human biology - How does an embryo know where to grow limbs etc

For example you have a cell or already a bunch of cells. Those cell(s) divide and after several week you have a grown organism, for example a human with limbs, several different organs etc. However, how do cells know where up, down, left, right etc. is? I know left and right can be defined clearly in physics, for example by the Wu experiment verifying parity violation really occur.

However how do cells define those directions? What are the mechanisms for them to grow into a certain direction and tell other cells to attain a certain property?

publications - How much informal writing should there be in a research article?

I am starting to write a research article in computer science area. While writing, I am using very formal terminologies and sentences which occasionally get quite boring. Sometimes, funny side of my personality pops up, and I end up writing some informal sentences which I have to delete later, picturing a very serious looking reviewer reading my paper draft. I always have this idea that a research article should be narrated like a story (keeping the facts and assumptions valid) to make it interested for the readers and stories often get quite informal. Don't they?

So the question is: How informal can I go in writing a research article even if my assumptions are correct? Do reviewers mind if the language used is not quite formal?

evolution - How to determine whether changes of an allele's frequency are due to genetic drift or selection?

Given that both natural/artifical selection and genetic drift are evolutionary mechanisms that influence how allele frequencies shift in a population:

Are there ways to determine whether a frequency shift for a specific gene/allele is due to genetic drift or selection? In other words: when we see an allele take over a population, is there a way to know whether it was selected or just 'got lucky'?

UPDATE: since apparently this issue is quite complex in experimental biology I want to clarify why I'm asking this and what I hope to learn.

I'm looking for a 'theoretical way' of determining whether the changes in allele frequencies in subsequent generations are the product of selection or mere drift.

I'm applying a genetic algorithm to the optimisation of websites, where each gene determines an aspect of the user experience of that website. The question is whether the alleles I see emerging in the fittest solutions (= the best user experience, rated by visitors) got there by chance or actually contribute to the fitness of the candidate solution (= make a difference in shaping the user experience).

graduate admissions - How to send a research proposal to find potential PhD supervisor?

I am trying to look for a PhD position by contacting potential supervisors through email. I have made a list of professors who I found interesting through searching some papers and their department websites. Now I decide to write to them for asking opportunity and in order to show my sincerity, I would like to attach a research proposal.

I know it seems not necessary to do this if my credentials are good enough, but in order to stay out of the crowd, I don't know if this is actually a good idea to attach a research proposal. Anyway, I want to have some advice on writing a research proposal in this situation.

1. What should the appropriate length be? 2 pages, 20 pages? with cited reference?



2. How much deviation is allowed with the professor's research interest? Because if everything are the same with the current papers, it seems I am just copying its content into the proposal.


3. Should I include all necessary experimental steps? (I am from engineering)


4. Any other suggestion on writing research proposal in this situation.

I don't know if it is worth the time to do this, I would like to know if you have also some suggestions in impressing potential supervisors solely through email.

Answer

In most branches of engineering, sending a research proposal to a prospective PhD advisor is not particularly helpful, unless you are providing your own funding.

The reason for this is that most PhD students are funded through grants obtained by the professor, either from traditional research funding agencies (NSF/DOE/DOD/NIH and their counterparts in other countries), or through industrial contracts. In such cases, the projects that are to be worked on are well-defined, so the possibility of deviating from those projects and using the money to fund other projects—such as the one you propose—are remote.

On the other hand, if you can provide your own funding, things change significantly. Under such circumstances, you could propose a project of your own design, so long as it fits within the general scheme of the professor's existing research (or moves slightly outside of it). However, proposing a project that lies too far outside of the mainstream typically is unlikely to be well-received, since the professor won't be able to provide much useful support.

However, even under such circumstances, the initial proposal should be more like a "white paper"—a faculty member, if he or she reads such a document at all, is not going to spend more than a few minutes reading it. So the initial idea will need to be compellingly presented in a short amount of space—two or three paragraphs at most.

The best way to show your interest in a professor's group is to explain how you could contribute to ongoing research in the group—that is, do you homework before writing to the faculty member. Your email should make it clear that you are writing the specific faculty member, and addressing the concerns and interests of their group. Anything that has the whiff of being a form letter will likely be ignored, unless your CV looks like a perfect fit for the research group!

How to prevent students from having an unfair advantage on exams, when they are held on different days?

I teach a writing course to different sections, across different days of the week. From the schedule, some students will take their mid-term exam early in the week, while others will take it later in the week. Recently, I found one student who was “just checking to see what the exam was like”, but was planning to go to another session to actually take the test. I realized there might be a variety of ways that students taking the exams on Friday would have an advantage over those taking it on a Monday.

I've taken the following steps in an attempt to address this problem:

• I build multiple tests, e.g. "A", "B", "C", etc., which are of similar difficulty, have the same types of problems, but different subjects. "A" is given to one section, "B" to another, etc.



• Provided a sample test that students can print and practice with and discuss with me in class.

Note that, there are several challenges to administering this:

• The classes are large, and the school offers me no assistance in managing the exams.


• Many students regularly attend my lectures during sections that they did not register for, so I will not easily recognize who belongs in which time.

Are there any additional steps I should consider to make sure the test is administered fairly?

conference - What is the significance of the overview slide in a presentation?

The first slide which follows the title page of my presentation is the overview slide. It has the title for each section to follow in the talk (thank you Latex!).

My question is how much time is to be spent on the Overview slide, given the talk lasts twenty minutes? Should I talk about each section's one-line-synopsis to let the audience mull it over? If the answer is no, how do I transition smoothly from the Paper Title Slide to the one on Motivation for the talk (For example : Why I love Science?).

ethics - Is it unethical to interview at a more prestigious program while currently enrolled in a PhD somewhere else?

I applied at two different PhD positions at universities X & Y a while back (both in EU, I prefer not to disclose identity for specific reasons, sorry).

I got into X and have been here for about 2 months, and I heard from Y a few days ago inviting me to interview with them. Y is more prestigious, and also many of my friends are there. (Note: Both positions had different starting dates, X was more of a start-earliest program, Y is for 2015 admits)

Considering I am more interested in studying at University of Y, would it be unethical for me to take up the interview with Y, after I am here for 2 months? (I am at X as a RA presently)

botany - What does the empty space in the bamboo stem do?

Is the empty space inside a bamboo stem a xylem? And why is the space so large?

Answer

No, its not xylem. Bamboo is a grass, and the stem (culm) of many grasses are hollow in the middle (see e.g. Grass Structures from Oregon state for some more info).

The exact reason for why Bamboo have hollow stems is most likely due to evolutionary contingencies. However, from a mechanical stability point of view, a hollow stem is much more rigid and stable than a solid (but much thinner) stem composed of the same amount of biomass (Niklas & Spatz, 2012, p. 191ff). So from the perspective of efficiency, the hollow stems of grasses are very useful. The solid node discs found in grass stems (and in other plants with hollow stems) are however really important for increasing overall stability and ability of stems to resist deformations, while only contributing to a very small amount of the total biomass.

human biology - How does the brain's energy consumption depend on mental activity?

What is the impact of mental activity on the energy consumption of the human brain?

I am most interested in intellectually demanding tasks (e.g., chess matches, solving a puzzle, taking a difficult exam) versus tasks with a similar posture but less demanding (e.g., reading a newspaper, watching TV).

I heard that energy consumption stays remarkably constant regardless of the mental activity (and energy consumption can be explained by elevated heart rate due to stress). However, it seems to contradict techniques such as fMRI, where the change in metabolism is measured (unless the relative change is really small).

gene expression - cell specialisation and their location

When we create new cells, how come they are of the 'right' type at the 'right' place? For example, when I make a new cell on my lips, it's obviously not the same as a new one in my kidneys.

Is the differentiation done by using a different part of the DNA each cell has? How does the mechanism of growing specific types of cells at a specific place work?

Answer

Yes differentiation is primarily about using only a portion of the genome as you pointed out. However, differentiated cells possess a kind of "memory" which enables the daughter cells to continue the usage of the same set of genes. This "memory" is enabled by epigenetic mechanisms which leave inheritable "marks" on the DNA such as methylation (I won't explain further as this would take an entire book).

