Easily confused

Earlier this week a colleague asked, "The Super Bowl is this week, right?"

"Yeah. Sunday."

"It's Sunday? I thought it was Thursday. Isn't it always on February 2?"

"Nope, you've got Super Bowl Sunday confused with Groundhog Day."

"Well, I knew something was happening Thursday."

Wishin' my week away

Now in the future, cloners won't make much money

This week I emailed an old friend the link to this article about a Japanese researcher's plan to clone a mammoth. They plan on using an elephant as a surrogate mother for an egg implanted with a nucleus from a mammoth cell taken from a specimen that was preserved in ice.

I wrote:

Remember when you used to say that some day they'd clone them successfully, and then they'd become pests and start knocking over your garbage cans in the middle of the night and you'd just shake your head and say, "Damn mammoths. Why'd they have to bring THOSE back?"

Well, looks like we're on our way.

He responded:

I only remember that because you brought it up and I thought, "yeah, that sounds like something dumb enough to come from my lips."

If you go to Eastern Europe though, you'll see some of the women and know that these Japanese researchers are wasting their time...Mammoths are alive and well.

Is he alive or is he dead? Has he thoughts within his head? We'll just pass him there. Why should we even care?

This week's seminar speaker was a guy who was involved with the sequencing of Ozzy Osbourne's genome. I wrote down some quotes from his talk (the only notes I took, and only because they were hilarious).

Ozzy's motivation for participating in the study? "Given the swimming pools of booze I've guzzled over the years, not to mention all of the cocaine, morphine, sleeping pills . . . you name it, there's really no plausible medical reason why I should be alive. Maybe my DNA could say why."

When they analyzed his genome, they found some unique gene variants, one of which was a protein that alters the way his body processes alcohol. Ozzy's response? "I used to drink four bottles of cognac a day. I'm not sure I need a Harvard scientist to get to the bottom of that mystery."

Ozzy possesses a gene that makes him more resistant to heroin addiction. His take on that? "I was never addicted to street heroin, 'cause it made me throw up. A terrible waste of booze."

Ozzy's genes make him slightly more likely to develop an addiction to cocaine. Apparently he didn't buy that: "This must be bollocks, because anyone who takes coke as much as I did gets hooked."

The presence of other alleles that they found mean that Ozzy is more likely to hallucinate while on marijuana. He did believe that one: "Makes sense, although I was usually loaded on so many different things at the same time, it was hard to know what was doing what."

He also has one region of his genome that contains DNA sequences from Neanderthals. Apparently it's very common for Europeans to carry Neanderthal DNA sequences. Pretty cool stuff in my opinion.

Kind of makes me want to go get my genome scanned so I can find out what unique traits I'm carrying. I doubt mine would generate as many headlines as this one does though.

Spent the night in Utah in a cave up in the hills

Last week I spent a few days in Moab, Utah for a scientific meeting. My boss, his master's student, and I skipped out on a session of talks so we could go check out Arches National Park.

The road through Arches:


Along the roadside:


Cairn marking the trail:


Stone steps:


Approaching Delicate Arch:


Delicate Arch:


We did this the morning of the day that park ranger got shot. Pretty crazy. I hope they catch the guy. We saw the beginning of the manhunt. There were well over a hundred law enforcement officials, and even an FBI helicopter.

And in case you were wondering, the meeting was fun (I knew a LOT more people there than I thought I would, including two very good friends), my talk was well received, and I'm told I did a good job even though I went into it with very little preparation (considering I was still writing it at the beginning of the session in which I was presenting - Who says procrastination never works?). Next year's is in Mexico. I'm already starting to lobby my boss to let me go to that one.

With the white unicorn across her shoulder

I gave a final exam to my summer students last Friday. I finished the semester with a little segment about Conservation Biology, including a bunch of stuff about human impacts on biodiversity. In that lecture, I talked about the effects of habitat fragmentation.

