Carolina Biological / Halobacterium spp. NRC-1 (from Tom Knight)
Mackenzie Cowell
Safe experiments with a good non-pathogenic organism.
A company devoted to high quality high school level experimentation.
Making Microbiology Manageable: The New Model Microbe, Halobacterium sp. NRC-1
From: Tom Knight <t...@csail.mit.edu>
Date: Thu, Jul 17, 2008 at 2:33 PM
Subject: Fwd: Posting error: DIYbio
To: Mackenzie Cowell <maco...@gmail.com>
Cc: Tom Knight <t...@csail.mit.edu>
Oh well.
Begin forwarded message:
From: nor...@googlegroups.com
Date: July 17, 2008 2:32:24 PM EDT
To: t...@csail.mit.edu
Subject: Posting error: DIYbio
You do not have permission to post to group diybio. You may need to join the
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From: Tom Knight <t...@csail.mit.edu>
Date: July 17, 2008 2:32:14 PM EDT
To: diy...@googlegroups.com
Cc: Tom Knight <t...@csail.mit.edu>
Subject: Carolina Biological / Halobacterium spp. NRC-1
Safe experiments with a good non-pathogenic organism.
A company devoted to high quality high school level experimentation.
http://www.carolina.com/category/teacher+resources/classroom+activities/making+microbiology+manageable-+the+new+model+microbe,+halobacterium+sp.+nrc-1.do?s_cid=em_ct_07152008
Mackenzie Cowell
Also, Carolina Biological Supply has no problem accepting credit card payments and shipping equipment / supplies to us at BetaHouse or the FabLab or wherever DIYbio headquarters gets dedicated space - so go check them out!
Of course, I still think we have a lot to gain by focusing on the DIY ethic. I am sure we could make successful diy alternatives to many of the things Carolina sells, such as their "Extremely Easy DNA Extraction Kit" - only $73.30! (it's just ethanol and some plasticware) - or the "Carolina™ Electrophoresis Equipment Package I", which only costs $1995.00.
That said, there will probably be times when it is wiser to use cheap, reliable, pre-fabbed consumables like invitrogen's e-gels (pre-cast, pre-stained, ready to go out of the box) instead of trying to make everything from scratch.
Mac
Bryan Bishop
> That said, there will probably be times when it is wiser to use
> cheap, reliable, pre-fabbed consumables like invitrogen's e-gels
>h+ethidium+bromide.do?keyword=egel&sortby=bestMatches>(pre-cast,
> pre-stained, ready to go out of the box) instead of trying to make
> everything from scratch.
Mac, have you sold out on us? :-) It's nice that they allow credit card
transactions, but really, buying products from companies is mostly
against the DIY concept. This is like trying to throw up an
instructable with the first step "Buy a kit". That's not do it
yourself. That's "do the credit card transaction yourself".
- Bryan
________________________________________
http://heybryan.org/
Engineers: http://heybryan.org/exp.html
irc.freenode.net #hplusroadmap
Jason Kelly
Jason Morrison
I hope we can produce a wide array of options that allows amateurs to make their own time/cost tradeoff decision, and learn a bunch along the way.
Mackenzie Cowell
Likewise, DIYbio might benefit from *low-cost, reliable* protocol kits instead of trying to build everything from scratch in a kitchen.
Mac
p.s. look for a shoutout in the video of our visit to the Boston FabLab (props to Ben)
Bryan Bishop
> what's wrong with kits?
Hm. Not much. I suppose this is the way to go about doing kits:
http://arduino.cc/ You get everything: the product, microprocessor
schematics, the interface, community support (it's the internet), and
so on. Historically kit purchases in nonelectronic areas involve less
than optimal documentation as unfortunate as this is.
Another way to say this is that the idea is to continuously minimize the
dependence on proprietary means of working with life. How is this
supposed to be done with proprietary kits all the time? Maybe for
bootstrapping, but as a requirement for group progress ? That's
definitely a sell out.
- Bryan
________________________________________
http://heybryan.org/
Engineers: http://heybryan.org/exp.html
irc.freenode.net #hplusroadmap
"Genius is the ability to escape the human condition;
Humanity is the need to escape." -- Q. Uim
Bryan Bishop
> I wouldn't be quite so harsh; I'm all for the knowledge and
> empowerment that comes from putting the R&D time into quality DIY
> protocols and schematics. At the same time, at least 6 of us spent 3
> hours a week or so back trying to run a gel - when looking at 18
> man-hours to run two gels (that didn't work), $8.75/kit seems rather
> cheap for a higher degree of confidence in success. At the very
> least, it's a good control against which to compare our own gel
> boxes.
Yeah, I agree that what I sent is harsh. But since this is diybio and
not buybio, ;-) ... speaking of which, those protocols and schematics
that you mention. I saw the writeup that someone sent to the list re:
the fun time with the group making a gel all at once. Was this written
up or documented or was there no documentation protocol in place? It
would be a shame if that was all wasted, undocumented effort. Without
documentation there's no way to improve on it so bringing it up in
discussion might become unfair, no?
