publications - How can editors and reviewers detect data manipulation?

I am preparing a paper in the field of Computer Science.

In order to report test results, we usually run a number of tests and report the average of those tests.

For each test, we generate random data.

Because of the randomness, at some points, the results may come out not as expected.

For instance, a graph may be like:

Usually, one should explain why on points 8, 11 and 12 there is a decrease on the plot. Probably, it is because of that randomness.

Not hand-crafting all the graph, but just manipulating a few points makes the graph acceptable:

Since three weeks or so, I work my ass off and try to figure out why my resulting graph looks like the first one. Sometimes I feel like yielding to temptation and just modify the raw data before I go crazy.

I believe, at this point the title became misleading, so let me make it clear:

I am not seeking an advice on data manipulation. I will not manipulate my data. However, I ask to myself "how the hell this can be detected?"

And now, I don't only ask to myself, but to whole community. How is this detected? For editors, referees out there, have you ever detected something like this?

Answer

The image manipulations reported on Retraction Watch are most of the time naive collages of gel photographs or spectrograms. They get caught, among other things, because repeating patterns in the noise appear on closer inspection, or linear disruption of the noise are visible, see this.

For 1D data, the case you mention, there is the Benford's law and other statistical tests that can indicate potential manipulation of data. It usually relies on human beings preferring certain digits over others, even unconsciously, thus generating data that has a non-random variability.

Also, many journals ask for graphs to be submitted in vector format, which means you are actually sending the data points, and not just a rendered figure. Things like editing out a few data points to smooth a curve will be apparent.

Now, to the best of my knowledge publishers and, even less so, reviewers don't systematically screen for these things, they only do so if they have suspicions, because the scientific publishing process is based on good faith. But if the paper gets any sort of attention it will get caught by post publication review.

Don't fabricate/manipulate data. It's adding unwanted noise to an already noisy signal, it's dishonest towards your coworkers, the people who fund you, the publisher and the readership, and it will ruin your career.

graduate school - What is the optimal number of times one should meet one's PhD. advisor?

I see sad students who meet may be once in a month and they complaint of not having enough progress. I have seen systems where the prof meets almost every few hours on weekdays and the prof is basically continuously working with the students. I see students who meet every 2-3 days or every week.

So what is the "right" frequency if at all? What is the good frequency?

Once the weekly(instant) gratification of getting full scores on the course homework is removed it is quite a challenge to keep a gauge of whether one has made any progress during the week. How does one measure progress during the week during one's PhD?

evolution - Are there genes in humans from the common ancestor of all organisms?

How long ago can human genes be traced? Are there any genes that go back unchanged to the beginning of life on Earth? And if so, how many?

evolution - Is there any evidence for secondarily poikilothermic vertebrate?

Is it possible that an endothermic physiology can evolve into an ectothermic (poikilothermic) physiology? I have a non-scientific gut feeling that it is irreversible. Whales and dolphins are evolved from land mammals, and they've remained warm blooded. While it doesn't give them any obvious advantage in the water, apparently they've compensated with massive amounts of body fat instead of devolving. If the ocean offers opportunity for mammals, then why haven't fish evolved to be warm blooded directly?

professors - Academic freedom and unpopular or offensive views

Academia values academic freedom. However, there may be some practical limitations on academic freedom. What repercussions might an academic face for voicing unpopular or offensive views in the name of academic freedom?

For example, how might a professor's academic reputation be impacted by publicly expressing views that support dictatorships (and other type of politicians) and their established crimes and violation of human rights?

Answer

First, academic freedom as it is commonly understood does not refer to one's views and publicly stated opinions, but to the freedom in which they conduct teaching in the classroom. The reference in US is the 1940 Statement of Principles on Academic Freedom and Tenure stating that

Teachers are entitled to freedom in the classroom in discussing their subject

But as a rule, academics do not get special treatment outside of the classroom with regards to freedom of speech. It's certainly not the case in the US, and I am not aware of any other country where it might be the case.

