microbiology - Does freezing microorganisms such as probiotics kill them?

Does freezing microorganisms such as probiotics kill them? If not, what is the process that allows them to "come back to life" after the temperatures are increased?

As an example, lets say you freeze a yogurt (whether it be Greek, Australian, Turkish, Indian, Russian, European, or Western) and eat it while frozen. Would the probiotics in the yogurt "come back to life" and be beneficial?

Specifically, I am referring to freezing refrigerated yogurts, and not products that are sold as "frozen yogurts".

What's the biological basis for this?

graduate school - “making it look good”- is it always important?

Recently I created a project report for the project that me and my classmate are working on. The project report goes to the external examiner to whom later we have to give a demo on our project.

Me being inclined to designing (web designing, graphic design, etc) I decided to make the project report look really good. A nice clean report with good choice of paper. And care taken while choosing font etc.

It turned out to be much much better than anyone else's report. BUT! The first thing I heard from other classmates was. "Making project report look good is of NO USE. Your project (Application) should be good enough and it's all that matters"

Is it true? from a general perspective of people. Does "making it look good" matter at all?

I couldn't find any other section more relevant enough to discuss this question. Please let me know if there is any.

Answer

A good-looking report will put me in the mindset that you took the assignment seriously, and aimed to turn in quality work. I think that counts for something, not nothing.

That said, if a report is just that – good looking, with little substance behind it – I will see through the façade very quickly, and all those superficial niceties might even count against you.

Assuming that's not the case, though, if two people turn in equally good work, yet one is formatted much more professionally than the other, that might earn an extra point or two – assuming I'm grading with some level of subjectivity, and not merely following a strict rubric. Shame on me, though, if I let mere appearance carry much more weight than that.

That all said, your classmates seem to be very shortsighted. Okay, maybe your extra effort will get you a 94 instead of a 93. Or maybe you'll just get a 93, with nothing more than a mental note that I thought your report looked really good. However, what you do in my classroom might – and perhaps should – extend far beyond my class. Presumably, you're in my class for an education, not merely for 3 or 4 credits. Get in the habit of turning in good work, and that might turn into something that translates into a valuable life skill.

One more thought: what's going to happen after you graduate, when all those folks from human resources ask you to include the names of three professors on your job applications? One of them might well call me, and ask, “What do you remember about this guy?”

Perhaps I'll answer, “Oh, I remember him. He always turned in exceptional work.”

Those two sentences might prove to be worth far more than an extra point or two on an assignment.

Incidentally, I had one student bring her term project into a job interview. They hired her, largely based on what they saw in that class project. Just a couple weeks ago, another student asked if my name could be listed as a reference.

“I hope they call me,” I replied in my email. “I distinctly remember how your work always seemed to go above and beyond what everyone else was turning in.” Imagine how that will sound in the ear of a corporate recruiter who is sifting through a pile of job applications.

It's your call. It's also your future.

publications - Transferring results of Google Scholar search to My Profile

Searching Google Scholar I find thousands of references, mostly to my poetry, but also to my articles and books. Is there any way of transferring some of these articles, books, and poems to "My Profile" without typing each in separately? Thanks!

evolution - Book recommendations for algorithms used in evolutionary biology

Do you have recommendations for a book that presents the different algorithm used in theoretical evolutionary biology?

I don't mean evolutionary or genetic algorithms (otherwise this question would not be a good fit for Biology.SE) but algorithms applied to evolutionary biology. I am not interested in statistical procedures and algorithms to reconstruct phylogenetic trees, to annotate DNA sequences or to find out synonymous changes by comparing sequences of closely related species. I am not interested in introductory book on programming.

I am interested to computational modeling applied population genetics, kin selection, game theory, population range expansion, simulating sexual reproduction, selection for different sex determination system, evolution for robustness/evolvability, evolution of codon usage, evolution of genetic code, evolution of cognition, evolution of multicellularity, …

I don't quite know if one book that encompass all these subjects exist. If not, I wold welcome suggestions of book that present the algorithmic used in some but not all of these subjects.

Searching a bit in amazon, I easily found tons of book but don't quite know if they fit my expectations. Below are some examples

Evolution as computation

Individual based modeling and ecology

Models and algorithm for genome evolution

modelling for field biologists

Practical computing for biologist

Evolution as computation

Genetic and evolutionary computation

Genetic algorithms+ data structures = evolution programs

The missing algorith

Cellular Model: Mathematical and theoretical biology, Algorithm, Data structure, Bioinformatics, Computational biology, Artificial life, Computer simulation

Natural-Artificial-Models-Computation-Biology

An-Introduction-Genetic-Algorithms-Paper

Answer

What you are describing usually falls under the category of computational biology or just mathematical biology. Unfortunately, the biggest part of this field is bioinformatics, or the application of statistical and/or dynamical programming techniques to sequence data. You exclude this in your question, and I would agree with you that it is a "boring" topic from a theoretical biologist's perspective, because it mostly uses computer science in a very standard way as a tool for experimental biologists.