- Bryan
________________________________________
http://heybryan.org/
Engineers: http://heybryan.org/exp.html
irc.freenode.net #hplusroadmap
Mackenzie Cowell
Mac
Bryan Bishop
> Well, I think that there is always going to be a gray area for the
> DIY ethic. The two extremes are building everything from scratch or
> ordering everything pre-built. I think most makers compromise
> somewhere in between. I don't have a problem buying $12.00 worth of
> screws and wire and plexiglass to build gel boxes from scratch... but
> I think it would be pretty ridiculous to synthesize those materials
> from scratch using a home-built forge and a plastic extrusion system
> and so on. So in many cases, DIY work involves using prefabricated
> materials.
I wouldn't call anybody out for not always using home forging methods
and so on. This is mostly because I'll admit there are other things
where attention should be focused on (amateur infrastructure projects).
But. The difference is between having identified and carried out the
homebrew, do-it-yourself method, having it documented, available,
ready, and functional, versus just skipping the step entirely and being
completely dependent on proprietary preparation. That's not good.
> Likewise, DIYbio might benefit from *low-cost, reliable* protocol
> kits instead of trying to build everything from scratch in a kitchen.
I am sure there are many people with many different choices, so maybe we
should be here to synthesize a broader picture from the technical
options we know of instead of keeping it all wrapped up in proprietary
kits.
> p.s. look for a shoutout in the video of our visit to the Boston
> FabLab (props to Ben)
There's a video? :-) I'll go look.
- Bryan
________________________________________
http://heybryan.org/
Engineers: http://heybryan.org/exp.html
irc.freenode.net #hplusroadmap
Bryan Bishop
> Agreed. Look for the first open-source DIYbio kits by September.
> We're focusing on three modular kits for the launch: sterile culture
> maintenance, DNA isolation, and gel electrophoresis. Maybe based on
> yeast, maybe on halobacterium NRC-1. You should help us develop
> them.
You make it sound like "we" means some group of people not on the list.
Are you having a little secret group within diybio or something? :-)
We're all in this together ... why not talk about it on the mailing
list? There's a number of ideas that would be worth talking about and
implementing, like the structured markup languages or object
serialization for functional protocol specifications, and the cullation
scripts I've hacked up for the git files, but if it's all behind closed
doors then how is it open source? etc.
Thomas Knight
Mine their own salt, synthesize their own lipids, Make their own DNA
from sugar and phosphorus. We'll put that Pasteur fellow in his place.
Bryan Bishop
> Right. Real Men don't use existing cells -- they build their own.
> Mine their own salt, synthesize their own lipids, Make their own DNA
> from sugar and phosphorus. We'll put that Pasteur fellow in his
> place.
Heh, that'd be awesome. I'd point out that these companies are made by
human beings and thus these products are somehow done by human created
processes, protocols, or machines of one sort or another, so it's not
magical or any sort of 'vitalism' that gives these companies something
that diybio amateurs can't have. It's proprietary lock out, and that's
about it.
BTW: I'm pretty sure I am made of cells and that my cells are making
DNA. Maybe I'm wrong. I haven't run a gel on it yet, so I haven't
checked.
ta...@museatech.net
In that vein, Intel got under my skin for the last time last week, too. So I rolled my own fab, complete with pvd, cvd and lithography machines culled from old banana skinning machines and used a low power chip design Andy Grove whispered to me.
I'll have the specs up on the wiki soon.
No stopping humans now.
Talli
Sent via BlackBerry by AT&T
-----Original Message-----
From: Bryan Bishop <kan...@gmail.com>
Date: Fri, 18 Jul 2008 13:48:55
To: <diy...@googlegroups.com>
Subject: Re: Carolina Biological / Halobacterium spp. NRC-1 (from Tom Knight)
Bryan Bishop
> On Friday 18 July 2008, Thomas Knight wrote:
> > Right. Real Men don't use existing cells -- they build their own.
> > Mine their own salt, synthesize their own lipids, Make their own
> > DNA from sugar and phosphorus. We'll put that Pasteur fellow in
> > his place.
>
> Heh, that'd be awesome. I'd point out that these companies are made
> by human beings and thus these products are somehow done by human
> created processes, protocols, or machines of one sort or another, so
> it's not magical or any sort of 'vitalism' that gives these companies
> something that diybio amateurs can't have. It's proprietary lock out,
> and that's about it.
This might be unfair since I didn't reference the other email.
The other:
> Hm. Not much. I suppose this is the way to go about doing kits:
> http://arduino.cc/ You get everything: the product, microprocessor
> schematics, the interface, community support (it's the internet), and
> so on. Historically kit purchases in nonelectronic areas involve less
> than optimal documentation as unfortunate as this is.
>
> Another way to say this is that the idea is to continuously minimize
> the dependence on proprietary means of working with life. How is this
> supposed to be done with proprietary kits all the time? Maybe for
> bootstrapping, but as a requirement for group progress ? That's
> definitely a sell out.
And here:
> On Friday 18 July 2008, Mackenzie Cowell wrote:
> > Well, I think that there is always going to be a gray area for the
> > DIY ethic. The two extremes are building everything from scratch
> > or ordering everything pre-built. I think most makers compromise
> > somewhere in between. I don't have a problem buying $12.00 worth of
> > screws and wire and plexiglass to build gel boxes from scratch...
