In Newly Created Life-Form, a Major Mystery • Hacker News Board

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

#141

Post by phkahler » Thu, Jun 23, 2016, 5:24 PM UTC

civilian wrote: post #99

phkahler wrote: post #89

Earlier quoted context omitted.

>> 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.

When dnautics says "different environment" he's not talking about the global environment, he's talking about the environment around the cell. A minimal viable cell should be able to survive on water, some dissolved gasses, and an energy source like glucose. Bacteria that have even smaller genomes are doing that by stealing components from other lifeforms. I'm not exactly sure what went wrong, but I think you're reall…

>> Bacteria that have even smaller genomes are doing that by stealing components from other lifeforms.

There are no bacteria with smaller genomes today, that was the point of making this one. I was not talking about the global environment either, but the number of options for what substances and concentrations may need to be present in the environment around a cell is certainly very large - making trial and error difficult.

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

#142

Post by smaddox » Fri, Jun 24, 2016, 2:59 AM UTC

alfiedotwtf wrote: post #104

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…

> As @sixQuarks has already written, finding the minimal amount of genes when there are 175 unknown ones and you don't know anything about their dependencies and relationships seems to be pretty much impossible. Is there any way at all at simulating the tests? I'd like to apply metaheuristics to search for which combinatorics work

This would require a quantum chemistry simulation many orders of magnitude larger and longer than what we currently capable of simulating. Though I suppose you could in principle use heuristics to greatly reduce the conputational complexity.

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

#143

Post by SilasX » Fri, Jun 24, 2016, 6:44 PM UTC

thaumasiotes wrote: post #72

SilasX wrote: post #53

Earlier quoted context omitted.

Also, isn't there an issue of "gene" being something of an unnatural category? Nature doesn't provide a clean labeling of what part of the sequence is "a" gene, and the term historically existed (AIUI) to denote regions that the researcher found to have phenotypic relevance. So I'm not sure it's helpful to phrase a minimum in terms of "n genes". See: https://en.wikipedia.org/wiki/Gene#Functional_definitions

> the term historically existed (AIUI) to denote regions that the researcher found to have phenotypic relevance That's Mendelian genetics. Geneticists focused on DNA as a physical molecule rather than a conceptual unit of inheritance use the same word to refer to a region of DNA that produces a protein. They're both important concepts, but they're not the same concept.

Okay I got the terms wrong but I think the core point stands: a gene is typically defined with respect to some research objective and area of interest, and is highly variable depending on what you're looking at. It doesn't (yet, at least) have a natural boundary. People looking at one phenomenon might see one boundary for a a gene, while others see another.

In fact, I think that term is great for comparison: "phenomenon". Asking for the "minimum genes for viable life" seems like asking for the "minimum number of natural phenomena to put a man on the moon". Are those two phenomena really just different manifestations of "gravity" or are they two things in their own right? "It depends."

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

#144

Post by gberger » Tue, Jun 28, 2016, 4:28 AM UTC

haberman wrote: post #95

gberger wrote: post #90

Earlier quoted context omitted.

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…

That's a great start at least! Posting something that is wildly wrong is the best way to get someone who knows more to interject with corrected information, so hopefully someone with expertise can confirm or deny.

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