About the place: each part of the body can produce cells locally (except for some tissues). For example the epithelial cells in your lips will arise from your lips. What signals the division of cells in response to a signal such as lets say injury is again a broad question. One simple mechanism is this (not an independent mode but just one aspect of a complex process): cells generally divide but stop dividing if there is no free space i.e. the cell is surrounded by other cells. This is called lateral inhibition of growth.

I would suggest that you pick up some good cell biology and molecular genetics books to understand these processes.

Cell Biology:

• Molecular Biology of the Cell - Bruce Alberts et al.


• Molecular Cell Biology - Lodish and Baltimore

Molecular Genetics:

• Molecular Biology of the Gene - James Watson et al.


• Genes - Benjamin Lewin

masters - mentioning MOOC's I took in my scholarship application

I'm preparing my application for a master degree scholarship, would it help to put the MOOC's I took in the application, I earned five MOOC certificates and expecting another two in the near future.

Answer

Yes! Why not? It shows that you go beyond what is required of you, and you have a genuine interest in learning. I always list certificates from MOOCs.

publications - How to respond to my name being included in acknowledgements of incorrect/misleading paper whose authors ignored my recommendations?

My colleagues (grad student + their advisor) from my department approached me, a fourth year PhD student in STEM, for comments on a manuscript written on a topic related to my research.

In two iterations over email, I pointed out serious logical fallacies in their arguments, instances of misleading references and attempts to skirt crucial issues in the paper. Most of the issues in the manuscript are still unresolved but the authors have thanked me for my comments in the acknowledgement section. I'm uncomfortable with my name being included in the acknowledgement section of an incorrect and misleading paper submission.

Would it be wise to politely request for my name to be removed from the acknowledgements?

Answer

How acknowledgments work is always a bit of a judgment call, but to me the following principle seems reasonable.

You are free to acknowledge anyone in any paper as long as what you acknowledge them for is factually accurate. If you have any reason to believe that the acknowledged party might take issue with the factual accuracy of what you write in your acknowledgments, it would be honorable to show them a draft of the paper and ask for their blessing on the wording of the acknowledgment. If this causes them to ask to be omitted from the acknowledgments, then it seems reasonable to honor this request unless you feel that removing this acknowledgment compromises academic integrity. (For instance, if you are including significant work of the acknowledged party, then just because they don't want you to mention that does not necessarily make it okay to do so. This creates a sticky wicket that other questions and answers on this site have addressed.)

I believe it follows from the principle that whether acknowledgments are acceptable depends more on what they acknowledge you for than whether they drop your name or not. For instance, suppose they thank you for "helpful conversations". If you did in fact speak (or write...) to them about their work, then if they say the conversation was helpful, how can you argue?

I think that most savvy academics understand that just dropping someone's name in the acknowledgments does not mean that the paper contains their imprimatur. Nevertheless it is shady to acknowledge someone -- especially someone very famous and eminent -- purely for the cachet that their name may convey to less than savvy readers. Here is a famous review of Marilyn vos Savant's book on Fermat's Last Theorem that calls out the author along these lines: she acknowledged some very famous mathematicians, who when contacted by her surely did not say anything to indicate that the material in her book was correct (not only does it contain errors, but it contains errors that any practitioner or serious student of mathematics would regard as bizarre).

In the case at hand: I think the OP would be within her rights to mention that she would rather not be acknowledged in the paper. Whether she wants to indicate that this is because she still finds the work to be significantly flawed depends on all kinds of social and political factors beyond the scope of this answer. As to that I would only say: in my opinion, simply very politely asking for your name to be removed from the paper without getting into why is probably a higher percentage strategy than indicating that the work is still problematic.

Added: Let me add that the principle above is meant to be on the minimalist side. In practice, if you think that someone is not going to appreciate being acknowledged in your paper for whatever reason, then unless there are academic integrity issues involved in omitting the acknowledgment it seems wise to do so. Once I acknowledged a friend of mine in a preprint in a way which was factually accurate but nevertheless embarrassing to him: he simply did not want to be associated with something that he viewed as intellectually trivial. I took his name out of the later drafts of the paper. This incident has made me think more carefully about how acknowledgments will be received by the acknowledged party.

publications - Elsevier actions following US sanctions on Iran

Elsevier has started circulating this letter as a consequence of the sanctions taken by the US against Iran to the editors of their journals:

Subject: US editors and reviewers can no longer handle submissions by authors employed by the Government of Iran

---

Dear Dr Bruno Granier,

The Office of Foreign Assets Control (OFAC) of the US Department of the Treasury administers and enforces economic and trade sanctions. As a result of OFAC sanctions we have been made aware that US editors, US Elsevier staff and US reviewers are now unable to handle scientific manuscripts where any of the authors are employed by the Government of Iran. This includes the research departments of the various oil and gas companies which are deemed to be entities of the Government of Iran. We realize that this OFAC regulation will cause some inconvenience in your role as an editor but Elsevier is legally obliged to ensure that all reasonable efforts are made to avoid submissions from Iranian government agencies and companies being handled by US editors, US Elsevier staff and US reviewers. Please be aware that editors, Elsevier staff and reviewers from outside the US may still handle these manuscripts and that this OFAC regulation does not pertain to manuscripts where the authors are based at Iranian academic and research institutes. Manuscripts originating from a clinical setting that are not government run, for example, a hospital or clinical practice are also exempt from this regulation.

To view the official OFAC regulation, please click here. In practice the result of these sanctions will mean that:

• Submissions where any author is based in Iran, and is not at an academic and research institution, cannot be handled by US-based editors, US Elsevier staff, US reviewers, or any US citizens based outside of the US.

• If an Iranian author has dual affiliations (eg. university and government), their submission cannot be handled by US-based editors, US Elsevier staff, US reviewers, or any US citizens based outside of the US.

• Affiliations of Iranian authors should therefore be checked, and any manuscripts which fall under this OFAC regulation delegated to a non-US editor, before handling.

• When assigning reviewers, affiliations of Iranian authors should also be checked, and any papers which fall under this OFAC regulation should only be sent to non-US reviewers. (As an editor you should do what is reasonable to determine the nationality of a reviewer e.g. check their email address. This check does not extend to emailing reviewers directly to confirm their nationality or location). Unless there is specific knowledge that a non-US-based reviewer is a US citizen, editors can send such submissions to reviewers based outside the US.

• If your journal workflow involves all submissions being handled by US-based Elsevier staff, they will reject these manuscripts outright before they reach you.

• Should there be no suitably qualified editor or reviewer, please reject the manuscript outright.

When rejecting manuscripts which fall under this OFAC regulation please use the new EES Decision Term "Reject - OFAC Sanctions" and the following text:

"As a result of OFAC sanctions all editorial staff who are US-based/US nationals are unable to handle scientific manuscripts which are authored by Iranian scientists, employed by the Government of Iran. Based on this OFAC regulation we are unfortunately unable to handle your manuscript. We wish you success with your submission to another Journal."

We apologize for the inconvenience this may cause. If you do have any questions please contact your Publisher.

Sent on behalf of Dan Lovegrove

Cretaceous Research

Has there been any public response, by US editors or reviewers, stating whether they will obey (or not) the instruction? Also, does this letter conflict with the Code of conduct and best practice guidelines for journal editors of the COPE (all Elsevier journals are members of COPE as of January 2008)?

Answer

The Office of Foreign Assets Control (OFAC) is an agency of the US Treasury that is empowered by US federal law to edict and enforce embargoes and economic sanctions. Thus, US journal editors are bound by its regulations, whether they like it or not. Violating them would expose them, and their employers, to liability. If they violated them willingly, the employer might also turn against them. I don't see how deference to the law is in violation of COPE guidelines (or academic ethics in the broader sense): though important in publishing, they do not have force of law (and specifically defer to the law in many areas).

Elsevier is not the only publisher affected by these sanctions, and as others, they are not happy with it:

We stand by our belief that generally speaking, restrictions on publishing are inappropriate, and any exceptions should be narrowly crafted. We will work with our other publishing house and industry colleagues, along with research communities and institutions, to analyze recent changes and continue to pursue appropriate balance in the laws.

