Fwd: [reprap-users] Reprapable Transistors and Batteries

[Bryan Bishop]

---------- Forwarded message ----------
From: Graeme Smith <grys...@telus.net>
Date: Thu, Dec 23, 2010 at 7:36 PM
Subject: [reprap-users] Reprapable Transistors and Batteries
To: reprap...@reprap.org


While I find the concepts of these two projects interesting there are a
number of caveats that work against doing this level of production in an
Open Manufactoring Paradigm.

1. NanoTubule design while replicatable, depends on nanoscale
stereochemistry to achieve. One way of achieving it is gas deposition on
a silicon substrate. Organic Thin Film technology however, can be done
with a much lower resolution, which is why RepRap designers are looking
at what is necessary for creating ink-jet technologies with a high
resolution. This can be done in the Thousandths of an inch scale, which
it is easily possible to control using a stepper motor.

2. Production of chemicals. While Organic Batteries are relatively easy
to make, once the paper is made, dopamelanin is a precursor, to both
dopamine, and melanin which are critical to human health. Dopamine being
used heavily in the brain as a Neurotransmitter, and Melanin being used
heavily in the skin to block UV rays. Further, these two chemicals are
only the most obvious byproducts of the precursor, a further refinement
into melatonin, is critical in humans to regulate the body clock that
synchronizes the individual cellular clocks. Care should be taken not to
create bio-chemical environments using common stomach bacteria that are
not bred to die in known lengths of time, if only because a mutation
that extends that time, means that the virus can escape the confines of
the manufactoring and destroy the health of humans by tagging along with
any that fail to meet prophylactic requirements.

As such, I strongly suggest not shipping the active cultures, but
instead planning a central production place for the bio-reaction, but
offering it to the Open Manufactoring Community in the form of a sheet
of paper, or a filament that can be extruded from a modified RepRap.

Graeme Smith


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--
- Bryan
http://heybryan.org/
1 512 203 0507

[John Griessen]

On 12/25/2010 03:26 PM, Bryan Bishop wrote:
> not shipping the active cultures, but
> instead planning a central production place for the bio-reaction, but
> offering it to the Open Manufactoring Community in the form of a sheet
> of paper, or a filament that can be extruded from a modified RepRap.
>
> Graeme Smith

Sure sounds like voluntary vendor lock in to me.

JG

[Bryan Bishop]

---------- Forwarded message ----------
From: Oren Beck <oren...@gmail.com>
Date: Sun, Dec 26, 2010 at 12:33 PM
Subject: [Open Manufacturing] Re: Fwd: [reprap-users] Reprapable Transistors and Batteries
To: Open Manufacturing <openmanu...@googlegroups.com>


RE: Biohazard Concerns.. Yes- those issues are potentially a species
decimation level risk if someone screws up in a worst "set of cases"
scenario.

Much of the work on preventing such issues has been dome by Science
Fiction writers- the "Wilfdire" facility from Andromeda Strain may be
*barely* adequate for some stupidly dangerous biohacks. IIRC it was
Paul Preuss who had a plot McGuffin involving shipping consumer
products that used a modded virus as a computing element.

Perhaps a few outreaches to the hardcore SF Fandom community to tap
that "Hive Mind" might be worth planning. Being totally serious. As
reading Frank Herbert's "The White Plague" forever altered my
perceptions of Biohazard dangers. If a writer can create that "worst
case" incident's conditions, we might use those same scenarios to
design our standards and practices guidelines. Jurassic Park comes to
mind as a fictional scary that some of us are already VERY mindful
of.

RE: the mundane mechanical considerations of hardware for fabbing
electronics. That too-might consider mining SF tech bases to direct or
suggest skipping design paths. I was taught the phrase:

AKICIF- All Knowledge Is Contained In Fandom.

Looking at the archives of the Usenet SF Fandom groups with a filter
for Biohazard terms might support my present wild haired thoughts on
finding sufficiently PRACTICAL paranoia:>

Same with the dissertations on mechanical design woven into the Doc
Smith "Skylark" and "Lensman" series books. Where a tracking
instrument's indicator needle was described as "having jewel bearings
stronger than those of a truck axle" supporting that needles estimated
single gram mass.

