Reignition

[jwslavin]

Greetings folks.  

I'm John Slavin and I recently took over administration of the ChiOpenSci list.  First and foremost, I suppose it's worth seeing if any folks no longer are interested in the group, and if so I can either direct you to removing yourself or can do so for you.  No need to junk up your inbox, aye?

I'm making it my mission to make an open science space in Chicago a reality and at the moment am doing my best to work with folks at PS1 to do so.  I'm interested in knowing who and when they would be able to start working with me to start getting the project functional.  I've proposed meeting on Tuesday nights over the PS1 list as the business and general meetings occur then.  If there are better suggestions for times, I'd like to work it out so let me know.  It would also be good to start developing an agenda and action plan for what could be achieved at such a meeting.

Please get in touch and let's make this a reality!

Cheers,

John

[John Slavin]

Howdy folks,

I'm searching for people who would be interested in working with me- and
some other folks I've been talking to about it- to open a new
Open-Science space sometime in 2014. The aim would be a space in
Chicago dedicated exclusively to scientific pursuits- be they chemistry,
biology, physics, etc; but outside of the typical academic/industrial
environments. I also hope to integrate an educational component,
working with local schools to provide hands-on experience with the
implements to youth.

If anyone is interested in participating, please either reply to the
thread or message me off list: jwsl...@gmail.com

Cheers,

John

[Ryan Pierce]

I've been doing a lot of thinking about science lately and its role in hackerspaces.

The trouble is that science has a lot of meanings. A lot of people think about it in terms of science done to academic standards, peer reviewed research published in academic journals, etc. And I think this is by far the most inaccessible form of science. The barriers of entry are high. It requires education, equipment and supplies, space, and time / motivation. Getting all these together is tough, and it appeals to a very limited number of people.

I'm focusing more at PS:One on, for lack of a better term, applied science, and I'd like to see more of that at the space. Already it has a solid foothold. So far we have a working electron microscopy lab, complete with a working SEM and EDX detector, sputter coater with carbon deposition attachment, ultrasonic cleaner (thank you! It has been very helpful for sample prep!) and, as of yesterday, critical point dryer. What can we do with that?

Well, for starters, we've got two members working on disassembling / reverse engineering ICs. They've already imaged the top of a wafer and are making plans to grind it to expose more layers. And I've done forensic analysis on lock pins to see the (very visible) effects of picking them. This has gathered interest nationally from TOOOL, an amateur locksport group.

We have other things in queue:

* Members have made a 3D printed large format pinhole camera. They want to measure the quality and size of various methods of producing pinholes.

* A member wants to do EDX analysis on vacuum tube parts to see what metals and alloys are being used.

* A member has discussed using EDX to examine tungsten welding electrodes for impurities and contamination.

* A member wants to start looking at insects.

None of this is ground-breaking research that is going to make it into academic journals, but that doesn't mean it isn't awesome in and of itself.

I'm also interested in expanding applied science at the space, using the SEM as a nucleus and growing outward. We have about 14 people certified on the scope, and I've been hearing a lot more requests for certification. Expanding the space needs to be considered carefully because square footage and funds are limited. But, for example, the critical point dryer could be used for aerogel production. I'd like to get a liquid nitrogen dewar, which will open up a whole lot of stuff. A binocular inspection microscope is on my wish list. And I think a fume hood would be a good next step. Heck, I ended up gassing the electronics lab one night gluing the rubber pneumo tubes on a polygraph machine with fumes that smelled like cat pee; a fume hood would have been very welcome. It supports the SEM in that it is needed to do gluteraldehyde fixing of biological samples. But we have some glassware too that I'm storing near the SEM, so it opens up new frontiers for chemistry and biology. We already have people who want to measure the caffeine content in Greg's insane "hacker fuel" and I'm hearing that needs a fume hood. And there is work now happening organically (pun intended) at the space with hydroponics, which could fall under the umbrella of applied science.

Bottom line: by broadening out to something like this, it can appeal to a wider audience than hard core scientists. People who are curious. People who want to play with fun technology. People who want to apply this stuff to projects they are already hacking.

I understand the desire to get a nice dedicated lab space, and I wish you the best of luck with this. But I'd also invite you and the rest of the Open Science group to consider working with what we already have at PS:One and participating in expanding this. I know it is short notice, but I'm running a SEM certification class Wednesday from 7-10 PM. Anyone is welcome to attend, even non-members from the Open Science list. (You'd have to join PS:One to complete the second hands-on part and be certified to use the SEM, but you can go to this class first before making up your mind.)

I think there is a lot of potential for synergy here, especially if we broaden the audience and scope.

