Galley Proofs

Final Race to Read list!

2010-09-09T07:26:00.000-04:00

Well, I didn't quite beat my count from last year, but I did at least make it to 10. Here is the final list:

1. I See Rude People (Amy Alkon)
2. The Cat Who Came to Breakfast (Lillian Jackson Braun)
3. The Cat Who Blew the Whistle (Lillian Jackson Braun)
4. If It Takes a Village, Build One (Malaak Compton-Rock)
5. A Better Pencil: Readers, Writers, and the Digital Revolution (Dennis Baron)
6. Bottled & Sold: The Story Behind Our Obsession with Bottled Water (Peter H. Gleick)
7. The Magician's Nephew (C.S. Lewis)
8. The Lion, the Witch, and the Wardrobe (C.S. Lewis)
9. If the Church Were Christian: Rediscovering the Values of Jesus (Philip Gulley)
10. The Insecure American: How We Got Here and What We Should Do about It (edited by Hugh Gusterson and Catherine Besteman)

Please click here to go to my GPLC donation page and make your donation today. Donations can be made through September 30.

As a reminder, this year I am matching all donations, up to $200.

If you cannot make a donation to GPLC, please consider volunteering with a local literacy program instead. Or, just read to your children!

Thank you!

Race to Read update (9/5/10)

2010-08-26T07:18:00.007-04:00

(If you're not sure what this is all about, check out my introductory post here.)

Here are the books I've finished so far:

Added 8/26/10:
I See Rude People (Amy Alkon)--an interesting read!
The Cat Who Came to Breakfast (Lillian Jackson Braun)--I am actually reading a lot of these right now, but I won't count all of them for Race to Read because they're just too easy to read.
Added 8/28/10:
The Cat Who Blew the Whistle (Lillian Jackson Braun)
Added 8/29/10:
If It Takes a Village, Build One (Malaak Compton-Rock)--very useful; highly recommended for anyone interested in volunteering or service, but unsure how to get started!
Added 8/31/10:
A Better Pencil: Readers, Writers, and the Digital Revolution (Dennis Baron)
Added 9/1/10:
Bottled & Sold: The Story Behind Our Obsession with Bottled Water (Peter H. Gleick)
Added 9/4/10:
The Magician's Nephew (C.S. Lewis)
The Lion, the Witch, and the Wardrobe (C.S. Lewis)
Added 9/5/10:
If the Church Were Christian: Rediscovering the Values of Jesus (Philip Gulley)

Second annual Race to Read for International Literacy Day!

2010-08-26T06:59:00.001-04:00

International Literacy Day is September 8. For the second year in a row, I've decided to participate in the Greater Pittsburgh Literacy Council's fundraising event: Open Up a Book, Open Up a Life.

Here's what I have in mind:

I will read as many books as I can between now (well, actually, August 22) and September 8. I'll keep a record of the books I finish here on the blog. If you'd like to make a donation, pick an amount to donate per book I read. After September 8, come back here to find out how many books I've read. Do the multiplication to figure out your total donation, then go to my donation page and make a secure online donation. Of course, if you'd prefer to just make a single fixed donation, you can do that, too. If you'd prefer to donate through the mail, that's also a possibility; just let me know.

You can donate any time between now and September 30. GPLC's tax ID number is, I believe, 25-1392652, if your company can make matching donations.

If you'd like to see the final list of books I read last year, you can check out the final post about it here.

If you're not able to make a monetary contribution, please consider donating some time to GPLC or to your local literacy group. Or, just pass the word along to others.

Thank you!

Usage tip double dip: poll/pole and roll/role

2010-06-23T06:10:00.001-04:00

So, after a long-ish hiatus due to factors beyond my control, I have returned. And what better way to return from hiatus than with a double dose of homophones?

A poll is a survey, typically used to assess people's opinions. A pole is a long, thin, generally cylindrical, typically vertical object. (Unless you capitalize it; a Pole is a person from Poland.)

INCORRECT:
We took a pole to decide what kind of food to have at the company picnic.
I always walk into that poll in the basement.

CORRECT:
A recent poll shows that most people are sick of taking polls.
Our garage's roof was unstable, so we put a pole in to hold it up.

A roll is a small, typically single-serving-size piece of bread; it can also refer to an object in the shape of a small cylinder. The word roll can also be a verb, meaning to move via rotation or (typically combined with up) to fold a flat object to form a cylinder. A role is the part an actor plays, or the function of a component of a system.

INCORRECT:
I love coming to this restaurant; they make the best dinner roles.
He made cabbage roles for dinner.
I used to love to role down the hill when I was a kid.
Make sure to role the dough evenly, or your cinnamon roles will look strange.
The actor playing the leading roll was not very good.
No one is quite sure what the roll of the senior vice president is, other than to look good on television.

CORRECT:
Please make sure to pick up some grinder rolls at the grocery store.
Pass me that roll of parchment, would you?
If your emergency brake is broken, your car may roll away.
I had so many posters that, when I rolled them up, the roll was two inches thick!
Do you know who had the leading role in that movie?
My role is primarily that of a troubleshooter.

Scientia Pro Publica 21!

2010-02-16T06:54:00.000-05:00

GrrlScientist hosts the most recent Scientia Pro Publica carnival. Check it out for links to some great science, medicine, and nature writing!

Links for the week of 2/8/2010

2010-02-15T09:58:00.001-05:00

Physical sciences:
Scientists from the Weizmann Institute of Science in Rehovot, Israel figure out how to get water to freeze at different temperatures by modifying the electric charge on the surface it is sitting on. (ScienceNews)

Plastic water? misc.ience describes how scientists are able to make hydrogels that retain their shape, but are made almost entirely out of water.

Biology:
Researchers at the University of Maryland shed light on how Egyptian bats track their prey. Rather than firing sound waves directly at it, they shoot to either side. This makes them less likely to locate prey, but once they have found it, they can follow it more accurately. (EcoTone)

Beware mussels bearing "gifts": Neuroskeptic describes a study of amnesia caused by toxins in shellfish.

It's now fairly common knowledge that bees dance to tell other bees where to find food. But a recent study in Current Biology shows that they also use short buzzes to tell each other not to go to a dangerous location. Ed Yong at Not Exactly Rocket Science describes the study.

Female crickets can apparently warn their young of environmental dangers: baby crickets born to mothers hunted by wolf spiders are more likely to freeze and hide when they detect the spiders. (Not Exactly Rocket Science)

Sociology/human psychology:
Also from Neuroskeptic: A study of whether antipsychotic medication can reduce psychotic experiences in marijuana users.

If you want to encourage altruism, lead by example...and cleaning that bathroom might not hurt, either. A recent study suggests that watching other people perform good deeds increases the observer's altruistic tendencies. Interestingly, smells associated with cleaning also seem to increase altruism. (Psych Central; Not Exactly Rocket Science)

Daniel Hawes at Ingenious Monkey-20 two 5 has an excellent pair of posts on factors affecting girls' success in math.

A number of bloggers have written about Inuk, an ancient Greenlander whose entire genome was recently sequenced. Gene Expression describes the genetic relationships between Inuk's people (which anthropologists call the Saqqaq) and other human groups. Ed Yong describes what we know about his appearance, and how we know it.

John Tierney of The New York Times describes a sociological study conducted using the Times' own records. As it turns out, articles that inspire awe and those that deal with complex topics are the most likely to be forwarded on. (I wonder if there might be selection bias--perhaps readers of The New York Times are more likely to be interested in complex or awesome topics?)

Is religion necessary for morality? A common belief (for lack of a better word) is that religions originally developed to provide a basis for morality--i.e., to give the members of the society rules to follow to keep the society functioning. A recent analysis of studies in moral psychology, however, suggest that religious training and beliefs do not affect how people make moral decisions. Instead, the authors suggest, religion may have filled other needs in early society, such as the need to feel in control of one's surroundings. (björn brembs blog)

Links for the week of 2/1/2010

2010-02-05T16:38:00.000-05:00

Since I don't seem able to put together a daily links post, maybe weekly will be more manageable. Within each group, links are posted in approximately reverse chronological order (most recent first). (Yes, I know some of these are from before Feb. 1. I never said what the error bars were on that date.)

First, DINOSAURS!:
Fossil Feather Colors Really ARE Written in Stone (Living the Scientific Life)
The renaissance of technicolour dinosaurs continues (and the gloves come off...) (Not Exactly Rocket Science)
Oldest feathered dino shows its colors (Science News)
Newly Described Bird-Like Dinosaur Predates Archaeopteryx by 15-20 Million Years (Living the Scientific Life)

Next: Running...ur doin it rong...(maybe):
Evo. Anthro. Study Suggests You Might Be Running Wrong (Laelaps)
New Nature Magazine Cover Story Shines More Light on Barefootin' (Runner's World Peak Performance)

How to not be annoying at the gym, courtesy of Peter at Obesity Panacea:
Appropriate Gym Etiquette
Annoying Gym Personalities
What to Wear

And finally, assorted other interesting things:
Seven habits of highly successful toads (Not Exactly Rocket Science)
Friday Weird Science: Preserving the Species (Neurotopia )
Un-Natural Disasters (In Terra Veritas)
Backyard Chickens: An Art, A Science, A Social Movement (Food Politics)
Dave Munger (formerly of the Cognitive Daily) has launched a new blog, The Daily Monthly. It's awesome.
Bees can learn to discriminate human faces (Arthropoda)
Playing to Learn (NYTimes Op/Ed)
Looking inside the structure of the Yellowstone caldera (Eruptions)
Power source for a light saber (Dot Physics)

Why migrate?

2010-02-05T15:54:00.001-05:00

Growing up in New Hampshire, I took the yearly migration of ducks, geese, and (less obviously, but more impressively) Monarch butterflies pretty much for granted. It never really occurred to me to ask why all of these animals migrate. If I had been asked, I probably would have made the (common) anthropomorphic fallacy and said that they migrate because they "want to," or because they "like it better" at their ultimate destination.

Think about it: migration--especially very long-distance migration, such as that performed by some shorebirds, which can migrate from the southern tip of Africa all the way to the Arctic--is incredibly resource-intensive. It takes a long time, requires enormous amounts of energy, and is pretty dangerous. For a behavior like that to survive and develop in a population, it must provide significant survival or reproductive benefits. There are three main hypothesis about what those benefits might be:

1. Increases in food resources. For example, migrating south might allow birds to avoid competing for the limited food available in New England in the winter.
2. Reduction in parasite load. For example, migrating out of an area during a parasite's main breeding season might allow a bird to avoid infestation by the parasite.
3. Reduction in predation pressure. For example, migrating to different areas during different times of year might allow birds (or their eggs or hatchlings) to avoid attacks by predators that are common during those times.

It's possible to test these different hypotheses by looking at exactly where different populations migrate to. For example, consider those shorebirds I just mentioned. They migrate to high northern latitudes from the southern parts of Africa. The range of latitudes to which they migrate is wide; some stop just below the Arctic circle, but others keep going nearly to the North Pole. Previous studies have shown increased food availability and reduced parasite loads at these high latitudes. However, until now, there have been few studies that produced quantitative data on how migration site affects predation risk. In the 15 January issue of Science, Gilg and Yoccoz and McKinnon et al offer substantial evidence to support the idea that migrating to high latitudes offers significant benefits in terms of avoiding predators.

McKinnon et al placed more than 1500 artificial shorebird nests at various locations in northern Canada, over a latitude range of about 3350 km. They monitored the nests for two or more summers and recorded how well they survived predation.

The result? For every one degree further northward a nest was placed, the risk of predation on the nest decreased by about 3.6%. Over the range of latitudes they studied, that translates to 65% lower predation on the northernmost sites than on the southernmost sites. This is a significant reduction, and suggests that predation may indeed play an important role in driving bird migration.

However, other studies of predation risk at different latitudes didn't show such a clear trend. McKinnon et al suggest that this might be because those other studies used real nests, which vary in size, health, etc. In other words, previous trials were not as well controlled as was this investigation. By using artificial nests, the researchers reduced other potentially confounding factors.

Gilg and Yoccoz add to the story by suggesting that an important factor influencing predation on the nests is the distribution of another common prey species, the lemming. Lemmings and shorebirds (and shorebird eggs) are common prey for the Arctic fox. By comparing the distributions of the lemmings and the shorebirds, Gilg and Yoccoz show that the shorebirds most commonly hunted by foxes are typically common only where lemmings also occur. They hypothesize that, in areas without lemming populations, the predation pressure on the shorebirds is too high for their populations to survive.

Together, these two articles indicate that there are many more factors influencing bird migration patterns than simply "because the birds like it better there."

Gilg, O., & Yoccoz, N. (2010). Explaining Bird Migration Science, 327 (5963), 276-277 DOI: 10.1126/science.1184964

McKinnon, L., Smith, P., Nol, E., Martin, J., Doyle, F., Abraham, K., Gilchrist, H., Morrison, R., & Bety, J. (2010). Lower Predation Risk for Migratory Birds at High Latitudes Science, 327 (5963), 326-327 DOI: 10.1126/science.1183010

Usage tip: pore vs. pour

2010-01-29T17:37:00.000-05:00

I have a research review in progress. Until then...

I read an email the other day in which the writer said he was "pouring over the image." Unless the image is liquid-proof, this could be problematic...

Pour refers to what happens to liquids when you tip their containers. If you're focusing a lot of attention on something, you're poring over it.

CORRECT:
I pored over every detail of Dumbledore's conversations with Harry to figure out what was coming next.
It was pouring out when I left work.

INCORRECT:
I don't want to spend hours pouring over tax guidelines, trying to figure out what deductions I can take.
I pored the oil into the saucepan before adding the garlic.

Links: 1/25/10

2010-01-25T19:54:00.001-05:00

Travis at Obesity Panacea has a good discussion on eliminating risk vs. minimizing risk, and the unintended consequences of trying to protect kids from getting hurt: No balls (or bikes, or skateboards) allowed

Mike Elgan at Computer World gives some updated cell phone etiquette rules.

Ammon Shea at the New York Times Magazine discusses whether texting might be changing the rules of spelling.

A research review at Science Daily describes how llama--yes, llama--proteins could be used to detect potent neurotoxins.

The Oatmeal gives his usual, unique take on a common grammar problem: How to use a semicolon.

Ed Yong at Not Exactly Rocket Science describes research indicating that echolocation in bats and whales may have been enabled by changes to the same gene.

New NSF-funded site on science education

2010-01-21T14:16:00.004-05:00

I just got this update from a friend (via LinkedIn):

A new NSF-funded site has just launched. According to the release:

"[The site is] dedicated to cataloging best practices in media-based science education and getting the word out about--and discussing--innovative new media-based science education programs and concepts (where media includes both traditional and new media). The site is located at:

http://www.mediasciencelearning.com/

To celebrate its launch (and help get its discussion areas quickly up to critical mass), the grantees (at their own expense, not NSF's) are giving away Zingerman's gift certificates to the best (and most prolific) contributors to the site's case discussions, located at:

http://www.mediasciencelearning.com/CaseStudies

Related to this, if you know of any great media-based science education programs that ought to be highlighted by this site (or you run one yourself and are looking for feedback, publicity, collaborators, or funders), you can submit it at:

http://www.mediasciencelearning.com/addacase/
"

Usage tip: sleight vs. slight

2010-01-20T17:02:00.007-05:00

Today's tip comes to you courtesy of Tetley tea, who puts short quips on the paper tabs of their teabags. One I got today said "False friends give slight-of-handshakes."

Clever idea, but wrong word.

Slight means small, diminutive, thin, etc. Sleight means cunning, skill, or dexterity. So, false friends actually give sleight-of-handshakes.

CORRECT:
The magician used sleight-of-hand to hide the ball under the table.
We need to take a slight detour to avoid the construction.

INCORRECT:
Don't try to fool me with slight of hand!
At the next intersection, take a sleight right.