Some other publishers, however, either have a different understanding of the law or are willing to (potentially) go to court over it:

A spokesperson for the American Geophysical Union, which has a dozen members in Iran, says AGU does not consider publishing to be a trade issue and "accepts paper submissions from anywhere in the world." The American Society of Mechanical Engineers echoes that view, as does AAAS, Science's publisher. "We do not put any restrictions on submission or publication of papers based on economic or other sanctions," says Monica Bradford, executive editor of Science.
                                                                                      [source: Wikipedia and references therein]

My advisor's new student copied parts of my PhD thesis; advisor doesn't care. What to do?

I wrote my PhD thesis a few years back. After I finished, my supervisor found another researcher and continued research with the apparatus I built, but along a different line of study. I met this student a few times and gave them advice and help when I could. They always had a hard copy of my thesis in the lab for reference; I also provided a PDF copy at the student's request.

The student recently finished their PhD and I looked at their thesis. The lit review, results, and findings are the student's own work. But, particularly in the middle section (describing the apparatus I built):

• Many paragraphs of their text is copied and pasted from mine, some without checking so that it makes false references;


• In other instances, the student has substantially copied paragraphs, but changed a few words here and there;


• One that particularly annoyed me was the copying and awkward re-hashing of my acknowledgements to my supervisor, very personal words;

I informed my former supervisor (with whom I have a good relationship) and he seemed not to want to know. He said that as long as it wasn't the results then it wasn't too important. He reckoned as the student was a good guy, he may not have known what plagiarism was, and perhaps did it by accident. He did offer to acknowledge or include me in subsequent journal papers.

Given that only some of the background text (rather than the results section) was copied, is it reasonable to pursue this further? What is normally done in such cases?

In particular, I was thinking to quantify the level of copying involved and ask my supervisor to withdraw the thesis until copied material is removed. However, I risk jeopardizing a fairly good relationship with my supervisor and possibly also with the small network of colleagues.

Answer

You have two options:

1. Not care about plagiarism enough to warrant getting involved.


2. Care about plagiarism to the degree you get involved.

There are arguments for both points here.

1. 
   

   It would be an obvious matter of record as to whose thesis was written first if anyone else happened to notice the similarities. Why get involved further? You notified the adviser, let him deal with blowback from letting a student plagiarize. Pushing the issue further would just compromise your relationship with your adviser. Whistleblowers rarely get rewarded properly anyway. And, cynically, some universities may not even care about a student plagiarizing parts of a thesis. It's more paperwork and labor for them to deal with and it's easier to just hope (from an administrative perspective) that the problem goes away.

   
   



2. 
   

   Based on what you have told us, it seems reasonable that your thesis was plagiarized from. You have contacted the adviser about this and he declined to do much about it. The graduate college and university administration, however, may not concur with your adviser. Plagiarism should be stopped on principle alone. I would report the offending thesis to the graduate college and see if they are willing to investigate it further. If you really wanted to do some nasty damage and the university declines to investigate, notify the local newspaper and see if they'll send over some junior journalist to write a spot on how your university is allowing plagiarism to occur.

   
   

Part of writing a thesis is learning to articulate in your own words what your research is about. This has to do with much more than just shoving original data in a table.

If your adviser told you the student "might not know what plagiarism is" then.....wow.....No one reaches graduate school and is completely oblivious to what plagiarism is. Let's be honest here.

For me personally, I would let it go. The network with my adviser is more important to my career right now. This is pragmatism, not principle, speaking.

zoology - Do octopuses have better eyes than humans?

I've read that unlike humans, octopuses have eyes "designed" the "right way", i.e. with the nerve fibers behind the retina, thus getting rid of the blind spot we humans have as well as theoretically improving eyesight.

Have there been tests to compare octopus sight with that of humans, and do they indeed have better vision than us?

Answer

There are a couple of advantages and disadvantages of possessing the eyes of octopuses.

• 
  

  The first advantage of the octopus eye is that it has no blind spot. This means that octopuses can see everything that is going on in their environment, and are more aware of predators and prey than some vertebrates. Also, they have many more photoreceptors than vertebrates, at roughly 20,000-50,000/mm² which means that their vision is much better than that of any human.

  
  


• 
  

  The disadvantage of the octopus eye is that it can not see in colour. The eyes possess no cones, only the invertebrate equivalent of rods. This means that octopuses can only distinguish between light and dark.

  
  

epigenetics - Can rats pass on memories of a maze to their offspring?

A friend of mine told me once about a documentary movie he saw some years ago. On this movie he saw scientists talking about particular experiment. This experiment involved rats and probably electrical traps. The rat had to get to the cheese, there were traps on the shortest route to it, and obviously it got shocked few times. What is interesting is that my friend says that when they took its offspring (probably born later) they avoided those traps.

I'm aware that its not how "genetic memory" works. Its not memory of individual, but of species (so it requires evolution). This is what I'm trying to explain to him, but he says "he knows what he saw".

Anyway maybe someone here is aware of such an experiment. I believe that he is wrong about something (or conclusions drawn where changed later), so I would like to find out more about it.

To sum up:

• Its not Tryon's Rat Experiment


• It involved: rats, traps (probably electrical), more then one path to cheese, rat's offspring and some sort of memory/learning amongst rats.

Answer

The phenomenon you're talking about was a fad in the 60's, called 'interanimal memory transfer'. It started out when James McConnell performed a later-discredited experiment in which he found that if you chopped up flatworms which had been exposed to some stresses, and fed them to other unexposed flatworms, the unexposed worms became wary of the source of stress quicker after eating their dead companions. He jumped to the conclusion that a 'memory molecule' was being transferred, and that the cannibal worms gained the food worms' memories of the stress.

People then started looking to see if they could:

1. repeat the experiments


2. find the same phenomenon in other animals

In the first case, nobody could replicate the experiments in worms, but because McConnell was such a PR genius he managed to convince the public that his results were valid (see Rilling, 1996 for more on this).

In the second case, Frank et al. (1970) and others tried working with rats - I think this is the experiment you're talking about in the question. They found various interesting results including that if you trained rats to run through a maze by using particularly stressful negative reinforcement (like electrocution), then those rats' children would be able to learn the new maze much faster. However, Frank et al. didn't make the same mistake as McConnell - first of all they wondered if the parent rats might be leaving a scent trail. So they used duplicate mazes with the exact same design, putting the children into clean mazes. The children of adults who had already learned the maze continued to outperform the control rats - the explanation was not scent trails.

Next they wondered whether it might be that the second generation rats had been born with a higher wariness as a result of the stress their parents suffered; i.e. it could be a hormonal transfer from mother to child (e.g. cortisol, the stress hormone).

Frank et al. tested their hypothesis by torturing some rats for a while (rules about animal welfare were not strict in the 70's). They would lock some rats in a small jar and bash them about for a long time, then kill them, chop them up, and take out their livers. They fed the livers to other rats, and found that after eating the livers the other rats learned the maze much faster. They interpreted the results in what now seems a sensible light: the stressed rats were producing high concentrations of a stress-signalling molecule. When those rats either had children or were fed to other rats, they passed on high doses of the stress molecule. This raised the alterness and wariness of the receipient rats so that they were much quicker to learn which parts of the maze were dangerous.

There is no evidence that the child rats actually 'remembered' the maze - they still had to find their way around, but they were extremely wary of the electrocution plates and so avoided them, finding the safest way to the end. This is not a case of genetic memory.

brain - How do our eyes see an inverted image?

How exactly do our eyes see an inverted image of what we are looking at? Does it have something to do with the shape of our lens (i.e. convex)?

zoology - Species identification; clusters of big plump red bugs in Taipei

I saw these red insects in Taipei near XinBeitou MRT station in the last week of April 2017, around lunch time. They were fairly active and would keep checking each other out with their antennae for a moment and then move on to the next. What struck me was the wide range of sizes and development in the groups. I didn't notice any feeding or mating that I could recognize, just a lot of walking around and checking each other out.

