“God likes matter. He invented it” (C.S. Lewis): A talk by Kenneth Miller at the University of Maryland

On Thursday I came back to my office to find a ripped-down poster haphazardly taped to my door, announcing a talk Friday by Ken Miller--the author of popular books about evolution, such as this year’s Only a Theory. The culprits, a couple friends of mine in the department, had misunderstood Miller’s stand on evolution due to vague wording in the poster, and stuck it on my door to piss me off.

They didn’t know of course, that I just finished Only a Theory last week, loved it, had no idea Miller was coming to speak, and was overjoyed to be informed of it. Needless to say, they were annoyed that the guy wasn’t in fact a creationist, and I wasn’t in fact pissed off. The talk was wonderful though. He is as good of a speaker as he is a writer. I think he fills a very needed role in the evolution/creationist debates—as a Christian himself, he is able to speak directly to fears that evolution and theism are fundamentally incompatible. As Miller points out, people’s beef with evolution is not really scientific, it’s philosophical—the fear that evolution takes away our ability to be moral human beings with purpose in our lives.

His talk was basically a summary of OAT, but for those who haven’t had a chance to read it yet, I’ll outline the talk for you here.

He started off with an overview of all the legal challenges to evolution that have been cropping up within only the last four years: there have been two federal trials (outlined below) and two state elections (OH and KS) that hinged on questions of evolution. Anti-evolution measures were passed in six state legislatures during this period, and 44 states had local measures passed in counties or in individual communities.

At the federal level, there was the 2004 case in Cobb County, Georgia, where the school board decided to put warning labels on the inside of the local high school biology textbook (written by Miller, incidentally). The stickers read, “This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered." Miller pointed out that the scientific definition of “theory” is not “we don’t really know,” and really a theory is of a higher order than a fact, since theories explain sets of facts. Additionally, he protested that the sticker conveys a false sense of certainty about all other fields of biology, and implies that, for instance, ecology and cell biology should not “be approached with an open mind, studied carefully [or] critically considered.” Kind of insulting to all biologists, really.

And then of course there was the famous Dover trial in 2005, for which he served as an expert witness for the side of science. In this case, the local school board was guided by the Discovery Institute’s booklet, “Intelligent Design in Public School Science Curricula: A Legal Guidebook,” and bought two sets of the Intelligent Design textbooks “Of Pandas and People” for the school library, as recommended by the booklet. The board also demanded that the biology teachers re-write their curricula to include intelligent design. They refused. The school board pushed back, demanding then that the teachers at least use an intelligent design lesson plan that the school board wrote for them. They refused. The school board finally asked the teachers to just read a statement to the class about the “weaknesses” of evolutionary theory and the teachers once more refused, forcing the school superintendent to come in and read the statement to the classes while the teachers stood outside. There was immediate protest from the community, of course, and a first amendment lawsuit was quickly filed against the Dover Area School District.

A group of scientists, including Miller, volunteered to serve as expert witnesses. Miller noted in his talk that despite ID proponents’ eagerness to subpoena “evolutionists” for a courtroom trial and force them to speak under oath, 5 of 8 ID witness volunteers dropped out of the case (including William Dembski, who wrote the document linked to in this paragraph).

The details of the ruling and the evidence is really quite fascinating, and you can find a thorough summary at Wikipedia along with a link to the judge’s decision. (The judge ruled, by the way, on the side of evolution.)

Miller then went on to outline just some of the purported evidence for Intelligent Design. In his talk on Friday, he just went over one major piece of the ID case—the “irreducible complexity” of the bacterial flagellum, but his book has many more, all of which he carefully considers and thoroughly destroys.

Michael Behe, one of the major ID theorists, defines irreducible complexity basically as the inability to produce a complex structure piece by piece while maintaining one function. For example, you couldn’t evolve a mousetrap because a mousetrap with only a couple of its parts is no longer a mousetrap—all of the parts are necessary for its mouse-catching function. The IDers say that the bacterial flagellum is an example of such an irreducibly complex structure, as it would not be able to function as a flagellum without any of its parts.

As Miller described in his talk and in OAT, the major problem with this argument is that it assumes that modern-day biological structures have evolved from earlier structures with similar functions. The fact is, as structures evolve, they often acquire radically new functions. (See my earlier post on the tryptophan operon for a biochemical example of this.) The same goes for the bacterial flagellum. It turns out that the base of the flagellum has incredible homology with another bacterial structure called a Type III Secretory System, used by bacteria to pump poisons. Additionally, other parts of the flagellum are made of a number of other proteins that exist elsewhere in the cell, performing other functions. So, unlike the predictions of the Irreducible Complexity argument, it is in fact possible to “take away” parts of a complex biological machine and have it still function—it’s just a different function.

At this point in the talk, Miller switched gears. He asked: well, if the best arguments the IDers can come up with don’t hold water, why is there such popular support for ID? He put a lot of emphasis on a quote from an NPR interview about evolution with former Sen. Rick Santorum, which I think is significant enough to reproduce here in its entirety:

"It has huge consequences for society. It's where we come from. Does man have a purpose? Is there a purpose for our lives? Or are we just simply the result of chance? If we are the result of chance, if we're simply a mistake of nature, then that puts a different moral demand on us. In fact, it doesn't put a moral demand on us."

Miller’s point was that Santorum--and approximately half of Americans--reject evolution because they see it as materialistic to a fault: denying souls, denying order, purpose, and meaning. Essentially, Miller argued, the design movement has forced science into a corner: out of opposition to the ID movement, scientists find themselves having to take the exact opposite position—that there is no design in the universe.

Miller argued the opposite: the universe has a design; it is the design of evolution. Basically, he said that evolution is an inherent, predictable property of life. It explores adaptive space in a predictable way, filling the same ecological niches with similar types of organisms. All organisms and biological structures do have a function, but it is a function that is driven by evolution. Miller went through several examples--such as the elegance of the genetic code, the specificity of proteins, the homology between different sorts of animals—-to illustrate this evolutionary “design.” He would probably note that the fact that I just put the word “design” in quotes in that last sentence is a sign that I am a scientist who has become afraid of the word because of its attachment to the anti-science ID movement. We, as the science-loving public, must reclaim that word, he argued. Regardless of our own beliefs about religion, we must show that the design of evolution does not mean our species and our lives are ruled only by chance and accident--we can still have purpose in our lives, and we are not "mistakes." Science’s derided materialism is its virtue, not its downfall, because it allows science to find natural explanations for natural phenomena. The ID movement was founded on an opposition to this materialism but Miller (like C.S. Lewis in the title of this post) argued that materialism shouldn’t frighten us, as a society, away from science. The scientific process cannot make claims about good and evil; this is society’s job as a whole. Science, and specifically evolution, Miller argued, will not make us immoral. It will only teach us about our place amongst the life on Earth, a place uniquely suited for us and our lives, each with its own unique purpose for the greater good.

Miller deftly answered the questions from the audience after his talk. This is obviously a man who has given many, many talks to diverse audiences, has heard every possible question, and has thought about all of them. His answers were eloquent and well-considered. If there were any IDers in the audience, they did not speak up in the Q&A period. As a friend and I discussed afterwards, they really wouldn’t have much to protest in the talk. Miller really covered all of the bases, and as a practicing Roman Catholic, could hardly be told that evolution is threatening to religion. If you haven’t yet read Only a Theory I suggest you pick it up at your local library. Not only does it thoroughly annihilate the ID position from every angle (useful reading for when you are forced to argue with a creationist) and discuss the larger anti-science implications of the anti-evolution movement, but it also provides a useful and much-needed perspective on the relationship between evolution and philosophical questions of morality and purpose. Read the book, and if you are lucky enough to see an announcement of a talk by Ken Miller, go and see him--and bring your friends.

Increase in Measles Cases

The CDC has issued a press release on an increase in the number of measles cases in the U.S. this year, with 131 cases reported so far. Of those measles patients, 95 were eligible for vaccination but 63 of them were not vaccinated because of their--or most likely their parents'--belief that vaccines are "dangerous."
I'm not sure how much evidence there need to be to convince parents that the MMR vaccine, and/or the preservative in it, do not cause autism. Obviously, piles of evidence accrued from gigantic longitudinal studies of thousands of children over many years are not enough. (see here, here, here, here, and here, for starters.) Will an epidemic of preventable, deadly infections be the only thing that will change some people's minds?
If people want to put themselves in harm's way because of their willingness to believe a bunch of pseudoscientific wackaloons, that's their problem. It's a terrible shame that they're putting their kids at risk too.

