Being dissed by the Genome web

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Jim H

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Mar 16, 2009, 8:18:57 AM3/16/09
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http://is.gd/nx6x

An interesting diddy in this months Genome Technology about DIYbio.

Jeswin John

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Mar 16, 2009, 8:27:07 AM3/16/09
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Yep, Folks like her said the same about Apple. We'll see in a few years what happens.

They see us building gel boxes and think thats it. Actually, the fact that you can build a $200 piece of equipment cheaply should say alot. She also forgets most here aren't biologist so the E coli example was stupid. We learn by making mistakes. Thats the whole point

Len Sassaman

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Mar 16, 2009, 10:40:37 AM3/16/09
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This is a somewhat insulting post, too. The statement:

"Recently, one of the poster projects for the group, an effort to make
melamine-detecting bacteria, suffered a setback because the people
involved in the project were unaware that certain plasmids can only
replicate in certain groups of bacteria. That's right -- you can't just
put an E. coli plasmid in Lactobacillus and assume that it will work."

is wrong. Yes, we were well aware that "you can't just put an E. coli
plasmid in Lactobacillus and assume that it will work"; our mistake was in
thinking that we had a suitable shuttle vector. Stupid mistake? Yeah. But
as a professional scientist in another field, I'll say that stupid
experiment mistakes happen all the time. I'd hardly call it a set-back
that we discovered our GFP was e. coli only -- I viewed it as a
break-through. It meant we could go back to trying heat shock on the
little buggers.

Biologists could learn something from programming wisdom, where it's well
known that the bugs you tend to spend most of your time on are the really
stupid, right-in-your face ones. That's what this was -- a really stupid
bug in our experiment that was right in front of our faces and we didn't
notice or think of it until we'd worked out a lot more complicated
scenarios first. That's just how it goes sometimes.

That said, I have no dispute with this statement: "It's hard to ignore the
learning curve, no matter what we'd like to think." Meredith and I have
spent years studying biology, as have many of you who are active in this
community, and as *will* many of you who become active in this community.
Nowhere did we ever say that DIYBIO meant "learningless bio". On the
contrary -- committing yourself to biohacking as a hobby means committing
yourself to an intense education program.

What's interesting about diybio is that self-education, group education,
informal study, etc., is now possible. In the 80s, some of the world's
best electronics designers were hobbyists. I expect in the 10s, some of
the world's best genetic engineers and cell biologists to be hobbyists.
Don't be surprised if institutionalized academia is threatened by this.



--Len.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Tito Jankowski

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Mar 16, 2009, 11:09:56 AM3/16/09
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"Wilbur Wright knows nothing about flight! :cackle:"

Tito

Sent from my iPhone

On Mar 16, 2009, at 7:40 AM, Len Sassaman

Nathan McCorkle

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Mar 16, 2009, 11:32:08 AM3/16/09
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"Nor are they strictly biologists; many DIYbio members, as they're known, are engineers and programmers, and they're determined to do biology in a new way and change the world."

"Still, the idea of treating bacteria like programmable robots is new to me, especially when it's clear that some of these programmers know very little about their biological operating system."


Now we are getting people from multiple disciplines to be interested in the same problems... this is a good thing, we need new ideas and approaches. I also feel like programmers in the game can help to reduce the person-hours needed, not immediately, but eventually we will have much more useful and fruitful computational methods to cut out a lot of problems.

-Nate
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

Daniel Singh

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Mar 16, 2009, 12:18:28 PM3/16/09
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Hi Nate,
 
just a thought, dont u have systems biology as a paper in your course, that deals with these
aspects, also the binary algebra, logic gates, flow of info, etc etc do parallel systems in biology
like promoters, inhibitors, intron, exon, homeostatsis, etc etc.
 
People from diverse backgrounds in DIYBio is an amazing thing where we can learn off each other
and improvise on almost many things.
 
regards
 
Daniel Singh

Bryan Bishop

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Mar 16, 2009, 12:59:58 PM3/16/09
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On Mon, Mar 16, 2009 at 9:40 AM, Len Sassaman wrote:
> This is a somewhat insulting post, too. The statement:

Len, you didn't explicitly say it, but you might as well have with the
ending you included. Essentially, it seems like instutitionalized
academia got through somebody's hands and took control of some fingers
to produce a rant- this same behavior might appear in the future,
maybe it won't, but at least we know how to spot it (more or less).
Institutions aren't bad, but sometimes things make me wonder. :-)

> is wrong. Yes, we were well aware that "you can't just put an E. coli
> plasmid in Lactobacillus and assume that it will work"; our mistake was in
> thinking that we had a suitable shuttle vector. Stupid mistake? Yeah. But

I'm not sure how stupid it is. I would admit that it was stupid if
there's a quantified method of determining, analytically, whether or
not some plasmid will work as a target to a given organism. To my
knowledge this doesn't really exist- so far, my understanding of
plasmid design has been "eh, figure out if there are any nucleotide or
codon biases in the organism's genome, and just make sure you make up
a vector that exhibits a similar bias." But maybe there's more to it,
and I'm just uneducated- so anybody should feel free to send me papers
or references on this topic. But anyway, if there's no quantification
of predictive plasmid design, then I don't know how stupid it can be.

> as a professional scientist in another field, I'll say that stupid
> experiment mistakes happen all the time. I'd hardly call it a set-back
> that we discovered our GFP was e. coli only -- I viewed it as a
> break-through. It meant we could go back to trying heat shock on the
> little buggers.

I actually have a hard time following this reasoning. Your GFP plasmid
vector was ecoli only, so you want to heat shock the cells- why? To
increase the chances of inducing competence to (as well as
acceptance/integration of) this vector? And if so, then the vector
isn't truly ecoli only. Right? So then why call it ecoli only?
Confusion.

> That said, I have no dispute with this statement: "It's hard to ignore the
> learning curve, no matter what we'd like to think." Meredith and I have
> spent years studying biology, as have many of you who are active in this
> community, and as *will* many of you who become active in this community.
> Nowhere did we ever say that DIYBIO meant "learningless bio". On the
> contrary -- committing yourself to biohacking as a hobby means committing
> yourself to an intense education program.

