A non-designing woman

Before I get into that, I hope you’ll send positive thoughts to my dear Cousin Shane. His awesome Dad, John, passed away yesterday. You all know that I love Shane like a brother, and it pains me to see him hurting. John loved road trips, cars, and Route 66. I wish him pleasant travels. Be careful on the highway out there. (One of his favorite things to say to Shane.)

In the interest of not letting myself fall back into the abyss of sadness, I will try to keep my mind occupied by writing a few things about the documentary I watched yesterday afternoon before I got Shane’s phone call. My friend Darren recommended it to me, and I can tell you that it is well worth watching.

“Judgment Day: Intelligent Design on Trial” was a Nova episode on PBS. It deals with the Kitzmiller vs. Dover trial in 2005 in which concerned citizens brought suit against the school district for trying to insert intelligent design into the science curriculum. (The link is the Wiki article, which is pretty good and jibes with what I saw in the documentary.) I recall reading and hearing about this, but didn’t pay close attention at the time. I suppose I probably felt that it was a no-brainer, not realizing how much sway the equal-timers had upon our school districts.

To sum up: a couple of fundamentalist Christian school board members decided that teaching evolution in science class wasn’t giving the students the full picture. When their proposal of an additional textbook promoting intelligent design was rejected, they took matters into their own hands and secretly purchased the textbook from the Discovery Institute, a conservative think tank that advocates for the teaching of intelligent design (AKA creationism) in our high schools. A battle of wills ensued, in which the science teachers refused to add ID to the curriculum, the superintendent required that they read a statement stating that evolution was “only a theory” that had significant gaps, and that some see intelligent design as an alternative possibility; the teachers refused to read the statement, so the assistant superintendent came into their classrooms and read it to the students.

As concerned parents got wind of this from their kids, one of them called the ACLU, and we were off to the races! This was a battle that had continued to brew after the Scopes trial of 1925, with many people refusing to accept the exclusion of creationism from the science classroom. (Eight decades, America? Really? Really?!) There was no jury here; it was heard by district court Judge John E. Jones III, a conservative appointed by George W. Bush, and his decision would be the final one on the case.

The plaintiffs presented a stellar group of witnesses, several scientists explaining the basic premises behind evolution and how scientific experimentation has supported the premise. Not only did they explain the science behind it, they explained how scientific inquiry itself works. In even more devastating testimony, they demonstrated that the ID textbook that had been sent by an “anonymous donor” to the science classrooms came from the Discovery Institute, and they showed that earlier drafts of the book had used the word “creationism,” which was altered in subsequent versions to read “intelligent design.” In other words, the concept was still the same--a religious one--and all they had done was change the phrasing. In yet more devastating testimony, they provided statements from a conservative advocate saying that the problem with the intelligent design movement was that they had no theory; if they were going to promote ID as an alternative to evolution, they had to come up with one.

In the most devastating testimony of all, they showed one of the fundamentalist school board members stating on camera that “creationism” needed to be taught alongside evolution, which showed that there was clear religious promotion there. Worse, they caught both of the fundamentalist school board members perjuring themselves when they said they didn’t know who they “anonymous donors” were; they had orchestrated the entire thing, and one of the board members’ fathers had written the check.

The defense countered with experts of their own, but their arguments were meticulously destroyed by the lawyers for the plaintiffs. The concept of “irreducible complexity” (which posits that there are some biological systems that are so complex that there is no function if one part is missing...the example of bacterial flagella was used, and was refuted) was discussed and proven wrong; one witness’s statements that no scientist has bothered to research or write about the complexity of our immune system was discounted in a very graphic way when he was handed numerous papers and a stack of textbooks that dealt with exactly that subject matter. The dismantling of every argument put forth about why ID is a legitimate scientific endeavor was a beautiful thing to see.

Judge Jones took some time to deliberate the case, and found that ID was not a scientific theory, and was, in fact, just another name for creationism. As a religious concept, it has no place in the science classroom. He also found that the two school board members violated the First Amendment in the Constitution by promoting a religion in the classroom. He also noted that the board members who had perpetrated this ID promotion because of their religion seemed to have no qualms about repeatedly committing perjury.

