evolution - What is meant by `individuals do not evolve, populations do`?

My university professor stated that "individuals do not evolve, populations do". But aren't populations made up of individuals? That's like saying when a compound changes in stability, none of the elements' properties change. If someone could clear this up, that would be great.

Why don't authors include in their publications the duration of the research?

I've noticed that most papers do not say explicitly (or at all) how much time did the research take. This excludes certain types of studies, such as epidemiological studies that usually say that the study's cohort was followed for some-and-some months etc., but what I mean is that in most papers there is no actual indication of how much time the study\set of experiments took. I believe this type of information could be useful for readers, especially for readers that would like to perform similar experiments for their own research.

So why is this information not required from authors?

(I realize that it's sometimes hard to pinpoint the date when a person begins and finishes a research project, but it could still be useful to give an approximation in months. This way a reader could get a better estimation if such a project is reasonable for their own research, at least from time investment considerations.)

synthetic biology - What are common causes of unexpected ligation products?

I digested two plasmids, one with EcoRI and AgeI and the other with EcoRI and XmaI. Digests looked as expected, so I purified the respective fragments and set up the T4 DNA ligation (AgeI and XmaI sites are compatible).

After E.coli transformation, culture and miniprep from 12 of the resulting cultures, I digested the isolate from the minipreps with BclI to confirm I had the correct product (because there was one BclI site in the insert and another one in 1.4kb away in the backbone). The results of this digest clearly show that there are two different ligation products: four lanes share one banding pattern and the other eight share a pattern which is different from it.

I checked both plasmids for other restriction sites of the enzymes used which I overlooked before, but found none. Because EcoRI and XmaI/AgeI sites are radically different (AATT vs. CCGG), I would exclude the possibility of the insert being ligated in reverse orientation.

Are there any common causes of unexpected ligation variants besides unnoticed restriction sites and reverse ligation?

Answer

A second investigation has suggested that the ligation product in question was indeed the vector, without ligated insert!

The vector also contained a BamHI site close to the XmaI site, so in a subsequent digest with EcoRI and BamHI, I was expecting to see the same band sizes that I ligated together in the first place.

All colonies contained plasmids that produced the long (vector) band, and the same eight as before produced the shorter (insert) band as well. However, those four which were aberrant in the previous experiment were this time lacking the shorter band.

This means the eight colonies with two bands contained the desired ligation product, while the other four contained a plasmid which was restricted at a single site (undigested it would have produced three bands like the control).

As the BamHI site was in the vector and untouched throughout the whole process, I conclude that those four were missing the EcoRI site, which should have been regenerated during the ligation, and hence indeed the EcoRI site and the XmaI site must have been ligated without insert somehow.

Long story short

This means that either

• An exonuclease digested the sticky ends of the vector away, or


• The sticky ends simply degraded by chance

resulting in a blunt-ended re-ligation of the vector without insert and consequently loss of the EcoRI site.

I believe these to be quite important things to consider in cloning - in subsequent experiments I have had several colonies growing on negative control plates (i.e. colonies transformed with a control ligation that contained no insert), all of which were probably due to loss of sticky ends and blunt ligations, resulting in functional plasmids that conferred ampicillin resistance despite containing an undesired plasmid.

research process - Can teaching help one's studies?

Most of the questions about teaching assistantship portray TA'ing as a waste of time that only damages research. Although I am not TA'ing this year I consider applying for a TA position next year, because I feel I kind of missing it and it actually helps me to focus on my research.

Are there any clear benefits of TA'ing for one's studies and research?

Answer

Of course, it depends on how much teaching you would be doing, and how many hours a week it would take you, but generally, I would consider the following pros/cons points:

Pros:

• Teaching might allow you to meet other people than those you are doing research with, and interaction with different people can be useful in terms of research (for instance, you can find a nice collaboration idea with a prof or another TA).


• Teaching brings more immediate rewards (positive and negative) than research. When I was doing my PhD, I was also teaching (about 60 hours per year), and sometimes, when I was stuck with some research problems, it was a nice feeling to interact with students and to feel "productive".



• Teaching is a good training to clearly explain ideas and concepts, which an important skill to write good papers.


• Teaching provides you a different activity aside from research, and can help you focus (as you said yourself).


• Teaching is good on a CV, and if you consider applying at some point to a lectureship/professorship position, then having done some teaching during your PhD can allow you to do some more research-oriented postdocs after (and thus get potentially more papers), so it's somehow a good time investment to do it when you're not expected to produce a huge amount of papers.

Cons:

• Teaching takes some time, especially if you are teaching in a field where you are not an expert.


• The downside of the immediate rewards is that sometimes, you can get frustrated because of the teaching, and that can have an impact on your research production.

In conclusion, I would say that being a TA has really clear and acknowledged benefits, as long as it does not take too much time on the research activity (I would say no more than a day per week during the official periods of teaching).

Publishing a conference version of a journal paper at the same time ? (copyright issues)

This may be a question repeated many times, but I want to know your opinion.

I submitted a journal paper for an algorithm (Computer Science). Fearing that the review process take too long, I decided to submit a short-version conference paper, while the long version is under-review. I received the journal review comments, and re-sent the modifications to the journal. Meanwhile, the conference paper was accepted. But the camera-ready is not sent yet.

The problem is that both papers are about the same idea. There is also some copy-pasted parts in both papers. But:

1) the editor of the journal was not informed about the conference paper (I heard that I should tell the journal about any published papers - but note that the conference paper is not yet published - not even the camera ready is submitted),

2) the organization organizing the conference, is not the same that manage the journal. I have been told that there are conflicting copyrights.

The proposed solutions (that colleagues told me about):

a) submit both as is !

b) submit both (but with change in text).

c) do not submit the conference paper (but I heard this can be harmful)

d) tell the editor now (but honestly, the journal is way more important than the conference).

evolution - Extraretinal photoreception in mammals?

A Finnish firm Valkee sells light-ear-plugs against thing such as jetlag. I asked a researcher in Aalto university how do they really work and he responded "why would evolution have lead to photoreceptive cells in ears?" -No direct answer. I asked a well-respected professor who said she did not know this area well enough. Now Valkee guided me to the publications such as Penetration of light into the brain of mammals (1963) and Spectral characteristics of visible radiation penetrating into the brain and stimulating extraretinal photoreceptors (1979). Related to the first one, I found this (1980) from the references:

"It is now fully accepted that the perception of light by extraocular photoreceptors plays a significant role in synchronizing endogenous rhythms with the environmental light-dark cycle in non-mammalian vertebrates"

Things such as certain birds and lizards apparently have extraretinal photoreception aka photosensitive cells not in eyes (this is how I understand it). Now the publication continues

"The limited number of mammalian species tested to date and the near exclusive reliance on nocturnal animals leaves open the possibility of extraocular photoreception in some adult mammals (Rusak & Zucker, 1975; 1979)."

Now according to a skeptical researcher in my university, there is only one paper supporting photosensitivity in mammals' brains: Wade et al (PNAS 85 (1988) 9322-9326 with rats. My professor in system sciences was extremely scornful when I even asked this question on a seminar course about brain -- he did not specify his reasons and pretty much labelled my thinking as inexperience. Now I am not sure whether researchers are even speaking about the same issues: too large disparities between opposing and proposing teams for the assumed effect apparently through the mechanism called "extraretinal photoreception in mammals". I am very curious.

Helper questions

1. 
   

   What are the mechanisms by which a led in ear would affect a mammal such as a homo sapiens? You don't get D vitamin because of no UV light. You get very-very light heat because of tosslink connection. So it cannot sense the heat as antidote against things such as SAD and jetlag. Other mechanism?

   
   


2. 
   

   Is the "extraretinal photoreception in mammals" just placebo or does there exist scientific proofs for it particularly with large mammals about the size of homo sapiens?

   
   



3. 
   

   Why would evolution have lead to extraretinal photoreception in mammals?

   
   


4. 
   

   Do the terms "extraretinal photoreception" and "non-eye photosensitive cells" mean the same thing? Other terms for the same thing?

   
   


5. 
   

   Now eyes are developed very late in cell-division with mammals. Do born-blind mammals and later-blinded mammals experience extraretinal photoreception differently? If led-light (non-UV light) has an effect on large mammals, then I expect this may be possible to see by analyzing results of mammals with different-developed visual-cortexes.

