A Drunken Walk Through Science

Is Britain Waking Up?

2008-07-25T16:54:00.002-04:00

There has been a 40% drop in homeopathic prescriptions in the last two years by general practitioners in the U.K.

Perhaps the fact that British folks became so enamored with the stuff backfired on homeopaths. With large sample sizes, doctors may have been able to clearly see how useless the stuff actually is.

Fantastic Article

2008-07-24T16:43:00.002-04:00

For the vast amount of credulous people in the U.K., there seem to be some pretty intelligent ones with the ability to grab the public's attention. This one wrote an outstanding article on two recent black eyes in the British CAM field.

This warms my heart to see a major news outlet publish such a scathing piece. Coupled to Amanda Peet's outing as a thoughtful celebrity, I'm in one of those waxing moods about our society. Could it be that the tides are starting to turn a bit? Oh, I'm sure that momentum will go back and forth many times in my life, but it's moments like this that make it good to be a skeptic.

Bad Study. Bad, Bad Study.

2008-07-22T17:08:00.002-04:00

This study is what you call junk science. Upon seeing the title of this article I said to myself - "I bet this is a very small study, published in an obscure alternative medicine journal, measuring some subjective variable, and funded by a juice company". Well...

"Published in the Journal of Alternative and Complementary Medicine, the randomized, placebo-controlled, double-blind clinical trial claims to be the first study reported from outside China that has examined the general effects of consuming goji berry juice."

and...

"The current study was funded by Arizona-based FreeLife International, a goji berry juice supplier. The study was also conducted by FreeLife employees."

and...

"A total of 35 people were recruited for the study. All participants were healthy adults, and were randomly assigned to either a goji berry group or a placebo group."

and...

"Participants were given a questionnaire at the start and finish of the test period, where they were asked to give ratings (0-5) of general feelings of well-being, neurologic/psychologic traits, gastrointestinal, musculoskeletal, and cardiovascular complaints as well as any adverse effects."

Pretty convincing, no? Here are the "results":

"According to the study authors, "significant differences" between day one and day 15 were found in the goji berry group."

Awsome!! Significant results?! That's almost unbelievable!!! But, how significant are we talking here?

"Around 50-60 percent of people in the goji group reported feelings of good health, contentment, and happiness."

Wow! 50% of the people feel good? Wait, how many people in the normal population would say they feel good?

Here's the clincher:

"The placebo group reported two statistically significant changes during the 14-day period - heartburn and feelings of happiness."

Actually, I'm not sure what this statement means. The control group had increased heartburn? Was that from not drinking goji juice, or was it from the crazy placebo juice they gave them? And I'm going to go ahead and assume they meant that the placebo group had decreased happiness. Is this study even ethical? Giving people heartburn and sadness seems kind of mean.

My New Favorite Celebrity

2008-07-17T19:22:00.002-04:00

Could somebody please pinch me?

An interview in the magazine Cookie with actress Amanda Peet has momentarily paused my usual eye rolling in the direction of Hollywood. Critical thinking in Hollywood is no longer an oxymoron!

This mother of an 18 month old daughter took a long look at the issue of childhood vaccination, and - *gasp* - came to the only logical conclusion!

"I was shocked at the amount of misinformation floating around, particularly in Hollywood," says Peet"

Wonderful, now if we can only get her to speak to a certain booger eating blond? Not after this observant gem, eh?

"Frankly, I feel that parents who don't vaccinate their children are parasites."

I think I've found my new Hollywood crush. We finally have a legitimate movie star on the side of logic and reason. They should name an award after her. In fact, I'm going to name an award after her.

Beginning today I will give out the "Amanda Peet Award for Excellence in Logic In Spite of the Apparent Handicap of Celebrity".

Incidentally, the irony has not escaped me that she will be starring in the new movie version of the credulous TV classic 'X-Files'. If she could come down on aliens and psychics next, I'd be much obliged.

Oh the Irony

2008-06-25T11:09:00.002-04:00

This article tells you everything you need to know about psychics - they are self-deluded proselytizers. I especially love the text below the picture of a local psychic on the side-bar. It reads:

"Mesa resident and psychic reader Don Davis sits at his work station in Wellspring Metaphysical Books in Mesa. Davis doesn't believe that a license for psychics in Mesa would help keep the con artists out."

Um, yeah. Keep fightin' those con artists buddy. What's that called again, when you attribute your own undesirable traits onto other people in order to distract from yourself? Hang on, I have to look that up for a sec... ah yes, it's called Freudian projection.

Another Child Killed by Faith

2008-06-20T08:54:00.004-04:00

I'll never cease to wonder how these people can justify these things to themselves after the fact.

In this case, unlike the many, many other cases around the country, the kid was old enough to think for himself. Unfortunately he was irreversibly indoctrinated by his parents for 16+ years to believe that God would save him. But now what? God did not save him. Furthermore, God saves scads of people every year who have the exact same condition. He lets them live even though they get this evil treatment from a hospital. Doesn't that tell us quite a bit about God's will? If he hates medicine so much, wouldn't he kill all of those people who seek the treatment, and let people like Neil Beagley live? Aren't faith healers and Christian Scientists presuming to understand God's will?

I know these people have an astonishing capacity for mental gymnastics when it comes to these things, but how about dropping the cognitive dissonance just a smidge, huh?

Gasp A Well Thought Out Article On Vaccines!

2008-06-19T08:45:00.002-04:00

Alright, so it's on the Opinion Page of the Indianapolis Star. It's still a very well written article that describes the tactics of the anti-vax crown to a tee. And it summarizes the evidence for the safety of vaccines, uh, also to a tee.

There is also some troll leaving inane comments below the article, so we should counter him by leaving positive comments in support of Richard Feldman.

Homeopathic Challenge

2008-06-18T09:56:00.002-04:00

Here's a wise British fellow who is putting his money where his mouth is. Homeopathy is becoming a pretty major problem in the U.K., and this guy is offering money for proof that it works.

For those who don't know, homeopathy is the practice of prescribing water to cure any disease. That's it in a nutshell anyway. You can read about the ridiculous details in this great four-part blog at Science Based Medicine. The crazy thing is that people of influence (questionable though it may be) such as Prince Charles have been promoting it, despite it being proven worthless time and time again.

With Randi's challenge coming to an end, I think that these local challenges are going to be popping up more and more. It's really a nice way to take the true believers to task.

Alternative Medicine Awareness

2008-06-17T11:00:00.003-04:00

As described in this Telegraph article, A Department of Health Report in the U.K. is recommending measures to "stamp out poor practice among herbalists". Unfortunately is sounds like a similar plan to requiring the licensing of psychics. Especially since any practice of CAM can be described as "poor", since it is useless.

The article says there are ~2,000 herbalists working in the U.K., and the CAM market earns 200-million pounds a year (that's probably like $50, right?). The report plainly states that there is "little evidence for many of their claims". Yet they recommend that practitioners study for honors degrees in herbal medicine or acupuncture, or otherwise demonstrate their proficiency and knowledge. How about proving that it works first?

Definiton of Skeptic

2008-06-15T15:20:00.003-04:00

Thank you Dr. Novella!

Just the other day I was trying to explain to a friend about my local skeptical group, which I am actively involved with. He kept cutting me off and asking simple questions like "so you don't believe in anything?", and "are you skeptical that the holocaust took place?".

I slowly conveyed to him the definition of skepticism and, since he too is a scientist, he conceded that it was a worthwhile movement. But, he added, we obviously have a perception problem and should change our name to something less pejorative. (There are many problems with this suggestion, not the least of which is that it has been tried and failed as pointed out in Dr. Novella's blog).

Anyway, it was nice to see on the SGU blog a (fairly) concise definition for skepticism:

"A skeptic is one who prefers beliefs and conclusions that are reliable and valid to ones that are comforting or convenient, and therefore rigorously and openly applies the methods of science and reason to all empirical claims, especially their own. A skeptic provisionally proportions acceptance of any claim to valid logic and a fair and thorough assessment of available evidence, and studies the pitfalls of human reason and the mechanisms of deception so as to avoid being deceived by others or themselves. Skepticism values method over any particular conclusion."

Link to this anytime someone asks "what is a skeptic"?

Vice-President Material?

2008-06-15T14:53:00.003-04:00

I saw an interview with Bobby Jindal this morning on NBC. Now, I had heard various reports of this guy's inanity, but I was pretty shocked to hear him say on national television that he wants his children to be taught "alternative theories" to evolution (read: creationism).

And this is who the Republican's are claiming to be the frontrunner for the VP spot? I did a little research and found this fantastic opinion piece by (the amazing) Barbara Forrest. We should all keep an eye on what she says about Jindal, because she seems to be keeping an eye on him.

It's imperative that we get some sort of campaign going that very clearly and logically explains to the average American why teaching alternative theories to evolution does not equate to teaching the problems within evolution. The issue is that it sounds so very reasonable on first glance, that people are disarmed by it and say "why not teach the controversy"? In fact, teaching the controversy is not what these people want at all (despite the clever catch-phrase). Debates within evolutionary biology should be and are taught. What they want is to downgrade the definition of science so that it includes their personal beliefs. There was a nice interview on Science Friday this week with Ken Miller (listen here, it's ~30 min). He did a great job of explaining it and I'd love to hear if he had some ideas as to how to convey these points to people across the country. The best part of the interview was when a 10 year old kid called in and asked Dr. Miller if he thought evolution was being forced upon children. He responded by saying (I'm paraphrasing here) "no more than algebra is being forced upon them".

This is something that genuinely scares me because the public can grab onto the "teach the controversy" thing very fast, and having a legitimate VP candidate (and future pres candidate) makes it that much more likely that they will. Are the evolutionists prepared for the battle?

More Hollywood Credulity

2008-06-14T13:30:00.003-04:00

I've heard two separate interviews given by M. Night Shyamalan in the past week. Both were on science oriented shows, and both left me wanting to pound my forehead against the nearest concrete wall. Last week Ira Flatow interviewed him on NPR's Science Friday, and this week Steve Mirsky did the same on the Scientific American weekly podcast (here and here).

