Bacteria have rights too!

Before you start laughing, please consider this: isn’t it at least a bit appalling to grow hundreds of millions of innocent little creatures just to be able to harvest a part of their DNA?

During my internship, I’ve grown countless erlenmeyers of bacteria just to harvest a plasmid or a phage. It’s something you do thoughtlessly, just inoculate some broth with a bit of your freezer stock and the next day you’ll be able to harvest. However, they still remain living organisms and don’t always do what you want. As a rule, if you’d like them to grow not too much, they always grow extremely fast, and if you’d like them to grow fast, they always take their time and you can spend hours waiting until they FINALLY duplicate.

Of course, I kill millions of bacteria just by doing the dishes. That’s not the point. I’m merely wondering -how far have we gone, using other organisms as a source for ‘ingredients’…

It’s not just bacteria, there are also a lot of immortalized cell lines (some stemming from aborted fetuses) that we use for virulence studies. These studies are very valuable – and yet, these cells living in plastic bottles, it feels wrong. These cells were once part of a multicellular organism and now they’re living their lives as individuals in medium that sort of replicates their native circumstances. What did they ever do to us?

Researchers using animals often say that they never forget to respect them – by their sacrifice we can study virulence, physiology, cures for diseases, etcetera. Perhaps we as microbiologists shouldn’t forget to respect our bacteria…

Does this sound stupid? Personally, I don’t think so. I still do a miniprep on my E.coli. But sometimes I pause to think about the ‘order of nature’, what force gave us humans the power to do this to entire cultures of organisms… And of course, the Creator who made this all possible, comes to mind. Let’s not forget the One by whose virtue we’re allowed to explore all of this… but I wonder whether he actually meant us to do this to his creation.

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On presentations

All master students have to do a literature presentation so I wasn’t exempted from that, even though I don’t have a background in the life sciences. It was a lot of fun but also quite stressful. After all, it was my first presentation in English and it was about a subject which I researched quite well, but I’ll never know as much as my audience does. In the end, everything turned out alright… but I’ve never been so nervous for a presentation.

You see, medical students at my university are literally drilled in doing presentations. Once in two weeks you needed to give a 30-minute  presentation about your group’s  ‘study assignment’ (a patient case and the theory connected to it). Presentations were graded, taking account things like ‘eye contact’, ‘body language’, ‘use of voice (inflection etc)’ — and there was also one item on which ‘content’ was scored. So, eventually, almost everyone became proficient or at least comfortable with giving a presentation in Dutch. For me, content was never a problem, but rather the ‘form’ – I’m usually quite nervous etc. So I got a lot of feedback and a lot of opportunity to try it, and most importantly, I got the experience so I knew I can do it (not perfectly, but I can do it) so that’s a great confidence booster.

However, when presenting in English, everything changes. Instead of being mindful of body language and how fast I talk and stressing important words, I’m thinking about grammar, sentence structure and pronunciation. English is really difficult in that aspect. For instance, compare the words ‘analysis’ and ‘analyze’. The stress is on a different syllable, even though the words are similar. So I manage to mess up and stress the wrong syllable – and then, halfway the word, I notice and I stop talking and think – what was I saying again?  The same goes for the ‘difficult to pronounce’ words – those words using sounds and sound combinations not encountered in Dutch (the th sound, the word ‘mechanism’ (ARRRGGGGGHHHHHHHHHHHHHHHHH)) . Really, I’ve stopped and restarted a word countless times…

But… somehow, they liked the presentation. I felt like I’d done a horrible job. I actually felt rather awful. And yet, several people whose opinion I value, came to me and told me in private that they really thought it was good and interesting and etc.

Apparently, everyone apart from the people in my curriculum, really only care about the content. They are used to people stuttering in English, they are used to people not knowing which word to use – — because we (Dutch people) are all in the same boat regarding our language skills. So they have learned to disregard the form and listen to what the person is actually saying instead HOW.

And that was an important revelation for me. Yes, I really need to improve my English presenting skills (sorry, didn’t watch enough TV series without subtitles, like my husband and no I didn’t know that disguise isn’t pronounced like dis-gweeze) – but perhaps our curriculum has gone too far in only grading form and not content?

Slightly less depressed :)

Fortunately, the ‘everything-goes-wrong’-streak broke, several experiments finally went the way they should and the results are looking quite promising. It also helps a lot that there’s a Christmas break – finally some time away from the lab! Now I’m finally able to properly enjoy the daylight again, usually I leave when it’s still dark and I return when it’s dark again.

Still, I’m feeling a bit ambivalent toward the internship, as I’ve come to realize that the supervision isn’t as optimal as it should be. At first, being left to work on your own is quite liberating – no one could see how I fumbled around with the pipettes on the first day- but in the end, it’s nice to have someone check in on me every once in a while. Especially as it feels as though I’m dragging people away from their Very Important Stuff when I’ve got a question (or don’t know what to do).

Fortunately, there are still quite some days of holiday left, so I’ll thoughougly enjoy that and go back to work with a fresh mindset! Or something like that…

I hate making mistakes.

