neurophysiology - Is our color vision calibrated to sky, vegetation, and blood?

Our color vision is based on three types of receptors (cones) which are sensitive to three distinct locations on the spectrum: 420–440 nm, 534–555 nm, and 564–580 nm. We label them "red", "green", and "blue", but these names are arbitrary. However, their locations on the spectrum may not be arbitrary.

I notice that they correspond to the colors of the three most important things in our natural habitat: sky (the above), vegetation (the below), and blood (the sign of potential food or alarm, depending upon whether you are the hunter or the prey).

Am I on to something here, or am I just dreaming in technicolor?

Answer

Short answer

Color vision is not based on a calibration to the sky, vegetation and blood. The current leading theory of the development of trichromatic vision in humans is based on the foraging of fruit in our primate ancestors.

Background
The places of red, green and blue wavelengths in the spectrum are physically defined and, therefore, not arbitrary; see this question on Biology SE.

Before continuing, it is good to mention that trichromacy (the presence of red, green and blue cones in the retina) is typical for primates. For example, dichromacy (<500 and >500 nm cones) is the most common configuration in mammals. The split in red and green photopigment in primates developed relatively late in evolution (30-40 mln years ago), inferring trichromacy in primates from a dichromatic ancestor. Note that many avian and aquatic species may be tetrachromats or up (4 or more photopigments) (Nathans et al. 1999), with the mantis shrimp featuring no less than 10(!) different photopigments (Cronin & Marshall, 1989).

It is believed that the red-green-blue system in primates has evolved due to its benefits for identifying fruit on a background of foliage, and to assess the ripeness of fruits. The food of monkeys typically consists of fruit, and young leaves. Young leaves are light-green, while ripe fruits are often yellow (e.g., bananas) and orange (e.g. oranges, mangos) (Osorio & Vorobyev, 1996). Unripe fruits typically contain chlorophyll and resemble the color of foliage (green). Hence, to discern ripe, nutritious fruits (yellow-orange or 570-620 nm) from foliage (green or 495-570 nm - frequencies mentioned were copied from wikipedia), it makes sense to have good resolution in the red-green area. The red opsin has its maximum at 530, and the green at 560 nm. The blue has its peak a lot lower at 425 nm (Nathans et al. 1999). Hence, the red and green opsins, which evolved late in evolution, are both right in the "ripe fruit area" and have absorption spectra very close together. Hence, there is a lot of color sensitivity (high color resolution) in the red-green area, which covers reds, oranges, yellows and greenish colors. This gives primates a very high sensitivity to recognize fruits, and especially ripe fruits in a green background. The resolution in the green-blue range is smaller (blues, purples).

As a background: color vision in trichromats works by color opponency, and specifically a yellow-blue and red-green color opponency. This means there exists no yellowish blue hue, or a reddish green (De Valois & De Valois, 1993). The red-green opponency means that we have exquisite sensitivity in the red-green pathway, as red cones suppress green cone output and vice versa. In other words, there is a high color acuity in the red-green area that helps to recognize fruits.

As a side note: The trichromat color vision scenario in primates supports the notion that cats (for example), being predators with dichromatic vision, do not benefit from being able to identify ripe and unripe fruits, as mentioned by @GoodGravy. In contrast, cats need excellent night vision and motion sensitivity, being nocturnal hunters. Indeed, color vision versus night vision, and color vision versus high motion sensitivity are both trade-offs that do not go hand in hand (Kelber et al, 2002).

<sub>References
- Cronin & Marshall, Nature (1989); 137-40
- De Valois & De Valois, Vis Res (1993); 33(8): 1053-65

- Kelber et al., Biol Rev (2003); 78: 81–118
- Nathans et al., Neuron (1999); 24(2): 299–312</sub>

mathematics - Is solving all of the exercises in a textbook a good idea?

Is solving all of the exercises in a textbook a good idea? I'm particularly concerned with textbooks on mathematics. I have this obsession that I should solve all of the problems that a textbook has. It takes a lot of time and energy but usually I'm satisfied with the end result being me having a better understanding of that particular subject.

Any similar experience of this sort? How's this going to work in the long-run?

Answer

It depends enormously on your personal objectives, apart from your personal predilections. For example, if a significant goal is to advance your understanding of mathematics, then obsessing over exercises (many of which are contrived busywork in undergrad textbooks, and sometimes in grad-level textbooks in the U.S.) is a dubious investment of your personal resources.

For one thing, apart from the articiality of some of the exercises, many of them will be semi-incomprehensible if you've just read the chapter they appear after... but obvious after you've read further! A significant reason for this is that mathematics has developed with various goals in mind, so that the most important enduring concepts and facts refer to important phenomena... not just to some artificial choice of linear logical development as is the common style in textbooks.

On another hand, if you do not aim to be a professional mathematician, or if somehow you have a lot of spare time, sure, why not do whatever you want? Indeed, another common trap of studying mathematics is being too obedient about following some syllabus or textbook, as opposed to following one's own curiosity and interests. It is subtler to parse the situation that your impulse is to do all the exercises... :)

Another practical point is that, at some point, probably soon, unless you severely restrict what books you look at, there's no way you'll have time to do all the exercises in detail, even if you are a whiz-kid. There are too many, and sometimes they are prankish. For example, the "exercises" in Atiyah-MacDonald's "Commutative Algebra" (a misleadingly slim volume) are mostly "theorems" one would find in other books on the same topic.

And, then, there's the point that novices' "solutions" to difficult exercises are often severely suboptimal, even if "successful". Sure, it's good to think about issues, but, at the same time, you'll be able to approach those questions far more wisely later (if you still care, and the things haven't become completely obvious anyway!).

But certainly no one is "required" to do all the exercises, despite some propaganda on the internet. For that matter, it is probably not optimal for most peoples' circumstances and goals. Still, taking an extreme stance, maybe the world will end tomorrow, and if you want to spend the evening doing exercises that you find enchanting, I'd be the last one to try to discourage you. :)

publications - "Due to many requests, the submission deadline has been extended" is this real?

following different CS conferences I see the following phrase very often:

Due to many requests, the submission deadline has been extended.

Or something similar to this.

I won't overestimate if I said 80% of the conferences (I have followed) have this attitude. This brings me to the question of whether this is true or people (conference organisers) admit a lie when say this. Why does this attitude exit in CS conferences? Do other fields experience the same thing?

Answer

Warning: personal opinion.

I view conferences that regularly shift submission deadlines as a little suspect. You're right that this happens in CS conferences, and it soon becomes pointless because everyone expects the extension ("Nobody expects the extension!!"). But your estimate of 80% is rather off. Almost none of the (many) conferences I submit to have deadline extensions for submission of the full paper.

And don't underestimate the level of pleading that goes on. People will always ask for an extension if they have even a smidgen of hope that the pleading will work. It's only when a conference takes a firm stand for many years that people stop asking.

writing style - Citation: refer to author or paper?

What is the British English way of referring to a source in-text.

Is it plural because there are two authors, like this:

X and Y (2011) describe ...

Or is it singular because you are referring to a singular source, like this:

X and Y (2011) describes...

So what I am asking is whether you refer to the source or to the authors?

Answer

In literature I generally see references to people much more than to source. When faced with ambiguity, I prefer choosing what sounds more correct grammatically, even if the difference is slight.

In the example above, it should be 'X and Y (2011) describe', because the verb 'describe' would apply to an animate subject (person) rather than an inanimate subject (source). Similarly, demonstrate, suggest, propose, hypothesise would be apt for people.

The source would be better referred to when using 'inanimate verbs' like contains, comprises, constitutes etc.

Examples:

X and Y (2011) propose that trees be considered sapient.

X and Y (2011) contains compelling evidence for trees to be considered sapient.

publications - Mentor trying to be first author?

I was on an internship with professor A at University B in China. We were working on a computer science project. During the internship I implemented professor A's idea and got some results. Three weeks ago I finished a paper draft and left University B for a new internship. Me and professor A were planning to submit the paper draft to a conference (deadline: May 20).

Until yesterday (May 17), the order of authors was: me, professor A, other students & collaborators in the lab... And professor A had no objection with that. However, last night I received an email from him. He said he wants to be the first author... His reason was for intellectual properties and patent issues. My understanding is that because I was merely an intern at University B, if the first author was me, it would cause IP troubles for him?

