[Hplusroadmap] Hplusroadmap Digest, Vol 5, Issue 2

Tue Mar 4 17:46:41 CST 2008

Dan,
the idea would be that it's difficult to run designed circuits in a genetic
system because there is so much noise from the endogenous operating system
already there.  If you can minimize that then there is a better chance that
your system will operate as planned.

however, you raise a very good point, why not just try and silence it as
nature does, rather than remove it completely.  I don't know if anyone is
trying that strategy.  could be done in yeast via histone modifications.

cheers,
John

On Tue, Mar 4, 2008 at 1:00 PM, <hplusroadmap-request at heybryan.org> wrote:

> Send Hplusroadmap mailing list submissions to
>        hplusroadmap at heybryan.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://heybryan.org/cgi-bin/mailman/listinfo/hplusroadmap
> or, via email, send a message with subject or body 'help' to
>        hplusroadmap-request at heybryan.org
>
> You can reach the person managing the list at
>        hplusroadmap-owner at heybryan.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Hplusroadmap digest..."
>
>
> Today's Topics:
>
>   1. cellular chassis (Tiago Catarino)
>   2. Re: cellular chassis (Dan Bolser)
>   3. Re: cellular chassis (Bryan Bishop)
>   4. Re: cellular chassis (Bryan Bishop)
>   5. Re: cellular chassis (Dan Bolser)
>   6. Question about current DNA sequencing technology? (Dan Bolser)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 Mar 2008 09:11:00 +0000
> From: "Tiago Catarino" <chromatinpt at gmail.com>
> Subject: [Hplusroadmap] cellular chassis
> To: hplusroadmap at heybryan.org
> Message-ID:
>        <dfdcd80803040111p6802ac38tbcfd1ee2cc6c6d3e at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> In yours opinion which are the minimums cellular components to have a
> human
> cell? If we have different pieces which are the basics one to build a
> functional cell?
>
> Thanks
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://heybryan.org/pipermail/hplusroadmap/attachments/20080304/f67f3d35/attachment.html
>
> ------------------------------
>
> Message: 2
> Date: Tue, 4 Mar 2008 10:29:27 +0100
> From: "Dan Bolser" <dan.bolser at gmail.com>
> Subject: Re: [Hplusroadmap] cellular chassis
> To: "Transhumanist Technical Roadmap" <hplusroadmap at heybryan.org>
> Message-ID:
>        <2c8757af0803040129y3fadfaf3g94cce103d9787631 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On 04/03/2008, Tiago Catarino <chromatinpt at gmail.com> wrote:
> > In yours opinion which are the minimums cellular components to have a
> human
> > cell? If we have different pieces which are the basics one to build a
> > functional cell?
>
> Red blood cells are functional... Don't they lack most of the major
> organelles? They only exist (function) in a pre-existing cellular
> context. This is why the idea of 'function' can be hard to quantify -
> you always need to take context into consideration when you define
> function (re: meaning).
>
> Yeast cells are among the most basic free living eukaryotic (modern)
> cells, AFAIK they have all the same organelles as human cells (as far
> as organelles are defined). However human cells have more specific
> cellular complexes (sometimes called micro-compartments). Not only do
> we have more complexes, the ones we share with yeast are often more
> complex (involving more different proteins).
>
> Other 'simple' modern cells are the obligate intracellular parasites
> (protists). They look very simple, but they are in the evolutionary
> process of discarding all the machinery needed for free living.
>
> Bacteria do all right with much less in the way of cellular machinery.
> Mycoplasma genitalium is the smallest known free living bacteria, with
> about 400 genes (compared to 6000 in yeast / 36,000 in humans).
>
> Frogs have a lot of DNA and some viruses as few as four genes.
>
> Basically, good question! Not sure if any of the above helps. Why not
> look at some 'standard' cell types and identify the common cellular
> components?
>
>
>
> >
> > Thanks
> >
> > _______________________________________________
> >  Hplusroadmap mailing list
> >  Hplusroadmap at heybryan.org
> >  http://heybryan.org/cgi-bin/mailman/listinfo/hplusroadmap
> >
> >
>
>
> --
> hello
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 4 Mar 2008 07:10:09 -0600
> From: Bryan Bishop <kanzure at gmail.com>
> Subject: Re: [Hplusroadmap] cellular chassis
> To: Transhumanist Technical Roadmap <hplusroadmap at heybryan.org>
> Message-ID: <200803040710.09834.kanzure at gmail.com>
> Content-Type: text/plain;  charset="utf-8"
>
> On Tuesday 04 March 2008, Tiago Catarino wrote:
> > In yours opinion which are the minimums cellular components to have a
> > human cell? If we have different pieces which are the basics one to
