A sample of the Ebola now raging in West Africa has, by recent count, 18,959 letters of code in its genome; this is a small genome, by the measure of living things.
Does this mean mean Ebola is essentially about 38 kilobytes?
Does this mean mean Ebola is essentially about 38 kilobytes?
Here's the complete genome of the pandemic strain (scroll down a bit):
http://www.ncbi.nlm.nih.gov/nuccore/KJ660346
Here's the paper sequencing it. ([edit]: I just realized the New Yorker article is largely about this exact paper -- I commented before reading, sorry). Note that five of the authors died before publication; there's a short tribute accompanying it.
http://www.sciencemag.org/content/345/6202/1369.full
http://news.sciencemag.org/health/2014/08/ebolas-heavy-toll-...
Here's another phylogeny of this strain, including github repo:
http://currents.plos.org/outbreaks/article/phylogenetic-anal...
It is simply incredible to me that it could be so small (in an information sense).
This article (gzipped) is 22KB, more than 4 times as much information.
The genetic information is really the 4.8 kB of "code" PLUS the entire information already contained in the cellular hardware reading it. One doesn't make sense without the other.
At the very bottom, the whole thing depends on the laws of quantum mechanics in this universe, governing the minute details of molecular interaction. That, too, should be considered to go into the "code". Make a tiny change to the Plank constant, and the Zaire ebolavirus code will do something very different.
I liken DNA to a paper tape containing one of two punches: MAN or MOUSE. Feed it into a bio-replicator and get a man or a mouse. Does the paper tape define the man? Of course not.
I don't think that really captures it. Yes, it requires external machinery to actually do anything, but DNA is much more information dense and carries much more of an exact definition of the organism to be produced.
Personally, I prefer the analogy of compiler source code. Sure, it can't do anything on its own. But it defines how an working external system (another compiler or an functional cellular environment) can produce a second possibly different system
My understanding of biology is very limited. I've heard how physically small microbes are in every article out there. But never how information-small they are. Fascinating from a software developer's perspective.
I wonder what code golf for a virus would look like.
> Viroids are plant pathogens that consist of a short stretch (a few hundred nucleobases) of highly complementary, circular, single-stranded RNA. Viroid genomes are extremely small in size, ranging from 246 to 467 nucleotides (nt), and consisting of fewer than 10,000 atoms. In comparison, the genome of the smallest known viruses capable of causing an infection by themselves are around 2,000 nucleobases in size. The human pathogen hepatitis D virus is similar to viroids.
> Viroid RNA does not code for any protein. Their replication mechanism uses RNA polymerase II, a host cell enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid's RNA as template. Some viroids are ribozymes, having catalytic properties which allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.
Source: http://en.wikipedia.org/wiki/Viroid
In case you were wondering what a ribosyme is
> A ribozyme (ribonucleic acid enzyme) is an RNA molecule that is capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes.
Source: http://en.wikipedia.org/wiki/Ribozyme
The action of ribozymes led to the RNA world hypothesis, as the mechanism for how you could have a simple system from which DNA and proteins can come as later optimizations on particular aspects. Some ribozymes are able to go as far as catalyze the building of their own RNA structure in the right environments (albeit, with limited success so far).
You hit near it when you gzipped the article -- consider a genome to be an incredibly compressed format, able to explode into a truly stunning amount of information, stored in a relative paucity of raw data.
P.S.: It's 37918 bits, about 4.6 kB
/note="immunosuppressive region; other site"
...
/note="transmembrane anchor; transmembrane region"
Is that why people die? Cells make too much of that stuff?
Fun fact: The victim's body continues producing cells for several hours after death. In rare cases this (in conjunction with post-death bloating) causes the cadaver to "explode"
524..2671 /gene="NP" /note="Ebola nucleoprotein; Region: Ebola_NP; pfam05505" /db_xref="CDD:147601"
"http://www.ncbi.nlm.nih.gov/pubmed/9657001?dopt=Abstract"
"DNA vaccines expressing the envelope glycoprotein (GP) or nucleocapsid protein (NP) genes of Ebola virus were evaluated in adult, immunocompetent mice. The vaccines were delivered into the skin by particle bombardment of DNA-coated gold beads with the Powderject-XR gene gun. Both vaccines elicited antibody responses as measured by ELISA and elicited cytotoxic T cell responses as measured by chromium release assays. From one to four vaccinations with 0.5 microgram of the GP DNA vaccine resulted in a dose-dependent protection from Ebola virus challenge. Maximal protection (78% survival) was achieved after four vaccinations. "
The article is from 1998. Interesting why there is still no vaccine. And this is on the virus structure - GP envelope - with attached antibody from human survivor http://www-als.lbl.gov/index.php/contact/163-structure-of-th...
http://mtpr.org/post/getting-closer-ebola-vaccine
(Rocky Mountain Lab in Montana is where a large portion of the ebola research in the nation if not world the world happens and mtpr had gotten some really good interviews as a result.)
I can remember seeing pictures of some Malians getting it.
There are only four nucleotides ("letters") in RNA. You can encode them with two bits.