Now, regarding the impact of unpopular or offensive views on reputation, it will heavily depend on your colleagues! I personally find that, while freedom of speech is highly valued in academic circles in general, Academia as a system is a rather conservative institution and I suspect you would not find much more sympathy for extreme views than in any other workplace.

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NB: Academic freedom is also used to refer to a US jurisprudence applying to universities and colleges; in that sense, it is unrelated to rights and duties of an individual teacher.

teaching - How to deal with a lazy class?

Imagine that you want to conduct your undergraduate classroom in a more creative way and introduce practical projects as a part of the final grade. However, students are lazy to embrace extra activities, and all of them decide not to deliver any report.

The department does not like the trouble of failing all students in a course because of an extra project.

What would you do to implement change when students are widely resisting? Or as @JeffE suggested, How to deal with a department that does not give its instructors autonomy in assigning grades?

Additional Description: In fact, I want to change the grading system to reduce the weight of final exam, and add to small projects (e.e.g writing a one-page about the topic under consideration). The lazy class prefer to deal with one final exam instead of continuing homework. The school does not support this method, but they do not stop me as long as there is no trouble.

Answer

It's a very difficult position you are in. The school does not want you to fail all the students and it seems the students might know that and are cooperating to overrule you. This is the like the two prisoners (in the Prisoner's Dilemma) finding a way to coordinate their actions. In this case, as I said, you have a very difficult situation.

It seems to me that three major issues in this case:

1. 
   

   The school says they give you power but they really don't. If this is the case, then you must deal with your boss (or higher) to find out what you can do and what you cannot. One way to test that power is to tell your boss that you will fail all the students because they are actively resisting course requirements. If your boss says that you must find a way to get the students to do the work, then you know you do not have any power and you must decide if this is acceptable to you or not. If not, go somewhere else (if you can). Otherwise, you have to live with it.

   
   



2. 
   

   You may be out of touch with what the students are capable of doing. This is quite common for new teachers. For myself (when I was starting to teach undergraduate students), I thought the students would all be hard-working and dedicated to their studies but later found that they were just like most undergraduates trying to get around the work and they didn't understand the importance of studying or the importance of their university degree. I was comparing them to my graduate-level classmates (since those were my most recent memories) but that was clearly wrong of me and I was far too expecting and too strict. If you are putting on them more than they can do, then perhaps you need to reflect on the requirements you've created. Are they really reasonable for the students you are teaching?

   
   


3. 
   

   The students might simply not understand how to do what you are asking them (this is related to point 2). Some students (especially 'unprepared students') need more attention and more explanations in order to do the work required in higher education. You might need to spend more time on general study skills (inside and outside of class) and less time on course content. That is, teach them how to research, how to write a lengthy report, etc. as opposed to simply teaching them about Theory A, B, and C.

   
   

There is a fourth issue which I raised in the initial paragraph and that is the students might be working together to overpower your authority. If this is the case, you must balance between finding out why they feel the need to do that - see points 2 and 3 above - (and solving the underlying problem) and maintaining your own power of authority (which requires you to challenge them back but then you're back to dealing with point 1 above).

graduate admissions - What should go in a diversity statement if I believe I have had no relevant experiences?

So I am completing the application for UCSB, and they ask me to write a Personal Achievements/Contributions Statement, however, I feel I have nothing to say, since I have never experienced anything like examples they give. So what should be talked about in this kind of essay except examples they give?

Here is what on their application:

Personal Achievements/Contributions Statement

UC Santa Barbara is interested in a diverse and inclusive graduate student population. Please describe any aspects of your personal background, accomplishments, or achievements that you feel are important in evaluating your application for graduate study.

For example, please describe if you have experienced economic challenges in achieving higher education, such as being financially responsible for family members or dependents, having to work significant hours during undergraduate schooling or coming from a family background of limited income.

