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.

Self-education

While I’m a big fan of formalized education (having been in school for 24 years now–yikes), I think it’s equally important to know how to teach yourself about the things that interest you.  Therefore, at any given time, I’m reading one or two non-fiction books about topics that interest me.  Currently, I’m reading two of them:  Lies My Teacher Told Me by James W. Loewen and Ever Since Darwin by Stephen J. Gould.

Lies is a book about American history.  The author (a historian) surveyed some of the most popular high school American history textbooks and wrote about the many inaccuracies found in those books.  It can be a bit depressing to read, though–not just because kids are being taught inaccurate information about American history–but because inevitably the inaccuracies are centered around sugar-coating events in American history.  So, mostly, I’m reading about the dark side of American history, so to speak.

Ever Since Darwin is a collection of essays about evolution written by Stephen J. Gould.  I have mostly shied away from blogging about evolution because it seems as though no other topic can bring the trolls and fanatics to your blog faster than talking about evolution (unless it’s talking about the need to improve the situation for women in science) and I just don’t need that kind of tsoris.  However, my blog is pretty low traffic, so I’m hoping it won’t be too much of a problem if I talk a little about my impressions while reading this book (this may be ridiculously naive of me, but I’m going to go ahead with it anyway).

I first read Ever Since Darwin about 8 years ago (just before I started grad school) and I’ve pretty much forgotten everything I read with a few exceptions.  This is not so much a statement about the material or the writing, but more of a statement about my ability to remember anything I have not specifically decided to commit to memory or taken notes about.  However, given the current trend of challenging the teaching of evolution in our schools, and being a scientist who is very interested in public science education, it seems to me that I should probably know more about the intricacies of the theory of evolution than I currently do.  Therefore, the last time I was in California (which is where the vast majority of my book collection resides, along with my husband), I tucked Ever Since Darwin in my carry-on and have been reading a bit at a time, making notes in the margins and in the space left at the ends of essays (note to self:  if ever I write a non-fiction book, try to make sure there’s at least half a page of blank space at the end of each chapter for people to make notes–and wide margins).  The fact that the book consists of relatively short essays is a bonus for me at this stage in my life because I rarely have solid chunks of time in which to read.  With this book, whenever my brain doesn’t feel like it’s about to blow a fuse (which, sadly, is not very often), I can read an essay and take a couple of notes without needing to make a huge investment in time.  So far, I have only read the introduction and about three essays in the first section.  Sometime soon, I hope to write a little about what I thought about those essays.  Stay tuned.

A different kind of microscope

I apologize for the light posting around here.  Unfortunately, it’s likely to continue until I finish these experiments.  I might find a little more time for blogging while I’m writing my thesis–who knows?

Lately, I’ve been spending my time trying to learn how to use a confocal microscope and bend it to my will.  The score so far is:  Confocal-5, Elisabeth-1.  But, I think I’m getting the hang of it.

A confocal looks much the same as a regular fluorescence microscope.  However, there are a few key differences in the way that the fluorescent image is acquired.   First, instead of using a mercury bulb to shine light on your sample to cause the molecules to fluoresce, a laser beam is used.  Second, the microscope is set up in such a way as to filter out much of the fluorescence not in the current plane of focus.  Third, instead of being able to look directly at the image using the eyepiece, the image is scanned with a special electronic scanning apparatus that is controlled via a computer.  The image is then displayed on the computer screen.

There are many advantages to this system, however, I am using it for a very simple reason.  I need to be able to collect an image from a sample in which my fluorescent molecule gives off infra-red light.  My regular microscope can’t do that whereas the confocal microscope can.  On the one hand, it’s good for me to learn how to use this important instrument.  On the other hand, I feel a little silly for using it for my stated purpose.  It feels a bit like using a supercomputer to write an article because it’s the only one that has the word processing program you like.  The confocal microscope has tremendous power but I’m only using it for it’s most mundane purpose.  In a way that’s good, I suppose, because I’m learning how to walk before learning how to run, but I still feel like I should be doing something a bit more profound on the scope than collecting an infrared image.

