Thursday, April 30, 2009

Education Optional?

The web site talks about a new law proposed in the province of Alberta that would allow parents to allow their children to "opt out" of classes that offended the religious beliefs of their parents.

According to the web site:

"The new rules, which would require schools to notify parents in advance of 'subject-matter that deals explicitly with religion, sexuality or sexual orientation,' is buried in a bill that extends human rights to homosexuals. Parents can ask for their child to be excluded from the discussion."

Of course despite being part of a human rights bill and using sexual preferences as the specific example, it applies to evolution as well.

As one blogger puts it (at ):

"This is a very stupid move by stupid people that will produce more stupid people.

"It neglects a fundamental property of education: that in order to learn, you have to be exposed to many new and sometimes difficult ideas. We teach about subjects that no one thinks are good, because you need to know about them to have an informed opinion. The Holocaust was horrible and painful — shall we allow children to avoid exposure to it? Fundamentalist parents may gnash their teeth in fury at the very idea of evolution — but how can they disagree with it rationally, if they don't even know what it is?"

This is simply another example of that anti-intellectual character of religious conservatives.

Ten Specific Predictions of Evolution

Here's a sample list of very specific predictions made by evolution. There are many more that I did not include. I got most of them from the talkorigins web site at

1. We should not find any early hominid fossils (such as Australopithicus, Ardipithecus, or Kenyanthropus) in Australia, North America, South America, Antarctica, Siberia, or on any oceanic islands removed from Africa.
2. No birds will have mammary glands or hair.

3. No mammals will have feathers (even though feathers are an excellent means of insulation).

4. No fish or amphibians will have differentiated or cusped teeth, since these are only characteristics of mammals.

5. We should never find mammalian or bird fossils in or before Devonian deposits, before reptiles had diverged from the amphibian tetrapod line. This excludes Precambrian, Cambrian, Ordovician, and
Silurian deposits, encompassing 92% of the earth's geological history.

6. We will never find a living or fossilized true chimera such as Pegasus, Mermaid or Griffin.

7. We will never find birds with both wings and arms, since the evolution of wings necessarily means the loss of arms.

8. No marine mammal (such as dolphins, porpoises and whales) will have gills despite the fact that gills would be very beneficial.

9. No reptile or mammal will have eyes without retinal blind spots. This is because poor design cannot be "fixed" by evolutionary processes, even if correcting the problem would be beneficial for the organism. The only "fixing" that is allowed evolutionarily is relatively minor modification of what already exists.

10. All living things on Earth will share the same nucleic acid genetic material.

Creationists will undoubtedly respond that many of these things are simple evidence of a common designer. In fact, if true, that designer is not very competent.

Consider prediction 10 in relation to the recently well-publicized swine flu. That flu jumped from pigs to humans. That is only possible because pigs and humans share the same genetic code. So a truly competent designer would have, presumably, used different genetic codes in pigs and humans in order to prevent the possibility of such an event from taking place. Note that this is NOT explained by the "Fall of Man" since the genetic codes in humans and pigs can't have changed since the [mythical] Garden of Eden.

There are many other predictions made by evolution.

There are NONE made by creationism.

Unless, of course, some creationist can come up with a similar set of predictions which, if not found to be true, would falsify their beliefs.

The Swine Flu Virus is EVOLVING

Someone on TV today used the correct word when describing the Swine Flu that we've heard so much about in recent days: EVOLVING.

They said that it is evolving, which it is.

Everyone else says that it is "mutating". It's doing that as well, but presumably some of the mutations are negative or neutral. The word EVOLUTION is more appropriate.

Here's an article from It's titled "Swine Flu Is Evolution in Action"

Anyone who thinks evolution is for the birds should not be afraid of swine flu. Because if there's no such thing as evolution, then there's no such thing as a new strain of swine flu infecting people.

For the rest of the population, concern is justified.

The rapid evolution of the influenza virus is an example of Nature at her most opportunistic. Viruses evolve by the same means as humans, plus they use tricks such as stealing genetic code from other viruses.

"The strategy is what makes the flu so virulent and often keeps the microbes one step ahead of scientists who would destroy or neutralize them.

Pigs to you

While much of the modern controversy over evolution centers around whether humans evolved from non-human primates (scientists overwhelmingly agree this is the case), some people still try to poke holes in the theory of evolution, one of the most solid theories in science. In addition to evidence from ancient fossils and modern DNA studies, one of the many lines of evidence supporting evolution is that it can quite simply be seen in action among some species that evolve particularly rapidly, such as fruit flies.

But on no stage does evolution unfold more quickly or with more potentially sickening or lethal consequences for humans than among viruses. It is, to pass on a scary phrase used among scientists and marketers, viral evolution. And you could be the star host of this all-too-often deadly show.

The sudden ability of the new swine flu virus to hop from pigs to humans and then to skip from person to person, at least in Mexico, is an excellent example of evolution at work.

“Yes, this is definitely evolution,” said Michael Deem, a bioengineer at Rice University in Texas.

Deem studies how evolution is affected not just by mutations but by the exchange of entire genes and sets of genes. Viruses, which are basically packets of DNA with a protein coat, are really good at this. Viruses are also really good at exploiting the fact that we humans cough and sneeze without covering ourselves and generally don't wash our hands frequently in a day.

“Viruses have evolved to exploit human contact as a way of spreading,” points out Peter Daszak of the Wildlife Trust, whose team 14 months ago predicted just this sort of evolution in an animal flu, coming from Latin America to the United States after evolving to infect people.

David Schaffer, a professor of chemical engineering and bioengineering at the University of California at Berkeley, explains the mechanics of how a flu virus morphs:

“For flu, there are multiple ways that diversity can arise (the virus has multiple strands of RNA in its genome, and it can mix and swap strands with different flu variants to give rise to fully novel variants ... in addition, each strand can individually mutate),'” Schaffer explained this week.

"Furthermore, in this case, the 'enhanced' property from the virus' point of view is the ability to infect humans. So, this is viral evolution.”

There's more including a discussion of whether or not viruses are alive.

But all of this shows that evolution is all around us and we see it in everyday life. Moreover it also demonstrates an example of beneficial mutations - at least from the perspective of the virus.

Tuesday, April 28, 2009

The First Cell

This is from an artilce by Carl Zimmer
From the November 1995 issue, published online November 1, 1995
I believe that it's the best explanation for how the first cell formed that I can find.

To most who search for life's origins, genes are everything. But as David Deamer keeps reminding them, without a container for those genes, there can be no life.

Part of the definition of life, says David Deamer, is that it is in a place.

Deamer is not uttering a koan in a Zen monastery. He’s sitting next to a microscope in a biology laboratory at the University of California at Santa Cruz. Deamer is a hard-core biophysicist, but still there is a monkish quality to him.

It comes not just from his unnervingly gentle manner of speaking but from his entire approach to science. This is a man who, in contemplating the pattern of nucleotides in DNA--represented by the letters A, C, G, and T--was reminded of musical notation. By allowing the letters to stand for notes instead of nucleotides--and using E as the equivalent of T--he turned human DNA into hypnotic melodies, available now for your meditative pleasure on both tape and CD. Deamer himself likes to hum the insulin gene. This is a man who isolates chemicals from meteorites and asks guests in his lab, Do you want to smell outer space?

It doesn’t hurt to have such a cosmic view of things in Deamer’s chosen field of study: the origin of life. Deamer is unusual even among the few dozen researchers in his field, and not just in his discography. For most of the others, explaining the origin of life means explaining the origin of the genetic code: How did DNA arise from chemical reactions on the early Earth? How did the original building blocks of today’s genetic code assemble themselves into crudely self-reproducing units? Were the first life-forms based not on double-stranded DNA but on single-stranded RNA?

For the past 18 years, though, Deamer has been gently reminding his colleagues that these questions define only part of the puzzle of life. DNA does not float loosely through the oceans. Life is constrained in a place--or, to be more specific, within a boundary. Life is chemical interaction, and for that interaction to occur, life’s molecules must be close to one another. Without a physical boundary of some sort, without a skin, a bark, or a cell membrane, an organism is nothing more than a diffusing blur of molecules. To explain how the first creature came to be, you have to explain how its innards got to be distinguished from its surroundings. In other words, you’ve got to explain how the first single- celled creature got encapsulated in a cell.

Over the years Deamer has persistently been teasing out some answers to this thorny question. Now he has reached a milestone. Under conditions something like those on the early Earth, he can create something like a cell: an enzyme-carrying bubble that draws in nutrients from its surroundings and crafts them into genetic material. Call it a quasi cell-- and say that Deamer has created quasi life.

A cell membrane’s importance to life is often underappreciated, says Deamer. People say, ‘Well, it’s just a little bag.’ But it’s much more. It’s the interface between life and everything that’s outside. The membrane of any cell has to do many things at once. It has to be impermeable enough to keep essential things (like DNA) in and harmful things (like viruses and poisons) out. Yet a cell membrane can’t form a perfect seal. It has to be able to flush out waste and heat from its own system and take in nutrients from the surrounding medium. And the first cell membrane, like the membranes of many single-celled organisms today, probably had to be able to collect energy as well.

When Deamer began his work on membranes as a graduate student in the early sixties, biologists were just learning what membranes were made of: thin films of oil composed of molecules called lipids, tadpole-like things with little heads and long tails. The heads are made of charged groups of atoms, such as sugars or phosphates, while the tails are long chains of uncharged carbon and hydrogen atoms.

All cells exist in a watery world. A water molecule, though neutral, can behave as if charged because of its polar structure: the oxygen atom pulls the electrons of the two hydrogen atoms toward it, making the oxygen end of the molecule more negative and the hydrogen more positive. This polar structure is the basis for an interesting relationship between water molecules and lipids: the lipid’s charged head can form a weak bond with a water molecule, but the uncharged tail cannot. Thus, in a cell wall, lipids are usually arranged in sheets made of two layers, with the lipids in each layer pointing in opposite directions. The water-loving heads contact water both inside and outside the cell, while the water- loathing tails stay tucked safely within the wall’s oily interior.

Arranged this way, lipids make surprisingly good barriers. A neutral or a weakly polar molecule, like water, can pass through without much effort--thus ensuring that cells won’t dry out. But a fully charged molecule, or ion, trying to fight its way through the uncharged lipid tails needs a lot of energy--10,000 times more energy than that needed by a water molecule. That’s why if you try to dissolve salt in oil, it’s not going to work; it’s just going to sit there, says Deamer. Thanks to lipids, therefore, a cell can keep out harmful ions while holding in ions it uses in the production of energy.

