Transapient Musings of an S6 Archailect

The biotech toolkit project and the prospects of the bioreactor

Bryan Bishop, 2008-06-13

Author's introductory note. There are a number of DIY (do-it-yourself) free and open source (or shareable and public) projects accessible through the internet including the biotech toolkit, OpenWetWare, diybio, biopunk, biogang, and so on. Because of modern software architecture and technologies, there's the availability to use revision history systems such as git to proliferate collaborative community effort in the same way that the free and open source software (F/OSS) communities have successfully demonstrated (see GNU and Wp's article on 'open source'). In the following document, a simple system of user-oriented software, policies and physical technologies will be presented that emphasizes design strategies and minimizes wasted effort. Additionally, when one reads "community", this means any particular community, since everything can be copied and effortlessly applied in new contexts, thereby allowing anybody -- or any institution (societies, governments, regulatory committees, etc.) -- to have their say.

Anybody who has kept up with modern biology will have noticed bioinformatics. What's interesting about bioinformatics is that it is the application of computational methods, including databases and programming, towards the investigations within biological science research institutions. It allows ridiculously large datasets to be managed with automated machinery, both in terms of robotic arms to fetch yeast knockout libraries and in terms of processes running through databases to find interesting information, like possible cures to diseases, the similarities between different genomes, understanding ecologies or ecosystems and the development of seemingly innumerable advancements in both engineering and science. Although a great deal of these databases and programs are available to the public, what "grounding" is there? In other words, there is a limited availability of tools and machinery that people could use to do interesting things with, as long as their are the ridiculously high barriers to entry to set up labs and other things that, traditionally, require funding to get grants for and such.

The idea of do-it-yourself biotech kits and engineering design is that we can get rid of that overhead with a "bootstrap-once, use-many" system. The idea of the biotech toolkit project ( http://biohack.sf.net/ ) is to make a resource of organized, computationally-tractable (but also, most importantly, human-readable) information on how to implement this social knowledge that has been accumulating in scientific journals and other paper repositories for the past 40 years of computer-usage. What this allows is that through simple collaborative frameworks like git ( see gitweb.cgi or /biotech.git), individuals can contribute to a larger project and include valuable information that would otherwise be lost to obscure dead-tree format books and such. The difference between this and a wiki is small, but an important one. A wiki can be implemented on top of git (like ikiwiki or dokuwiki). However, the majority of wikis out on the web today use something called revision control or history, and usually this is implemented within the wiki software itself -- meaning that the development history of git, svn, cvs, monotone, etc., are completely ignored in place of custom implementations that are not nearly as robust and usually require database projects (MySQL, PostgreSQL, etc.). What this means for end-users, people clicking around and adding information, means little except that the usable set of functional possibilities is expanded rather than restricted by conventional wiki software.

Having information on protocols and materials is an interesting first step, but it is certainly missing the broader picture of what could be possible. This is where the bioreactor project steps in. Simply put, the bioreactor is a biologically "mostly" self-replicable kit that makes all of the materials one would need in order to modify the organisms involved in the bioreactor itself. The reason why it is 'mostly' self-replicating is because of the requirement of a chasis, which will probably be metal, plastic, or some other material to encapsulate different tanks or different cell cultures and so on. The bioreactor is being designed to incorporate all materials necessary, into the genomes of the organisms involved. Friends would be able to make a new bioreactor for another friend, and a chain of proliferation and exponential growth could be developed. Individuals could use it to test out new ideas, to try out do-it-yourself biogerontology experiments, to make biomolecular compounds and run them through purification processes, etc. There are many, many possible uses of such a bioreactor.

The main component of this bioreactor is the idea of a DNA synthesizer incorporated into the biology itself, perhaps an in vitro DNA synthesizer, hopefully in vivo. This component (still a subject of active R&D) would allow new strands of DNA to be implemented on the spot without the use of bulky DNA synthesizers using silicon manufacturing that, frankly, not everyone has access to. The in vitro DNA synthesizer (writozyme) may require either a "retarded" polymerase or protein-based oligonucleotide synthesis. All of the development patterns of the biotech toolkit, the repositories, books, information, communities and so on effortlessly map over to the bioreactor project, with all of the benefits and more.

Resources on git

Git - fast revision control system (asynchronous, amorphous, distributed development)
http://en.wikipedia.org/wiki/Git_(software)
http://savannah.gnu.org/maintenance/UsingGit
http://kerneltrap.org/Linux/Git_on_Windows
http://git.or.cz/gitwiki/InterfacesFrontendsAndTools (for graphical user interfaces)

Google TechTalk on git or see below:

Here's a video on the toolkit and git.

There's also an IRC channel (#hplusroadmap on freenode).
http://freenode.net/
http://irchelp.org/

Maybe you'd like to see the wiki?

