Anybody else find it suspicious that 2 quanta magazine stories were the top two stories on HN today?
In Newly Created Life-Form, a Major Mystery
131–140 of 144 posts
Re: In Newly Created Life-Form, a Major Mystery
#132Earlier quoted context omitted.
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] I was a fly on the wall for most of the group meetings and even contributed some unpublished results (there were transposons that were causing problems by shuffling the t…
> Most of the mystery essential genes are vague cell wall proteins. Probably what is going on is that if you knock out too many of these genes, you lose cell wall turgidity and the cell becomes nonviable. So what is important is not so much which of these genes you have, but how many of them you have. Sounds like dependency hell. Gene A only works in the presence of Gene B which only works when there's Gene C which n…
In this simplified system, the number of these cell wall genes in the genome is proportional to the quantity of the cell wall proteins produced. It's more of a quantity issue, rather than a dependency issue. For example, having more developers usually results in more lines of code written in a given period of time, especially in enterprise. The quality of code might be questionable but the quantity is usually there.
Re: In Newly Created Life-Form, a Major Mystery
#133Earlier quoted context omitted.
> Most of the mystery essential genes are vague cell wall proteins. Probably what is going on is that if you knock out too many of these genes, you lose cell wall turgidity and the cell becomes nonviable. So what is important is not so much which of these genes you have, but how many of them you have. Sounds like dependency hell. Gene A only works in the presence of Gene B which only works when there's Gene C which n…
> Sounds like dependency hell. Random mutations are like that. It's almost like no-one was planning out how these things should work, and whatever did work stuck. Weird, huh?
In other words, God writes spaghetti code.
Re: In Newly Created Life-Form, a Major Mystery
#134Re: In Newly Created Life-Form, a Major Mystery
#135Earlier quoted context omitted.
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…
> A minimal viable cell should be able to survive on water, some dissolved gasses, and an energy source like glucose. M. mycoides certainly does not survive on that. Mycoplasmas need cholesterol and lipids because they lack the HMGCoA reductase pathway and FAS, so all the media you grow them on are enriched for that (started as FBS, but we found horse serum worked great and was cheaper). In general, I think you need…
Hell, we found an intranuclear parasite that didn't even have its own ATP synthase, glycolytic pathway or any other obvious way to generate ATP.
Re: In Newly Created Life-Form, a Major Mystery
#136Earlier quoted context omitted.
> Sounds like dependency hell. Random mutations are like that. It's almost like no-one was planning out how these things should work, and whatever did work stuck. Weird, huh?
In other words, God writes spaghetti code.
God writes code that writes code that writes code ... that writes spaghetii code
Re: In Newly Created Life-Form, a Major Mystery
#137TL;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…
> That's the most interesting point to me, I deeply believed that organisms share the same basic set of genes.
It should seem obvious in retrospect. Turing machines have many incarnations as different instruction sets in modern CPUs. I don't see why cells wouldn't have analogous multiple expressions, unless your deep belief was that there was only one way for protein chains to replicate.
Re: In Newly Created Life-Form, a Major Mystery
#138That should be us.
Re: In Newly Created Life-Form, a Major Mystery
#139So it's like a unikernel of life?
It's closer to a microkernel.
Re: In Newly Created Life-Form, a Major Mystery
#140How 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…
141.9 kB! In the future, I expect there will be a demoscene of biosynthetics.