Friday, October 16, 2020

An Update for 2020

Hello, dear reader!

After a long hiatus, I have returned to update and refresh this site. The year is now 2020, we are living through the covid-19 pandemic, and it feels like everything has changed.

I am still tutoring and writing. I had a baby in 2018, and I shifted my freelance commitments from full-time to part-time to be a (mostly) stay-at-home parent to our young son. Samuel is now almost 2.5 years old. He is wonderful--so smart and funny. I have been working on a personal essay about the decision to become a parent, and I look forward to publishing it on this site when it's finished.

Because of my scheduling constraints around childcare, I have a small number of tutoring students with whom I am working this year. Being able to work this semester (fall of 2020) has felt like a lifeline. I'm so glad to have this connection to the outside world during a time when it feels like we still live under the threat of a deadly virus. A few of my sessions are done in person, with both of us wearing masks and hand-sanitizing before and after sessions. It is a risk to be meeting in person, and we remain vigilant about our health and potential covid symptoms. For now, our risk seems to be okay. I've remained healthy, though the pandemic has turned me into a hypochondriac. Every sniffle, every cough, every sore throat makes me think I have covid.

I've been doing more writing and editing work, which I have loved. For four years, I've been a science writer for Dook Dook Ferret Magazine, a magazine for ferret owners which is published through Ferret-World. Austin Writing Shop, a small business I own and run with Courtney Stoker, has been helping clients with job-seeking and school applications. I am working on two books, one solo and one with my friend, Lewis Weil, the founder of Money Positive. (Full disclosure: my partner is a member of the Money Positive team.) And I have a bunch of ideas for essays that I want to write, some of which I plan to publish on this site.

In short, I am absolutely swimming in inspiration.

For now, I am not seeking new tutoring students, but because things can change rapidly, feel free to get in touch with me if you are looking for a math or science tutor. Even if I am unable to work with you or your student, I can give you resources to help you find a tutor.

I wish you all the best! Stay safe and stay healthy.

Friday, May 22, 2015

Five Ways We Should All Try to be Like Scientists

Be brave in front of the Universe, its grandeur and magnificence.  Paraphrased from Carl Sagan

My recent post for The Grad School Series got me thinking about the intellectual benefits of science PhD training.  I no longer work full-time in a lab, but I feel I’ll always be a scientist at heart.  My training shaped me as a person, and I know I’m a better human for having survived that experience.  Here are five ways in which I think we should all strive to be more like scientists.

* Be willing and able to admit when you are wrong.

THIS!  This.  My goodness, we could use more willingness to be wrong.  I’m not saying that you have to like being wrong, but the faster you can admit you are wrong, the faster you can get back on track.  Experiments do not move forward if you can’t admit your hypothesis was wrong or your methodology was flawed.  Life often follows the same rules.  (And it’s okay to make mistakes.  Really.  In my experience, people are far more forgiving of mistakes when you come forward and tell the truth.)

* Be open-minded and skeptical.

Many people underestimate how open-minded scientists have to be about their work.  Science is a strange profession, full of unexplained data and experimental backfires.  We become more effective at this work by embracing that possibility that we are wrong.  Being a scientist has made it easier for me to listen to criticism and to see things from another person’s perspective.  It has softened my hard edges.  I’ve learned that there is often more than one side to a story, so I am slower to judge. 

* Be meticulous when it counts most.

I have my flaky moments, as most of us do.  But science has honed my ability to focus when it really matters.  In an world filled with distractions, I think this skill is invaluable; it’s one that has pulled me through tough spots again and again.

What does being meticulous outside of the lab look like?  For me, it’s a way of defining short-term goals.  Some tasks require intense focus, like driving in bad weather.  Other tasks ask us for some grace, like supporting a friend who just needs some love, not advice.

I try to make sure that my meticulousness is balanced with the understanding that we all make mistakes.  I’m not a religious person, but I need grace in my life, for me and for those around me.  