> > but I think it would be pretty ridiculous to synthesize those
> > materials from scratch using a home-built forge and a plastic
> > extrusion system and so on. So in many cases, DIY work involves
> > using prefabricated materials.
>
> I wouldn't call anybody out for not always using home forging methods
> and so on. This is mostly because I'll admit there are other things
> where attention should be focused on (amateur infrastructure
> projects). But. The difference is between having identified and
> carried out the homebrew, do-it-yourself method, having it
> documented, available, ready, and functional, versus just skipping
> the step entirely and being completely dependent on proprietary
> preparation. That's not good.
- Bryan
Bryan Bishop
> In that vein, Intel got under my skin for the last time last week,
> too. So I rolled my own fab, complete with pvd, cvd and lithography
> machines culled from old banana skinning machines and used a low
> power chip design Andy Grove whispered to me.
Comparing DNA extraction and running gels to running a microprocessor
fabricator is retarded. But if you really want to be a jerk and argue
the microprocessor side of things, let's go talk about how the industry
started and how these guys were buying camera lenses down the street
and shinning down on giant boards of wax to etch out giant circuits
instead of beginning with the admittedly complex CVD chambers and Si
pulling. Even before this in the vacuum tube era -- it is people who
made these things [at first]. BTW, since cells are building DNA all the
time, and doing PCR and the like, diybio has more meaning in this
regard than semiconductor manufacturing as much as I'd like it to be
otherwise:
http://heybryan.org/semiconductor.html
http://heybryan.org/graphene.html
http://heybryan.org/instrumentation/instru.html
^ I'm definitely trying and looking. bio's been around a bit longer.
- Bryan
________________________________________
http://heybryan.org/
Engineers: http://heybryan.org/exp.html
irc.freenode.net #hplusroadmap
John Cumbers
I'd try not to be so blunt about other people's suggestions, Mac's suggestion for a social network would strengthens the DIYbio goals for an institution, and the Carolina Biologicals http://www.carolina.com is the cheapest place for high school labs to buy organisms and reagents without having the hassle to do everything yourself..
John
John Cumbers, Graduate Student, SETI Institute
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 371 Moffett Field, CA 94035, USA.
cell +1 (401) 523 8190, fax +1 (650) 604-1088
Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA
Bryan Bishop
> I'd try not to be so blunt about other people's suggestions, Mac's
> suggestion for a social network would strengthens the DIYbio goals
> for an institution, and the Carolina Biologicals
> http://www.carolina.com is the cheapest place for high school labs to
> buy organisms and reagents without having the hassle to do everything
> yourself..
John, I didn't say anything against social networking in of itself, just
that the website in particular didn't seem all that professional, up to
date, or with the professional web/social-networking standards of our
time. I wouldn't mind if there happens to be a group or tribe or
whatever other social structure they implement on that website -- it's
not in my interest to stop that, ever -- but the same would go for any
other existing social networking website, whether we talk about
facebook, linkedin, myspace, beebo, and the others that I am sure I am
neglecting. The institution for the amateur should leverage these
computational tools that we rely on and be honest with their use and
histories; for instance, FOAF is a way of users specifying their own
social network in relation to others, and some websites have begun to
implement it last time I checked (I participate in some mailing lists
that have social networking website programmers popping up all the
time, I think it's from the dataportability.org group), and it's just
one thing to look for to see if something is really up to professional
standards. In truth it's a way for us to leverage the ridiculous
popularity of facebook, myspace, twitter, youtube in a way that brings
it back to being about community for the diybio topics that we're
interested in, instead of proprietary lock-in on those servers, since
this is amateurs doing -our- thing instead of buybio -- which requires,
admittedly, 'new stuff' and new ways of formulating these stuffs to
make it all work out for us. And it's not like it's impossible to do
this .. all of the tools are available at our finger tips. So it'd be
nice if we were to use a specific social networking website that it
would be up to date with data portability standards so that we could be
more inclusive instead of limitting and so on, so that we can develop
the servers or architecture/system (the biotech toolkit project has
been mentioning this for a while) that makes all of this information
work for 'us' (well, anyone). Not just the limited buttons on a social
networking website :-) or whatever uptime they might boast :-).
As for the Carolina stuff, because of the ways that businesses are run
it's not in their interest to provide us with information that would
keep us from vendor lock-in, and so it's more like indoctrinating all
of those high school kids into the stereotypical scenario and
perpetuating nonDIY knocking-down-barriers work. :-( It would be easy
for someone else to outcompete Carolina, so that's why they don't go
open and help us out. It has to be us that goes in and retrieves the
literature and documentation on how to make it happen. If we end up
with the RDF and specific documentation on how to do it, fine, I'd say
go ahead and recommend purchasing the kits. But as long as it's
perpetuating dependencies that can't be salvaged in the case that
Carolina (un)miraculously fails :-( then it's just square one and we've
got nothing. That's not good. I have nothing against people doing the
work with the kits, again I'm not going to go physically stop anyone
from doing work :-), but I'd really like to point out how it's not
quite the solution we're all hoping for with a 'diybio group'.
