Importance of being dumb - oh science...

Taking break from student horror stories for a minute I recently came across an interesting article, which I have linked at the bottom (free access) for those that are interested.  The gist of the article, which we will go into more detail about in a moment, refers to the need of stupidity in graduate school and to be successful in science.  I had an interesting applied moment when I read this in light of my graduate career so far.  I remember reading an opinion paper (which I cannot find now for the life of me) in a journal that talked about how being in graduate school makes you feel stupid, even though being in school means to some degree you are pretty darn smart.  Recently, with my comps (ideally) looming next semester I've heard more than a few talk about the need for absolute humility while taking the oral component - in short explain what you know while never appearing as though you think you know everything.  Let's discuss.

First off, graduate school does make you feel stupid.  Part of this level of education is not taking regular classes but having them as seminar or discussion - to integrate advanced topics and reasoning.  Prepare as you will, the professor will always lead the discussion in a way that you never thought of and there's always someone else that says something profound (well, it's not always actually profound, but you're little brain makes it feel that way).  You'll find yourself scrambling to write down every word and still walking away only half following what the hell just happened.  This mixes very interestingly with the societal pressure to cut the tall weeds (aka it is often socially unacceptable to be the really really smart one) and the academic pressure to weed out the scrubs (aka figure out who really doesn't know much).  Most new students are too afraid to say anything, afraid to sound stupid or to come across like they are "attacking" another idea.  So you sit, smile, and nod your head.



Of course, this doesn't last.  Here in my 3rd year of my PhD I find myself participating more often, especially in classes or seminars with a large proportion of graduate students.  Still keep pretty pursed lips though in large scale settings with lots of faculty.  I'm not really a shy person, but what do you do?  Just try.

Now onto the comps piece.  We talked a little bit about this before but for the conversation to continue we all need to be on the same page.  For a PhD student, the only way to move from "student" to "candidate" (aka even be considered for grants or graduation) is to take comprehensive exams.  This differ from department to department and school to school.  Usually there's a mixture of written and oral exams.  Some use a mock grant proposal and defense.  Others use large scale tests.  My department has a week of essay papers for the written.  Each day a different committee member (minimum of 5, and trust me that's ALL you need) will send you a set of questions each day.  They will require you to produce facts from papers you have read as well as extrapolate and apply them to the questions.  Assuming you pass these there is a day of orals, whereby you sit in front of your committee and for 4-6 hours they verbally ask you questions.




Okay, enough on that drama for now.  I am more than sure as they approach and I sink in deep for survival there will be more on that.  The point of that conversation is to move it further.  Another student in the department (with another adviser) was telling me horror stories of her first failure and her second try (you only get 2) in which she passed.  She told me one of the biggest differences was attitude.  She's a smart cookie and going into her first one felt confident.  Responding to this her committee became very aggressive and would outwardly tell her that they didn't like whatever thought process she had followed to get to an answer, even if it wasn't technically wrong.  Afterwards her adviser berated her for her performance, leading her to almost quit.



Thankfully she didn't quit and when she tried again she went in with her head down.  She was still able to think through answers but by being less confident she got more positive responses and received much less aggression from her committee (plus she passed).  Now take any story with a grain of salt but it seems to me that part of the point of comprehensive exams is to show you how much you DON'T know (or can't know YET) and look for you to show signs of humility and "absolute" stupidity.  Keeping in mind of course that these exams also look for you to prove you do know the basics in your field and would be a respectable representation of it (not "relatively" stupid).

This brings us to the paper I mentioned at the beginning of this conversation.  The author actually teases at my assessment above, stating if a student is able to answer all the questions posed to the fullest it is the committee that failed the exam.  By that feeling of absolute stupidity it pushes us to question and inquire, to keep moving beyond the bounds of current knowledge to learn and regain the feeling of shock and awe at the complexity of the universe.  If we ever feel like we know anything, then we stop learning and stunt the learning of those around us.  In the universe of science, you shouldn't feel like you know what you're doing because that's what leads to the big discoveries.  So feel absolutely stupid but know that you're not relatively stupid.  You know a lot, but you can't know everything!

Check out the article.  It's a well written essay that is easy to follow, even if you don't get into science itself per se.

Swartz, M.A. 2008. The importance of stupidity in scientific research. Journal of Cell Science 121: 1771.
http://jcs.biologists.org/content/121/11/1771.full.pdf+html-

Let me know what you think or share related experiences.  Your story can only lead to inform others coming through and make those who have felt it feel less alone.


"Do not be afraid of defeat. you are never so near victory as when defeated in a good cause" Henry Ward Beecher

TA: It's always worth it

I know the past couple of weeks I have spent so time doing a little student bashing and talking about many of the frustrating features of being a teacher.  So here I'm going to put forth some examples of students that DID care and DID really freakin' give me everything they had.  The thing to remember is, no matter how many students you have swear at you or walk out, if you have EVEN ONE that comes out a better person, that you were a successful teacher.

1. So even when a student is not necessarily successful with his/her actual grades, it is often clear when a student putting forth a concerted effort to change their path.  Student A (again, different than all the other student A's from past weeks) was a mess from the start.  He sat at the trouble lab table and after 3 quizzes was looking pretty desolate.  However, after the third quiz he actually came into my office to talk to me about it (a miracle in itself).  He wanted to go over the quiz and discuss how he could change his study habits to improve his grade and ultimately not fail the exams or class.  Not only did he come in to my office every week to study but moved tables, sitting with a group of final year nursing majors (a good find in an anatomy course-I was pretty fond of them myself).  He still did fairly poorly in the class, which I largely akin to poor test taking skills, not learning problems.  However, he was teetering on the edge of the D/C range so I was able to bump him up due to clear effort and participation. He cared and put the effort in to make a difference.  Those situations always make me care so much more AND feel good about what I do.(ps does anyone else think this button looks less than adorable and innocent?!)
2. Student B begins to put a counter balance on all the stupid excuses I've ever gotten.  I received it via e-mail initially.  It came in during class, but of course I didn't get it until directly afterward.  It had been particularly snowy this year, seemed every week for a while had the University shut down for at least part of one day.  The e-mail was not actually from a student, but from a mechanic.  Apparently, the student had slid on the ice and another car plowed right into her.  She was fine but was so worried about missing class she asked the towing company that retrieved her totaled car to contact me.  Phone, address, and manager.  Completely legitimate.  For something like this I would have probably not pushed too hard even without the e-mail but in addition when she sat in the next day's class she brought me the DAMAGE ESTIMATE.  The problem with situations like these is because she went so far beyond the call of duty, I have A LOT of trouble dealing with most other excuses! 
3. For my final piece of evidence I present to you the following image I made from an actual e-mail.  I received this e-mail after my first semester of teaching Anatomy and Physiology (second semester teaching ever).  It was a particularly arduous class to teach, most of the students were a little younger and it was partially filled with athletes that were "just wasting time until drafted."  I was exhausted and a little disheartened (this is the same class I had the plagiarism issues I referred to before).  A wonderful student sent this to me the last week of the semester (technically finals week but labs don't have finals).  Enjoy this and hopefully it lifts your day like it always lifts mine. 

Next week I've got some unusual students that give me a head tilt just thinking about! Got some happy stories? Please share! Every TA has a bad day, class, or even semester! Share the love!


"When I was younger I thought success was something different. I thought, " When I grow up, I want to be famous. I want to be a star. I want to be in movies. When I grow up I want to see the world, drive nice cars. I want to have groupies." But my idea of success is different today. For me, the most important thing in your life is to live your life with integrity and not to give into peer pressure, to try to be something that you're not. To live your life as an honest and compassionate person. To contribute in some way." Ellen DeGeneres

TA: above my pay scale II

Alright, as promised some more stories.  These little ditties probably rate as the most astonishing and brazen students I've ever had.  Step out into the bathroom and recollect yourself between classes kind.  My advice for all of these situations? P p p poker face p p p poker face.  NEVER let a student know they've gotten to you, even if you have to be stern to get them to behave.  To a naughty student, your emotional reaction is winning and will likely feed them to do it again.  Same goes when you get goofy answers or excuses, practice your stock teacher face.  It's your best weapon.




My first semester teaching I noticed that I was having a huge attendance drop off after the mini lecture portion (aka not looking at the lab materials).  It's hard with college students since you have a little less power (but should be able to assume some degree of maturity).  Below are a list of reasons I've heard to miss class or tests.  This is through all my years but after my first semester I learned to kill that down to a much smaller proportion.