The whole documentary was excellent (if you have a couple of hours, and want to see more about the arguments put forth, I really recommend it), but there were a couple of things that I found of particular note. The witnesses for the plaintiff took particular pains to address the usual complaint of creationists that “evolution is just a theory.” (I’ve encountered that argument often, myself.) A quote from “The Princess Bride” is applicable here. Theory...“I do not think it means what you think it means.” A scientific theory is not an immutable fact; it is a body of thought that maintains, like all science does, that there may be modifications as more is discovered. Evolution is an ongoing investigation. Nothing has appeared to refute its claims, but more and more evidence is being found that confirms it. The scientists at the trial pointed out that the advent of molecular techniques, some of the most sophisticated tests to date that can provide incredibly detailed information, have only confirmed the theory of common ancestry. If anything were to disprove evolution, it would be looking at encoded information on a genetic level. Instead, we are finding incredible similarities between our own genetic code and that of other hominids, especially chimpanzees.

Speaking of that, another thing that creationists like to toss out is “I don’t know about you, but I didn’t descend from no ape!” Not only is that grammatically incorrect, it shows a complete ignorance about the entire concept. I shouldn’t have to say this, but I suppose I will: evolution is not a straight stick poking up out of the ground, with one-celled organisms at the base and us brilliant humans (ha) at the top. It is a tree with many branches. There have been many twists and turns along the way, with offshoots happening constantly over the millennia. Genetic mapping continues to show the similarities and where divergence took place.

After his decision, Judge Jones was accused by conservative groups of being an “activist judge.” Remember, he was appointed by GW Bush. He and his family received death threats, and one of the fundamentalist school board members said the judge is a “jackass.” Doesn’t that old-timey religion just make you feel all warm and fuzzy?

Finally, the documentary showed a local pastor who said that he was “personally offended” that the kids were being “indoctrinated” with evolution, without hearing alternative viewpoints. If you want your kids to hear alternative viewpoints, go ahead and teach them that at home. Your alternative viewpoint is not a valid scientific theory. It is based on your religious beliefs, and as such, has no place in the science classroom. As for you being “personally offended”...cry me a river, dude. The Constitution guarantees us all certain rights. The right to not be offended isn’t one of them. Get over it, and keep your religion out of my science.

There’s a vacancy in the handbasket

Did anyone catch the story over the weekend about the Methodist minister in North Carolina who lost his job? Apparently, he’d posted something on his Facebook page in support of a book coming out soon, in which author Rob Bell takes issue with the usual dogmatic view of Hell. That didn’t sit well with the higher-ups in the church, and Chad Holtz is now looking for a job.

I do realize that there may be more to the story; Holtz wrote more about his feelings on the firing, but went into no details. He wasn’t upset by the firing, just said that he wasn’t able to take the parishioners in the direction they needed to go. I looked him up on Facebook and sent a friend request. It seems that quite a few other people had the same idea, and he has hundreds of new friends, the majority offering support. (Of course, there was the usual contingent of the “You’re going to burn in hell” folks.) I left a note saying that although we don’t have the same belief system, I applaud his willingness to question.

Some of the subsequent posts I’ve seen mention his faith, his continuing studies, and his morning prayers. As I’ve said here often, I have no problem with what people want to believe, as long as they don’t get all up in my business, as long as they keep it out of my government, and as long as they don’t harm others with their words. But I can’t help but wonder....

If he took the big step of questioning one of the tenets of his faith, that of the existence of the biblical version of hell, why did he stop there? If his readings, ponderings, meditation, and prayer let him to doubt the veracity of people being cast into the Fiery Pits™, why not keep going and begin to question some of the other dogma that he subscribes to? If I were him, I would also think seriously about why his church was so unhappy with his thoughts on the matter that they saw fit to remove him rather than answer the question or discuss the topic.

I suppose I already know the answers to those questions, though. I know how very hard it is to break out of something that you’ve believed all your life. I know how questioning things that you’ve taken for granted because of blind faith can lead to a dramatic shift in how you view the world around you. I know it’s difficult to be different. And I know that if there’s one thing the church--any church--hates, it is people asking questions that aren’t easy to answer, and people who won’t toe the party line. Anyone who dares to question, or points out the contradictions, errors, and inadequate explanations in whatever holy book happens to be in question, is viewed as someone to be distrusted and silenced. That in itself makes me wonder about the legitimacy of the organization. If you’re afraid of questions, maybe your dogma isn’t all that great to begin with.