   
   


6. 
   
   

   Does this statement "Light penetrates deep brain areas, eye's receptors have developed from receptors of old CNS." by Humancharger justify the extraretinal photorecetpion?

   
   

P.s. I presupposed in this question that extraretinal photoreception is the effective mechanism by which light-in-ear would affect a mammal. It is also possible that there are other mechanisms -- I am not an expert with the terminology here, anatomically and physiologically challenging.

evolution - Height and natural selection in humans?

I watched the documentary "Evolve" recently and in the segment on "size" Scott V. Edwards, Harvard evolutionary biologist mentioned the idea that humans might evolve to be 7' tall in 'hundreds of years'. (I think this may have been taken out of context... I have emailed him to find out, but do not expect a response from someone so busy)

The reasoning goes that the trend in the past 100 years has been greater height, and women show a strong preference for men who are taller than they are. (Though a large share perhaps all of this difference has been due to diets higher in protein at an early age)

I wonder, though, if this is only part of the story. The preference women have is not just for tall men, but for a man who is taller than she is. Likewise, men seem to prefer woman who are shorter than they are. There is even cultural pressure: the classic western image of a couple on wedding cake always shows a man who is about 4" (to scale) taller than the bride.

Thus, women who are short have an advantage as they have a greater pool of men to choose from. (Colloquially, simply ask any 6' tall woman if she feels her height helps her find dates.)

Let's say that men seek women who are shorter than they are, but no more than 8" shorter. Women seek men who are taller than they are but no more than 8" taller. Given that the current average height for men is 5'8" and for women it is 5'4" (and distributed normally SD 2.8") will we have selective pressure that leads to greater or lesser height? (This is, obviously, oversimplified, but it is a starting point.)

Answer

@kate has what is probably the more correct answer for the observed pattern.

But as an experiment, I set up a basic simulation to approximate the conditions that you lay out:

1. Starting mean heights of 5'8" (172.72 cm) and 5'4" (162.56 cm) with standard deviations of 2.8" (7.112 cm). I used cm, because it's easier than dealing with inches.


2. Males will not mate with females that are taller than themselves.


3. Females will not mate with males more than 8" taller.


4. Males will not mate with females more then 8" shorter (follows from #3 above).

The problem that I quickly ran into was that, by truncating part of the normal distribution, the variance in height at each generation gradually decreased. After about 20 generations, the means weren't evolving because there was so little variation in height.

Human height is one of the most studied quantitative traits, going back over 100 years to some of the very first statisticians (Fisher, Galton). Height is a polygenic trait with very high heritability (h² = 0.8)¹. Genome-wide association studies have reported 54 genes involved in determination of human height².

Imagine that each of these 54 genes has just two alleles: a and b. a gives a +1 to height. b gives a -1 to height. So aa would be +2, ab or ba 0, and bb -2. The sum of all those alleles is correlated to height. So if all 54 were aa, then the height would be +108.

The problem comes in when people only mate with taller people. Over time, the proportion of b's will decrease, and the proportion of a's will increase, but only to a point. Once all the alleles are fixed at a, there won't be any room left. The genetic variation will be exhausted. Without the input of new alleles, height will cease to evolve.

1 Lettre, G. 2011. Recent progress in the study of the genetics of height. Hum Genet 129:465–472.

2 Visscher, PM. 2008. Sizing up human height variation. Nat Genet 40(5):489-90.

peer review - Are reviewers supposed to know each others' identity, after the reviewing process is finished?

I reviewed an article and submitted my review along with a short letter to the editor. As a service the journal permits to see the decision letter and the other review. However, I am also able to see the other reviewers' letter to the editor, which is signed with a name. My own short letter to the editor I did not sign with my name.

Is this supposed to be? If not, should I do anything in particular if I do find out by accident?

The issue is somewhat addressed in some of the answers for the question Are reviewers allowed to discuss their review with each other?. One answer states you're not meant to find out, while another one states once you've submitted your own review, it is normal to know who the other reviewers are and be able to see their reviews. There are two different issues here:

1. Knowing the other reviewers' identity during the reviewing process.



2. Knowing the other reviewers' identity after the reviewing process.

Is case (2) normal?

Edit: I might add that the policy of the journal is not a double-blind: the full list of authors and affiliations of the manuscript were purposefully disclosed to the reviewers.

pcr - When designing primers how important is the GC clamp?

I'm designing a set of primers and reading about the principles of primer design one of which is:

GC Clamp: The presence of G or C bases within the last five bases from the 3' end of primers (GC clamp) helps promote specific binding at the 3' end due to the stronger bonding of G and C bases. More than 3 G's or C's should be avoided in the last 5 bases at the 3' end of the primer.

From here.

My question is how essential is it to have a GC clamp?

Answer

It's hard to provide an objective answer. If you have a decent length and good complexity, even a single terminal 3' G or C would do. Of course, one has to take into account the primer's overall GC:AT ratio and things like annealing temperature.

Here's a link to diverse opinions on the topic and it has this nugget (which I subscribe to when possible):

FWIW, my preferred offerings to the PCR gods are primers with a single G or C 3', FWIW. Seems to keep 'em happy most phases of the moon.

publications - Why patents are not cited in papers as that of journal papers?

I couldn't find papers that cite patents. Is it OK to cite patents? If yes, what are the reasons for scarce patent citations?

Answer

There are certainly papers citing patents, mostly in engineering fields. So, yes it is certainly OK to cite a patent.

Now patents have an entirely different purpose than scientific articles. They usually contain detailed descriptions of methods and devices and (sometimes wild) speculations about practical applications of these. Useful to protect potential commercial use, but not really to scientists wanting to build on existing knowledge.

More specifically, what they typically don't contain are original experimental data, or other means of scientifically evaluating the described methods or devices.

Very often, if the development of the patented method or device has led to scientific discoveries, these have been published separately as articles (or conference proceedings for the fields where that applies). Those will be much more scientifically informative, and hence more likely to be cited in academic articles.

ethics - Teaching a class likely meant to inflate the GPA of student athletes

Premise

My department recently finalized the faculty teaching assignments for the Fall 2019 semester (starts at the end of August 2019). As these assignments were being discussed a few weeks ago, my department chair approached me and asked my "interest" (her word) in teaching an "explorations" (again her word) class that students could take to learn more about our department and our discipline.

She had a pre-written syllabus that she had composed. The proposed work load for the class essentially consisted of having 80% attendance at a weekly 50-minute class period and filling out a course review at the end of the semester (10% of the grade was to come from a nebulous "class participation" score). This class would be worth three (3) credits, which would be the typical credit given for a class that met for three 50-minute periods a week and had several exams, weekly homework, etc. Some examples of classes in my college (STEM) worth 3 credits:

All names and course numbers are effectively fake. These are all real classes at my university, but I have completely made up the numbers to mask the real classes.

• Math 3340 Differential Equations.



• Math 3870 Algebraic Number Theory.


• Phys 2200 Electromagnetism.


• CoSc 3130 Compilers and Interpreters.


• Stat 4650 Bayesian Inference.


• CoSc 3270 Intro to Machine Learning.


• CoSc 4270 Advanced Machine Learning.


• Chem 3510 Organic Chemistry I.


• Chem 3520 Organic Chemistry II.

(CoSc is Computer Science. This is not what my university calls it. I did this literally just so that every class only had a 4 letter abbreviation).

I told the department chair that I was not interested in teaching the class and made the passing observation that it seemed like the class was rather simple for a three credit class. She told me that, yes, it is a rather simple class, but that this was okay, since it was "targeted at the athletes from our university." The class is open to any student at the university, but it requires departmental signature to add the class.

I feel that this may be treading a fine line that borders on academic fraud, such as this scandal at the University of North Carolina. This is exacerbated by the fact that I have now discovered that there is not only one version of this class, but three (XXXX 3910 Explorations I, XXXX 3920 Explorations II, XXXX 3930 Explorations III) versions of the class.

The classes meet concurrently (e.g. Tuesdays at 2 p.m.) in "different" rooms, however it is really just one big room that can be subdivided into three classrooms with accordion curtains. (Each section of the room has a separate door to the hallway and a separate room number). So the "Explorations" classes can effectively be taken all at once by signing up for all three classes and then just sitting in the big room and "participating."