Look at RepRap's or MakerBot's LAUGHABLE by comparison FDM fabbed ABS
slides for a lesson in WHY looking at both SF and traditional machine
designs is going to be needed to fab Bioscale Electronics. I saw a
demo of the differences in dimensional accuracy between an ancient
Bridgeport Mill- and the average Darwin Fab unit. Not to disrespect
RepRap et all- but we're sadly delusional to overlook that there's a
several orders of scale divergence in repeatable dimensional
resolutions between our BEST current Fab gear and that IIRC 50? year
old tech in a Bridgeport mill.

Enough for now- hopefully my wild suggestions bear fruit.

> reprap-us...@lists.reprap.orghttp://reprap.org/mailman/listinfo/reprap-users
>
> --
> - Bryanhttp://heybryan.org/
> 1 512 203 0507

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[Russell Whitaker]

On Sun, Dec 26, 2010 at 11:52 AM, Bryan Bishop <kan...@gmail.com> wrote:
>
>
> ---------- Forwarded message ----------
> From: Oren Beck <oren...@gmail.com>
> Date: Sun, Dec 26, 2010 at 12:33 PM
> Subject: [Open Manufacturing] Re: Fwd: [reprap-users] Reprapable Transistors
> and Batteries
> To: Open Manufacturing <openmanu...@googlegroups.com>
>
>
> RE: Biohazard Concerns.. Yes- those issues are potentially a species
> decimation level risk if someone screws up in a worst "set of cases"
> scenario.
>

I think the word Oren's looking for in a "worst case scenario" is
"extinction," which denotes a 100% species loss, rather than
"decimation," which denotes a 10% reduction.

--
Russell Whitaker
http://twitter.com/OrthoNormalRuss
http://orthonormalruss.blogspot.com/

[Russell Whitaker]

Me to Oren: "Oren, you seem to have accidentally replied privately to
me; shall I cc my reply
to the list?"

Oren to me: "yes- CC to list please:>"

- me

---------- Forwarded message ----------
From: Oren Beck <oren...@gmail.com>
Date: Sun, Dec 26, 2010 at 1:05 PM
Subject: Re: [Open Manufacturing] Re: Fwd: [reprap-users] Reprapable
Transistors and Batteries

To: Russell Whitaker <russell....@gmail.com>

Actually- I picked the 10% figure to intentionally remind us that
"homo sometimes sapient" is awfully hard to kill despite our best
efforts :>

Oh, I don't doubt that we "could" perform species suicide if it for
whatever warped reason became someone's goal. It's from the reality of
humans being simply not often capable of anything 100% even as a goal.
Look at Australia and Rabbits then revisit the Cobra and Mongoose
lesson from several islands.

Close, but not 100% of 100% even with the inclusions of Passenger
Pigeon etc. The only closer to 100% extinction fear that wakes me up
in cold sweats is fearing how close we have come to extinction of
Common Sense as a working concept. That's the one which would indeed
be most logically be soon followed by a new dominant species on this
planet.

--
Oren Beck

816.729.3645

[greenhouse flower]

The conducting polymer of interest is polypyrrole, and precursors to
its biosynthesis do not have to be dopamelanin, but one or multiple
analog molecules or enzymes that performs one or more of the
biosynthetic steps. In a similar way, for example, organic chemists
have multiple ways to organically synthesize a molecule, which could
take 17 steps or 12 steps, and use different precursors. By studying
the biosynthesis of polypyrrole, alternative synthetic (or natural)
pathways can be suggested.

Additionally, polypyrrole is one of multiple conducting polymers, and
the biosynthesis of single and/or copolymers was an is being suggested
(in my first email), rather than focusing exclusively on dopamelanin
and other precursors. For example, other conducting poymers include
polyacetylene and stable nitroxides in organic radical batteries
(ORB). This is also based on research in the past 5-10 years, thus it
is very early to know which conductive polymers might be better
integrated into an engineered biological synthesis pathway. Lastly, if
synthetic approaches are considered, I'm curious to speculate on
whether the ideal synthetic molecule would be one that is designed to
decompose into natural sub-parts, such that it is not observed to
undergo unstudied chemical reactions, by using micro/chemical array
analysis of reactivity to common and likely relevant compounds.

In my previous e-mail, I discussed more about the biological
environments, though when I submitted it, I think my session logged
out and am not sure if it was received, but I can re-send it with some
updated edits.

