#science advice

[cancerbiophd]

Hey Julia!😊 It's been good to see your posts about your work and we get to see through into life of a researcher in a way. I have this very silly doubt. How one thinks what topic one should go with while making a research proposal? Like if someone's interested in molecular biology and neuroscience so how do you get think about it in a scientific manner? I have always been curious about how one can be a great scientist and contribute more to science.

Hi anon! Well I’m very glad to be your window into research/grad school. And anything I haven’t shared yet I’m always very happy to answer in an ask, like this one!

How to go about thinking about a subject in a scientific manner is a very good question. 

The short 5-step answer is:

Learn about what’s currently known about the subject, such as through classes, reading the literature, going to seminars, or from other researchers. 

Identify knowledge gaps that interest you

Pursue those knowledge gaps as doable research projects. And I say doable because we are confined to available technology, money, space and time, etc

And hopefully make a meaningful discovery, and contribute that to society by communicating that discovery (through presentations at conferences/seminars, publishing papers, etc)

Then repeat the whole process with another knowledge gap :)

If you’d like to know more of the nitty gritty details, here are links to some of my other posts:

How to come up with a PhD research project (in the life sciences, ie involving lab work)

How to learn more about the subject to identify knowledge gaps

How to design a good experiment

Tips on writing papers for publication

How to think like a biologist

Let me know if you have any other questions about this process (or anything else)!

[6-phds-and-no-sense]

Science babe, I ask for some wisdom. Not a lot of people take me seriously, even though I get a lot of A’s in my science classes. My parents don’t even think I’ll become a scientist, I’ve been told I don’t fit the ‘type’. I know it doesn’t matter that I’m really into patterned socks and glittery eyeshadow, but I’m curious. Will no one take me seriously in upper academia, or are they willing to actually look at my report card?

Am I science babe now?? I will accept this. This is good.

As to your question: I have been considering this sent you sent it in, and I don’t have a sure answer for you. Some disciplines are harder than others, just because the demographics haven’t quite shifted away from being mostly straight white dudes. That said, I found that undergrad was much, much better than high school (where I’m assuming you are now? forgive me if I’m wrong). A lot of what I have to say is through the lens of being a cis white lesbian, so it may not apply exactly to your particular experience.

When I was in high school, I also got A’s in all my science classes. Towards my senior year, when science classes were electives instead of required, I was one of a handful girls in most of the upper level science courses. Despite being on par with all the boys in my class, I was told over and over again that if I got into a good university, it would only be because I was a girl and they needed to ‘fill a quota.’ This persisted even after I did better on the SATs than them, and after I got 5s on my AP exams. So, I went into undergrad expecting to fight people constantly and have to prove how smart I was.

A few things happened. One: half the people in the chemistry department were women. Two, almost everyone was extremely nice and just very excited to be doing science (and the ones who weren’t were not well liked). I didn’t have to be the smartest to be taken seriously. I just had to be serious about the work and reasonably pleasant to people. Good professors can tell which students are working hard and trying to understand the material. 

(Side note: Everyone currently in college or about to go to college. Go to office hours! GO TO OFFICE HOURS. Go o o o to of fice hours. Let these people know your face. A B student who goes to office hours every week and does their best gets better recommendations than an A student who only talks to the professor while dropping off assignments.)

I work at a different university now. I spend most of my time helping graduate students with their experiments. I suspect you know this, but there’s not really a ‘type’ of person who excels at science. There are a lot of people with bright blue hair, or people who dress high femme, or people who wear t-shirts and jeans. They all do well and are taken seriously. (I talk too much about Pacific Rim, but like. There are definitely scientists who dress like Newt. Many are lesbians. They do fine. I hope to see many of them hired as faculty.) It’s hard when your parents believe you aren’t the sort of person who can do science, but I very much doubt your parents are scientists (and if they are, they’re jerks).Some links that you may find helpful on this particular issue:https://www.500queerscientists.com/ 

https://500womenscientists.org/

http://www.scienceupdate.com/spotlights/african-american-scientists/ 

(ps if someone has a more comprehensive list for current scientists of color that would be neat and I would appreciate that link)