Trickery and Sex in the Firefly World

This is not news in the scientific world, but it’s news to me—I ran across this in some reading I have to do for a seminar tomorrow. Further evidence that bugs are awesome:

Fireflies, lightning bugs, or Lampyrids (if you were the nerdy type). Who didn’t spend innumerable summer evenings in childhood chasing after these beetles, empty pickle jar in hand? But you might not have known of the high drama and Shakespearian trickery that was going on among these insects right there in your own childhood backyard.

There’s multiple species and genera of Lampyrids in North America, each with its own characteristic flashing pattern. Males and females of the same species locate each other for mating using these unique signals. However, females of the genus Photuris have evolved a deadly trap: they lure males of other genera by imitating their own females’ flashes. When the males come a-courtin’, the Photuris females pounce, and devour them with gusto.

You may wonder how the Photuris females ever mate, if they’re always on the prowl for dinner during mating time. Turns out that male Photuris capitalize on their female’s predilection for firefly meat by imitating the flashing patterns of males of other genera—the very insects that the female is trying to lure to their death! Some Photuris males go even farther in their imitation, by flashing not only the right pattern, but also at the right time of night, in the right location, to be even more convincing as the potential prey.

In some species of Photuris this imitative behavior has gone so far that the species has completely lost the ability to produce its own unique flashing pattern, instead conducting all its business using signals stolen from others.

I’m unaware of any papers that detail what happens next, after the flash exchange—how does the male Photuris end up as the mate, and not the dinner of the female? I’ll do some more searching because this has piqued my interest, and let you know if I find an answer.

The Darwin Particle

My father works with the particle accelerator at Fermilab in Illinois. As a child, when I would visit him at work and we would walk through the underground tunnels where the beam-control equipment was kept, the towering machines on each side of the walkway would terrify me: they thundered, blinked, screamed "Warning: Radiation" to me at every turn.

Now CERN has built an even bigger, scarier accelerator. And all I have in my lab is jars of termites.

Fortunately, we biologists now have our own accelerator to terrify our progeny with. At last, the final secrets of evolution are within our reach.

The Black Widow Spins Her Deadly Web... Well, Sometimes.

I always get disproportionately excited when I read about a new discovery showing behavioral complexity in invertebrates. Of course, now that we understand the incredible intricacy of honeybees' language, these sorts of things shouldn’t surprise me too much. But I still love this stuff, wherever it pops up.

Black widows alter their web architecture to be better insect traps as they get hungrier. A neat little paper in this month’s issue of Animal Behavior [76(3):823-829] describes how this happens.

When a black widow spider is well-fed, it uses that energy with gusto—spinning out lots of thread, but making a chaotic, disordered cloud of a web near the opening to its hideout. This kind of web is called a ‘tangle-based’ web, and for all that thread, isn’t really that sticky.

However, take a spider who hasn’t been fed for a week, and watch her spin a web. That jumble becomes a well-engineered, efficient killing machine. Instead of making a jumble of undifferentiated, generic thread, the spider uses three different kinds of silk structures to spin a very specific trap (using less thread overall):
(This image is taken from the original paper)



SH is the silk sheet, a flat plane on which the spider can easily maneuver, supported by a network of threads (ST). Anchoring the web to the substrate are the very sticky gumfooted threads (GF), which are kept under constant tension.

The researchers set up homes for 112 juvenile black widow females, fed half of them every day for a week, and the other half nothing for a week. After the members of each group spun their characteristic webs, the webs were imaged to quantify the structural differences between them. Then the researchers saw what happened when half of each group was then moved to the other group’s webs, and then fed.

Under most metrics used, the researchers found that it was indeed much easier for black widows of both types to catch prey when the spider was using a hungry spider’s three-thread design, rather than the chaotic mass of thread of a fed spider. It seemed that the silk sheet made it easier for the spider to sprint out towards its prey. The prey may have alerted the spider to its presence by touching the gumfooted threads and sending out vibrations, and perhaps was slowed down by those threads’ especial stickiness.

Why would black widows switch between a poor web and a good web, though? Wouldn’t it be better to just maintain the efficient functionality of the three-thread design whether the spider was hungry or satiated? This is especially head-scratching when you consider that it uses up more silk to make the jumbled webs of the full spiders. The spider would be using up energy both to modify the web as well as to make the loads of silk needed to the tangle-based web.

Consider this though: the authors point out that many spiders are prone to killing more prey than they can eat, and just leaving the extra prey rolled up in silk on their webs. It’s also been documented that some spiders may just eat themselves to death if able to catch too many prey. Perhaps the switch to the poorly-trapping tangle-based web is a smart move by the black widows, at the very least saving them the energy of pursuing and killing more prey than they can use, at the most sparing them a fate like Monty Python’s Mr. Creosote. The authors also suggest that the tangle of web of a fed spider might serve as a predator defense in those times in which it doesn’t need the web to serve as a food trap.

I think the behavioral plasticity that can be built into such a small animal is really fascinating, and the adaptability of the webs of these spiders is just another example of that. So three cheers for the black widow (one for each part of her web)!

And one more that we aren’t one of the flies who get caught by her web when she’s hungry…

On the Jury—Part II

This entry is a follow-up to last week’s “On the Jury—Part I.” If you haven’t yet read that entry, do so before reading this one.


After the closing arguments had taken place, the judge gave us his final instructions and we were sent into the deliberation room. I was very apprehensive at this point. After hearing all of the evidence throughout the two days of the trial, I did not feel supremely confident that the defendant had committed the crime. In fact, the thought that we might convict him and send him to jail put knots into my stomach. My worry was that I was the only one who would feel this way, and I would have to argue against eleven rabid, blood-thirsty conviction cowboys, I would have to refuse to budge, everyone would hate me, and the jury would be hung. At least this way the defendant would have a chance, though. My worst fear was that my innate agreeability would allow me to be convinced and the defendant would go, possibly innocently, to jail, and I would hate myself for the rest of my life starting the next morning.

No pressure.

Filing into the deliberation room, everyone was visibly on edge. Some made too-loud jokes and laughed nervously. Some looked down at the floor and didn’t talk to anyone. Everyone was very polite to one another. Our foreman was an older woman with a gentle demeanor who had been burglarized and robbed many times without ever having had a conviction, but was nevertheless chosen to be on the jury. She read again to us from the judge’s printed instructions and the legal descriptions of the two crimes we were meant to deliberate on: burglary in the first degree and theft over $500. Then it was silent. “Well,” said the foreman. “Should we begin?”

It turns out I needn’t have worried about being the only one with doubts. From a quick survey of the jury after the first few brave people had spoken up, everyone was feeling uneasy about the case. We began compiling a list of the holes in the case on a whiteboard in the room. The board quickly filled up with all the jury members’ particular hang-ups with the evidence. Where was the physical evidence linking the defendant to the crime scene? Why weren’t the watches ID’d as the Jones’ until today? Did the defendant’s complexion really change from uneven and pockmarked to smooth and even between March and August? Why didn’t they bring in a bloodhound to do a definitive trailing of the path of the burglar? Where were the jacket and the hat? Why didn’t they do a line-up of the defendant with other young black guys of light builds? Why on earth did no one check up on the defendant’s alibi? The list went on. Excited chattering groups quickly broke off from the main group, each discussing their own certain takes on the evidence. I was sitting near a middle-aged Hispanic hairdresser and several young women of my age: a black woman, a woman of color of indeterminate race, and another white woman. All of us expressed our disgust in the incompleteness of the evidence and the police’s investigation. The hairdresser weighed in with her professional opinion that the defendant was not, in fact, wearing cornrows in his mugshot.

The mood in the room became almost spirited once we realized, with relief, that we were all more or less on the same page. We opened up the burglar’s backpack, given to us with all of the other physical evidence for our deliberations, and passed around the odd contents remaining after the Jones’ property had been returned to them. There were red and gold candy wrappers covered in Chinese characters and some sort of flyer with an unknown Asian script on it. All the women I was sitting with guffawed when a pink-wrapped Maxi pad was removed from the pack. I hypothesized that the burglar had stolen the backpack and bike from a Chinese girl on his way to the Jones’ neighborhood and everyone laughed in agreement. And an item that one of the lawyers had briefly mentioned to be a “band-aid” was actually a disposable razor blade. “Good thing they actually looked hard at the contents,” somebody noted sarcastically.

The watches were passed around with a slightly different attitude. They were, indeed, gorgeous and expensive watches. Very heavy, with an aura of wealth and success. People handled them gingerly in their plastic evidence bags. I noted to the group that the gold Omega watch that was ID’d by Mr. Jones on the stand that day was of a standard, classic design, shared with most men’s watches. Of course it was gold, which made it more special, but imagine how many watches there existed that looked more or less like this one. There were no engravings or other unique features. We didn’t have the appraiser’s report that would have listed this watch among the other appraised jewelry inherited from Mr. Jones’ deceased parents, either. “I bet these don’t belong to that boy,” said one of the jurors. We murmured an agreement. “But I’m not totally sure they belong to those people either.”

