Life blog

Kickstarting a great new documentary

I'm a film hack. Yeah, some of my short vids have hundreds of thousands of views or even millions, and some (nameless) have contributed to big donations, but I'm still a hack. Last fall I had a very very brief moment of insanity when I thought, just thought, fantasized, really, that, maybe, I could do a documentary on iGEM, synthbio, and DIYbio.

Y'see, we're living in the early days of a renaissance in Biology. Wouldn't it be great to capture all that, travel the country, talk science in a broad-sweeping documentary?

But then I realized what it would take for me to do it: being a hack, it would be much harder to get to the level I wanted. The gap between my skill level, equipment access, time, and money and what was needed was way too large, even to try and fund it via Kickstarter.

But then, at iGEM 2010, I bumped into two guys whom I had initially met at iGEM 2009, and who now had a cool project they were working on (see video below).

Yeah, it's a documnetary about synthetic biology.

And they are raising funds via Kickstarter.

And I pledged $300. Don't know about you, but $300 is a big deal for me. But, it's also a big deal that this documentary get made.

Will you join me and help these guys get the funds they need?

These guys have great style, sensibility, and focus (loved the trailer, below, and check out the cool excerpts). It's gonna be an awesome documentary and will kick ass at Sundance. But only if you join me in helping them.

What are you waiting for? Head over to Kickstarter and pledge something. Wouldn't you say 25 bucks should help?

And then get all your friends to help out too.

 

Are scientists afraid of blogs and tweets?

Nature has a nice wee article (no subscription required to read this one, FTW!) on the state of what one might call "informal" peer review - the challenges and questions to published works that come from blogs and tweets and the like.

For those of us who have been talking about the changes needed in the whole infrastructure and culture of science discourse (particularly the lock publishers have on research papers), this Nature article holds no surprises. Indeed, it comes off making some scientists seem a bit whiny.

The article points to some recent events where scientists have been skewered online for papers or claims made. This reminds me of the early days of blogging when folks were trying hard to control the message and were freaking out when anyone said anything.

The paper does have some great examples and quotes though. For example, David Goldstein, from Duke's Center for Human Genome Variation, is quoted saying, "if the work is solid, it hold up over time". And the efforts by PLoS with comments on papers, how arXiv.org works, and ratings from F1000 are good to show to those who are probably reading the article to figure out how to survive the blogosphere.

My favorite comment by the author, though, is:

One solution may lie in new ways of capturing, organizing and measuring all these scattered inputs, so that they end up making a coherent contribution to science instead of just fading back into the blogosphere.

I've been harping on this for a while and still think there's an opportunity to create a solution like this. I think there is a lot of good thinking, plenty of examples in other industries, and folks are doing parts of this solution, such as trying to think of other ways to change how we calculate the impact of a paper (à la Technorati or through real-time stats), author ID systems, or ways to turn the science paper into the social object. The article also mentions Jason Priem's work on alternate paper metrics (alt-metrics).

It feels like 2004 all over again as another industry discovers the power of devolving the power back to the masses. And the Web was initially designed by scientists, for scientist - what's there to fear?

UPDATE 28jan11: Related to this topic, Zachary Knight has an incisive commentary on how all this was protrayed.

Image from Mike Babcock

Human microbial ecology - cool study

I mentioned a few weeks back a review in Nature about a trio of scientists studying the contributions of gut microbial ecology in preemies that get necrotizing enterocolitis (NEC). Sneaky, sneaky, it turns out that a paper on this work was posted that the review didn't mention or link to. I subsequently found a great article out of the UC Berkeley media relations team that is an even better review of the work, with some excellent quotes from the investigators themselves.

Link: Scientists sequence gut microbes of premature infant

It's a fascinating story. The microbes in preemie feces were collected daily and either sequenced completely or identified by 16S rRNA sequences. The investigators were then able to visualize a time course of the abundance of different microbes (image to upper-right) and to start to understand the contributions of these microbes to pathology, particularly NEC.

It's cool to see the shifts in population as the gut microbes settle in. Interestingly (and not surprising), there were some microbes that are known to be pathogenic, but didn't really affect the preemie's health.

The thought, though, is that there might be some strain specificity within microbe species, or something related to the balance of all the other bacteria. This seems to correlate well with the findings from folks studying the contribution of gut microbes to immune system development.

If you're into developments in human microbial ecology (which I highly recommend new grad students study), I urge you to read this paper (here's the link from the article linked above) and the back story in the article linked above.

What do you think of this?

Image from the paper showing a time course of the gut microbial species

Doing stand-up at IgniteAmherst Feb 8th

Just a note that I'll be doing a 5-minute stand-up act at IngiteAmherst at the Eric Carle Museum of Picture Book Art (125 West Bay Road, Amherst, MA).

Link: IngiteAmherst: Making stuff

Our theme is "Making Stuff". Our valley is steeped in a rich history of making stuff, from the straw hat industry of Amherst to Holyoke and Springfield and Northampton. That tradition continues and we'll hear thought-provoking Ignites from folks Making Stuff in our valley.

There'll be folks talking about Fish, Games, Museums, and Biz. I'll be on hand to give a whirlwind tour of DIYBio (working title "The past, present, and future of making stuff through biology").

My plan (working on talk today) will be about all the ways we use biology to make stuff, starting with practical microbiology (of course), then making the leap to synthetic biology, and then spending some time showing examples of all the cool things happening among DIYbio folks. Of course, the emphasis will be on all the "making". And, I'm sure as I develop the outline, I'll start winnowing away the extra and find that one thing I am excited to focus on.

Let's see what actually turns out. The talks will be pecha kucha - 20 slides automatically flipping in 5 minutes - which I've never done before. Thankfully, I do NOT think 5 minutes is too short to share something that excites me.

Looking forward to a great evening!

Functional roles for noise in genetic circuits

I have a thing about noise (see my ramblings here). And as folks try to turn elements of biological circuits into well-behaving engineered parts, I’ve been trying to put my finger on why biological noise means so much to me.

A series of articles in Nature back in September covered the cost of feedback control, the fundamental limits on the suppression of molecular fluctuations, the functional roles for noise in genetic circuits (subscription required for all three).