Please describe if you have any unusual or varied life experiences that might contribute to the diversity of the graduate group, such as fluency in other languages, experience living in bicultural communities, academic research interests focusing on cultural, societal, or educational problems as they affect underserved segments of society, or evidence of an intention to use the graduate degree toward serving disadvantaged individuals or populations.

ethics - Should universities give extra time or related accommodations for students with mental illnesses?

Based on this question: Is it unethical to accept extra time on exams when I still do well?

To my knowledge, I don't think my university or home department has a policy on extended time exams or a "disability office". In my entire stay in the university, I have heard of only three people with mental illnesses. Two graduated. One is still in the university, but I have not yet asked her. It seems like she is entitled to have extra time on exams or homework or something that evens the playing field.

Are there any legitimate reasons a university may have for not allowing extra time or something for mentally ill students, assuming of course that the student can prove mental illness? It seems that they ought to give extra time or something to be fair to students.

Relevant links: this comment, this answer, this answer.

As an undergrad student, how should I ask a professor for an opportunity to do research with them?

I was wondering what I should do in this situation as an undergraduate student:

About a month ago, I applied for and did not get into a program that allows first-year students to work on research projects that professors put forward, with the intention of introducing students to research, which included a research stipend, housing, etc.

I was very interested in the professors topic of research, and was wondering if it would be okay for me to ask the professor for the opportunity to work with him essentially as an unpaid intern, as I would really like the opportunity to learn more about the topic.

Would he view this attempt to do research under him as desperate? Or would he appreciate the opportunity to have an extra research assistant?

I know that the answer would depend on the professor himself, and on my relationship with him, but how do professors in general feel about students coming up to them and asking to be a part of their research?

Answer

Absolutely, with no qualifications, approach the researcher and ask what it would take to do research in his/her lab. As a first-year undergraduate student, it's very likely that you don't have the knowledge to contribute to the projects. So approach humbly, asking what you can do to prepare yourself. Ask for suggestions for a review paper or a few research reports that would bring you up to speed. Ask if you can attend lab meetings as a fly-on-the-wall to absorb the controversies and decisions being made day-by-day. The very worst possible case is that you're told, "no." If so, you're already there. Next worst is that you invest your time and get only an education out of it. That's not so bad. You'll be positioned very very well for next year.

Good luck!

publications - Attitudes towards self-plagiarism

I am planning to write several papers exploring various aspects of the same scientific question. Each of these papers must have an introduction which motivates it and explains the relationship between the problem and what others have studied in the past.

It would be fantastic if I could simply copy-and-paste the same introduction, or, at least, 90% of it. This seems to me to be ethically unproblematic. After all, I need to say the exact same things every time, and I certainly don't mind the self-plagiarism. Am I hurting the reader in any way? I suppose I might be, if the reader desired an introduction which consists of original material, but that is an odd desire, isn't it? Its the research, the stuff that follows the intro, that is original.

Sadly, I have gotten wind that the majority of the research community apparently does not agree with the sentiments expressed in the previous paragraph. This leads me here to ask a series of related questions:

1. 
   

   To what extent is self-plagiarism in non-technical bits considered acceptable? I often see authors recycle paragraphs but I have never seen anyone cut-and-paste the entire section outright.

   
   

   I'd be particularly interested in learning whether norms on this vary across different scientific communities.

   
   



2. 
   

   How often do scholars find themselves trying to same the same thing in different words to avoid self-plagiarism?

   
   


3. 
   

   Supposing I insert a sentence to the effect of: "The introductory section 1.2 is taken verbatim from the author's earlier paper [1]." How likely are journal editors and reviewers to complain about this?

   
   

By the way, I am fairly certain they would be very likely to complain about a sentence to the effect of "We refer the reader to [1] for motivation to study this problem and a discussion of its relation to prior work."

evolution - Could humans and chimpanzees hybridize?

In some cases two species can hybridize. For example, Tigers and lions can hybridize to produce "Ligers".

Would it also be possible for humans and chimpanzees (or any other species) to hybridize ? If not, what would be the likely cause of failure?

Why do some hybridization matings produce offspring, like the Liger, and some not? What mechanisms prevent hybridizations?