The Issue

Despite my declining having any interest in teaching one of these classes, I have been named as the instructor of one of the classes. The department chair and a new adjunct hire have been listed as the professors over the other two classes. Students have registered for the class and it looks like out of 21 students on my class list, 19 are student athletes.

I spoke (informally) with our associate dean about this class soon after my department chair first approached me about the class. At that point I had not yet been assigned to teach the class. He informed me that the dean had signed off on these classes in order to "engender interest in the college." Most student athletes at my school do not major in STEM fields.

I'm not sure how high this goes. I do not want to lose my job over being unwilling to get up in front of some student athletes and talk about interesting things in my field. If the class was worth fewer credits, I would feel better about participating. But as it is, I feel uncomfortable being associated with the course. If it were worth fewer credits, I might be more favorable to the thought of teaching the class.

Should I blow the whistle here?

---

Addendum

I do not have tenure. I am relatively new to the department. I think this is why the department chair is asking me and an adjunct professor (new hire) to cover these classes.

I mentioned that I had been assigned to teach this class to one of my senior faculty. His assessment was essentially "Oh yeah, sounds fishy. But if [Dept. Chair] got it approved, must be on the up and up, right? Ha ha ha...."

Grade break down for the class is as follows:

• 10% Participation (On an integer scale from 0-10).


• 10% Course Evaluation (Filled out = full marks, not completed = zero).


• 80% Attendance:
  
  
  
  • There are 10 total class meetings (we do not meet every week)
  
  
  • You get 1 point for each class period you attend up to and including your eighth class period attended. (Max score of 8/8).
  
  
  
  
  

The class is not pass fail. ABC grades are assigned.

So, if you participated at a level 9 (whatever that will mean), filled out the course evaluation, and attended 5 class periods total, your score would be:

9% + 10% + (5/8)*80% = 69% in the course.

If you participated at a level 3, did not fill out the course evaluation, and attended 7 class periods total, your score would be:

3% + 0% + (7/8)*80% = 73% in the course.

Answer

You wondered "how high does this go?" At my university, the football coach's salary is 7 times the president's. Who do you think answers to whom? The chancellor, the president, the provost, the dean and your chair could all agree with you and nothing would be done. (And if they were the sort of people who agreed with you, then they would not be the chair, dean, provost, president, or chancellor.)

You're new and adjunct, and so have a very weak position. I'm pretty sure this is why you were assigned the course. Options:

1. 
   

   Refuse to teach the course and hope that the there's enough bad publicity when you are fired, that the school quietly removes the course. You'll be unemployed, but will have done a service.

   
   


2. 
   
   

   Teach the course in such a way that the students actually have to work and learn things. Milk the "participation" for all it's worth. If you do it right, you'll never get the course again. (E.g. Lead a discussion each meeting on the topic of "Why major in STEM." Point out that the very course they're in is robbing them of their opportunity to get a real education. They're essentially slave labor for the billionaires who really own the athletic teams. They're playing pro-football for free and getting in return a worthless degree in "Undergraduate Studies" which won't qualify them to sell used cars. Wouldn't a STEM degree be more valuable and satisfying? That's on-topic for the course and should prevent you from having to teach it again. OR perhaps, choose a nice, science-y book and require that "participation" means taking turns reading aloud from the book. When this uncovers that half your students can't read....)

   
   

publications - Acknowledging the discussion with someone in the paper but excluding this person as a reviewer: how to do this?

While writing a paper I discussed its first draft with a certain colleague (he is from a different university, so it is not likely that he will be automatically ruled out as a reviewer as suggested in the Visoft's answer). He made a few helpful suggestions but by and large didn't like the paper: he would like the results to be compared with the ones one could obtain using his favorite method -- but this is a separate piece of hard work, and his favorite method is, to put it mildly, far from being universally recognized by the community of experts in the field.

I would like to acknowledge his helpful suggestions in the paper but at the same time I would like to rule him out as a possible reviewer (some journals give you an opportunity to let them know whom the paper should NOT be sent for review).

QUESTION: How should one word the acknowledgment of this colleague's helpful suggestions in the paper in a way compatible with excluding him as a possible reviewer, so that the editor who will handle the paper does not get confused by the whole situation and honors my request to exclude this person from the list of possible reviewers?

Also, which is the best way to state the reason for excluding this person from the list of reviewers (conflict of interests, or something else)?

Thanks in advance.

evolution - Why is the strength of genetic drift inversely proportional to the population size?

I saw a concept on the Internet that says "the strength of genetic drift is inversely proportional to the population size". I don't know why they are inversely proportional? Can somebody explain? Thank you all!

Answer

Plane Crash Analogy

4 people in a plane crash

In a small aeroplane, there are 2 people that wear a blue shirt and 2 people that wear a green shirt. The plane crashes, half of the people died. The 2 survivors are those wearing the green shirt… well, nothing so surprising!

400 people in a plane crash

In a very big aeroplane, there are 200 people that wear a blue shirt and 200 people that wear a green shirt. The plane crashes, half of the people died. The 200 survivors are those wearing green shirt… This is quite surprising!

Genetic Drift

The same logic applies to genetic drift. Genetic drift is caused by events that modify the reproductive success of individuals in a random way (independently of their genotype). We usually referred to this as random sampling. At each generation, individuals are randomly chosen to reproduce and some genotypes might just happen to be chosen more often than others at a given draw (=at a given generation). Genetic drift pushes the frequency of allele slightly away from what would be predicted. According to the Wright-Fisher model, the frequency of alleles (of a bi-allelic gene) in a haploid population (to make it easier) in the next time step is given by:

$$p' = \frac{p \cdot WA}{p \cdot WA + (1-p) \cdot Wa}$$

where $p$ is there frequency of an allele at time = $t$ and $p'$ is the frequency at time = $t+1$. $WA$ is the fitness of the genotype which frequency is $p$ and $Wa$ is the fitness of the genotype which frequency is $1-p$. If the population is infinite, the predictions of this equation are exactly correct.

Now if we say that meteorites fall and half of the individual get killed. The probability of getting killed by a meteorite obviously does not depend on genetic predisposition, it is a question of chance! If you look at a population of 1 million individuals, half of them having the genotype $A$, the other half having the genotype $a$. It is very unlikely that more than 60% of all individuals that get killed are of the same genotype. Therefore, the meteorites won't change much the frequency of the genotypes. If you look at a population of 4 individuals 2 are $a$ and 2 are $A$, 2 of them get killed by a meteorite. Well, you have a probability of one half that the two survivors are of the same genotype and that the genotypes frequency would have changed drastically.

Genetic drift refers to these changes in allele frequency which are due to random events (such as meteorites) and the strength of genetic drift indeed depends on the population size for probabilistic reasons. The greatest the population size, the lowest is the strength (or the relative importance) of genetic drift.

How to model genetic drift

There are three famous models of genetic drift that all lead to very similar expectations. I shall just name them here but I will not develop the underlying mathematics.

• 
  

  Wright-Fisher model of genetic drift

  
  
  
  
  • Not to confuse with the Wright-Fisher model of selection written above
  
  
  • It models genetic drift as a random sample of the previous generation and hence uses a binomial distribution.
  
  
  
  
  


• 
  

  Moran model

  
  
  
  
  • It is based on a birth-death model (a type of Markov model).
  
  
  
  


• 
  

  Kimura's diffusion equation model

  
  
  
  
  
  • It is an extension of the above two models for a case of continuous time.
  
  
  
  

degree - What are "all the rights and privileges pertaining thereto"?

It is common language in graduation ceremonies, at least in the United States, to hear a degree conferred with "all the rights and privileges pertaining thereto." How would one discover what the rights and privileges pertaining to a MA or PhD degree actually are?

Answer

I don't think any of the seven previous answers attempts to address the question from the body of the post:

How would one discover what the rights and privileges pertaining to a MA or PhD degree actually are?

The first thing to do would be to check the university's website for its regulations, which may go by different names. E.g. in Cambridge they are Statutes and Ordinances, and by reading them you can discover, for example, that both MAs and PhDs are members of the Senate (unless they have resigned or are suspended) and as such can vote in elections to the Chancellorship.

If you can't find the regulations, believe them incomplete, or need clarification on some point, then the next thing would be to write to the university. Again, the name of the body or title of the person equipped to answer the query probably varies: it would probably be reasonable to make an initial approach to the Alumni Office, the Dean's office, or the Vice-Chancellor's office, and to request that should their department not be the correct one that they point you in the right direction.

graduate school - Is it okay for professors to completely copy another professors' notes, assignments, and exam questions word for word from another university?

