Update: More thoughts on uncomfortable research

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

The Intersection
DrugMonkey

Uncomfortable research

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

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

On the shoulders of giants...

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.

Scientia Pro Publica 7

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

Using geometry to find a rainbow

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!

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.

If the Girl Scouts had badges like these...

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)

Fascinating

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.

Primary sources and creationism

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.

Vaccine safety and creationist nonsense

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.

From opposite ends of the spectrum

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.)

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?

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.

Efficiency and food security

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.

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

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.)

Rant but good

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.)