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.

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*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.

So, what does an expensive microscope look like?

A few months ago, I took a picture of the microscope I work on to show my family.  Here it is:

Some closer shots:

This scope allows me to look at my slides and take pictures of them.  It’s not a top of the line fluorescence microscope, and it’s a few years old besides, but it’s nice scope with good optics and it gets the job done.

Recently read books

I mentioned in a previous post that I was (some might say) obsessively reading fantasy books. Fantasy is the genre I indulge in when I need to relax or escape from whatever is going on in my life at the moment.

Right now, I’m reading books by Raymond E. Feist. I read the first few of his Midkemia books quite a number of years ago (10 or 11, I think) and haven’t read anything since then. I have just finished his two latest (in paperback), Flight of the Nighthawks and Into a Dark Realm, which are set in the same world as those first few books I read years ago. In fact, I seem to have jumped over a good 6 or 8 books in the series to get to these. Normally, I don’t like to do that (I prefer to read a series in the order in which it was written), but I was at the university bookstore and their fantasy selection is rather small so these were the only ones of the series available. Fortunately, the author writes these books in sets of trilogies so that I’ve essentially started at the beginning of a new storyline, so I’m not horribly confused (which would not be relaxing at all). The last book in this most recent trilogy has been released in hardcover, but I’m not sure I want to spend the money on a hardcover right now.

In general, I tend to buy books rather than borrow them from the library. First of all, because I love books and love owning books and love the feel and smell of books so I much prefer to own a book than borrow a book. Second, because I often read books over and over again and it’s easier to do that if I own it. Third (and possibly most importantly), I really suck at returning books to the library. Therefore, I rack up huge fines and in the end it is not much cheaper for me to borrow a book from the library than to buy the book (if it’s a paperback). When I was a kid, I ended up with so many fines the library wouldn’t allow me to check out books anymore (I had no way to pay the fines). So, I would read books in the library. This required me to hide whatever book I was currently reading so that nobody could check it out until I was done. I’m not sure if the librarians ever caught on. The books were always where I had stashed them, so if the librarians did know, they were kind enough to allow me to keep the book on hold, as it were.

At any rate, I’m now going back and reading the books in between the first books I read in the series and the books I just read starting with the trilogy just before this one. Of course, I know which characters make it to the next trilogy so the life-and-death passages are not so gripping, but I’m still enjoying them.

Trying to NOT falsify data

The vast majority of the data for my paper consists of photographic images. I have five figures and all but one of them are going to be mostly photographs. These images are of my cells and the images are supposed to answer the following question: where is Protein 1 when I do something severe to Protein 2?

Now, these data are exclusively qualitative. So, you would think that there wouldn’t be much of an issue with image processing. As long as I show images that look like what the cells actually do look like through the scope, then I’m fine, right?

Well, there exists in this world a program called Photoshop. With it, you can do any number of things to photographic images. For instance, I can take an image that looks like this:

And turn it into this:

And then, I can crop the image so that it looks like this:

But, should I? And why would I want to?

First of all, is the first image representative of what I see through the microscope? No. There is way too much green background (green that is not in spots) in the cells. That is most definitely not what they look like when I look at them through the scope. So, I can attempt to subtract out the green background. However, I can’t get rid of all of it because when I look through the scope there is a bit of green background fluorescence (cells naturally have some green background fluorescence). Besides which, when I try to get rid of all of it, I end up losing the greens spots which are my data.

Even more concerning, what if that green background is not actually background, but diffuse staining of my protein throughout the cell? That would mean that not all of my protein is found in spots. So, by getting rid of the background, I could be getting rid of data. If my purpose in showing this figure is to say that all of my protein is in these particular green spots and I manipulate the image to show that you only see green in spots, then I am misrepresenting my data.

