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In Newly Created Life-Form, a Major Mystery

quantamagazine.org

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Re: In Newly Created Life-Form, a Major Mystery

#21

Post by jhoechtl »

chubot wrote: post #11
maxerickson wrote: post #8

Earlier quoted context omitted.

If I understand correctly, they built the technology to synthesize arbitrary genomes. So they remove genes by omitting them from the synthesis.

The article says they tried the additive/synthesis approach first, which didn't work. And then they tried the subtractive approach, starting with M. Mycoides. And in that case they were left with a lot of "unexplained" genes. But he reminds us that the subtractive process entirely depends on the starting cell. I would like to hear more about the difference between additive and subtractive methods -- it wasn't entirel…

This reads to me as: They took a working system and did parts away until the system failed (or did stgh "odd" towards failure). Then they were looking at the pieces they took away and guessed what functionality these pieces have.

Re: In Newly Created Life-Form, a Major Mystery

#22

Post by davnn »

Retric wrote: post #14
davnn wrote: post #10

TL;DR: Venter and his collaborators originally set out to design a stripped-down genome based on what scientists knew about biology. ... With the right tools finally in hand, the researchers designed a set of genetic blueprints for their minimal cell and then tried to build them. Yet “not one design worked," ... So the team took a different and more labor-intensive tack, replacing the design approach with trial and e…

Not all life has DNA.

Do you know an article about that? Did not find anything about a life form without DNA, except http://news.nationalgeographic.com/news/2010/12/101202-nasa-....

The definition of life itself is not really obvious to me either, some sources count viruses as life other don't.

Re: In Newly Created Life-Form, a Major Mystery

#23

Post by jhoechtl »

0xfeba wrote: post #20
davnn wrote: post #10

TL;DR: Venter and his collaborators originally set out to design a stripped-down genome based on what scientists knew about biology. ... With the right tools finally in hand, the researchers designed a set of genetic blueprints for their minimal cell and then tried to build them. Yet “not one design worked," ... So the team took a different and more labor-intensive tack, replacing the design approach with trial and e…

> I deeply believed that organisms share the same basic set of genes. Many groups of organisms do. All organisms is a tall order, if you think about it.

The more I think about that the more makes me believe that the Genome is not the smallest order which defines "life".

Maybe all is hidden behind getting blurry because of Heisebergs uncertainty principle.

Re: In Newly Created Life-Form, a Major Mystery

#24

Post by alextheparrot »

chubot wrote: post #11
maxerickson wrote: post #8

Earlier quoted context omitted.

If I understand correctly, they built the technology to synthesize arbitrary genomes. So they remove genes by omitting them from the synthesis.

The article says they tried the additive/synthesis approach first, which didn't work. And then they tried the subtractive approach, starting with M. Mycoides. And in that case they were left with a lot of "unexplained" genes. But he reminds us that the subtractive process entirely depends on the starting cell. I would like to hear more about the difference between additive and subtractive methods -- it wasn't entirel…

Additive method: Synthesize genomes with the genes you expect to be necessary, pretty much an optimization problem on the number of genes where you continually try to remove genes that were in previous iterations.

Subtraction method: After reading a bit of the paper, they utilized Tn5, which causes a DNA sequence to be arbitrarily inserted into the DNA (Random locations). This randomly disrupts genes, causing them to likely not function correctly.

Here's the logic: If all genes were necessary we would expect no cells to live that had mutations.

If no genes were necessary we would expect all cells to have mutations at about an equal rate relative to the space they occupy. (Assuming no bias by the Tn5, but that's a nuance)

What they instead found was that some cells grew, but there were certain genes that were not mutated, meaning that they are likely necessary.

They also classified a few things like studying the growth of the cell (Slow growing, but still viable was classified as "quasi-essential") and implanting their minimal genome in another species, which failed giving evidence that a subset of genes that are sufficient for survival are not necessarily sufficient in all cells.

Re: In Newly Created Life-Form, a Major Mystery

#25

Post by Lyaserkiev »

davnn wrote: post #22
Retric wrote: post #14

Earlier quoted context omitted.

Not all life has DNA.

Do you know an article about that? Did not find anything about a life form without DNA, except http://news.nationalgeographic.com/news/2010/12/101202-nasa-... . The definition of life itself is not really obvious to me either, some sources count viruses as life other don't.