The main review mentions that noise is a nuisance in the design of deterministic (engineered) circuits. But goes on to show that noise in biological systems provides critical functions that are hard to achieve with deterministic circuits.

Noise in biological systems is unavoidable, there are limits to how much a feedback system can reduce noise. And the review goes on to discuss many areas where noise is integral to the stability or responsiveness of a process, such as gene expression coordination, state-switching, positive feedback, differentiation, and in development.

How might we understand this noise and actually engineer it into our deterministic circuits?

One thing, though, that tempers my bias towards keeping noise in biologically engineered circuits is that digital electronics also had their start in a noisy analog world. Will engineering biological circuits be forever mired in the analog noisy world of biology or will these circuits eventually be complex enough to exhibit the precise nature that biological engineers seem to want? Should biological engineers seek to incorporate noise into their calculations or strive to limit stochastic fluctuations?

Really, that’s a bit beyond my ability to understand circuit design and noise and all, so I leave it to smarter folk than I. :-)

Image from BarelyFitz

 

The subtlety of life - clever codon usage

Here’s a paper from September I haven’t had a chance to comment on.

Zhang et al reported in Science (review, paper - subscription required) how two almost identical protein sequences can have different translational modifications. In this case, β-actin and γ-actin are 98% identical, the differences are marginal and don’t explain why one protein is modified with arginine and the other is not.

The difference is actually quite subtle - there is one amino acid in the protein sequence that is lysine in both proteins, but the codons in the RNA are different. That difference is enough to change the relative translation speed of β-actin so that it rapidly folds and gets arginylated but not degraded as happens in the slower translation of γ-actin. In the end, this affects the relative lifetime of each protein in the cell, leading to differential functions.

That’s so cool.

It seems like every so often, things we view as well understood turn out to have another layer of subtlety built in. For example, differential codon usage is usually considered a synonymous change, nothing momentous. Sure, there’s been studies of codon usage relative to the abundance of corresponding tRNAs and how that might be used to modulate abundance of a protein (a quick Google search revealed some interesting codon-usage papers). But I think this case is novel, differential codon usage actually affecting the post-translational modification of a protein simply by tweaking the speed of translation.

How might we create a codon usage table that takes into account tRNA abundance, contribution to translational speed of different codons, and speed of post-translational processes to be able to model and predict things like the differences between the functions of β-actin and γ-actin.

Also, how prevalent is this subtle effect on post-translational modification and how susceptible is it to breaking and causing trouble in a cell?

image from Science review (found via Google images, mind you)

Co-operative evolution of the immune system in humans?

Lee and Mazmanian, from Caltech, published this great review in Science on microbes in the gut and how different bacteria might have been involved in the evolution of the human immune system.

Link (subscription required): Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System? by Yun Kyung Lee and Sarkis K. Mazmanian

They discuss research that shows different bacteria modulating the maturation and function of different types of T-cells. And this modulation not only affects what happens immunologically in the gut, but also the rest of the body.

The thought is that this modulation not only keeps the body from rejecting the bacteria outright, but also might provide a protective environment favoring that bacteria, including keeping out other competing bacteria. They also suggest some potential connection with auto-immunity as well.

How cool is that?

Of course, all this requires a proper balance of bacterial populations and T-cell modulation - any imbalance can lead to disease. Indeed, they use the term “pathobionts” for bacteria that normally colonize the gut without adverse affects, but still remain pathogenic under certain circumstances.

There has been lots of research in understanding the molecular mechanisms that underly our relationship as host to a whole ecosystem of bacteria in and on our body. This review provides a great overview of what’s known about the potential modulation of the evolution of our immunity. It’s worth a read if you can get the paper.

Image from striatic

More on bacteria and asthma

There’s a theory going around to explain the rise in asthma: we’re too clean. Research in the past 5 years has slowly been teasing out how this might be.

Link (subscription required): Bacteria and Asthma: Untangling the Links by Jennifer Couzin-Frankel, Science

Scientists have been studying the difference in the incidence of asthma in babies born by cesarian and babies born through vaginal birth, where they are exposed to birth canal bacteria and fungi; or the incidence in children who receive lots of antibiotics or not. Children who are born by C-section or receive lots of antibiotics have a higher incidence of asthma.

Another study is comparing the bacterial flora of children from farms and from non-farm rural settings - farm kids seem to get less asthma.

So far, the link between bacterial diversity and asthma has been an association not proof that bacteria are causing or inhibiting the development of asthma. Yet, it does point to a future where we are less aseptic, less clean in the post-Pasteurian sort of way.

What do you think?

Image from net_efekt

The new germ theory

Lizzie Buchen from Nature (link below) wrote a great article on some cool work folks are doing to change the way we view bacteria.

For example, one group (like a joke, it’s a microbiologist of extremophiles, a neonatologist, and a human microbial geneticist) is studying the effect of bacteria on a devastating intestinal disease in premature babies. They want to know if there’s a role or not for bacteria in this disease.

What’s interesting is that up to now, most understanding of bacteria in humans has been stuff that is pathogenic and can be cultured easily. Bringing in someone who is skilled at finding and characterizing microbes from extremely inhospitable places might help discover new things about our own microbiota.

I don’t know if it’s because I’m all interested now in human microbial ecology or if indeed there has been a resurgence in the study of human microbiology, all I know is that not a week goes by without a new paper or review in this area.

Quite exciting, isn’t it?

Here’s the article: Microbiology: The new germ theory in Nature (no subscription required FTW!).

Commentary on Synthetic Biology: Either. Or.

Either "Scientists should NOT be allowed to create artificial life"

Or "Scientists SHOULD be allowed to create artificial life"

Is this really the distinction? So black and white? And when is life artificial?

I guess the Economist is starting this discussion to answer those questions.

Images from James King (who I suspect might have been invovled)

DIYBio meet-up - Folk Microbiology

It was a night of culture - yoghurt cultures. Vaughn Tan shared his passion for yoghurt with about two dozen captivated future yoghurt makers. He spoke about the biochemistry and microbial ecology of the process - ways to optimize the proteins in the milk, effects of inoculation temperatures, the activities of the different bacterial populations in the culture.

