Finding Every Species

And Then by Alien54 · 2003-01-12 17:15 · Score: 3, Insightful

put a patent on every single one for purposes of commercial exploitation

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Re:And Then by divide+overflow · 2003-01-12 18:56 · Score: 5, Insightful

I think it's possible that somebody wildly overestimated the scope of the project. Or wildly underestimated the resources that could be applied to it. Or both.

Many different factors caused the project to take less time than initially planned, not the least of which was clever algorythmic techniques to speed up the decoding process. All of them combined led to a quicker result.

As I understand it, the vast majority of pure research is being funded by private companies now. So even if that research is being done at universities-- which it is, largely-- it's being paid for with corporate dollars. Which, some people's opinions to the contrary, is not inherently a bad thing.

I believe you meant "basic" research rather than "pure" research. Basic research (as opposed to "applied" research) is "experimental and theoretical work undertaken primarily to acquire new knowledge without a specific application in view". There has been a general decline in spending on basic research by corporations in recent years due to the high cost and uncertainty of return on the investment, leading to the shift of basic research to universities. This has had good and bad effects on universities, who have benefited from the funds but have also found increasing limitations and restrictions placed upon them by their corporate sponsors. For example, there have been well documented reports of drug companies putting restrictions in grant contracts to public researchers preventing them from telling the public of any hazardous effects of their drugs, even when those same drugs are in current use by the public.

So their is no black or white answer to which is better, public or private research. Perhaps it is good to have both, just as it is good to have a multiplicity of competitors in a market economy. It may just help to keep everyone honest.
Re:And Then by alext · 2003-01-13 14:35 · Score: 3, Insightful

Hardly single handedly - all their sequence data was from public research.

And they didn't win - the public effort was described in Nature magazine, and the Celera one in Science, both on the week of 12th Feb 2001.

However, Celera's attempt to violate the international Bermuda agreement of 1996 and turn our own genes into proprietary information did act as a spur to the public effort. Thank goodness they were able to respond.

Good freakin' luck by D4Vr4nt · 2003-01-12 17:16 · Score: 1, Insightful

Good freakin' luck..

As the pesimist I am, I say this is impossible. What about all the stuff that is so deep in the sea we can't even get to?

I think we'd have better luck finding life on Mars. :P

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Shouldn't be too hard... by Quaoar · 2003-01-12 17:17 · Score: 3, Insightful

List of species known gets larger each year...

List of species that aren't extinct gets smaller each year...

The two numbers will eventually meet.

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Re:Shouldn't be too hard... by Twirlip+of+the+Mists · 2003-01-12 17:29 · Score: 4, Insightful

You forgot to take into account the rate of speciation. About which we basically know nothing. Lots of theory and fossil evidence, but as to the rate of speciation occurring today, we know nothing.

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Re:Shouldn't be too hard... by f97tosc · 2003-01-12 20:42 · Score: 3, Insightful

You forgot to take into account the rate of speciation. About which we basically know nothing. Lots of theory and fossil evidence, but as to the rate of speciation occurring today, we know nothing.

Well, we know almost nothing about how speciation occurs, but one can make estimates of the rate. If there are 10 million species today, and almost all of them evolved within the last million years, then the rate is probably ten per year, give and take an order of magnitude.
This numbers also illustrate that new the number of new species are not really relevant within this time frame. If 100 or a 1000 or 10000 new species form within the next ten years is of little consequence to a project aiming to categorize 10 million species.
One caveot to all this is that in reality speciation is probably not linear but rather happens more like in bursts. To your point, that would indicate that if we are in the middle of such a burst (which I never have heard suggested, btw) then sure that could mess up our calculations.

Tor
Re:Shouldn't be too hard... by dandelion_wine · 2003-01-13 08:01 · Score: 3, Insightful

Man. Ok, where to start.

You remember those breath-mint commercials? Trim looking woman is sucking away on one while telling you that it's only a few calories each, so you can work them off "walking, working... breathing " (wink, wink). Well, yes. True. Only a few calories. Except anyone who's seen someone order two diet specials knows that it's not a few calories. It's a few more calories. In the same way that people who say "No one can make a difference in pollution -- it's too big a problem" forgets that it was a lot of individuals who made the problem in the first place. Everyone adding their bit.

