Corante

Corante: technology, business, media, law, and culture news from the blogosphere
<$MTBlogName$> OUR PUBLICATIONS:
Corante Blogs

Corante Blogs examine, through the eyes of leading observers, analysts, thinkers, and doers, critical themes and memes in technology, business, law, science, and culture.

The Press Will Be Outsourced Before Stopped

Vin Crosbie, on the challenges, financial and otherwise, that newspaper publishers are facing: "The real problem, Mr. Newspaperman, isn't that your content isn't online or isn't online with multimedia. It's your content. Specifically, it's what you report, which stories you publish, and how you publish them to people, who, by the way, have very different individual interests. The problem is the content you're giving them, stupid; not the platform its on."
by Vin Crosbie in Rebuilding Media

Travels In Numerica Deserta

There's a problem in the drug industry that people have recognized for some years, but we're not that much closer to dealing with it than we were then. We keep coming up with these technologies and techniques which seem as if they might be able to help us with some of our nastiest problems - I'm talking about genomics in all its guises, and metabolic profiling, and naturally the various high-throughput screening platforms, and others. But whether these are helping or not (and opinions sure do vary), one thing that they all have in common is that they generate enormous heaps of data.
by Derek Lowe in In the Pipeline

Disrobing the Emperor: The online “user experience” isn't much of one

Now that the Web labor market is saturated and Web design a static profession, it's not surprising that 'user experience' designers and researchers who've spent their careers online are looking for new worlds to conquer. Some are returning to the “old media” as directors and producers. More are now doing offline consulting (service experience design, social policy design, exhibition design, and so on) under the 'user experience' aegis. They argue that the lessons they've learned on the Web can be applied to phenomena in the physical and social worlds. But there are enormous differences...
by Bob Jacobson in Total Experience

Second Life: What are the real numbers?

Clay Shirky, in deconstructing Second Life hype: "Second Life is heading towards two million users. Except it isn’t, really... I suspect Second Life is largely a 'Try Me' virus, where reports of a strange and wonderful new thing draw the masses to log in and try it, but whose ability to retain anything but a fraction of those users is limited. The pattern of a Try Me virus is a rapid spread of first time users, most of whom drop out quickly, with most of the dropouts becoming immune to later use."
by Clay Shirky in Many-to-Many

The democratisation of everything

Over the last few years we've seen old barriers to creativity coming down, one after the other. New technologies and services makes it trivial to publish text, whether by blog or by print-on-demand. Digital photography has democratised a previously expensive hobby. And we're seeing the barriers to movie-making crumble, with affordable high-quality cameras and video hosting provided by YouTube or Google Video and their ilk... Music making has long been easy for anyone to engage in, but technology has made high-quality recording possible without specialised equipment, and the internet has revolutionised distribution, drastically disintermediating the music industry... What's left? Software maybe? Or maybe not."
by Suw Charman in Strange Attractor

RNA Interference: Film at Eleven

Derek Lowe on the news that the Nobel Prize for medicine has gone to Craig Mello and Andrew Fire for their breakthrough work: "RNA interference is probably going to have a long climb before it starts curing many diseases, because many of those problems are even tougher than usual in its case. That doesn't take away from the discovery, though, any more than the complications of off-target effects take away from it when you talk about RNAi's research uses in cell culture. The fact that RNA interference is trickier than it first looked, in vivo or in vitro, is only to be expected. What breakthrough isn't?"
by Derek Lowe in In the Pipeline

PVP and the Honorable Enemy

Andrew Phelps: "Recently my WoW guild has been having a bit of a debate on the merits of Player-vs.-Player (PvP) within Azeroth. My personal opinion on this is that PvP has its merits, and can be incredible fun, but the system within WoW is horridly, horribly broken. It takes into account the concept of the battle, but battle without consequence, without emotive context, and most importantly, without honor..."

From later in the piece: "When I talk about this with people (thus far anyway) I typically get one of two responses, either 'yeah, right on!' or 'hey, it’s war, and war isn’t honorable – grow the hell up'. There is a lot to be said for that argument – but the problem is that war in the real historical world has very different constraints that are utterly absent from fantasized worlds..."
by Andrew Phelps in Got Game

Rats Rule, Right?