I'm guessing he means RNA viruses https://en.m.wikipedia.org/wiki/RNA_virus

Re: In Newly Created Life-Form, a Major Mystery

#26

Post by kens »

meursault334 wrote: post #2

Article summary and Article http://www.cba.mit.edu/docs/papers/16.04.minimal.pdf edit: appears to be the full article (scroll down past summary)

I encourage people to read the one-page summary and at least the section headings in the full article.

To answer a few question that have come up:

How did they synthesize the genome? By creating short sequences of DNA and joining them together step by step to make larger sequences. They chemically synthesized short DNA sequences and assembled them into 1.4 thousand base pair (kbp) fragments. Five fragments were assembled into 7 kbp cassettes, which were assembled in yeast to generate 1/8 chunks of the genome, and these chunks were assembled in yeast to create the full genome. (See figure 2.) To try out deletions, they could replace a 1/8 chunk, rather than synthesizing the whole genome.

Why can't they delete all the non-essential genes? Bacterial have a lot of redundant genes, where two different genes provide the same essential function. Just like redundant disks, you can remove one, but not all of them. And you'll get different of minimal genomes depending on which gene you keep.

One interesting thing is that because the growth medium provides almost all the necessary nutrients, they could remove a lot of the metabolic genes, but needed to keep a lot of genes to transport molecules across the cell membrane. You can imagine a minimal cell constructed the opposite way.

The article doesn't mention that in their first synthetic bacterium (2010), they encoded text (actually HTML!) in the DNA to provide a secret watermark. See http://www.righto.com/2010/06/using-arc-to-decode-venters-se...

Re: In Newly Created Life-Form, a Major Mystery

#27

Post by gtycomb »

sixQuarks wrote: post #7

I'm afraid it's not the individual genes themselves that are important to life, but a specific combination of those genes. Further complicating the problem is that we have no idea how many genes comprise an "essential group". Is it a combination of 2 genes? 3, 5, 10? When you're talking about 175 unknown genes, the combination of all of these is a huge number. It's like finding a needle in a haystack the size of the…

I am thinking of George Boole (boolean algebra and logic) who wrote in the 18th centuary -- that a symbol (an individual gene in this case) in itself is not meaningful but that its meaning depends on how it combines with with other symbols. Quote- "..the validity of the processes of analysis does not depend upon the interpretation of the symbols which are employed, but solely on their laws of combination. Every system of interpretation which does not affect the truth of the relations supposed, is equally admissible, and it is true that the same process may,under one scheme of interpretation, represent the solution of a question on the properties of numbers, under another, that of a geometrical problem, and under a third, that of a problem of dynamics or optics." (Boole 1847)

Re: In Newly Created Life-Form, a Major Mystery

#28

Post by alextheparrot »

jhoechtl wrote: post #23
0xfeba wrote: post #20

Earlier quoted context omitted.

> I deeply believed that organisms share the same basic set of genes. Many groups of organisms do. All organisms is a tall order, if you think about it.

The more I think about that the more makes me believe that the Genome is not the smallest order which defines "life". Maybe all is hidden behind getting blurry because of Heisebergs uncertainty principle.

If you consider the genome to be information, life is effectively the process that information supports by encoding a method to accomplish the process. Replicating and using energy in a coordinated manner are two processes of life, but their information-based encoding can differ significantly based on the method used.

Re: In Newly Created Life-Form, a Major Mystery

#29

Post by Retric »

davnn wrote: post #22
Retric wrote: post #14

Earlier quoted context omitted.

Not all life has DNA.

Do you know an article about that? Did not find anything about a life form without DNA, except http://news.nationalgeographic.com/news/2010/12/101202-nasa-... . The definition of life itself is not really obvious to me either, some sources count viruses as life other don't.

The definition of life is a tricky question. The most obvious example is red blood cells dump their DNA. So they can't replicate, and virus can't target them. However, insect drones also can't reproduce and are considered alive so it's a little more open to debate than you might think.

As to life without DNA. The methodology is somewhat in question for this but here is a more in depth link: http://science.sciencemag.org/content/332/6034/1163.full Now, this is really 1:1 with DNA just using slightly different chemistry, but it's hard to call something DNA when you swap out one of the building blocks.

Other examples are hard to locate in large part because you can't direct detect this stuff.

Anyway, my point was while a virus is 'stuck' using DNA as it needs to infect things that use DNA. However, they can use RNA internally.

PS: For a really out there example, prions seem really close to life.

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