I’ve never been what you might call docile. I’m often quiet and shy (it’s true!), but if something doesn’t make sense to me, I’m going to ask questions...and I want answers. If your answers are inadequate, I’ll wave good-bye and go merrily along my way.

I am glad that Pastor Holtz dared to question, and dared to go public with it. I hope he doesn’t stop asking questions, both of his church and of himself. It might lead him to a place he’d never anticipated.

Beth’s Books

I don’t intend to turn this into a book blog—you all know I’ve got more interests than just that—but I’ve read a couple of good ones recently and wanted to write about them. They both have to do with politics, so that’s in keeping with one of my favorite subjects!

First is The Great Derangement by Matt Taibbi. I first became familiar with Taibbi as a columnist for Rolling Stone, when my friend Darren recommended his writing to me; one of Taibbi’s most memorable articles there dealt with the tea partiers. Taibbi’s style is irreverent and, to borrow a word most often used with another RS writer, gonzo. The subject of this book is twofold. He writes about our broken political system, in which our politicians follow the money and influence. Public airing of legislative procedures on C-SPAN is usually limited to important things like renaming post office branches; the big-ticket stuff goes on behind the scenes, in late-night meetings, with little public discussion. Taibbi is obviously left-leaning, but he shares equal contempt for the politicians of both sides.

I try to stay engaged and informed when it comes to politics, but it’s disturbing to think that my participation matters very little in the process. I’m not going to relinquish my right to vote, and I’m not going to become overly cynical about politics in general. It’s easy to do that, and the truth of the matter would probably lead any halfway intelligent person to that conclusion. But simply opting out is not a viable alternative to me. It’s still discouraging to think about just how much corruption is taking place, though.

The other subject matter I found even more fascinating. The heathen Taibbi decided to check out the fundamentalist evangelical faction by going undercover and joining Pastor John Hagee’s church in San Antonio. You might remember Hagee as the guy who said that Hurricane Katrina was God’s punishment on a New Orleans that embraces and celebrates homosexuality. Yeah, that guy. I found Taibbi’s experience to be fascinating. I wasn’t really surprised at any of the dogma expressed by those in the church; I’ve heard plenty of similar things throughout my life. I suppose I found it fascinating because I’ve heard it all before. It’s the party line.

Taibbi participates in a weekend getaway with the church. He progresses far enough up the ladder to be invited to a workshop about how to witness to people, and joins two other church members in a rather embarrassing visit to a mall to evangelize. One exchange that I found particularly amusing is when Matt role-plays with the group leader in learning about how to talk to people about the good word. When the group leader asks him if he feels that God would judge him according to the ten commandments, Matt says it’s an irrelevant question because he doesn’t believe in God. When the group leader protests that it’s written in the Bible, Matt says he doesn’t care, because he doesn’t believe in the Bible. This throws the group leader for quite a loop. Matt says, “I’m just repeating what non-believers might say. That’s all.”

In a previous life, I recall having discussions with someone who just kept quoting scripture. I said something to the effect of, “Can you please just talk to me and tell me what YOU think, rather than quoting scripture at me?” He couldn’t do it. He was so far up the ass of the church he’d joined that he just couldn’t stop the conditioned response and rote regurgitation of what what being fed to him. I found Taibbi’s conversation so fascinating because it’s interesting to see how people respond to someone telling them that not only do they not believe that the Bible is the literal word of God, they don’t even believe in God. It seems to really perplex them...like it is just so far outside their realm of possibility that they just can’t wrap their minds around it.

The book ended on a rather sad note. After heading back to New York, he eventually came back to San Antonio to have lunch with one of the women that he’d become friends with in the church. She was having a hard time, because she was wasn’t fitting in at the church...she didn’t know how to play the political games there (and just like any place that involves a large number of people, there ARE political games), and she wasn’t feeling accepted. (I’ll have more to write on this topic soon.) Anyway, Taibbi is an excellent writer, and this is an excellent book. Highly recommended!

Next was Game Change by John Heilemann and Mark Halperin. This was an account of the presidential primaries for the 2008 election, and the election itself. Like many of you, I followed that election very closely, and I remember so much of what is discussed in this book. Sometimes verbatim. The title of the book comes from how seemingly small things loomed large in this particular race, and ended up being game changers. A phrase, a look, an indiscretion, a misspoken word, a wrong note struck. A vice-presidential pick that came as a complete surprise, and after initially firing up the base, went horribly awry.