If you’re still with me after this ramble, some science school advice!1a. When you’re looking at universities, check the faculty pages for people like you. Are they hiring women? People of color? Or is it all white dudes?1b. For labs you might want to intern in, check to see what the graduate students look like. 1c. A diverse faculty does not guarantee a friendly environment, and a very whitebread faculty does not guarantee a surplus of -isms. That said, departments with diverse faculty tend to work harder to support diverse students. My undergrad experience was greatly improved by having a bunch of women as professors in my department.2. Grades are important, especially if you want to go to grad school, but I think doing internships is maybe more important than classwork. Internships are the best way to find professors and graduate students willing to cheerlead and mentor you. These are the people you can go to when you need advocates or just a perspective check. Exactly how you get an internship in a university lab differs by university, but where I went to school we literally just e-mailed professors we liked until one said yes. (*Or, if you’re taking a class with a cool professor you would love to work for, ask during their office hours if they’re accepting undergrads!)3. Make friends. These don’t have to be good friends that you hang out with all the time, but have at least like, one person in each class that you can work with on assignments or ask to pick up worksheets etc for you when you’re sick. The nice thing about science majors is that you are often forced to have lab partners, which is like a class assigned friend that does not require you to initiate any social contact yourself. (Some lab partners will suck. Do not rely totally on this method.)4. There is no way to guarantee anyone will take you seriously. What you can do, though, is take yourself seriously, and take your classmates seriously. People will take cues from you. Learning to advocate for oneself is super, absurdly hard, but it’s a good skill to start learning. Calling people out for their rude behavior is also hard to start doing, but immensely satisfying. Upper academia will continue to have its problems, but it’s getting better all the time.5. When you find the people that take you seriously, treasure them. Cheerlead their work too. University is the time to find your people who will help push you through the rest of your career.

I think, if you decide you want to be a scientist, that you will be. 

I hope you found this helpful! Please message me privately if you have any specific questions. (or send more anons!)

[cancerbiophd]

Hi Julia! I'm just starting my PhD, and my supervisor gives me a lot of freedom and independence. While I appreciate that, I'm not sure where to start tackling my project. I've done a lot of reading, but I'm having trouble designing good experiments. Do you have any suggestions?

Hi anon!

I have a post here outlining one possible path to take when designing your thesis project–however, it does involve communicating with the PI almost every step of the way. I do think that PI involvement is pretty crucial for the development of a PhD student, so if there’s a way for you to have weekly one-on-one meetings with your PI, I think you’ll find that would be really beneficial. 

In the meantime, let’s talk about experimental design. It’s a very important skill we learn during grad school, and one of those skills that separates someone with a PhD and someone without. It’s part of the “Ph” part of the degree, after all! So if you’re not getting the mentoring necessary to learn how to properly design experiments, then that’s a huge foundation of your PhD that’s missing. If your program (or any related programs) has a class on experimental design, it would be worth taking (I took two different experimental design courses, on top of regular guidance from my PI, and years later I’m still learning so much about the nuances of experimental design). Regardless, as a minimum requirement for a PhD mentor, your PI should be teaching you proper experimental design and results interpretation. Otherwise they’re just a warm money-pumping-lab-having body for the next 4+ years and that’s not what you, a PhD student, are here for, or deserve.

However, I do understand the reality that is busy PIs and large labs. If your PI is really hard to get a hold of, you can try finding other mentors to help guide you, such as: other senior members in the lab (like the lab manager, research specialists, post-docs, even other grad students), your committee members, the PI next door even. I get advice from as many people as I can, because sometimes even if my PI is available, she may not have the best expertise in certain situations. 

As a supplement, I would also recommend finding online resources on experimental design. A quick google search of “experimental design in biology” lead me to this awesome video from Khan Academy that covers experimental design at its simplest. 