In the early sixties biophysicist Alec Bangham of the Animal Physiology Institute in Cambridge, England, made a remarkable discovery about lipids: they can put themselves together. When he extracted lipids from egg yolks and threw them into water, he found that the lipids would naturally organize themselves into double-layered bubbles roughly the size of a cell. Bangham’s bubbles soon became known as liposomes.

Deamer was intrigued when he learned of these cellular shells. In 1975 he went to England to work with Bangham, taking a sabbatical from the University of California at Davis, where he then taught. Together Bangham and Deamer thoroughly studied the self-created liposomes, figuring out ways to increase their volume. That work helped open the door to subsequent research that has made it possible to use liposomes to carry drugs and repaired genes into the body. And those discoveries have attracted an intensely interested audience of biotechnology firms.

But it was then, 20 years ago, that Deamer and Bangham also realized that liposomes might have provided life’s first shelter. Previously, researchers had assumed that membranes were always built the way they are now--by an intricate system in which DNA provides the blueprints for the structure, and RNA ferries the instructions to the cell’s protein-making factories. If so, then genetic molecules had to exist before membranes. But studies of liposomes demonstrated that if lipids existed at the dawn of life, they would naturally, and quickly, have formed simple, albeit empty, membranes.

If there were lipid-like molecules on the early Earth, says Deamer, there must have been membranes that would have predated life. They would have been just hanging around there as little bubbles until something came along to inhabit them. These bubbles might have engulfed early molecules that had the crude ability to replicate. The liposomes would thus be able to protect them from their harsh surroundings and concentrate them so that they could react (and evolve) quickly and efficiently.

When he returned to Davis, Deamer pursued the membrane first hypothesis, experimenting with mixtures of three compounds researchers believed existed on the early Earth: fatty acids, glycerol, and phosphates. In the right concentrations, he found, they formed into lipids, and in turn, the lipids spontaneously assembled into liposomes. Now Bangham’s ponderings had turned into some real chemistry, and Deamer’s journey to life’s genesis had begun.

The waves that crash on the shores around Santa Cruz must first travel over the jungles of kelp in Monterey Bay. They pick up some of the flotsam of the underwater forests: loose seaweed, the rare seal’s corpse, fragments of countless dead plant and animal cells. As the waves come closer to land, the lipids in this cellular debris rise to the surface and lift their water-hating tails to the air. The waves mix them together and they join into bubbles. This cream-colored foam is different from the normal silver froth of churning water; its bubbles are so stable that it holds together on the water’s surface. Sometimes when the waves reach the coast, the foam shoots through channels of rock like eggnog blasted from a fire hose. Other times it collects offshore into long ribbons, then rides up onto the sand and into tide pools, where it sits quivering in the wind.

A short trek inland, in a grove of redwoods, is Deamer’s new lab, where he has been for the past year. Santa Cruz is a more appropriate setting for his work than the flat farms around Davis; what is happening down on the beach is much like what Deamer thinks happened at the dawn of life.

To demonstrate those first steps, Deamer repeats an experiment he first did a dozen years ago. At the time, he explains, many researchers resisted the membrane-first hypothesis precisely because a liposome is so impermeable. A conceptual barrier that everyone then had in their head was that there couldn’t have been membranes on the first forms of life because you couldn’t get big molecules inside them. But there’s actually an easy way, he explains as he picks through a frosty tray of assorted vials he has taken out of the laboratory freezer.

He opens a jar of lipids, extracted from egg yolk, and mixes some of the clear oil into a small test tube of water. To the naked eye the water seems unchanged, except that it has taken on a slightly milky quality; in actuality it is now full of microscopic bilayered bubbles. Deamer extracts a few drops from the mixture and puts them on a glass slide. With the casual precision of a veteran chef, he then adds dried white threads of DNA from salmon sperm to a second test tube, where they turn gooey. He spikes the solution with a fluorescent stain and adds some of these DNA drops to the lipids on the slide. Why don’t we get the hot plate going? he says to Ajoy Chakrabarti, his postdoctoral researcher. Chakrabarti switches it on and puts the slides on its surface.

That’s our tide pool, Deamer says, nodding toward the hot plate. Imagine a primitive sun beaming down on that. We’re going to let it dry down. The bubbles are moving around, and pretty soon, as the water leaves, they touch. They fuse and you have enormous planes of lipids. If anything is in between, it gets sandwiched between the planes.

After a few minutes of primordial heat, the lipids and DNA on the slide have dried into a thin film. Deamer fills his tide pool again by adding a few drops of water. He puts it under a fluorescent microscope, and Chakrabarti turns out the lights. Looking through the eyepieces, you can see lipids squirting out from the dried film into the surrounding water. At first they writhe like snakes; gradually they swell into bubbles. Some of them are dim, but others glow with the intense fluorescent green dye attached to the DNA. The glow is clear proof that as the planes of lipids curled up into vesicles, the DNA that had been sandwiched in between them got trapped inside.

There are many exotic new ideas these days about where life originated. Some researchers say the grand event took place around the furnaces of underwater hydrothermal vents; others look in the spray of ocean bubbles; and still others prefer clay. But Deamer’s choice is tide pools, an idea that harks back at least as far as Darwin’s warm, still ponds. Twenty years ago researchers showed that the wet and dry cycles of actual tide pools could bond together several precursors of RNA. It seemed reasonable to think that these pools could have been the cradle for genetic molecules, and it was likely that liposomes would have sloshed into the pools as well. All this organic stuff is accumulating on early beaches, Deamer says, and the sun is heating and drying it, and lots of natural experiments are taking place that I’m trying to re-create in the laboratory.

But a decade ago Deamer began to have doubts about the materials he was using. Astronomers and geologists were discovering that Earth had a violent infancy--hundreds of millions of years after the planet had formed, giant asteroids and comets still crashed into it, burning off its young atmosphere and boiling away its oceans. In the process, they also destroyed all the chemicals that researchers assumed were in liberal supply on the early Earth, including the building blocks of lipids. There were some naive aspects, but I was playing by the rules of the time, Deamer admits of his early research. Still, given that there must have been a first cell, it had to have a source of lipid molecules. It had to.

Research now suggests that the source was extraterrestrial. Comets and meteorites evidently brought seeds of creation to replace the ones they had destroyed, in the form of hundreds of different organic carbon molecules synthesized when the solar system was a swirling disk of gas and dust. After the last atmosphere-killing impacts--about 4 billion years ago--smaller comets, meteorites, and dust from space could, in the space of a few hundred million years, have brought enough organic carbon to cover the planet in a layer ten inches deep.

Deamer wondered whether space could also supply him with his membranes; specifically, he wondered whether he could dig them out of a 200-pound meteorite that had fallen in Murchison, Australia, in 1969 and that was positively tarry with organic carbon. In 1985 he traveled to Australian National University in Canberra to study it. The question was, he says, are there any things in the meteor that form bilayers? If so, it would be fair to assume that after impacts of similar meteorites in the ocean billions of years ago, such substances could have washed up onshore in a tide pool, dried, and then been rehydrated.

Deamer ground a piece of the Murchison meteorite and extracted the organic carbon, made it into a slurry, dried it, and then added water again. I took that ordinary extract and put it on a slide; I didn’t know what I was going to see. It was a wonderful surprise--the whole slide began to fill with these beautiful little vesicles. I started taking pictures immediately. It’s like what they say about seeing a UFO--you want to get your shots in. I can remember running downstairs to a lunch group of my colleagues and showing the pictures, and they looked at them and said, ‘From meteorites?’ It was pretty hard to believe.

Since then Deamer and his co-workers have tried to figure out exactly which of the meteorite’s molecules form these membranes. We found a few things we can identify. The problem is that meteorites are such complicated things with hundreds of chemicals, and we’re stuck with just a few precious micrograms to analyze. One substance they have isolated is nonanoic acid, a chain of nine carbons, and they’ve managed to form membranes with it. Yet their membranes fall apart sooner than the ones formed from Deamer’s original stew, which suggests that the true membrane formers are probably still hidden.

Incidentally, it was during this work that Deamer found the aroma of outer space--it smells like a musty attic. Think about it, he says after some observers put their nose to the vial of meteoritic organic carbon. You now have molecules in you older than the Earth. Deamer jokes about marketing it as a cologne--Chanel Number Five Times Ten to the Ninth, he’d call it.

The scent of meteorites, though, might put researchers on the trail toward discovering how the first organisms harnessed energy. The musty odor comes chiefly from a group of chemicals named polycyclic aromatic hydrocarbons, or PAHs for short, that are made of hexagons of carbon and hydrogen atoms linked in various arrangements. PAHs are unpleasant stuff--you can find them coming out of almost any tailpipe--but they may have made life possible on early Earth. Some years ago researchers discovered that when a PAH is exposed to light it can give off an electron. That’s what chlorophyll does for plants, explains Deamer. Plants capture the energy of this free electron and use it to bind together carbohydrates. It’s possible, Deamer thinks, that in a similar manner PAHs could have supplied energy to early cells. He has managed to incorporate PAHs into lipid membranes. Now, he says, we’d like to make them capture energy in a useful form. Nobody’s particularly impressed yet, but we think we may be able to capture carbon dioxide and use the light energy to attach it to something else.

Deamer was encouraged by this work--he had found hints that meteorites supplied material to form membranes that could have enclosed complex genetic molecules and could have trapped energy. But how do you get from there to a cell? One big problem was that these early membranes would simply have been too good at separating what they enclosed from the environment outside. A cell needs to pull in ions and toss them out all the time, so it overcomes its membrane’s impermeability with intricate channels, pumps, and shuttles. Swallowed by a liposome, a primitive genetic molecule would have been unequipped to manufacture channels through the membrane. The liposome would not be a shelter but a prison--or at least, so it seemed.

People think that membranes are permeable to nutrients and ions only if you put a channel through them, says Deamer. That’s the end of the story, because that’s the way it’s brought up in textbooks. But he has recently discovered that the textbooks are wrong.