- Bryan
John: what does the arrogancemeter say this time?
ta...@museatech.net
Date: Fri, 18 Jul 2008 14:46:00
To: <diy...@googlegroups.com>
Subject: Re: Carolina Biological / Halobacterium spp. NRC-1 (from Tom Knight)
Bryan Bishop
That's one way to do it, or you can use any other number of options:
http://en.wikipedia.org/wiki/List_of_social_networking_websites
http://en.wikipedia.org/wiki/Comparison_of_social_networking_software
As long as we look for compatability, especially with respect to
frameworks to implement -- the asynchronous git journals and
repositories and such, instead of static lock in. OpenWetWare has some
journal support, and some blogs, and the (computational) power of
blogging is that everything is kept in separate files when the system
is flatfile, or separate table entries when it's database driven.
Working it into a social model is left for someone else -- I'm just
telling about the software architectures that could really do some good
work in relation to the overall web of bioinformatics and amateur
biology -- since the Boston group is really good at being Boston and
applying its own flavor. See:
http://heybryan.org/manufacturing_ecology.html (below)
This is just as easily doable with throwing up a FOAF RDF/XML file on
the diybio.org server (I'm assuming someone in this group actually has
ftp/ssh access), and maybe a service for aggregating these people and
their files together if that's what we want to go for (we (in this
group) haven't actually discussed this, just made vague allusions to
it). And then we can maybe do an update pushing service for protocols
or something if we want. But the other options, like throwing up a
drupal install, aren't hard either. I actually don't use drupal any
more, but I hear good things of it.
I used to have a list somewhere of a few hundred different social
networking websites and software packages. I'll keep on looking for it.
- Bryan
Here's the content of:
http://heybryan.org/manufacturing_ecology.html
It was an email I received from Eric Hunting a while back.
> If we are to realize an integration of society to informatics and
> then to production -to create what writer Bruce Sterling has recently
> dubbed 'an Internet of things'- then the key rests in how we digitize
> the spectrum of modes/methods of process representation for our
> collective knowledge of fabrication in some standardized and modular
> way. This also relates to the subject of courseware development since
> that field faces a similar issue of how to deal with a very great
> diversity of knowledge with a uniform structure for its presentation,
> communication, and the evaluation of knowledge retention. You could
> say courseware represents this same problem going in the opposite
> direction. (this is why, in TMP2, I feature an Open Courseware
> project in the same section as the Open Source Everything project.
> They are both important as means to cultivating a Post-Industrial
> culture and their development will likely feature much cross-over
> between the two pursuits) As you noted, defining a specific semantic
> structure for this is a vast and challenging task. It's no wonder you
> assumed at first it would be a task demanding AI to accomplish. It
> looks virtually impossible on the face of it. I think, though, that
> in a study of how we really do this representation today and have
> done it in the past -which really is something few people have ever
> seriously and systematically examined- rest the keys to this. I don't
> think we can realize any ideal system. What's probably more important
> is that any system devised allow for free evolvability because, just
> in the act of pursuing this, we're going to learn some new things
> about how our own civilization and culture work that we didn't
> realize before. The forest we never noticed for the trees, so to
> speak. And that, along with the advancing technology of our tools, is
> going to feedback on the later design of such systems.
>
> The graphic representation of fabrication -usually craft fabrication-
> is something that has always interested me. It has an ontology that
> relates to some very unexpected things. For instance, to understand
> the history of DIY literature today you also have to know something
> about the history and culture of comic books because they both
> evolved in parallel with the same systems of graphic representation -
> particularly temporal representation- largely because there was often
> a cross-over in the artistic talent pools they relied on for
> illustration. One of my all-time favorite books is a fine example of
> this; Peter Auschwenden and John Muir's How To Keep Your Volkswagen
> Alive. It's like an underground comic book of the 1970s crossed with
> an engineering textbook and this style became a hallmark of 'softech'
> and sustainable building literature throughout the 70s and 80s. (I've
> often said I which I could get an artist like Auscwenden to
> illustrate for TMP) We also see the influence of -or perhaps the
> origins of- Taylorism in this through the similar modes of
> compartmentalization of tasks over time. Taylorism has often been
> accused of being a collection of psuedo-scientific baloney
> feeding-into the sociopathic tendencies of the executive class but it
> has its basis in the idea of the quantification of the physical
> parameters of tasks and the modularization of the processes of
> production, thus being the starting point for the modern science of
> ergonomics and the basis of much automation research.
>
> Another unexpected side to this is the evolution of toys, model kits,
> and product instruction manuals. In fact, in these this context comes
> full-circle with the design style of Lego and Japanese model kits now
> representing the state-of-the-art in the graphic representation of
> fabrication and now being mimicked in contemporary DiY literature,
> engineering and scientific visualization, and industrial and
> architectural design presentation. Indeed, the efficiency of these
> forms of graphic representation now allow for very different
> strategies of production and distribution. For instance, the growth
> in 'flat pak' furniture design epitomized by Ikea is based on the
> desire to off-load portions of product end-production to the consumer
> in order to reduce production costs and allow for more energy and
> materials efficient transportation of goods in flatter more compact
> forms. This is only possible where the visual representation of this
> final assembly is made comprehensible to the completely non-skilled
> consumer and often irrespective of their native language. For
> companies like Ikea, billions of dollars are now riding on this
> point. That this actually works at all is pretty amazing, when you
> think about it -even if a certain number of people often complain
> they never can figure out these kinds of assembly instructions.