So yes, Pinatubo did massive ozone damage. So do flatulent cows (ha ha). And forests need to burn down every now and again. But there's a reason there wasn't an ozone problem until recently! There's a reason we hadn't run out of cod until recently (even though we've had seals, supposedly the culprit, a good long while). There are natural checks and balances that we humans are successfully overcoming. I was in Southeast Asia not long ago doing, among other things, a little reef research (I was just an assistant). Well, turns out that most of the reef damage in the area was caused by tropical storms. Hey, great. Good to hear. Of course, there was a whack of damage caused by fishermen using nets, poorly placed anchors, and cyanide, amongst other things. There was also a lot of damage from snorkelers, many of whom (heh) could not swim, and felt the need to stand on the coral where possible. There was also the dedicated work of the conservationists who, in trying to kill every crown-of-thorns starfish (that destroys reef) either created many more in some cases, or destroyed reef while destroying the starfish. All not good. Of course, again, the storm did the most damage. But on its own that storm damaged reef might recover given time. But you know, add all those things together and that section of reef was a goner. Natural processes at that point were exacerbating the situation (proliferation of those c.o.t. starfish and sea urchins, for example, both likely due to different human-added pollutants).

So, yes, I like to knock people's delusions of grandeur as much as anyone, and if Phil down the street comes out tearing his shirt off, screaming in guilt, "It was me! Me! I destroyed the ozone layer" I'll be the first to use that handy label. But collectively? Yes, absolutely. We're fucking the planet six ways from Sunday.
Re:Shouldn't be too hard... by Twirlip+of+the+Mists · 2003-01-13 18:15 · Score: 3, Insightful

Have we even scientifically defined the concept of "species"?

I thought we had, and said as much in another post in this thread, but I was corrected. It seems like the idea of a species is a nebulous one at best, and at worst downright nonsensical.

Besides, upon further reflection, wouldn't any project like this necessarily run up against a sort of Heisenberg effect? In order to be absolutely certain that you have catalogued every species on the planet, you have to examine every organism on the planet. Single-celled organisms, too. And examining a single-celled organism on the genetic level would necessarily result in the destruction of that organism. Practically speaking, this would happen with any microscopic organism; we simply can't learn about them without squishing them to see what goo comes out.

So carried to its natural conclusion, a project like this would would mean absolute genocide for untold teeming billions of microscopic and single-celled organisms.

Wish I'd thought to post this a few days ago. Surely it would have been good for an "insightful" mod point or two. ;-)

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That doesn't sound possible by spooje · 2003-01-12 17:20 · Score: 3, Insightful

Is that even theoretically possible? Since new species are always evolving wouldn't there always be new species to name?

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But what is a species? by OmegaGeek · 2003-01-12 17:31 · Score: 2, Insightful

I should start by saying that I think this is a noble project. The shadow that humanity is casting across the earth threatens to leave all other species in oblivion, except for those we have genetically engineered or deemed economically beneficial.

A major technical problem, however, is trying to define the limits that constitute a species. This is sometimes tricky with animals, and in some families of plants, it is practically impossible. (If I remember my bio 101 correctly from all those years ago). The project sounds similar to what Lineus and the other naturalists were trying to do just before Darwin and the evolutionists bollixed everything up.

I only hope we leave enough other species around so that when we go, the cockroaches inherit a viable planet. And in case they are listening, "we salute you, our insect overlords". Or perhaps an inanimate carbon rod will save us all.

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Re:skeptical by MillionthMonkey · 2003-01-12 17:42 · Score: 3, Insightful

Not going to happen. They would first have to come up with an adequate universal definition of a species, and they haven't done that in the last 150 years (Darwin addressed this issue).

The lack of a definition for "species" is a problem for humans who like definitions, not for nature, which doesn't care if things become hard to define.
Some things, like pornography and race, are just not easily definable. Usually people use the standard of recognition (i.e. "I know it when I see it") which works well enough for most purposes.