More evidence that simple classroom interventions can have positive effects on achievement

2010-01-19T19:04:00.021-05:00

Reading the article I summarized yesterday reminded me of a pair of articles I read recently on a related topic. The first was published in the 1 September 2006 issue of Science, and the second was published in the 17 April 2009 issue. Both describe the results of affirmation exercises on student achievement.

For the first article, Cohen et al. studied two groups of seventh graders (approximately 120 students per group), about half European-American and half African-American. They randomly assigned students to one of two groups (an experimental group or a control group). Students in both groups were given short (~1 paragraph) writing assignments. Students in the experimental group were instructed to choose and write about values that were important to them; those in the control group wrote about values that were unimportant to them.

The intervention occurred at the beginning of the fall semester during the experimental year. Researchers followed up on students' fall semester grades to evaluate the effectiveness of the intervention.

In the second article, the researchers describe the results from a third experiment (a third set of students given the assignment), plus additional data on the students from the original groups, two years later.

This is where it gets interesting. As you read the following, keep in mind that this intervention took about 15 minutes and involved no special equipment, no curriculum modification, and no teacher preparation at all.

African-American students in the treatment group showed significant increases in GPA (~0.24 points) compared to their peers in the control group. African-American students with the lowest achievement going into the class (and the lowest expectation for achievement in the class) had an increase in GPA of 0.41 points compared to their peers in the control group. These effects were present even two years later. What's more, students in the treatment group were less likely to be held back or assigned to remedial classes. Students in the treatment groups also reported more positive self-perceptions, even over the long term.

European-American students showed no differences between control and experimental groups. In fact, the treatment reduced the "achievement gap" (the observed difference in performance between African-American students and their white classmates) by approximately 40%.

The researchers hypothesize that the affirmation exercises act to break a recursive cycle of failure. To quote, "A feedbackloop, with psychological threat and poor performance reinforcingone another, can create worsening performance over time. Students'poor performance may also cause them to be seen as less ableby their teachers and less worthy of attention and mentoring,increasing the likelihood of lower performance." In other words, students who fail early--and therefore assume that they are less capable--have lower expectations of achievement. Those low expectations can become a self-fulfilling prophecy: students expect to do poorly, so they do.

Because the affirmation exercises focus students on things they value, the exercises can increase students' feelings of self-worth. By reinforcing students' self-esteem, the exercises help to break students out of the failure feedback loop.

The differential effects of the treatment on African-American and European-American students may arise because of the so-called "stereotype threat." A common stereotype is that African-American (and other minority) students perform poorly compared to white students. Therefore, minority students are more likely to fall into a feedback loop when confronted with failure--students' awareness of the stereotype makes them more conscious of their performance, and if they do poorly, they think they're conforming to the stereotype, which puts them under more pressure, which makes them do even more poorly...you get the idea. Even minority students who perform well may experience negative stereotyping effects--their awareness of the stereotype (again) puts pressure on them, which negatively affects performance.

The researchers hypothesize that doing the affirmation exercises helps to reduce the psychological "threat" of stereotyping, allowing students to perform better.

Together, these two papers provide additional evidence that even short-term, simple interventions can make significant strides in closing the achievement gap between white and minority students. As in the article I reviewed yesterday, the effects of this simple exercise were most pronounced for the most at-risk students (low-achieving African-American students), and the exercise had no downside for high-performing students. The results also suggest that such interventions might have long-lasting positive effects. Obviously, these kinds of exercises will not solve all of the educational issues facing the country--but they are cheap (in terms of both time and money), easy, and effective.

(And by the way, the older article is available--full text--for free online at www.sciencemag.org.)

Cohen, G., Garcia, J., Purdie-Vaughns, V., Apfel, N., & Brzustoski, P. (2009). Recursive Processes in Self-Affirmation: Intervening to Close the Minority Achievement Gap Science, 324 (5925), 400-403 DOI: 10.1126/science.1170769

Cohen, G. (2006). Reducing the Racial Achievement Gap: A Social-Psychological Intervention Science, 313 (5791), 1307-1310 DOI: 10.1126/science.1128317

Things I learned at ScienceOnline2010

2010-01-18T17:14:00.004-05:00

Might as well jump on the bandwagon...

10.5 Things I learned at ScienceOnline2010:

1. Science bloggers, and people who willingly spend an entire weekend in RTP with them, are pretty amazingly cool people.

2. There's too much attention paid to failing kids, and not enough to the awesome ones.

3. In all the huffle about NCLB and K-12 STEM education, we may have overlooked an important group who are just as excited and interested in science: adults (and here).

4. Food on ocean research vessels is awesome. (Who knew?)

5. Fact-checking isn't just making sure you got the science right. Oh, and it's not always clear what constitutes a "fact."

6. Minorities are edging out whites in the use of handheld devices.

7. Apparently, college students no longer check their email.

8. Google is working on a brain implant, so you can be constantly online.

9. Working online and using social media can allow people to be judged more by their thoughts than their appearance. But that might not necessarily be a good thing.

10. The North Carolina Museum of Natural Sciences is very large. And, it hosts an insect festival every year in which one can consume stir-fried crickets and meal worm pie.

10.5. The Sleep Number Bed is the world's most expensive air mattress...and that's about all it is.

Focusing students' attention on the relevance of science improves educational outcomes

2010-01-18T08:38:00.003-05:00

In the discussion about improving science education, the focus often falls on large-scale programs. However, some studies are suggesting that even short-term, small interventions in classrooms can have significant effects on student achievement. In the 4 December 2009 issue of Science (okay, I'm a little behind in my reading...), Hulleman and Harackiewicz investigate the efficacy of short writing assignments on student interest and achievement in science.

It's generally well accepted (and logical) that students with an interest or stake in the material they are learning perform better, work harder, and retain more of what they learn. However, it can be difficult to identify causal relationships between various interventions and student success, because many programs that do produce good results include a lot of different components, not all of which are focused on increasing student interest in the topic.

Hulleman and Harackiewicz hypothesized that activities that draw students' attention to the relevance of instruction to their everyday lives would lead to an increase in achievement. They also hypothesized that the increase in achievement would be largest among students who started out with low expectations of their own abilities--that is, students who think they will do poorly in science would benefit more from these interventions than students who already think they will do well.

To test these hypotheses, the researchers performed an experiment involving 262 high school students. The students attended two different high schools, were taught by seven different teachers, and were enrolled in three different science courses (biology, physical science, or integrated science). Nearly all (92%) of the students were ninth-graders (the remaining 8% were tenth-graders). About half (52%) were female. The majority (66%) were white; 15% were African-American, 12% were Asian, and 8% were Hispanic. The experiment spanned a single academic semester, but data were also collected on about 40% (100/262) of the students' grades for the following semester.

The students were randomly divided into two groups (one experimental group and one control group). Slightly more than half (136/262) of the students were in the experimental group. The teachers did not know which group each student had been assigned to. Each group was assigned to write between one and eight short essays over the course of the semester. Students in the control group wrote summaries of the content they were learning in the class. Students in the experimental group wrote essays describing the relevance of what they were learning to their own lives. (It was not clear whether that context was provided to the students or whether they were expected to identify it themselves.)

At the beginning of the semester (before the experiment), the researchers surveyed students to learn their expectations of success in the course and their interest in science. They also surveyed the students at the end of the semester to reassess their level of interest in science and to learn their future plans for careers in scientific fields. Students' grades during the semester were also monitored.

The results suggest that even this type of simple, short-term intervention can significantly improve student results, at least for those students who start the class with low expectations. Students with low expectations who were in the experimental group had significantly higher grades--"nearly two-thirds of a letter grade", to be exact--than those in the control group. Low-expectation students in the experimental group also showed significantly increased interest in science compared to those in the control group.

Among students with high initial performance expectations, there were no statistically significant performance or interest increases from the intervention. In other words, students who thought they'd do well in the class generally had the same grades (and post-class interest in science), regardless of which group they were in.

Although these results are encouraging--they suggest that teachers can increase the likelihood of student success, especially for the most at-risk students, through a few simple writing assignments--the sample size was small, and relatively homogeneous. Larger studies involving more students, especially minority students, would increase the reliability of the results. Until then, though, these results certainly suggest that these kinds of assignments can't hurt, and could be very helpful.

Hulleman, C., & Harackiewicz, J. (2009). Promoting Interest and Performance in High School Science Classes Science, 326 (5958), 1410-1412 DOI: 10.1126/science.1177067

Some more useful science online resources

2010-01-17T11:43:00.004-05:00

Scivee--share your science online!

SciNet--a new social network for scientists of all stripes, from AAAS.

Periodic Table--interactive periodic table. h/t Staten Island Academy student in ScienceOnline session. (Play with the temperature slider and see how the states of different elements change!)

Miss Baker's Biology Class--some really amazing student projects, blogs, etc.

Staten Island Academy's blog community--a great role model for student blogging.

Usage tip: affect vs. effect

2010-01-17T07:05:00.007-05:00

In nearly all cases, affect is a verb (meaning "to have an influence on"), and effect is a noun (meaning "result" or "influence"). Thus:

CORRECT
That movie had a strong effect on me.
The news report affected me greatly.
How does gravity affect matter?
What are the effects of solar radiation?

INCORRECT
The book I just read really effected me.
I don't drink because I don't like the affects.
Can you describe some of the affects of commercials?
Will Internet usage effect how we learn information?

One way I often remember it is this: Just like a comes before e in the alphabet, you have to affect something before you see an effect.

Just to confuse things, of course, there are situations in which affect is a noun, and in which effect is a verb. However, those usages are not parallel like the ones above.

Affect as a noun is almost exclusively used in psychology (and by people who are not in psychology but who want to sound like they are). In that context, affect refers to a person's behavior, mood, and general emotional state. (Also in this context, the word is pronounce "A-fekt", not "a-FEKT".)

Effect as a verb means "to put into motion" or "to cause". In this context, the word is pronounced "ee-FEKT", as opposed to the more common "uh-FEKT". It's almost always (at least in my experience) used with "change," as in "to effect a change". Again, this is an uncommon usage.

In general, to figure out whether to use affect or effect, try replacing the word with another noun or verb. If you can replace it with a verb, use affect. If you can replace it with a noun, use effect. But please, whatever you do, do not use impact!!

Some cool science and education web sites, courtesy of ScienceOnline2010

2010-01-16T10:56:00.018-05:00

FieldTripEarth--free data, plus info from real, live research programs going on all over the world.

NESCent--the National Evolutionary Synthesis Center. More (lots more) free data, plus educational materials on cutting-edge evolution research. (I think when the speaker demonstrated this, half the room started drooling at the data that are available...)

EduWeb--a source for online/digital, educational games on science, technology, history, and art.

Dryad--another open access data depository.

PRI's The World Science--weekly science podcasts, news stories, etc.

Scitopia--a peer-reviewed-research search engine.

Fold.it--play computer games for SCIENCE!

Spot.us--donate to journalists needing funding to cover their stories.

Science for Citizens--find research projects looking for volunteers.

Pandemic II (game)--play the bad guy. Design germs, infect people, get points!

Science Cheerleaders--learn basic science facts, find citizen science projects, and take a brain makeover quiz!

Interesting word for today: graben

2009-11-30T15:44:00.005-05:00

According to the American Geological Institute's Glossary of Geology, 4th edition, the definition of graben is the following:

"graben (n) An elongate trough or basin, bounded on both sides by high-angle normal faults that dip toward the interior of the trough."

Breaking it down a bit:

A fault is a crack in a rock body along which the rock has moved--i.e., the rock on each side of the fault has moved relative to the rock on the other side. Most faults are tilted relative to Earth's surface--they're not perfectly vertical. Therefore, there is a body of rock "above" the fault and a body of rock "below" the fault. The rock "above" the fault is called the hanging wall. The rock "below" the fault is called the footwall:

The hanging wall and the footwall can move in two different ways. In a normal fault, the hanging wall moves down relative to the footwall. In a thrust fault, the hanging wall moves up relative to the footwall:

A graben is a valley bounded by high-angle (i.e., steep) normal faults on both sides:

Sorry about the blurry images. Blogger's thumbnails aren't that great. But you should be able to see the images in all their glory by clicking on them...

An open letter...

2009-11-06T14:01:00.002-05:00

...to the leftover Halloween candy lurking throughout my house.

Dear Evil, Yet Strangely Delicious and Compelling Ones,

Please, leave me alone. Seriously. Why can't you bother my husband for a while?

Please?

Thanks,

Kate, who wishes to remain cavity- free and to not have to purchase new pants

Update: More thoughts on uncomfortable research

2009-11-05T06:07:00.001-05:00

A few more science bloggers have added their thoughts on drug addiction research:

The Intersection
DrugMonkey

Uncomfortable research

2009-11-04T16:50:00.003-05:00

There are a couple of good posts up at ScienceBlogs (at Bioephemera and Adventures in Ethics and Science) about the double standard applied to drug addiction research, and the ethics thereof.

To sum it up succinctly, BioE points out the apparent double standard of research into how to help people quit smoking tobacco = GOOD! but research into how to help people quit smoking pot or crack = BAD! She also points out the (possibly larger) societal costs associated with illegal drug use and addiction and (validly, in my opinion) questions why spending money to try to avert those costs is considered a waste of money. She also touches on issues involved in funding research on other "uncomfortable" topics, such as HIV transmission in transgendered prostitutes.

Dr. Free-Ride, as is her wont, addresses some of the ethics involved in avoiding research on behaviors considered to be "moral failings." She asks (again, validly, in my opinion) "...are we committed to a one-strike policy with bad choices, with no room for compassion or fresh starts? Is that really who we want to be as a society?"

My answer is a resounding "Hell, no!"

And as both Dr. Free-Ride and BioE have asked for others to post their thoughts, I thought I would.

I'd like to write more on this, but between the two of them they've pretty well hit all the points I would have made.

Go forth, read...and then do something about it!

This requires a new label category

2009-11-01T09:13:00.006-05:00

Between this and the Sesame Street Martians, I think I need a new category: "I wish I'd thought of this!"

h/t to Dr. Isis

Check it out!

2009-11-01T08:42:00.001-05:00

Suzanne Coldwell--a friend of mine from high school--and her family have an alpaca farm! How cool is that??

Check out their new website and blog.

Darn, I wish I'd thought of this...

2009-10-31T07:45:00.005-04:00

Although I'm not sure my husband would've gone along, and it just doesn't have the same effect if there's only one.

Kind of reminds me of a time I went to my chemistry professor's Halloween party in college. A group of his students came dressed as letters and numbers--a.k.a., the letters and numbers Sesame Street is "brought to you by". It was brilliant.

h/t Orac at Respectful Insolence

Usage tip: its vs. it's--with bonus visual aid!

2009-10-30T06:32:00.005-04:00

So you think you've figured out how to use the apostrophe. The apostrophe is used to indicate possession and to take the place of missing letters in a contraction. No problem! You've got it down.

And then, along comes...its.

English being English, you know there has to be an exception to every rule (and several exceptions to each exception, too, in most cases). Well, its is it.

Use its to indicate that it owns something. Use it's to replace it is.

Correct:
The dog carried its bone to its den.
It's a nice day for a walk.
It's got a big scar on the back of its head.
It's a zombie! Run!

Incorrect:
The bird used newspaper in it's nest.
Its too late to watch TV tonight.
Its carrying its baby in it's mouth.
Its after your brains!

And just when I thought I had finished with The New Yorker ad fail, I get this week's issue and see this:

An open letter...

2009-10-23T16:19:00.002-04:00

...to the random folks I passed on my bike ride to class last night.

Dear Rockin-Out D00d:

I totally get that your music is, like, so awesome that you have to listen to it ALL THE TIME, even when you're walking somewhere. And I totally respect you for wearing earbuds so we don't all have to listen to it.

However, if you are walking on a joint walking/biking path, it would probably be a good idea to make sure your music isn't so loud that you can't hear my bell when I ring it. Or, at least, if you're going to use it to block out the pesky noises of Pittsburgh, then dude, don't walk down the middle of the path. Pick a side and stick to it. That way, when I need to pass you, I don't have to hold my breath that I might hit you (since you didn't hear the bell).

