
First life with 'alien' DNA - jamesbritt
http://www.nature.com/news/first-life-with-alien-dna-1.15179
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kjhughes

      “If you read a book that was written with four letters, you’re not
      going to be able to tell many interesting stories,” Romesberg
      says. “If you’re given more letters, you can invent new words, you
      can find new ways to use those words and you can probably tell more
      interesting stories.”
    

He needs a better way to motivate his work to a lay audience without losing
those whose immediate response will be dismissive because binary can tell
interesting stories in two letters.

~~~
kyberias
That quote sounds rather silly, I agree, but if you think about it, these
results don't have too many immediate applications or benefits that would
resonate with a layman. Therefore it's challenging to try and explain the
importance of this achievements to a wider audience. In this light, I kind of
understand the book example.

~~~
toufka
Honestly, it actually is a pretty good example, but you need to be creative.

If I tell you that your book can only have 26 characters, you'll say, 'great,
who cares, that's the whole alphabet'.

But imagine the books you cannot write: No punctuation, no foreign languages,
no mathematics, no accents, etc. Give yourself an escape character, and all of
a sudden, you have access to a LOT more creativity.

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sanxiyn
Since the actual paper is paywalled, can someone answer this question?

This paper uses d5SICS-dNaM base pair. How does it compare to dZ-dP pair in
the following paper? I checked that two pairs are different.

Enzymatic incorporation of a third nucleobase pair. (2007)
[http://www.ncbi.nlm.nih.gov/pubmed/17576683](http://www.ncbi.nlm.nih.gov/pubmed/17576683)

~~~
tomkinstinch
The major accomplishment of the paper referenced in the original article is
that they demonstrated the feasibility of unnatural bases in vivo. The work in
the Yang, et. al. paper occurred in vitro, whereas the Malyshev paper was in
an E. coli system. Malyshev, et al. noticed that the unnatural bases were
being degraded in the space between inner and outer cell membranes
(periplasm), so they added a membrane transport protein to import the
unnatural bases into the cell. From there, the E. coli was able to incorporate
the unnatural bases into replicates of an introduced DNA segment (plasmid)
using its endogenous replication machinery. They also demonstrated that the
unnatural bases were not a hinderance to growth, and they they were not
excised by the DNA repair enzymes.

There have been other papers demonstrating the use of unnatural bases in
various cases in vitro (some cited in the paper), but this is notable because
it is a thorough example of use in vivo. Peter Schultz has done similar work,
as well as exciting work on unnatural bases in tRNA.

The bases in the Yang paper and those in the Malyshev paper both exhibit
Watson-Crick bonding geometry, and pair by hydrogen bonding. One distinction
of those mentioned in the Malyshev paper is the presence of a sulfur
substituent, though there is no mention of its participation in the bond.

------
CrLf

      "Malyshev sees the ability to control the uptake of
       foreign DNA bases as a safety measure that would prevent 
       the survival of alien cells outside the lab, should they 
       escape."
    

This reminds me of that line from Jurassic Park where Ian Malcom says: "I'm
simply saying that life, uh... finds a way."

Anyway, this is interesting in the sense that perhaps the role of humanity in
the big picture of life evolution is to do exactly this kind of thing...

~~~
trhway
if we can imagine each civilization to have its own "black box" what would be
typical last words recorded by it?

"ability to control the uptake of foreign DNA bases as a safety measure that
would prevent the survival of alien cells outside the lab, should they escape.
But other researchers, including Benner, are trying to engineer cells that can
make foreign bases from scratch, obviating the need for a feedstock"

sounds like a darn good candidate :)

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techwatching
Is there some behaviour that can't be coded with natural base pairs?

~~~
tomkinstinch
In addition to the applications mentioned by toufka, one would be data
storage.

There has been some work[1] done on using DNA as a medium of high-density
self-replicating storage for digital data, and it would be exciting to have
another couple bases to work with.

1\.
[http://www.nature.com/nature/journal/vaop/ncurrent/nature118...](http://www.nature.com/nature/journal/vaop/ncurrent/nature11875/metrics/news)

~~~
JunkDNA
What would be exciting is if the bases had properties that made them amenable
to easy read operations using non biological means. Currently it takes 1 - 3
days fort a DNA sequencer to read what is effectively a few gigabytes of data
in a human DNA sequence. That is painfully slow for any practical use. However
if we had DNA bases that had atomic properties that could interact with some
sort of electronic device, we might be able to engineer a sequencer that is
quite easy and cheap. In fact, we might even be able to design an enzyme that
translates regular DNA into a synthetic form for easy sequencing (similar to
how RNA polymerase turns DNA to RNA)

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hrjet
Is there a term for Singularity due to runaway evolution of an artificially
created species?

~~~
toufka
Keep in mind, life has been trying to 'runaway' since it was made. We're
really good at biological warfare. A species from much earlier in our
evolutionary history wouldn't stand a chance against a modern organism. We're
_really_ well optimized. It would be very very difficult for a novel organism
to get a leg up on the few billion years of adaptation we've accumulated, for
this particular environment in which we live.

~~~
meric
"A species from much earlier in our evolutionary history wouldn't stand a
chance against a modern organism [in the modern environment]". I doubt most
species would stand a chance going back in time to an Earth with no oxygen!

------
gweinberg
Four isn't the interesting number, 20 is.

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d64f396930663ee
Ugh, that headline.

~~~
Kequc
It's a good thing they put quotes around 'alien' otherwise I wouldn't have
been tempted to click on it.

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dekhn
Somewhere in La Jolla, Peter Schultz is asking why he's not getting credit for
having done this... years ago.

~~~
cjensen
Assuming Wikipedia describes Schultz's work correctly, this is a different
achievement.

DNA is essentially an instruction set. Each instruction is three base-four
digits (a sequence of three base pairs). A single instruction is either STOP,
START, and for every amino acid there is one or more ADD AMINO ACID TO
SEQUENCE instruction.

Schultz altered the interpretation of some of the ADD AMINO instructions so
that a different, non-natural amino acid is added.

This new creation alters the mechanism by changing from a base-four
instruction set to a base-eight instruction set. As a side benefit, bacteria
based on this new mechanism cannot reproduce in the wild.

~~~
dekhn
The interesting part of schultz's work is the use of modified tRNA adapters.
Personally, I think this is a far more tractable approach.

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callesgg
Currently I would say it seams kind of useless, he could have spent his time
on something better...

~~~
tstactplsignore
Right why doesn't he move to SV and work on Serious Real Problems like how to
get people to click on ads and the latest Laundry As A Service app?

~~~
callesgg
I was thinking more like doing something with the DNA.

To me this seams like adding the letter ö and ä to the English alphabet there
is no need for them. If we put them in the alphabet we still won't use it
cause they have no purpose.

