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?
> 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.
Arrogance is so unbecoming.
>> 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?
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.)
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
2) The performance attributes that existing customers do value improve
at such a rapid rate that the new technology can later invade those
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?
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".
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
> 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.
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."
"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)
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
I'm not sure that it's safe to assume that people who are incredibly
clever aren't also incredibly stupid.
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.
> 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
> 2. Could DIY biologists tackle problems with pollutants?
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
> 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
(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.
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.