>
> Curiously, the formal world of engineering and industry does not seem
> have ever pursued as sophisticated a scheme for communicating its
> knowledge as the craft world nor ever sought a standardization in
> semantics as in the world of science. There are standards in drafting
> and patent documentation and, quite recently, standards in
> documentation for engineering committees but in general this culture
> has been more concerned with the restriction of the flow of
> technology information as a means to maintain market share (and for
> engineers, job security...) or cultivate monopolies and so the
> implementation of technology has tended to depend heavily on the
> engineer as interpreter of very disorganized information and the
> general spread of
> technological knowledge has tended to be illicit, based largely on
> deliberate information theft and the reverse-engineering of
> competitors products. So we have a kind of technological Tower of
> Babel today. This is probably why we ended up with the situation NASA
> and the new space entrepreneurs now find themselves in with having to
> reverse-engineer museum and junkyard hardware from the Apollo era
> because, after 40 years of neglect, no adequate documentation exists
> for much of the technology that once put men on the Moon. One would
> think this impossible for technology representing one of the historic
> peaks of human accomplishment, but there it is.
>
> Another area of this that has long been a focus for me is the
> evolution of modular building systems and architecture, because of my
> personal need for and interest in alternative and non-toxic housing.
> Modular component systems are vexing because they've always been a
> more efficient strategy to make just about anything and yet, in the
> construction trades in particular, most of those proposed or
> developed have been dismal failures while in areas like electronics
> they've been astoundingly successful. In fact, in the context of the
> computer this was so successful that it resulted in an entirely new
> industrial paradigm that had gone largely unrecognized today; the
> industrial ecology.
>
> Most modular hardware systems have often been developed by designers
> and inventors with a poor grasp of the logistics of industrialization
> and so frequently fail miserably when their developers give
> insufficient focus on market cultivation through application
> diversity, never bridging the gap in unit production volumes
> necessary to justify the tooling for their production. There's a
> presumption that simply because something seems more rational in
> design it should automatically be embraced by the market. Reality
> doesn't work that way. So these top-down modular systems have a hard
> time getting off the ground. Modular component systems that evolve
> from the 'bottom up', so to speak, by being driven by market forces
> -as was the case in electronics- have tended to be much more
> successful even if less efficient. How these emerge is a bit of a
> puzzle. In the field of electronics it was associated with the
> development of an abstract symbolic language employed as a very high
> level design tool. In other words, the modularity of electronic
> components has its origins in the symbolic engineering language of
> schematic diagrams with components being developed to directly
> translate that language into hardware. Electronics engineers
> originally had to make the components to match their schematic
> designs from scratch and on-demand. By designing circuits for
> schematic modularity they inadvertently created a certain
> standardization and reusability of components parameters that
> afforded manufacturers a potential market volume that would justify
> mass component production. These parts were 'functionally modular' in
> terms of their ability to equate to uniform performance parameters.
> Standardization in physical form-factor followed suit as compelled by
> the need for ready physical component integration, though has never
> become quite absolute. In other words, every electronic component
> represents an independent domain of possible form factors bounded by
> the topological and electrical constraints of its mandatory component
> interface standards. An IC may have an infinite number of internal
> variations in structure but to be useful must have standardized
> external sizes, shapes, and pin arrangements. There's a programming
> analogy here -one that's becoming more literal as we move toward the
> use of generic data processing hardware like field programmable gate
> arrays running virtual circuits as the basis of full computers. (with
> FPGA programming is the same as circuit design and code optimization
> has a topological component to it) Circuit design is done on an
> abstract level independent of specific physical hardware form even if
> those symbolic elements equate to specific pieces of hardware. This
> is like high level programming. After this the standard form factors
> of the components come into play through circuit board design as
> modular graphic elements employed in layout and simulations to model
> the thermodynamics and EMF field behavior of specific hardware
> configurations. This is very much like the interpreted or 'bytecode
> based' programming language in that one is still dealing in a layer
> of abstraction based on simulation software. (the architectures of
> 'emulator' systems and circuit design and simulation platforms like
> VHDL did, after all, emerge from the architectures of interpretive
> programming systems) And finally we get to the physical hardware
> implementation which may be performed with automated manufacturing
> systems and so we're down to the 'machine code' level of a
> programming analogy. It seems that electronics may be the only
> technology at present where we have this complete a spectrum of
> standardized semantics at each of these levels of development, and
> this, again, seems related to the fact that electronic is the only
> industry so far to have actually implemented an industrial ecology
> where this sort of information must be pretty freely and efficiently
> communicated. The only industry that does work, more or less, in
> non-linear systems of development and production. This probably also
> related to the astoundingly rapid pace of evolution in this
> technology compared to any other.