Derek Lowe: "So, you're developing a drug candidate. You've settled on what looks like a good compound - it has the activity you want in your mouse model of the disease, it's not too hard to make, and it's not toxic. Everything looks fine. Except. . .one slight problem. Although the compound has good blood levels in the mouse and in the dog, in rats it's terrible. For some reason, it just doesn't get up there. Probably some foul metabolic pathway peculiar to rats (whose innards are adapted, after all, for dealing with every kind of garbage that comes along). So, is this a problem?.."
by Derek Lowe in In the Pipeline

Really BAD customer experience at Albertsons Market

Bob Jacobson, on shopping at his local Albertsons supermarket where he had "one of the worst customer experiences" of his life: "Say what you will about the Safeway chain or the Birkenstock billionaires who charge through the roof for Whole Foods' organic fare, they know how to create shopping environments that create a more pleasurable experience, at its best (as at Whole Foods) quite enjoyable. Even the warehouses like Costco and its smaller counterpart, Smart & Final, do just fine: they have no pretentions, but neither do they dump virtual garbage on the consumer merely to create another trivial revenue stream, all for the sake of promotions in the marketing department..."
by Strange Attractor in Total Experience

The Guardian's "Comment is Free"

Kevin Anderson: "First off, I want to say that I really admire the ambition of the Guardian Unlimited’s Comment is Free. It is one of the boldest statements made by any media company that participation needs to be central to a radical revamp of traditional content strategies... It is, therfore, not hugely surprising to find that Comment is Free is having a few teething troubles..."
by Kevin Anderson in strange
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

The Loom

« A View From the Left (Sigh) | Main | Bush, Frist...McCain »

August 24, 2005

The Kanisza Virus

Email This Entry

Posted by Carl Zimmer

kanisza.jpgScientists have been making some remarkable discoveries about viruses recently that may change the way we think about life. One place to start understanding what it all means is by looking at this picture.

You can't help put see a bright triangle with its three corners sitting on top of the black circles. But the triangle exists only in your mind. The illusion is known as a Kanisza triangle, and psychologists have argued that it plays on your brain's short-cuts for recognizing objects. Your brain does not bother to interpret every point of light that hits your retina in order to tell what you're looking at. Instead, it pulls out some simple features quickly and makes a hypothesis about what sorts of objects they belong to. It's fast and pretty reliable, allowing you to make quick decisions. For getting us through our ordinary lives, it's good enough. But as a guide to objective reality, it is far from perfect. What's really weird about the Kanisza trinagle is that even when you accept that it doesn't exist (cover up the circles and watch it disappear) you can still can't stop yourself from seeing it. You just have to accept that your brain's short-cuts are fooling you.

Scientists have documented lots of illusions that may expose many other mental short-cuts. And it's possible that one of them may interfere with the way we think about life. For most of the history of Western thought, natural philosophers tried to divide up living things into species and other groups on the belief that each group shared an underlying nature--an essence. Birds all have feathers, setting them off from other animals. People always give birth to people, rather than rabbits or trout. But recent psychological research suggests that essentialism is not something we come to after years of careful thought. We are essentialists from childhood. (For a nice summary of this research, see this recent article by University of Michigan psychologist Susan Gelman.) Children seem to put things into categories and come to believe that there are deep, non-obvious differences between the categories, even if they don't know what those differences are. The essence of these things is stable, children believe, and intrinsic--particularly when those things are species.

Why do we have this essence-perceiving faculty in our brains? One possibility--an adaptationist explanation--is that it helps us to predict how things will act, and allows us to come up with a reliable response. If you meet a lion, you don't need to sit down and get to know that individual lion to figure out how it will act. A lion is a lion, and you run. Of course, that particular lion might be blind or tame or a guy in a lion suit. But you're probably better off just letting the essence of lions be your guide.

Essences can act as a rough guide to organizing the world. A bird guide distinguishes different species by their unique colors and shapes. But our essentialist brains can also get us into trouble. In the 1700s naturalists could not draw clear lines between species of plants that could clearly hybridize. The discovery of the platypus in the early 1800s--an animal that nursed its young like mammals but laid eggs unlike any other mammal--posed an enormous headache. When Darwin and other scientists began arguing that humans shared a common ancestry with chimpanzees and gorillas, anatomists such as Richard Owen desperately tried to find traits in the human brain that would firmly set us apart--signs, as it were, of our unique essence. Owen failed, and today's research on the human genome helps to show what a futile effort he was making. Humans are different, just like each species is, but they are also linked to other species by common descent. They have no more of a special essence than the branches on a tree.