The page's predecessor?. It's not quite the predecessor, for manufacturing is still the central focus, however biology provides some useful pieces that can be used to kickstart a number of interesting projects -- especially bioinformatics, which has excellent protocols and support that manufacturing, sadly, simply can't match at the moment (and thus sucks for the basis of a description of what I'm talking about).

A Galactic Internet?

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What applications and knowledge could such a powerful internet that spreads across the galaxy, or even the universe, bring us? Moonbrains, jbrains, mbrains, sjbrains, etc. See Orion's Arm and the megascale engineering mailing list.

What's mine is mine: Brain scans reveal what's behind the aversion to loss of possessions

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Did you ever wonder why it is so difficult to part with your stuff? A new study reveals fascinating insights into the specific neuropsychological mechanisms that are linked with the potential loss of possessions. The research, published by Cell Press in the June 12 issue of the journal Neuron, has important implications for both neuroscience and economics and may even explain why you are reluctant to sell your iPod.

Which Cognitive Enhancers Really Work: Brain Training, Drugs, Vitamins, Meditation or Exercise?

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Can 'brain training' software really increase useful, everyday cognitive function?

Although wisdom may come with age, our brains don't get any faster. Many areas of cognitive function decline over time: attention wavers, processing speed decreases, memory starts to crumble.

All kinds of methods for fighting back against this brain-wide slow-down have been suggested. There is training with computer programs, popping pills, taking nutritional supplements, meditating or even getting some more exercise.

Some want to ward off the scourge of a rapidly ageing population: dementia. Others are looking for competitive advantage against younger, faster brains.

So: what to choose? These methods, along with many others, are often presented as though they're all roughly equivalent, but this isn't true. The scientific evidence currently available is much stronger for some of these options than others.

This post examines what the research currently tells us about each method for cognitive enhancement and delivers a verdict on each.

1. Brain training

Computer programs that promise to improve cognitive function have become all the rage in recent years, mostly on the back of the success of Nintendo's 'Brain Age' game. Many other companies have now jumped on the bandwagon and the market for brain fitness software reached $225 million in the US in 2007 according to a report from SharpBrains.

But what about the science behind the hype?

Certainly cognitive training has been shown to be effective in a few randomised controlled trials, but the evidence is still quite limited. The first large study in older adults without dementia failed to find an improvement in daily functioning from the training, but it did slow decline. Also, this study's method has been criticised.

Other studies have found benefits for specific groups such as children with attention deficit hyperactivity disorder (ADHD) and dyslexia. Whether advantages gained by these groups might be effective for others is a matter for debate.

The real challenge for brain training is showing that practising one type of mental skill transfers over into other real-life benefits. Doing puzzles like Sudoku or completing crosswords probably only improves your performance on those specific tasks.

One new study, though, does suggest that training working memory can increase fluid intelligence - what we use to solve problems which don't rely on things we already know. The study, recently published in The Proceedings of the National Academy of Sciences, found that gains in fluid intelligence were proportional to the amount of working memory training completed.

Unfortunately this is still early-stage exploratory research and many are not convinced that the actual products available on the market are beneficial. Sandra Aamodt, the editor in chief of Nature Neuroscience and Sam Wang, a Princeton University molecular biologist explain in the New York Times:

"In the United States, consumers are expected to spend $80 million this year on brain exercise products, up from $2 million in 2005. Advertising for these products often emphasizes the claim that they are designed by scientists or based on scientific research. To be charitable, we might call them inspired by science -- not to be confused with actually proven by science."

It's telling that the best-selling brain training software - Nintendo's 'Brain Age' - has the lowest level of clinical validation according to a market report from Sharp Brains.

Verdict: Evidence for the benefits of cognitive training for everyday functioning is still very limited. Brain training software currently available is mostly 'inspired by science' rather than based on it. Treat marketers' claims with extreme scepticism. Side-effects are probably limited to repetitive strain injury and a depleted wallet.

2. Drugs

Until recently the main chemical cognitive enhancer most people used was caffeine. But there are a whole batch of new drugs that could challenge caffeine's dominance as the safe stimulant of choice. Of these, two well-known for their 'off-label' use are Modafinil (also known as Provigil) and Ritalin.

Modafinil was originally developed to treat narcolepsy, but is now used by many people as a cognitive enhancer. Studies reported by the Academy of Medical Sciences have shown that Provigil does indeed improve aspects of memory: mainly verbal working memory, planning performance, working memory and executive inhibitory control (ability to stay on-task).

Other important aspects of cognitive function such as attention, however, were not affected by Modafinil. This study found Modafinil did not enhance spatial memory span, rapid visual information processing or attentional set-shifting. This study also found that Modafinil did not enhance attention.