1. Student A told me he needed to get out of class early because his buddies were doing a weightlifting group.  I felt like I didn't need to say no, that is NOT even REMOTELY an appropriate reason to miss class.
2. Student B scheduled his dentist appointment over class.  When he asked to leave after only 30 min of class I asked how bad his teeth hurt. He said they didn't, it was just routine. Poker face. I told him that that will be unexcused since he opted to do it over class. Seriously?
3. Email 2 hours before the exam. Student asked to take the test in a later section of the week because he'd been busy with other classes and didn't have a chance to study.  Now I actually am very sympathetic to this concept and if a student comes to me before a test and says that a day is overloaded I'm happy to let them bump, it's all the same to me. But right before the test? Really?  Surely you jest.
4. Another student emailed me the day before the test, saying she'd had some away tournament and had been gone all weekend, therefore unable to study.  Now admittedly, I'm very UNsympathetic to this.  If you're paying to go to school to better yourself, school should come first .  Emergencies aside. I always hated being paired with these people in school.  That job is going to be costly when you have to retake courses and double your overall tuition spent because you were trying to get a couple extra bucks.  I worked through college, I get it.  But I also actually went to college.  In addition I had a student that was paying her own way through college and worked 40 hours every weekend and NEVER asked for an extension.  Given all that, I'm sure you can imagine what my response was.  She should have studied during the week or on the bus.
5. Noticed a student packing up his things after my talk was over. When I asked him what he was doing he told me he had all the materials. I told him he didn't even do the lab. He responded by saying that the class was completely optional. P p p poker face.  I told him that class was certainly not optional.  I did make a big mistake here though. About 20 minutes later I look up and don't see him. I asked out loud if he had decided to leave. Timid yes' and much quiet followed.  Yeah, that was definitely inappropriate of me.  Poker face fail.  

And the piece de resistance, the 3 worst situations I've faced.

1. For the first paper homework in one of my classes I noticed a rampant amount of textbook copying and plagarism.  I talked to the LC and got the okay to allow them to do rewrites.  I sent out an email explaining the situation.  I said if they wanted they could rewrite any questions that fit the bill and write 1 paragraph on defining plagarism and get any/all credit back.  If not, they would receive the grade from what they had already turned it.  HEAVEN ALMIGHTY!!!  You would not believe the angry emails I received, telling me what a hard a$$ I was being and that it wasn't fair they had to do rewrites over their spring break. Now bear in mind that I had to continuously grade through this whole period and it was optional. Moreover, they wanted to be told which questions were bad and worth rewriting, like it would be no time drain for my to grade, hand back, and regrade (and defeat the entire purpose of the exercise in the first place).  Besides, realistically you know if you copied text from somewhere, you're just looking to see if I noticed... I actually had a student tell me he didn't have time for this $h**.  I wanted to scream TAKE THE EFFIN ZERO THEN IT'S LESS WORK FOR ME!  It's not my fault that either they were lazy or their previous courses had failed them.  "No good deed goes unpunished. No act of charity goes unresented!"  I made a handout that I give out now BEFORE, defining it and giving examples of good answers and plagarism/copying.  NEVER AGAIN!! 
2. While grading a homework, I found 3 girls' answers to be all the same.  Now, it's always funny how much students think we DON'T notice this, but usually it's really freakin' obvious.  We read all the answers back to back AND we have the same textbook you do. Put on your try face.  Now this was particularly obvious because the answer made no sense whatsoever.  I had no idea what they were talking about and was pretty sure one of them spent too much time in the thesaurus (they think they're clever, like we have no vocab...).  When confronted, two of the girls admitted they were roommates (LEAST FAVORITE THING).  They took the zeros.  The other came in and said she had asked for help from the other two but had rewritten it.  So I asked her to explain it.. She balked and admitted she just copying the answer from a facebook message (DAMN YOU FACEBOOK!).  She said, I quote "I guess I should understand an answer before I write it down huh?"  Oh honey, I don't even think you understand the depth of this mistake...
3. I gave a pop quiz in my lab based on a reading their lecture professor assigned.  A quick 5 question quiz, general enough to just see if they even opened the book.  Now I actually don't believe in pop quizzes, and understand the panic and groans that ensued.  Luckily for them the quiz was extra credit, which they found out afterwards.  This method works well, you're like a hero.  Well almost always, one student that I would normally call a very good student apparently found the situation particularly frustrating.  In red pen down the front of the quiz he wrote, "I don't know and I don't f****** care."  Of course, he used the actual expletive.  Needless to say I was stunned.  I took it to the LC who told me there wasn't anything I could do about it but give a zero, which on extra credit really isn't a punishment in my opinion.  The kid was super docile after I handed it back.  Still, I will never forget it.

Next week I think I'll lighten the mood.  I have some good stories too.  And I'll have done some regrading so I see a "stupid things kids write" section coming soon too!  Stay tuned and please leave comments!!

"Speak when you are angry--and you will make the best speech you'll ever regret." Laurence J. Peter

TA: Above my pay scale excuses

Hey guys.  So this is a segment I have deemed to call "above my pay scale."  The excuse types found herein are true examples of things that not only make you go "oh mercy" but are just viable enough so you can't ignore them or are long running issues that you'd like to run from.

Student A (not student A from last week): Student was missing from the first 2 weeks of class, which if you're teaching a lab, only meets once a week, so that's a significant proportion of class time as it is. So, after taking role and marking him absent I assumed he dropped and crossed his name off my paper roster (TAs are almost NEVER EVER given updated rosters. EVER.)  About half way through my mini lecture of course, guess who comes strolling in?  Right, so I tell him he needs to see me after class and carry on, can't spend precious class time on someone who doesn't think class time is precious right? So after class he comes up and asks what I need. REALLY?!  You can't possibly imagine why I would want to talk to you?!  So I ask him why he's missed class so much.  Are you ready?  Turns out he was TAing another class during this same timeslot so he needed to get that fixed before abandoning his class to come to mine.  I ask if he had spoken to our Lab Coordinator (LC).  Of course, he said no, he didn't think he had to.  I had to stare for a moment, thinking you teach and you still thought you didn't need to let anybody know why you were missing class.  I told him he was unexcused until he talked with the LC.  He said nah, he'd pick it up.  Yeah okay whatever buddy, do as you wish, you're now above my pay scale to argue with.



Student B:  Student B had pre-emailed me (good girl) that her mom had a medical emergency and she needed to miss that week's classes. I gave her the go ahead (I'm a momma's girl myself).  After THREE weeks of no communication she comes in to take the final lab practical.  She's obviously allowed to take the test and I ask her to see me after, wondering how she was even going to complete the exam with half of the lessons completely missing.  After class she has the last 3 weeks homework assignments (given to her by friends) and a note from her mom that read, "XXX was home with me. I fully expect her to be responsible for her missing work."  So, after the 8th grade, that kind of note means NOTHING, but she was a good student so I tried to humor the situation.  I asked her what was going on and that I needed something more substantial.  I told her I believed there was something real to her absence but I couldn't be favoring her by going on her word.  She told me her mom was sick and it wasn't her place to talk about it.  They didn't go to the doctor so she only had her mom.  At this point I assume her family was under a delicate situation and likely there was some mental illness at check here.  Still, it broke all my University Sanctioned rules to run with it.  I took the first homework, from when I had given her the go ahead to miss.  I told her very seriously to just talk to the LC.  If I get the go ahead from her then I would love to grade the other homeworks.  The student backed off and said she didn't want to start a fuss.  I told her I didn't have the power to say okay but the LC did, and that I believed what she told me. She said she'd think about it.  She didn't.  This was painful because I still believe something was wrong but at my level I'm not allowed to make decisions like that without any sanctioned excuse.  She still passed, but two zeros did some damage.



I've got more to come for next week, and I've only been teaching 3 years. If you've got any good stories or insights SHARE!!!


"Integrity without knowledge is weak and useless, and knowledge without integrity is dangerous and dreadful." Samuel Johnson

TA: excuse note stories

Ah excuses, easily the biggest bane of any teacher's existence, ever.  And at the college level, we've gone well beyond, "The dog age my homework."  The tales you will hear will range from the astonishing, to downright infuriating.  Of course they're not all lies, but even the truth tellers tend to go out of their way to make things messy.



