permaculture

[Toby Hemenway <toby@patternliteracy.com>]

Dredging up my old career as a geneticist:

On the positive side, the materials used in CRISPR technology come from 
bacteria, so the source organisms are very familiar, found everywhere, not 
endangered, and well understood. It allows extremely precise targeting of 
specific gene sequences, making it much more accurate than the restriction 
enzymes commonly used in genetic engineering.. Restriction enzymes clip DNA 
at a very limited number of places, so when a geneticist uses them to cut out 
a gene, they get  other gene sequences along with the target gene that then 
go into the production system and the final product. From that point of view, 
CRISPR is much more efficient, predictable, and carefully targeted.

Also, since the changes are permanent, we know more about what’s being 
released into the environment. With the old tech, as the organism loses the 
new inserted gene, it turns into something new and even less predictable, 
sort of a chimera that is half engineered and half randomly mutated. I’d 
rather have the GMO stay the way it was designed.

On the negative side: the same greedy, ignorant, shortsighted criminals who 
brought you Roundup Ready and terminator genes will use CRISPR to make 
products that we don’t need and that will have all kinds of unforeseen 
negative consequences, just like the old genetic engineering techniques. It’s 
not the tech that’s the problem, it’s the people who use it, and their bosses 
who make them do stupid things with it.

I don’t know what to make of the talk of altering the human genome. That was 
the scare-mongering rumor passed about when genetic engineering first 
appeared in the 1970’s, and it’s still prohibited by the Asilomar agreement, 
AFAIK. But now the scientists themselves are talking about doing it, not just 
opponents of the process. The wikipedia article says that 4 labs are looking 
into modifying human embryos. Too bad those embryos don’t have a voice in the 
decision.

One of the major CRISPR researchers, Jennifer Duodna, has a very clear video 
on the technique, https://www.youtube.com/watch?v=SuAxDVBt7kQ
and a TED talk as well. How bizarre that her surname ends in “DNA.”

As with so much new tech, it’s exciting and depressing at the same time.

Toby
tobyhemenway.com

Just out: my new book on urban permaculture, The Permaculture City. Order it 
at your favorite bookseller or get a signed copy from me at  
http://tobyhemenway.com/book/the-permaculture-city/