Giovanni

> reprap-us...@lists.reprap.orghttp://reprap.org/mailman/listinfo/reprap-users
>
> --
> - Bryanhttp://heybryan.org/
> 1 512 203 0507

[greenhouse flower]

> From: Graeme Smith

"Care should be taken not to
> create bio-chemical environments using common stomach bacteria that are
> not bred to die in known lengths of time, if only because a mutation
> that extends that time, means that the virus can escape the confines of
> the manufactoring and destroy the health of humans by tagging along with
> any that fail to meet prophylactic requirements.
>
> As such, I strongly suggest not shipping the active cultures, but
> instead planning a central production place for the bio-reaction, but
> offering it to the Open Manufactoring Community in the form of a sheet
> of paper, or a filament that can be extruded from a modified RepRap.

First, I am suggesting bacteria or yeast, not necessarily "common"
stomach bacteria, as I did suggest uncommon genetic compositions.
Secondly, BioBricks or other standardized part repositories could
provide the genetic elements that could be transformed into an
otherwise unmodified organism, and those parts can be shipped to
developers and researchers without an active culture. Unmodified
organisms could then only later be "activated" for production after
proper protocol steps are performed as tested and validated by a
safety peer review. Third, bacteria are not a "virus," as they do not
depend on a host for replication, but exist on their own, and
relationships with another organisms may be categorized as mutual,
parasitic, or commensal. Furthermore, A synthetic or modified bacteria
or yeast that only exists for a short duration analagous to heavier
elements on a periodic table would not fit any of the above
categories. They are not viral in nature, but would not survive
either, unless a mutation caused a bypass in prophylactic
requirements. Using a partially or fully synthetic platform for core
machinery has advantages because the modified core replication
requirements cannot be be found naturally. A recent suggestion is the
orthogonal systems to lessen unexpected interactions, as suggested in
this Nature article:
http://www.nature.com/news/2010/100120/full/463288a.html
"To transcribe DNA into RNA, the team uses a polymerase enzyme that
recognizes genes only if they have a specific promoter sequence that
is not present in the cell's natural genes. Similarly, the system's
orthogonal 'O-ribosomes', which translate RNA into protein, can read
only 'O-mRNA' that contains a specific sequence, and O-mRNA is
unreadable by natural ribosomes."
Each synthetic assembly part could raise the improbability of genetic
or chemical element exfiltration by a fold-factor, by creating a
platform of artificial nutrient/ribosome/polymerase scarcity for the
bacteria or yeast organism and contributes to a more secure
microenvironment. The aspect of synthetic biology's "uncommon"
presence in nature can be used in a advantageous way because it limits
its migration potential based on the artificially modified nutrients
that have been localized in the growth medium that are needed for
survival. In other words, if an ordinary bacteria can survive on
glucose and water, a synthetic bacteria that can only survive on a
rare, artificially-made or artificially-prepared organic compound that
isn't edible to any other natural organism, that synthetic organism
would not be able to stray from the food source (manually-added) and
survive if its food source can't be naturally found.

Giovanni

[Graeme]

On Dec 26, 12:41 am, greenhouse flower <giovanni.lostu...@gmail.com>
wrote:

> First, I am suggesting bacteria or yeast, not necessarily "common"
> stomach bacteria, as I did suggest uncommon genetic compositions.
> Secondly, BioBricks or other standardized part repositories could
> provide the genetic elements that could be transformed into an
> otherwise unmodified organism, and those parts can be shipped to
> developers and researchers without an active culture. Unmodified
> organisms could then only later be "activated" for production after
> proper protocol steps are performed as tested and validated by a
> safety peer review. Third, bacteria are not a "virus," as they do not
> depend on a host for replication, but exist on their own, and
> relationships with another organisms may be categorized as mutual,
> parasitic, or commensal.

Sorry don't know how that Virus snuck in, but you did mention E-coli
as an option if I remember right.

>Furthermore, A synthetic or modified bacteria
> or yeast that only exists for a short duration analagous to heavier
> elements on a periodic table would not fit any of the above
> categories. They are not viral in nature, but would not survive
> either, unless a mutation caused a bypass in prophylactic
> requirements.

