

'Artificial life' breakthrough announced by scientists - blogimus
http://news.bbc.co.uk/2/hi/science_and_environment/10132762.stm

======
phaedrus
This is surprisingly like the first step you'd take if you were about to start
hacking the firmware on an embedded board: before you change bits, you upload
a known good firmware to prove your programming process is working correctly.

~~~
JeanPierre
But the next steps looks more like software on a computer: You'll have to fix
all those compilation-errors on first run, then look out for bugs in the
software. Finally, when you ship the software, people use it and report other
bugs. And since you can't update running processes at the current moment, you
need to terminate and replace it.

------
glymor
Better write up: [http://arstechnica.com/science/news/2010/05/first-
functional...](http://arstechnica.com/science/news/2010/05/first-functional-
synthetic-bacterial-genome-announced.ars)

~~~
rms
Or <http://www.sciencemag.org/cgi/content/full/328/5981/958>

~~~
raimondious
My favorite part from that article:

 _So that the assembled genome would be recognizable as synthetic, four of the
ordered DNA sequences contained strings of bases that, in code, spell out an
e-mail address, the names of many of the people involved in the project, and a
few famous quotations._

~~~
Evgeny
I guess sooner or later the random mutations may make these string
"corrupted".

~~~
Devilboy
I hope they included checkbits!

~~~
zackattack
it may be a misconception but i think that checkbits are a feature of organic
dna?

~~~
biotech
Yep! There is some error-checking built into dna-replication. The protein that
does the replication is called DNA Polymerase. From its wikipedia article:

Error correction is a property of some, but not all, DNA polymerases. This
process corrects mistakes in newly-synthesized DNA. When an incorrect base
pair is recognized, DNA polymerase reverses its direction by one base pair of
DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base
pair to be excised (this activity is known as proofreading). Following base
excision, the polymerase can re-insert the correct base and replication can
continue.

------
jamesbritt
Gripe: "artificial life" already has a somewhat lengthy history of usage,
referring to emulating biological activity or traits in software or hardware.
It's often shortened to just alife or a-life.

It's related to genetic algorithms, genetic programming, and the like.

It would be nice if the using-real-chemicals-and-alive-stuff hacking were
called "synthetic life", or something to distinguish it from existing
terminology.

~~~
nooneelse
That use maybe should have been "simulated life" all along, so as to be more
exact. This is a living organism that is artificially made, "artificial life"
applies to it just as much as the other subject. Though the more specific
terms that capture the way in which their somethings are artificial are good
too.

~~~
jamesbritt
'This is a living organism that is artificially made, "artificial life"
applies to it just as much as the other subject.'

Maybe. But if you end up with a living organism, then that it's not artificial
life; it's life (albeit artificially manufactured) . Whereas the software
stuff is never anything but artificial.

Long run I'd expect anything that's alive to be called life, regardless of the
process that lead to it.

------
orblivion
Call me a luddite, genetic engineering gives me the willies.

~~~
bh42
Luddite.

In all seriousness, the dangers brought up in the article can only come from a
person lacking significant knowledge of bacteria.

Unimaginable numbers of bacteria permeate every part of the world, including
miles within the earth, deep sea volcanic vents, radioactive waste, the rain
drops falling on our heads, and us, up our noses, in our skin pores, our guts,
etc.

Those simple bacteria evolve at staggering rates, and swap genes like DJ
Danger Mouse mixing tracks.

Any new synthetic, or extraterrestrial, or magical, life form would have to
compete. And unless you believe in magic it is unlikely to out-compete in a
pre-existing niche.

The grey goo danger often thrown at nano-tech, is possible only if we violate
one or more of the basic laws of thermodynamics.

And when it comes to antibiotic resistant bacteria, well we are already doing
a great job of breeding those within ourselves.

But if you grew a barrel full of MRSA and then poured it down your toilet, the
SA wold quickly lose its metabolically expensive MR. Because there is no
Methicillin in the sewer, the resistance to Methicillin is a disadvantage. And
the only way the Staphylococcus aureus could survive is if it dumped this
feature.

But luckily you're probably taking antibiotics so you are a niche where MRSA
can out-compete and thrive.

~~~
WilliamLP
> And unless you believe in magic it is unlikely to out-compete in a pre-
> existing niche.

Cars are faster than land animals. Planes are faster than birds. Not being
constrained by needing to have come from slow gradual iteration might open
some possibilities, some terrifying. Biology doesn't produce the wheel.

To consider this as a possibility is not to believe in magic.

~~~
CWuestefeld
> Cars are faster than land animals. Planes are faster than birds.

There's no comparison.

I'm sitting here looking out the window at my car, and there are caterpillars
out there that are moving faster than it. Not only that, but that caterpillar
can refuel itself. And it'll turn itself into new ones next year. In the
meantime, my car will sit and rust.

Really, it's the height of hubris to think that we can engineer something that
works as well as what untold generations has evolved.