This book is worth a read just for the chapter that deals with McCain’s choice of Palin as his running mate, and his campaign’s attempts to...dare I say it? Yes, I dare. His campaign’s attempts to put lipstick on a pig. Inadequate vetting and a candidate unwilling and perhaps unable to learn the basics of what she needed to know were a recipe for disaster. I don’t take this book as the full truth, but based on everything I’ve read and what I’ve seen of Palin, I know that this woman doesn’t belong anywhere near the White House. When McCain chose her, I felt that he was pandering to the conservative base and attempting to garner female voters, and I condemned him for making a purely cynical choice; I still feel that way, and I still feel that he traded what little honor he had left in order to make a last-ditch attempt to get votes. If he truly thought that she was capable of being the leader of the free world if something happened to him, it shows what a doddering old fool he is, and that he put his victory in November above his country. I’ll just say it outright: if you think Sarah Palin is capable of running this country, you don’t have its best interests at heart. Neither did McCain.

Halperin and Heilemann aren’t lapdogs for the Democrats. They speak of Obama’s sometimes overwhelming arrogance; they speak of Clinton’s poorly managed campaign and the harm that President Clinton inflicted upon it; John Edwards’ all-too-human failings are examined, and Elizabeth Edwards’ irrational behavior is addressed.

I suppose that much of the book was political gossip, but I read enough during that campaign to know that it wasn’t far off the mark. It was a fun and interesting read, and an enjoyable reminder of what was truly a historic and game-changing election. I think it had a happy ending, too!

Tell ‘em how it’s done, Ted

Thursday evening, I was very pleased to attend a lecture given by journalist Ted Koppel. He’s well-known for his amazing hair, and I was delighted to find out that he’s much more than a pretty ‘do.

He began by talking about how he wanted to conduct his lecture and subsequent question and answer session in a way that we seem to have lost lately...he wanted to have a civil discourse. He bemoaned the lack of civility in the current atmosphere of discord and hatred, and he seemed to transcend party politics, showing that it IS possible to be a voice of reason in an unreasonable world.

He spoke at length about the state of journalism today. When he started out, news divisions were not moneymakers for the three networks. It was a given that they would lose money. They operated under the credo of reporting what people needed to know. Matters of importance to the national interest, things that they deemed worth knowing. They felt they were providing a certain level of public service, and reported accordingly. With the advent of “60 Minutes,” the networks realized that news could make money, and that’s when things changed. Instead of giving the people what they needed, they made the shift to giving people what they wanted. After all, ratings meant money, and if people wanted lighter news and entertainment stories, they drove the ratings. He gave the obvious example of the news cycle last week: Libya, our budget crisis, the devastation in Japan...and what was the number one news story? Charlie Sheen, of course. He seemed saddened by this, and so am I.

This was a fairly conservative crowd, but Koppel pandered to no one. He said that FoxNews is obviously biased and partisan...but so is MSNBC. He said that talk radio is most definitely not journalism, said that NPR is great journalism (with a full disclosure that he does occasional work for NPR) and we must continue to fund this national treasure, and that the New York Times is the best newspaper in the world (while admitting that there would be some there who disagree and think the NYT is far too liberal). He talked about the travesty of not raising taxes in a time of war, saying that it was negligent to go to war without funding it by raising taxes, and that it has never been done in our country until now.

He spoke at length of what is going on in Libya, and had some thought-provoking questions. If our goal in Libya is a humanitarian one, why didn’t we intervene in Sudan? The Congo? Ivory Coast? Millions are being slaughtered in these places, so why did we not stop those regimes from killing their own citizens? His point was that there is always more to the story, and there are always national interests that might not be expressed overtly. He illustrated this with a story about a supposed conversation between Charles DeGaulle and David Ben Gurion. Some argument or incident occurred, and Ben Gurion told DeGaulle, “I thought you were my friend.” DeGaulle replied, “Men have friends; nations have interests.”

Someone asked him a question and said that it seems that Israel is our only friend in the middle east. After the questioner rambled on a bit longer, Koppel began his response by saying, “I’m going to have to disagree with your basic premise there, about Israel being our only friend in the middle east.” He went on to say that we may not like everything that certain nations do, but when it comes to diplomacy, friendship is a relative term. After all, the Shah of Iran was our good buddy for quite some time, despite his oppressive regime; when the people finally gave him the boot, we ended up with the Ayatollah Khomeini. He brought up the point that although we may get rid of Mubarak in Egypt, or Qaddafi in Libya, we have no way of knowing who or what will replace those regimes. Will they be friendly to us? We don’t know that yet. He said that we seem to think that democracy just somehow magically happens, but it is actually a long, drawn-out, and often bloody process.