That is one of the issues, using DNA based biologicals, you cannot
predict that a mutation will not bypass prophylactic requirements
because you cannot predict which mutations will happen and when. As a
result, I suggest that the real problem is to limit the number of
locations to those where prophylactic mechanisms are fairly strong,
and monitored for failure.

>Using a partially or fully synthetic platform for core
> machinery has advantages because the modified core replication
> requirements cannot be be found naturally. A recent suggestion is the
> orthogonal systems to lessen unexpected interactions, as suggested in
> this Nature article:http://www.nature.com/news/2010/100120/full/463288a.html
> "To transcribe DNA into RNA, the team uses a polymerase enzyme that
> recognizes genes only if they have a specific promoter sequence that
> is not present in the cell's natural genes. Similarly, the system's
> orthogonal 'O-ribosomes', which translate RNA into protein, can read
> only 'O-mRNA' that contains a specific sequence, and O-mRNA is
> unreadable by natural ribosomes."

Ok, that sounds good in principle, but what I wonder about, is how
easily a mutation can knock-out the promoter sequence, and so, make
the RNA readable by natural ribosomes.

> Each synthetic assembly part could raise the improbability of genetic
> or chemical element exfiltration by a fold-factor, by creating a
> platform of artificial nutrient/ribosome/polymerase scarcity for the
> bacteria or yeast organism and contributes to a more secure
> microenvironment. The aspect of synthetic biology's "uncommon"
> presence in nature can be used in a advantageous way because it limits
> its migration potential based on the artificially modified nutrients
> that have been localized in the growth medium that are needed for
> survival. In other words, if an ordinary bacteria can survive on
> glucose and water, a synthetic bacteria that can only survive on a
> rare, artificially-made or artificially-prepared organic compound that
> isn't edible to any other natural organism, that synthetic organism
> would not be able to stray from the food source (manually-added) and
> survive if its food source can't be naturally found.
>

Ok, so this is a little like the arsenic phosphate switch found in
some high arsenic environments? The only way to spread the micro-
organism, is to spread the specific environment it is based on?


> Giovanni

[Giovanni Lostumbo]

The E.coli was cited only in quotations of a publication, of which I
only mentioned to borrow concepts from, because of the ability of
bacteria to produce a polymer, not a conducting polymer, seemed
relevant, but that's not the same as suggesting that I want to use
E.coli to do that. I I can see the confusion. My writings are very
dense and interdisciplinary (Many of my concepts are suggesting to
test and apply meta-ideas to other fields) That paper is here:

"Users of 3D printers such as the RepRap that use polylactic acid
> (PLA) have potentially an inexpensive and robust way of harvesting the
> bioplastic as has been reported: "Biosynthesis of polylactic acid and its
> copolymers using evolved propionate CoA transferase and PHA synthase" (Nov
> 2009) and "Metabolic engineering of *Escherichia coli* for the production
of
> polylactic acid and its copolymers" (Nov 2009)."
http://blog.reprap.org/2009/11/bugs-brew-pla-direct.html
http://www3.interscience.wiley.com/journal/123188458/abstract
http://www3.interscience.wiley.com/journal/123188463/abstract
From the first link: "However, they are presented as granules in the
e.coli, it is not deposited. The researchers lysed the cells and used
a centrifuge to extract them. On top of that the PLA was identified
with mass spec, so I'm not sure what the purity is like."

Thus, what I would want to borrow from that technique towards a
hybridization with the techniques behind this paper:
http://x-journals.com/2010/microbes-reprogrammed-to-ooze-oil-for-renewable-biofuel/

is exploring membrane secretion of polymers, to understand how
conducting monomers of polypyrrole can polymerize, and how to achieve
a high degree of polymerization for it to become insoluble in water as
Dr. Albert Mihranyan has replied. Alternatively, if there is a
mechanism to line up bacteria or yeast in a row so they simltaneously
secrete monomers, which are readily polymerized with enzymes designed
for the lattice of polypyrrole (or the conducting polymer of
interest).

This is a bit like searching for two completely brand new techniques,
and applying discrete, modular parts to a new cell system/factory that
allows two isolated machinery aspects (biosynthesis and membrane
secretion) to be combined to produce a new function- secreting not oil
for renewable biofuel, but a polymer, and thirdly, a conducting one.

"but what I wonder about, is how
> easily a mutation can knock-out the promoter sequence, and so, make
> the RNA readable by natural ribosomes."