(And I'll apologize for the tangent, but this is also the fatal conceit of
those who believe that any central authority can manage our economy any better
than the market can on its own.)

~~~
weavejester
_"Really, it's the height of hubris to think that we can engineer something
that works as well as what untold generations has evolved."_

Why? Technological progress through logical deduction is patently more
efficient than evolution through natural selection. Modern technology has
already far surpassed the capabilities of natural organisms in a number of
areas, all within a geologically minute timespan.

Just because a caterpillar can self-replicate, doesn't make it better than a
car in every single respect, otherwise we'd be riding caterpillars to work. In
terms of self-replication and regeneration, nature has us beat (for now). But
if you want to send packets of information halfway around the globe, there is
no biological process that comes anywhere close to our technological
capability.

 _"(And I'll apologize for the tangent, but this is also the fatal conceit of
those who believe that any central authority can manage our economy any better
than the market can on its own.)"_

But it can, or at least, a market with regulatory oversight is more efficient
than a completely unregulated market place.

Natural environments and unregulated markets suffer from very similar
problems. They don't magically gravitate toward the most efficient solution;
very often they'll do incredibly stupid things that would leave an intelligent
observer scratching their head.

However, natural selection does produce very _robust_ ecosystems, which is why
life has flourished for millions of years, and why caterpillars will outlast
your car.

Logically, the best approach is to combine natural selection with intelligent
oversight. Left to its own devices, an unregulated market has a tendency to
fall into traps which benefits an individual or subgroup for a short time, but
disadvantages the market in the long run. The Prisoner's Dilemma, the Tragedy
of the Commons and the Market of Lemons are all common effects that can be
circumvented by intelligent regulators, but would cause great damage to any
market left to its own devices.

~~~
bh42
_Modern technology has already far surpassed the capabilities of natural
organisms in a number of areas, all within a geologically minute timespan._

They key words here are: "in a number of areas"

In a number of areas indeed. Can a plane fly without oil drillers, oil
refiners, fuel trucks, and jet fuel?

Or in a more generalized form: For some X, thing Y is better at X.

Having said that, I in no way belong to those people who think that nature is
magical and humans can never do better.

We can quite easily make incremental improvements some of the time.

Note that I consider it an improvement if it still does everything else
equally well and some new things better.

If on the other hand, it can't do some things, then it is only useful in _a
number of areas_.

So a plane is not an improvement on a bird, but a bird immune to some
pesticide would be an improvement IF that immunity didn't have a huge cost.

Or we can say it's better only when lots of that pesticide is in its
environment and worse otherwise.

~~~
jacquesm
I think quoting oil drillers is not really opportune at the moment if you want
to give an example of how the damage from technology is going to be 'limited'.

~~~
bh42
See there's thing thing called an apple and this other thing called an orange.

And there's this discussion about artificial and natural micro organisms
competing in the same niche. Like using light energy to capture CO2 for
example.

And then there's oil drillers.

------
eduardoflores
Announcement here [http://www.jcvi.org/cms/research/projects/first-self-
replica...](http://www.jcvi.org/cms/research/projects/first-self-replicating-
synthetic-bacterial-cell/overview/) with the press release, a FAQ and some
fact sheets (and the video is promised to be available soon)

------
danielharan
So when do we get dinosaurs?

------
stavrianos
they've got root

------
mortenjorck
DNA: Now jailbroken.

------
tocomment
Here are my questions about this, hope you smart folks don't mind chiming in:

How do you physically put DNA into a cell? A very small needle? Or is there
something fancier?

How were the synthesized pieces of DNA produced? Very tiny robotic hands
pushing the molecules together in the right sequence?

How did they stitch together the synthesized pieces of DNA? What would say
which pieces go with which?

~~~
aheilbut
Bacteria will often take up DNA from their environment, and this ability,
called "competence" is widely used in molecular biology. In this case, they
treated the cells with a chemical called polyethylene glycol, which increases
the efficiency by which the cells can pick up the DNA molecules. The procedure
for transplanting genomes was described by the same group in a paper in 2007.
It is possible to use a small needle ("DNA microinjection") to inject DNA into
cells; one can also use an electric field to disrupt the cell membrane and
force DNA into a cell, which is called electroporation. In this case though,
the PEG transformation was sufficient (and because these artificial
chromosomes were so large, they might not survive being shot through a needle
or zapped with electricity too well).

The initial pieces of DNA (oligonucleotides) are synthesized chemically - the
components are added to a reaction one at a time, and the reaction is
controlled so that at each step, only one base gets added. There is a lot of
chemistry optimization and QC to be able to make relatively long fragments
accurately. They ordered the building block pieces (1080 bases long) from a
company called Blue Heron, which specializes in putting together long DNA
molecules.

The sequences were designed to be partially overlapping, so that the
complementary sequences could fit together. Overlapping pieces of DNA can be
combined by a process called homologous recombination. There is existing
machinery in the yeast cells that they used to join together such
complementary sequences. The molecules were assembled hierarchically, so they
first made 10kb fragments, then put 10 x 10kb together to make 100kb
fragments, and then finally put the 10 100kb fragments together. The
overlapping sequences at the ends determined which fragments will stick
together.

~~~
tocomment
Wow thanks. That explains a lot.

