotinin, or alternative drugs tranexamic acid or aminocaproic acid, had been routinely given to prevent blood loss during heart surgery - but approximately 6 per cent of patients given aprotinin died within 30 days of surgery, compared to 3 per cent given the alternatives. Bayer has responded by pulling the drug from all countries where it remained in the supply chain.
Sanofi loses patent appeal: Sanofi Aventis has lost its appeal over a US court’s 2007 decision to strike down patents for the French pharmaceutical firm’s anticlotting drug Lovenox. The court had ruled that the patents were unenforceable because the company had failed to disclose certain information to the US patent office. Sanofi earned €2.6 billion (£2.1 billion) from Lovenox in 2007 - but may now face competition from generic copies of the drug.
Energy
Biofuel ventures: German firms Süd-Chemie and Linde have agreed to collaborate to develop and market second generation biofuel production plants. The companies say their biotech approach will deliver ethanol or related fuels from cellulosic biomass - Süd-Chemie contributing biocatalysis and bioprocessing expertise, Linde providing engineering know-how.
Meanwhile, US firms DuPont and Genencor have announced they will form a 50-50 joint venture to develop a low cost technology to make cellulosic ethanol. The companies will invest an initial $140 million over the first three years, and will initially target corn and sugarcane waste as a feedstock.
Last year I wrote a guide to the most accessible and well-written psychology blogs online. I have just finished updating this guide and I'm pleased to see the vast majority of these blogs are, more or less, still going strong a year later.
As ever I'm always on the lookout for accessible, fresh blogging in psychology and related fields. So if you'd like to suggest your own blog or someone else's work for inclusion then leave a comment below or drop me an email.
Following many, many others, I finally got myself a SlideShareaccount and uploaded a recent presentation on MetWare, our metabolomics data warehouse project. Some spoilers: SQL, RDF/SKOS, JSF.
Lots of visitors are hitting the Sciencebase site look for information on stem cell research. It is a subject I’ve written about before, both on this site and elsewhere, but I thought it might be useful, given that my alma mater is at the forefront of stem cell research in the UK, to provide a FAQ on the subject of stem cells. Just to be clear, usually when the media uses the phrase stem cells, they really mean human embryonic stem cells, but that occasionally takes print journalists over the wordcount, so it’s commonly abbreviated to stem cells, so for the sake of brevity, I’ll do the same here.
What are stem cells?
Stem cells are primordial cells that can divide without limit and differentiate into the various types of cell used to build our livers, hearts, bones, brains, skin, and other organs, blood cells, nerves etc. More details.
Where are stem cells found?
Pluripotent stem cells, which can form any cell type, can be harvested from human embryos that are just a few days old.
What do researchers do with harvested stem cells?
Harvested pluripotent stem cells can be cultured in the laboratory to create “stem cell lines” for research and development.
What can be done with cultured stem cells?
A cultured stem cell line can multiply indefinitely in the lab, so once produced researchers can use the same line without having to harvest new stem cells.
What might stem cells be used for?
Cultured stem cell lines can be “engineered” to differentiate into specific cell types, which researchers are hoping can be transplanted into a patient to treat a wide range of problems, including cancer, spinal cord injury, stroke, burns, heart disease, diabetes, birth defects and neurodegenerative disorders, such as Parkinson’s and Alzheimer’s disease.
Have researchers cured diseases with stem cells?
Not yet, stem cell research is little more than a decade old and is very much in the experimental stages. Legal, funding, and ethical issues in the US, UK and elsewhere have slowed stem cell advances during this time to some degree.
Aren’t bone marrow transplants using stem cells?
The well-known bone marrow transplant uses the blood stem cells found in bone marrow and has been used to treat a range of diseases, such as leukaemia, for four decades.
Do embryos have to be used to harvest stem cells?
Not necessarily, the umbilical cord is being researched as an alternative source of stem cells that would sidestep some of the ethical issues associated with embryonic stem cells. There is also research into using tissue-specific stem cells from adult donors.
A much more detailed FAQ on stem cell research can be found on the ISSCR site.
Kristy M. Ainslie, Casey M. Kraning, Tejal A. Desai (Paper from Lab Chip) Kristy M. Ainslie, Lab Chip, 2008, DOI: 10.1039/b800604k To cite this article before page numbers are assigned, use the DOI form of citation above. The content of this RSS Feed (c) The Royal Society of Chemistry
So, yesterday I was chatting with my pal Lee Kottner (personal stylist to Jen-Luc Piquant, and an occasional guest blogger at the cocktail party), who lives in New York City, and I asked her which of the myriad of events she was planning to attend at the upcoming World Science Festival. Her response: "Festival? There's a science festival?"
