You would think...

...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

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

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

The growth of Wal-Mart over time...

(thanks to Mike the Mad Biologist for the link)

Darwin progress

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

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...

"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

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

(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)