Answer

The concept of a human/chimp hybrid is called a humanzee. No humanzees have ever been recorded despite the fact that sexual intercourse between humans and chimps have been recorded on several occasions. This suggests that male-human/female-chimpanzee is not capable of producing viable offspring, at the very least.

As to why, several reasons will contribute: humans and chimps have a different number of chromosomes, making cross-fertility unlikely (although animals with different chromosome numbers can and do breed so this isn't absolute). Humans and chimps are anisomorphically quite different (i.e. the ratios of limbs are different and so on) so it's quite plausible that the growth patterns are not compatible. I'm not aware of any exhaustive studies into reasons why cross-breeding is impossible but it's also quite plausible that there are changes in the chemistry of fertilisation, etc. that will limit cross-breeding.

I'd note, finally, that there's evidence from the X chromosome that the human line continued to have some level of interbreeding with chimps for some million years after the initial split (Patterson et al, 2005^†).

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^† _{I see that there are some later publications that have disputed the claims made in that paper. So I'll leave you to judge the merits of the arguments.}

evolution - Why are there nail growth differences between humans and other mammals?

When a cat is growing, his nails are growing with him to some extent. A grown cat has a fixed nail length that is not extending.

By contrast, human finger nails just keep on growing, so we have to cut them to keep an aesthetically pleasing look.

Nature clearly has a mechanism to control nail growth.

What is the most probable reason as to why this is not implemented in humans?

Answer

Cat claws are growing all the time, like horse hooves, or human nails. However, cats and horses usually use their claws/hooves, so they get shortened through mechanical action.

An indoor cat may need their claws trimmed if it doesn't use them enough (that's why cats will want to scratch everywhere), or if has supernumerary toes that don't normally touch the ground. Similarly, cattle that doesn't get to move will suffer from hoof overgrowth, which appears to be very uncomfortable to the animal.

Consequently, if you were to use your fingernails more often for digging and scratching, you wouldn't have to trim them all the time.

publications - Should a colleague receive authorship for identifying a research gap and reviewing a manuscript?

A colleague of mine identified a research gap / problem and reviewed a manuscript of mine addressing said problem. Otherwise, he/she had no other contribution to the conceptualization and execution of the solution and to the writing of the paper.

Does he/she deserve authorship? I don't believe so but I have acknowledged his/her contributions in the acknowledgements section. If this is not standard practice in science, I am more than happy to include his/her name in the list of authors.

Answer

Identifying a research gap and reviewing a manuscript does not seem to warrant authorship to me.

Things would be different if your colleague had also worked with you in designing the study, experiment or research project to address the gap she or he identified. Or if your colleague had written part of the manuscript, say the summary of the existing state of the art.

Different disciplines have wildly different conventions on what constitutes enough contribution to warrant authorship. For instance, the American Psychological Association offers resources and a helpful scorecard. At the first link, we find:

An author is considered anyone involved with initial research design, data collection and analysis, manuscript drafting, and final approval. However, the following do not necessarily qualify for authorship: providing funding or resources, mentorship, or contributing research but not helping with the publication itself.

This does not seem to cover your colleague's contribution under the specific conventions in psychology.

I suggest you look over the websites of associations in your field, and/or of relevant journals/conferences, perhaps the venue where you are considering submitting your work. There may be similar resources specific to your field.

teaching - How to motivate students to do readings

I am planning on teaching a couple of math-y classes next semester that will involve a large amount of in-class group work and discussions, and relatively little lecturing. There will be required outside reading for almost every class (3x/week), but as I am at a large public university where student work habits are not generally great, I am worried about making sure students stay up on the reading for each class. Also, the students will probably not be in the habit of doing reading for math classes.

Currently, to encourage students to stay up-to-date on the readings, this is what I am thinking of doing:

1. Use books that are relatively easy to read and hopefully interesting for the students (closer to popular books than textbooks when possible), and try to make each individual reading assignment short.