The reason many use Modafinil is that it doesn't seem to have any short- or long-term side-effects and it is not addictive (although it's lack of side-effects may well have been exaggerated). For example it doesn't increase blood-pressure or heart-rate, as caffeine does. It may give you a headache, though, just like caffeine.

Ritalin was originally developed to treat ADHD yet adults have begun using it as a cognitive enhancer. It seems to work best in young people, enhancing spatial working memory and cognitive flexibility. Effects on other aspects of cognition such as verbal learning and long-term memory are relatively small.

In most people Ritalin tends to improve mood, increase activity and arousal, but it's effects are more varied and can include anxiety, tiredness and lowered mood.

Verdict: Amongst the chemical cognitive enhancers Modafinil is currently fashionable for grown-ups. But is it really that much better than caffeine? This study and this study suggest that in warding off sleep Modafinil is no more effective than caffeine - and caffeine is legal and readily available. Probably better to stick to tea or coffee.

3. Nutritional supplements

There are all kinds of claims for the abilities of nutritional supplements to enhance cognition. For example, vitamin B6 has been found to enhance memory (but far from conclusively) and there are many other claims being made by marketers for vitamins E, B12, folate, neurosteroids and so on.

However, in reviewing the research the Academy of Medical Sciences points out that most of the studies are few, far between and small in scope.

Verdict: Unproven, but probably not dangerous as long as you're not exceeding the recommended daily allowances. On the downside supplements can be costly.

4. Meditation

Meditation, like nutritional supplements, is another modern cure-all, but what does the evidence tell us about its effect on cognitive function? A forthcoming review of the research published in the Annals of the New York Academy of Sciences looks at the effects of meditation on cognitive function.

There is some limited evidence that meditation can benefit cognitive function overall, and memory in particular. But this research is at a very early stage and needs to be replicated by different researchers.

A major problem in this research is the fact that there are many different types of meditation. It might be that there is some kind of common active ingredient in meditation, but this has yet to be identified.

Verdict: Meditation still has to be considered unproven as a cognitive enhancer but it probably won't do you any harm, plus it's free.

5. Exercise

Whether you're old or young, fit or even suffering from a neurodegenerative disorder, aerobic exercise has been found to be beneficial for cognitive health. Randomised controlled trials, along with reviews of many of these trials (such as this one in Neuromolecular Medicine), have shown that exercise improves cognitive function across the board. It has also been found to be particularly good at enhancing executive control processes (e.g. planning and working memory).

Exercise is also thought to encourage the growth of new brain cells. In the past scientists always thought that neurogenesis - growing new brain cells - was impossible in humans. New studies, though, have shown that we can grow new brain cells.

Research reviewed in Neuromolecular Medicine suggests physical exercise can promote neurogenesis in the hippocampus - an area of the brain thought to be important in memory and learning.

Verdict: The evidence for exercise boosting cognitive function is head-and-shoulders above that for brain training, drugs, nutritional supplements and meditation. Scientifically, on the current evidence, exercise is the best way to enhance your cognitive function. And as for its side-effects: yes there is the chance of an injury but exercise can also reduce weight, lower the chance of dementia, improve mood and lead to a longer life-span. Damn those side-effects!

The results are in (for now)

Even though exercise is the current winner for enhancing cognition, this might change in the future. Maybe better drugs for enhancing brain function will be developed - possibly en route to improved treatments for conditions like Alzheimer's. Or maybe studies on nutritional supplements, brain training software or particular forms of meditation may provide firmer evidence.

Maybe.

On current evidence exercise is clearly the best method for increasing useful everyday cognitive functioning. And in the future we may even have exercise regimes that are specifically targeted at enhancing cognitive function.

E-Mail After Death: Revenge or Rapture?

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Youvebeenleftbehind.com lets saved Christians send e-mails from heaven.

Open Source Drug Discovery gets Funding

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Mat Todd reports on the Synaptic Leap:

We've been successful in securing a large government grant with an open source component. The 3-year project concerns the enantioselective synthesis of PZQ for a low price, with the World Health Organisation as partner. (PDF of the Uni Sydney outcomes is here). The funding comes from the Australian Research Council (the main government funding agency in Australia). We wrote the proposal emphasising the possibilities inherent in the open source approach to doing science, and we're very pleased that this was seen as positive by an official grant-funding agency. The funding will allow us to increase our efforts on using TSL to drive our project forward much faster.