MNS is, in my eyes, a talented screenwriter and director. All the same, I personally lost interest in his movies after Signs revealed his now obvious belief in a greater power that gives the universe some sense of order. That's easy to show in a universe that you've created on your own where aliens are attacking Earth and ghosts speak to small children. I see no evidence for such order in the universe that I currently reside in.

In these interviews he made it quite clear that he believes there are certain things in our universe that we do not understand, and in fact, will never be able to fully understand. This is utter BS. There are indeed many, many things that we do not yet understand. And some of those things we may never get around to understanding. But there is nothing inherently not-understandable in the universe. Except, perhaps, that last sentence that I wrote. Otherwise though, we base our lives on the premise that there is a reason for everything - arguments from ignorance aside.

He also stated that he became interested in Einstein's increasing belief in God as he aged. Say what? He clearly did not do his research on this, because it has been so thoroughly debunked that had he simply googled 'Einstein' + 'Personal' + 'God' this is what he would have found at the top of the list. And the notion that he became more interested in god later in life can be summed up in this quote from 1954 (he died in 1955):

"It was, of course, a lie what you read about my religious convictions, a lie which is being systematically repeated. I do not believe in a personal God and I have never denied this but have expressed it clearly. If something is in me which can be called religious then it is the unbounded admiration for the structure of the world so far as our science can reveal it"(1).

Religious folks love to portray Einstein as a believer in order to prove that someone who understood so much about the nature of the universe thought that it was designed by a creator. This is clearly not the case. He used the term 'God' frequently, but only when speaking about the natural order of things. And he clearly felt obligated to set the record straight late in life because his quotes were being so abused by people of faith.

A good and thorough review of "The Happening" can be found here. I'm sorry Mr. Shyamalan, but you're simply talking about things that are out of your your league. Scientists can't go about their jobs with the premise that there are "forces at work beyond our understanding". Research would hit a standstill. All progress would end. That sort of speak can only seem logical when you start from an ideology and move out from there. And that's just not the way science works.

1. Dukas, H., Hoffman, B. Albert Einstein: The Human Side

51st

2008-06-13T10:37:00.001-04:00

I totally missed the fact that I was making my 50th post. So I'll celebrate my 51st. Yay! (that's enough celebration for now)

Sasquatch Ree-Ward

2008-06-12T08:30:00.002-04:00

This seems a little redundant, but there is now a $1-million prize being offered by Bushnell (the binocular manufacturers), for verifiable evidence of a bigfoot sighting. This seems to be quite shrewd of them, since they will never have to pay. On the surface it's free advertising.

There may be a downside to the scheme though. By now everyone has heard that Randi will be (sadly) ending his decade-long challenge to reward any verifiable paranormal action with $1-million. The reason? It became too difficult to deal with all of the kooks trying to win the money. I predict that Bushnell will have to close this offer sooner, rather than later, for the same reason. It's no longer free advertising if you have to pay someone to sort through hundreds of blurry photos, or strange hair samples, or bags of feces! Not to mention the lawsuits that will undoubtedly be brought up by those who feel their evidence was valid. Those who believe in bigfoot, tend to not be the most logical of folk.

Keep an eye on this company to see how it works out for them.

The Secret Lives of Herbs

2008-06-11T17:45:00.002-04:00

An interesting article in the NY Times science section this week on recent findings that a particular species of plant can recognize its relatives.

Research by a Canadian group (Ontarian, to be exact), found that the Great Lakes sea rocket (the perfect name for a beach weed), aka Cakile edentula, appears to be able to distinguish between plants that are related to it, and those that are not (published in Biology letters - and if anyone can tell me why this was buried in this journal, I will be forever grateful).

The bottom line here is that plants do not have consciousness (which should go without saying...). But through some yet unknown mechanism they are able to sense when they are in a pot with siblings, and they decrease their root allocation in this situation compared to when they share a pot with strangers (i.e. non-related plants). Presumably, the plants can tell through some chemical signal when they are surrounded by other plants, allocating to their roots in order to out-compete them. Somehow the signal is different when the surrounding plants are siblings, resulting in decreased allocation (and fitness, importantly). The difference in allocation seems pretty significant, and the error bars are not enormous. The question remains - what signals are given off by sibling plants telling them to decrease allocation (maybe whoever answers that will have themselves a Science paper).

The world is a fascinating place on it's own, so please do not try to explain this by invoking psychic ability of plants!

Oops, and Phony Degrees

2008-05-23T09:44:00.002-04:00

Alright, I've been pretty tied up at work. We're actually submitting a paper next week, so that has been taking up most of my free time. I really need to get back into this blogging thing because it's the only activity that keeps me half sane.

One thing that I wanted to mention was a fantastic story on the May 22nd Nature podcast. Unfortunately, I didn't get all the details as I was at the gym when I was listening to it. But a nice sounding English gentleman did a story on British schools that give phony science degrees for non-scientific studies (e.g. homeopathy and other alt med practices). It is a real problem that is not limited to the U.K. I'll write more, and cite things properly when the transcript is uploaded to their webpage, or I re-listen to that segment, whichever comes first.

For those of you who think that we should be open minded about these things, and that people should be able to get any type of medical treatment they are willing to pay for, I say, you're right... to a degree. When $120 million a year is being spent on researching things that we already know do not work, and when passive acceptance of alt medicine is contributing to an overall decline in our national health care, that's when I begin to disagree. And fake degrees contribute to that overall attitude.

Magnets for Fighting Cancer? It's Even Cooler Than it Sounds!

2008-04-21T10:27:00.002-04:00

Now, I'm a big-time skeptic. So when I saw the title of this article had to do with magnets, "Tiny Magnets Offer Breakthrough In Gene Therapy for Cancer", I rolled my eyes and expected the worst. You know what I was imagining, a bracelet that supposedly improves blood flow to the problem area (in this case a malignant tumor), but in actuality does nothing at all...

But when I read the article, I realized it was legit. Researchers from the UK were using gene therapy to treat cancer cells, but were having difficulty getting enough of the monocytes localized to the tumors. Monocytes are a form of immune cells, but in this case they are being used as a carrier for genes that are meant to aid in the fight of cancer. The researchers overcame the problem by loading the monocytes with ferromagnetic nano-particles. They were then able to sequester the therapeutic monocytes to the tumor by holding a magnet over it (results to be published in the journal Gene Therapy in June).

It's unlikely that the magnet is strong enough to actually pull the particles from other parts of the body to the problem area, but they probably flow around the body in the bloodstream, and the magnet concentrates the particle-containing cells in one place. It's like panning for gold with a sieve, only the magnet is the sieve for magnetic particles. There's a long way to go before something like this is proven to be safe and effective in humans (the article didn't say which model organism they used, but it was probably done in mice), but the idea is so cool I just had to write about it.

If you're worried about how a magnet might affect your blood, always remember that the iron in your blood cells is non-ferromagnetic, meaning it has no magnetic properties. So it should be safe, at least based on what we know now.

Expelled, Exposed, Expunged

2008-04-18T13:32:00.003-04:00

Alright, here is the best analysis of Ben Stein and Mark Mathis's movie that I have come across, written by two of my favorite people when it comes to conveying science to the public; John Rennie and Steve Mirsky.

This is on the heels of a question and answer session, where the editors of SciAm got a chance to grill Mark Mathis about the movie. It's definitely worth listening to if you have 75 minutes to spare.

The bottom line: These guys are being insanely dishonest. Utterly, and unabashedly dishonest. It's not that I don't expect it from creationists, and there's nothing novel about this conclusion. It's just that it will never cease to shock me when I come across individuals who so brazenly flaunt their ideological blindness. They know they are lying, but they don't care. They're no better than a snake oil salesman who tells you his cure-all potion is fool proof, then sneaks off to the next town before you realize it's nothing more than scented water. It's depressing more than anything, really, that such people are getting our attention. But you can't ignore them. They must be answered.

Fortunately, the movie is getting absolutely panned by all major critics.

Skeptologists

2008-04-18T10:50:00.003-04:00

Here's something we should all be pulling for. A skeptical TV show! I mean, Mythbusters is great and all, but how about something a little more scientific?

*Edit - I forgot to mention that they are asking people to write emails stating that this is a show that they could get behind and watch. Please take a moment to do so here. I would actually pay for cable if this show was on TV.

Just Following Orders

2008-04-14T17:28:00.002-04:00

I'm a good soldier.

Expelled

Loss of Legs, or Acquisition of Traits?

2008-04-10T10:08:00.003-04:00

French researchers uncovered a 92-million year old fossil of a snake with two "unmistakeable leg bones". The interesting thing here is not that we have a beautiful example of a transition fossil (or a fossil of a descendant of a transition species), we have plenty of those, but it's entertaining to watch creationists once again move the goal-posts for the burden of proof on evolution.

Over at AiG they have scrambled to explain away such a nice bit of evolutionary history. Here's a funny quote:

"Bible believers should be wary of rushing in with comments about the serpent in Genesis. This fossil was probably formed in Noah’s Flood, hence the creature it represents was in existence some 1600 years after the cursing of the serpent to crawl on its belly."

Not quite sure where the evidence for this lies, or even what it is supposed to mean. So basically, serpents where cursed to crawl on their bellies, but then another snake with small hind legs was designed? (Incidentally, why did god curse some lizards and not others? And while I'm at it, why curse any of them just because the devil dressed up like a one? Seems sort of reactionary if you ask me). He was, however, kind enough to leave rudimentary legs on the cursed serpents. Is this because he felt bad for them having to copulate without legs? I'm sure we can all imagine how difficult that would be, and it was kind of him to make this beneficent gesture. Maybe he felt bad for overreacting.

They also go to the oft utilized but always silly - scientists debate the details, therefore they are wrong - argument:

"The findings are controversial. Some evolutionists claim that snakes came out of the sea, from something like a mosasaur. Others insist on a land-based origin. The controversy still rages. In other words, the fossils are open to interpretation."

