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Author: Subject: Do-It-Yourself DNA
Magpie
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[*] posted on 30-12-2008 at 11:44
Do-It-Yourself DNA


The website given below tells about some home biochemistry that, so far, seems to be acceptable to the media, possibly the general public, and more questionably the 3 letter agencies charged with guarding our wellbeing. These folks have "homemade" lab equipment and experiment in their dining rooms, kitchens, etc.

It seems hypocritical for the media, etc to think that this is cute but come down so hard on us regular home chemists. But I do hope the positive publicity continues. More of this just might help our cause.

http://www.huffingtonpost.com/2008/12/25/do-it-yourself-dna-...

Edit: Oops. I just read the 3 pages of comments from Huffington readers, a fairly high level discussion. This article just may turn out to be negative publicity for the home chemist. :(

Edit 2: The Associated Press picture of Ms Patterson working in her lab:



[Edited on 30-12-2008 by Magpie]

[Edited on 30-12-2008 by Magpie]

[Edited on 30-12-2008 by Magpie]

DNA.jpg - 12kB
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[*] posted on 30-12-2008 at 14:11


I don't know Magpie.

When I see people write things like this:
"It's time to write your State and Federal leaders and demand legislation to outlaw this dangerous practice.

Due to the secrecy with which it can be conducted, it will have to carry a very high penalty if discovered.

This is a serious danger to the public. As such, the legislation should be equivalent to terror!st acts with equivalent consequences."

I wonder about it.

He goes on to say:

"Dangerously foolish!!

Manipulating the genetics of organisms in an uncontrolled environment by unskilled "hobbiests' is a disaster waiting to happen. It's not a matter of IF, but rather WHEN one of their mutants is loosed on the public.

I work as Molecular Biologist in a Bio-safety Level 3 laboratory and this idea sounds like a nightmare to me. I don't trust half the Ph.D.'s I work with, let alone some curious "know-it-all" who read a few journal/news articles and thinks, "I can do that!"

A little bit of knowledge is a dangerous thing! In this case, it could be the end of us all... If you live near Ms. Patterson, I suggest not shopping at the same grocery store."


I understand his concerns. I suppose if I worked in his lab setting, or in a facility that worked with say, chemical weapons, I'd probably have a ''leave-it-to-professionals" opinion about all of science. I do feel that way about super toxic chemicals and/or dangerous bacteria and viruses, us as amateur chemists or biologists should have nothing to do with that outside of a properly equipped lab. But I also understand that much of that can't happen by accident, or at least not easily--there must be some intent to do that. There are some of us here at sciencemadness that have extremely sophisticated home laboratories which nearly rival professional labs with regards to equipment and chemicals. Still though, I doubt any of us could pull off a nerve agent (or would dare try, for that matter) accidentally or intentionally.

Also, how many people that have enough interest in science to do it at home, aren't professionals? Chemistry is my livelihood and I am positive that there are many professional chemists on this board. The fact is, even if I work in a research laboratory, it doesn't mean I do not have other research interests that I pursue outside of my career. I love synthetic inorganic chemistry, but it's not my job--it's my hobby.

Like many things, I think this comes down to opinion. For me, I do not think it is that bad to do legitimate science at home or in a private laboratory. Even as a hobby, I think it should still have regulations placed on it though, so as to prevent any abuses (mainly with waste, exposure, other safety issues). I truly believe that a home laboratory can be made as safe as any professional lab--it is a question of quantities, and a question of commonsense. Woelen's laboratory is a good example-- based off the quantities he experiments with and his high level of responsibility, I would probably feel safer working in his lab at his scale than in many professional laboratories.

I also don't believe that an amateur could just so easily make a WMD and hurt a lot of people with it. If he has that type of skill, he's probably no amateur and that is what would concern me.




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chemoleo
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[*] posted on 30-12-2008 at 16:26


I really doubt an amateur would be able to pull this off - linking a melamine-detecting gene to expression of green fluorescent protein in lactobacillus.
This requires more than just cursory interest, this (simple) project could take a year in a professional lab to make it work. An untrained beginner? No way!!
Not to mention equipment, hugely expensive enzymes and access to some rather nasty reagents. Can a private person order all the reagents, order genes and plasmids and have them sequenced?