New skills for a new era

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Continuing previous thoughts are science education and what people should know, here is an interesting one. Melanie Swan has a new post on her blog about required skills in a hyperconnected, technology-centric world. She writes

the educated person of today must be able to express thoughts in a variety of technology-based media

She goes on to say that this new literacy requires, in addition to writing, a knowledge of “computer software, 3d printing, virtual worlds, synthetic biology and visual storytelling”. While I don’t completely agree with that list, it is clear that our education is not adequate for a world that is changing very fast. Take something like The Bug. Right now, it is something for a select few, but I remember my childhood, playing with mechano sets, DIY gliders, etc. The Bug is today’s mechano set. The other day I talked about peope doing molecular modeling at home, as a hobby. Technology is changing so fast these days that we can essentially never catch up, so what do we do? How do we encourage and deliver this new literacy.

While our education system(s) needs to change to accommodate technology, and not simply pay it lip service, the real impact will come outside of the classroom. Summer camps emphasizing knowledge and technology, an exposure to new ways of communicating, etc. That’s where we, as early adopters can really help. It is also why I am optimistic about the future. For a while there was a big gap in the technological awareness between generations, but that is not likely to be true with the generation that I belong to, or indeed those a little older. Will there be a generation of geeks? Highly unlikely. Human society is not going to change overnight, but if we get more people involved from a young age and make them appreciate, embrace, and respect science and technology, and how they enable us to communicate and explore, then we’ll all be in a better place.

All of this sounds fairly Utopian, and if you catch me in more cynical moments you’re likely to get a much more grumbly response, but even then I don’t see why we can’t get there. Perhaps we will need to just because our video games will force us to :).

On a related note, a lot of us have wondered about the future of libraries. I believe that they should be the gatekeepers of information, providing expertise in tools that help us find and manage information in a virtual world (these libraries will inherently be virtual). I wonder what role they could/should play in helping people with this new literacy.

The hidden universal distribution of amino acids biosynthetic networks: a genomic perspective on its origins and evolution

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Background:
Twenty amino acids are the universal building blocks of proteins. However, their biosynthetic routes do not appear to be universal from an Escherichia coli-centric perspective. Nevertheless it is necessary to understand their origin and evolution in a global context - i.e. to include more 'model' species and alternative routes-. We use a comparative genomics approach to assess the origin and evolution of amino acid biosynthetic alternative network branches.
Results:
We predicted a core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids, suggesting that this core occurred in the last common ancestor by tracking the taxonomic distribution of amino acids biosynthetic enzymes. Additionally, we detail the distribution of two types of alternative branches to this core: i) analogs - enzymes that catalyze the same reaction (using the same metabolites) and belong to different superfamilies; and ii) 'alternologs' - herein defined as branches that, proceeding via different metabolites converge to the same end product-. We suggest that the origin of alternative branches is closely related to different environmental metabolite sources and life-styles among species.
Conclusions:
The multi-organismal seed strategy employed in this work improves the precision of dating and evolutionary relationships among amino acids biosynthetic branches. This strategy could be extended to diverse metabolic routes and even other biological processes. Additionally, we introduce the concept of 'alternolog', which not only plays an important role in the relationships between structure and function in biological networks, but also as shown here, has strong implications on their evolution, almost equal to paralogy and analogy.

The Open Science Web

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David Recordon has a nice, optimistic post about the Open Web. I have long felt that the web is the ultimate platform, and the past few years have only strengthened this opinion, as we make the web more programmable and start leveraging it as a multi-way communication medium (in conjunction with such technologies as XMPP). Much of the tech community is focused on leveraging this web around social networks. My hope is that we in the scientific community can take this to the next level, literally connecting data and information first and then the people.

We are producers and consumers of data. The data lies in our labs, in our papers, in central repositories, on web sites and services; a mishmash of static and dynamic data of all types. We use these data to derive information and hypotheses. Call me conceited but as a scientific community we are probably the stewards of a decent, important, chunk, of the worlds collective intelligence. Except that now we have the ability to bring a distributed collective intelligence to life. What do we need?

An open data web: We are getting there. I am convinced that this is inevitable and more optimistic as time goes on. Not only is the open data web a necessary requirement for us to arrive at the next era in scientific discovery, it will be the primary driving engine. In the sciences, especially the life sciences, the Semantic Web is going to play a key role in how we find data and relationships, not only among pieces of data, but bringing people and knowledge together
Participation: Not just from the early adopters, but the scientific community at large. I am actually less optimistic about this, although I have a feeling that’s just my cynical side. We have an opportunity here folks to really take the next step to solving new problems, leveraging our distributed knowledge
Bursty Work: This is my mantra, but needs participation. In discussions about The BioGang, the issue of critical mass has come up, but if you look at what’s been happening recently, we are slowly taking steps there. A community of software savvy scientists, eventually tapped into wet lab scientists can truly come together for what I hope will be a new era of science. Is it going to happen in the next five years? I seriously doubt it, but we’re just planting seeds at this time. A decade? Now we’re talking. Will be fun to see what happens

Aside: After meeting Matt Wood, discussions with Pawel over time, and seeing the activity over on FriendFeed, I am even more optimistic that we can have an impact as a community of like minded geeks with a diversity of interests and skills.