This is factually incorrect, but more importantly, it's stupid. Scientists debate the details, but either way, they agree that the snakes evolve. You can't have your cake and eat it too. If you believe that scientists are completely wrong about evolution, you can't use their arguments to support your own. They're wrong, remember?

There was, at one point, a debate as to whether snakes lost their legs on land or in water. There was fossil evidence that suggested it may have happened in the ocean. In the end researchers used molecular techniques to create a family tree of snakes and lizards, and found that the only ocean-dwelling lizards known (they're now extinct, but are closely related to monitors) are too far up the evolutionary tree to be the descendants of snakes, suggesting that legs were lost on land and then some snakes moved back into water. It's still possible that another fossil will come along and change that, but this is what the evidence says for now.

Another contradictory point made by AiG:

"Even assuming it could be established that the ancestor of snakes today had legs, creationists have no problem in principle with loss of features through natural processes. Development of leglessness is not evidence for molecules-to-man evolution, which requires addition of newgenetic information. Loss of legs could be achieved through degeneration of the DNA information sequences that specify leg development."

How is this any different from evolution? Loss of a feature is gain of a trait. In fact, they've explained this one aspect of evolution fairly nicely in the last sentence. However, for this to explain the loss of legs, you have to believe in natural selection. You believe that degeneration of DNA leads to new traits, and that these traits can then be selected for if they are advantageous. If you don't believe that it's advantageous, then how could degenerate DNA persist in snakes? So, if you agree that natural selection can occur from loss of information, why are things like gene duplication so hard to accept? They have been observed and documented! It really boils down to an argument from incredulity, or one from ignorance, take your pick. You can't imagine, or don't understand how such a thing could happen, therefore it didn't. Not exactly convincing logic there.

I know, I know. I'm arguing against people who have already made up their minds. But the fallacies here are unforgivable.

Massimo Pigliucci and Scientific Objectivity

2008-04-08T15:21:00.004-04:00

I was able to attend a talk this past weekend by Massimo Pigliucci, which was put on by the NYC Skeptics. It was quite good, and I have since caught up on Dr. Pigliucci's blog. He's a fascinating guy with a ton of great insight into scientific truth and objectivity (by the way, you can view the slides for his talk here).

I took exception to one thing that he said in his talk, but it was a minor, minor point. He suggested that most scientists would take the side of the correspondence theory of truth, which is to say that scientific theories are true if they approximate reality. He goes on to make the great point that reality is dependent on our position, since we all see things a little differently.

I would suggest that that we scientists think a theory is true if it matches our observable, measurable reality. This, I think, is positionally independent because it is open to modification. All of science is pending further data. Now that's objectivity!

This is only a slight variation on what he says, and I think he made the same point at the end of his talk when discussing how we can define truth. My only complaint is that not all scientists are so arrogant to assume that we are in position to know what is real. We just measure what we see, and call it a spade.

World Science Festival in NYC

2008-04-03T10:09:00.002-04:00

Good news! Brian Greene - famed string theory proponent - and his wife Tracy Day (plus a smattering of other prominent NYC scientists and science supporters) have put together a science festival in NYC (link to a NY Times article about it here). I'm all for it of course. Hopefully it takes off and the city becomes invigorated about science. Take a look at the prominent list of speakers who will be there:

to name a few. If you live in or around NYC, and are even remotely interested in science, I recommend going. For whatever that's worth.

Exp(os)elled!

2008-03-31T09:18:00.002-04:00

I know, I know. I'm a little late to the party. Everyone was abuzz about the Myers/Dawkins move theatre scandal... and it was priceless. It took over the internet so fast I saw no reason to post about it. But now I want to link to Eugenie Scott's anti-Expelled webpage; expelledexposed.com

Go there now and go there often. Link to it if you have a blog or a webpage. As Genie mentioned on the SGU podcast this week, how great would it be for this to come up every time someone googled Expelled? I'll tell you the answer... super-great.

I'm Lame

2008-03-20T10:24:00.004-04:00

It's true, I suck. I've been so busy lately I haven't had time to write anything. Every time I sit down and start, I become distracted with something else. What can I say, I'm not a professional blogger... yet

Anyway, I recently finished reading Niel Shubin's Your Inner Fish. I give it a big thumbs up. It's an extremely approachable book, that details some of the vast amounts of evidence for evolution. It also nicely explains how fossils are found, dated, and analyzed. My favorite part though, was towards the end when he described several evolutionary byproducts - physilogical problems we acquired because because our evolution went a certain way (for example, why we hiccup and why we get hernias). It's good for two reasons; it certainly educated me about these details, and it will make (hopefully) some people wonder 'why would god design us with big holes in our abdomen where our gonads are supposed to be when it occasionally leads to our spilling out? Good Stuff!

Downtime

2008-03-05T09:19:00.002-05:00

It's been a few weeks since I've posted. I feel bad about that, but hey, I've been busy. I'm writing a paper, which is extremely exciting for me, but also extremely time consuming. Anyway, I want to post something so I thought I would pass along this interview that I heard with Dave Acer on the Skepticality podcast. I'm embarrassed to say that I had never heard of this TV show, nor had I heard of Dave Acer (I don't have kids, and I don't watch TV). But I'm glad to see anything that promotes critical thinking in kids at an early age. It doesn't take away from a child's imagination to ask them to think carefully about the likelihood of something being true. Anyway, give it a listen. I think I'll buy the DVD for my nephews.

I'm Considering Changing the Name of this Blog

2008-02-19T17:48:00.002-05:00

This frog from the late cretaceous has the greatest name ever: Beelzebufo ampinga. But the really interesting part is what the frog has taught them about the geography of the continents during that time (ca. 65 million years ago).

This devilish amphibian seems to be related to several species of South American frogs, yet the discovery was made in Madagascar off the eastern coast of Africa. This means that there must have been a path for animals to cross over the continents, and it was probably through Antarctica.

I'd leave the Americas for Madagascar too if given the chance. All the cool animals live there

The Colors of the Moon

2008-02-18T08:16:00.001-05:00

Sweet.

http://www.wltx.com/FYI/story.aspx?storyid=58596

Alright, I Admit it

2008-02-17T23:01:00.002-05:00

I was wrong yesterday. There's nothing wrong with the things I was railing against. I just wish the skeptic community was a little more diverse, but in the end it's a great movement. One that I'm proud to call myself a part of.

Consider my tail between my legs

Scienticians Says, I'm Sciencing as Fast as I Can!!!

2008-02-17T14:39:00.002-05:00

I don't know why I found this so funny (well, actually I do. It boils down to my mixed-Groening quote in the title).

"Columbus Given Exterior Science"????

Really? Isn't there a good amount of science going on already on the exterior and interior of something so sophisticated as a space-station?

Turns out they meant that the Columbus part of the ISS is being fit with some new apparatus for performing experiments. Was that so hard to say? What's with the vagaries Brits? Just kidding, I love you guys, and the BBC.

It's actually a cool set of experiments. They are testing how the solar environment affects various biological samples.

Abuses in Science

2008-02-17T14:25:00.002-05:00

No, I'm not talking about scientists acting like catholic priests. I'm talking about the well documented anti-science stance that has been taken up by this lame-duck administration. I came across this webpage (actually I heard about it on Science Friday this week), which documents the laundry list of abuses of science perpetrated by this administration over the last 7 years.

It was put together by the Union of Concerned Scientists, a coalition of scientists who have been monitoring it all. And the list is astonishing. It's a fun way to go through these things (as fun as something so shocking can be, I guess), but more jaw-dropping than any individual claim is the unexplainable pattern of deceit and mistreatment of science. I know, I know. There is nothing new about this, we've been hearing about it for years. But I think there are still people out there who would place this under the conspiracy theory fold and brush it off. This is a nice resource to keep handy when trying to convey exactly how bad, and how much worse this administration has been than previous ones (including prior republican admins). Basically, with all of the well referenced stories summed up here, it's hard to deny that they are simply a bunch of dicks.

A Lack of Skepticals

2008-02-16T18:43:00.002-05:00

I got a chance to see Rebecca Watson, author of the blog Skepchick and co-host of the Skeptics Guide to the Universe Podcast, speak this afternoon at a lecture sponsored by the NYC Skeptics Society. She was speaking about the lack of women in the skeptical community and showed some interesting figures on how critical thinking and scientific reason break down the gender lines. Basically, it doesn't look good ladies. More women than men believe in things like creationism, big-foot, psychics and all sorts of other stupid crap. And less women can be found in the skeptical community in general. Now, I find it highly unlikely that there is any fundamental reason causing women to be more prone to woo. I think that social tendencies have forced women away from science at a young age, and pushed them towards fields that do not emphasize critical thinking. Plus, I have to admit that the skeptical community is full of male nerds and dweebs. I wouldn't go anywhere near it if I were a self-respecting woman. The skeptical movement needs to do two things to bridge this divide:

1. Promote science education to girls at a very young age. Get them thinking critically about science and everything they learn, get teachers to change their preconceived notions about boys being good at math and science and girls being good at humanities. I see no reason to think that sex would have bearing on this at all.

2. Skeptics, please stop talking about Star Wars, Star Trek, Dungeons & Dragons, World of Warcraft, and comic books (all science fiction and video games really). It's lame, and it has nothing to do with the cause. Think about it, if the skeptical community is full of people who look and act like the Comic Book Guy character from The Simpsons, why would anyone pay attention. Let's stay keen to cultural interests, and try not to alienate people.

Sorry about that rant, but I was a little disappointed with the people who made up the bulk of the NYC Skeptics Society. I mean, I am a total fucking nerd, but I try keep in tune with cultural trends, and not act with an air of superiority. Not trying to pick on people, but it all ties together. Skepticism will not have a major impact if it does not cater to the masses at least a little. Still, the NYC Skeptics Society seems like a great organization trying to promote critical thinking and logic, so I guess I should not complain too much.

Man, I'm a jerk.

4 Horsemen

2008-02-08T08:54:00.000-05:00

I haven't had a chance to watch these yet, but it looks great. Dawkins, Dennett, Hitchens, and Harris in one room. Sounds intriguing, no?