Complex systems
The coolest thing Vaughn explained was about the three key populations of bacteria in yoghurt, their optimum growth temperatures, and how he varied inoculation temperatures to encourage the right populations of bacteria to grow. He pointed out that the usual yoghurt recipes keep the yoghurt culture at a single temperature; this likely diminishes the cultural diversity, reducing the quality of the yoghurt. It was clear that Vaughn’s delicious yoghurt benefitted from a multi-organismal systems understanding.

Ancient cultures
Of course, he brought samples (tasty!) and encouraged everyone to take a bit home. The story around this strain was that Vaughn got it from the Google yoghurt three years ago, and the Google cook apparently got the strain from India, where it was already 500 years old, so we joked that the strain was 503 years old.

But Vaughn mentioned that these complex cultures are always changing, so they really are not the same culture when folks take samples to new places. Also, most cultures come from a previous one unless someone starts one from nature, so it’s highly likely this culture might be even older than we think.

Vaughn was also encouraging us to take some home as an insurance that this strain never dies out. That made me feel that I’ve become part of Vaughn’s network of apprentices, carrying the “flame” of this strain.

Here's the culturing guide for download.

The cultured crowd
Vaughn led a great discussion, and the audience was quite engaged. Mac posed a great question regarding the copyright of strains, if there were legal ramifications to using strains taken from commercial yoghurts, such as from Vaughn’s favorites Stonyfield and Seven Sins (I think that's what it was called). I joked that commercial strains could be fingerprinted for copyright protection.

In the spirit of Folk Microbiology, Keegan brought his microbial battery. It also uses a heterogeneous bacterial culture of aerobic and anaerobic bacteria to create a useful electric gradient.

Also, I brought a few bottles of my own home-brew (an IPA) for everyone to enjoy. Alas, my brew was started with commercial yeast, most likely mono-cultural, though, no doubt, itself an old strain. Vaughn urged me to experiment with lambic-style open-air inoculation of my beer, with the potential benefits of a heterogeneous culture. Heh. Could be interesting. And since sometimes I inoculate with a bottle from the previous batch, I could then start my own strain of beer yeast to hand down to future generations of home brewers.

Awesome experience
As an aside: I brought my 15 year old son along. My highlight of the evening was watching his wonder as he met with everyone, saw their demos, read some books off the shelves, and, basically, saw that there are many ways to express one’s curiosity and creativity. From dirt batteries, to electronic poi, to ancient bacterial cultures, his expanding world was pure joy for me.

Do we need a DIYbio academy?

Among my many ideas I have lying around is some form of institute to support the DIYbio community. This is different from the meet-ups happening in places like Somerville, San Francisco, Houston, and New York. And this is a bit more than what DIYbio.org is providing (sharing of ideas within the community).

This idea adds some pieces that seem to me to be missing (please correct me, of course). I’ve been turning over these thoughts for some time, and since nothing has really materialized (remember, I have a high idea-execution quotient), here are my thoughts.

In my notes, I call it the Molecularist Academy (why? check out the URL above). But the name is inconsequential, what’s important is the mission - Funding, Education, and Outreach.

The mission supports seeding of money - to jump-start activities; legitimacy - practitioner education and safety (certification?); and advocacy - promotion and community education to communicate what DIYbio is about and what folks are up to.

Funding
There are a few interesting funding models out there, such as Kickstarter, Biocurious, and Awesome Foundation. My thought is to create a traditional funding system backed by large sponsors and donors to provide DIYbio-specific grants for exploration, seeding ideas, and to support activities. This funding system would have someone actually reaching out to sources such as biotech industry associations (around here, the Mass Biotech Council), leading biotech businesses (around here, Biogen, Genzyme, NEB, among others), the NIH and NSF, institutes like the Wyss and Venter Institutes, universities, and community organizations.

I do think there’s a bit of a local focus needed, as I feel the biggest contributions DIYbio can make is actually in the local communities the different groups have sprung up in.

And by creating a formalized fundraising and granting structure, the hope is to build an endowment that lasts as the DIYbio community grows. (and I've wondered about alternate ways to fund and legitimize practitioners, in an HHMI-sort of way - more in another post)

Which leads to the next mission focus.

Education
I carry a lot of baggage from my institutional science days, so I am always stuck between letting a thousand flowers bloom and hoping folks don't kill themselves or others while futzing with biotech tools.

The education part of the Academy would set up courses and seminars to teach techniques, science culture, and, most importantly, safety certification. The Academy would be vetted by existing safety organizations and provide legitimacy to the practitioners. And, there would be a structure of re-certification and continuing credits sort of education.

Safety is a big deal and my brief foray into how to communicate it made me realize that it’s much more than just putting up a bunch of pages of regulations and recommendations. Folks like the FBI and the local regulatory bodies likely want more structure.

As part of this Education mission, I’ve also been trying to gauge the need for a patent clearing system, to make sure DIYbiologists are working with the appropriate product licenses, which suggests the Academy should work with tools providers to create special DIYbio tinkering licenses.

And that leads to the third and final part of the mission.

Outreach
This is public outreach, outside the community.

I’ve spent less time thinking of this part as the folks from DIYbio.org already seem to be doing a good job of reaching out to the public and news groups to explain what DIYbio is and can do, and reaching out to agencies who should consider the implications of DIYbio.

And I know there’s been talk of extending this outreach to courses and seminars to engage schools, local communities, and influencers to make DIYbio part of public thinking.

Outreach should also include working with regulatory and policy agencies to take DIYbio into consideration when revising or creating regulations and policies. DIYbio.org has been very good here too.

And, finally, as part of outreach, would we need to have an Asilomar-type event, bringing stakeholders together to hash out the future of Natural Philosophy in the 21st Century, particularly as it pertains to Biology and non-institutional biologists?


There it is
So there’s my Academy, supporting funding, education, and outreach to promote DIYbio. Of course, this could be built upon the existing DIYbio.org structure. I just wanted to get these ideas out there.

What do you think?