That is something I plan to look into too and I discuss that below.

> Ok, so this is a little like the arsenic phosphate switch found in
> some high arsenic environments? The only way to spread the micro-
> organism, is to spread the specific environment it is based on?

Correct, that sounds like an applicable analogy. From that recent
news, phosphate in the DNA backbone apparently is replaced with
arsenic at rates of up to 11%, in addition to lipids and ATA
(adenosine-tri-arsenate?) The analogy works even without using arsenic
(i.e. a silicon based organism instead of carbon, though that hasn't
been observed) If knocking out an amino acid synthase, thus requiring
addition of amino acids such as L-glutamine (or proline/arginine,
etc), then natural uptake of a plasmid or lysed bacteria that contains
Glutamine synthetase on a auto-(self-excising)-transposon in the
genome/plasmid it would be less likely.

"I suggest that the real problem is to limit the number of
> locations to those where prophylactic mechanisms are fairly strong,
> and monitored for failure."

"That's what I was referring to when I wrote:

"I would look to the history of biologically-produced
pharmaceuticals, transgenic organisms/crops, and such compounds
produced by bacteria- antibiotics, insulin, etc, for guidance as to
the likelihood of a microbe escaping a bioreactor factory and
hybridizing with non-GMOs. I think some safeguards could be used such
as using less than minimal media, which could prevent the growth of
the bacteria unless certain minerals were added manually, rather than
automatically."

Using combinatorial/permutational genetic BioBrick parts could
decrease the mutation count.
There are computational mechanisms that I studied, such as the
likelihood of a point-mutation as a function of the number of base
pairs, and the repair accuracy of the DNA polymerase's error checking
subunits. If I recall correctly, they're in the 1x10^-6 range:

"In general, the mutation rate in eukaryotes and bacteria the rate is
roughly 10-8 per base pair per generation[4]. The highest mutation
rates are found in viruses, which can have either RNA or DNA genomes.
DNA viruses have mutation rates between 10-6 to 10-8 mutations per
base per generation, and RNA viruses have mutation rates between 10-3
to 10-5 per base per generation[4]. Human mitochondrial DNA has been
estimated to have mutation rates of ~3×10-6 or ~2.7×10-5 per base per
20 year generation (depending on the method of estimation)[5]; these
rates are considered to be significantly higher than rates of human
genomic mutation at ~2.5×10-8 per base per generation[1]. Using data
available from whole genome sequencing, the human genome mutation rate
is similarly estimated to be ~1.1×10-8 per site per generation [6].

RNA has a drastically higher mutation rate than DNA because of several
DNA repair systems that can correct changes before they become fixed
in the genome as mutations.[7]"
http://en.wikipedia.org/wiki/Mutation_rate
Those mutations would have to be addressed for each susceptible gene
at risk of mutation towards having genetic and organismal
transferrability to other (external) microenvironments.

Combining abiotic conditions with some synthetic parts could decrease
the mutation rate, though I'm not sure if that number would have to be
extreme (e.g 10^-90 or 10^-900+) as a many-fold reduction, but I'm
very curious as to what computational biology can integrate into it
and if such algorithms are used by industries that use bacteria/yeast
to yield synthetic/natural compounds.

[Giovanni Lostumbo]

*(e.g 10^-90 or 10^-900+) isn't in reference to improving the DNA
repair accuracy of the polymerase, though that could be done while
reaching some enzymatic limits
, but rather the unlikelihood that all propylactics were bypassed
(e.g. ten x10^-9 prophylactic modifications to one of: genome(5) +
media (4)=10^-900 if that's applicable)

On Dec 29, 1:20 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>
wrote:

>  The E.coli was cited only in quotations of a publication, of which I
> only mentioned to borrow concepts from, because of the ability of
> bacteria to produce a polymer, not a conducting polymer, seemed
> relevant, but that's not the same as suggesting that I want to use
> E.coli to do that. I I can see the confusion. My writings are very
> dense and interdisciplinary (Many of my concepts are suggesting to
> test and apply meta-ideas to other fields) That paper is here:
>
>  "Users of 3D printers such as the RepRap that use polylactic acid> (PLA) have potentially an inexpensive and robust way of harvesting the
> > bioplastic as has been reported: "Biosynthesis of polylactic acid and its
> > copolymers using evolved propionate CoA transferase and PHA synthase" (Nov
> > 2009) and "Metabolic engineering of *Escherichia coli* for the production
> of
> > polylactic acid and its copolymers" (Nov 2009)."
>

