Kay Aull, Mac Cowell & Hugh Reinhoff on New Hampshire Public Radio today
Mackenzie Cowell
Public Radio's (http://www.nhpr.org/) "Word of Mouth" program,
starting at 12:00 noon EST, which will have a blurb on Amateur
Science. You can tune in here:
http://nhpr-sc.streamguys.us/listen.pls.
Hugh has been profiled in Nature, MAKE magazine, and most recently
Wired (see Raj's email below) because he is single-handedly sifting
through his daughter's genome for the genetic basis of his daughter's
mystery disease, working out of the family attic.
I anticipate talking about the size, history, and activities of the
community, ranging from experimental biology to naturalism (both
micro- and macroscopic) to low-cost, open-source hardware development.
I'll try to mention the gel box 2.0 project, the bioweathermaps
project, melamine-sensing yogurt, and the development of several
"garage" and community labs around the country. Kay will help and is
also going to talk about her upcoming work to sequence the allele's
for one of her genes.
If anyone has any suggested talking points or tomfoolery (want me to
read the first 20 bp of your favorite gene on-air?), please let me
know.
Mac
On Tue, Feb 3, 2009 at 7:28 AM, Rajagopal <vrg...@gmail.com> wrote:
>
> All members pl read this
>
> http://www.wired.com/medtech/genetics/magazine/17-02/ff_diygenetics
>
> and explain the similar lab work and usefulness...
> Raj
> ----- Original Message -----
> From: "Rajagopal" <vrg...@gmail.com>
> To: <diy...@googlegroups.com>
> Sent: Tuesday, February 03, 2009 5:07 PM
> Subject: Re: Monitor 360 Interviews
>
>
>> Hi
>> All are worried about legislations and rules of the fed to run labs.But if
>> a person does an individual experiment at home what is the law?
>> Is there any ban on this?
>> VR
>> ----- Original Message -----
>> From: "Mackenzie Cowell" <m...@diybio.org>
>> To: <diy...@googlegroups.com>
>> Sent: Tuesday, February 03, 2009 4:50 PM
>> Subject: Re: Monitor 360 Interviews
>>
>>
>>>
>>> NIH Office of Biotechnology Activities guidelines on Recombinant DNA:
>>> http://oba.od.nih.gov/rdna/rdna.html - all NIH-funded work must
>>> comply. Compliance is broad, and most institutions make the NIH
>>> guidelines policy. Doug Ridgeway and others have started a DIY guide
>>> pulled from sources like the NIH here:
>>> http://docs.google.com/a/diybio.org/Doc?id=dfxdf7dw_115d3gq2wc7
>>>
>>> The CDC Biosafety in Microbiological and Biomedical Laboratories
>>> (BMBL) 5th Edition:
>>> http://www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm
>>>
>>> More broadly, the CDC Biosafety Index:
>>> http://www.cdc.gov/od/ohs/biosfty/biosfty.htm
>>>
>>> City of Cambridge Recombinant DNA regulations:
>>> http://www.cambridgepublichealth.org/services/regulatory-activities/rdna/overview.php
>>> - this requires anyone doing recombinant DNA work to annually pay a
>>> fee and get approval of a community review board. I don't know of any
>>> other cities that do this in the US, but the UK and Japan may have
>>> similar rules at a national level.
>>>
>>> Michigan State University review process for work involving
>>> Recombinant DNA: http://www.biosafety.msu.edu/rdna/rdna_index.htm
>>>
>>> Chapter 5 of the Molecular Biology Problem Solver, "Working Safely
>>> with Biological Materials" would be a good place to begin:
>>> http://www.scribd.com/doc/10960397/Molecular-Biology-Problem-Solver
>>> (scribd page 154).
>>>
>>> A British Journalist pointed me towards some UK regulations:
>>> HSE Leaflet on Contained Use: http://www.hse.gov.uk/pubns/indg86.pdf
>>>
>>> The GMO regulations: http://www.opsi.gov.uk/si/si2000/20002831.htm
>>>
>>> I think we should curate this list on the wiki and at diybio.org
>>> somewhere. At the end of this thread lets port it over to those
>>> sites. A good goal might be to categorize the resources into "Must
>>> Read", "Good to Know" and "Referece" categories..
