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

http://news.nationalgeographic.com/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/

by mikeleeorg • 13 years ago

183 66 13 years ago

news.nationalgeographic.com

pvnick7• 13 years ago

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

tshadwell2• 13 years ago

So how do you classify life?

burke• 13 years ago

...compulsion to shove things into neat little cubbies...
So how do you classify life?

I believe that's the point.

pvnick7• 13 years ago

Are you asking "how do you define life?" or "how do you separate organisms from each other?"? Regarding either question, I don't think anybody has a good answer, and that's what's so fascinating, because it really seems to be a metaphysical question rather than a scientific one.

makmanalp• 13 years ago

Do we really need to classify it down to 8 taxonomic levels? At the last few levels I bet it tends to get really arbitrary. Or, we could have a variable-depth tree. Make it more specific only when you need to.

baddox• 13 years ago

I think the underlying point is that while humans have an extremely strong (and undeniably useful) urge to classify things into clean groups, not everything lends itself to being so classified. The human urge to classify things is what makes possible paradox like the sorites paradox.

colinm• 13 years ago

1) Dead.

2) Alive.

3) Somewhere in between.

EarthLaunch• 13 years ago

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.

pvnick7• 13 years ago

I agree, and that's why I said "Modern classification schemes." The current system doesn't work, and bioinformatics is blasting it away at such a speed that it can't seem to keep up. The current response seems to be just bandage it up, like a novice PHP developer's first web app devolves into spaghetti code because he doesn't know what an MVC framework it.

otisfunkmeyer• 13 years ago

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.

CreRecombinase4• 13 years ago

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.

dnautics4• 13 years ago

well, they kind of are bullshit, in the same way that the bohr model is bullshit, and that quantum mechanics is bullshit, too. It's not REALLY what's going on, but rather a simplification that gets your feeble brain to the point where it can do something useful. You'll eventually learn a model that's less bullshitty, that gets you doing one slightly more useful thing, but it's still bullshit.

It really is bullshit, but it is useful bullshit.

pvnick7• 13 years ago

You seem to have allowed the intricacies of the subject to distract you from my meaning. All of that is true, and there are obvious macrostructures, such as those you mentioned, which are credible. However, the worship of phylogenetic classification schemes which attempt to disambiguate even the most minute details of living organisms are not useful except maybe in the nichest of fields and to boost bioinformaticists' egos.

danmaz74• 13 years ago

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

JunkDNA3• 13 years ago

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).

teej• 13 years ago

This is frightening and fascinating at the same time. Thanks for sharing.

pvnick7• 13 years ago

I actually agree with you regarding bioinformatics, and the subject you describe is one which I'm exploring as a career path. I was describing an indictment of classification schemes, not bioinformatics, and it seems there are plenty of respondents here that have misunderstood me. Which I suppose is either an indictment of the care with which I constructed my original comment or a lack of attention to the other comments I've made in this thread.

Edit:

Also, hi Mike!

ronaldx2• 13 years ago

if you're developing an antibiotic...

Beautiful examples in theory, but blown out of the water in practice.

In the current age of bioinformatics, practical modern antivirals and antibacterials are not being identified, not at all[0].

As such, I find it awkward and outdated to claim that novel drug discovery is a great testament to phylogenetics and bioinformatics.

Can anyone offer a practical example of how bioinformatics has genuinely been (pref. statistically) useful in successful drug discovery? I would also be interested in evidence that existing antibioitics could have been discovered more effectively, using new methods ab initio.

[0] e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2095086/ "the success rate of discovery has gone down"

mathattack• 13 years ago

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.

tokenadult• 13 years ago

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.

arkades• 13 years ago

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.

wissler• 13 years ago

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.

jergosh• 13 years ago

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.

grannyg00se• 13 years ago

"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?

FrankenPC• 13 years ago

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

quasque4• 13 years ago

Many types of viruses[1] are like this by virtue of their high replication rate and RNA's poor error correction while copying (in comparison to DNA). It's one of the reasons why anti-viral therapy can be so tricky in viruses like HIV, as it's such a rapidly moving target.

As as analogy to computer viruses and other malware, the effect is very much like the polymorphic program code found in some of these, albeit not going as far as to derive new functionality as biological mutations can, through the combination of mutation and selection.

[1] https://en.wikipedia.org/wiki/Viral_quasispecies

quasque4• 13 years ago

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.

dnautics4• 13 years ago

exactly. The DNA database definitely suffers from the streetlight effect.

ChuckMcM• 13 years ago

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• 13 years ago

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

minor_nitwit• 13 years ago

In a a way Evolution itself is debugging by printf. It's actually even more basic - trial and error all the way down.

JoachimS• 13 years ago

That is actually very interesting. How well would our (in)ability to parse what code (SW) does without actually running it transcend to genes. STA for genes?

Are genes Turing Complete. ;-)

quasque4• 13 years ago

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• 13 years ago

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

Daniel_Newby2• 13 years ago

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.

tiatia• 13 years ago

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

An image without a scale it worthless..

draugadrotten• 13 years ago

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.

JunkDNA3• 13 years ago

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.

pvnick7• 13 years ago

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

platz• 13 years ago

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

marcosdumay• 13 years ago

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.

Daniel_Newby2• 13 years ago

It has neither a membrane nor cytoplasm.

beat• 13 years ago

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

guard-of-terra• 13 years ago

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• 13 years ago

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.

AaronLasseigne• 13 years ago

"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• 13 years ago

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.

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

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