Microbe Monday: 1/2 lesson, 1/2 rant

Last week at the International Conference on Gram-positive Pathogens, there were talks (and posters) on Bacillus anthracis and Clostridium difficile. While listening to some of these talks and poster presentations, I was forced to endure a phrase that grinds my nerves. What is that you ask? It's the phrase: "The dormant spore."

It bugs me because it's (1) incorrect and (2) redundant.

(1) Why the phrase is incorrect.

Bacteria don't make spores. Members of the genera Bacillus and Clostridium undergo sporulation, but the product is an endospore, not a spore. A spore is the result of asexual reproduction, an endospore is not.

Now, I realize that if you are giving a talk about endospore or sporulation that you are going to say the word endospore multiple times. I don't think it is a big deal if people drop the word endospore for spore for the duration of the talk if they at least refer to it correctly in the beginning. This is fairly common. Referring to an endospore as a spore didn't even use to bother me at all until I met multiple people working on endospore-forming bacteria that did not realize the difference.

(2) Why it's redundant.

An endospore is a dehydrated, highly-refractile product resulting from a series of biochemical and morphological changes known as sporulation. Endospores are resistant to ultra-violet radiation, extreme temperatures, chemical disinfectants, dessication and pressure. They are metabolically inactive, i.e. dormant.

Using the phrase dormant spore (or dormant endospore) is the same as saying frozen ice.

It might seem silly, but it bugs me.

Anyone want to share their scientific pet peeves?

Argh.

Sometimes I think the universe is trying to determine just how far I can be pushed before I completely lose my mind. I can tell you right now, it’s not that far. In general, my fuse is pretty damn short. Patience is not a virtue I possess and I do not fear or avoid confrontation. However, I really do try to keep myself under control, especially at work. If you compare myself of today with myself of 10 years ago, you would find significant improvements in this arena, but if you compared me to myself of just one year ago, you would probably find little improvement.

Then there are weeks like this, where you might find it difficult to see any progress no matter which version of myself you compared me with. It feels like 10 million little things are going wrong. No, none of them are worth losing my mind over, but as they add up, I find myself dangerously close to the breaking point.

As an example, let me describe a 1-hour portion of my day yesterday:

• Our lab possesses multiple thermocyclers and right now, we are down to one. I think fixing one of them would be nice, you know, just in case that last one decides to die. Yesterday, the last thermocycler died. Fortunately, it was some sort of issue with a fuse and was repaired quickly, but considering I cannot do what I need to do without PCR, I was pretty damn irritated.
• I send DNA for sequencing. I get results using one primer, but no results using the other primer. I use the sequencing facility's primers. If it were my DNA, then neither primer should have yielded a result. Therefore, I think it is their primer and that they should re-run the samples for free. They are not under that impression.
• I open the -80 C and a mountain of tubes fall all over the floor. Someone decided that balancing an open box precariously near the front of the freezer was a dandy idea. I want to leave their stupid shit all over the floor, but I pick them up and shove them back into the freezer.
• After picking up all the tubes and replacing them in the freezer, I try an locate the strain I need, only to find that whoever got into the stocks previously completely rearranged all the boxes and since they are covered in frost, I have to remove them one by one, open them and pull out a vial to determine which box I am in. No, I don’t fix the order, because I am annoyed as shit.

This kind of irritating crap has happened every day this week. I am so ready for the weekend. I need to rest and reboot. I really hope next week is significantly better.

Things...

Although my work schedule this week was pretty darn relaxed, thanks to the poorest planning possible, my after work schedule was busy, busy, busy. There just wasn't ample time to post. However, I thought I would hammer out this brief post that is a hodge podge of things I considered writing about.

