Why yeast? Part I

I volunteered to be the speaker at a Jr. Science Cafe in a couple weeks. The idea is that middle school and high school students will come and listen to me talk a little bit about science and we’ll have a discussion. My topic is using yeast as a model system. However, last night, I tried explaining to a layperson why we use yeast and I found myself floundering a little bit. Why do we use yeast?

Well, for one thing, it’s easy to work with. You don’t need a lot of special equipment. Just a regular incubator set at 30 degrees Celsius and a shaking incubator set at 30 degrees celsius. Another couple of incubators are good so that you can change the temperature for temperature sensitive mutants. And you can grow yeast on your benchtop as well–it just takes a little longer. Contrast that with mammalian tissue culture (mammalian cells grown in dishes). You need a special hood to maintain sterility. You need fancy incubators that pump carbon dioxide into them.

Yeast don’t take up a lot of space. You just need space for the incubators and glassware. Mice, another good models system, take up a lot of space. And you have to have a special facility in which to house them, special protocols for the care and treatment of the mice and how you are going to use them in your experiments. There are very specific rules about how you take care of animals that are used for research purposes. Even fish, which seem pretty straightforward, have special protocols for maintenance.  Nobody cares how we treat the yeast.

And yeast are cheap. All of those special facilities for animals cost a lot of money to maintain, money that has to come out of your grants. Even tissue culture is expensive. Because it’s so easy to contaminate your cells, you use lots of disposable pipets and bottles, unlike with yeast where everything is reusable once it’s been cleaned and sterilized. Also, tissue culture requires the cells to be grown in special media which is bought pre-made and is quite expensive. Yeast media is cheap and you can make it yourself.

So, yeast are convenient. But there’s more to yeast than convenience (see Why yeast? Part II).

No common ground

Last Friday, I got into a cab that had the radio on to Science Friday. I wasn’t really paying attention (I was thinking about my upcoming trip to NYC) when all of the sudden, the cab driver says that the effort scientists are putting into figuring out the differences between chimps and humans is “a big waste of time and money.”

Uh-oh.

I knew what was coming. I knew that I was a biological scientist in the presence of a creationist and I knew I had a duty to make the case for evolution. But, the whole idea seemed overwhelming. First of all, I didn’t want to tick off the driver, I mean, I was sort of at his mercy sitting in the back of his cab. Second, I felt singularly unqualified to make a case for evolution. I accept evolution (I hate the term “believe in” as though it were in article of faith) but I don’t know enough to have an argument with a creationist about it. As I told my husband later, I don’t have any talking points prepared for this situation. All I’ve got is a set of disjointed facts that I can offer up (and several are molecular biology related so I’ve got to deal with the fact that most people don’t know a damn thing about molecular biology). My argument would have been something like, “Fossils! Homologous genes! In vitro evolution!” Hardly convincing.

So, first I asked why he thought looking for the differences between chimps and humans was a waste of time and money. As I thought it was because he believed that God created humans fully formed and since scientists did not want to take God into consideration, they were never going to find the answers they are looking for. I tried to explain that divine intervention is not a scientific argument and therefore scientists cannot take God into consideration as it were (despite their own personal beliefs about faith). Somehow this led to a discussion in which the driver asserted that Darwin wanted people to become atheist and that’s why he came up with evolution, as though the theory of evolution was simply a means to make people atheist.

So, I tried to shoot that down. But, unfortunately, Cab Driver had read about the life of Darwin and I haven’t (where he read about the life of Darwin, I am not certain and probably would be scared to find out) so he asserted that Darwin became atheist after the death of a child. Whether this is true I couldn’t say, but I could at least argue that if what Cab Driver said was true, that didn’t necessarily mean that acceptance of evolution leads to atheism because lots of people lose their faith in God after a tragedy. To which Cab Driver agreed so I guess I came out the winner (?) there despite my lack of actual knowledge.