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watson.fawkes
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[*] posted on 30-12-2008 at 17:08


Quote:
Originally posted by chemoleo
I really doubt an amateur would be able to pull this off - linking a melamine-detecting gene to expression of green fluorescent protein in lactobacillus.
This is exactly the sort of stuff that iGem is all about. For those who've never heard of it, it's a genetic engineering contest for undergraduates. It has an emphasis on making "standard parts" available as open source. Here's this year's winning entry.
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[*] posted on 30-12-2008 at 17:22


From the article:
"Once you move to people working in their garage or other informal location, there's no safety process in place," he said

Translation: My anti-science lobby group has no power over what you do in your garage, unlike government and universities where when we whine loud enough our extremist veiwpoints cause curtailing of science.

EDIT: One poster on that site seems to be the cause of much of the BS on the comments section.

[Edited on 30-12-08 by The_Davster]




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[*] posted on 31-12-2008 at 11:04


"Edit: Oops. I just read the 3 pages of comments from Huffington readers, a fairly high level discussion. This article just may turn out to be negative publicity for the home chemist. "

You're right. This is very disconcerting.




"There must be no barriers to freedom of inquiry ... There is no place for dogma in science. The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors. ... We know that the only way to avoid error is to detect it and that the only way to detect it is to be free to inquire. And we know that as long as men are free to ask what they must, free to say what they think, free to think what they will, freedom can never be lost, and science can never regress." -J. Robert Oppenheimer
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[*] posted on 1-1-2009 at 17:58


I doubt she could pull it off too. I realize that transfecting DNA into bacteria isn't that hard but even if you succeed in transfection the gene must be expressed for it to do anything. Of course I must admit I am amazed at the fact that it is so easy to buy bacteria, culturing supplies, reagents etc. All of which can be obtained without violating any laws.
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[*] posted on 2-1-2009 at 06:26


I have serious doubt that she will obtain any interesting results. I am no biogenetics expert at all, but I think that it is incredibly hard to do experiments in this field.

But if this Meredith Patterson does get results, then I can imagine that the risk is not acceptable. Chemistry certainly has its risks, but at least, chemicals cannot reproduce and spread into the environment while multiplying themselves. A living organism is another matter. So, I understand some of the concerns of people who gave comments on the article. On the other hand, some comments are rather harsh and do no good to home experimenting in general.

I personally think that the activities of this woman are not good for the attitude of the general public towards home experimenting. I have a much better feeling with the acitivities of a guy like Mr. Deeb, whose lab was raided some months ago. I personally think that tinkering with life forms is beyond the border of the acceptable what can be done at home.




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[*] posted on 18-7-2009 at 00:27


I find the idea fascinating and wish I had the knowledge to do it. I've been thinking about going to uni in fact just to learn about biochemistry and genetic engineering but seeing as your average plasterer makes more than a genetic engineer and it takes years to learn I've been unable to convince myself to do it (sorry, I think genetic engineering is more important and takes longer to learn than plastering and the pay is insulting!) Since the people who do it obviously do it for the love not the money though they can be exploited which is sad.

Back to the relevant point I don't think it should be illegal to do this sort of thing at home if you have the knowledge but being required to have the correct safety equipment seems a reasonable legislation, we don't really want that bacterium you modified to possess the waxy coat of tuberculosis and express oil/paint stripper/pepper spray/whatever escaping and ending up in the environment.

[Edited on 18-7-2009 by everythingischemistry]
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[*] posted on 24-7-2009 at 12:30


Interesting.

I don't think you'll create anything dangerous out of this, because it would be purely random (by accident). Genetic engineering can be done several ways. I think these guys are just using the method where they suspend the plasmid in the culture, heat weaken the bacteria, and force the bacteria to absorb the plasmid. Other than that it would seem too hard to do in a home laboratory.