Which brings us to viruses. Viruses have traditionally been considered fundamentally different than "true" organisms, such as bacteria, animals, and plants. That's because all viruses that scientists studied were just simple bags of genes, made up of tiny bits of genetic material encased in protein shells. They were not truly alive, because their few genes could only be copied and turned into proteins with the help of a cell's biochemical machinery. Outside a cell, they were inert, lifeless packages drifting through the world, waiting to bump into a new host.

Last year this essence of viruses began to blur. Scientists discovered a gigantic virus capable of making 150 proteins, including enzymes for repairing DNA and for translating a gene's code into protein. Its entire genome is 1.2 million base pairs long--about twice as long as the smallest genomes of parasitic bacteria. These viruses are not rare flukes. Just a few days ago, scientists reported on how they plumbed a database of DNA gathered by Craig Venter from the Sargasso Sea and found signs that there are a lot of these giant viruses floating out in the oceans.

Today, viruses from another part of the world blurred their essence even more. Scientists reported in Nature the discovery of strange viruses from hot springs in Italy. The viruses reproduce inside microbes, and when they burst out of their host, they do not remain inert. Instead, they continue developing, growing tails made out of filament-shaped proteins that are encoded by their own genes. It's not clear from the report whether the viruses can make the proteins themselves, or if their hosts make them and then squirt them out into the surrounding water. But whichever the case, the scientists conclude that viruses "may be even more biologically sophsticated than previously recognized."

The discoverers of the "living" virus compared some of its genes to those of other organisms and argued that it has an ancient history, descending from organisms that lived four billion years ago, before the major branches of life had emerged. Some critics have argued that these viruses actually stole the genes from their hosts and incorporated them into their own genome, but the original team has rebutted them in a paper submitted to Virus Research. It is still possible that these viruses stole some of their genes from their hosts, because the evidence of viral gene theft is now overwhelming. On the other hand, viruses seem to have sometimes donated their genes to their hosts. Some researchers have even argued that many of the key components of our own cells, from DNA-copying enzymes to DNA itself--began as viruses.

So try to ignore that urge to see viruses as a separate kind from us, just as you try to ignore the triangle that isn't there. Despite what we may think, life is a wonderful blur.

Comments (12) + TrackBacks (0) | Category: Evolution


COMMENTS

1. linguist on August 24, 2005 03:26 PM writes...

"Children seem to put things into categories and come to believe that there are deep, non-obvious differences between the categories, even if they don't know what those differences are....Why do we have this essence-perceiving faculty in our brains?"

It is this instinctual ability (I would say "drive") that allows us to acquire language. Mental categories such as 'noun' and 'verb', 'part' and 'whole', 'self' and 'other' are arguably the earliest forms of reasoning humans do. We'd likely have no language, culture, or science without this use of categorization.

Permalink to Comment

2. BC on August 24, 2005 03:48 PM writes...

For most of the history of Western thought, natural philosophers tried to divide up living things into species and other groups on the belief that each group shared an underlying nature--an essence. Birds all have feathers, setting them off from other animals. People always give birth to people, rather than rabbits or trout.

When I talk to creationists, they seem to have this very idea as one foundation of their worldview. And when they say things like, "I don't believe in evolution because I've never seen a dog give birth to a cat" or "I've seen a dog and I've seen a cat, but I've never seen a dat", they are arguing for an essentialist understanding of the world. Those of us who have compared genomes of species, however, realize how flawed this reasoning is.

Permalink to Comment

3. Andrew Brown on August 24, 2005 04:30 PM writes...

Essentialism is surely related to Pascal Boyer's ideas about "templating", which, he argues, is the process by which belief in supernatural beings is generated. A ghost is, for example, just like a person, except that it has no body. But in all other respects, it fits the "person" template, and certainly the "animate" one. So you might say that it is essentially animated -- from that, a short step to believing that there is some essence of animation.

Permalink to Comment

4. Doug on August 24, 2005 06:46 PM writes...

This 'essentialism' sounds pretty much the same as Eleanor Rosch's (http://en.wikipedia.org/wiki/Eleanor_Rosch) Prototype theory (http://www.strath.ac.uk/ecloga/Giannakopoulou.htm), so I don't think it's a recent discovery. I doubt that intelligence is possible without categorial perception.

