DIY Biotech Book
Bryan Bishop
The biobarcamp guys and others are planning to do a do-it-yourself
biotech book. The idea is to make a book that introduces and includes
information on how to make and use the biotech equipment, the
do-it-yourself scene, and so on. There's already significant content in
the biotech toolkit ( http://biohack.sf.net/ ) *however* there's also
tons of information from other communities that really needs to be
integrated into something new -- a book -- so I'm sending out this
email as notification of where everybody is. It looks like nobody is
keeping notes on it yet, so I'm taking the initative and organizing
everything here:
http://heybryan.org/mediawiki/index.php/Book
Feel free to edit it ruthlessly, copy it to another wiki, whatever. The
content for the book itself should be up on a wiki, so feel free to
link over to new pages with content dumps of related interest. There's
going to be a lot of contributions, but we can sort through it in the
end and discuss what we want to finally include and what not and so on.
I'm also emailing this to a number of mailing lists. Mailing lists are
limited for large collaborative projects like this where we don't have
everyone on the same page and copying emails between too many mailing
lists has this tendency to be a not-so-good of an idea.
So, to provide a medium to more quickly organize people from different
groups, I'm hanging out on IRC in #hplusroadmap on freenode and hope
others will join me. There's a good number of contributors interested
in this project there (>10 normally). There's also #biology,
#bioinformatics, ##neuroscience, and a good number of other communities
on freenode that we can dive into. Here's how you can access it:
http://irchelp.org/
http://freenode.net/
irc://irc.freenode.net/#hplusroadmap
Anybody using Firefox can use Chatzilla. Window users can use mIRC or
something. And people on linux can apt-cache search IRC | grep IRC and
get something that looks good.
I'm also going to propose a 'cycle' of contributions to follow so that
we have somewhat of a pulse that can beat out content. Wikipedia has a
community pump, for example. There's a few options over at twitter, but
in general, I think we'll get a pump going (aggregator) through IRC and
then decide on twitter or whatever. Twitter is down all the time, so
somebody else might have a better idea than I.
In the mean time:
http://twitter.com/biotecher
http://pimm.wordpress.com/2008/04/14/follow-biotecher-a-solution-to-find-all-biotwitters-in-1-place/
http://twitter.com/attilacsordas
http://twitter.com/kanzure
http://twitter.com/mndoci
I'm emailing this over to a lot of different communities into this sort
of thing -- the neuralensemble group that focuses on the computational
neuro side of biotech, the longevity groups, etc. All of these people
are awesome and have good ideas to contribute, so I'm hoping some of
them will click on the biotecher twitter, show up on the IRC
discussions, and end up making an even more amazing resource for
individuals.
- Bryan
---------- Forwarded Message ----------
Subject: Re: [BioBarCamp] BioBarCamp topic/session suggestions
Date: Saturday 07 June 2008
From: Bryan Bishop <kan...@gmail.com>
To: bioba...@googlegroups.com
On Tuesday 03 June 2008, Attila Csordas wrote:
> Hi All,
>
> This will be a lengthy email (sorry), but with good chance, it covers
> a lot of topics that will be discussed at BBCAmp. The reason for that
> length is that I include the Tentative Table of Contents of the so
> called *BioTech Geek Guide* as I would like to organize the closing
> session of the BBCamp with Deepak and Ricardo with the interactive
> participation of you all. Let me explain:
>
> The *Biotech Geek Guide* is also an
> idea<http://pimm.wordpress.com/2008/02/28/lets-compile-a-biotech-for-
>it-folks-book-and-publish-it/>fed by a Twitter stream, just like the
> BBCamp idea. Deepak complained about
> the tech world's ignorance about health & genetics (a recurrent
> theme) and then I suggested to write/edit/compile a biotech, biology
> book for IT folks specially and publish it as an O'Reilly book.
