IVF 5: In which I cause trouble

Today I had yet another ultrasound, this one to serve as a baseline for imaging my follicles over the next couple of weeks. Dr. Earnest Resident was plumbing my sparkle hole, while Dr. BigShot watched and grunted. Nurse Blondie was standing by, as of course was devoted Dr Hyde (who longs for the day when they let him run the ultrasound machine--we are both aching to push all the buttons on that sucker).

My ovaries were demurely tucked out of sight, so Dr. Earnest had to press on my abdomen as she moved the ultrasound wand at odd angles to get a glimpse of the follicles. “1, 2, 3…” she counted through my right ovary. When she hit “..11, 12…,” Nurse Blondie gave me an “aren’t you the impressive egg-layer” sort of look. The combination of the relief that I was producing plenty of follicles, the funny smirky smile on Nurse Blondie’s face, and the vaguely tickly feeling on my abdomen--I burst out laughing.

What happens when you laugh? Well, all your abdominal muscles tighten up. Dr. Earnest, who had been intent on the ultrasound screen, gave a startled “Ooh!” and scooted backwards as her hand flew off my now-rigid stomach, as though she were worried I had somehow ruptured mid-exam.

Then we all had a good chuckle. After everyone stopped laughing, Dr. Earnest had to restart the counting--it’s not like she could hold her place. This should have calmed me down, but instead I was beset by a horrid fit of the giggles. It was all I could do not to laugh some more, particularly after she re-counted my twelfth right follicle. I tried to think of sad things (dead puppies?) but the giggles are the giggles, and this was probably their least efficent follicle-counting mission ever. Not to mention when she switched over to the left side, and once again we reached 12--I was squirming with suppressed laughter, and Dr E eventually gave up after 14, saying to Nurse Blondie, “Let’s just call it 15+.”

I have to have perhaps four or five more follicle-measuring ultrasounds before they go in to retrieve the eggs (for which I will be anesthetized--and after today's performance, they'll probably want me two degrees warmer than dead). If the giggles recur, I will need to start bringing a Russian novel to the stirrups.

Team of Lab Rivals

There's been lots of talk lately about whether Obama is Lincoln-ishly shaping his Cabinet to include a spread of viewpoints, many distinct from his own, in order to avoid the self-reinforcing groupthink that can set in among like-minded people.

How well does such an approach work in the lab? I was thinking about this today when Advisor announced that he wanted to discuss possible plans for a New Fancy Microscope we might get. He wanted advice. (Actually, he only asked for advice from GradStudent and Other New Postdoc, but I elbowed my way into the discussion because I was in charge of acquiring an NFM in GradLab. Neither of the other two male trainees has done such a thing. So hmmmph.)

All three of us could be charitably described as opinionated. And it is the rare day that we are opinionated in the same direction. We get along reasonably well, but none of us would be mistaken for a retiring violet.

Accordingly, lively discussion ensued. We disagreed with each other's "facts," we disagreed with each other's interpretations, and generally hashed it all out at length.

At the end, though, there was a consensus about the steps forward. We all agreed that Advisor should get a quotation from a particular company, should look into the details of another company's product, and should talk with two or three people about their own NFMs.

I'm fairly sure that this debate served to identify some critical choices and to consider all options on the table. I'm equally sure that if any one of us had not been in the room, some of those options would have been discarded much earlier in part due to some people's "facts". So although my labmates sometimes rub me the wrong way, there's something to be said for this team of rivals idea.

If only we could achieve similar agreement over freezer defrosting.

Pizza and DNA

Those two things just don't go together, do they? Oh but they do, and it's called a Vendor Show.

I would love to work in industry just long enough to find out the profitability details on vendor shows. The economics of these things, especially the small ones that happen near-weekly at any large biomedical institution, have always baffled me.

Swarms of hungry graduate students and postdocs and techs descend like locusts on whatever free food is available. In the mornings you'll get coffee, bagels, doughnuts; lunchtime means pizza; afternoons there are sugar bombs in the shape of cookies or even ice cream.

The vast majority of attendees have not even a passing interest in the product being sold. I have literally never heard someone say, "Hey, I was thinking about getting a Promega enzyme, so I think I'll hit up their vendor show tomorrow for more information." In fact if I were to hear such a thing, I would fall off my seat laughing. Hello, Captain Internet?