I further tried to explain that there are scientists who believe in God and accept evolution. Cab Driver argued this was not possible, it had to be one or the other because the two were mutually exclusive. The problem here was that he was equating belief in creation with belief in God. Now, here we get into the idea of a literal interpretation of the Bible versus a non-literal interpretation of the Bible and this was really beyond my ability to debate.

Fortunately, we had arrived at my destination, so I paid Cab Driver, who thanked me for the good conversation (!) and I went on my way.

I left this conversation feeling very uneasy and even a little ashamed of my lack of knowledge. This is exactly the kind of situation in which contact between the public and a scientist can foster understanding of evolution and instead of diving right in, I held back because I wasn’t sure what to say. True, I also didn’t want the guy to kick me out of his cab on Lake Shore Drive, but still, the fact that I felt completely unprepared for this conversation while Cab Driver felt fully prepared for this conversation having “read up” on the subject because, he said, he wanted to know more about it was, well, embarrassing. Never mind the fact that where he got his information might not be a reputable source, the fact is he had actually bothered to become more informed and I haven’t. I just haven’t.

Beyond that, we had no common ground theologically, either. He’s right, you can’t believe in a literal interpretation of the Bible and accept evolution. You can’t believe in Adam and Eve and the Garden of Eden and simultaneously accept that people evolved from lower primates, you just can’t. So, where do you go in that sort of argument? There really isn’t anyplace.

I suppose I just have to accept that I did the best I could. There wasn’t anything more I could have said or done and I’m not sure that more knowledge on my part would have persuaded him that evolution is valid. What I hope, though, is that when he thinks about scientists and God and evolution, he’ll remember that once he had this girl in his cab who was a scientist, who believed in God, who accepted evolution and who was nice and didn’t yell at him and didn’t call him an idiot for his beliefs and tried to explain her point of view without being insulting. So that, when he hears about scientists and evolution he doesn’t automatically think of atheism, doesn’t automatically think of unreasonable people. I suppose that’s the best I can hope for.

A day in the life

People often ask me what it is I actually do in lab (not what I’m studying, but what I physically do with my time in the lab). Here’s a rundown of Thurs. Sept. 4:

10:20–Arrive in lab

10:30-11:30–extract DNA from bacteria

11:30-11:35–Label tubes, check yeast cultures to see if they are dense enough for an experiment (they’re not), watch a mock fight between two labmates who are using giant pillow boxing gloves

11:35-11:45–Set up and start running DNA gel of a PCR product.

11:45-12:00–Write on blog, check email, send email.

12:00-12:40–Buy lunch, come back to lab, eat lunch at desk while reading blogs.

12:40-12:50–Stop running gel from earlier, visualize DNA, swear because it looks like crap, print out picture of crappy gel, throw away gel, clean up gel running apparatus.

12:50-1:10–Design and set up new PCR and start running it.

1:10-1:30–Discuss with labmate possible alternative strategies to get around PCR problem.

1:30-2:30–Work on planning alternate strategy to get around PCR problem; check to see if yeast cultures are ready for another experiment (they’re not).

2:30-3:00–Hunted down reagents for yeast experiment. This took a lot longer than it should have.

3:00-4:00–One yeast culture finally ready for experiment. Start purifying protein from this culture. Freeze bacteria cultures in our frozen stock collection during the down time in the experiment.

4:00-4:20–Go get tea with labmates.

4:20-4:40–Freeze bacteria cultures in our frozen stock collection. While doing this, have discussion with labmates about letter in Science about publishing.

4:40-5:30–I have no idea what I did during this time. I forgot to write it down for the blog. How can I lose track of an hour? Probably checked email, wrote in lab notebook, planned experiments for tomorrow and chatted with a few people.

5:45-6:45–Other culture finally ready for experiment. Do protein purification experiment with yeast from this culture.

6:45-7:45–Streak yeast plates, start bacterial cultures to freeze and purify DNA from tomorrow, send DNA for sequencing (we have a facility that does all of our DNA sequencing).

7:45–leave lab

This was a pretty typical day.  Usually, I’d talk to my adviser once or twice in there but he’s out of the country at a conference.  Also, I came in a little later than usual.