I have a professor who used the same lecture notes, same assignments, and same exam questions word for word from from another professor at a different university (who posts his notes, assignments, and exams online). She mentions she "makes her own exams", however the questions are identical to the online past exam and assignment questions.

It's a masters level class and the exam questions are quite specific. We are given an abstract to read and then asked to perform calculations/analyze the abstract.

Is this common or "allowed"?

How much time before (possible) effect of US sequester is felt on grant funding?

When a US institution that manages grant programs (such as NSF) suddenly sees its funding cut, as will be the case after the US sequester takes effect in March, how long does it take for that cut to trickle down onto grant programs and grants?

Namely: Can grants already started get cut (like, they tell you you'll lose 20% funding for the last year)? What about grant programs where the selection was already announced, can they make changes to that? Or will it “merely” impact the number of grants they can fund from now on?

(I know that the government will move, and though the situation is stupid, it's not as much of a dead-end as it is pictured… this question assumes that the sequester goes in effect, and not deal is made to lessen its impact.)

---

This question was spurred by today's PhD Comics:

Answer

See the NIH answer below on what's happening to grant budgets, at least for their agencies. It sounds like there is some budget trimming for the amount awarded for new grants, but they're trying to mitigate that somewhat. Where I think there's going to be a much greater impact is with new awards - with less money, and not wanting to hamstring grants with further cuts, they're simply likely to make less awards.

As for how much time before the possible effect of the sequester hits? It already has. Several people I've spoken to who do program planning, grants work, etc. for the Federal government have expressed the feeling that, because of the level of uncertainty about what money they'll have in the future, funding agencies are being very conservative about what they commit to spending. We could see this in the last budget cycle and the near shut-down - funding slowed to a crawl for a bit, and then when the continuing resolution got passed, there was a small "bump" as agencies spent out money they hadn't yet promised "just in case".

So if the sequester goes through, what that will really do is make those conservative, "We better not spend $$$ until we know we'll have it" plans a reality, followed by more severe paylines etc. in the next grant cycle.

So worst case: It's already here, we're just not committed to it yet.
Best case: The next funding cycle.

Edit: The actual answer has come from the NIH: http://grants.nih.gov/grants/guide/notice-files/NOT-OD-13-043.html

The NIH continues to operate under a Continuing Resolution as described in NOT-OD-13-002, and therefore all non-competing continuation awards are currently being funded at a level below that indicated on the most recent Notice of Award (generally up to 90% of the previously committed level). Final levels of FY 2013 funding may be reduced by a sequestration. Despite the potential for reduced funding, the NIH remains committed to our mission to seek fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce the burdens of illness and disability.

Should a sequestration occur, NIH likely will reduce the final FY 2013 funding levels of non-competing continuation grants and expects to make fewer competing awards to allow the agency to meet the available budget allocation. Although each NIH Institute and Center (IC) will assess allocations within their portfolio to maximize the scientific impact, non-competing continuation awards that have already been made may be restored above the current level as described in NOT-OD-13-002 but likely will not reach the full FY 2013 commitment level described in the Notice of Award. Finally, in the event of a sequestration, NIH ICs will announce their respective approaches to meeting the new budget level.

publications - Should CV include special note about published 'cover articles'?

I just published an article and, when I saw the journal, I was surprised to discover that they put my article on the cover.

My question is, should I update my CV to make special note of the fact that my article was not just published but is the cover story in a particular journal?

Answer

A cover article is noteworthy, but not all noteworthy material goes on all CVs. I include a note about cover articles on my CV iff I am also including citation counts. I only include this extra information if the CV is for something that is trying to evaluate the "impact" of my research.

human biology - Relative sweetness

I have noticed that when I eat something sweet, then afterwards, I eat something else that is sweet, the second sweet food is not as sweet as it usually is. I am pretty sure many others have a similar experience before too. Why does this happen?

genetics - What does it mean to clone a gene?

When I look up information related to the identification of disease genes, texts will often refer to the gene being "first cloned." What does "clone" mean in this context? Is it simply a synonym for discovery?

Answer

Usually this is used in the context of gene analysis and further characterization. What is done, is that a piece of foreign DNA (either generated by digesting genomic DNA (from human or mouse for example) or by PCR amplification) digested at the end of the DNA to have matching open ends with a bacterial vector.

The DNA of interest is then ligated with the vector and can then be replicated in bacteria and isolated easily in great yields. This plasmid can then further analysed (by restriction analysis, sequencing etc.), the gene or its promoter manipulated and mutated, or in case of protein coding genes the gene overexpressed in the cells. All this is useful to analyze the function of unknown genes. See the figure for a schematic overview (from Campbell AP Biology Book 8th edition, via this website):

Technically making a clone means that you generate multiple genetically identical daughter cells from one precursor.

publications - Should I do anything when I see several references that are not used in the text?

In a linguistics paper I read, I noticed that several references in the bibliography are not actually used in the text. This is for about 10-15% of the references the case. Should I do anything with this? I always thought that all references must be used in the text, because even if they are just suggestions for further reading you would want some explanation why it is relevant and what you can find where.

I only know the author through their work and do not know the editors. The paper is from 2011. The references are rather general. They are relevant to the paper, but you would want page numbers with them unless you are familiar with them. They are all from different authors and different institutes. It is likely that the references were used in previous versions of the text.

Answer

There's nothing inherently wrong with this. It's sometimes done to mention sources that provided general background information, or that the author suggests for further reading, but which weren't needed to support any specific claim within the paper. Some journals don't allow this, but it's a matter of style.

Even if the journal didn't want this, or if those references were included by mistake, it's a harmless error which just wastes a little bit of space.

If you have good reason to suspect that references were given in bad faith purely for padding, or to increase citation counts of other articles, then that would be misconduct - whether they were cited in text or not. But otherwise I don't see that this represents anything improper, and there is nothing you should do about it.

conference - Talks vs. poster presentations: Which is better for advertising your research and building research networks?

I'm looking into applying to present at a conference for undergraduates in mathematics this summer. When I apply, I have to either apply to give a talk (~20 minutes) or present a poster.

From what I've read on this site, it seems posters are often looked down on relative to talks, especially in mathematics. However, one advantage of a poster session is that I can have a back-and-forth discussion which is impossible in a talk. I think this is especially important for my research, since the computations in the subject are notoriously tricky and will trip up even experts if they aren't paying close attention to the details.

What are the relative advantages/disadvantages of each format? Which is a better way to advertise my research and network with other researchers in my field?

Answer

It depends on what you want to do. If you feel like at this point in your research it would be more beneficial to converse than to present, then I'd say that a poster session is the right venue for you. It's true that talks are considered a bit more prestigious than poster sessions, but you really should go with what you think will be more valuable for you, and for the conference attendees.

It's worth noting that you could always do a poster presentation this year, get the feedback that you covet, and then return next year to do a talk, and let everyone know how your research went over the subsequent year. That kind of progression is not a bad thing.

Also, if you are in the early stages of your research, it might not be ready for a talk. When I attend a conference talk, I'm expecting there to be some significant findings. Sure, talks might be more "prestigious," but, if there are some holes in your research, you could end up discrediting yourself. People aren't expecting the same level of maturity in the research during a poster session. So, as I said before, forget the prestige aspect, and choose what is more fitting based on your goals, and on what you have to share at this point in your research.

publications - Why is the date left out of some academic papers?

Being somewhat familiar with referencing of academic papers as a source, it has struck me as odd why authors would leave out some date on their paper. The date could be the day the author completed the paper on or submit date or published date etc. Certainly it would be of help to others who would want to reference their work? So, does anyone know if there is a specific reason why certain authors leave out a date on their papers?

Answer

There is often a substantial delay between when the author finishes a paper and when the paper is actually published. The author may not be totally aware of the publishing date. This is why the authors do not include the date.

The date is generally found in/on the book/proceedings that the paper is published in. This is the date that should be used for referencing a paper.

evolution - How to calculate the effective population size ($N_e$) with overlapping generations?

From this Source: If generations are overlapping, then the effective population size $N_e$ does not equal the population size $N$.

