Back at Clashing Culture

It's been a little while since I've posted anything at the science and religion blog Clashing Culture. But my co-bloggers over there have kept the place free of cobwebs. I spent a little bit reacquainting myself for the ever-present creation vs. evolution issue this weekend. There's a Texas School Board meeting this Friday to decide science standards for the next 10 years. And of course, some last minute insertions by the board's chair have the scientific community worried that creationism will find its way into science text books... It turns out that the chair of the board Don McLeroy has written an anti-evolution book Sowing Atheism and calls clergy who accept evolution morons. Sounds like the typical anti-intellectual name calling that makes this issue so frustrating to folks like me who just want to get along. In not very related news, one of creationism's champions, Ken Ham, has taken to leveling hypocritical complaints about radio interview ambushes. Read more at Clashing Culture.

Read more about the Texas School Board issue here and the Clergy Letter Project here.

Pride

What! You haven't heard of pyroptosis?

It's the hottest thing in cell death!

Well, except for my wife...

Science News

Among many other strong choices for science advisers, it appears an outspoken advocate for curbing greenhouse gasses has been selected to serve as chief science adviser for the Obama administration. John Holdren, a past president of American Association for the Advancement of Science, had to cancel a meeting at Harvard to fly to Chicago. According to journalists who are familiar with these escapades, this probably means he is meeting with Obama about a job. The AAAS blog reports this, as does a NYTimes blog. About climate change, he says,

I am one of those who believes that any reasonably comprehensive and up-to-date look at the evidence makes clear that civilization has already generated dangerous anthropogenic interference in the climate system…. What keeps me going is my belief that there is still a chance of avoiding catastrophe.

Sounds pretty okay to me. He also was involved with Pugwash and was part of the crew that accepted a Nobel Peace Prize in 1995 for nuclear non-proliferation work.

What I want to know is if he will get an office IN the White House. You may recall that GWBush kicked his science advisers out in favor of them occupying space down the street.

More than Meets the Eye.

I love living in a world where this is news.

When the transformer malfunctioned, operating temperatures rose from below 2 Kelvin to 4.5 Kelvin -- extraordinarily cold by most standards, but warmer than the normal operating temperature.

Isn't this so much better than what's her name's what's it called?

Teenage Sex

In the past 16 hours, I've removed extensive perineal condylomas (laser ablation) from a 14 year old and removed a tubal ectopic pregnancy (laproscopic excision) from an 18 year old. Well, I "assisted" with the procedures... Ectopics occur in 2% of pregnancies, are fatal to the fetus and very dangerous to the mother. They must be removed ASAP - hence the call at 10:30 tonight. Genital warts are far more common. I think every human is infected with at least one of the more than 100 human papillomaviruses (HPV). Some of these viruses cause plantar warts, others are to blame for genital warts, yet others predispose women to cervical cancer. If you have an immune deficiency, the virus can turn you into a tree. HPV ranges from benign to deadly. (GUESS WHAT! There's a vaccine for the HPV's that most often lead to cervical cancer! If you're reading this, you're too old - you've already been exposed. But your 10 year-old-daughters haven't. Give them Gardasil. They'll thank you...)

But this gets me back to the point of this entry. Teenagers are having sex. Remember back in the '90's? There was lots of talk about safe sex, safer sex, harm reduction, and a catchy little phrase, "safe, legal and rare." What was the outcome of such openness? Some say there was hypersexualization of pop culture. Wait a minute... Wasn't it an earlier generation that subscribed to free love? Hmmm... It turns out that a concerted campaign to educate teens of the risks of sex and ways to make it safer ACTUALLY reduced the amount of sex teenagers had. Whoa...

Any scientist who's tried to publish the results from a new knockout mouse knows that showing an effect of the intervention is not enough. You need to also show the 'rescue.' Basically, turn the mouse back to the way it was before the change and see if the outcome reverts. Well, whadaya know? The last 8 years HAVE BEEN JUST THAT! Abstinence only, no talk of condoms, no pregnancy preparation no nothing with public money have all combined to flip the culture from the previous decade. That decline in age of first intercourse and encounter frequency stops. It's been in a holding pattern. Well, at least kids aren't having more sex... yet... Teen pregnancy is up this year (first time in 15 years!) and 1 in 4 teenage girls have an STD.