Now here’s a quick and dirty 4-step crash-course on experimental design (from my experience in doing biology research):

1) Start with a testable and feasible research question:

This is based off a hypothesis/prediction you make, which in turn is based off the knowledge gaps in your research area

It can be as simple (one experiment) or as complex (aka the focus of your entire dissertation) as you want it to be

It should be testable: you actually have a way to figure out the answer

And also feasible: given your time, ethics, and resources (eg. equipment available, funding, people who can help you)

This is something that reading the literature, or talking to your PI, can help with. 

(Divide up your research question into sub-questions if necessary)

“Yes” and “No” research questions are totally ok. Sometimes it’s as simple as “does my cell line constitutively express this receptor, yes or no?” or “does Treatment X induce my cell to secrete Protein Z, yes or no?”

2) Come up with a method to answer the question:

I like to first go into “fantasy” mode. Like, what would the perfect assay be to answer this? I pretend it’s the year 3050 and whatever I think of we can do. For example: “ah if only i had xray vision and the ability to tell apart a human tumor cell from mouse bone marrow and can see just how many of these tumor cells end up in the bone with my naked eye!” Thinking like this first lets you get to the bottom of “what do we need to solve this problem?” 

Ok, time to go back to the present. We can’t see tumor cells through bone with the naked eye, but what do we have that allows us to do so indirectly? How can I tell the difference between a human cell and a mouse cell, and also quantify that? 

Another part of the design process where reading the literature and/or talking to your PI and other researchers would help with, especially if you don’t know what you don’t know. 

Like if I have no idea that something like intracellular fluorescent labeling and flow cytometry existed to solve my question at hand, I couldn’t even use that in my experiment

Determining the method you will use is sometimes the most time-consuming part imo. If it’s something you or the lab haven’t done before, you’ll need to do a lot of research into the methods (what’s the best reagent? concentration of reagent? do we have access to equipment necessary? do i need specific controls? what’s the specificity and sensitivity of this assay? are there background issues i have to contend with (eg. autofluorescence))? It may take a few tries with optimization before getting the method down for your purposes. And as you can see, it can be super involved, so getting advice and help from your PI or another expert would be really helpful (and time saving!)

3) Design the experiment on paper with the proper variables, controls, and replicates:

I like to pretend I’m solving a murder mystery and I have to convince the jury that Suspect A, with weapon C, is the one who dun it. How do I go about designing an experiment that will eliminate all possible suspects and murder weapons (and thus convince the jury)? 

Sometimes it helps to draw a predicted results graph of your experiment; seeing it in its “final” form may help you realize some controls or treatment combos may be missing. 

Once you’ve designed the experiment, go over it with your PI (or another expert), to make sure it’s sound.

The number of replicates (technical vs biological) you may need will depend on statistical analyses, like power analyses and what kind of statistical experimental design (eg. one-tailed vs two-tailed) you’ve decided beforehand. If this all sounds new, then that’s something you’ll need expert advice on (like from your PI), or take a class in (like biostats), or do lots and lots of independent research (perhaps the most time-consuming and mistake-prone choice). At a minimum though, we always need at least 3 values to perform any stats (so if you’re just running something up the flagpole, n=3 is a quick and dirty thing to do first). 

4) Predict the outcomes of each of your variables and controls and do some thought exercises

Ask yourself if these predicted results will answer your question

If it only answers part of your question, what else do you need?

If it doesn’t really answer your question, what should be changed? 

What if the opposite of what you predicted happens? What would that mean? 

If all this seems super overwhelming, then I think it’s a sign to seek out specific help on experimental design, like your PI or a class. Again, it’s part of your PhD training, but it’s not something you need to, or should, learn all by your lonesome self. 

Good luck with your training and research! I hope you find a good path forward. 