Everyone wondered about Mrs. Coons’ ID of the burglar and the defendant as looking “just like DeAngelo Barksdale from The Wire.” “Hey, have any of you guys ever seen The Wire?” asked one of the jurors. We all looked around the table at each other. “Wow, a room of twelve people where nobody watches cable tv!” somebody exclaimed. So that piece of evidence went by the wayside because of all of us were pop-culturally incompetent.

“I am so angry with all of the lawyers and the police for putting us in this position!” exclaimed a middle-aged real estate agent with a strong twang from the other end of the table. “I can’t believe that they expect us just to send this guy to jail with this kind of evidence.” There were vigorous affirmations of this sentiment from all around the table. At this point, we had been deliberating for about an hour or so. The conversation had slowed. The foreman asked us if we were ready to start deciding the actual verdict. We were.

She suggested that we go around the table, each of us stating what verdict we would give and a brief statement of why. And so we did. Everyone had his or her own reason that was the strongest in their mind. The stutterer came out slowly and red-facedly with his verdict of not guilty from lack of definitive evidence. The African immigrant with the strong accent and the young Hispanic man—who was probably profiled by the police all the time—both opined that the police hadn’t bothered to go any farther in their search than the first black man they saw, and thus the defendant should be not guilty from lack of strong evidence. I said not guilty, for an overall lack of evidence but especially the seemingly bogus watch ID. The real estate agent with the twang was most unconvinced from the lack of DNA or fingerprint evidence. Others had their own reasons.

One juror, a middle-aged, well-spoken white man, agreed that the evidence was, in fact, less than would be desired in a number of instances. “But how would you explain the witnesses’ positive ID’s of the defendant if he weren’t the guy, though? I just don’t know.” He was the only one who did not say “not guilty.” After everyone had said their piece, there was a pause, and all heads turned toward this one man. He looked around and then looked down. “I agree with things that people have been saying,” he started. “I’m uneasy because of the witnesses’ identification of the defendant,” he continued. “But I’ll say ‘not guilty,’ too,” the man finished in a rush of quiet words.

With relief palpable in the room, the foreman filled out the verdict form and went through the double-knock routine at the door to inform the judge’s clerk, a young, type-A law student. After several minutes we were called back in to the courtroom. We filed in, while clerks, defendant, lawyers, and the audience—the defendant’s friends—stood silently, watching us. I noticed gratefully that neither Mr. Jones nor his neighbors were in the courtroom. I didn’t want to have to feel their hatred when we let the man off whom they were convinced was guilty.

“Who will speak for you?” questioned the courtroom clerk.

I pointed at the foreman, and she stood up and said, “I will.”

“How do you find the defendant for the charge of burglary in the first degree?” asked the clerk.

“Not guilty,” said our foreman, enunciating clearly.

With this, a movement went through the courtroom. The defendant’s friends gasped, exclaimed, cried out, began hugging each other. The defendant stood, immovable, face a mask, as he had been throughout almost all of his trial.

We repeated the same verdict for the second charge. Some other stuff might have been said, but I didn’t notice because I was watching the defendant go over to his friends and be overtaken by a mass of jumping, giggling, back-slapping, bear-hugging, and crying. I wondered if two of them lived in the Jones’ neighborhood after all. Tears came to my eyes and my hands were shaking. One of the friends looked over to us and said, “You guys did good today. Real good.” I looked down, too overcome to look at them any more.

When I got home, the first thing I did was to look up The Wire’s web page and find out who plays D’Angelo Barksdale. It’s an actor named Larry Gilliard, Jr. Feeling apprehensive, I went to Gilliard Jr.’s bio. When it came up, I squinted at the small picture in disbelief and enlarged it.

The character D’Angelo Barksdale looks nothing like the defendant. Nothing. NO. THING. I actually laughed out loud as I stared at the picture. I just couldn’t stop laughing. Sure, they are both young black men with slight builds. But their faces are totally different. The defendant’s face was defined, in my opinion, by large eyes with very heavy lids that I never saw reveal more than half of his eyeballs. He also had a very broad nose and well-defined cheekbones. Larry Gilliard, Jr. has light lids over his fully-visible eyes, and a more oval, smoother face. It’s hard for me to describe how little they look like each other. I even went and looked at a picture of Gilliard Jr. as he appears in the tv show, in case I was thrown off by the preppy sweater and smile he wore in his actor profile. No, even in a picture of him playing a street punk he looked nothing like the defendant. For Mrs. Coons to describe the defendant as looking just like D’Angelo Barksdale would be like her describing, say, Audrey Tatou as looking just like Natalie Portman because they’re both young, slender white women with short brown hair. I mean, it’s totally ridiculous. It’s the kind of mistake you’d make if, for example, you were a Mozambican living in the bush who really didn’t have any interaction with white people at all, and only saw them occasionally on other people’s tvs when the electricity was working.

Looking at this picture made me feel more confident that we had done the right thing as a jury. There was clearly an element of racism in the conviction, although it seemed unconscious. The witnesses had obviously seen a real burglary and the real burglar. But they were eager to help their neighbor, and were unfamiliar enough with black men in their every day lives. So much so that they were able to convince themselves that this young black man with suspicious goods in his pocket and sweat on his shirt was in fact the very same young black man they had seen robbing their friend’s house. The police really don’t have enough resources to thoroughly investigate every burglary, and didn’t bother to look too hard for evidence to fill in the gaps after getting the positive ID from the neighbors. No one was lying. No one was trying to mislead anyone. But people make mistakes and oversights out of a conviction of something. But they weren’t able to convince us with their conviction due to a lack of real, hard evidence. Although the defendant had very likely robbed somebody that day, suspicion alone could not convince us of the link between the defendant and this particular burglary. In my firm belief now, after the trial, we the jury were able to make the right decision to not send him to jail. To my surprise, the system of American justice—at least in this one case—worked as designed.

Your Vote Needed!

Hi folks

There is a call for submissions on a new site called Carnival of Evolution, which publicizes good original writing on evolution in the blogosphere. I think I'd like to send something over.

What is the best evolution-related post so far on this blog, in your opinion? Leave your vote in the comments.

Thanks!

On the Jury--Part I

On Monday and Tuesday of last week, I served on the jury of a criminal trial. It was my first time ever being called in for jury duty, and I got called in for the first trial that day in the Montgomery County Circuit Court. Beginner’s luck, I guess. I’m really glad I got chosen, because it was an extremely enlightening look into the process of justice in my county—haphazard, gray, but in the end as fair as we could possibly muster. We hoped.

There was a parade of eyewitnesses, each with his or her own details to add, own perspective, own biases, and own errors. Read through this account of the incident and of the testimony of the witnesses and the police officers on the scene. You’ll agree, I think, that it would have been a hard case to decide. What would you have done?

The case was a break-in. The defendant, a black kid from south-east DC, was being charged with first-degree burglary of a home in the wealthy Maryland suburb of Olney, and with the theft of goods from that house. There was one thing we knew for sure in the case—that the house was broken into, and things were stolen. The rest, including and especially the involvement of the defendant, was frustratingly ambiguous.


This picture illustrates the neighborhood and the action that occurred during and after the crime. (You'll probably want to click on it to see a larger version.) The house with the red square around it was the one burglarized, belonging to Mr. and Mrs. Jones and their two daughters.

Just after 12pm on St. Patrick’s Day of this year, Mrs. Adams, a part-time nurse, was sitting in a chair at her bedroom window (at house marked by “A”), suffering from back pain. She noticed then a young black male with a backpack riding a bike down the street (red arrow). “That’s odd,” she told the jury she was thinking, “school is in session now—why isn’t he at school?” (“That’s odd,” she didn’t tell the jury she was thinking, “why is there a black kid in our neighborhood?”) She immediately noticed that his height was 5’8”, the same height as her son. She also noticed that the kid rode his bike straight into the gap between the Jones’ house and the Butler’s house (B). Then he came back to the front of the Jones’ house, and rang the doorbell. Then, oddly, he started jumping up and down in front of their windows, waving his arms madly and peering inside the house. There was no response from inside. He walked over to their garage, looked in the garage window panels, and finally went back around the side of the house.

Mrs. Adams immediately called Mrs. Butler, a stay-at-home mom. “Mrs. Butler,” she asked, “do you see a bike parked alongside the Jones’ house? She did. “I think something funny is going on. I’m coming over, let’s watch their house.” From Mrs. Butler’s big picture windows they couldn’t see the back of the Jones’ house. But they strategized that with a vantage point on the other side of the Jones’ house, at the Coons’ house (C), they might be able to catch what was going on. Mrs. Adams called Mr. Adams, who worked from the basement of their house. As he was coming over with his digital camera, they spotted Mrs. Coons, a stay-at-home-mom, carrying her baby out with her to get the mail. Mr. Adams ran over to her and told her to go back inside for safety; something was going on. They both went over to her place and set out to wait on the Coons’ back porch, camera ready.