The following are things that I

don't give a rats ass about, yet keep seeing in the media:

• Sarah Palin. Seriously people, why is this woman still discussed. I don't want to read about or listen to anything she says, whether I agree with it or not.
• Tiger Woods. I am not his wife, therefore his extramarital affairs do not hold any bearing on my life. I don't need an apology from him and he didn't let me down. He did let his wife and children down and that is who he should apologize to. The only people that owe me an apology are the news media, for irritating me with the Tiger Woods coverage.
• The attire of snowboarders. Earlier this week I read an article about a snowboarder, Nate Holland, who was whining about other snow boarders wearing tight pants. Apparently, he feels this "betrays the anti-establishment culture that birthed snowboarding" and blah, blah, blah, wah, wah, wah. First of all, you are competing as part of a team sponsored by three huge American companies while wearing faux jeans. Puh-lease. Get over yourself. I thought that was pretty random until today when I read an article about how Japan is all in an uproar about how a Japanese snow boarder appeared "disheveled." Good thing he didn't arrive doing something actually bad like, abusing a child.

don't understand:

• gay republicans.
• why anyone thought it was a good idea to remake We are the world? I am all for donating money to help Haiti. However, I don't need to get anything in return, especially not some awful song that makes my ears bleed. That remake, like most remakes, sucks some serious ass.

I am happy about:

• In less than 10 weeks (hopefully) I won't be pregnant. I do not understand women who enjoy this part. It's uncomfortable, it's gross and it drags on forever.
• A good friend of my found gainful employment after and exhausting search in a shitty economy. Congratulations again!!
• My primers arrived today.

Grrrrrr

My lab collaborates regularly with another lab located at an institution near by. This lab could do some nice clinical work, but unfortunately a dumb fucking donkey (DFD) of a “post-doc” works there. DFD is a combative and uniformed researcher who started working in this lab over 10 years ago. In that time, DFD managed to chase off every decent post-doc and grad student that attempted to enter the lab. The post-docs left because DFD steals ideas and presents them to the PI as his or her own and the grad. students left because they don’t enjoy getting yelled at and treated like idiots. From all accounts the PI isn’t aware of any of this and on the contrary, thinks DFD is an asset to the lab.

Anyway, I had a run-in with DFD when I presented at our last “group” meeting. Fortunately, I knew it was going to happen because at the previous group meeting, DFD went on a 10-minute tirade about how a particular protein doesn’t bind a substrate even though everyone else reports that the interaction does happen. You see, DFD can’t replicate this interaction, therefore the interaction can't possibly occur. After this meeting, I discussed this conversation with Magnum, PI as we both know this interaction does occur. In fact, the apparent KD for this interaction is in the nM range. We concur that DFD is in fact a DFD.

Fast forward to a month later. I am presenting my data, which includes the previously mentioned protein binding nicely to the previously mentioned substrate. DFD goes in for the kill and repeats the tirade from the previous meeting. I let DFD speak because I am prepared with no less than 10 different accounts from multiple labs, demonstrating that this protein binds to this substrate, which I subsequently share with everyone in the room. The last piece of evidence I bring up is the crystal structure showing the very same protein binding to the very same substrate. DFD just stares and eventually replies, “Oh.” I move on with the rest of my talk.

Enough already

My plans for the evening were to eat, shower, veg. out on the couch and watch TV. However, my plans were fatally flawed because there is nothing worth watching (yeah, I know, I know, this is not new). It seems like television programming consists largely of the following:

1. Shows featuring people who raise a litter of children.

I do not find birthing, managing, raising, conceiving or even being around 8-17 children interesting or remotely entertaining. I also resent that these shows appear to portray these families as having financial difficulties when they are clearly getting paid to appear on the program.

2. Shows about brides.

Jesus fucking christ people! The commercials alone make me want to blow my head off. Who are these stupid bitches, the douchebags who are marry them, the friends who put up with them and the awesome parents that raised such a waste of space? Actually, I don't want to know. Besides, are weddings that interesting? No, they're not.

3. Shows about housewives, fictional or not.

Seriously, these are not housewives. These are people that worship money. They are stupid, embarrassing and completely devoid of any actual personality. Also, please tell me the whole wife-swapping crap is almost over. How about a show about a woman who works and raises a child or children? I guess since she might not have enough time to fake-bake, get drunk over lunch, gossip or shop for designer clothes at every opportunity, that it just wouldn't be very interesting.

4. America's next top _____________.

OK, America's Next Top Model was entertaining for a few seasons and I really liked Project Runway, but exactly how many more renditions of this theme are we going to go through? I thought that we reached the bottom of the barrel with animal grooming, but who am I kidding, something even more ridiculous is surely on the horizon.