It doesn't take the chairman of the department of population and family health at Columbia University to point out that "abstinence education spends a good amount of time bashing condoms. So it's not surprising, if that's the message young people are getting, that we're seeing condom use start to decrease." But John Santelli went ahead and stated the obvious in a Washington Post article that got me all riled up after a day of medical treatment of the effects of teen sexuality. Sure, comprehensive sex ed will be blamed. (Hey, Jimmy! we sure learned some swell things in school today - you want to do some homework later?) Oh, and don't forget about R-rated movies. And the internet. And hormones. And those perverts at Planned Parenthood.

Humans cannot divide asexually. If we don't talk about the consequences of our species' tendency to rely on genetic recombination, someone else will. It will be your kids' doctors, delivering their babies or treating them for gonorrhea, HPV or worse.

"Just say no!" didn't work for drugs. It looks like it doesn't work for sex, either.

Let's talk...

Thinking Back On The Lab

My wife tells me I'm a hypocrite because I like reading PhysioProf's posts at his blog and at DrugMonkey. Those familiar with both PhysioProf and me immediately will know why. For everyone else: foul language usually makes me cringe.

One of the reasons I like reading his blog is that his insight reveals a connection with science, teaching and mentorship that I resepect. Exhibit A:

[One] thing to keep in mind ... is that by the time you reach the end-game of grad school, are finishing up the last few experiments, and are beginning to write the thesis, it is highly likely that you will be pretty much completely disgusted with the science underlying your project, life in the laboratory, and science as a career. This state of mind is a natural consequence of the grueling process of earning your PhD, and does not reveal anything particularly salient about how you really feel about a life in science.

It is similar to how Army recruits feel at the end of basic training: drained, exhausted, miserable, and wanting to quit. But this is no time to make life-altering decisions, such as leaving science for some other profession. As soon as the thesis is accepted, a huge weight lifts, and over the course of a few months, you begin to remember the joys of a life in science.

He sure hit the nail squarely, here. Except for one thing.

I'll let you know when the weight lifts.

Total Eclipse of the Heart

I mean moon. Total eclipse of the moon. And for West Coasters, it's at a reasonable time! 7:30 PM! Here's NASA's diagram explaining when to look on Wednesday night:


If you live in a different time zone, go to this page. 'Supposed to rain or snow in Spokane, so I'm not going to get my hopes up for seeing it this time. At least I witnessed the full lunar last August in Seattle.

Double Dipping

It's time for the Super Bowl, and you know what that means - you'll be going to a Super Bowl party. The folks over at ScienceBlogs are making a big deal about double dipping - you know, the socially scorned practice of going back into the spinach dip or salsa with a chip that you had already munched. Dr. Free-Ride, Greg Laden, OmniBrain and Tara Smith all have chimed in. Evidently there's a lot of bacteria that gets transferred in the mouth to chip to dip to chip to mouth pathway. 10,000 bacteria. That sounds like a lot. Or is it?

1) How many of those bacteria cause disease?
2) How many of them do you not have in your mouth already?
3) What's the equivalent transfer from multiple hands going into the same snack bag?

Frankly, I'd rather get someone else's mouth bacteria than their hand bacteria. Because you know what hand bacteria is the same as? That's right, folks: butt bacteria. And butt bacteria can cause real problems.

And there's one more thing. If you really want to stay healthy during the Super Bowl, don't bother with safe dipping. In this case, I advocate dip abstinence. What's in those dips? Mayo, cheese, sour cream, butter; this equals fat, fat, fat, salt salt salt. And that's before we consider the chip... Now I don't have any evidence behind this, but my hunch is that this stuff will kill you faster than the bacteria you'll pick up this afternoon.

Just say no to dips and chips. You'll avoid anxiety over bugs, and your waist will thank you.

Dear Reviewer,

Dear Reviewer,

It's only been a few weeks since we last wrote, and we've been talking on and off for a little while now, but I feel like I hardly know you. The space between us is so vast, sometimes I wonder whether our inter-continental attempts to communicate are lost. Your cut and paste letters arrive in my mailbox, dog-eared from forwarding and labeled with a baffling cipher. Even so, seeing the message awaiting my expectant eyes causes my heart to skip a beat. You surprise me every time - always waiting until I've almost forgotten about you to postmark your note. This roller coaster can't be healthy can it? I want to get on the page, reviewer. Help me to be on the same page as you.

When it comes down to it, you and I share a love. You know who I speak of. Beauty and Truth are her nicknames. Maybe you've had a few spats with her, too. For me, every time we make up and move on, she becomes more important to my life. I know I am just one small tool in her quest, but us together, my friend? We empower her! Without yours and my relationship, dear reviewer, she has no legs, no foundation. Her name means to split, to cleave; she is knowledge.