I thought he struck a very realistic note about international diplomacy. It’s not always black and white, and we walk a fine line between helping people and intervening in their affairs. (I’m reminded of the Star Trek Prime Directive.) In our current situation, it’s very easy for anyone not in the President’s shoes to be talking about what they would or wouldn’t do. I suspect that any of us in that situation would struggle with the decisions that need to be made, and not make any of them lightly.

One thing that Koppel mentioned several times was that we “need to be informed.” It’s a complex world out there, with complex problems, and as citizens, we need to pay attention to what is going on out there. Although he didn’t say this, I’ll continue the thought. There is nothing wrong with being entertained. I think we all need that if we want to keep our sanity in an increasingly insane world. I enjoy my books, my music, movies, TV shows...but balance that with knowing what is happening in your community, your state, your country, and your world. It belongs to all of us, and we owe it a little more attention than we do some drug-addled pseudo-celebrity’s latest shoplifting spree or coke-fueled Vegas party weekend.

I enjoyed his lecture immensely. Ted Koppel is a class act, and we are all better informed because of him. He worked hard to do his job for many years, and he inspired me to continue to work hard at being informed.

What have I become?

No, I haven’t become Sarah Palin. [shudder] When I got up yesterday and started checking some of my feeds, I saw on one that Sarah Palin’s speech in India was going to be livestreamed. I was still waking up, not ready to go out and workout at the moment, so I thought what the hell? It was starting right then, so I popped on over to the site to watch a few minutes of it. I figured I wouldn’t be able to last more than about ten minutes, but I ended up watching the whole stupid thing! Why, and how, and what is wrong with me?!

The why and how is because there were a few like-minded individuals there, and we started having a pretty good time laughing at Palin. (I even made a new Facebook friend out of it!) Now, the live chat consisted mostly of Palinbots who think she’s beautiful and smart and the next President of the United States, and they obviously didn’t care much for me and my wisecracking new pals. They started calling us trolls, and I’d be lying if I said that didn’t give me pause. I thought about it: Am I a troll? Am I one of those mouth-breathing, window-licking obsessives who love nothing more than to stir up trouble and hurt others?

I really didn’t have to think about it for long. The answer is no. I went there with the intention of listening to Palin’s speech and perhaps finding some blog fodder (which I did!). This was not any sort of conservative site dedicated to praising Palin (like Palin's own Facebook page is). This was a site from India that was livestreaming the speech, and I had every right to be there. I also had every right to criticize Palin and her speech, and I did that. I didn’t make my attacks all that personal, and probably the worst thing I said is a line that I used on Facebook some time ago, saying that her jacket looked like the lining of a whore’s coffin. (I cracked myself up on that one!) I made several comments about things she said in her speech…many of the things she said were just generally stupid and outrageous. Her speech was typically tortuous and twisted, full of run-on sentences that, when she stops speaking, make you go, “What the fuck did she just say?” In short, nothing new. Except for one thing that I’ll get to in a moment.

I wasn’t there to attack any of the Palinbots, and I did not do so. I attacked Palin, yes. This was not a Palin site, this was a site that was open to all, and to all opinions. I didn’t just get called a troll, though. When the guy introducing Palin said that a poll showed that she was the frontrunner in the Republican primaries, I wondered what poll, because none that I’ve read recently show her as the frontrunner at all. Quite the opposite. She’s tanking. Even plenty of Republicans don’t want her to run. One of the Palinbots wrote this: “Beth shove a poll up your a$$, then you’ll know what poll.” Haha! I was like, “Really? Shove a pole up my ass? No thanks, it’s not even noon here yet.” The person had a snappy comeback: “Better a poll than your fist.” What does that even mean?