Update

2008-02-07T18:45:00.000-05:00

Great shit has been going down at pharyngula since my last post. Basically, PZ's rabid and plentiful readers have torn apart the review article, which I discussed. On top of it being a terrible piece of crap, it turns out the bastards plagiarized parts of it! How big are their balls?! Seriously, you are going out on a limb to force your creationist viewpoints into a scientific journal, but your unwilling to take a few extra hours to word things in your own way? That's just laziness. We're fortunate that these people are, in fact, so lazy because it will help to stifle some of the claims which will inevitably be made by creationists. I can hear them now: 'Extra! Extra! Creationist Research Published in Peer Reviewed Journal (it was plagiarized). Read All About It!(it's fraudulent)'

Anyway, I wrote a note to the Editor-in-Chief, Mike Dunn of Dublin, Ireland. Basically, I said - in the nicest way possible - that I was extremely disappointed in the editorial board and its review process, and will find it extremely difficult to take articles that they publish seriously in the future because of this fiasco. He replied quickly with a stock response, essentially saying that they are looking into the matter urgently and that "Clearly we hope to achieve an early and satisfactory resolution to this matter". Fair enough. But allow me to make a suggestion. When you decide to retract the publication of the paper - this is, without doubt, the only option based on the plagiarism alone no matter the reprehensible content - please explain to your readers how something like this managed to get happen. Regardless of how embarrassing it is for your journal, please, please, please explain to us exactly how it went down. It might just teach us something about the peer-review process, and its flaws in these matters. If these two authors managed to take advantage of the system in order to inappropriately get their views published in a scientific journal, tell us how they managed to do it. It just might help you save some face, but more importantly it may help other journals keep on the look-out for such rogues

Mito-What???!!!???

2008-02-06T14:06:00.000-05:00

Who the hell are these people? I came across this review article today (link to the abstract found here), and it grabbed my attention. Now, without giving too much info about myself - I like to remain mysterious - I work in a proteomics lab, and my thesis is rooted in this field, so I think it's not too forward of me to say that I know something about and think very highly of the field in general. I'm not an expert on mitochondrial biochemistry or anything, but as soon as I saw the title of this article, I nearly shit myself.

Mitochodria, The Missing Link Between Body and Soul: Proteomic Perspective Evidence??????

Seriously, how did this title stand up to peer response, let alone the article itself? (I'll say now that the article was a might difficult to read due to the fact that the authors were clearly not experts in the English language, but I don't think this was a matter of translation errors, for reasons that should become clear).

First, let me explain something about the type of article that this happens to be. A review article differs significantly from a research article. A review is meant to summarize all of the available literature within a particular field, sometimes that which has taken place over a specific period of time. Often the author(s) will go slightly out on a limb and hypothesize about what is the most likely explanation for a particular phenomena, and even propose experiments which would prove or disprove said hypothesis. What a review article should not do is overreach its grasp and try to predict something, when there is not a significant body of evidence to support it. This is exactly what has happened here.

The authors happen to call themselves the Mitochondrial Research Group (so you can imagine how high their pedestal for these admittedly important organelles is), at Inje University in Korea. I've never heard of this place, but that doesn't mean it's not a perfectly good institute. It does make you wonder how someone from a fairly unknown place can get away with stretching things so much, but I guess that's a little unfair, and besides the point.

In the abstract they say:

"These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative."

Wow. That's all I can say. Wow. The hypothesis that mitochondria arose from bacteria that took up residence within other cells is a long-standing one, that has withstood quite a bit of criticism to implant itself in the scientific mindset. Maybe they made that statement in the abstract just to grab our attention... oh, wait. They said it again:

"In accordance with this disciplined performance, the work looks at recent proteomics evidence that disproves previous
lines of thought on mitochondrial evolution in eukaryotic cells."

To be fair, the endosymbiotic theory is still a theory (as plainly stated in its name), but one with mounds of evidence to back it up. You better have some real good data to feel comfortable saying that you have disproved it. Let's see what they've got...

"A recent new interpretation in the proteomics front broadens our scope of understanding toward a better realization of the mitochondrial–cellular integration with the intimate relationship to other organelles. This relationship expands its coverage from the tiny peroxisomes [45] to the giant ER (Fig. 1). This shared relationship, however, is basically essential rather than complementary for cell survival."

OK, that sounds reasonable, so far. They are basically saying that cells cannot exist without mitochondria. Nothing outrageous there. The thought is that the symbiotic relationship between pre-mitochondrial bacteria and other cells is what allowed multi-cellular life to form. Not that mitochondria are a parasite. Anyway, what else have they got?

"Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life."

Damn children! That's a hell of a leap. I can't quote everything in the paper that lead up to this statement, but I can say that none of it was very convincing. Basically they tried to claim that there was zero evidence for an intermediate between a bacterial endosymbiont and a mitochondria, which is untrue. Then they say that a majority of the mitochodrial proteome is synthesized from nuclear DNA and transported into the mitochondria. Fair enough, but what does this prove? Nothing! The whole idea is that this happened so long ago that things will have changed drastically, and the host cell has adapted its processes to take advantage of the endosymbiont. It doesn't surprise me at all that the mitochodrion is contributing so little to the process, it's the host cell that is taking advantage of a specific mitochondrial function. And to say that it is more likely the fingerprint of a creator? I can say with 100% confidence that there is more evidence for the endosymbiotic theory than for the creator theory, so you have betrayed yourselves. You're a couple of creationists trying to shoe-horn your creation myth into science. Shame on you, and shame on the journal for publishing this.

Just, unbelievable.

DS

*Edit (5 minutes later)*
Son of a bitch!!! PZ Meyers totally scooped me. Why is reading Proteomics anyway? It's a middle-tier proteomics journal that I barely read, and I'm a proteomics guy!

Karma Chameleon!

2008-02-05T09:44:00.000-05:00

Poor old chameleons. They've lost their most defining characteristic. Everyone knows that chameleons change colors in order to blend into their surroundings. I mean, that's what it means to be a chameleon, right? WRONG! Turns out their colors make them stand out. I guess we're going to have to come up with another descriptive for people who blend in. If we were being honest, we would call them octopi

Amazing!

DS

The Mind-Body Experience

2008-01-26T11:15:00.000-05:00

There is a nice interview with medical historian Anne Harrington in Salon today (by Katharine Mieszkowski). She is chair and professor of the History of Science at Harvard, and has a new book out titled "The Cure Within: A History of Mind-Body Medicine" (reviewed by the NY Times here). It sounds to me that she may be going a little too easy on people who promote the notion that we can heal ourselves with our minds, but she seems more interested in where the notion came from than whether it is right or not. It's easy to tell from the interview though, that she does not think the data holds up for most of these notions.

Sounds like it could be a good read, and I might have to check it out.

DS

1000 Human Genomes Project

2008-01-25T11:00:00.000-05:00

Interesting article about the new plan to sequence 1000 human genomes over the next 3 years (sorry if you don't have access to that article, try this one). We are step-wise approaching a new age of enlightenment, and it's amazing to watch it unfold.

It's the next logical move in understanding how our genetic material makes us who we are. Having so many genomes sequenced and at our disposal will make it easier for researchers to make confident conclusions about which genes cause certain traits. For example, imagine a researcher comes across a patient with a rare disease, which has not been traced to a particular mutation. All the Dr has to do is sequence the patients genome, then search a database which contains the 1000 genomes to see if there are any patients with the same affliction. If there are, Doc can then align the 2 (or more) genomes and see if any SNP's or haplotypes stand out.

This strikes me as a perfect primer situation. Once these genomes become publicly available, researchers who utilize it can deposit the sequences of their own patient's genome into the database. So the more people utilize it, the more useful it becomes. 1000 sounds like a very reasonable starting point to get people using it. Once enough sequences are deposited, diagnosing genetic disorders will become a thing of ease.

A small technical note, it looks as though they plan on using shared sequences to move the project along quickly. By looking specifically for stretches of DNA that show a lot of variation, they can streamline their efforts. It will be slightly less complete than if they were to sequence the entire genome, but equally useful.

It can be utilized by researchers who are interested in what causes any type of trait, not only diseases (although that's obviously the most useful). Let's say I want to know what gene causes red hair, or an excess of moles on a person's skin. With enough sequences it will become almost trivial. We're not quite there yet, but it is coming soon.

The Tiktaalik Goal Post

2008-01-24T09:08:00.000-05:00

This was just too much. Over on the Discovery Institute webpage, Casey Luskin is trying to explain away the marvelous Tiktallik rosaea find of Niel Shubin and his group. I guess I shouldn't be that surprised, they usually start grasping for straws when something so convincing comes into play. This time Luskin uses so many logical fallacies that it is hard to know where to begin. First he uses a favorite ploy of the ID'ers by moving the goal posts of proof. Next he sets up a straw man argument by saying that "evolutionists boast about the size of the previously large "gap" in this transition, and how Tiktaalik solves all these previously unanswered questions". He rounds it all off with the equally fallacious (and equally commonly used by the ID'ers) argument of incredulity. In other words, he doesn't see how the evidence could fit and therefore it doesn't.

Here we have an ideal example of an animal that shares features of a fish and the first tetrapods (four legged animals). It had fins scales and gills like a modern fish, but its flat head, neck and ribs were more like similar to those of early tetrapods. Moreover, the truly amazing thing about the find is that they predicted that it would be there! The fossil record and molecular evidence suggested that there should be a flat-headed fish in a fossil bed from that time period (375 million years ago), and it was. This further solidifies the predictive power of evolutionary theory.

Yet Luskin chooses to ignore all of this beautiful evidence and instead sets up a straw man by saying that evolutionists believe that this answers all of the questions about the fish to tetrapod transition. I can assure everyone that no biologist thinks this.