2. Give simple quizzes on the reading once a week or so



3. Generally try to make sure the in-class activities are closely related to the assigned readings.

Are there any other effective techniques that would help encourage students to stay current on the reading?

Note: while I want them to read certain things before each class period, I do not want to give a reading quiz every class period.

Answer

I require students to fill out a short summary sheet of the reading prior to the start of class for classes with small group work based on required reading. The summary sheet looks something like a structured abstract of the reading. In total it is less than 200 words of writing. I make my summary sheet available after the class. Based on feedback, the students like the sheets since they help them in reviewing for the exams. It also helps them gauge differences between what I think is important and what they think is important.

I divide the class into groups based on if the students have completed the sheet or not. Generally, I tell students to go to one side of the room if they have completed the sheets and the other side if they have not. I and the students can then quickly visually inspect the sheets to see if they are completed or empty. The groups of students who have completed the sheet get to work on the group activity, for which having the sheet is useful. The groups of students who have not completed the sheet work on the sheet and if time allows work on the activity. I make it a point to reassign students if the sheet is filled out with nonsense.

human biology - Elevated position effect on recovery times from upper respiratory infections at rest?

In nursing school, they advice for people with upper respiratory infections to be in a slightly elevated position at the head region when sleeping. My intuition of the reason is that the lymphatic drainage to the venous arch works better; gravity helps to drain the lymph to the venous system; not only the heart. Bacterial infection of the pharynx occurs in a prolonged exposure of the concentrated lymph.

I got today exact information about exact positions to relieve the body most when sleeping:

• 5-10 % angle to relieve body most, while gravity helping to suck the lymph from the throat; can be helped with the hormone motilium (domperidone)


• more than 10 % is for other conditions

Is there any studies about the effect of elevated sleeping position on the recovery time from the upper respiratory infection?

evolution - What did pangolin scales evolve from?

Were they developed anew or a heritage from fish?

proteins - Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks?

I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks:

Isotopes

If the mass spectrometer you are working with has sufficient resolution look at the isotopes, a singly charged ion will show isotopic peaks that differ by 1 mass unit, a doubly charged ion will show peaks that differ by 0.5 mass units and so on. This is another way to deduce the charge state of a peak and thus the mass.

So let's suppose the spectrometer has a sufficient resolution to look at the different isotopes. It's not really clear for me at which peak I have to start. So to summarize my questions realted to this topic:

• Which peak do I have to look at when determining the charge based on the isotope distribution?
  


• Why would the peaks differ 0.5 mass units (see above)?

update


source: http://mascot.proteomix.org/help/mass_accuracy_help.html
When looking at the above graph, there is a difference of 1 amu between the different peaks.

• What do the isotopes have to do with the charge?


• What does this charge (and isotope distribution) tells us about the peak on which we zoomed in to create the above graph?

Answer

If you have an ion of mass 100 and charge 2, the m/z ratio (let's exclude the root) will be 100/2=50. If you have isotopes, then you expect to find several peaks for a given fragment. For example, the masses of different isotopes of the same molecule could be like: 100, 102, 105 and 107. In this case the spectrometer will detect four peaks, instead of one, for the same molecule (will look something like this): 100/2, 102/2, 105/2 and 107/2. The charge of all that peaks is the same.. it's only the mass that differs.

The page you linked simply makes an example, "singly charged ion will show isotopic peaks that differ by 1" example m=10 z=1 m/z =10, for the isotope m=11 z=1 m/z=11 (difference of 1). If you have a doubly charged ion m=10 z=2 m/z=5 and for the isotope will be 11/2=5.5 (difference of 0.5).

So, if you take the spectra of a compound and you see the isotopic peaks having a distance of 0.5 among each other, you are looking at a doubly charged ion, if the distance is 1, it's a singly charged ion.

What do the isotopes have to do with the charge? Given that the isotopes peaks are around 1 units far from each other, you can conclude that the ion you are looking at has 1 charge.

The last question is not clear to me.

zoology - Is there such thing as Animal non-verbal body language?