And to the loving couple,

It's great that you're taking an afternoon walk together, and the river trail is a beautiful place to do it. But please understand that A) it's a mixed-use trail, which means I as a bicyclist have as much right to the trail as you do; B) it's not a very wide trail, which means I as a bicyclist pretty much take up half of it; C) it's a lot easier for you two to walk single-file or move over than it is for me to shorten my handlebars to avoid hitting you; and D) that bell ringing behind you means "Hello, I'm riding a bicycle, and I'd like to pass you because I'm traveling faster--can you please move to one side for a couple of seconds?"

I'm glad I didn't hit either of you. And I don't begrudge you your space on the trail. But if you're going to walk side-by-side, at least, please, walk on the right instead of in the middle. That will give the rest of us plenty of space to go by you.

And finally, to the buttmunch in the car who honked at me,

Dude, get over it. Bicycles are vehicles too. It's just as illegal for me to ride on the sidewalk as it is for you. (And seriously. Have you seen some of the sidewalks around here? Do you know how much it hurts to go over uneven brick like that on a bicycle seat?!?) I'm riding as far to the right as I can. Deal with it.

Kate

On the shoulders of giants...

2009-10-23T16:13:00.003-04:00

Thanks to Dr. Isis, my complaint about the Intel ad generated an actual response from Intel. Kelly Feller apologized both here and on Dr. Isis's blog for any offense the ad caused.

I do appreciate the apology. I am sure that the intention was not to offend. And I do respect Intel's "Rock Star" line of ads in principle; I like that they're trying to bring visibility and cachet to science and engineering. I suppose when you put together as many ads as they do, a few are bound to flop. But still--maybe this incident will reduce the chances of this particular type of flop in the future.

At any rate, thank you Dr. Isis for bringing some visibility (and for agreeing with me, even though I wear sneakers for non-running purposes), and thank you Intel for a quick and polite response.

Am I the only one...

2009-10-21T13:23:00.003-04:00

...who finds this Intel ad (from the inside back cover of this week's The New Yorker magazine) vaguely insulting?

Because apparently the geniuses at Intel are far above such plebian activities as physical exercise. After all, really smart people are all skinny nerd-boys who subsist on junk food and chess. If you're low-brow enough to actually exercise, you wouldn't stand a chance against those "big brains" at Intel.

I know it's just an ad. But to me it propagates a false dichotomy: either you're smart and don't care about your physical wellbeing, or you're a gym rat with a brain the size of a ferret. Never mind the large number of studies that have found correlations between physical exercise and concentration, focus, and stress relief (something I'd imagine the Intel folks would know a lot about).

The ridiculous imbalance in X and Y chromosomes also bothers me. Yes, I realize that there is a big gender imbalance in Yoga classes (mostly XX) and technology R&D (mostly XY). But come on. If you're going to go to big lengths to show racial diversity (you can't tell me the two non-white d00ds are there by accident), at least show a chick in one of the games!

I'm not sure if the person in the white coat in the game on the far left is supposed to be a girl. But even if it is, come on, you couldn't pick someone with identifiable female features? Way to support even MORE smart-people stereotypes! (I.e., smart women don't look like women. We all have short hair, dress like men, and never wear makeup. Okay, that might be true for me. But I think Dr. Isis, among others, might have something to say about it.)

I think the folks who do the advertising for Intel deserve a big "congratulations" for taking great strides in making non-scientists even more likely to think that scientists find them stupid. Way to go, Intel!

Final results for Race to Read

2009-09-08T17:27:00.002-04:00

Well, I wasn't sure I'd make it to 10, but I did. Eleven, actually. For the record (this is also available on the original post), here are the 11 books I read for the GPLC International Literacy Day fund raiser:

1. The Good That Men Do (Andy Mangels and Michael A. Martin)
2. What Einstein Told His Cook: Kitchen Science Explained (Robert L. Wolke)
3. Kobayashi Maru (Michael A. Martin and Andy Mangels)
4. Proust and the Squid: The Story and Science of the Reading Brain (Maryanne Wolfe)
5. Holy Hullabaloos: A Road Trip to the Battlegrounds of the Church/State Wars (Jay Wexler)
6. Prime Directive (Judith and Garfield Reeves-Stevens)
7. Speaking Up: The Unintended Costs of Free Speech in Public Schools (Anne Proffitt Dupre)
8. Memory Prime (Gar and Judith Reeves-Stevens)
9. A Suitable Vengeance (Elizabeth George)
10. When Gay People Get Married: What Happens When Societies Legalize Same-Sex Marriage (M.V. Lee Badgett)
11. The Kobayashi Maru (Julia Ecklar)

To make your donation, visit my fund raising page.

Thanks!

FINAL RESULTS: Race to Read for International Literacy Day

2009-08-19T10:26:00.013-04:00

International Literacy Day is September 8. I've decided to participate in the Greater Pittsburgh Literacy Council's fundraising event: Open Up a Book, Open Up a Life.

Here's what I have in mind:

I will read as many books as I can between now and September 8. I'll keep a record of the books I finish here in this post. If you'd like to make a donation, pick an amount to donate per book I read. After September 8, come back here to find out how many books I've read. Do the multiplication to figure out your total donation, then go to my donation page and make a secure online donation. (Or, if you'd prefer to donate through the mail, just let me know.)

(Of course, if you'd prefer to just make a single fixed donation, you can do that through the donation page, too.)

You can donate any time between now and September 30. GPLC's tax ID number is, I believe, 25-1392652, if your company can make matching donations. [h/t to Erin for reminding me to look this up!]

If you're not able to make a monetary contribution, please consider donating some time to GPLC or to your local literacy group. Or, just pass the word along to others.

Thank you!

BOOKS I'VE READ:

1. The Good That Men Do (Andy Mangels and Michael A. Martin)
2. What Einstein Told His Cook: Kitchen Science Explained (Robert L. Wolke)
3. Kobayashi Maru (Michael A. Martin and Andy Mangels)
4. Proust and the Squid: The Story and Science of the Reading Brain (Maryanne Wolf)--Recommended!
5. Holy Hullabaloos: A Road Trip to the Battlegrounds of the Church/State Wars (Jay Wexler)--Recommended!
6. Prime Directive (Judith and Garfield Reeves-Stevens)
7. Speaking Up: The Unintended Costs of Free Speech in Public Schools (Anne Proffitt Dupre)
8. Memory Prime (Gar and Judith Reeves-Stevens)
9. A Suitable Vengeance (Elizabeth George)
10. When Gay People Get Married: What Happens When Societies Legalize Same-Sex Marriage (M.V. Lee Badgett)
11. The Kobayashi Maru (Julia Ecklar)

Usage tip: everyday vs. every day

2009-08-05T15:32:00.004-04:00

This one crops up so often, it's practically an everyday occurrence. (ha, ha, ha...sorry.)

Here's the difference between everyday and every day:

Everyday is an adjective.
Every day is an adverb.

But that doesn't really matter. You want to know how to use them correctly, right? Here's a handy rule of thumb:

If you can replace the term in your sentence with occasional or frequent or any other adjective and have the sentence still make grammatical sense, chances are you should be using everyday. If you can replace the term with Tuesdays or sometimes, you should probably be using every day.

For example:

WRONG
This shampoo is best for every day use.
Everyday, I walk my dog.
People should try to exercise everyday.
Luckily, loud street arguments are not an every day occurrence in my neighborhood.

CORRECT
You can use this shampoo every day.
Some trainers say you should run every day, but I think that's too much.
He's trying to prove that he's an everyday guy.
Let's try to make laughter an everyday event.

The mystery of the rotating seeds

2009-07-17T07:33:00.011-04:00

If you live in a temperate deciduous climate, you probably know what a maple tree is. And if you’ve been in a maple forest during spring or fall—or, really, any time of year—you’ve probably seen maple seeds. They look a bit like badminton birdies, only flattened: a heavy, solid "nut" at the bottom, with a single "wing" above. The wing helps the seed fly relatively long distances (for a plant)—up to a few kilometers in some cases.

A maple seed. From http://commons.wikimedia.org/wiki/File:Maple-seed.jpg.

Watching a maple seed fly is an interesting experience—they flutter and twist very rapidly. Because they twist and spin as they fall, scientists say they autorotate. In fact, they autorotate quite stably—a factor that allows the wind to carry them far from their parent trees.

Maples aren't the only trees with autorotating seeds—hornbeams, for example, have similar winged seeds. In all of these seeds, the autorotation is thought to help create extra lift on the seed, enabling it to travel farther from the parent tree. (Rambling offspring are a benefit for plants, because plant seedlings compete with surrounding plants for soil nutrients, sunlight, and water. If they land too close to the parent tree, they end up competing with their own parents—which benefits neither parent nor offspring, and therefore is detrimental to the survival of the species.)

Maple seeds and other autorotating seeds produce surprisingly large amounts of lift as they fall, considering how small and relatively slow they are. This is similar to the wings of many insects, which can produce a lot of lift from a relatively small surface area. Insect wings create this lift through the production of a leading edge vortex (LEV)—that is, a maelstrom of disrupted air along the edge of the seed that is "cutting through" the air as the seed falls. (Think of a wing—one edge of it is pushing through the air as it moves forward. The other edge trails along behind. The edge cutting through the air is the leading edge.)

In the 12 June issue of Science, Lentink et al report results of an investigation into the motions of maple seeds as they fall. Because the LEVs generated by insect wings help the insects produce significant lift, the researchers reasoned that maple seeds might produce similar LEVs.

Maple seeds are relatively small, and studying them while they fall can be challenging. This is especially true if one is interested in observing the flow of air over and around the seed as it falls. Therefore, as an initial test, Lentink et al built a scale model of a maple seed that was somewhat larger than a real seed. To make studying the movement of the air over the seed easier, they attached the model seed to a large arm inside a tank of mineral oil.

It may not be immediately clear how putting a model seed in mineral oil can be used to study the flow of air around a real seed. It turns out that this works because air and mineral oil are both fluids—substances that can flow in response to stress (pressure). As it happens, all fluids behave pretty much the same way under specific kinds of stress, provided that their differences in viscosity (resistance to flow, or thickness) are taken into account. The main difference viscosity makes is in the force required to move through the fluid—as you know if you've ever tried to walk under water. The more viscous the fluid, the more force is required to push through it, and the more slowly it returns to its original position. This latter property is the reason that many fluid dynamics studies are performed in oil or water, rather than air: the higher viscosity of a liquid makes observing its flow paths much easier. The path the liquid follows around the object is the same as the path that air would follow, so the results of the study are easily transferred to air.

Lentink et al used digital particle image velocimetry (DPIV) to make an image of the fluid flow around the model seed as it "fell" through the oil. DPIV is a technique that uses laser light, high-speed cameras, and computer integration to determine the velocity (speed and direction) of the fluid moving around an object in various locations. In DPIV, tiny particles are suspended in the fluid. During the experiment, as the fluid is moving, rapid flashes of laser light shine on the fluid, making the suspended particles visible for brief instances. A high-speed camera photographs the particles during each flash. The images are fed into a computer, which analyzes the locations of the particles during each instant. Because the computer knows the location of each particle at specific instances in time, it can calculate the velocity of each particle over time. Once the computer has calculated the velocities of the particles, it can create a three-dimensional image of how they move (and, by extension, how the fluid moves).

Using DPIV, Lentink et al identified a very pronounced LEV along the model seed. To confirm that their model seed accurately represents real seeds, they placed real maple seeds in a vertical wind tunnel. They adjusted the wind speed in the tunnel so that it matched the air speed the seeds would experience as they fell. As a result, the seeds hovered in place, but still spun the same way they would if they were actually falling. They recorded the motions of the seeds as they rotated. They were also able to create images of the flow of air around the seeds. The experiments with the real seeds confirmed the results seen in the model studies: maple seeds do, indeed, produce significant LEVs as they fall.

By comparing the maple seeds to other plant seeds, Lentink et al showed that the rotation of the maple seeds, and the resulting development of the LEVs, allows maple seeds to fall more slowly than non-rotating seeds of a similar wing loading (wing loading is the ratio of seed weight to surface area). Therefore, maple trees (or hornbeam trees, or other trees with rotating seeds) can produce heavier seeds (which can contain more food for the embryonic tree), but those seeds can still travel far enough from the parent trees to avoid competition.

Maple and hornbeam trees are not the only organisms to make use of the extra lift provided by LEVs, though. Hovering insects, bats, and possibly some birds also benefit from the production of LEVs along their wing edges. It makes me wonder whether "winged" marine organisms might generate similar vortices along their wings as they "fly" through the water.

Lentink, D., Dickson, W., van Leeuwen, J., & Dickinson, M. (2009). Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds Science, 324 (5933), 1438-1440 DOI: 10.1126/science.1174196

Normally I'm against Twitter, but...

2009-07-14T10:47:00.004-04:00

...in this case, I think I'll make an exception:
(see the original at PHD Comics.)

Calling PA residents!

2009-07-10T13:27:00.004-04:00

If anyone who reads this blog is a resident of Pennsylvania, please contact your senator and representative today to ask them not to cut state funding for public libraries. Public libraries provide important services to those most in need during tough economic times: students, the elderly, the un- or under-employed, and other underserved populations. Many public libraries provide assistance with education and job searches. They provide free entertainment in the form of books, magazines, music, and videos. Many host tax preparation workshops, educational seminars, and social activities for seniors, children, non-native-English speakers, and the disabled.

Public libraries rely on public dollars to stay in operation. If you live in Pennsylvania and have ever used, might ever use, or know someone who uses, a public library, please write to your state congresspeople today.

If you live in an area served by the Carnegie Libraries of Pittsburgh, please attend one of the town hall sessions they are holding to determine "...the future direction of public library service to the community of Pittsburgh" (quoted from an email I received today):

WHO: Hosted by the leadership of Carnegie Library of Pittsburgh and moderated by representatives from the League of Women Voters of Greater Pittsburgh.

WHAT: A brief program will be presented outlining the financial situation faced by Carnegie Library of Pittsburgh. Individuals are encouraged to comment about Library services.

WHEN & WHERE:
Thursday, July 16 at 7:00 p.m.
CLP - Main; Lecture Hall, 4400 Forbes Avenue

Saturday, July 18, at 10 a.m.
Carrick High School; Auditorium, 125 Parkfield Street

Tuesday, July 21 at 7:00 p.m.
CCAC-Allegheny Campus; SSC Auditorium, 808 Ridge Avenue

As a library volunteer, I thank you!

Scientia Pro Publica 7

2009-07-07T08:28:00.001-04:00

...is now available at Greg Laden's Blog. Check it out!

Good news for paleontologists?

2009-06-23T16:49:00.021-04:00

Paleontologists, as most folks know, study fossils (or, more generally, the evidence of past life of any kind). By examining the types and distributions of fossils in rocks of various ages, paleontologists can give us insight into how life on Earth has evolved. Thanks to the study of fossils, we know, for example, that Cambrian oceans were full of trilobites, that the Mesozoic Era was dominated by giant reptiles, and that giant "terror birds" once roamed South America.

Yes, fossils are undoubtedly vital to our understanding of life on Earth. However, although fossils are the only evidence we have for the existence of past life, they have--like all evidence--limitations. Foremost among these is the preservation bias. There's a reason nearly all the fossils you'll see in a museum or private collection are fossils of shells, bones, and teeth: hard parts are much more likely to fossilize than are soft parts.

This means that critters like the sea squirt and the cuttlefish, cute though they may be, are unlikely to appear in the fossil record. Their bodies are entirely (or almost entirely) made of soft tissue, which decays rapidly once they die. About the only way soft tissue can be preserved is through mummification or other direct preservation methods; and they are pretty darned uncommon.