> > build a functional cell?
>
> http://heybryan.org/mediawiki/index.php/Minimal_cell_project
>
> - Bryan
> ________________________________________
> Bryan Bishop
> http://heybryan.org/
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 4 Mar 2008 07:11:11 -0600
> From: Bryan Bishop <kanzure at gmail.com>
> Subject: Re: [Hplusroadmap] cellular chassis
> To: Transhumanist Technical Roadmap <hplusroadmap at heybryan.org>
> Message-ID: <200803040711.11279.kanzure at gmail.com>
> Content-Type: text/plain;  charset="iso-8859-1"
>
> On Tuesday 04 March 2008, Dan Bolser wrote:
> > Basically, good question! Not sure if any of the above helps. Why not
> > look at some 'standard' cell types and identify the common cellular
> > components?
>
> An interesting methodology would be to do gene-knockout on a
> microarray-like environment for the rapid testing of a few million
> different genomes, knocking out a few genes here, a few there, looking
> for increasingly minimized cells. That work.
>
> - Bryan
> ________________________________________
> Bryan Bishop
> http://heybryan.org/
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 4 Mar 2008 14:35:21 +0100
> From: "Dan Bolser" <dan.bolser at gmail.com>
> Subject: Re: [Hplusroadmap] cellular chassis
> To: "Transhumanist Technical Roadmap" <hplusroadmap at heybryan.org>
> Message-ID:
>        <2c8757af0803040535ma88101evf1bbecf129adf21a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On 04/03/2008, Bryan Bishop <kanzure at gmail.com> wrote:
> > On Tuesday 04 March 2008, Dan Bolser wrote:
> >  > Basically, good question! Not sure if any of the above helps. Why not
> >  > look at some 'standard' cell types and identify the common cellular
> >  > components?
> >
> >
> > An interesting methodology would be to do gene-knockout on a
> >  microarray-like environment for the rapid testing of a few million
> >  different genomes, knocking out a few genes here, a few there, looking
> >  for increasingly minimized cells. That work.
>
> Yup. Some standard studies deal with 'dual knock out lethality' when A
> alone and B alone have 'no phenotype' (non lethal deletions) but AB
> removed together = lethal, then we can assume that A and B are
> functionally coupled. There have been some high throughput studies of
> this kind done in yeast.
>
> Still, why would you want to do this other than from a theoretical
> perspective? i.e. if you don't really care about studying the minimal
> genome, why attempt to produce one at all? What practical use would
> such a construct be that a full genome would not be?
>
> Every tissue type has a 'full' genome, but each tissue type has a
> different function / expresses a different program. While a 'minimal
> linux install' can be practically useful, what practical use is a
> minimal cell?
>
> I am just curious because the emphasis on biohacking seems to be
> practicality rather than theoretical understanding. I don't see any
> immediate practical use for such a system...
>
>
>
> >
> >
> >  - Bryan
> >  ________________________________________
> >  Bryan Bishop
> >  http://heybryan.org/
> >  _______________________________________________
> >
> > Hplusroadmap mailing list
> >  Hplusroadmap at heybryan.org
> >  http://heybryan.org/cgi-bin/mailman/listinfo/hplusroadmap
> >
>
>
> --
> hello
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 4 Mar 2008 15:53:03 +0100
> From: "Dan Bolser" <dan.bolser at gmail.com>
> Subject: [Hplusroadmap] Question about current DNA sequencing
>        technology?
> To: Hplusroadmap at heybryan.org
> Message-ID:
>        <2c8757af0803040653g70039fddl23fd918edc199059 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Sorry for the dumb question, but what is the current 'state of the
> art' DNA sequencing technology? How fast? How accurate?
>
> What is 'next generation' sequencing (in real terms?).
>
> Any info on the wiki?
>
> It would be really great to see a time line of DNA sequencing
> technology ... any links?
>
> I just found out that there is a 'brand new' Solexa machine in the
> building where I work, and to my shame I don't even know what that
> means!
>
> Thanks for any pointers to material that will let me catch up on this
> field.
>
>
> Dan.
>
>
> ------------------------------
>
> _______________________________________________
> Hplusroadmap mailing list
> Hplusroadmap at heybryan.org
> http://heybryan.org/cgi-bin/mailman/listinfo/hplusroadmap
>
>
> End of Hplusroadmap Digest, Vol 5, Issue 2
> ******************************************
>

-- 
John Cumbers,  Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address:  Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://heybryan.org/pipermail/hplusroadmap/attachments/20080304/01fc34d9/attachment-0001.htm 