#biology phd

[lichenaday]

I know this blog is lichen focused, but I also consider it a science blog and a space where I can talk about my experiences in science and academia. My most recent field work involved catching, handling, and ringing birds at a bird observatory, and I wanted to talk a little about the harsh realities of working with wild animals that I feel like don't get represented enough. I think it's important to paint a fair and realistic picture of what the world of animal research looks like, as it often gets misrepresented in media.

Wild animals do not like being handled. You have probably heard some story or seen some movie that makes it seem like you are somehow gonna connect to the animals you are working with and reassure them that you mean them no harm. No no, you are a big scary predator and they have no idea what is happening, and they scream, bite, and fight like hell to get away from you. This runs the gambit from kinda funny to mildly annoying to actually making it hard for you to work to making you feel bad for putting these animals through this stress. There will be no special magical wild animal friendships, trust me.

Animals are DIRTY. Like I know you know that on some level, but you don't really know it until you are up close and personal with them. In the case of the birds I work with, this usually means shit. Lots and lots of shit. On them, or you, on every surface and article of clothing you have. And you may think "in the grand scheme of poops, bird poops aren't so bad." But let me tell you: in sheer quantity and viscosity, bird shit beats them all.

PARASITES. Now we are not anti-parasite on this blog in general, they have their place in the ecosystem just like everything else. But personally, I don't really enjoy having to see them or experience them up close and personal. I'm talking ticks, fleas, mites, intestinal worms, louse flies, etc. Just . . . no thanks.

Animals get injured, and having to see these injuries up close and knowing there isn't anything I can do about it is hard. Be they old wounds, new, or the very rare wound that can occur during the catching and handling process, it can really get you down looking at an animal that you can't help.

Animals are unpredictable. Like, most of this field is about *trying* to predict their behavior, but animals are true disciples of Murphy's Law, and I swear they get off on frustrating scientists and their well laid plans and hypotheses. For me, this meant that the birds I was working with just didn't show up in the predicted numbers. This was frustrating to me on a how-the-fuck-is-my-project-gonna-work-out-now? level, but also on a worried-for-the-health-of-the-birds-and-the-planet level. If you enjoy work that is predictable and dependable, wildlife biology isn't for you.

I wat to be clear that I LOVE what I do, and I wouldn't trade it for the world. The work I and other wildlife biologists do is incredibly important and I am not saying this to cast a disparaging light on the field. But so many wildlife biologists I have interacted with are not like, bleeding heart, sensitive babies like me, and didn't adequately prepare for the mental and emotional toll of working with wildlife. I think the field selects for folks who are able to compartmentalize their love and empathy for animals, and I don't like that. I think we need people like me in the field, but I think they should be prepared for the reality of it, that's all. Or maybe I just need to vent lol.

[ladyflamewing]

May I also suggest getting to know a friendly scientist or other academic professional? I'm a Biology PhD and a current college professor, and I am always happy to talk about those individual words or jargon that makes research difficult - it's literally my job!

I am becoming aware of the effect a lack of trust in the media has had on people, paired with a dearth of research skills.

[skwpr]

Incredibly Healthy Habits For Students

The most commonplace advice on good habits for students. This crucial component of a healthy relationship is not to be overlooked.

1. Don’t over-stuff your backpack.

Unless a professor tells the class to bring a textbook – keep that thing at home/in your dorm. Also, try not to carry too much with you anyway. At most I have a spiral or two, my computer. It’s not only unnecessary, but it’s heavy. It wears you down over time just adding stress and annoyance that you don’t need.

2. Work out every week.

Finding time to run a mile or two, play some basketball, or lift weights is important. It was a huge stress reliever for me and it also made me happier.

3. Stop Putting Things Off.

You know you should be finishing homework instead of going out every night. The crazy thing is, we ALL KNOW what we should be doing. But a lot of us still don’t get anything done. I’m in awe of the number of times I have put off studying or reading. However, every time I come to the simple conclusion that getting it done in the beginning is waaaaaay easier than trying to finish the task later.

4. Socialize.

Involvement in college is a spectrum. One extreme includes hobbits who stay in their dorm or apartment all day and the other includes social butterflies who are out on the town every night having fun with friends. Your goal is to find a happy medium. You don’t want to be closed off but you also want to interact with people every once in a while.

For me, this was the hardest part. I do not like to make acquaintances, but for myself I decided that it would be useful. I stepped out of my comfort zone.

5. Eat Healthier.

This is the most predictable advice I can give you. What you put in your body matters.

6. Drink more water.

Drinking water is one of the most essential healthy habits for students.

7. Know When To Say NO.

If you get your work done first, you will have time to have fun without any grief or regrets.