Cheers,
Ryan


> On Nov 26, 2013, at 9:06 AM, John Slavin <jwsl...@gmail.com> wrote:
>
> Howdy folks,
>
> As was discussed earlier in the year I'm interested in an Open-Science space, but have decided that maybe the workshop isn't the best place for it. This is mainly due to cleanliness issues and maintaining a controlled environment, only slightly related to the space considerations. As that is the case, I'm searching for people who would be interested in working with me and some other folks I've been talking to about it, and open a separate space sometime in 2014. The aim would be a space in Chicago dedicated exclusively to scientific pursuits- be they chemistry, biology, physics, etc. I also hope to integrate an educational component, working with local schools to provide hands-on experience with the implements to youth.

>
> If anyone is interested in participating, please either reply to the thread or message me off list: jwsl...@gmail.com
>
> Cheers,
>
> John
>

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[John Slavin]

I totally agree with your points Ryan, there are some more specific
drawbacks that I feel are worth mentioning. I'm interested in getting
what could be considered a proper instrument room together, which I
don't believe would be fitting to put in a workshop area. Having
instruments with open ports, such as UV-VIS or IR spectrometers, that
also have optical mirror systems would not work out well as signals are
dependent upon those surfaces being clean. It's not as much an issue
with an SEM, as the working components and sample chamber are separated
from the environment by a vacuum.

That said, it's not necessarily out of a desire to explicitly not work
with PS:1, I'd still be happy to work there and really support PS:1.
It's more that the space offerings right now would not fit the profile
of what would work. I'm more inclined to lean toward the applied
science aspects, even; in fact much of what I'm interested in doing
would not be novel in any way, shape, or form. However, I don't think
what I want to do would work well when oils are being vaporized nearby
or wood dust is splashing about.

I might suggest, if people's ears were open to the idea (and it seemed
potentially successful) having a satellite of PS:1, i.e. a location that
was still part of the organization but not at the main facility. I
would support that, and if there were some willingness to support it at
least in part financially I would be even happier to do so. Of course
the issue there is still whether there would be enough interest within
PS:1 to support a motion toward that end, which is entirely dependent on
convincing people that it would be sufficiently used. It could be
something like a $1000/month facility in a shady part of town, for all I
care. This separate space could later merge with the main facility
again, once PS:1 expands to a new space.

Let me put it this way, I'll support whichever direction makes a
functional space become a reality faster. Having these conversations, I
suppose, is the best place to start.

Cheers,

John

[Ryan Pierce]

I posted something last night and it didn't seem to go through. Or are posts to this list moderated? Apologies if you get this multiple times.

Hi John,

I guess the question in my mind is what you consider a functional space.

An "instrument room" in PS:One isn't going to happen any time in the near future. There just isn't the support for it right now. That said, I think equipment and space should be the least of your concerns. The most important element is building a community of people that will actually use it.

I'm going to address the elephant in the middle of the room. From my limited perspective as an outside observer, Open Science was tried at PS:One and it failed. A considerable amount of cool equipment came in the doors, space got allocated, and from what I could see, none of it was ever used.

The idea of renting a room and getting a UV-Vis and/or IR spec seems to me like it is heading in the same direction. There's got to be a support base first. I think it is very important to start small and make logical expansions from there. Even if right now you had a bunch of backers to go in on a lab with you, what's to say they'll stick with it, and it won't similarly end up as a bunch of equipment in a space that nobody uses, with the added downside of a rent payment?

Now, that said, we've already got a kickass electron microscopy lab at PS:One, complete with the goodies (CPD, sputter coater) I mentioned earlier. And we've got a community of 15 people certified to use it, with a bunch more people in queue. I've got a system in place to train people to use it effectively. That's a really good start, and it is addressing both the equipment and the community dimensions. My goal is to keep growing the community, to find new and interesting ways to use what we've got, and to expand *IF AND ONLY IF* there is support for it. I think we are really close to the point where we can justify a fume hood. Especially if you'd bring in yours, so there isn't a significant cost element. Then get people using it, and we can see where we go from there. Who knows? PS:One is rapidly growing, and has arguably outgrown the building it is in already. If applied science can become respected there (and the way for that to happen is by people DOING it, not just talking about it) then, should PS:One move or rent the whole building, it would be easier to justify the dedicated lab room.

Can we work together to get applied science happening at PS:One, with a strong community supporting it, while using what already exists there?

Cheers,
Ryan

[Ryan Pierce]

[John Slavin]

Well, I for one can say that I would be using the equipment, fairly
regularly, so that's at least one issue taken care of ;) The exception
to this of course is that it would be a single user at this point rather
than a community, which I see as a problem, as well. That said, tying
educational components to it- much like trainings on the SEM- would be
what ultimately determines use in the long run rather than just having
it there.

If you don't mind me saying, I find it funny that the statement keeps
being made that I need to build a community when that's the explicit
purpose of sending these emails, i.e. to get people to say they want to
work with it and then go from there. We're definitely on the same
page. Pardon the reflexive statement, I'm just wondering what you think
needs to be done beyond this (my thoughts are below) at the moment.