Firstly, every year you will always have at least one student e-mail you the DAY a major paper is due or a test will occur.  Always.  And it's always some variant of "I'm so busy I didn't have time to do it!"  Normally my rule is, if you came to me with a legitimate issue BEFORE said date, I will probably roll with it if it doesn't start too many issues.  Examples of complete inability of students to follow this philosophy:

1. Student A shattered his dominant arm mid week that a paper was due.  You don't really need a note for this, they show up with a cast.  So I gave him an extension to go down to disabilities resources and get help with writing.  Easy!  If he had told me the day of or day before though, hell to the no.  You shouldn't be writing the paper 2 hours before class anyway and putting if off until then certainly doesn't earn you an extension.  Of course, this kid ended up turning it in later than the extension date anyway so he still could have lost points.  Round two had no excuse besides, "I forgot!"  Regardless the paper was terrible so the score was low enough that not only could I tell he'd written in that Saturday to turn it in in the middle of the night (it was due Friday) but I couldn't even justify taking off an additional 20%.
2. Student B sends me an e-mail after hours on a Friday. She states that she is leaving for a conference in an adjoining state with her club and won't be back until late Tuesday, therefore missing the field trip we have on Monday. She says she will go to the Thursday class. So, I have two major issues with this e-mail.
1. It's a conference, which means you knew about it more than 12 hours in advance so either you are lazy and didn't bother to use a pre-excuse as an actual pre-excuse or you fibbing. I made her show documentation so it was legit, but seriously, she's known since the first week of school, what?
2. I HATE (hate hate hate hate hate) when students skip the request stage and immediately assume they can jump in where ever or just get the notes and that's just fine and dandy. As a student you are SUBORDINATE. You have to ask. And in this case we had full classes so she couldn't just pop on to another day, there wasn't room in the vans. 
3. The first week of school contained labor day, so Monday labs were missed. However, the instructor decided that all safety training needed to be done that week. Therefore the students needed to hop in to one of the other 3 labs that week or to my extra session on Friday. Student Splinter Group C ignored the requirement and the very important step of TELLING ME. 
1. Did I mention all I require is communication? You know that first day whether you will have issues or not. It's like the pre-excuse, I just don't care as much when you show me you don't either!! 
2. Anyway, I digress. Come the following Monday I had 7 students who had not only missed training the last week but ignored even talking to me about it in class. I held them after and asked why they skipped. The average response? "I just got the information from somebody else taking the class." 
3. So...I was pretty sure I hadn't certified anyone else to do safety training. I told them training is more of a piece of paper and I needed them in the training with a signature of completion if they wanted to stay in class. Furthermore, since they skipped class without discussion they received an unexcused absence.
4. I actually had a student tell me she couldn't e-mail me because she didn't have access to the internet. Apparently for 7 days. I asked if she had been on campus at all, since we have free computer access. What I didn't ask was if her legs were broken so she couldn't walk up to the instructor's or my office either, the location of which were given in lecture multiple times. Miraculous healing she must have had.

 

Next week I'll post some more serious excuse situations. Have some good stories of your own? Let me know!!

"The history of our race, and each individual's experience, are sown thick with evidence that a truth is not hard to kill and that a lie told well is immortal." Mark Twain 

TA: tips and tricks of the trade

Now I want to start this off by reminding you that this in no way is the perfect set of rules for a TA.  Every TA is different, and so is every class, course, professor, student, and coordinator.  Take them with a grain of salt and use them carefully!

I'm going to spend this week going through a list of dos and don'ts.  Definitely question, comment, and add on!  I always love these conversations!!

DOs:

1. Be energetic.  
1. Students can smell weakness and feed on it like the brain slugs from Animorphs.  Sound confident and it really does go a long way.  
2. My first year teaching I was driving a van load of students to a lake field trip.  Along the way they said they could tell that it was Nematobrycon's first time teaching (the other TA, also female).  Of course I told them it wasn't and that she deserved respect, teaching wasn't easy.  Truth was though they had us backwards, I was the noob and Nematorbrycon was a seasoned veteran so to speak.  The difference is I am loud and bouyant while she is quiet and short on speech, lending her to look unsure of herself regardless of her competence. 
2. Be engaging.
1. Every chance to get to bring in student participation, do it.  If nothing else they'll be less likely to fall asleep.  It also helps to get a good feel for students and to learn names.  Teach Socratically.  The goal remember is to teach them how to learn, so by giving them some basics you can help them through just about anything.  
1. Use candy as a bribe, that works.  Just make sure they know they can't eat it until they leave (no food in labs ya?). 
2. My coordinator also recommends "danger colors." I've never had to employ this method but basically you draw a color randomly and go around the room so anyone with that color on will have to answer. Depends on the students I think how well they would respond.
3. Speak and write confidently.
1. Give the students assurance that you know what you are babbling on about. Even if you feel like it's a weak subject for you, prewrite your board work and think about what you say. Fumble around or need to change something on the board and you will lose them fast. Super fast.

Don'ts

1. Never say "Try harder"
1. Seriously, never say this. Chances are the student is trying to their capacity (whatever that is) and even if they're not it's a very frustrated piece of advice. You look like a complete pompous douchebag and they will likely stop trying altogether and feel you are entirely unapproachable. Which you are.
2. Never say " I don't know"
1. Even if you don't know, there are other ways to handle the situation that doesn't make them lose their faith in you.
1. Try attacking it socratically, can you think through it together?
2. Is it really pertinent? If not say that's above the level required for the course and in an effort to stay on track let it slide for now. After class, look it up and have it open for THEM as a resource.
2. Does it matter? Are they asking what the obscure stuffed animal in the corner is that was likely extinct 400 years ago? Then a "mmm I'm so sure on that one" is probably just fine.
3. HOWEVER, NEVER EVER LIE to your students. For one they take what you say is truth and you can severely harm their learning. Moreover if they figure out you fibbed you lose all their confidence AND, again, you look like a pompous douchebag, albeit an incompetent one.
3. Never let students run the joint.
1. Some freedom in a lab setting is great, it teaches responsibility and add comfort to their learning process, allowing them to focus more. Some informality at this level works too, be friendly and you'll likely get more active discussion. However, there will come a time when you need to stomp on a student. Be sure that when push comes to shove no means no. Some of them will tests boundaries, make sure you set a solid example.
4. Stay away from "wrong"
1. Especially if you are in a discussion moment within the lecture and asking for feedback, telling a volunteer straight out they are wrong can slow the discussion down dramatically. Make sure to smile and keep a positive flow. Say things like "well that's a good start" or "okay what it we thought about it this way." Try to redirect without spurning their attempt.

That's a solid review. Drop in your questions and comments and we can add more. Next week I think some funny horror stories to bring in the realism!

"Good teaching is one-fourth preparation and three-fourths theater." Gail Godwin

Teaching: Rules of survival as a TA

Okay, back again from a trip home.  Remember my family lives out of state from me.  Classes started today so back to the old grindstone and back to weekly posts.  We've done a lot of learny learny so let's take a break and talk about something else!

While in grad school one of the ways you're likely going to draw a paycheck is by being assigned as a T.A., or teaching assistant.  In the sciences, this generally means you run a lab and/or a tutoring session.  In total you will likely hold class about 6 hours a week, plus grading, plus classroom preparation, plus running open lab times and office hours.  They'll pay you for about 20 hours a week.  Let's just say you get very quick at grading.  I personally LOVE teaching.  Even when classes are at their worst.  This week I'm going to walk you through how a standard week for a science TA goes.  Next week I'm going to clean house with some nice do's and don't tips to help you along your journey.  This is a great topic for questions or experiences.

A week of teaching actually starts the week before.  At the end of the previous week you'll meet with your TA coordinator, your other TAs (usually anywhere from 2 to 6 of you total) and, rarely, the professor who teaches the lecture portion of the course.  You'll spend a little time making sure there weren't any major issues and the rest of the time getting the handouts and outline for the lab next week.  Although the coordinator will go over major chunks of material and go over pitfalls, they will not be teaching you the material.  Whether it's rusty, or even a little new, it is your responsibility to learn the material.  Don't panic though, you've already been through college and aside from some crap you were forced to learn that you DON'T remember there is a real benefit.  As I try to tell my own students, it's not about what you can memorize, it's about how you build your tool box that will allow you to tackle any problem that any teacher throws at you.  You absolutely have the ability to teach yourself just about anything and certainly have enough base knowledge to hack it.  I recommend making a detailed outline of the information you have to cover.  Not only will it ensure that you don't miss any major points when giving your talk but it will also make a good, discreet resource if you get a tougher question.

