Re: [DIYbio] Re: civil disobedience and diybio

I think synthetic organelles could help increase the specificity of
the chemistry. Synthetic organelles and a shuttling system.

On Tue, May 28, 2013 at 6:10 PM, matt harbowy <hbergeronx@gmail.com> wrote:
In poking around to support my response to this, I came across an excellent
example of why this is not just a political or regulatory problem.

In my head, I started to go through a "use case analysis" of a hypothetical
research project. I wanted to come up with something practical, that might
even be a project someone here is willing to take on. So I chose diabetes as
the problem, and settled on galegine, a natural anti-diabetic found in
galega officianalis. or French lilac.
http://en.wikipedia.org/wiki/Galega_officinalis. Not surprisingly, after a
little searching on publicly accessible journals, I found a link to "Furman
and Coxon et al"- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438274/ and,
according to the article, pure galegine is hard to get but is "easily
synthesized" from "benzyl amine" and 2-methylpseudourea sulphate, both
available from Sigma.

But wait- I thought galegine was also known as N-dimethylallyl guanidine: I
woundered how they could have gotten an allyl from a benzene, which if you
have synthetic chemistry experience is a huge red flag. So I managed to find
a non-free publication, "Coxon and Furman et al"-
http://www.ncbi.nlm.nih.gov/pubmed/19422230 which correctly shows the rather
complicated synthesis of galegine. I quote:

1-(3-Methylbut-2-enyl)guanidine Hemisulfate 1 (Galegine) and General
Procedure for Synthesis of Guanidine Hemisulfates.


A mixture of 4-bromo-2-methyl-2-butene (19.4 g, 1.0 equiv, 130 mmol) and
potassium phthalimide (29.8 g, 1.2 equiv, 161 mmol) were suspended in DMF
(200 mL) and stirred at 120 C for 1 h before heating to 160 C and stirring
for a further 18 h. The mixture was poured over ice and washed with
dichloroethane (5 × 50 mL), and the organic phases were separated and
combined before washing with sodium hydroxide solution (0.1 N) (2 × 100 mL)
and water (2 × 50 mL). The organic extracts were separated, dried over
anhydrous magnesium sulfate, filtered, and concentrated to leave a crude
solid that was crystallized from cold ethanol to give the intermediate
2-(3-methylbut-2-enyl)isoindoline-1,3-dione (25.6 g, 93%) as a white solid;
mp 100-101C


A mixture of 2-(3-methylbut-2-enyl)isoindoline-1,3-dione (10 g, 1.0 equiv,
46.6 mmol), ethanol (100 mL), and hydrazine hydrate (85%) (2.9 mL, 1.2
equiv, 51.1 mmol) were stirred under reflux for 1 h, cooled, hydrochloric
acid (1M) (5.2 mL, 1.2 equiv, 51.1 mmol) added, and then refluxed for a
further 1 h. The mixture was allowed to cool, filtered, and the residue
washed with cold water (100 mL) before reducing the filtrate under vacuum to
give the intermediate 3-methylbut-2-en-1-amine hydrochloride (4.4 g, 78%) as
a white solid; mp 95-97C

2-Methylthiopseudourea sulfate (6.95 g, 1.0 equiv, 150 mmol) and
3-methylbut-2-en-1-amine (9.1 g, 2.0 equiv, 100 mmol) were dissolved in
water (100 mL) and ethanol (100 mL). The mixture was stirred at reflux for
18 h, connected to a series of bleach traps, before cooling and reducing
under vacuum to give a white crude solid. The compound was suspended in
water (30 mL) and heated until it barely dissolved before allowing to slowly
cool upon which a white solid began to form. After allowing the formation of
the solid to continue overnight, it was collected by filtration and dried in
the oven to give the title compound (5.4 g, 62%) as a white solid; mp
216-218C



It turns out that you get a related compound, N-benzylguanidine. The class
of all the compounds has been patented
http://www.google.com/patents/US5373008 but this patent is now expired and
the entire class of compounds should be free of patent, including the
leading indication and first line therapy, metformin
http://en.wikipedia.org/wiki/Metformin.

So why do I mention this? Let's start off thinking about some of the
research plans someone might take toward finding "open source" diabetes
drugs. They might just be tempted to hack the minimal procedure from
"F&Cetal" instead of following the correct procedure of "C&Fetal". The
lingering doubt I have about this work is, what if the paper principally
authored by Furman actually studied benzylguanidine instead of galegine?
What is the differences of approach between Furman's lab and Coxon's lab
that results in the difference in reported experimental procedure? Who
edited and checked these papers? By simply following published research, it
would be so easy to fool yourself when synthesizing drugs.

At least with synthetic chemistry, I can fall back on the methods of
chemistry to give myself at least some confidence that what I think I have,
I can be sure I have, because proton and carbon NMR and mass spec and
melting point and FTIR, while they all have flaws, eventually suss out the
truth.

Now move on to bioengineering: let's say you engineer a recombinant cell
line to produce galegine. As with the chemical synthesis, actually
recovering the free base is not easy, and when you add up all the possible
side reactions that might make various contaminants, it could be really
difficult to isolate the multigram quantities of any compound you would need
to do a study n=1. You might just get a mixture. You might get poison. You
don't know- and even if you are successful, the next person you give the
drug to might die of lactic acidosis because you "happen" to have a gene
that prevents that side effect. Who knows? Although we know metformin
inhibits a particular enzyme(s?) involved in gluconeogenesis, we don't
really know what giving somebody metformin does to the body, or why some
people react so badly to it. As much as we don't know about metformin, we
know even less about galegine, except that every animal reacts slightly
differently to it.

So, even in a pure libertarian utopia, drug research is fraught with
difficulties on where to start and tons of conflicting theories on what we
know. That's not to say doing some basic investigation in a DIY lab couldn't
do some of the groundbreaking early stage research that might gain us some
critical insights into the why and how of diabetes. There are GREAT projects
to be had. But DIY medicine is more than just bad politics: hacking ceases
to be science when you stop following scientific best practices. N=1
experiments are interesting and all, but they're not science. The politics
and regulation is, in large part, a way to shut down random people from
poisoning each other, as happened all the time at the turn of the 20th
century. For the chemical example, google "elixir sulfanilamide". For the
biohack example, google "a horse named Jim", the ultimate in N=1 biohacked
medicine and a case study on where biohacking could go very, very wrong.

Do you really want to get your medical care from "a horse named Jim?"

-matt





On Monday, May 27, 2013 3:45:05 PM UTC-7, Reason wrote:


http://www.fightaging.org/archives/2013/05/civil-disobedience-and-diybio.php

From a point of view of materials and time it is not costly to set up a
home
laboratory for the purposes of synthesizing chemical compounds or even
perform simple procedures in biotechnology - raising bacteria, assaying
genes in lower animals, and so on. It is, however, illegal to just forge
ahead and do this in most US states or in much of Europe due to the many
prosaic, stupid laws that encrust the body politic....

--
-- You received this message because you are subscribed to the Google Groups
DIYbio group. To post to this group, send email to diybio@googlegroups.com.
To unsubscribe from this group, send email to
diybio+unsubscribe@googlegroups.com. For more options, visit this group at
https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups
"DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an
email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio?hl=en.
To view this discussion on the web visit
https://groups.google.com/d/msgid/diybio/e85425a3-4ff8-4076-8d3f-a1cfc0033621%40googlegroups.com?hl=en.

For more options, visit https://groups.google.com/groups/opt_out.