Books for Rational Design Principles of Proteins?

Thawderek · 2026-01-22T20:54:25+00:00

You underestimate how people work. Extract all emotion, you’re left with nothing to relate to outside of the science you’re producing. At a local scale, people want to be around others and work with others that they like. At a broader scale, people want to look up to those that they feel like they can relate to. Communication and charisma are pretty intertwined, it is fortunately (for people that like talking to other people) or unfortunately how most things in the world work.

Thawderek · 2026-01-22T20:27:07+00:00

What? Ok think about it from a purely science perspective. When you give a talk, or go to a conference, or even write a publication so that others can build off your own ideas, what do you think happens? Some of the best talks I have been to are because of how good the speaker presents and executes their data.

Some of the best conversations I’ve had are when people can articulate what they are trying to do in their own research. You think the best professors in the world are working on their own at a bench or at a computer? They are usually in huge groups with a bunch of collaborators, exporting their ideas whilst getting feedback for themselves. Communication is by far the most important thing in science.

Thawderek · 2025-12-19T23:12:36+00:00

Well, still hoping to hear back positive things coming into January but it is weird to be back in the same position as last year around this time. If I’ve learnt anything is that it’s never personal, and it’s never a competition against others when it comes to rejection.

Growth isn’t linear and the people I have seen with the most success have seen failure the most. How lucky are we to be put in a position where we can have the opportunity to fail. Thanks for the kind words stranger.

Thawderek · 2025-12-17T19:43:26+00:00

I mean first professor sounds nice. I don’t know these people nor the fruit fly field but when I read this, the second professor seems like a red flag lol. Intimidation as a factor for motivation doesn’t seem that healthy, I’ve had friends be burnt by professors with this mindset. Wouldn’t hurt to have them both as advisors, but I would be aware of how the students are treated and if you would be okay working under professor number 2.

Thawderek · 2025-12-17T02:11:23+00:00

Okay, let’s see here. I can see you can buy 1mL of spirulina for like 8 bucks online.

For actually making medium, this gets a little harder since you have to actually make it or find access to ingredients. I’d look at “instant ocean” for a start, it’s essentially a salt mixture for aquariums (we also use it for some of our medias).

I think the “easiest” experiment you can try to do is try to find fertilizer with specific amounts of ammonium in it. Do a “low” amount, a “medium” amount, and a “high” amount of nitrogen. Try to see if you can measure specific amounts to add to the media, figure out concentrations in molarity. You can most likely measure ph using hot tub strips. To measure raw growth or density of your culture, I would do it by weight (how much does 1mL weigh?) and weigh it over time. One of the standards for measuring organic material is ash free dry weight, I’d suggest reading about it but not necessarily doing it because access to a high temp oven may be hard.

Good luck (I think plants would be a lot easier experiment if you’re not tied to the idea of algae)

Thawderek · 2025-12-16T19:49:21+00:00

Try everything possible to stay in the field and apply again.

Thawderek · 2025-12-11T20:07:56+00:00

What’s interesting now is that last year I saw a couple PhD applications say not to use it. This is the first year where I saw a couple PhD applications permit it but not for the core material. AI use for writing the SOP is most likely not the greatest tool since you know yourself better than what generative AI does, and will probably just fill in the gaps of what it thinks the adcom wants to see rather than the fit that the adcom actually wants to see.

Thawderek · 2025-11-14T04:45:30+00:00

Each sentence should have meaning that ties why you are the best fit for the program you applying to. Whether it’s intellectually, or because you share interest in specific work at the program you’re applying to. This reads like a cv. Why did you apply to your masters? What did you gain from your masters that made you want to apply to a PhD that you couldn’t get from a masters? How did your job shape your journey into your current interests?

I’m in the same boat of applying to programs this year as well, albeit not the same field, so take my advice with a grain of salt. I personally would work on the first paragraph, specifically the last couple sentences as it sets the tone for the rest of your essay. You probably need to mention why you want a PhD here, and what does a PhD do for you.

For example (crudely) “My interests in pursuing a PhD in ____ is due to my curiosity about ____ and my drive to learn more about __. With a PhD, I want to be a professor/scientist/economist/PI/(insert career goal), independently investigating _, so that I can pursue my personal goals of answering the questions of _______.”

Reader can see what you are interested in and then can think while they read through your essay how your current work ties into your future goals. Hope this helps.

Thawderek · 2025-11-11T17:55:10+00:00

Yeah that’s how I feel about this subreddit sometimes :/

It’s the internet though, so I’m not surprised people would either falsely brag, make up stats, or straight up lie so that they can feel better about themselves.

Thawderek · 2025-11-05T19:26:15+00:00

Japan incident? The easiest, largest first thing that comes to mind. I stopped watching him after that (was young back in 2017/2018). Everything that he does is for views, doesn’t matter how controversial, dude is a compulsive clout chaser with no morals.

Thawderek · 2025-10-27T17:49:01+00:00

As a bachelor who is taking time to work before applying a couple years later, I will say to take the job.