[cancerbiophd]

Hey Julia, I have both a scientific and I guess personal/self-confidence question. I'm a first year grad student and my knowledge base is still quite narrow. When reading a paper, how do you distinguish between an experiment that was sloppily done and just not understanding why they did things the way they did? My group was assigned to present on a paper and we found numerous flaws/stuff that just didn't seem to pass a basic sniff test. (1/4)

While discussing it, I kind of led the charge on “Holy shit there are so many things wrong with this” and my groupmates agreed and found some odd things as well, but I wonder if we just got carried away? By basic sniff test I mean stuff like: only having 2 mice for an elaborate experiment but measuring them multiple times to increase the n so they could do stats (my instinct is this is wrong and confuses technical and biological replicates but I know some people do it), injecting mice with a viral vector but not injecting an empty vector into a control, surgical intervention w/o a mock, graphs where the means don’t look too different and there’s high variation but the p is very low, unconventional stat tests when there’s a more “obvious” one (makes me wonder if the obvious one didn’t give significance), doing 3 diff treatments on the same mouse at diff times then treating the measurements of outcomes from those treatments independently, etc. It looked like there was so much questionable stuff that it’s almost unbelievable to me which is part of why I’m doubting myself. It’s a pre-print and hasn’t been published despite being on bioRxiv for 1+ yr, but I know lots of good articles languish under review. We’re planning on talking to our prof to better understand it/clarify whether these are red flags or just us not understanding but I’m scared of appearing arrogant/like I’m critiquing something I just don’t understand.

Hi anon!

Whoooooo babEY that is an. Interesting paper for sure. 

But firstly, to answer your question:

Q: How does one distinguish between an experiment that was sloppily done vs just not understanding the experimental design?

A: Basically gaining more experience in experimental design/research and knowledge of the field. It’s gonna take time and effort and trial and error and having a mentor to walk you through stuff (hence why journal clubs are great!). One piece of concrete actionable advice I do have is if you find anything in a paper that seems odd, try to find a similar design in other (reputable) papers and see what they did, aka gauging what’s “standard in the field”. If something conflicts (and there are always conflicts in research as we learn more and more each day), try to come up with your own conclusion, being as un-biased as possible. 

And be picky while reading papers! Honestly, when I read papers, I treat everything with skepticism until proven otherwise. Science is a tool created by inherently flawed humans to understand nature, and the process is similar to a murder trial with a gazillion potential suspects and a gazillion more murder weapons. The evidence to convict suspect A and weapon B has to be really really robust to convince the jury. My PI’s PI’s (grand-PI?) method for reading papers is as follows: He reads the title first, then goes straight to the figures and figure legends, and then he formulates his own conclusions based off those data alone, before seeing if it agrees with the authors’. He warns that reading what the authors write may bias the reader towards possibly wrong conclusions. 

As for those specific points from the paper you pointed out–I agree with you that those all do seem questionable, even having not read the paper personally myself. Your group is right to discuss those, and it’s great that you’re going to talk to a professor for clarification! 

A point I have to mention here before closing off: so my understanding of BioRxiv is that it’s also a space to get casual feedback from peers before the formal peer-review process. A “pre-print” by definition is something that hasn’t gone through the formal review process yet, so I would expect some papers to be in a “works in progress” mode. This article seems like it may still very much be in those preliminary stages (hopefully!); maybe the data were gathered for a poster or grant proposal, and the authors decided to throw it in BioRxiv for more feedback/put down their flag on this specific experimental design. Therefore, I would suggest looking at the paper with that paradigm in mind–I would frame my thought process as “this is wrong as of now, but the authors could make it more robust by doing xyz”. This broader application would also be a great training exercise to gain that experimental-design-experience I was talking about earlier. 

Hope this helps! And if you want, let me know what your professor says about the paper; I’m really curious as to its actual status (casual pre-print vs has it actually been accepted for publication?).

[cancerbiophd]

Hi! I am about to start a PhD program and I just got a new laptop... I was wondering if there were any particular programs or extensions you'd recommend for grad school, particularly for STEM programs? (I know this probably varies in each field and even in each lab, but are there any basic must-haves?) I have a Mac! Thank you!