There are plenty of birds around (this is quite a green area) but I didn't notice any interest by birds in eating them.

I've also included a screenshot from google maps so you can see the location and the trees growing in these concrete structures.

The body of the largest individual is probably 2.5 centimeters long.

Answer

I'm fairly certain these true bugs belong to the species Leptocoris vicinus, and carry the nickname of "soapberry bugs", which is specific to the subfamily Serinethinae. They're quite common in urban areas of Southeast Asia, which coincides nicely with where you encountered them.

Also, you had mentioned,

There are plenty of birds around (this is quite a green area) but I didn't notice any interest by birds in eating them.

Soapberry bugs, as well as many other types of insects, are able to freely congregate in large numbers, and in such exposed places, due to their bright coloration. Having such a bright color may indicate to some predators that the prey in consideration is toxic, a phenomenon referred to as aposematism.

source

source

And then, here's a map of their distribution, with Taipei holding marker #37. (source)

An interactive version of this map can be found here.

Can my UK PhD permit me to use the title "Dr.-Ing." in Germany?

I'm moving to Germany in a couple of weeks and I'll be setting up as a freelancer. I'm just curious about my title though.

I got my PhD in the UK in 2015, it states "Doctor of Philosophy" on the certificate, as usual, but my research was in Computer Science, specifically experimental application of Computer Science techniques to Engineering problems (in fact, my work was actually funded by an automobile company based in Germany whom I visited quite regularly).

I'm no longer in academia, but last summer I was briefly at Hannover University, where somebody suggested that I would be eligible for the Dr.-Ing. title instead of the plain Dr. title.

Fact is, I would like the Dr.-Ing. given the technical nature of my freelance work, but I am not sure whether I am legally allowed to use it.

Can anybody advise me?

Answer

One important thing you need to know about the German Doktorgrad is (alongside other non-academic titles) that its use is restricted by federal law. Adding a Doktortitel to your name in public without being entitled to do so is a punishable offence. This means that you should not trust any answer that you get from the Internet on this topic. Make sure that you verify whatever answer you get with an official side. One way of doing so is pointed out in @Cachapa's useful answer from the point of view of someone who already went through this.

Having said that: First of all, a British Doctor of Philosophy is indeed considered equivalent to a German Doktorgrad. You can verify that using this database (unfortunately only available in German). This means that you're fully qualified for whatever position or task that requires a Dr.

However, while you're entitled to use your PhD in public as an academic title, it is not possible to convert your PhD into a German Doktorgrad, and doing so might be an offense according to German law. This is based on a statement issued by the Kultusministerkonferenz (the "Standing Conference of the Ministers of Education and Cultural Affairs of the Länder in the Federal Republic of Germany"). These are the crucial points:

• Akademische Grade sind in Deutschland rechtlich geschützt.


• Der ausländische Grad muss ordnungsgemäß verliehen sein.



• Die Umwandlung eines ausländischen Grades in einen deutschen Grad ist nicht möglich (…).

My translation:

• Academic titles are protected by the law in Germany.


• A foreign title has to have been granted lawfully.


• It is not possible to convert a foreign title into a German title.

This statement is very explicit in my opinion, and it means that you cannot just add Dr.-Ing. to your name if you haven't been granted the title by a German university. It also means that no German university can grant you a Dr.-Ing. simply because you have a foreign equivalent title.

Yet, you can use your PhD in public, because it's acknowledged as an academic title. Plus, the Kultusministerkonferenz has decided that EU members can also choose to use Dr. instead of the designation used in their country of origin, this is regulated in (2) in the "Vereinbarung über begünstigende Regelungen der 'Grundsätze für die Regelung der Führung ausländischer Hochschulgrade'" (thanks to @Pont for pointing that out), but this does not include the "-Ing." part. To quote:

1. Hochschulgrade aus Mitgliedstaaten der Europäischen Union (EU) oder des Europäischen Wirtschaftsraumes (EWR) […] können in der Originalform ohne Herkunftsbezeichnung geführt werden.

This means that academic titles from the EU, the EEA may be used as part of the name in their original form without stating their origin.

2. Inhaber von in einem wissenschaftlichen Promotionsverfahren erworbenen Doktorgraden, die in den in Ziff. 1 bezeichneten Staaten oder Institutionen erworben wurden, können anstelle der im Herkunftsland zugelassenen oder nachweislich allgemein üblichen Abkürzung […] wahlweise die Abkürzung „Dr.“ ohne fachlichen Zusatz und ohne Herkunftsbezeichnung führen. […] Führung beider Abkürzungen ist nicht zulässig.

This means that a holder of a doctorate from one of the countries described in (1) may decide to use the abbreviation Dr. instead of the abbreviation that is usually used in their country of origin, but without the addition of an abbreviation indicating the title-granting discipline – that's the part referring to the -Ing. suffix. Also, it's not possible to combine both abbreviations, i.e. "Dr. Schmuddi, PhD" is not allowed.

Of course the UK has decided to leave the EU, and as it is, it's not clear yet how this will affect this regulation. In the current form of the "Vereinbarung", that regulation will not apply automatically to UK PhD holders any more. I am so very much not a lawyer, but in my understanding, a PhD from the UK will not be entitled to use Dr. any more once the UK has left the EU, unless the Kultusministerkonferenz revises the "Vereinbarung". I'm pretty sure that they will do that very soon by adding the UK to the list of countries in (4) (alongside Australia, Israel, Japan, Canada, and the US). Yet, you never know.

human biology - Why is the brain dependent on glucose?

The strict dependence of the (human) brain on glucose has always been puzzling to me. While ketones can substitute for a portion of the brain's energy needs, it cannot substitute completely: blood glucose levels below 2--3mM somewhere causes serious neurological problems and can lead to unconsciousness.

Other body tissues are not strictly dependent on glucose, but can oxidize amino acids as well, which is a good backup solution since there is always lots of protein around. But not the brain.

In terms of evolution, this strict glucose dependence must be a major drawback --- falling unconscious just because you don't get enough sugar is probably a bad thing out in the wilderness, when the lions are after you ... So there must be a very important reason.

So why is the brain so dependent on glucose?

evolution - Evolutionarily, why do male rats and horses lack nipples?

Developmentally male rats don't have nipples because (reddit)

Testosterone release in the fetal male rat happens before the stage of mammogenesis where the teat is formed whereas other species halt that same process after the teat is formed.

According to the same page, male rats and horses (and mice) are unique among non-monotreme mammals in not having nipples.

Male humans have nipples because there's no evolutionary pressure for them not to. (Why do men have nipples?) Then, why was there selection for males to lack nipples in the case of mice, rats, and horses?

(Apparently, male horses lack nipples because "female horses have their nipples between their hind legs, and in males, that real estate is used for other purposes". (Straight Dope))

Evolutionarily, why do male rats and horses lack nipples?

Answer

Male mice lack nipples too. Mice are frequently used for embryonic research as they are small and reproduce quickly. It is thought that male mice do develop nipples, but that they regress during development (Wysolmerski, 1998).

In general, it is thought that mammalian organisms develop as females by default when there is no male (Y) chromosome present (Hughes, 2004). Notably, X_ individuals and XY individuals with certain Y-chromosome deletions also develop as females. Basically, it is testosterone that suppresses female features. Hence, also boys with testosterone production, but without the appropriate receptors also develop as females.

Hence, men have nipples because females do (Simons, 2003).

The development of nipples is a pretty complex process (Wysolmerski, 1998). Disruptions in the process cause regression. Indeed, in mice, the tissues typical for nipples do develop in males during embryogenesis, but degenerate within a few days, leaving no trace of nipples at birth.

Hence, given the mouse example, I think that every mammalian male species develops by default nipples somewhere in development like mice, but that development is halted at various stages across species. The later in development it halts, the more it resembles female nipples. When it is stopped very early after gestation, they regress completely, like in mice.

Why is there a difference between species as to when the nipple development halts? Because the nipple developmental sequence is complex (Wysolmerski, 1998), and because evolution typically prefers losing things over gaining them, it is likely that by happenstance one of many crucial genes was lost in males, but selective pressure was simply too small to be of any significant advantage over males with slightly better-developed nipples. But from here on, it is guessing.

