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That's like forking someone's program, but not understanding two thirds of the code. (What's the big deal? It happens!) If you take someone's 4000-5000 line program and whittle it down to 473 lines which are still somehow useful, "newly created" doesn't apply in full honesty, let alone if you don't know what a third of those lines do.
In this analogy, they're not looking for the code to "work". They simply want it to compile.
Forgive my complete ignorance, but how do they even count genes? Given a very long string of base pairs, how is it possible to know where one gene ends and the next one begins? Do genes overlap?
That's like forking someone's program, but not understanding two thirds of the code. (What's the big deal? It happens!) If you take someone's 4000-5000 line program and whittle it down to 473 lines which are still somehow useful, "newly created" doesn't apply in full honesty, let alone if you don't know what a third of those lines do.
In this analogy, they're not looking for the code to "work". They simply want it to compile.
Thinking if it like: Just remove files from the OS until it wont start :)
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…
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.
you can download the human genome from here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.... (it is recommended to use ftp, see: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/). it is an ~800mb download.
if it takes 800 mb to store 3.3 billion bases, i would assume it takes (531k / 3.3b) * 800 mb = 0.141 mb to store this genome.
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.
the cellular genome size of RGD3.0, the organism with a 473 genome, is 531kbp according to the paper. this means that the genome encompasses ~531,000 nucleotides (base-pairs). for reference, the human genome encompasses approximately 3.3-billion base-pairs. you can download the human genome from here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.... (it is recommended to use ftp, see: http://hgdownload.…
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…
[1] https://www.amazon.com/Creation-Life-Make-Steve-Grand/dp/067...
Earlier 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…
>> 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.
I'm not exactly sure what went wrong, but I think you're really misunderstanding something dnautics said.
Earlier quoted context omitted.
the cellular genome size of RGD3.0, the organism with a 473 genome, is 531kbp according to the paper. this means that the genome encompasses ~531,000 nucleotides (base-pairs). for reference, the human genome encompasses approximately 3.3-billion base-pairs. you can download the human genome from here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.... (it is recommended to use ftp, see: http://hgdownload.…
Thanks! By the way, when you say "you can download the human genome", presumably this is the genome of a specific individual whose DNA was sequenced? What person is that?
genomic regions with higher variability between individuals are annotated separately and are not represented in the main chromosomal sequence, but can be aligned to it as such.