Then, inside the Butlers’ house, Mrs. Adams and Mrs. Butler heard a loud, rhythmic banging from the back of the Jones’ house. The women called 911 and reported a probable burglary at the Jones. On the 911 tape, the jury heard Mrs. Butler, frantic and trying to be calm, shakily telling the operator what was going on, with Mrs. Adams in the background telling Mrs. Butler to tell the operator the few descriptive details she noticed about the burglar when she saw him on the bike—race, height, that was about it. Minutes passed. Neither the Adams or Mrs. Butler or Mrs. Coons saw anything. Mrs. Butler grew increasingly frustrated on the phone, begging the operator to send the police faster, demanding to know why they weren’t coming.

Then, suddenly, the burglar appeared on the Jones’ back deck, walking down the steps. He looked up, and made eye contact with Mrs. Coons for a second. Mr. Adams was fiddling with his camera at the time, switching between movie mode and still mode once he realized his card is full. He only managed a shot of the sky in his rush to take the picture and never saw the burglar’s face. Mrs. Butler saw the side of the burglar’s face and gave this description to the 911 operator: “He’s got on blue jeans, a gray jacket with navy blue panels down the sleeves, and a black skullcap. Slight build, young African-American man.”

The burglar hopped on the bike, backpack bulging, and took off through the backyard, along the treeline (aqua line). “He’s getting away!” Mrs. Butler wailed to the operator. “You’re just going to let him go!?”

At this point, Mr. Adams, a trained runner, jumped into action, leaping off the Coons’ porch and sprinting after the escaping burglar through the grass. He started to gain on the bike. “You’d better ride faster!” Mr. Adams taunted the burglar. The burglar looked back and saw Mr. Adams’ approaching figure, deciding to leap off the bike and start running on foot (first tick mark). Mr. Adams started to gain more ground on the fleeing burglar. “You’d better run faster!” he jeered. The burglar seemed to agree, dropping the backpack (second tick mark). At that point, the burglar seemed to disappear into thin air.

Mr. Adams looked to the right, a downhill slope into naked trees, and didn’t see anyone. But to the left was the beginning of an abandoned road, partially obscured by a large mound, which he couldn’t see around. (You can see the road, a narrow strip, coming up out of the bottom of the picture just after the end of the aqua line, going north). Afraid of being jumped, Mr. Adams proceeded slowly around the mound. Nothing. Gone. The burglar was nowhere in sight. In capitulation, Mr. Adams turned slowly around and returned to the abandoned backpack and bike, carrying them back to the house.

At that point the police had arrived and the women were giving their statements to the officers who had arrived at the house. Mrs. Coons had had the best view of the burglar, when they had looked each other in the eye. She told the police that he looked a lot like D’Angelo Barksdale from The Wire. He had a very broad face and a medium coloration, she said, with an uneven complexion, as if he had had pockmarks. The police took the bike and backpack as evidence. They also tried to fingerprint the bike and the house, to no avail. Mr. Jones was called and summoned home from his job as a bank manager.

Meanwhile, about 10 minutes after the burglary, the defendant was seen by a cruising police car running out of a nearby cul-de-sac (yellow arrow), drenched through two shirts with sweat, wearing a purple tshirt and jeans. No jacket. His hair, in a buzz cut, was exposed. No hat. He had on very distinctive white and purple shoes, matching his shirt. He was 5’8”, African-American in his late teens or early twenties, and of a fairly light build. The police were on the alert and pulled up behind him, making him stop. He told them his name and where he was from—southeastern D.C., 30 miles away. Then they asked him what he was doing so far from home. He came to see a friend, the defendant stated. The friend wasn’t home, so he was on his way to his girlfriend’s to get a ride home. The police officers asked where the friend and the girlfriend lived, and the defendant indicated this. The location of their houses was not recorded and was subsequently forgotten by the police.

Have you been on the pavement the whole time? asked the police. The defendant indicated in the affirmative. Then how come you’ve got mud all over your shoes? The defendant shut up and stared at the pavement.

He was put in handcuffs by the police and sat down on the curb to wait. The witnesses were driven past the defendant in a squad car. That’s him, said Mrs. Butler. That’s definitely him. In his pockets the police found a pocketknife and two expensive men’s watches.

The defendant was booked later that night.

Meanwhile, Mr. and Mrs. Jones were sorting through their goods that were recovered from the backpack. This task was made more difficult by the fact that Mr. Jones had recently inherited a lot of jewelry from his newly-deceased mother and father, and the couple was not intimately familiar with all of the jewelry. The thief had ransacked their living room, where there were the inherited jewelry boxes, recently back from the appraiser’s, as well as a Wii, a Game Boy, and games for each of the game systems. All of this stuff was stolen, and all the contents of the backpack were immediately returned to the Jones’ after it was identified as theirs. The missing Game Boy and the games were not found inside the backpack.

One of the police officers showed up with the watches and pocketknife from the defendant’s pockets. The couple was not able to identify them as theirs. The police took those items as evidence, where they stayed for months, claimed by no one.

Meanwhile, a canine unit arrived. The officer, Mr. Adams, and the dog—a German shepherd named Vlerk*, re-traced the steps of Mr. Adams’ chase. The dog took off running, following the path of the chase. Now, one thing about German shepherds is that they are not bloodhounds. They do not follow a particular scent. They are trained to follow the most recent human scent, along with scents of recently-disturbed vegetation. The dog led them to the abandoned road, just after the point where the backpack had been dropped. At first Vlerk led the officer down to the right on the road, but then he got confused and stopped. The canine officer helped Vlerk re-establish a trail, one that led instead up to the left, past the mound of earth and north on the abandoned road. The dog led them enthusiastically to the first cul-de-sac north along the road. Then he stopped again. No trail was re-established. The officer and the dog poked around some of those houses there, looking for a thrown-away jacket and hat. None were found after a couple minutes. They wandered aimlessly up the abandoned road, across the through street, and north off the map. They didn’t find anything after 20 minutes and so everybody went home.

This is the story we heard at the trial, knit together from the testimony of Mr. and Mrs. Adams, Mrs. Butler, Mrs. Coons, two patrol officers, the canine officer, and Mr. Jones. However, there are some additional points I’d like to make about the testimony.

When both Mrs. Butler and Mr. Adams were brought up to the stand, they were asked to describe the defendant as they saw him that day sitting on the curb in handcuffs, detained by the police. They both said that he was a young black man, lighter build, about 5’8”, with cornrows, looking exactly like the defendant in the courtroom. The problem was, as we saw later in the mugshot, he was wearing no cornrows that day. He had grown his hair and braided in the rows only since being in prison awaiting trial.

Another interesting moment came when Mr. Jones finally took the stand, near the end of the second day of the trial. The prosecution lawyer had him look at photos all of the stolen loot found in the backpack, and re-identify everything as his. Then, he brought up the watches found in the defendant’s pockets. “Do you recognize these?” asked the prosecution lawyer. “Yes. Yes, that gold one, that is definitely one I inherited from my father. That is it.” This was the first time he had identified that watch as his in the five-plus months since the burglary had occurred.

We never heard from the defendant.

There is also a geographical note that should be made. Notice on the map the orange line. This line is accentuating a 6’ tall fence that runs all along the left side of the abandoned road as it runs north. The prosecution assumed that this was the general route the burglar had taken. But if the defendant were guilty, look at the route he’d have to take to get from his last-seen position at the end of the chase to the location where he was stopped by the police—he’d have to leap this 6’ tall fence, or he’d have to run all the way north to the end of it, turn back and run south along the other side of it and end up in that other cul-de-sac, and then turn around again and run out of it before being spotted by the police cruiser.

How do you see the evidence in this case? How would you have ruled if you were on its jury? Leave your comments; I’m curious to see how other people view this situation. After a couple days, I’ll write a post about our deliberations and our verdict.




*This is the only name that is not changed in this blog post.

***POSTSCRIPT

one important note on the testimony that I forgot to add. When Mrs. Coons came up to testify, she identified the defendant as also looking like D'Angelo Barksdale, just like the burglar she saw face to face. However, she was hesitant, as she did not notice an unevenness of coloration like she saw on the burglar that day. No pockmarks, either. So she determined she was "75% sure" the defendant was the burglar.