Technorati Tags: Open Web, Open Science, Bursty Work

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Built for Speed: Printing Buildings

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Contour Crafting is an effort to scale up rapid prototyping/manufacturing (a billion dollar industry to make 3 dimensional parts) and inkjet printing techniques to the scale of building multi-story buildings and vehicles. The process could accelerate the trillion dollar (US only) construction industry by 200 times. Projections indicate costs will be around one fifth as much as conventional construction. (Land prices are unchanged, so the actual prices of homes would not change as much in say Hawaii, Tokyo, Manhattan or San Francisco). Using this process, a single house or a colony of houses, each with possibly a different design, may be automatically constructed in a single run, embedded in each house all the conduits for electrical, plumbing and air-conditioning. [H/T to a reader Bonesteel] Contour crafting could be one part of a new manufacturing revolution

The machine will cost between $500K to $700K for average size (2000 sq ft -- 200 m2) detached houses. This is not much given that a concrete pump truck is now $300k-$400K. Note that with one machine numerous homes can be built. The first commercial machines to be available this year, 2008. The machine will be collapsible to form into an easy truck load. The unloading and setup will take between 1-2 hours.

Behrokh Khoshnevis is the visionary who has been driving this concept. He is the Director of the Center for Rapid Automated Fabrication Technologies (CRAFT) and Director of Manufacturing Engineering Graduate Program at USC.

Initial plan is to use the technology for emergency shelters and low-income housing in underdeveloped countries (Mexico, with the demand for nearly 500,000 houses per year, seems to be a good starting choice for implementation), almost immediately after its development they will address local building codes for commercial deployment of CC in the US.

Because of the unprecedented speed of CC construction, attendant improvements in the construction inspection process will be required. They plan to develop advanced sensory systems and information technologies for automated real-time inspection and feedback to municipal computers overseeing ongoing CC construction activities at various locations.

Competing Construction Automation
There are two categories of automation considered by the Japanese construction companies. The first uses single task robots that can replace simple labor
activities at the construction sites. Single task robots can be classified by four different types- concrete floor finishing, spray painting, tile inspection, and material handling.

The second category consists of fully automated systems that can construct high
raised steel buildings or steel reinforced concrete buildings using prefabricated
components. An example of this approach is Big-Canopy, which is the world’s first automated construction system for building a precisely defined concrete structure and has four independent masts supporting an overhead crane which delivers components at the control of a simple joystick. All tasks are scheduled and controlled by a centralised information control system. The introduction of robotics at construction sites has contributed to productivity, safety, and quality improvements. Yet, the contribution of robotics at current levels is not revolutionary and current automation approaches are still geared toward conventional processes. Automating conventional processes (such as using a brick laying robot) is invariably expensive, hence the associated cost saving is minimal. Fast changing construction requirements and project complexities create complicated requirements and exceptional challenges for automation technology to meet.

The Big Canopy construction system can be divided into the following subsystems:
· a roof supported by four tower crane posts, which are situated outside the building
· a complex hoist system with three cranes mounted against the roof
· a jib crane on the roof to mount and to dismantle the tower crane posts
· a high-speed construction lift to all floors
· all components bar-coded for easy identification
· a material management system to manage the flow of materials and components

The Big Canopy automated construction system ensures good working and environmental conditions, shorter construction time (about 13% less), less waste and improved overall productivity (0.9% less cost).

There are Prefabricated homes
Modular homes
Panelized homes

Panelized home construction can complete the project in 90 days from the time we begin to dig. Custom plans generally take four-to-six months from start of construction to finish. The weather-tight shell finished in days, as opposed to the many weeks required with "site framing."

So all prior efforts to improve building construction are vastly inferior to contour construction if contour construction delivers on its goals.

Three subsystems are required to build a complete house in one day. The Extrudable Materials and Fabrication (EMF) thrust will research and develop materials, extrusion systems, and structures built by extrusion of materials. The Modular Components and Assembly (MCA) thrust will research and develop the non-extrudable components required by the grand challenge such as reinforcement, electrical, plumbing, and sensor systems and on the robots required both to assemble these components and to deploy the extrusion systems developed by the first thrust. The Integrated Software Systems (ISS) thrust will research and develop the software needed to go from design through construction, including planning and controlling the behavior of the multitude of robots to be developed by the previous thrust, and providing the logistical support required for constructing a house in a day, or beyond this to constructing a full community in a small number of days.