The joys of shared equipment

I’ve written a little bit about the microscope that I use to look at the results of my experiments.  The scope belongs to the department, meaning it’s shared by several labs.  In order to use it, you have to schedule time on it.  Of late, it seems like it’s booked up like crazy–to the point that today I had to come into lab way earlier than usual in order to do this experiment so that I could look at the results this morning because the scope is booked until 8pm today.  I am not a morning person.  So, despite the fact that a large portion of the American population is at work at 8AM, for me to get here by 7:30AM (having showered and eaten breakfast beforehand and even *gasp* wearing makeup) is a miracle on the order of giving sight to the blind.  Usually, I roll in around 9 or 10 or sometimes even 11 (along with the majority of my lab, including my adviser).  This means that I stay later in the day (7 or 8pm) but for me that’s infinitely preferable to getting up at the ungodly hour of 6:30AM.

Cleaning out the cobwebs

Look at the dust that has accumulated on this thing!  It must be an inch deep at least!  There are dustbunnies the size of tumbleweeds rolling around in here.

I think it’s time I dusted this thing off, cleaned up the corners a little, and use this space for its intended purpose.  I can’t promise much, but a post a week seems reasonable.

Now, if  someone would pass me a broom and some swiffer cloths, I’ll get to work cleaning this place out and maybe put up a science-related post in a day or two….

Writing Goals

I’m currently reading a book called Time to Write by Kelly L. Stone.  The synopsis on the back reads:

In Time to Write, more than 100 professional writers from across genres–including [names of lots of authors omitted]–share their secrets to finding time to write.  And if they can find the time to write, then so can you.

As the lack of posts on this blog can attest, I am having difficulty finding time to write.  It’s not that I don’t enjoy writing–I do, very much–it’s that I’m swamped with labwork and so writing gets pushed to the back-burner.

Now, don’t get all excited thinking I’m suddenly going to become an extremely prolific blogger.  Because, I’ve been thinking about it, and there’s one bit of writing that I really should start doing.

I need to start writing my thesis.

Just the thought of it scares me.  It seems like such a big project!  Much bigger than any writing project I’ve ever tackled before.  So, I’ve started breaking it down into smaller, more manageable pieces.  Thinking about it as a series of smaller projects has really helped with the anxiety I’ve been feeling about it.

Time to Write recommends establishing writing goals with short-term and long-term goals.  Here are the goals I’ve written

Long Term Goal:  Submit Thesis to Committe
Completion Date:  Sept. 12

Short Term Goal:  Write Introduction chapter
Completion Date:  June 12

Mini-Objective 1:  To spend one hour a day taking notes for intro

Mini-Objective 2:  Spend 10 min a day writing (to be increased as time progresses)

Mini-Objective 3:  Read two papers a day

Now, I don’t think I’m going to be able to finish writing my thesis by Sept. if I only write for 10 minutes a day until then.  I know I’m going to have to ramp up at some point.  I’m counting on two things:

1. If I start by making it a habit to write 10 minutes a day, then it will not be too difficult to gradually increase that to a much longer time.
2. Sometime in the next couple of months, I will be finished with my experiments and it will then be my job to write as much as a possibly can every day.

I know there will be a time when all I do all day long is write my thesis.  I expect this time to come around July or so which is why I’ve given myself until mid-June to finish the Intro chapter.

I have no idea how well this will work, but I’m willing to give it a try.

Yes, there are scientists who believe in God

Recently, over at ScienceBlogs, there has been a bit of a rumpus about science, religion, atheism, creationism, intelligent design, and framing science–all centered around an incident involving PZ Myers,* and the movie Expelled.   This prompted Janet of Adventures in Ethics and Science to write a post in which she says:

…while Myers and Dawkins are having their say, theistic scientists should also speak up. They should explain to non-scientists how their belief and their scientific activity can coexist. And, they should explain how the scientific discourse can work — and how it can be tremendously productive — while involving scientists with such divergent views on things like faith.