> http://blog.reprap.org/2009/11/bugs-brew-pla-direct.htmlhttp://www3.interscience.wiley.com/journal/123188458/abstracthttp://www3.interscience.wiley.com/journal/123188463/abstract

> From the first link: "However, they are presented as granules in the
> e.coli, it is not deposited. The researchers lysed the cells and used
> a centrifuge to extract them. On top of that the PLA was identified
> with mass spec, so I'm not sure what the purity is like."
>
> Thus, what I would want to borrow from that technique towards a

> hybridization with the techniques behind this paper:http://x-journals.com/2010/microbes-reprogrammed-to-ooze-oil-for-rene...

> ...
>
> read more »

[Giovanni Lostumbo]

Speciation and divergence on proteobacteria is not something I'm
knowledgeable in, so whether horizontal gene transfer and conjugation
are with bacteria high arsenic conditions still requires scrutiny, so
the analogy in that sense wouldn't apply to genes or cell contents in
arsenic dependent organisms, yet when lysed or conjugated are
components discrete from arsenic substitution (e.g. one promoter/
operon on an arsenic rich genome may not have arsenic on any of its
base pairs, and could be transposed to a nearby microenvironment where
that DNA is transposable).

On Dec 29, 1:27 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>

wrote:
> *(e.g 10^-90 or 10^-900+) isn't in reference to improving the DNA
> repair accuracy of the polymerase, though that could be done while
> reaching some enzymatic limits
> , but rather the unlikelihood that all propylactics were bypassed
> (e.g. ten x10^-9 prophylactic modifications to one of: genome(5) +
> media (4)=10^-900 if that's applicable)
>
> On Dec 29, 1:20 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>
> wrote:
>
> >  The E.coli was cited only in quotations of a publication, of which I
> > only mentioned to borrow concepts from, because of the ability of
> > bacteria to produce a polymer, not a conducting polymer, seemed
> > relevant, but that's not the same as suggesting that I want to use
> > E.coli to do that. I I can see the confusion. My writings are very
> > dense and interdisciplinary (Many of my concepts are suggesting to
> > test and apply meta-ideas to other fields) That paper is here:
>
> >  "Users of 3D printers such as the RepRap that use polylactic acid> (PLA) have potentially an inexpensive and robust way of harvesting the
> > > bioplastic as has been reported: "Biosynthesis of polylactic acid and its
> > > copolymers using evolved propionate CoA transferase and PHA synthase" (Nov
> > > 2009) and "Metabolic engineering of *Escherichia coli* for the production
> > of
> > > polylactic acid and its copolymers" (Nov 2009)."
>

> >http://blog.reprap.org/2009/11/bugs-brew-pla-direct.htmlhttp://www3.i...

> ...
>
> read more »

[Giovanni Lostumbo]

from: http://x-journals.com/2010/microbes-reprogrammed-to-ooze-oil-for-renewable-biofuel/

Liu realized that if cyanobacteria could be cajoled into overproducing
fatty acids, their accumulation within the cells would eventually
cause these fatty acids to leak out through the cell membrane, through
the process of diffusion. To accomplish this, Liu introduced a
specific enzyme, known as thioesterase, into cyanobacteria.

Photosynthetic microbes called cyanobacteria offer attractive
advantages over the use of plants like corn or switchgrass, producing
many times the energy yield with energy input from the sun and without
the necessity of taking arable cropland out of production. (Biodesign
Institute, Arizona State University)

Photosynthetic microbes called cyanobacteria offer attractive
advantages over the use of plants like corn or switchgrass, producing
many times the energy yield with energy input from the sun and without
the necessity of taking arable cropland out of production. (Biodesign
Institute, Arizona State University)

The enzyme is able to uncouple fatty acids from complex carrier
proteins, freeing them within the cell where they accumulate, until
the cell secretes them. “I use genes that can steal fatty acids from
the lipid synthesis pathway,” Liu explains noting that thioesterase
acts to efficiently clip the bonds associating the fatty acids with
more complex molecules. "

"...A second series of modifications enhances the secretion process,
by genetically deleting or modifying two key layers of the cellular
envelope—known as the S and peptidoglycan layers—allowing fatty acids
to more easily escape outside the cell, where their low water
solubility causes them to precipitate out of solution, forming a
whitish residue on the surface. Study results show a 3-fold increase
in fatty acid yield, after genetic modification of the two membrane
layers.