I know mathematical formulations in order to find the effective population size $N_e$ when the sex-ratio is biased $\left(N_e = \frac{4N_mN_f}{N_m+N_f}\right)$ or when the population size varies cyclically through time $\left(N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}\right)$.

What is the effective population size in a population with overlapping generations?

Answer

There are many different ways to do this, depending on what assumptions you make on e.g. stable age structure, distribution of offspring, haploidy/diploidy, population growth etc. As you probably know, there are also two main approaches to effective population sizes, namely ones based on:

1. the rate of inbreeding ($N_{e,i}$)


2. the increase in variance of allele frequencies ($N_{e,v}$), and they can sometimes differ a bit from each other.

An early attemp to calculate effective population size with overlapping generations comes from Felsenstein (1971), which is based on life table information. This paper includes several derivations, both on inbreeding $N_e$ and variance $N_e$. As an example, the formula of inbreeding $N_e$ for a diploid population is:

$N_e = \frac{N_1T}{1 + \sum_i^\inf l_i s_id_i v_{i+1}^2}$

Here, $T$ is the generation time, $l_i$ is the survival up to age i, $s_i$ is the survival from age i, $d_i$ is the probability of death at the end of age i (i.e. 1-$s_i$), and $v_{i+1}$ is the reproductive value of individuals in stage i+1. However, this is assuming a constant population size and a stable age distribution, so some rather restrictive assumptions. The paper also includes models for haploid populations, and I haven't gone through it carefully.

A couple of more recent papers that calculate $N_e$ for overlapping generations are Engen et al. (2005) and Engen et al. (2007). These papers use diffusion approximations to derive several formulas for $N_e$ under different assumptions, for age-structured density independent populations. One model for a haploid population in a fluctuating environment is:

$$\begin{align} N_e & = \frac{N}{\sigma_d^2T} \text{, with} \\ \sigma_d^2 & \approx \sum_{i=0}^k \frac{\lambda^{-2}}{u_i} \left[\left(\frac{\delta\lambda}{\delta b_i}\right)^2\sigma_i^2 + \left(\frac{\delta\lambda}{\delta s_i}\right)^2 s_i(1-s_i) + 2\left(\frac{\delta\lambda}{\delta b_i}\right)\left(\frac{\delta\lambda}{\delta s_i}\right) c_i \right] \end{align}$$

where $T$ is the generation time and $\sigma_d^2$ is the demographic variance. In the lower equation, $\lambda$ is the deterministic growth rate (dominant eigenvalue), $u_i$ is the proportion of the population in stage i (a component of the stable age distribution), $b_i$ is the expected number of offspring with variance $\sigma_i^2$, $s_i$ is the survival rate of stage i (with binomial variance), and $c_i$ is the covariance between reproduction and survival. You really need to dive into these papers to fully understand how these equations are derived and how the variables are defined (will take up far to much space here). However, at its core, it is using a diffusion approximation on an allele at a selectively neutral locus.

There are many other papers out there deriving effective population sizes, under different assumptions and restrictions, but the ones cited above should be a good starting point, and by looking at citations to and from these you should get a decent overview of the topic. Many textbooks also cover ways to calculate effective population sizes with overlapping generations, e.g. Hedrick (2011) and Felsenstein (2013, free pdf).

In citations, how to find out if it's a compound name?

I have a paper that I want to cite in my own work, in the form "J. Wayne" (for John Wayne) in the bibliography part of the paper and Wayne in the body of the paper.

The full name of the author appears on the paper as Aaaa Bbbb Cccc, and is typically a non-western name. Say, consider something like John Fitzgerald Kennedy, but let's assume you never heard of them, and they obviously are from a different culture, and you don't know if their last-name is Kennedy or Fitzgerald Kennedy.

Should I note it in my Bibtex file as Kennedy, John Fitzgerald or Fitzgerald Kennedy, John ? This will change things when printed with last-name only, it will appear either as Kennedy or Fitzgerald Kennedy.

So, more generally, is there an academic naming convention for this kind of situation ? Edit: To be more precise, what I want to know is if there is a standardized way for an author with such a name to sign his paper, for example Aaaa Bbbb-Cccc, so no ambiguity is left for the reader. Or for the reader, if one has a guaranteed way to know this (seems not).

I must add that I have seen the considered author cited as Bbbb or as Cccc, one of these being obviously incorrect (even both could be).

Answer

No.

(aeismail has already addressed nicely how to deal with this, but what follows is too long for a comment.)

As far as I know, there's no standard way (i.e., the same for every name no matter the culture) of indicating which components of a name are considered to be the last name. In fact, even the concept of last name is different from culture to culture and may even be absent -- see http://en.wikipedia.org/wiki/Category:Names_by_culture. Even in Europe, you can get quite complicated naming systems. So you are really trying to identify the "main professional name", whatever that may map to in a given culture. To identify it from the list of names as written within that culture, you have be familiar with the specific naming conventions (maybe the Wikipedia page helps, or if you know someone from that culture, you can ask them).

It's worth keeping in mind that getting it right serves two purposes:

1. 
   

   Making sure everybody knows the person you refer to, even if they don't know the full name.

   
   


2. 
   
   

   Showing courtesy towards that person.

   
   

While the second point is the only one of importance when addressing the person directly ("Dear Professor/Dr. X"), in your case the first point is actually more important: If (say) a referee wants to check the bibliography whether you cited a relevant author's works, they would expect to find them in a certain form. If everybody uses the same (wrong) way of parsing the name, it would arguably be the right thing to do to follow that choice.

(Finally, you could also chicken out and just list all authors in full, native name order; in Bibtex, you can do this by wrapping the full name in curly braces.)

Is it possible to submit a PhD thesis with two authors?

We are two students working in the same field under the supervision of the same professor within his chair and all of our publications are done together.

Hence I am curious: Is it generally possible in academia to submit a PhD thesis with two authors?

Answer

A few answers have noted that PhD theses with two authors do exist, and that is interesting trivia.

However, I think it is useful to address your underlying issue. I.e., what is the best strategy to adopt when you are collaborating closely with another PhD student, you are working on a similar topic, and you have the same supervisor?

This situation arises for many PhD students (I can think of a few), yet they still work out a way to write their own thesis.

If you are publishing joint papers, then you may want to think about ways that you and the other student can be the lead author on different papers. You probably also want to formalise the description of who made what contributions to each paper. I know at my institution, papers that form part of a PhD need to have a statement signed by all co-authors listing the contribution of each author.

You want to think about how your thesis can be distinct. You should work with your supervisor to carve out your unique focus.

bioinformatics - Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein coding genes in the human genome. Is this something to do with splice isoforms, like those from SpliceProt, or another splice isoform database or tool?

Answer

Well you are assuming one sequenced genome/proteome per NCBI tax id. That is no longer true. So if you click on the proteome filter it decreases by half. Which gets you into the 60,000 range. Now not all of these are "different" conceptual proteins, many are artifacts from the way GenBank/EMBL/DDBJ interact with the TrEMBL section of UniProtKB i.e. they are not normalized in db speak.

So for the human case you also want to add the Swiss-Prot filter to get a decent proteome that gives you about 20,000 proteins. Corresponding to the predicted/confirmed human gene count.

In all bioinformatics databases you need to pay attention to difference between database records and biological concepts. They rarely map cleanly one to one. In this case an UniProt record is not a protein, but information about a protein and a different record could have information about the same "protein". Or at least the same under some definitions of "same".

See the announcement of the draft human proteome in UniProtKB

The known isoforms are most often stored in the alternative products section of an UniProt entry. In some rare cases when the splice variant has a completly different biological function they are described in separate UniProt entries. For UniProtKB/Swiss-Prot Human there is a near 1 to 1 relation between genes and proteins. Cases as above and fusion proteins are the exceptions to this rule.

TrEMBL tries to automatically reduce redundancy in INSDC by auto merging entries in the same taxid and now proteome that have an identical reported sequence. However, variations of single gene products due to mutations and or limit what auto merging can do. For example there are 8 records for the P53 gene in TrEMBL today. Many of them from mutants, i.e. cancer genomes etc...

botany - Why doesn't the herbicide 2,4-D damage lawn grass?

I sometimes use 2,4-Dichlorophenoxyacetic acid to control broadleaved weeds in lawns. It is selective, and quickly kills the dicot weeds, while other plants are unharmed.

