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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

#81

Post by julienchastang »

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.

This comment is not as absurd as everyone seems to think. It is possible that life started out as RNA[1] on Earth or elsewhere in the galaxy[2].

[1] https://en.wikipedia.org/wiki/RNA_world [2] https://en.wikipedia.org/wiki/Panspermia

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

#84

Post by misiti3780 »

Has anyone else here read Nick Lane's new book - The Vital Question - I just finished it and this article really seems like a continuation of some of his theories he talks about.

I found about the book from HN, and have since bought every single other book by him, almost done with Life Ascending now, which is also amazing

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

#85

Post by haberman »

How much information is 473 genes? How many bytes does this represent, in a compact but "raw" encoding? What about if you compressed it with gzip?

Also what are the raw/compressed sizes for a human genome?

I have wondered this for a long time but never seem to find a concrete answer.

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

#86

Post by cowsandmilk »

rcthompson wrote: post #33
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…

My understanding is that all known organisms share at least the ribosome RNA genes. Unless you're counting viruses, which is not exactly fair since they hijack the host's ribosomes.

but there is RPL1 up to RPL41, and same for RPS and then MRPL and MRPS , so despite the similarities, one can argue different organisms may have different rRNA genes.

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

#88

Post by dnautics »

dekhn wrote: post #60
dnautics wrote: post #39

Earlier quoted context omitted.

with a handful of exceptions (for example TER units, and DnaA, which seems to need to be close to the replication origin), for most microbes, placement and arrangement don't matter. I believe they wanted to modularize the bacteria by placing cassettes of common functionality (e.g. all the tRNAs together) in parts of the genome. I don't know if they are still are working on that, or how it went. In yeasts, the tRNAs h…

I thought most bacterial have their critical biochemistry genes arranged in a specific order so that they can be all be cotranscribed (for efficiency): https://en.wikipedia.org/wiki/Gene_cluster#Prokaryotic_gene_...

Ah yes - that's true - I was thinking of operons, not genes. But you can shuffle operons without too many broader consideration of genomic structure. Some prokaryotic organisms seem to have all of their operons pointing in-line with DNA replication (pointing origin -> ter) but IIRC switching the direction of those doesn't seem to make much of a difference either.

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

#89

Post by phkahler »

dnautics wrote: post #35
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 worked in the synthetic biology lab (on a different project) while the early stages of the Syn3.0 was being done, and also have paid several visits to chat with them in the meantime. [Proof: first author on http://dx.doi.org/10.3390/ijms16012020 ] I was a fly on the wall for most of the group meetings and even contributed some unpublished results (there were transposons that were causing problems by shuffling the t…

>> Firstly what constitutes "minimal" depends on what you feed the organism.

So maybe the environment needs to be changed to support an organism with a smaller genome. The world today is certainly different than when life began. It's probably difficult to evolve the environment, so they'd need to understand what goes wrong with gene deletions and figure out how a different environment could help.

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

#90

Post by gberger »

haberman wrote: post #85

How much information is 473 genes? How many bytes does this represent, in a compact but "raw" encoding? What about if you compressed it with gzip? Also what are the raw/compressed sizes for a human genome? I have wondered this for a long time but never seem to find a concrete answer.

From [1], "Mycoplasma genitalium: it has only about 480 genes in its genome of 580 070 nucleotide pairs." So in average, each gene is 1200 nucleotide pairs.

A nucleotide is one of [A,T,C,G]. So that means it encodes 2 bits of information.

473 * 1200 * 2 = 1 135 200 bits, or 141.9 kilobyte.

Of course, this is coming from a software developer using numbers from Google, so I might be wildly wrong.

[1] "Molecular biology of the cell" by Bruce Alberts

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