Size and depositional environment also play a role in preservation bias. Larger body parts may be more likely to be preserved and fossilized than are smaller body parts, because it takes large parts longer to break down (thus allowing them more time to be buried and mineralized--although this isn't a hard-and-fast rule). Similarly, critters that die in the water are much more likely to be preserved, because they're more likely to be buried before they decay completely.

Ultimately, preservation bias means that our understandings of life on Earth are inevitably biased toward largeish, ocean-dwelling animals with shells, bones, and/or teeth. This is why we know so much more about trilobites than we do about, say, ancient jellyfish.

Of course, paleontologists acknowledge this problem, and make attempts to compensate for it. One way to try to compensate for preservation bias is to use so-called "live:dead" ratios. For example, suppose in a particular ocean ecosystem 30% of the animals are bivalves, 25% are bony fish, 35% are crustaceans, and 10% are "squishies" such as anemones and jellyfish. That critter composition is known as a "live assemblage" or a "life assemblage" for that ecosystem. (I made up those numbers. They probably bear almost no relation to realistic numbers--and those particular types of critters may not occur together. Just bear with me for the sake of demonstration.) To try to correct for preservation bias, a scientist might count the number of dead critters in each category. (I should note that this type of analysis would be based on numbers of individuals, not numbers of remains--so two clam shells would count as one clam, for example.) This "dead assemblage" or "death assemblage" can then be compared to the life assemblage to figure out relative preservation rates. If, for example, 30% of the living critters are bivalves, but 40% of the remains are bivalve remains, then bivalves would have a higher preservation rate than other critters in the ecosystem.

Potential problems with this method are probably obvious: How do you know which types of modern environments to compare ancient remains to? How do you know that preservation rates in remains are the same as fossilization rates? How do you know preservation rates for different types of critters are the same today as they were then? What happens if the ecosystem changes rapidly--do the death assemblages still accurately reflect the life assemblages?

In the May 22 issue of Science, Western and Behrensmeyer present data that may help to address the last two of these questions. They used a 40-year record from the Amboseli ecosystem in Kenya to study the relative preservation rates for large mammal (15 kg-4000 kg) bones. Previous studies have shown that the life and death assemblages for these mammals are similar at specific points in time; that is, at a given time, the proportions of different species in the life assemblage are similar to those in the death assemblage.

A variety of factors have caused the Amboseli environment to change quite rapidly since the 1960s. Woodlands have shrunk, grasslands have expanded, and swamps have doubled in size. These environmental changes, in addition to direct human actions, have substantially affected the mammal populations in Amboseli during that time. The ratios of different types of organisms--grazers vs. browsers, for example--have changed as a result, and overall species diversity has declined.

Bone and live animal surveys were conducted during two time periods: 1975-1976 and 2002-2004. The bones studied during those times could be separated into subintervals based on how long ago the animal died; this allowed the researchers to divide the samples into four subintervals (1964-1969, 1970-1976, 1993-1998, and 1999-2004). They also used census data to determine the numbers of live animals in various groups during those same time intervals.

For each of the time periods, the researchers compared the proportions of different organisms in the life assemblages with those in the death assemblages. They used these data to determine how well the death assemblages "track" or represent the life assemblages. What they found is pretty interesting:

Statistically significant correlations between live populations and bone counts for the different time intervals indicate that organisms that make up a larger fraction of a living community also make up a proportionally larger fraction of the bone assemblage for that community. In other words, at least for this ecosystem, you can use the death assemblage as a pretty direct proxy for the life assemblage--if 50% of the individuals represented by the death assemblage are medium-sized grazers, then you can infer that about 50% of the organisms in the ecosystem (on average) over the time period you're looking at were medium-sized grazers. You can also use the death assemblages to study how populations in the ecosystem changed over time; the ratios of grazers to browsers in the death assemblages roughly paralleled those in the life assemblages for the same time period. They were able to distinguish changes in population composition over time scales as small as 5 years; they were even able to "predict" ecological structure from the death assemblages (and those predictions were largely confirmed by the life assemblages).

Western & Behrensmeyer's data could be very useful for paleontologists, particularly large-vertebrate paleontologists; the data suggest that bone distributions in death assemblages can be used to infer population and community structures for ancient ecosystems. With some assumptions about ecolosystem properties, bone assemblages can also be used to infer other properties of ancient ecosystems, such as species richness and productivity.

Obviously, these data have limitations; Amboseli is a relatively dry terrestrial ecosystem populated by relatively large mammals, so it's not clear whether the same correlations apply to marine ecosystems, wetter (or drier) terrestrial ecosystems, or to those inhabited primarily by smaller organisms or invertebrates. Additionally, because all of the remains studied were relatively recent (40 years isn't long enough to produce fossilization or even significant burial in most terrestrial ecosystems), it's not clear how the processes of preservation, burial, and fossilization might affect the death assemblages. (Although they do note that partially buried bones--a "pre-fossil" assemblage--seem to show the same correlations as unburied remains.) But studies like these are still very important in determining the error bars (accuracy) of ecosystem studies based on fossil assemblages.

Their data also suggest that studies of death assemblages in modern ecosystems can be of use to scientists studying the effects of human actions and other phenomena, as well as to those wishing to confirm (or obtain) estimates of vertebrate population sizes and compositions.

Western, D., & Behrensmeyer, A. (2009). Bone Assemblages Track Animal Community Structure over 40 Years in an African Savanna Ecosystem Science, 324 (5930), 1061-1064 DOI: 10.1126/science.1171155

This is possibly one of the coolest shows ever...

2009-06-20T20:02:00.002-04:00

So I took today off to be a lazy bum, which means I watched way too much PBS. One of the WQED digital channels, the Create channel (13.2 for those in Pittsburgh with a digital air signal), is doing a marathon of the show Make.

This is the coolest show I've seen in a long time. It's basically half an hour of people talking about and demonstrating how they make a variety of gadgets and gizmos. It's really pretty neat--things one might never think of, like using an old VCR to make an automatic cat feeder, or building kinetic sculptures.

They have a website, and it's got archived videos of their shows. Check it out!

What's the signal, and what's the noise?

2009-06-16T15:41:00.019-04:00

As anyone who listens to the (non-satellite) radio knows, signal-to-noise ratio is an important consideration when analyzing a data set. If the ratio is too low, all you get is static. But what if that static actually contained its own signal?

The idea of useful information being "hidden" in apparent noise is nothing new--after all, cosmic background radiation was once thought to be just noise (and for many applications it still is). But in the May 22 issue of Science, Peter Bromirski outlines a rather unusual case of noise-becoming-signal: seismological evidence for climate change.

Geologists use seismographs to record the movements of the crust. Most of the time, the crust doesn't move much, aside from a background "hum" that results from Earth's natural oscillations. That hum can actually show up on seismograms; it has a period of 1-8 minutes or so. Occasionally, though, an earthquake--geologists also sometimes call it a "seism"--causes the crust to move much more emphatically.

During an earthquake, the movements of the crust cause the seismograph needle (or the digital analogue) to move in a specific way. The speed, amplitude, and duration of that motion are related to the motion that occurred to cause the earthquake, as well as to the composition and structure of the materials the resulting seismic waves passed through to get to the seismograph. By studying seismographs from around the world, geologists can infer where and when the earthquake occurred, what caused it, and how the waves it produced traveled. The background hum is just noise, and it's generally ignored.

The thing about seismographs is that, for the most part, they're terrifically sensitive. It's not unusual for them to detect trains and traffic. And, as Bromirski points out, under the right conditions they can also detect ocean waves, particularly those produced by big storms.

During a large storm over the ocean, high winds blow over the ocean's surface. The wind transfers energy to the water, which is where the big ocean waves come from. That energy can generate "microseisms" in the ocean crust. (A microseism is exactly what you'd guess from the name: a very low-amplitude vibration in the crust.) The vibrations produced by wave energy travel through Earth, just like those from an earthquake, and they can be detected on seismographs, too. Therefore, hypothetically, one could use seismogram records to determine the average storminess of the oceans over time.

The use of seismograms to study storminess has a few advantages over more common methods. For one thing, there are accurate seismograms that go back to the early 20th century--as far back as 1930, in some areas. These seismograms were all collected using pretty much the same technology and have similar precision, so they're readily comparable. This is unusual in climate science; many of the techniques commonly used to study recent climate change are fairly...well...recent, so the records don't go very far back or, if they do, they're much less precise.

Another advantage to using seismograms is that the global seismograph network (which has become more and more widespread over time) allows for comparisons between signals from different areas. This can allow scientists to infer the approximate paths and durations of storms in a region. In some cases, microseisms can give information about wave frequency and duration along specific coastline regions, data that may be hard to obtain otherwise.

Some studies using these long-term seismic records do suggest that Earth is becoming stormier: the ambient noise on the seismograms has increased over time.

Some researchers are also studying ways to use storm-driven microseisms to study more than storms. An important use of earthquake seismogram data is the study of Earth's interior. It's similar to the use of ultrasound to see inside the body: just as the path of a sound wave through your body depends on the density and structure of the organs below the skin, so the path of a seismic wave depends on the composition, temperature, and structure of the rock within Earth. Typically, seismologists use earthquake-generated seismic waves to study Earth's interior, because they're very high amplitude and generate strong signals. However, earthquakes are relatively rare and unpredictable. "Background" microseisms produced by storms and wave activity may provide a more long-term and consistent energy source for the study of Earth's interior.

Bromirski, Peter D., 2009. "Earth Vibrations." Science 324: 1026-1027. doi: 10.1126/science.1171839.

Using geometry to find a rainbow

2009-06-16T08:51:00.002-04:00

Chad Orzel at Uncertain Principles has a neat little post up about rainbows.

And you thought geometry could never come in handy.

I think it's pretty neat that the angle made by two hands is nearly scale-invariant. I wonder what that angle is for chimpanzees or other apes whose arms are longer relative to their bodies than human arms are?

Scientia Pro Publica 6!

2009-06-16T07:33:00.002-04:00

Scientia Pro Publica, the best in science/nature/medicine blogging for the general public, is now posted at Mauka to Makai. Yours truly has a post up!

Check it out.

Usage tip: complimentary vs. complementary

2009-06-15T09:43:00.002-04:00

For me, the easiest way to remember the difference between these two is to remember the definitions of compliment (something nice you say about someone) and complement (something that completes a set or group).

Something that is complimentary is either a) free or b) flattering. (Maybe another way to remember it is to think "I like things that are complImentary". Or maybe that's just really corny.)

Something that is complementary completes a set, matches a pair, or fills out a group. Angles, base pairs, and wines can be complementary, but statements and newspapers generally aren't.

So, you can sip complimentary coffee while contemplating the complementary angles on the rafters above your head. But if you start encountering complimentary angles, you might want to get your eyes (ears?) checked...

Usage tip: enormity

2009-06-12T17:04:00.004-04:00

Enormity does not refer to size. It means "horribleness" or "horrendousness."

If you talk about the enormity of a situation, make sure it's something terrible.

(My trusty Webster does allow the use of enormity to mean "enormous size or extent", but qualifies it by saying that it's considered "a loose use by some." Count me in that "some!")

If the Girl Scouts had badges like these...

2009-06-12T16:35:00.004-04:00

I just discovered Science Scouts. I was a Girl Scout for more than 10 years, and earned my share of badges. But none as cool as these!

As far as I can tell, I've earned 13 of them:

The "I've named a child or pet for science" badge (Sandy's real name is Sanidine. She prefers Sandy because it's less pretentious.)
The "Works with acids" badge (Including both HF and aqua regia, plus the standard highly concentrated nastiness.)
The "I've set fire to stuff" (Levels I and II) badge (No self-respecting chemistry major--or Girl Scout!--has NOT earned these two.)
The "Somewhat confused as to what scientific field I belong to" badge (Probably pretty self-explanatory...)
The "Experienced with electrical shock (Level III)" badge (I grabbed an electric fence once. Actually, I think I've had contact with electric fences twice. Comes from growing up in the country...)
The "I know what a tadpole is" badge
The "I've done science with no conceivable practical application" badge (But don't tell the NSF.)
The "Has frozen stuff just to see what happens" (Levels I and III) badge (I haven't had much experience with dry ice.)
The "Arts and crafts" badge (I'm about to start a crocheted DNA molecule...and realized that the one in the sample photo twists the wrong way!)
The "Talking science" badge
The "I blog about science" badge

(h/t Chad Orzel)

It's all in your head

2009-06-03T16:02:00.018-04:00

I think most of us are pretty willing to accept that the "will" or "urge" to move originates in the brain, and that the nerve stimulus that initiates the movement also originates in the brain.

What you might not know (I didn't) is that those two impulses--wanting to move, and initiating the movement--may actually happen in different parts of the brain.

I suppose it's not really surprising that this should be the case; the brain is, after all, a pretty big place (from a neuron's perspective), and obviously everything doesn't happen all in one spot. But in the May 8 issue of Science, Desmurget et al give pretty good evidence that the area that starts your body moving is distinct from the area that actually generates the urge to move.

The researchers studied seven human patients undergoing brain surgery for tumors. All seven were conscious during the surgery (possible because the brain, although the largest concentration of nervous tissue in the body, has no actual pain receptors on its surface), so they were able to answer questions. (Although it's not made clear in the article, presumably the patients were on several medications to relax them, but they were still conscious.)

In brain surgeries like this, doctors sometimes stimulate areas of the brain near the tumor to identify what parts of the body (or personality) may be affected by the surgery. In this case, the researchers used a similar technique to learn more about how the brain works.

During each surgery, several different regions of the patient's brain were stimulated with a small electrical probe. The shocks varied in intensity and duration. The researchers repeated the stimulations up to four times for each location, to check for reproducibility.

What they found out strikes me as pretty interesting. It turns out that, for several of the patients, when parts of the inferior posterior parietal cortex were stimulated, the patients felt an urge to move one or more body parts (arm, lips, chest, etc). If the stimulation was repeated with a higher intensity, the patients thought that they had actually moved that body part, even though no movement actually occurred. (The researchers report that one patient even said "I moved my mouth, I talked, what did I say?", although no mouth movement or speech was observed.)

Additionally, when portions of the premotor cortex were stimulated, the patients did actually move some of their body parts. When the stimulation was increased, the movement became more pronounced. However, and this was the part that I thought was kind of neat, the patients were completely unaware that they had moved at all. In fact, when they were specifically asked, the patients denied that they had moved, even when the movement was quite significant (e.g., raising an arm, or making a fist).

During the procedures, the researchers monitored the electrical signals in the patients' muscles as well. They saw no evidence of muscle movement when the parietal cortex was stimulated, even when patients were sure they had moved.

As an interesting side note, Desmurget et al report that stimulation of the right inferior parietal cortex caused patients to want to move their left limbs--hands, arms, feet, etc. However, stimulation of the left inferior parietal cortex seemed to prompt a desire to move the lips, or to talk.

References:
Desmurget, M., et al, 2009. "Movement Intention After Parietal Cortex Stimulation in Humans." Science 324: 811-813. doi 10.1126/science.1169896
Haggard, P., 2009. "The Sources of Human Volition." Science 324: 731-733. doi 10.1126/science.1173827

UPDATE: This post appears in the June 15 Scientia Pro Publica at Mauka to Makai.

Plus, they look a lot better on a shelf.

2009-05-29T10:02:00.003-04:00

Check out the highly scientific comparison of Kindle vs. books over at Bookgasm.

Personally, I particularly like that the scenarios they chose are so realistic and statistically likely.

(h/t John at Confessions of a Science Librarian)

Fascinating

2009-05-28T15:58:00.003-04:00

Ed Yong at Not Exactly Rocket Science has a post up about the "bacterial zoo" living on your skin.

It's really pretty amazing how many different little critters are hanging around all the time--and what a huge fraction of them are actually perfectly harmless.

It makes me wonder--when you see those articles in magazines etc. talking about all the different kinds of bacteria living on your keyboard, phone, desk, etc, they never actually say how many of them are pathogenic. My guess is that, unless you've recently had a bacterial infection, most of those bacteria the media like to use for scare tactics are actually quite harmless. But I could be wrong. Anyone have any data on that?