Image from tiseb

As an aside, I was looking more into Biocurious and see they are thinking the same things, though still with a crowd-funded model.

Culture as Augmented Reality?

I was listening to Wade Davis' Long Now talk about the wisdom of ancient cultures. Like all Long Now talks, it got me thinking. One thing that Wade said that stuck out was that other cultures are not failed attempts at being us, but other interpretations of what it means to be human.

He did mention one thing that rubbed me a bit the wrong way. When mentioning Amazonian indians who have a hallucinogen that is made from two parts from two plants, he cited the usual disbelief from our culture of how this came about. He did mention that the indians reply that the plants speak to them. But I feel he failed to say that these indians are as scientific and explorative and systematic about their world as we are and that what was figured out generations ago is now part of how they interact with nature - the plants indeed do speak to them.

He also mentioned Songlines, the songs indigenous Australians sing when traversing the outback. The songlines are an interesting mix of information and culture used to navigate the world.

That got me thinking: Are songlines a form of augmented reality? Indeed, thinking about how the plants "talk" to Amazonian indians, might culture, our encoding of information and norms and etiquette and stories, just be an augmentation over the world, and augmented reality?

By the way, the rest of the talk was mind-blowingly awesome. Listen to it.

Image from StormyDog

Moderating panel on "Healthcare 2.0: The Impact of Social Media on Health Information"

Babson College's Health and Life Sciences Club are hosting their 7th annual industry forum tomorrow. I'll be moderating a panel on social media and health care.

The panel will be at 1:15-2:45 at Knight Auditorium at Babson in Wellesley.

It's a great spread and I think we'll cover a bunch of interesting topics. We have folks from pharma, hospitals, media, and patient advocacy. If all the panelists agree, there will be an audio recording as well, which I'll share here as soon as I can.

Link: Healthcare 2.0: The Impact of Social Media on Health Information

Social media has proven to be a powerful tool for connecting patients, caregivers and doctors. Blogs and niche social media sites are connecting patients dealing with disease and illness in a way that wasn’t possible just 10 years ago. This shift has empowered patients to take control of their health through the support of individuals in similar situations. How will these environments continue to evolve and what future role will they play in the treatment paradigm?

Panelists:

• Charlie Schick - Senior Web Producer, Children's Hospital Boston (Moderator)
• Tony Cotrupi - Principal, PARTNERS+simons
• "e-Patient Dave" deBronkart - Patient Engagement Consultant and co-Chair, Society for Participatory Medicine
• Ben Heywood - Co-Founder and President, PatientsLikeMe
• Shwen Gwee - Lead, Digital Strategy and Social Media, Vertex Pharmaceuticals

Image from State Records NSW (Australia)

I'm giving a brown-bag at UMass Amherst on DIYbio and Synthetic Biology on 07apr10

I'm going to be out at UMass Amherst visiting my PhD advisor, Craig Martin. He's been so kind to let me do a brown-bag discussion around DIYBio and Synth Bio:

Brown Bag Lunch
Presentation and Discussion
Do-It-Yourself Biology, Registry of Standardized Parts, iGEM, and more

ISB Conference Room 145
Wednesday, April 7, 2010
12:15pm

Alas, there was zippo name-recognition for DIYbio and Synth Bio (so much for all those news articles). So, Craig asked me to make a summary of some sort.

What it means to me:
DIYBio is basically about increasing the tinkerability of biology. While there are some who think there's science in DIYBio ("citizen science"), the current buzz is around making biology simpler and more accessible outside of institutional settings - hacking, basically. Folks are making $100 gel boxes, isolating bioluminescent microbes from squid, building Dremel-based centrifuges, isolating DNA from strawberries, or trying to figure out ways to make something equivalent to Arduino for biology. It is a nascent "movement" drawing a lot from the Open Source way of doing things and is still about hacking and having fun and introducing people to the tools of biology. But, as in other areas, the expectation is that interesting things will happen when tools became cheaper and more approachable. How will that impact institutional science?

Synthetic Biology, of the Biobricks flavor, seeks to create a standardized registry of characterized biological parts to aid in the engineering of specified micro-organisms. Much like standardized electronic parts paved the way for the electronics industry, the expectation is that standardized biological parts will lead to better engineering of micro-organism. Showcasing what can be done, there's an annual jamboree for genetically engineered machines (iGEM) where micro-organisms have been engineered to produce various pigments, electrically stimulated light production, and detect explosives and toxins. How will things change as it becomes easier to create defined biological machines?

So what's the sales pitch? Why should anyone out at UMass care about these topics?
DIYBio and Synthetic Biology are re-arranging the way non-scientists engage with biology. It's not really about science, but about making biology more tinkerable, more hackable, more approachable so that the messiness goes away and creativity can shine. Designers, engineers, and other non-biologists are making biological tools and experimenting in fun and practical ways. From melamine detectors to mine detectors, from bioluminescent bacteria in squid isolated in the kitchen to electrically induced light production in a lab, biology is starting to be more than just about biology and more about machines. What does this mean to academic scientists? How might this change the future of biological science?

 

Enthusiastic?
I guess I just want to get the word out. I feel that these two topics are changing the way folks view and use biology. And I think is some ways, making biology more accessible outside of the institutional setting will change what we can do with biology by opening access to whole new swaths of creative people.

What do you think of my descriptions here?

Image from daisybush

Developing thought on biological tinkering and biological machines: Sure, biology-as-products exists today, in the form of breeding, brewing, bio-pharmaceuticals. But for me, in those cases the biology is serving the biology (as in, the protein is the drug, or the organism is the end-product). These engineered machines are using biological tools for non-biological purposes (such as toxin detectors or pixel generators)

An author ID system is essential to the future of science publishing

Nature recently wrote an article on a proposed Author ID system. I find this momentous.

In my vision of the Future of Science Publishing, which is highly based on the way we currently use the Social Web, one of the key sticking points was the need to authenticate authors. By authenticating authors in a kind of OpenID way, authenticity, reputation, citations, publications, and activity streams could be automatically managed.