Since he has set up this straw man that there is 100% confidence in the field, he then moves on to knocking it down. He attempts to do so by looking at the fin skeletons of Tiktaalik and the other early tetrapods. They do not look similar enough to him, so he brushes off the entire find as unimportant since, as he says "I would assume that documenting how fins turned into feet would be one of the more important aspects of the fish-to-tetrapod evolutionary story". (He also seems, unbelievably, to think that Panderichthys is more similar to the tetrapod skeletons and I really don't know what to say about that. This is a subjective argument which he tossed in, but cannot really make. Has he been trained in comparative anatomy? I doubt it.) Well, if you can't see the similarities, they must not exist, right?

Well Mr. Luskin, you assume wrong. There are many fundamental differences between fish and tetrapods, not just that one can walk and the other has fins. These anatomical features are spelled out very clearly on Shubin's webpage so I won't go into it here. On top of it all, these differences evolved at different rates. So yes, there are more fossils to be found that would ultimately show a smoother transition between Tiktaalik and the early tetrapods, but this beautiful fossil still provides a vast amount of evidence that a transition does indeed exist.

Let's try to be a tiny bit objective (I know, I'm asking way too much her) about this and not make logical fallacy after logical fallacy. Next time, try making an argument that at least utilizes a few facts, not just your opinions. As you point out, we will find another fossil in the future that solidifies this transition even more. But contrary to your statement, we will not claim that we knew vary little about the transition before, nor will we claim to know it all after. As someone smart once pointed out (mockingly towards an ID'er, naturally), every time we find a transition fossil, we create another gap. But we make the gaps smaller, and we increase what we know by orders of magnitude. You can't keep moving the goal posts. There is currently sufficient evidence to show that fish evolved into tetrapods. But what will it take to convince you? By paying attention only to the gaps, you are missing the big picture. You are claiming that a TV show is no good because you watched the commercials. Not exactly convincing my friend.

I'm back baby

2008-01-23T19:56:00.000-05:00

I was out of town for close to a week attending to some family business. I'm back now though, and I'm glad to be.

There are a few things I hope to write about in the next day or so, but for now I just wanted to thank Karl at Inoculated Mind (a top-notch blog if ever I saw one, aye) for including my Shermer write-up in the most recent tangled bank (#97 to be precise).

2008-01-17T09:34:00.000-05:00

From my favorite comic strip; 'Tom the Dancing Bug'.

The Believability of Godlessness

2008-01-16T10:32:00.000-05:00

I was lying in bed last night contemplating my godlessness, as I often do after drinking several imperial pints of local brew, and a few thoughts passed through my groggy mind. For various familial reasons I have been considering people's belief in the afterlife, and why it is considered to be comforting for so many. Personally I am perfectly comfortable with my heaven-less eternity, in fact it makes me appreciate life all that much more. I'm not looking over my shoulder at a god who wants to send me to hell at the first sign of indiscretion, or asking for forgiveness for every little mistake.

Anyway, believing in the afterlife is fine for some people. What I don't understand is why it is so difficult for people to even imagine that there may not be one. It seems pretty obvious to me. Think about it, of the >99% of the species that exist on earth today which are not humans, we do not think that they go to some heaven or hell. There is no dog heaven, or bee hell, or fern purgatory. So why then, is it so unbelievable that we may not exist beyond our current existence? Considering the major difference between ourselves and those other animals is an awareness of our own consciousness, isn't it much more likely that the idea of existence after life would arise from that self awareness rather than that we have been chosen for an afterlife because of it? If dogs and bees can simply stop existing, why can't we?

The point is, don't act so freakin' surprised at people who don't believe in the afterlife. It's not that hard of a concept to grasp, it's just a different way of thinking. It doesn't make life any less endurable, in fact in my case, it has made it more pleasant*.

*and before you ask, it's not because I feel I have carte blanche to do whatever I want. I'm a good, honest person. So there.

The New-New England

2008-01-15T13:33:00.000-05:00

Here's an interesting article on which direction the temperatures are heading, at least in the Northeast United States. The reason that I post this is not to try to convince the world that global warming exists, at this point I doubt there are very few (rational) people left who doubt this. The argument has shifted to a debate over whether or not it is being caused by man (ah, the old moving goal-posts).

I do, however, think it's interesting that it is beginning to hit us where we live in a dramatic, quantifiable way. Will this be enough to make people change there ways? Stay tuned, but I think it may take a more forceful showing by the government before this country changes its ways significantly. Also, it's nice to have some more solid numbers to cite when people say things like "brrraaapppp, global warming can't exist, durh, it's freezing outside!"... idiots

Academic Life

2008-01-13T08:48:00.000-05:00

As a grad student in the sciences, I find that I have a difficult time conveying to people what I do, what I plan on doing, and how I do it. Of course part of this is due to the inherent difficulties involved in explaining hard science topics to people with zero background in science. But I am starting to think that there is something even more fundamental than that which is not getting across, and therefore confusing the whole situation. And that is basically that people don't understand the type of graduate school that I attend, they don't understand what a post doc is, and they don't understand what the long-term career options for someone with my background would be. They don't understand the whole cascade of events that lead to a scientific career, and they therefore are unable to comprehend what scientists do. Maybe if we make this crystal clear, it will be a first step in breaking down that wall, so let's break it down in a chronological fashion (I will intersperse some anecdotes from a made up scenario when I think it might help):

First, some definitions:

The Primary Investigator (aka the PI)- The head of the laboratory. He is a professor, faculty member, and mentor to his post docs and students.

PhD (aka Doctor of Philosophy) - An advanced academic degree, usually given in the sciences or humanities. Often has a research focus.

Qualifying Exam (aka Quals, Prelims, Comps) - An exam given to PhD candidates which determines if they are competent to pursue the remainder of their thesis.

Graduate School in the Sciences - Basically, if someone wants to do any kind of scientific research; biomedicine, chemistry, physics, cell biology, biochemistry, etc., one needs a graduate degree in one of these fields. For simplicity, I will focus on the biological sciences I am most familiar with that area. This would include biology as well as areas like biochemistry, cell biology, biophysics, molecular biology, and microbiology. There is a ton of overlap in these fields, so avoid getting bogged down in the details of the names. There are a few programs around the country which give out masters degrees in hard sciences, but not many. This is typically not thought of as all that useful for someone who wants to do their own research down the line (it can be useful for someone going into industry, because they might be in a more business oriented job that requires some science background). For the most part, when someone gets an undergraduate degree in science, and they are interested in pursuing research as a career, they apply to PhD programs. Most universities have a separate PhD program for each department.

PhD Programs - The best thing about these typed of programs is that they pay you to attend. Typically, they give all of their students a yearly stipend which can run between $18,000 and $25,000. Not much but it's enough to get by on for 5 or 6 years, while you are in your early to late 20's. This is the typical length of time that you would spend in grad school. Often the first 2 years are spent taking classes. In the first year we do rotations along with classes. Rotations are essentially try-outs for a few labs at the university to see which type of research we want to go into. It's both a try-out from the PI's perspective (do we fit in with the lab?) as well as from ours (is this the type of lab we want to be in?). In the second year, we have decided which lab we want to work in, but are still taking classes (this can vary depending on the program). At the end of our second year, most programs require us to take some sort of right-of-passage test, often called a qualifying exam (or qual, see definitions). The format of this can vary from a multiple choice exam, to an oral exam, to a more research oriented oral presentation. It is however, extremely stressful and can be quite difficult. It essentially determines whether the program believes that you are good enough and smart enough to continue with a thesis in their department. If you fail, which happens with surprising frequency (again, depending on the place), the department will often give you a masters degree and send you on your way. This, I believe, is another reason why masters are not particularly useful in the sciences. They are probably thought of as someone failing to get a PhD, rather than someone achieving a masters (not to knock anyone with one, just my observation). Anyway, once you pass your qual you are ready to working towards your thesis.

The Thesis - Actually, by the time the end of your second year rolls around you have probably already figured out what you want to work on, and it will typically take another 3 to 4 years in order to accumulate enough information to be considered worthy of a thesis. The term thesis itself has several meanings. It is the central argument of a paper or proposition. It is also the name for the physical document which is the summation of your 5-6 years of graduate work (this definition is interchangeable with dissertation). So there is some understandable confusion when someone says "I'm in grad school working on my thesis". Typically this is not what a person who is, at that time, writing their actual thesis would say (if they were doing that you probably would not see them for several months anyway). What they mean is that they are busily working in the lab to accrue enough data to support their thesis. Usually a student is required to propose their idea for a thesis topic (called a thesis proposal) around the beginning of his/her 3rd year, after qualifying for continuing her/his education. The student must select a few faculty members to make up his thesis committee. This group will judge the students proposal, determine whether it is a) achievable and b) worthy of a potential thesis, make suggestions and send the student on his/her way. Typically students meet with their committee members yearly, so they can assess the progress and guide them in the right direction. It's a particularly useful part of grad school as the committee members are often very knowledgeable people who are there specifically to help.

As an example, let us say that Jimmy applied and was accepted to the biochemistry department at Cornell University. He spent his first year rotating in 3 different labs, a fly genetics lab, a structural biology lab, and a cell division lab. All the while he was taking classes on Cell Biology, Gene Expression, and Human Genetics. You'll notice that there is a seemingly wide range of fields that Jimmy is learning about. That is typical as even though each of those labs has an area which they specialize in, there are many techniques and principles which would be used in each lab. Additionally, even though Jimmy will choose a fly genetics lab to work in, it behooves him to learn as much as possible because, as we shall see in the post doc section, he will most likely choose to work in an area that differs in some way in the future.

So at the end of his first year Jimmy chose the structural biology lab, and started discussing with the PI what type of research project he is interested in pursuing. Jimmy, it turns out, would like to know the 3-dimensional structure and function of a protein from a bacteria which is involved in infecting humans. The PI and Jimmy plan out a loose course of action for the next several years which will hopefully allow them to understand a significant amount about this protein. If they succeed in shedding light on the details of this protein, JImmy will have enough data to write his thesis, and will have supplied the world with a little bit more information about a disease causing bacteria. Not bad, but it's still a long way off. He spends most of his second year toiling away in the lab, trying to work out conditions for isolating large amounts of this protein from the dangerous bacteria, all the while taking another 2 classes in order to fulfill the requirements of his program. By the time spring of his second year rolls around, he realizes that his approach has not worked as well as he had hoped, and he needs to alter his approach. But now his quals are coming up and he has to put everything on hold so that he can study for them. He passes his oral exam, and submits his thesis proposal to the dean of his department which is accepted.