As you noticed, it is also standard to use computational models in theory papers as a way of simulating things. I think this is the sort of resources you are asking for. Unfortunately, specific algorithms are seldom standardized or reused in this area. Typically, each paper (or sequence of related papers) uses their own models.^[1] As you read a lot of papers, you will find some common themes, but these are just standard ideas of theoretical biology expressed as simulation. I doubt that comprehensive books exist, and even if some do their utility is not clear to me due to a lack of specific algorithm (re)use.^[2] However, the most commonly used techniques are to either to solve differential equations numerically (which most would classify as mathematical modeling) or run agent-based or population-based models. General resources on these exist, and here are some discussions for the latter other SEs:

Finally, do not confuse 'computational modeling in theoretical biology' with 'algorithmic biology'. Algorithmic biology is a new field that views ecological and evolutionary dynamics as computatioanl proccesses. Instead of using mathematical tools borrowed from physics (as is standard with the dynamic systems approaches to mathematical biology), it uses the tool of theoretical computer science (note that this is a type of math that has very little to do with programming the laptop infront of you). I know of only two books in this field:

Notes

1. In general, I consider these sort of models as heuristics and I am skeptical of their usefulleness beyond rhetorical devices/examples.


2. I think that literature reviews would be interesting computational modeling in specific subfields. In fact some colleagues and I have wanted to do this for the smaller area of evolutionary game theory (This answer can serve as a starting point for some algorithmic considerations of EGT).

etiquette - How to deal with uninterested students during an optional exercise session?

Last week I taught my first exercise session. I am a PhD student so the kind of classes that I will teach are exercise sessions about what the Professor explained in the theory class. They essentially have to work problems and I have to explain and help them with their approach in solving them.

Students of the same year are divided into small groups. I had about 25 students and from what I noticed: 17 were working hard, 7 were working more slowly with less interest and 1 was watching videos with his smartphone.

I tried to get his attention in a kind way several times (by going to him and telling something like "I know that videos are funnier than this theoretical stuff but if you want to practice for the exam you should do also exercises") but even if he stopped and started to read the exercises then he always restarted watching videos.

Since I will not assign grades and this kind of class is not mandatory, his participation will change nothing in his final grade. So at a certain point I just wanted to ask him why is he attending. There are many seats outside the class where he could sit and watch videos, but I just stopped to get his attention and I left him watching videos. I made this decision because he was watching videos/surfing the web without audio and without annoying the other students.

What is the best way to deal with these situations?

Answer

Do you prefer more or less authoritarian style?

More authoritarian: "If you come to my class, I assume you wish to be taught by me and respect my time. In other words, you are to work on your assignments. If you do wish to watch videos or to Facebook, that is fine, but please do not do that in my class - it is disrespectful to me and in fact also to your fellow students who come here to learn. Feel free to leave to watch, and to come back when you are done and wish to return to the exercises."

More liberal: "It is everyone's own responsibility to learn and I will help you to understand the material and how to master it. If you do not wish to engage in it, that is your free decision, but you need to be aware that this is your own responsibility to engage with the material in order to benefit from it [and pass the exam]." - say it once at the beginning, and then perhaps one more time in the middle of the semester. That's it.

Modify as required, this is just a coarse line of action, YMMV.

job search - Is it worthwhile to find a teaching letter writer who can also speak to research abilities?

When applying for academic jobs in the US, one is often asked for a recommendation letter from someone who can attest to your teaching abilities.

Should you try to find a teaching-letter-writer who can also speak in some way to your research? (For research-focused jobs, since you get to submit a bounded number of letters, this could be a sneaky way to get more research content into the letters.) Or do search committees for research-focused jobs generally not read teaching letters deeply/at all?

---

I am personally in mathematics. I am assuming the answers will not be too field-dependent (please correct me if I am mistaken), so I left it out of the main body of the question.

Answer

Search committees that I know read all the letters written for the candidates in whom they are interested, though of course some people read some letters more closely than others. I will admit that at my "research-focused" university, I often read teaching letters very briefly. In my defense, many teaching letters are not worthy of more than a very brief reading. They simply do not separate out the candidate or provide any really incisive or useful information. If teaching letters are to be believed, then approximately 99.5% of all candidates are above average teachers. Why do I find myself skeptical of this?

That said, I don't really see much advantage to "hiding" research in a teaching letter (or vice versa). If you get a teaching letter written by a "research professor", then they may be a little nervous about not mentioning the research whatsoever or feel through force of habit that they must say something. But really, when we read a teaching letter we want to hear about teaching, so saying something at the beginning like "Dr. Ray has asked me to write about her teaching, and so I will" would be fine.

You speak of a "bounded number of letters". That must be true, but the supremum may not be what you think. In most jobs that I know of, nothing stops you from submitting more letters than the number they ask for. Past a certain point maybe it looks obnoxious: I remember one candidate for an assistant professor position that had nine letters of recommendation (8 research, 1 teaching, I think). I felt that was a bit much but we certainly didn't disqualify the guy or write back to say how many of the letters we had burned without reading. In fact he made the short list and almost got an interview.

I would say: if you want to send one or two more letters than the application asks for: just do it. If you want someone to talk about your research, don't have them do it in a way that other people might not read, or might read but dismiss because they are expecting to hear about the teaching. Just get another letter. For that matter, it is increasingly common to get more than one teaching letter even for a research job, even though I know of no research job that asks for more than one.

reference request - University policy of publishing student course evaluations: Prevalence and pros and cons

These days it is very common to have some course evaluation towards the end of a course, in which students respond to standardized questions on a numerical scale (e.g. between 1 and 5) and can additionally give free-form comments.

Sometimes individual lecturers make student comments (and their responses) available to the cohort in which the survey was taken and the next cohort, to show that they are open to critique and how they respond to it.

I am, however, more interested in cases where there is a departmental/faculty/university-wide policy to consistently publish evaluation results for all of their courses (averages of numerical data only, or perhaps the free-form comments as well) to the current and future cohorts.

• Is it common for universities to have a policy of publishing student course evaluations?



• What are advantages and disadvantages of doing this?


• Has this been looked at in the educational literature?