I'm willing to work with you to build open (applied) science at PS:One,
and looking at doing things in baby steps might not be a bad idea. My
main desire in this is to make it an active course of action, meaning
having people commit to working on the project. I'd put a few ideas on
the table for an action plan 1) a motion to install the fume hood
(honestly, my dues lapsed at the space, mainly because the money I had
for it is now tied up in storing the hood- will be resolved if a plan
gets formed-, so I need a full member to sponsor said motion), 2)
meeting up to brainstorm the argument for doing so, and 3) finding time
to regularly discuss the direction of the project and scheduling
accordingly. I'm also going to slap a 4th point on- getting at least a
flammable and acid storage cabinet- just because I like to think
responsibly :) and I think it would be good for the space to have those
anyway, noting some of the chemicals stored around there.

I know a few folks outside of PS:One that I could potentially convince
to join forces with all this from other areas where I've been talking
about it. I'm not sure whether some of them can become dues paying
PS:Oner's at this point, but they'd at least be able to help with
getting it together.

Otherwise, once a hood is installed, I will be able to begin working out
of it immediately. Again, I'm concerned about the cleanliness issues,
especially for some of the projects I'm thinking of up the road, but if
we can start making things happen at PS:One earlier than opening a new
space, then I think I can at least think of some engineering controls in
the meantime to help deal with those issues. As for the instruments, I
have access to some as it is that I can probably hop on at will- so it's
less an issue for me. It's a vision I have to have this stuff
accessible and available to the novice outside of standard settings,
just like the SEM. Can it wait? Sure, I guess.

Side point, how possible would it be to used the EDX for powders? I can
imagine scintering them to a substrate as an option. Anyway, I need to
do some trace metal analysis for part of what I'm interested in doing,
and not having access to an ICP-Mass Spec I thought using the EDX might
be a good option...

So, when would you want to talk beyond email?

Cheers,

John

[John Slavin]

I changed your settings to be unmoderated. Sorry, I saw it last night
and didn't submit. Shouldn't be a problem in the future.

Cheers,

John

[Ryan Pierce]

Regarding the reflexive statement, I'm entirely in favor of building community. There is a razor thin balance here. On one hand, people value doing above talk. There needs to be something in existence that people can gravitate around and start using. But at the same time, expanding too fast with the stuff and not having a community to back it up is problematic. It looks like one person's pet project, or it gets unused, as what happened with Open Science 1.0 at PS:One.

I suggest a two prong approach:

Fume Hood

You've got to get dues current again. And I need info. Specs. Dimensions of the fume hood. Type of power (volts, phase, current) that it needs. Is it complete, or is it missing stuff? What needs to be done to get it working? Is it just a matter of moving it, plugging it in, and putting up some flexible duct to join it to the building exhaust? How heavy? Where is it? What would it take to move it?

If this is easy to do and cheap, then, while not a slam dunk, I think this can be done soon at PS:One. Now if it needs a bunch of extra stuff, then we've got more of a hard sell.

Applications:

You've got your work. If you can do some outreach with it, that would be cool.

I'd like to fix biological samples for the SEM in it.

It also has an immediate use by the membership for anything that generates fumes. Mixing lye for soap making. Certain glues and paints drying. Etc.

SEM

I'm looking for cool applications of it that can interest people and inspire more work with it. Anything you can come up with would be much appreciated.

EDX for powders: How stable are they in a vacuum? You can embed particulates in double sided carbon tape, however depending on the thickness of the powder granules, you might find yourself picking up signal from the carbon in the tape itself. Scintering it into something solid would work, too. EDX only picks up elemental signatures, not molecular signatures like a mass spec. And the detector is only rated to pick up elements as low beryllium. (I have some metallic beryllium to test this with, which I'd like to do next time we get LN2, but carbon is the lowest I've tried to observe, and I did succeed.)

The big factor here is getting LN2. I have a supplier but we need a dewar. I have a lead on a 10L dewar for $100 plus shipping. I've been struggling with whether I should buy this, or hold out for a larger dewar (say 20-35L) with a withdrawal device so that one purchase of LN2 can simultaneously go to the scope and other things in the space. (Ice cream....) Still if you've got stuff that needs EDX now, I may just jump on it.

We should talk. I'll send you my phone number offlist.

Cheers,
Ryan


> On Nov 28, 2013, at 1:41 PM, John Slavin <jwsl...@gmail.com> wrote:
>
> Well, I for one can say that I would be using the equipment, fairly regularly, so that's at least , one issue taken care of ;) The exception to this of course is that it would be a single user at this point rather than a community, which I see as a problem, as well. That said, tying educational components to it- much like trainings on the SEM- would be what ultimately determines use in the long run rather than just having it there.