The day before the final I got this email from one of my students:

I'm also still confused on the Edge Effect... can you explain that for me again? Is the Edge effect in correlation with fragmentation?

I wrote back to her:

Edge effects are definitely correlated with fragmentation. There are some species that do well at the edge of a forest (e.g., deer, elk, etc.), and others that need to be deep in the forest because they can't survive close to the edge (e.g., most of your mythical creatures like unicorns, centaurs, sasquatch, etc.). So, the more fragmented the habitat becomes, the closer those organisms that would be in the middle of the forest are to the edge, so they wouldn't survive as well.

I am nothing if not a professional.

I've got science for any occasion, postulating theorems formulating equations

In one of my classes this week I was explaining the scientific method to my students.

"The first step is observation, which is basically just that you notice something and start thinking about the reason why that's what you see. Then you develop a hypothesis that might explain your observations, and make predictions based on that hypothesis. Next you design an experiment to test the hypothesis, you analyze the results of the experiment, and draw conclusions based on those results. You can determine if the results support the hypothesis, and if they don't, you come up with an alternative hypothesis and test that."

Then I gave them an example of something that I'd been talking about in my other classes this week: sexual selection in guppies.

"Male guppies have colored spots all over their bodies, which turns out to be a way that females choose which males to mate with. People have done experiments to show that, but it all started with someone making the observation that males are brightly colored and females aren't. Then they came up with a hypothesis about it being related to female mate choice, and designed a set of experiments to test that. Think about it. You could basically set up a tank with a female and two different males, one brightly colored one and one dull one, and sit and watch to see which one the female mated with. It'd be like watching fish porn. But that's probably not the kind of stuff you want to go look up on YouTube."

I probably should have left the last two sentences unspoken.

So sentimental, not sentimental no

Once again, it's time to share the highlights from my TA evaluations from last semester. As always, these are taken verbatim from the evaluations themselves, so don't blame me for spelling and grammatical errors.

The Lab
What was your favorite lab exercise? Why?
- Pig disection. We Disected a PIG!
- Push ups. It gets me pumped.
- Invertebrate diversity I and II. Because worms, clams, and crawfish are probably the most exciting organisms to dissect. Also the starfish gonads get me excited.

Which lab experienced was most informative and educational for you?
- [Field Trip]. On the ride up, a fellow student said to his friend, "Why does anyone come out here? There's nothing out here, and Vegas is 15 min away!" I learned people can be dumb. And I'm a biased jerk.

What was your least favorite lab exercise? Why?
- Everything with plants, hate plants.
- Invertebrates =( gross

What is the major weakness of the lab?
- The pine cones suck
- Some ppl suck

The Laboratory Instructor
How would you rate your lab instructor as a teacher?
- Bill Clinton!

Assess your lab instructor's knowledge about the topics covered
- Pro!!!
- Freakishly thorough
- He knew everything we needed to know . . . and nothing more.
- He is smart, yo!

Assess your lab instructor's examination policy, fairness, and grading.
- Very fair! Especially in all situations.

What were his/her strong points?
- Being a damn good man.
- You are awesome, [Minnow]! Hot and helpful.
- Pure awesomeness.
- Euthuastic*

How could he/she improve?
- By giving me more 10/10.
- Listen to better music. Just kidding! :)
- Build a time machine and convince former self to not get married.
- In every way imaginable. Just kidding. Nah, just kidding again. No, just kidding. Again.

Then there was the guy who merely wrote "I &hearts [Minnow]" across the entire page, and also signed his name. Should I be flattered? Or afraid?







*Pretty sure they meant enthusiastic.

I'm in love with the size of a desert

A few days ago I went with a friend to survey abandoned mines. A day spent doing that beats a day working on manuscripts any day of the week. My friend put me in charge of taking pictures of things. Here are a few of the pictures I took.