>
> With the Open Source Everything project idea I was thinking not just
> about cultivating and disseminating Open Source knowledge to make end
> products but also about the evolution of standardized semantic and
> visual systems for representing their 'recipes' as I tend to call
> them because you need more than just 'plans' to explain how to make
> things. You have to represent a fabrication process, not just an
> end-form. And you need to standardize to make the information
> portable, modular, and reconfigurable across networks, across
> languages, etc. Making that work would take experimentation and
> evolution, hence another reason for employing a group project. I've
> often been critical of the sorts of silly things the Make and
> Instructables blog participants seem to focus on. I keep thinking;
> "What's with these people and their toys? Where's the open source
> car? The open source hand-tractor? The refrigerator? Wind turbine?
> Compact gas turbogenerator? Water purifier? Things that would really
> shake-up this world if they were open source." But I've also come to
> realize there's more going on with these blogs than just people
> sharing instructions for making toys. The real 'craft' of these blogs
> isn't in the stuff people are making. It's in the language they are
> cultivating to communicate the instructions for making things. You
> could be able to make Faberge eggs but your social status on these
> blogs is based not on how impressive your personal end-results but on
> your ability to communicate techniques in a way that is effective and
> entertaining. So it's really the evolution of another kind of
> literature going on here -a sophisticated mixed- media literature for
> fabrication knowledge. Right now it's a pretty messy, fast, and loose
> system but I'm noticing some consistent structure emerging as people
> interact with each other's recipes and refine them. This is the
> latest branch of evolution in DIY literature and it is adapting old
> schemes from that to new media with some interesting results.
>
> Concerning T-slot; T-slot framing is a system of modular building
> that is common in current industrial automation and laboratories.
> it's the current 'state of the art' (more or less) in the evolution
> of so- called universal building systems. It's had a very powerful
> impact on the evolution of automation because it is doing -albeit
> slowly- for machine tool systems what the modularization of
> electronics did for the computer. T-slot is based on a system of
> aluminum profiles in standardized dimensions (standardized in
> cross-section profile dimensions and fittings but not in unit frame
> piece length) based on a square section with a T shaped slot in each
> face. Simple fittings with recessed or hidden bolts mounting in these
> slots allow the profiles to be connected together in many way,
> usually forming simple box frame structures but sometimes in trusses
> and space frames. Tubular channels in the profiles also function as a
> means of distributing pneumatic or hydraulic power or as conduits for
> wiring, allowing the framing to function as a system bus with the
> appropriate fittings. T-slot is made by many companies to common
> standards and a vast assortment of passive and active components have
> been developed to integrate with it, allowing for the increasingly
> easy on-demand construction of complex automated systems and lab
> equipment. It's very commonly used for robot prototypes, particularly
> when they have to be fairly tough, large, and real-world functional.
> The three biggest manufacturers of it in the world are MK and Bosch
> HQed in Germany and the 80:20 company in the US. (which, curiously,
> took its name from the Pareto Principle) T-slot appeared on the
> market sometime in the late 1970s or early 80s as a building system
> for custom machines and industrial structures and became a
> replacement for commonly used framing systems based on pre- drilled
> or spot-welded angle-iron and flats, extruded or roll-formed alloy
> channel, and 'trilap' joined wood in the Box Beam or Matrix systems.
> It's sometimes called the engineer's Tinker Toy or Lego. NASA was one
> of its early adopters, which helped give it prestige among engineers,
> aiding its rapid proliferation. Intended originally for industrial
> automation, today it's ubiquitous in that market and most every
> machine-manufactured product in existence today has probably passed
> through some piece of machinery with a T-slot structure. It has
> greatly reduced the cost of developing automated manufacturing
> systems and adapting them to rapidly changing product designs, making
> automation more economical than it has ever been. It's produced an
> automation integration and consulting industry very much the the
> computer consulting and Value Added Reseller industry. However, it's
> applications have steadily been spinning off in all directions and
> you can now find it used for everything from reconfigurable power
> tools for model-makers to office furniture and most recently as the
> basis of a plug-in architecture system for prefab housing -which is a
> use I'm personally very interested in.
>
> Currently, I have been slowly researching material for a T-slot
> Source Book akin to the legendary Suntools Box Beam Source Book of
> the 70s or Ken Isaac's How To Make Living Structures of the 60s and
> have been looking for novel 'recipes' for T-slot based structures as
> well as other similar contemporary building systems, like the rod and
> socket framing I mentioned and others like the N55 space frame
> developed by the N55 design group in the Netherlands.
> (http://www.n55.dk/) I'm currently hoping to build a recumbent bike,
> Dobsonian telescope, and fabber from T-slot and hope for my own
> future non-toxic home to be T- slot based. I've been hoping my
> relationship with the Jeriko House company -one of the few current
> developers of T-slot based housing- may lead to obtaining a workshop
> for this research along with that home.
Julie E Norville
The SYBR gels from Carolina biological supply are nice because they
optimize for
safety in a lot of ways (even though SYBR stain is proprietary. . . )
-The SYBR gels so far seem to be safer than the ethidium bromide gels,
and thus
they may not need to be disposed of as hazardous waste. They can also
run in a
shorter time than standard gels. A disadvantage is that they are more
expensive. It is also nice that the power supply comes with the gels.