Another person apparently looked up my profile on Facebook, because he asked, “Beth, what did you think of the most pro-abortion president in history speaking at ND?” I didn’t take the “pro-abortion” bait. I mean, really, who is “pro-abortion?” I’m not. I’m pro-choice. I don’t think our President or anyone else is wanting more women to have abortions. (Of course, if the Republicans get their way and strip funding from Planned Parenthood, that’s exactly what they’ll get. But that’s a topic for another day.) I merely said that I thought it was a great speech and it was an honor to have the President in my town. I didn’t mind the question, because it wasn’t asked in a nasty way, so I answered it honestly and respectfully. There were comments about President Obama “vacationing” in Brazil, and there were really lovely comments about Michelle being a “fat skank.” I think some comment was made about their daughters having abortions, but I don’t recall exactly what it was.

I insulted no one there except for Palin, and I really wasn’t that nasty with her. I honestly despise the woman and I think she’s an idiot, and I was laughing at the stupid shit that she said. I don’t think that makes me a troll. Just someone who thinks Palin is an idiot. There are actually quite a few of us who feel that way, Palinbots, and if your “gal” decides to run, you’ll encounter a lot more of this, and much worse than what I gave you yesterday. I found it astounding to see the vitriol directed against the President and his family (there was also some directed against Palin and her family, but that wasn’t coming from me), especially his “taxpayer-funded vacation to Brazil.” Somewhere along the line, it seems that diplomatic trips by the President of the United States became a deplorable thing, and I get the impression from these people that they think it’s a matter of the welfare family in the bad part of town—and oh yeah, they’re black people, doncha know—sucking the country dry in order to have their fun gallivanting around the world and eating like pigs. And they wonder why we think they’re racist. Has anyone ever seen a bunch of people so pissed off about any other President taking trips overseas, meeting with foreign heads of state, and attending or giving state dinners? Yeah, me neither. There’s a reason for that, and it’s quite obvious to me.

Back to Palin’s speech. What is probably getting the most attention from the media is something she said in response to a post-speech question about China.

I personally have huge military concerns about what is going on in China. What's with the build-up? You don't see a tangible outside threat … to that country. Is that just for a defensive posture? How can that be? Stockpiling ballistic missiles, submarines, new-age ultramodern fighter aircraft. It certainly means America needs to be vigilant looking at what China is doing.

Gee, what other country has no tangible outside threat, but stockpiles weapons and spends more than any other country does on their defense budget? What country is currently in the midst of TWO WARS, and now possibly beginning a third? Which country might that be, Sarah? Holy fuck, what a goddamn idiot. (I couldn’t help but laugh at the “new-age fighter aircraft” remark. Are new-age fighters powered by crystals? If they THINK of the missiles as fired, do they fire?)

Kanwal Sibal, former foreign secretary and columnist in India, said this about her statements concerning China:

I am surprised at her openness when speaking about the Chinese threat, especially when she is on Indian soil. China will not fail to notice this.

So thanks a lot, Palin. You have no official capacity as an American agent; your “job” is as a ClusterFox commentator, you give rambling speeches that make little sense, and you and your ghostwriter Mansour have sold some books. You travel to another country and make careless remarks about a country with whom we walk a fine line when it comes to debt and humanitarian concerns. Let the diplomats deal with such matters. Let those who were duly elected work on these things. Write your little Facebook notes—excuse me, post the little Facebook notes that Mansour writes for you—and for the sake of the world, shut the fuck up.

And oh yes...please run in 2012!

Infection Connection: PCR

First of all, thanks to everyone for their kind words of support. Things are definitely rough lately, but we all get by with a little help from our friends. Thank you.

I got a book shipment today, and it’s always fun to open up that box and pull out book after book of fun stuff. (One of the places I order from is Edward R. Hamilton, a place which has overstocks and closeouts. What is really cool is that if you send in your order via snail mail, using a check, it’s a flat-rate $3.50 for shipping. In this shipment I got nine books, at an average of $5 per book. What a deal!) This time I ordered from their Science and Nature catalog, and I found some good ones about Microbiology:

• Emerging Epidemics: The Menace of New Infections
• The Secret Life of Germs
• Good Germs, Bad Germs
• Case Files: Microbiology
• The Life and Death of Smallpox
• Vaccine

They all look pretty good. I skimmed through the Case Files one (I always loved the case studies when doing continuing education at the lab) and I was still able to figure out most of them (or at least be in the ballpark) and answer many of the questions. The first one was a farmer who owned cows and presented with a black eschar on his arm. I said, “Anthrax!” Winnah winnah chicken dinnah! Anyway, it made me think about how much I still love Microbiology, and since I was in need of a good diversion, I decided to write an Infection Connection entry I’ve been wanting to do for a while.