I suspect that Sandra was really meaning to say that the "learning
curve" can only be climbed and conquered in university environments
(which come with their own baggage on those curves and learning
distributions), which I disagree with. Indeed there might even be a
conflict of interest from Sandra, since she's practically promoting
universities as the Solution :-).

> What's interesting about diybio is that self-education, group education,
> informal study, etc., is now possible. In the 80s, some of the world's
> best electronics designers were hobbyists. I expect in the 10s, some of
> the world's best genetic engineers and cell biologists to be hobbyists.
> Don't be surprised if institutionalized academia is threatened by this.

- Bryan
http://heybryan.org/
1 512 203 0507

Tito Jankowski

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Mar 16, 2009, 1:18:04 PM3/16/09
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Hi everyone,
I appreciate that Sandra interviewed Jonathan Cline and went to a
Seattle DIYbio meeting -- most will assume what "DIYbio" means and
leave it at that. Sandra came out and tried the kool aid. And I know
that if Sandra is truly excited about DIYbio, she'll love hearing
about and contributing to the other DIYbio projects in motion.

Since DIYbio is an open community, I encourage Sandra as a journalist
to respond to your concerns -- publicly on this list diy...@googlegroups.com
, or privately to the individuals.

The worst thing *we* can do right now is assume what she meant.

Tito

Daniel C.

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Mar 16, 2009, 1:46:06 PM3/16/09
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In March, 2009, Sandra Porter, PhD wrote:
> I suspect that if the DIYbio project makes a contribution, it may be because
> it's caught the imagination of people like me, professionals who are jumping
> in to voluntarily offer advice

Arrogance is so unbecoming.

William Heath

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Mar 16, 2009, 1:46:48 PM3/16/09
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Ditto.

Meredith L. Patterson

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Mar 16, 2009, 1:59:30 PM3/16/09
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Sorry for top-posting (I know it chaps some people off), but messages
are out of order and I think everyone's context is important here.

I don't think Sandra would have known about my enormous vector braino
had I not posted about it to this very list. My ass is showing, in
public, for anyone who cares to read the archives of this list.
Whoops! I made a n00b fuckup! Oh, and better yet, the "d'oh" moment
was when someone anonymously posted a comment to my blog along the
lines of "hey, you might want to take a closer look at the origins of
replication that plasmid has..." -- yep, I had to be handheld through
that realization.

But you know what? This is the internet, and people are awesome enough
to just drop by and *hand* me those realizations. And I learn, piece
by piece, day by day.

Even a totally failed experiment teaches me things. The very first
time I cultured bacteria from yogurt, I was so proud about the awesome
bubble-free plates I poured (that were about 4x as thick as they
needed to be, whoops), and didn't find out until several hours after
I'd started incubating the plates that lactic acid bacteria grow
better in a CO2-enriched environment. (They're facultative anaerobes.
I knew that, but hadn't put two and two together.) That led to some
unintentional science comedy while my then-housemate and I tried to
figure out how to *create* such an environment. (Note: a 1L one-arm
Erlenmeyer half full of vinegar, with a hose on the arm leading to a
ziploc baggie, and careful coordination with sodium bicarbonate and a
cork, is not the answer. A party balloon stretched over the neck of a
2L soda bottle works way better.)

And I did get some growth, even on that first batch. Looked like I'd
even managed to keep it halfway sterile.

Anyway, now I've gotten the hang of autoclaving, pouring plates,
incubating anaerobes, performing serial dilution, tube cultures,
making and inoculating stabs and slants, pelleting and washing, safe
disposal techniques ... all pretty simple and straightforward once
you've had some practice, but working out how to make it so that you
*can* practice is an exercise unto itself -- for now. (Bryan, we'll
get there eventually. :P)

The fear of being wrong can be almost crippling to some people. I've
really never understood this, I guess my brain just doesn't work that
way. Yes, it's a pain in the ass to discover that many hours of work
have been wasted, but the fact that I made a mistake in execution
doesn't mean that my plans are somehow impossible. Hell, all I had to
do was pop on the list, describe my problem, describe a possible
solution I was considering, and courteously ask whether any of the
more bio-experienced folks could comment on its feasibility. I got
solid answers, told people "thanks!", and went on my way.

What I like so much about this list is that this is a place where
skill and understanding speak for themselves, and where people are
willing to help others along their way toward answering interesting
questions. I'm not interested in academic ego battles, and I'm glad
the rest of y'all generally aren't, either.

Cheers,
--mlp

Len Sassaman

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Mar 16, 2009, 3:26:12 PM3/16/09
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On Mon, 16 Mar 2009, Bryan Bishop wrote:

>> as a professional scientist in another field, I'll say that stupid
>> experiment mistakes happen all the time. I'd hardly call it a set-back
>> that we discovered our GFP was e. coli only -- I viewed it as a
>> break-through. It meant we could go back to trying heat shock on the
>> little buggers.
>
> I actually have a hard time following this reasoning. Your GFP plasmid
> vector was ecoli only, so you want to heat shock the cells- why? To
> increase the chances of inducing competence to (as well as
> acceptance/integration of) this vector? And if so, then the vector
> isn't truly ecoli only. Right? So then why call it ecoli only?
> Confusion.

We now have an explanation for why our current plasmids didn't work; once
we have the right plasmids, we can go back to where we started -- heat
shock -- since we ruled it out when the real problem could simply have
been the incorrect origin of replication. (We know that heat shock for
gram-positive organisms is more difficult than for gram negative
organisms, but we've researched appropriate protocols. And if that doesn't
work, electroporation and sonication are the other possibilities.)

> I suspect that Sandra was really meaning to say that the "learning
> curve" can only be climbed and conquered in university environments
> (which come with their own baggage on those curves and learning
> distributions), which I disagree with. Indeed there might even be a
> conflict of interest from Sandra, since she's practically promoting
> universities as the Solution :-).