I understand that food is, comparatively speaking, cheap. Perhaps a small vendor show, of the weekly bagel and coffee variety, costs ~$100. Pizza lunch, $150.

How much do the sales reps earn? They always show up in pairs, like Mormons, and their time probably costs the company what, another $200, taking into account travel etc? There's also the advertising flyer drop ("Free pizza tomorrow! Downstairs, outside the conference room!"). So we're only looking at an outlay of $300-400 plus some shiny brochures.

Still, I cannot wrap my head around how this junket is profitable. Sure, if just one attendee decides to buy their PCR machine, costs are recouped. But who decides on lab purchases based on the quality (or mere presence) of free chocolate chip ice cream sandwiches?

Of course, visibility is part of advertising too. Even if no one picks up your brochures (for use as anything but a brownie-plate, that is), you've still implanted the VWR brand name in their little skulls. In this sense, vendor shows are just like the adverts on the back page of Nature, only cheaper and probably further-reaching (who looks at the physical journal any longer?)

Nonetheless, I remain mystified that these biomedical companies regularly survey their entire operation, ask themselves, "What can we do to be a leader in the field?" and conclude, "Give away free pizza."

I would be happier with improved navigation on their websites, myself.

InADWriMo update: Ugh

I didn't get jack done on my November writing project this week. I did collect some data for a completely different unfinished project, so I guess that's nice, but only managed to read one paper for the November project.

I did do the rest of the my figure-scrunching very early in the week, though, so at least that gets crossed off the list. There's still one figure that hasn't been scrunched because it mostly hasn't been made. I'm supposed to be making a prettified picture from some imaging data, which leads me to my question of the day:

How can Photoshop be such a complicated menu-y program, and yet contain no simple way to average two (or more) images together? Yes, I know I can layer them all and adjust the opacities. Yes, I know I can "apply image" to add two images together. But why no straightforward averaging function?

(Perhaps it exists in modern-day Creative Suite. But I am using [don't laugh] PS 7.0, and it is like a tundra. For this, at least.)

IVF 4: Enter at your own risk

We are beginning the in vitro fertilization cycle, and as Abel "As you wish" Pharmboy requested, I am going to blog the daylights out of this sucker. The fun (?) part about IVF is that it takes ~6 weeks and encompasses many, many delightful procedures, so there will be no shortage of topics.

I will also post intermittently about Science during this time, and InAdriwriMoWhatsIts Progress, but this post serves as notice that if you visit this site any time between now and Christmas, you may be reading about my vag. The IVF posts will all be titled as such, as fair warning.

What you've missed so far: I had a hysterosalpingogram (= dye + x-ray visualization of my inner bits), and I have to say that I have the prettiest uterus ever.

Figure 1. Dr Jekyll's uterus really is this hot.

Ok, that's some other lady's uterus, but the sentiment is correct. Does it or does it not look like a beautifully filled pyramidal neuron? That is, if an apical tuft resembled a speculum. I was delighted, insofar as that was possible from my position. (This doctor's office, excitingly, didn't have stirrups but instead padded bars to drape your legs over. It looked sketchy but was actually way comfortable. Petition, ladies.)

Last week I had a "trial transfer," in which the doctor guides a cannula into the cervix and injects a little saline to mimic the procedure that will occur on the real embryo transfer day. Ahead of time, the nurse asked if it would be ok if a resident, rather than the Fancy IVF Doctor, took a turn. "Sure!" I said, ever eager to encourage medical education.

The resident had some difficulty figuring out a route through my (apparently labyrinthine?) cervix. "Ahah!" she finally exclaimed, after a particularly firm twist of the guide tube. "I'm through. I felt it."

"Me too," I replied. Oh, how we all laughed.

Today was the first hormone injection. I have been taking birth control pills for ten days now to suppress ovulation, and now we add in shots of Lupron, a gonadotropin releasing hormone agonist. This drives crazy activity in the pituitary, followed by a fall-off during which luteinizing hormone production is suppressed, as is ovulation. Don't want those little yolk sacs jumping off yet!

Anyhow, these injections are the easy subcutaneous ones. The nurse instructed us (well, me) to inject in the abdomen, after pinching up a roll of skin. Now, I've given many injections to many animals in my time, but of course I have a particular interest in getting these right. So this morning over breakfast I googled for more instructions.