Alright, so then the week of teaching you'll have 2-3 sections you teach.  I personally like to break them up over the week, other TAs prefer to compound it up and do them all in a row and be free.  It's a balance and you need to decide what makes you the most comfortable.  So you teach and I won't go into any detail here and will go into lengthy tips and advice next week.  Before the end of the week you will also have to have 2-3 hours of office time, usually over 2 days throughout the week.  This makes for great grading time as students tend not to show up so much to these.  They come a lot right before the test and right at the end of the semester-aka times you don't care that they are trying to squeak by.  You do get a few good ones who put forth the effort.  I've used this time in the past to bring in students that need a talking to as well.  Generally in lower level courses but when I've flagged cheating or plagiarism I use this time to talk to the student face to face.  We'll talk more on this later, both in tips and as a particular horror story of mine.


Regardless of what method you use and how the semester goes, the best thing I can say is KEEP A PAPER TRAIL. If a student has an excuse, print out the email or photocopy it.  If you give extensions, write it down.  While you're grading, on your master sheet make note of what you accepted and what got half credit.  Post reminders on open lab times or office hours.  There will always be one student who will say "well my friend wrote basically the same thing on his test and got credit" or " I didn't know you had time for us to look at the specimens again!" Make sure if they run crying to the coordinator that you have something that shows, yes you did.  Then it's the coordinator's problem and likely WAY above your pay scale to deal with.  More on this next week!


"For every person who wants to teach there are approximately thirty people who don't want to learn--much."
W. C. Sellar and R. J. Yeatman

Speciation II: isolationism-ishy

Let's continue to think on and discuss this issue of speciation.  As opposed to the genetic concept, which we discussed last time, we're going to look at the other two popular versions of the biological concept and the ecological concept.  Hang tight!

The biological species concept is one of the more well known models and although it centers around several pieces of evidence, the core piece deals with reproductive isolation.  We've discussed this idea a little in the past when talking about the African Cichlid fish and again last time, in part, with the ring species example.  This isolation however, has many parts to it.  For the sake of simplicity, we'll talk about two general sections

1. Pre-zygotic isolation: Isolation that occurs before the completion of the zygote.  At the risk of over-generalizing and simplifying we'll refer to this as pre-mating.  These are the things most people think of-mate choice, mate and species recognition, behavior, etc.
2. Post-zygotic isolation: This isolation is a little less well known and can be a little more difficult to understand.  These are isolations that occur AFTER mating, basically penalties for poor mate choice.  Generally these refer future of the offspring.  This can be things like zygote mortality, sterile young (cannot produce offspring of their own like a mule), or a poor mix of adaptations (mom is adapted to one and dad is adapted to another and the middle ground isn't well adapted to anything).

The thing I want to reinforce here is that speciation is in fact a PROCESS by which species come about.  Usually you see these species first experience some post-zygotic isolation that will be reinforced by pre-zygotic isolation.  Generally a species isn't truly called until there is no survival of any young and that there is no choice mating between the different populations. 

Now the ecological concept seems a little more straight forward.  The idea here is that the species experience isolation based on their ecological niche, things like habitat choice, nesting, food choice, life-cycle and timing.  An example would be birds that choose marshier habitat and those that choose higher ground, dry habitat.  Different habitat and attracting different partners, thusly reducing the change of cross breeding.  Here you consider that the species are now filling (or starting to fill) different ecological roles.  

As you can imagine as straight forward as this can be (to breed or not to breed) there is a lot of space for haziness too.  With a shifting environment and climate you can be on the brink of isolation and suddenly end up with hybrids between the populations that are even more well adapted than either of their parents.  There are plenty of cases where, as with the ring species example, although you can identify clear separate species, they are not finite and have hazy zones in the long line that got them there.  So where do we draw the line?  If we are more strict we lose the potential to understand discrete ecological impacts and in some cases destroy chances of species or populations of receiving government protection because they they don't qualify under endangerment laws.  If we are more flexible with our definitions we get widespread confusion and, as some birders and avian biologists can tell you, infinite updates on what species are and which are mere groups.  And, as I mentioned in the last speciation post, you get some cranky extreme creationists that run with it like it's on fire.  So what do you think?  What is a species?

Feel free to post with your comments, this is a controversial and ever changing topic! I'm happy to discuss! I have the book I referenced and some additional sources from a class I took!

Until next time!

"It is by universal misunderstanding that all agree. For if, by ill luck, people understood each other, they would never agree." Charles Baudelaire

Speciation: What the and the why hows??

Speciation (process of species forming) seems simple enough on the surface.  Over time adaptation and evolution drive a divergence between two populations.  Let's take a population of birds.  The population splits as it colonizes around a large mountain range.  As each subset of the original population colonizes farther and farther around the mountain range, each subset is undergoing natural and sexual selection pressures.  Of course, these pressures are not the same on both sides of the mountain, you have different light, weather, environment, predators, nesting sites, etc. When the two subsets reach the other end of the mountain range and re-converge they no longer recognize each other as of the same species.  They choose different nest sites and even sing slightly different songs.  They are both different from each other and from the original source population.  This particular mechanism is referred to as "ring species."  The image below shows why.

As a side, when looking for an image to help show this I found a lot of creationism websites that use ring species and speciation as reason to show evolution does not exist.  They cite that such species are not stead fast and singular and thereby are not showing evolutionary process.  To this I say, by being fluctuating and changing they certainly aren't showing that they were put on this Earth in their perfect form then are they?  Ecology and evolution are messy, that's why they're so interesting.  If anyone actually knew the straight answer to everything, they'd get paid a lot more.

Now that aside, that issue of fluctuating species is the major point I actually want to talk about.  Apparently unbeknownst to our extreme creationist friends, it is not necessarily speciation that does the fluctuating, it is the way in which we define it.  Our example above shows speciation, up to three species total in the end.  The problem arises when we try to draw lines.  What about all of the colonies in the middle?  They're a little bit of everybody and would probably breed with more than one group.  What are they?  Hybrids may be the answer.  Mixes between two populations.  But that leads to all sorts of problems.  Let's take a step back first and look at why defining species is so hard in the first place.  Don't worry, we'll get back to this later.

Two guys named Coyne and Orr took time in their 2004 book on Speciation to figure out just how many different ways we had to identify species. Nine. Nine MAJOR ways with sub groups among them.  These range from change of habitat, to reproductive isolation, to genetic change, to biochemical effects and so on.  Now firstly I'd like to dispel the "genetics is the answer to all" idea.  I more than understand and respect using genetic code changes, especially since genetics of course is one of the necessary basic constructs for evolution to occur.  But bear with me and follow me through an example.

When I took my Phycology course (study of algae) I was confronted with a interesting and (at the time) frustrating situation.  We were in lab learning to identify different species of algae.  I was identifying one using the standard dichotomous key.  For those of you who are unfamiliar, a dichotomous key takes characteristics for a given specimen and splits them into 2 groups-Spines are present or absent.  You follow the pathway for your given sample and if you play your cards right you use these split characteristics to arrive at the proper identification.  See below for a very general example.


Now, when I had reached the end of the road I had two choices that led to two related but separate species.  The way to tell the difference was by color.  More specifically, I had to decide whether my specimen was "dark lime green" or "apple green".  Ooookay, so I was stumped, thinking what is the actual difference between these colors (since my 64 crayons box was at home) and was it distinct enough for the average person to get right, even with the correct illumination.  So I brought my professor, here on the Triggerfish, over and explained.  Hand on my heart, the conversation went thusly.  Triggerfish quickly told me the answer.  I was surprised and asked how it could tell.  Triggerfish responded that it just knew.  I asked if the coloration was useful, it replied no, there was almost no way to make a correct assessment based on that.  (Okay, so for you following along by in large these two species look the same).  When I asked how it knew, Triggerfish replied that it knew the genetic coding for the species in the area (Okay so the genes were different).  I then asked in the two species had any ecological differences, looking for habitat choice, temperature tolerance, nutrient requirements.  The answer? No. Bluntly.  (So functionally these species were identical).  Then angry Triggerfish walked away.  I promise you will hear about Triggerfish again, it was a particular thorn in my side and the side of my other grad student counterparts.  Facebook page dedication and all (of course not under Triggerfish, combined with a terminator spoof if I recall).  I'll discuss this in my teaching posts as well, "I just know" and "try harder" are things you never tell a student.



Anyway, I digress, my point is these two algae were separated into different species groups because they were genetically distinct somewhere in their lines of code.  This to this day seems completely pointless to me, different shades of green and a little obscene if you will.  Moreover it shows that what seems to be the most straightforward way of assigning species isn't any more irrefutable than some of the others.  There's always a dance of where to draw the line, and people will argue violently on where to draw the line.

Next time we'll hit on other popular ways to define species and where those have pitfalls as well.

Don't forget, questions or comments are welcome!