Environmental benefits
Globally more than 40 percent of all raw materials are consumed in the construction process. Each of the 6 million new houses built in the United States have 3-7 tons of waste from construction.

FURTHER READING
This concept is like the inflatable electric car idea. Rethinking the process for how a major segment of our economy works to enable cost breakthroughs.

Inflatable cars and scaling up printer technology for making buildings are the kind of powerful ideas that could enable acceleration of economic growth even without successful development super technologies (like fusion, molecular nanotechnology or super artificial intelligence). It is similar to how Henry Ford's mass production methods accelerated economic growth at the beginning of 1900s. However, there is no reason we cannot re-invent the car and construction and develop super technologies. So even without molecular nanotechnology there
could be a step up in economic growth rate with ideas like this and inflatable electric cars. These ideas are also very compatible with a nanofactory world.

Youtube Contour Crafting videos

Center for Rapid Automated Fabrication Technologies at the University of Southern California

The goal of the Center for Rapid Automated Fabrication Technologies (CRAFT) is to develop the science and engineering needed for rapid automated fabrication of objects of various size up to mega-scale structures such as, boats, industrial objects, public art and whole building structures.

Selective Inhibition sintering (SIS) method is capable of making plastic as well as metallic parts without the use of laser.

Megascale fabrication article

The perils of power tool amputation

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Newsweek has a fascinating article on 'body integrity identity disorder', a condition where people feel they need to have a limb amputated to become normal and often go to extreme lengths to have their arm or leg removed.

BIID, otherwise known as apotemnophilia, is often confused with amputee fetishism, where sexual gratification is linked to ideas of amputation. However, they seem quite distinct in most cases.

Although its not widely studied, the desire seems to be much more about the feeling of being comfortable in one's body rather than anything explicitly sexual.

The Newsweek article discusses the condition and looks at some of the latest scientific research on this seemingly strange desire, but suffers from some rather sloppy thinking about the mind and brain. For example:

BIID is attracting the attention of researchers who suspect that the condition may be related to other body image disorders—including anorexia, body dysmorphic disorder, and gender identity disorder—that at first glance may seem entirely psychological, but may be linked to physical differences in the brain.

All psychological changes are related to physical differences in the brain, so this is a completely bogus distinction.

Whenever you read a sentence like this translate it into the language of theories and evidence.

In other words, '[conditions] that might seem better explained by solely psychological theories now need to be updated as evidence on biological brain changes becomes available'.

The piece then goes on to repeat a common but trashy fallacy that you can describe any brain difference as something that is 'hard wired'.

Despite these disastrous misunderstandings of the fundamentals of neuroscience, the piece is actually quite good.

It's interesting that while the medical viewpoint is that BIID is linked to other body image disorders, the people who have these desires do not feel it is a disorder at all.

I was struck by the fact that a couple of people who have acquired amputations anecdotally report that they feel much better afterwards.

This is in marked contrast to people with body dysmorphic disorder who after plastic surgery to 'fix' their self-perceived distorted body part typically do not feel 'cured'. Or those with anorexia who do not feel satisfied even when they are at a near-fatal point of emaciation.

It would be fascinating to follow-up people who have BIID after they've acquired a successful amputation to see how they fare.

If their desires disappear, they do not become newly fixated on amputating another limb, or experience improved mental health and life-satisfaction as a result, how far can we go in saying its a mental illness?

I've had a search and, sadly, found no such studies.

Link to Newsweek article 'Cutting Desire'.

Full Fledged Space Power

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NASA chief urges Europe to build manned spaceship

"NASA encouraged Europe on Thursday to develop its own manned spaceship, which would give the world -- and particularly the U.S. -- another way of reaching the international space station. Europe became "a full-fledged space power," the agency's administrator said, when flight controllers at a European Space Agency center guided an unmanned cargo ship to the international space station in April, successfully delivering food, water and clothes."

Body position affects memory for events

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This article was originally posted on March 27, 2007

When we see a familiar face, or even a photo of a favorite car or pet, we're often flooded with memories from our past. Sometimes just seeing a person or object that's similar to the ones in our memory will trigger recollections we never knew we had. Maybe you've had a memory triggered by a scent or the texture of an object. Sometimes emotions such as happiness or anger will spur vivid memories, too.

A new study adds an unexpected method to the list of ways to spur memories about our past: body position. That's right: just holding your body in the right position means you'll have faster, more accurate access to certain memories. If you stand as if holding a golf club, you're quicker to remember an event that happened while you were golfing than if you position your body in a non-golfing pose.