Modern cells contain lipids with tails 16 to 18 carbon atoms long, with the rare 14-carbon tail appearing in some microbes. Tails with 12 or fewer atoms don’t appear in any cell membranes, anywhere. To determine the effect of tail length on permeability, Deamer prepared lipids with a range of tails and tried to make liposomes with them. By measuring how well they could trap charged dye molecules, he could measure their impermeability. Short tails, he found, couldn’t form bilayers at all; the best they could manage were little clumps of particles. Lipids with tails of at least 16 atoms, on the other hand, formed tightly sealed liposomes that held their dye stubbornly. However, tails with 10 to 14 atoms could also form liposomes, though they were leaky. The tails evidently weren’t quite long enough to form a permanently stable barrier, and occasionally some of them would jiggle around and create a pore. No longer is it a pure oil across there, Deamer explains. You’ve got a defect that creates a space through which ions can leak. The defect might last for only a millisecond, but you have billions of ions striking a membrane per second, and if something opens even for a microsecond, maybe ten ions will squirt through.

In 1990, Deamer started trying to toss ions through these pores. Potassium ions, he found, would go through nicely. In 1992, Chakrabarti managed to slip amino acids, which are three times bigger than potassium, through the leaky membrane. Perhaps, the researchers speculated, the earliest membranes were made of such short-tailed lipids; then, once the first cells had the genetic machinery up and running to make protein channels, they could make lipids with longer tails for better insulation without starving themselves. But Deamer and Chakrabarti still faced an intimidating challenge. For their hypothetical scenario to work, they would have to show that truly significant biochemistry could happen inside their liposomes. And to achieve that kind of chemistry, they would have to provide an encapsulated enzyme with a steady diet of much bigger genetic molecules. If the potassium was the size of a walnut, these molecules might be the size of a watermelon, explains Deamer.

At this point, Deamer and Chakrabarti teamed up with molecular biologists Gerald Joyce and Ron Breaker, at the Scripps Research Institute in La Jolla, California, who have made the study of an RNA-based artificial life something of a specialty. The researchers began by forming liposomes out of 14-carbon lipids and used Deamer’s tide pool method to capture an enzyme known as an RNA polymerase. In modern cells this enzyme grabs nucleotides and puts them together into RNA. Four nucleotides are needed to make real RNA, but for simplicity’s sake, Deamer and his co-workers used only one.

They then put these polymerase-loaded liposomes into a beaker of water in which two other molecules were floating. One was the nucleotide-- the watermelon. The other was protease, an even larger enzyme that acts like a molecular razor blade, cutting any other enzyme it meets into bits and pieces. (For anyone who works with enzymes, protease is a dirty word, says Chakrabarti.) They let the liposomes sit for three days, then added a dye that could seep through them and bind to RNA. In theory, if the nucleotide could slip through the pores of the membrane, it would be assembled into RNA by the polymerase. The dye would attach to the RNA and signal the researchers that the procedure had worked. The protease was too big to get inside the liposomes, but it would prevent any RNA from forming outside their protective walls.

We didn’t know if we’d see anything at all, says Chakrabarti. But we saw all these vesicles glowing red with RNA. I hadn’t expected it to be so dramatic. The liposomes had indeed allowed nucleotides to enter through their pores, and the polymerase had assembled them into RNA. The researchers thus showed that primordial liposomes forming in tide pools could have performed some essential cellular tricks.

As an analogy to early life, their quasi cell has obvious limits, Deamer and Chakrabarti know. It builds simplified RNA, using only one nucleotide rather than the full complement of four, and once the RNA is produced, it can’t do anything--it simply fills up the liposome. Joyce and Breaker, however, have the expertise necessary to take the quasi cell another step toward life. Over the past five years, they have perfected a method for making RNA evolve. Simply stated, they put loose RNA strands in a beaker and give them a job to do, such as cutting DNA; the ones that do the best are rewarded with offspring. The researchers place the selected RNA in a bath of loose nucleotides and enzymes and allow it to produce millions of copies of itself. They use this process to evolve the RNA by making the copying process slightly imperfect. Some variants do the designated task better than their ancestors, and they in turn are rewarded with progeny.

Deamer and his colleagues now want to put this whole loop of reactions inside their liposomes. There’s no guarantee it will work. They’ll have to sandwich the RNA, two enzymes, and two necessary primers in the lipids and hope that all five molecules get trapped in some of the liposomes. Then they’ll need to supply all four nucleotides in the water surrounding the liposomes and hope that the molecules can get into the liposomes fast enough to let the RNA direct its own reproduction.

Even if they succeed, many questions will remain before anyone will be able to build a functioning cell. How does it manage growth and division--a process that demands mind-boggling choreography even in a microbe? How exactly is this dance powered with energy? Yet there are far fewer questions to answer now than anyone expected. These things we’re now doing would have been unthinkable a few years ago, says Chakrabarti. It would be great one day to walk into the lab and say, ‘I think I’ll start up a cell today.’

I’m pretty sure in the next five or ten years we or somebody else will put together a system of molecules that can take a source of energy and make more of itself in an encapsulated environment, says Deamer. It’ll be technically alive, but if we put it out to compete in any natural environment, something will eat it long before it has a chance to make its way up the evolutionary ladder. It’s going to be a big deal when somebody gets to it, but this mystery of how genetic information came into the biosphere--that’s going to be unknown for years to come.

Deamer isn’t going to lose his patience, though. As we work our way toward the first living state, we find things all along the way. You pick a direction and start walking. That’s really what I’m doing. You may never know exactly how life began, but you’re going to learn a lot along the way.

Monday, April 27, 2009

More Contradictions related to Religion

The web site discusses two planks in the platform of the Oklahoma Republicanparty. They are adjacent planks 4 and 5 :

4. While the objective study of philosophy and religion can be beneficial, public schools should not be endorsing any specific religion or philosophy. We believe that students and teachers should enjoy the right of free exercise of religion.

5. We support posting the Ten Commandments and our Nation's motto, "In God We Trust," in all public schools in recognition of our religious heritage. U.S. citizens. We support teaching the intent of our founding fathers, the original founding documents, and the difference between a democracy and a republic.

Note that those are EXACT contradictions of each other in ADJACENT recommendations!

First they say don't endorse any specific religion or philosophy but then they endorse a specific religion or philosophy: the Ten Commandments from the Judeo-Christian religions.

The influence of religion appears to weaken people's basic brain functions.

Sunday, April 26, 2009

Religion as byproduct of useful cognitive processes

The web site has approximately an hour long presentation on how religious beliefs evolved. It turns out that organized religion is sort of like a parasite.
The web page includes some interesting claims, suchas this:
"Morality is doing what is right regardless of whatwe are told.
"Religious dogma is doing what we are told, no matterwhat is right."
Exactly correct!
The idea that somehow organized religion has improved our moral values is one of the ultimate unsupported assertions.

Friday, April 24, 2009

H.L.Mencken on how to handle superstition

The web site gives a quote from H.L. Mencken while he was reporting on the Scopes"Monkey Trial" in 1925. Here is that quote:

"Once more, alas, I find myself unable to follow the best Liberal thought. What the World's contention amounts to, at bottom, is simply the doctrine that a man engaged in combat with superstition should be very polite to superstition. This, I fear, is nonsense. The way to deal with superstition is not to be polite to it, but to tackle it with all arms, and so rout it, cripple it, and make it forever infamous and ridiculous. Is it, perchance, cherished by persons who should know better? Then their folly should be brought out into the light of day, and exhibited there in all its hideousness until they flee from it, hiding their heads in shame."

A perfect description of how creationism should be treated.

Tuesday, April 21, 2009

Dictionary of Evolutionary Nomenclature - Letters V and W

Van Valen, Leigh: An evolutionary biologist who came up with the model of the Red Queen -- the living chess piece that Alice encounters in Through the Looking Glass who must keep running as fast as she can to stay in the same place -- as a metaphor to explain evolutionary patterns. His studies involve genetics and systematics, and involve a wide range of topics, including the evolution of biotas and of mammals.

variance: A measure of how variable a set of numbers are. Technically, it is the sum of squared deviations from the mean divided by (n-1) (the number of numbers in the sample minus one). Thus, to find the variance of the set of numbers 4, 6,and 8, we first calculate the mean, which is 6. We then sum the squared deviations from the mean (4 - 6)2 + (6 - 6)2 + (8 - 6)2, which comes to 8, and divide by (n-1) (which is 2 in this case). The variance of the three numbers is8/2 = 4. The more variable the set of numbers, the higher the variance. The variance of a set of identical numbers (such as 6, 6, and 6) is zero.

Vermeij, Geerat J.: Biologist at the Center for Population Biology of th eUniversity of California, Davis, and author of Privileged Hands: A Scientific Life. Vermeij, blind since age 3, combines autobiography and description of the evolutionary "arms race" between intertidal predator and prey species. Wider research interests include economic relationships between organisms and ecosystems and their implications for human organisms.

vertebrates: The group (specifically, a subphylum) of animals, descended from a common ancestor, that share the derived character of an internal skeleton made of bone or cartilage.

vestigial: Any structures that have been greatly reduced in size and function over evolutionary time to the extent that they now appear to have little or no current function.

virulence: The disease-producing ability of a microorganism.

virus: A kind of intracellular parasite that can replicate only inside a living cell. In its dispersal stage between host cells, a virus consists of nucleic acid that codes for a small number of genes, surrounded by a protein coat. (Less formally, according to Medawar's definition, a virus is "a piece of bad news wrapped in a protein.")

vitamin A: A member of a chemically heterogeneous class of organic compounds that are essential, in small quantities, for life.

Von Mutius, Erika: A pediatrician and allergist, Dr. von Mutius's research interests include the epidemiology of childhood asthma and allergies with a focus on environmental predictors and gene-environment interactions.

Vrijenhoek, Robert: A senior scientist in the areas of evolutionary biology, marine biology, and conservation, Vrijenhoek studies the ecological and evolutionary consequences of genetic diversity in animals. His research efforts have focused on the evolutionary and ecological consequences of sexual and asexual reproduction in Mexican poeciliid fish (genus Poeciliopsis), as well as invertebrates in deep-sea hydrothermal vents.

Wake, David: A professor in the Department of Integrative Biology at the University of California, Berkeley, Dr. Wake's research emphasizes analysis of evolutionary patterns and the processes that produce them, ranging from functional morphology to evolutionary genetics and population ecology. Amphibians and reptiles are the focus of his work.