UPDATE: Here's a link to the "official" summary of the article from Science.

Canine dimensions

2009-05-18T15:33:00.004-04:00

Okay, apparently Sandy isn't as spectacularly cute as I think she is, because no one wanted to look at her long enough to estimate her dimensions.

This makes Sandy sad, but she'll get over it.

But, I did say I would explain the reason for the challenge in a few weeks. Being a woman of my word, I figured I ought to follow through.

All of the people to whom I've sent photos of Sandy who have subsequently met her have remarked on her size. Apparently, people expect her to be quite a bit larger than she actually is. This led my husband and I to wonder how people judge the sizes of objects when they have no reference points. We concluded that Sandy's proportions must be more similar to those of large dogs than to those of small dogs. I was hoping for some independent data to support this hypothesis. Alas, it was not to be.

(end note: Sandy, demonstrating a typical dog attention span, has now recovered from her disappointment.

)

Primary sources and creationism

2009-05-18T15:04:00.003-04:00

Chad at Uncertain Principles has an interesting post up about the difference between the humanities and the sciences with respect to primary sources. I was all set to make a short comment, when it occurred to me that what I was about to comment on actually spawned a more interesting thought:

My comment was going to be that a critical difference between many (most? all?) humanities primary sources and those in science is that, in science, the primary sources (especially old ones, like Principia) are more than likely no longer totally valid. Once Nietzsche wrote down his ideas, they were there--it's not like someone could come along and "disprove" them. That's the whole point; they're subjective. Most humanities primary sources are--the point of them is to present a position and defend it, in one way or another, but the position and the defense are both subjective. They might be more or less well-supported or more or less relevant, but they're still opinions, and therefore can't be disproved.

The same can't be said for many (most? all?) science primary sources. No one who knows any better claims that The Origin of Species is completely in line with modern evolutionary theory, because we've made discoveries since it was written. (I.e., Darwin didn't have all the facts. Neither do we today, which is why biologists in 150 years probably won't be citing papers published today as definitive references.) Not having read Principia (or even Cliff's notes of it), I can't say that's the case for it as well, but I would imagine it would be. Even in my relatively specific field, there are a few "primary" references that a lot of people go back to, but only for certain things--because the rest of the article has since been replaced by something more specific. This constant reexamination, replacement, updating, etc., of the "going thing" is a fundamental part of science, and it's the reason that it's considered questionable in a lot of fields to cite papers that are more than a few years old: we might have learned something since then that totally overthrows the previous paper. (The time scale of "acceptably recent" varies field-to-field, but it's always there.)

This led me to a thought: I'm wondering what fraction of the struggles we have with creationists might be due to a fundamental difference in the perceived importance of primary sources. A lot of creationism "arguments" against evolution are based on Origin, even though any competent biologist (or, really, any intelligent person who's taken high school biology) should be able to tell you that a great deal of the text in Origin is only somewhat correct, if not flat-out wrong. But a lot of the people arguing against evolution come from backgrounds that are, shall we say, not steeped in the fundamental concepts of science. (This isn't to say there aren't scientists who are creationists; there are. But my impression is that the vast majority of creationists are not scientists and have very little scientific training.)

How much of the problem could be attributed to creationists being more familiar with the humanities "method", and therefore reading the "original" texts and interpreting them, without bothering to think about anything that's come after them? It's completely appropriate in, say, philosopy or literature to read a primary source and then draw your own conclusions and opinions about it. And your opinions are just as valid as those of others who have read the same text and drawn different opinions. (Which isnt't to say there aren't "accepted" interpretations of many famous works, or that dissenting with those interpretations won't open you to ridicule or censure.)

How many creationists who think evolution = Darwininsm read Origin, interpret it in light of common knowledge, and then view works based on Origin (i.e., most of modern biology) as simply others' opinions?

I don't think this is the primary problem or stumbling block; I think that's more likely to be a combination of a poor mainstream understanding of the nature of science and the tendency of creationists to be indoctrinated into an absolute belief system. But I think this also might be part of it.

Usage tip: i.e. vs. e.g.

2009-04-30T16:35:00.001-04:00

Short and sweet:

i.e. means "that is" or "in other words". e.g. means "for example".

Vaccine safety and creationist nonsense

2009-04-30T16:26:00.003-04:00

Todd W at AntiAntiVax has an excellent post up addressing some of the most common "arguments" against vaccination. Check it out.

(h/t Phil from Bad Astronomy)

I also recently found an excellent source for refutations to creationist "arguments" against evolution. It's quite comprehensive in scope, although each specific anti-argument is a bit brief.

Usage tips (double dose!): insure vs. ensure and tenets vs. tenants

2009-04-29T12:29:00.003-04:00

The use of insure vs. ensure might seem fairly straightforward, but I've found multiple instances of its misuse even in that bastion of copyediting, fact checking, and solid writing, The New Yorker. So here we go again:

To insure something means to agree to provide payment to the owner of the thing if something happens to it. You insure your house, your car, and your health. Unless you're talking about something an AllState agent would sell you, you shouldn't be using insure.

To ensure something means to guarantee or make sure that it happens. You insure your health in case you get sick, but you try to ensure good health by eating right and exercising.

So:
incorrect: We hope that the investment in science research today will insure advancements in quality of life in the future.
incorrect: You're required to ensure your car in most states.

I've also seen multiple incorrect uses of tenants to mean tenets. A tenant is a resident of a building. A tenet is a fundamental principle. Thus, religions have tenets, but (one would hope) not tenants.

So:
incorrect: The tenants of Buddhism include rejection of dukkha, or desire.
incorrect: The tenets of the building sued the landlord for negligence.

On the importance of aspect ratio in estimating canine dimensions

2009-04-19T11:20:00.004-04:00

I have a challenge for anyone who reads this post (all two of you):

Here is a picture of my dog, Sandy.
Using only this picture for reference, please answer the following questions:

1. How tall is Sandy (floor to top of shoulder)?
2. How long is Sandy (tip of nose to base of tail, assuming her neck is stretched out)?
3. How much does Sandy weigh?

You may give your answers in Imperial or metric units. Estimates are fine. And if you have the urge, feel free to explain where your estimates came from. I'm especially interested to know if you have ever owned a dog, and if so, what kind(s).

If I get enough responses, I'll post an analysis (highly scientific and rigorous, of course). If I get only a few responses, I'll still post an analysis, but it'll be less interesting.

Regardless of the number of responses I get, in a week or two I'll post again explaining the rationale behind this challenge.

And it's not just the gammas...

2009-02-18T16:24:00.018-05:00

(Sorry for all the insectoid posts; Science just seems to have the most interesting articles on our six-legged friends lately!)

It's not just gamma male beetles that benefit from fake-outs. According to an article by Barbero et al., some species of butterfly also benefit from mimicry--of ants, of all things.

Ant society is very complex; most species include a number of different "genders" and societal roles, all of which are rigidly defined. (Emancipation has not yet come to the ant world.) Certain castes of ants are more valuable, and therefore more highly protected, than others. The extreme of this is, of course, the queen, who receives the most care and attention.

Although most of the communication necessary to keeping such a complex society running is chemical (e.g., pheromones) and physical (i.e., physical contact), apparently some of it is acoustic. Adults in certain ant subfamilies can produce "stridulations" (which I assume sound something like scraping noises, although I could be wrong) to communicate. Within these subfamilies, different castes produce different sounds (and larvae and pupae produce no sounds at all).

A number of ant species are also parasitized by the larvae and pupae of other insects. Barbero et al focused specifically on the butterfly species Maculinea rebeli, which parasitizes the ant species Myrmica schencki. M. rebeli larvae and pupae can infiltrate M. schencki nests and fool the ant workers into taking care of them. A significant characteristic enabling the butterfly caterpillars to survive in the ant nest is their ability to produce chemicals that mimic the chemicals produced by the ant larvae.

However, M. rebeli larvae and pupae apparently show higher "social status" than would be expected simply from the chemical mimicry. For example, M. schencki workers will rescue M. rebeli larvae and pupae instead of "dummies" that have been painted with the same chemical mimics. In addition, M. schencki queens will sometimes treat the butterfly larvae and pupae as rivals; at the same time, the ant workers treat the butterfly larvae like queens. This discrepancy led Barbero et al to guess that perhaps the butterfly larvae and pupae are able to produce acoustic signals that increase their status in the ants' social heirarchy.

As it turns out, they may be right. M. schencki workers and queens do produce distinct stridulations (i.e., they sound different to the other ants), and M. rebeli larvae and pupae produce sounds that are more similar to the queen ant sounds than to the worker ant sounds.

To test their hypothesis, Barbero et al carried out a number of tests. First, they recorded the sounds produced by the ant workers and queens. They played those sounds to "naive" worker ants. (They also exposed control groups to white noise and to silent speakers.) The worker ants showed more interest in the ant noises than the white noise or the silent speakers. In addition, the noises from the queens caused the workers to become more alert and to assume postures that are associated with "serving" the queens. This test confirmed that worker ants do respond to acoustic signals from other ants.

Next, the researchers recorded sounds from butterfly larvae and pupae. They played those sounds to similarly "naive" worker ants. The ants responded to both larval and pupal calls in the same way they responded to the queen ant calls.

Based on their observations, Barbero et al conclude that M. rebeli larvae and pupae are first able to enter an M. schencki nest through chemical mimicry. Once they are inside, however, acoustic mimicry may also play an important role in preventing the ants from rejecting them.

Barbero, Francesca, Jeremy A. Thomas, Simona Bonelli, Emilio Balletto, and Karsten Schönrogge, 2009. "Queen ants make distinctive sounds that are mimicked by a butterfly social parasite." Science 323: 782-785. doi: 10.1126/science.1163583

More insect phenotypic funkiness

2009-02-18T15:58:00.005-05:00

Like the male members of many species, male beetles fight over female beetles. And, like male deer and antelope, many male beetles sport formidable (for a beetle, anyway) horns, spines, and mandibles, which they use to intimidate (if not outright harm) other males. In the February 6 issue of Science, Rowland and Emlen report that some male beetles take a different tack: instead of fighting over the ladies, they pull an Achilles and "dress" like them.

Rowland and Emlen conducted statistical analyses of body size and horn, mandible, or spine length for several different species of beetles. Most previous analyses had assumed only two main male phenotypes for each species (e.g., big horns and small horns, with hornless males being classified in the "small horns" phenotype). Rowland and Emlen, however, found that several species of beetles actually show facultative male trimorphism--that is, the males actually demonstrate three distinct phenotypes (alpha, beta, and gamma). Alpha males have large bodies and large horns (or mandibles, or spines). Beta males have smaller bodies and smaller horns (mandibles/spines). Gamma males have the smallest bodies and no horns (you get the idea).

The differences in phenotype are facultative because they don't seem to be related specifically to genotype. Instead, the main factor determining whether a male is alpha, beta, or gamma seems to be his body size at maturity--beetles that get lots of food and good living conditions end up as alpha males (big bodies = big horns), while beetles that get less food and are smaller at maturity end up as betas or gammas.

Alpha, beta, and gamma males also seem to employ somewhat different mating strategies. Alpha males have the typical pissing contests for access to mates--for example, some alpha males will guard the burrows where the ladies are living, and fight off all comers. Beta or gamma males, though, are sneakier: they might dig side tunnels into the burrows and cuckold the alphas without ever having to fight them. In some other species (e.g., cuttlefish), "gamma"-type males actually get in with the ladies by "cross-dressing"--for example, some male cuttlefish can change color to mimic female cuttlefish, thus allowing them to get in close enough to mate with the females while the other males are busy showing off.

According to Rowland and Emlen, previous studies (and phenotypic analysis methods) have assumed that the majority of beetles display male dimorphism, rather than trimorphism. They suggest that alternative analyses may be necessary to detect trimorphisms--apparently, some of the traditional analyses did not detect all three male morphs in the beetles they studied.

I suppose the moral of the story is, if you're an alpha male, you might want to check the skirts of the ladies in your harem!

Rowland, J. Mark, and Douglas J. Emlen, 2009. "Two thresholds, three male forms result in facultative male trimorphism in beetles." Science 323: 773-776. doi 10.1126/science.1167345

Darwin in Context

2009-02-12T15:45:00.026-05:00

I've been trying to figure out what to write about for my Blog for Darwin entry. I've been reading Origin, but I haven't finished it yet (the last few chapters are not nearly as interesting as the first few). Even so, as I've been reading, I haven't really been struck with any brilliant insights or profound thoughts. One thing that has occurred to me a lot, however, is just how much we've learned since Darwin's time. So, I thought that for my BfD contribution, I would outline what was going on in science while Darwin was doing his thing. I'm hoping it might give some insight into what Darwin did and didn't know, and how his ideas may have been influenced by what was going on around him.

Disclaimer: I am not a historian; the summary below is not intended to be exhaustive. I'm mainly going to focus on the big ideas and events; if you're interested in the gory details, there are a plethora of excellent books out there to satisfy you, I'm sure. Also, please note that I've done my best to verify all of the information below, but I'm not an expert in this stuff. Any errors are solely my responsibility. If you find any, please let me know!

Chemistry
By the 1800s, the study of chemistry was becoming modernized. In the 1600s and 1700s, naturalists began to discover general laws that govern natural processes. Both Boyle's law and Charles's law (on the properties of gases) had been discovered by the early 1800s; a number of gaseous elements and compounds (including oxygen, nitrogen, and nitrous oxide) had been isolated and described.

John Dalton proposed his atomic theory in the early 1800s; although his concept of the atom (i.e., hard, solid, indivisible sphere) has since been replaced, his work on the conservation of mass and the law of definite proportions still underlies much of modern chemistry. His law describing the partial pressures of gases in a mixture is still used today.

The early 1800s also saw the publication of Avogadro's hypothesis (i.e., that equal volumes of gases at the same temperature and pressure contain the same number of molecules).

In the mid 1800s, Lord Kelvin proposed the idea of absolute zero and an absolute temperature scale.

What Darwin didn't know: Most elements were not identified or isolated until after the 1860s. Electrons were not discovered until the late 1800s; the concept of the atom as we know it today (i.e., nucleus of protons and neutrons surrounded by electrons) was not developed until the twentieth century. The nature of chemical bonding was also unknown in Darwin's time, as was the periodic table and the notion of periodic properties.

Physics
Electricity and magnetism were the order of the day in eighteenth and early nineteenth century physics. Franklin "discovered" electricity in the late 1700s; Ohm's law was proposed in the 1820s; Oersted discovered evidence of a magnetic field around a current-carrying wire in 1820; Faraday discovered electromagnetic induction in the 1830s; Joule and Helmholtz proposed the law of conservation of energy in the 1840s.

Newtonian mechanics were well established by the 1800s.

What Darwin didn't know: Radioactivity, quantum physics, relativity, and nuclear physics were decades to centuries away in Darwin's time.

Biology
As Origin does a pretty decent job of summarizing what was going on in evolutionary biology (such as it was) at the time it was written, I won't spend space on that here. In the mid-1800s, the idea that all living things are made of cells was just beginning to take hold; spontaneous generation was beginning to be discredited. Taxonomy was becoming more rigorous. Paleontology was starting to become a well-established field; most naturalists accepted that the majority of the fossils being unearthed around the world represented organisms that no longer exist.

What Darwin didn't know: Genetics and the theories of inheritance had not been discovered when Darwin did his work; a story I've heard (which I have not verified) is that Darwin had Mendel's papers on his desk when he died. Molecular biology, most of microbiology, and, of course, genomics were completely unknown. The germ theory was still a few years off, as was the discovery of many disease-causing microorganisms.

Earth Science
Naturalists were just beginning to come to grips with Earth's immense age during the late 1700s and early 1800s. The best consensus was that Earth was a few hundred million years old at most; these estimates were based on rates of physical processes (such as sedimentation and cooling). Radioactivity was unknown, so both a method for accurate dating and a mechanism for keeping Earth "warm" for long periods of time were lacking.