<sub>References

- Hughes, N Engl J Med (2004); 351(8): 248-50
- Lawrence, Nature News, August 1999
- Simons, Sci Am, September 2003
- Wysolmerski et al., Development (1998); 125: 1285-94</sub>

botany - How does the sensitive plant detect vibrations?

The sensitive plant (Mimosa pudica) is a remarkable little plant whose characteristic feature is its ability to droop its leaves when disturbed:

Apparently, this ability to droop rests on the cells in the leaves of the sensitive plant being able to draw water out of themselves through changes in intracellular ion concentrations, which makes the leaves less turgid.

What I'm hazy about is how the plant "senses" vibrations. Plants don't really have a nervous system to speak of; how then does the sensitive plant "know" to droop when disturbed?

publications - When should I write a thank you letter to the author of a scholarly paper?

If I read a scholarly paper and find it interesting and beneficial, should I write a short thank you letter to the author? Should I send the thank you letter from a .edu email address?

Answer

It certainly wouldn't hurt, and as a published author myself, I would say it would be very nice feedback, particularly if you include details about:

• 
  

  specifically any particular points/methods you found useful.

  
  


• 
  

  A brief outline of how you are extending the work.

  
  


• 
  

  Perhaps any question you have about the article.

  
  

This could be a good way to make yourself known in Academia, especially if the author is an influential scholar in your field. However, a caveat, don't overdo it - in terms of being 'over the top' complementary or too many 'rapid fire' letters/emails.

But, it would more than likely be appreciated as it would be a validation of the author's work.

publications - Which articles don't need experimental results?

I see that every paper which propose (present) something (new) (over existing methods) should possess an experimental result section and some tables and figures and numbers. Some papers may be rejected if they don't follow this format regardless what they are going to say. They may are needed for the evaluation of the method or comparison of it with the related methods.

I myself, when read some papers, based on the arguments in them, propose a new or more general techniques which covers their shortcomings. Or I may propose a new formalism or tool which can be shown that is novel or useful.

However, providing some experimental results for them is not always easy. Some measures should be defined and samples should be gathered to get some statistics ( for something that you know works in practice). In fact some times, I don't know how can I offer such results or whether it is necessary or not.

Then, I would like to know which type of researches need those quantities and tables and diagrams?

Or in the other words, which articles don't need a results section? How can I write or put my arguments to show that it doesn't need further evaluation.

I give some examples to show my problems (first I should say my filed of study is computer science):

• There are some grammar or annotation scheme to build a linguistic corpora for English, there is no such corpora for Persian, I justified a similar scheme for building such a corpora for Persian based on the language features, Should I provide (experimental) results?


• I developed a software which filter a webpage and remove noise and reformat the content to enhance readability and comprehension for non native English speakers ..... I used the results of another article on reading comprehension which didn't implement a web tool for their foundings.. Should I provide (experimental) results?


• There is an algorithm for converting a linguistic corpora specially designed for English language, I generalized it to cover some other languages and justified that with some arguments, should I provide results?


• I proposed a formalism for extraction rules for a data extractor from webpages, I provided many examples how it works, and how it is more robust, understandable and easier to use and based on previous tools and methods and how it borrowed their features ..., should I provide (experimental) results? ......

graduate admissions - Answering "Why do you want to become a research mathematician?"-type questions in a statement of purpose

How should one address the classic "Why do you want to become a research mathematician?"-type question that is normally asked in the statement of purpose when applying to Masters (and also) programs?

I've read (and I bet so has any admission board) lots of statements beginning with

(*) "I've always loved numbers and solving problems, which is the most rewarding thing of my life"

(or variations thereof), which seems like a rather lame way to start off.

I do have an enthusiastic love for mathematics and the challenges of research work, and have some "philosophical" reasons to dedicate myself to it (I've been mostly inspired by Prof. Thurston's answer to this question which was asked on MathOverflow), and a somewhat defined (although broad) area that deeply arise my interest (which I surely should mention). However, I'd really like to avoid seeming unprofessional (or outright creepy) as in passage (*), and trying to convince anyone that I've always been in love with my field "ever since I could take my first trembling steps". So my question is:

What points should you keep in mind to address the question "Why do you want to become a research mathematician?" in a statement of purpose without seeming unprofessional but communicating your genuine and deep passion? And what is actually expected?

---

A related question is Choosing research ideas to include in a statement of purpose.

Answer

I can't speak for all mathematics graduate admissions everywhere, but when I was on the admissions committee for my department (UGA) we generally did not take the statements of purpose all that seriously. Most statements of purpose are indeed a bit dull and similar to each other. The particular question "Why do you want to become a research mathematician?" is certainly not explicitly asked across the board (somewhat crankily I could ask "Why are you asking that for a master's program? The degree needed to become a research mathematician is a PhD. Depending upon your local academic culture, getting a master's degree could either prepare you to enter a PhD program or it could be totally unnecessary for that.").

It's not a bad question, but to me a very acceptable answer -- really the best answer -- is because I really enjoy mathematics, I am good at it, and I am eager to learn and do more of it. Not to brag too much, but I am in fact a research mathematician. Why did I become one? Please see the above bold-faced text: even with the benefit of many years of retrospective, I don't really see a better answer than that. In fact, honestly I think the bold-faced answer is probably better than the wordier answers I gave in my early 20's: how mathematics is the best field because it has an amazing internal consistency and a level of rigor and certainty unmatched by any other intellectual endeavor, how mathematical theorems are eternal so proving them is a form of immortality, and so forth. Yikes. It's not so much that I don't believe these things anymore but rather that I don't find these beliefs very interesting or distinctive: I think they fall nicely under "because I really enjoy mathematics".

The problem with taking the personal statement too seriously is that the ability to write an excellent personal statement -- especially an unusually interesting or insightful one -- is only weakly correlated to success in a math PhD program. I looked at personal statements to see whether they were adequate, e.g.:

• 
  

  Do they use flawlessly correct grammar, syntax and punctuation? Do they express their (not so complicated) ideas clearly? Do they convince me that this student has strong enough writing skills not to be dragged down by this in the future? (Many STEM-types have alarmingly weak writing skills, and for sure it drags them down. I take the GRE Verbal score very seriously.)

  
  


• 
  

  Do they avoid gross misconceptions about what a math PhD program and a math research career will be like? I don't expect an incoming math PhD student to really understand either one: most don't, but they learn eventually and adapt accordingly. However some students are clueless so far beyond the norm that it becomes a risk that as soon as they arrive they'll think "Wait, what is all this??" and drop out in their first semester.

  
  


• 
  
  

  Do they seem like a responsible person and not a snowflake who thinks that graduate school is a summer camp that they get paid to attend? (It happens...)

  
  


• 
  

  Do they avoid sounding too weird? Yes, mathematicians can be weird, like many people, and the amount of allowable weirdness in the mathematical profession is probably greater than most. But it is still only a finite amount, and I know people who have the intellectual skills to be a mathematician but not the requisite level of socialization. It's not pretty but it's true.

  
  

If you avoid these and similar negatives in a personal statement and mostly just evince a sincere, not terribly pretentious or twee "I really like math", then I suspect you'll do fine with this part of your application. You would in my department, certainly.

publications - Difference between a letter/short article and a full length article?

After 3 weeks from submission, I recieved the below email from the editor in chief of an applied math journal, asking whether I would consider changing my manuscript from full length article to a letter/short article, giving primary reason that the article length is short, so it would suit a short article/letter, and mentioning that the journal publishes short articles of high quality along with full length articles in all regular issues. I was asked to give my decison. I had a look at the letters/short articles of that journal from previous issues and found that they are no different, except in length. So I am not understanding the difference.

I am not able to interpret, whether I have been strongly adviced by editor, and that I better go with it. The editor already had that article with him for 3 weeks, so he might have had a look at it and might be giving strong advice. I also don't fully understand the difference between both modes of publishing. Do these two have different academic values?