I think that this list is proof of the incorrectness of that statement,
then. I don't think anyone would challenge the statement that Meredith,
Jonathan, Mac, Kay, Tito, etc., are biologists or biological engineers or
bioinformaticists. If you go about your research in a scientifically
rigorous way, it doesn't matter if you're unaffiliated. (I think it is
important that people in this community publish academic papers from time
to time, and attend their conferences -- bridging the two communities will
be important for you.)


--Len.

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

JonathanCline

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Mar 16, 2009, 4:08:44 PM3/16/09
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On Mar 16, 7:18 am, Jim H <gah...@gmail.com> wrote:
> http://is.gd/nx6x
>
> An interesting diddy in this months Genome Technology about DIYbio.

Sandra mentioned she had an interesting bioinformatics project to me
over the phone and sounds like she pitched it to the Seattle group. I
invited her to post it here as well. Haven't seen it yet, though I'm
still curious about the details. There are a lot of computational
projects which CompSci types could more easily ramp up on, and make a
much-needed impact to bio. One note of conflict of interest not
mentioned in the article: Sandra does have or is starting her own
bioinformatics training business, so open source and/or DIY may not
agree with her commercial interests.

I didn't expect to have to explain synthetic biology (or biobrick
abstraction-methodology) during the interview -- I keep assuming those
in the field (esp. university instructors) are aware of the progress
related to / stemming from synthesis. It shows how far the Syn Bio
crowd, or even Systems Bio crowd, still has to go in order to really
make inroads for the new technology (Endy and others obviously have
been evangelizing for quite some time; and they're much more expert
than I am. The article shows how tough it can be). It's curious how
the "let's make biology easy to engineer" idea gets panned, when it's
obviously a solid evolutionary (not revolutionary) scheme and highly
plausible at varying degrees.

If anyone is interested in the MP3 of the talk, email me & with
sufficient interest I'll post it. The article makes me feel very good
about the direction some of us are going in: commercialization of the
projects, offering buildable kits, etc. When the market incumbents
reject obvious innovation on their own products, it means they aren't
paying attention -- which provides a great opportunity for a startup
to flourish (i.e. grab the market from the sleeping bear). Only the
paranoid survive, as Grove would say, the rest get eaten.

Openwetware is open source applied to bio, and open source leverages
the "long tail" for success. This means a project can make 1000
mistakes -- like Edison on his light bulb -- without a penalty
typically forced by corporate or academia work environments. Open
source means that even small, incremental project contributions will
add up to a superior (or comparable) product in the long term. All
input is considered without budget, schedule or "political" bias.
This is a huge departure for those indoctrinated into "professional"
work environments, so it's common for a knee-jerk reaction of "Haha,
you won't get anywhere with that" type of response. (Read "The
Cathedral and the Bazaar", and read "The Long Tail".) In the long
term, the results speak for themselves.

I do feel a little misrepresented as "DIYBio project manager." I'm
one of many who is working on skunkworks biotech engineering (on the
DIYBio list or off), and I always state that. DIY has a strong meme
today though, so I guess that's what sticks.


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

Daniel C.

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Mar 16, 2009, 4:57:49 PM3/16/09
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On Mon, Mar 16, 2009 at 2:08 PM, JonathanCline <jnc...@gmail.com> wrote:
> When the market incumbents reject obvious innovation on their own
> products, it means they aren't paying attention -- which provides a great
> opportunity for a startup to flourish

There is a lot of historical precedent for startups which take away
the low -- almost undesirable -- end of a market from large companies,
then grow steadily and slowly into higher and higher markets until
they've eaten away at the foundation of the companies they originally
took the "crappy" customers away from.

There are two articles in the Harvard Business Review about this phenomenon:
* "Disruptive Technologies - Catching the Wave" by Joseph L. Bower and
Clayton M. Christensen, HBR January - February 1995
* "Meeting the Challenge of Disruptive Change" by Clayton M.
Christensen and Michael Overdorf, HBR March - April 2000

There are several examples given - yes, Apple is one of them, but on
the losing end I'm afraid - but the pattern is the same in each case.
Large, established companies are focused on selling large, expensive
products to large, well financed customers. IBM ignored the
minicomputer market because their customers were large commercial,
government and industrial companies who saw no immediate use for
minicomputers. IBM listened to their customers, gave them the large
systems they were asking for, and in the end had their market taken
away by the (much-evolved) minicomputers.

This pattern occurs all over the place, in almost all markets. There
are two important characteristics that disruptive technological
changes usually have:

1) They typically present a different package of performance
attributes -- ones that, at least at the outset, are not valued by
existing customers.
2) The performance attributes that existing customers do value improve
at such a rapid rate that the new technology can later invade those
established markets.

There is a lot more good stuff in the article, and as I read it with
DIYbio in mind it's pretty clear that we're going through a textbook
example of disruptive technologies. The great part is that it's
almost impossible for large corporations to see disruptive
technologies coming - they're blinded by good management practices
(yes I said GOOD management), honest feedback from their customers,
and a hundred other factors.

Someone is going to get rich off of DIYbio. Possibly a lot of people.
Anyone want to place bets on who it will be?

-Dan

Jeswin John

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Mar 16, 2009, 5:19:53 PM3/16/09
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Not just in the computer field but even Watson and Crick faced naysayers. DIYbio is going to get both positive and negative criticism but lets hope that there's more positive than negative

digitalbio

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Mar 16, 2009, 5:28:25 PM3/16/09
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Uh, Jonathan, you wrote <a href="http://scienceblogs.com/digitalbio/
2008/12/diy_bio_clone_at_home_but_kill.php#comment-1300887">in your
comment</a> that you were Meredith's project lead. I'm accustomed to
the project lead being the same person as the "project manager." I
apologize for not realizing that this could differ in other places.

To be honest, though, you worried me quite a bit by discussing E. coli
and Lactobacillus as if all bacteria are interchangeable.

I have also suggested two ideas for DIYers:

1. A DIY biology project idea: making yeast that sense heavy metals
http://scienceblogs.com/digitalbio/2009/01/a_diy_biology_project_making_y.php

2. Could DIY biologists tackle problems with pollutants?
http://scienceblogs.com/digitalbio/2009/01/could_diy_biologists_tackle_pr.php


And, I haven't written yet (here) about ideas for DIYers to use
bioinformatics to do biology. When I wrote about that idea before,
people said I was being condescending.