  • Forgetting to add DNA
  • Confusing test tubes (adding #1 tot the new one labeled #3 etc)
  • Adding the wrong amount of… DNA, medium, enzyme, you name it…)
  • Selecting the wrong settings for the… PCR machine, power source for gels/blots, heat blocks
  • Tipping over fragile things
  • …..

I do try really hard, I write out all the steps, think things through, but somehow, stupid mistakes continue to happen. Usually, they can easily be fixed but sometimes they result in having to throw out all of the experiment and starting all over…

I’ve put a lot of thought into ‘WHY?!!!!!!!!’ I think the answer is really simple, actually: I wasn’t trained to do this. Where students of the life sciences get lots of lab time, I haven’t spent more than 20 hours in a lab. All experiments were completely prepared – we didn’t have to do dilutions or OD-measurements, we just ‘put stuff together’. They did try to make us understand what was happening but, usually, these explanations were really boring and it wasn’t on the test anyway. True, I did choose this internship myself because I thought I liked doing things in the lab.

I do. I think it is really interesting and it is awesome to ‘mess around with DNA’. However, when almost everything that can go wrong goes wrong due to an oversight on your part… it isn’t so much fun anymore. It’s completely different from medical-type things, where you also need to work systematically and carefully. You need to think about everything in advance – decisions on the spot usually have disasterous consequences.

The point is – I’m trying really hard. Asking lots of questions, asking for verification. Some things do finally go well. Yet I’m getting more and more frustrated that these mistakes actually happen, that I still work rather slowly (stress / lack of time really is the ideal disaster recipe…).

Would I like a career in research? I don’t think so. The thought that this will be coming to an end really comforts me. I do like digging for answers in cells, but, apparently, medical students in the Netherlands really aren’t made for this.


Three weeks in!

I didn’t know a better title. It’s been a wonderful experience so far. No, not everything is perfect but I am finally getting to know what research is like when you do it full time – and that was the goal of this internship! I’ve still got five months to go so I hope I can keep this excitement alive…

What I like:

1) They are leaving me alone to work with extremely expensive equipment / dangerous chemicals. Of course, they are always available to help and they made sure I got good instructions – but I like it that they trust me (even though I’m not scientifically trained).

2) The serenity of lab work. It’s quite Zen like when you need to make an enzyme mix for 10 eppendorf tubes. Actually, I get so caught up in the work that easy things like that can take me an hour. (sorry!). I do try to speed it up but then I forget things like adding the DNA…

3) The fact that we’re really on top of things. During literature meetings, the impact on our research is discussed and sometimes they set out an entirely new course based on just one article.


What I don’t like:

1) My own mistakes. I lost an entire week because I apparently did something wrong in one of the first and fundamental steps. No one holds it against me, but it is very frustrating when something like that happens.

2) My lack of reasoning abilities in these matters. For instance, how to judge when a gel is finished. My supervisor usually say something like ‘just let it run until the first band reaches 2/3 of the gel’.  But WHY?! I finally found out myself but it’s quite annoying when you have to blindly trust them without knowing the reasons behind it.

3) Sometimes things go wrong even though it’s not your mistake. I wouldn’t be able to do this for a living. I know it’s not important whether my project yields results, but it’s just a limited amount of time. Some people have worked there for YEARS and of course there are periods in which nothing happens. How can you keep motivated when everything fails? (for instance, they tried to work with a new strain of the particular bacteria and it just wouldn’t stay alive no matter what they did.)

4) The interpersonal relationships are just like high school. Lots of gossip etc. etc. I heard from friends/relatives that ‘the workplace’ is always like that, but it’s still a bit of a disappointment.

Half a doctor does NOT mean half a scientist

It feels a bit like when I was doing the primary care internship and tried to explain to my supervisor that I heard some ‘ rumbling’  in the patient’s lungs. Well, worse. Now I don’t just lack the correct vocabulary, I lack the knowledge and the skills as well. I knew it was going to be a challenge, but apparently, Dutch medicine students are very ill prepared for basal research. (alright, and that I forgot that red blood cells don’t have any DNA… let’s blame it on Mr. Grey Rat’s premature demise.)

So I spent the first three days of my internship reading up on my research and watching my supervisor put a piece of DNA in a plasmid. And feeling rather stupid, as my fellow research internship students (bachelor students of biomedical sciences) don’t have any problems with understanding my resarch. So now I need to hurry up with understanding it myself…

Things I learnt:

  • The meaning of the words ‘putative’, ‘moiety’ and ‘periplasmic’ (FAIL, I should have known that one)
  • Don’t push your pipette when you’re in 1 μl of fluid. It will start to foam and you might almost fail the blot you are doing
  • Scientists are also very good at pimping
  • After 4 hours, reading the NEJM and the BMJ ‘for fun’ is better than trying to figure out at how enzyme-ase catalyzes 1,2,3-alpha-protein to 2-7-beta-protein.
  • Finally being allowed to pipette something makes me ridiculously happy.