I feel deceived. But, should I feel like this? I was counting on a first-author paper because I'm planning to apply for a PhD program in the US. One paper may not mean a lot to someone who's published a lot. But for someone who hasn't published yet, it means something.

Looking on the Internet, I found something that might explain professor A's motivations: In China specifically, corresponding authors are often underappreciated by universities and research institues. This might be the case for University B. Given professor A is relatively young, he may want first authorship for promotion.

Summary of my questions:

1. Should I go discuss with professor A and try to persuade him to let me be the first author?



2. If I want to apply for a PhD program in the US, would being the first author be more helpful or being the second author is as well helpful?

Edit:

1. My affiliation for the paper has always been University B. I didn't mention my current university or internship in any sense.


2. I emailed back to professor A yesterday, saying I think I should be the first author, because I did most of the work; because the idea was originated from him he should be the corresponding author. He replied this morning, saying he agree with what I said. He explained that because I was doing an internship in his lab and not a student of University B, putting me as the first author could cause IP and patent troubles for University B... So this problem is fixed now.

Do human populations differ in core body temperature?

Human body temperature is a very complex and tightly regulated system. Hypothermia or fever of only 1-2K (i.e. changes of about 5%) already cause major symptoms and changes of 3-4K (i.e. about 10%) are life threatening. Many humans live under relatively cold outside temperature conditions and maintaining an inside 36-37 degree C in these conditions is very energy consuming (most probably a reason why the body temperature in the periphery is several degrees lower), indicating very strong evolutionary constraints on not changing the core temperature too much (I remember a professor in biology classes in university saying that most fungi have a growth minimum around 37 degree C). However, other mammals have higher or lower body temperatures than humans which suggests that the 36-37 degree C of humans are not a universal gold standard (in mammals).

Probably, for a long time in hominin evolution maintaining the core body temperature was not extremely energy consuming due to tropical conditions. This could have changed during the out-of-Africa migration some 100-60 thousand years ago. Of course this is somewhat difficult assess because early modern humans started to wear protective clothing. In fact, wearing clothes is a most probably adaptive trait to save energy while maintaining core body temperature. Still, it is unclear to me whether physiological adaptations took place as well. Furthermore, there is considerable variation between individuals and also within individuals, the latter in response to environmental conditions and/or behaviour (e.g. exercise), which in principle allows natural selection to change the trait and also shows that slight shifts in body temperature are not harmful individuals.

My question is: Are there significant differences in core body temperature between human populations? Please note that my questions is not why the (average?) human core body temperature has this particular value or why it is different from other mammals or birds.

There is a somewhat related question (also on Skeptics.SE) about lower core body temperature in Japanese people. As far as I know, this difference is rather a measurement thing than a real biological difference, so my question remains unanswered.

research process - How much time do researchers spend on writing grants?

As a potential future researcher I would like to know how much I could focus on my research and how much distraction grants cause. My research interest lie in theoretical cs and logic, however the answers should include other areas so that they may be useful to other readers too.

Specifically, how many hours of your working day on average is dedicated to grant related issues - searching a grant, writing a grant proposal, writing the final report for the funded projects, etc.

I heard in an informal talk that this can be as much as half of the time of the researcher, say 5 hours, Monday to Friday. In such circumstance, I do not think I would be able to focus on the research.

Answer

In my case (pure mathematics) it is about two or three weeks of hectic activity before the October 1 NSF deadline once every 2-3 years. I cannot say that I do nothing else during that time but it definitely distracts me quite a bit. What helps is that we (I and a few my colleagues and friends) often apply for collaborative research grants (so we have well-established separation of labor when writing, which increases the speed noticeably).

The reports are easy if you have something real to show. I would say it takes me at most a couple of hours to write mine. Recommendation letters and reviews usually take much more time.

ethics - How to deal with corresponding authors not sharing submission steps? (E.g. Peer reviews & Decisions)

I am a 3rd-timer postdoc, and I often run into this issue. Over my career I have greatly benefitted personally of responsible peer review and participating in the elaboration of 'Response to Reviews'. Moreover I am very wary of publishing ethics, and open discussion of papers after publication.

This is often what happens: the 1st author of a paper where I am a co-author assigns a PI as last corresponding author. This PI is usually older and actually less invested in the project, but wishes to handle the submission. This person will however not share any correspondence with editors or submission files with authors other than the first (and I suspect even then not in full). I am thus left in the dark about discussions over papers where quite often I made a major part of the writing and experiments, and the only specialist about core topics being discussed.

I have tried asking for the details of peer review and was ignored, every time this happened. On a most recent case I received editorial notification of submission of same paper from two different journals within the time span of just 5 days, and now I fear somebody pulled a duplicate submission! This kind of attitude has made me reluctant of handing the position as corresponding authors to others, particularly to PIs, which is politically not good.

Thus I ask: How do others deal with such a situation?

UPDATE 1 (24.01.2018): I have just sent an email to the PI politely asking again for the peer reviews stating I will follow up with the journals if there is no reply.

UPDATE 2 (25.01.2018): First author responded informally providing the dates of all submission and general reasons for two rejections. The details didn't really add up, but given a casual tone perhaps it wasn't precise (e.g. I suspect this person is not aware of the difference of editor x reviewer). I still asked again for the Reviewers reports, and was left with the impression the 1st author did not (care to) see them either. She said she'll ask the PI.

In case I get no response I am not sure on how to proceed (e.g. if I want to see peer review from a previous journal).

Answer

I have decided to post my final update on this as answer to anyone arriving here in the same situation.

The following line of response worked: I have written a formal email (in English, which is not our language of choice for communication) to the first author and PI asking again for the results of previous submissions and to be duly warned of future submissions. I implied (by stating I could just contact the journals but 'felt that was the role of the corresponding author') I'd contact journal editors if ignored for more than 5 days.

Within less than 12h the first author responded informally describing generally what had come out of previous submissions. I still asked (informally) for the peer reviews and she said she had to ask the corresponding author for it (PI, last author). By that I understood this 1st author had also not seen the result of peer review, and told her this was not fair on her as well.

Finally after 5 days the PI contacted me formally, and in English (unexpected because it is not easy for him to write in English) excusing for the time taken, informing any future submissions would be correctly reported, and attaching the results of previous peer reviews. I am formally thanking him for the attention given.

I cannot say how the PI feels about this (I now live on the other side of the planet) nor whether there will be further collaborations. Whatever the reasons, his response was appropriate, thus I am recommending this line of action. On a personal note, I would not have escalated this to the journal editors unless I was sure there was something else out of place.

Thanks to all for the suggestions given.

cell biology - RNA or ribosome, which one moves during translation?

During translation ribosomes decode the genetic information present in the mRNA and protein synthesis takes place. During this process which of those two does move, the ribosome or the mRNA?

human genetics - Initial population when i count backwards?

My question is dealing with how many ancestors it took to produce me:

• --> to produce me it took 2 people (my parents) = ($2^1$) people = 2


• --> one generation further included = ($2^1 + 2^2$) people = 6


• --> in the past 500 years my pedigree chart contains 15 generations, so $2^{16}$ people = 65.532 people to produce me (-2 to be completely correct)


• --> when i calculate back to 35.000 year ago I get a larger number *)


• --> when i calculate to all humans 2.400.000 ago I get a ridiculous large number *)



• --> when i include up to all mammal grandfathers and grandmothers 60.000.000 years ago the total number takes pages to scroll *)

*) see: http://ed.je/2L6 for the actual numbers did not want to clutter here.

*) I took 3 generations per 100 years to let the numbers be small as possible.

So, I think I'm making a mistake somewhere. Only I don't know where: to create a child you need 2 parents. And to create a parent you need 2 further parents. But somehow calculating back to "all mammals" just related directly to me would mean $2^{1.800.001}$ mammals walking around 60 millions years ago being my direct predecessor back then.

So where am I going wrong? Somehow I can't figure out where my error lies (I've not studied Biology though).

I visualize a pedigree tree (reverse pyramid) starting with me and then logically each parent needs to be born out of 2 other parents just calculating my way up.

Answer

Your calculations are the following. Assuming non-overlapping generations, the number of ancestors you have in the last $t$ generation is given by:

$$\sum_{i=1}^t 2^t$$

This sounds correct. But there are some very strong assumptions:

• 
  

  Generations are non-overlapping. A more realistic model would need to consider $t$ as a continuous variable a give a probability of reproducing which depend on the age of the individual.