And after talking to you, and attending the meeting in Seattle, I got
the impression that DIYers might not be interested. All of those
ideas involve making discoveries about biology, none of them involve
writing software or doing programming.


I was hoping that DIYers might be interested in discovering new
viruses, like I wrote about <a href="http://scienceblogs.com/
digitalbio/2008/09/do_mosquitoes_get_the_mumps.php">here</a>.


Anyway, my response to the points above is <a href="http://
scienceblogs.com/digitalbio/2009/03/
diy_bio_programming_culture_an.php">here</a>.


Bryan Bishop

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Mar 16, 2009, 5:36:28 PM3/16/09
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On Mon, Mar 16, 2009 at 4:28 PM, digitalbio <digit...@gmail.com> wrote:
> Uh, Jonathan, you wrote <a href="http://scienceblogs.com/digitalbio/
> 2008/12/diy_bio_clone_at_home_but_kill.php#comment-1300887">in your
> comment</a> that you were Meredith's project lead. I'm accustomed to
> the project lead being the same person as the "project manager." I
> apologize for not realizing that this could differ in other places.

That's right. One meaning of "project lead" is like somebody who leads
you to the story, but doesn't lead the story itself. But it is
ambiguous, so we'll have to see how Jonathan clears this up, since
"project lead" can also mean "The Leader".

Daniel C.

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Mar 16, 2009, 5:46:06 PM3/16/09
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On Mon, Mar 16, 2009 at 3:28 PM, digitalbio <digit...@gmail.com> wrote:
> Anyway, my response to the points above is
> http://scienceblogs.com/digitalbio/2009/03/diy_bio_programming_culture_an.php

Just FYI, Sandra, this is a plain text mailing list, so adding html
tags doesn't actually translate well for all mail clients.

From your blog post:

> I managed to offend some people by suggesting doing biotechnology
> successfully at home might mean that you actually have to learn some
> biology.
>
> Funny, huh?

It wasn't your suggestion that learning is important that was
offensive. Rather, it was the condescending air which was widely
inferred from statements like the closing "Funny, huh?" quoted above.

Mackenzie Cowell

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Mar 16, 2009, 9:09:53 PM3/16/09
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I was unable to post the following as a comment to Sandra's recent blog post.  When I tried, I got an opinionated "Comment Submission Error: Text entered was wrong.  Try Again." error message (http://skitch.com/macowell/bekyd/discovering-biology-in-a-digital-world-comment-submission-error).

==========================================

Dear Readers,
you may wish to check out one of the main threads discussing Sandra's GT article on the DIYbio google group [1].

Dear Sandra,
Thanks for posting your followup to the diybio discussion about your GT article.  I don't think you put your foot in anything and I think most people enjoyed your comments and suggestions.  I particularly liked your DIYbio project ideas, such as engineering heavy-metal detecting yeast [2].  

I think new diybio and iGEM teams benefit greatly from having the input of an expert like yourself when brainstorming project ideas to help them choose ideas that are likely to be achievable with existing methods and techniques, which you are familiar with.  But I also think that the fresh, blue-sky perspective brought by newcomers helps them imagine novel new territory.  Together, the combination is very powerful, and I wish there were more experts like you helping brainstorm diybio projects.  Maybe we should start a new google group just for that purpose - I am sure the thousands of iGEM students this year would find it indispensable.

Speaking of DIYbio model organisms like Baker's Yeast, I just want to clarify that the species of Acinetobacter suggested on the list [3] as good fit for diybio was Acinetobacter baylyi [4], not Acinetobacter baumannii [5].  Just mentioning the Genus of the organism is ambiguous, since Acinetobacter is a large genus and A. baylyi is not pathogenic like A. baumannii.  This sort of confusion concerns me because it demonstrates how easily a journalist could negatively portray innocent work with ADP1, so maybe we should just stick with yeast.

Anyway, I hope you aren't put off by the critics.  The loudest/most frequent voices, especially on mailing lists, should not be taken to represent the majority opinion.  I hope you keep you project ideas and advice coming and perhaps share your bioinformatics idea with the group.

Cheers!
Mac

[1] http://groups.google.com/group/diybio/browse_thread/thread/3a1108bbb90d50e2
[2] http://scienceblogs.com/digitalbio/2009/01/a_diy_biology_project_making_y.php
[3] http://groups.google.com/group/diybio/browse_thread/thread/d993bb976d0a20d0/31225ec90747cd8f?lnk=gst&q=ADP1+which+is+naturally+competent#31225ec90747cd8f
[4] http://openwetware.org/wiki/Acinetobacter_baylyi_(ADP1)
[5] http://en.wikipedia.org/wiki/Acinetobacter_baumannii


Alec Nielsen

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Mar 16, 2009, 9:32:46 PM3/16/09
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Sandra, I think it's unfair to say that we aren't interested in the computational aspects of DIYbio. There are many people on-list who discuss bioinformatics, areas where programmers can contribute, and the interface of computers and biology. Even here in Seattle, there are hobbyists who already do (or want to start) biomodeling, writing software, and doing digital biology. I'm one of those people who wants to start, and I'm glad to have an expert in the neighborhood. (I read your blog regularly, and I find it interesting and helpful as an amateur).
 
Anyways, we're due for another Seattle DIYbio meeting, and we should all meet up and talk about this more. Certainly, a large percentage of DIYbio-ers work in labs, or have previously, which sometimes gives the impression that we're primarily interested in biohacking. But, saying that we *only* want to do wet-things is a hasty assessment that isn't entirely true. I'm going to post on the DIYbio-Seattle list about the next meeting now, and I hope to see you there!
 
Alec

digitalbio

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Mar 16, 2009, 10:12:46 PM3/16/09
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Hi Alec,

Another meeting would be good. I got the impression from the first
meeting that most people were interested in doing synthetic biology,
not digital biology, but maybe that was wrong.