The most important relationship you make in your life is with yourself. It’s genuinely all a mind game. You have to learn to trust yourself by putting yourself first so that you can enjoy what life has to offer you. Having fun with this grey cloud of regret and worry about work you haven’t finished is just not fun at all. So have fun and be yourself but learn when to say NO. You’ll be forever grateful you did in the long run.

8. Give Yourself Grace.

One of the biggest downfalls for me was stressing out. Stressing over school work, time management, boys, networking, and the list goes on. It’s important to shut all the negative voices out.

There’s only one you so treat yourself with respect. If there are things you need to fix, make a plan and make it happen. If that fails, adjust the plan. No one is perfect and I wish we would collectively tell ourselves it’s going to be ok. Because it will be!

[miss-biophys]

Work on a scientific article

What it actuallly entails:

Come up with an idea, define an interesting problem

Do thorough literature research. Maybe similar stuff was already done. Define the knowledge gap well.

Plan in detail, how we can solve the problem, design experiments

Reach out to potential collaborators, agree with them on a plan

Buy necessary equipment, chemicals

Do pilot experiment, optimize the conditions to get reliable data

Perform experiments, calculations, make everything multiple times so it's reliable

Analyze the data

Urge collaborators to deliver their parts

Coordinate your progress with the collaborators

Manage the collaborations, organize meetings

Be diplomatic, you don't want to make enemies in academia

Agree with direct colleagues, who worked on it, what will be the message of the article. Will it be a long story and we need to add some more data? Or will it be short and right to the point and we write a short "letter"?

Do literature research again. Maybe new stuff appeared, and for sure your data must be confronted and discussed with already known facts.

Write the first draft of the article

Send it around for feedback, first only to direct colleagues from your lab

Incorporate the feedback, maybe do more experiments and more analysis

Rewrite the manuscript

Send it around the second, third, fourth, fifth... time

Incorporate the feedback

Send the manuscript to all collaborators.

Wait for the feedback, urge everyone to give it, maybe you don't have all data from all the collaborators yet

Incorporate feedback

Prepare the manuscript for journal submission

Get approval from all co-authors

Submit the manuscript

Wait for editor response, hopefully they send it to reviewers. If not, you need to rewrite a bit the article to adhere to the new journal's format and send somewhere else.

Get reviewers' reports, deal with them, reply truthfully, make effort to explain everything even if you know that the reviewer's suggestion is just impossible or irrelevant. Be diplomatic.

Maybe you need to do an additional experiment, analysis, or rewrite a major part fo the manuscript. This can take months.

Submit revised manuscript with all the changes

Wait for editor's nad reviewers' comments in the second round. You can get many rounds of review and still get rejected.

Finally get a "Congratulations, your manuscript has been accepted for publication"

Pop a shampagne! You deserve it!

What part of this do you usually do in different career stages:

BSc. and MSc. students: Perform experiments and analyze data

PhD students: Do all the experimental and analysis parts, write the manuscript, discuss with their supervisor and direct colleagues, incorporate feedback. But does not have to come up with their own idea and manage collaborations and diplomacy.

Postdocs: Do literally everything on the list

Group leader/Professor: Do the thinking and managing parts, help with writing and feedback, provide discussions and insight. Do not perform actual experiments and analysis.

Being a postdoc is the transformation between the student and the group leader.

As such, we just have to do all these tasks. It's stressful. It's challenging. It's definitely not boring. I am taking every opportunity to get a student, who can help with the experimental repetitions so I have time for all the other stuff.

[honey-marrow]

[foxscarf]

24.11.23

I finally finally broke through the cloning lab work we've been stuck on for two weeks! We're behind on the project plan/schedule, but I feel more 'in it together' with my supervisor now, and I'm hopeful that we're on top of it and I'll get to do cool data collection over the next few weeks!! It'll be a busy time but yay. ❤️✨🧪🥼

At first was really annoyed about having to stay late this evening (on a Friday night!), as I needed help and had to keep waiting around for my supervisor to have time; but in the end I got really engrossed in understanding a problem and designing some primers by myself, and I'm super proud of that! It's very confusing with the type of plasmid we're constructing (a hairpin vector for any molecular microbiologists reading this lol❤️) so I think I did really good.

And then I actually finally got back to art and drawing this whole long evening when I had the flat to myself!!

30/100 days of productivity

[panic-flavored]

Some Stobotnik for MerMay!

❤️💙 when the hot fish man the government hired you to study is more fascinating than 100% of the humans you've met (and he loves all your diabolical ideas) ❤️💙

[ladyflamewing]

Friends, I have won literal awards for my teaching, and I still have moments every single semester where I go, "But what if I'm actually terrible at this?"

It really doesn't ever seem to go away.