Finally, by cropping the image, am I selecting a subset of images that look like what I want them to look like rather than what the majority of cells actually look like? I have no choice about cropping the image–I can’t possibly include the whole thing in the paper. The first image I showed you isn’t even the entirety of the original image. The original image is 18 x 11 inches in size, whereas my final image for the paper is probably going to be 1.5 inches in size. In order to be able to include more cells, I can resize the image to be 11 inches wide and I have done that with the actual image I’m going to use for my paper. Then, I can crop the image so that it’s only 1.5 inches wide–but only if the cells I include are representative of the majority of the cells I see when I look through the scope.

The Journal of Cell Biology has this to say about image manipulation:

No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The grouping of images from different parts of the same gel, or from different gels, fields, or exposures must be made explicit by the arrangement of the figure (i.e., using dividing lines) and in the text of the figure legend. If dividing lines are not included, they will be added by our production department, and this may result in production delays. Adjustments of brightness, contrast, or color balance are acceptable if they are applied to the whole image and as long as they do not obscure, eliminate, or misrepresent any information present in the original, including backgrounds. Without any background information, it is not possible to see exactly how much of the original gel is actually shown. Non-linear adjustments (e.g., changes to gamma settings) must be disclosed in the figure legend. All digital images in manuscripts accepted for publication will be scrutinized by our production department for any indication of improper manipulation. Questions raised by the production department will be referred to the Editors, who will request the original data from the authors for comparison to the prepared figures. If the original data cannot be produced, the acceptance of the manuscript may be revoked. Cases of deliberate misrepresentation of data will result in revocation of acceptance, and will be reported to the corresponding author’s home institution or funding agency. [emphasis added]

It’s somewhat tricky ground. I have to try to get rid of some of the green background in order to make the image true to what I see when I look through the scope, but if I get rid of too much of it then I’m massaging the data. Add to that the fact that I took these images a couple of weeks ago and am only now getting around to processing them which means that my memory of what things truly looked like when I looked in the scope is a little bit fuzzy. Do I really remember it having less green background or is that what I remember because ideally there would be less green background? Because of this, I’m going to repeat the experiment and process the images immediately after I collect them.

As you can see, it is relatively easy to manipulate your data to the point of falsification, even if you don’t mean to. The vast majority of scientists truly intend to present their data in a way that is truthful, but it is difficult to completely eliminate personal bias. I would love for all of my images to look like that last one, but that’s not reality and to present that image in a paper would be misleading. In some ways, I wish the image collection and processing were being done by someone other than me–someone who is not emotionally attached to the project in the way that I am. On the other hand, then I would have to trust that person to not manipulate the data in a way that is not truthful.

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.

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*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….

MIA

I’ve been having a hard time finding time to blog recently. Mostly, I get up in the morning, go through my morning hygiene regimen, eat breakfast, go to lab, come home, eat something small, take a shower and go to bed. That doesn’t leave much time for blogging. I was thinking about this the other day (albeit in the context of why other knitters are able to complete a sweater in a reasonable amount of time) wondering how anyone ever managed to even do laundry when I realized that most normal people have several hours between the time they get home and the time they go to bed. I vaguely remember when that was true for me, too, but I think it’s going to be awhile before I get back to that sort of sane schedule.

One disadvantage to being a scientist in the molecular biosciences is that it is virtually impossible to stop in the middle of an experiment due to the fragile nature of our samples. In some experiments, there are certain defined stopping points, but you really cannot stop until you get to one. It’s a bit like making cookies. You can freeze cookie batter, but it’s better if you finish adding all of the ingredients and mixing and so on before you freeze it. This is very comparable to my labwork because I am often freezing things (or putting them into the fridge) until the next day.

Anyhoo, the immunofluorescence experiments I’ve been doing have required that I grow my cells in special conditions for 8 hours, then start four hours of work. I can’t grow the cells for longer than 8 hours or I might have them grow overnight which would make things easier. No, I must grow them for 8 hours, then incubate them in fixative for 2 hours, then spend another hour preparing them for the antibody incubation and then I can stop until the next day. And, I always I think to myself, I’m going to go home for an hour or two in the afternoon before I start the fixation, or for dinner during the fixation, but I get busy doing other stuff and I never manage to take a break.

Anyway, the bottom line is, posting may be scarce until I get these particular experiments behind me.