-It would be nice if we could hack the gels so that they could be used
more than
once.
-Something we may want to find a way to make (if we can) is a blue light
transilluminator for visualizing SYBR stained bands on a gel (currently the
ones available would be rather expensive for a high school student.) They are
made with leds and possibly a blue and an orange filter, but unlike a uv box
(that is used to visualize ethidium bromide gels) the blue light
transilluminator should be harmless for the user--good from a safety
standpoint
(and also less harmful for the dna itself.) (I don't know if a black
light will
let us visualize the bands with a SYBR stained gel?)
example transilluminator
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Nucleic-Acid-Purification-and-Analysis/Nucleic-Acid-Gel-Electrophoresis/nucleic_acid_gel_electrophoresis/Transillumination.html
Mario Raya
David Wine
--David
--
David Wine
+1 617.548.8694
Mario Raya
Mario Raya
Talli Somekh
sarcasm clearly cannot withstand the onslaught of hyperlinked facts.
at this rate, you might have a chance to overthrow the Cambridge cabal
of synthetic biologists who are so intent on locking out the universe
from their machinations by having coming up with ideas via pre-
historic analog conversation rather than the more advanced, almost
telepathic medium of digital wikis.
i don't really mean to be harsh, but i haven't really participated in
a silly mailing list flame war in at least 5 years and this one is
just making it so easy to satisfy that craving...
talli
Bryan Bishop
> The SYBR gels from Carolina biological supply are nice because they
> optimize for safety in a lot of ways (even though SYBR stain is
> proprietary. . . )
I have had positive experiences with SYBR Gold stains before, so I'd
recommend it if especially over EtBr.
> -It would be nice if we could hack the gels so that they could be
> used more than once.
Awesome idea, yes, definitely. Have you seen the suggestions to use
artificial gels? The latest I remember hearing of was the silicon gel.
"Entropic trapping and sieving of DNA in nanofluidic channels"
http://www.hgc.cornell.edu/biofab/entropic.htm
http://www.hgc.cornell.edu/biofab/gel.htm
> The first result of lambda DNA movement in this channel shows the
> possibility of a new kind of sieving device for polymers and
> macromolecules. In a flow of very low concentration of DNA,
> individual DNA molecules were retarded by the entropic barriers posed
> by the interface between thin and thick region of channel. Below a
> certain driving electric field, this effect decreases the mobility of
> DNA drastically, suggesting a trapping of DNA molecule.
>
> Recent experimental results shows that there is actually a difference
> in mobility between larger and smaller DNA molecules. In contrary to
> our intuition from conventional gel electrophoresis, larger DNA
> molecules turned out to move faster than smaller ones in this
> channel.[3] This is due to the fact that DNA molecules are heavily
> deformed and stretched when they enter the thin gap, and this
> deformation energy barrier, not the entropic free energy difference
> between spherical and compressed molecule, is the relevant energy
> barrier in the escape of DNA molecule.[4]
>
> This separation device is a very promising candidate for an
> alternative of gel electrophoresis, Several advantages over gel
> electrophoresis or other newely emerging technologies include, (1) It
> is not a time-consuming pulsed-field technique but requires only a dc
> field to control the device. (2) It is peculiar because one can
> recover the longer DNA molecules first, in contrast with the gel
> electrophoresis where longer molecules are generally 'stuck' at the
> first part of the gel. (3) It is very easy to control the gap size
> (or etch depth) and there is no practical limit in terms of how
> narrow they can be made. Therefore one can easily optimize the device
> for a desired length range of DNA for an efficient separation. (4)
> Since we are making use of only z-directional size constriction, we
> could make a large area of this structure on a Si wafer for a
> paralleled operation of many samples.
>
> To see a video clip of the DNA molecules moving in the channel, click
> here. This page will load two large avi files which requires
> appropriate plug-in to see.
http://news.bio-medicine.org/biology-news-2/Artificial-Gels-Could-Speed-DNA-Sequencing-13341-1/
> Stephen Turner, a graduate student working under Harold Craighead,
> Cornell professor of applied and engineering physics, described his
> biochip research in a talk, "DNA Motion in Nanofabricated artificial
> Gels," today (March 25) at the centennial meeting of the American
> Physical Society in the Georgia World Congress Center.
<snip>
> replacing the organic gel with a tiny solid-state device, called an
> artificial gel. electrophoresis gels consist of a maze of
> interlocking polymer molecules that leave many tiny openings through
> which moving DNA molecules must navigate. Using the same techniques
> used to make electronic circuits, tiny passageways can be carved on a
> silicon chip.
>
> Turner's artificial gels are forests of vertical pillars with sizes
> down to 100 nanometers (nm) thick and 100 nm apart. (A nanometer is
> one billionth of a meter.) They are smaller, Craighead believes, than
> earlier versions of artificial sieves, an achievement made possible
> by using the Cornell Nanofabrication Facility's electron-beam
> lithography tools, which can lay out features much smaller than those
> used so far in commercial integrated circuits. Ordinarily such
> devices are made by etching a cavity in the silicon, then gluing on a
> cover to create a channel through which the DNA sample can flow.