 * Learn to live with doubt.

Who wants to live with doubt?  No one, that’s who.  And yet, that is what we have in this world.  There will always be uncertainties, and I think it behooves us spiritually to learn how to make peace with our doubts.  I am all about making plans for an uncertain future, but I recognize that life is what happens when you are busy making plans**.

Scientists who are working at the edge of our knowledge, as I did for ten years, are working on the cliff’s edge of doubt.  It provokes intense anxiety.  Paradoxically, I think that working for so many years under those conditions has made me less anxious.  Because I realized that in the face of the unknown, I would still find my way forward.  I believe the same is true for most of us.  But denying our doubt is not the answer: I say embrace it and move forward as best you can.

* Approach problems with a collaborative spirit.

Science taught me how to troubleshoot with the best of ‘em.  Shit would go wrong, and it was my job to figure out how to get things back on track.  Now I apply this strategy to my life outside the lab.  My general MO is to assume that there is a mutually agreeable solution.  I am more open to collaborative problem-solving and more willing to listen.  I’m able to prioritize problem-solving, and guess what?  That means it’s easier to solve problems.

Science is so much more than the scientific method.  It’s an approach to life that transcends lab work and scientific articles.  And because we do science in pursuit of the truth, a scientific worldview is a toolkit that we can employ whenever truth is the highest priority. 

** RIP, John Lennon.

Wednesday, April 22, 2015

Should You Sign Up for a Science PhD Program?

I’m dusting off The Grad School Series to bring you this post!  The question above is one that is near and dear to my heart as a person who was always on an “alternative” path even while pursuing a PhD followed by postdoctoral research.  My path, like so many, has been one of mixed success: I was able to complete my PhD in six years with several publications under my name, but my years as a postdoc were mostly a flop.  And yet, I don’t regret the time I spent on my PhD and consider myself very lucky to have that experience under my belt.  After a few “wilderness years” and the panic of not knowing what to do with my life, I’m very happy with where I am now and where my career interests are taking me.  While a PhD is certainly not necessary for tutoring, it was through my PhD work that I discovered genetics, which is by far my favorite subject to teach.  It was also through my PhD that I discovered a deep love for science and the scientific method.  I also learned patience and great troubleshooting skills, which are essential for excellence in teaching.

In this post, I will highlight the most common reasons that people choose to pursue a PhD in science and I’ll share my thoughts on each.  No matter what your reason for going after that PhD, there are ways you can set yourself up for career success after you reach those three little letters.

* I want to be a professor.

Who wouldn’t want to be a professor?  The excitement of leading a research team, the chance to be brilliant, the possibility of saving people’s lives through your work…it really is an incredible career to pursue.

But it is now rare for a PhD scientist to become a research professor.  According to this analysis, 14% of biology PhDs obtain a tenure-track position within six years of graduation.  The numbers are a little more encouraging for PhD-trained chemists and physicists, with 23% of the chemists and 21% of the physicists landing those prized positions.  In my experience, for the biologists who do land a tenure-track position, they do it after spending ten years in a postdoc position (or even several postdoc positions).  Academic science is a pyramid scheme: only a few can make it to the top.

The truth is that a lot of talented, hard-working science PhDs simply grow tired of waiting for a job to appear or (perhaps more commonly) they decide to move on with their lives and look at other jobs.

If you have your heart set on being a professor, what can I say to make your long, long journey better?  Well, for one thing, I have seen people on this path land a tenure-track position.  My colleague Dr. Bridget Lear, who was a postdoc in my PhD lab, is one such person and I’m happy for her: she was a great mentor to me when I was in graduate school.  Another encouraging observation is that people on the tenure-track path are able to transition successfully into science industry.  I think their talent and ambition can work very well in the private research sector.

If you’re able to stay patient and engaged with your research while waiting for a tenure-track position, then perhaps the waiting won’t be quite so painful.  But more often than not, I think a lot of PhD scientists decide to throw in the towel on waiting.  I’m sure at some level, it feels like failure, and if that happens to you, you’ll have to find a way to make peace with those feelings of failure.  Here’s a chilling account of one such person’s experience.