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[John Slavin]

Ryan,

I see your point, and do want to avoid issues with having something there that just takes up precious space.  It's just a question of where to start for me, such as email lists vs. meetings, etc.

Can you let me now when a good time to call would be?  I don't want to ruin dinner :)  Also, I'm going to answer some of the questions here, just so others can see it.

As for the other parts:

Hood:

75x32x81" 115V, 60Hz, 16.1amps.  It's complete, but I had to take it apart significantly to get it stored.  All tolled it wouldn't take more than 3 hours to put it back together, and that's a very liberal estimate on the time.  One thing I want to do for integrating is switch the location of the blower that came with it, moving it from below the hood area to above.  I think the way it was engineered it was meant to be tied into an HVAC system, with the lower fan to bolster air flow.  The lower fan is more than sufficient to function on its own, but I also have some small fans to integrate into the air lines that would increase flow, even more.  Moving it requires renting a trailer, $25 bucks; it's currently stored around Western and Diversey.  It's 1100lbs, but I moved it into storage myself, actually did most moving of it myself.  One alteration I want to make is putting it on locking casters, but I need someone to drill holes because the metal does not take to my bits and hand-held drill.

The only thing it would probably need is some extra ducting and it should probably vent to outside rather than going into the main system.  There's already an empty port to the roof, relatively near where it would go (in my mind).  It shouldn't be too difficult to do.

SEM:

What it would be is inorganic catalysts (some organic content, depending on the catalyst).  Depending on the sensitivity, which I'm not sure of for the PS:One scope, I want to see the purity of them mostly in terms of other metal contaminants.  I think either drying an aliquot on glass or the carbon tape could work.  The glass drying plan would take care of some of the concern for vacuum issues, I believe, and also use less of the catalyst in the process.  I can't say what amount of organics might come off from the ones with organic ligands (some will, undoubtedly, as equilibrium effects would be in play).

I won't be able to do anything with the EDX until I have access to a hood, though... 

Otherwise, one thing I want to buy is a nitrogen generator, which can be had for around $1000 on ebay.  If it were tied to something like:
http://benkrasnow.blogspot.com/2008/08/diy-liquid-nitrogen-generator.html
it would be awesome because we'd have purge gas as well as LN2 for much, much cheaper than rental/purchase.  I think jumping on a $100 10L dewar is a good idea, though.  That's really cheap and I'd say worth it.

Just let me know when you're available.

Cheers,

John

[Pete N.]

Hi Gang - I'm Pete, aka Bioguy on the IRC channel.  I've been a full member of PS1 now for about a month, and looking forward to getting involved.

By profession I have been a pharmaceutical microbiologist for over 15 years, and have experience in growing up microbiological cultures.  I've talked to a number of people on site, including Ryan, Sacha, and Everitt, and would be excited about re-igniting this group for 2014. 

It sounds like we all have the same basic goals, but the devil's in the minutiae.  Maybe we can set up a time when we can all meet at the pumping station to brainstorm and develop ideas?

Thanks, and looking forward to meeting you John!

[ChemHacker]

Pete is now a manager of this group.  I'm moving out of Chicago - who wants ownership of this mailing list?

[Ryan Pierce]

I'm happy to do it. I'm in contact with Pete and others at PS:One about doing more science.

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[John Slavin]

Howdy folks,

I must apologize for my absence these past few months, considering the discussions from December on the SEM list, etc.  Directly, in December my family decided to move to Virginia this coming summer.  I've been considering how that plays into my involvement at PS1, what I should do with the hood that's collecting dust, and how to afford it all.  Ultimately, I do want to continue with an open science project here, for however long that takes and I can be involved; but as I explained to Ryan in November, I'm paying $60/month to store the fume hood I have.  Adding $40 a month for membership is extending my budget much further than I can afford (I honestly can't even afford the storage at the moment, but I have no options to get rid of the hood, so....).

Long and the short of it, I'll reiterate my desire to help out until I depart but I'd like some help figuring out how to get rid of the monkey (hood) or getting it into the space.  If folks can figure out a way to use it for pure bio, then I'm fine with foregoing my uses.  If folks think we can find a temporary space for me to do some welding- I'm trained to stick weld, have figured out brazing, and could probably handle MIG/TIG- and work on converting it, then I'm more than happy to either do it myself or work with folks to do that, too.

I hate this situation and really regret my jumping the gun on the hood; and I also mourn the fact that this might seem to be coercive (i.e. collectively deal with the hood or say goodbye to me) because it's not meant to be that way.  I'm just dealing with recovering from a shit job situation, still; supporting a family, and generally trying to curb my enthusiasm to make sure I make solid decisions. 

So that's my piece.  I'm happy to meet up with folks if I'm welcome and am more than willing to do the leg work to schedule a meeting.  I'll do my best to also stay in the conversation from now on too, regardless of my personal BS.