Wallace, Alfred Russel: A British naturalist and contemporary of Charles Darwin. Wallace conducted research on the Amazon River and studied the zoological differences between animal species of Asia and Australia, developing a theory of evolution similar to Darwin's.

Ward, Peter Douglas: Professor of geological sciences at the University of Washington in Seattle, where he is also adjunct professor of zoology and of astronomy. Author of several books on biodiversity and the fossil record, Including Rivers in Time: The Search for Clues to Earth's Mass Extinctions and Rare Earth: Why Complex Life is Uncommon in the Universe (with Donald Brownlee).He is the principal investigator for the University of Washington's portion of the NASA Astrobiology Institute.

Wegener, Alfred: A German climatologist and geophysicist whose book, The Origins of Continents and Oceans, was the first to propose the concept of continental drift (the forerunner to the theory of plate tectonics), as well as to suggest a supercontinent called Pangaea, which Wegener suggested had fragmented into the continents as we know them today. His ideas remained controversial until the1960s, when they became widely accepted as new evidence led to the development of the concept of plate tectonics.

White, Tim: A paleoanthropologist with University of California, Berkeley's Laboratory for Human Evolutionary Studies, White is known for his meticulous fieldwork and analysis investigating early hominid skeletal biology, environmental context, and behavior. With an international team of colleagues, he discovered and named Ardipithecus ramidus and Australopithecus garhi.

wild type: The genotype or phenotype, out of a set of genotypes or phenotypes of a species, that is found in nature. The expression is mainly used in lab genetics to distinguish rare mutant forms of a species from the lab stock of normal individuals.

Wilford, John Noble: A New York Times reporter and winner of two Pulitzer Prizes for his national reporting of science topics, and for his work on the Challenger explosion and the aftermath. While at the Times he served as science correspondent, assistant national news editor, and director of science news.

Wilson, E.O.: A biologist and professor at Harvard University since 1955. Wilson has won two Pulitzer Prizes for his books On Human Nature and The Ants, and has received numerous honors for his research and conservation efforts.

Dictionary of Evolutionary Nomenclature - Letters T and U

tarsier: One of three species of small nocturnal primate belonging to the genus Tarsius, found in Sumatra, Borneo, Celebes, and the Philippines. They have a naked tail measuring 130-270 mm (about 5-11 inches) long, which makes up about half the total length of their bodies (220-460 mm, or 8-19 inches). Tarsiers have enormous eyes, large hairless ears, and gripping pads at the end of their digits. They are mainly arboreal, using both hands to seize insects and small vertebrates such as lizards.

taxon (plural taxa): Any named taxonomic group, such as the family Felidae, or the genus Homo, or the species Homo sapiens. Also, a formally recognized group, as distinct from any other group (such as the group of herbivores, or the group of tree-climbers).

taxonomy: The theory and practice of biological classification.

terrestrial: Living on land.

tetrapod: A member of the group made up of amphibians, reptiles, birds, and mammals.

thecodont: The thecodonts were a diverse group of Triassic reptiles that included large four-legged carnivores, armored herbivores, small, agile two- and our-legged forms, and crocodile-like aquatic reptiles. They gave rise to crocodiles, dinosaurs, and pterosaurs. The term Thecodontia is no longer used, as they are a paraphyletic group. The thecodonts are therefore an evolutionary grade of animals, rather than a clade. Most palaeontologists now use the term "basal archosaur" to refer to thecodonts. As a group, they are defined by certain shared ancestral features, such as teeth in sockets, an archosaurian characteristic that was inherited by the dinosaurs. The name thecodont is actually Latin for "socket-tooth." Members of the group show a general trend toward a more upright, less sprawling stance, with the hind limbs especially being progressively positioned more directly beneath the body, until some could walk upright on two legs.

theory: A well-substantiated explanation of some aspect of the natural world that typically incorporates many confirmed observations, laws, and successfully verified hypotheses.

theropod: The theropod (meaning "beast-footed") dinosaurs are a diverse group o of bipedal dinosaurs. They include the largest terrestrial carnivores ever to have lived, as well as many quite small species. Theropods typically share a number of traits, including hollow, thin-walled bones and modifications of the hands and feet (three main fingers on the hand, and three main (weight-bearing) toes on the foot). Most theropods had sharp, recurved teeth for eating flesh, and claws on the ends of all of the fingers and toes. Some of these characters were lost or modified in some groups later in theropod evolution. Theropod fossils are fairly rare and often fragmentary. Fossils of small theropods are especially rare, since small bones are harder to find and are weathered away easily.

Thiagarajan, Sivasailam: The president of Workshops by Thiagi, Inc., his organization helps people improve their performance through games and simulations.

trait: A characteristic or condition.

transcription: The process by which messenger RNA is read from the DNA forming agene.

transfer RNA (tRNA): A type of RNA that brings the amino acids to the ribosomes to make proteins. There are 20 kinds of transfer RNA molecules, one for each of the 20 main amino acids. A transfer RNA molecule has an amino acid attached to it, and contains the anti-codon corresponding to that amino acid in another part of its structure. In protein synthesis, each codon in the messenger RNA combines
with the appropriate tRNA's anti-codon, and the amino acids are arranged in order to make the protein.

transformism: The evolutionary theory of Lamarck in which changes occur within a lineage of populations, but in which lineages do not split (i.e., no speciation occurs, at least not in the sense of the cladistic species concept) and do not go extinct.

transition: A mutation changing one purine into the other purine, or one pyrimidine into the other pyrimidine (i.e., changes from A to G, or vice versa, or changes from C to T, or vice versa).transitional fossil: A fossil or group of fossils representing a series of similar species, genera, or families, that link an older group of organisms to a younger group. Often, transitional fossils combine some traits of older, ancestral species with traits of more recent species (for instance, a series of transitional fossils documents the evolution of fully aquatic whales from terrestrial ancestors).translation: The process by which a protein is manufactured at a ribosome, using messenger RNA code and transfer RNA to supply the amino acids.

transversion: A mutation changing a purine into a pyrimidine, or vice versa(i.e., changes from A or G to C or T and changes from C or T to A or G).

trilobite: An extinct marine arthropod common from the Cambrian to Permian eras(570-245 million years ago). Trilobite fossils are abundant in rocks of this period. Trilobites were 10-675 mm long, and their flattened oval bodies were divided into three lobes by two longitudinal furrows. They had a single head shield, which bore a pair of antennae and, in many species, insect-like compound eyes. This was followed by more than 20 short body segments, each with a pair of forked appendages. Many trilobites apparently burrowed in sand or mud, preying on other animals or scavenging.

tuberculosis: An infection of the lungs, accompanied by fever and a loss of appetite, caused by the bacillus Mycobacterium tuberculosis.

tunicate: A group of simple chordates, including sea squirts (class Ascidacea)that live attached to rocks, and the salps (class Thaliacea) that float in the sea. Tunicates are small marine animals, cylindrical, spherical, or irregular in shape, ranging from several millimetres to over 30 cm in size. They have a saclike cellulose tunic covering the body; water is drawn in through a siphon and food particles are filtered out. The free-swimming tadpole-like larvae show the major characteristics of all chordates. They subsequently undergo metamorphosis, losing their chordate features and becoming adults. One group (class Larvacea) retain their larval characteristics throughout life.

typology: (1) The definition of classificatory groups by phenetic similarity to a "type" specimen. A species, for example, might be defined as all individuals less than x phenetic units from the species' type. (2) The theory that distinct "types" exist in nature, perhaps because they are part of some plan of nature.(See also idealism.) The type of the species is then the most important form of it, and variants around that type are noise, or "mistakes." Neo-Darwinism opposes typology because in a gene pool no one variant is any more important than any others.

unequal crossing-over: A crossing-over in which the two chromosomes do not exchange equal lengths of DNA; one receives more than the other.

Dictionary of Evolutionary Nomenclature - Letter S

Saag, Michael: Dr. Saag is director of the AIDS Outpatient Clinic and associate professor of medicine at the University of Alabama, Birmingham. He is also associate director for clinical care and therapeutics at the UAB AIDS Center. Dr. Saag's research activities focus on both clinical and basic aspects of the human immunodeficiency virus. He serves on several state and national advisory panels, including the NIH/NIAID AIDS Clinical Trials Group Executive Committee.

sagittal crest: A ridge of bone projecting up from the top midline of the skull, running from front to back. It serves as a muscle attachment area for the muscles that extend up the side of the head from the jaw. The presence of asagittal crest indicates extremely strong jaw muscles.

Schneider, Chris: A biologist and professor at Boston University whose research focuses on the evolution of vertebrate diversity in tropical systems and the scientific basis for conservation of tropical diversity. He uses a variety of molecular genetic methods, such as DNA sequencing, to study speciation, systematics, and biogeography of terrestrial vertebrates, with an emphasis on reptiles and amphibians.

Schultz, Ted R.: An ant systematist at the Smithsonian Institution, Dr. Schultz studies the evolution of the symbiosis between fungus-growing ants and the fungi they cultivate.

science: A way of knowing about the natural world based on observations and experiments that can be confirmed or disproved by other scientists using accepted scientific techniques.

Scopes, John: The 24-year-old teacher in the public high school in Dayton, Tenn., who was the defendant in the "monkey trial" of 1925. He agreed to be thefocus of a test case attacking a newly passed Tennessee state law against teaching evolution or any other theory denying the biblical account of the creation of man, and was arrested and tried, with the American Civil Liberties Union backing his defense.

Scott, Eugenie C.: A human biologist specializing in medical anthropology and skeletal biology. As executive director of the National Center for Science Education, Scott is an advocate of church/state separation in schools, ands peaks widely about science, evolution, and natural selection.

Scott, Matthew P.: A professor and researcher whose work in developmental biology explores how homeotic genes orchestrate differentiation and multicellular organization.

sedimentary rocks: Rocks composed of sediments, usually with a layered appearance. The sediments are composed of particles that come mostly from the weathering of pre-existing rocks, but often include material of organic origin; they are then transported and deposited by wind, water, or glacial ice. Sedimentary rocks are deposited mainly under water, usually in approximately horizontal layers (beds). Clastic sedimentary rocks are formed from the erosion and deposition of pre-existing rocks and are classified according to the size of the particles. Organically formed sedimentary rocks are derived from the remains of plants and animals (for example, limestone and coal). Chemically formed sedimentary rocks result from natural chemical processes and include sedimentary iron ores. Many sedimentary rocks contain fossils.

selection: Synonym of natural selection.

selectionism: The theory that some class of evolutionary events, such as molecular or phenotypic changes, have mainly been caused by natural selection.

selective pressures: Environmental forces such as scarcity of food or extreme temperatures that result in the survival of only certain organisms with characteristics that provide resistance.