"In science the credit goes to the man who convinces the world, not the man to whom the idea first occurs."
Sir Francis Darwin

Paleoecology: A long-term complicated relationship. I can't break-up, my CD's are in his truck

Sorry about the delay, I was on a bit of vacation. Not thinking about school or work in real life and the internet universe as well. I'll make it up to you though!

Now, continuing on my previous train of though.  There are many ways in which ecology gets complicated and tends not to look as pretty as the previous post shows.

Let's look at some of my MS (Master's of Science) work as a starting point.

I worked in a field called paleoecology in order to tie in aquatic species with water quality to look at pollution affects on a lake over time.  Diatoms (see Fig. 1) are a form of algae that is made up primarily of silica, and therefore fossilizes in the sediment of the lake they live in when they die. What we can do then is take a core of the lake bed. Each year a new layer of sediment is added to the bottom of a lake. We can take a core of a lake, date it using chemistry (such as Lead 210 dating) and compare what things are in each layer of the core with the associated date.  This allows us to track ecological community changes (the relative number of each species or population of diatoms in a year) through time.  NOW in addition to all that knowledge you can also run chemistry on the surface of the lake bottom (before the chemicals mix or breakdown).  You can compare the water chemistry (things like nitrogen, phosphorus, oxygen, pH, or temperature) with the species found and their relative numbers. This can tell you the preference and tolerance of these species to a given water chemistry factor. So species that have a lot of individuals fossilized at the same level as the water chemistry you tested do very well in those conditions (say high nitrogen, which remember is basically a fertilizer).  Species that are low in numbers (or not in the sample) do poorly under those conditions.  With me so far?
Fig. 1: Diatoms
Fig. 2: A core from the bottom of a lake (depth of mud at bottom)

Okay then so here's the kicker, with the relationship of species to water chemistry, you can look back at older layers of the lake sediment and count the number of species and individuals that are fossilized.  Once you know the community structure, you can use that information to estimate what the water chemistry was likely like!  You can start to understand how a lake has change over hundreds or even thousands of years!!

Now of course, is where is starts to get dirty.  Remember this is still ecology.  So what happened with me is, after 2 years (normal length of a MS program), it didn't work.  But in a way that's what made the project really interesting (and of course at the time very frustrating).  When I ran my estimates and compared them to known emission rates of nitrogen from the area they were exactly inverted! My model checked out well against expected ecological relationships (we call it r squared, or how tightly the relationship of your data is). For something more linear like chemistry or physics you would never accept and r squared value below 0.8 or so (on a scale of 0-1).  In ecology? Remember 0.4 is fantastic and numbers like 0.1 are not even unusual.  The reason is that there are many factors that effect an organism and its habitat and the variable you are testing is likely only one piece of a much larger puzzle.  That doesn't mean it's not important, it just means it's complicated and intertwined.

In my case what we think may be happening is one particular species tends to completely dominate the older sediments, and the problem it this species is a known generalist (often can do well in many different conditions and it quite good at competing with other species for a limited resource).  I proposed that the model needed to be able to ignore such species.  More in depth later.  As a result I have a very controversial paper in lieu since the model has been used for 30 years.  So it's been hard to publish.  See previous Science post for likely reasons why...



"Science is facts; just as houses are made of stones, so is science made of facts; but a pile of stones is not a house and a collection of facts is not necessarily science."  Henri Poincare

Ecology-drama and "it's complicated" written all over it

There are so many ways in which ecology becomes complicated.  The last example is a beautiful one-well studied, fairly well understood, and fairly simple.  The cichlid fish example works so beautifully because there happens to be only 2 major selection pressures driving coloration-sexual selection and water clarity.  But what if there was more to it?  What if suddenly a visual predator was introduced to both clear and murky systems?  Or what if there was increased fishing pressure?  More or less plant material?  Stark changes in diet?  Variables can add up very quickly and have enormous effects.

For example, salmon change to a beautiful bright red during breeding season in order to attract mates.  The bright the red, the more likely you are to pair up because you are PERCEIVED to be more fit.  Now a certain type of salmon called Kokanee got landlocked and now live in a lake system.  Most salmon derive their beautiful red color from their food, which contains a carotene for red coloration.  To adapt to their new environment, the Kokanee salmon improved their ability to obtain (sequester) red coloration from their food, which has much less carotene than the ocean available food of their counterparts.  Both Kokanee and "regular" salmon turn red during breeding season but if the regular salmon get into the lake system they are unable to turn red, because they cannot sequester such small amounts of carotene, and therefore are not chosen to breed, regardless of their actual fitness level.  A simple change in diet shifted mate choice based on coloration to a completely different and isolated level!  And of course, we have speciation as well much like the cichlids, which I do want to say is not necessary when these things occur.



Nothing gets this complicated variable idea across more than thinking about how to design an experiment.  For example, a study that aimed at looking at predation on small rodents by their larger, wolf and fox, predators took the home site of the rodents and fenced it off, denying access to the predatory mammals.  It is a tried and true method, good for animals or to protect plants or even insects from their known predators.  It didn't work here though, because the posts along the fence line attracted hawks and small falcons that wanted a perch, thereby increasing predation on the rodents via a predator that usually accounts for a very small amount of predation (if you're going to stop and rest why not grab a snack while you're at it?).  Oops.  So here even though we've removed the predator that based on observation and testing is the primary influence on the rodent life cycle, you see how moving one thing out of a niche (space/resource/habitat used by an animal in relations to others it shares said space with) how easy it is for something else to move into the open slot.



It is because species and their environments are so intermixed that these things happen.  There is no such thing as a food chain, only food webs.  One creature eating only one other species is the exception, not the rule.  Specializing can be good-if the source is available you become very efficient at handling and deriving nutrients from one thing.  However, the environment is shifty and even poor panda probably regrets it's monogamous relationship status with bamboo.  Moreover more than one thing will determine a species or individuals fitness-habitat, shade, food, water, nutrients, substrate, predation, etc.  Then, each of those factors is controlled by any number of additional factors, habitat for example-competition for space, degree of visibility required, predation, hunting, community of plants, nutrients, flooding, fires, access to mates, etc.  You can see how one thing rarely dictates the response of a given species.

To sum this up let's think about how this looks graphically.  You have your species and the response of said species (i.e. weight, survival, food choice, etc).  On the graph you get a huge cloud of points through which you draw a line, which represents your variable.  The line will likely trend the points with an r squared of maybe 0.1 or 0.2.  In other words, your variable can explain the response of the species about 10-20% of the time.  Seems low considering in chemistry you need above 80%.  But makes sense right?  It has to be one serious pressure to make up 80% of the life response of an individual!  Think about what controls your day to day activities?  Some things are certainly more important than others, but no one thing controls you.  Ecology sets out to find the more important things, from which we can glean the most information about that species in that environment.  Hence why the possibilities are endless!!

Stay tuned! Next week I'll talk about what I did my master's work in and how it puts a whole new twist on this complicated relationship!!



"When one admits that nothing is certain one must, I think, also admit that some things are much more nearly certain than others." Bertrand Russell

Ecology: complicated and delicious, just like your ex's facebook status

Ecology was truly love at first sight.  Now I'm not normally one for complicated relationships, but something about ecology has always made my toes tingle. Ecology is the study of the relationship of species and their environment. Like all relationships, this one is dirty, convoluted, and complicated.  Like a good relationship though, I can also be very rewarding and exciting.  Upfront the idea of ecology may seem very simple. You take a species and see how it responds or affects its habitat.  And it's insanely relevant, answers to those questions can help inform conservation, forestry, zoos, climate change, habitat management, zoning, invasion, biological control, and so on.  You also end up incredibly well rounded, using mathematics theory, statistics, experimentation, laboratory control, cross departmental collaboration, biology, physics, chemistry, aquatics, animal behavior, and evolution. Okay, so now you can see how this can get so complicated.

My bio stats professor once said that ecology will always be a strong career because there's never any way to answer everything about even one question. Realistically, the possibilities are endless.  You could have 9 hypotheses to test and none of them be the correct theory.  Moreover, ecology is almost never controlled by one variable. Let's look at the situation that originally got me interested in ecology my junior year in college as a simple starting point.

I still have the original article, I never got rid of it.  It's a 1997 article in Science (one of the top 2 science journals in the world, likely only second to it's London counterpart, Nature).  "Cichlid Fish Diversity Threatened by Eutrophication That Curbs Sexual Selection."  Okay, let's look at this concept bit by bit.