  
  


• 
  

  Never two related individuals mate together. Otherwise, you paternal grandfather might be your maternal grandfather. In reality we are all somehow related, we have a common ancestor (Hey Bro). For example if you consider that your parents are siblings and that their parents are siblings and so forth… then you don't need more than 2 great-great-great-great-grandparents. In order to keep track of such events (inbreeding), you need a stochastic model and you would need to know the population size $N(t)$ as a function of $t$.

  
  

Tracking the change of population size through time is part of a very big in biology which is called population biology. For example you will find in this post a model of population growth of two interacting species (prey-predator)

etiquette - How frequently can you ask for a personal reference without being disrespectful?

When applying for post-doctoral and faculty positions you are typically asked for three (sometimes more) reference letters to support your application.

Given that it is competitive out there, it also makes sense to apply for all positions that are good matches to your qualifications and career development goals (in the case of post-docs).

Sometimes this may mean asking for several reference letters (or pre-application "can you support me if required?" requests) in a short space of time.

Also, there may only be a small pool of people (i.e. 3 or 4) who know your work sufficiently well to give an excellent reference.

I have also been told that referees want to help you out, and that there is no reason to fear asking them. And, that in many cases once a letter is written it can typically be quickly repurposed. But there must be a breaking point.

How do I manage this without being disrespectful? How many requests in a given unit of time is too many, or harms my credibility? I am asking this question in this forum, as I am interested in the norms in the academic world, which are often somewhat different than the rest of the working world.

graduate admissions - Course of action after failing a (non-maths) course in hopes of entering grad school for maths?

I'm currently a second year student in a general science program with a specialization in mathematics (it's kind of like a double major, almost). I'm hoping to go to grad school for combinatorial optimization, operations research, or some other pure math stream. The problem is, I failed a cell biology course this semester (that just ended).

There are no medical reasons as to why I failed, just a matter of poor judgement when it came to choosing courses (I took an extra course than needed - the cell bio one - so that I could get it over with and take a computational biology course next year which requires this cell bio course), as well, I'm part of a major faculty society at my school and I'm doing research (non-math) with a group. All these factors lead to cell bio being my last priority and to sum it up, I have a U (0) in it, because I didn't pass.

My question is, how will this look on my grad school application? Overall, I'm a good student, I had about a 3.8 cgpa last year and at most I think this will bring it down to about a 3.4-3.5. I'm sure the next few years I'll do much better in my courses and can hopefully bring my cgpa back up to it's original glory, but for now I'm kind of at a loss as to what to do, especially given that there isn't really anyone to talk to at my school (Canadian) about maths grad school (I went to see an adviser and was told I'd get an email with some helpful info, but haven't received anything yet). I am going to write the GREs and hopefully do well in that and I'm considering taking the Putnam to further enhance my application.

I'm very sorry if this is a duplicate of a question, but so far, people have had different (I'd think more severe) circumstances, i.e. medical, failed course was taken as a high school student, etc. If anyone was in a similar situation or have dealt with this and could help me out, I'd really appreciate it. Thank you!

interpersonal issues - What can I do if a student in my lab threatens to tell lies about me, and my advisor doesn't want to fire her?

I'm doing my Masters right now and I am a new lab member (I've been there for just 4 months). A undergrad student didn't like it when I told her to follow biosafety rules when handling dangerous chemical reagents. So by e-mail she said she would tell our advisor lies about me and that he will believe in her because she's there for 2 years and he likes her, and I am a newbie.

I took that issue to the advisor, who read the e-mail that she sent and he was 100% supportive of me. However, they used to go the same church and he either pities her or really likes her, I don't know. Then he asked me to forgive her. But I can't, I can't even look her in the face anymore. I think she's evil and mean: she even told me I'm making my own grave and would spread lies about me to him. Now he knows the truth about her, but I think their personal relationship is blinding him. He should fire her! But he wants her there, so...

I don't want to change labs because I really like my PI. How should I deal with this situation?

She and I will have a one-to-one meeting next week, and my advisor told me she will apologize to me in that meeting, but I'm still worried she can sabotage my experiments in the future. We are not in the USA.

UPDATE: I had another conversation with my PI today, and he's dealing with this situation as "teenage fighting" - his words, not mine. He's being complacent about all of this and laughs about my worries and insecurities. He does not think that abusive and threating language from a student to another to be a big deal.

Religion plays a big role here I guess. He does not want to fire her in ANY hypothesis. Same religion; knows her parents and so on...

I really really like him, but I don't know if I do anymore. I think he's not providing a safe mental health environment for me...

He was too perfect to be true...

UPDATE 2

She lied, lied and lied again and it blew up on her face! Now, ALL* lab members wanted her to go. The PI cut her funding, and she finally left our lab! Now we can live at peace, right? Not so fast...

*She has a friend (just one - and also an undergrad like her) that is still here. And he's full of revenge! Another sociopathic liar. Sabotage is being a big issue here. All mice from a PhD student were found dead inside their cages. We cannot prove anything, but they had a fight two days earlier... Also, controlled drugs are now missing, and my PI is being once again complacent about it. I can denounce him to our correspondent DEA, but it could backfire somehow, I don't know. He still likes me, but I don't think I like him anymore. Actually, nobody in our lab trust him anymore.

Answer

She has been mean to you, not the PI. He clearly signals that he likes you and your work. You say that he also realises she has an immature attitude. I think that you are in a good position here, unless you mess it up.

The superviser clearly sees the situation and - in veiled form - tells you to be the mature part of the interaction. When he tells you to forgive her, that's very clearly what he means. In short, at this stage, you have to show maturity. Clearly, you need to work on that (I quote your response: "Hahaha...." - SE is not the place for such formulations).

You should not worry too much to prove that she lies about you, as the superviser made very clear that he will not pay heed to her stories about you (why otherwise would he have emphasised that you are one of the brightest students he had?). He has sent you a clear message of confidence.

Whether he likes her or not, you do not know, but it seems very clear, even through your report, that he takes pity on her. He will not fire her; it is not your job to make him do so. He also will not remove you, unless you decide to go. He seems a very reasonable person.

As for her using threatening language, you have a number of options: when she does that, you ignore it. Or else, you find a reason for yourself to go away, without responding, to some made-up excuse (for yourself), such as the bathroom. Or else, you respond: "This is not the place for threatening language. Please refrain from such language, it is inappropriate to talk like that to your colleagues." - or something along those lines. In a cool, calm, and collected manner. If she indeed has the maturity of a 12-year old, she may not absorb the words, but she will absorb the tone.

She presses the buttons where she sees an effect in. If you signal to her that you have no business with her, and that you are unaffected by her threats, you will become an uninteresting target.

Forget about winning/losing. You just do not have to play her game, you decide which games you play, and which ones you don't.

Bottom line: stay away from her; relax, the PI trusts you; and follow your maturity level and do not let yourself be dragged down to hers. She is not the one to set the agenda, your PI is, and he unambiguously signalled his trust in you. When he sets the meeting, if she apologises, graciously accept the apology (even if you do not believe in it, take it at face value), but still stay away. Her safety procedures are not your business anymore - you have made your case.

physiology - How are long time periods measured in biological systems?

Biological systems are pretty good at measuring fairly long times, for example, menstrual cycles (month), or puberty (years). Counting days or years seems to be implausible, and chemical concentration also seems implausible. What are the physiological processes that are involved in keeping track of such long periods? Is it just a long sequence of finite state changes?

I understand there are environmental correlates such as seasonal changes and relative position of celestial objects to measure the relative time, but regardless of these external cues, I suspect that a pretty good internal clock for longer time scale could exist. For example, the time to menopause can actually be thought of as a counting mechanism of a shorter clock which is the menstrual cycle. But, how does the body know when to stop growing? I cannot think of biological processes with such long time constants that is stable.

Answer

The short answer is: we do not know exactly, although we do have some insights.

I will take the example of puberty.

Although a clear definition of puberty is lacking, it is quite clear that it corresponds to a period where gonadal function starts.