However, the principle of uniformitarianism was pretty well accepted, having been proposed in the late 1700s. As I mentioned above, paleontology was becoming more rigorous and "scientific," although some of the interpretations of fossils--especially dinosaurs--were rather interesting.

The idea of a global geologic column or time scale was becoming increasingly popular. Indeed, Darwin makes many references to the accepted contemporary time scale (although the time scale of the mid-nineteenth century bears little resemblance to our modern one).

What Darwin didn't know: The theory of plate tectonics was still about a century away. Radiometric dating (and an understanding of how radioactive decay has heated the planet) wouldn't be developed for quite a while, so Earth's true age was unknown to Darwin. In addition, research into the fossils and strata of the planet was generally restricted to Europe and North America, so Darwin's (and everyone else's) ideas about geologic history (and paleontology) were accordingly limited.

Well, there you have it: the two-bit tour of the state of science in the 1860s. I hope this is helpful to someone. If I had time, I'd go into more detail...yet another item to add to my "things to do when I win the lottery" list!

If the Egyptians had only known...

2009-02-10T16:52:00.012-05:00

According to legend, one of the way the Egyptians were punished in the time of Moses was with a swarm of locusts.

Locusts are insects that look a bit like big grasshoppers. They're a classic example of what's called phenotypic plasticity. An organism's phenotype is basically its observable characteristics--behavior, color, size, etc. (Phenotype is the outward expression of genotype; genotype is the specific group of alleles that an organism has. Most--all? I'm not sure--genes have at least two alleles, or "flavors." The classic example is, of course, Mendel's peas; the gene that controls flower color in pea plants has two alleles, purple and white. A pea plant's flower-color genotype is the particular combination of alleles that it has; its flower-color phenotype is the particular color of flower it produces.)

Organisms such as locusts that demonstrate phenotypic plasticity can undergo significant changes in behavior, appearance, etc due to changes in their surrounding environment. Locusts are a classic case because the change is so dramatic. If you take two locusts and put them in a box, they will pretty much avoid each other--that is, assuming they're demonstrating the "solitarious" phenotype. This is pretty much the default position for locusts; most of the time, they hang out by themselves (not a lot of singles bars in their neighborhoods, I guess).

Now if you had put, say, 20 or 30 solitarious locusts in that box and shut them in for a couple of hours, they would be quite changed when you opened the box. They would be swarming together, and they would have changed in appearance (from kind of boring and green to a rather striking, Steelers-like combination of yellow/tan and black...sorry, couldn't help it). They would be demonstrating the "gregarious" phenotype.

Solitarious (top) and gregarious (bottom) desert locusts. Image from Dr. Tim Matheson, University of Leicester

Locusts in the gregarious phase are the stuff of legend. These are the critters that mow crops down to the roots and blacken the skies. (Presumably, the Egyptians crowded their locusts.)

The cause of the transition from solitarious to gregarious has been known for a while, at least in broad strokes: being in the presence of lots of other locusts makes a locust more gregarious. In a recent article in Science, Anstey et al identify the mechanism that triggers the transformation.

There are two different sets of stimuli that can make a locust more friendly: mechanical and "cephalic." Mechanical stimulation involves being jostled by other locusts; in contrast to most humans, most locusts become more friendly when strangers stroke their legs. Cephalic stimulation involves the sight and smell of other locusts; locusts apparently have really great makeup and cologne. Both types of stimuli cause the locust's central nervous system (CNS) to produce (what else?) serotonin. (Yes, that serotonin.)

Previous researchers established that serotonin levels are higher in locusts undergoing the solitarious-to-gregarious transition. Anstey et al set out to determine the limits of this relationship. They did four main experiments: first, they figured out whether artificial stimulation of the individual sensory pathways could stimulate serotonin production and gregariousness. Then, they tested whether serotonin antagonists (i.e., chemicals that block the action of serotonin) could prevent the onset of gregarious behavior. Third, they determined whether artificially increasing serotonin levels was enough to induce gregariousness. Finally, they determined whether giving the locusts a serotonin precursor (i.e., a chemical that is easily converted to serotonin) increased their sensitivity to environmental stimuli.

In the first experiment, the researchers either stroked the hind legs of solitarious locusts, stimulated the nerve connecting the legs to the CNS directly, or put the locusts in a cage that allowed them to see and smell (but not touch) other locusts. In all cases, the locusts switched from solitarious to gregarious, and serotonin levels increased, suggesting that either type of stimulation is sufficient to induce gregariousness.

Next, they injected some of the locusts with serotonin antagonists (they also, of course, injected others with just saline--this was the control group). After the injections, the treated locusts (the ones that received the antagonist) were significantly less responsive to stimuli than the control locusts; treated locusts did not become gregarious, even when exposed to stimuli that caused the control locusts to boogie down. This relationship showed that inhibiting the action of serotonin prevents the "phase change."

In the third experiment, Anstey et al applied serotonin directly to the locusts' nerves (again, they also used a control group that received just saline). They also injected a third group of locusts with a serotonin agonist (i.e., a chemical that increases the activity of serotonin--the opposite of an antagonist). The treated locusts became much more friendly, but the control locusts remained aloof. In other words, just increasing serotonin levels (without actual stimuli) can make solitarious locusts more gregarious.

In their final experiment, the researchers determined whether increasing the ability of the locusts to produce serotonin would cause them to become more gregarious after only a small amount of stimulation. Typically, a solitarious locust has to hang out with other locusts for a couple of hours before putting on its party shoes. However, when solitarious locusts were injected with a serotonin precursor, 30 minutes of exposure was enough to get them dancing.

There's some hope that these results might lead to new possibilities for locust control. Individually (i.e., in the solitarious phase), locusts aren't too much of a problem--no more so than, say, grasshoppers, really. It's only when they start to swarm that they become economically disastrous. If a way could be found to prevent locusts from become gregarious, even when crowded, then locust swarms could be controlled. (Too late for Rameses, of course.) Such possibilities are still in the future--currently, there is no locust-specific serotonin antagonist that can be applied appropriately--but it does give some hope.

Until then, there is one thing we can definitely conclude: keep the locusts away from the Prozac!

Anstey, Michael L., Stephen M. Rogers, Swidbert R. Ott, Malcolm Burrows, and Stephen J. Simpson, 2009. "Serotonin mediates behavioral gregarization underlying swarm formation in desert locusts." Science 323: 627-630. doi 10.1126/science.1165939

Stevenson, P.A., 2009. "The key to Pandora's box." Science 323: 594-595. doi 10.1126/science.1169280

(Yes, I know this isn't quite 1,000 words. But it's pretty darned close!)

Blogging for Darwin

2009-02-10T16:24:00.004-05:00

I joined the Blog for Darwin blog swarm (which means I have to actually finish Origin soon, so I have something to write about). Check it out--it's pretty cool.

I haven't decided yet what to write about; I'm having a hard time coming up with anything super profound. I'll wait and see if any inspiration strikes as I keep reading.

Thanks to Newton's Ocean for the link.

From opposite ends of the spectrum

2009-02-05T10:48:00.003-05:00

Apparently, the downturn in the economy is causing some of us to become a bit too obsessed with language.

On the other hand, some are just giving up in disgust (or despair?).

And some are robbing stores with bat'leths.

(Thanks to Lou for the first link, erv for the second, and Gwynne for the third.)

You would think...

2009-01-23T16:31:00.006-05:00

...that in 200 years, the anti-science crowd would have come up with some new objections to evolution. Apparently not: Check out this quote from Origin.

Long before the reader has arrived at this part of my work, a crowd of difficulties will have occurred to him...These difficulties and objections may be classed under the following heads:--First, why, if species have descended from other species by fine gradations, do we not everywhere see innumerable transitional forms?...

Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some other animal with widely-different habits and structure? Can we believe that natural selection could produce, on the one hand, an organ of trifling importance, such as the tail of a giraffe...and, on the other hand, an organ so wonderful as the eye?

Thirdly, can instincts be acquired and modified through natural selection? What shall we say to the instinct which leads the bee to make cells, and which has practically anticipated the discoveries of profound mathematicians?

These questions, of course, have many parallels in the standard litany of "problems" with the theory of evolution often spouted by creationists and intelligent design proponents. Is this yet another example of Darwin's apparent prescience? Or is it more accurate to say that Darwin's statements echo those of modern-day denialists because they are building on the "work" of those who came before, who undoubtedly read Darwin? If the latter, it's really a shame they didn't read the whole book. Even if they'd read a few pages further on, they would have come across this beauty:

When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science.

Perhaps it might be better said that Vox populi, vox veritas "cannot be trusted in science." But the sentiment still holds: Just because most people think it's so, doesn't make it so. The fact that so many people argue that we should teach the Bible as science because "most Americans believe in God" speaks to a fundamental lack of understanding of the way science is done. But I'm not the first to make that statement, nor will I be the last.

Self-catalytic RNA enzymes

2009-01-16T16:15:00.019-05:00

GumbyTheCat recently posted about a study in which researchers created self-replicated RNA enzymes. There was a bit of discussion in the comments about what those enzymes are all about and whether they are, indeed, "true" enzymes (i.e., proteins).

As I have access to Science magazine online, I was able to read the actual article (Gumby's post was based only on the abstract, I think), and so I can now answer the question of what, exactly, an RNA enzyme is, and how the research group got it to replicate itself.

An RNA enzyme, it turns out, is not a true enzyme. That is, it isn't a protein made up of amino acids. It's actually a strand of RNA. The particular RNA enzymes this group made look kind of like a capital T with one side of the crossbar a lot longer than the other. Like all RNA, they're made up of nucleotides (a nucleotide is a molecule consisting of a sugar molecule--ribose, in the case of RNA--a phosphate group, and a nitrogenous base). (I am forced to conclude that the "RNA" in "RNA enzyme" is an adjectival form, rather than a description of what the enzyme catalyzes.)

To understand how the enzyme works, you first need to know a bit about bonding in nucleic acids (DNA and RNA). What follows is a brief discussion; details can be found in any introductory biology textbook.

A single strand of a nucleic acid is a polymer (a really big molecule made up of a lot of similar, smaller subunits called monomers). As mentioned above, the monomers in nucleic acids are nucleotides. When nucleotides join together to form a nucleic acid, the sugars and phosphates bond together to form a "backbone." The nitrogenous bases stick off one side of the backbone. There are five nitrogenous bases that can form nucleotides: thymine, adenine, uracil, guanine, and cytosine. They are abbreviated T, A, U, G, and C, respectively. A, T, G, and C are found in DNA; RNA contains A, U, G, and C. So, a single strand of RNA looks kind of like half a ladder; the rungs are A, U, C, and G molecules. A double-stranded nucleotide (such as DNA) looks like a full ladder; the base in each "rung" is bonded to another base on a rung on the other side of the ladder. The bonded bases form a full rung. (Of course, a DNA molecule really looks like a twisted ladder, but the physics of why it twists isn't important for our purposes here.)

These bases aren't just any random molecules, though. As it turns out, their molecular structures force them to bond together in specific ways: A can bind only with T or U, and G can bind only with C (and vice versa, in each case). In a double-stranded nucleotide, therefore, each rung is made up of either a C-G pair or an A-T (or A-U if it's RNA) pair. You can probably see the beauty of this arrangement: it means that if you have one half of a double strand of RNA or DNA, you can construct the other half.

As I mentioned before, the RNA enzymes in this study look like lopsided Ts. The stem of the T is actually a double strand of RNA: part of the RNA molecule has bonded to itself. (A similar structure is found in some kinds of RNA that take part in transcription and translation in eukaryotic cells.) The crossbars of the T are single strands of RNA.

Each enzyme forms from two smaller pieces of RNA: a straight piece (called "B") and a piece that looks like a regular (i.e., not lopsided) T (called "A"). The straight piece binds to one of the crossbars of the T-shaped piece to form the lopsided T (which the researchers refer to as "E", for enzyme).

Each enzyme (and each sub-enzyme piece) actually exists in two "mirror-image" forms (i.e., E and E', A and A', and B and B'). The mirror-image forms can bind to each other because of the way the bases pair. However, A doesn't bind to A', or B to B'. Instead, A binds to B', and B bonds to A'. The A-B' combination forms E; the A'-B combination forms E'. [EDIT: the previous sentences should read "Instead, A binds to B, and B' binds to A'. The A-B combination forms E; the A'-B' combination forms E'."] The drawing below shows my lame attempt to summarize.

Essentially, when the researchers put some E into a mixture of A, B, A', and B', the A' and B' pieces bonded to the E to form molecules of E'. Once there was some E' in the mixture, the A and B molecules could bond to it to form new E molecules, and Presto! self-replicating RNA.

Of course, it wasn't really that simple. And actually, the not-simple part is kind of cool: The original E that the researchers used wasn't very efficient at catalyzing its own formation. So, basically, the researchers evolved it. They generated new A and B with mutations--variations in the sequences of bases on the backbone--and selected the ones that formed E that could replicate itself most quickly.

Because they have groovy tools (such as polymerase chain reaction machines) and computer to do the analysis, they were able to try a whole lot of different combinations in order to find the set of A and B that produced the most efficient E.

All in all, a really groovy little study!

Lincoln, Tracey A., and Gerald F. Joyce, 2009. "Self-sustained replication of an RNA enzyme." Sciencexpress. published online 8 January 2009; 10.1126/science.1167856.

More Darwin progress

2009-01-16T15:45:00.005-05:00

Well, I've made it through chapter 3. Here are my impressions so far:

First, I'm really impressed with Darwin's writing. I wish modern research results were presented in as readable and understandable a way. Yes, he's using rather flowery Victorian prose, and he tends to overuse the semicolon and the hyphen--but then, there are a lot of people who do that today, and some of them run the government. And at least he's managed to refrain from quoting anything in French (or, worse, German...) since the "Historical Sketch." And at least he doesn't capitalize random words.

Second, I've been very interested to see exactly how much Darwin didn't know--and, given how much he didn't know, how much he got right. It's mind-boggling to think that he managed to get the main ideas right when he didn't even know about genes. (A friend of mine recently told me that they found a copy of Mendel's paper on Darwin's desk after he died--apparently, he just didn't get around to reading it. Imagine what he might have done with Origin if he had!)

On his blog, John mentions that he scribbled in the margins of his book the modern terms for the concepts Darwin presented in chapter 3. I have to admit, I was tempted to do the same thing in my copy (although the thought occurred to me back in chapter 1). I find it fascinating that many of the ideas that Darwin apparently had to defend are taught in high-school biology today. For example, consider this, from chapter 1:

Indefinite variability...has probably played a more important part in the formation of our domestic races. We see indefinite variability in the endless slight peculiarities which distinguish the individuals of the same species, and which cannot be accounted for by inheritance from either parent or from some more remote ancestor.

Mutations, anyone?

John points out several other examples from ecology.

I was also reassured to learn that the debate about what constitutes a species has been going on since before Darwin. I was tempted to think that it was the offspring of the digital age--i.e., the need of modern scientists to cut into chunks things that are naturally continuous.

More to come...

I don't know if this is cool or creepy

2009-01-15T10:14:00.002-05:00

The growth of Wal-Mart over time...

(thanks to Mike the Mad Biologist for the link)

Darwin progress

2009-01-09T16:34:00.005-05:00

I started On the Origin of Species last night. I'm reading a slightly different version than John is--he's reading the first edition, and I'm reading the 6th (which, according to the book jacket, is the last edition to have had edits made to it by Darwin himself). However, the introductions are apparently sufficiently similar that I can understand his discussion of the introduction. (Plus, I have to admit that I'm glad he didn't get through chapter 1 last night, either. One of the problems with doing most of my reading in bed is that I periodically fall asleep before I've finished.)