Senut, Brigitte: An anatomist at France's National Museum of Natural History. In2000, Senut and Martin Pickford discovered Orrorin tugensis, a proto-hominid dated at 6 million years old.

separate creation: The theory that species have separate origins and neverc hange after their origin. Most versions of the theory of separate creation are religiously inspired and suggest that the origin of species occurs by supernatural action.

sexually dimorphic: When males and females of a species have considerably different appearances, which may include size, coloration, or other features, such as special plumage.

sexual selection: A selection on mating behavior, either through competition among members of one sex (usually males) for access to members of the other sex or through choice by members of one sex (usually females) of certain members of the other sex. In sexual selection, individuals are favored by their fitness relative to other members of the same sex, whereas natural selection works on the fitness of a genotype relative to the whole population.

sex chromosome: The chromosome or chromosomes that influence sex determination. In mammals, including humans, the X and Y chromosomes are the sex chromosomes (females are XX, males XY). Compare with autosome.

Shubin, Neil: A paleontologist who is known for his work on early tetrapods (any creature with four limbs). He presented a hypothesis of general patterns of the development of tetrapod limbs which changed the way scientists think about this field. The study of limbs is crucial to evolutionary science; one example of why this is important is that human development would have been impossible without limbs.

sickle cell anemia: A disease in which poorly formed red blood cells cannot bind correctly to oxygen, resulting in low iron, blood clotting, and joint pain.

Simpson, George Gaylord: One of the most influential paleontologists of the 20thcentury and a leading developer of the modern synthesis. He wrote hundreds of technical papers in addition to many widely read popular books and textbooks, and was a leading expert on Mesozoic, Paleocene, and South American mammals.S mall, Meredith: A professor of anthropology. Her research interests include primate behavior and ecology; mating strategies; reproduction; and the evolution of human behavior. Small's publications include Female Choices: Sexual Behaviour of Female Primates, What's Love Got to Do With It?, and The Evolution of Human Mating.

Smith, John Maynard: An eminent evolutionary biologist and author of many books on evolution, both for scientists and the general public. A professor emeritus at the University of Sussex, his research interests include evolution of human mitochondrial DNA sequences and investigation of evidence for extensive recombination.

Smith, Tom: An ornithologist and conservation biologist, Smith is executive director of the Center for Tropical Research at San Francisco State University. His work combines basic research in ecology and evolutionary science with applied research in conservation biology. Among other issues, Smith is interested in the role of ecological gradients in speciation and maintaining species diversity.

social Darwinism: A doctrine that applies the principles of selection to the structure of society, asserting that social structure is determined by how well people are suited to living conditions.

spacer region: A sequence of nucleotides in the DNA between coding genes.

speciation: Changes in related organisms to the point where they are different enough to be considered separate species. This occurs when populations of one species are separated and adapt to their new environment or conditions(physiological, geographic, or behavioral).

species: An important classificatory category, which can be variously defined by the biological species concept, cladistic species concept, ecological species concept, phenetic species concept, and recognition species concept. The biological species concept, according to which a species is a set of interbreeding organisms, is the most widely used definition, at least by biologists who study vertebrates. A particular species is referred to by a Linnaean binomial, such as Homo sapiens for human beings.

sponge: A member of the phylum Porifera, marine and freshwater invertebrates that live permanently attached to rocks or other surfaces. The body of a sponge is hollow and consists basically of an aggregation of cells between which there is little nervous coordination, although they do have specialized sets of cells that perform different functions. One set of cells causes water to flow in through openings in the body wall and out through openings at the top; food particles are filtered from the water by these cells. Other cells construct a stiffening skeletal framework of spicules of chalk, silica, or fibrous protein to support the body.

stabilizing selection: A form of selection that tends to keep the form of a population constant. Individuals with the mean value for a character have high fitness; those with extreme values have low fitness.

stepped cline: A cline with a sudden change in gene or character frequency.

stromatoporoid: Stromatoporoids, once thought to be related to the corals, are now recognized as being calcareous sponges. Sponges similar to fossil stromatoporoids are found in the oceans today. Like modern sponges, stromatoporoid created currents to pump water in and out of their body, where they filtered out tiny food particles. Fossil stromatoporoids can be massive, chocolate-drop in shape, tabular, encrusting, cylindrical, or even arm-shaped("ramose"). There are two main groups of fossil stromatoporoids that lived in different eras, the Paleozoic and the Mesozoic. After their appearance in the Ordovician, the Paleozoic stromatoporoids were dominant reef builders for over100 million years. The second group of stromatoporoids, from the Mesozoic, may represent a distinct group with a similar growth form. They were also important contributors to reef formation, especially during the Cretaceous.

subduction zone: A zone where rocks of an oceanic plate are forced to plunge below much thicker continental crust, along margins between adjoining plates. As the plate descends it melts and is released into the magma below Earth's crust. Such a zone is marked by volcanoes and earthquakes. See plate tectonics.

substitution: The evolutionary replacement of one allele by another in apopulation.

supernatural: Relating to phenomena that cannot be described by natural laws, cannot be tested by scientific methodology, and are therefore outside the realm of science.

symbiosis: A relationship of mutual benefit between two organisms that live together.

sympatric speciation: Speciation via populations with overlapping geographic ranges.

sympatry: Living in the same geographic region. Compare with allopatry.

syntax: The rules by which words are combined to form grammatical sentences.

systematics: A near synonym of taxonomy.

Dictionary of Evolutionary Nomenclature - Letters Q and R

quantitative character: A character showing continuous variation in a population.

radioactivity: The emission of energy due to changes in the nucleus of an atom. Such spontaneously released radiation is a characteristic of certain elements and at some levels can be harmful.

radiometric dating: A dating technique that uses the decay rate of radioactive isotopes to estimate the age of an object.

Rak, Yoel: An Israeli paleoanthropologist and anatomist whose research interests include facial morphology of fossil hominids. Rak was part of the team that found a 2.3-million-year-old skull fragment from the genus Homo at Hadar, Ethiopia.

random drift: Synonym of genetic drift.

random mating: A mating pattern in which the probability of mating with another individual of a particular genotype (or phenotype) equals the frequency of that genotype (or phenotype) in the population.

recanted: Withdrew a statement or opinion; disavowed a former assertion.

recapitulation: A partly or wholly erroneous hypothesis stating that an individual, during its development, passes through a series of stages corresponding to its successive evolutionary ancestors. According to the recapitulation hypothesis, an individual thus develops by "climbing up its family tree.

"receptors: Proteins that can bind to other specific molecules. Usually on the surface of a cell, receptors often bind to antibodies or hormones.

recessive: An allele (A) is recessive if the phenotype of the heterozygote (Aa)is the same as the homozygote (aa) for the alternative allele (a) and different from the homozygote for the recessive (AA). The allele (a) controls the heterozygote's phenotype and is called dominant. An allele may be partly, rather than fully, recessive; in that case, the heterozygous phenotype is nearer to, rather than identical with, the homozygote for the dominant allele.

recognition species concept: A concept of species according to which a species is a set of organisms that recognize one another as potential mates; they have a shared mate recognition system. Compare with biological species concept, cladistic species concept, ecological species concept, and phenetic species concept.

recombination: An event, occurring by the crossing-over of chromosomes during meiosis, in which DNA is exchanged between a pair of chromosomes of a pair. Thus, two genes that were previously unlinked, being on different chromosomes, can become linked because of recombination, and linked genes may become unlinked.

reinforcement: An increase in reproductive isolation between incipient species by natural selection. Natural selection can directly favor only an increase in prezygotic isolation; reinforcement therefore amounts to selection for assortative mating between the incipiently speciating forms.

relative dating: The process of ordering fossils, rocks, and geologic events from oldest to youngest. Because of the way sedimentary rocks form, lower layers in most series are older than higher layers, making it possible to determine which fossils found in those layers are oldest and which are youngest. By itself, relative dating cannot assign any absolute age to rocks or fossils.

reproductive character displacement: The increased reproductive isolation between two closely related species when they live in the same geographic region (sympatry) as compared with when they live in separate geographic regions. A kind of character displacement in which the character concerned influences reproductive isolation, not ecological competition.

reproductive isolation: Two populations or individuals of opposite sex are considered reproductively isolated from one another if they cannot together produce fertile offspring. See prezygotic isolation and postzygotic isolation.retina: The back wall of the eye onto which images are projected. From the retina, the information is sent to the brain via the optic nerve .

ribosomal RNA (rRNA): The kind of RNA that constitutes the ribosomes and provides the site for translation.

ribosome: The site of protein synthesis (or translation) in the cell, mainly consisting of ribosomal RNA.

ring species: A situation in which two reproductively isolated populations (see reproductive isolation) living in the same region are connected by a geographic ring of populations that can interbreed.

RNA: Ribonucleic acid. Messenger RNA, ribosomal RNA, and transfer RNA are its three main forms. These act as the intermediaries by which the hereditary code of DNA is converted into proteins. In some viruses, RNA is itself the hereditary molecule.

Dictionary of Evolutionary Nomenclature - Letter P

paleoanthropologist: A scientist who uses fossil evidence to study early human ancestors.

paleobiology: The biological study of fossils.

paleontologist: A scientist who studies fossils to better understand life in prehistoric times.

paleontology: The scientific study of fossils.
Pangaea: A supercontinent which began to break apart into the modern continents about 260 million years ago, causing the isolation (and separate evolution) of various groups of organisms from each other.

panmixis: Random mating throughout a population.

paradox: A seemingly absurd or contradictory, though often true, statement.

parapatric speciation: Speciation in which the new species forms from a population contiguous with the ancestral species' geographic range.

paraphyletic group: A set of species containing an ancestral species together with some, but not all, of its descendants. The species included in the group are those that have continued to resemble the ancestor; the excluded species have evolved rapidly and no longer resemble their ancestor.

parasite: An organism that lives on or in a plant or animal of a different species, taking nutrients without providing any benefit to the host.