What really excited me is that this author ID system, the Open Researcher and Contributor ID (ORCID), is backed by 23 organizations, including Thomson Reuters, Nature Publishing Group, Elsevier, ProQuest, Springer, CrossRef, the British Library and the Wellcome Trust. In short, those most threatened by the dismantling of the science publishing system are taking an active role in reforming it.

Furthermore, these companies recognize that this system not only brings recognition to authors in huge multi-author projects, but "could also be assigned to data sets they helped to generate, comments on their colleagues' blog posts or unpublished draft papers, edits of Wikipedia entries and much else besides."

That's brilliant.

They also mention the Digital Object Identifier (DOI), a unique indetifier for papers, books, and "scholarly publication." An ORCID and a DOI (and an immutable time stamp) is all that's need to release science publication from its current story-contained-in-single-paper so that each morsel of info can be labeled with a OCID/DOI/Time stamp and be linkable, comment-able, embed-able, feed-able, and search-able. Just as Tim Berners-Lee intended.

While this is a promising direction, I think the current edifice of science publishing is still going to be around for a while, so outfits like Mendeley will still add a layer of value for some time to come.

So, what do you think of this development? Do you think ORCID will radically change the way we share science information?

Institutional science needs to change

I was having lunch with some old ex-lab friends. Unlike me, who left the lab at the end of the 90s, all three of them have kept on doing research and medicine and have their own labs with students, post-docs, and techs. The good news is that their research is progressing, the bad news is that funding is tighter than ever.

I had asked them who was writing a grant (of course, knowing that one always is writing some grant). There was an awkward pause as all three of them seemed to be lost in their thoughts, then they gave me an update of where things were at, since last I was in science, listing some stats to show how things were getting tighter.

When I left research, I had the naïve idea that I would no longer need to hustle for money. But, we all know, the biz world is just the same. Yet, for sure, the biz world seems to have a multitude of revenue and funding options that don't seem to be available to institutional scientists.

I feel that the whole endeavor of Science (I come from a biology background, so my thoughts are around that area, really) has been stuck in the 60s - the way we fund science, the expectations of the apprenticeship (PhD and Postdoc), the publishing and reputation cycle, the job progression - all seem to have been built in a model that came into being in the science boom of the 50s and 60s and really hasn't changed.

Am I missing something? I've been out 10 years, but it seems like nothing has improved. Funding is tighter, people still can't get academic jobs, and publishing is getting more onerous.

How do I envision the future of institutional science?

I'm not sure.

I've mentioned how science publishing could change, taking cues from the current way we use the Social Web. I think DIYBio points to how science could change how we explore the natural world and who does it. And, brilliant folks, like at Biocurious and Pink Army Coop, are looking at ways to diversify how we fund and participate in funding the future of science.

In summary, the business of institutional science is sclerotic and the clues to how we move forward are right in front of us. And, as usual, institutional culture is in the way of this change.

Do you think the way we do science should change? Can it? Will it in our lifetime? How do you envision the future of science or are we fine the way we are?

Image by caterina

Hacking microscopes - DIYBio meetup 13dec09

We had another gathering at The Sprouts. Mac, Jason, Jason, Dave, Kay, and I (with my son) gathered and talked about moving forward with safety stuff (pages, FAQs, and questionnaires), logo stuff, and playing around webcams.

We were going to do some wet-work, but the webcam seemed more interesting and we played with them, building a set up to see if we can use them like the folks at Hackteria.org did. In the process, we ended up taking microscopes apart so that we could have more fine control over the height of the slide.

Kinda funny to break up microscopes to build one.

Here are some pics of the afternoon (no video this time):

Book review: The Manga Guide to Molecular Biology

I had the good fortune of being sent a book by No Starch Press called "The Manga Guide to Molecular Biology." The book is a great introductory molecular biology text book explained through a manga-style narrative.

On the story side, it is very funny. Two girls, have been sent to their professor's private island for summer school. Under his and his assistant's tutelage, the girls gradually learn about proteins, DNA, transcription, and molecular cellular processes. The girls use a virtual reality machine to see molecules and processes up close and their string of questions serve to make the reader think through the topics.

Of course, as part of the girls' growth through the book, tempers flare, jokes are made, and embarrassing situations crop up - all drawn in manga style.

The narrative serves well to walk the reader though the topics, especially since the girls themselves have an inkling about the subject but are discovering it more in depth. Also, the topics, to me, seemed quite compete. The drawings and explanations alternate with pages of expository text (sprinkled with dialogue) to move between a high-level view and some detail.

It may not be "Genes," which I used in grad school, but it's a very good introductory text. I handed it to my son, who is in high school, and it has been helpful to him in his biology projects (and I think he found the storyline quite engaging, too).

I recommend this book as a fun introductory molecular biology text book. Graphical narratives are a great way to explore science and math (check out this amazing one on Mathamatics and Logic). No Starch Press has other manga books on Stats, Databases, Physics, Electricity, and Calculus.

If you want to know more about the book, here's an excerpt. Also, below, is a video by Joanne Manaster (@sciencegoddess), reviewing the book in her own inimitable style. The Manga Guide to Molecular Biology (Excerpt)

Book info, from the publisher, No Starch Press:

"The Manga Guide to Molecular Biology" by Masaharu Takemura, Sakura, and Becom Co., Ltd. August 2009, 240 pp. $19.95
ISBN-10 1-59327-202-2
ISBN-13 978-1-59327-202-9

Rin and Ami have been skipping molecular biology class all semester, and Professor Moro has had enough—he's sentencing them to summer school on his private island. But they're in store for a special lesson. Using Dr. Moro's virtual reality machine to travel inside the human body, they'll get a close-up look at the fascinating world of molecular biology.

Join them in "The Manga Guide to Molecular Biology," and learn all about DNA, RNA, proteins, amino acids, and more. Along the way, you'll see chemical reactions first-hand and meet entertaining characters like Enzyme Man and Drinkzilla, who show how the liver metabolizes alcohol.