I work in a BSL 2 lab as an intern/research, and I'm still scared of catching Strep or Staph. Something real evil would be to give Strep resistance to antibiotics. I doubt anyone could do that, much less distribute it. Most biological weapons require fine grade silica, and forcing the bacteria into dormancy as spores, or immediate weaponization. Biochemistry reagents -- unless you are doing acrylamide gels, ethidium bromide stuff, are rather easy to obtain. One would need common bacterial cultures, some vitamins, and some salts. Now dying, staining, and acrylamide/ EthBr is rather dangerous as it involves toxic and carcinogenic chemicals. But other than that, reagents for simple insertions involving heat transfer doesn't seem hard.
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[*] posted on 24-7-2009 at 13:20


Some of the commenters on the article are just repeating the tired old arguments that were made about all recombinant work, even that done by professionals, soon after the first recombinants were created in the 1970's. There were international conferences to hash out allowable and proscribed techniques and organisms. Many people said the sky would fall, but it didn't.

Recombinant DNA has been taught in high school, and even middle school, lab courses for more than 20 years. See http://www.genome.ou.edu/HHMI/workshop.pdf for an example. The educational science companies sell kits with all the goodies for high school teachers. Most companies don't sell them to individuals, however.

When I took a recombinant DNA lab course at a major university we didn't use any biosafety precautions that couldn't be used at home, except when we labeled probes with radioactive nuclides. We just wore labcoats and gloves and disinfected everything at the end with bleach. Pretty much everything can be done without using pathogenic organisms, unless of course you are studying pathogens per se.

Deserving greater concern would be the group with malicious intent who learned the genetic sequence for a virulent pathogen (e.g. smallpox) form the sequences published on the web, then ordered the sequences from the mail-order firms that supply them and splice them together to make a virulent virus. Several years ago a university group performed such a trick and created a virulent poliovirus. This was widely reported in the news media and generated a lot of concern.

A random mutation is much more likely to destroy an organisms mechanism of pathogenicity, for example by deleting a critical region of a gene encoding for toxin, than it is to somehow create a superbug with enhanced pathogenicity. Genetic engineering is to today's students as amateur chemistry and rockets were to students in the 1960's.
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[*] posted on 24-7-2009 at 15:54


Quote:
Genetic engineering is to today's students as amateur chemistry and rockets were to students in the 1960's.

Most of the things you say is correct, but that last statement is ....horsecrap...sorry.
The complexity, empirical knowledge, reagents (enzymes, substrates, equipment), never mind in depth knowledge of the field, are all things required in genetic engineering, but not necessarily for amateur chem and rockets. It's not even worthy a comparison!

Nonetheless, it is a very interesting point that scientists used to be very worried about genetic engineering, and indeed in the 70s things were strictly regulated. As no incidents ever occurred, these rules were relaxed.

This begs one question: E coli, present in our very guts, doubles in 20-40 min, depending on conditions. The adaptation rate, as well as mutation rate, should be staggering - so why is it that there's a 'stable' E coli genome sequence that is published, which persists in all our guts, why is it not that thousands of people succumb to random mutations occurring all the time on E coli? In fact, why is it that E coli (or any other organism replicating fast) hasn't covered the planet with a thick bacterial mat a million times over? Why are these organisms so stable (genetically speaking) despite their adaptation and mutation rates?

It's a bit of a brain teaser...




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[*] posted on 24-7-2009 at 17:42


Quote: Originally posted by chemoleo  
Quote:
Genetic engineering is to today's students as amateur chemistry and rockets were to students in the 1960's.

Most of the things you say is correct, but that last statement is ....horsecrap...sorry.
The complexity, empirical knowledge, reagents (enzymes, substrates, equipment), never mind in depth knowledge of the field, are all things required in genetic engineering, but not necessarily for amateur chem and rockets. It's not even worthy a comparison!

...


Read the first post. Look at the hyperlink.

Sorry you missed my point: middle and high school students are being exposed to molecular biology and some acquire the in-depth knowledge of which you speak. I guess you've never been to the Intel science competition for high school students where molecular biology is commonplace.