5. Shows about psychics and/or the paranormal.

It's not real. Besides, you are never going to convince me of a paranormal experience by presenting my with a professionally edited and produced video.

The only thing that makes the existence of these shows tolerable is watching Joel McHale poke fun at them on The Soup.

Note: Aside from ANTM and Project Runway, I've never actually made it through an entire episode of a single one of these shows, so I am more than willing to admit that my assessment of how tedious and annoying they are might actually be wrong. Maybe at the end of each episode, everyone learns a lesson and serves food to the less fortunate.

My two cents on how to behave as a seminar spectator

Usually my irritation with any seminar is directed at the seminar speaker. This is because, in my experience, the vast majority of scientists and scientists-in-training give awful talks. However, today I want to post about the other end of the spectrum, the seminar attendees. During my final stretch of graduate school I barely attended seminar and as a result started forgetting about all the little annoying and rude things people do while someone is trying to present their data. After attending exactly two seminars, my annoyance level is right back to where it was when I started my vacation from seminar last September.
At my last institution there were a couple of people that just didn't seem to get it. One faculty member arrived late for every single seminar by at least 20 minutes. Frankly, if I miss the first 20 minutes of a seminar I don't even bother attending. Not only is it rude to the speaker and disruptive to walk in so late, I would have missed all the important background information. Another regular offender was a faculty from another department. This person slept through every single seminar they attended. Thankfully there was no snoring, but this person would be completely leaned over into the seat next to them. I think this is extremely rude, especially for a faculty since it gives the impression that sleeping at work is OK. Why not just tell the speaker that their data sucks and is so boring you couldn't be bothered to stay awake. The invited speakers don't know it happens every time, so what else are they going to think.
In my new department, I already know to avoid sitting next to one person in particular during seminar. Unfortunately, I learned the hard way...I sat next to them in one seminar and behind them (not by choice) in another.
The behavior exhibited by this person is extremely offensive and way worse (in my opinion) than sleeping or arriving or leaving late or early. This person is on of those who, for whatever reason, feel the need to comment on the talk, out loud, for the duration of the seminar. Unfortunately, they are also the person who answers questions for the seminar speaker, before they get the chance themselves. In seminar #2 they were even shushed by the person next to them.
First of all, the constant comments: If you have something to say, then raise your fucking hand, wait to be called on and then say it. If you don't have the balls to do that, then shut your pie-hole. Second, don't answer questions for the speaker while they are answering. Sure, you can answer a question if no one else knows the answer, but the first voice heard after a question is asked should be the speakers, not some random audience member. * It is not your seminar. If you want to answer questions, then you need to give a talk.
I think most of the people that do this are just insecure and really want the people around them to think they are smart. For me, this backfires, just like it does when people regularly talk about how awesome, good-looking, or smart they think they are.** Frankly, if you are that awesome, smart or hot, then you wouldn't need to tell me, because I would easily figure it out. I also feel that the amount of times that you mention these things is in direct proportion to how awesome, smart or hot you are not.
The take home message: Suck it up and act like a professional. Try not to disrupt everyone with your late arrival or early departure, don't use seminar as your personal nap time and please, for the love of god, realize that NO ONE wants to hear your color commentary on the seminar. And finally, know this: if we wanted to hear your answers to the questions, we would ask you.

*This goes for advisers whose students are presenting their research. Let them take a crack at answering the question before you swoop in and save the day.
**This applies to parents who constantly talk about how their kids are geniuses. Statistically speaking, it is unlikely every single kid is a genius. In fact, if a parent uses the word genius (not in a kidding way) while speaking about their child, I just stop listening and go into the regularly scheduled head nods with a "wow" and a "really" thrown in every now and again.

