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Garage Biology in Silicon Valley – synthesis

March 11, 2010

Garage Biology in Silicon Valley

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A couple of weeks ago I made a whirlwind trip to San Francisco that turned out to be all about garage biology.  I started off with a talk to the California Assembly Select Committee on Biotechnology.  Here are my slides (Carlson_CA_Assembly_February_2010.pdf), which focus on the role of small business and garage hackers in creating innovation in the Bioeconomy, and here is the agenda (PDF).  See my recent post on "Micro-Brewing the Bioeconomy" for the details of craft brewing as an example of distributed biological manufacturing.  I also did an event at the GBN for the book, and I'll post a link to the recording when it goes live.

I spent most of one Saturday hanging out at a garage biology lab in Silicon Valley.  When I walked in the door, I was impressed by the sophistication of the set-up.  The main project is screening for anti-cancer compounds (though it wasn't clear to me whether this meant small molecules or biologics), and the people involved have skillzzz and an accumulation of used/surplus equipment to accomplish whatever they want; two clean/cell-culture hoods, two biorobots (one of which is being reverse engineered), incubators, plate readers, and all the other doodads you might need.  They aren't messing around.  I didn't get into the details of the project, but the combination of equipment, pedigree, and short conversations with the participants told me all I needed to know.  That doesn't mean they will be successful, of course, just that I believe they are yet another example of what can be attempted in a garage.  This sort of effort is where new jobs, new economic growth, and, most importantly, desperately needed new technologies come from.  Garage innovation is at the heart of the way Silicon Valley works, and it is envied around the world.

IMG_0174.jpgI continue to get push back from people who assert that "it is really too hard" to hack biology in a garage, or too expensive, or that garage labs just can't be up to snuff.  This sort of dissent usually comes out of National Labs, Ivy League professors, or denizens of the beltway.  All I can say to this is — Doodz, you need to get out more.

So why am I not telling you the who and the where for the photos above?  Because, like many garage biology hackers, they are a little skittish given the way the Uncle Sam has been off his rocker for the last few years when it comes to mis-perceived biothreats (Shoot first, Google later).  The people who built the lab pictured above are pursuing a project that is technically well beyond anything discussed on the DIYBio list, and while they may be watching the DIYBio conversation they don't advertise what they are up to.  It would be better for all of us if we could rest assured that conversations about this sort of work could proceed in the open without guys showing up in biohazard suits with weapons drawn — Youtube, at the 00:00:48 mark.  Words fail to describe this video.  Or, rather, I have plenty of choice words to describe the quality of the investigation and planning that went into an armed assault on the residence of an art professor whose many previous public shows and events included biological technologies including hacked bacteria — and indeed I have shared those words with the appropriate individuals in DC, and will do so again — but it won't do my blood pressure any good to go further down that road here.

While the innocuous art professor may be back at work, and while some may view this as water under the bridge, it is not my impression that Federal law enforcement officials truly understand the impact of their behavior.  (Here, I will try again: Dear Feds, You are making us less safe.)  The response to errant "enforcement"efforts (or "career enhancement", depending on your perspective) is exactly what you would expect — people stop talking about what they are doing, making the job of sorting out potential threats all that much harder.  I recall giving a talk in DC in 2003 or so wherein I made this point to a room full of intelligence types (domestic and foreign), and only about half of them — predominantly the younger ones — understood that information was their only tool in this game.  The notion that you could effectively produce safety through prohibiting garage biology and related efforts is the height of folly.  See, for example, "And the Innovation Continues…Starting with Shake and Bake Meth!" for the latest on the effectiveness of domestic prohibition of methamphetamine production.  The effect is — surprise!!! — more innovation.  Just like it always is.  However much garage biology we wind up with, we will be much safer if practitioners are willing to discuss what they are up to without worrying about misdirected badges, search warrants, and guns. 