Hi there! And congrats on the start of your PhD adventure!

I would recommend these programs (they’re great for both Mac and Windows unless otherwise specified):

Mendeley Citation Manager - a (free!) way to save and organize papers using a browser plug-in, along with a Word doc plug-in so you can insert in-text citations and automatically build a reference page when writing. If you’re going to just get one program on your computer, get this one!

GraphPad Prism - for all your graphing needs! I use this program exclusively for all my data visualizing, and it can also do some basic statistics. It does cost $$, but your institution or lab may already have a license/subscription. 

NIH ImageJ - free image analysis software (eg. cell counting, quantifying western band intensity, etc), and since it’s open source, there are lots of plug-ins available to download. 

R Studio / R Project - free statistical software. It’ll take some time learning (via tutorials or someone showing you), but it’s a pretty awesome program. I don’t personally use it for stats, but I know many colleagues who do. 

Box Sync or Dropbox - to easily share files between computers (like protocols with everyone in the lab, or editing manuscripts with multiple authors). I personally like Dropbox better and am willing to pay for more space (Box Sync sometimes has delays in syncing). 

BioRender - If you’re a biologist, this thing is a lifesaver when it comes to creating figures/schematics. Full access is free to students for private use (like presentations). 

Google calendars, or some sort of electronic calendar - for scheduling your day, because grad school gonna be hecticccc! 

Bear - A note-taking app for Macs and other Apple products. I don’t personally use it (I like physical notes), but my lab mate uses it to keep track of all the notes during his meetings with our PI; it’s basically his electronic notebook. He’s been using it for years and says it works really well. 

Hmm I think that’s all that I have on my computer (that aren’t super technique specific) and what I’ve heard work well for my colleagues. I hope there are some options in there that work for you!

I hope your PhD journey goes well! 

[cancerbiophd]

Two questions if you don’t mind? :) one: which are your fave medicine/science blogs on here? And two: what are some good (online) resources for medical and/or generally scientific articles, news, resources etc? Thanks a lot! 😊

Hi!

I have a recs page here, and studyblrs have their study subjects/majors/focuses listed next to their URLs (and the majority of them are STEM focused). A bit further down the list has a bunch of really neat science-focused non-studyblr blogs, with some of them focused on science/medical news. 

(And let me know if any of the links don’t work/are wrong! Sometimes blogs get deleted by their owners, or my copy+pasting of links messes up)

Other online resources:

Wired is a great technology/science news source (may require a subscription to read some articles though)

Science News is also another website with exactly what their title is

ResearchGate (basically LinkedIn for researchers) has a forum and is my go-to when I have a question related to science/research (usually I start with a google search and it leads me there bc someone else had the same exact question answered already)

Khan Academy has a surprisingly thorough Biology and Health & Medicine sections for any basic info

Great youtube channels include SciShow and Kurzgesagt

And, PubMed is still my go-to to find original science reviews and articles. More and more of them are open access now, and if you’re a university student, your university may have access to many of the articles behind paywalls. 

And usually, a google search for anything will lead to some great resources, from videos to amazing websites. 

My #science-advice tag has a few science resource masterposts (from other users) peppered in that you might find useful, such as this STEM resource masterpost here. 

Hope this helps! Happy science-ing!

[cancerbiophd]

hiii, i love your blog 💖💖💖 i’m going to start my first year of veterinary school this september. i’d like to get my vet phd and work as researcher in the biomedical or biochemical field, and maybe get a genetics masters or something similar. is there any tips or anything you’d wish you knew before becoming a researcher? seriously i can only speculate what is it like to work as researcher so anything would be very much appreciated. thank you!!! have a great day 💓

Hi anon! Congrats on starting vet school! I just wanna gush and say I have the utmost admiration for vets and if I were to rank occupations based on pure “goodness” vets would definitely be in like the top 3 so I love you with all my heart already. 