What are these people talking about? (Part 4)

I am referring to this story.
It states that:
"The DNA linked the anthrax used in the mailing to a flask used in Bruce Ivins' lab at the U.S. Army Medical Institute of Infectious Diseases, said the source, who was not authorized to speak publicly about the case."
Can you identify the part of this phrase that tells the reader that the writer has no idea what they are talking about? It is this part: "DNA linked the anthrax used in the mailing to a flask." Not only do flasks not have DNA, but they are used, sterilized, washed and resterilized. I doubt a culture started in 2001 would still be sitting in a flask this many years later. What (I think) they mean to say is that the DNA matched the DNA of a strain that Bruce Ivins had a stock of in his lab. Alternatively, if the labs at USAMRIID were searched and samples were taken, then maybe they mean that the DNA from the letters matched a sample of culture taken from a flask in Ivins' lab.
I know this is picky, but how am I supposed to know what else the writer did and did not interpret correctly when they clearly do not have the science background needed? Besides, this is not the first thing I've read since Friday that wasn't accurate.

This story, released by the AP contains a couple of strange staements and I am not sure what to make of them. The statements are as follows:
1. "Although the Army lab where Ivins worked had long been on the FBI's radar, scientists were unable to pinpoint the specific strain used in the attacks until about a year ago."

The B. anthracis strain isolated from a victim of a recent bioterrorist anthrax (Bacillus anthracis str. A2012) was sequenced and a paper describing the unique genetic markers associated with strain A2012 appeared in the journal Science in 2002. Furthermore, you can find the nucleotide sequnce in the NCBI database.

2. "The new genome technology that tracked down Ivins was either not available or too expensive to use often until about three years ago."

I don't know what new genome sequencing technology would be needed for a strain that is already sequenced. Any thoughts?

Discussing the media's case for and against Bruce Ivins (Part 3)

I want to take some time today to discuss the different points the media makes public regarding Bruce Ivins' involvement in the intentional release of Bacillus anthracis spores through the US Mail during 2001.

Before I begin, I want to state that my opinion remains the same regarding Bruce Ivins; I don't know. Until I see the actual evidence, which I hope is released soon, I can't render an opinion on his involvement. With this post, I hope to demonstrate that the information presented by the media is not evidence of guilt, but is circumstantial at best.

1. Bruce Ivins stood to gain financially from the aftermath of the intentional release of B. anthracis spores through the US mail by way of money from patents or increased federal spending on anthrax-centered research. Reported by, Los Angeles Times,
If Ivins were listed on anthrax vaccine patents, then one would expect him to benefit financially if and when these products went to market. Any inventor of a process or product that was utilized would benefit in the same way, including scientific investigators. Isn't this a major reason for obtaining patents in the first place? I also want to point out that one quote from a Los Angeles Times article states that Ivins was only going to receive “tens of thousands of dollars, but not millions.”

Many scientists benefited from increased federal spending on research directed at B. anthracis. Some of these scientists were working with the organism before 2001, while many others jumped on the anthrax bandwagon when a significant shift in research money was directed toward B. anthracis research. I also want to point out that money for research is awarded to a laboratory and goes toward paying salaries of post-docs, graduate students, research assistants and technicians, rental of laboratory space and purchasing of equipment, supplies and reagents. Some of this money might pay a portion of the lead investigators salary, but this amount is determined by the funding agency, not the investigator. * Furthermore, since Ivins was employed by the government, I am not sure that the increased funding for his laboratory would have effected his salary the way it might effect an academic investigator working at a university. **

Conclusions
From what I can gather, Ivins potentially stood to gain tens of thousands of dollars from a patent and possibly an increase in salary. Professionally, he might have received an increase in money for his research resulting in the ability to hire more people and purchase more supplies and equipment, all of which should benefit any labs research.

2. Ivins was a mentally unstable sociopath. Reported by CNN, Los Angeles Times
In almost every article I read, Jean Duley's court testimony that resulted in a restraining order against Ivins as well as his forced removal from USAMRIID is cited. From what I gather, Ivins stated that, in addition to purchasing a gun and a bulletproof jacket, that he formulated a plan to kill co-workers. First of all, I think Duley did the right thing by reporting her information to the authorities. If she hadn't and Ivins did murder his co-workers, Duley would suffer severe public criticisms by the news media for her lack of action.
However, I don't know what to make of her claims that Ivins was diagnosed "forensically" (what ever the hell that means) as being a sociopath and a homicidal killer, that he attempted to murder and poison people and that he plots revenge killings. Really? Where are these reports? How does she have this information? If someone attempted to murder or poison someone, wouldn't there be a police report, even if no charges were filed?
Again, an unbiased presentation of the facts would require that a claim like this be substantiated. Why, because validation helps the readers decide how much credit to give Duley. Who is to say she isn't fabricating or embellishing some of this to make her point? Moreover, corroboration benefits her as well.