2,4-D is a synthetic auxin, a class of plant hormones. It is gets taken in through the stomata on the leaves, and is transported to the meristems of the plant. This causes uncontrolled, unsustainable growth, and the plant wilts, and dies.

Why doesn't this affect most monocotyledons?

Answer

According to this link from Purdue, the seed of the answer is this:

The herbicide is used to kill broadleaf weeds, which are dicots, while monocot grasses, such as sorghum and corn, are more resistant. That's because grasses inactivate 2,4-D inside the plant, while broadleaf dicots do not.

But on the other hand, Song 2014 has this to say about 2,4-D:

However, the underlying molecular mechanism of how auxinic herbicides selectively kill dicots and spare monocots is not understood yet (Grossmann 2000; Kelley and Riechers 2007; McSteen 2010). The mechanisms of auxin biosynthesis, transport, and signal transduction are conserved in monocots and dicots make this question more complex (McSteen 2010). Early research has proposed that the selectivity of auxinic herbicide is because of either limited translocation or rapid degradation of exogenous auxin, altered vascular anatomy, or altered perception of auxin in monocots (Monaco et al. 2002; Kelley and Riechers 2007). Auxin transport is influenced by plant vascular systems (Mattsson et al. 1999; Scarpella et al. 2006). The difference in vascular tissue structure between dicots and monocots may contribute to the selectivity of auxinic herbicides. In monocot stems, the vascular tissues (the phloem and xylem) are scattered in bundles, and lack a vascular cambium; in dicot stems, the vascular tissues are form ed in rings and possess a cambium.

So in other words, we don't know yet. It seems to be very strongly tied to auxin transport, but we do not have the full mechanism of action; since auxin is such an important plant hormone, and the pathway is therefore highly conserved (that is, the genes tend to be nearly identical on the parts of the sequence that affect the phenotype), the general conclusion is that the pathway itself is not affected, but an accessory pathway clears up auxin in levels excess of any normal amount in monocots.

Edit: Whoops, got the author's first/last names mixed up.

publications - Order image from freelancer

I am writing a journal paper. In order to illustrate my work, I need to include an image of the whole system that I have built. The problem is that I am not very talented to make good images, so I would like to hire a freelancer to create a professional image. My questions are:

• Is it allowed to add an image that was not done by me?


• Is it ethical?



• If yes, what kind of contract I need to sign with the freelancer so that all the rights belong to me after the payment?

Many thanks.

publications - What does author order indicate?

When you look at a paper, what order to you assume the authors are in? Most important/most work done first or alphabetical? In my group we usually use alphabetic order, but I've been wondering if that might create a misleading impression with lots of people.

On a related note, would you expect the name of a PhD student to be always first on publications related to her/his work?

Answer

The answer is strongly conditional on discipline and, to a lesser extent, country of origin. Conventions vary widely, as does the degree to which they are institutionalized. For instance, in some fields (e.g., Philosophy), co-authorship is not common and there is no convention about attribution, so absent an explicit note people are are likely to think the more senior author is the primary one. In Sociology, co-authorship is common and the convention is that the first author is the lead author unless there is a note indicating equal authorship. In Economics, co-authorship has become increasingly common over the past few decades but the convention is to list authors alphabetically, regardless of degree of contribution. In some fields the primary author may be determined by looking to see if there's a note specifying to whom correspondence should be directed, regardless of order of authorship on the paper.

Meanwhile in many lab-based science disciplines, where it's sole authorship that's rare, author order is governed by different norms. In some fields, the first author is the one who is primarily responsible for the paper (what that means can vary, too), the last author is the lab head or primary grant-holder, and the order of authors in between is sometimes influenced by other norms. But other conventions exist, too. Knowing what they are and how to interpret them is part of one's socialization into a discipline.

To make things more complicated, some fields—or some journals, or some labs, or some individual authors—may have their own rules or conventions designed to clarify things by listing credit more explicitly. Even worse, there may be a kind of hermeneutics of author-order where people parcel out credit to different contributors regardless of order of authorship, as when someone says "Sure, X is the first author and Y helped him write it up but it's obvious the paper was Z's idea".

In your case, if your lab or unit is using a convention that's not standard in your field the most straightforward solution is to make a note of this in your articles. This isn't an ideal solution because papers will still be cited or referenced without people paying attention to your clarifying note, but there isn't much you can do about that.

pharmacology - Derivation for drug half life

The formula in textbooks for $t_{\frac{1}{2}}$ of a drug following first order elimination is generally given as $$t_{\frac{1}{2}}= \frac {\ln(2).V_d}{Cl}$$where $V_d$ is the volume of distribution and $Cl$ is the clearance.

Shown below is my attempt to derive the formula but I don't know where I'm going wrong.

Assuming first order kinetics of elimination, the rate of elimination ($R$) would be proportional to the plasma concentration ($Cp$)

$$ R = Cp . k$$

Where $k$ is the rate constant.

For calculation of $t_{\frac{1}{2}}$, since this is a first order elimination, $$ t_{\frac{1}{2}} = \ln(2)/k$$ Substituting, $$ t_{\frac{1}{2}} = \frac{\ln(2).Cp}{R}$$ Since $ Cl = R/Cp$, substituting would give, $$ t_{\frac{1}{2}} = \ln(2)/Cl$$

Since both the formulae don't match (this one doesn't have a $V_d$ term at all!), where have I gone wrong? Also then how is $Cl$ different from $k$?

According to the correct formula, $k=Cl/V_d$. How is that so?

EDIT

Volume of distribution is the apparent volume of blood the drug takes up and is given by $$V_d = \frac {Dose}{Pc}$$

Clearance is the volume of blood that has been cleared of the drug in unit time and is given by $ Cl = R/Cp$

Correct me if the basic definitions themselves are wrong.

Answer

Well, $Cl = R/Cp$ is correct, but $R$ is not $Cp \cdot k$.

Given $X(t)$, the actual quantity (ie weight or moles) of drug in the system, $R$ should have the dimension of $\frac{dX(t)}{dt}$, that is $weight \cdot time^{-1}$ or $mole \cdot time^{-1}$ because the base definition of clearance is given by $$- \frac{dX(t)}{dt} = Cl \cdot C(t)$$.

The volume of distribution $Vd$ comes into play when converting from $X(t)$ to $C(t)$. Following the same steps as you did :

$$ R = \frac{dX(t)}{dt} = \frac{dC(t)}{dt} * Vd = C_p \cdot k \cdot V_d$$ because (due to 1st order kinetics) $$\frac{dC(t)}{dt} = Cp \cdot k$$

Substituting, $$ t_{\frac{1}{2}} = \frac{\ln(2)}{k}$$ $$ t_{\frac{1}{2}} = \frac{\ln(2) \cdot C_p \cdot V_d}{R}$$ Since $ Cl = \frac{R}{Cp}$, substituting would give, $$ t_{\frac{1}{2}} = \ln(2) \cdot \frac{1}{Cl} \cdot V_d$$ $$ Cl = \ln(2) \cdot \frac{1}{t_{\frac{1}{2}}} \cdot V_d$$ $$ Cl = k \cdot V_d$$ $$ k = \frac{Cl}{V_d}$$

How much customization of letters of recommendation is necessary?

While I know that students are encouraged to "tailor" their applications to the particular school or program they're applying to, does the same hold true for the people writing letters of recommendation on their behalf? In other words, is it possible just to change the "addressee" portion, and use a greeting such as "Dear Members of the Admissions Committee," or is more personalization required?

Just to clarify here, I'm referring to the "pro-forma" parts of the letter, rather than the actual content of the recommendation per se.

Answer

I have two levels of customization. Firstly, if the letter is for an internship at a lab, or an application to grad school or a job, I tailor the qualities that I emphasize and link those qualities to the specific job.

A second level of customization is if I have any connection to the institution (for example, when writing letters of recommendation for AT&T Labs - where I used to work - I might mention this explicitly in order to convey that I understand the local culture)

This is above and beyond the usual pro-forma customizations for the addressee etc.

teaching assistant - Lecturer in a course I'm TA'ing refuses to give feedback on student assignment

I am a teaching assistant in an undergraduate bioinformatics course. A few weeks ago the students in the course handed in the final assignment (which is worth 80% of the final grade), which we (me and the other members of the course staff) are currently in the process of grading.