This, in turn, is derived from the activation of the gonadotropin system, which consists of two main cell types:

1. 
   

   a small number of neurons located in the preoptic area of the hypothalamus (a nucleus at the base of the brain) called the GnRH neurons. GnRH is the Gonadotropin-releasing hormone, a small peptide that stimulates the production of gonadotropins from the pituitary.

   
   


2. 
   

   the gonadotrophs, a specialised group of cells in the pituitary (a gland located underneath the brain) which produce two hormones, called luteinizing hormone (LH) and follicle-stimulating hormone (FSH) which stimulate the gonads to produce various hormones, such as estrogen.

   
   

In mammals, the secretion of GnRH, and thus LH/FSH varies during the course of the menstrual/estral cycle. This cyclicity lasts several days (4-5 days in rodents, ~1 month in humans) and entrains the cyclical secretion of estradiol (E2) from the gonads.

Note that this is a sort of self-sustaining cycle, as cyclic levels of E2 will then allow for cyclic GnRH secretion and so on.

But, back to your question: how does the GnRH/LH/E2 system "wake up" at puberty?

The exact mechanism is still unknown, but recent work has found an important mediator, called kisspeptin, that is produced from two population of neurons in the hypothalamus, called the kisspeptin neurons.

Kisspeptin has been shown to be a very potent activator of GnRH neurons and work in the mouse has shown that these neurons appear at the time of puberty, their number increasing dramatically between 25 and 31 days (puberty is at around 30 days in mice).

Postnatal Development of Kisspeptin Neurons in Mouse Hypothalamus; Sexual Dimorphism and Projections to Gonadotropin-Releasing Hormone Neurons - Clarkson and Herbison - Endocrinology, 2006

Similar work exist in the monkey: Increased hypothalamic GPR54 signaling: A potential mechanism for initiation of puberty in primates - Shahab et al. - PNAS, 2005

In humans mutations in either kisspeptin, or its cognate receptor GPR54 results in disturbances of pubertal maturation because of underactivation of the system (hypogonadotropic hypogonadism) or hyperactivation (precocious puberty).

So, now the question is shifted: why do kisspeptin neurons show up only at puberty? We don't know for sure, but it looks like increased levels of E2 could be important for this.

Again, we get into a self-sustaining cycle. Growth of the body generates an increase in E2 production (possibly due to increased volume of the gonads?), which, when over a certain level permits the development of kisspeptin neurons, which will then stimulate the GnRH neurons, resulting in increased LH and E2. We then have more E2 and this makes kisspeptin neuron grow even more etc etc.

From: Postnatal development of an estradiol-kisspeptin positive feedback mechanism implicated in puberty onset. - Clarkson et al. - Endocrinology, 2009

teaching - A few students requesting to cancel lectures due to their personal reasons. What should I do?

I give lectures to postgraduate students. The number of students in this batch is very low (< 20). The lectures are foundation lectures for the course. We are only into the basics of the course.

A few (maybe 4) students of this batch are requesting to cancel two lectures as they won't be available for personal reasons. In fact, they are going to attend a workshop. In my university, attending workshops that are not fully recommended by the department is considered 'personal interest'.

One option is to ignore their request and ask them to study the topics covered during the lectures or with the help of students present during the lectures. If they could study these topics themselves or with friends, they wouldn't have requested me to cancel these lectures.

What should I do in this case?

I could ask this question to my head of the department, but, I don't know how this will turn out for students. They should not feel that they were not allowed by the head to attend this workshop.

I do understand that there will be variations of opinions on my question as per the different academic rules of universities but I still want some insights from experienced academicians.

Answer

If you do this for a minority, then you will have to do it every time a few students have some excuse.

I suggest that you don’t consider this and make it clear that if they miss lectures then it is up to them to catch up on material.

Providing double or triple repeats of lectures due to a few absences, especially if unpaid, is not a good use of your time.

Some students will want to rationalize their choices and make sure which they attend - some workshops can be valuable. If you think one workshop is very worthwhile then you could consider re-scheduling for all, but that depends on your schedule, and yes, I have done this for similar reasons involving the majority.

Based on a comment> I always provide the material used in class - notes & worked example on Moodle as well as further practice problems (some 10 to 20 for each topic with solutions) for those who attend as well as those who do not.

Master's thesis results used to publish a new research paper?

few years ago I did my Master's thesis at University, when I worked in a lab and was performing various experiments on different materials. The thesis defense I held officially in front of commission, and the thesis is available on Internet.

As I was looking for some research papers, I discovered that there is this new publication, which uses the results I got during the experiments, as well as few other Master student who worked on their thesis. Our names are mentioned at the end, where authors are thankful for our assistance. I have two questions:

1. Is is possible to use and publish results which were actually already part of someones Master's thesis?


2. If these results of experiments were used in the new publication, is it right just to mention names of persons who performed them, and not putting them as co-authors?

Thanks!

application - Reapplying to same PhD program after one year, should I state I applied the previous year?

I was wondering if someone who is reapplying to the same program after it was not accepted the previous year is seen as a negative thing.

If in the application form I am asked if I applied the program in the past, should I state that I did or would that look bad on my application?

Why is this question been asked? And does not really matter what my answer is? The university clearly states that all application material is destroyed after a few months. Thus the admission commitee look at this question?

Answer

Lying on an application form is a really bad idea, it would probably destroy any chance you could have to be accepted. So, if the question is asked, you probably should answer truthfully.

As for why it is asked, it also depends on how a program works. If it's a very competitive program, maybe your application was good, but there were just better candidates than you. In that case, it could be worth applying again. If, on the other hand, the committee just decided that your application was not good enough, then applying again is risky. In any case, you would have to demonstrate that you have significantly improved your application during the last year.

evolution - How did people's liking of ceremonies evolve?

Habitual group activities are prevalent across many animal species, particularly in mammals, especially in primates.

However, I do not see any evolutionary benefit of this. 'Ceremonies' take time, and in many cases seem to exert more energy than they reap. Note at this point I am not talking about hunting groups, but rather about group activities that serve a purely social purpose (mourning is a good example of this and is present in elephants, chimpanzees, bonobos, and probably more). This costs significant amounts of resources, time, and energy which apparently could be better spent hunting, foraging, traveling, mating, or grazing.

I'm interested in finding a timeline, and explanation, of why and how this phenomenon of higher social rituals (perhaps using mourning as an example) evolved throughout the mammalian kingdom.

A cursory google revealed nothing about how this 'liking' of interaction evolved.

graduate admissions - How to respond to an unofficial PhD offer?

I applied to 10 schools and have heard formally from 3, 2 rejections, 1 admission. I just received an email from another school (a very good one) saying that they are seriously interested in me, but would like to know if I am still interested in them. While I am very interested in this program, which is in my top 4, since I have not heard from the other 6 schools, I am not ready to make a decision. Does saying yes now mean I am committed to accepting their offer?

graduate school - Grades in a PhD program

I am a math grad student who has completed the qualifying exams within my first two years. Lately, I have been taking a few non-core courses, which allows me to put most of my time on my own research. In one of these non-core courses, I received a low grade: B-. I certainly have the a good Cumulative Grade Point Average: 3.9 -- well above what is required for "normal progress".

Question: How important/serious is getting a grade below 3.0 in this one course at this point in a PhD program? Any feedback is much appreciated.

phd - Does improving systems count as “research experience” in grad application?

Like What is exactly meant by “research experience” in grad application? but situation-specific:

• 
  

  Between graduating master's in 2016 and applying now for PhD admissions for 2018-9, I started teaching maths at a branch of a company that is something like Kumon.

  
  


• 
  

  During this time, I looked up Google Sheets and SQL programming to learn on my own supplemented by my experience with Excel in master's and then created paperless spreadsheet templates.

  
  



• 
  

  I wasn't guided, instructed, requested or paid to do this, but I did improve processes at work.

  
  

Could said looking up then creation count as "research" ? If so, how? If not, why?

From other post:

As a rule of thumb, the more that what you did was something other people could not have done

Additional comments based on aforementioned:

• 
  

  Well I think what I did would've been pretty simple for a/an CS/Engineering/IT/ICT person but not just any employee in my company could've developed the paperless systems I made.

  
  


• 
  

  Also, the IT department in my company didn't for reasons I guess I'm not allowed to disclose.

  
  

Answer

No. Research is working towards creating new knowledge (not just knowledge that you didn't have, knowledge that is genuinely new to experts in your field, too) that advances the state of the art in your field.

