
Biggest Virus Yet Found, May Be Fourth Domain of Life? - mikeleeorg
http://news.nationalgeographic.com/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/
======
pvnick
As I study biology and microbiology in college, the more I realize that
taxonomy and phylogeny classification schemes are essentially bullshit.
Bioinformatics and evolution research have shown "life" to be much more
ambiguous and mysterious than we could have ever imaged. Modern classification
schemes are so arbitrary and error-prone as to be essentially just a painful
way to satisfy scientists' compulsion to shove things into neat little cubbies
and has the negative side-effect of scaring students away from an otherwise
fascinating subject. The professors I've spoken with tend to agree.

Edit: added "classification schemes" after taxonomy and phylogency to clear up
confusion

~~~
tshadwell
So how do you classify life?

~~~
burke
> ...compulsion to shove things into neat little cubbies...

> So how do you classify life?

I believe that's the point.

~~~
tshadwell
I'm sure the author means dislike for the current system for trying 'too hard'
to classify life, not dislikes it entirely, or out goes our ability to
describe life with words entirely, which I think you'll agree is a pretty
important faculty.

------
quasque
Discoveries such as this just go to show how arbitrary the definition of
"life" is.

One might argue that viruses are not life because they are obligate
intracellular parasites - but many species of bacteria are too. It used to be
that size was the distinction: viruses as small, simple particles and cells
much bigger, but large complex viruses also blow this argument out of the
water.

The only thing left that really distinguishes the "life" of cells and the
"maybe-not-maybe-life" of viruses is the presence of ribosomes to synthesis
proteins. Maybe one day we'll find a virus-type replicator that also contains
ribosomes - and what then?

Then there is also the issue of simulating life _in silico_ \- at which point
does it stop becoming just a simulation and can be considered 'actually'
alive?

Personally I think these questions are best debated in the context of
philosophy and ethics rather than taken as something that the domain of
science ought to provide conclusions to.

~~~
leot
My favorite exploration of this topic is found in Maturana and Varela's
"Autopoiesis and cognition: the realization of the living". Cells have to
"work" to preserve their ability to go on preserving their ability to ...
(etc. recursively). Viruses don't.

[http://en.wikipedia.org/wiki/Autopoiesis](http://en.wikipedia.org/wiki/Autopoiesis)

------
AaronLasseigne
"Each about one micron—a thousandth of a millimeter—in length, the newfound
genus Pandoravirus dwarfs other viruses, which range in size from about 50
nanometers up to 100 nanometers."

That is a horrible use of units.

~~~
karpathy
I thought the same thing exactly. I usually convert everything on molecular
scales in terms of proportions to the nearest tangible entity. (I find nm too
abstract and harder to remember)

A single hydrogen atom has diameter of about 10e-10 meters.

A single nanometer is 10e-9 (i.e. about 10 hydrogens stacked)

Viruses are on order of 50-100 nanometers => ~500-1000 hydrogens across.

These viruses are 10e-6 meters, or 10,000 hydrogens across.

That's too many to imagine and hard to remember, so other useful dimensions I
sometimes use are

diameter of DNA helix is about 2nm (20 hydrogens across)

the size of X chromosome, which is roughly 7um.

the size of a cells in our bodies vary around 10-100um.

so, the best way to get a sense of scale for this particular virus (imo) is to
imagine it as 1/7th of size of an X chromosome. Or as 10x bigger than an
average virus.

------
grannyg00se
"93 percent of pandoraviruses' 2,500 genes cannot be traced back to any known
lineage in nature. In other words, they are completely alien to us."

Is this as significant as it sounds? Did they just find life that may have
origins different than anything else on earth?

~~~
ChuckMcM
Absolutely, there are 2,500 genes that we didn't know about.

Now it could be that if any one of these genes shows up in any of the "known"
lineages (as it might if a retro-virus carrying it injected it) that it causes
the host to die before reproducing. It could be that they are pandemics
waiting to happen, it could be that they are code for additional eyeballs.

The challenge is that we do not yet (as far as I can ascertain) have a way to
looking at a gene and identifying all of the effects that gene has on a cell
or an organism. What we have are organisms with genes, that we are 'debugging
by printf' by essentially commenting them out and seeing what happens.

Once our knowledge base flips, and we understand genetics at a
information/programmatic level, we would be able to evaluate these 2500 genes
and see if there is anything useful here.

~~~
Zikes
93% of 2500 genes, so ~2325 we didn't know about.

------
guard-of-terra
Maybe it was once an unicellar predator that hunted bacteria which during
evolution gained the "idea" of using prey cells' machinery to do some of its
biochemistry. So it didn't eat bacteria, rather plundered those.

Then during evolution it eventually lost every other piece of own
biochemistry, eventually becoming a virus.

~~~
svachalek
I read about the mimivirus it mentions in the article a few years ago, and it
mentioned that was one hypothesis. Another is that it went the other way
around; before cells were invented life was just increasingly complicated
self-replicating molecules and cellular life evolved out of them. In that case
the virus-like ancestors would have evolved to prey on their self-sustaining
descendents.

I think the uniqueness of this virus' genes suggests that whichever direction
it happened, it happened very early in the history of life.

------
JunkDNA
Whenever I read about findings like this, I'm reminded of just how much our
requirement that microbes need to grow on a piece of glass distorts our view
of them. If we could observe them as easily as animals in the wild, that would
open whole new avenues of research.

~~~
pvnick
Very relevant xkcd comic: [http://xkcd.com/1217/](http://xkcd.com/1217/)

------
tiatia
"An image of a Pandoravirus particle, created using an electron microscope."

An image without a scale it worthless..

~~~
draugadrotten
> An image without a scale it worthless..

Not so. If you read the article, it says each is about one micron—a thousandth
of a millimeter—in length.

------
platz
why even call it a virus, if it shares so little in common with what we know
as actual viruses?

~~~
marcosdumay
It's a wall of protein with nucleic acid inside that reproduce by exploiting
other organisms' cells. Don't get blinded by the differences, the similarities
are much bigger.

------
beat
I think technically, it's a worm, not a virus. :)