1. The species: Cichlid fish are found in many places in the world, although warm water.  They are well studied for their species divergence by population.  In other words, often when a population of cichlids becomes isolated in a lake or water way they specialized and diverge.  If they are reintroduced to the population they come from (the source) there will no longer be any breeding between the populations.  
2. Eutrophication: In aquatics, the water quality and clarity is often generalized into 3 majors groups
1. Oligotrophic: clear crystal water with little algal blooming or fertilizer
2. Mesotrophic: moderate clarity with some algal blooms likely giving the water a hue of blue or green for parts of the year
3. Eutrophic: murky, dark water with little clarity and high algal blooms giving the shoreline a very green color. SO when we say "eutrophication" we mean a lake that is moving (or being pushed) towards poor water clarity and quality.  In this case reducing vision within the water column. 
3. Sexual selection: Alright so this term should be more familiar since we talked about it in my evolution post.  Specifically here it is important to know that females choose their male mates based on color and color brightness.  So there is selection pressure on the males to be a certain color and to be a very bright variant of that color.  Think about how this would be different if there were a predator? 
4. So the kicker with this research is that over time, as the lake becomes more euthrophic and more murky, the females have less ability to visually choose their males and often do so indiscriminately.  They breed across the lines of sub species as well, no longer able to choose by color.  As a result, there is no benefit for the male to invest a lot of energy in being colorful so there is a reversal (another term you know!) to being dull fish.  The males and females were becoming dull grey in color and the populations were almost completely intermixed again as a result!!!

Alright, I will continue to talk about ecology next week and how it becomes more complicated.  If you have any questions so far, let me know!

"Science is one thing, wisdom is another. Science is an edged tool, with which men play like children, and cut their own fingers." Sir Arthur Eddington

Science-how the study itself adapts and evolves!

Science!  One of the things that is often misunderstood and misconstrued is scientific theories (and the process by which they are derived).  One of the major problems for this is scientists have established their own little world with its own lingo and set of standards.  The good thing?  These standards have a very good tenancy to hold up (as in relation to society-more on this in a bit).  The bad thing?  Nobody normal gets it.  Mercy sometimes I don't get it, so let's talk about some of the things that science does that incidentally fuels the anti-Darwin fires.

1. THEORY: A theory as the average person thinks of it is a constructive thought process by which a philosophy or belief is based according to perceptions and observations.  Again, I cite the Annunaki (the reptile aliens from a previous post), which is a theory that aliens had intermixed with humans. The theory arose from ancient Sumerian text and carvings.  The beings have traits apparent in certain (select?) humans and the whole shebang.  The term is actually not even caught by spell check it is so common.  They even tie in the the UFO theories and the Builderberg Group/New World Order theories.  They all sound new, they're not mainstream, and honestly some of them are just plain crazy.  
2. HYPOTHESIS V LAW: The problem is scientists don't use the word theory as we just described it.  The term "hypothesis" would tie up much more closely to this definition-a series of ideas or questions built on observational framework.  A scientific theory comes much further down the process line.  First you have a hypothesis, then you propose how to test it, you test it, get results, and draw conclusions based on your test and the subsequent set of results.  For any long standing scientifically accepted theory, that process needs to be performed many times by many different people (repeatable results). Very similar to scientific law.  In fact, the law of gravity is actually a theory according to scientific terminology, but I don't see very many people jumping off the building in order to fly home.   
3. SOCIETY: Science, like every other construct is the black duck of society.  You follow what people want to hear or you get squished.  Example-Ptolemy was able to explain heavenly bodies in motion with an Earth at center basis, he used concentric circles so technically the pattern matched the data.  What was more important was that it matched societies view so it stuck around for 1600 years, even though Galileo figured out the real pattern much sooner than that.  But what happened to Galileo?  Oh, he died in prison...  Now Ptolemy did not screw with data and forcefully misconstrue anything, based on what he had to work with and his observations it fit the pattern fine.  The issue here is that poor Galileo got squashed when he had a DIFFERENT idea, and it took almost 200 years to make it mainstream.  Society also governs what's important, or what types of things scientists should focus on.  AIDS research didn't really go into full swing until the 1990's, but was discovered in the 1970s and named.  However, because of the stigma, it wasn't "important" for mainstream research so it was very difficult to get funding.  It's kinda like that city law that so many accidents need to happen in an intersection before they'll budget in a stoplight.
4. WRONG: Like I just mentioned, sometimes science gets it wrong.  Sometimes it's completely innocent-trying to draw conclusions based on only a few pieces of evidence.  But you have to start somewhere in order to make progress.  Sometimes though, people do bad things, which I'm sure doesn't surprise anybody.  And let's face it, this isn't a construct isolated to the sciences, or even to our society.  However, the example I want to use I've actually seen brought up in a Darwin v God debate.  His name was Johann Meckel.  He made a very famous move in the early 1800s.  Meckel believed development of an embryo mirrored evolution (not that strange of an idea in the early 1800s).  He spent several years of his life studying it.  The issue was (of course) that it just isn't true, the development of an embryo does not mirror the procession of evolution through time.  Instead of admitting his failure, he was so passionate and emotionally tied to his idea that he forged drawings and had them published.  These drawings were even used in textbooks for a couple of years until someone figured out his masking attempt.  That's the perk about science, it has to be testable and repeatable by someone else.  Of course, the drawings have been stricken from teaching and his name only comes up to demonstrate a very bad point.  In fact it took me 10 minutes and 5 pages in google images to find his little faux pas (he went on to do some other quite spectacular things medically).  The point is that even though science makes mistakes, it is able to admit the issue and adapt to new information (even if it takes a while) which is certainly more than can be said of other passionately driven constructs.  No societal construct is perfect!  

Evolution: let's get this straight people!

Being in the science field I've seen some pretty interesting misunderstandings about the theory of evolution.  Some funny and some scrape your eyes out painful.  Although the first painful argument I often hear is about evolution being a "theory", that merely stems from people not understanding scientific processes and scientific theories as they differ from your drunk roommate insisting the entire human race is partially controlled by lizard space beings called the Annunaki (this is a real CONSPIRACY theory, check it out).  However, I will delve into that in a later post.

For now I think I will take you through the basics of evolution, in a way I teach all my little youngens in my vertebrate evolution course.  As with class, feel free to ask questions, I will post answers.

Natural Selection: fundamental mechanism (process) by which evolution occurs.  It is based on the struggle for existence and organisms' competition for space and resources.  This includes migration, mutation, genetic disease, and death.  Natural selection requires 3 basic constructs to occur:

1. Variation: individuals within a population differ from each other in their traits (also referred to as phenotype or characteristics)
2. Inheritance: aforementioned traits need to have a genetic basis.  AKA I can pass my awesomeness down on to my children.  (Please note, traits for this CANNOT be acquired-e.g. picked up by the parent through the course of life-it needs to be in the DNA code.  Therefore if you adhere a horn to a horse and have that horse breed, its foals will not be born or develop horns [again, real study way back in the day, check it out])
3. Fitness: given competition and limited resources, not all individuals will have the maximum capacity to reproduce. The struggle for space, food, and survival will cause a gradient in success for mating and offspring.  Therefore, this inequality means individuals will contribute differently to the next generation (high fitness=higher contribution).

Sexual Selection: secondary mechanism that is based not on actual survival but on a potential mate's perception of your fitness.  E.g. red coloring in bird.  Being red does not make you a faster runner but indicates since you are very brightly colored and alive you're probably good at escaping predators.  This includes mate choice, coloration, size, combat, display, plumage, etc.  In some cases, sexual selection can actually work in the opposite direction of natural selection.  Certainly male peacock tail feathers do not benefit them for survival but the ladies think it's awfully sexy!


Constraint: evolutionary limits.  Evolution IS NOT progress towards a perfect organism.  Evolution is more like an engineer piecing together the best option out of some mismatched hunks.  Bear in mind that evolution (generally) occurs over a very long time, and many of the traits you see weren't developed to survive in THIS moment, they were developed THEN.  As their landscape, competition, and resources change they are constantly changing too.  But you don't get to wipe your slate clean every time, you have to use what you've got.  Pigs don't have wings, not because wings wouldn't be beneficial to a pig but because the pig's body design would certainly not support flight.

Teleology: explanations of a trait based on its PERCEIVED purpose rather than natural (mechanistic) origins.  Many non evolutionists fall into this trap, as have some scientists (everybody makes mistakes, it's what you do with them that matters, see later Science post for more on this).

Contingency: chance historic events.  These are things like catastrophes (lightning, eruptions, etc) or continental drift that may strongly impact the evolutionary path but is not based on fitness.  Sort of being in the wrong place at the wrong time kind of idea.