Programming/IT/engineering work is not research, unless it is undertaken to create new knowledge.

Examples:

• Writing code to simulate a physical system, so as to answer questions about its behavior that have not been addressed yet, is part of doing research.


• Writing code to implement a new kind of wireless communication system, so as to evaluate its performance, is part of doing research.


• Writing code to help me organize my students' homework submissions is useful work, but it's not research.

career path - Pros and cons on working in an industrial research lab without a PhD

I am from engineering, and I would like to know if I am able to find a job in industrial research lab after finishing my master, will there be any advantage or disadvantage compared with entering the same lab after finishing PhD? Possible advantage may be that I have more industrial experience as I enter the lab earlier, and possible disadvantage may be that without a PhD position I cannot be promoted to certain senior positions or lead a project. Are these true? Are there more advantages or disadvantages for this?

Answer

For many research positions in industry, a PhD is a requirement to apply for the job. With just an M.S., you simply cannot be considered for these positions. Some research jobs I have seen in industrial labs are available to candidates with either a PhD or an M.S. with several years of industry experience, but I don't see as many of these.

Industrial research labs often also have non-research positions (e.g., staff programmer) that do not require a PhD. However, these positions tend to not be on the research "track": you cannot easily be promoted from "staff programmer" to "junior member of technical staff" in many companies. If you are interested in doing creative research, staff programmer jobs are not a direct path to research scientist jobs.

Smaller companies tend to be more flexible, so that it may be easier to get a research job without a PhD in a tiny company than a large global one.

Of course, this can vary by industry and geographic region. (My experience is in the field of telecommunications and computer networks, in the United States.) You can find out more about your particular field of interest by going to the "Careers" page of the labs you are considering, and looking up the requirements for the jobs that you would like to do.

However, as a rule, if you are interested in doing creative research (and not just working in a support position in a research lab), you will have more opportunities available to you with a PhD than without one.

graduate admissions - Is a letter of recommendation from an employer useful, when the company has shut down?

I worked for a while with a company developing software, at which I also used mathematics (my field of undergraduate study) often. I was close with my employer until the company shut down, but we still keep in contact every so often.

When applying to master's programs, alongside the normal letters from my undergrad professors and research advisor, would a letter of recommendation from this employer hold any weight? I know he could write a very positive one, but it would be more concerned with work-effort, attitude, etc than anything academic.

Answer

There are quite a few issues to be careful about when considering a recommendation letter from an employer. Some examples:

1. Make sure they understand the culture of academic recommendation letters. In industry, lots of the time recommendations are more-or-less a token statement that someone worked for you and didn't cause any issues. Academic recommendation letters are very different, so make sure they have an idea of what kind of letter to write.



2. What exactly is the background of your letter writer? This is a bigger issue with PhD (or research-based masters) recommendations, but if your recommender doesn't have the background or credentials to understand what it takes to become a successful researcher or academic, then it's unlikely that they will be able to speak intelligently about whether you have those traits.


3. How common are industry to graduate school moves in your field? In a field like mathematics or physics, my guess is that most candidates do not have significant work experience and any work experience is usually far removed from the subject material. In a field like that, the people evaluating your profile are more likely to discount an industry recommendation, especially if it comes from a non-PhD, non-researcher. On the other hand, fields like business or engineering have many more applicants from industry and are probably used to seeing those recommendation letters, so it is unlikely to put you at a significant disadvantage.


4. How well are your other bases covered and what are your alternatives? If you have recommendation letters that already focus on your undergraduate classes and research, then it may be more valuable to have a letter describing traits you exhibited in the workplace than another "he got an A in my class" letter.

In general, an employer's letter is never going to be as good as a great letter from an active researcher that you worked closely with. But most applicants don't have three of those on hand. Can a letter from an employer be useful? Definitely. Given the alternatives, is it the optimal decision for you? It's possible, but that depends on a lot of factors that you should probably spend some time thinking about.

peer review - Do you list journals you have reviewed for on your CV?

Is it acceptable to list the journals you have reviewed papers for on your CV? Is it common? Do you think it’s recommended?

On the one hand, it shows that you are engaged in this necessary part of scientific research that is peer-review. On the other hand, it sounds a bit useless, because everyone actually reviews papers for journals, and it is actually an unverifiable information (reviewers are confidential).

Answer

On the one hand, it shows that you are engaged in this necessary part of scientific research that is peer-review.

That's one of the major reasons why people list it. If your CV is being viewed as part of a performance review or hiring decision, or even for awards, this constitutes "service to the community" and indicates that you're a good citizen.

It's a noisy signal for the reasons you indicate, and so it doesn't carry a whole lot of weight compared to things like technical committee memberships and leadership roles, but it's part of the larger picture. Moreover, for more junior researchers who haven't yet had the chance to take on leadership roles, this is a good signal of service.

physiology - Is there nutrient absorption in the large intestine of hindgut fermenters?

In hindgut fermenters, plants are digested in the caecum by microbes. I want to know whether hindgut fermenters can absorb the nutrients obtained from the digestion in the large intestine because the absorption of digested materials is not the main function of the large intestine in other animals. I know some hindgut fermenters reingest the materials created in the caecum, but I think not all hindgut fermenters perform this behavior. I want to know the main site of absorption after the caecum.

Answer

I have divided this answer into a section on horse and rabbit. While there are many other hindgut fermenters, these species are good illustrations of different ways hindgut fermenters can digest and absorb nutrients from their food.

Horse

As you know, absorption of "nutrients" occurs along the intestines, but at varying degrees at different sites. Most compounds are primary absorbed in the small intestine of the horse. This includes protein, glucose (soluble carbohydrates), fats, calcium, and magnesium.

Any carbohydrates that are not absorbed in the small intestine reach the hind gut. Here they are fermented by bacteria to short-chain volatile fatty acids (VFAs) and lactic acid. Horses can use the VFAs (propionate, butyrate, and acetate) as an energy source, but a diet too high in grain can also lead to excessive lactic acid production in the hindgut, and as a result the horse may experience colic. As your question pertains to the hind gut, a nutrient of main concern is therefore volatile fatty acids.

The hindgut of the horse is very long and developed. To review with the anatomy of the horse hindgut, it consists of the caecum, ventral colon, dorsal colon, transverse colon, descending colon (or small colon), and rectum.

In a study in 1974, RA Argenzio et al. determined that among the parts of the horse hindgut, most VFAs were produced and absorbed in the ventral colon, 8-12 hours after feeding. This is depicted by the graph below, which shows a large negative net production of VFAs after 8-12 hours (i.e. more VFAs absorbed than produced). Note that the caecum and dorsal colon are also important sites of VFA production and absorption.

The hindgut is also an important site for phosphorus absorption in the horse, unlike many other species that primarily absorb phosphorus in the small intestine. This is thought to be because most of the dietary phosphorus in the horse in phytin phosphate, which must be exposed to the enzyme phytase produced by the microbial flora in order to be absorbed. Studies such as Schryver et al. (1972) and T. Matsui et al. (1999) have shown that most phosphorus is excreted by the small intestine and caecum, and most is absorbed in the dorsal colon and small colon. The figure below from Schryver shows the net absorption of phosphorus on the various experimental diets. Note that this is oriented opposite to the VFA figure above; absorption is positive rather than negative on this graph.

---

Rabbit

To begin with the rabbit anatomy, you will note that the colon of the rabbit is much less developed than that of the horse. However, both are hindgut fermenters, and what they do have in common is a very large caecum.

As in the horse, much of the digestion and absorption of nutrients occurs in the small intestine. This includes protein, fats, and simple carbohydrates (glucose), as well as some vitamins.

Also like the horse, the digestable material not absorbed by the small intestine passes to the caecum, where it undergoes fermentation by the microbial flora. The large fibrous material passes directly to the colon, where water is absorbed and forms hard faecal pellets, while the small digestible material passes through reverse peristalsis into the caecum. What is different in a rabbit to a horse, however, is that the about 8 hours after feeding, the caecal material is packaged into a small pellet called a caecotrophe. As or shortly after the caecotrophe is excreted, the rabbit re-ingests the caecotrophe. As this food has been digested once already, the small intestine is better able to absorb nutrients from it.