The lecturer in charge of the course wants to give the students only their final grades for this assignment without any feedback on why points were taken off. Her justification for this is that she do not want students to pass the feedback to the next class that will take this course and thus avoid copying of answers. While she did not say so explicitly, my impression from some things she did say is that by avoiding a more detailed feedback she hopes to discourage student from appealing their grades. My university's regulations state that a student can appeal any grade, but in the appeal form the student must specify exactly which question/part of the assignment they appeal and why do they think that points were taken off unfairly, so no feedback - no appeal and thus no extra work for the course staff.

I am rather uncomfortable with this attitude for several reasons:

1. 
   

   From a didactic point of view I think that merely giving a student their final grade without any indication what was his/her errors is wrong is it does not allow them to improve.

   
   


2. 
   

   Not giving feedback will not prevent students from passing their work to the next class. It will just mean that the errors of student from this class will propagate to the next class.

   
   

On the other hand, I am uncomfortable from insisting on this issue from several reasons:

1. 
   

   This is my first year as a TA, whereas the lecturer has been giving this course for many years, so it is possible that her judgement is better then mine, even though it seems wrong to me.

   
   


2. 
   

   It is unlikely that I will teach this course again (I intend to graduate and move to another university later this year). Thus, even if I do manage to persuade the lecturer to give a more detailed feedback, I will not be around to face the consequences she is afraid of whereas she will, so insisting on this may be a bit unfair to her.

   
   


3. 
   

   The other TAs in the course do not seem to share my opinion (they did not voice any strong opinion of this matter).

   
   
   


4. 
   

   I do not want to start a confrontation with the lecturer, as I might need a reference from her in the future.

   
   

There is still a window of a few weeks until we are supposed to give the grades, so theoretically I can reopen this discussion.

Basically, I have two questions:

1. Given all of the above, should I attempt to persuade the lecturer to allow more detailed feedback?


2. If I should, how can I persuade her?

EDIT

Some additional information that seem relevant is light of the comments and answers:

1. 
   

   As per the lecturer's instruction we keep a detailed record of the grading of the assignment (this also includes that lecturer, with respect to the parts of the assignment that she grades herself). So detailed feedback is available. Thus we can rule out the possibility of laziness or unwillingness to waste time on detailed grading.

   
   


2. 
   

   Assessment and feedback during the course Many of the classes in the course included practice sessions during which the students were supposed to complete on assignment. These assignment were not handed in or graded, but were meant solely for the students' learning. During these sessions the students were able to consult the course stuff if they did not understand or were unsure about a certain question. In addition there were two midterm assignment, each worth 10% percent of the final grade (I would mention that at my institution it is quite normal that the final exam/assignment makes 80% or even more of the final grade, but is not normal not to give feedback on it). For the first of these midterms we did not give students individual feedback, only the final grade. We did mention in class some frequent errors and issues in the assignments. Formally students were allowed to approach us for more detailed feedback but as far as I know few if any did that. For the second midterm assignment we give detailed feedback. The in the grading policy between difference between the two midterm assignments is that the first assignment was submitted only electronically via the course website and in the second assignment the student were also required to hand in a hard copy of the assignment. The lecturer refused to allow feedback on the electronic submission because this would be easier to pass to the next class. Initially she wanted to require hard copy submission of the first assignment too (presumably to allow detailed feedback). When I asked prior to the issuing of the assignment to the students why an electronic submission is not enough she changes it an electronic submission only. I did not realise at the time that this would deprive studetns from feedback. She only inormfed us about that after the assignments were handed in and we were about to start grading.

   
   

Answer

No, you should not confront the lecturer again ("reopen") over this issue. That would not be an efficient use of your time.

You've talked to the course instructor. She has explained to you her justification. Presumably she's observed both cases of giving and not giving feedback for the final in the past (you have not). You do not have the power to compel her. You don't have other allies on the grading staff. You are ending your engagement there in the immediate future. You will not deal with this issue again. Move on.

Keep this in your list of "things I think I could improve on when I become a lecturer" for the future. Hopefully this will be a memorable case to experiment with later on your own. And you'll get to observe another institution's practices for comparison in the meantime. You may well be right, but you triply don't have the time to redirect this in your current position.

awards - What date should I use for graduation?

When graduating from a university in the UK you are often conferred with an award before the graduation ceremony. I am therefore seeking clarification as to what date should be written on documents such as job application forms.

• For an bachelor's degree, do I use the ceremony date or the award date?


• For a PhD, do I use the date of the viva voce or the ceremony date?

Answer

You should use the date conferred. Universities will have an official date where all degrees for the term are conferred on everyone. This is usually not the same date as the graduation ceremony as there can be multiple graduation ceremonies across multiple days, but trying to keep track of all of them would be confusing. It's much simpler to just pick one day after all the ceremonies and say all degrees are official as of that date.

That being said, I've never heard of an employer (or anyone) who really cares about the particular date as long as it's clear that you've already met all of the requirements of graduation.

respiration - Effects of smoking tobacco compared to inhaling other smoke

How much less dangerous is breathing smoke from burning wood and coal compare to smoking tobacco?

Edit: Sorry. I should have made the question clearer.

If this were an experiment, it would be set up like this. Subject 1 is a control, so he is exposed to smoke from burning tobacco for a year. Subject 2 is exposed to smoke from burning maple leaves for a year. Subject 3 is exposed to smoke from burning pine needles for a year. The other subjects continue in this fashion, being exposed to smoke from many different sources. The rats are examined for lung cancer through this year and for the remainder of their lives. What would the expect results of this experiment be?

phd - How to overcome the feeling that I don't know many things about my research tool?

I am a 6th year PhD in computational chemical engineering. I have extensively used Lammps for my Molecular dynamics simulations. However there are many aspects of the modeling tools that I have no idea about ( like the time integration procedures used, the algorithms to make parallel computing possible...etc). This makes me feel bad about myself. I know that it is not possible to know everything and an important part of PhD is research output, so not all attention can be diverted into learning everything about the tool.

But, my question is, what to do if that bothers me greatly? I don't feel like a potential expert in my research and I feel like that's something to worry about.

How does one feel like an expert or become confident about their research/technical abilities? Does that come from acknowledgement of the deficiencies and being humble of the fact that probably I won't know many aspects of many things?

Are there any advice you would like to give a new PhD graduate to ensure a satisfying research career?

genetics - How is haemophilia dominant in human females?

In human females one X chromosome is inactivated forming a Barr Body. Then how is it that haemophilia is dominant?

Suppose a female has one normal X chromosome and one chromosome with the haemophilia gene. Now suppose that the normal X chromosome is inactivated — will the female show haemophilia?

Answer

X-linked Hemophilia is caused by the lack of production of the clotting factors VIII or IX. It is not inherited dominantly, but instead inherited in an X-linked recessive manner.

These proteins are produced in multiple regions around the body. In a female heterozygous for the gene coding for Factor VIII or IX, X-inactivation would randomly prevent one of the chromosomes from expressing its allele. Therefore, the production of active Factor VIII or IX would only occur in half the cells which have the faulty allele inactivated.

However, half the production of the relevant factor results in a close to normal phenotype, as the hemophilic phenotype would not manifest unless the clotting factor activity levels are very low.

This Medscape article on hemophilia states that:

Normal values for FVIII assays are 50-150%. Values in hemophilia are as follows:

Mild: >5%

Moderate: 1-5%

Severe: < 1%

Therefore, despite X-inactivation reducing the production of clotting factors by 50%, the heterozygous female still displays the healthy, non-hemophilic phenotype.

While the clotting factor concentration can only be reduced to approximately 50% of normal, it is still possible for heterozygotes to suffer from mild hemophilia. This is because other genetic factors may also affect the hemophilia phenotype.

For example, the gene encoding FVIII may have point mutations which reduce the effectiveness of the protease, therefore reducing activity levels below the expected 50%. Mutations in regulatory elements or interacting proteins may also result in hemophilia due to the regulatory elements downregulating the expression or activity of the protein.

Approximately 40% of cases of severe FVIII deficiency arise from a large inversion that disrupts the FVIII gene. Deletions, insertions, and point mutations account for the remaining 50-60% of the F8C defects that cause hemophilia A.

Low FVIII levels may arise from defects outside the FVIII gene, as in type IIN von Willebrand disease, in which the molecular defect resides in the FVIII-binding domain of von Willebrand factor.

advisor - What's wrong with my e-mail to potential PhD supervisors?