Together with Ami and Rin, you'll learn all about:
• The organelles and proteins inside cells, and how they support cellular functions
• The processes of transcription and translation, and your genes' role in synthesizing proteins
• The pieces that make up our genetic code, like nucleotides, codons, introns, and exons
• The processes of DNA replication, mitosis and cytokinesis
• Genetic technology like transduction and cloning, and the role of molecular biology in medicine

Whether you need a molecular biology refresher or you're just fascinated by the science of life, "The Manga Guide to Molecular Biology" will give you a uniquely fun and informative introduction.

Masaharu Takemura is a Lecturer at the Tokyo University of Science in biology, molecular biology, and life sciences. A Doctor of Medical Science, Takemura has written several books about biology.

The need for Plain English DIYbio Safety Guidelines

When we were setting up the wetspace over at The Sprouts, there was a lot of discussion about safety. We were all interested in safety, but Mac was clearly stressing that the future of DIYBio depends heavily on showing that DIYBio can be done safely.

At the set up we had three people, Kay (an active DIYBiologist), Manuel, and Charles, who have (recent) academic and corporate lab experience, and me with academic experience (if a bit hazy from years of inactivity). Together we (mostly them) were able to go over what was needed to make the wetspace safe for reagents, working, disposal, and so forth (especially for The Sprouts).

Highlighting these concerns, the iGEM competition was closed to non-main stream scientists, partly due to safety issues. And the DIYBio-NYC folks are inundated with media request, to see what they are up to, particularly to allay any community safety fears.

I've been doing some investigation and I can't really find a central place for "Plain English" Safety Guidelines that are relevant to DIYBiologists. I envision a wiki where links and info are collated and annotated, training videos, lists of where to get or how to make safety enclosures and equipment, links to downloadable material safety data sheets, lists of suppliers and agencies and safety companies (such as disposal), and so on. But the key thing is that it would be easily accessible and tailored for the DIYBiologist.

This is one aspect of ensuring safety among DIYBiologists, but there are a few more and I am still figuring out how to offer them.

I am not sure _where_ this wiki should be. A quick look at Open Wet ware shows that all the safety info is lab-specific or hidden behind firewalls (understandable, since it's about institutional rules and such).

So, my questions are:

1) Is this a good idea? (I know it is)
2) Where should this wiki be?
3) Who wants to be part of it? (I don't think it should be an open wiki, but curated by a few people. And, of course, since I mentioned it, I should be part of it.)

Increasing tinkerability - explaining DIYbio

I was with my father this Thanksgiving and he asked me about "that Biology thing" I've been getting involved in. He's known for some time that I've been increasingly focused on science in the past few years and that, with my move back to the Boston area, I've been meeting up with scientists and biohackers.

I explained to him what Synthetic Biology and DIYbiology were all about. I showed him my video of my last DIYbio activity, who were the characters involved, what the impact has been so far.

Being a biz guy, he kept asking me what was the "end goal," to help him wrap his head around what would motivate folks to tinker with Biology. He wanted to know if there was a scientific goal or if there were products folks wanted to build.

After a long circular discussion, he finally realized that the field was so nascent that, really, the goal was to "increase the tinkerability" of Biology. 

Of course, that conclusion is filtered through my view of where these areas are at. Right now, engineers and non-institutional biologists are mostly focused on simplifying and domesticating Biology. Issues like science and products will arise naturally as the accessibility and malleability of biological systems increases.

What do you think? Do you think that's an appropriate assessment?

Image from Matt Biddulph

Video: DIYBio meetup 22nov09

We had a DIYbio Cambridge Boston Sommerville meetup this past weekend to get familiar with a nice new hackspace, The Sprouts, to come up with a project for the next few months, and to move and set up equipment in the current space.

The great folks at The Sprouts actually want a wet-space for DIYbiology. They gave us some space and they even had some equipment. We added to that the equipment Mac picked up from a failed biotech.

The whole moving, setting-up thing was quick. We had Kay, Mac, Manuel, Paul, Charles, Jason, and I there, so the "many hands" made the work lighter.

I was happy to see things happening, space being set up, projects being set. Of the things on my to-do list, a few have been now knocked off, allowing me to join existing set-ups.

I took some video of what we were up to.

One last thing: I am so pleased with The Sprouts. They only opened in August, but show great promise. I hope that our group can be part of their growth and give back as even more than they have already so generously given us.

Mac, Sophia, and the philosophy of 21st-century Biology

Mac has written two short but deep posts, inspired by a talk by Sophia Roosth. What inspired Mac was Sophia's "anthropological insight" that DIYbio is "domesticating" Biology.

While I don't feel that it's an explicit doctrine, domestication of Biology is indeed the spirit of what DIYbiologists are up to. It's something that arises from the curiosity, openness, and tinkering that represents the DIYbiolgist "ethic." Sophia puts it in terms of "episteme" (Knowing) and "techne" (Doing).

Biology, as a discipline, is young in many ways - "science" itself is a product of the Enlightenment. And, as a focus of understanding, Biology is old - Aristotle was a biologist.

But domesticated Biology is at the core of civilization: thousands of years ago folks were breeding animals and plants, and brewing beer, bread, yogurt, and wine. These are the heart of Genetics and Microbiology and Biochemistry.

Mac made a recording of Sophia's talk. It's brilliant and really expresses DIYbio (and synthbio) as it is today and where it can lead. It's a must-listen for anyone interested in the future of Biology.

She makes a very nice story of the mind-sets of institutional and non-institutional scientists. And she pivots around the Homebrew Computer Club analogy as a way to think of the where DIYbio is going.

In many ways, she reminds me of the talks Dana Boyd gave, back in the day, as she watched the early evolution of social networking - Sophie brings together a range of threads from different disciplines to provide some coherence and understanding of the events and thinking unfolding right in front of us. Sophie has articulated what DIYbiologist just knew, just "did," in their hearts.

I think her insights just accelerate the nucleation of the "movement" at these early stages of exploration.

Go listen to it.

Image from pusgums

"The Machinery of Life" - a great book for molecularly-minded folks

I've been meaning to share this for the longest time. I've had this book for ages and never tire of it.

"The Machinery of Life," by David Goodsell, is an illustrated journey through cells and proteins and macromolecules - at scale.

What I like about the book is that it attempts to show what it really looks like if you're the size of a molecule - the crowding, the relative sizes, and so on.