Conclusion:
The claims made by Duley, his treatment for depression and apparent suicide paint the picture of a mentally unstable man, but it does NOT mean that he sent B. anthracis spores through the US mail in 2001? The depression and bizarre behavior of late could be a result of the intense scrutiny of the investigation.

3. Bruce Ivins conducted unauthorized "tests" outside of secure lab areas. (Having internet problems, cannot link right now. Will update ASAP.)
This is another one of those statements that tells you the reporter(s) doesn't have a clue about the topic that they are reporting on. In my opinion this is referring to a containment breach that occurred in 2002, where Ivins disinfected an area outside of a secure lab that was accidentally contaminated with B. anthracis. Ivins disinfected the area and as part of this effort, he performed "tests" to determine if contaminants remained. It doesn't appear that Ivins was at fault for the contamination, but as the lead investigator, he was at fault for not reporting the incident. The actual "testing" that he did would have occurred whether he reported the incident or not. The contaminated area must be cleaned and subsequent tests would be required to ensure that the area was safe and all B. anthracis had been removed. This is common protocol.

4. Bruce Ivins was an organ playing, church-attending, egghead who wore ill-fitting clothes. Reported by CNN.
This is information that might make one believe Ivins did not mail B. anthracis spores to unsuspecting people. Granted, I don't really thing that the news media want to paint a picture of an innocent man, wrongly accused, but if I feel that I must look at these statements as well if I am going to be fair. (Sadly, there aren't very many.)
First of all, going to church does not preclude one from killing other people. Remember BTK? This serial killer was elected president of the Congregation Council at his church.
The fact that Ivins fit the stereotype of a scientist (quiet, unassuming, poor fashion sense) is not evidence either. Remember Ted Bundy? Part of his success stemmed from the fact that he didn't look like a serial killer.

The take home message: Until the evidence agains Dr. Bruce Ivins is made public, there is no way to know if he is responsible for mailing B. anthracis spores.

Who do I think did a good job with this story?
Time. Check it out.

*I welcome any comments from lead investigators with federal funding that might want to elaborate on how allocation of salary from grant money occurs. I know there are several variations, depending on the academic institution.
**I have only worked in an academic lab, so I have little knowledge of external funding for government laboratories and how it would be allocated for salary, equipment, etc. I also do not know how internal money works in these types of institutions either. If you know about this, please feel free to comment and explain.

I'm not convinced about Dr. Bruce Ivins (Part 1)

But I am convinced that there is not a single journalist with a functioning brain left in this country. The reporting about Bruce Ivins, his apparent suicide and looming indictment by the federal government underscores what the media is today: biased and uninformed.

Let me start with the label "anthrax letters."
I hate this phrase since anthrax is a disease, not a letter. However, these two little words tell you everything you need to know about the quality of the information you are about to receive. For the record, jackass reporters: Bacillus anthracis is the causative agent of the disease anthrax. Said another way, the letters contained B. anthracis spores not anthrax.

The intentional release of B. anthracis spores through the mail occurred before I entered my graduate school lab. However, the increased security resulting from this release is something I deal with everyday. I want to post on this incident, but it will likely require multiple entries since I am too irritated right now to comment on everything. (I am saving the bullshit about testing his anthrax "cure" for later when I am calm.)

Right now I want to comment on CNN's interview with Tom Ivins, older brother to Bruce Ivins. If you haven't listened to it, please do. It will only take a couple of minutes. Now, take a look at this CNN news story, paying specific attention to use and placemnt of the Tom Ivins quote, "I tried to stay away from him."