Finishing Grad School - Once the proposal for the thesis has been accepted, the student toils in the lab for another few years. Not to sound self-pitying or anything, but we often work long, painful hours with very few results. We're like baseball players, if we get something to work 3 out of 10 times, we're all-stars. Most of what we try does not work. That's why you have to have a very specific personality to enjoy research. You can't get discouraged, and you can't expect too much. Anyway, this is the time that I find to be the most difficult to explain to non-science people. We are no longer taking classes, but we aren't working at a job. I often interchange work and school when describing what I do. Sometimes I feel as though it is more accurate to say that I have a full-time job, because saying that I'm in school gives the impression that I do nothing except attend classes and study. That's really not the case. I personally work 10+ hours in the lab/day during the week, and another 15 or so on the weekends. Plus I often come in at 3am simply because my experiments don't care what time it is. Add in the reading that I do at home in the evenings and I certainly work more than any non-scientists that I know (except, frustratingly, newly graduated lawyers).

Let us now return to Jimmy's hard-working adventures in crystallographyland. He returns to the lab to rework his approach and gather some data. While he failed in his first year in the lab to purify the protein in any significant amount, it was not a total waste of time. He was able to optimize the conditions of is purification so that, in the end, he had a small amount of highly pure protein. He also was able to clone the gene which encodes for this protein, which meant that he could try and express it in large amounts in some other type of cell. He does this, optimizes things, works long hours in the lab at all times of day, and ultimately gets his hand on large amounts of the desired protein. He crystallizes it and determines the 3-D structure using x-ray diffraction. This takes many months, but in the mean time he has designed an assay for the activity of the protein, and makes several mutants, which in the end reveals how that protein helps the bacteria to infect humans. Overall, this body of work took him 3 years. When he presents it to his thesis committee, along with a paper that he authored and published, they tell him "good job, go write your thesis". He takes another 6 months to write, as well as finishing a few "loose-end" experiments. He submits the thesis to his committee, and prepares his defense. He presents his thesis work in a public lecture and then his committee asks him tough but important questions about his work and what it means. He answers them appropriately, and they award him a PhD. It took 5+ long years, but it was worth it, because now he can go on to a pot doc, which is not exactly a huge change. Wait, that wasn't worth it at all! Jimmy is pissed!

The Post Doc - This term is a shortening of 'Post-doctoral researcher'. So it means someone who has received their PhD is doing some more research. Grad students and post docs work in the same labs, but most often a grad student moves to a new lab upon graduation. Basically, this is an advanced but in-between stage. In grad school we kind of learn how to do research, and many of the underlying principles of research, and a whole lot of background in whatever general field we are entering. When we move on to a post doc, we are essentially thought of as independent researchers who must come up with our own experiments and projects. As with many things in this field, there is not really a clear demarcation in these things. Good grad students who are trained well by their PIs often have the capacity to think creatively about their project, and often times post docs need a little help from their advisors in designing experiments. However, by the time they are finishing in the lab, a post doc should really be quite competent at thinking creatively and critically, and have a good idea of a research project that is heavy enough so that they could start up a lab based around that idea. I think this is the main point of a post doc; to hone one's experimental skills as well as one's publication record enough to where universities will consider you for a faculty position.

Faculty Life -Now, I am nowhere near starting a lab, but even from my distant vantage point it looks like a daunting task. First you have to convince a department at a university that your ideas are original and important enough to warrant a significant chunk of startup money and lab space. Then, if you are fortunate enough to get that, you have to convince the US government (some other grant agency) of the same thing so that they will give you renewable grant money for your research. The odds of getting a position get slimmer and slimmer every year, and the odds of getting both are shrinking to nothing (especially with this administration and their cutting of funding for basic research). But if you are fortunate enough to get those things, you still have to be hard-working and fortunate enough to get enough good results so that your department will grant you tenure. Once tenure is granted, you can finally relax, a little bit anyway. There's a myth that tenured faculty do nothing, but I have never seen a single person stop working once they receive tenure. In fact, I think that most of the greatest work is done after tenure, possibly because they no longer have pressure to get positive results (except for the pressure to maintain the non-guaranteed grant money will keep coming in). They can move over to some more risky projects which may or may not work, but which are potential home-runs. Anyway, a young PI only has so much time in order to accomplish what is required for tenure. We call this a tenure clock, and it begins ticking the moment he/she sets foot on campus. It's usually somewhere between 5-10 years, but it depends on the institution and their policies. If they do not accomplish enough, their tenure committee will deny them, and their career can be in jeopardy. Often when this happens a PI will move to a smaller university or switch to more teaching duties, or leave academia altogether.

So you can see that academia is a high-risk, low reward type of career. Grad school is long and demanding, but at least they pay for it. Professors don't get paid that much on average, although a tenured professor can make a decent living and the job security is unbeatable. Aside from that, I believe there are 2 reasons for people to enter this line of work:

1) We want to change/save the world. This can be a little misleading, because realistically we are not going to make much of an apparent difference. However, the research that we do can lay the groundwork for more research which can ultimately lead to cures for diseases, or new technology that will better people's lives. This is what we tell ourselves at least.

2) We are insatiably curious and have questions that need answering. This, I would guess, is the most common reason. I often tell people that I am not, by any means, altruistic (so take me out of category 1), I just enjoy science very much, and happen to be pretty good at it. What else can I say?

So if you are a grad student/scientist and have been having trouble explaining to your parents or friends what you do, feel free to pass this along. Also, if there are other areas that could use clarification, I'd be happy to edit this with those in mind.

DS

Michael Shermer's Book Lecture

2008-01-10T09:07:00.000-05:00

So last night I went to the New York Academy of Sciences to watch Dr. Michael Shermer talk about his new book titled The Mind of the Market. The talk was part of the NYAS Author's Series which is apparently one of their public gateway programs. Overall it was a nice evening (the wine and cheese helped), and I strongly encourage any scientists in New York to get involved with the NYAS, become a member, go to some talks, etc. If for no other reason, go for the amazing view of lower Manhattan from the 40th floor of WTC Building 7. Unbelievable.

Anyway, before giving my thoughts about the lecture/reading (just to be clear, I have not yet read the book), let me declare my predisposition on this matter. For one thing, I am an unyielding skeptic. I am a card-carrying member of The Skeptics Society, of which Dr. Shermer is a founding member, and I read Skeptic magazine front to back the moment it reaches my apartment. However, I have noticed that I differ greatly with several of Dr. Shermer's views in the past.

Furthermore, as other bloggers have noted, his newest book was given a very interesting review on amazon by Dinesh D'Souza (and other conservatives) who trumpeted it as putting a positive evolutionary spin on free trade. Now, I hate D'Souza and think he is a spineless leach (I won't get into why now), but I vowed not to let a positive review by him automatically translate to a negative review by me. On the other hand, having read this review, I did not put it past Shermer to make these types of claims as he has made no bones in the past about jumping back and forth across political lines (i.e. he's a libertarian).

My main reason for concern is that I get a little antsy when people try to shoe-horn evolutionary explanations for human behavior. Don;t get me wrong, I love learning why we do the things that we do, and more often than not there is an evolutionary component to behavior. What kind of gets me is when people offer a change in our behavior to satiate some evolutionary need. Unfortunately, even if the explanation fits nicely as it often does, there is still no guarantee it is the bona fide root of that behavior pattern. So my opinion on these types of exercises is they are fun and interesting, and can be very educational in some cases, but it is wrong to extrapolate from them that we should modify our society in order to more comfortably fit our "nature". It is a huge leap to begin solving problems from hypothetical explanations.

The reason that I went through all of that before discussing Dr. Shermer's talk is that I believe he was greatly misrepresented by D'Souza in this particular case. It did not sound to me like he was proposing that a free market system would be better for America, only that he thinks that our evolutionary past would predispose us to making good decisions if given a chance to do so in an open system (keep in mind here that I have not read the book, I'm only interpreting what was discussed at this particular event). This immediately addresses my main concern about translating a theory about our behavioral evolution into a drastic societal change.

In any case, his evidence was fairly convincing. He mainly cited things like Prisoner's Dilemma, which is a game theory scenario that posits a series of choices to people. There are many variations on this problem, but typically two people are given a choice to take all of something, share something, or give up something and there are a series of consequences for each choice. The bottom line is that most of the time, people choose to collaborate with the other person because the consequences are mutually beneficial. That was a poor description, but the outcome is all that matters. It seems as though humans are hard-wired to work together, because the benefits will outweigh the cost (the cost being a slightly lower payoff than making the "take all" choice). Similar experiments were performed on monkeys, and they made the same choices suggesting that it was a very early adaptation in our ancestors.

He also claims that most hunter/gatherer populations were egalitarian in nature, and that simpler societies make use of trade in order to establish trust and to firm up relationships. This, he suggests, means it is in our nature to do behave appropriately in issues of economics. Again, it's an interesting theory, but it would be a huge leap to say that a free market would benefit our society. For one thing, we have essentially been outside the realm of evolutionary pressure for a very, very long time. So even though many humans may have some predisposition to behave appropriately in a free market scenario, a few bad eggs would have grave consequences for the rest of society. And these bad eggs have not been weeded out by natural selection. it reminds me of the hawk/dove scenario that Dawkins has discussed. When a mutant hawk behavior is introduced to a stable population of doves, that behavior would take over. But this is no longer a stable situation, so the population would ultimately swing back to an equilibrium. However, if there is no pressure on the hawks, ESS does not apply and hawks would dominate the population. He answers this concern by saying that we of course need some rules, and that sending them to prison would be like selecting against those people. Not 100% about that, but it's a debatable point.