I'm flying to Tennessee on Thursday to give bioinformatics workshops
at a conference, and writing a grant after that, so I'm pretty
committed until after April 5th. After that, I should have some time.

I have some good news too, I talked with someone today from Science on
Tap. There are some open slots this summer, so I will try to get DIY
bio on the schedule and will coordinate more once I get the open dates.

Nathan McCorkle

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Mar 16, 2009, 10:19:02 PM3/16/09
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I think making statements in your blog like this :
"When students or researchers work with E. coli in a place like a school or lab, they have both the equipment to kill the bacteria afterwards, and someone around who knows that autoclaving your cultures is an important thing to do.

Your average kitchen, on the other hand, doesn't have an autoclave, and or even a pressure cooker. I don't know know if your average DIY biologist knows it's a bad idea to pour E. coli down the sink."

and this:

"Unless home cloners use proper safety techniques, like autoclaving or pressure cooking their cultures, they will be sending antibiotic resistant E. coli out into the environment at the end of their experiments."

just seem odd to me, because it is coming from someone with a PhD.

I am a big fan of open source software, I have been using linux almost exclusively for at least 2 or 3 years, and started playing with it when I was about 10 (I am almost 22 now). I am also a big fan of DIY bio, I have been in an accreditted biotech program for 2 years, and have been playing with it since I was about 15.

My first piece of DIY bio equipment was a used pressure cooker from the goodwill, without it I would have gotten NO WHERE. That was when I was in high school planning on going to college for computer science, it took me a long time not to get pole beans to die!

My point is, if you are uneducated and don't have a way to sterilize media, reagents, etc... and you don't know about the importance of sterile technique and how strict you must be...  you just aren't going to get anywhere. You're never going to make a superbug and pour it down the drain to infect Mayberry, Aunt Bee, and the Griffith kid. You're never going to get past step 1.

I asked a prof that I did summer research with after my first year here, something about how people are scared of genetic engineering, and he bluntly responded "people that rant about the dangers don't know anything about science". Now given the situation with drugs and their metabolites getting passed through our waste treatment plants, maybe a superbug poured down the drain might have a slight chance of survivng, but I really doubt it. 

Oh, and I found that 30% of Indians have a pressure cooker  (sorry I tried for the last hour to find U.S. statistics, and could only find some stuff from uga.edu that was more about canning)

(http://www.google.com/url?sa=t&source=web&ct=res&cd=2&url=http%3A%2F%2Fwww.nfhsindia.org%2Fdata%2Findia%2Findch2.pdf&ei=dfq-SdLrFIqvtwfO2YH3Cw&usg=AFQjCNEDACXsRsa1fVxoScJiKUd5uzS8_w&sig2=KjnTKBcYW9aJfEHj_JvXRQ)


-Nate

Nick Taylor

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Mar 16, 2009, 10:58:07 PM3/16/09
to diy...@googlegroups.com

> I asked a prof that I did summer research with after my first year here,
> something about how people are scared of genetic engineering, and he
> bluntly responded "people that rant about the dangers don't know
> anything about science".

The flipside of which would appear to be "People who do know about the
science don't seem to see any potential dangers outside their field of
expertise"

I'm not sure that it's safe to assume that people who are incredibly
clever aren't also incredibly stupid.

digitalbio

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Mar 16, 2009, 11:50:19 PM3/16/09
to DIYbio
Nathan,

You must not read the discussions here very often. There was one guy
who wanted to isolate and work with his own E. coli. Yikes!

It would be irresponsible to suggest that people work with bacteria
without sterilizing their cultures afterward, but I have seen that
written here and elsewhere. And so, I point out those things.

And I try not to make assumptions about prior knowledge.

When I was on sabbatical years ago, I spent time in a cutting edge
genetics lab where people were growing E. coli to make clone
libraries. Interestingly, I found that the people in the lab (post
docs, grad students, and techs) didn't know much about microbiology
and they certainly weren't really growing E. coli. So, I try not to
assume that people know those sorts of things, unless they have Ph.D.s
in microbiology.

Sandra Porter
Discovering Biology in a Digital World
http://scienceblogs.com/digitalbio

Oh, BTW - I fixed the commenting problem on my blog, so you can post
comments now. Our blogging platform, Moveable Type has a bug in the
captcha filter.

Daniel C.

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Mar 17, 2009, 12:03:59 AM3/17/09
to diy...@googlegroups.com
On Mon, Mar 16, 2009 at 9:50 PM, digitalbio <digit...@gmail.com> wrote:
> You must not read the discussions here very often.  There was one guy
> who wanted to isolate and work with his own E. coli.  Yikes!

You are mistaken, Sandra, and you should read more carefully before
you go on about things like this. I am the person in question, and I
never suggested that anyone -- least of all myself, stricken as I am
with obsessive compulsive disorder -- attempt such a distasteful act.

Len Sassaman

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Mar 17, 2009, 7:20:31 AM3/17/09
to DIYbio
On Mon, 16 Mar 2009, digitalbio wrote:

>
> Uh, Jonathan, you wrote <a href="http://scienceblogs.com/digitalbio/
> 2008/12/diy_bio_clone_at_home_but_kill.php#comment-1300887">in your
> comment</a> that you were Meredith's project lead. I'm accustomed to
> the project lead being the same person as the "project manager." I
> apologize for not realizing that this could differ in other places.

Perhaps the misconception is that you think that there is an organization
called DIYBIO? In the sense that that term is used on this list
(interchangeably with biohacking), it's not an organization. It's a
movement, or a label.

But yes, it is a mistake to equate "project lead" with "project manager".
I'd have a look at how open source software projects work (ones of the
three to seven person team size; projects like Firefox, etc., do generally
have product managers and other middle-management overhead.

> To be honest, though, you worried me quite a bit by discussing E. coli
> and Lactobacillus as if all bacteria are interchangeable.

For many of our purposes, they are. We're essentially talking about
nanotechnology, without waiting for the nanoassemblers. If e. coli and l.
acidophilus will perform the same desired function within the same
specified criteria, it doesn't matter which we use.