But life goes on and so will you, even if you don’t become a research professor.  And if you do make it?  Congratulations!  Go forth and do some kick-ass science.

* I want to teach college.

This is why I pursued a PhD in neuroscience: I really wanted to teach at the college level.  And I am, in a way, though it looks different than what I imagined twelve years ago when I was applying for grad school.

The good news is that great science teachers are very much appreciated by their students and the general public.  Great science teachers provide so much value.  The real questions you’ll have to grapple with are:

How devoted am I to teaching specific subjects to specific students?

How much money do I need to make to be satisfied?

Do I want to teach at a single school, or am I willing to teach at multiple locations?

Community colleges are frequently hiring adjunct professors, but adjuncting carries with it a host of drawbacks, including poor pay, no health insurance, multiple locations, and the struggle to teach enough classes to make ends meet.  My friend Courtney, who taught as an English adjunct professor for three years in Houston, has shared many horror stories with me about how hard the adjuncting lifestyle was.  And yet, she loved teaching.  I don’t think she regrets the time she spent teaching, but it was not financially sustainable.  Courtney and I now run Austin Writing Shop, which is a business dedicated to helping students at all levels become better writers.

My dream was to teach at a small, liberal arts college like the one I attended and loved.  That’s not what I do now, and I’m okay with it.  I arrived at a fork in my road where I realized that being able to choose the city in which I wanted to live, with the partner I loved, was more important than my job.

The bottom line is that if you want to teach science, I think there are tons of ways to do so.  You’ll find a way to teach, and you’ll find a way to make money doing it, too.  I was able to get some of my first teaching experiences by volunteering and tutoring at a low pay rate, and those jobs showed me, without a doubt, that teaching is what I am meant to do.  So even though I didn’t make much money doing them at first, the confidence I gained was invaluable and propelled me to try full-time tutoring. 

* I have another job in mind that requires a science PhD.

Awesome!  You’ve got a career path lined up for yourself, and now you just gotta get a science PhD to make it happen.

But…what if you change your mind halfway into your PhD?  Or what if that job isn’t waiting for you when you graduate?  Many things can change between starting and finishing a PhD—interests, the economy, relationships, family life.  My best advice is to take a step back and ask yourself if your PhD training is teaching you skills that you will be able to parlay into a good job in a few years.  While the specific job may not be there any more, your skills are yours—make them work for you! 

* A science PhD will teach me useful, marketable skills.

Maybe…but what does “useful” mean to you?  What about “marketable?”  So much depends on what you like to do and what you want to do.  I think one of the best things a science PhD student can do for herself is to be proactive about getting the training she wants.  One of the best decisions I made before graduate school was choosing a lab where lots of techniques were used: behavior, genetics, molecular biology, biochemistry, even electrophysiology.  While I didn’t learn every single technique, I learned a lot and I took all those skills with me when I left.  I’m a better teacher now because I am so well-versed in biology. 

* I love science and just want the chance to study it deeply.

Yay!  I love this reason for going to grad school.  Doing something because you love it is so pure and beautiful.  That being said, you’ll still want to spend some time thinking about what you might want to do after grad school.  Having an eye trained toward graduation and beyond will help make that transition easier and less painful.  If you aren’t sure what you might want to do, check out these useful career-planning links:

- You Need a Game Plan

- myIDP (a guide to creating your own Individual Development Plan, a strategy to identifying and getting what you want out of your career in science)

(As an aside, let me say that I had the chance to meet Dr. Phil Clifford, one of the developers of myIDP, and he was so kind, encouraging, and pragmatic.  I’d say that it was one of the highlights of my postdoc years, and I’m delighted to pass along his words of wisdom by sharing the links above with you.) 

* A PhD will make my family proud.