I guess the question is 'where should the line between free market and what we have today lie'? If we take away all of the rules then most people would behave, but the hawks might take over. If we have too many rules, we may not be getting the full benefit of our collaborative disposition. It's too complicated a matter for conservatives to blithely suggest that we should move towards a completely different economic situation. I won't even delve too deep into the hypocrisy here. If you don't believe that evolution can explain human behavior as D'Souza has stated (in fairness, he has said that he believes in evolution, but that it does not explain things like why we are here, or why we do things, only god can explain that), you can't then turn around and agree with someone who is proposing an evolutionary support for free markets. Whatever.

In any case, Dr. Shermer was a very engaging lecturer. He was witty and entertaining, and clearly knew his shit. My interpretation of his stance is that we evolved in a free market, 90% of our history was within a simplified free market, and therefore we would behave in a surprising way if we returned to it. I don't think he was necessarily condoning a sudden reversion to it, but again, that's my interperetation. I'd be interested to hear what other skeptics thought about him or his book.

DS

Scientists Advise Government to Teach Evolution - How Controversial!!!

2008-01-04T13:41:00.000-05:00

A report was given to the government today which emphasized the importance of teaching evolution in schools. No big surprise there, since the group consists of scientific advisors from the National Academy of Sciencesas well as it's Institute foe Medicine.

No big shock here, but I think that it underscores an important issue. Namely, there is no controversy surrounding evolution! I'm probably preaching to the choir here, but if any of you are ignorant enough to fall into the newest ID catch phrase "teach the controversy", please do not bring it up until you have read the information withinreport discussed above. You really cannot speak on the topic with any authority until you have gone through all of the scientific evidence. If you still have doubts, bring up your specific questions and we can discuss them one by one. (If you don't want to read the book, check out this link).

DS

Edit: There was also an article published this month in the journal FASEB which is aimed at encouraging scientists to "become more involved in the promotion of science education, including evolution" (press release found here). I think it's great that major science groups are unafraid to promote science and empiricism, and willing to criticize those who want to teach pseudoscience and woo in our schools.

Herbs and Medicine

2008-01-02T11:27:00.000-05:00

Here is a great post about the misleading dichotomy between pharmaceuticals and medicinal herbs (incidentally it is a new blog on science and medicine which looks like it will be very good). It is specifically referring to a web article in the New York Times about a medicine hunter in Peru named Kilham (the blog is far more informative than the NYT article).

This is an old debate that seems to be one of those things where people just can't grasp a very basic principle which would make things very clear. Basically, botanicals (or herbs, or medicinal herbs or whatever) are themselves drugs. They just haven't been put through the rigorous trials that pharmaceuticals have to go through. In fact, many pharms are derived from natural products, as are many poisons. So an herb may in fact have some sort of helpful compound within it, but there is an equal chance that it will have a harmful one. We cannot know for sure unless it is tested in double-blind experiments. In any case, the bottom line is that there is nothing inherently good about botanicals, nor is there anything inherently bad about pharms. In fact, there is no difference except one has to have been proven to be effective and relatively safe. Of course, sometimes even pharms are not as safe as we think, but that is another issue.

Happy New Year!

2008-01-01T10:31:00.000-05:00

I resolve to get a few readers and comments!

Breakthrough of the Year

2007-12-31T11:07:00.000-05:00

I'm ripping off Science Magazine here, but since it's New Years Eve I want to do some sort of wrap up of science in 2007. I just happen to agree with them that this is the most important achievement in science this year, but they got it out first.

Anyway, Science announced their 2007 Breakthrough of the Year in this weeks issue (article written by Elizabeth Pennisi). The winner was sort of a culmination of technological advancements over the past few years coupled to a long-standing goal in the field of human genomics. It is best described as the assessment of human genetic variation.

First, let's take a step back. The sequencing of the human genome several years ago was a major achievement for human medicine, but not necessarily for the reasons that most people think. What the sequence of the human genome actually is has always been a common area of confusion within the public. "What does it actually mean? We always hear that our genes make us who we are. I'm very different from any other human, so it follows that my genes must have some differences, right? So then, how can there be one single sequenced human genome?" Great questions. Let me try and clarify a little, it will help to point out why this was such a major breakthrough.

There are indeed some major genetic differences between all humans. The fact remains though, that when you look across a population (at every human being for example), there is what we call a consensus sequence for the genes in our cells. There are approximately 3,000,000,000 base pairs in every one of our cells. A majority of those bases, however, are exactly the same from person to person. In fact, it is estimated that there are only 15,000,000 base pairs that differ consistently from person to person. If you think about it, that is only 5% of the 3,000,000,000 total bases. So we can sequence a mixture of DNA from several people (this was how it was originally done) and get a very good idea of the concensus sequence of the human genome. Additionally, it is really just a compilation of those 15,000,000 differing base pairs [we call them SNPs (Small Nuclear Polymorphisms)] which make us individuals. If you do the math, that leads to a possible 50,625,000,000,000,000,000,000,000,000 (i.e. 50,625 billion-trillion-trillion) individuals with at least one differing base pair. That is just a number and not very meaningful, but you can see how the magnitude of it makes sense considering there is some 6,000,000,000 people in the world. That means that less than 0.000000000000000012% of the possible combinations of SNPs are being used today (man I hope my numbers are right, I did a lot of rounding and simplified things by ignoring insertions/deletions and other complicating factors).

To be clear, try not to put too much stock into these numbers. I am just using them to illustrate a point which will hopefully become apparent at the end of this paragraph. The 250,625 billion-trillion-trillion number does not actually represent the potential number of individuals, and there are two contrasting reasons for this:

People probably need a minimum number of distinct SNPs in order to actually appear distinct. I couldn't even guess what this number is, but it would decrease that 50,625 billion-trillion-trillion number by some significant factor.
Our appearance is dependent on the amount of the given gene that is expressed (i.e. the amount of the gene product that is present in our cells), which also has a genetic component to it, but I don't want to drag out here. This complicating factor would increase the number of potential individuals, mitigating to some extent the logic in point 1.

The main issue here, which I hope to get across, is that we can be, and are, very different from each other while still having mostly identical DNA. In fact, the most recent study shows that any given individual shares 99.5% of her/his DNA with any other person.

Ok, moving on. Hopefully I have answered the first part of my own hypothetical question. The original human genome sequence was a consensus type of study that generalized most of the sequence features in our genomes. Now, in order to make the human genome useful, we need to be able to sequence the genomes of individuals. And that is exactly what Science (and me too) dubbed the breakthrough of the year. We are finally starting to see some progress in this important area. We are finally able to look at our own DNA sequence, and because we can compare it to other people's sequences, we can learn how the differences affect our appearances (and more importantly our health!). The studies that are geared towards understanding these relationships are called Genome-wide association studies, and there have been more than a dozen of them this year.

The first individual genome sequenced was that of J. Craig Venter, of the institute bearing his name (JCVI). This is no surprise since he was the person who privately funded one of the two original sequencing projects in the late '90s. It took about 4 years, and was finally published this fall. In any case it was a huge accomplishment, and as sequencing technologies become cheaper, better and faster we are going to see this become commonplace. Already there are companies set up to sequence the genomes of individuals (although we should be wary of these claims until the companies have shown they are reliable), and the more sequences we have from individuals, the more data we have for the Genome-wide association studies, and the more we will know about how our genes affect disease and other traits. Exciting, no?

From a scientific perspective, this was a fascinating study because it actually showed that we are even more different than we ever expected. Until the Venter study, it was believed that we shared 99.9% of our DNA with all other humans. We now estimate it to be closer to 99.5%. You may think "hell, both are very high numbers so what's the diff?" Well, it means we were off by a factor of 5 before, so it just goes to show that we have ton of work to do in this field. I think that we are finally starting to see the results from the human genome project that we were expecting all along.

Whale Ancestors

2007-12-19T16:41:00.000-05:00

I was going to write something about this Nature paper which fills in some of the questions about the ancestors of whales. However, PZ Meyers beat me to it. It's pretty fascinating, but oh well. I have another idea, which I'll write about in a few hours.

DS

Whoo

2007-12-17T22:07:00.000-05:00

Well, my posting has been sporadic to say the least. What can I say, I'm still working this thing into my schedule, which is cramped.

Today I'd like to discuss a common misconception about evolution. You can get this information anywhere, and there are clearly more established blogs which I have directed you to in the past. Also, check out this good site for all of your argumentative needs. But I specifically want to address one very depressing error, which I read this evening in a salon.com article. The article discusses the "new atheists" (whatever that means) and has this sentence at the end of the opening paragraph:

"How can a person of faith reconcile the apparently random, meaningless process of evolution with belief in God?"

This is utter bull-plop! Bull-plop I say! There is not a single statement that more accurately predicts that the person making the statement knows absolutely nothing about the topic of evolution. And if you know not about a topic, you are hardly in position to write an article about it. Granted, the article was not specifically about evolution, but who are we kidding here? Evolution is at the heart of this debate.

Anyway, back on point. Evolution is not random. Let me say that again. Evolution is not random. Ok. That was unnecessary, but, whatever. Random events, aka mutations, clearly play a major role in evolution. However, the beauty of evolutionary theory is that natural selection chooses favorable outcomes, and discards negative ones. This is the exact opposite of evolution. So many people think that if a single designer is not involved it must therefore be random. It is not random. Do not say that it is random. It is not. I hope I have made this clear.

Nuclear Pore Complex Structure

2007-11-30T23:08:00.000-05:00

This is just mind-blowing. In the link is a pretty decent explanation of the research, as well as links to the papers and a video interview with two of the (many) authors.

The nuclear pore complex (NPC) is the gatekeeper of the nucleus. Eukaryotic cells (including the cells that make up humans and other higher organisms) contain a nucleus which contains the cell's genome. The nuclear envelope is the barrier which encases the genome, however it has to be selective in what it keeps in or out. In other words it has to somehow let in specific molecules that are necessary for a huge number of nuclear processes, and allow other molecules to exit. The way it does this is through NPCs. NPCs poke big holes in the nucleus, but act as the gatekeepers of these holes. They prevent molecules from entering or exiting the nucleus unless they have a ticket, er, actually, that is, unless they are associated with transport proteins.