Imposter syndrome is wild lol cause I’ve had multiple people tell me they think I’m good at my job and that I’ll do really well in the grad program I’m enrolled in but still am convinced that I’ve tricked them all and failure is imminent. It really makes me wish I could see inside peoples minds to see how they perceive me. One coworker told me they think I’m really confident and that I never seem to get stressed and I’m like lol it’s a good thing you can’t see the constant clusterfuck of self doubt and stress that’s inside of my head.

I'm 37 years old, I make really good money in a great career, and I still can't believe people on the internet listen to my advice. I'm terrified that some day one of you will go:

Imposter syndrome: she's real!!!

[wolftozier]

niche au i will never get around to writing: entomologist richie tozier

[lichenaday]

One of the things I really like about being a PhD student is that I don't really have average days. I don't have any teaching commitments at the moment so I can kinda just plan my own work schedule. This takes A LOT of self discipline which I don't have tons of so it can be challenging at times, but also means I get to work at my own pace. Since I don't have an average day, here's a peak at what I am up to today.

I wake up around 7:30/8. That's the time my cats have decided is wake up time, so I have little choice. Today we have a lab meeting over zoom at 10, so after running to the store to pick up cat litter and cat food, I head into the office.

I live about an hour away from my lab via train (I can't afford a place in the city), so my long commute is taken up listening to podcasts and staring out the window.

The lab meeting goes long today (as it does most weeks) and then it's on to EMAILS. I have a lot going on at the moment as I am planning my field work in Iceland in 2 WEEKS jeez how did it get here so fast! I also have to submit a presentation abstract for a botany conference I am attending in a few months. Luckily my supervisor was able to edit it last night so I can submit it today.

Then I go for a walk because the weather is nice and I need it.

My office is at the botanical garden so it is hard to resist. Spring is here! My misery can end!

Then it's lab work time.

They are doing construction on our normal lab so I have to go use the one in the creepy basement. I get a stern talking to from one of the other lab folks for not signing up for a scheduled time slot, which I didn't realize was a thing since it is my first time working in this lab. So I scurry away to figure out how to do that.

It's a lot of running up and down this grand stair case back and forth between my office upstairs and the lab in the basement.

I am running an agarose gel on some PCR products to see if I was able to amplify fungal DNA in some rest samples. I have to do this using ethidium bromide which is a hazardous chemical™. The German "danger" skull and crossbones doesn't have teeth for some reason?

My gel results are not good and so it is back to the drawing board on that one, but this was just a test anyway.

I am also working on extracting spores from lichen apothecia, which involves sticking apothecia on the lid of a petri dish, watering them every day for a week, and praying that they rain down spores into the dish below. Pipetting a drop of water onto each apothecia is tedious, but also satisfying.

Now I just have to kill time until I head out to choir rehearsal @ 7:00PM. So I go back to emails, annoying my coworkers, and my side hustle editing for an academic blog.

And that's what my day looked like. Some days I do more lab work, most days I do a lot of writing, and soon I will be doing LOTS of field work which is my favorite!

[sillysparklyspaghettios]

GENIUS IDEA: what if we fixed air pollution by turning all the carbon in carbon dioxide emissions into diamonds and become rich 😱😱😱😱🤯🤯🤯🤯🤔🤔🤔🤔😲😲😲😲

[inheritance-beyond-genes]

17.05.24

After a depressive episode i decided to reromantisize my relationship with living things. One thing i used to enjoy a lot is fielwork which i am not doing anymore so i sneaked into other's people projects yesterday. Felt so energised and passionate even for short time!

[some-sort-of-ecologist]

some thoughts on doing science as a PhD drop out

I saw this post on Facebook and it so perfectly summed up the gatekeeping aspect of doing research on a charismatic species. Ultimately the gatekeeping led to me quitting the PhD program, but I hadn't even really realized it until I read the way this person verbalized it.

When I did my undergrad thesis, I worked on reintroduced elk that no one really knew existed beyond a tiny group of biologists. Any research about these elk was exciting and GOOD, because so few people had the funding to study them. I got so much support from biologists and so much "wow, that's so cool, I had no idea we had elk here!" from the locals.

I love research. It plays up my strongest skills - outdoor field work, intense observation, patience, technical writing, and analysis. I love collaborating with people and seeing how we can ask new questions together.

I moved on to caribou for my masters and predators (wolves, bears, and cougars) for my PhD. Suddenly everyone and their dog had an opinion on these species. How they should be managed. Whether they should be studied or left alone. Whether my particular study had any value. And I heard about it. All. The. Time.

I started dreading talking about my research. I was so scared of people thinking my methods weren't rigorous enough, or I wasn't asking the right question, or I wasn't using the right statistical analysis for my question. It seemed like everyone I met had some sort of investment or special interest in my species, some reason why I had to consider their advice.