Email:

---

Dear Mr. XXXX,

I am writing to ask if you would consider to change your submission, XXXX, to a Letter from a Full Length Article. The reason for my request is based on the short length of you manuscript. XXXX Journal publishes short papers of high quality. Please let me know of your decision. The official review process will not proceed until we hear from you. Thank you.

Kind regards,

XXXX

Editor-in-Chief

Answer

In my experience, there is no real difference between "full" articles and "short" articles except for length.

Many journals, especially more recent online-only ones, do not bother with this distinction at all. An article is simply as short or as long as the article turns out to be. Even with journals that do make the distinction, it often has little impact of the de facto length of the material once supplementary material is included---all that is affected is the fraction of the published "iceberg" that is "above water" in the main text. The peer review process is generally the same, and the perceived value the same, just simply some are shorter than others.

In terms of visibility and citations, short articles are typically just as visible (as you have noticed). I have never seen a citation attempt to distinguish between short and full articles, and most citation formats have no way that one could do so. For those who are affected by publication statistics (e.g., impact factor), that's not affected either: these are calculated by journal, not by article category within a journal.

In short: some things are just shorter than others, and that has little effect on their significance. The editor thinks your article will work better in "short" than "long" format, so take their offer or risk rejection pointlessly.

citations - How to use results/ideas from a paper I reviewed?

I recently reviewed a paper (general applied mathematics context). During the review, I realized that the fairly general ideas introduced in the paper can potentially be applied to a specific problem in a similar context. The authors did not mention this application in their paper, so I suggested to add a short comment about it in my review.

I later started thinking about the application in more detail and tried out some things, which actually seem to work quite well for this application. Now, the paper is still in the review process and might take some time until it gets published. What is the proper way how to proceed here in order to use the ideas and results which I in my exclusive position as a reviewer saw? How can I refer to the paper that is still under review? How can I best discuss the ideas with my co-workers (and potential co-authors) without disclosing that I reviewed the paper?

The paper under review is not available online on any preprint servers such as arXiv etc

Answer

You can't ethically do anything based on ideas from this paper until it is made public (by the authors as a preprint, or by the publisher). In particular, before that point you can't refer to the paper, you can't use the ideas without referring to it, you can't publish or otherwise disseminate results based on it, and you can't discuss it with other people, including your collaborators. It can be really frustrating to know something important and be unable to tell anyone else for the time being, but there's no way around it ethically.

The reason is that submitting a paper for publication is not considered to release it for other use or dissemination until it is actually published. The people involved in processing and evaluating it (most notably the editors and reviewers) have an ethical obligation to keep all information about the submission strictly confidential and not to use it to gain any personal advantage. Once it is published of course it can be treated the same as any other paper, and in the meantime the authors can choose to make information publicly available via preprints or talks (in which case others can follow up on this information as appropriate), but nobody else is authorized to release any information before publication beyond what the authors have chosen to share, or to use it for any purpose other than reviewing the paper. Otherwise it has the same ethical status as using material you stole off the authors' desks.

There's no reason why the research community has to work this way in principle, but it's the system that has evolved over time. (Note that as recently as the 1930's, famous physicists were not all in agreement as to how peer review should work.) It's possible that in the future we will move to systems such as submitting for publication only after releasing a preprint. That seems to be the trend in some fields, but we haven't yet made a full transition if we ever will, and the community's ethical principles still offer protection to authors who choose not to distribute their paper before publication.

Nobody signs a non-disclosure agreement when reviewing a paper, but the ethical principles are well established. Deliberately violating them would be a serious form of misconduct, which could easily be career-ending if it was more than a minor or technical violation.

Pete L. Clark asks in the comments whether referees are allowed to prepare follow-up papers, as long as they don't distribute them before the original paper becomes public. I.e., does the "you can't ethically do anything based on ideas from this paper" really mean you can't do anything, or just that you can't disseminate anything yet? (Let's assume it's a single-authored paper that is not discussed with anyone else in advance.) My interpretation is that nobody can stop you from thinking a little, and you may not even be able to stop yourself, but actively working on and writing a paper of your own would be abusing your position as referee. There probably isn't a consensus as to exactly where the line is for what's strictly forbidden, but either side of the line could still look terrible. If you want to publish work you began thinking about as a referee, I'd strongly recommend against doing it so quickly that's it clear you had to have known about the original paper in advance.

Incentives for professors to write recommendation letters

Is one incentive their ability to communicate their perceptiveness to people in their general community?

Are there other incentives?

advisor - Dealing with a PhD student reneging on an agreement to appear in social media

Inspired by this question, I have a similar but somehow different problem.

I recently assumed a tenure-track position. One of my strategies for a visible start is to have a strong presence in social media. We have a youtube channel in which students regularly explain their achievements. Or sometimes we post short educational materials. We also prepare brief videos for each publication as some publishers promote the videos.

However, one of my PhD students refuse to cooperate. I specifically asked him in the interview (both video chat and email questionnaire) if he is willing and ready to prepare such video materials for the group, and he firmly answered YES. Now, he claims it is not part of the job description for a PhD.

I first preferred to ignore this conflict, but now other students are reluctant to do so. Now it is more a matter of my authority.

Since I am new, I do not want to take the case to the department head or other officials.

outward appearance - What do people usually wear to conferences?

I'm going to my first conference in about a month, where I will be presenting a poster.

How do people usually dress for conferences? Do I need to dress more smartly than usual? Is formal dress (e.g. a suit) normal? Or does no-one really care?

I'm a PhD student, if that makes any difference, and both my university and the conference are in the UK. It's a biology conference.

Answer

It depends a lot on the event (some gatherings are more formal than others) and on your status (win a Nobel prize, and you can wear anything you damn well want), but in general, you're not really expected to wear anything fancier to an academic conference than you would for a normal day at work or in class.

In practice, most people do tend to dress up a little bit, just to look their best, but still, even if you just wear your normal clean everyday clothes, you're not going to embarrass yourself (any more than you usually do, at least). As the other answers note, "smart casual" is the usual style here.

Nothing says you can't wear a suit if you want to; I see people do that all the time in conferences. Then again, some of those people also wear a suit to work every day, so...

Still, if you're in doubt, why not ask your advisor (or someone else in your group who's been to similar events before)? That's part of their job: to teach you the basics of academic work, which certainly includes presenting your work at a conference.

molecular biology - Effect of single nucleotide deletion or insertion on primer annealing

How is primer annealing, and, consequently, PCR amplification affected by single nucleotide deletion or insertion inside the primer ?

Imagine a primer like this:
GCGTCATAAAGGGGACGTG (primer)
and the corresponding part of template DNA has one G missing, so it looks like this:

GCGTCATAAAGGGACGTG (template).

The possible pairing could be
GCGTCATAAAGGGGACGTG primer
GCGTCATAAA_GGGACGTG template
or
GCGTCATAAAGGGGACGTG primer
GCGTCATAAAGGG_ACGTG template
or anything in between.

Is it possible that amplification with such primer would be completely disrupted in normal real time PCR at 60°C annealing? Could this completely disrupt the amplification?

If the mismatch was substitution-like, I would be pretty confident, the primer would be still functional and amplification would occur. In the extreme case, it would be at least residual amplification at late Ct. There are a lot of data, how substitution mismatches affect primers and I also have a lot of personal experience with that.

Unfortunately, the deletion mismatches are less studied plus googleproof. The only indication I have found is this work:
Lipsky RH, Mazzanti CM, Rudolph JG, Xu K, Vyas G, Bozak D, et al. DNA melting analysis for detection of single nucleotide polymorphisms. Clin Chem. 2001;47:635-44.
In that work, single nucleotide deletion had similar or lower affect on melting temperature than substitution mismatch. But it was about longer oligos. Examples:
Effect of deletion:
133 bp fragment, 67 % GC, deletion SNP at position 43, delta Tm (homo-hetero duplex) = 1.2°C
Effects of substitutions:
152 bp fragment, 43 % GC, substitution T to C at position 68, delta Tm (homo-hetero duplex) = 0.9°C
100 bp fragment, 41 % GC, substitution T to C at position 42, delta Tm (homo-hetero duplex) = 1.4°C
163 bp fragment, 60 % GC, substitution C to T at position 86, delta Tm (homo-hetero duplex) = 2.2°C
110 bp fragment, 59 % GC, substitution G to A at position 66, delta Tm (homo-hetero duplex) = 3.8°C

Questions:
1. Can you recommend me literature about how deletion mismatches inside (not at the very end of !!!) primers affect annealing and PCR ?
2. Would You guess the primer in my example would be still functional , at least partly, or would You expect no amplification at all ?