A mine entrance


Scary structure - we could hear dirt falling here, so didn't proceed any further


The area where five of the openings were


I made a comment about the harsh conditions these miners were working in, and my friend said, "I know. You look out at that, and it all makes sense why Nevada has legalized prostitution." He's got a point. We almost had to go get some prostitutes ourselves, and we were only out there for a day, and we weren't even blasting holes with dynamite or moving ore carts or anything.



The mines were fenced off in order to let people know to be safe and stay out


Some were fenced off better than others


This mine was one of my favorites


Even if it had experienced instability at some point as evidenced by this giant rock that had fallen from the ceiling


The mine was old enough, and damp enough, that some miniature stalactites had formed


Guano!


This was the mine with the coolest entrance. Fine. I admit it. I'm a sucker for a good 'Keep Out' sign.


This looked a little more stable than the wooden structure pictured above, but we still didn't go down. Safety first!




This mine was really cool too, in part because of the rails for the ore carts. Turns out that's not just something you see in old Scooby Doo cartoons and Donkey Kong video games after all.


The same tracks from the inside of the mine looking toward the entrance.


Guess what else we saw. Bats!!!






So there you have it. A slightly more exciting day in the life of Native Minnow.

Make it somehow all seem worthwhile

A few months ago I submitted a manuscript for publication in a scientific journal. For those of you who don't know how the process works, the manuscript gets an initial look to make sure the formatting requirements are met, and that the subject matter is appropriate for the journal. If both those things seem to be okay, then the editors send the manuscript to other researchers who are familiar with the subject for external review. Those reviewers will go through the manuscript, and produce a list of concerns such as problems they see with the analyses, problems they have with the conclusions that are drawn based on the results, etc. The reviewers then send those comments back to the associate editor who is handling the manuscript, along with a recommendation of whether or not they feel the paper should be published in the journal. The associate editor will also read through the manuscript and provide comments, and based on those and the recommendations of the other reviewers will make a recommendation to the journal editor. All of this usually takes a few months.

Last week I received comments for the paper I submitted, and they were all favorable. However, there are some issues that one of the reviewers felt needed to be addressed, so I've been revising the manuscript to deal with those. Some are more time consuming than others, and that's when I begin to wonder why all the comments can't be like some of those from the associate editor:

"Line 35: Please include references that support this statement.
Lines 311, 323: may be extra spaces at the end of sentences.
Line 408: Period at end of sentence is strange - possibly bold or larger font.
Line 415: large-water not large water"

Those are the easy ones to deal with. That said, I'm almost done revising, and the paper will be accepted once I resubmit it to the journal (which will hopefully be in the next couple days) . The only bad part is that it's merely a side project that should've been published years ago.

That's right, I'm the egg man

During yesterday's lecture, I started talking about how changes in temperature can cause a protein to change its shape and lose its function.

Then, for an every day example, I gave my students the example of a fried egg. Here's my quote:

"When you heat the egg, the protein changes shape, and the clear part becomes white. When you cool it back down, the egg stays white, so those proteins do not regain their function. They do however, retain their deliciousness."

I repeated that to a friend later in the day. He said it's a wonder that I don't have at least one student off him/herself every lecture.

The whole valley looks like someone's body, and all the people look like little scars

One more post about my trip to Idaho, and then I'll shut up about it. I swear.

I met the Evilutionary Biologist. Pretty cool guy, although I had no idea that he'd be so ultra-competitive when playing shuffleboard on a warped shuffleboard table. He and JC Marshall (who did a post-doc at Yale) beat me and my friend in every game we played. When I voiced frustration to JC Marshall about that he said, "That's what happens when you go up against two members of Skull & Bones."

"You're not in Skull & Bones though."

"I cannot confirm nor deny that."

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A mini Reese's peanut butter cup is probably not worth crashing your car into the Salmon River over, just because you are trying to unwrap that rather than focus on staying on the road.



However, that didn't stop me from trying.

You may be thinking that it's time for an intervention, but I'm not an addict. I can quit anytime I want.