Parish, Amy: A biological anthropologist and primatologist whose research focuses on the social behavior of bonobos ("pygmy chimpanzees," or Panpaniscus). In addition to comparative work with chimpanzees (Pan troglodytes)and endocrinological investigations, Dr. Parish studies reciprocity in chimpanzees, bonobos, and hunter-gatherers.

parsimony: The principle of phylogenetic reconstruction in which the phylogenyof a group of species is inferred to be the branching pattern requiring the smallest number of evolutionary changes.

parthenogenesis: Development from an egg cell that has not been fertilized. The term for a certain form of asexual reproduction that is found in some lizards, insects (notably among aphids), and certain other organisms.

particulate: (as property of theory of inheritance) A synonym of atomistic.

paternity: The identity of the father of an offspring.

pathogen: A microorganism that causes disease.

pathological: Related to or caused by disease.

penicillin: The first antibiotic discovered, penicillin is derived from the mold Penicillium notatum. It is active against a wide variety of bacteria, acting by disrupting synthesis of the bacterial cell wall.

peripatric speciation: A synonym of peripheral isolate speciation.

peripheral isolate speciation: A form of allopatric speciation in which the new species is formed from a small population isolated at the edge of the ancestral population's geographic range. Also called peripatric speciation.

pesticide-resistant insects: Insects with the ability to survive and reproduce in the presence of pesticides. These resistant variants increase in frequency over time if pesticides remain present in their environment.

Petrie, Marion: A behavioral ecologist at the University of Newcastle in the U.K., Dr. Petrie's research interests include the links between sexual selection and speciation, and how males and females assess genetic quality in a mate.

phenetic classification: A method of classification in which species are grouped together with other species that they most closely resemble phenotypically.

phenetic species concept: A concept of species according to which a species is aset of organisms that are phenotypically similar to one another. Compare with biological species concept, cladistic species concept, ecological species concept, and recognition species concept.

phenotype: The physical or functional characteristics of an organism, produced by the interaction of genotype and environment during growth and development.

phenotypic characters: Individual traits that can be observed in an organism(including appearance and behavior) and that result from the interaction between the organism's genetic makeup and its environment.

pheromone: A chemical substance produced by some organisms and emitted into the environment to communicate with others of the same species. Pheromones play an important role in the social behavior of certain animals, especially insects and some mammals. They are used to mark out territories, to attract mates, to lay trails, and to promote social cohesion and coordination in colonies. Examples are the sex attractants secreted by moths to attract mates and the queen substance produced by queen honeybees, which controls the development and behavior of worker bees. Pheromones are usually volatile organic molecules which are effective at very low concentrations, as little as one part per million.

photoreceptor cell: A cell, functionally part of the nervous system, that reacts to the presence of light. It usually contains a pigment that undergoes a chemical change when light is absorbed. This chemical change stimulate selectrical changes in the photoreceptor that, when passed along and processed by other neurons, form the basis of vision.

photosynthesis: The fundamental biological process by which green plants make organic compounds such as carbohydrates from atmospheric carbon dioxide and water using light energy from the Sun. The process has two main phases: the light-dependent light reaction responsible for the initial capture of energy, and the light-independent dark reaction in which this energy is stored in the chemical bonds of organic molecules. Because virtually all other forms of life are directly or indirectly dependent on green plants for food, photosynthesis ist he basis for almost all life on Earth.

phylogeny: The study of ancestral relations among species, often illustrated with a "tree of life" branching diagram, which is also known as a phylogenetic tree.

phylum (plural phyla): One of the highest levels of taxonomic classification. See taxon.

phytoplankton: Microscopic aquatic organisms that, like plants, use photosynthesis to capture and harness solar energy.

Pickford, Martin: A paleontologist at the College de France in Paris. In 2000,Pickford and Brigitte Senut discovered Orrorin tugensis, a proto-hominid dated at 6 million years old.

Pinker, Steven: A psychologist and professor with a special interest in language, linguistic behavior, and cognitive science. Pinker's publications include the popular science books The Language Instinct and How the Mind Works.

placental mammals: A group (specifically, an order) of mammals in which the young develop inside the mother, attached to her and nourished by a specialized structure called the placenta. In placental mammals, the young are born in an advanced stage of development. Compare with marsupial and monotreme.

placoderm: An extinct bottom-dwelling fish that was among the first to develop jaws and paired fins.

plankton: Minute or microscopic animals (zooplankton) and plants (phytoplankton)that float and drift in water, usually near the surface. In the top meter or two of water, both in the sea and in freshwater, small plants can photosynthesize, and abundant microscopic life can be observed. Many organisms that are sessile (attached to a surface) as adults disperse by means of a planktonic larval stage.

plan of nature: The philosophical theory that nature is organized according to a plan. It has been influential in classification, and is a kind of idealism.

plasmid: A genetic element that exists (or can exist) independently of the main DNA in the cell. In bacteria, plasmids can exist as small loops of DNA and be passed between cells independently.

plate tectonics: The theory that the surface of Earth is made of a number of plates, which have moved throughout geological time to create the present-day positions of the continents. Plate tectonics explains the location of mountain building, as well as earthquakes and volcanoes. The rigid plates consist of continental and oceanic crust together with the upper mantle, which "float" on the semi-molten layer of the mantle beneath them, and move relative to each other across the planet. Six major plates (Eurasian, American, African, Pacific, Indian, and Antarctic) are recognized, together with a number of smaller ones. The plate margins coincide with zones of seismic and volcanic activity.

Poisson distribution: A frequency distribution for number of events per unit time, when the number of events is determined randomly and the probability of each event is low.

polyandry: A reproductive system in which one female mates with many males. Seahorses and jacanas are examples of polyandrous species, which are less common than monogamous or polygynous species.

polygyny: Reproductive strategy in which one male mates with several females. Lions, peacocks, and gorillas all have polygynous mating systems. Compare with polyandry and monogamy.

polymorphism: A condition in which a population possesses more than one allele at a locus. Sometimes it is defined as the condition of having more than one allele with a frequency of more than five percent in the population.

polyphyletic group: A set of species descended from more than one common ancestor. The ultimate common ancestor of all species in the group is not a member of the polyphyletic group.

polyploid: An individual containing more than two sets of genes and chromosomes.

population: A group of organisms, usually a group of sexual organisms that interbreed and share a gene pool.

population genetics: The study of processes influencing gene frequencies.

postulate: A basic principle.

postzygotic isolation: A form of reproductive isolation in which a zygote is successfully formed but then either fails to develop or develops into a sterile adult. Donkeys and horses are postzygotically isolated from one another; a male donkey and a female horse can mate to produce a mule, but the mule is sterile.

prezygotic isolation: A form of reproductive isolation in which the two species never reach the stage of successful mating, and thus no zygote is formed. Examples would be species that have different breeding seasons or courtship displays, and which therefore never recognize one another as potential mates.

primate: A mammal belonging to the order Primates (about 195 species), which includes prosimians, monkeys, apes, and humans. Primates probably evolved from insectivorous climbing creatures like tree shrews and have many adaptations for climbing, including five fingers and five toes with opposable first digits (except in the hind feet of humans). They have well-developed hearing and sight, with forward-facing eyes allowing binocular vision, and large brains. The young are usually produced singly and undergo a long period of growth and development to the adult form. Most primates are arboreal, but the great apes and humans arelargely terrestrial.

prokaryote: A cell without a distinct nucleus. Bacteria and some other simple organisms are prokaryotic. Compare with eukaryote. In classificatory terms, the group of all prokaryotes is paraphyletic.

proofreading enzymes: Mistakes during DNA replication can be recognized and repaired by proofreading enzymes. A mismatched nucleotide may occur at the rat eof one per 100,000 base pairs, causing a pause in replication. DNA repair enzymes perform a proofreading function and reduce the error rate to one per billion. Many complex mechanisms have evolved to repair damage and alterations in DNA, which can occur as a result of damage from ultraviolet radiation, X-rays etc. as well as from errors during replication. (Over 50 genes have been found in yeast to be involved in repair mechanisms).

prosimian: One of the group of primates that includes lemurs and lorises; the other two primate groups are tarsoids and anthropoids.

protein: A molecule made up of a sequence of amino acids. Many of the important molecules in a living thing -- for example, all enzymes -- are proteins.

protozoa: A group of unicellular, usually microscopic, organisms now classified in various phyla of the kingdom Protoctista. They were formerly regarded either as a phylum of simple animals or as members of the kingdom Protista. Most feed on decomposing dead organic matter, but some are parasites, including the agents causing malaria (Plasmodium) and sleeping sickness (Trypanosoma), and a few contain chlorophyll and carry out photosynthesis, like plants.

pseudogene: A sequence of nucleotides in the DNA that resembles a gene but is nonfunctional for some reason.

pupa (plural pupae): The third stage of development in the life cycle of some insects, including flies, butterflies (in which it is the chrysalis), ants, bees, and beetles. During the pupal stage locomotion and feeding cease and metamorphosis from the larva to the adult form takes place. The adult emerges by cutting or digesting the pupal case after a few days or several months.

purine: A kind of base in the DNA; adenine (A) and guanine (G) are purines.

pyrimidine: A kind of base. In DNA, cytosine (C) and thymine (T) arepyrimidines. In RNA, cytosine (C) and uracil (U) are pyrimidines.

Dictionary of Evolutionary Nomenclature - Letters N and O

Nagel, Ronald: A hematologist and professor at Albert Einstein College of Medicine. His research includes molecular, biochemical, and physiological studies of genetic red blood cell defects, including sickle cell.

natural selection: The differential survival and reproduction of classes of organisms that differ from one another in one or more usually heritable characteristics. Through this process, the forms of organisms in a population that are best adapted to their local environment increase in frequency relative to less well-adapted forms over a number of generations. This difference in survival and reproduction is not due to chance.

Neanderthal: A hominid, similar to but distinct from modern humans, that livedin Europe and Western Asia about 150,000 to 30,000 years ago.