Polymerase Chain Reaction (PCR) is a powerful laboratory tool developed in the past couple of decades. Dr. Kary Mullis is generally credited with the development of the technique (and won the Nobel prize in Chemistry for it in 1993), although his research built upon the work of others, as do all inventions and techniques. Shoulders of giants, and all that. I recommend Mullis’s autobiography, Dancing Naked in the Mind Field. He’s brilliant, but a real character, and has put forth some pretty bizarre and disproven ideas. He credits his usage of LSD with his realization of how PCR could work. [shrugs] Who knows? It really is an amazing development in science, and maybe it took that expanded leap of imagination to get him to that point.

Anyway, it’s a pretty amazing thing, and I think by the time I’m done with you, you’ll think so, too! (haha) The way it works is that you mix up this cocktail that includes the sample to be tested, free nucleotides (Remember ACTG, the building blocks of DNA? Adenine, Cytosine, Thymine, and Guanine. They only fit together one way: Adenine pairs with Thymine, and Cytosine pairs with Guanine.), a DNA primer that will target a specific strand in the organism for which you are testing, and Taq polymerase, an enzyme derived from the bacterium Thermus aquaticus, an organism that thrives in high temperatures. (I’m sure I’m not the only person who always thought of “Tak!” from Stephen King’s book Desperation whenever saying “Taq polymerase.”) A few other things are in there, like a buffer for stability, and some various ions that facilitate the reaction. I’ll explain in a moment why Taq polymerase is so important.

When you get your cocktail together, you place it into a thermal cycler. This is an instrument that can reach high temperatures quickly, and then cool down quickly. At the high temperature (usually around 90° Celsius), the DNA strand in the sample denatures, i.e., the hydrogen bonds in the double helix are broken, and the DNA strand zips apart. Think of running a chainsaw down the rungs of a ladder. The thermal cycler then drops down to a lower temperature, around 60°C, at which point the DNA primers form hydrogen bonds (this is called the annealing phase) with the target strand of DNA. The thermal cycler then goes up to 72°C, which is the temperature where Taq polymerase is most effective, and the enzyme causes the free nucleotides in our cocktail to go to the site where the primers are and they begin to extend the strand of DNA. If the next nucleotide in the sequence is Thymine, an Adenine nucleotide will attach to it, and so on. Are you still with me?

What is essentially happening here is that we are duplicating that original strand of DNA in our patient sample. We split the strand at the high temperature; the primers attach to the target strand at the low temperature; the primers tell the nucleotides where to go at the medium temperature, and a new strand of double helix is formed. We have made an exact copy of that original strand of DNA, all in the matter of minutes (because the thermal cycler is capable of rapid temperature fluctuations). What’s next? We do it all over again. We now have two identical strands of DNA, and we do the process again and are left with four strands; the next cycle gives us eight strands. We let these cycles run for as long as necessary, usually up to 40 cycles. At the end of 25 cycles, there are more than 33 million copies of our original DNA strand. I don’t know about you, but that STILL blows my mind!

Why is this important? There are a couple of important reasons from a microbiological perspective. One, some infections involve a very low number of organisms. And if the organisms are damaged because the patient is already on antibiotics, they may not be able to be cultured. If there are only fragments of the organism available, or very low numbers, the PCR method can still target the specific DNA strand and increase it exponentially so that there are large numbers of DNA strands which we can test for. Second, traditional culture methods can take a while, and PCR can provide much quicker results. The best example I can think of is that in the lab where I worked most recently, we did a PCR test for Group B Streptococcus, an organism that can cause life-threatening infections in newborns if the mother carries the bacteria and delivers vaginally. Culture can take up to three days; PCR can be done in a matter of a couple of hours. If a woman goes into labor and hasn’t already been tested for Group B Strep, the PCR test can mean the difference between a vaginal birth with antibiotic prophylaxis and a C-section with its attendant complications. If a baby picks up Group B Strep from a vaginal birth, it can result in meningitis or septicemia, both of which can kill. Rapid diagnosis is key, and PCR provides that.

I was going to mention why Taq polymerase is so important. Because this enzyme is so heat-tolerant (it doesn’t denature at the 90°C temperatures used in the PCR process), it allows for a closed-system procedure. In other words, you can take it through numerous cycles without “killing” it, so that you don’t have to stop after every cycle and add more polymerase. You just mix up your cocktail, pop it in the cycler, and walk away until it’s done. This allowed for a practical application in the clinical lab; companies can put together systems that are affordable for larger hospital and reference labs.

