
‘Minimal’ cell raises stakes in race to harness synthetic life - superfx
http://www.nature.com/news/minimal-cell-raises-stakes-in-race-to-harness-synthetic-life-1.19633
======
dghughes
I wonder would it be possible to accelerate a synthetic cell's evolution via
software?

If you already know exactly what's in the cell (you built it!) could a
computer speed up its life via a software model and jump ahead to something
more complex which you build as version 2?

~~~
toufka
You'd be hard pressed to beat biological evolution...

A liter of e. coli can have upwards of 100s of billions of cells. Which can
double every 90 minutes. Try to run that many instances of a full
environmental simulation in software. That's 1L of bacteria. Scaling that up
to 100L is pretty easy. Try to do that on your super computer...

A straightforward evolutionary experiment to find resistance to an antibiotic
can literally run trillions of trials in a stupid simple overnight culture.
Slowly increase the dose of an antibiotic in a few liters of bacteria over the
course of a day or two and see what survives.

~~~
meric
Perhaps it would be more practical to use biological components to accelerate
software...

~~~
dnautics
As someone who codes and does a lot of wet biology/chemistry... What
calculations would you suggest be accelerated biologically?

~~~
ajuc
Sth paralelizable. Like pathfinding, or factorization.

Could we do a bacteria that reproduces with part of genome changed in
predictable way - like

    
    
        ... 100 ... ---> ... 110 ... -> ... 111 ...
                    \               \-> ... 101 ...
                     \
                      -> ... 010 ... -> ... 011 ...
                                    \-> ... 001 ...
    

And then checks that number in some way and signalizes somehow when it arrived
at solution ? For example by releasing a toxine that kill others and
reproducing without changes from that point on.

If we could, we could beat exponential-time problems in linear time as long as
there's enough space and growth medium :)

~~~
IanCal
The interesting problem you hit is although you suddenly CSV do things in
linear time, you now have an exponential space problem.

So suddenly your problem scales from test tube to swimming pool to ocean
sizes.

~~~
ajuc
Right, so in the end constants matter, and the question is - are bacteries
smaller than computers are fast?

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pak
This article is self-contradictory.

In the second caption: "Each cell of JCVI-syn3.0 contains just 473 genes,
fewer than any other independent organism."

In the main text: "In a 1995 Science paper, Venter’s team sequenced the genome
of Mycoplasma genitalium, a sexually transmitted microbe with the smallest
genome of any known free-living organism, and mapped its 470 genes."

Which is it? Venter would have seemed to disproven his own claim to novelty,
unless we've found new genes in _M. genitalium_ 's genome since 1995.

Edit: As with most biological terms, part of the problem is the fuzziness of
the definition of "gene". More recent studies claim _M. genitalium_ has 525
genes [1], but that might be including tRNA and ncRNA regions. I'd still
object to the article's poor editing. Also, let's get down to brass tacks
here: we've only trimmed a 580kb genome down to 531kb (9% reduction). Clearly,
life is already pretty damn efficient.

[1]
[http://www.cell.com/cell/fulltext/S0092-8674(12)00776-3](http://www.cell.com/cell/fulltext/S0092-8674\(12\)00776-3)

~~~
greeneggs
The figure caption is misleading. By "smallest genome" they mean fewest base
pairs (531,000 base pairs, compared to 580,000 in Mycoplasma genitalium).

~~~
pak
That's not what I'm getting at. If _M. genitalium_ really has only 470 genes
by whatever counting scheme we've chosen, then the claim that "each cell of
JCVI-syn3.0 contains just 473 genes, fewer than any other independent
organism" is simply mistaken.

~~~
marxidad
It's possible that a different counting scheme was chosen for either case.

------
Terr_
Often this topic makes me think of some of the fictional technology present in
Deus Ex, released back in 2000, e.g:

> The cells of every major tissue in the body of a nano-augmented agent are
> host to nanite-capsid "hybrids." These hybrids replicate in two stages: the
> viral stage, in which the host cell produces capsid proteins and packages
> them into hollowed viral particles, and the nanotech stage, in which the
> receiver-transmitter and CPU are duplicated and inserted into the protective
> viral coating. New RNA sequences are transmitted by microwave and translated
> in to plasmid vectors, resulting in a wholly natural and organic process.

------
nsxwolf
Minimal cell, or minimal genome? I don't think we're anywhere near capable of
creating a synthetic cell, minimal or not.

~~~
tosseraccount
Minimal genome ... which also means the minimal viable cell. They are trying
to figure out what is the minimal amount of genes to create a cell that can
survive and reproduce.

Craig Venter, the researcher from the Nature article, claimed to have built
"artificial life" earlier in 2010. The new Nature article is reporting he's
claiming to have made a "new species".

An article on Venter's group's 2010 work:
[https://www.theguardian.com/science/2010/may/20/craig-
venter...](https://www.theguardian.com/science/2010/may/20/craig-venter-
synthetic-life-form) ...

 _" Craig Venter and his team have built the genome of a bacterium from
scratch and incorporated it into a cell to make what they call the world's
first synthetic life form"_

The recent 2016 Science journal article is here :
[http://science.sciencemag.org/content/351/6280/aad6253](http://science.sciencemag.org/content/351/6280/aad6253)

 _" JCVI-syn3.0 is a working approximation of a minimal cellular genome, a
compromise between small genome size and a workable growth rate for an
experimental organism. It retains almost all the genes that are involved in
the synthesis and processing of macromolecules. Unexpectedly, it also contains
149 genes with unknown biological functions, suggesting the presence of
undiscovered functions that are essential for life. JCVI-syn3.0 is a versatile
platform for investigating the core functions of life and for exploring whole-
genome design."_

One question I would have is "Are there homologs to the 149 unknown function
genes in the human genome"?

~~~
kyberias
The original article uses these concepts interchangeably: minimal genome and
minimal cell. They basically define the minimal cell as a cell with a minimal
genome.

E.g. "Because our minimal cell is largely lacking in biosynthesis of amino
acids, lipids, nucleotides, and vitamins, it depends on the rich medium to
supply almost all of these required small molecules."

~~~
dekhn
I don't think it necessarily follows that a minimal genome has the minimal
cell or vice versa. It really depends on how much support structure (the rich
media) is provided and the specific details of how the genome produces the
cell structure, and the cell structure details.

One can imagine little cycles of genes that all need each other, but don't
actually provide any extra fitness. IIRC the Venter method can't identify and
remove those sorts of cyclic dependencies if the cycle is more than 1-2 long.

------
justsaysmthng
> Church says that genome-editing techniques will remain the go-to choice for
> most applications ...

George Church is kind of a sarcastic name for a genetic scientist..

But the ethics question is more open then ever. Didn't you immediately think
about how cool it would be if we could program these organisms to do stuff ? I
did. Could you then program it to become multi-cellular ?

How long before this can be achieved ? 10 years ? 50 ?

However, "Because it’s there" is a worrying motivation to pursue this
knowledge, because the pandora's box it opens is very real.

We're getting closer to the point were we can play God and achieve magical
technological feats.

But are we mature enough to handle the powers that this technology bestows
upon us ? Do we really need this technology now ?

~~~
nsxwolf
The first genetic scientist was a priest so not really...

------
horsecaptin
Hopefully they're not creating something airborne with an unending thirst for
life.