When taken out of the context of the phone interview, this remark implies that Bruce Ivins is so strange/dangerous/bizarre that his own brother chose to avoid him. In my opinion, this is exactly what the reporter was going for (that's called sensationalism, by the way). In the context of the full interview, with the idiotic anchor John Roberts, Tom Ivins comes off as someone with an ax to grind. Furthermore, when Roberts asks T. Ivins why he tried to stay way from his brother, Tom Ivins responds with some incoharant babble about his two other brothers (of which Bruce is one) sharing a room together and growing up together. He never really gives a reason. Tom Ivins' parting statement regarding his brother is "He can go to hell as far as I'm concerned."

Maybe CNN should just stick to what it does best, fluff reporting about idiot celebrities. The days of CNN being a reputable hard news agency are long gone.

Watchdogs...ruff

I am not against government or agency watchdog-type groups. I think the majority of the time we are better off for them. Accountability is a strong motivator to do the "right thing." However, I think some of these groups could do more harm than good.

For example, the anti-vaccination groups.
I think these people mean well, but people that understand how vaccines work and can critically think about scientific data, know that what anti-vaccine pushers are saying doesn't really make any sense. I don't want to go into too much detail because I think that Dr. Steve Novella does an excellent job of explaining the errors and misconceptions of the anti-vaccine movement on his NeuroLogica blog. These groups have been in the news touting their belief that vaccines are to blame for the increases in the number of children that are diagnosed with autism. Originally they proposed that thimerosal (an organic mercury compound) was to blame. Recent scientific studies show no connection. Furthermore, despite removal of thimerosal from vaccines, autism cases have continued to increase. Still the anti-vaccination movement persists.
The major problem here is that these groups might (and one might argue, aim to) encourage parents not to vaccinate their children. Even a small decrease in the percentage of immunized people in a population can seriously compromise herd immunity. If you are immune compromised (cancer, transplant recipient, elderly) herd immunity is vital.

Example 2 (a group near and dear to my heart): The biosafety or biosecurity watchdog organizations.
These groups might obtain information (like meeting minutes) under the freedom of information act and then compare these minutes to incidents reported to the CDC. If they find an incident mentioned in a meeting, but not reported to the CDC, the group reports the lab and institution to the CDC and the media. There are serious consequences to not reporting incidents.
My lab includes a BSL3 laboratory and we work on a select agent, so any type of exposure to the organism, whether it is actually putting someone in danger or not, is written up and reported. Additionally, whenever we use the bacteria, we record this activity (in detail) in a log. Fine. No problem. (I'm not even going to get into all the security precautions we take. This is another blog entry on its own.)
What irritates me, is when a watchdog group sees that an incident (that was reported to the proper agencies) happened within a BSL3 or BSL4 and decides to send out press releases to the media painting the incident as a near catastrophe that puts the publics health at risk. I read one news article where a watchdog group member discussed the problem of "rogue" labs within the US that are working on select agents. WTF is a rogue lab? Is it in a motor home with foil over the windows like a meth lab? Where is this "rogue" lab information coming from? If they know of them, why aren't they reporting them to the CDC?
In other articles, I have seen these people describe the number of reported incidents that occurred within BSL3 and BSL4 laboratories. The numbers might seem high, but they are not discussed with any context. This number doesn't reflect safety unless you compare it to how many times a lab member does an experiment in a BSL3 or BSL4 lab without an incident occurring. Of course, we don't have to report that.
Let's think about this for a minute. People are going to make mistakes and have accidents. It's fact. This is one of the reasons why certain research is done in a BSL3 or BSL4 environment, and not in the hallway of an elementary school. The accidents that happen within a BSL3 or BSL4 laboratory are already contained by virtue of where they occur. The only people exposed are those within the lab itself. Even so, the lab members (if following proper protocol) should also be safe in many of these scenarios because they are wearing protective clothing, face protection or are vaccinated. So, if you hear about an incident happening within a BSL3 or BSL4 be glad, that is where it is supposed to occur.
Personally, I think it is unethical to scare the public when there is no real danger.

The point? If you are going to guard the public from harm and are concerned about peoples health and well-being; great. Just educate yourself first so your advice or opinion is more likely to help.