---

EDIT after your inputs:
This online application " mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting " thinks, deletion mismatches are more destabilising than substitutions, at least for short primers. For my own example, it calculated delta Tm (homo-hetero duplex) = 12.9°C . If I try substitution mismatches instead, delta Tm (homo-hetero duplex) is in interval 3,8°C to 5,7°C.

New question
If you have experience as similar as possible to my case, which is 19 nt long primer with single nucleotide deletion in the comlementary template at position cca 6 - 9 from 3' primer end, annealing temperature used at 60°C, please let me know if You achieved amplification or not. Please, give me a respective reference, if you have it, so I will quote it in my review :-) .

Also, I am still interested in general info, as long as the topic is narrow enough to be about single nucleotide deletions or insertions in primers. (Not substitution mismatches).

conference - What is an extended abstract?

Some conferences ask for an extended abstract. What are the differences among "abstracts," "extended abstracts," and "full papers?"

Answer

An abstract is a preliminary submission that summarizes the contribution of a paper. There are usually strict limits on the length of an abstract, either in terms of words or of total characters (rarely do they exceed 1000 words or 5000 characters; they are often substantially shorter than this.

An extended abstract and a full paper are nearly the same; the primary difference is that an extended abstract tends to be somewhat shorter than a full paper; I've seen extended abstracts from 2 pages up to 6 pages, while conference papers run from 4 up to about 12 or 15, depending on the space allotted.

One other important difference—outside of computer science, extended abstracts almost never go through a formal peer-review process before being published, while a conference paper will typically have at least one reviewer. (I think this is the case for almost all such papers, but there may be exceptions.)

Non academic career options for PhD in Math

I am thinking of getting my M.S. in Computer Science. I chose C.S. because I enjoy programming and because its a solid choice, career wise. Low unemployment, good pay, all that jazz.

But my real passions has always been math and lately I have been thinking about swapping and going for my graduate degree in Math. If I went the math route I would probably go full PhD (since I don't think there is much you can do with just a Masters in math).

But as much as I love math, I can't see myself being a math teacher. I would want to work in research or industry, applying math to solve real world problems.

What kind of non-academic jobs are there for someone with a PhD in math (or what is the best resource to see what jobs are out there)?

phd - What should I put in the introduction chapter of my thesis?

I have to start writing my thesis. My topic for research is work life balance in IT sector - a comparative analysis of male & female IT professionals in Pune.

I need help in writing the first introduction chapter. what all should be included in this chapter & what should not?

publications - How is the H-Index of a journal related to its grouping in SJR?

How is the H-Index of a journal related to its grouping in SJR?

I was searching for journals for submitting my first manuscript.

I came across this site https://www.scimagojr.com which very well lists the journals and also groups them into four groups Q1,Q2,Q3,Q4.

I have the following two questions:

1. 
   

   I found instances where a journal with low H-Index got grouped in Q2 and a journal with higher H-Index got grouped in Q4.How is this possible?

   
   


2. 
   

   Is this grouping of SJR well-defined?Is it more prestigious to publish in Q1 than in Q2?Is Q1 journal considered to be of higher value than Q2?

   
   

This is somewhat related to my previous question How are journals evaluated?

Answer

They are different indices, measuring quite different things, and shouldn't be expected to be highly correlated.

• The H-index is simply the number h of articles that have received at least h citations.


• The Scimago Journal Rank (SJR) only considers documents published in the journal in the last three years, and weights them depending on the prestige of the journals the citing papers were published in. The idea is that a citation is "worth more" if it's from (what SJR determines to be) a highly prestigious journal. (Interestingly, the prestige factors are determined self-consistently, using an algorithm like Google's PageRank.)

1. I found instances where a journal with low H-Index got grouped in Q2 and a journal with higher H-Index got grouped in Q4. How is this possible?

The H-index is strongly linked to the number of papers the journal publishes, see this answer. Hence, it's quite possible for a small selective journal to get a low H-index, but high SJR ranking. Conversely, a large journal with lower standards is likely to eventually publish enough highly cited papers to achieve a high H-index.

2. Is this grouping of SJR well-defined?Is it more prestigious to publish in Q1 than in Q2?Is Q1 journal considered to be of higher value than Q2?

It's well-defined in the sense that there's an objective algorithm to calculate it, and it seems to do a decent job at capturing the trends in the fields I'm familiar with. A Q1 journal will generally be more prestigious than a Q3/Q4 one, but there might be exceptions, especially as any measure can be and will be gamed. However, if there's say one journal just above the Q1/Q2 cutoff, and one just below it, I wouldn't take Scimago's word for it. While it's useful as a rough guide, it ultimately, like most rankings, is no substitute for experience. Look where leaders in your field publish, where the papers you read are published, and discuss journal quality with colleagues or mentors.

funding - How do you "grow your own" post doc opportunity?

I am a finishing doctoral student (graduation in ~7-9 months) and I would love to get an year or so of postdoctoral experience. I've come to understand that a postdoc is generally paid by funds created for the project (s)he is a postdoc for.

How should I go about "growing my own" postdoc opportunity? In other words, how should I go about soliciting for funds for research ideas? I know it is a rather daunting task. Although I have participated in writing several proposals (some of which were accepted), I have never been the PI or co-PI for any of those projects -- generally just one of the grad students working on it.

I am at a US university and have already taken at look at NSF's website.. Being an international student, I don't have all the options available to domestic candidates.

This is what I've thought of so far:

1. Come up with feasible research idea and approach advisor.


2. Discuss idea and possible collaborations.


3. Try to categorize it into NSF's or any other funding agencies categories.


4. Write a proposal in the summer and submit it during the next window of opportunity.

Any pointers, tips or funding agencies I might also look at?

Some background: I am a PhD candidate in Mechanical engineering with emphasis on fluid dynamics, applied mathematics, energy systems and space systems.

Answer

From what I've seen, you've just described perfectly what many professors would view as the "ideal postdoc". As one of the main goals of your postdoctoral training is to gain experience writing your own grant proposals, your four steps are very close to what you should be doing.

The most crucial part for you will be finding a postdoctoral advisor with whom you get along. As is typical in research settings, look for someone with significant research experience who has a successful record of getting proposals funded. Given that this is your goal, this is possibly more important now than their publication record. You should be able to find this out by asking around the department and speaking to graduate students, and even just asking the advisor directly about their recently funded grant applications. Once you find someone, everything else should go fairly smoothly.

1) Come up with feasible research idea and approach advisor.

2) Discuss idea and possible collaborations.

You should do this both on your own and through talking to your advisor. Remember that one of the main factors driving whether a postdoctoral grant is accepted is previous experience of both the postdoctoral fellow himself and the advisor; consider ideas in areas where you have experience doing research and your advisor has experience mentoring.

While you can consider collaborations, my postdoc advisor told me that at most I should consider one other collaborator, other my advisor himself, as collaborative proposals are more complicated, both from a submission and administrative standpoint.

3) Try to categorize it into NSF's or any other funding agencies categories.

Your advisor should already be aware of relevant funding opportunities.

4) Write a proposal in the summer and submit it during the next window of opportunity.

I assume you wrote "summer" because you were thinking of a particular grant, but different opportunities have different grant submission deadlines. Again, talk to your advisor to see which grants the thinks would be a good fit for you, and check out their respective deadlines.

entomology - Do ants really dispose of their own dead, and how/why?

I just read this from Wikipedia's Swarm Behavior article:

Despite the lack of centralized decision making, ant colonies exhibit complex behaviour and have even been able to demonstrate the ability to solve geometric problems. For example, colonies routinely find the maximum distance from all colony entrances to dispose of dead bodies.