NOW, given the information above the way origins are traced and mapped is called PHYLOGENY.  Historically (aka before we started DNA sequencing everything) this was based on trait relationships, which in some cases were perceived since whether or not traits are similar because of function, common ancestry or common pressures is hard to tell.  You end up with two groups, or two and a half?

1. Homology: traits are similar because they are of common origin
2. Homoplasy: traits LOOK similar because two separate groups underwent similar natural selection pressures (like hopping mice in the African and American deserts-they're not related but they're traits are almost identical since there are only so many ways to deal with movement across sand!).
3. Reversals: this isn't so much a third group as much as a related issue.  Sometimes traits REVERSE or switch back to a previous evolutionary state due to a shift in selection pressures.  As you can imagine, this can really mess up how we try to order things. 

Many of these issues are starting to get worked out with DNA sequencing, where you can see and follow exact mutations and deletions in the code and follow them through time.  

Misunderstood information:

1. Missing link: there is no such thing and it wouldn't be necessary for there to be one.  Changes through evolutionary time are GRADUAL, you can tell because even today with our existing species there is an incredible amount of debate on what is a species and what is a subpopulation.  Certainly it is not any easier when you don't have the ancestor population with you as you make the comparison.  Not only is this process gradual, with small changes occurring and building up over time, but when it doesn't work the individual doesn't reproduce or they die quickly, such individuals are in low enough proportion that they don't contribute to the gene pool or the fossil record.
2. Species that are ill adapted to their system: sure, again GRADUAL.  Evolution takes time so often there is a little bit of a time lag between successful evolutionary adaptation and the landscape they are adapting too.

  

Remember, the idea is that through shifting adaptive landscapes (changes in their resources, climate, habitat, competitors, etc) exert pressure on a species.  The most successful (fit) individuals pass on their genes to the next generation (passing on awesomeness) while the less fit individuals do not (kill off lameness).  Therefore the next generation is proportionally more fit than the previous one and the pathway continues.  Sometimes there is more than one "equally" fit answer to a given problem or part of the population migrates and is presented with a new set of pressures.  This is (in part) how speciation occurs.  The success of some species over others within the same line and against sister lines is how evolution occurs.

There, now you all survived half of day 1 in my class.

"The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...' " Isaac Asimov

Applying to graduate school-The real journey begins

Step 5. Before moving to your new school.  This is going to sound lame, but seriously spend a lot of time at home.  I don't mean that dumpy little apartment that your trainer friend throws parties in (wherein you vomit off the back balcony as you recall from the previous post...) but your home home.  Mom, dad, little brother or what have you.  This may be the last time you get a chance to be a child and live free.  Things get expensive and very self-sufficient from here on out and you don't get whole summers and winter breaks off anymore.  Enjoy the babying while it lasts, trust me.



Now, if you've been following the timeline, you will likely spend 5-6 months preparing and applying for grad school, 2-5 months sweating for results, over $300 in expenses directly related to said applications (of course this doesn't include the running naked in the street bail money), and $? in moving expenses.  Not a process for the weak.  Loads of benefits, but not an easy path in life to take.

Since at this stage, you are heading towards or have finished your undergrad, here's a nice little tip list to keep your head on straight.  Basically, stop panicking because it really ISN'T a big deal and don't go through life being an entitled douche-bag.  See how politicians and political analysts act on tv?  Don't be them.  Unless you are going into that field, in which case douche-it-up because that's the only field that really pays in...
http://jezebel.com/5910701/congrats-new-grads-by-the-way-you-dont-know-anything

Before you panic and jump off the academic bus (or cliff, depends on your level of drama) remember, if you're even considering applying to grad school you obviously have an incredible amount of love and interest for what you do.  Good things in life never come easy and remember my first post-there are still a lot of fun perks that come from the process, and of course that papery degree thingy at the end that allows you to lead and do what you want in your field.  That's pretty great to.

"Anyone who has never made a mistake has never tried anything new" Albert Einstein

Applying to graduate school-Crocodile tears

So you've got your app in, now what? WAITING, LOTS AND LOTS OF WAITING

Step 4. Getting your response letters.  No matter how awesome you are (or how awesome you think you are...) you are going to get rejection letters.  And you can act tough, they suck.  It never feels good when you've been busting your butt at school, going out less than your athletic training major friend, and taking more hours of work than your course credits realistically reflect and then have someone say sorry, you're not good enough and all the butt busting was a waste of time.  It's not true of course, that butt busting means a lot in any competitive situation and that's all this is.  Many factors go into choosing grad students, previous work, courses, networking, and "goodness of fit," or how well you seem to match up.  I know it seems ridiculous since all this is based on a couple of emails, a crappy application, and (if you're super lucky) a phone interview.  Take my advice, open your letters (or emails or phone calls) in your room.   If it's good news run into the streets naked screaming and crying with glee (this may also be an additional expense tacked on to getting into school if you get caught though mind you).  However, if it's bad news you can recenter yourself private and cry or punch a pillow or what have you without any pity faces staring you down.



"I'm extraordinarily patient, provided I get my own way in the end." Margaret Thatcher

Applying to graduate school-Applying to sell your soul

Now that we've gotten all the prep work out of the way, let's talk about what happens during the actual process.

Step 3. Actually applying to said graduate schools.  SchoolSSSS, meaning more than one.  Never put all your eggs in one basket.  On the upside, the applications usually all want the same thing.  General information, upload your UPDATED resume, and some essays.  The essays are basically all the same and are another step of prostituting out your skills.  It's always, explain how you would benefit from education at this institution blah blah.  Honestly, look at the essays first on these apps and write out responses in word files that you can copy and paste from later.  Use spell check.  And make sure that when you use the same essay for different schools you still personalize parts for each university within the essay.  AND BE CAREFUL TO CHANGE OUT SAID NAMES AND STATEMENTS FOR EACH!  You will be doomed if you make that faux pas.  The other major requirement is the letters of recommendation, usually from 3 professionals you know.  Again, do not ask your supervisor at Macy's.  Professors and teaching assistants (labs, small classes) that you had a particularly good relationship with make the best recommendations.  The same goes for any supervisors on relevant internships you have had.  Make sure 1) that you did well in their class (B or up) and 2) you had a good attitude while in class.  I have definitely had students ask for letters of recommendation that got C's or in my notes (yes, your teachers keep notes on your behavior if they know you or the class is below 30 students) it will say "leaves early" "snippy" "disinterested and refuses to discuss class information."



Don't ask!  I'm usually gentle, the few times I've said no I'll fib a little "I'm very overloaded with work right now and don't feel I could give you an accurate representation" or "I'm sure there are other classes with would be far more beneficial to your endeavor than mine."  Heads up though, others are not always so friendly so be very careful how you choose them.  Moreover, think about what field you're going into.  It helps if you have more letters from that or similar fields than your yoga instructor and meditation course.  The final kicker here is getting your transcript sent.  You need to send 1 (sometimes 2, though why any place needs 2 official board copies I don't know...) to each school.  Subsequently, when you are accepted you will need to send the final transcript (aka post-graduation showing your degree earned) as well.  These babies run about $8 a pop, not a big deal until for 4 schools you realize you need to send 7 transcripts.  Don't let it take you by surprise.

"It is the mark of an educated mind to be able to entertain a thought without accepting it." Aristotle

Applying to graduate school-Academic debris

Step 2 in our multi-part pathway, taking your graduate school exams...

Step 2. The GRE (Great Ridiculous Excess, aka Graduate Record Exam).  Taking this test once will run you about $250 (at least it did back when I took it) and the scores are good for about 2 years.  So take this seriously, you don't want to go through it twice, for multiple reasons.  Technically, the are two forms of this test.  If you're lucky, you only have to take the general test.  Some schools will also make you take the subject test (generalized-biology, mathematics, physics, etc).  Keep that in mind in thinking about the cross between what schools you want to go to and what tests you need to take.  I'm quite convinced the GRE is designed to prove that you know nothing about a bunch of menial material (similar to comps, which prove you know nothing about really important things related to your field-more on this on a later post).  My advice, just get the little Kaplan book with practice tests (http://www.amazon.com/New-2011-2012-Premier-CD-ROM-Kaplan/dp/1607148498) and 7th grade breakdown of all the major material.  Take a practice test.  Relearn 7th grade math and word association.  Panic about the number of vocab words on the list that you don't (and never will know).  The best thing I did was hang out on middle school and high school websites.  It's not that you don't know it, it's just that for most people finding the area of a shaded section in an obtuse shape just doesn't come up in our daily lives.  (Those who know me often hear me vent about a similar issue in my Calculus I course, in which we spent 3 weeks finding the volume of a deflated inner tube...).  When you go to take the test in the little computer room, the worker will be fussy and basically want to strip search you.  And no matter what, you're still going to feel like you don't know enough.  And you can't, trust me.  One of the questions on mine was "What term refers to an Amish flower printed blanket?".  Not only did I not even have a clue what the answer was, but I was left thinking, where in life am I going that this is a deal breaking piece of knowledge??