>>>
>>> Mac
>>>
>>> On Tue, Feb 3, 2009 at 1:32 AM, JonathanCline <jnc...@gmail.com> wrote:
>>>>
>>>> It might be a good idea for everyone who has an intention on
>>>> fabricating anything to skim existing legislation (even if not in the
>>>> U.S.), as visibility into our project grow. Notable is:
>>>> The Bioterrorism Act of 2002,
>>>> http://www.fda.gov/oc/bioterrorism/Bioact.html
>>>> (don't over-react to the name, it covers a broad range of issues.)
>>>>
>>>> Is there a list of other regulations covering work related to
>>>> culturing, isolating, cloning, GMO'ing, etc. The result of any market
>>>> study/survey will likely act from existing regulatory frameworks, so
>>>> it's best to know the status quo.
>>>>
>>>>
>>>> ## Jonathan Cline
>>>> ## jcl...@ieee.org
>>>> ## Mobile: +1-805-617-0223
>>>> ########################
>>>>
>>>>
>>>> On Feb 2, 7:03 pm, Tito Jankowski <titojankow...@gmail.com> wrote:
>>>> > Hi everyone,
>>>> >
>>>> > As you may know, Monitor 360 is putting together a report on the
>>>> > DIYbio and biohacker community. Travis and Nils from Monitor 360 are
>>>> > interviewing with many of us.
>>>> >
>>>> > Please post your comments and feedback if you chat with Monitor!
>>>> > Overall, I enjoyed the interview and am excited about the project. I
>>>> > hope we get access to the final report - a compilation of these
>>>> > interviews through someone else's eyes would be valuable to our
>>>> > development.
>>>> >
>>>> > I phone-interviewed with Travis, who is in Cambridge, MA. On the topic
>>>> > of safety, my opinion is that our current projects (i.e. BioWeather
>>>> > Maps and Gel Box 2.0) exist because we do not YET feel comfortable
>>>> > doing wet-lab work due to cost, information, and safety concerns.
>>>> > Meredith and Kay are obviously exceptions to this. As well, I believe
>>>> > most DIYbio experiments require high school level knowledge - i.e.
>>>> > transforming bacteria. But rather than transforming dummy genes like a
>>>> > high school lab, we will be adding in complex, useful, DNA. Travis
>>>> > also asked about the best way to find out how many DIYbiologists
>>>> > exist. I said to check out this mailing list and lab equipment
>>>> > auctions.
>>>> >
>>>> > There's talk of Monitor hosting a workshop in San Francisco in early
>>>> > March.
>>>> >
>>>> > Best,
>>>> > Tito
>>>> >
>>>
>>> >>
>>
>
>
> >
>
Bryan Bishop
> Kay Aull and I will be joined by Hugh Reinhoff today on New Hampshire
> Public Radio's (http://www.nhpr.org/) "Word of Mouth" program,
> starting at 12:00 noon EST, which will have a blurb on Amateur
> Science. You can tune in here:
> http://nhpr-sc.streamguys.us/listen.pls.
Hope somebody can make a recording of this. Hugh Reinhoff has rapidly
earned a title akin to "the Iron Man of fatherhood" or something.
Don't know if anyone around here saw the last Iron Man movie, but it
had a fantastic opening sequence where Tony Stark builds a powered
exoskeleton in a cave in the middle of a desert. He just kind of
"snaps" and decides he's not interested in playing along any more ..
kind of like what Hugh's doing for his daughter?
> Hugh has been profiled in Nature, MAKE magazine, and most recently
> Wired (see Raj's email below) because he is single-handedly sifting
> through his daughter's genome for the genetic basis of his daughter's
> mystery disease, working out of the family attic.