Permalink to Comment

5. John Wilkins on August 24, 2005 08:52 PM writes...

For most of the history of Western thought, natural philosophers tried to divide up living things into species and other groups on the belief that each group shared an underlying nature--an essence. Birds all have feathers, setting them off from other animals. People always give birth to people, rather than rabbits or trout.

Sorry, Carl, but this is just wrong. Sure, philosophers tried to define formal essences, but species were always understood to be the reproduction of form. The earliest material essentialists are at best 18thC, and in my view after Darwin.

Ernst Mayr and G. G. Simpson are misreading the historical material.

Permalink to Comment

6. Dan S. on August 24, 2005 10:23 PM writes...

'Living' viruses . . . wow. Amazing world.

In structural anthropology (deeply influenced by structural linguistics), categorization -esp. binary oppositions - are very important; interestingly, things seen as being 'betwixt and between' as often - it's argued -viewed as being very special, powerful (for better or worse). For example, Levi-Strauss said that Coyote was a trickster in many Native American cultures because he crosses boundries - plant-eater/meat-eater, agriculture/hunting, life/death - and serves as a mediator, resolving contradictions between these things. Mary Douglas examined other anamalous animals - non-kosher foods in Judaism were those odd creatures that fell between categories and were therefore considered unclean (cloven hooved animals that ruminate are clean, non-cloven ruminants (camels) and cloven non-ruminants (pigs) aren't; among the Lele of Africathe pangolin - a mammal with scales found in trees - is given a special status, etc. . . .

"When I talk to creationists, they seem to have this very idea as one foundation of their worldview."

Evans - mentioned in the Gelman article (Evans, E, M. (2001). Cognitive and contextual factors in the emergence of diverse belief systems: Creation versus evolution.Cognitive Psychology, 42, 217–266.) - sees essentialism as a factor in the development of evolutionary or creationist beliefs in kids - it seems to be a bar to the devlopment of evolutionary explanations that can be overcome by experience & knowledge (fossils, etc - hey, animals can change!), but not if the cultural context strongly supports it -when it is "not only reified, but deified," in a nice turn of phrase, you get coherent creationist belief, when it's challenged, you can get coherent evolutionary beliefs. (This is a horrible summary - most of the article goes right over my head, and there's a lot more than this.

I tend to think that unfamiliarity not just of the fossil record but of living organisms may play a role in the evolution/creation bustup. Most people in industrialized societies just aren't familar with too many animals, especially, if you're not a farmer or science/nature buff. Most of the ones folks do know about are highly processed,either culturally (ie, Mickey Mouse) or literally (you mean meat doesn't just come from the supermarket in precut, plastic-wrapped pieces??!). Look around and you usually see pretty big gaps - cats and dogs, for example. Look at the Carnivora -even without fossil evidence - and essentialism seems maybe less tenable. But as the structuralists and the creationist discussions suggest, that won't necessarily make much of a difference, if there's strong support/preexisting commitment to it . . .

"Those of us who have compared genomes of species, however, realize how flawed this reasoning is."
It bewilders me - creationists (ID and otherwise) will talk about sophisticated (if probably meaningless) ideas about DNA and information and all, but don't ever discuss (at least that I remember) what might explain the pattern of relationships . . . Not even to go, well, yeah, this is where Darwinism goes wrong - just nothing. What's up with that? (Although probably if I look a little . . .)

Darn. I'm so concerned over this whole ID silliness that all sorts of cool stuff's just getting filtered through it. : (

Permalink to Comment

7. Dan S. on August 24, 2005 10:36 PM writes...

'Living' viruses . . . wow. Amazing world.

In structural anthropology (deeply influenced by structural linguistics), categorization -esp. binary oppositions - are very important; interestingly, things seen as being 'betwixt and between' as often - it's argued -viewed as being very special, powerful (for better or worse). For example, Levi-Strauss said that Coyote was a trickster in many Native American cultures because he crosses boundries - plant-eater/meat-eater, agriculture/hunting, life/death - and serves as a mediator, resolving contradictions between these things. Mary Douglas examined other anomalous animals - non-kosher foods in Judaism were those odd creatures that fell between categories and were therefore considered unclean (cloven hooved animals that ruminate are clean, non-cloven ruminants (camels) and cloven non-ruminants (pigs) aren't; among the Lele of Africa the pangolin - a mammal with scales found in trees - is given a special status, etc. . . .

"When I talk to creationists, they seem to have this very idea as one foundation of their worldview."