I don't mean to tell you how to be in this relationship. After all, I am many years your junior. Still in the cradle, really. And you! Where to begin? You have everything that I aspire to. The big house, the sweet toys, dutiful admirers... But think about when you were in my shoes. You know: with your name out in front. What was it that you needed from your young flings?

Do you feel the connection between us? You've already taught me a thing or two about life. But I have to admit: I want more out of our relationship. I'm going to make this easy for you. I want you to understand me in little chunks, so I am going to use that mainstay of my generation: the bulleted list.

• You would really help me out if you could write to me in paragraphs. Heck, I'd even take numbered lists. But a single long paragraph makes it hard for me to see you amidst the debris. It's like you don't have time for me or something.
  
• I've spent many sleepless nights of internal debate musing meaning, tense and commas; I get dressed up for you (but don't use too much makeup, just how you like); I even show you some of my vulnerabilities - the least you could do is use a spell checker. It would make what you write so much sweeter.
  
• You talk about yourself too much. Sometimes it's like you didn't even listen to me! I know that J. Doe et al did groundbreaking work. That's why I referenced two of their papers. You want another one referenced? I can do that for you. That's how much you mean to me.
  
• I sit at home reading every word of your letters. Take for example the time you said I looked like I was stained with weak grape juice. That really hurt. But I got through it. Acting on the wisdom of your comment, I actually made a discovery. (See figure below. Click to enlarge.) I never did hear what you thought about it. Am I to take this as an answer? Maybe we should both put this behind us.
  

• Why do you have to be so schizophrenic? First you love me. Then you hate me. Then you think you might go to a movie with me, but just as friends. What gives?

Please don't take offense to these comments and questions. It's just that I don't want you to be like my past reviewers. They seemed like mere flings compared to you. I feel like you and I have a special connection. We have the potential for real growth. If this doesn't work out between us, I just don't know if I can take any more rejection. I might have to turn away from it all. Maybe I'll take a vow of abstinence. You know as well as any how that may turn out badly.

Sincerely,

The Author

Science Then And Now

Have any of you encountered the creationist tracks extolling the Bible as a scientific text? In one I was recently referred to, evangelist Ray Comfort presents a perspective of science then and now to show just how well our knowledge today was predicted by the Bible. If you promise to read them all, I’ll offer some ideas about Biblical science. Keep in mind that my personal perspective is as a Christian and a scientist who sees very little in conflict with those positions.

1. THE BIBLE: The earth is a sphere (Isaiah 40:22). SCIENCE NOW: The earth is a sphere. SCIENCE THEN: The earth was a flat disk.
2. THE BIBLE: Incalculable number of stars (Jeremiah 33:22). SCIENCE NOW: Incalculable number of stars. SCIENCE THEN: Only 1,100 stars.
3. THE BIBLE: Free float of earth in space (Job 26:7). SCIENCE NOW: Free float of earth in space. SCIENCE THEN: Earth sat on a large animal.
4. THE BIBLE: Creation made of invisible elements (Hebrews 11:3). SCIENCE NOW: Creation made of invisible elements (atoms). SCIENCE THEN: Science was mostly ignorant on the subject.
5. THE BIBLE: Each star is different (1 Corinthians 15:41). SCIENCE NOW: Each star is different. SCIENCE THEN: All stars were the same.
6. THE BIBLE: Light moves (Job 38:19,20). SCIENCE NOW: Light moves. SCIENCE THEN: Light was fixed in place.
7. THE BIBLE: Air has weight (Job 28:25). SCIENCE NOW: Air has weight. SCIENCE THEN: Air was weightless.
8. THE BIBLE: Winds blow in cyclones (Ecclesiastes 1:6). SCIENCE NOW: Winds blow in cyclones. SCIENCE THEN: Winds blew straight.
9. THE BIBLE: Blood is the source of life and health (Leviticus 17:11). SCIENCE NOW: Blood is the source of life and health. SCIENCE THEN: Sick people must be bled.
10. THE BIBLE: Ocean floor contains deep valleys and mountains (2 Samuel 22:16; Jonah 2:6). SCIENCE NOW: Ocean floor contains deep valleys and mountains. SCIENCE THEN: The ocean floor was flat.
11. THE BIBLE: Ocean contains springs (Job 38:16). SCIENCE NOW: Ocean contains springs. SCIENCE THEN: Ocean fed only by rivers and rain.
12. THE BIBLE: When dealing with disease, hands should be washed under running water (Leviticus 15:13). SCIENCE NOW: When dealing with disease, hands should be washed under running water. SCIENCE THEN: Hands washed in still water.