> On Jul 4, 2016, at 8:49 PM, Steve Hart <stevenlawrencehart@gmail.com> wrote:
> 
> Hi Declan...yes I did my masters in bed after breaking my back..a great way
> to focus
> 
> By the way..there is plenty of those mongrels operating within the
> Permaculture world too.
> 
> Steve Hart
> 
> On 5 July 2016 at 09:53, scrooge McDuck <declan@planetmail.net> wrote:
> 
>> Well the reading I have done & stuff watched since my stroke has turned me
>> off GMOs big time. One of the few advantages of the stroke was that I
>> arrived in the 21st century. I discovered Permaculture. At night I watched
>> documentaries and torrents I had downloaded during the day rather than
>> suffer trash tv. So I became aware of the damage mankind is doing, and the
>> inherent evil of large super profitable businesses who focus on today's
>> profits rather than tomorrow's planet.
>> 
>> --
>> Declan Moriarty
>> 
>> Sent from my Android tablet with mail.com Mail. Please excuse my brevity.
>> On 04/07/2016, 21:20 Steve Hart <stevenlawrencehart@gmail.com> wrote:
>> 
>>> Yes Declan..it is another diversion from nature. What did we learn in
>>> Permaculture ? ? One that rings in my ears " work with nature not against
>>> her" because as we know...Mother nature always fights back. I've just
>>> started re-reading "Hidden Nature" by Bartholomew a biography on
>>> Schauberger...a must for all in the Permaculture network...Steve Hart
>>> 
>>> On 5 July 2016 at 00:52, Lawrence London <lfljvenaura@gmail.com> wrote:
>>> 
>>>> On Mon, Jul 4, 2016 at 5:45 AM, scrooge McDuck <declan@planetmail.net>
>>>> wrote:
>>>> 
>>>>> What often horrifies me is where they get these 'crisper genes' from -
>>>>> often from sources we would do more than raise an eyebrow at. I have
>>> few
>>>>> facts, but I'm not comfortable with what I do know.
>>>>> 
>>>>> Regards
>>>>> 
>>>>> Declan Moriarty.
>>>>> 
>>>>> *Sent:* Sunday, July 03, 2016 at 10:13 PM
>>>>> *From:* "Lawrence London" <lfljvenaura@gmail.com>
>>>>> *To:* permaculture <permaculture@lists.ibiblio.org>
>>>>> *Subject:* [permaculture] Crisper gene technology - are there
>>>>> (John d'Hondt: Will this new powerful gene modification technology
>>> have
>>>>> implications for permaculture, changing the genetic makeup pf
>>> generations
>>>>> of organisms, including those in the wild?)
>>>>> 
>>>>> Crisper gene technology - Google Search
>>>>> 
>>>> 
>>> https://www.google.com/search?q=Crisper+gene+technology&ie=utf-8&oe=utf-8
>>>>> 
>>>> 
>>>> From Wikipedia:
>>>> https://en.wikipedia.org/wiki/CRISPR
>>>> CRISPR
>>>> From Wikipedia, the free encyclopedia
>>>> <https://en.wikipedia.org/wiki/File:Crispr.png>
>>>> Diagram of the CRISPR prokaryotic antiviral defense mechanism.[1]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid20056882-1>
>>>> 
>>>> *Clustered regularly interspaced short palindromic repeats* (*CRISPR*,
>>>> pronounced *crisper*[2]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-sawyer2013-2>) are
>>>> segments
>>>> of prokaryotic <https://en.wikipedia.org/wiki/Prokaryotic> DNA
>>>> <https://en.wikipedia.org/wiki/DNA> containing short repetitions of
>>> base
>>>> sequences. Each repetition is followed by short segments of "spacer DNA
>>>> <https://en.wikipedia.org/wiki/Spacer_DNA>" from previous exposures to
>>> a
>>>> bacteriophage virus or plasmid <https://en.wikipedia.org/wiki/Plasmid
>>>> .[3]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid20125085-3>
>>>> 
>>>> The *CRISPR/Cas system* is a prokaryotic immune system
>>>> <https://en.wikipedia.org/wiki/Immune_system> that confers resistance
>>> to
>>>> foreign genetic elements such as those present within plasmids
>>>> <https://en.wikipedia.org/wiki/Plasmids> and phages
>>>> <https://en.wikipedia.org/wiki/Phage>,[4]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-4>[5]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid17379808-5>[6]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid19095942-6> and
>>>> provides a form of acquired immunity
>>>> <https://en.wikipedia.org/wiki/Acquired_immunity>. CRISPR spacers
>>>> recognize
>>>> and cut these exogenous genetic elements in a manner analogous to RNA
>>>> interference <https://en.wikipedia.org/wiki/RNA_interference> in
>>>> eukaryotic
>>>> <https://en.wikipedia.org/wiki/Eukaryote> organisms.[3]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid20125085-3> CRISPRs
>>>> are
>>>> found in approximately 40% of sequenced bacterial
>>>> <https://en.wikipedia.org/wiki/Bacterial> genomes and 90% of sequenced
>>>> archaea <https://en.wikipedia.org/wiki/Archaea>.[7]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid17521438-7>[note 1]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-8>
>>>> 
>>>> By delivering the Cas9 <https://en.wikipedia.org/wiki/Cas9> nuclease
>>> and
>>>> appropriate guide RNAs into a cell, the cell's genome
>>>> <https://en.wikipedia.org/wiki/Genome> can be cut at a desired
>>> location,
>>>> allowing existing genes to be removed and/or new ones added.[8]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-nature99-9>[9]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-vb99-10>[10]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid26121415-11>
>>> CRISPRs
>>>> have been used in concert with specific endonuclease
>>>> <https://en.wikipedia.org/wiki/Endonuclease> enzymes
>>>> <https://en.wikipedia.org/wiki/Enzymes> for genome editing
>>>> <https://en.wikipedia.org/wiki/Genome_editing> and gene regulation in
>>>> species throughout the tree of life
>>>> <https://en.wikipedia.org/wiki/Tree_of_life_%28biology%29>.[11]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-12>
>>>> 
>>>> Cas9 was the first nuclease discovered, followed by Cpf1, which was