> Turner used a new technique in which the channel is filled with a
> "sacrificial layer" that can be etched out after a covering layer is
> deposited. This allows much more precise control of the height of the
> channel, he explained.
>
> The researchers are still at an early stage, running DNA samples
> through the biochip to see how fragments of different lengths can be
> identified. They mount the chips between two microscope slides, glue
> small reservoirs to each end to hold a few drops of a water-DNA
> mixture, place the slides on a microscope stage and apply an electric
> field, then watch and measure what happens, tagging DNA molecules
> with fluorescent dyes to make them visible.
So that's one option. The fabrication of these artificial gels is rather
intense, with the nanolithography and nanofabricational setup required
for it. It's just one alternative. I am sure there might be others.
DNA electrophoresis in microfabricated arrays:
http://www.nano.umn.edu/research_projects/2007/DNA_Electrophoresis.pdf
Was that it? Hm. This one might be the one I'm thinking of:
http://web.archive.org/web/20020909121552/http://polymer.matscieng.sunysb.edu/dina01/
> Performing electrophoresis on a flat silicon chip, introduced in this
> research paper, promises to alleviate these drawbacks, allowing for
> fast, efficient, automated results of high resolution quality.
> Electrophoresis was performed using 1 kb Ladder DNA with a high
> resolution of 300 bp at a relatively low electric field of 4.5 V/cm
> (This is comparable to capillary electrophoretic performance at much
> higher fields >100 V/cm). A double-logarithmic plot of mobility of
> the DNA chains (μ) vs. number of base pairs (N) shows that there is
> indeed a length-dependent mobility when performing electrophoresis on
> a chip.
Anyway, there was a group that had a silicon surface that you could
electrically drag DNA molecules through and get some serious results.
The staining was typical, but it wasn't a gel.
Any others?
- Bryan
David Wine
Jason Morrison
David Thompson
> -Something we may want to find a way to make (if we can) is a blue light
> transilluminator for visualizing SYBR stained bands on a gel (currently the
> ones available would be rather expensive for a high school student.) They are
> made with leds and possibly a blue and an orange filter, but unlike a uv box
> (that is used to visualize ethidium bromide gels) the blue light
> transilluminator should be harmless for the user--good from a safety
> standpoint
> (and also less harmful for the dna itself.) (I don't know if a black
> light will
> let us visualize the bands with a SYBR stained gel?)
I have this info second-hand, but a friend of mine says his PI found a
blue light box for ~$25 on ebay and it works with their SYBR gels. I
don't know what use this box was originally intended for, but I do
know that colored light boxes are sold for 'light therapy'. I imagine
they can be found for much less than whatever invitrogen is asking.
I'll ask for more specific info.
Also, first post here. Mac, John Cumbers, and Jason Morrison know me
(hey). For those that don't, I'm a grad student at Harvard just
finishing up my first year. I'll be doing something related to
synbio, though I don't know what. I may start attending some DIYbio
events.
Andrew Perry
source of safety should be the MSDS.
I don't really want to 'muddy the waters' on the issue of DNA dye
safety, but check out Rosie Redfields analysis of EthBr vs. SYBR
stains: http://rrresearch.blogspot.com/2006/10/heresy-about-ethidium-bromide.html
Conclusion: It would be misleading to call SYBR "non-toxic". SYBR may
be less _mutagenic_ relative to EtBr, but it is still _toxic_.
Despite Rosie's analysis which suggests that counter to popular lab
superstition, both stains probably aren't that dangerous unless you
are exposed to high doses, in DIYBio experiments I'd still be wearing
gloves, and obviously would avoid ingesting any stain. Within reason,
it's better to be safe than sorry ....
Other DNA staining options are Methylene blue (as DIYbio'ers have
already tried), Crystal Violet, and Gel Red (from Biotium):
http://bitesizebio.com/2008/03/03/ethidium-bromide-the-alternatives/
There is also a company on eBay providing free/cheap "GR Safe DNA Gel
Stain" to for scientists in non-profit organizations (USA only) ... if
DIYbio can classify itself as a non-profit which contains some
scientists, someone could probably buy some, maybe even get a free
sample ...
: http://tinyurl.com/6ejgul
I haven't been able to find the MSDS for "GR Safe DNA Gel Stain", but
there is a patent out there somewhere ...
Andrew
On Jul 19, 8:52 am, "Mario Raya" <marior...@gmail.com> wrote:
> Link to the manual ---http://probes.invitrogen.com/media/pis/mp33100.pdf
Norman
You'll need an emission Wratten 47/47B? pre-filter (I'm currently
testing to filter out green background) + amber/orange post filter.
Don't buy the SYBR safe filter from Invitrogen, which is a ripoff. It
filters the wrong wavelength and DOES NOT WORK, possibly it was a
yellow filter meant to be for UV (defeats the whole purpose of using
SYBR safe to avoid DNA damage) Their product information is very
incomplete. Tech support is no help because they don't really provide
any detail info on what it is.
CodonAUG
I have been using GelRed stain from Phenix Research. It has roughly the same spectra as Ethidium bromide but is non-toxic and drain disposable. It works great.