Cheers,

John

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[Pete N.]

Hi John, pleasure to meet you. :)

And Ryan, thanks for our brief chat the other day while showing me around the SEM!

I think right now the most important thing is to get a core team together to talk about short term and long term goals of Open Science at PS:1.  It looks as though there have been some strides made in the past, but I don't know how far these have come along.  My original idea was about building a yeast library to support the Beer Church.  A biosafety cabinet would be good for this, but it is not vital.  Once this goal has been achieved and shows practical application, next step would be to create a BSL-1 laboratory, but that takes time, effort, resources, and maintenance.

As I mentioned before, I am a microbiologist by profession and have worked in Laminar Flow Hoods, Biosafety Cabinets, Half-Suit Isolators, RABS, etc., and in classic aseptic environments down to Class 100/ISO 5.  I am very familiar with biosafety cabinets and their usage, but typically the hoods I have used are self-sufficient, with a HEPA filter on top.  John, do you have a manufacturer / model number for the Biosafety Cabinet you have been storing?  I've only seen 6-foot BSC's for sale recently, and those usually retail upwards of $15K, not including yearly calibration and maintenance.

I'm going to be at Zee's Genetics/Extremophile seminar on Tuesday March 2nd; Maybe we hold an impromptu brainstorming session on the hood, SEM, and open sci in general?  Would love to meet all Open Sci enthusiasts. :)

-Pete

On Wednesday, October 30, 2013 11:17:22 PM UTC-5, jwslavin wrote:

[John Slavin]

Hi Pete,

Pleasure to meet you as well :)

The hood I have is a Baker model B60-112M, with on top HEPA filter as you mentioned.  I got it from Abbott for $475 back in November- excluding transport and storage costs.  It is a beast to move, but I started making some modifications to make it easier to handle such as getting it on casters rather than being entirely free standing.  We can discuss the details more in person if you'd like.

I'm amenable to going to the talk Tuesday (which I assume you mean the 4th?).  Would you want to talk before or after the event?

Cheers,

John

--

[Ryan Pierce]

Hi John and Pete,

I've spent a lot of time talking with the leadership and key members of PS:One about science, space issues, etc. A few things to understand about PS:One:

They advertise themselves as a do-ocracy, and this is true. Doing cool stuff, especially if said stuff is visible to the membership, gets you cred. Talking about doing stuff is just hot air.

They advertise themselves as a do-ocracy, and this is false. As much as they speak of JFDI and members having a right to "hack the space", that isn't true beyond the trivial. While one person told me to JFDI and bring John's bio cabinet in, several others told me that doing so would be most un-excellent and I would destroy any goodwill I had with the space. Equipment needs to be brought in and space allocated for it through coalition building and reaching consensus with the powers that be.

Space is increasingly at a premium and PS:One is operating in scarcity mode. They are becoming obsessive about every square foot and have a penchant for throwing things out. It looks like people opened up two gel electrophoresis machines, possibly to scavenge for parts, and there is a galvanostat/potentiostat in the "please take this home or it will be thrown out" pile. There are 300+ members and no sign of this is slowing down. People are running scared.

Open Science had a golden opportunity at PS:One, and they fucked it up. They got space back when space was was available, moved in a lot of equipment, and DID NOTHING WITH IT. This has since caused a lot of people to believe that science can't be done at a hackerspace. Attempts I'm making at promoting science there are now a major uphill battle. 

Also, there is a massive distinction between a tool (as in, something that already works) and a project. Right now the general thought is that it would be better to buy a $6000 CNC router than have a member build the same thing for $2000 in parts. With a project, you have to trust that a user will follow through and justify the space they're taking up. Case in point: the space had a second SEM. The owner did little with it. Nobody could repair it. People became irate about the space it was taking up and forced it out in short order.

Regarding John's bio-cabinet, it is a non-starter for several reasons:

1. We first need a fume hood. A bio cabinet is a one trick pony. It's awesome if you are doing bio research. Yeast library, etc. But if you want to work with volatile and potentially flammable vapor-producing chemicals, you are SOL seeing as a bio cabinet will concentrate them, not exhaust them.

2. A fume hood is easier to sell to the members because it is dual use so non science people can get behind it. Solvent bonding laser cut acrylic, washing the commutator of a motor in mineral spirits, doing hot acetone vapor treatment of 3D printed squirrels, etc. Lots of people have been "gassed" at the space with people doing smelly things, and while the rule is "Take it to the loading dock", that isn't a great option in winter, and the person doing it is still exposed to the fumes.

3. While I know John says he can convert the bio cabinet into a fume hood, that means it is a project, not a tool. And, frankly, I think it would be a waste, seeing as a bio cabinet is far more specialized.