Nelson, Craig: A professor of biology and environmental affairs at Indiana University in Bloomington. His research focuses on evolutionary ecology.

neo-Darwinism: (1) Darwin's theory of natural selection plus Mendelian inheritance. (2) The larger body of evolutionary thought that was inspired by the unification of natural selection and Mendelism. A synonym of the modern synthesis.

nervous system: An organ system, composed of a network of cells called neurons, that allows an animal to monitor its internal and external environment, and to move voluntarily or in response to stimulation.

neural: Related to nerves and neurons.

neutral drift: Synonym of genetic drift.

neutral mutation: A mutation with the same fitness as the other allele or alleles at its locus.

neutral theory (and neutralism): The theory that much evolution at the molecular level occurs by genetic drift.

Newton, Isaac: An English physician and mathematician, considered the culminating figure of the scientific revolution of the 17th century. He is best known for his explanation of gravity and for laying the foundation for modern physical optics.

niche: The ecological role of a species; the set of resources it consumes and habitats it occupies.

Nilsson, Dan-Erik: Professor Nilsson heads the Functional Morphology Division of the Department of Zoology at Lund University in Sweden. His main research interest is the optics and evolution of invertebrate eyes.

Nilsson, Lennart: A Swedish photographer who began as a photojournalist, Nilsson soon began exploring new techniques such as the use of endoscopes and electron microscopes to photograph the inner mysteries of the human body. He published a book entitled A Child is Born of his photographs of the beginning of life, and made a number of films, including the mini-series Odyssey of Life, a coproduction between WGBH/NOVA and SVT Swedish Television.

nitrogen fixation: A chemical process by which nitrogen in the atmosphere is assimilated into organic compounds. Only certain bacteria are able to fix atmospheric nitrogen, which then becomes available to other organisms through the food chains.

nomadic: Having to do with nomads, people who live in no fixed place but move in search of food or grazing land for their animals; of a wandering lifestyle.

notochord: A flexible skeletal rod running the length of the body in the embryos of the chordates (including the vertebrates). In some simpler types, such assea-squirts, only the free-swimming larva has a notochord; in others, such as the lancelets and lampreys, the notochord remains the main axial support, and invertebrates it is incorporated into the backbone as the embryo develops.

Novacek, Michael J.: Paleontologist with the American Museum of Natural History. Dr. Novacek's research interests include evolution of and relationships among organisms, particularly mammals. He is the author of Dinosaurs of the Flaming Cliffs, an account of AMNH's Gobi Desert expeditions.

nucleotide: A unit building block of DNA and RNA. A nucleotide consists of a sugar and phosphate backbone with a base attached.

nucleus: A region of eukaryotic cells, enclosed within a membrane, containing the DNA.

numerical taxonomy: In general, any method of taxonomy using numerical measurements. In particular, it often refers to phenetic classification using large numbers of quantitatively measured characters.

Nurse, Paul: A pioneer in genetic and molecular studies who revealed the universal machinery for regulating cell division in all eukaryotic organisms, from yeasts to frogs to human beings.

O'Brien, Stephen J.: A geneticist at the National Cancer Institute whose research interests include the evolutionary history of the immunological response in mammals to retroviruses like HIV. With his colleagues, he discovered a mutation that can protect individuals from infection by HIV, the virus that causes AIDS.

order: The taxonomic classification level between class and family. For example, within the class Mammalia, there are several orders, including the meat-eaters, who make up the order Carnivora; and the insect-eaters, grouped together in the order Insectivora. The orders in turn are divided into families; the order Carnivora includes the families Felidae (the cats), Canidae (the dogs), andUrsidae (the bears), among others. See also taxon.

organelle: Any of a number of distinct small structures found in the cytoplasm(and therefore outside the nucleus) of eukaryotic cells (e.g., mitochondrion andchloroplast).

organisms: Living things.

orthogenesis: The erroneous idea that species tend to evolve in a fixed direction because of some inherent force driving them to do so.

Owen, Richard: A 19th-century British comparative anatomist, who coined the word "dinosaur" to describe a breed of large, extinct reptiles. He was the first to propose that dinosaurs were a separate taxonomic group. Owen opposed Darwin's theory of evolution, but ultimately his work helped support evolutionary arguments.

ozone layer: The region of the atmosphere, generally 11-26 km (7-16 miles) above Earth, where ozone forms in high concentrations. The ozone layer absorbs ultraviolet radiation, shielding Earth from its damaging effects.

Dictionary of Evolutionary Nomenclature - Letter M

macroevolution: A vague term generally used to refer to evolution on a grand scale, or over long periods of time. There is no precise scientific definition for this term, but it is often used to refer to the emergence or modification of taxa at or above the genus level. The origin or adaptive radiation of a higher taxon, such as vertebrates, could be called a macroevolutionary event.

macromutation: Mutation of large phenotypic effect, one that produces a phenotype well outside the range of variation previously existing in the population.

malaria: A sometimes-fatal disease transferred to humans by mosquitoes, infecting the bloodstream.

Malthus, Thomas: A British economist and demographer best known for his treatise on population growth, which states that people will always threaten to outrun the food supply unless reproduction is closely monitored. His theory was in opposition to the utopians of the 18th century.

mammals: The group (specifically, a class) of animals, descended from a common ancestor, that share the derived characters of hair or fur, mammary glands, and several distinctive features of skeletal anatomy, including a particular type of middle ear. Humans, cows, and dolphins are all mammals.

mammary glands: Only found in mammals, these are specialized glands that canp roduce milk for feeding young.

mandible: A part of the bony structure of a jaw. In vertebrates, it is the lower jaw; in birds, the lower bill; in arthropods, one of the paired appendages closest to the mouth.

Margulis, Lynn: A biologist who developed the serial endosymbiosis theory of origin of the eukaryotic cell. Although now accepted as a plausible theory, both she and her theory were ridiculed by mainstream biologists for a number of years.

marsupial mammals: A group (specifically, an order) of mammals whose females give birth to young at a very early stage of development. These newborns complete their development while sucking in a pouch, which is a permanent feature on the female. Examples include kangaroos and opossums.

mastodon: An extinct elephant-like mammal.

Mayr, Ernst: Mayr's work has contributed to the synthesis of Mendelian genetics and Darwinian evolution, and to the development of the biological species concept. Mayr has been universally recognized and acknowledged as one of the leading evolutionary biologists of the 20th century.

McGinnis, William: A professor of biology at the University of California, San Diego. Discover (with Mike Levine) of homeoboxes, the sequences of DNA that are characteristic of homeotic genes, which play a central role in specifying body development. His current research uses both genetics and biochemistry to examine such questions as how molecular variations in the Hox genes that specify the head-tail pattern of an organism can generate variety in animal shapes during evolution, and what the molecular changes were that allowed single-celled animals to become multicellular.

meiosis: A special kind of cell division that occurs during the reproduction of diploid organisms to produce the gametes. The double set of genes and chromosomes of the normal diploid cells is reduced during meiosis to a single haploid set in the gametes. Crossing-over and therefore recombination occur during a phase of meiosis.

meme: The word coined by Richard Dawkins for a unit of culture, such as an idea, skill, story, or custom, passed from one person to another by imitation or teaching. Some theorists argue that memes are the cultural equivalent of genes, and reproduce, mutate, are selected, and evolve in a similar way.

Mendelian inheritance: The mode of inheritance of all diploid species, and therefore of nearly all multi-cellular organisms. Inheritance is controlled by genes, which are passed on to the offspring in the same form as they were inherited from the previous generation. At each locus an individual has two genes -- one inherited from its father and the other from its mother. The two genes are represented in equal proportions in its gametes.

Mendel, Gregor: An Austrian monk whose plant breeding experiments, begun in1856, led to insights into the mechanisms of heredity that are the foundation of genetics today. His work was ignored in his lifetime and only rediscovered in1900. See Mendelian inheritance.

messenger RNA (mRNA): A kind of RNA produced by transcription from the DNA and which acts as the message that is decoded to form proteins.

metabolism: The chemical processes that occur in a living organism in order to maintain life. There are two kinds of metabolism: constructive metabolism, or anabolism, the synthesis of the proteins, carbohydrates, and fats which form tissue and store energy; and destructive metabolism, or catabolism, the breakdown of complex substances, producing energy and waste matter.

metamorphosis: One or more changes in form during the life cycle of an organism, such as an amphibian or insect, in which the juvenile stages differ from the adult. An example is the transition from a tadpole to an adult frog. The term "complete metamorphosis" is applied to insects such as butterflies in which the caterpillar stage is distinct from the adult. "Incomplete metamorphosis" describes the life histories of insects such as locusts in which the young go through a series of larval stages, each of which bears similarities to the adult. Metamorphosis in both insects and amphibians is controlled by hormones, and often involves considerable destruction of larval tissues by enzymes.

metazoans: All animals that are multicellular and whose cells are organized into tissues and organs. In the simplest metazoans only an inner and outer layer can be distinguished.

microbe: A nonscientific and very general term, with no taxonomic significance, sometimes used to refer to microscopic (not visible to the unaided eye) organisms. The term often refers to bacteria or viruses that cause disease orinfection.

microevolution: Evolutionary changes on the small scale, such as changes in gene frequencies within a population.

Miller, Geoffrey: Author of The Mating Mind, Miller is known for his research on evolutionary psychology and sexual selection. He believes that our minds evolved not only as survival machines, but also as courtship machines -- at least in part, to help us attract a mate and pass on genes.

Miller, Ken: A cell biologist and professor of biology at Brown University. Miller's academic research focuses on the structure and function of biological membranes. He is the coauthor of widely used high school and college biology textbooks, and he has also written Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution.

Miller, Veronica: A German virologist whose research has focused on HIV-AIDS. Miller was the first researcher to announce that an interruption in drug treatment among AIDS patients may result in reversion of drug-resistant virus to its wild type. This led other researchers and clinicians to explore "structured treatment interruptions" among some patients as an experimental treatmentoption.

mimicry: A case in which one species looks more or less similar to another species. See Batesian mimicry and Müllerian mimicry.

mitochondrial DNA: DNA found in the mitochondrion, a small round body found inmost cells. Because mitochondria are generally carried in egg cells but not in sperm, mitochondrial DNA is passed to offspring from mothers, but not fathers.

mitochondrion: A kind of organelle in eukaryotic cells. Mitochondria produce enzymes to convert food to energy. They contain DNA coding for some mitochondrial proteins.

mitosis: Cell division. All cell division in multicellular organisms occurs by mitosis except for the special division called meiosis that generates the gametes.