Flip-Flopping Functions at the Drop of a (Leucine-Shaped) Hat

Conceptualizing evolutionary change is a difficult thing. If something has changed from A to B, and if A and B have drastically different forms or functions, it is often hard to envision the gradual changes that must have occurred between them. This difficulty is exacerbated if an intermediary form seems impossible, maladapted, or even just neutral. It’s easy to see how this conceptual difficulty might have led some people to reject evolution entirely.

However, a new paper in Nucleic Acids Research reminds us that intermediary forms are not always necessary in evolution. Resch and Striegl et al. [36(13):4390-4401] report a sudden switch in function in the evolution of a regulatory protein, which changes between two mutually exclusive modes of action with just one amino acid change. No conceptually impossible intermediate necessary!

Before I get into the paper, let me back up and go over some background you’ll need to understand it. The paper focuses on a bacterial repressor protein. In bacteria, repressor proteins stop transcription of a gene by binding to a certain spot in DNA, called the operator. Let me explain. Normally, for DNA’s information to be used, it first has to be transcribed into RNA by RNA polymerase. RNA polymerase binds to the DNA and travels along it, letting out a growing string of newly-transcribed RNA as it passes along. Before beginning to transcribe the actual gene in the DNA, however, the RNA polymerase must pass over the operator. If nothing is bound to the operator, the RNA polymerase can just continue on and complete the transcription. If, however, a repressor protein is bound to the operator, it physically blocks the RNA polymerase from passing, thus preventing the gene from being transcribed and “read.” (If you’re not a biology person and can’t picture this process blindfolded with your hands tied behind your back, check out this video.

There’s an added level of complexity when you consider what is regulating (controlling) the repressor. There are two completely opposite ways of doing this. One is through an inducer, which is a molecule that binds to a repressor, preventing it from binding to the operator. The second is through a co-repressor, which binds to the repressor, helping it bind to the operator. So, inducer → gene expression, co-repressor → no gene expression. Two totally different options. To illustrate, see the pictures and captions below:

This is a set of genes called the Lac Operon, which is regulated by a repressor and an inducer. Notice how the repressor (maroon oval) is always bound to the operator to prevent transcription, unless the inducer (blue oval) attaches to the repressor causing it to fall off and allowing transcription to occur.

This one is a picture of the Trp Operon, regulated by a repressor and a co-repressor. Normally, the repressor (U-shaped orange thingie) is not bound to the operator, and gene transcription occurs. However, when the co-repressor (blue hexagon+pentagon) is present, it binds to the repressor, allowing it to bind to the DNA, stopping transcription.

The take-home message from this is that repressor-mediated gene regulation can occur in two opposite ways: two things binding together to stop transcription, or two things binding together to allow transcription.

In the paper by Resch and Striegl et al., they describe how one regulator switched between the two opposites listed above in just one small evolutionary step. The regulator in question is called TetR, pictured below, bound to its operator on a strand of DNA:

TetR is involved in tetracycline resistance in bacteria. (Bacteria have a habit of quickly evolving resistance to whatever antibiotics we throw at them, and they’ve done particularly well with tetracycline—there is not just one but at least three different mechanisms for tetracycline resistance in bacteria. For an interesting review, check out this paper by Speer et al. from 1992. TetR works like the regulator in the Lac operon in the example above. Its normal position is to be bound to the DNA, preventing transcription of its tetracycline-resistance genes. Antibiotic resistance is often costly for bacteria, and they generally only activate their resistance when it’s needed. In this case, the resistance is needed when tetracycline is present in the environment. The tetracycline acts as the inducer, binding to TetR, which causes it to release from the DNA, allowing transcription of the resistance genes. When tetracycline is removed from the environment, TetR is able to bind to the DNA again.

The weird thing is, there’s several mutant versions of Tet-R (called revTet-R) that have exactly the opposite behavior. revTet-R cannot bind to DNA unless tetracycline is present, much like in the example of the Trp operon, above. In the mutant, tetracycline suddenly acts as a co-repressor, not an inducer. (This results in tetracycline in the environment turning off the tetracycline-resistance genes, and in the genes being on once tetracycline goes away.) Even weirder, one of these mutants is only one amino acid different than the sequence of the original Tet-R—the 17th leucine in the chain is replaced by a glycine. How could a change of just one measly amino acid in this large, complex protein change induce a completely opposite behavior from the one it originally possessed?

The authors and their team used a variety of biochemical procedures to answer this question. They raised the revTet-R mutant bacteria, broke open their cells, purified the contents to get out the revTet-R protein, broke it up, then sequenced the bits. Then they determined its three-dimensional structure with and without attachment to tetracycline.

Here’s a picture of the two molecules taken from the article, going through their processes of binding tetracycline and DNA, side-by side. The line drawings represent the overall structure of Tet-R and its variant. The left-most, vertical arrangement (A-C) is revTet-R, and the horizontal arrangement (D-F) is of Tet-R. The “effector” is tetracycline, and it binds to that little oval in the center of the egg-shaped part of the protein.

Let’s start with the standard Tet-R, images D-F. Notice that the helix α4 (the rectangle) functions like a pendulum, swinging up and tightening in the two ball shapes tight in close to the main egg-shape when tetracycline (the effector) is present. This prevents DNA from being able to fit into the binding site to attach. But in the absence of tetracycline, the pendulum swings down, opening up the binding site to DNA. However, in revTet-R, in the absence of tetracycline (A) the amino acid chains that are normally rolled up into two balls no longer want to bind up together. Instead, they are loose and free, and don’t make any of the three-dimensional structure necessary to bind DNA. The slight change in amino acid sequence in the mutant is enough to screw up the whole DNA binding apparatus. However, when tetracycline is bound in (B), all of a sudden everything tightens up, and the result looks a lot like (D): Tet-R with tetracycline. But, because of that amino acid substitution, the normally tightly-bound DNA binding site is not as tight as it usually is. This weakness allows DNA entry into the binding site even when tetracycline is attached, resulting in revTet-R to have an opposite action to Tet-R.

So from just one single amino acid change, this protein called Tet-R completely reverses its function, but through a completely different mechanism and set of conformational changes than it goes through normally. This just wows me with its level of specificity—with all the thousands of amino acids in this protein, just one change can screw everything up in such a drastic way. Not just to break it—which is easy—but actually to reverse it through a whole new mode of action. I’d imagine that creationist folks would say this is evidence of the delicacy of life, how everything is too fragile and precise to have arisen on its own without being designed. But I would argue that this incredible ability to change gears is evidence for the power of random change—how even if an organism’s environment suddenly does a 180, random mutation is sufficient to allow it to go with the flow and allowing the species to adapt in a radical manner to whatever its ecosystem can throw at it. Obviously in this case, a revTet-R mutant doesn’t seem very well-adapted to a bacterium’s normal environment. Turn off your tetracycline-resistant genes in the presence of tetracycline? (It was generated in a laboratory through random mutagenesis, not evolved naturally in the wild.) But it’s a great living analogy for the power of mutation to do crazy, seemingly-impossible things. Obviously evolution often occurs through slow steps and many intermediates, especially for larger, more complex organisms. But this paper shows that it doesn’t always have to happen that way.

Valley Girls Know What They Want: Sexual Selection and Elevation in Finches

Each year as spring comes, opening your window will invite in a cacophony of ebullience from the male songbirds in your neighborhood. They find a good spot, puff out their chests, and sing their hearts out to any ladies of their species who might be listening. The females then choose the male with the best song, because he is more likely to be healthy and able to pass on good genes to his offspring. But odds are you live in an area that’s relatively low in elevation, unless somehow this blog’s gotten picked up by an Alpine sheepherder with a satellite internet connection. If you were, however, to travel up to very high elevations one spring to hike in alpine meadows or pine forests, you may notice that you’re not getting nearly as much of a show from the local bird populations. They don’t sing with as much gusto or showiness, even though they may look very much like the birds from back home. So what gives?

Emilie Snell-Rood, from the University of Arizona, and Alexander Badyaev, from Indiana University, did notice this. In a new paper in Oecologia [157(3):545-551] they are the first to prove this variation is a function of elevation. As their study group they chose a large group of finches, called the Cardueline finches, which contains 126 species with the widest elevational range of any living subfamily of birds in the world. Many of the finches that live at lower elevations have very close relatives at higher elevations, which sets up a perfect study system to test for elevation-based differences between species.