Hell, yeah, there's a World Science Festival! It takes place May 29 through June 1, and it is going to be teh awesome. It worries me that Lee, of all people, hadn't yet heard of it, because she's pretty plugged into that sort of thing. Time to get the word out people! Alas, I will not be able to attend the festival personally, but here's my Top Ten list of the events I would be attending, if I lived anywhere within easy driving (or Amtrak/subway/bus) distance of NYC (and could split myself into multiple clones since many of them directly conflict with each other). You can see a complete schedule of all events here; there's even a blog.
1. Parallel Worlds, Parallel Lives, Thursday, May 29th, 6 - 8:30 PM, The Paley Center for Media. Any fans of the multiverse out there? This event is tailor-made for you (and all your doppelgangers in parallel universes). Hugh Everett III was a theoretical physicist who devised the Many Worlds theory in the 1950s as a way of explaining what happens to all the other possibilities once the wave function collapses in quantum theory. His son, Mark Oliver Everett, is a musician with the alternative band Eels ("Souljacker Pt 1" has been on my cardio workout playlist for a couple of years now). Many Worlds languished for a very long time as kind of a fringe theory, but it's enjoying a bit of a resurgence. So much so that NOVA has produced a documentary about Everett pere et fils, detailing the younger Everett's "personal journey to understand the the astounding contribution that his reclusive father... made to physics." PBS will air the documentary this fall; now is your chance to see it first, and also participate in a panel discussion with Mark Everett, Michio Kaku, and Max Tegmark, moderated by Brian Cox.
2. Toil and Trouble: Stories of Experiments Gone Wrong, Thursday, May 29, 7:30 - 9:00 PM, The Moth at Symphony Space. Failure is an integral part of the scientific process: without it, no progress would ever be made. But for some reason, we only hear about the successes -- maybe everyone's concerned about losing their funding. The Moth is a renowned storytelling collective, fostering the art of the raconteur in the 21st century, so it's a perfect venue for scientists to tell their stories of experiments gone wrong -- horribly wrong! -- and other writers to explore, in narrative form, their ongoing relationship with science. String theorist Jim Gates will be on hand, along with cosmologist Michael Turner, Lucy Hawking (a.k.a., "Spawn of Stephen"), and novelist Nathan Englander.
3. The Brain and Bourne, Friday, May 30, 5:00 - 8:00 PM, The Museum of Modern Art. As a proud princess of pop culture science (I'd wear the tiara more often, but it itches), it is killing me -- just killing me, I tell you -- to miss this fantastic session. They'll be screening The Bourne Identity, and afterwards, the producer/director Doug Liman and neuroscientist Giulio Tononi will participate in a panel discussion exploring the science behind the entire Bourne trilogy: brain function, memory, personality and identity, among other issues. Award-winning screenwriter and producer James Schamus, CEO of Focus Features (Brokeback Mountain, Lost in Translation, Atonement), will moderate. Maybe if we close our eyes and wish really, really hard, Matt Damon will show up, too. Hey, we can dream. Apparently MoMA's Film Department has acquired the trilogy for its permanent collection. They've got taste, those curators. Bring your own popcorn and Twizzlers.
4. IJK, Friday, May 30, 7:00 - 8:30 PM, The New Victory Theater. French theater troupe Compagnie 11 will present "a witty, physics-inspired showcase of sonic juggling." Sonic juggling, people! That's gotta be pretty cool. The name "IJK" refers to mathematics' designators of direction in a 3-D world. Apparently, "the show explores space and movement in a balancing of light and dark that weave whimsy with geometry." Once Compagnie 11 has wowed the audience with their skills, Heidi Hammel of the Science Science Institute in Boulder, Colorado, will talk about some of the connections between the acrobatic antics and cosmic motion: the planets, comets, and galaxies.
5. Armitage Gone! Dance: The Elegant Universe, Friday, May 30, 7:30 - 8:30 PM, Works & Process at the Guggenheim Museum. You've read the book (or the first few chapters anyway), you've seen the NOVA special, and you've been wondering what the Brian Greene string theory franchise would dream up next. Wonder no more: string theory meets modern dance as famed director/choreographer Karole Armitage debuts a new work inspired by Greene's bestselling book. The performance "blends music, dance, text, and projected imagery to create a vibrant portrait of the universe as revealed by cutting-edge physics," and will include discussion by the aforementioned Jim Gates and composer Lukas Ligeti, who wrote the score. (Jen-Luc Piquant wants to know which dancer will play Peter Woit. C'mon, he has to be in there, too! Every performance piece needs some central conflict.)