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Nothing illustrates a person's glaring lack of intellect more than saying "These species have been shown to show . . ." during their talk.

And yes, I really said that.

The moral of this story? I am an idiot.

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And of course, some pictures from the road:

We drove through a real gullywasher (several actually - I'm not used to standing water on the highway)


And passed a stretch of a historically important trail



We spent a little time in downtown Boise




Spent an afternoon checking out Palouse Falls


And the channeled scablands of eastern Washington


The Palouse



There were plenty of wildflowers



And other scenic views along the way





Go ahead and admit that you're a little jealous. It's okay.

I'm so smart, too bad I can't ever get anything figured out

I just got back from a conference in Moscow, Idaho. It was nice to get away, even if it was work related. I gave a talk, and listened to plenty of others. My brain is entirely full. Who am I kidding? My brain was full after listening to the first talk.

My friend and I arrived just before the registration desk closed the evening before talks began. In a weird coincidence, the very first person we saw at the conference was the one other guy from our university who was attending and who happened to be walking up to the registration desk at the same time. The next person I saw was a friend who was working on his Ph D when I was working on my MS, and one of the next was a guy who was a post-doc at the same time. Strange that I would travel a thousand miles away from home, to a conference where I didn't expect to know anybody, and have that happen.

Before we got to Moscow, my friend and I made a wager. He set the over/under on hot girls who would be at the conference at ten. I took the under on the condition that they had to be legitimately hot, not just biology hot*. I won. There were only six**. Six hot girls out of 1200 registered attendees. That's a mere 0.5%. And you wonder why I'm single.

My friend told me he'd give me $1000 if I'd end my talk by saying, "And with that, I'd be happy to take any questions . . . Ladies!" He wouldn't have paid up if I had, but even if he would have, it wouldn't have been worth committing career suicide over, so I didn't. Not that I would've been able to say it with a straight face anyway.







*Biology Hot - a girl who is average looking, but when compared to other female biologists stands out as unusually attractive.

**And one of those may have been a duplicate.

Call it education it was somewhere in between

Thursday night. Last lab of the day. Most of the students are gone, but the diligent ones are making sure they've seen everything. As they're nearing the end of it, one group starts talking about going out for drinks afterward since apparently nobody has classes on Friday anymore.

Student 1: [Minnow] do you want to come out with us tonight?

Me: No.

Student 1: Why?

Me: For one, you're my students. But even if you weren't, I need to get up early tomorrow so I'm going to go home and go to bed.

Student 2 (who earlier had been talking about how he'd been dumped by his girlfriend of five years: Are there going to be women where you're going tonight?

Student 3: Why are you asking that? You of all people should know that women are nothing but trouble anyway.

Student 2: That's true.

Student 4: I know. We really are trouble. I don't even know what you guys see in us.

Student 1: I know what we see in you.

Student 4: There is that.

Student 2: No, I don't need that. I can take care of that myself.

Me: Alrighty then. How about we change to a new subject?

Student 5 (pointing to her lab manual): Yes, let's change the subject. So, getting back to lab stuff, I was wondering if you could help me answer this question.

[The Question: Most ferns are monoecious, having antheridia and archegonia on the same gametophyte. How might a plant like this avoid self fertilization?]

Me: I thought we were going to change the subject.

Now throats'll be slashed and flags'll unfurl

They say that a picture is worth a thousand words. I was going through some old notes from a conservation biology class, and found a couple of examples that demonstrate the saying perfectly. Well, almost perfectly.


Example 1: The Cichlids
One day in class we had a prolonged discussion on the high levels of diversity of cichlid fishes in the Rift Lakes that have formed in eastern Africa. These fish represent a textbook example of an explosive radiation. There are estimates of nearly 1000 species of cichlids in these rift lakes, even though the rift lakes are relatively young in geologic time. The lakes formed as a result of plate tectonics because the plate that eastern Africa sits on is slowly pulling away from the rest of the continent. This has resulted in the formation of a deep valley that has filled up with water in some parts. Hence, any organisms living within these lakes had to get there within a relatively recent time frame, and the sheer number of species found there suggest that they must have evolved at an accelerated rate.