In their study Snell-Rood and Badyaev used sonographs to get a “picture” of each species’ song. With this they were then able to quantify different aspects of the songs’ showiness, for example number of notes, length, pitch range, etc. They then analyzed the relationship between these variables and the maximum elevation of the birds’ range. They were able to control for other factors that are known to vary with song complexity and might have otherwise confounded their results, such as body size, bill size, and habitat type. Once these confounding factors were controlled for, any existing differences between species’ songs would be more likely to be due only to elevational distances. They did find, in fact, that between “sister species,” the species with the lower breeding territory was more likely to sing elaborate, loud courtship songs than their counterparts higher up the mountain. Lower-elevation species also had longer songs with more notes. For an example of the kind of showiness in these carduelines, check out the song of the pine grosbeak, one of their lower-elevation species. Although I can’t find a file online of the song of its sister species—the crimson-browed finch—to use as a comparison, you can clearly hear the complexity and length of the pine grosbeak’s elaborate song.

The interesting thing about this variation in song complexity with elevation is that it correlates to differences in the breeding behavior and family lifestyles of these birds. The cardueline finches at lower elevation need more elaborate songs because there is more sexual selection in these species—the females spend more time evaluating and choosing mates, who are more showy in song and in plumage than the females. This is because, for these lower-elevation birds, the males don’t always really do much to help raise the offspring. Any contribution they will make to the next generation will be through good genes, which must be evaluated at the offset by the female through some proxy like song or plumage brightness. At higher elevations, a far more important predictor of offspring success is the amount of help it receives from its parents. Since food is much more scarce farther up in the mountains, both parents are required to forage for food to feed the baby birds. The male’s success lies in his ability to care for his young, not in convincing a female that he’s worthy of a copulation with her. He then does not need to invest as much in elaborate, difficult songs as his polygamous counterparts down in the valleys.

Next time you hear an effluence of birdsong through your window, or up on a hike in the mountains, try to pick all the songs apart as you listen and analyze them. As in most things in nature, there is more going on than it seems.

I'm Back!

An apology to the myriad 3 fans who missed me while I was gone. Expect the posts to keep rolling with the same pace as they did before now that I am back at home and in my old routine. Although I may have to alter that pace once classes start... I've still got a good week and a half though until that point to get some good posts in though.

I'm actually taking a science journalism class this fall semester, so I'm hoping to be able to get some good stories through projects for that class that I can post up here. At the very least it should give me some tips to improve my writing.

In any case, keeping reading for a brand-new post on a brand-new research article.

Susan's Snazzy Arthropod of the Day: Mastotermes darwiniensis

I know some of my dear readers are less than fond of our termite friends, but as I'm pretty sure that my readership is still restricted to acquaintances in the U.S., you don't have to worry about it eating your house. It’s Mastotermes darwiniensis of Australia, the only extant member of the termite family Mastotermitidae. Apparently the common name is the Giant Northern Termite or the Darwin Termite. All the termite biologists I know, however, just call it by its genus name since that is pretty darn specific, it being such a phylogenetic loner.

The thing that makes Mastotermes so cool is its evolutionary significance. Upon its description a hundred or so years ago, it was the clue that made biologists pretty sure that termites are very closely related to cockroaches. This suspicion was confirmed last year with the first comprehensive phylogeny of roaches and termites using molecular data: In the roach family tree, termites are just one branching limb nestled in the tree, and Mastotermes is the branch closest to the roach trunk.
Below are pictures of a generic termite, Mastotermes side-by-side, with a generic cockroach right underneath.


You, a layperson, can easily see some of the striking similarities between Mastotermes and the cockroach. On the extended wings, do you see how Mastotermes and the cockroach both have that extra lobe coming out of the back end of the hindwing? That’s called the anal lobe. It’s found in all cockroaches, and no termites except for Mastotermes. The nerve patterns between Mastotermes and the cockroach are similar as well. Additionally, you can see the differences in the shield behind the head (called the pronotum, which covers the prothorax): on the generic termite it’s pretty small, but much larger in Mastotermes, as large as its head—much closer in size to the cockroach’s greatly expanded pronotum. You may also be able to infer from these drawings that Mastotermes is also quite a bit larger than other termites, closer in size to a roach. Other morphological similarities between Mastotermes and the cockroach that you’re not able to see in these drawings are the 5-segmented tarsi (feet) with pulvilli (adhesive pads), the ovipositor (egg-laying tube) in the females, the oothecae (egg masses), the row of spines along the tibiae (a leg segment), and possession of the same kind of gut microbiota. None of these features are shared by the other termites.

So it seems that both the morphological and molecular data point to Mastotermes representing a “transitional form” in termite evolution from a roach-like ancestor: i.e. it branched off early in termite evolution and still retains many of the ancestral cockroach characteristics. (Note: creationists commonly claim that no transitional forms exist, thus evolution is wrong—despite the overwhelming evidence. Next time you have to talk to one, remember Mastotermes.) Of course Mastotermes is a modern animal, and can’t be confused with the actual transitional form between roaches and termites that lived in the early Cretaceous or before. But since it seems to have kept many of those ancestral features, it’s a pretty good proxy in many respects.

As you probably know, termites are highly social creatures—they live in colonies of extended families where most individuals are altruistic and only a couple individuals reproduce. (Note that “social” in the context of evolutionary biology has a much more specialized meaning than it does in conventional speech.) Though some roaches live in simple family groups, none are truly social like the termites. So if we were interested in learning about the evolutionary steps in between family living in the roaches and true social (“eusocial”) behavior in the termites, it seems like Mastotermes would be the perfect place to look, because of its half-roach, half-termite appearance.

Wrong.

The odd thing about Mastotermes is that while it is morphologically primitive, and has not changed its physical appearance much in many millions of years, its behavior and social structure are highly complex, and as derived as the termites that have evolved most recently of all. Mastotermes builds huge underground nest structures that contain extensive gallery construction and tunnel excavation; it forages far afield from the nest, and has been known to damage structures over a hundred yards away from its colony. Full-grown colonies contain over a million individuals, with rigid caste structures and obligatory sterility for the worker forms. This is a lot like the most-derived, most-recently evolved termites, like the great mound-builders of Africa. In contrast, the most termite-like cockroach and the next-most-primitive termites after Mastotermes all live and eat inside one piece of rotting wood, have very flexible development, do not have obligatory sterility in the worker forms, build no galleries and no tunnels, and are have many fewer group members.

Mastotermes is thus a weird chimera of primitive morphology but derived behavior and development. If it were translated into, say, the primates, it would be a lemur with a big brain, language capabilities, and maybe a car. I think it’s a great example of the complexity of evolution, and shows how even within a single species vastly different evolutionary paths can be taken in different areas of one genome.

The Scala Naturae and Evolution

People often have misconceptions about the process of evolutionary change. I find that one of them is often that evolution is sort of a giant ladder. Life is arranged on this ladder in order of primitive to advanced, with each organism in its place. As evolution progresses, organisms can step up, reaching greater heights of perfection and complexity, climbing until at last, the pinnacle of human perfection is reached. This idea of evolutionary change actually has very deep roots, back to at least the Middle Ages.

The great chain of being, or scala naturae, was a medieval philosophical concept that was the basis of thinking about the order in the world for much of western history. In the great chain of being, all living things are organized from most perfect, at the top, to least perfect, at the bottom, in a continual series of gradations. Of course, God is above everything. Below God is the King, below the King are the lords, and so on. Eventually the chain reaches the last serf, and starts down into the animals. Every animal is ranked according to medieval man’s idea of its nobility, its complexity, and its usefulness to man. Lions and tigers and the like are at the top, ladybugs are above flies, oaks are above the demonic yews, and snakes are at the very bottom of all animals. All of these are then in turn above the minerals. Once microorganisms (animalcules) were discovered by Antony van Leeowenhoek in 1683 (in the plaque of an old man’s teeth), they fit perfectly in that gap between animals and minerals.

Once evolution was accepted by the mainstream scientific community, these ingrained ideas of “the order of nature” became the unconscious basis for the evolutionary ordering of life. The scala naturae was originally meant to be a fixed chain, with each thing’s place immovable, but with minor adjustments the same idea could be read as a ladder instead, a progression through time. And of course, who is at top, but man. Sean Nee has a great article about this in the journal Nature [435: 429] from 2005. He writes how any published phylogeny that includes humans inevitably will place humans at the top of the tree, even when they could correctly be placed in some other ordering. This isn’t coincidental. If you still have your high school or middle school biology textbooks lying around, take a look at them. You’ll notice how they will start out their discussions of living things with viruses and bacteria and other single-celled things, progress through plants perhaps, into insects and squirmy things, through reptiles and birds, and finally into the mammals, with the very last section being about human evolution: the pinnacle, the peak of God’s creation evolutionary history. It’s very deeply engrained in our cultural psyche.