(Now don't get me wrong, I value constructive criticism from colleagues and appreciate suggestions for improvements, but these were constant, unending comments from people outside the field, people working on different species, and people I didn't ask for advice.)

Anyway. I didn't have any real kind of community or support from peers during grad school, especially compared to the network of Elk People I had during undergrad, and it, combined with the effects of the pandemic on the world, eventually led me to quit my PhD. Talking about my project felt hostile, no matter who I was talking to (and especially my labmates), and my heart wasn't in it.

The thing is, I love research. I love wildlife. I would love to pursue a PhD.

I think I just need a less charismatic wildlife.

[skwpr]

🔆📝 HOW TO KEEP YOUR LIFE ORGANIZED 📝🔆

1. The 3 most important tasks. Write down the top 3 tasks you need to do during the day. Start your day with them, and then you won't have another day where you've managed the small things and there's no time left for the important things.

2. Make a task list. Every morning, make a list of tasks that you need to do during the day. This list will help you stay on top of your scheduled to-do's and make you more organized.

3. Do only one thing at a time. When you focus on just one thing, the work progresses a lot better than if you do several things at once, jumping from one thing to another.

4. Do it now. If something needs to be done, do it right now. Don't put it off for a minute, because then you'll find other reasons why that action needs to be postponed or not done at all.

5. Clear your workspace.Remove from your field of vision all unnecessary and superfluous things that can distract you.

6. Simplify, simplify, simplify! Find methods to simplify your actions so you can get your things done in less time with less effort.

7. Keep things in order. You don't want to throw things around your apartment or office. Put each thing in its place and then you will not need to spend time looking for them.

8. Sign up for a time planning service. Nowadays, there are many different services on the internet that help you plan and do what you have planned. You will be able to keep your to-do lists under control, work on them through your phone, get reminders on your phone or e-mail and more.

9. Examine your daily routine.Analyze your days. What takes up the most of your time, what you are often distracted by, what activities do little good. Try to remove habits from your life that interfere with your life.

10. Add color. Those who like to work with different colors can try creating a to-do list in different colors so you can see important to-do's at a glance.

11. Let others do.Some to-do's are worth delegating to other people (work or home).

12. Be positive.If you are not able to make your life organized in one day, you should not despair. Try, try, try and you will see that you and your life will start to change.

13. Set goals. It helps a lot to speed up the process of work if you clearly see the end goal you are moving towards.

14. Set a deadline.Understanding that you have a definite time limit on a task, you will be less distracted and relaxed.

15. Encourage yourself. When you finish some hard work, an important task or some project, then do something nice for yourself, maybe even celebrate the event. Positive emotions will help you in the future and make life more joyful.

[katiajewelbox]

Plant Immune System Part 3

The plant immune system is the topic of my PhD thesis, which I'm currently writing following several years of lab-based research as a PhD student at Imperial College London under the supervision of Professor Colin Turnbull.

Here's an introduction to my research, which focused on how certain plants defend themselves against aphids.

Aphids are an important insect pest that threaten agriculture worldwide. As we learned in the previous post, plant resistance (R) genes control resistance to specific pests and pathogens through interaction with effectors from the invaders. Since examples of R gene-dependent aphid resistance have been documented in different plant species, aphid-specific R genes may enable the development of resistant crops.

In the model plant Medicago truncatula, there are some varieties that are resistant to aphids and other varieties that are susceptible to Pea Aphids (Acyrthosiphon pisum). Whether the plant is resistant also depends on the variety of aphid. In my project, the A17 plant is resistant to PS01 aphids but not to N116 aphids, while the DZA plant is susceptible to both aphid varieties.

What is the key difference in the resistant versus susceptible plants? Resistant A17 plants have a portion of their genome “Resistance to Acyrthosiphon pisum 1” (RAP1) which determines resistance to PS01 aphids, but the genes controlling the defence response and physiological defence mechanisms remain unknown. Two candidate R genes located in RAP1, designated “RAP1A” and “RAP1B”, may control resistance.

My main objective in my PhD project has been to determine whether RAP1A and RAP1B control aphid resistance, and to investigate the RAP1-mediated defence response. I look forward to sharing the findings in publications and in talks next year!

Image credit: Original diagram by Katia Hougaard with images from the Turnbull Lab.

#katia_plantscientist#science#biology#research#plants#botany#plantbiology#phdproject#plantbiology#plantscience#sciencecommunication#diagrams#phd#imperialcollegelondon#phdthesis#medicago#aphid#plantimmunesystem#pestsandpathogens#plantpathology#womeninscience#plantbiologist

[mardistudies]

april 3rd

chile, im still playing catch up, but i spoke with my advisor and we found a way to make this semester easier for me. the down side is that i’ll be doing work this summer too, but it’s okay. i just gotta do my best yk.