Maybe he should get a batcave? But more seriously, I'm wondering what
sort of computational infrastructure we could help him acquire for
genome sequence analysis- sifting through a genome by hand sounds like
something a bioinformaticist can help with. So, Mac, could you extend
our offer for assistance to him on the show maybe? Don't know how
helpful the community can be overall, but it's better than nothing.
> I anticipate talking about the size, history, and activities of the
> community, ranging from experimental biology to naturalism (both
> micro- and macroscopic) to low-cost, open-source hardware development.
> I'll try to mention the gel box 2.0 project, the bioweathermaps
> project, melamine-sensing yogurt, and the development of several
> "garage" and community labs around the country. Kay will help and is
> also going to talk about her upcoming work to sequence the allele's
> for one of her genes.
Good luck. I look forward to hearing how it turns out. :-)
> If anyone has any suggested talking points or tomfoolery (want me to
> read the first 20 bp of your favorite gene on-air?), please let me
> know.
polymerase (DNA directed), delta 1, catalytic subunit 125kDa
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=156616275&uids=&dopt=fasta&dispmax=5&sendto=&from=begin&to=end&extrafeatpresent=1&ef_CDD=8&ef_MGC=16&ef_HPRD=32&ef_STS=64&ef_tRNA=128&ef_microRNA=256&ef_Exon=512
http://www.bioinformatics.org/sms2/rev_trans.html
MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQSVLEGVADGQV
PPSAIDPRWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRGSVPVLRAFGVTDEGFSVCCH
IHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRDSRGGRELTGPAVLAVELCSRESMFGYHGHGPSPFL
RITVALPRLVAPARRLLEQGIRVAGLGTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKEK
ATQCQLEADVLWSDVVSHPPEGPWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPF
LRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPF
LGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEQKEDVQ
HSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVPLSYLLSRGQQVKVVSQLL
RQAMHEGLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKL
GLTEDQFIRTPTGDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSV
YGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAE
AMALGREAADWVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV
ANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGKQAHVELAERMRKR
DPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQQLAKPLLRIFEPILGEGRAE
AVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLSHQGAVCEFCQPRESELYQKEVSHLNALEER
FSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLRRFGPPGPEAW
which is:
atggatggcaaacgccgcccgggcccgggcccgggcgtgccgccgaaacgcgcgcgcggc
ggcctgtgggatgatgatgatgcgccgcgcccgagccagtttgaagaagatctggcgctg
atggaagaaatggaagcggaacatcgcctgcaggaacaggaagaagaagaactgcagagc
gtgctggaaggcgtggcggatggccaggtgccgccgagcgcgattgatccgcgctggctg
cgcccgaccccgccggcgctggatccgcagaccgaaccgctgatttttcagcagctggaa
attgatcattatgtgggcccggcgcagccggtgccgggcggcccgccgccgagccgcggc
agcgtgccggtgctgcgcgcgtttggcgtgaccgatgaaggctttagcgtgtgctgccat
.. and then it carries on like that for an unpleasantly long time.
Tito Jankowski
we make to help you?
Tito
Mackenzie Cowell
scientists looking for meaningful projects like his to work on and ask
him to make a TED-style wish that we all could help fulfill. He
already has started a website, mydaughtersdna.com, for people to talk
about and help solve mystery diseases like his daughter's. Necessary
but not sufficient, I think.
Mac
Bryan Bishop
> I will definitely tell him about the potential legion of amateur
> scientists looking for meaningful projects like his to work on and ask
> him to make a TED-style wish that we all could help fulfill. He
> already has started a website, mydaughtersdna.com, for people to talk
> about and help solve mystery diseases like his daughter's. Necessary
> but not sufficient, I think.
His response basically indicated that he needs to know about Amazon's
Mechanical Turk, which is basically equivalent to distributing tasks
to many different individual people- the same model that spammers use
to solve captchas (by using random humans around the world to decode
the text in the image). An alternative would be for him to upload the
genomic information to the net and describe the tasks that need to be
done. It sounds like some programming can solve the problem of
"looking through the data".
Mackenzie Cowell
show. I will email him to learn more about the turkability of his
problem.
Sent from my iPhone