                               

Anyway, your scores come back in the hundreds and most schools, if they even post a minimum only care about the total.  Many professors will admit they don't even take it into account.  Since the test is so pricey, the only way to make the system work for you is to have you list of potential schools ahead of time.  They'll let you send to so many for free during registration, but they charge you a hefty price after just to spite your indecision.

"It has yet to be proven that intelligence has any survival value" Arthur C. Clarke

Applying to graduate school-Selling your soul to the devil

Seems to me, the best place to start (at least for now), is at the beginning.  The application for graduate school is no less stressful than some of the stages within the degree process itself.  After getting past the idea of 2-8 more years of being a poor little student you have a long way to go.

Step 1. Looking at potential grad schools.  There are many websites through google and likely through your school that will allow you to search graduate schools by subject matter.  (http://www.gradschools.com/; http://graduate-school.phds.org/)  This is an okay starting point, maybe to find states or places in the world that tend to focus on your particular area of study.  However, in order to make any real headway here, you need to go to each of those potential universities' websites and scope them out.  Check out the grad school page and the homepage and get a feel for the environment.  Most importantly, go to the department(s) of interest and look at the faculty.  Read their little snipits about themselves and their research.  Ultimately, you're picking an advisor and topic more than you are the school itself.  When you find one(s) that pique your interest, e-mail them.  COMMUNICATE!!  This is where the soul selling begins.  You need to sex yourself up, really sell YOU in order to get attention.  After all, many times you are in very high competition.  Also note I refer to sexing yourself up academically, not in the horror movie running across the yard at night in your panties with the sprinklers on sexy.  Key difference.  In your first email, act like a rent-a-bride.  Be interested and suck up. Offer to send resume information and to chat more about what they do and where you are going. (Oh, and note: update your resume.  Basically redesign it but only list things that are relevant.  School, internships, serious jobs.  Probably your job at Macy's isn't going to matter anymore, though technically I suppose it shows you have a good ability not to throttle stupid people.  Your job at the library though, still good.).  Whatever the case, ultimately it's the faculty member that decides whether you get into grad school (assuming you pass all the basic requirements in admin for the U of course).  By the time you are ready to apply you want to have a good relationship with him/her and he/she WANTS to have you apply and use your app materials for the final decision.  Even after you have this good relationship, keep in contact every week or every couple of weeks.  Make sure you stay on their radar and use good things to talk about, publications, work, app stuff, etc.  Don't write about the weather, these people get enough junk mail and you'll likely be ignore.


Alright, this got a little longer than I originally anticipated. More to come, after all it's a multi-step process.  I'm signing off and leaving you with another deliciously dorky quote:

"Remember that there is nothing stable in human affairs; therefore avoid undue elation in prosperity, or undue depression in adversity." Socrates

Introduction

Not surprisingly I am a graduate student.  In the midst of my second year as a PhD student actually.  A little nobody in the big world of academia as it were.  But more on that later.  I got the idea for this blog from a class and some students of mine.  In the class we were discussing how scientists, as an overgeneralized whole, do not use new media like they should.  There can be great potential.  It had also come to my attention that many of my students were curious about academia, grad school, and beyond.  I also had a student from another university (with the intent of communicating with my advisor) contact me with a flutter of questions.  In all cases, I'm happy to oblige but I found myself reminiscing on what I went through when I was at that stage.  Terrified, confused, and oh so painfully naive.  I began thinking that there are precious few places in which academics can really go to ask questions and relate to one another on what goes on beyond the lobby doors.  Given the potential (and perhaps my naive dreaming that many will read this) for other scientists to follow me, I thought it would be a fantastic way to express and communicate scientific ideas and concepts at a scale well beyond anything I can do from my office, on a regular day at least. So, those are my goals with this blog 1) Present real life experiences in a way that others can learn from or relate to 2) Present real science (whatever that means I guess) and hopefully discuss and communicate with the scientific community as a whole (regardless of where or where not you are in your career).

Now, for the nitty gritty pieces.  It behooves me to say that whatever I say in here, though true to my beliefs and experiences, is not necessarily true in all circumstances.  The first thing I would always remind you is that every person, every advisor, lab tech, undergrad, grad, mentor, and mentee is different and will thereby foster different relationships.  You're welcome to take my experiences as advice (as they apply of course) but the best advice I could give here is "Adaptive Management."  Adjust to your surroundings and be flexible in the way you deal with things.  More flexibility will give you more bounce after all.  The second thing I want to say is I will be taking this semi-anonymously.  By that I mean I will be referring to real people, and some with very real academic careers.  Therefore you will not find any real names or places in this blog.  This will allow me to be more honest about the situation without worrying about hurting someone else in the process.  I'll make up names (likely to fill my fantasy void of stereotypic behaviors...) and places (my lab is actually divided into video game realms afterall) but the events themselves will be quite real.  And lastly, be sure to comment and discuss!  I love to see what others think and will be happy to do a topic based on what people want (need?) to hear.  So be heard!

For the posts I do put up, be patient.  They're disorganization may kill me since it'll be a mixture of things I experience now and some back experiences (plenty of those) I will refer to.  The chronology will be miserable.  More reason to request topics than to sift through my insane flow of thought ya?

Now, onto the more personal and the more fun.  As I mentioned before, I'm a grad student.  A second year PhD student with a long way to go.  I completed a 2 year Master's under another advisor in a semi-related field.  And obviously I have my BS.  I'm one of those crazies that has went straight through from undergraduate (standard college, 2-4 years) to my MS and now into my PhD.  It's one of those good/bad things.  I'm a female in my mid-late 20s.  My modest stipend allows me a little 2 bedroom apartment where I hide with my 8 year old blue russian cat and my partner.  My partner makes a particularly interesting person to vent too since he's a teacher (math if you can believe the insanity) so he relates to and sees things in a very particular light.  More on him later, often and regularly I'm sure.

At my school a PhD student makes around $20,000 a year (for reference equivalent of a McDonald's worker and a little less than a good construction worker).  The school covers your tuition credits up to 9 credits (keeping in mind 6 is full time for a grad-we put in more credit hours for one credit and have to work a full job within the U on top of that) and half of your forced student health insurance (more on that travesty later...).  You cover the other half of your insurance and the student fees.  Oh and living, if you can manage the whole being human thing of course :)  .  If you're like me and have some painful back bills from moving halfway across the country and refuse to live in a hovel with slanted floors you probably will take out student loans too.  I usually get ~12-14,000 a year, which breaks down into about $5000 a semester that I actually see, most of which is gone in a month or two paying of bills I'm behind on and honestly from getting excited from having spending money and, well, spending it.  If you're smart (and not like me) you'll save up chunks of this all year long since you'll be a lucky ducky to get paid in the summer.  If you're like me you like ramen and phone calls to mom.  You do get other perks though.  The whole learning thing of course, and pretty much free reign in the library (access to all kinds of stuff that I don't even know why they HAVE, but is cool anyway).  Finding an apartment is much easier, landlords respond really well to grad students as we tend to be quieter, have fairly steady income, and will be around for a couple of years.  And it's true, I'm definitely too old to be throwing up liquor 3 times a week over a balcony or what have you.  Besides, if the grad school will give you free beer, no reason to binge on it, enjoy the freebies. I get to travel lots of places too.  With part of my job being a field scientist I get to go in the field.  Basically get paid to boat on a lake, spend time in a national park, and put up and experiment on a coastline beach.  You get to go places to present your material too, to conferences.  Some in other cities, some in other countries and if you're good your school will give you money to do it.  Not a bad gig if you ask me.  Grad students can get really good freebies from the U.  Food, beer, game nights, bar discounts, ask and you shall receive sometimes.  Other times, as a close friend of mine would say, you drink away your grad school stress alone in lawnchair and spend all night drunkenly knitting under a dead tree.  Meh, it's a give and take world.

Those are my basics and for now that seems like a good start since I have no idea what I'm doing.  I'll sign off this first post with my favorite dorky quote. "My goal is simple. It is complete understanding of the universe." Stephen Hawking