Re:Not as easy as it sounds. by the+gnat · 2003-01-12 17:59 · Score: 5, Insightful

The current rate of discovery is a mere 10,000 a year. With an estimated 100 milion species, it'd take, well, forever.

I think the idea is to identify species based on a genomic fingerprint- the usual marker is actually the sequence of 16S RNA (part of the ribosome). They simply collect as many samples as possible and feed them into the sequencer, and then use computers to determine the relationships.

At least that's what I assume from the article. I don't really think this is worthwhile, because it's easy for two organisms to be nearly identical on the sequence level and still be non-mating. You could have a single polymorphism be the only thing separating two species simply because of change in color, metabolism, etc., coupled with reproductive isolation. In particular, 16S RNA is used for large-scale cladistics because it changes relatively little over time, but this means that the difference between an Amazonian Spotted Yellow Frog and an Amazonian Spotted Green Frog may be nil at that level.

If they're looking at entire genomes, on the other hand, the technology simply won't be powerful enough for some time, particularly if they run into weird or huge genomes. Our genome is small compared to some of the projects underway, and the problem with everything on that scale is figuring out the damn repeats.

Sure. by Suppafly · 2003-01-12 18:22 · Score: 3, Insightful

A hugely ambitious project to find and name every species on Earth within the next 25 years has been launched by scientists.

Haven't they been doing that for the last couple of hundred years? What makes them think the can do it in 25 when a few hundred years of science has just barely scrapped the surface.

Must not apply to microbes... by Tuxinatorium · 2003-01-12 18:41 · Score: 4, Insightful

There are so many varieties and they evolve so quickly, that it would be impossible to catalog all of them because there are constantly new species being made. Besides, the distinction between divergent strains of a species and different but related species is completely arbitrary on that scale, because they don't have sexual reproduction. In mammals, the ability to produce fertile offspring generally draws the boundaries between species.

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Re:The real question is by below_the_sea · 2003-01-12 20:03 · Score: 2, Insightful

The cataloging bit is not so much the goal here. Nor is completeness. As you can read in the article, the people who are currently trying to preserve parts of nature can't make proper decisions on which bits to preserve and which to neglect because of their lower conservational value.

Most conservation efforts start with identifying what's actually present inside an area. For a few groups such as birds, mammals, and butterflies, we have a pretty good knowledge of who's present, despite the occasional deer being discovered in Vietnam or the ten or so new bird species Peru has reveiled over the last few years. But in most groups, which actually account for 99% of biodiversity were are at a complete loss. So much for making sound judgements on where to make the next National Parks.

In order to know how much biodiversity actually needs to be preserved to for instance keep speciation going, or to keep extinction at a minimum, we have to get some basic insight into current state of affairs. Again, just knowing what species you're dealing with is a prerequisite if you want to obtain a global picture.

So from a practical point of view, completeness of the database is not essential. Getting our working knowledge of species from 1% to 50% would be a great step forward, and would probably be enough to obtain much better estimates of extinction rates.

As to how to even get DNA from all those millions of species, most of which have such small ranges and thrive in low numbers in inhospitable places, I can't say I have much of a clue either.

Anthropology by ndogg · 2003-01-12 20:30 · Score: 5, Insightful

They should start asking the indiginous people of the various places they go to about the animals they encounter, especially if they are nomadic. The folklore, myths, traditions, stories, etc. often serve purposes beyond that of creating a basis for religion. Many of them have been created to help them survive the environment they live in. Not only that, but they also seem to allow to live within these environments without destroying them. This is something anthropologists have known for some time now. Western biologists often have the bad habit of dismissing these things, particularly if they are tribal, under the misconceived notion that they are "primitive" and could not possibly understand the plants and animals around them, when in fact it's their vast amounts of knowledge of the plants and animals around them that allows them to survive.

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// file: mice.h
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Every species in 2028? by C+A+S+S+I+E+L · 2003-01-13 00:02 · Score: 4, Insightful

Here's an exhaustive list of every species which will be alive on the planet in 2028:

1. Man.

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