While the fish community represents a large amount of genetic diversity, the professor made the comment about how all the diversity might eventually be wiped out if the two plates separated completely. This would be because the rift valley would eventually fill up with sea water, which would obviously kill off any freshwater species. So it's a conundrum. While this system represents a classic example of rapid evolution (side note: there are fish so specialized in these lakes that they only eat the eyeballs or scales of other cichlids), it may also only be a blip on the screen of evolutionary time. That's if all these species eventually become extinct.

I'm not doing the conversation justice here, but I remember it as clearly as the day I sat in the classroom. However, here are the only notes I took during that conversation:





The second picture is the national flag for the country that will be sitting on the shoreline of the newly developed seaway: Dead Cichlid Nation*.



Example 2: Bees
We had another discussion about how we need to be mindful of changing environmental conditions when thinking about conservation and how it pertains to plant and animal distributions. Just because an organism occurs somewhere does not mean that it was always there, just like absence of an organism from a certain area doesn't guarantee that it's never occurred there. Anyone familiar with the fossil record knows that. This could be important when planning reserves. If possible, you want to conserve enough of an area that things can shift around if they need to. That usually isn't possible because of the financial obligations and politics, but it would be ideal.

The example our professor gave us when trying to illustrate this point was the continent of Antarctica. Today it is obviously covered with ice, but that hasn't always been the case. He mentioned a fairly recent study that talked about how Antarctica was once a much warmer place, and showed that bees migrated from Africa to South America across Antarctica (more recently than when all three continents were joined together to make up Gondwana).

Here are my notes from that discussion:



That would be the flag** for Frozen Bumblebee Nation.








*Incidentally, Dead Cichlid Nation would be one of George W. Bush's favorite countries because of the mass extinction rate associated with its formation - so glad that guy's not our president anymore.

**One of my lab mates looked at my notes while I was drawing these flags, and she interrupted the class by laughing too loud. The professor was not as amused. That may have been the reason why he started disliking me. I'm not sure about this.

Can you imagine the clones at war with the 'bots?

The people in my research group meet every Friday to discuss a recent journal article pertaining to the research we do. A few weeks ago our class was cancelled because most everyone was going to be out of town, so the grad student who was assigned to lead the discussion postponed her paper for a couple weeks. Her paper was to be on a study that used the entire mitochondrial genome to examine population structure of woolly mammoths. Once class was cancelled for the week, I decided to put off reading it until the week that we were going to discuss it.

The following week, another grad student (who studies birds) was having some difficulty settling on a paper, so called me to see if I had any suggestions. She mentioned that she wanted to have us read a paper that used the entire mitochondrial genome to address similar questions with bears. All I could remember was the journal and the complete mitochondrial genome part, so told her I thought that was the one the other grad student had already picked, so she decided to go with a different paper instead. It turned out that I was wrong, so the following email exchange went over our listserv.

Student 2: Hi. Sorry it's late, I wanted to do the bear papers but [Minnow] said [Student 1] was going to do, so found something else.

Student 1: What bear paper??? Unless bear = mammoth...

Advisor: Bears, Mammoths...all the same to bird people...

Student 3: Or fish people...

Me: You mean bears aren't mammoths? I thought they were the same species. My bad.

Student 4: When I read the email I assumed there must have been a new statistical phylogeography study on bears; that concluded mammoths were in fact nested in with the bears. [Minnow] confirmed to me that he knows mammoths aren't bears.

When we finally got around to discussing the mammoth paper, we ended with a discussion about the possibility of cloning a mammoth. One of the professors had this to say afterward: "Cloning a mammoth. That's not interesting. Cloning a Neanderthal, now that's interesting. Maybe we could clone eleven of them and see if they could play football. I'd pay to watch that."