4. It is too big. Something in the 3-4 foot range would be much better. Possibly even a tabletop portable hood. I've even heard people talk about the space paying to buy a smaller hood than accept a donated larger one.

I've given a lot of thought to how to advance science at PS:One. And I'm definitely looking for allies and champions here, provided they are willing to work within the realpolitik of PS:One rather than pie in the sky idealism. 

My game plan so far:

* Get people DOING stuff with the facilities we have. And make it visible.

* We have a freaking awesome scanning electron microscopy lab. Working EDX, Iiquid nitrogen supply, sputter coater, critical point dryer.... Nobody in the nation provides access to this for $40 a month. Get it utilized more.

* Look to partner with other groups to get more users of stuff into the space, get donations, etc.

* Work to change the image around science. To that end, I've been re-branding this as "applied science" because publication in refereed journals isn't as much the goal as trying to do something awesome that ends up on hackaday.com. Trying stuff for fun. (OK driving a nail with a liquid nitrogen frozen banana isn't by any means original research, but it is surprisingly awesome.) Or to learn. Or to improve upon a project you are hacking. Or to make art. I want this to appeal to a wide audience where you don't have to have a degree in hard sciences and a real experiment to play.

* Expand the SEM area with things that could help it. (I really want a binocular inspection scope for sample prep work.)

* I think the next piece of sizeable equipment we get should be a smaller fume hood. There is a user base to justify it.

* Then, see how what we are actually doing could be expanded, and where the logical next steps are. But make sure any expansion comes with a guarantee of utilization so we don't have a repeat of Open Science 1.0. Dual-use items that other areas are interested in would be ideal.

Any thoughts?

Cheers,

Ryan

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[Pete N.]

Indeed, the 4th.  My mistake.

I plan on getting to PS1 sometime between 6 and 7 on Tuesday the 4th, so let's discuss after the event?

Ryan is that fine for you?

[Pete N.]

Ryan - thanks for that insight.  I know you and I talked briefly about these details, which is why I was hoping we'd have an opportunity to talk to you more.  This response give me answers to some of the questions I had for you.  My communications with others have indicated to me this 'realpolitik' that exists, which help in addressing the root causes of the issue.

I think Ryan hits things on the head about 'Applied Science.'  In order to justify the existence of an open science initiative, we need to show crossover and a return to the other groups within PS1; this is the only way to generate buy-in.  Making the replacement part for the electric drill with the 3D printer is an excellent example of this.  The creation of a yeast library not only supports the Beer Church, but it also sets up an infrastructure for a biological laboratory, but it's primary purpose would be support of Beer Church.  However, now we have the procedures and infrastructure to make... our own yogurt.  Or Kimchi.  The point is - the open exploration is a 'nice to have,' but let's have a primary goal of showing an actual need or support of other projects.  Or, create an opportunity for a 'resource' for other projects.  We need to justify the existence of ChiOpenSci, either a monetary justification or a resource justification.

To be honest: The hood is not 100% necessary to create a yeast library.  The things I need more now are either an autoclave, or some source of presterilized equipment.  I haven't been to AmSciSurp in a while to see what's available, but I don't trust any sterility claims they might have.

My secondary consideration is biohaz waste.  No one wants to see petri dishes with stuff growing on it, especially our waste haulers in Chicago, who may go to an alderman on this.  I'm going to be sending emails to BioCurious and Diebel Labs to see what they do.

With regards to the fume hood: this isn't something I would use on a day-to-day basis, nor have I used it in day to day job in microbiology.  As soon as we are venting something, then the EPA gets involved.  I want to go through as little red tape as possible in moving things forward, and make sure we can facilitate bringing something productive from a science perspective immediately to PS1.  That being said, I don't know the rules regarding venting fumes.

If the hood is causing so much consternation, and people really have issues with square footage today... I don't know.  That's John's decision, as he's been storing this instrument on his own dime for a while.  In my opinion, there is not an immediate need for an 8 foot BSC, if we wish to sell it.  The cash we get from it could be use to offset some of the cost John has had in storing it, and maybe get that benchtop hood that Ryan spoke of.  But: seeing as I use these BSCs on a routine basis, I know what I would want.  An 8 foot biosafety cabinet would be very nice indeed, but not if I'm the only one using it, and if Ryan wants a completely different hood.  Our extremely good luck in having this BSC is offset by the specific needs we have for it, that may not justify have an 8 foot BSC.

But, the point of this all is: we need to do something to apply our open sci.  It is very easy for me to say "A micro lab is cool and I want one" but a wholly different thing to say:

• 'I'd like to justify the creation of a yeast library with microbiology infrastructure, because (1) we can provide yeast to the Beer Church so that they don't have to buy it, (2) We can isolate yeast from higher-end beer, for use by the Beer Church, and (3) We can isolate environmental yeast for experimental brews from our locally grown fruit."  That's phase 1.
• Phase 2 would be, "We can now collect organisms so that we can grow, harvest, and store organisms for (1) Ginger Beer production, (2) Yogurt production (3) Kimchi production..." etc. 
  