To be sure, I don't have reason to suspect anything but good intentions and productive work originating from the garage lab shown above.  Nor is a drug screening project likely to result in something scary.  But I certainly can't know they won't make a mistake.  I would feel more comfortable if they, in turn, didn't feel like they had to keep a low profile so that there could be open discussion of potential missteps.  This applies to individuals and governments alike: "Above all else, let us insist that this work happens in the light, subject to the scrutiny of all who choose to examine it." (PDF)  And I am waaay more concerned about what the government might get up to behind closed doors than I am about activities of individuals.  

Next week I am headed to DC for another biosecurity/bioterrorism discussion, which will be interesting in light of the recent "F" grade given to US biopreparedness by the President's Commission on the Prevention of Weapons of Mass Destruction Proliferation and Terrorism.  See also my earlier analysis of the report.  I mention this here because the US Government still doesn't get the role of garage biology in much needed innovation (see the slides above from the talk to the CA Assembly Committee for a list of important technical advances from small businesses and individuals — this discussion is also in the book).  Nor has the US Government clued into the PR job they have ahead of them with students who are gaining skills and who want to practice them in the garage.  Both the FBI and the Biological Weapons Commission Convention (sorry, Piers!) had a presence at iGEM in 2009 — as liasons to students the FBI sent Agents whose cards read "Weapons of Mass Destruction Coordinator".  !!!Calling Chiat\Day!!!

There continues to be a prominent thread of conversation in Washington DC that "biohacking" is somehow aberrant and strange.  But apparently DIYBio, you'll be happy to hear, is a group composed of the Good Guys.  Everyone should feel happy and safe, I guess.  Or maybe not so much, but not for the reasons you might think.

The creation of a false dichotomy between "DIY Biotech" (good guys) and "Biohacking" (bad guys) lends unfortunate credence to the notion that there is an easily identifiable group of well-meaning souls who embrace openness and who are eager to work with the government.  On the contrary, in my experience there are a number of people who are actively hacking biology in their garages who intentionally keep a low profile (I am not certain how many and know of no existing measure, but see discussion above).  This tally included me until a little over a year ago, though now my garage houses a boat under restoration.  These people often consider themselves "hackers", in the same vein as people who hack computers, boats (!), cars, and their own houses.  Yes, it is all hacking, or Making, or whatever you want to call it, and not only is it generally innocuous but it is also the core of technological innovation that drives our economy.  And without direct interaction, I do not believe it is practical to ascribe motivation or intent to an individual – including and especially an incorporated individual – operating in a garage.  Thus, I strongly object to the establishment of a conversation related to biosecurity in which the term "biohacker" has any pejorative connotations precisely because it perpetuates the misconception that i) this group is quantifiable; ii) that the group has any unified motivations or identifiable ethical norms (or anti-norms); iii) that it can realistically be currently addressed (or assessed) as a "group".

Hmm…with that, I have run out of steam for the moment, and have real work to do.  More later.

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Nonsense Detection – The UnScientific Method

March 10, 2010
the following table translates commonly used expressions found in research papers:

Published Translation

" It has long been known…."

I didn't look up the original reference.

" Of great theoretical and practical importance…."

Interesting to me.

" A definite trend is evident…

The data seem practically meaningless

" Three of the examples were chosen for detailed study.."

The others made no sense.

" Typical results are shown..

The best results are shown.

" It is believed that..

I think

" It is generally believed that….

A couple of other guys think so too.

" It is clear that much additional work will be required before a complete understanding of these phenomena is possible..

I don't understand it.

" Correct within an order of magnitude.."


" Statistically oriented projection of the findings..

Wild guess.

" Highly significant area for exploratory study.."

A totally useless topic suggested by my committee.

Source: Unknown

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Pain relief and improved nerve health linked to amino acid, agmatine

March 10, 2010

Agmatine, the natural metabolite of the amino acid arginine, may alleviate pain and benefit nerve health, according to a clinical study published online in the journal Pain Medicine.

The research, lead by neuroscientists Gad Gilad and Varda Gilad, found that people who took agmatine reported accelerated improvement in their neuropathic pain measures and in their health-related quality of life.