As an example, important nutrients that are able to be absorbed due to caecotrophy in the rabbit are the B vitamins such as niacin, riboflavin, folate, and cobalamin (vitamin B₁₂). One of the early studies on this topic is Kulwich et al. (1953).

Summary

The reason for the difference between the horse and rabbit is fundamentally an anatomical difference. Both species have a large caecum which enables fermentation of plant matter. However, the horse has a long, voluminous colon in which it can absorb many nutrients, but they will lose protein and other nutrients in this process because the colon is less adapted to absorb them. In coprophagic (rat) or caecotrophic species (rabbit), they do not have as long a colon, but can absorb vitamins and proteins lost in the faeces during the second pass through the gastrointestinal tract.

An excellent and very detailed review of the gastrointestinal tracts and nutrient absorption in a variety of species is this freely accesible paper by Stevens and Hume, "Contributions of Microbes in Vertebrate Gastrointestinal Tract to Production and Conservation of Nutrients."

References

Argenzio, R.A., Southworth, M., and Stevens, C.E. (1974) Sites of organic acid production and absorption in the equine gastrointestinal tract. Am. J. Physiol. 226:1043-1050.

Bugaut, M. (1987) Occurence, absorption and metabolism of short chain fatty acids in the digestive tract of mammals. Comp. Biochem. Physiol. 86B(3):439-472.

Hornincke H., and Bjornhag, G. (1980) Coprophagy and related strategies for digesta utilization. In Digestive Physiology and Metabolism in Ruminants, 707-730. Avi Publishing, Westport, CT.

Kulwich, R., Struglia, L. and Pearson, P.B. (1953) The effect of coprophagy on the excretion of B vitamins by the rabbit. J. Nutr. 49:639-645.

Matsui, T., Murakami, Y., Yano, H., et al. (1999) Phytate and phosphorus movements in the digestive tract of horses. Equine Vet. J. Suppl. 30:505-7.

Schryver, H.F., Hintz, H.F., Craig, P.H., Hougue, D.E. and Lowe, J.E. (1972) Site of phosphorus absorption from the intestine of the horse. J. Nutr. 102: 143-148.

Stevens, C.E., and Hume, I.D. (1998) Contributions of Microbes in Vertebrate Gastrointestinal Tract to Production and Conservation of Nutrients. Physiological Reviews, 78(2):393-427.

evolution - Variations in Genome Sizes

Why is there wide variation in genome size amongst groups of protists, insects, amphibians and plants, but less variation within groups of mammals and reptiles?

Answer

You're asking about the C-value enigma, in particular this kind of diagram:¹

The quick answer is that there is no "why" in evolution; things happen and if they're beneficial they tend to stick around more than the deleterious things. The longer, (slightly) more satisfying answer is non-coding DNA. Thanks to non-coding DNA the size of a genome doesn't even correlate to the number of genes. The human genome, for example, has over 20,000 genes but is less than two percent protein-coding; the flower Utricularia gibba, however, has over 28,000 genes with about two orders of magnitude smaller of a genome, due to the fact that its genome is 97% protein-coding. In short, there is no real meaning to be found in genome size variation due to non-coding portions, which while they are sometimes important regulators can often be just transposons (40% of our genome). I will also point out that all of those groups you mention have species with significant polyploidy.

---

The are a number of other interesting ideas. In the process of researching this, I stumbled upon the Animal Genome Size Database, which is an absolute gem of a treasure trove. It's an unbelievable mine where I've spent a good half-hour just reading. In particular, the statistics pages list interesting correlations for certain groups. Mammalian genome size, for example, correlates:

• Positively with red blood cell size, despite lack of nuclei


• Negatively with metabolic rate


• Not at all with developmental rate or longevity

For amphibians, however, there is:

• Positive correlation with red blood cell and nucleus sizes in both frogs and salamanders


• Negative correlation with developmental rate in many groups


• Negative correlation with brain complexity in both frogs and salamanders



• No strong relationship with metabolic rate in either frogs or salamanders


• Some association with intensity and frequency of metamorphosis

If you have time, I highly recommend reading through T. Ryan Gregory's PhD thesis entitled The C-Value Enigma. It's around 350 pages, but each chapter is in separate pdfs and is the most in-depth treatment I've seen, despite being about a decade old. It's been moderately life-changing for me to read, some of the interpretations he presents challenged my thinking on the subject of genome evolution entirely. Should genomes be treated as individuals, and what would that mean? I digress. Chapters 3, 4, 6, and 7 are what you'll want, in particular the last twenty or so pages of chapter 7.

Dr. Gregory now has a faculty position and his lab's research page is a little easier to read. I love this image:

As genome size increases in eukaryotes, the percentage of the genome composed of genes (white circles) becomes smaller. Conversely, the percentage of the genome made up of transposable elements (black circles) increases with genome size.

It seems like the best way to look at genome size and find some meaning is within a specific group. There are correlations, for example, that are present in frogs and salamanders, but not in either group alone. Some of the groups are very unbalanced; in insects, only Orthoptera tend to have very large genomes. Interestingly, a number of those groups also undergo some form of metamorphosis, but the correlations aren't what you might have expected: insects that develop quickly and metamorphose have smaller genomes, but "[i]n a more general sense, small genome size seems linked to rapid diversification... Conversely, insects without metamorphosis may possess very large genomes..."

publications - What should I do, as my submitted paper is still under review after 1 year?

I'd just submitted a manuscript to Robotics & Autonomous Systems Journal on Mar. 1st, 2015. Right after 1 month, its status changed to Under Review. I just waited up to Jan. 2016 and send a letter to editor-in-chief to clear the status of the paper and any potential problem due to this delay. He did say this after that 10 months!:

you are right with your criticism. However your paper deals with research topics, where only a few of roboticist are familiar with. Hopefully we can get now the final required review. Sorry for the inconvenience.

Now, 2 extra months are passed, yet the paper's status is still Under Review.

They should have considered responsibility regarding the case. They could easily announce us about their inability to find any interested reviewer for the manuscript, and we would find the other journal. I'm frustrated a little bit. As a matter of fact, I am reluctant to withdraw the submission as they have wasted my time, NOTICEABLY, over the last year. I wonder if they have completely neglected it.

Is there any way to handle this case, and ask them POLITELY and REASONABLY, leading to the finalization of this manuscript's situation?

Thanks

Edit: After 2 weeks from sending an email to the editor about the manuscript, he has not still replied.

Answer

I'm in a different field, but had a similar situation. I got a paper published in a journal in a matter of 6 months (submission to publication), then followed with another paper a month later. That paper was in review without notice for 6 months. After two unanswered emails, I politely asked for a decision on publication such that I might submit elsewhere if publication wasn't likely. This prompted them to respond that they were having trouble locating reviewers and asked for a list of potential reviewers. I received my reviews for the paper about 2 months later. It seems that if you suggest you might pull the paper and submit elsewhere, it may open a more honest conversation!

united states - Do they really mean "in all areas" and "will continue to be accepted until..." in Computer Science faculty opening ads in the US?

The following is an extension of the question Job applications reviewed "until the position is filled" (i.e. soft deadline): What does that really mean?.

In most US job announcements of faculty openings (of any rank) in computer science I've seen no hard deadlines for applications and no hard subdiscipline designations. (In Europe, this is different: the deadlines and the subdiciplines are typically hard restictions.) Most of the time, we see sentences such as

The search will focus on candidates in the areas X1, X2, and X3. However, outstanding candidates in all research areas will be considered.

and

Preference will be given to applications submitted before Date Y, but we will continue accepting applications until the positions are filled.

Wee see such phrases way too often and may consider them boilerplate in the meantime.

1. 
   

   Does the search team actually sometimes look at applications outside of the mentioned areas (X1, X2, and X3) and at the applications submitted after the deadline? Or are the above phrases introduced for some other reasons (legal, politics, ...), and the search team never looks at anything beyond the mentioned subdisciplines or anything past the deadline?

   
   


2. 
   

   Has anyone already been hired despite being outside of areas X1-X3 or beyond the date Y?

   
   


3. 
   

   In practical terms, if the applicant is a normal scientist but has missed the deadline, how long after that he/she should apply?

   
   


4. 
   
   

   In practical terms, if the applicant is a normal scientist, is on time, but the subdiscipline is slightly off, should he/she still apply?

   
   


5. 
   