> O'Reilly Books have the fame of being the definitive guides, intros,
> manuals in their technolgical fields. Ricardo came into the
> conversation too and 10 minutes later I emailed Tim O'Reilly with the
> suggestion and got almost instantly a very positive answer back
> followed by a detailed Proposal Guidelines that needs to be filled
> out to set up a schedule in order to get a final Yes or No answer to
> the publishing of the book. So we started to work (just a little in
> the lack of time) on it and I copy here what we've done basically the
> *Book Outline/Tentative Table of Contents*. The concept of the book
> later transformed into the *Biotech Geek Guide* which is too collect
> every cool, major topic together that could be of interest for a
> rookie/advanced biogeek, who is usually tech-savvy and biotech-savvy
> too.
I was talking with Deepak and others a few weeks ago about offering the
Synthetic Biology Toolkit as a basis for the book. There's tons of
content in the download and I think that it would be a good place to
start.
http://biohack.sf.net/
http://heybryan.org/mediawiki/
So the table contents, I would think, should focus mostly on (1)
protocols, (2) equipment -- mostly improvised, (3) introduction to the
online communities, including the broader world of bioinformatics,
programming, open source communities, friendly people to talk to on the
internet (seriously, an email address to me, Deepak, pimm, etc.),
diybio.org groups, etc. The entire field is very quickly moving along,
so it has to be a book that will not be dead in a few months (books
aren't good for content like that).
> And so we have an idea, an option to make a product (a book) out of
> it, and define or delineate the knowledge-base and topic sensitivity
> of current biotechnology, life sciences well tailored for IT people
> but we lack an essential component that is behind every good animal
> covered O'Reilly tech book: we lack the creative and critical
> community and we need authors and commenters in the spirit of open
> source and science. (That community also starts to form on FriendFeed
Woah, I think we /do/ have that community. Check out the biohack.sf.net
community. There's a good number of people on the mailing list. We just
need to get them rallied up on a project. :-)
> as *The Life
> Scientists*<http://friendfeed.com/rooms/the-life-scientists>room,
> earlier form is a simply
> Biotecher <http://twitter.com/biotecher>
> register<http://pimm.wordpress.com/2008/04/14/follow-biotecher-a-solu
>tion-to-find-all-biotwitters-in-1-place/>at Twitter.)
>
> But I think that the BioBarCamp could collect together exactly the
> Community that is needed for the succession of that book and the
> whole biogeek culture!!! The authorship, content and schedule is
> totally open at that point (publishing an O'Reilly book is not about
> money, really, at least I think so), I'd (and probably Deepak, if he
> is interested) serve as a kind of main editor, and the more coauthors
> and voices we have, the better the book will be.
Let's make it on a wiki, instead of requiring it a BioBarCamp-only book.
I don't know if BioBarCamp would be a good venue at which to write the
book, but for rapid outlining (sit there on a wiki and have a live
brainstorming session) it might prove an awesome mechanism.
> So by copying the content suggestions here, I'd like to invite you
> all to this hypothetical closing session and invite you to become
> future O'Reilly authors to define the biogeek culture. (Disclaimer: I
> am not an employee of O'Reilly Media, and if they say no I still
> think that the concept of the book is good enough to publish it
> elsewhere).
To _define_ the biotecher culture? I don't know about that. That one is
already in progress. For example, biopunk.org, the F/OSS communities,
the typical lab culture.
> 1. *All about bio* (introduction to the book). In the
> introduction we will discuss the the origins of biotechnology and how
> the field has evolved over the past 25 years? As biotechnology has
That's a pretty challenging part. Maybe we could start by looking over
at wikibooks and see if there's anything already written that we might
import. There's a lot of important people to mention from the field of
bio and biotech and so on, so we need somebody pretty knowledgable and
able to integrate all of the information together, showing the broader
vision that people started out with (or acquired), and then integrating
it all back together to make sense. I think this could be done if we
ruthlessly recursively read Wikipedia for the broad overview aspects,
but then we need to reinterpret in light of (1) actual research
articles (references to open access papers, etc.), and (2) an
interpretation in terms of the do-it-yourself culture.