Gad Gilad, also CEO of manufacturer Gilad&Gilad, told “Dietary agmatine may help people suffering from lumbar disc-associated radiculopathy, otherwise known as sciatica, to improve their quality of life by alleviating neuropathic symptoms.”

Agmatine, decarboxylated arginine, is a naturally occurring molecule widespread in low amounts in various plants, fish and meats.

Produced synthetically

Agmatine, branded as G-agmatine, is synthesized in living organisms by the decarboxylation of arginine. The product is produced synthetically for the company using a chemical reaction under regulated cGMP conditions.

According to the company, animal experiments have shown that agmatine produces effective neuroprotection in various models of nervous system trauma including stroke, epilepsy, diabetes and neurotoxins, effective reduction of neuropathic pain, anxiolytic and antidepressive effects. It also provides protection in models of heart and kidney injuries.

For humans, historical reports describe hypoglycemic effects and our clinical study indicates alleviation of neuropathic symptoms including pain and motor deficits,” said Gilad.

G-agmatine is thought to benefit health by acting as a shotgun targeting multiple molecular mechanisms critical for healthy nervous system functions. These include:

  • Modulating several neurotransmitters – molecules that transmit nerve signals (notably nicotine, glutamate, and noradrenaline)
  • Blockading membrane channels that transport key salts into cells (notably potassium and calcium)
  • Regulating nitric oxide (NO) production, a ubiquitous regulatory molecule
  • Serving a building block for polyamines, known neuroprotective molecules
  • Preventing processes that destroy extracellular proteins.

Neurologic functions

Gilad believes G-agnatine benefits specifically nerve health by modulating the above mechanisms. “The nerve cells are better conditioned to sustain insults due to fluctuating changes in metabolism or harsh external stimuli which we experience and thus, to be healthier as reflected by the execution of their neurologic functions,” he said.

Meanwhile, more than 20m US citizens cope with circumstances that affect normal peripheral nerve function, said the company.

The research, sponsored by Gilad&Gilad, was published in the journal Pain Medicine (Pain Med, 11: 356–368, 2010) will be presented at the American Academy of Neurology’s 62nd Annual Meeting in Toronto April 10 to April 17, 2010.

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Intendix, The Brain Computer Interface Goes Commercial (video) | Singularity Hub

March 7, 2010
intendix bci from gtec

Intendix is the first thought-to-type system you can buy that’s ready to use out of the package. BCI is going commercial. About time.

The world’s first patient-ready and commercially available brain computer interface just arrived atCeBIT 2010. The Intendix from Guger Technologies (g*tec) is a system that uses an EEG cap to measure brain activity in order to let you type with your thoughts. Meant to work with those with locked-in syndrome, or other disabilities, Intendix is simple enough to use after just 10 minutes of training. You simply focus on a grid of letters as they flash. When your desired letter lights up, brain activity spikes and Intendix types it. As users master the system, a few will be able to type as quickly as 1 letter a second. Besides typing, it can also trigger alarms, convert text to speech, print, copy, or email. Retailing for €9000 (~$12,250), Intendix isn’t cheap, but it’s the first thought to type system available that’s geared towards easy to setup personal use in the home. Brain computer interfaces just got more accessible, and that’s a step towards them becoming more common all over the world.

How commercially available is Intendix? Well they’ve entered the marketing phase where their advertisements don’t actually explain what the product does. I think it took Nike decades to reach that point:

Keyboards and computer mice are only going to take us so far. While some companies are focusing on touchscreens and other next step replacements, the brain computer interface (BCI) is the ultimate I/O device. The ability to directly communicate with machines using our thoughts will allow for greater speed, precision, and intimacy. EEGs, which measure brain activity through the surface of the skin, are a fairly common approach to BCI. We’ve seen them used for typing before, as well as controlling computerstagging images, or even commanding robots. While Intendix is simply a typing system, g*tec has been working on a Second Life control scheme using the same EEG cap:

EEGs have great temporal resolution for a BCI. This allows Intendix to quickly pick up which letter you are focusing on in a grid by flashing different rows and columns of letters and measuring your brain response. g*tec claims to hold the record for typing speed using an EEG cap as seen in this video of a precursor to the Intendix:

As Kurzweil mentioned in his speech about BCI to the MIT XPrize Lab, EEGs are limited in their applications. They have great temporal resolution, but spatially they lack the precision needed to really translate your thoughts into computer actions in a way that exceeds our current keyboard and mouse system. Eventually, we will need to know more than which centers of the brain are active, we’ll need to know about neocortical columns or even individual neurons. That may mean directly wiring electrodes into the brain. We’ve seen success in that arena already, both withspeech and motor controls. Of course, there could be better sensing technology that allows precise spatial and temporal resolution without sticking wires in your head. Projects like the BCI X Prize are aiming to develop them soon.

No matter how the computers of the future will read our thoughts, there’s little doubt that they’ll be communicating directly with our brains. Controlling the digital world will become much more intuitive when we can simply think commands to our devices. With the interconnectivity of social networks and electronic communication, that also means we’ll be able to talk with each other through our thoughts to some degree. The next generation’s Twitter could be broadcasting what we’re thinking. Literally. That level of BCI technology is fairly far off on the horizon, however. Right now we have Intendix; the ability to go to a store, buy a device, and start typing with my thoughts is enough to keep me happy for a while.

[image and video credits: g*tec]
[sources: g*tecIntendix site]

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Can You Hear My Heart Now? Digital Stethoscope gets iPhone App

March 5, 2010

March 5th, 2010 by Aaron Saenz  Filed under Gadgets, medical

digital stethoscope

ThinkLabs just gave their electronic stethoscope an iPhone App. Get ready for your doctor to go digital.

Need to prove you’re human? Doctors can now email your heartbeat using a digital stethoscope and new iPhone App from ThinkLabs. While the ds32a digital stethoscope has been around for years, the recent addition of an iPhone App opens great possibilities for its use. Once an auscultation has been performed, you can look at the digital sound recording on the iPhone (or iPod touch), save it, add notes or photos, and

 email it. This will allow for doctors to build databases of recordings for each patient and provide them with better care. That sort of innovation isn’t exactly cheap: the ds32a retails around $250, the App is $70, and a special jack is required (the recommended one from Belkin costs $70). Yet it’s not that far from a traditional stethoscope (~$100 depending on style) and provides a distinct advantage in application. This is the coolest use of a digital stethoscope we’ve seen in a while, and it’s a sign of the coming information revolution that will lead us into Medicine 2.0.

If we want to take advantage of remarkable stem cell treatments, genetic therapies, and nanobots, we’re going to need better diagnostics to help guide their applications. That’s why the growth in health monitoring is so promising. Right now, digital stethoscopes provide an active means to track patient data over several visits. Eventually, I expect that capability to be included in the vital sign monitoring patches we’ve seen from Toumaz and WIN. Such health monitors may also be able to contain specialized diagnostics like ultrasound, which have already started to become miniaturized. Doctors will be assisted by software that analyzes the information from these devices to help them treat patients, and they’ll probably keep track of everything on their smart phone or tablet computer. There’s no doubt, digital data is going to transform the medical profession. Kudos to ThinkLabs for getting on the wagon now.

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Fluorescent lighting increases nutrients in spinach!

March 5, 2010

New research indicates that fluorescent lighting typically found in supermarkets could boost the levels of vitamins C, K, E and folate in spinach, as well as carotenoids lutein and zeaxanthin.

A team from the USDA’s Agricultural Research Service (ARS) wanted to see how the presentation of spinach in supermarkets – usually in clear plastic containers at around 39F (4C) – affected nutrient levels.

Levels of folate were seen to increase by 84 to 100 per cent over nine days of continuous light exposure, the researchers found, while vitamin K levels were up between 50 and 100 per cent.

The findings could lead to new ways of preserving spinach and other vegetables so they pack the biggest possible nutrient punch, the ARS team concluded.

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Eat this Laziness! : 100 foods that boost productivity

March 1, 2010