   In practical terms, if the applicant is a normal scientist but the subdiscipline is slightly off and the deadline has passed, how long after that he/she should apply?

   
   

(An aside: Assume that the applicant cannot get this information directly by asking, e.g., due to the absense of contact data, and that the applicants network, including that of the supporting advisors if there are any, does not cover the location.)

This question seeks answers from folks who have participated in search committees, have supervised their work, or have received feedback as applicants. If it is the case for you, say so.

ethics - Who is responsible for detecting plagiarism in a PhD thesis?

Background I am asking this question in the context of the long running plagiarism scandal in Germany.The most prominent victim of the scandal of plagiarized doctoral dissertations by politicians was former defense minister Guttenberg. His doctoral title was withdrawn, and he resigned from his position. He was followed by several other politicians, and now even the German Education and Research Minister Annette Schavan is under suspicion of plagiarism.

The interesting thing is that for all these people, the plagiarism was detected only due to plagiarism detection wikis like VroniPlag and GuttenPlag, where ordinary people compared these doctoral dissertations with other published work. The only role of universities has been to respond to allegations that are especially well documented and have caused a reasonable amount of public uproar.

Don't the Universities themselves bear any responsibility for letting this plagiarism go undetected? In fact Guttenberg's dissertation was awarded a summa cum laude. It appears as if their is no mechanism whatsoever (at least in German universities) to detect academic fraud.

Is there any mechanism at all to detect plagiarism or fraudulent research in PhD dissertations (doctoral theses)?

I understand that there are probably country based differences and my experience is primarily with the German system. Still it would be good to know the seriousness with which academic fraud is taken in different countries. This appears especially pertinent to the maintenance of the credibility of academia in general and doctoral degrees in particular, and yet there seem to be no checks whatsoever!

Answer

The problem is that the PhD system is designed for people who intend to become researchers. For these cases, plagiarism is not at all a common problem. You are expected to published your research, and you will not have a successful career unless it is widely read and cited. That gives lots of opportunities to get caught, and the penalties for plagiarism are a huge deterrent.

To the extent you find plagiarism, it's generally people who do not want a research career, but instead view the PhD simply as an obstacle on the road to a teaching (or other) career. Probably the community should scrutinize these sorts of theses more carefully, but it can be hard to work up the energy to do so when most of them are OK, and when these theses really don't matter much for the research world.

The German politicians are pretty much the worst case scenario. In the US, the stereotypical case is educational administrators. Typically, you have a distinguished person who starts to feel the need for a PhD. Perhaps it's because they associate with academics and feel looked down upon, or perhaps it's because an academic endorsement would make the public value their expertise more. This student is very smart and accomplished, and nobody suspects them of any dishonesty. However, they are also very busy, often working on a PhD while pursuing other projects as well, and academic research is not a priority. At some point, they succumb to pressure and start taking shortcuts. Probably it starts with small things, but the shortcuts gradually grow larger. They rationalize that the thesis doesn't really matter anyway, because they have no intention of following an academic career track. After all, they have the knowledge and experience, and they deserve the PhD title, so what difference does one document make anyway? Meanwhile, the advisor probably doesn't spend that much time working with the student, and has no reason to suspect anything. The advisor really ought to be extra careful in cases like this, but that would seem like an insult to the student, so it's easiest just to trust them.

So my take on this is that plagiarism is not as widespread as news stories might suggest. It's just particularly likely to happen in cases where it would attract media attention.

ethics - Can we use students' class homework solution for research purpose?

A colleague of mine would like to compare 25+ different Java implementations of the same homework. Is it OK (ethically/legally in the US) to share my students' class homework solutions with him for his research purposes?

Answer

You need to run this by your Institutional Review Board (IRB), as you would any time you use data from human subjects for research.

From what you describe, it has a good chance of qualifying for an IRB exemption under one of these categories (if identifying information is removed before giving the data to the researcher):

• It is using existing data


• the data comes from normal educational practices

but even then, the IRB needs to be the one to make that determination.

metabolism - Statistical method for characterizing the relationship between body mass and metabolic rate

There is a dataset that contains body mass ($x$) and metabolic rate ($y$) from many different organisms. It is common to fit the data to the model of the form $y=ax^b$ and estimate the parameters $a$ and $b$ (see Kleiber's law and The Metabolic theory of ecology). In doing so, it is also common to log transform $y$ and $x$ and create the linear relationship log($y$)=log($a$)+$b$log($x$) and perform linear regression analysis based on the log transformed data. Is this approach better than directly estimating $a$ and $b$ based on nonlinear regression for $y=ax^b$ (because results are different)?

Do's and Don't's of Undergraduate Research

I was fortunate enough to get a position as a researcher for the Mayo Clinic's SURF Program this year. My PI's lab focus is on the the immune system's role in CNS axonal and neuronal injury, specifically through the lens of how innate and adaptive immune effectors interact w/ infected neurons.

Although I do research under a professor at my college and I volunteered for a state university lab during the previous summer, this is my first REU/SURF opportunity, and I REALLY want to make a good impression. Here are my questions:

What are the do's and don't's in terms of being a skilled and efficient researcher?

Since I am still an undergrad, I know that I will be a less useful asset to the lab than a grad student or post-doc, but what can I do as an undergrad to not burden my colleagues and PI?

Thank you all for your help! Wishing you all the very best!

advisor - Failing postdoc?

After a successful PhD in computer science (including some awards from top conferences, internship at top industry research labs, and a good number of citations to my ~15 papers) in a top-10 US school, I got a postdoc at a top-3 US school.

I had a number of postdoc offers and chose the one whose topic more far-related to my phd thesis, in order to learn new things, get out of the box, and show that I'm not a one-trick dog (or doc? ;) ). The topic is different but not too much far away (i.e., I didn't move from theory to systems, rather from algorithms to (applied) machine learning).

I've been in my new position almost 6 months and feel like a complete failure. I can't go on with one of the projects I was assigned to and it is not for lack of trying: I just don't understand the results I'm getting because I don't know the field well enough and I can't figure out what I am actually supposed to do to improve them.

My supervisor gets quite "adversarial" when I ask for feedback and I try to explain what I don't understand. On the other hand, he says that I'm very helpful on other projects, helping the students, and a valuable addition to the group, and he would have told me if it wasn't so. Indeed I think it is true and I'm doing a good job on other projects (which are not "mine").

The project I'm failing at could have a great impact on science (not just CS) on the long term, but I feel like any engineer trained in the field could lead it to completion, so I don't find it particularly exciting. I guess I'm missing the excitement I got when I had to prove theorems during my PhD. Right now, the project involves just messy data analysis, and a lot of try-and-error coding (mostly error), all without much feedback from the supervisor (who actually told me to ask the students...which I did and they weren't exactly helpful).

Anyway, this is getting me extremely stressed (I actually started seeing a therapist about this), and I'm thinking of moving away from this position, although I may have the possibility of renewing for another year (if my supervisor would even still consider the option, which he gave me when I started)

What are the pro/cons of moving away after 1 year with not exactly much positive work done yet, especially of which I could claim ownership? I believe that right now my supervisor would not, in the future, write me a very positive recommendation letter, in my opinion.

Note that I already have offers for next year, on topics more related to what I did during my phd.

research process - Is it ethical to require student work in exchange for letter of recommendation

Is it ethical for a psychology professor to expect volunteer work in the lab in exchange for a letter of recommendation? The rationale is that they are unable to judge a student's suitability for graduate school without evaluating their lab abilities. I can see the point, but it's difficult for a working student to volunteer for an entire four month long semester on the professor's schedule, which varies considerably.

publications - Should an intern who wrote most of a paper and where the first author contributed little request to be first author?

Background: A little over a year ago, I wrote a paper for an internship (during high school) at a major university medical center. My contribution to the paper was basically everything except conception and some editing/revision (mainly phrasing, not content). The author list, in order, is: immediate supervisor, me, other intern, senior person in group, and PI. The other intern put in about 3 hours of work which were not used in the final manuscript before disappearing to another country and not responding to my attempts to contact. My immediate supervisor, frankly, had very little contribution and is not giving the paper the attention I would like; they took a year to submit the paper (rejected the first time by a reach journal), is taking excessively long to resubmit or get back to me about it, and is usually radio silent.