It's a really fascinating book for someone like me who has his head in the (molecular) clouds. :-)

There is a review of the original edition (PDF). A nice phrase from that review was "cellular numeracy," referring to the way Goodsell places things in scales, making us realize the relative sizes of molecules and cells.

At the iGEM Jamboree I saw a color image from Goodsell. After searching a bit, I now know that there is a color edition of the book (just out in 2009?), updated with new molecules, too. You can see more on Goodsell's own pages at Scripps.*

I highly recommend this book for anyone messing with molecules, to get a good idea of what the macromolecular landscape truly looks like.

Enjoy!

*It's a shame that the Scripps pages are so 1999-ish. The site needs to be more visual and more up to date.

Building a Minimal Airplane?

At the iGEM Jamboree there was a lot of discussion of Minimal Cells, cells that have the fewest number of components to function as a laboratory organism. One of the key benefits is that it's a defined organism that does only what it needs to do and gets out of the way of the main things someone wants to use them for, say, to create an engineered machine.*

From the discussions, a few said that the route to a Minimal Cell was to subtract components from a current cell and see which ones were essential for operation.

That didn't sit well with me. And it took a while for me to develop an analogy to explain why.

To me, removing components from an existing cell to create a Minimal Cell is like removing components from a Boeing Dreamliner to see what's essential for an airplane (a Minimal Airplane could be like a Wright Flyer).

The mistake is forgetting that even bacteria are highly complex and evolved organisms with complex multi-subunit enzymes and structures. That complexity causes a limit to what can be removed, simply due to the complexity-overhead the bacteria has accumulated over billions of years.

In the plane analogy, the Dreamliner has a ton of essential components, say fly-by-wire, that really were added in evolution, replacing a simpler version, such as manual flying. The function, "controlling the flaps," is what's important, not the component. And the fly-by-wire system makes a whole load of other systems essential (complexity overhead), but which could be dispensed with in a manual system.

Makes sense?

I suppose I am of the school of bottom-up rather than top-down construction of Minimal Cells. And I suppose these discussions have already happened. [Indeed, Foster and Church's 2006 paper "Towards synthesis of a minimal cell" is a good foundation paper.]

I'm not trying to knock on all those working on Minimal Cells. here is a benefit to top-down reductionism, teaching us which pathways and functions are essential, even if we are not finding out the ideal components.

I'm just trying to develop a metaphor for myself to help me think of how to build a Minimal Cell.

That's all.

Image from Boeing

*Heh, one interesting thing I noticed at the iGEM Jamboree was a vocabulary developing around synthbio - machine, quorum sensing, chassis - words I've never used before in biology and that come from engineer-speak. I like it. :-)

DIYbio and Main Stream Scientists - 2004 all over again?

Back in 2004 I was flying all over the place, promoting blogging. It was the year The Blogger entered the public eye, came out in magazines, built empires. One of the great debates was the clash between Main Stream Media (MSM) - the newspapers, publishing houses, and TV stations - versus the citizen journalist, the bedroom blogger, the unwashed masses of online writers.

MSM, of course, said that bloggers were not accurate, were not honest, were temporary, that only MSM was the font of Truth and quality information. Well, so much has happened since then. I feel there is still a place for professional journalism, but blogs have settled into their niches, providing a "long tail" (there I said it) of content of varying quality and scope. And, well, blogs today aren't the same as blogs 5 years ago, in the end, they are still just an online publication.

But watching the style and aspirations of the DIYbio crowd reminds me of those days. It seems that the friction between DIYbio types and Main Stream Scientists - the labs and institutes - hovers around the same issues as in the day of blogger vs. MSM.

And I think the change will be just as profound and the outcome just as mundane.

Image taken from Six Apart's post

DIYbio at iGEM 2009

iGEM for me was the first time I got to meet folks in the DIYbio "movement." The DIYbio folks from NYC and Boston had a meeting the first night to discuss where things were going. They all knew each other and had collaborated in some areas.

It was nice to see the easy flow of ideas and decisions. As with iGEM, this group is in a very early stage. But already some things are becoming clear as to what it's going to take to keep growing.

One more thing (and I might be inviting a flame war): there is clearly some friction between the iGEM folks and the DIYbio folks. Part of this resides in prejudices towards amateur biologists (unfounded), part in worries about safety (well founded), part in the small difference in culture.

DIY home base
One of the things that happened is that iGEM required teams to be affiliated with an institution. That was a way to ensure safety concerns (indeed, the FBI was a sponsor of the Jamboree, go figure). Independently, the DIYbio groups in Boston and NYC (and I) realized that, while it would be nice to actually do kitchen biology, groups need some sort of entity with which they can buy supplies, teach safety and techniques, and, of course, enter into iGEM.

I'm all for it. In the past months, reading and following and talking to DIYbio folks, my thoughts on hack-spaces has evolved to include more than just a bench, but also seminars, safety certification, mini-grants, and even a store (check out Pearl Biotech).

I was also glad to finally meet Mac, one of the leaders in DIYbio. He's recently purchased a lab trailer, full of equipment. He's now looking for space (too bad my ample backyard is so far from town). His goal is to build this out as a hack-space, also hoping to mix novice and experience biologists, to get some culture and skills transfer.

That's super. I look forward to getting more involved. Mac has a ton of projects in mind and could use some help. And I want to learn from the DIYbio NYC folks who recently formed a non-profit and are acquiring space so that they can get out of their living rooms and get a nice space to play around in.

This is going to be fun.

And here's a video of the folks at the meeting:

Report on iGEM 09, from a newbie

This iGEM was my first. I'd read about it, talked about it, but this is the first time I've been immersed in it.

OK, so I wasn't part of a team, so I told folks I was a "lurker." That was out of the ordinary, since most folks were either staff, team members, or volunteers (which is what I should have done to save the registration fees - maybe).

Clever little undergrads
I'm not going to go into details as to how the teams got to the Jamboree. Suffice it to say that anyone who wanted to come, came; also, the teams were undergraduates who thought long and hard on what they would build and then built everything over the summer.