We're sticking with l. acidophilus for a number of reasons -- 1, the
glowgurt project is something that Meredith and I have been kicking around
for a lot longer than the melaminometer -- merging the two just seemed
sensible given the existing work on glowgurt; the scurvy cure experiment
has to be l. acidophilus based; and people have an irrational fear of e.
coli that they don't have for "yogurt bacteria".

> I have also suggested two ideas for DIYers:
>
> 1. A DIY biology project idea: making yeast that sense heavy metals
> http://scienceblogs.com/digitalbio/2009/01/a_diy_biology_project_making_y.php
>
> 2. Could DIY biologists tackle problems with pollutants?
> http://scienceblogs.com/digitalbio/2009/01/could_diy_biologists_tackle_pr.php

These are two very similar problems. I think Meredith has posted about
some ideas we've had on this topic, as well as research we've been
following with respect to the use of various mushrooms for heavy metal and
other toxin cleanup -- you might check the archives.

> And, I haven't written yet (here) about ideas for DIYers to use
> bioinformatics to do biology. When I wrote about that idea before,
> people said I was being condescending.

Given the number of professional bioinformaticists on the list, I find
it surprising and unlikely that someone would find you condescending for
having mentioned bioinformatics. It's a daily part of life over here.
(Heck, Meredith's two CodeCon presentations (2005 and 2006) were both
based on ground-breaking bioinformatics software.

Are you sure you weren't being perceived as condescending for some other
reason? (Such as, perhaps, assuming that there are no professional
biologists or bioinformaticists on this list, or that the amateurs know
less than the professionals?)

> And after talking to you, and attending the meeting in Seattle, I got
> the impression that DIYers might not be interested. All of those
> ideas involve making discoveries about biology, none of them involve
> writing software or doing programming.

You'd be hard-pressed to find a single thing that every biohacker agreed
was interesting.

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Len Sassaman

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Mar 17, 2009, 7:36:41 AM3/17/09
to DIYbio
On Mon, 16 Mar 2009, digitalbio wrote:

> So, I try not to assume that people know those sorts of things, unless
> they have Ph.D.s in microbiology.

Are you seriously saying that someone needs a PhD in microbiology before
you will credit them with some common sense? I'm in general agreement that
assumptions about people's knowledge can be dangerous -- but you're
assuming highly educated and intelligent people are idiots because they
don't have PhDs in microbiology. I can see how that would be
condescending.

(Yes, I'm calling people who do e. coli experiments without an
autoclave/pressure cooker, and who flush the results of their experiment
down the sink, idiots. What else would you call them?)

Newcomers to biohacking need "lab techniques 101", not "microbiology
comps" to get them on the right track.

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Daniel Wexler

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Mar 17, 2009, 9:02:57 AM3/17/09
to diy...@googlegroups.com
E. coli goes down the drain all the time, from your bowels to the
toilet. Also, use bleach to kill recombinant bacteria if you don't have
an oven or pressure cooker or stove top to boil water. Or simply put it
in a box to air dry.
Dan

Nathan McCorkle wrote:
> I think making statements in your blog like this :
> "When students or researchers work with /E. coli/ in a place like a
> school or lab, they have both the equipment to kill the bacteria
> afterwards, and someone around who knows that autoclaving your
> cultures is an important thing to do.
>
> Your average kitchen, on the other hand, doesn't have an autoclave,
> and or even a pressure cooker. I don't know know if your average DIY
> biologist knows it's a bad idea to pour /E. coli/ down the sink."
>
> and this:
>
> "Unless home cloners use proper safety techniques, like autoclaving or
> pressure cooking their cultures, they will be sending antibiotic
> resistant /E. coli/ out into the environment at the end of their
> some stuff from uga.edu <http://uga.edu> that was more about canning)
>
> (http://www.google.com/url?sa=t&source=web&ct=res&cd=2&url=http%3A%2F%2Fwww.nfhsindia.org%2Fdata%2Findia%2Findch2.pdf&ei=dfq-SdLrFIqvtwfO2YH3Cw&usg=AFQjCNEDACXsRsa1fVxoScJiKUd5uzS8_w&sig2=KjnTKBcYW9aJfEHj_JvXRQ
> <http://www.google.com/url?sa=t&source=web&ct=res&cd=2&url=http%3A%2F%2Fwww.nfhsindia.org%2Fdata%2Findia%2Findch2.pdf&ei=dfq-SdLrFIqvtwfO2YH3Cw&usg=AFQjCNEDACXsRsa1fVxoScJiKUd5uzS8_w&sig2=KjnTKBcYW9aJfEHj_JvXRQ>)

Nathan McCorkle

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Mar 17, 2009, 9:50:18 AM3/17/09
to diy...@googlegroups.com
Dan, drying could leave the DNA intact so that other organisms could take it up, I doubt the plasmids would survive any subsequent lysis intact, but the fragments could be taken up by horizontal transfer.

My point about not getting anywhere without some sterilization device seems to have gone unheard. There is no need to worry about people engineering something and not having the means to deactivate it, IMO, you need to have an autoclave/pressure cooker to begin with, the only remaining step is to let people know these organisms should be deactivated before disposal.

Even if you're not doing GE, autoclaving waste can is still a good idea just because some things like fungal contamination can sporulate and get all over your lab leading to further contam problems.

-Nate

Meredith L. Patterson

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Mar 17, 2009, 10:44:04 AM3/17/09
to diy...@googlegroups.com
On Tue, Mar 17, 2009 at 2:50 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> My point about not getting anywhere without some sterilization device seems
> to have gone unheard.

I'll just reiterate this, because if you're working with any kind of
cells (single-celled organisms or tissue culture), you're going to
need sterilization equipment to protect the cells from the surrounding
environment much more than you'll need it to protect the surrounding
environment from your cells. If your plates/slants/tubes/whatever get
contaminated with another organism, that can ruin your results, so
sterilize your equipment first, srsly.