So now we have a practical application and wouldn't be cloning Neanderthals just to see if it could be done.

Did you think I wouldn't recognize this compromise, am I just too stupid to realize?

Now it's time to share some tips on how to write, as given to me by my advisor:

"Simplification is always good. You should assume* that the people who are reading your work are stupider than you."

I'm not sure if I should take that as a compliment or an insult.








*And people wonder why scientists tend to be arrogant. With training like that, how can we help it?

I tell you what mathematically I'm having it, I want to live on science alone

Do you ever have those days where you wonder why you chose your profession? I had one of those yesterday as I was trying to make it through a paper describing a computer program that looks like it'll do something I've been trying to figure out for a while now.

Here's an exerpt:

The goal is, therefore, to determine for each i from 1 to n such λ(i, z_i, k_i), where z_i = 1 or 2 and 0≤k_i≤K_max, that the resulting solution has the maximum V. In order to do it, we estimate for each λ(i, z_i, k_i) the maximum V of all the solutions containing that configuration. For any a_i in F consider strings F' =a₁a₂…a_i and F" = a_ia_i+1…a_n. For each λ(i, z_i, k_i) denote the maximum V of all the aligned solutions of F' that end with λ(i, z_i, k_i) as P(i, z_i, k_i). Denote the maximum V of all the aligned solutions of F" that begin with λ(i, z_i, k_i) as Q(i, z_i, k_i). Let for a particular λ(i, z_i, k_i) the sum of the corresponding P and Q be the maximum of all aligned configurations at i. In that case, the maximum V of all the solutions of F containing λ(i, z_i, k_i) equals the maximum V of any solutions of F.

And on it went, just like that, for another six pages. I didn't understand any of it. I showed it to my advisor and he said something like, "Well, with that many equations, it must be right."

Words to live by.

You could follow logic or contest it all

If you haven't already guessed, I am always able to entertain myself, even while doing something as mundane as writing an exam. For example, here's a question that I put on the test my students will be taking today:


Consider the following chemical reaction: Fe + CuSO₄ → FeSO₄ + Cu. In this reaction, Iron (Fe) loses electrons and Copper (Cu) gains electrons. Copper is acting as a(n) _____________.

a) oxidizing agent
b) enzyme
c) reducing agent
d) deionizing agent
e) selfish jerk

You've just gotta smile and hang out with intelligent people

I'm back. Did you miss me?

No?

Oh.

Well, that's a bit awkward, isn't it?

Anyhoo, the meeting was pretty cool. I got to leave the heat of Las Vegas, see some old friends, hear some smart people talk about smart things, etc.

A few thoughts from the meeting:

- Generally speaking, biologists are not a particularly attractive group of people (present company excluded, of course).

- Whoever suggested it would be a good idea to drive to Minneapolis from Las Vegas in order to save money is an idiot.

- I am an idiot.

- After driving for twenty-seven hours over a three day period one relishes the chance to walk everywhere, even if it takes 30 minutes to reach the destination.

- It's a little scary crossing bridges in Minnesota.

- Even with talks going in nine concurrent sessions, there are still times when there's nothing worth listening to.

- Really smart people make everything sound so easy.

- I am incapable of walking on a footbridge across the Mississippi River without singing "1814 took a little trip . . ." in my head.

- I need a better way of dealing with stress.

- When presenting your research at a national meeting it is best to meet the expectations of your audience rather than presenting a talk that is too elementary.

- I'll try to remember that for next time.

- Sometimes when you don't know what you're talking about it's best to take the entire time allotted without leaving any time for questions, especially when the audience includes a few of the leaders of your field of study.

- It's not good to joke about how you're glad you didn't allow time for questions from certain "big named" scientists in the audience to ask you about something you wouldn't know the answer to when one of the "big names" you specifically mention is standing ten feet behind you.