I admit, I can’t really relate to this one personally.  My parents have always encouraged all of their children to pursue their own interests, so when I decided to pursue a PhD, it was not a big deal.  It was always my choice.

I generally think that making big life choices to make other people happy is a bad idea.  I’m American and a product of the hyper-individualistic American culture, so of course my opinion here is heavily influenced by my cultural background.  And truthfully, research is too fucking hard to be doing it for someone else.  You need to want that PhD for you.  I’d say that if your family is pressuring you into grad school, give research a try (see my post on summertime research for more thoughts on this) and see if you enjoy it.  You might even need to dabble in a few areas of research to find the best fit.  But when it comes time to apply to PhD programs, I think you need to be clear on why you are applying.  If it will make you proud, then go for it!  You need a lot of enthusiasm for research to survive the 5+ years of grad school.

* A PhD will make me proud.

I find this reason interesting; I’m generally intrigued by what motivates people.  I think that deep down, this was a huge reason I went to grad school, and finishing my PhD is still one of the accomplishments of which I am most proud.

It’s perfectly fine to start here with your journey into grad school.  But then make the choice to dig deeper, to find more things that motivate you and make you excited to do research.  Also see my links above for career planning to help guide you toward success on your terms.

* A PhD will make people think I’m smart.

Well…maybe.  Grad school may also shred your ego because everyone there is so smart and talented and motivated.  Success in research requires a certain humility that asks your ego to step aside.  I found that the more open I was to learning, the better I became at doing research.

I will say, however, that there are times to stand up for what you believe to be true, whether it’s defending your own data, describing your role in a conflict at work, or not taking on projects that you know you don’t want to do.  You gotta learn when to hold ‘em and when to fold ‘em.

Don’t go to grad school so that other people will think you are smart.  Work on the insecurity that is leading you down that path instead.  You can always get some research experience while you sort out your insecurities by, for example, landing a job as a lab technician. 

* I don’t know what else to do with my life.

Hmm…perhaps you don’t want to commit to a PhD program until you figure this out?

I have mixed feelings about this reason.  On the one hand, grad school can be a great place to be while you figure out your life path.  There are tons of opportunities, cool things to learn, smart people—all great things to be around when you are young and uncertain.  And lots of people who do earn PhDs end up doing something different with their career than what they had imagined during graduate school.  On the other hand, you do need to be pretty motivated to do well in graduate school.  It’s not a place you can just “hang out.”  You gotta work—in your classes, in the lab, on your thesis.  If you don’t know why you are in grad school, I fear that you may simply coast toward failure because you didn’t have an inner light guiding you toward goals.

I’d be careful about pursuing grad school if you just don’t know what else to do.  It’s not a place for slackers, but it can be a good place for the curious.  And if I’m honest, finishing my PhD required me to commit again and again to reaching my goal.  There are so many moments of doubt and frustration in research.  For me, the only way to move forward was to acknowledge the doubt and commit AGAIN to my project and my path toward the PhD.

* * *
Whew!  That was a long post.  Do you have any questions for me?  Feel free to leave them in the comments below, and I’ll address them there or in a future post.  I really enjoy writing this series and hope to keep it going with more good content.

Thursday, September 4, 2014

LESSON: Selection Pressure, Part Two

In this lesson, we’re going to pick up where my last lesson on selection pressure left off.  Here’s the link to the first lesson if you’d like to familiarize yourself with that first.

Today’s lesson focuses on how selection pressure changes allele frequencies over many generations.  Our sample problem is a follow-up to the scenario in my first lesson:

Despite your good work in Capitol City last time, the strange epidemic persisted and all individuals who lack Factor G are now sterile.  Individuals who lack Factor G are genotype gg; individuals who produce Factor G are GG or Gg and have normal levels of fertility.  How many generations will pass until the recessive g allele has a frequency of less than 1%?