--mlp

Marco Mena

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Mar 17, 2009, 12:09:59 PM3/17/09
to diy...@googlegroups.com
Actually, most any sterile disposable labware, tools, and media that one needs to get started with microbiology can be purchased pre-sterilized, so it isn't strictly true that you need an autoclave to work with cultures.  Of course, if someone is buying pre-sterilized equipment, they will likely know that proper disposal via bleaching/autoclaving is also important, but the "not getting anywhere" part isn't exactly true, unfortunately.
- Marco

ridgway

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Mar 17, 2009, 12:45:27 PM3/17/09
to DIYbio

Hi Sandra,

On Mar 16, 8:12 pm, digitalbio <digital...@gmail.com> wrote:

> I got the impression from the first
> meeting that most people were interested in doing synthetic biology,
> not digital biology, but maybe that was wrong.

Just as a note on the potential confusions of new buzzwords, "digital
biology" is being used essentially synonymously with "synthetic
biology" where I hang out. Craig Venter's TED talk has a similar usage
-- the "digital" is referring to the discrete coding of biological
information by DNA bases. I've also seen "digital biology" being used
to refer to artificial life (the programs created by computer
scientists on a computer, not reproducing chemical organisms in a wet
lab) and also the Benveniste "water memory" homeopathy fraud. Great
buzzwords get reinvented and reinterpreted over and over, so those of
us who use them have to get used to re-explaining what we mean by
them. (And the same goes for "synthetic biology", "systems biology",
etc.)

I think it's great to see you getting involved with DIYbio. My
personal opinion is that it is the educational domain where DIYbio
could have the largest near-term impact.

doug.

Citizen Jimserac

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Mar 18, 2009, 8:48:28 AM3/18/09
to DIYbio
Pardon me, while I agree with your description of digital biology, I
must register an objection, and I understand this is off topic,
regarding the characterization of Benveniste's water memory
experiments as a fraud.

Skipping over a recapitulation of the travails of Benveniste, it
should be pointed out that a Homeopathy skeptic named M. Ennis heard
about the furor and decided to repeat experiments of another French
researcher. She was convinced that high dilutions, in which all
molecules of the stimulant have been diluted away, could not possibly
stimulate a biological effect. She was astonished to find, however,
that they did. She and several other labs repeated the experiment and
3 of the other 4 labs got positive results. She published the
results in Inflammation Research vol 53, p181.

These results have been repeatedly confirmed as recently as in 2007
and 2008 by other researchers, and there is no known scientific
explanation.

Since the researchers have quite genuine scientific credentials and
are publishing in reputable journals, I object to calling eitehr their
research, related theories, or consequently Homeopathy, a fraud.
This unfortunate characterization was started by anti alternative
medicine fanatics and professional skeptics such as those involved
with the now discredited quackwatch which now owes hundreds of
thousands of dollars in legal judgements against it. Despite loud
protests that they; are supporters of science, the methods and tactics
of their innuendo say othewise.

A 2001 BBC documentary supposedly "repeated" Ennis' experiment with
"negative" results. Intrigued, Ennis expended some effort in
contacting the producers and eventually they sheepishly admitted that
they had never intended to exactly repeat her experiment and their
researcher that performed the TV experiment also admitted that he had
added aluminum chloride, which kills the basophil cells involved in
the test, thus ruining results from the outset. A Weak-ee-pedia
article (anonymous authors) still wrongly claims that Ennis'
experiment was repeated with negative results in the documentary.

Last but not least, much attention has been given to the "Amazing"
Randi. The editor of the prestigious Lancet, a known rabid anti-
Homeopathy foe, agreed to let Benveniste publish his experiment but
only if Randi and another stage magician were present to "expose"
trickery. As one might expect, these non-scientists turned the lab
into a circus, performing card tricks, distracting the scientists and
it is not much of a surprise that the results turned negative, with
the added help of some sloppy controls and procedures on the part of
the researchers. Randi later exploited this and gained worldwide fame
with his $1,000,000 "challenge". After 5 years of negotiations with
Randi, Greek Homeopathist George Vitoulkas expended incredible time
and energy following Randi's directives and allocated rooms and
personnel in a Greek hosptial to perform a test agreeable to Randi
only to be told that all negotiations were "discarded" and Vitoulkas
was required to begin the negotiations all over again. Incredibly,
at his website, Randi claims that it was Vitoulkas who had
withdrawn. The full story can be found at Vitoulkas' website.

The latest profiteer to attack Homeopathy with a "challenge" of his
own is Dr. Edzard Ernst, author of a recent book and the world' first
Professor of alternative and complementary medicine. He may well be,
but in an exchange with him at Abel Pharmboy's blog, he openly
admitted that he is an MD and has no advanced degrees or additional
training in Homeopathy or any other system of alternative medicine.

In the light of the above and from recent research we can conclude
that Homeopathy has no known science behind it but does have a huge
clinical and case history basis, which, just as in modern medicine,
confirms its efficacy well above placebo.
(A 2005 Lancet article claiming to deny this has been totally refuted
in a recent Journal of Clinical Epidemiology article).

So calling legitimate researchers, or their areas of research "frauds"
is totally improper and actually subverts all scientists in every
discipline. You may personally think Homeopathy the craziest nonsense
that ever was, a feeling I happen to have with theories such as the
"many worlds" theory of Quantum Mechanics, but impugning the
reputation or motivation of genuine researchers is unscientific and
should be avoided at all cost.