To improve the fatty acid production even further, the group added
genes to cause overproduction of fatty acid precursors and removed
some cellular pathways that were non-essential to the survival of
cyanobacteria. Such modifications ensure that the microbe’s resources
are devoted to basic survival and lipid production."

This approach seems to suggests that if the bacteria were programmed
not to replicate (removing cell-division machinery perhaps like
keeping a eukaryote cell in G1 phase but maybe with prokaryotes?
Yeast, again is an option), mutations theoretically would not occur
because cell-division wouldn't be induced because all of the
production of a compound would occur in the parent generation. The
cells wouldn't divide- they'd only be devoted to "survival and lipid[/
compound of interest] production" as described above.

On Dec 29, 1:49 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>

> ...
>
> read more »

[Cathal Garvey]

This thread is very much "Too long, didn't read" for me, I'm afraid. But I will add some thoughts I often have about mutation rate.

Mutation rate in DNA is kept in check by DNA mismatch repair and by having careful polymerases. Diploid organisms also have comparisons between their different alleles as an option in cases of catastrophic damage.

For evolution to occur at any appreciable rate, these systems must be imperfect. In other words there cannot be a perfect natural DNA copying mechanism, or the organism would be unable to adapt and would rapidly go extinct.

This leaves the question of how accurate DNA synthesis can be in principal as a very open issue. It is very possible we could reduce or effectively eliminate mutation and evolution in synthetic organisms.

That's all I have to add for now! :)

> knowledgeable in, so whe...

> ...
>
> read more »

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[Giovanni Lostumbo]

"As a result, students may leave an introductory biology course with
the ability to recite the reactions in the Calvin cycle but still
believing that plants obtain most of their mass from the soil rather
than from the atmosphere, that plants photosynthesize but do not
respire, or that the mass of a decomposing organism will primarily
return to the soil."
http://news.slashdot.org/story/11/01/07/1833206/College-Students-Lack-Scientific-Literacy

I'm interested in how microrganisms and their byproducts return to the
biosphere cycle.
"With the growing recognition of the importance of collective
phenomena in evolution especially[10–13], but also in ecology[14–18],
immunology[19, 20], microbiology[21–23] and even global climate
change[24–26], it is timely to assess the extent to which a condensed
matter physics perspective—with its unifying principles of collective
behavior arising from interactions—can be illuminating in biology."
http://arxiv.org/abs/1011.4125

On Dec 29 2010, 2:23 pm, Giovanni Lostumbo
<giovanni.lostu...@gmail.com> wrote:
> from:http://x-journals.com/2010/microbes-reprogrammed-to-ooze-oil-for-rene...

> > > >  "Users of 3D printers such as theRepRapthat use polylactic acid> (PLA) have potentially an inexpensive and robust way of harvesting the

> ...
>
> read more »

[Giovanni Lostumbo]

And how Entropy/The Second Law of Thermodynamics might fit into this.
(e.g. if it doesn't return to the biosphere, or in a partial/alternate
way)

On Jan 7, 2:10 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>
wrote:

> "As a result, students may leave an introductory biology course with
> the ability to recite the reactions in the Calvin cycle but still
> believing that plants obtain most of their mass from the soil rather
> than from the atmosphere, that plants photosynthesize but do not
> respire, or that the mass of a decomposing organism will primarily

> return to the soil."http://news.slashdot.org/story/11/01/07/1833206/College-Students-Lack...

> ...
>
> read more »

[Giovanni Lostumbo]

On Jan 7, 2:22 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>

> ...
>
> read more »

[Giovanni Lostumbo]

On Jan 7, 3:39 pm, Giovanni Lostumbo <giovanni.lostu...@gmail.com>

> ...
>
> read more »

[Cathal Garvey]

...is there any new text here not already quoted twice? I'm afraid I'm seeing nothing but quoted text?

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[Giovanni Lostumbo]

Hi Cathal, Sorry, I just renamed the subject because the title was funny, but I wanted to change it back to it's original topic.