The Loom

The Kanisza Virus

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

  1. #1 linguist
    August 24, 2005

    “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.

  2. #2 BC
    August 24, 2005

    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.

  3. #3 Andrew Brown
    August 24, 2005

    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.

  4. #4 Doug
    August 24, 2005

    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.

  5. #5 John Wilkins
    August 24, 2005

    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.

  6. #6 Dan S.
    August 24, 2005

    ‘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, 217266.) – 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. : (

  7. #7 Dan S.
    August 24, 2005

    ‘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, 217266.) – 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. : (

  8. #8 Dan S.
    August 24, 2005

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

  9. #9 Christian Tanzer
    August 25, 2005

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

  10. #10 Torbjorn Larsson
    August 25, 2005

    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.

  11. #11 Gun Of Sod
    August 25, 2005

    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.

  12. #12 hoopman
    August 25, 2005

    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…