Dr Jekyll: Hmm, it says on this website that you shouldn't do sub-Q injections in the abdomen if you're really skinny.

Dr Hyde: [breezily] I wouldn't worry about it. You're not that skinny.

[pause]

Dr Jekyll: Dearest, that's the sort of conclusion you're supposed to let me arrive at on my own.

MoranTech: We will never be rid of him.

While I was off Obamarama-ing, BlogFodder (ne Tech) was given a project to complete on his own. It was to be a repetition of the small project I trained him on the previous week, only with fewer of those complicated dilutions. The catch of course being that he had to do it all on his own, without my coaxing.

(For those of you who missed some of the later comments--if BF had been hired as my tech, he'd be out the door. But he's here mostly to do a project of Advisor's devising, and be an extra pair of hands for the rest of us when he's free.)

Against all expectation, BF performed just fine on his lonesome. The slides look ok, if not lovely, and he appears to have gotten the dilutions right, thus supporting the hypothesis several readers voiced, that he just goes all weak-kneed under my judgmental eye.

Today, Advisor was having BF look through the slides and compare them to an atlas. When I stopped by the microscope for unrelated purposes, BF asked me a couple of questions about the comparison.

Because I am a naturally bossy helpful person, I looked at his tissue, gave him a few pointers, and went about my business.

Later, Advisor came to me. "Jekyll, I am quite happy with BF. I gave him some slides to compare to the atlas and he appears to have figured out the best landmarks to use!"

Jekyll: "Ohhh. Um, I helped him out."

Advisor:[disappointed] "You helped him figure out the landmarks? So my test was not really a test?"

In other words, BF had his big test this week, and somehow I failed it.

InADWriMo 2 (Obama 63 million and counting)

I just fired off the revised and refined manuscript draft to GradAdvisor for a brief communication-type item. First InADriWriMo item, check!

I'm excited about the format--this is a paper whose previous drafts have given me heartburn, because it felt as though we were welding together two related-as-second-cousins experimental results. As a result, I always seemed to be shortchanging one half of the picture, or dwelling at excessive length on the other.

In a recent chat, I suggested to Advisor that we consider breaking the paper into its two immiscible halves--one as a brief communication with the flashy finding; the other as a regular length journal article with the more workmanlike "resolved outstanding issues in our subfield" part. After some discussion, we decided to give this a try. I am immensely more satisfied with the current version of the manuscript (flashy brief bits...mmmm....) since it no longer drags along the manacle of virtuous-but-slightly-dull Figures 3 to 6.

We are still missing one necessary bit of information (see to-do list item 3) but I don't think it will influence the manuscript dramatically, so this seemed like a good time to get this draft to GradAdvisor for first thoughts.

Incidentally, the journal we are planning to send this to recommends that the text not exceed about 1200 words. You thought I whined about the word limitations on the abstract of my last paper--skinnying this one down will be hellish. We're currently at 1470 words without any of the missing data....we'll see how this goes.

Yeeeeeaaaaaa

aaaaaaaaaaahhhhhhhhhhhhhh!!!!!!!!

Our swing state went blue! We had a very interesting time at the polls doing GOTV--we had a preprinted list of Obama supporters who were considered flaky (first-time voters, irregular voters, etc) and every time one came in we crossed them off the list.

Then at 2p we took the "walk list"--the houses canvassers were supposed to visit to get out the vote--and cleaned off the list anyone who had already voted in our precinct. In effect, making the last ditch 4pm GOTV effort more efficient and targeted by eliminating anyone who had already done their civic duty. Then we took the list and knocked on doors in one neighborhood, although everyone we chased down had already either voted or wasn't home. Still, we felt all participatory and stuff.

Around 5:30p we went back to the hotel and watched TV until Hopey won and gave his speech, and cried ourselves into a stupor (ok, the beer might have had something to do with it too.) The line about how his daughters had earned their puppy just slayed me. I mean, c'mon, PUPPIES.

Anonymoustache, nice job in in! Razor thin margins but it looks like you're holding on--amazing! JP, equal props to you for holding the margin under 10%, it appears.

Tomorrow a return to lab, and normalcy (?) Tonight, a bath of relief that--since neither Dr Hyde nor I is running for office--for the first time, I am actively proud of my country for something it did, as opposed to something it was.