> evolved, it has had a significant impact on the world around us, from
> how we approach problems to how we try and cure disease, to the
I think it's important to emphasize just how awesome disease curing can
be. I wasn't aware of the World Health Organization's attempt to cure
polio via a world-wide campaign until a few years ago. That was a
terribly massive medical front that I doubt can be emphasized enough.
And what would happen if people were able to do that on their own? Hrm.
> environment and even to DIY hackery. The world of biotechnology is
> also increasingly moving towards a systems level approach, as begin
> to look at our bodies as interconnected, complex machines, changing
> the way we try and cure diseases. We will also propose that biology
> is the ultimate information science and lay the grounds for later
> discussions on the data challenges and the information that can be
> gleaned
> 1. the biological mindset
> 2. biotechnology in general
> 2. biology basics In this chapter we provide a brief introduction
> of the building blocks of biology. Here we go a little beyond what
> you might find in the mainstream media and tell you about how we
> function and highlight the complexity of human biology
> 1. The building blocks (DNA, RNA, protein, organelles, membranes,
> extracellular matrix, tissues, organs, body). *Do we need
> anything else here? Don't want to make it too technical.*
So, a list of general componentry that people can investigate in trying
to make their projects a reality. Not just "building blocks of life",
but 'parts and tools that you can use to do cool stuff'.
> 3. methods -
I suspect that including a CD of protocols wouldn't be a bad idea. We
could start with protocols-online and OpenWetWare. In fact, if there's
going to be a CD, let's include the biohacking toolkit and the entire
wiki output of major wikis like OWW, biodatabase.org, biohack, etc. And
then we can probably also include the portions of Wikipedia that are
relevant. This is critical. There's no way that we can talk about
everything in a book that we all want to be published in a reasonable
amount of time ... so a CD, plus the book as more of a creative 'index'
(in discussion format) to the contents, might be a good idea.
> 1. the lab The par excellence biologist of our time is an
> experimental scientist working at the bench with different tools and
> methods: DNA, RNA:
> isolation, amplification, quantification, protein: western
> blot, SDS PAGE,
> antibodies immunocytochemistry organelle: isolation of
> mitochondria, lysosomes (centrifuge), cell: in vitro cell culture
> 2. Biology in silico
http://heybryan.org/mediawiki/index.php/Computational_biology
> 1. Bioinformatics
> 2. Modeling and simulation
http://heybryan.org/mediawiki/index.php/Computational_biology
> 4. Postgenomic
> 1. proteomics
http://heybryan.org/mediawiki/index.php/List_of_bioinformatics_databases
> 2. HapMap
> 3. Protein Structure Initiative (Structural Genomics)
CASP?
> 5. Systems Biology Over the past few years, it has become
> apparent that the traditional reductionist approach to biology was
> very limited. The human body is extremely complex, a function of
> interconnected pathways and networks. In order to cure many
> diseases, it becomes necessary to study the human body at a systems
> level, getting a deep understanding of various pathways and networks.
> By combining large quantities of data, complex mathematical
> modeling and advanced computer models, systems biologists are
> developling predictive models of organisms and biological systems
> which will not only help us develop better, more potent drugs, but
> also develop new fuel sources, clean up the environment and
> potentially hack the human body. 6. The future of biotech
Re: future of biotech. George Church is supposedly making some
incredibly cheap biotech equipment (polonator.org and so on);
sequencing for everybody on the planet; do-it-yourself pharmacy; brain
augmentation; etc.