I think my main point about what to know before becoming a researcher is actually experiencing what a researcher’s day to day life is like, aka is this the lifestyle that works for you? Because as with any occupation, something that looks great on paper may not work out in person, and vice versa. For example, I thought for the longest time I wanted to be a medical doctor, but then I started shadowing doctors and volunteering at hospitals and I realized that’s actually not the work environment or lifestyle I want, and what I had thought what being a doctor was like was actually me romanticizing certain aspects of it. “Only speculating” what an occupation is like before diving into it is not a wise decision for any of us. That’s like adopting a dog without knowing anything about how to care for a dog, ya know? 

It’s important to me that research is, without a doubt, the path you want to take. It’s pretty disappointing and challenging for anyone to realize that after years of our life and thousands of dollars, that what we’re doing now is actually not what we want to continue doing. 

So I would highly recommend one of the following before you set in stone your path to research (and hopefully vet school will offer some of these opportunities!):

visit a lab (preferably one in the field you’re looking into)

shadow a researcher in a lab

maybe even volunteer in a lab if possible

and/or have an informational interview with a researcher (so kinda like what you’re doing now by talking to me, but asking questions like: what’s a “day in the life” like? what are some of the challenges you face? what personal characteristics are necessary for your job/position?) and btw i am totally open for you to ask me these questions on an ask or chat!

To get you started, I can tell you about the characteristics of a scientist/researcher (from my own personal experience and opinions). This can at least give you an idea if this is the world you can see yourself be a part of. 

So, a life sciences researcher:

Gets into the nitty gritty super-detailed parts of the science. We take the big picture view and zoom in and in and in and dissect down into the smallest details sometimes. So even though we may be studying a specific disease, our research may focus on a single signaling pathway or protein. 

Loves every aspect of solving a scientific problem, and is ok with constant setbacks and failures. It’s the thrill of the chase and of finding the puzzle pieces and how they fit together. Some days are super frustrating, some days are just ok, and there are very few days that are great. Basically we gotta be ok with being disappointed 90% of the time, but throughout it all, we’re satisfied with just being immersed in awesome science.

Science is slow; we have to take our time to figure things out. Instant gratification is not the name of the game. One research question can take months of digging through existing literature to design a project; one experiment in that project can take hours of design to make sure we have all the controls and the calculations are correct; and one project can take years until the results are conclusive. 

We’re ok with not making an immediate impact on the world. Every lab pushes the boundaries of what’s known by a teeny tiny bit, and it’s really the collective work that spans years that may change the world. So it’s not like diagnosing a patient where the results I get today is going to make a huge impact tomorrow. 

We can thrive with both working alone and as a team. Though we can work by ourselves on individual experiments, science as a whole is definitely a collaborative effort, and labs are always made of a group of people that collaborate with other labs. 

Going off of the collaborative nature of science, we don’t have to know everything. I just have to be an expert on my niche field, and if I need help with say… calculus, I get help from someone who’s a pro at math. 

Good at communication. The amount of written and oral communication that goes into scientific research is just astounding: writing (and lots of it, even outside of academia), presentations, meetings, emails, phone calls, etc. After all, what good do our discoveries do if we can’t tell the world about it? 

Scientists aren’t stuck to only doing lab research; there are many job opportunities for us outside of academia such as industry (like working in biotech and pharma companies), science writing/communication, teaching, outreach, and even as medical liaisons that work with doctors (if you want to bridge the two fields).  

How to think like a biologist if you’re interested in learning some more!

I hope this helps! Let me know if you have any other specific questions (like if you wanna chat with me about my life as a researcher). Good luck in your journey to becoming a vet! May all your patients/subjects be adorable in their own furry, feathery, and scaly ways, and also easy to work with :)

[cancerbiophd]

when i get frustrated with my research (ie getting results that i did not expect), i have to always remind myself:

there are no such things as “good” or “bad” data

there are only “reliable” or “unreliable” data

and at the end of the day, the data are what the data are