What's PEG? The electrical method you mentioned?

So if the DNA pieces overlapped did that overlapping base pairs somehow get
removed when the pieces were joined? Otherwise I'd think the next final DNA
sequence would look a lot different from what they were intending to copy.

~~~
aheilbut
PEG is the abbreviation for PolyEthylene Glycol. Just a chemical they add that
makes the transformation work more efficiently.

DNA, as you probably know, is a double-stranded molecule, and the strands have
complementary sequences. When the overlapping pieces are joined, one strand of
one molecule overlaps with its complement on the other piece, and vice versa -
the pieces aren't just joined end-to-end.

see <http://en.wikipedia.org/wiki/Homologous_recombination> for all the
details.

------
cb18
Perspective:
[http://www.theatlantic.com/science/archive/2010/05/ventners-...](http://www.theatlantic.com/science/archive/2010/05/ventners-
not-all-that/57046/)

(I am not currently well-informed enough in this area to either advocate or
not this perspective, just providing it.)

------
MikeCapone
This is a huge deal, and I'm not surprised to see that Craig Venter had
something to do with it. Kudos!

~~~
joe_the_user
This is a nice step for technology and a _really_ huge deal for human culture
and religion.

A certain _Someone_ said once "Let the earth put forth vegetation, plants
yielding seed, and fruit trees bearing fruit in which is their seed, each
according to its kind, upon the earth."

That certain Someone later said: "Behold, man has become like one of us..."

~~~
metamemetics
I can't decipher which English-speaking reader of the New Revised Standard
Edition post 1989 you are referring to, _how elusive_!

------
yu
Nature article
[http://www.nature.com/news/2010/100520/full/news.2010.253.ht...](http://www.nature.com/news/2010/100520/full/news.2010.253.html)

Nature asks and eight experts comment on significance
[http://www.nature.com/news/2010/100520/full/news.2010.255.ht...](http://www.nature.com/news/2010/100520/full/news.2010.255.html)

------
sheldonwt
Advancements like this make it feel exciting to be young and have so much time
ahead of you. The future is bright. Science is key.

~~~
jjs
_Advancements like this make it feel exciting to be young and have so much
time ahead of you._

What, you're still using your original telomeres?

------
zokier
This is awesome. Literally, awe inspiring. We now have a compiler for the code
which is DNA. Now we just need a "Hello, world!" app :)

~~~
jacquesm
We'll see if it is awesome, if the compiler is buggy it might turn out to
create a 'killall' app instead.

This is great news, but with this new power comes also a very large
responsibility.

------
dmn001
very informative video on guardian from Craig Venter:
[http://www.guardian.co.uk/science/2010/may/20/craig-
venter-s...](http://www.guardian.co.uk/science/2010/may/20/craig-venter-
synthetic-life-form)

------
itistoday
Oddly enough this makes me feel a bit impotent. Here I am playing with my 1's
and 0's... like a caveman. :-p

~~~
Anon84
You're using base 2 (0 and 1), they are using base 4 (A, G, C and T)... Not
that different, really.

~~~
dublinclontarf
Could this mean a step towards biological computers?

------
amichail
They just copied the genome of an existing micro-organism.

Making changes to the genome to accomplish some task is much harder to do.

~~~
geebee
You're probably getting negged because you appear to be disparaging the
accomplishment. But yeah, they did copy over an existing dna structure, they
didn't create one from scratch.

However, the scientists did (according to the arstechnica article, posted
above) have to remove a section of the DNA (something to do with the bacterium
cutting DNA originating in yeast into small pieces... sigh, wish I understood
this sort of thing). So they did actually make modifications to the genome, I
think...

~~~
raimondious
To be disappointed that they used existing DNA to do this is uninformed. We
are _so_ far away from synthesizing a completely novel form of life from
scratch. This step is needed before we ever get close to designing our own
cell — it's the leap from using hand tools to CNC.

~~~
geebee
I agree that disappointment in this accomplishment is crazy, it's an amazing
feat

That said, people can sometimes go batty and start thinking something was
achieved when it wasn't. I think it's reasonable to clarify that this isn't a
full realization of "artificial life" just yet (though it clearly is a partial
realization, as the scientists did alter the genome (also, apparantly they
removed potentially disease-inducing strands of DNA, according to the
NYTimes). The poster who got negged expressed this distinction in a fairly
dismissive fashion that appeared to disparage the achievement. But you should
be able to point out (diplomatically, one would hope)that a monumental
achievement isn't an even more monumental achievement without being accused of
minimizing the achievement itself!

------
run4yourlives
Mandatory:
[http://www.reddit.com/r/science/comments/c6dea/synthetic_lif...](http://www.reddit.com/r/science/comments/c6dea/synthetic_life_breakthrough_announced_by/c0qeydc)

~~~
michael_nielsen
That comment can safely be ignored. It makes lots of vague accusations about
Venter, and one concrete accusation - that Venter is responsible for patents
on genes involved in breast cancer. That accusation is wrong: it's a reference
to the BRCA patent by Myriad genetics, which has nothing to do with Venter.