This list is a clever attempt by certain Creationists to claim the Bible as scientific. This doubtless is a rhetorical tactic in the effort to confer legitimacy to the Genesis accounts of creation. There are two main problems with this presentation: 1) Science did not exist until the sixteenth century and 2) The Bible is not a scientific text.

At the foundation of each of these claims is that science is not merely about predictions. Science combines innovation and idea with a rugged process of hypothesis testing and repeated fine-tuning to formulate a theory that when applied to unknown situations can explain them to the best of our ability. Unlike Ben Stein’s perception of science as a static entity unchanged since the days of Charles Darwin, elements of science are always in flux.

Right – my points:

1. The SCIENCE NOW/ SCIENCE THEN dichotomy is flawed most simply because the world view in the ancient world was not scientific. Sure there were glimmers of it all over the ancient world – Egypt, Greece, South America, India, China, Arabia – but the progression of thinking of something, testing it objectively and using the results to formulate predictions just hadn’t come around yet. Humans were stuck describing, categorizing and guessing. (This, by the way, worked pretty well for us most of the time.) It is as unfair to claim the then prevailing world-views as science then as it is to claim astrology as science today. Each has made predictions about the world, but only science as we know it today can be tested. (Also recall that ‘science’ wasn’t even a commonly used word until the early 19th Century!)

2. The Bible is not scientific. If it were, the writers would have incorporated those flawed (SCIENCE THEN) explanations into its stories. The world would not have been created in six days; it would have been vomited by a scarab. I admit, this second point is not as strong. It actually makes me sound like I’m in a “Yes it is/No it’s not” argument. Even so, I don’t think I have written enough recently of my opinion that the Bible is not a scientific text. The absence of there even being science when it was written aside (see point 1, above), few in Christendom or the Jewish or Muslim worlds would identify these texts as scientific. What else was there to describe in these verses but items in the natural world? Referring to rocks does not make your novel a geologic text. Even the references cited in the list above are oblique references to physical phenomena. Check out the Job 38:19-20 text. I’m pretty used to sorting out metaphors in the Bible; maybe that’s why identifying these verses as referring to the propagation of light was so hard. By the way, in this section of his trials, God is speaking to Job in the midst of a terrible storm. It is often interpreted as emphasizing the power of God and the finite knowledge of man, both in the ways of the world and the ways of Heaven.

These are my raw thoughts on this matter. If I didn’t have to study up on anemia and GI disease tonight (how appropriate!), maybe I could formulate some more succinct arguments. I guess I will have to leave some of that up to you, dear reader.

Big hat tip to Tangled up in Blue Guy.

SMFPNIS For Two Days In A Row!

Science is big news in Spokane! This picture of molecular anthropologist Dr. Brian Kemp made a splash above the fold on the front page of today's Spokesman Review. Using molecular techniques he devised as a graduate student at UC Davis, he has established the age of native peoples in the Western Hemisphere to exceed 15,000 years. Check out the Discover Magazine story, or the original report in the American Journal of Physical Anthropology. The story in Spokane's paper was to feature how prominent Washington State University is becoming on the national research scene. He actually did the work as a post-doc at Vanderbilt. It seems as though he is setting up a new lab at Wazzu.

If Seattle's papers would stop trying to pick apart the University of Washington for animal research policy, human subject trials and medical mistakes and focus on the positives of having a world class university in the backyard, maybe it would be easier to fund higher education in this state.

Wondering about the acronym in this post's title? Go here.

Too Legit To Quit?

How long can a newly minted PhD last without having a first author paper to his name?

Evidently, about 3 months...

Robey TE, Murry CE. Absence of regeneration in the MRL/MpJ mouse heart following infarction or cryoinjury. Cardiovasc Pathol. 2008;17:6– 13.

The text is available with subscription here. Email me or post a comment if you would like a .pdf.

This is the lead article in the first issue of the 2008 volume of Cardiovascular Pathology. Who says you can't publish negative results? If you recall, there was a bit of a splash earlier this decade about a funny mouse that could (amazingly!) regenerate its heart after injury. To catch up about how this over-hyped story has played out in the last 7 years, read this nice review.

It took a year for this to go to press after it was accepted, hence the lag between earning the PhD and being published. There are more on the way, hopefully including a pair I polished up for submission last Friday. But none will receive the fanfare I afforded this one. There is just something special about the first time.