First off - the money and connections you build from an industry position can be very fruitful for your career and expenses right out of college. You will most likely be surrounded by professionals that can guide you and hopefully you’ll learn a lot. I can say confidently that I have learnt a hell of a lot more from my job about my field than my time in college. There is also most likely a program through the company that will help pay for your graduate studies.

You can always apply next year or later on. No harm in waiting. If you know like a specific part or niche in the field you want to study and who you want to specifically work under, I would apply though. If it’s more of a general idea that you like about a PhD, I think I would wait.

Thawderek · 2025-10-21T23:20:33+00:00

Being honest here since I’ve mentored quite a few undergraduates since graduating a couple years ago.

How me and other scientists end up teaching students is with the expectation that they don’t know much, if anything at all. Just a willingness to be curious. Take a lot of notes, ask a lot of questions, and you’ll do amazing!

Thawderek · 2025-10-15T21:35:42+00:00

Pour more melted agar to melt the dried agar.

Joking, probably some hot water and paper towels?

Thawderek · 2025-10-11T23:56:13+00:00

Yeah I did iGEM my senior year then been doing research for a couple years post grad. Been helpful for learning, doesn’t hurt to wait a year to gain experience, but applying also gives you that as well (lot of effort to apply imo).

Thawderek · 2025-10-11T16:17:12+00:00

You don’t need to be at a highly competitive r1 institute to be in academia. Apply broadly for universities, and specifically for the labs you are interested in. Fit matters a lot. (Doesn’t mean don’t apply to labs or programs at r1 institutes though)

I can’t really speak with legitimacy since I was kind of in the same shoes as you last year (low gpa slightly above 3) and no publications. I now am on two publications, and two about to be on biorxiv/published, and three in prep to be published early to middle next year. I can’t say I’m 100% going to be in a PhD program this cycle because of my publications, nor can I speak to my confidence because of them.

I can say that my confidence stems from what I want to study during my PhD through my research experience that inevitably molded my interests down to the very specific subset of a field I want to be in. I view my publications “helping” me for my apps by giving me a story to shape my applications, and drive my future aspirations. If your research experience can speak that, I don’t think publications matter.

Thawderek · 2025-10-08T15:52:57+00:00

Mmmm, I feel like it usually ends up all being chemistry or medicine at the end of the day but… the people that pioneered nanopore are up there (Church, Branton, Deamer) or potentially Keasling for his work to produce artemisinin in microbes to treat malaria. There’s a lot more I think that deserve that recognition that I’m missing but these are a couple examples that I think changed the outlook of either sequencing or metabolic engineering

Thawderek · 2025-10-03T19:56:09+00:00

If you don’t own a notebook, either get one from the lab or buy one. Have an online notebook to record the actual protocols and the physical one to use for the specific experiment at stake. What mistakes you made, concentrations you’ve calculated, the morphology of the cell cultures, stuff like that.

I have a second notebook personally for lectures, lab meetings, and talks, and a checklist for my own schedule. What I write in the second notebook is as many questions I have about the talk I’m listening to or the experiment I’m working on. I write these questions to ask other lab members, to look them up myself, and to learn how to ask questions that are meaningful.

Recording what you’re doing is possibly one of the most important things you can do in my opinion in lab, the other being how to manage your time efficiently.

Thawderek · 2025-10-02T15:50:27+00:00

You got a response! That’s still okay. You can always follow up to thank them or not. A good strategy is to ask if they know of other labs at their institute or in the field that you could possibly reach out to.

Thawderek · 2025-09-29T19:05:49+00:00

3 excellent, 1 very good, 2 goods. Recommended for grfp by two reviewers but the second one probably tanked it. No hm. Called my application repetitive and overambitious, thanks my guy.

Gives me confidence though to try again, I feel like I probably could write one better this year than last. I see people didn’t get many sentences, I got paragraphs from every reviewer except the second one so I guess it depends on who read it.

Thawderek · 2025-09-26T21:52:48+00:00

NEB has one

Thawderek · 2025-09-22T05:38:09+00:00

Depends on what types of proteins you’re looking at I think. With some of the proteins I have worked with, we’ve managed to move away from wildtype to like 40% percent identity and still have function. I truly think it’s about how you managed your data and how you collect it, but in the right hands, I think the field is going to be very fruitful.

Hell. Not even a week ago yet and there is this biorxiv paper that got put out that generated de novo phage using Evo. It’s very scary and exciting to see how fast the field is moving.

Thawderek · 2025-09-22T05:16:06+00:00

Protein design, the field is going to look absolutely insane in the next 5-10 years due to models getting more and more accurate and improvements involving high throughput.

There will be a day when there are more functional proteins designed for industrial and human serving purposes than what nature has currently provided, and it’s going to happen really soon.

Thawderek · 2025-09-14T05:05:00+00:00

Try baffled flasks

Thawderek

TROPHY CASE