At the end of his post, John mentions his surprise that Darwin acknowledges his and Wallace's nearly simultaneous arrival at the concept of natural selection. That didn't surprise me very much, because the preface to the 6th edition consists of an "Historical Sketch of the progress of opinion on the Origin of Species, previously to the publication of the first edition of this work." In it, Darwin summarizes the work of various key players in the study of the origin of species. The first person he discusses in any depth is Lamarck (although he gives passing reference to Aristotle, as well), and his summary extends to publications and presentations by Huxley and Hooker in late 1859, the same year the first edition of Origin was published.

I found the historical sketch to be quite an interesting read (despite his penchant for quoting works by French authors in the original language). Although it pains me to admit it, my knowledge of the history of the theory of evolution is abysmally lacking. I was surprised at the sheer number of researchers that had done significant work (and reached conclusions in line with, if not completely similar to, Darwin's) prior to the publication of Origin. Of course, I know that Darwin held off publication of the book for a while after formulating his ideas. But I do find it refreshing that he acknowledges the influence of others on the generation of his ideas.

Another line in the introduction that I found interesting: "No one can feel more sensible than I do of the necessity of hereafter publishing in detail all the facts, with references, on which my conclusions have been grounded...For I am well aware that scarcely a single point is discussed in this volume on which facts cannot be adduced, often apparently leading to conclusions directly opposite to those at which I have arrived." (p. 2)

I was struck by the apparent prescience of this statement: could Darwin, perhaps, have been anticipating the likes of Ray Comfort?

Interesting word for today: kobold

2009-01-09T16:25:00.002-05:00

According to Webster's New World College Dictionary, 4th edition, the definition of kobold is the following:

"kobold (n) Germanic folklore: 1 a helpful or mischievous sprite in households 2 a gnome in mines and other underground places"

The roots of kobold are not Greek, but German: Middle High German kobolt (a household spirit), to be precise.

I think it might be fun to have a kobold, provided it was of the helpful, rather than mischievous, sort.

The more things change...

2009-01-08T15:51:00.003-05:00

"Tertullian expressed contempt for philosophical inquiry and ordered his flock to renounce worldly curiosity. He asked, "What has Athens to do with Jerusalem? What has the Academy to do with the Church?" He demanded unquestioning acceptance of the Orthodox position: "God's son died: it is believable precisely because it is absurd. He was buried but rose again: it is certain because it is impossible!""

(from The Alphabet Versus the Goddess, by Leonard Shlain, p. 245. Published by the Penguin Group. (c) 1998)

Blogging Darwin

2009-01-08T15:23:00.004-05:00

John Whitfield is embarking on a quest: He's going to read On the Origin of Species by Darwin's birthday (Feb. 12). Not only that, but he's blogging about it.

Having just picked up a copy at my local half-priced bookstore--and despite being in the middle of three other books--I think I'm going to try to follow along. I can't guarantee that I'll respond to every chapter, but as I've never actually read it, I figure now's as good a time as any. If nothing else, by the end I'll at least be able to counter quote-mining creationists with "Have you actually read the book?" and not be hypocritical.

Book Review: Tested

2009-01-07T15:36:00.009-05:00

(First, an apology: Sorry for the long delay in posts. I blame the holidays. Sorry if my hiatus has caused problems for either of the people who ever visit...)

I don't remember a lot about third grade. I remember even less about how I was taught reading and math in third grade. In math, I remember that we did a lot of Mad Minutes. (For those unfamiliar with the concept, a Mad Minute is a 30-problem math test that students try to complete in--you guessed it--one minute. The problems start out easy--for example, I think Mad Minute 1-1 is multiplication by 1--and get progressively harder. A Mad Minute minimally tests mathematical skill; it's more a test of a student's ability to memorize a list of 30 numbers and write them down in one minute.)

In reading, I remember we used a basal reader (although I didn't know that's what it was called), and that we were put into reading groups, each of which got a different reader. (I was in a group called the "Odd Balls," so named because there was only one boy in the group. I think the groups were roughly homogeneous in terms of level--certainly the others in my group were among the higher students in the class.) I remember we also did a lot of writing: short stories, poems, etc.

If I had attended third grade at Tyler Heights Elementary in Maryland, I would have learned math by rote. I would have learned to read by reading the same passage each day for a week and answering the same types of questions over and over again. I could have gone to another classroom and heard their teacher saying pretty much the same thing my teacher was saying, because all the teachers would have been reading from the same teacher guide, and their district curricula would have dictated when they would move from one topic to another. I would have learned how to write 3-4 sentence Brief Constructed Responses to standardized questions (such as, "What features of the instructions make them easy for third-graders to follow?"), but I would have done almost no other writing. And I would have spent most of the year learning how to take the Maryland State Assessment (MSA).

At least, that's what the third graders profiled in Tested: One American School Struggles to Make the Grade, by Linda Perlstein, experienced. In Tested, Perlstein describes a (school) year in the life of the third grade at Tyler Heights Elementary in Annapolis. Tyler Heights was listed as a "failing" school under No Child Left Behind (NCLB). In one year, they turned their test scores around and had an MSA pass rate of more than 75%. The school was widely touted in the press as a "success story," which is what caught Perlstein's attention. In Tested, Perlstein attempts to answer the questions "How did Tyler Heights turn its scores around?" and "What do those test scores mean?"

Tyler Heights was praised as a success story largely because most people expected it to keep failing. Most of the students at Tyler Heights are poor and non-white; many of them are homeless, have absent parents, or do not get adequate food at home. (The school serves both breakfast and lunch to its students to help ensure that most students get at least two good meals a day.) The school receives so much Title 1 money that it sometimes has trouble spending it all. Many of its students don't show up for school; some of them show up when school is closed, because their parents don't pay attention to closures. In short, it fulfills every stereotype of a failing school.

Perlstein got permission from the school to essentially live in the building for an entire school year. She was allowed to interview students, parents, teachers, and administrators, and to report her observations and interviews. It's hard to believe that such freedom would be granted in this day and age, but the result is as exceptional as one would hope: Perlstein's book is informative, well written, and gripping. Her descriptions of day-to-day life at Tyler Heights are vivid; I could almost hear some of the students' and teachers' voices by the end of the book.

The story Perlstein tells in Tested is one that probably will not surprise most educators: Tyler Heights got its scores up by drilling students every day on how to answer the questions they would most likely see on the MSA. The only types of questions they ever saw were those that were similar to MSA questions; the only content they covered was content within the testable limits of the Maryland Voluntary State Curriculum (which isn't really voluntary, since the MSA is based on it, and thanks to NCLB, students have to pass the MSA for a school to continue to receive funding).

The book focuses primarily on the reading curriculum (possibly because it's harder to argue about how to write a test that truly tests students' ability to do math). Tyler Heights uses a program specifically designed to raise students' test scores; because most reading tests focus exclusively on reading comprehension, students spend almost no time writing, reading for fun, or doing any of the other things that help get kids excited about reading. (At one point in the book, Perlstein relates a situation in which students who had finished an exam early were reading silently at their desks. The teacher was told that students who finish early must go back and continue working on their answers; they were not to read "fun books" outside of designated time slots.)

As would many educators (okay, maybe I'm inflating myself a bit, but someone who writes textbooks and lessons is still an educator, right?), I found the stories Perlstein tells about a typical Tyler Heights third grade day disturbing. The curriculum seemed designed to drum out of students any vestige of curiosity they might have; the reading curriculum certainly was unlikely to instill in any child a love of reading, or an ability to write coherently. It's especially disturbing because one could argue that these kids are the ones most in need of that kind of inspiration.

But although I found the stories disturbing, sadly, they did not surprise me. It doesn't take a rocket scientist to predict that if most of a school's funding (or even a significant portion of it) is based on whether students pass a standardized test, that school is probably going to focus on giving students as much practice on that test as possible. (There's a good reason most students' scores on the SAT increase the second time they take the test: practice, as they say, makes perfect.)

Don't get me wrong; I don't necessarily think the administration at Tyler Heights made a bad choice in implementing the programs they have. As long as NCLB controls funding and public perception of school success, schools will continue to focus on getting kids to pass the test at any cost. And in a community with almost no parental support for education (percent attendance at parent-teacher night at Tyler Heights rarely reaches double digits), there aren't a lot of ways to get those test scores up other than drill, drill, drill. But just because I understand the administration's decision doesn't mean I think all is well in schools like Tyler Heights (because I'm sure there are hundreds of schools around the country in a similar situation). Of course, I could go off on a long, long rant about my thoughts on public education today--but this is supposed to be a book review, so I'll stop there.

Tested should be required reading for anyone curious about the effects of NCLB (or high-stakes testing in general) or the realities of teaching in a low-income, urban school district. Heck, they should put it on the mandatory reading list for the U.S. Department of Education. (Do they even have one of those? If they don't, they should!) But when you do read it, be prepared to be disturbed and saddened (and a little inspired, too).

Tested: One American School Struggles to Make the Grade
Linda Perlstein
Henry Holt and Co., 2007 (1st edition); Holt Paperbacks, 2008 (Reprint)
ISBN 978-0805080827 (hardcover), 978-0805088021 (paperback)

Interesting word for today: metagnathous

2008-12-01T17:19:00.004-05:00

According to Webster's New World College Dictionary, 4th edition, the definition of metagnathous is the following:

"metagnathous (adj): 1 having the points of the beak crossed, as in the crossbills 2 having larvae that feed by chewing and adults that feed by sucking, as in butterflies and moths"

Yet again, the roots are Greek: meta- (between, among, along with) and -gnathous (having a jaw). Words that share meta- as a root include (among many others) metaphysics, metamorphosis, metagenesis, metacarpal, metabolism, and metagalaxy. -gnathous is a bit more obscure, but Agnatha (a class--or superclass, depending on who you ask--of animals, comprising the jawless fishes), gnathite, and gnathic are some of them. I suspect that words like gnashing and gnaw are also related, but I can't confirm that with my dictionary.

Efficiency and food security

2008-12-01T17:11:00.003-05:00

The Corpus Callosum has an interesting post up about the relationship between efficiency and food security. The main premise is that efficiency, as measured by "the market" or by standard economics (i.e., number of X per dollar spent) is probably not the best way to measure the effectiveness of a food supply system.

This seems to me to be a primary problem in allowing the market to "work." The fundamental assumption in that view is that monetary cost is exactly equal to total cost of a product/widget/service. But, of course, companies can externalize most of their non-monetary costs (some would say the real costs--such as environmental destruction, poverty, poor health, insecurity, etc). So the model's fundamental assumption is flawed: monetary cost is much less than actual total cost.

Eventually, people will realize that it makes a lot more sense to have a lot of (fully employed and tax-paying) small farmers growing a variety of foods using a minimum of (non-renewable) resources than to have a couple of (tax-avoiding, outsourcing) big companies growing one kind of (resource-intensive) food. I hope I'm around to see it--because if it doesn't happen soon, I suspect that the people who end up in that world will have lived through a lot of really bad conditions in order to get there.

Effective measures

2008-11-17T12:03:00.002-05:00

I just heard on the radio that Citigroup is cutting thousands of jobs and is taking other steps to cut costs to help it survive.

My question: How much are they cutting the pay and bonuses of the top managers? I find it completely unacceptable that top managers routinely talk about "the good of the company" but aren't willing to forgo their bonuses or seven-figure salaries to make things better. They're perfectly willing to cut other people's pay, but heaven forbid they should not get a bonus!

And don't even get me started on using bailout money to give bonuses so that people won't leave and go to other companies.

A friendly note to car makers

2008-11-14T07:28:00.001-05:00

When advertising your giant gas guzzlers, please don't use the phrase fuel-efficient to describe vehicles that get less than 30 mpg on the highway. News flash: 23 mpg highway is not fuel efficient. Just because it's better mileage than other gas guzzlers doesn't mean it's fuel efficient. It just means its more fuel efficient than other gas guzzlers.

Clearly, this is a hysterical LOLcat

2008-11-13T15:57:00.000-05:00

Yes, I admit, I enjoy the LOLcats. Especially this one. I'm actually finding myself looking for reasons to use it!

more animals

Read this review! (And then read the book!)

2008-11-12T12:18:00.005-05:00

GrrlScientist has a great review of one of my favorite nonfiction books (it even makes my list at the bottom of this blog), Bottomfeeder: How to Eat Ethically in a World of Vanishing Seafood, by Taras Grescoe. Unfortunately, she beat me to it; I was planning to write a review of it, too. Hers is good enough that I don't think I have to. Guess I'll pick another one of my favorites, instead.

Go! Read the review! Then read the book. And most importantly, act on it!

UPDATE: There's an interview with Taras Grescoe over at oceana. Read it here. (If that link dies or shows up as subscriber only, you can also read an excerpt of the interview here.)

Photos that won the election

2008-11-08T05:31:00.002-05:00

PDN (Photo District News) has put together the top five photos that their staffers think helped President-Elect Obama win the election. Check it out.

(Thanks to Greg Laden for the link.)

I think my favorite of the bunch is one that didn't actually make the top five: The photo of then-Senator Obama with his feet up on the table, showing the holes in the soles of his shoes. I wonder how long he wore those shoes before those holes got there? I'm inclined to say that they were not new shoes...I mean, it's not like candidates are putting serious miles on their shoes. Yes, they travel a lot--but they drive. Or fly. Or train. And once they get there, they stand. Not activities likely to put quarter-sized holes in good-quality dress shoes. My guess is they're the same shoes he's been wearing for a while. (I understand completely--it's almost impossible to get me to give up a comfortable pair of dress shoes. Do you know how hard it is to find comfortable flats?) I don't know, something about that kind of makes me respect him a bit more. I mean, he's obviously not hurting for money--but he's wearing worn-out shoes.

Of course, it's possible the shot was totally staged, and all of his shoes are brand new. It's also possible that he thinks those shoes are good luck, or that they're his "lounging around calling staffers and reading briefs" shoes (in which case, I suppose he should get used to wearing them...), or something. But maybe, just this once, I'll be optimistic. :)

Expected, this was!

2008-11-05T07:12:00.002-05:00

So, in case you're living in a dark hole somewhere (in which case you probably aren't reading this anyway), Barak Obama (I guess spell check programs will have to start including his name now...) has won the presidency. And not just won. He WON. By a very large margin.

To me, the most impressive thing isn't the victory itself, but the fact that several devoutly Republican states--Indiana, Florida (somewhat), and Virginia spring to mind--went for Obama. I think that speaks to effective outreach.

Now we just have to hope it actually works...

Big government = bad?

2008-10-27T08:03:00.001-04:00

McCain is making a lot of statements lately condemning the Democrats' desire for so-called "big government." While I agree that unnecessary bureaucracy is inefficient and wasteful and should be avoided, I'm still not quite sure why "big government" is such a horrible thing. Who else is going to control the country, if not the government? Recent events have shown that business leaders are completely incapable of suborning their own greed for the greater good. That's the JOB of the government, for crying out loud.

And aren't the Republicans the ones pushing all the wiretapping programs and the Patriot Act and all that? What is that, if not big government? (Oh, right. Those are REPUBLICAN programs that will protect us from evil people who want to destroy us. Big government is fine as long as they control it and are using it to spy on us. But as soon as we want to use government to keep people from going broke, or to make sure everyone can afford to see a doctor when they're sick--watch out! Socialism on the way!)

Expected, this was not!

2008-10-21T06:56:00.001-04:00

But it's still pretty cool...

Huh?

2008-10-10T11:13:00.002-04:00

Check out this letter that was sent around a community in Virginia. Apparently, voting for a black man for President is racist, and the only way to prove you're not racist is...that's right...vote for the white guy!

So, according to this reasoning, the best way to support gay rights is to support man-woman-only marriage.

I really just don't have enough illogic to be able to figure this out.

(Thanks to Ed Brayton at Dispatches for the link.)

Rant but good

2008-10-06T08:03:00.002-04:00

Check out GumbyTheCat's discussion of what's wrong with American politics. I don't have a big long critique of this one, mainly because I agree with pretty much all of it.

If I get time, I may write a longer discussion--but right now I have to get to work. (Argh.)

Response to an open letter

2008-10-04T06:50:00.008-04:00

GumbyTheCat recently wrote an open letter to creationists. Here it is.