As far as the post's title, what's up with PhD students slaving in the lab for years and then deciding not to pursue a career in academic science after all? I don't know. Check back with me in a couple of years.

Science and Peace

Did you hear? Science won the Nobel Peace Prize this year.

The Nobel committee said that Al Gore “is probably the single individual who has done most” to create worldwide understanding of what needs to be done to halt the damage caused by greenhouse gas emissions. With this award, the committee also implicitly support the positive role of science in decisions made abut mankind's future.

Way to go, Al!
Way to go, science!

Pondering Placebo

Here's a brainteaser for you:

You are skeptical about the efficacy of an alternative medical treatment. In fact, you believe said treatment works through the mechanism of the placebo effect. You do, however, accept the physiological reality of placebo. Indeed, you have the feeling that placebo is a legitimate therapeutic modality - a sugar pill works better than not doing anything at all. If you persist using said alternative medical treatment to gain the desired effect of placebo, is this cure still a placebo?

Anyway, I used this logical twist to convince my wife to try the generic version of Airborne. Evidently, if it wasn't invented by a schoolteacher, it costs $3.00 less for 120% of the doses. Then I asked the same question of the checker. He brought it upon himself by pointing out that we were trying the generic... Now he's thinking, "What a nerd."

Soooo Different

Wow.

Medicine is way different from science.

Details later...

Not Too Late

If you are reading this real time, which according to my Sitemeter, means there will be 3 or 4 of you, here is the information about when to view tonight's lunar eclipse from the West Coast. Click on the image below for all sorts of information.Other time zones stats are here. What a great chance for a break. And there are no clouds in Seattle right now! I'll see how my new nifty little point and shoot digital camera holds up to a mooning.

Thank Bora for the link!

Chris Mooney at YearlyKos

UW's Forum on Science Ethics and Policy is bringing ScienceBloggers Chris Mooney and Matt Nisbet to give their Speaking Science 2.0 talk in Seattle on October 5. Mooney is on a book tour for Storm World. He also recently participated in the YearlyKos Science Blogging panel in Chicago. The talks were televised on CSPAN and posted to YouTube. Chris has embedded his full talk from that event in three clips up over at his blog. Some of these same topics will probably turn up in the October 5 talk in Seattle, but don't let that keep you from turning out for their free, live and in person presentation at the Pacific Science Center.

Post Wrong About Stem Cells

There is still a long way to go to educate the public about embryonic stem (ES) cells. In yesterday's Washington Post election blog, John Solomon (a Post staff writer) made a blatantly false statement about ES cells. He wrote,

Many religious conservatives, including President Bush, oppose the scientific use of embryonic stem cells because the cells often come from aborted fetuses.

Right... Does a journalist have to be a science writer to check his facts? Here is the truth of the matter: Embryonic stem cells NEVER come from aborted fetuses. They are derived from 5-day old blastocysts generated in the context of in vitro fertilization clinics. This embryo has never been in the uterus, and is a ball of about 100 cells. A correct replacement sentence could be: Religious and other conservatives object to ES cell use because they cells taken from a structure that occurs 5 days after fertilization.

I wonder how widespread this misconception is.

Civic Scientist Role Model?

I want to be like this when I grow up. So excited about science! So talkative about science! As a bonus, Neil deGrasse Tyson blows Jon Stewart's mind.



I particularly like, "You carve through what is known and you come to this precipice between what is known and unknown, and that is where the research scientist lives."

Special K: Cures What Ails Ye

Ketamine is an injectable drug used in anesthesia that works by blocking the NMDA receptor in the brain. It is known on the streets as "Special K" because of its dissociative and hallucinogenic effects. (You're removed from pain and worries and see crazy stuff.) I use ketamine in the lab for rodent sedation and pain reduction.

A recent press release from the NIH, reported by Science Daily, announced a newfound effect of this drug: anti-depressant. Evidently one sub-anesthetic dose reduced the symptoms of depression in patients resistant to all other anti-depressant therapies. The effect was not trivial. From the NIH press release:

Depression improved within one day in 71 percent of all those who received ketamine, and 29 percent of these patients became nearly symptom-free within one day. Thirty-five percent of patients who received ketamine still showed benefits seven days later. Participants receiving a placebo infusion showed no improvement.

That is something else! Due to its status as a controlled substance and the hallucinogenic side effects, it may be a while before this treatment gets approved. It is exciting none-the-less that there could be an entirely different approach to treating depression.