http://www.innerspacefoundation.org/
http://heybryan.org/recursion.html
> 1. Next generation sequencing
http://heybryan.org/mediawiki/index.php/DNA_sequencing
Is pyrosequencing still next generation? There's also scanning tunneling
microscopy for DNA (like ZS Genetics plans to be doing later this
year). The STM setups technically don't cost much, but getting the
reoslution needed to do nucleotide-by-nucleotide scanning, ehh. That
gets tricky. See:
http://heybryan.org/instrumentation/instru.html
http://heybryan.org/graphene.html (sort of)
> 2. Personal Genetics - Genomics
Also, the $0 genomics project. Community sequencing projects, brief
notes on how to deploy something like that (run around with cotton
swabs and baggies and refridgerators in a van), etc. Also, the
prospects of viral gene therapy in relation to personal genomics; the
prospects of downloading genes from the internet from "gene pools"
(i.e., "hey, look at this!" blogs).
> 3. stem cells-regenerative medicine (A) The chapter covers the
> basic concepts: stem cell, uni-, mult-, pluripotency, embryonic,
> adult, induced pluripotent, cancer stem cell, stem cell niche, tissue
> regenerative potential, regenerative medicine.
The biohacking toolkit includes some papers by Yamanaka re: iPS cells.
I'm still looking into protocols for adult fibroblast extraction and
colonies, but it's looking interesting.
> 4. tissue engineering
http://heybryan.org/mediawiki/index.php/Neuropod
organotypical neural slices, also see the heart-in-a-jar and prospects
of the brain-in-a-jar projects. Stem cell engineering too. Hrm. Ah, and
most importantly, the in vitro meat stuff.
http://heybryan.org/mediawiki/index.php/Meat_on_a_stick
> 5. The biology of our age: the biology of aging
Emphasis on how to do "anti-aging research" in your own home.
http://sens.org/
http://grg.org/ has some people that we might want to contact (Coles?
Aubrey?)
> 6. synthetic biology* *Perhaps we can get Jason or someone to
> do this. My preference is that we stick to non-famous people but
> interview Drew and others extensively.
http://syntheticbiology.org/
http://partsregistry.org/
http://biobricks.org/
http://biohack.sf.net/
http://diybio.org/
> 7. biotech DIY: set up your low budget lab at the backyard
> The idea of doing biological experiments with current
> biotechnological methods and conducting research projects at home is
> very new. There are already many names in use referring to the same
> concept: bioDIY, home biology, biotech DIY, garage biology. All you
> people need is a short course
> in biotech basics, a few thousands of dollars, some tinkering
> capability, and enough spare time and space. The beautiful retro idea
> of tinkering with
> digital devices in a garage, conveyed by the
> Make<http://www.makezine.com/>magazine, can be extended to biotech
> too, and some projects were already
> published in Make backyard biology issue like the Home
> Molecular Genetics including DNA isolation.
By the way. There's a few projects out there (bioreactor project from
the biohacking group) that are trying to make a completely biological
setup for do-it-yourself biology experimentation. For example, in vitro
DNA synthesis.
http://heybryan.org/mediawiki/index.php/In_vitro_DNA_synthesizer
And also having cells generate the proteins (T7, etc.) necessary to do
transcription, or other various reactions that will be needed. This
way, the entire kit is self-replicable except for the metal or plastic
chasis.
> 7. Applications
> 1. industrial biotech
Might want to mention something about 'industrial ecology' and the
biosphere as another ecology and how this could all fit together
productively for various interests.
> 2. Drug Discovery
> 8. The Web and biotech
> 1. Google and biotech Google's interindustrial power reached
> the biotech sphere through its investment into 23andME and backing
> George Church's Personal Genome Project amongst others. While
> personal genomics is
> in the focus of Google's recent interest, its connection with
> the biomedical
> sector is much more complicated. Google Health
> 2. Virtual medical education and web 2.0 in medicine
Maybe the diybio.org guys would like to run some of those virtual
educational seminars eventually. I've been holding weekly lectures on
IRC on freenode in #hplusroadmap for a while now, but it's really just
whenever people feel like showing up and pestering me about some
awesome topics. Anybody is welcomed to join and contribute. :)
- Bryan
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