>>>> discovered in the CRISPR/Cpf1 <
>>> https://en.wikipedia.org/wiki/CRISPR/Cpf1>
>>>> system of Francisella novicida
>>>> <https://en.wikipedia.org/wiki/Francisella_novicida>.[12]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid26422227-13>[13]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid27096362-14> Other
>>>> such
>>>> systems are thought to exist.[14]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-:3-15>
>>>> 
>>>> CRISPR/C2c2 from the bacterium Leptotrichia shahii
>>>> <https://en.wikipedia.org/wiki/Fusobacteria> is RNA-guided CRISPR
>>> system
>>>> that targets RNA rather than DNA, and can either cleave single-stranded
>>> RNA
>>>> targets or knock them down <
>>> https://en.wikipedia.org/wiki/Gene_knockdown>.
>>>> [15] <https://en.wikipedia.org/wiki/CRISPR#cite_note-pmid27256883-16>
>>>> 
>>>> The CRISPR interference <
>>> https://en.wikipedia.org/wiki/CRISPR_interference
>>>>> 
>>>> technique has many potential applications, including altering the
>>> germline
>>>> <https://en.wikipedia.org/wiki/Germline> of humans, animals, and food
>>>> crops. The use of CRISPR for genome editing[16]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-17>[17]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-18> was the AAAS
>>>> <
>>>> 
>>> https://en.wikipedia.org/wiki/American_Association_for_the_Advancement_of_Science
>>>>> 's
>>>> choice for breakthrough of the year in 2015.[18]
>>>> <https://en.wikipedia.org/wiki/CRISPR#cite_note-19> Bioethical
>>>> <https://en.wikipedia.org/wiki/Bioethical> concerns have been expressed
>>>> about the prospect of using this nascent biotechnology for editing the
>>>> human germline.[19] <https://en.wikipedia.org/wiki/CRISPR#cite_note-20>
>>>> <>
>>>> Bitter fight over CRISPR patent heats up : Nature News & Comment
>>>> <
>>>> 
>>> http://www.nature.com/news/bitter-fight-over-crispr-patent-heats-up-1.17961
>>>>> 
>>>> www.nature.com/news/bitter-fight-over-*crispr*-patent-heats-up-1.17961
>>>> Nature Jan 12, 2016 -
>>>> Use of the *technology* in research has exploded, thanks to
>>> *CRISPR*–Cas9's
>>>> relative simplicity and versatility compared to other gene-editing ...
>>>> <>
>>>> http://www.radiolab.org/story/antibodies-part-1-crispr/
>>>> Hidden inside some of the world’s smallest organisms is one of the most
>>>> powerful tools scientists have ever stumbled across. It's a defense
>>> system
>>>> that has existed in bacteria for millions of years and it may some day
>>> let
>>>> us change the course of human evolution.
>>>> <>
>>>> 
>>>> I listened to an interview on public radio last week with an (the?)
>>>> inventor of the CRISPR technology currently in intense development.
>>>> 1) He insisted and will campaign for development and use of CRISPR to be
>>>> completely in the public view, interactive with the public and not
>>> behind
>>>> closed doors. He said that this is the way forward for maximum progress
>>>> with and best use of CRISPR.
>>>> 2) He described it this way. With conventional gene splcing the GMO
>>>> organism can eventually shed the modifications to its genetic makeup.
>>> With
>>>> CRISPR it can not.because it inserts a gene segment plus a tool (spacer)
>>>> that keeps it in place and protects it from evolutionary changes. In
>>> other
>>>> words it makes permanent changes to an organism's genome such that, as
>>> any
>>>> organism modified with CRISPR reproduces, those changes are retained in
>>> any
>>>> offspring and for generations forward. [this is my take on what he said
>>>> several days ago - I tried to find the interview and name of the
>>> researcher
>>>> but without luck],
>>>> 
>>>> So, Declan, what "questionable" materials are sourced for use in CRISPR.
>>>> BTW they are talking about modifications to the human genome with this
>>>> promising technology. .
>>>> --
>>>> Lawrence F. London
>>>> lfljvenaura@gmail.com
>>>> https://sites.google.com/site/avantgeared/
>>>> https://plus.google.com/u/0/b/116100117925365792988/+Avantgeared/posts
>>>> https://ello.co/permaculture
>>>> https://lists.ibiblio.org/sympa/arc/permaculture
>>>> permaculture mailing list
>>>> permaculture@lists.ibiblio.org
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>>>> http://lists.ibiblio.org/mailman/listinfo/permaculture
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> Kia ora Ehoa
>>> 
>>> [image: Picture]
>>> *Steve Hart*
>>> *Ecology Architect*
>>> *Designer, Teacher, Builder of Ecologically Sustainable Resilient
>>> Environments, through Urban Design, Architecture, Landscape Architecture
>>> and Systems Ecology.​*
>>> Skype: tipenemanawa
>>> Phone: +64 220 75 62 11
>>> 
>>> Permaculture Global Design:
>>> www.permacultureglobaldesign.org
>>> 
>>> The Permaculture International College
>>> www.permaculturecollege.eu
>>> https://permaculturecollege.academia.edu/SteveHart
>>> 
>>> GAPPS The Global Alliance for Permaculture Partnerships and Solutions.
>>> www.permaculturepartnerships.com
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>> 
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> 
> 
> -- 
> Kia ora Ehoa
> 
> [image: Picture]
> *Steve Hart*
> *Ecology Architect*
> *Designer, Teacher, Builder of Ecologically Sustainable Resilient
> Environments, through Urban Design, Architecture, Landscape Architecture
> and Systems Ecology.​*
> Skype: tipenemanawa
> Phone: +64 220 75 62 11
> 
> Permaculture Global Design:
> www.permacultureglobaldesign.org
> 
> The Permaculture International College
> www.permaculturecollege.eu
> https://permaculturecollege.academia.edu/SteveHart
> 
> GAPPS The Global Alliance for Permaculture Partnerships and Solutions.
> www.permaculturepartnerships.com
> permaculture mailing list
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