This thing they call life

[Rüdiger Trojok]

Hey everyone!

I am having some kind of theoretical issue right now, that is that I need to define life.

It is part of a job that I am doing for the Technikfolgenabschätzungsbüro beim Deutschen Bundestag,

discussing the implications of synthetic Biology. Some guy argued that Darwinian evolution is unpredictable

and that only cell free systems should be used for safety reasons – and to trash all other approaches.

I want to explain why cell free systems are nice, but you lose to much of the special functionality of cellular production

by restricting it to that.

So now I am currently trying to update the picture on life and evolution, supplementing it with

recent insights in this domain of research to convince him why hacking life is cool and what the thing is actually about.

Would be awesome to get your support, as this guy I am arguing against is a well established old biochemistry professor,

who got at least ten times as much money and time and personnel to bring up his arguments compared to me,

so a crowdsourced update on life and evolution would rock it J

 

A brief pitch by you of the main argument of the literature you cite would be ideal.

I will of course feed back the info I collected to the community, after some digestion time.

 

Can you help me with some cool papers you know about such terms like:

·         adaptive evolution (Lamarckian style)

·         Horizontal gene transfer

·         directed Hypermutation

·         the functional role of membranes

·         origin of life hypothesis

·         energetic of evolution

·         information concept (syntax and semantics, system of reference)

·         information storage (is it only DNA?)

·         Epigenetics

·         you name it

 

 

Best,

Rüdiger

 

[Tom Hodder]

On 20 February 2014 14:06, Rüdiger Trojok <ruedi...@googlemail.com> wrote:

 

Some guy argued that Darwinian evolution is unpredictable

and that only cell free systems should be used for safety reasons

that's a bit like saying "only gun-free guns" should be used for safety reasons.

There are a few edge cases, but most writers on the topic regard cells as "the smallest unit of life" (Allen & Cowling, 2011) and therefore a system without cells would be devoid of meaningful life;

http://infohost.nmt.edu/~klathrop/7characterisitcs_of_life.htm

1. Living Things are Composed of Cells:

...

Allen, T. and Cowling, G. J. (2011) The Cell: A very short introduction, Oxford, Oxford University Press : [distributor] Oxford University Press Distribution Services.

http://www.amazon.co.uk/The-Cell-Short-Introduction-Introductions/dp/0199578753

[Lisa Thalheim]

Hey,

I don't think defining life is your problem - defining synthetic biology is.

The other guy's position makes sense if he views synbio mainly as a means of production - which is kind of understandable, since synbio advocates have often been selling it as such in the past (think biofuels and artemisinin). Before this background, it kinda makes sense to limit synbio to cell-free systems.

So, your problem lies in convincing the other guy that synbio is about more than synthesizing biomolecules in large vats.

Stuff like this may be a good starting point for that: http://www.ncbi.nlm.nih.gov/pubmed/24434884, http://www.ncbi.nlm.nih.gov/pubmed/24061539

Cheers,
Lisa

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[Ruediger Trojok]

the thing is that in that discussion we have already come to terms that synbio as it was advocated mostly in the past, was a PR coup by some american companies and professors, without much substance. now it is to figure out where the actual potential lies, somewhere between current genetic engineering and some future version of synbio.
therefore it is important to define the matter we are talking about, to find access points where programming life (in a broader sense) will work and how this might turn out. all of this is in the context of this european regulation debate,
and i am trying to convince the people to not even further crack down on technology development as they already did on gene-tech. This needs good arguments though, thats why i asked for your input.
the mammalian cell-hacking approach by fussenegger is a good example, thanks for the links.

[Mega [Andreas Stuermer]]

I will look more deeply into it. but my first impression was: How the heck would you e.g. produce vitamin B in cell free systems?

In a cell you largely benefit that all kind of precursor substances are already present. Else you would have to extensivey chemically synthesize the precursors, which makes it useless for what I understand.

[Andrew Willoughby]

It's like trying to explain an engine without pistons :(

[CodonAUG]

I would posit that viruses are an example of life.  Viruses use their environment (cells being part of their environment) to propagate themselves.  Viruses respond to environmental changes via evolution (evolution being a change in allele frequency with each generation).

Lamarackian evolution is wrong.

Directed hypermutation -- read up on MHC production in humans.  There is a variable region in the gene used to make cell receptors that gets hyper-mutated to create variation.

Origin of life hypothesis -- Its just a hypothesis and it is one that is literally impossible to prove as the stuff basic life is made from doesn't leave evidence behind.  But take a look at this experiment and follow-ups:http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment

Information storage -- RNA is used as information storage by viruses.  Epigenetic factors, which influence gene expression, are heritable (to an extent) and are a type of information -- they can be made up of protein or DNA.

[Ute Kuntz]

 

Hi,

Lamarckian evolution is wrong!

If you need basic information on evolution, and all its stuff you should read - "evolution" from Stearns (a book)  -There is info about the definition of evolution, def. of life, hypermutation, adaptive evolution, horizontal gene transfer, information storage ...... All the information you need! This book is the best for evolutionary biologists to understand evolution, life and its context. And there are remarks of syn.bio and experiments.

Good luck.

Cheers, Ute

 

Gesendet: Donnerstag, 20. Februar 2014 um 15:06 Uhr
Von: "Rüdiger Trojok" <ruedi...@googlemail.com>
An: 'diybio' <diy...@googlegroups.com>
Betreff: [DIYbio] This thing they call life

--

[Nathan McCorkle]

On Feb 23, 2014 12:54 AM, "Ute Kuntz" <ute_...@web.de> wrote:
>
>  
> Hi,
> Lamarckian evolution is wrong!

Even in the context of epigenetics?

[Cathal Garvey]

Also, Rudiger said to me on another channel that he was talking about
meta-evolutionary niches; if you imagine the cell as the unit of life,
rather than the multicellular "organism", then T-cells exhibit something
resembling lamarckian evolution.

But yes; in the context of what we usually consider "evolution" in
Eukaryotes, lamarck was wrong. Things are woolier in bacteria and
archaea of course; there are occasional gene systems that have odd
serial-generation microevolutions that could be called "lamarckian" in
the right context..

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