At least two local high schools here teach multiple courses in these subjects and have better labs than some community colleges.




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[*] posted on 24-7-2009 at 18:19


Quote:

At least two local high schools here teach multiple courses in these subjects and have better labs than some community colleges


Is this in the US?
My schools most advanced biology course is AP biology, and all you do in there is eat donuts and mix starch and iodine together for some osmosis crap, let alone have a lab better then some colleges!?
That is very impressive!





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entropy51
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[*] posted on 25-7-2009 at 10:44


Yes, it is in the US. They are "science magnet" schools, not your typical public high school. Science is mostly taught by PhD's. They have facilities up through and including NMR. A lot of the lab equipment is donated by big companies. They often have multiple finalists, and frequently winners, in the Intel Science Talent Search http://sciserv.org/sts/

These are the students that would have been chemistry geeks in years past, but now do supercomputing and molecular biology.
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[*] posted on 30-7-2009 at 07:12


Just for fun I sometimes like to toy with the idea of the things that would be possible with generally available chemicals and some home build and/or cheap equipment. :)

A number of things would defenitely be in reach for DIY home experimenting. The genome and proteome of sequenced organisms is freely accesible through NCBI. Media and thermostat controled incubators for growing and even transforming bacteria probably pose no real problem as well and the isolation of DNA requires no more than a few solutions of chemicals that are generally available. I've even read about people construction their own purification columns by applying glass wool instead of the expensive commercial sillica columns. A -80 is no requisite for the storage of GMO's, as alternatives exist. Gel electrophoresis is not that difficult as well, etbr can be replaced by methylene blue and freely purchased for the treatment of fungal infections of fish held in aquaria.

Mutaginizing agents in combination with an appropriate selection marker (that what you want to select for) would provide an easy method of screening for mutants without the need to know the details of the mutations involved. This method of accelerated evolution requires no more than a large scale approach and time and is still used to obtain mutants today.

However, I think it is safe to say that at the basis of cloning or manipulating a single particular gene is the extremely versatile PCR reaction. Apart from the fact that oligos and taq are not that expensive anymore, it does require an expensive piece of equipent. In the earlier days this was performed by the immersion of the reagents in water baths at the required temperature, though this was extremely time consuming. On the other hand, searching somewhat on the internet I could buy meself a PCR machine for under $600. :D(Features fast ramping, lol)

http://www.labx.com/v2/adsearch/detail3.cfm?adnumb=391505


Here however the list of DIY things probably quickly ends, western blotting, protein purification, protein activity assays, sequencing, qPCR, etc etc all require enzymes and equipement that are extremely expensive and require knowhow to operate.

At this moment I guess that the potential of genetic engineering at home is well beyond the level of brewing your own beer, but still a long, long way from profesional labs.

[Edited on 30-7-2009 by nitro-genes]
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[*] posted on 3-10-2009 at 07:14


A couple of years ago I wanted to do a PCR reaction at home. I found companies very reluctant to sell to me as an individual. The excuse they always gave was that their lab kits contained "chemicals", and because of this they could only sell to schools. In one particular case, the only "chemical" I saw included was a calcium chloride solution! But they said sorry, if it has any chemicals in it at all, we cannot sell it to the public. My attempts to persuade them that this chemical is simple ice melter had no effects.

Finally I found a place, called WardSci, that would sell to individuals. That was my worst buying exprience ever. They charged exorbitant prices, not only for the materials, but for shipping as well. Then, even with the high prices for shipping, it took weeks to get my order. When it finally arrived, it was missing two reagents. I sent them E-mails repeatedly complaining about this and they never responded at all.

Hodges
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[*] posted on 3-10-2009 at 12:48


Quote: Originally posted by Isilla21  
The fact is, even if I work in a research laboratory, it doesn't mean I do not have other research interests that I pursue outside of my career.


Agreed, I'm not professional - I'm a student, but I also have interests in chemistry other than my syllabus. Hence the home lab :)




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