Even more fascinating than the facts about body position and memory is how they were learned. A team led by Katinka Dijkstra actually had young adult and older adult volunteers assume different body positions while asking them to remember particular events from their lives. Sometimes the body position matched the memory:

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In which I get funded: The Comparative Biogerontology Initiative

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I’m on a team that just got awarded a Keck Futures Initiative grant. This is the fruit of the NAKFI conference we attended last year on “The Future of Human Healthspan.” It was an unusual conference: instead of giving individual talks, the participants were split up into “task groups” that were each assigned a different question related to the biology of aging. At the end of the conference, each group gave a presentation. (The proceedings are available in overpriced booklet form here or as free HTML here).

Our group started off with one subject (stochasticity of gene expression) but took a sharp left turn and ended up thinking more broadly. We ended up focusing on what evolutionary biology might teach us about aging.

Within groups of species that share a given body plan (e.g., bats, birds, dogs, or primates), there is significant variation in maximum life expectancy, and we believe this variation is genetically determined. In other words, natural selection has performed dozens of parallel “experiments” in which more or less similarly constructed organisms end up with different lifespans, based on variations in a range of factors (some known or long-suspected, like antioxidant enzymes, and others as yet undetermined). Some of these factors may be unique to specific body plans, whereas others might be universal. The challenge we set ourselves was ambitious: How can we use the “data set” (i.e., variation in lifespan among related organisms) to identify novel determinants of longevity? Thus was born the Comparative Biogerontology Initiative.

We soon realized that we’d need a great deal of expertise, not only from within biogerontology but also from other fields, some with which we often have dealings (biostatistics, computational biology) and others with which we have almost no interaction in our daily professional lives (veterinary medicine, pathology, histology, comparative physiology). Identifying the relevant experts is a profound challenge in itself: How does one identify expertise in a field in which one has none? Hence a lot of what we’re going to be doing at first is figuring out who our collaborators will be — leading to the contorted mission statement:

These researchers will hold two meetings with senior scholars to develop a plan to test hypotheses about biological factors that control lifespan and healthspan, and compare tissues from multiple species of animals. The scholars are pathologists, comparative physiologists, methodologists, statisticians, and experts in the biology of aging.

“Hold…meetings…to develop a plan to test hypotheses”…no doubt, this will inflame the sensibilities of those who advocate a more direct frontal assault on the problem of aging; indeed, if this were all we were planning to do, they would have a point. We know a lot about aging and it makes sense to move forward aggressively where knowledge is already extensive — but those efforts are being undertaken already, and will continue. All of us are keeping our day jobs.

The CBI was conceived not as a replacement for more direct studies of more relevant models (like humans), but as a complement: by carefully examining aging in understudied organisms, and by systematically identifying the factors that contribute to their differential longevities, our hope is to discover entirely new determinants of aging and lifespan. By bringing in expertise from around the scientific world, including disciplines that don’t usually overlap with biogerontology, our hope is to break new ground in the biology of lifespan (and, if you like, to open new fronts in the battle against aging). In the process, we’ll learn more about the evolutionarily conserved bases of aging throughout the animal kingdom, identify new biomarkers of aging, and pose enough new questions to keep the next generation of biogerontologists busy for years to come.

The other members of the team are, dare I say it, eminences grises of biogerontology — some of whose work and thoughts (e.g., Steve Austad and Richard Miller) we’ve discussed here in the past (and one of whom is my current boss, Judy Campisi). I’m personally thrilled for a chance to work with and learn from them.

And who knows? After we hold our meetings to develop a plan to test a hypothesis, we might actually test one, and then I can blog about it here. Watch this space for further developments.

Why do online opinions evolve differently to offline ones?

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The way in which opinions form, spread through societies and evolve over time is a hot topic among researchers because of their increasing ability to measure and simulate what’s going on.

The field offers some juicy puzzles that look ripe for picking by somebody with the right kind of insight. For example, why do people bother to vote in elections in which they have little control over the result when a “rational” individual ought to conclude that it is not worth taking part.

A similar conundrum is why people contribute to online opinion sites such as Amazon’s book review system or the Internet Movie Database’s (IMDB) ratings system. When there are already a hundred 5-star reviews, why contribute another?

Today Fang Wu and Bernardo Huberman at the HP Laboratories in Palo Alto present the results of their analysis of this problem. And curiously, it looks as if online opinions form in a subtley different way to offline ones.

The researchers studied the patterns of millions of opinions posted on Amazon and the IMDB and found some interesting trends. They say:

“Contrary to the common phenomenon of group polarization observed offline, we measured a strong tendency towards moderate views in the course of time.”

That might come as a surprise to anyone who has followed the discussion on almost any online forum but Wu and Huberman have an idea how moderation seems to evolve. They suggest that people are most likely to express a view when their opinion is different from the prevailing consensus because such a contribution will have a bigger effect on the group.