Anyway, the NPC is too big to get a crystal structure, but still sub-microscopic enough that it is hard to make out the fine details like where specific components are. This study was a real tour de force because it compiled molecular restraints from biochemical and proteomic experiments into a program that generated a most likely conformation of the NPC. It's a thing of beauty too. It's like a donut with spaghetti in the middle. The spaghetti is too thick for large molecules to pass through, while little ones can squeeze through with ease. Additionally, if a molecule is associated with the right transport factor (or if it has a ticket), the spaghetti lets it pass. Donuts and spaghetti! It makes perfect sense!

BizZay

2007-11-30T22:53:00.000-05:00

Oh man. Had a busy November with various familial obligations and research objectives to meet. Lots of good stuff going on though. And now I'm home sick on a Friday night. yay. I loved the NOVA special on the Dover schoolboard trials. It's hardly worth talking about since so many others have given their thoughts (like here, and here). Good stuff though. Check out Monkey Girl by Edward Humes if you're interested in more details about that particular ID fiasco. There were lots of fascinating characters and ins-and-outs and what-have-yous during that whole trial. Humes did a fantastic job putting it together in his book. One thing that I did not notice in the NOVA special that was a great point in the book was that judge Jones was quoted as regretting his decision to keep cameras out of the courtroom. He said the scientific evidence was so overwhelming, and was presented in such an organized way that everyone should have been privy to it (my intereperetation of his words). To bad. An oppurtunity missed if you ask me, but it was still a landmark victory for logic and common sense.

ERV's Translation

2007-11-10T09:13:00.001-05:00

OK, here is ERV's 'parentification' of her debate with Michael Behe. If you can't tell I truly enjoy reading her blog, and everyone should check it out regularly. As soon as I get a chance I'll make a list of all of the science blogs that I read daily.

DS

Yaaaaaaaaaayyyyyy! (yay!)

2007-11-08T13:56:00.000-05:00

My first comment. What a rush. And from ERV, one of my favorite science bloggers, too! She previously posted a great 'parentification' of this argument, and has promised to post a second, more detailed one soon. This is nice because I don't have to research all of the details and translate it, and because she is clearly much more of an authority than I on the subject so it will be 100x better that anything I could do. I'll post the link when it arrives.

DS

Might as Well

2007-11-05T17:33:00.000-05:00

Even though this helps her not at all (because I have yet to get any readers [I'm a pathetic beast, I am]), I would feel remissed if I did not link to a beautifully worded and elegant article by ERV. She responds to Michael Behe, who I can only describe as detestable at best for his fraudulent claim to be a scientist, all the while misrepresenting bad science and ignoring good science in his quest to debunk evolution. I really don't need to say much about it as she takes care of him so thoroughly that there is nothing left to explain.

I'm a little confused about Behe's motives in all of this. I suspect that he was never a particularly good scientist, knew this, and saw an opening in society as a "scientist"-spokesperson for intelligent design (ID). Pretty shrewd, but his bit is getting old as he seems to just be mailing it in these days. He doesn't even try to make a reasonable argument anymore. He makes it too easy for intelligent bloggers like ERV to tear him apart. I guess it was inevitable all along.

DS

Open Access

2007-10-26T08:59:00.000-04:00

Here's an interesting article about open access journals. Basically, Senator Inhofe (R, Oklahoma) tried with all of his might to prevent a bill from being passed which called for open access to government (NIH) funded research. The bill called for all research to be made public no more than 12 months after publication. Seems pretty reasonable, right? If the government (and taxpayers) are paying for something, they should have the right to read it. So why would this guy put so much effort into putting the kibosh on it? Turns out one of his largest campaign donors is Elsevier, which in turn is one of the largest scientific publishers in the world. It's amazing how these things work. Inhofe is one of the most deplorable characters in politics today, and has been for a while. But now I think I'll be boycotting Elsevier journals due to their underhanded ways.

Still No Comments... But Nobel Prizes to Discuss!!!

2007-10-09T08:47:00.000-04:00

I'm ok with the lack of activity, even though it probably means that nobody has read my first post. Maybe I'll put a little more effort into spreading the word. I guess I should write more as well, but I've been a bit busy for the past week. Anyway, I'm thinkin' I'll post a long one describing one of the winners of the Nobel this year. If you don't know (I'm speaking to the void right now since I have yet to attract any readers) the prize for medicine was awarded yesterday, physics was today, and chemistry will be out tomorrow. If anyone is out there reading, waiting, observing... I'll be happy to parentify* any of the work that lead to one of the prizes. Maybe I'll take a poll. Send comments if you have a preference!

*Parentification is the tentative term that I will use for explaining science in everyday terms. I think it fits because a) I have to do it all the time with my parents b) I don't think my parents are dumb, so it is very different from 'dumbing things down', and c) a famous scientist once said that all scientists should know their material well enough to explain it to their parents (actually he said grandmother, but in this context I take them to be interchangeable), so practicing this will be good for me.

A Flip-Book Animation of Translation Initiation

2007-10-02T14:53:00.000-04:00

The dynamics of proteins while they go through biological processes fascinates me. Most of biochemistry and related fields involves measuring things indirectly and, after going to great lengths to validate hypotheses, scientists are able to make useful statements about the process at hand. It can however, be difficult to say things definitively about dynamics. Let me explain a little further.

An enzyme is a biological macromolecule that performs a specific chemical reaction within a cell. There are millions of different types of enzymes within each cell, whether we're talking about an individual cell within a human body or a single-celled bacterium. Each of these enzymes is a series of amino acids strung together, and each have evolved a specific amino acid sequence over the millennia which conveys a specific function to each enzyme. Now, typically the activity of (or the chemical reaction specific to) a particular enzyme involves the following: 1) the enzyme binds a substrate (the compound being chemically altered by the specific reaction of the enzyme) 2) the enzyme modifies the substrate 3) the enzyme releases the substrate. Hopefully you can see how this would be important for a cell or an organism. If you have ever wondered how we metabolize food into energy, it's through this process. Frequently there are many enzymes involved, like people working at different steps on an assembly line. Each enzyme binds to the substrate, modifies it into something more useful, and shoves it down the conveyor belt to the next enzyme which follows the same process, and so forth until the substrate is no longer a substrate, but a product which our bodies can utilize (e.g. an amino acid for making new proteins). So, biochemical analysis of a particular enzyme typically gives us the following information about it; we can find out what substrate it binds to, how strongly it binds to it, and what the product is. We can even learn about the specific mechanism the enzyme employs to perform its chemical reaction. This is all extremely important information, but there is something missing. What does the enzyme look like when it is undergoing it's process? Does it change the way it looks, allowing the substrate to bind? Does it change shape again when the product is ready to be released? These are the dynamics of the enzyme. To be fair, biochemistry (with it's long and powerful reach) can tell us a little about these problems and has in the past. The information learned has tended to be hard-fought and (dare I say it?) inferred from indirect evidence.

Now a recent article published in Cell called 'Structured mRNAs Regulate Translation Initiation by Binding to the Platform of the Ribosome' (Marzi et. al. Cell 130, 1019-1031, 2007) shows that this information can be determined directly. The work was a collaborative effort between groups from France and the US, and it visualizes the discrete stages of translation. Translation is the process whereby a message RNA (mRNA) is relayed into a protein. This is how genetic information is carried out within a cell. DNA is "transcribed" into mRNA, which is "translated into a protein. Proteins carry out a bulk of the processes within a cell (they make up enzymes as well as structural molecules that give cells their shape). Anyway, the ribosome is the enzyme that converts mRNA into protein. Follow? I hope so. In this paper, they literally take pictures of the ribosome while it is binding to mRNA. The cool thing that they show is that there can be structural features in the mRNA which prevent it from being translated (think of a tangled ribbon on a cassette tape which will not go into the tape). The ribosome binds to this knotted mRNA, but temporarily shoves it off to the side because it is not in the correct state to be translated. When the mRNA is in the correct state (i.e. unknotted), it moves to the correct region of the ribosome and is translated as normal. The great thing about this paper is that it shows a series of pictures that essentially describes the steps leading up to the translation of a "knotted" mRNA. So we know, with pretty great resolution where the mRNA molecule binds at each stage. It's like watching a movie of a biological process, or more accurately, a flip-book style animation. It's great. They used a technique called cryoEM which I won't get into today (maybe another time, or ask if you're interested), but it's basically the use of a very powerful microscope to look at things that are much, much smaller than the size of a bacterial cell (I'm talking millionths of a millimeter here). They use a clever trick to trap the various stages of the process so they can take these snapshots.

Ok, so why is this important? I guess one can argue for the general utility of a system that shows where substrates are bound to enzymes when they are going through their functional cycle. Drug companies like this kind of information because the drugs that they design are often inhibitors of these processes. Additionally though, translation of mRNA is a fundamental process in all organisms. If we want to ask ourselves "where did we come from?' we need to understand the biological processes that make us who we are. Some processes are specific to humans. Some are specific to vertebrates, and many still are present in all organisms from the simplest bacterium to us. Translation is one of these, and this means that it was probably one of the first processes to evolve and one that is critical to life, as we know it. Therefore understanding the details of such a process is critical to understanding ourselves. Being able to watch a critically important process take place is a major goal of biology. We aren't yet even near a stage where we can point a camera at a region of a cell and watch what happens, but this was a step in that direction.

First... Blog Post... Ever

2007-10-01T18:42:00.000-04:00

OK. I'm new to this game, so I'll start small. My goals are simple. I just want to talk about my opinions on various scientific/societal issues that may catch my fancy. As a graduate student I do a pretty hefty amount of reading, and I'm always trying to think of how best to pass this information to the general public in a not-dumbed-down but easy to understand way. Hopefully I can use this as a forum for trying out various styles and techniques for disseminating these all too important and sometimes hard to comprehend issues. And if anybody reads it they can let me know if I'm supplying anything useful. If so, maybe it will evolve into something interesting. If not, I'll kill it, and finish my PhD. Wish me luck!

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First... Blog Post... Ever

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