• From that, I can develop a budget for what I would need, what are one-time costs, what are re-occuring costs.  Do I need to pay money for special waste pickup?  Can I buy microbiological media from Becton Dickenson, or can I make it on my own from agar-agar and potatoes?  What is the upkeep?  Etc. 
  
• Then I also outline how I can save costs:  Instead of buying a plastic test tube rack from VWR for $10, maybe I can have the 3D printer guys make me one for less.

In short, it's about synergy and planning.  JFDI will fall into place once we have both of those in a concrete rather than abstract form.  In the meantime, I would suggest we collaborate with each other to create practical applications, justifications, and budgets for what we want.  Space may be at a premium, but PS1 has money in the bank, and people are already planning on what to do with it.  At the last board meeting, they talked about wanting proposals, and I think we need to strike while the iron is hot.

I look forward to talking to you both, and anyone else, on this in greater detail on Tuesday!

-Pete

[John Slavin]

Pete and Ryan,

Yeah, the politics are an unfortunate part of the situation and another reason I decided not to push the issue before.  I'm also on the same page for making sure that it is an "Applied Science" endeavor as it will definitely encourage some of the other side of the space to get involved. 

I didn't really mean to reopen the can of worms concerning the hood.  It seemed to be dead in the water in terms of getting it into the space- as much as I appreciate Ryan trying to discuss it with the SEM list and at the space- but I wanted to explain my situation in terms of my relationship with PS1.  To clarify what I meant before, if there's a space *other than* PS1 that I can work on it, then I can; if we can get it into PS1 (which I again don't think will happen) fantastic.  Otherwise, I'm happy if folks can brainstorm ways to sell it asap.  If I can get 50% of what I've spent so far back, I'm happy.

Otherwise, for most of my goals I want/need a fume hood.  Call it a lack of imagination ;) but I have a few different projects that I've been pining over since September.  Those projects were the primary purpose for my getting involved at PS1 in the first place, as long as the infrastructure could be accomplished.  I've grown to appreciate during my quest the need for open science, especially seeing as its closest relative in Chicago doesn't seem to see the need as much.  So, I'm definitely happy to help with actually making that aspect happen, even if I'm limited in how I can make use of the final product.

Just for clarification, is this is a project of PS1 or is it independent, but mainly composed of PS1 members?  I'm asking because I want to know what I should plan to do in terms of my membership, which is currently nonexistent.

Cheers,

John

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[Ryan Pierce]

I own a very nice computer controlled autoclave. I am happy to sterilize stuff for people, provided they don't mind that I'll do it at home and bring it back the next time I'm there. I've also saved scint jars from Sacha's cache of stuff which looked like they could survive autoclaving and are a good size for making agar slants. I'd originally really wanted to do this, as a Wyeast smack pack is a considerable cost relative to the other ingredients, so it could help brewing.

Unfortunately, brewing at PS:One has not been happening all that frequently. The problem is that the Kegerator fridge is having a defroster issue, and we had originally envisioned using kegs for dispensing. It may be fixable but getting inside the freezer side to work on it is no longer advisable for me as it really hurts my back. This is a shame. (Any help here would be greatly appreciated.) I'd envisioned lots of brewing awesomeness. Fabricating stainless steel brewing gear with the TIG welder. RFID controls on the tap system. Using EPICS (free SCADA software designed for physics experiments) to control PID loops to regulate the mash process. Etc.

Another reason I want a fume hood: fixing biological samples for SEM. We have a critical point drier. But generally you need to cross-link proteins with glutaraldehyde or paraformaldehyde first. Osmium tetroxide is often used as well, but even with a fume hood, the toxicity and volatility of it make me strongly question whether it belongs at a hackerspace. Uranyl acetate... no way. Now I find it interesting that someone apparently left ampules of paraformaldehyde in a cabinet in the space. No idea who or why.

[Steven Finkelman]

John,

Look into a place called The Plant on the south side. Today, their web site is having some problems. The plant was always about growing things, aquaponics and having one stream support another. Beer castoffs, fed to fish, fish poop for fertilizing plants. A vault for mushrooms. One process waste stream is used as the next process input. The developed tech to support the processing. IMO a very interesting setup, 

Their goals are more aligned with your interest than you will find at PS1. Contact Nick, who is growing fungus there. Nick is a phD graduate from Northwestern and the Chicago botanic garden and his interest was soil ecology and fungus. Likely, they are already setup for inoculation and sterilization. 