Or as Dr Hyde says, "We don't have to leave the country!"

InADriWriMo 1; Obama 95

Two unrelated bits stuffed into one post:

On Saturday I hacked valiantly away at the Manuscript of Excessive Length, and I would say that all but the last two paragraphs (out of 10) are ready to give to GradAdvisor for a read. I also worked some on scrunching the figures, but haven't yet quite miniaturized them to my satisfaction.

--------

We arrived in SwingState yesterday pm with unreasonable giddiness. We are in an extended-stay suite hotel, with quite functional kitchenette. It feels a little like being at home, although obvs not. We are therefore referring to this as our Staycation Away From Home.

Yesterday evening we phonebanked for get-out-the-vote efforts. One of the phones we used had had the digits all rubbed off the keys, it had been used so much. We had lots of pro-Obama responses, with the only exception being some people complaining they had been called TOO MUCH by the Obama campaign. If this is our biggest problem, we are doing ok.

And I got to talk to a real live undecided voter! I don't know anyone in my normal life who is undecided or at least who is willing to admit that to me. This young woman said she was leaning Obama but she works in a doctor's office of McCain supporters who said that Obama would ruin health care. I talked her through some important basic points ("No, Obama is not going to socialize health care. Everyone with an employer-based health care plan, like you and me, will be able to keep that plan as long as they're happy with it") and she seemed to be happy to hear it.

Then she wanted serious details on how Obama was going to guarantee accessible health care for the uninsured and pointed her to the website (where she was headed anyhow--she said she was using this Sunday to read up on the candidates' positions on everything (!!)).

Here today, probably gone next week

I gave Advisor the summary of the Week of Fodderousness. Advisor said he was fine to fire the guy if that's what I wanted.

I said that I wanted to give BF one week. In the coming week, he will have to do the type of experiment I showed him this week, all by himself. There will be calculations, even. (Advisor: "Push him.") If he can't pull his act together, he is a goner.

In brighter news, today Dr Hyde and I early-voted at the county registrar. I expected it to be all momentous and teary, but in the event we were running late to a doctor's appointment and so it was mostly impatient. Oh reality, you letdown.

I counted the people I could see on line with us. 10 of the 40 were African-American (although of course people may self-identify differently than I estimated). For you nascent BFs out there, that's 25%.

According to the US Census, our county is less than 6% African-American.

So that was pretty cool.

And made me resent the hour-long line much less.

-----------------------------

We leave Sunday for a swing state GOTV effort. Hope you all are also doing your best, wherever you are, to encourage voter participation. The entire meaning of a democracy is that we vote. Even if your state is "safe" either way, your vote--your participation--your voice--your improved popular vote count for Obama--matters (plus there's all that down-ballot stuff!)

I doubt I'll be blogging between now and the The Great Hangover Either Way Wednesday, so I leave you with: V O T E. How will you ever explain it to your kids if you decide to sit this one out because you have two Westerns to run on Tuesday? Yeah, that'll matter in twenty years.

Oh, and for my foreign readers, sorry about the last 8 years. We're going to try to make up for it on Tuesday.

EPIC FAIL

I have to say, I was not looking forward to the point in time when BF stopped providing me with, well, BF. Ugh on going back to soul-searching posts about supplemental data or whatever.

Thankfully (?), not yet!

Today many things became clear:

Jekyll: We'll be diluting the secondary antibody 1:200, meaning 1 part antibody for 200 parts final solution. We've already figured out that we have a total final volume of 4.8 mL. How much antibody do we need?

BF: [writing]

   1      x
 ----- = -----
  200    4.8 mL 

Jekyll: [sigh of relief]

BF: [writing]
4.8 = 200x
So, we'll need to divide 200 by 4.8.

Jekyll: [suddenly gripped by dread]

BF: [writing]

     _______
4.8 | 200

Jekyll: [crying on the inside]
Don't take shortcuts on the math. You need to divide each side by 200 to isolate x, so that should be 4.8 divided by 200.

BF: Oh, right.

     ________
200 | 4.8 

[ominous pause]

Jekyll: [helpfully] Instead of working in milliliters, you could put that in microliters so the math is easier.

BF: Uh, so it'd be...480 microliters?

Jekyll: [suppressed inward sigh] No, let's walk through the conversion.