Evans - mentioned in the Gelman article (Evans, E, M. (2001). Cognitive and contextual factors in the emergence of diverse belief systems: Creation versus evolution.Cognitive Psychology, 42, 217–266.) - sees essentialism as a factor in the development of evolutionary or creationist beliefs in kids - it seems to be a bar to the devlopment of evolutionary explanations that can be overcome by experience & knowledge (fossils, etc - hey, animals can change!), but not if the cultural context strongly supports it -when it is "not only reified, but deified," in a nice turn of phrase, you get coherent creationist belief, when it's challenged, you can get coherent evolutionary beliefs. (This is a horrible summary - most of the article goes right over my head, and there's a lot more than this.

I tend to think that unfamiliarity not just of the fossil record but of living organisms may play a role in the evolution/creation bustup (Evans touches on this a bit, I think, asking parents about the importance, etc of nature-related kid activities.) Most people in industrialized societies just aren't familar with too many animals, especially if you're not a farmer, don't live in a rural area, or aren't a science/nature buff. Most of the ones folks do know about are highly processed,either culturally (ie, Mickey Mouse) or literally (you mean meat doesn't just come from the supermarket in precut, plastic-wrapped pieces??!). Look around and you usually see pretty big gaps - cats and dogs, for example. Look at the Carnivora -even without fossil evidence - and essentialism seems maybe less tenable. But as the structuralists and the creationist discussions suggest, that won't necessarily make much of a difference, if there's strong support/preexisting commitment to it . . .

"Those of us who have compared genomes of species, however, realize how flawed this reasoning is."
It bewilders me - ID and other creationists will bring up sophisticated (though probably meaningless) ideas about DNA and information and all, but as far as I can remember don't ever suggest any explanation for the pattern of relationships . . . Not even to go, well, yeah, this is where Darwinism goes wrong - just nothing, even folks who know many facts about bio. What's up with that? (Although probably if I look a little - they must, right?)

Darn. I'm so concerned over this whole ID silliness that all sorts of cool stuff's just getting filtered through it. : (

Permalink to Comment

8. Dan S. on August 24, 2005 10:40 PM writes...

oops - it looked like it bounced, so I edited a bit and reposted . . .sorry!

Permalink to Comment

9. Christian Tanzer on August 25, 2005 03:21 AM writes...

George Lakoff gives a very interesting account of essentialism and human categorization in his book 'Women, Fire, and Dangerous Things'.

Permalink to Comment

10. Torbjorn Larsson on August 25, 2005 07:24 PM writes...

I have never been bothered by virus lack of metabolism since I have used the essentialistic device of healthy human vs infected human (from virus, bacteria, parasite). The infected human is a more complex metabolic system and the specific nature of the infection agent does not matter.

Permalink to Comment

11. Gun Of Sod on August 25, 2005 09:14 PM writes...

It's great to hear about another discovery that blurs the line between the categories of species, any new transition organism is another example of evolution in action.

The problem of course is that for every new example of transition organism discovered, there now opens up two new gaps in the evolutionary record for evolutionists to defend, although I think at some point the differences are going to get so negligable that IDer's are going to have to admit to the fallacy of their hypothesis (maybe this is to reasonable to hope for?).

One thing I would like to find out about, and perhaps someone here could answer my question? From my understanding the ID hypothesis posits that there is some point in the process of ambiogenisis which required the intervention of some outside intelligence in order to proceed. Is there any clearly defined point that they say this must have happened at; was it during the development of amino acids, proteins, RNA, DNA, cell membranes, prokaryote, eukaoryote?

Can anyone help with this, I would like to get on the offensive concerning this debate, and so far most of the positions I have heard are contradictory or not defined.

Permalink to Comment

12. hoopman on August 25, 2005 11:52 PM writes...

Now THIS is just mesmerizing. THIS is so much more interesting than debating I.D. Thanks for the great stuff, Carl. I haven't seen this one anywhere else yet.

Repeat:
I will avoid Deepaks blog...
I will avoid Deepaks blog...

Permalink to Comment


EMAIL THIS ENTRY TO A FRIEND

Email this entry to:

Your email address:

Message (optional):




RELATED ENTRIES
Talking at Woods Hole
Invisible Gladiators in the Petri Dish Coliseum
Synthetic Biology--You are There
Manimals, Sticklebacks, and Finches
Jakob the Hobbit?
Grandma Manimal
Hominids for Clinical Trials--The Paper
The Neanderthal Genome Project Begins