6. Science of Disney Imagineering, 12:30 - 1:30 PM, NYU Skirball Center. (Also at 10:00 AM and 3:00 PM on the same day) The kids should love this one. Scientists and engineers from Walt Disney Imagineering will pull back the curtain and reveal the science behind that Disney theme park magic. They'll talk about the chemistry of creating colors and of fireworks, and how to make smog and other special effects. Maybe they'll even explain why the animatronic Jack Sparrow recently added to Disneyland's Pirates of the Caribbean ride looks so creepily more lifelike than the older ones. (Animatronic technology has come a long way, baby!)
7. Cool Jobs, Friday, May 30, 4:00 - 5:30 PM, NYU Kimmel Center for University Life. Okay, I already have a pretty cool job, but in an alternate universe, I'd totally be a forensics specialist like Peter Diaczuk. He's the real deal, director of forensic science at the John Jay College of Criminal Justice, where he spends his days (and probably the occasional night) researching everything from underwater fingerprints, blood spatter patterns (we just blogged about this!) and how bullets ricochet off different surfaces. He won't be the only cool scientist on hand for this multimedia event, intended to inspire curious minds of all ages: oceanographer and marine botanist Sylvia Earle will be there, as well as Christopher McKay, a planetary scientist with NASA Ames Research Center, molecular biologist Betty Pace, and one of the Walt Disney Imagineers, Ben Schwegler, who specialized in developing sustainable, energy-efficient theme parks.
8. Science of Sports, Saturday, May 31, 3:00 - 4:30 PM, NYU Coles Sports Center. How often do you get the chance to see Olympic athletes and NBA players in the same room as physicists and physiologists? This program promises "a lively mix of action, audience participation and video, creating the excitement of a live sporting event." Physics, biomechanics, biochemistry and so forth all have some bearing on all kinds of sports, from running and skiing, to basketball and bicycling -- even the martial arts.
9. QED: A Reading, Saturday, May 31, 8:00 - 9:30 PM, Columbia University's Miller Theater. It's Feynman. It's Alda. It's Alda playing Feynman in a reading of the classic play by Peter Parnell. 'Nuff said.
10. Plague in Gotham, Sunday, June 1, 2:00 - 3:00 PM, New York Historical Society. The NYHS has a new exhibition about the deadly cholera outbreaks in 19th century New York City -- I actually wrote about cholera epidemics last year -- and they figured, what a nice way to bring in leading epidemiologists and disaster-preparedness officials to discuss how well we are equipped, in the 21st century, to deal with a possible global pandemic. (Hurricane Katrina's aftermath did not inspire confidence in our organizational infrastructure.) They will also be showing excerpts from a new TV miniseries version of The Andromeda Strain.
There's so much more to choose from. Oh, and there's also a Science Street Fair, Saturday, May 31, 10:00 AM - 6:00 PM, Washington Square Park/NYU. Two years ago, I participated in a similar event, manning a booth to demonstrate the physics of the fight (i.e., martial arts). We won't be there this time around, but there'll be lots of other cool stuff going on. Jen-Luc sez check it out!
Frontal lobe damage changes performance on the 'Pepsi challenge'. Isn't the world a better place now we know that?
Philosophy Nowreviews 'Freedom and Neurobiology' by John Searle.
In an article for Salon, our recent interviewee neurologist Robert Burton gets stuck into a high-tech huckster promoting expensive SPECT scans to diagnose Alzheimer's and herbal supplements to treat the brain disorder.
Channel N discovers a video lecture by Antonio Damasio on the neuroscience of emotion.
Psychologist Charles Fernyhough turned every moment of the first three years of his daughter's life into a research project notes The Telegraph as they review the resulting book.
Treatment Online on research that has found that variations in serotinergic neuroreceptors may indicate severity of depression.
13 ways to quickly improve your decision-making are discussed by PsyBlog.
The Age has a fantastic article on the psychology of risk and why we're so bad at judging it.
"The Change You Deserve". The slogan for antidepressant drug Effexor, and now, the slogan for the US Republican party!
Furious Seasons notes that a recent study on bipolar disorder being overdiagnosed is being supported by leading bipolar researchers.
APA psychology magazine Monitor has an excellent article on how research with deaf people who can't sign might shed light on the fundamentals of cognition.