         1000 uL
4.8 mL x ------- = 4800 microliters
          1 mL

BF: Oh right.

     ________
200 | 4800 

[pause]

Wow, it's been so long since I've done long division.

[excruciating pause]

Uh, 2.4?

Jekyll: [gasping and appalled, yet inwardly joyful that she can later share this precious moment with some anonyfriends] Let's think about the decimal point....


And I'm even sparing you the tedious calculations on getting the 4.8 mL number in the first place.

The good news is, it is now perfectly clear that BF has some sort of math disability, by which I might or might not mean "stupidity." I have no idea how he made it through college (calculus, anybody?) although presumably a calculator was involved. [Or a systematic cheating scheme via his frat.]

The bad news is that he is still in my lab. Tomorrow I will talk with Advisor about the path forward.

I am a broken record

I'm rechristening Tech "Blog Fodder" because that is clearly his role in my life.

Episode 1: So close.

Jekyll: We're going to dilute this antibody 1:1000. That is, one part antibody per one thousand parts total solution. So if we want a final volume of 1 mL, ie 1000 microliters, how much antibody should we add?

BF: Um, one microliter?

Jekyll: [relieved] Yes! That's right. Now we want to make a 1:2000 dilution, again with a final volume of 1 mL. How much antibody do we need?

BF: Uh, 0.2 microliter?


Episode 2: Do as I say, not as you think.

Jekyll: While I'm gone at journal club, add 0.2 mL of this solution to each well of the 24-well plate. There will be leftover solution, but don't throw it out because we'll use it later.

BF: Ok.

[1 hour elapses]

Jekyll: I'm back. Hey, how come there's such a large volume in these wells?

BF: Well, there was a lot of leftover solution, so I just added it all to the wells so as not to waste it.


Episode 3: OH REALLY?

Jekyll: Doing all these molarity and concentration calculations is going to be really important, and I think it would be good if you practiced them. Here are a few websites that have tutorials on how to calculate these things. You should review them and do the practice problems. Later this week I'll try to find a chem textbook so you can go over the material on solutions.

BF: Yeah, I guess you found my weak spot in math!

Jekyll: That's ok, molarity and concentrations just take some practice.

BF: It's been a long time since my last chemistry class.

Jekyll: Oh? What did you major in--psychology?

BF: Neurobiology. I took chem as a freshman and then orgo as a sophomore, but that was over two years ago so I'm rusty.

Jekyll: Hm, what lab classes did you take?

BF: Well, none in bio.

Jekyll: What?

BF: The lab classes were only required for pre-meds, and I wasn't pre-med. I want to go to graduate school.


Let me help you out with that decision, young man. You should not even go near heavy machinery, let alone graduate school.

Gaaah. Advisor has been away for a few days but he will want a report on BF when he returns. I plan on telling the truth. Advisor will undoubtedly ask me if we should fire him. I have to make a decision.

OTOH, if you watch like a hawk, BF can do what he's told. He is indeed improving his hand steadiness by means of forearm support etc. And we really just need a tech for menial tasks that do not involve much thinking. If he can conquer molarity, he should be fine.

OTOH, why does anybody with two university-level chem classes and a B.S. in neurobiology still need to conquer molarity?

Quick tips

Vocab time!

Rostral = noseward.
Caudal = tailward.

Dorsal = topward/backward.
Ventral = tummyward.

If you ever wish to tech in a bio lab, these would be good words to learn.

Let me further suggest that if you learn them, you get them correct, and not reversed.

And as a final suggestion, if you do somehow find yourself getting them wrong in front of your mentor, do not turn the incident into a joke by saying, "Oh, yeah. Just checking if you were paying attention!"

That is all.

I'm not sure that's as reassuring as you think it is.

Thanks all for your helpful tips on hand steadiness. I showed Tech the dissection today and later this week will watch him do one, with the benefit of the various ideas you gave me.

However, Tech just keeps on losing points in my book. Here's today's episode:

Jekyll: The dissection we'll be doing can seem a little gruesome, but I want to assure you that the mice are deeply anesthetized.

Tech: Oh, well, whatever. They're just rodents.

Jekyll: Well, it's still extremely important that we make sure that the animals are not experiencing any pain.

Tech: Sure, because the animal rights people would complain.