Thanks
CJ

On Mar 17, 12:45 pm, ridgway <ridg...@dridgway.com> wrote:
> Hi Sandra,
>
> On Mar 16, 8:12 pm, digitalbio <digital...@gmail.com> wrote:
>
> > I got the impression from the first
> > meeting that most people were interested in doing synthetic biology,
> > not digital biology, but maybe that was wrong.
>
> Just as a note on the potential confusions of new buzzwords, "digital
> biology" is being used essentially synonymously with "synthetic
> biology" where I hang out. Craig Venter's TED talk has a similar usage
> -- the "digital" is referring to the discrete coding of biological
> information by DNA bases. I've also seen "digital biology" being used
> to refer to artificial life (the programs created by computer
> scientists on a computer, not reproducing chemical organisms in a wet
> lab) and also the Benveniste "water memory"homeopathyfraud. Great

Rajagopal

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Mar 18, 2009, 10:43:57 PM3/18/09
to diy...@googlegroups.com
I am fascinated by the discussions.I would like to take the discussions into
practical innovative domains instead of harping on too much technicalities.
Techonlogy is ok if if is diy and is an enabler of assessments and
experiments with useful results.
1.what is effect of baceria from plants and animals on human bodies.
2.what is the effect of nano particles on bacteria as it is a quantum level
intervention?
3.New specific bacteria collection and development and growth.
4.what are the improvised equipments required in specific cases.?
5.diy microscopic examination with cheap chinese lasers(red) etc.
6.how to collect bacteria from plants?
7.DNA mutatation in situ without separation from the cells.
8.Toxic,metal eating,plastic eating bacteria collection and lab methods to
multiply them.
9.Petroleum hydrocarbons producing bacteria.How to collect and develop
further.
10.what are the activites feasible by DIY folks?
Merely separating DNA etc and later confirming the sample from big labs are
only small steps.
11.Effect of proteins and macro molecules on the cell structure and walls.
12.An educational discussion giving effects of pH and other common chemicals
like Ammonia,H2O2,various alcohols,DMSOetc on microbes and their culture.
13.Even nomenclature which is wayward and unilateral can be systematised by
somebody who is interested in that area.
I am working on separation of proteins and macro molecules.The push pull
mechanism for separation of amines is not that much effective.Still it yield
70% results in a number of cases. Such simple methods can also be discussed
by sub-groups.
14.Simple alternative to PCR,electrophoresis,chromto graphic methods can be
discussed to begin with.

Raja

Rajagopal

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Mar 18, 2009, 10:56:19 PM3/18/09
to diy...@googlegroups.com
Homeopathy cannot be brushed aside.Metals and other molecules on dilution
take up nanolevels and give such effects.Similar to this is the Ayurveda
treatments in which pruification is done through sives several times.If you
are interested understand "Vastrakayam" ie passing the powder through a
muslin cloth several times and using the resultant powder for treatment or
preparation of medicines.This powder passes through the nano-pores of
"vastra" ie cloth and the resultant powder has more nao-concentration.thus
the Indian medincine system accepts this a sure treatment with good and even
excellect results.There is no need for denigrating any system by the
wasteful complications without understanding the process.
Also pouring of warm oil on the head and body is an ayurvedic treatment
which changes the -OH groups on the skins and other crevices by interaction
with oleo-resins in the oil thus producing a change which is proven with
results of amelioration and good health.

These are real and practical examples.
Raja
----- Original Message -----
From: "Citizen Jimserac" <Jims...@gmail.com>
To: "DIYbio" <diy...@googlegroups.com>
Sent: Wednesday, March 18, 2009 6:18 PM
Subject: Re: Being dissed by the Genome web



Mike Barnkob

unread,
Mar 19, 2009, 8:51:11 AM3/19/09
to DIYbio
Please stop this homeopathy spam. Homeopathy has nothing to do with
science or this topic.

Mike

E. M. Muralidharan

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Mar 19, 2009, 8:55:25 AM3/19/09
to diy...@googlegroups.com
I have just been lurking around here for some time but the "off topic' comments on Homeopathy provoked me enough to write this. Today there is no science in homeopathy or ayurveda - you just believe what their  bible says.   If advocates of Homeopathy want to demonstrate it is a science then it would not do to simply rebuke Randi or the editor of Lancet or Nature ( the Benveniste paper appeared in Nature not Lancet). And Randi's $100......00 challenge came before the Nature debate. Some basic tenets of chemistry, physics and biology as we know it today would have to be revised  if the incredible homeopathic dilutions did have any biological effects.  That I think cannot be done in the cavalier manner being adopted by the alternative medicine folks today.

 Raja, are we talking   of nano levels here?  And is it not possible to test homeo or ayurvedic  formulations by the classical double blind randomised clinical trials rather than rely on anecdotal evidence? One has to account for placebo effects too. The  liberal use of  pseudo scientific terminology is so typical of the alternative medicine. I am not denigrating anything but we need some more science not just  alchemist's notes  or ancient palm leaves to go by.   

Murali

Citizen Jimserac

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Mar 19, 2009, 8:58:26 AM3/19/09
to DIYbio

On Mar 19, 8:51 am, Mike Barnkob <mbarn...@gmail.com> wrote:
> Please stop this homeopathy spam. Homeopathy has nothing to do with
> science or this topic.
>
> Mike
>

While Homeopathy was off topic, I do not post spam.

Also, I will again object to innuendo against Homeopathy
while perfectly legitimate scientific researchers are researching it.

You might as well have said that the "many worlds" theory
of quantum mechanics has nothing to do with science.

Please don't allow your opinions, however strongly held, or your
opinion as to what is or is not science, to be held as a standard for
anyone else.

Citizen Jimserac

Darth Mencken

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Mar 19, 2009, 11:32:37 PM3/19/09
to DIYbio
Professional contempt and jealousy toward amateurs! Yes, many of us do
other things on the side. And yes, newcomers do often make mistakes.
Course we'll make mistakes. Don't professionals, with their vastly
greater educations and budgets, also make mistakes?

On Mar 16, 8:18 am, Jim H <gah...@gmail.com> wrote:
> http://is.gd/nx6x
>
> An interesting diddy in this months Genome Technology about DIYbio.

Rajagopal

unread,
Mar 20, 2009, 4:20:52 AM3/20/09
to diy...@googlegroups.com
AS a chemical researcher I understand what you say.The categorisation as alternative medicine and proper medicine etc is not proper.As a original thinker if you devote your attention to fundamentals even the chemical reactions can be questioned.Philosophy of chemistry is the subject area for convinience.
Pl understand vastrakayam and sputams and methods adopted.
Also please go though the practical experiments where metal atoms and ions work on macro molecules.These areas are still virgin grounds.Why an isotopic metal ion seeks a cancerous tissue more than its normal variety?
Raja
 
 
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