And, in the comments, Amber writes:

As a theistic person who thoroughly enjoys science… it is daunting and discouraging to read ScienceBlogs. Where are the theistic scientists? Are there any? Are they immediately unheard and disrespected? Where is their voice? Is there any chance that a scientist can be theistic and spiritual (or is that somthing different) and also be included as a peer in the scientific community?

I am a practicing Catholic.  I have never been shy about saying so in the company of other scientists.  I don’t flaunt it, rather it is simply a part of my life and as such gets mentioned in a casual way much the same as any other aspect of my life might get mentioned (well, except for that one time I doused my lab bench with holy water because I was going through a particularly rough patch with my experiments) (how do you get holy water?  You boil the hell out of it!  Hahahaha!  Or you know, you ask your grandmother to send you some).

There are 11 people in my lab.  There are two Christians, one practicing Jew, one non-practicing-but-still-believes-in-God Jew, and one Hindu.  Everyone else is some sort of agnostic or atheist (this includes the boss).  The atheists do not denigrate the theists.**  The boss obviously does not think that you can’t be a good scientist if you believe in God because, if he did, he would’ve kicked me out long ago.  So, as far as I can tell, bashing of theists is mostly a blogosphere phenomenon.  And yes, it can be particularly bad over at ScienceBlogs.

There are several reasons that I, as a scientist who believes in God, do not blog about my belief in God.  First of all, I am blogging about my life as a graduate student, my work in lab, and scientific concepts I find interesting.  Religion plays no role in any of those things, so I don’t blog about it.  Second, I really have no interest in having the likes of PZ and other atheists coming over to my blog and insulting me for my belief.

Catholics are a minority in Iowa.  Most people are some Protestant denomination of Christianity.  Some of those denominations do not look too kindly on Catholics.  “Heathen” is probably the most polite term they would use to describe me.  I once had a babysitter tell me I worshiped idols.  My grandmother recently told me about my grandparents’ mailbox being blown up (yes, by some sort of homemade bomb-like thing) because they were Catholic.  This happened when I was about 3 or 4.

I felt discriminated against outside of Iowa, too.  I have had people immediately go on the offensive as soon as they find out I’m Catholic.  I’ve been told that the church is corrupt and the proof is that the pope keeps warehouses of gold in the Vatican.  I’ve been told that I worship idols so many times, I’ve lost count.  I’ve been told that I worship Mary.  I’ve been asked to explain some bizarre, obscure papal command from the 15th century that I’m not even sure actually exists.  I’ve had people try to tell me that the current Church is morally bankrupt because we sell indulgences (there are a large number of people out there who think the Church hasn’t changed a bit since the Middle Ages.  They are wrong).

Frankly, I’m sick of it.  I’m sick of uninformed people telling me what I believe instead of asking me what I believe.  I’m sick of them not believing me when I tell them what I believe (and what the actual Church policy is).  And yet, I love my Church so when confronted with these sorts of things, if the person shows any signs of being at all reasonable and willing to hear what I have to say then I will attempt to educate them.  But there’s a difference between being willing to defend my Church and my faith when forced to do so by the situation I am in and actually deliberately putting myself in a situation in which I expect to be belittled.

The bottom line is, I have not seen any signs from the atheist scientists who are vocal about being atheist scientists that they are willing to listen to another perspective.  Therefore, I am not willing to engage in a discourse with them.

Finally, the reason I don’t blog about science and religion is because I have no particular agenda to convince scientists that you can believe in God and still do science or convince laypeople that you can do science and still believe in God.  Maybe one day it will be higher on my priority list, but right now I don’t have the inclination, the patience or thick enough skin to do it.

——————————————

*Normally, I would link to him but I don’t want to draw him over here so that he can call me an idiot. 