There was no citation.

Is it true that ants dispose of their own dead? If so, how and why? I would've though it would be much better to just eat their own dead, which would be a "free" food source allowing the colony to reclaim some protein and nutrients. It would cost much more energy (and risk) to transport dead ant carcasses away from the hive.

human anatomy - How do we sneeze?

When a stimulus triggers the sneezing pathway, known as the trigenimal nerve network, how do the droplets from a sneeze get created within the nose? What affects the size of these droplets?

How is sugar in fruit metabolized, or digested and used?

I thought before, in general, when we have sugar in our food, then the sugar goes in our bloodstream, and if there is too much sugar, then insulin is secreted by our pancreas, and the sugar is pushed into our cells for storage, and to lower the blood sugar (and the insulin may over do it, causing our blood sugar to be too low).

But then recently I heard that sugar in fruit goes through a different route: it goes directly to the liver, and not moderated by the pancreas and insulin? How does it work?

How long does it usually take for published articles to show up on Google Scholar?

The title pretty much says it all - what's the typical delay with which Google Scholar indexes newly published articles? (Note I'm not talking about citations, but about the article showing up at all.)

Edit: the article in question went for over six months after being published (in a well-regarded Springer journal with its own Wikipedia page) without appearing on Google Scholar, until it received a citation, at which point it was added to Google Scholar almost immediately. One more motivation to write papers that get cited. :)

Edit 2: Another article in an even more mainstream journal took a little over seven weeks.

Answer

My article showed up in a few days. Since google is crawling, I believe (although I am not certain), that updating other sources such as policy, government, medical repositories and other resource hubs that allow you to update fields, add links etc, without needing to upload the article, increases the external links with the article page. This might not be necessary to expedite the process, but if the article is not showing up within the normal period of time (which could be a week), I believe this would be a good step to take. This advice also applies for anything else such as websites and blogs. Actually my repository link showed up in google before the actual journal page did!

genetics - Interbreedability between current humans and his ancestors

I want to know the first point of time in the past when genomes have diverged so far from modern human genomes so that they both (human and ancestors) are not interbreeadable anymore and can be seen as separate species.

Answer

Considering only post-zygotic isolation and based on below discussion, I would tend to think that 20th century human could interbreed with our ancestors living a 1 to 2 millions years ago. I would give a range between 100k years and 8 MYA for safety.

Concept of species

The post How could humans have interbred with Neanderthals if we're a different species? makes a good introduction to the difficulties behind the concept of species.

Pre-zygotic isolation

Anatomically speaking, it is probably possible to get a spermatozoid cell from a 20th century man start fusing with a Homo abilis ovule (and vice-versa). The potential pre-zygotic isolation will rather be caused by aesthetic appearance.

To the risk of sounding posh, I would say that Homo abilis hairy face does not exactly fall within my standards! I suspect it will be the same for many of us, humans of the 20th century. It is hard to really know how much time one needs to go back to consider that we don't disgust each other enough to refuse mating together. There are a few reasons why this is hard

• Reconstruction (esp. facial reconstruction) is often too inaccurate to really allow to tell how ugly their faces were.


• It is going to be super hard to tell what they would just about our faces today! I bet they'd laugh at our ridiculously small jaws!


• It is hard to fully separate the environment from the person. In middle-age (in Europe at least) people would bath a few times in a life-time. Again I would consider this not in my standards!

But let's focus on post-zygotic isolation.

Post-zygotic isolation

Humanzee

The humanzee (Homo sapiens sapiens × Pan) (also known as the chuman or manpanzee) is a hypothetical chimpanzee/human hybrid. An unsuccessful attempt to breed such a hybrid was made by Ilya Ivanovich Ivanov in the 1920s. There have been occasional reports of human-chimpanzee hybridization, notably regarding a performing chimp named Oliver during the 1970s, but none of them have been confirmed. Similarly, the possibility of a chimpanzee–gorilla hybrid, known as a koolakamba, also remains unsubstantiated.

There is no evidence of humanzee but it is important to realize that the idea of such hybrid is not fully unthinkable. Human and chimpanzee share a common ancestor about 6 millions years. So, if a humanzee is consider eventually possible, I would quite definitely consider that a H. abilis (~1 MYA) or H.erectus (~2 MYA) and 20th century human could well interbreed if we were to live at the same time.

Sumatrans and bornean orangutans can hybridize (Malinson, 1984) despite that their lineages have split about 1.3 MYA!

So putting all of that together and follwing some vague intuition, I would personally tend to think that 20th century human could interbreed with our ancestors living a 1 to 2 millions years ago. I would give a range between 100k years and 8 MYA (MRCA with gorillas). But really, it is a rather vague intuition.

See also CrashCourse > How to Make A Humanzee

evolution - Junk DNA and "random" mutations

I'm somewhat irritated by "mutation" generally being described as a fully random factor in evolution: pure randomness does not seem like something that can survive in a long evolutionary process.

And some basic evolution in some long-lived organisms appears to happen in quite fewer generations than one would consider plausible considering just natural selection over an unbiasedly mutated genetic base.

So I'm wondering whether there have been attempts to view mutation itself as a process influenced by evolution. For example, couldn't "junk DNA" result in a susceptibility to certain mutations that is determined by environmental factors, like amount and constitution of nutrients, ambient temperatures and others.

The overall discussion of mutagenesis I can find focuses entirely on "damage", again basically assigning all mutations a negative or at least undirected character (like more mutations occuring under stress, with the "aim" being more likely to have more random mutations where one offspring might be more successful than the stressed parent by chance).

In a similar vein, I don't see not much of anything about evolution and competition of gametes: how different environmental factors influence which of an abundance of eggs mature and which of the (asexual) male gamete reproduction mutation in the testes will be favored over time or under environmental conditions.

Basically all of evolution and natural selection seems about how to survive into fertility and select a partner, and that's it as genes are constant apart from random cosmic radiation or toxic substances.

I think that this kind of viewing the message in the DNA as isolated from its medium just does not sound like something that would survive billions of years without something less random replacing the pure randomness.

So are there any major studies trying to figure out whether certain mutations leading to better adapted phenotypes occur in a non-random manner (namely not just affecting mutation rate but also direction) in response to environmental circumstances?

students - Should I hide the fact that I did a group assignment completely by myself?

Three students and I were assigned a small (~14 hours of work) group project. Because there was no effort on their side to meet and work, my e-mails regarding their progress remained unanswered and from previous experience I know that their quality of work is much lower than mine, I decided to do it myself and already spend around 10 hours doing ~2/3 of the work. The reaction of the others was something along the lines of "Wow, thanks man. This looks great. You're the man!"

Later I asked them to help me out with the rest because I had another assignment due and thus my time was limited but the contributed work was much less in quantity than what I asked for and also of very low quality, hinting that they did not bother reading the assignment thoroughly or did not really spend time actually thinking of something substantial to contribute. As it stands now I will have to do the remaining 1/3 by myself as well.

Because I had a question for the lecturer I was writing him an e-mail and one of the sentences was

I already did most of the work but we need to...

then I thought whether it would be better to write

We already did most of the work but we need to...

The reason I even mention it, is that it is very close to the submission deadline and I do not want him to think that I/we only started now. My intent was not to slip by this information and blame the others.

Is there any reason to be "diplomatic" and actively hide the fact that I did everything myself?

I am mostly interested in the impression I will leave on the lecturer. On the one hand I do not feel like I owe the others anything, on the other hand I also want to avoid the lecturer seeing my behavior as tactless or arrogant.

Answer

Personally I would dodge the issue using

Most of the work is done, but we need to...

I don't think it will really matter which option you go with, but that way you don't have to worry about it.

Anyone setting a group project knows that it is fairly likely someone will end up doing all the work. If they don't take any action to avoid that (and it sound's like they haven't in this case), then presumably they don't really care.

I understand that you want to get the credit for doing the work. But I agree it might come across as tactless to point out the situation in your email. It might be more productive to separately have a conversation with the lecturer about why they haven't taken steps to avoid the situation occurring.