Burgeoning research on the neuroscience of mystical experiences is discussed in the The New York Times.
BBC News reports that music can enhance the taste of wine. If only it could do the same for brussel sprouts.
The brain is not modular: what fMRI really tells us. An article in Scientific American Mind discusses limitations of brain scanning.
Deric Bownds covers a study that finds our facial touch sensitivity is enhanced by viewing a touch.
The excellent ABC Radio National's All in the Mind discusses the neurobiology of nicotine addiction and concerns about new anti-smoking drugs.
Developing Intelligence covers a fascinating study on time distortion due to visual flicker.
The Wall Street Journal on the possibility of the US Goverment awarding Purple Hearts, a medal for soldiers wounded in battle, for cases of PTSD (thanks Kyle!).
Looks like NASA is finally disposing of the tooling used to build the orbiters, which had been moved to storage at Michoud a few years ago: No more new orbiters (if anyone really wanted to build any)....
On net@nite I heard that Dipity, a great site for mashing up timelines uses Freebase as one of its information sources. An excellent example is this timeline for Marillion embedded below
Earlier today, on Friendfeed, Alex Iskold described an “aha” moment for Powerset, which I have been quite underwhelmed by thus far (although it has a gorgeous UI). When I browsed over to the search link, it seemed to be that the reason the results appeared as they did were because they came from Freebase, whose structure made the query very powerful. Wonder if others think that’s the primary reason as well? The Wikipedia results for the query were not that impressive.
So what do these results tell us? Well, perhaps there is value in taking data and adding structure the way Freebase and dbpedia are doing. The ability to generate different representations, etc is quite powerful. I can already envision what Pierre might do with some of these tools and the work he has been doing with Freebase and Wikipedia.
These examples are somewhat trivial, but it is not difficult to imagine more interesting scenarios, perhaps to represent protein interactions, or trying to find non-obvious relationships and linkages. Will be interesting to see what kinds of applications are developed on the backs of these data platforms
Nuclear fission is the process in which a nucleus decays into two fragments. For large nucleii, this process is a complicated one in which the nucleus undergoes several stages of deformation before tearing itself apart.
In recent years, physicists have predicted that fission ought to be affected by the presence of electrons in orbit about the nucleus. That’s because any change in the shape of the nucleus naturally affects the electrons which tend to absorb energy making fission less likely. And the more electrons there are, the more energy they absorb. But the effect has never been observed because ordinary, naturally ocurring elements simply don’t have enough electrons to make this effect significant.
Today, Vlad Dzuba and Vic Flambuam at the University of New South Wales in Australia have calculated the strength of this effect for superheavy elements which would have more electrons. They say that although the effect is tiny for naturally ocurring nuclei with fewer than 100 or so protons, it would be hugely significant for these larger nuclei. In fact, they calculate that an atom with 160 protons would have double the expected half life because of this effect.
That could have significant implications for how much of this stuff we’re likely to find because elements that decay quickly tend to be rarer) . Last week, arxivblog reported on the potential discovery of element 122 (with 122 protons). Perhaps the groups looking for superheavies should be setting their sights much, much higher.
Editor's note: The current thinking is that Scott Parazynski's summit window is centered on 22 May. Weather and human traffic are the main factors affecting Scott's progress to the summit.
Our original plan did not work out in terms of comms and updates we planned to do from from Base Camp. So ... here is the back up plan: post your comments below. If you simply want to wish Scott "good luck, best wishes, etc." post that and I will do a head count. If, however, you have something a bit more expansive to say - please post it. Please try and make it simple so that I can condense it down to something I can efficiently convey to Scott and that he can keep in his oxygen-starved brain. Longer comments will be left online for Scott to read when he gets back home.
Scott will be the first human to both fly in space and summit the highest peak on our planet. What does this mean in terms of personal determination and endurance? In terms of exploration and pushing frontiers? As a preview of things to come - and of risks to be taken - on other worlds?
We won't see a similar combination and alignment of first accomplishments again until someone summits the highest lunar peak - or Olympus Mons on Mars.
Send your thoughts to the summit of Mt. Everest. Give Scott something to think about. Be a part of this unique climb.
Further updates and fresh images from Mt. Everest at Everest On Orbit
One of the things I've been hoping to see with the Automotive X PRIZE is major companies with large-scale manufacturing capabilities entering the competition. I like to see the small teams and their innovative approaches, but I also like to see "dinosaurs" (as some NewSpace people refer to the large government-oriented companies in their industry) grow "fur". They can do things that small companies can't - each has its advantages.