In my last lesson, we figured out that when gg individuals cannot reproduce, the frequency of g drops from 0.3 in the parent population to 0.231 in the first generation after selection.  The simple formula for figuring out g’ if gg individuals are not reproducing is g’ = g/(1+g).

Here, g’ refers to the frequency of g in the next generation.  (And if you want to see the derivation of that simple formula, see my last lesson.)

If we do the math, we see that after one generation of selection, g decreased by 23%:

Slide 1 cropped

So how do we find the generation at which allele g is less than 1%?

Before we jump to those calculations, let’s consider what these numbers really mean.  After the first round of selection, the frequency of g is 23.1% or 0.231.  This number includes the individuals who are gg, even though they are sterile.  Why is that?  Because when Gg heterozygotes mate, their children will be:

1 GG: 2 Gg: 1 gg

The fact that Gg individuals have normal fertility means that there will be gg children, even though those children are not able to reproduce.

Also, let’s consider the number of Gg heterozygotes in the population after one round of selection pressure.  Again, the frequency of g is 0.231.  The number of Gg hets = 2pq.

2pq = 2(0.769)(0.231) = 0.355 or 35.5%

35% of the population here is Gg, which means that g is being propagated by about a third of the population (a substantial fraction!).

Let’s move on to the calculations to determine when the frequency of g will be less than 1%.

I doubt that you’d be asked to solve a problem like this on an exam without being able to use Excel or a similar program.  The calculations are easy on a spreadsheet but very tedious to do by hand.  I used Excel to solve this problem.  Here’s what my spreadsheet looked like to set up the calculations:

Slide 2

Here are the entries I put into Excel to set up this spreadsheet: 

Cell B1: 0.3 (original value of g before selection)

Cell B6: =B1/(1+B1)

(this is the calculation for g after each round of selection: g’ = g/(1+g))

Cell B7: =B6/(1+B6)

Cells B8-B14: Copy/Paste from cell B7 down to B14.

From the image above, you can see that after 9 rounds of selection (Row 14), the frequency of g is 0.081 or 8.1%.  So we’re not done, and we can continue our calculations by copy/pasting Cells A14 and B14 until we reach…

Slide 3

…Cell 102!

We’re looking for the generation at which q drops below 0.01, which happens to occur at the 97th generation of selective pressure.  What’s so interesting to me as a geneticist is that g (or q, in Hardy-Weinberg terms) can persist for so long when gg individuals are sterile.  This example illustrates why recessive deleterious alleles are not easily eliminated from the population.  As long as Gg heterozygotes are healthy, then g will be in the allele pool for a long time.

So that was a lesson on selective pressure and Microsoft Excel techniques.  Got questions, comments, or something else to say?  Tell me in the comments below! 

Thanks for reading!

A Little Something Inspirational

As your new semester gets underway, remember that…

“Education is not filling a bucket, but lighting a fire.” ~William Yates

Happy learning to you!

Monday, September 1, 2014

LESSON: Selection Pressure and Changing Allele Frequencies

We’ve used Hardy-Weinberg equilibria to determine phenotype frequencies in a population.  The Hardy-Weinberg equations assume that a population is stable.  In other words, allele frequencies are not changing—there’s no selection pressure.

But what happens when selection is acting upon a population?  Theoretically, we understand that selection will favor certain alleles or allele combinations over others.  This will shift the balance of alleles toward a new equilibrium.  If we know the magnitude of the selection pressure, we can calculate the effect of selection on allele frequencies.

Let’s work through a sample problem to unpack this set of questions. 

You and your medical team are summoned to Capitol City, where a strange epidemic has rendered 9% of the population sterile. Working rapidly, you discover that there’s a strong correlation between Factor G, a protein found in blood, and the fertile residents: all the fertile residents test positive for Factor G, but all the infertile residents test negative for Factor G. Later genetic and biochemical tests reveal that the population of Capitol City carries two alleles for a gene that is necessary for the production of Factor G such that G is dominant to g. All the fertile residents are genotypically GG or Gg. All gg individuals are now sterile. The original frequencies of G and g were as follows:

G = 0.7

g = 0.3

After the epidemic, what are the allele frequencies of G and g in the next generation?