While I enjoyed it and thought it was almost completely valid, I do have an argument to two of his points: first, that creationists know that the stuff they spout is lies (i.e., that they're deliberately lying); and second, that their blind faith will ultimately push more and more people toward reason.

I take argument with the first point because, as far as I've seen, most creationists/intelligent design proponents do actually believe what they are saying. They truly do--for them, it's not a matter of ignoring evidence, it's a matter of faith. They truly believe that fossils were put there by god to test our faith. They truly believe that the Bible is the literal word of god. They're not saying these things knowing that they are lying (which is Gumby's assertion); they really do believe that they know The Truth, and that they have to spread that truth or they (and those they don't spread the truth to) will go to hell. Of course, that doesn't mean that there aren't some creationists who don't have doubts. But as odious as the tactics and belief system are to me, I don't agree with the "fundamentalist/evangelical-Christian-as-conspirator" theory: I really think that most of them think that they're doing this "for our own good." (I.e., I don't think they're deliberately spouting what they know to be lies in order to brainwash people so they can take over and rule the world and oppress everyone else. They really think things would be better if everyone had blind faith in the big G. As I said, I don't agree with that belief--but I don't think they're doing what they're doing with evil intentions.)

My second argument with Gumby's letter is the premise that continued spouting of creationist dogma will turn more people toward reason. As much as it pains me to admit it, I think the vast majority of people (okay, perhaps I should say Americans, since I don't know a lot about the cultures of other countries or parts of the world) actually don't want to learn more. Science (and a scientific understanding of the world) is hard work. It takes time and effort to really understand what we know, think we know, don't know, and don't know we don't know--and fundamentally, people are lazy. They're not curious about the world; they don't want to think about it or have to try to work things out in their own minds. That is the appeal of blind faith religions: they make all the decisions for you--and even better, they tell you that following those decisions will guarantee you happiness after you die. All you have to do is stop thinking. I can see how that would appeal to a lot of people. And certainly, the creationist explanation of where we came from is a lot easier to understand (and much more appealing to human vanity) than is the scientific explanation. I mean, really, all you have to do is read one book--instead of thousands upon thousands of research articles. Is it any wonder so many people choose that belief? And because a fundamental tenet of that faith is acceptance of what the authority figures tell you, if those authority figures (who don't have any more scientific understanding) tell you that there's no evidence for evolution, or that all the evidence is made up/incorrect/circular, then you believe it (because if you don't, you'll go to hell).

Maybe I'm just feeling pessimistic this morning. But I think that the sheep-like tendencies of people to follow the easy path are not going to just go away if we allow creationists to keep spewing anti-science. I think most of those people truly don't know how (or don't want) to think for themselves...and the only way to combat that is to teach them how to think for themselves, and give them an incentive to do so.

As for how to do that...Well, that's the real question, and I'm not sure I know the whole answer. Certainly part of it has to be better outreach and science education. But part of it also has to be a culture shift. Intellectualism, reason, and critical thinking have to be accepted as positive traits, instead of as "elitist" and overbearing. I have a few ideas about how to fix science education. But I have no clue how to change a culture. Any ideas?

(hat tip to John Wilkins over at Evolving Thoughts for the link)

Usage tip: conflate vs. confuse

2008-09-26T06:53:00.004-04:00

I've seen a lot of misuses of the word conflate lately. Many folks seem to be using it as a cooler-sounding synonym for confuse, as in "don't conflate political ambition with political knowledge."

I have to quote Inigo here: "You keep using that word. I do not think it means what you think it means." (The Princess Bride)

According to my trusty Merriam-Webster (11th edition), this is the definition of conflate:

"conflate (vt): to combine or mix (two variant readings into a single text, etc.)"

And here's the definition of confuse:

"confuse (vt): 1) to mix up; jumble together; put into disorder 2) to mix up mentally; specif. a) to bewilder, perplex b) to embarrass; disconcert c) to fail to distinguish between; mistake the identity of"
(both definitions from p. 306)

Notice the subtle (or not so subtle?) difference here. Confuse means just what everyone thinks it means. If you confuse A with B, it means you don't know the difference between them, or you think they're the same thing. Conflate, on the other hand, doesn't mean what one might expect. If you conflate A with B, it means you combine them and come up with something that's related to both, but different from either.

If you're trying to say that someone has mistaken X for Y, then you need to say that the person has confused X and Y. Use conflate only when you mean that someone has taken multiple (slightly different) statements and combined them into one.

Nice cream!

2008-09-25T16:44:00.005-04:00

For those of you who haven't heard, PETA (People for the Ethical Treatment of Animals) recently sent a letter to Ben & Jerry (yes, that Ben & Jerry). Their position is, apparently, that B&J should start making ice cream with human breast milk, instead of with cow's milk.

Don't get me wrong--I'm all for the ethical treatment of animals. I don't like factory farming, and I don't think treating heifers with rBGH is a good idea. I won't eat veal, I try to eat "happy meat", etc., etc. I was once even a PETA member. But I do think it's possible to take a good idea too far (which is why I am no longer a PETA member). Breast milk ice cream? Because, apparently, there's a huge surplus of human breast milk out there?

The Straight Dope Message Board has a rather amusing take on it. They asked their contributors to come up with Ben & Jerry-worthy names for human milk ice cream. There are some clever folks over there. Check it out.

My personal favorites? Butterscotch Nipple, Thanks for the Mammaries, and Titty Fruitti.

(hat tip to Orac over at Respectful Insolence)

Sandy and the House Centipede

2008-09-25T16:31:00.014-04:00

I had an amusing interlude this morning. I was in the kitchen getting a glass of water and I looked in on Sandy (my dog). She was curled up in a little brown Ball-O-Sandy on the Purple Chair, which is her usual status at 6:45 in the morning. Just as I was going over to tell her how cute she is, she suddenly leapt off the chair, dashed across the room, and pounced with alacrity on a spot on the baseboard. Just before she landed, I spotted what looked like a small freight train scooting across the moulding. "Ah-ha!" I thought to myself, "It's a million-legged bug!" (That's the scientific name. The more commonly used name is "house centipede" or—if you want to be really dull--Scutigera coleoptrata.)

Sandy has a great passion for catching and mauling all manner of arthropods (an activity we encourage, given that we share our house with a large number of them), so needless to say she was ecstatic to see one with more than twice the usual number of legs. She grabbed it, munched for a minute, and spat it out (this is her usual method—if they're still moving after that, they're still fun, so she goes after them again). The poor million-legged bug was lying on the floor, twitching, covered in dog spit and (thanks to the dog spit's adhesive qualities) dog hair. I expected Sandy to jump back in and give it the coup de grace. However, Sandy had discovered that, in addition to having way more legs than the typical cockroach, centipedes also have way more venom. In case you were wondering, a dog that has been bitten in the mouth by a house centipede looks remarkably like a dog with peanut butter stuck on the roof of its mouth, although with slightly more lip-curling. To save Sandy from further issues (she sometimes lets her excitement about creepy-crawlies overcome her basic good sense), I threw the centipede outside.

After doing some research, I learned that a centipede bite is rarely any worse than a bee sting. (Sandy didn't even yelp when it bit her, and she certainly seems to have recovered—although I think the belly rub probably helped.) I also found out that house centipedes eat cockroaches and other unpleasantness—thereby also discovering why Sandy tried to eat it (aside from the obvious "fun" factor): she was eliminating the competition!

So, I learned that house centipedes (aside from being really eww-y) are good to have in your house, if you can keep them away from the dog. Sandy also learned something: avoid crawlies with too many legs. (Although somehow I doubt she'll remember that in the heat of the moment next time.)

Here is a picture of Sandy:

And here is a picture of a house centipede:

(image of house centipede from Horror Wallpaper; images not to scale)

Even if...

2008-09-04T16:32:00.004-04:00

There is a great deal written out there about the problems with Intelligent Design's "arguments" that supposedly "refute" the theory of evolution. I won't go into them here (although I may in the future), but suffice it to say, they pretty much all fall into one or more of the following categories:

misinterpretation (either deliberate or out of ignorance) of legitimate scientific data;
quotes and/or data taken completely out of context and tortured into implying something other than what they actually imply;
self-contradictions (or contradictions of other arguments made by the same person or organization);
fallacies of logic;
applications of valid scientific theory and/or concepts to things they have no business being applied to; and
outright lies.

However, as a thought experiment, suppose for a moment that every single argument made by Intelligent Design proponents were completely scientifically accurate. Suppose, if you will, that the theory of evolution really were as full of holes and problems as they'd like us to believe.

Even if that were true...Intelligent Design STILL would not be a valid scientific theory, and it STILL would not belong in science classrooms.

One point that I don't think is made often enough in the "debate" between Intelligent Design proponents and real scientists is this: proving one theory false is not equivalent to proving another theory true. (Not that you can prove a theory. But you know what I mean.)

They'd like us to believe that, if they can "prove" that the theory of evolution is invalid, scientists will magically just accept Intelligent Design. Allow me to use an analogy to illustrate how silly this argument is.

Imagine a really big party. Hundreds of people in a really big room, all milling around. Suddenly, a gunshot rings out, and someone falls down dead. Further suppose that there are security cameras in this room that catch the whole thing on tape. You can see the shooter's face--can even see the color of her eyes. What's more, there are 15 eyewitnesses that claim to have seen her shoot the victim. The gun has her fingerprints on it and is ballistically matched to the bullet in the victim. There is gunpowder residue all over her hands. And, she has a motive.

In court, the defense tries to get the shooter off by arguing against the validity of all of the evidence. Then, in the closing statement, the defense council says the following:
"Ladies and gentlemen of the jury, the evidence clearly does not show that my client shot the victim. Therefore, it must have been the doorman who shot the victim."

How likely do you think it is that the jury would convict the doorman, just because it couldn't possibly have been the defendant who shot the victim?

Disproof of one theory does not equal proof of another theory. A scientific theory is based on evidence. If there's no evidence to support it--and especially if there's no possible way to collect evidence to support it--then it cannot be a valid scientific theory!

If Intelligent Design really were science...

2008-08-26T16:53:00.003-04:00

Imagine the state of scientific endeavor if real science followed the same rules as Intelligent Design.

When Oersted observed a compass needle moving when the compass was placed near a current-carrying wire, he would have said, "How interesting! Our current understanding of nature can't explain that. A supernatural Directing Agent must be causing the compass needle to move. Since I can't ever know how the Directing Agent works, I guess there's no way for me to figure out why the compass needle is moving. I guess I'll go study something else."

When Rutherford observed alpha particles bouncing straight back from a sheet of gold foil (an event, to paraphrase him, as unexpected as if he had fired a bullet at a tissue and it had bounced), he would have said "Fascinating! Our current atomic model can't explain this. There must be a supernatural Directing Agent causing it. Maybe I'll move to Hawaii and retire."

When scientists first had enough data to see that most earthquakes and volcanoes occur in specific regions, rather than being scattered randomly over Earth's surface, they would have said, "Hmm...thermal contraction shouldn't produce patterns like those. They're much too complex. It must be a supernatural Directing Agent doing it. Well, I guess we can stop looking for another explanation now! Let's have a beer!" (They were, after all, geologists.)

When Mendel observed that pea plant characteristics don't always breed true, he would have said, "Goodness! That's unexpected. Our current understanding of of heredity can't explain that. Must be God's work. I guess I'll start eating spinach, instead."

Intelligent Design isn't just not science. It stifles inquiry. It's--dare I say it?--designed to keep people from asking questions.

And for the record, "God did it" is not a valid scientific explanation.

Interesting word for today: thanatocoenosis

2008-08-26T16:48:00.003-04:00

According to the American Geological Institute's Glossary of Geology, 4th edition, the definition of thanatocoenosis is the following:

"thanatocoenosis (n): a) a set of fossils brought together after death by sedimentary processes, rather than by virtue of having originally lived there collectively; b)...all the fossils present at a particular place in a sediment" [note: I trimmed some of the definition a bit]

The word comes from the Greek thanatos ("death") and koinos ("general" or "common").

Thanatocoenosis shares a root with thanatology (the study of death), thanatophobia (the fear of death), and thanatopsis (a view or thought about death).

This was also another word I considered as a title for this blog, but rejected because it's hard to spell...

1000 words

2008-08-20T09:40:00.005-04:00

One of my favorite lazy-Saturday-afternoon-with-a-book book series is Lillian Jackson Braun's The Cat Who.... In one of them (I can't remember which), she makes reference to an activity that the main character's English teacher used to have him do: pick a topic from a dictionary or encyclopedia and write 1000 words on that topic.

I think this is a pretty cool idea, and an interesting way to practice writing without going back over the same topics over and over again.

So, I am going to try to start doing that. I will post the results here. We'll see how it goes! With any luck, I'll learn some interesting things, and you'll get more interesting posts.

Interesting word for today: catachresis

2008-08-17T07:57:00.005-04:00

According to Webster's New World College Dictionary, 4th edition, the definition of catachresis is the following:

"catachresis (n): incorrect use of a word or words, as by misapplication of terminology or by strained or mixed metaphor" (p. 229)

The roots of the word are (what else?) Greek, from kata, which means "against" or "down," and chresthai, which means "to use."

Other words using the prefix cata in a similar way include cataclysm, catabolism, cataclastic, catacomb, catadromous, and catafalque. (Perhaps some of those will become words of the day later on...)

On a side note, I almost called this blog Catachresis...but decided that naming my blog after something I wish to avoid might not be the wisest of ideas.

Usage tip: like vs. such as

2008-08-14T11:19:00.005-04:00

Both like and such as are commonly used to compare two (or more) things. However, if you wish to write clearly and unambiguously, it's important to understand the distinction between the two.

When used to compare two or more things, the word like essentially means "similar to" or "in the manner of." In contrast, such as essentially means "for example."

Therefore, the following two sentences have different meanings:

Carnivores like wolves generally have large, sharp teeth.
Carnivores such as wolves generally have large, sharp teeth.

The first means that most carnivores that are similar to wolves have large, sharp teeth. It implies that carnivores that are not similar to wolves--say, for example, sharks--do not have large, sharp teeth.

The second sentence tells us that a wolf is an example of a carnivore, and that most carnivores--including wolves, and including sharks--have large, sharp teeth.

The insertion of a comma can affect meaning, too. A "like XXX" phrase enclosed in commas generally means you're making an explicit match or link between two things. In essence, you are equating the two. For example:

Seals, like dolphins, are mammals.

This sentence is using dolphins as a referent and stating that seals are similar to dolphins in the specific way described in the sentence (i.e., they are both mammals). In a sentence of this form, the noun after like is generally assumed to be more familiar to the reader than is the subject of the sentence. (I.e., this sentence suggests that the writer expects the reader to be more familiar with dolphins than with seals.) This sentence is correct as written. Replacing like with such as in this case would make the sentence incorrect, because a dolphin is not a type of seal. If we wanted to use such as in this sentence, we'd have to change dolphins to a type of seal (e.g., "Seals, such as the Weddell seal, are mammals.").

Unless you want to make that explicit link between the two things, you generally want a "such as XXX" phrase inside your commas. For example:

Some actors, like Jonathan Frakes, are quite tall.

There's nothing really wrong with this sentence, if you are trying to get across that Jonathan Frakes is quite tall, and that some actors resemble him in being quite tall. But if you were trying to give Jonathan Frakes as an example of a tall actor, rather than as the definition of a tall person, then you would use such as:

Some actors, such as Jonathan Frakes, are quite tall.

(This sentence would also work with including instead of such as, but I won't go there right now.)

Boring First Post

2008-08-13T16:04:00.002-04:00

Yes, boring--I have several ideas for posts, but haven't had the time to think them through. But as my blog looks incredibly weird without any posts at all, I wanted to put at least one up--just to see how it looks.

More to come later. I hope to use this blog to review books I've read; talk about interesting topics in science, grammar, and education; and generally write about anything else that strikes my fancy.