
Scientists have created a living organism whose DNA is human-made - Osiris30
https://www.nytimes.com/2019/05/15/science/synthetic-genome-bacteria.html
======
olliej
No.

They really didn't.

In this case the claim that it's a fully synthetic genome is fairly suspect,
basically it boils down to this:

A codon is 3 base pairs. Giving 64 possible codons.

Each codon codes for an amino acid except for 3 (I think?) stop codons.

This results in more unique codons than there are amino acids.

As a result some amino acids are represented by different codons.

In this paper all they did (not saying it's nothing, but it's definitely not
what the headline says) was remove that redundancy. Effectively they ran sed
over the genome of E. Coli (I think, I read it this morning which was hours
ago), and replaced every occurrence of an alternative codon with a single
"standard" one. Then they plonked it into an existing cell and it reproduced.

The biggest challenge was probably ensuring the correct construction over the
3 million odd base pairs in their root strain. Note that of 3 million base
pairs, they only made 18000 changes, far from a synthetic genome.

It should not be surprising that given a correct assembly the bacteria
reproduced - by design the experiment only replaced codons with a different
equivalent codon.

~~~
TeMPOraL
> _It should not be surprising that given a correct assembly the bacteria
> reproduced - by design the experiment only replaced codons with a different
> equivalent codon._

I am surprised. I was under the impression that while two codons may code for
an equivalent protein, bacteria do play shenanigans with DNA, like re-reading
the same genome multiple times with shifted read frame. I don't think codon
equivalence is preserved when you shift the read frame by 1 or 2. Moreover, a
DNA molecule with changed codons is slightly different chemically at that
place - which means a protein that might have previously attached there for
some reason now might not.

~~~
sanxiyn
You are right. If you read the paper, they de-duplicated all out-of-phase
(shift 1 or 2) overlapped genes. Simple search and replace wouldn't have been
viable due to these overlapped genes.

~~~
TeMPOraL
Thanks. Should've read the paper before commenting.

~~~
mic47
Actually, your question and followup answer is valuable addition to the
discussion.

------
JakeAl
No, it is not artificial life, they synthesized life from that which already
gave rise to life. This is an important distinction because what they did
involves growing and manipulating existing systems. It's no more artificial
than a an animal which has been bred, this is just on the level of molecular
genetics. If we ever transcend, creating human/"machine" interfaces will
require such technology. No you won't jack in like Neo, no we won't download
our souls and thoughts to a computer, synthetics will replace organics slowly.
The computers and people will meet in the middle.

------
nsxwolf
I will keep moving goalposts until a genome and cell are synthesized atom by
atom.

~~~
kazinator
You just revealed where your goalposts will end up when they stop moving, so
that's effectively where the goalposts are.

~~~
gpm
Maybe he means atom in the original sense of "indivisible particle", in which
case it appears we can count on the physicists to keep moving the goalposts
further ;)

------
kazinator
No. Scientists didn't create the full biochemical environment in which a
genome's meaning is evoked.

~~~
JoeAltmaier
This is so often overlooked. DNA is nothing without the machine to 'run' it.
Which is incredibly complex in itself, more so than the DNA?

~~~
dekhn
there are some DNA enzymes.
[https://en.wikipedia.org/wiki/Deoxyribozyme](https://en.wikipedia.org/wiki/Deoxyribozyme)

------
xedeon
This sounds like the Genesis of the movie Splice.

------
jimworm
No it's not. It could be DRM for the biotech industry though.

------
jhoechtl
Does it reproduce in a non-deterministic way? If so ...

~~~
kumarharsh
Data scientists have a hard time predicting the states and decision paths of a
Neural Network! I doubt we'd even make a serious attempt at predicting
reproduction for life in this millenium (or maybe ever!)

------
millstone
"Life" means splitting hairs finer and finer. Are bacteria alive? Viruses?
Prions? The distinction is ultimately meaningless.

~~~
olliej
Bacteria are alive by all standard definitions of life.

Generally viruses and prions are not considered alive as they are not
(theoretically) capable of self replication.

Viruses don't have any of the mechanisms required for self replication - they
only reproduce if a different organism is coerced into duplicating the virus's
genetic material. Specifically the virus genetic material gains precedence
over the cell's own material once the cell dissolves the protein shell.

Prions are literally misfolded proteins - saying they're alive is not
different from saying any arbitrary polymer is alive - plenty of
polymerization processes essentially have the same construction behaviour:
rely on the bond affinities to morph neighboring identical molecules into
identical construction.

~~~
dekhn
Prions definitely self-replicate. the criterion for life is metabolism
addition to self reproduction

~~~
ncmncm
No, they don't. When they come in contact with another, already synthesized,
protein of identical composition, they alter it to match their own shape. That
is a far cry from replication or reproduction. The other protein has an equal
role, in its readiness to conform.

Other molecules alter the shape of proteins not like themselves, in otherwise
similar ways. We don't call them alive, either. Prions are interesting in that
their action produces more identical action, in an exponentially growing
fashion, unlike other, otherwise similar, processes.

If you like, you could say the prion's shape, itself, reproduces, given a
substrate of conformable prionic proteins. That makes it more like a meme.

~~~
dekhn
I got my phd in biophysics from UCSF, where the prion work was originally
done, and all my professors used the term "replication". That was a colloquial
term for "catalyze a structural transfer in an exponential way". I think that
really does qualify for replication in a limited way.

However, arguing over this terminology is irrelevant.

~~~
ncmncm
Agreed. The exponential character makes it eerily similar to life processes.

I wonder whether anyone has measured temperature reduction in a runaway prion
replication process.