Open science is all about being able to pursue research outside of the university/industrial/grant science realm where access to information/journals is very expensive if you are outside the system. It's also a reaction to   government pays money to fund research and that research is not available to the general public, but only through the established systems.  In Chicago, it was started at PS1, when there was a more diverse interest in the rest of the universe. IMO the people who could have made a success of it left before it developed enough to be self sustaining. Open science at PS1 failed initially because of the diversity of interests, everything from deep space and subatomic physics to psychological studies. There was no agreement of goals and it was more talk than actual work. I don't recall that there was any work other than some discussions of papers and vague ideas that were never implemented. In the second instance, People had equipment but no real ideas on implementation. A lot of university labs in the area have surplus. It's tempting to pick up cool shit for a cheap price and then look for an application for it. Space at PS1 was not really available for any kind of lab setup. 

Pursuing Open science at PS1 will end up being a fruitless task that will sap your energy. I know this because I was there. I left last june. The organization is more about tech than it is about science. The place is not conducive to sterile bio work. The location in the space that would be part time available to you is in the middle of a wood/metal shop and it is a mess in bio terms. Politically, it's a difficult kettle of fish if the goal doesn't have some kind of immediate gratification to a large enough portion of the membership. Otherwise, the amount of disrespect your equipment and area will be depressing. IMO, ps1 is too big, too general with too many diverging interests and  too many moving parts to sustain a project like yours. 

Maybe even a better idea is to develop a bio hackerspace on your own where bio is first and the space you acquire should be setup to be minimally bio clean, have vents already installed, and waterlines, electricity and bench space installed. In order to build a hackerspace from scratch, you should advertise and hold meetings until you can attract a minimum of 4 to 10 people of like mind, in your case, micro biology, who are willing to donate enough time, energy and funds in order to purchase your own facilities.  They also need to be tuned to bioclenlieness from the get go. A core have to have the necessary expertise to make it  bio or have a sincere desire to learn and teach others. Look up the term 'design patterns for hackerspaces' that was originally presented at CCC as 28C3 for details on how to grow a hackerspace. 

IMO Some models for sustainability are better than others. PS1's model is that  anyone can pay and use the equipment in a space, with a minimal amount of training use the stuff there. In a bio space, I like the country club model better, that is new people need to be around the space for some time, have members sponsor new membership. Hold a vote for new members to become full members. Also a cap on the number of members should be maintained at less than 110. The cap at 110 is the difference between community of friends and impersonal place to go. 

Fwiw.

Steve

[Pete N.]

All,

Based on the levels of frustrations experienced here by you all, I'm pretty certain that I shouldn't expect the outcome would be different now versus when you all tried before.  Still, I think we should make a go of it one more time.

John, you make some pretty compelling arguments.  I don't have the time or energy to try to create a new bio-based hackerspace in chicago, but the Plant seems like some good place to collaborate with... which of course, is the essence of scientific exploration.  I may give them a call, along with BioCurious, Seibel Laboratories at Goose Island, and maybe a few other contacts of mine in the industry.

I'm going to make it for the PS:1 Board meeting and the general Member meeting this Tuesday the 4th, and then go to Z's extremophile presentation at 9.  I figure that after that would be a perfect time for us to discuss open sci together in person, and understand the frustrations of everyone involved from those who have hit the brick wall before.  Once we have a core team together, I think we should announce at the march 11 "300 seconds of fame" a re-ignition of Chicago Open Sci.

[Ryan Pierce]

I'll be there tonight, John, and I'm happy to talk to you in person about all this.

Cheers,

Ryan

[Pete N.]

Hi everyone - Pete here:

Ryan and I had a good conversation about plans and goals about open and applied sci, and we both agreed that a strong foundation is where we want to begin, and that foundation is built by actually doing things.  We also discussed the status of the hood that John has in storage, and while I think the use of this instrument would be a boon, I think it's not necessarily needed /right now,/ nor do I see a time in the foreseeable future when it would be in active use.  Ryan and I came to the joint decision that if John wants to sell the hood he has graciously stored for PS1 all this time, he should certainly do so, and use what profits he makes to re-imburse himself for storage costs.

In the meantime, I do get the vibe that open and applied sci are still part of the culture here at PS1, and everyone has some general idea of what open sci looks like and what they want to do with it.  But, just as an orchestra is made of individual members who have to individually practice their particular instrument, I think that the concept of open sci is going to grow organically out of the groups and individuals that move forward and JFDI on their own accord.

From my personal standpoint, a 'yeast library' will support the needs of groups within PS1, but more than equipment, what I need to do is create infrastructure to support yeast cultivation: namely procedures, sanitization practices, growth media recipes, and disposal protocols.  I also need to do some research on disposal regulations to make certain that proper techniques are being followed, and when that's finished, present that to the board so that they know that nothing I am doing will impact the physical operations of PS1.

So that's where I am at!  I will be giving a '300 Seconds of Fame' talk on March 11th summarizing my goals above.

Thanks - Pete