I have a pretty good relationship with the PI, who seems somewhat aware that my immediate supervisor is not being responsive or attentive. It's from work done during high school, so I don't have very much experience with these politics.

• Can and should I ask the PI (or someone) about changing the order of authors?



• and what actions would be appropriate for me to take to try and get the paper finally submitted relatively soon?

publications - How do I go about publishing a paper without a university affiliation?

I graduated with a B.S. degree and I have been working in industry for a few years as a software engineer. I am very interested in reinforcement learning, a sub-field of machine learning, and I am interested in performing research and publishing a paper on that topic.

The problem is, in my city there are no professors working in this field (or related fields) who could help me. I contacted other professors in different cities and they rejected my help request for a variety of reasons (such as I am not their student, they don't know me, they are busy, etc.).

Still, I want to perform research and publish a paper. I can't attend school as a full time student and my collaboration requests were not successful. Given all that, how can I publish by myself?

1. How to choose a research topic?


2. Should I read all the papers on this field?


3. How to decide which problem to work on or which is not obsolete? I don't want to work on something which no one is interested in.



4. Should I read and study all the prerequisite material, or fill in the gaps during research efforts?

publications - Questions about authorship rank and academic politics

Disclaimer! I am a first year CS/Applied math master student so I do understand very little in how academia works. I am trying to fix it before I go into PhD.

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I have discovered a scientist who works in the field I am interested in. This scientists is very successful career-wise. The scientists finished a prestigious university and had stays in very good places. Now the scientists is an assistant prof in a high-ranking US university.

However, literally >90 % of his papers were written in co-authorship (as a rule, not the first nor the last author) with other more experienced researcher who we recognized as leaders in the fields. In fact, the only solo paper the scientist has is ones thesis! All PhD students so far have been also co-advised.

I have very little research experience but it seems to me that coming up with a good idea one can further develop is the trickiest part. Implementation (or, sometimes, even writing down actual proofs) is a technical work. I guess that the coauthorship was earned for some implementation work. It seems to me that there are much more people capable of / actually doing these technical work both in academia and in industry who do not get such recognition as the aforementioned scientist.

I may be envy but I find very little proofs of that scientist actual skills. Instead I have a feeling that the scientist makes very wise political decisions or is good as self-advertising.

Also I did very limited empirical studies and found that researchers who have highly-cited solo papers tend to have higher (4K +) citation counts then those who have almost exclusively co-authored papers.

My question is many-fold:

1. 
   

   is what I have described normal? Update. Is it normal to have almost exclusively co-authored papers?

   
   


2. 
   

   what should I do to mimic that behavior. It does not seem to be noble at all but apparently this is how successful academia people work.

   
   


3. 
   

   Are indeed funding and promotions based on citation counts? If this is not the case, how those researchers without solo papers are assessed?

   
   



4. 
   

   Is it true that those researcher who has successful solo papers are much better supervisors?

   
   

Update. I am talking here about theoretical research in CS/Applied Math. I guess in other fields there are many more opportunities for equally valuable contributions of many sides.

Answer

I should point out one of the most famous of co-authors in math: Paul Erdős. Erdős never won a fields medal or even wrote a seminal paper as a solo author. What he did do was "wander" around to different universities and help people solve problems. He was an extremely prolific writer (over 1500 published manuscripts) and is considered one of the greatest mathematicians of the 20th century. The ultimate mathematical Renaissance man who could seemingly work on any problem. I think you would have quite a bit of difficulty in arguing that because Erdős never wrote a classical mathematics paper as a solo author, he was not a tremendous mathematician. (Though to be fair, in the past decade, his paper "On Random Graphs" can now be considered a classical work of mathematics. It just took 50 years for the work to become highly applicable).

I relate this story because having lots of co-authors does not necessarily mean having bad skills. Now I am not saying your professor is the second coming of Paul Erdős (I can't think of anyone currently in academia who can claim that mantle) but they might have other skills you are not giving them their due credit for.

Never underestimate the power of being able to organize a group of smart people and get them to work together on the same problem.

To answer your questions specifically-

1. 
   

   It's neither normal or not normal. Tenure positions are rare enough that there are certain metrics that are highly predicative (e.g. individuals who are ahead of the publication curve for their field tend to get hired in tenure positions) but there is no conclusive metric. Individually, there is enough variance within each position that you cannot really say.

   
   


2. 
   

   Collaborate! Having only solo author publications is probably not wise (unless you are in a field that is big on monographs). Having a variety of publications where you are first author, second author, and a middling author show your ability to collaborate and be a team player.

   
   


3. 
   

   Yes, clout does increase likelihood of getting accepted. Being a big wig with 10,000 citations at an elite university means you are more likely to get a grant than someone with a handful of publications from an R2. But to be fair, the qualities that led that person to be a big wig probably translate into their writing and research caliber as well.

   
   



4. 
   

   I have never seen any research or evidence that suggests that.

   
   

publications - Telling PhD supervisor I published a paper about my thesis without telling them or listing them as authors?

I am in my 3rd year of PhD. In my program, it is a requirement for PhD students to graduate with a paper that is published in a Scopus Index journal.

Before I entered, and during my PhD, I had already published a few papers to a Scopus index peer reviewed journal (for topics not based on my thesis). At the moment, I am trying to publish a paper as a part of my thesis (with my supervisors' names), but my supervisors keep criticizing the paper and making me rewrite it again and again. This has been going on for two years.

However, I did submit another paper (a part of my thesis) under my own name and without my supervisors' knowledge, and it was accepted. This paper was done without any intellectual contributions from my supervisors - no writing or reviewing. When I told my supervisors about the paper (but not its acceptance,) they were angry that I hadn't included their names, and they asked me to include their names in it. Unfortunately, the editor said I couldn't as I had submitted it initially as one author only.

I am aware that it is my fault that I didn't ask them beforehand, but I know in my heart that if I had included them, it would have taken months or years to even get their approval. In all honesty, they would have ended up demotivating me. I am now really scared to tell them that it has already been published and I cannot add their names.

Can you give me any advice how to handle this situation?

Answer

The answers here are generally explaining the fact that supervisors should not be omitted from the authorship as they are supposed to direct and contribute to the research.

The critical problem is, you are saying that they did not contribute at all, and they, naturally, did not write or review the published article. Still they try to add their names as authors when they learned about the article submitted. You can not be an author if you did not even review the article, just this information is sufficient to see that the ethical misconduct is mostly on their side.

Your problem is, you can not both submit an article without making "such" people authors and at the same time maintain a good relationship with them. A one-author paper is, for me, much better than giving credit to the people who disregard the functioning of the academy, by both hardening the situations unnecessarily and also making academic misconducts. Even if you somehow get your advisors' names added to the paper, they will never ever forget this. At the same time, you shake the ethical ground of your publication by this act of "correction", and it may, in the end, cause the rejection to your paper. All the while, you will still be considered untrustworthy by your advisors, quite rightly in their perspectives.

Your only choice is to forget about updating the author names, and find some other ways to correct your relationship with the advisors.

And please keep in mind that in academy, at least in Turkey, almost everyone faced in a situation that more than the bulk of work done by someone and just because their advisors don't like them they don't give authorship to the corresponding researcher. And these advisors made their Ph.D. in top-tier universities of USA. I think you will most likely face such problems from now on.

publications - Is it acceptable to publish a paper using an affiliation with a former employer?

Recently I've changed jobs, and consequently the field of research has also changed. But I'm still getting proposals for publications in the previous field, and it is interesting for me to accept some of them. My concern is about which affiliation to use: on one hand I gain all the knowledge in that field while working on the previous employer, also I hope they can cover my expenses related to the publication. On the other hand, I do not work for them anymore, and my current company has very little interest in my old field of research, and probably will not support it financially, but I think it is wise to mention them as well. As a compromise I'm thinking to put the previous employer in the affiliation, and the name of my new employer in the footnote, something like "currently at XYZ". Surely I'll discuss this issue with both, although the opinion of the community is also very valuable.

Answer

If you have written the publication only with the resources and support of the former employer, then it is perfectly acceptable to do what you have written, and list the old address as your address for the "active" affiliations, and include a "present address" affiliation to show your updated physical location.

However, if your new employer does provide financial support, then you should list them accordingly. This is especially important if any of the actual research that makes its way into a publication has been performed while working for the new employer using their resources.