Let’s define a new term first.

* Fitness, W.  Fitness is a measure of reproductive success and should be a value between 0 and 1.  If there is no selection pressure reducing the reproductive success of a genotype, then W = 1.  If a genotype cannot reproduce (as in our sample problem above, where gg individuals are sterile), then W = 0.

So for our sample problem:

For GG, W = 1

For Gg, W = 1

For gg, W = 0.

We’ll make use of these values below. 

Now we need to dive deeper into the math to connect s to Hardy-Weinberg equilibria.

Slide1 cropped

Slide2

We could have predicted that if q2 = 0, then p2 + 2pq = 1.  So that set of calculations confirms our prediction, but we still have no idea what p and q are after selection.  We need another set of equations for that task.

Slide3

Slide4 cropped

Slide5 cropped

Slide6

Slide 7 redo cropped

Slide 8 cropped

And there you have it!  Now it’s your turn: what if the epidemic, rather than making gg individuals sterile, reduced their fertility by 50%  What would the frequency of G and g be after one round of selection pressure?  (I’ll provide or confirm the answer in the comments when someone asks for it.) 

References:

Comprehensive Genetics coursepack, 2014 version, published by Dr. John Ellison, Texas A&M University

Saturday, August 30, 2014

What Happens During My Tutoring Sessions?

August 26 2014 iPhone 025

I’ve been in a few situations in the past week which have got me thinking that people have preconceived (and inaccurate!) ideas of what happens during a tutoring session.  I want to offer some insights into what I do as a tutor.

My sessions are, as a rule, student-led.  As a tutor, I am here to meet my students’ needs, and I want their needs to guide our sessions.  That means I’m not following a script or a checklist.  I’m listening to my students, hearing their concerns, their confusions.  I’m finding them on the map of learning and meeting them there.

A tutoring strength of mine is flexibility.  Because I don’t have preconceived notions of what any given tutoring session should look or feel like, I feel very free to make each session unique.  That’s not to say that I feel compelled to reinvent the wheel, but I think there is enormous power in the collaboration between tutor and student.

Allow me to be give you some concrete examples of what can happen in my tutoring sessions.

* We can start from “I’m totally lost in this class.”  It’s not uncommon for students to tell me they are lost and frustrated with a class.  I have such love and admiration for their willingness to tell me how they are feeling.  That takes courage.  When a student is lost, we start a dialogue so I can find a starting point for our lessons.  From there, I can create entire customized lessons to help my student build a base of knowledge.  Generally, I think that simple is better in these situations.  Yes, science is large and complex, and I don’t mean to diminish that truth.  But we learn new ideas in bite-sized chunks, and I think it’s better for my student to walk away from a tutoring session with one new idea that they understand rather than five ideas that leave them confused and frustrated.

* Lessons can be improvised from homework, practice problems, or class notes.  Much of what I do is teaching mini-lessons that are centered around exam preparation.  Feedback from students on these tutoring sessions has been really positive, so I’m happy to keep going.  My students crave more than the right answers.  They genuinely want to understand the how and why of their subjects.  I strive to create interactive sessions so that my students are actively engaged as we work through the material.  Many students want to participate, and I’m happy to co-create our learning environment with them.

* Yes, sometimes we work through homework assignments together.  We do homework together.  Homework is the bread and butter of learning.  Again, my students are seeking an understanding, not just the right answers.  When we work through the homework, we’re having a conversation.  And if a mini-lesson is needed, then that’s what we do together.

* I share resources, advice, and exam strategies.  I’m aware that many students feel the pressure to get it all done, so time is of the essence.  

And now it’s your turn: have you ever worked with a tutor?  What was your experience like?  Would you work with a tutor again?

(And if you have any questions for me about my tutoring, feel free to ask them below in the comments!  Happy learning.)