Jekyll: [pause] Well, of course we comply with IACUC regulations, but these animals are in our care and only exist because we breed them, and so there's a strong moral ground for treating them as well as possible.

Tech: Don't worry, I'm not going to go all Jeffrey Dahmer on them.


?????????

This is only a loose transcript, duh, and Tech's apparent disinterest in animal welfare is hard to get across. His tone of disregard when he said "just rodents" was a shock.

Before now, I've exclusively trained labbies who were if anything terrified of causing discomfort to mice. That was a great starting position, because it let them work backwards to a position of comfort as they learned proper handling techniques etc.

I have never had to train someone with this sort of attitude. I am at a loss.

I asked some friends for help on this (thanks, friends!) and they gave two primary suggestions:
(1) Ask my Advisor to sit down with Tech and reinforce that animal treatment is of paramount importance, and that disrespect for animals will not be tolerated.
(2) Make Tech read the whole damn IACUC protocol to get a sense of exactly how much thought and care goes into animal treatment, and make it plain that he has to get on board.

Dr Hyde also thought that I should emphasize that if I ever see him mistreating an animal, his ass will be fired pronto.

I think these are all good suggestions. My issue now is implementation.

I've been lucky up til now that basically all of the people whom I helped to train were already awesome. The downside is that I have little to no experience telling people to shape the fuck up. To be honest I am a bit afraid of it. I do not think I have natural managerial talent. My bad tendency is to fume privately (or bloggily!) that a trainee is screwing up, rather than have the nerve to address it head-on.

I am irked that Tech has arrived with such minimal baseline skills. I am dubious about his shaky hands. However, these are presumably tractable problems. I don't know whether respect for animal life is a tractable problem.

But as Dr Hyde points out, no one is going to teach him but me. If I shy away from teaching him, or if I just ask Advisor to fire him (which has certainly crossed my mind....), then perhaps his next mentor won't lick him into shape either.

Apparently I shouldn't have been asking you-all for suggestions about shaky hands, I should have been asking what to do if he doesn't care about the tail-pinch response. Sigh.

How do I pull together the demeanor for the appropriate mix of teaching him, educating him, and scaring the poop out of him?

Mememememe

DrDrA tagged me for the six-things meme, and I perhaps overthought it. Anyhoos, here are the rules:

1. Link to the person who tagged you.

2. Post the rules on your blog.

3. Write six random things about yourself.

4. Tag six people at the end of your post and link to them.

5. Let each person know they’ve been tagged and leave a comment on their blog.

6. Let the tagger know when your entry is up.

1) I am an infant about spiders. A few nights ago before dinner, we spotted a spider on the floor but then couldn't find it. Not three minutes into the meal, I looked down and--you guessed it--spider was crawling on my shirt. I shrieked, stood up so fast I knocked over my chair, and started peeling off all my clothing. After Dr Hyde stopped laughing, he did what he always does and caught the spider for release outdoors. For this I married him.

2) I do not keep a clean house. My parents always did. I admire clean houses. But mine is regularly a disaster. I regret this, but not enough to do anything about it, except when guests visit.

3) I am better at the Times crossword than virtually anyone else I know. Also, Scrabble. The corollary is that if I don't win a game of Scrabble, I am upset and sulky.

4) I once slept with a guy I met on a plane.

5) Although I am generally a good cook, I regularly make the mistake of thinking that if 1 tsp of [ingredient] would be good, then 2 tsp would be even better! It turns out, this is only true of cinnamon, cardamom, and ground coriander. Pretty much everything else, no. Knowledge doesn't stop me, though.

6) When I was younger, I had insomnia. I would lie awake for an hour or two just thinking--replaying conversations, imagining futures, etc. Eventually I found that the best way to shut my brain up was to memorize poetry. A sonnet is about the right length, although once during extreme insomnia/boredom I learned "To His Coy Mistress." After I've spent 45 min or so memorizing a piece, I can focus on repeating it and thereby fall asleep. Something about the rhyming and scansion helps. To this day, if I really can't sleep I will get up and find a book of poetry, or repeat poems I already know. I know a number of poems by heart, plus some unusual song lyrics ("Antimony arsenic aluminum selenium").


I tag Juniorprof, juniorprof, JrProf, JP, Joon-yah, and JUNIORPROF. And Anonymoustache, if he feels like it.