I was impressed with the creativity the teams showed. There was light-induced vanillin production (for the aroma), electrically-induced light production (creating pixels - see video below), various detectors (for toxic metals and mines), and inducible pigment production (to free us of the boring tyranny of all the usual fluorescent reporter proteins).

While some might call for something applied to come out of all this, I am content to see the participant's enthusiasm; their learning of how to solve problems, think, and communicate results; the multi-disciplinary nature of teams, mixing engineers, biologist, sociologist, designers, mathematicians, physicists, artists, and programmers; and the gathering of like spirits to exchange information and dream up even more exciting things.

Keeping up with the E colis
For me, it was heaven. I had not been immersed in this field in so long. It was good to try to figure things out, talk about how decisions were made, and learn all the clever techniques and solutions folks came up with.

Of course, at the end, I started dreaming up some of my own "machines." Who knows if I might be able to build one someday.

E. chromi
I was particularly pleased with the winning team - Cambridge - for their creation of inducible pigmentation in bacteria. Through a network of connections, I had met the irrepressible Daisy Ginsberg, a designer from London who has been exploring the future world where synthetically engineered biological organisms are established and integrated into society. Daisy coined the term Kingdom Synthetica to add to the Eucarya-Bacteria-Archaea Kingdoms that we already have.

Daisy, and her partner in design-crime, James King, worked with the Cambridge team to help them explore the sociological and design aspects of what the team was building.* They got the team to think of a future that had colored bacteria and what that would mean. For example, one team talked about color-poachers killing rare wild-life for color genes; or, global battles over patenting of colors (for example, the Dutch if China were to patent Orange).

The best example of the future was colored poop, formed by these color producing bacteria detecting metabolic states and reporting it through color production, say green for an ulcer or red for vitamin deficiency (see picture). This colored poop was the sensation of the Jamboree. James and Daisy walked around with a silver valise, telling their whole story and ending with opening the valise, much to the surprise of their audience.

It was very fun.

Naming gaming
Daisy christened the Cambridge bacteria as E chromi (@echromi on Twitter). And they presented their colored poop to the MOMA in NYC, so don't be surprised if the valise ends up there.

Other teams also named their bugs, as in Essencia coli (Team KU Leuven) and GlueColi (Team ULB-Brussels).

Once again, these names just point out that this Jamboree is more than a bunch of geeks building gadgets, but a whole way of thinking and mixing and creating. This is all so embryonic and what will come out of it no one really knows. But what is sure is that mixing folks from different background in a fertile playground with no dominant player is a sure way to come up with lots of interesting things.

Now I'll go off and start building my E coliroid (hm, what might that be?).

Here are some images and video that I took at iGEM:

*One nice feature of the competition was a thorough list of judging criteria, nudging the team to do more than just building something. Most interestingly, teams were encouraged to do a sociological survey around ethics, society, and synthbio. This added non-scientists to the teams. One of the most interesting findings (as these we mostly qualitative, due to experimental design constraints) was that folks were against genetically modified organisms (GMO) in general, but were fine with GMO use in humanitarian work, such as toxic waste or mine detection.

Vestiges of the past in our tools: Fruit fly culture bottles

In a previous post, I discussed how we've forgotten techniques and instruments of the past. These techniques and instruments could come in handy as garage scientists try to build their labs.

In that post, I mentioned that folks keep fruit flies in plastic bottles that look like milk bottles (well, only if you know what a milk bottle looks like, otherwise, it's just another oddly-shaped bottle). In case you're wondering, the use of milk bottles goes back to the days of Thomas Hunt Morgan, the genetics genius who chose the fruit fly as a model organism. Somehow, he and his contemporaries did a ton of great science without the kits and super equipment we have today.

What do you think?

I think these vestiges are really cool and I like seeing them wherever I can (and I have a ton of stories about these vestiges). 

Do you know of any more?

Image from wikipedia.

Oh, what we've forgotten...

In this new era of natural philosophers (neo-natural philosophers?), where the cost of buying science kits and instruments can be an obstacle to amateur science, I keep thinking back to how science was done many years ago. What were the tools used? What were the different reagents of the day? How can this lost knowledge be applied today to circumvent barriers to modern reagent and instrument access?

I remember when I was a tech at MIT, back in the late 80s. There was an old Worthington molecular biology catalog with reagents and enzymes. For restriction enzymes, there were two: EcoRI and BamHI. Talking around the lab, our PI told me how "in the day" everyone had to purify their own restriction enzymes. 

To me, that was fascinating. By the late 80s, the New England Biolabs catalog was already full of a ton of enzymes and kits. And, huh, it was so easy to sequence DNA by doing nested deletions of M13 vectors and using the kit's primers. And then you could purify plasmids with CsCl gradients and gobs of Ethidium Bromide in milligram balanced tubes and a wicked cool ultra-centrifuge. 

State of the art, man!

As the junior tech in that lab at MIT, I was also responsible for keeping the fly stocks alive, transferring them on a regular basis from old bottles to new bottles. As per fruit fly science convention of the time, the flies were kept in small glass milk bottles, with cardboard plugs. I wonder how old our bottles were, but I was told that it was getting harder to find the bottles or even the cardboard plugs.

When I went over to the Whitehead to do some experiments, I saw that they all had plastic containers - in the shape of a milk bottle. It was the future, but in the image of the past. I wonder if folks today know why they still use such oddly shaped bottles to store flies in.

Straddling the past and future, that lab was a treasure trove of old stuff. I once opened a drawer at the lab and found a ton of capillary tubes with different color markings and sizes. These were actually glass micro-pipettes, calibrated and used with a mouth adapter (oh, my!), and eventually replaced by Gilsons with disposable plastic tips.

In summary, there are a ton of techniques and tools that have been knocked aside by kits and newer instruments, mostly for convenience (because I am a science history enthusiast, I have a ton of these stories). For those enterprising neo-natural philosophers, if you long for some kit or instrument, imagine back to the day when you got your hands dirty and didn't just buy your reagents. You might find some ideas how to create your own reagents and tools.

Image of pigments from hyperscholar, to remind you that "in the day" artists ground and mixed their own pigments to make paint. No kit for them!