I recently sent some e-mails to potential supervisors asking information for a PhD with them, I obtained no answers. I share my doubts and then copy the standard mail I sent.

1. I sent it to 5 different professors in different universities, is the sample too small to expect some answers? I know professors are flooded with e-mails so it could be normal not receiving answers.


2. Can you point out something I did wrong in my email such as: too long, too short, harsh, too many details, not many details, grammar mistakes (I'm not a native speaker), anything, to help me improve for future e-mails?


3. How do I have to take these silences? Should I solicit an answer or simply accept that they are not interested in answering?


4. I sent them on a sunday night, is this a bad moment to send such e-mails? if it is what are the best days and time to send them?


5. Feel free to give me any kind of advice you think could be helpful.

Here's a copy of my e-mail

Dear professor XXX, I'm a student of XXX at the university of XXX thinking about applying for PhD in FIELD X, therefore your group at the university of YYY attracted my attention. I'd like to ask two questions about the possibility of being admitted at your university:

1) Is there a good chance your group is going to look for PhD students in 2019/2020?

2) Is the topic of the master's degree thesis fundamental for a strong application? For example, what are the chances that a student with a thesis in TOPIC Y would have his application taken very seriously into consideration by a group like yours?

This is a very important question for me as it will have a great impact in my application strategy and maybe in the selection of the advisor for the thesis.

Thank you in advance for your time and help if you decide to answer me.

Best regards,

ZZZZ

Addendum 1: as suggested by iayork I have to be more precise and state that I'm European writing to professor in Europe and that I wasn't trying to bypass the application system by writing to them but instead following. As suggested I share the example of a professor I didn't write to: https://www.ics.uzh.ch/~jyoo/home.htm In the section jobs he says he has to be contacted for information by possible PhD students. Another example from a university I didn't write to: http://www.en.physik.lmu.de/promotion/berechtigung/index.html The point 1 is to find an advisor getting in touch with him/her

Addendum 2: Since it's creating a bit of confusion I have to precise that Topic Y in the letter is far from the research interests of the group contacted, I should have been more explicit in the mail and here explaining that the point of that question was to know if I had a chance even with such a thesis, and in case of negative answer I would change my master thesis advisor and topic to produce a thesis that allows me to have a chance to be taken in consideration by the group.

Thank you in advance for any help.

physiology - What is the human energy consumption by organ?

The human brain uses about 25% of the human body's metabolic energy. How are the other 75% spent, in terms of portioning to its various systems?

I thought this could be answered by a simple search, but I can't find the answer after searching very hard. I only got dieting advices.

I am envisioning the best answer to look like

Answer

Percent of basal metabolic rate by organ (BC Campus Open Education):

• Liver and spleen : 27%


• Brain: 19%


• Skeletal muscle: 18%


• Kidneys: 10%


• Heart: 7%


• Other tissues (lungs, intestine, skin, bone, fat tissue, glands...): 19%

Basal metabolic rate by 1 kg of specific organ tissue (kcal/kg of organ/day) (Table 5 from American Journal of Clinical Nutrition, 2010):

• Heart: 440 kcal/kg


• Kidneys: 440 kcal/kg


• Brain: 240 kcal/kg


• Liver: 200 kcal/kg


• Skeletal muscle: 13 kcal/kg


• Adipose tissue: 4.5 kcal/kg


• Residual tissues (lungs, intestine, skin, bone...): 12 kcal/kg

cell biology - How would the human body adjust to sleep times if we were to live in a place with different day lengths?

You sleep at night and are active during the day that's how things work for humans, but theoretically if a human whose parents lived on earth were to be born in another planet resembling earth but the difference was that this planet has an 8.5 hour day, what kind of changes will this person undergo?if a human who grew up on earth suddenly had to move to this planet how would his body adapt? what would be the difference between a person who moves to this 8.5 hour day planet with the person that was born there? and would the person who was born on this planet be active for 4.25 hours and then sleep for the other 4.25?

ethics - Can I learn the course material for the first time while I'm teaching it?

If I'm going to give students the course X in next semester. Should I have full understanding of the subject before I teach them or can I learn about the topics before I go to the class and then teach them?

The idea that I want to reach is it good to study the subject in the same semester or should I study before?

Answer

. . . the first time I was in a statistics course, I was there to teach it. - John Tukey

In my experience, it's definitely better to learn about it beforehand. If you are really pressed for time, then start reading the textbook or course material from the back, because you really need to know the direction in which the course is going before you teach the material.

Too many times, I have done the opposite and tried to learn the subject at the same time as teaching it. This is really fun and certainly helps you to see things from the perspective of the students, but is not ideal from a pedagogical point of view, as you are too likely to be blindsided by something. The same goes for courses which are part of a series. For example, I once taught a linear algebra class and left out determinants because we were running out of time and we didn't "need" them for the exam. Next term, I got an irate email from the instructor of Linear Algebra 2...

The best possible prepartion for teaching the course in X is having taught it before.

job search - How do hiring/promotion/grant committees assess individual applicants who've authored papers with huge teams

While reading this slightly-too-snarky question, I was reminded of a slightly more serious question I’ve wondered about from time to time: how does being one of the 1000+ authors on a paper like the LIGO discovery or one of the CERN collaborations influence your career? I’m used being in a field (mathematics) where most papers have between one and three authors (I’ve written with three separate four-person teams, and people have often considered this a bit exotic), so when reading a CV, one can reasonably ascribe most of the “credit” for a paper to any of the authors.

If you’re in a situation where you have to judge the research output of a scientist (like a hiring or tenure committee), how does seeing a paper from an enormous collaboration change your thinking? What do you if you have make a decision between candidates whose publication lists are identical (due them being in the same collaboration)?

career path - Should I use a not-self-hosted website for both blogging and collecting academic materials?

Several researchers in my subfield (and in mathematics in general) use not-self-hosted wordpress.com subdomains for their 'professional blog' (to blog about their research, their latest papers, or any topic related to their interests). Few of them use some pages of their blog as 'professional websites' too (to upload their CV, list of publications, material for courses, and so on).

I've made up my mind to start blogging myself; also, I'd like to create a webpage 'independent' from the one on a subdomain of my current institution (to make my life easier when I'll change place and to have some more flexibility).

Should I use a not-self-hosted website for both blogging and collecting academic materials?

So far, these are the results of my research (in and outside my department) on the topic (but I'd like to examine some more objective and expert points):

"Pros"

• 
  

  I like that it is easy to use and set up (without any need to set up (and pay) your hosting yourself and actually "code" your website -- which would be hard since my knowledge of computer science and programming is very limited). Plus, some free themes are nice, essential, and easy to navigate.

  
  


• 
  

  I like the idea of connecting blogging and actual academic work.

  
  
  

"Cons" (i.e. the points that I'd mostly like you to address)

• A friend of mine (who is not in academia anymore) implied that not-self-hosted websites look very unprofessional and cannot be fully optimized and personalized. Is the perception of not-self-hosted websites as unprofessional a real thing in the academic world? (In my opinion, on the contrary, seeing a website of the form namesurname.com could leave the impression of great pretense).


• It has been pointed out to me (by a much senior researcher) that having "serious" (or at least would-be serious) research achievements on the same website as "more relaxed, informal, or expository blog posts" may be detrimental to the perception of the research itself. I strongly disagree on this point, but I'd like to do a reality check to see if this is actually a potential issue or just an "old-styled-man's viewpoint".


• These subdomains and (mostly) the themes can be unstable (or be no longer updated/supported) and thus force me to redo the set-up at some point in time. Specifically, they may be more unstable than the website of a university. I really don't know about this, so I'd like to check, but I've heard it from a grad student in computer science.

Answer

In academia, an amateurish-looking website can almost be worse than having no website at all. Now "amateurish" here does not mean "made yourself"; it instead refers to sites that use bad design practices (lots of garish colors, ill-chosen animations and transitions, poor design choices that make it hard to find information). However, there is not necessarily a strong link between poor design and web host. So, you can and should decide if the web host makes sense for you.

I know a number of researchers who have their websites that are hosted by sites such as Google Sites, but they do look professional enough to pass muster. On the other hand, the main issues for a web site in academia is that you are able to find the information you need. A bare-bones text-based website (which many people still use) is perfectly acceptable if you can access a researcher's CV, lists of interests and publications, and get contact information.