***Although I did have one–a pretty good friend, actually–ask me if I believed in young earth creationism.  I stared at her as though she had just asked me if I do kinky things in my bedroom involving a feather boa and five dancing sheep.  Okay, first of all, I’m a cell/molecular biologist.  I cannot possibly do the sort of work that I do if I think the earth is only 6000 years old because that would mean that I don’t accept evolution.  Second of all, I’m married to an astrophysicist.  If I tried to tell him the earth was 6000 years old, he would laugh in my face.  And then file for divorce.  There is no way he would respect me intellectually if I was a young earth creationist.  And there’s no way he could be married to me if he didn’t respect me intellectually.

Blog blah

Lately, I’ve been finding it difficult to write in my blogs.  I’m also way behind in reading some of the blogs I normally keep up with.  Some of this is just science overload, I think.  I was reading a popular science book, reading science blogs, writing a science blog and working in a lab all at the same time and I think I experienced some kind of upper limit and now, in backlash, I’ve read three fantasy genre books in the last five days.

I really wanted to keep this a strictly science blog and talk about my scientific interests but, ironically, I think that might be easier to do on a regular basis when I’m not actually doing research science.  For one thing, labwork takes up the bulk of my time.  Because of this, I have little time for leisure activities and less patience for studying and writing about science in what leisure time I do have (which seems to be about 15 minutes a day, but I suspect it may be slightly more than that).

So, my choices seem to be:

1.  Shut down this blog
2.  Keep this blog only about science and write in it very infrequently
3.  Write about things other than science when the mood strikes and write about science when I feel like it.

Of all of these, number 3 seems like the best option.   So, that’s what I’m going to do.

Banner Images

You may have noticed that the banner images have been changing every so often (or you may not have because you’ve never been to this blog before; I am currently on my 3rd (4th?) banner).  This isn’t because I’ve been unhappy with the banners that I have, but because I have these images that I take on the microscope, many of which will never be published, so I figure I may as well do something with them.*  The details of what is in the images can be found by clicking “Header Image Details” under pages on the left.

—————————

*I’ve also considered printing a few and hanging them up in my living room, but I think that may be a little too geeky….

First post

Where to start? I have chosen to call this blog SECular Thoughts. This is a bit of an inside joke. My graduate research involves proteins in the yeast secretory pathway. These proteins are Sec16 and Sec12. In yeast, a gene name is in all caps and from that I get the SEC in SECular Thoughts (gene names are also italicized but I couldn’t figure out how to make the header do that, sorry). Feel free to groan at the pun.

This is not my first blogging experience. I’ve been playing around with blogs for awhile and have kept a knitting blog and a personal blog. Both of those have been good experiences for me. Now, I want to blog a bit more seriously about science and what it’s like working in a lab. I am on my way to a science blogging conference and so it seemed that now was a good time to start a new blog.

I am currently a graduate student at a large research university in the Midwest. I am hoping to graduate fairly soon. Considering I’m in my eighth year of graduate school (!), it would be surprising if I wasn’t hoping to graduate soon. At any rate, much of my life is consumed with doing the experiments that will get me my thesis material that will get me my degree, so I’m not sure how much time I’ll actually have to blog. Right now, I’m aiming for at least one post a week (I find it better to aim low and be pleasantly surprised when things go better than to aim high and be disappointed).

The image found in the banner is a photograph of some of my yeast cells. It is typical of the type of data I collect in my experiments. In this image, there are actually about 20 cells (you can’t see the outlines of the cells because of the type of light I am shining on the cells). In these cells, Sec16 is fused to green fluorescent protein (GFP) while Sec12 is in red (the way I get Sec12 to look red is a little complicated). One way you can determine that there are several cells in the photo is that each ring of Sec12 represents one cell (not because it’s defining the boundary of the cell but because it’s in a circle around the nucleus of the cell and there is only one nucleus per cell). Each cell only has a few of the green spots. This is because Sec16 is found only in certain places in the cell. Normally, Sec12 would perfectly co-localize with Sec16 (that is, it would be found in red spots and these spots would overlap the green spots), however, these cells are actually overexpressing Sec12 (that is, making much more of it than it normally would). When I overexpress Sec12 in these cells, it becomes delocalized–it is found in regions different from the ones you normally see it in.