Müllerian mimicry: A kind of mimicry in which two poisonous species evolve to look like one another.

modern synthesis: The synthesis of natural selection and Mendelian inheritance. Also called neo-Darwinism.

molecular clock: The theory that molecules evolve at an approximately constantrate. The difference between the form of a molecule in two species is then proportional to the time since the species diverged from a common ancestor, and molecules become of great value in the inference of phylogeny.

molecular geneticists: Scientists who study genes and characters through as a fleshy, muscular body. The phylum Molluscaincludes snails, bivalves, squids, and octopuses.

"monkey trial": In 1925, John Scopes was convicted and fined $100 for teaching evolution in his Dayton, Tenn., classroom in the first highly publicized trial concerning the teaching of evolution. The press reported that although they lost the case, Scopes's team had won the argument. The verdict had a chilling effect on teaching evolution in the classroom, however, and not until the 1960s did it reappear in schoolbooks.

monogamy: A reproductive strategy in which one male and one female mate and reproduce exclusively with each other. Contrast with polygyny and polyandry.

monophyletic group: A set of species containing a common ancestor and all of its descendants, and not containing any organisms that are not the descendants of that common ancestor.

monotremes: A group (specifically, an order) of mammals whose females lay eggs. The young hatch and continue to develop in the mother's pouch, which is present only when needed. Two species of spiny anteater and the duck-billed platypus are the only living monotremes.

Moore, James: The author, with Adrian Desmond, of an authoritative biography of Charles Darwin, Moore has made a 20-year study of Darwin's life. With degrees in science, divinity, and history, he has taught the history of science at Harvard University and at the Open University in the U.K.

morphology: The study of the form, shape, and structure of organisms.

Mueller, Ulrich G.: A zoologist and professor whose research aims at understanding microevolutionary forces and macroevolutionary patterns that govern the evolution of organismal interactions, particularly the evolution of mutualisms and the evolution of social conflict and cooperation. Mueller's current research focuses on the coevolution between fungus-growing ants and their fungi and the evolutionary ecology of halictine bees.

Murray, Charles: An author and policy analyst who has written many controversial and influential books on social policy. He is coauthor with Richard J. Herrnstein of The Bell Curve: Intelligence and Class Structure in American Life(1994). He has also written Losing Ground: American Social Policy 1950-1980(1984), which argues for the abolishment of the welfare system, The Underclass Revisited (1999), and Income, Inequality and IQ (1998).

mutation: A change in genetic material that results from an error in replication of DNA. Mutations can be beneficial, harmful, or neutral.

Dictionary of Evolutionary Nomenclature - Letters K and L

Kegl, Judy: A linguist who works on theoretical linguistics as it applies to signed and spoken languages. Among her research interests is a study of Nicaraguan Sign Language.

Kimbel, Bill: An anatomist, Kimbel worked with Don Johanson and assembled Lucy's skull fragments. In 1991, Kimbel and Yoel Rak found a 70 percent complete skeleton of Australopithecus afarensis.

kingdom: The second highest level of taxonomic classification of organisms (below domains). Classification schemes at the kingdom level have changed overtime. Recent molecular data have generally reinforced the evolutionary significance of the kingdoms Animalia, Plantae, and Fungi. The single-celled eukaryotes once lumped into the kingdom Protista are now known to be very diverse, and not closely related to one another. The prokaryotic organisms once lumped into the kingdom Monera are now considered to belong to separate domains: Eubacteria and Archaea. See taxon.

Kirchweger, Gina: An Austrian biologist interested in the biological evolution of skin tone. Her essay, "The Biology of Skin Color," concerns the evolution of race.

Kluger, Matthew: A researcher whose work on lizards demonstrated that fever is beneficial and can improve the immune response to infection. The implication for humans is still being researched, but evidence indicates that mild fevers can have a number of important immunological functions that allow us to better fight bacterial and viral infections.

Knowlton, Nancy: Dr. Knowlton is professor of marine biology at the Scripps Institution of Oceanography, University of California San Diego, and staff scientist at the Smithsonian Tropical Research Institute in Panama. Her primary research interests concern various facets of marine biodiversity. These include the nature of species boundaries in corals, elucidating biogeographic patterns in tropical seas, the ecology of coral-algal symbiosis, and threshold effects in coral reef ecosystems.

Kondrashov, Alexey: A population geneticist specializing in mathematical analysis who has studied the evolutionary role of slightly deleterious mutations. He has theorized that a primitive organism's strategy for protecting itself against damaging mutations may have been the first step in the evolution of sexual reproduction.

Kreiswirth, Barry: Director of the Public Health Research Institute TB Center in New York, Dr. Kreiswirth uses DNA fingerprinting to study the evolution of antibiotic resistance in Mycobacterium tuberculosis, the pathogen that causes TB.

Lamarckian inheritance: Historically misleading synonym for inheritance of acquired characteristics.

Lamarck, Jean: An 18th-century naturalist, zoologist, and botanist noted for hisstudy and classification of invertebrates, as well as his evolutionary theories. He traveled extensively throughout Europe and was elected to the Academy of Sciences, where he introduced the principles of heredity and acquired characteristics.

land bridge: A connection between two land masses, especially continents (e.g., the Bering land bridge linking Alaska and Siberia across the Bering Strait) that allows migration of plants and animals from one land mass to the other. Before the widespread acceptance of continental drift, the existence of former land bridges was often invoked to explain faunal and floral similarities between continents now widely separated. On a smaller scale, the term may be applied to land connections that have now been removed by recent tectonics or sea-level changes (e.g., between northern France and southeastern England).

larva (and larval stage): The prereproductive stage of many animals. The term is particularly apt when the immature stage has a different form from the adult. For example, a caterpillar is the larval stage of a butterfly or moth.

law: A description of how a natural phenomenon will occur under certain circumstances.

Leakey, Maeve: A paleoanthropologist at the National Museums of Kenya, Maeve is the discoverer of Kenyanthropus platyops and Australopithecus anamensis. She is married to Richard Leakey.

Leakey, Mary: A British paleoanthropologist described as "a real fossil hunter" and "the real scientist in the family." Her discoveries, some in collaboration with her husband Louis Leakey, included the 1.75-million-year-old skull which first showed the antiquity of hominids in Africa, jaws and teeth of an earlyHomo species, and fossilized footprints of bipedal hominids.

Leakey, Richard: The son of renowned anthropologists Louis and Mary Leakey, Richard continued their work on early hominids from 1964 until the 1980s, making a number of significant fossil finds in the Lake Turkana area and serving as director of the National Museum of Kenya. Later he devoted his energies to conservation and politics.

Lee, Melanie: A molecular geneticist and microbial biologist, who in the 1980s collaborated with Paul Nurse on novel research that demonstrated the commonality of the genetic code between yeasts and humans. Dr. Lee later took her molecular skills into the pharmaceutical industry, and was a leader in moving pharmacology away from animal models and toward the use of recombinant DNA technology for screening potential new therapies. She now heads the research division of Celltech, an international biopharmaceutical company, where her team works on drug discovery and development of new therapies, mainly for the treatment of inflammatory and immune diseases.

lek: An area of ground divided into territories that are defended by males for the purpose of displaying to potential mates during the breeding season. This form of mating behavior is known as lekking, and occurs in various bird species (for example the peacock) and also in some mammals. The dominant males occupy the territories at the centre of the lek, where they are most likely to attract and mate with visiting females. The outer territories are occupied by subordinate males, who have less mating success. Over successive breeding seasons, younger subordinate males tend to gradually displace older individuals from the most desirable territories and become dominant themselves. The lek territories do not contain resources of value to the female, such as food or nesting materials, although males of some species may build structures such a sbowers that form part of their display.

lemur: A small, tree-dwelling primate that belongs to the group called prosimians.

lethal recessive: The case in which inheriting two recessive alleles of a gene causes the death of the organism.

Levine, Michael: Professor of genetics and development in the Molecular and CellBiology Department at University of California, Berkeley. Levine was the discoverer (with Bill McGinnis) of homeobox sequences in the homeotic genes Antennapedia and Ultrabithorax while a postdoctoral researcher with Walter Gehring at the University of Basel, Switzerland. His current research involves analysis of gene regulation and patterning in the early Drosophila embryo;s tudies of embryonic development in the tunicate, Ciona intestinalis, focused on the specification of the notochord and tail muscles; and a critical test of classical models for the evolutionary origins of the chordate body plan.

lineage: An ancestor-descendant sequence of (1) populations, (2) cells, or (3)genes. linkage disequilibrium: A condition in which the haplotype frequencies in a population deviate from the values they would have if the genes at each locus were combined at random. (When no deviation exists, the population is said to be in linkage equilibrium.)linked: Of genes, present on the same chromosome.

Linnaean classification: A hierarchical method of naming classificatory groups, invented by the 18th-century Swedish naturalist Carl von Linné, or Linnaeus. Each individual is assigned to a species, genus, family, order, class, phylum, and kingdom, and some intermediate classificatory levels. Species are referred to by a Linnaean binomial of its genus and species, such as Magnolia grandiflora.

Lively, Curtis: A professor of biology who studies population biology and the ecology and evolution of host-parasite interactions. His laboratory is involved in detailed studies of the interaction between a parasitic trematode and a freshwater New Zealand snail in which both sexual and asexual females coexist.

locus: The location in the DNA occupied by a particular gene.

Lovejoy, Owen: A paleoanthropologist and consulting forensic anatomist, Lovejoy is known for his analysis of early hominid fossils. His research includes work on Lucy (Australopithecus afarensis).

lycophyte: Commonly known as club mosses, lycophytes were among the first seedless plants to appear on Earth. Along with horsetails and ferns, these made the planet more hospitable for the first animals.

Lyell's notion of gradual change: Also called uniformitarianism, Lyell's notion was that Earth has been shaped by the same forces and processes that operate today, acting continuously over very long periods of time. For example, the ongoing erosion caused by flowing water in a river could, given enough time, carve out the Grand Canyon.

Lyell, Charles: A 19th-century scientist considered a father of modern geology. Lyell proposed that the geology of Earth is shaped by gradual processes, such as erosion and sedimentation. Lyell's ideas, expressed in his landmark work, Principles of Geology, greatly influenced the young Charles Darwin. Darwin and Lyell later became close friends. While Lyell initially opposed the idea of evolution, he came to accept it after Darwin published On the Origin of Species.