They tested the idea by looking at the contributions of people who added detailed reviews against those who simply clicked a button. Sure enough, those who invest more effort are more likely to have an opposing view. It is these opposing views that tend to moderate future views.

By contrast, sites such as Jyte in which users can only click a button to give their opinion tend to show herding behaviour in which people copy their peers, just as they often do offline.

Wu and Huberman’s analysis raises more questions than answers for me. But they point out that the study of online opinions has been neglected until now. That looks set to change.

Ref: arxiv.org/abs/0805.3537: Public Discourse in the Web Does Not Exhibit Group Polarization

Carnival of Space Week 57

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The Carnival of Space 57 is up at Out of the Cradle

This site contributed an article about some problems with lorentz propulsion tests but success with the SpaceX Falcon 9

International Space Development day 1

International Space Development day 2

International Space Development day 3

Babe in the Universe also had International space development coverage

There is covereage of the Mars Phoenix lander

Check out the carnival for more.

The meaning response

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I am currently reading Daniel Moerman's "Meaning, medicine and the 'placebo effect'". As well as containing many interesting asides, the book discusses what is at the heart of the so-called placebo effect: patients' response to the meaning of their treatment. Moerman calls this the 'meaning response'. This response to meaning explains why two inert pills produce more cures than one inert pill, and why inert injections are even more effective (because "everybody knows" that injections are more powerful than pills). But importantly, it is possible to show that doctors are as important in producing the meaning response as patients. Gracely et al (1985) looked at the effect of placebo on pain in patients having their wisdom teeth extracted. The study was set up as a standard double-blind (neither the doctor nor the patient knows if the patient is getting a real medicine or an inert placebo), with the possibilities being a placebo, fentanyl (which usually reduces pain) and naloxone (which usually blocks reduction in pain, so could be expected to increase the pain of the procedure). The twist was that for the first half of the experiment the doctors, but not the patients, were told that a supply problem meant that no patient would be getting the pain-relieving fentanyl. In the second half the doctors were told that the problem had been resolved, so that now the patients might receive fentanyl. By comparing levels of patient pain in the placebo condition is possible to gauge the effect of doctor expectations on the meaning response of the patients. In this condition patients are all receiving inert substances, and they all 'know' the same thing: they might receive a placebo, pain-relief or 'pain-enhancement'. The doctors don't tell them about the supply problem and, for that matter, they don't know themselves for definite what the patient is given. The only difference is that for the patients in the first half, the doctors think they know that pain-relief is not a possibility, whereas in the second half it is. The graph of the results, copied from Moerman's book is below:

As you can see, patients in the PN group --- those whose doctors thought they might receive pain-relief had a large pain-relieving placebo effect. Those in the PNF group --- those whose doctors thought they couldn't receive pain-relief --- didn't have a pain-relieving placebo effect.

What I think is interesting about this study is, firstly, it confirms the need for rigorous double-blind controls in studies of medicine and, secondly, just how significant an effect this subtle manipulation has. The doctors don't know anything definite, and they certainly aren't telling the patients what they suspect or guess, but somehow --- a look? a slightly brighter smile? a slightly lowered tone? --- they communicate their knowledge of the probabilities to the patients who then experience a real change in their levels of pain because of it.

A striking aspect of the meaning response is that one could suppose that patients have control over their experience of different levels of pain. After all, we know that the pills are inert. Could we just imagine ourselves a 'placebo effect' in all situations where we have unnecessary pain? Sadly, normally we can't do this --- the meaning response doesn't work like that. Doctors are required to give patients permission to feel less pain. Perhaps a fundamental part of the creation of meaning is that it requires other people.

Update: A great recent post by Vaughan 'placebo is not what you think', which deserves to be linked up with this post

Refs

Gracely, R. H., Dubner, R., Deeter, W. R., & Wolskee, P. J. (1985). Clinicians' expectations influence placebo analgesia. Lancet, 1(8419), 43.

Moerman, D. E. (2002). Meaning, medicine, and the "placebo effect". Cambridge University Press: New York.

Electrically controlled microvalves to integrate microchip polymerase chain reaction and capillary electrophoresis

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Govind V. Kaigala, Viet N. Hoang, Christopher J. Backhouse
(Paper from Lab Chip)
Govind V. Kaigala, Lab Chip, 2008, DOI: 10.1039/b802853b
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Carbon nanotube field effect transistors for the fast and selective detection of human immunoglobulin G

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Cristina C. Cid, Jordi Riu, Alicia Maroto, F. Xavier Rius
(Communication from Analyst)
Cristina C. Cid, Analyst, 2008, DOI: 10.1039/b805301b
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Grant Gopher

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URL: http://www.grantgopher.com/

American company that specialized in locating open funding opportunities across all funding categories in all fifty states.