This view of evolution and nature, obviously, is flawed. With this sort of idea it’s natural to visualize a whole-organism progression; a collective complexifying of all the organism’s parts simultaneously. However, organisms are mosaics of derived and primitive features [spoiler warning, see next post!]; our own genome contains remnants of retroviruses; our mitochondria were originally free-living bacteria. Furthermore, plenty of “simple” organisms have immense super-powers that we, the apex organisms, can only dream about, like the ability to survive in environments with and without oxygen, like facultatively anaerobic bacteria. The erroneous view of a progressive ladder implies that “simple” modern organisms are somehow ancestral organisms simultaneously, leading to the “men from monkeys” fallacy of human evolution and the recent portrayal of the platypus genome as “a cross between a reptile's and a mammal’s.”

A much better view of evolutionary “progress,” one that at least gives us an idea of our true place in the universe, is one like this one. Notice the small insignificant little “Homo” down there on the bottom left of this branching bush. (Compare that tree to this one though, to see how the same sort of information can be flipped around to feed that old human ego some more. Why are animals at the top? Bacteria are the ecologically dominant life-form, after all.) Or perhaps a web would be better, to show the interlinking of life: fungi and algae, joining to form lichen; retroviruses and humans, our genomes inextricably intertwined. Or perhaps the map could be of just one single organism, color-coded, labeled, showing the differential evolution of all the various parts—the parts that have slowed down their development, the parts that have gone off into something totally novel, the parts that happen to be very similar to its relatives.

Perhaps the reason why so many people have trouble accepting evolution is that they still have these ingrained ideas about it, based on the centuries old scala naturae. If you really start to look around at the world, nature doesn’t seem to fit such a rigid view, such a strict, ordered progression. If this is how people think of evolution, no wonder they reject it. If we are able to recognize these deeply embedded cultural preconceptions in our own minds, it would go a long way in helping us embrace the odd complexity of the world, the riotous transformations over evolutionary time, and our own place—a small side branch, nestled among the apes and the protists and the dandelions, a great vantage point from which to watch evolution unfold around us.

A Simple Question

So here’s a statistical question for you. Now, mind you, this is a question that ground my graduate-level experimental design class to a halt for at least half an hour, and that also brought my boyfriend and I into something resembling not a discussion, but an actual argument. Pretty heavy stuff, for statistics.

Here’s the situation: You are a botanist and you want to study the effect of two different light regimes on petunia growth—let’s say 12h light and 12 dark, and 18h light and 6h dark. You have 40 little petunia seeds planted in pots waiting for you, and your university has 2 environmental chambers for you to use. You put 20 pots in each chamber, set the light timers, and start the experiment. After the prescribed number of days on this program, you measure all your petunias, and begin to analyze the data.

Now here’s the question, and I’ll phrase it a couple different ways: How many experimental units do you have? In other words, how many independent data points? How many degrees of freedom will you get in an analysis of these data?*

Answer: 2 experimental units, 2 independent data points. 0 degrees of freedom.

“What???!!” you may splutter. “But there were 40 petunias!!” You thought there were going to be 40 experimental units and 19 degrees of freedom, didn’t you?

Well, what did happen to those pots of petunias? The problem stems from when they were all put into only 2 environmental chambers. Once in an environmental chamber, the light turned on and shone into the entire room. The light was applied to all the pots together, as a group. If the lightbulb, say, started flickering and going out in one room, it would be flickering over all those plants together. In other words, the treatment (the light) was applied to one unit, the room. Therefore the environmental chamber as a whole becomes the unit of experimentation, not the individual plants. If the experimenter were to ignore this, he would be committing the mortal, yet frighteningly common sin of pseudoreplication.

Pseudoreplication occurs when there is a lack of independence between supposed experimental units, when the treatment is applied collectively, not individually. What this means, practically, is that each of your little units you are assuming are independent are actually irrevocably linked to each other, in a way that can mask the effect that you’re actually trying to see.

Now let’s suppose that there’s a problem with one of the lights, the one in the chamber on the 12/12 regime. That light tends to flicker when the MRI machine next door gets turned on. It’s new, and people don’t generally tend to hang out in environmental chambers and read the Times and have a coffee, so it hasn’t been noticed yet. But every single petunia in that chamber collectively feels all of those light flickers. In fact it happens frequently enough that it negatively affects their growth—all of them, together. So when the data are collected, the plants in the 12/12 room are just a little bit shorter than they might have been otherwise. Their growth was stunted just enough that those plants’ heights are less than those of the plants in the 18/6 room. When the experimenter analyzes those data (not realizing yet that the experiment is pseudoreplicated), he finds a significant difference between the two and concludes that an 18/6 light regime for petunias helps them grow taller. What he doesn’t realize is that he hasn’t detected a difference due to light regime, he’s detected a difference due to faulty wiring—not at all helpful. Incidentally, even if he did finally recognize the pseudoreplication, he wouldn’t be able to analyze the results. With only one (true) experimental unit in each light regime, he wouldn’t be able to take an average and compute the variation around that average—there’s no variation because with only one data point, there’s nothing to vary. Without that, he can’t figure out if his two treatments truly are different from each other outside of the range of normal background variation. No conclusions can be made, and the entire study is wasted.

It’s easy to imagine other situations in which the pseudoreplicated nature of this study could screw up the results: a careless undergraduate props the door to one of the chambers open for a minute, forgets about it when his girlfriend calls, and then goes to lunch. In the meantime that room loses all its humidity through the open door. Or one of the lightbulbs burns out and nobody notices it for 8 hours. Et cetera.

Experimental units are independent when treatments are applied to each one individually. If this study used little light lamps for each plant, they would truly be the independent experimental units, because each one would be receiving an independent treatment. If one of the bulbs flickered and screwed up the growth of that one plant, the results overall may not be affected much, because there’s still 19 other independent data points in each that will all be averaged with the screwed-up one. Not ideal, but not the end of the world. Doing it this way sounds like a lot more work, but sometimes correct experimental design calls for a little more creativity and effort in order to get it right, and get valid results.

You roll your eyes and tell me that I’m being entirely impractical and unrealistic. “OK let’s assume that this is a well-funded university that can afford a decent electrician. Everything in the rooms has been tested and checked out. They’re fine. They’re completely monitored in every way so that if something goes wrong it’ll be noticed immediately and fixed. Stop being such a curmudgeon.” Yes, probably everything will be fine. But what if there is some variation that you don’t know about yet? You can’t monitor something you don’t know of. You have to design your study well enough, and with all precautions in place, to take care even of the most unforeseen circumstances. Only then can you get results that prove what you say they prove, with as much confidence as you think.

Pseudoreplication is everywhere. For example, a major study in my thesis area is pseudoreplicated, and sometimes I wonder if I’m the only one who’s noticed. (A developmental hormone was applied to some insects. The experimenters squirted hormone onto filter paper in the bottom of a Petri dish, and let groups of insects walk around on it and absorb it. Thus, the experimental unit here was not the insect, It was the Petri dish. But you can bet that each insect was treated as independent in the statistical analysis.) I know that sometimes I tend to lazily skim over the methods sections in papers to get to the conclusions. It’s a temptation, and a strong one, too, when there’s so much to read and so much else to do. But so much can go wrong in those dry methods sections. If we biologists can’t be trusted to always remember the lessons of our statistics classes way back in grad school, then all of us have to be on guard to catch our colleagues’ mistakes, before those unnoticed mistakes become accepted and cited in future research, even though they may well be completely erroneous.











*”data” is plural. “These data.” Not “this data.” Really. Don’t be That Guy**

**In normal situations “That Guy” might refer to the dude at the bar with his shirt tucked into his underwear who can’t figure out why all the girls are shooting him down. In nerd circles, it refers to the person who uses “data” as a singular noun. Hopefully it’s not the same person who also has his shirt tucked into his underwear, or he’ll never get a date.

How You Can Get Involved In Local Education

I just stumbled across this site, www.donorschoose.org. It's a way teachers can post the cost of specific material needs they have in the classroom, for potential donors to search for projects they want to support. All entries are indexed by state, so you can look for something close by. Most of the needs are basic things like art supplies, dictionaries, or school supplies for kids who can't buy their own, and usually cost only a couple hundred dollars total. All entries include pictures of the teacher or students, and once all the money is collected, each donor to a specific project will get personalized thank-you notes from the kids in the classroom and a photo of all of them with the materials your donation helped to buy.
I'm really excited about it because it's local, and it's direct. There's no money wasted in overblown bureaucracy, and you know exactly where every cent of your donation is going. A small percentage of the total cost of each project, which is listed up front, and which you have a choice in contributing to or not, goes to donorschoose.org for their work in screening project proposals, sending materials to the schools, and organizing thank-you notes. It's highly efficient, transparent, personal, and beneficial.
One troubling question that this brings up though, is why teachers have to go searching for private funds to buy books, like this teacher from Maryland who wants to buy age-appropriate books for her students. Or even dry erase markers, in this case in New York City. Why don't our school districts have money for these things? Why do teachers need to beg strangers for funding for basic educational materials for their classrooms instead of receiving it from the state?
There's several needy projects listed for my state, but I decided to give some bucks to this one, which needs only $66 more in order to complete funding for a classroom microscope in a high-poverty elementary school in Maryland. The microscope comes with prepared slides, and will be the first microscope that any of the students have ever used. The first time I ever used a microscope, it was astounding. It opened up an entirely new way of thinking about living things, and it would be great to help some less-fortunate kids around here have the same experience.