There are other molecular methods in use in labs, including DNA-RNA hybridization and ligase chain reaction. These have definite differences, but they are all based on the molecular level rather than traditional culture methods. We did one molecular procedure to identify the species of mycobacteria in a culture; those are the organisms that cause TB and other infections, but they can be notoriously slow-growers. We can now identify a case of TB in a matter of several days rather than several weeks, which is hugely important from an epidemiological standpoint.

Twenty years ago, I remember my supervisor at the lab where I worked in Indianapolis telling me, “Eventually we’ll be able to take a sample and test it directly using DNA probes.” He gave the example of testing a sputum sample for TB directly, rather than processing and culture. We had just started doing DNA probe testing (sort of the beginning of molecular testing in the clinical lab) for Chlamydia and gonorrhea. Molecular methods are both more sensitive (able to detect lower numbers of organisms) and more specific (targeting only certain organisms, resulting in fewer false positives). Paul was right. It only took two decades to get to the point where molecular testing is a part of routine diagnostic testing, and the patient is the big winner here. Better, more accurate, and faster tests can mean shorter hospital stays, quicker recovery, and less chance of passing on serious infections like TB to others.

It really is a revolutionary testing method, and I am very glad that I got to see it unfold during the course of my career.

Paint It Black

It’s been a rough few days, and there are still more to come.

My stepfather-in-law was recently diagnosed with Stage III lung cancer, and is not doing well at all. He’s not strong enough to handle either chemo or radiation, so the goal now is to make him as comfortable and as pain-free as possible. In the short-term, the plan is to pick him up at the nursing home in a couple of weeks, bring him home to enjoy a NASCAR race and a martini with his son and the rest of us, and take him back after a couple of hours. We got together Friday with his son and daughter-in-law and had an honest discussion about some very difficult subjects.

Friday was also the day that my Dad had his stroke a year ago.

Another family member (no longer family by marriage, but still held in high esteem by many of us...I won’t say who it is out of respect for their privacy) is seriously ill and in the hospital recovering from surgery. The recovery isn’t going as well as planned, and all involved are very concerned.

Today was a meet-up with my family at my Dad’s grave site. While there, I also went over to my Cousin Donny’s grave, my paternal grandparents’ grave, and an uncle and aunt’s site. After that, we all went to grab a bite to eat and happily had some laughs and discussions...of course, some of the discussions were about an unsolved murder from 1904 that my sister was researching at the museum, as well as the death and destruction in Japan and the fears of a nuclear core meltdown. Good times, eh? We then watched a slide show that my niece put together. I was dealing pretty well, but I got pretty choked up at seeing tailgating pictures from when we took Dad and Cousin Shane to a Notre Dame game. You all know that was one of the special things that Dad and I shared. We were sports buddies and that was always one of our topics whenever we talked. Unfortunately, my niece included pictures of his service at the cemetery, and that was like a punch in the gut. I didn’t want to see that...didn’t want to see the looks on all of our faces as the flag was presented to Mom.

Tomorrow is the anniversary of his death. I know the first year is the hardest, and I know it will continue to get better and less painful. Mom told me that one of my sisters told her that she has a hole in her heart. I understand what she was saying, but I don’t feel that way. I still miss him like crazy, but he will always be in my heart.

[Side note: I’m curious what you guys think. Do you often visit the graves of loved ones? Mom and Dad were always big on that, going around to various relatives’ graves on Memorial Day. I’m kind of not that way. I still miss the ones that have gone on and always will, but I think of them every day. Visiting their grave isn’t a necessity for me. Having said that, I’ve got an idea for something I want to put on Dad’s stone. More to come.]

Anyway, I’ve been in a very dark place for a few days. I’ve felt at times that I was surrounded by death. This is unusual for me, and I know it will pass. (There is probably a certain measure of winter fatigue setting in, too.) In the meantime, I’ve tried to handle things the best I can. I know I haven’t said the right thing all the time, and as John Mellencamp sang, if I’ve done any wrong, I hope that I’m forgiven. I know there will be more tough times ahead, but I can only continue to do what I can to help others to get through them. As for myself, I have to turn my head until the darkness goes. And it will.