Here's the news I've been waiting for, from X PRIZE Cars:
The Tata Group is one of India's largest and most respected business conglomerates, with revenues in 2006-07 of $28.8 billion or Rs129,994 crore (not including Corus financials), the equivalent of about 3.2 per cent of the country's GDP, and a market capitalisation of $66.26 billion as on April 30, 2008. Tata companies together employ some 289,500 people.
X PRIZE Cars notes that Tata Motors alone is pretty big. Now we'll have to see how the other major auto manufacturers react.
The accompanying press release mentions some other new contestants:
Other recent entrants to the Letter of Intent program include Motive Industries of Canada, Western Washington University, Hybrid Electric Vehicle Technologies, Inc. of Chicago, IL and TTW Turin Italy of Turin, Italy. Rock and Roll Hall of Famer Neil Young also intends to enter his 1960 Lincoln Continental conversion into the competition, along with his partner Jonathan Goodwin.
There's a lot more news in this recent X PRIZE Cars post.
Jason Rosenhouse of EvolutionBlog linked to an article by Steven Pinker in The New Republic:
The Stupidity of DignityConservative bioethics' latest, most dangerous ploy.This spring, the President's Council on Bioethics released a 555-page report, titled Human Dignity and Bioethics. The Council, created in 2001 by George W. Bush, is a panel of scholars charged with advising the president and exploring policy issues related to the ethics of biomedical innovation...Many people are vaguely disquieted by developments (real or imagined) that could alter minds and bodies in novel ways. ... Traditionalists and conservatives by temperament distrust radical change. Egalitarians worry about an arms race in enhancement techniques. And anyone is likely to have a "yuck" response when contemplating unprecedented manipulations of our biology. The President's Council has become a forum for the airing of this disquiet, and the concept of "dignity" a rubric for expounding on it. This collection of essays is the culmination of a long effort by the Council to place dignity at the center of bioethics. The general feeling is that, even if a new technology would improve life and health and decrease suffering and waste, it might have to be rejected, or even outlawed, if it affronted human dignity.
Although the Council includes two heavy hitters of neuroscience...
Floyd E. Bloom, M.D. Professor Emeritus in the Molecular and Integrative Neurosciences at The Scripps Research Institute, and the founding CEO and board chairman of Neurome, Inc.
Michael S. Gazzaniga, Ph.D. Director of Sage Center for the Study of Mind, University of California, Santa Barbara.
Although the Dignity report presents itself as a scholarly deliberation of universal moral concerns, it springs from a movement to impose a radical political agenda, fed by fervent religious impulses, onto American biomedicine.
The report's oddness begins with its list of contributors. Two (Adam Schulman and Daniel Davis) are Council staffers, and wrote superb introductory pieces. Of the remaining 21, four (Leon R. Kass, David Gelernter, Robert George, and Robert Kraynak) are vociferous advocates of a central role for religion in morality and public life, and another eleven work for Christian institutions (all but two of the institutions Catholic). Of course, institutional affiliation does not entail partiality, but, with three-quarters of the invited contributors having religious entanglements, one gets a sense that the fix is in. A deeper look confirms it.
But why are ice cream cones undignified?? Because that's the view of Leon Kass, the former chair of the Council. As Pinker explains:
Kass has a problem not just with longevity and health but with the modern conception of freedom. There is a "mortal danger," he writes, in the notion "that a person has a right over his body, a right that allows him to do whatever he wants to do with it." He is troubled by cosmetic surgery, by gender reassignment, and by women who postpone motherhood or choose to remain single in their twenties. Sometimes his fixation on dignity takes him right off the deep end:
Even a book review in Studies in Christian Ethics found Kass's squeamishness to be excessive (Clark, 1996):
Much that he has to say is significant, and even cogent. But it is one thing to draw attention to such neglected topics as the duty of hospitality, or good table manners, and another to spend such energy denouncing minor shifts in public appetites: ’the walking street eater ... is a being led by his appetite ... this doglike feeding, if one must engage in it, ought to be kept from public view’. So eating a hamburger ’on the run’ is really wicked: not - we must presume-because it’s bad food badly cooked, not because its purchase finances bad farming practices, but because it’s too impatient, too ’uncivilised’, because it imposes our ’ingestions and chewings’ on others.
With ice cream in hand, President George W. Bush departs Manning's Ice Cream and Milk in Clarks Summit, Pa., Thursday, Oct. 19, 2006. White House photo by Paul Morse.