Biggest Virus Yet Found, May Be Fourth Domain of Life?

So how do you classify life?

There's no harm in defining and categorizing things. The harm would be in forgetting that categories should be based on reality, but don't define reality (a Platonic mistake).

When new information blasts away an existing categorization scheme, then a new one does need to be made.

Perhaps the answer lies in tagging. Rather than a hierarchical categorization, everything is just tagged and thus searchable. That way you don't have to keep trying to fit everything into preexisting categories... Seems to be the direction most other things are heading as well.

If you find phylogeny to be "bullshit", your biology and microbiology professors have truly failed you. Evolution by natural selection has produced the wonderful diversity that is life. Phylogenetic reconstruction is the tool biologists use to understand the history of all life on the planet. The fact that some living organisms engage in lateral gene transfer, or that there is no definition of species that perfectly applies to all living things is no reason to abandon perhaps the most fundamental and central pursuit of biology. Who we are as humans is inextricably tied to our mammalian, primate, vertebrate and multicellular ancestry, and we know this by virtue of the wonders of phylogenetics.

"Essentially, all models are wrong, but some are useful." George E.P. Box

There are a great many biologists and bioinformaticians who don't "get" phylogenetics. Please, please don't be one of them. I worked with some world class evolutionary biologists in the drug industry early in my career and I was blown away by how useful this often ignored corner of biology has become when married with modern bioinformatics techniques.

Here's an example: let's say you're trying to develop a new drug against a virus. You can isolate huge numbers of the virus from infected individuals and sequence the DNA very cheaply. Using selective pressure analysis you can look for regions of DNA that are being selected for over multiple generations of the virus. Why? Because these might be important for survival. If your drug can target those regions of the protein, the virus will have an uphill battle mutating and creating resistance to your drug.

Here's one more: You can use phylogenetic techniques on individual proteins to see how closely related they are. Why do this? Because if you're developing an antibiotic, you want to know that the bacterial version has a sufficiently large evolutionary distance from the human version. Now you can do this at scale for huge numbers of bacterial proteins and identify the ones with the biggest distance from their human orthologs. This allows you to identify bad antibiotic targets upfront before pouring all sorts of money into experiments (or at the very least, going into said experiments with your eyes wide open).

Growing up it seemed crazy having to memorize these arbitrary taxonomy schemes when things intuitively didn't seem so black and white. I guess every model has it's shortcomings.

Are you studying those topics as a biology major, or as a student of some other major subject? There actually is a lot of criticism among biologists about how far behind the textbook representation of those topics is compared to the professional literature of biology. If "cladistics" is not a familiar term to you from your undergraduate education, that would be diagnostic of a poorly designed biology course, for example. See

http://www.evolution-outreach.com/content/6/1/11

for a discussion of this issue and other issues about problems in biology education.

To my understanding the classifications tend to be "lies we tell to children", much like the simplified atomic models sold to first-year chemistry classes. If you're a biology major, you never really need to get the Chemistry PhD's version of atoms, right?

Very broad classifications tend to be useful, in that by definition they group similar organisms. Beyond that level of detail they're useless, yes, but beyond that level of detail you're already going into the level of expertise where you're expected to recognize their uselessness. Cell Biology PhDs may or may not realize it, but they're working on tyrosine kinases, not classifications.

It's not "bullshit", it's just doesn't come with the same kind of guarantees that religion does. Our knowledge is refined and expanded over time. This is perfectly natural.

The problem is when people are taught in an authoritarian manner, and then they run into places that method breaks down, and so throw the baby out with the bathwater. As you have done.

> 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.

What do you mean by "modern classification schemes"? If anything, molecular phylogenetics helped clarify earlier attempts at classification which used common morphological features.

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

> Maybe one day we'll find a virus-type replicator that also contains ribosomes - and what then?

Mimivirus, another giant virus, has its own gene for an amino-acyl t-RNA synthase, an enzyme that loads an amino acid onto a transfer RNA to be used in making proteins. That's awfully close to a ribosome component.

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.

Either that or it randomizes it's genetics so much that it is more like a random seed generator. The Darwinian god bug.

No it doesn't imply anything about origins of life - but the lack of any homologous sequences in known species (including other viruses) that have been sequenced does illustrate the vast gaps in the totality of genetic data collected and indexed so far.

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.

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.

Very relevant xkcd comic: http://xkcd.com/1217/

> 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.

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.

It has neither a membrane nor cytoplasm.