A Fast-Forwarded Look at How Our Oceans Might Be in a Few More Decades

This is scary stuff, when you get right down to it: With atmospheric CO₂ concentrations rising, where does it all go? Well, lots of it goes into the ocean. There, it's estimated to have caused a 30% increase in hydrogen ion concentration since the beginning of the last century. An increase in H⁺ levels means a drop in pH as the ocean becomes more and more acidic.

Our oceans are turning into vats of acid.

Does that scare you?

It should scare calcareous organisms more, since they're the ones who will be bearing the immediate brunt of ocean acidification: as acidity increases, their calcium carbonate shells disintegrate. Many, if not most of, the ocean's coral reefs, clams, snails, etc are threatened by this. And of course, not only them, but the ecosystems--and economies--based around them. Detailed discussion of the mechanisms and effects of ocean acidification has been made before, you can find one at wikipedia.

We might be able to visualize some of the effects that ocean acidification will have in our children's lifetime right now, according to a new letter in the journal Nature. [454:96-99] Hall-Spencer et al. use marine CO₂ vents in the Mediterranean as a natural experiment to see the correlation between high carbon dioxide levels and marine life community structure. The vents they monitor flux in CO₂ output normally throughout their existence, and they chose vents that emit only CO₂, without poisonous sulphur compounds or heat. Thus, they were able to limit confounding effects other than CO₂, and come to stronger conclusions about the association of CO₂ and reduced numbers of calcifers in the ocean.

They found a 30% reduction in species numbers (mostly calcifiers) near the vents versus the control sites. Coral reef cover (from Family Corallinaceae, the red algae corals) was 60% outside of the vent areas but only 0% within it. (*poof* Gone.) As if to take these Corallinaceae's place, a number of algal genera grew fantastically within the CO₂-rich regions near the vents. These algae include some of the most invasive algae species in the world, like sargassum, which forms thick, floating mats, and Caulerpa, which is already threatening the Mediterranean with its ability to crowd out all other species.

Sea urchin numbers were also significantly lower around the vents, juvenile gastropods were nowhere to be found, and adult gastropods' shells were flimsy. Barnacles seemingly were able to close themselves off to protect themselves from the acidic water, except for the lowest-pH sites, where they, too, were decreased in number.

The results of this study by Hall-Spencer and his team corroborate theory as well as earlier experimental studies of a more limited nature that couldn't take into account ecosystem-scale effects as well as this study could. The authors acknowledged that their work with vents could not perfectly model world-wide ocean acidification due to temporal variation in pH at the vents, the patchiness of the high CO₂ regions in the ocean landscape due to the nature of the vents, and other abiotic factors that may have had some effect. And of course, it's correlational and not causational. Nevertheless, this study provides valuable insight into the drastic effect that anthropogenic sources of CO₂ may have on ocean ecosystems if greenhouse gases continue to be emitted at the present rate.

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note: 15 minutes after posting this, I realized with a big, forehead-slapping "duh" that in this post I was committing the very same error I was deriding in my earlier post about the incorrect inference of causation from observational studies. I had to go back and edit myself. How embarrassing...

Susan's Snazzy Arthropod of the Day: Zonocerus elegans

This is Zonocerus elegans, or the "elegant grasshopper." Native to southern Africa, it was commonly found in the area in Mozambique where I used to live. Its species name, though, refers only to its coloration, not to its locomotion: it has got to be the most ungraceful, clumsy excuse for a grasshopper I've ever seen. When it hops, it rarely ever seems to land how one might expect it wanted to; instead of hopping in a manner that would allow it to proceed in a straight, efficient path, it tends to sort of slowly flop, landing sideways or backwards or sometimes not even on its feet. Maladaptive? Nah, you don't have to be an effective escape artist if you're as nasty-tasting as these guys are. They have a predilection for eating poisonous plants and sequestering the toxins as a predator defense. Additionally, they secrete a foul-smelling yellow goo when handled, and taste accordingly. Most things won't touch them, and they often can be a pest in agricultural settings.
Unfortunately for Z. elegans, though, some humans like funny-tasting stuff. The Pedi people of South Africa, for example, traditionally enjoyed them as a relish with porridge. I'm not certain how they dealt with the sequestered poisons; perhaps the concentrations are generally too low to affect humans, or the poisonous substances (generally cardiac glycosides or pyrrolizadine alkaloids, even cannabinoids) are degraded upon cooking.
In any case, other than their zesty flavor, I'm sure the Pedi also enjoyed how darn easy they are to catch. I would have liked to have been shown the proper way to catch them and cook them up. Nowadays, though, Z. elegans doesn't have as much to worry about. With entomophagy and other traditional diets on the wane in southern Africa, this pretty insect must be breathing a little grasshopper sigh of relief as it flounders off into the sunset, uneaten.


Photo by Lambert Smith, from insecta.co.za. Used with permission.

Kneeling at the pipes: a poem by Marge Piercy (dedicated to Amy W. and her roommates)

Princely cockroach, inheritor,
I used to stain the kitchen wall with your brothers,
flood you right down the basin.
I squashed you underfoot, making faces.
I repent.
I am relieved to hear somebody
will survive our noises.
Thoughtlessly I judged you dirty
while dropping poisons and freeways and bombs
on the melted landscape.
I want to bribe you
to memorize certain poems.
My generation too craves posterity.
Accept this dish of well aged meat.
In the warrens of our rotting citites
where those small eggs
round as earth wait,
spread the Word.

Score One More for Evolution--Magical Disappearing Fish Eyes

OK PEOPLE. Evolution is a fact. The details are up for grabs--that's how science goes. The book of Genesis, the seven days, the whole shebang, is an allegory, ok?
Now, can we just get over it and stop being stupid jerks and ruining kids' science educations? Really.

So we all know that deep down in dark caves lives oodles of weird animals without eyes. You've got your blind shrimp, your blind isopod, your blind salamander, and your blind fishy friend, the charismatic Astyanax jordani, the subject of a big huffy fit courtesy Casey Luskin at the Discovery Institute.

Luskin's argument is that loss-of-function mutations--i.e. mutations which occur randomly, screwing up a functioning gene so it "breaks"--are not contrary to the idea of intelligent design. The idea seems to be that God created something a certain way, and then something in our imperfect, corrupted world caused some oops to happen in the DNA that messed up God's perfect design. Ignoring the flaws in that argument for a moment (If that were so, and loss-of-function mutations were just unfortunate mistakes, how would they get fixed in a population? Could it be--gasp! natural selection??), let's examine Luskin's claim briefly.

He claims that the only thing that "Darwinism" (what a bad, incorrect term) cannot explain is gain-of-function, when an organism actually acquires a new trait.

Unfortunately for him, this loss-of-function in Astyanax jordani is actually a GAIN-of-function: a developmental gene called sonic hedgehog is actually upregulated, which increases skin sensitivity (beneficial to cave life, no?) while having the side-effect of disrupting eye development. PZ Myers has a great discussion of the flaws in Luskin's "argument" and the details of how A. jordani lost its eyes over at the Panda's Thumb.

Take that, Discovery Institute.

Educational Support in Mozambique

When I was in the Peace Corps, I served as a secondary school biology teacher in rural Mozambique. There, I encountered a whole lotta kids and a whole nottalotta teachers, crammed into school buildings with few supplies. In some cases roofs were even threatening to fall down on students' heads; they had never been replaced after being bombed out by RENAMO during the civil war, the contractor having absconded with the donated repair funds. The kids were like kids everywhere, sometimes curious, sometimes bored, sometimes awesome, sometimes little shits. There were a number of generally undereducated yet dedicated teachers, working from 7am with the beginning of 1st period of the first school shift, until past 10pm when the sixth period of the 3rd shift ended, five days a week, three trimesters a year. And then there were a whole bunch of corrupt jerks who were only still there because there was such a desperate teacher shortage. I read now about how the Mozambican government is putting in place a new program to support and supervise teachers and schools. I hope it stops those corrupt jerks I knew from deliberately lowering students' grades after barely teaching at all for a whole trimester in order to extort money and sex from them to pass. I can't wait to see the day when Mozambique has enough trained teachers to kick the predators and the thieves out of their school system.