Have there been any studies done on the animal use of their bodies to signal, communicate or express their emotions, particularly to members of other species (ex: humans)?

I've been observing a very intelligent indoor-outdoor cat who has been doing the same sideways stretching posture every day he met me. There has been a number of other postures that the cat has been using - tearing at a carpet with claws, or dragging himself against the carpet by using claws that I've repeatedly observed.

Another cat was thumping her head against a door to "knock" and indicate that the cat is outside.

To me, these gestures appeared as clear expressions of intent or emotional state.

Other experiment involved "trained" geese at a local pond who would indirectly approach humans to ask for food. Their body, neck and head position appear to indicate intent (is the animal grazing towards the human or away from the human).

Yet another experiment involves nesting birds who start to clearly express their displeasure at me located near their nesting area. They repeatedly produce high pitched screech until I move away.

For example I repeatedly see geese assume this gesture to intimidate other geese.

As a human, I'm very conditioned to vocal and eye related coordination, and this "non-verbal" language is fascinating to me.

Have there been any studies in how indoor/outdoor - partially domesticated animals communicate with humans?

Is it true that this communication uses their entire body and not just the vocal cords?

Is there some "foundation" language that would be similar among members of the same species, or is it entirely a learned skill that has nothing to do with evolutionary adaptation?

Finally, is there some sort of a brain complexity cut off at which level the animals can no longer understand if they are being communicated with?

Answer

The closest reason that I know of for such behaviour is simple conditioning!

B. F. Skinner conducted some fairly famous experiments with pigeons, where he put hungry pigeons in cages, and randomly administered the food. The pigeons associated the foods arrival with whatever they happened to be doing at the time (be it looking to the right, or bobbing their heads). They would then keep trying this until more food came out (randomly), and the pigeons 'superstition' was confirmed. See the wiki.

I realize this is not concrete, but it seems to me that they are not 'communicating' as such, they are simply repeating what has worked before. It is your anthropomorphication that has meant this seems like deliberate communication in my opinion. Although I'm sure it could be argued that all communication is having been 'conditioned' to use words/gestures to get your meaning across.

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Update (14.6.12)

Just read the abstract for this paper (published yesterday) that finds that experts in dog behaviour can interpret the ('socially relevant') posture of a dog in a similar way to that of a human. We can therefore interpret the body language of an animal (in this case, dog), if we are familiar (you do not even have to have owned a dog necessarily) with the kinds of postures adopted. So the dog does not have to consciously 'communicate' for us to interpret their emotional state (happy/sad/angry/...).

In terms of human-pet communication then, there seems to be more emphasis on the human interpretation of the natural postures adopted by animals, than the animals themselves. Pets may behave very differently to animals in the wild, but it comes back to what the specific human is used to. If you have had a lot of contact with pet dogs you are in a better position to associate the current behaviour of a pet dog with the correct emotional state. No doubt the animal with subconsciously adjust their behaviour to achieve the 'correct' human interpretation, and thus get fed, or whatever.

human biology - Why do people have antibodies against other blood types?

The ABO blood type divides each blood type according to whether they have the "A" and "B" antigen(s) (AB has both, O has none). People also have antibodies against the antigens they don't have (AB has none, O has both), even before they have ever come in contact with those antigens.

Why do people have antibodies against these antigens they have never come in contact with? This isn't the normal situation for the immune system (e.g. for a virus or the blood type rhesus factor)

Answer

According to the Wikipedia entry for the ABO blood group system:

Anti-A antibodies are hypothesized to originate from immune response towards influenza virus, whose epitopes are similar enough to the α-D-N-galactosamine on the A glycoprotein to be able to elicit a cross-reaction. Anti-B antibodies are hypothesized to originate from antibodies produced against Gram-negative bacteria, such as E. coli, cross-reacting with the α-D-galactose on the B glycoprotein.

The cited reference is Van Oss, CJ (2004) Letter to the Editor: "Natural versus Regular Antibodies The Protein Journal 23:357, available here. This source contains this statement:

..."we have known for more than four decades that these bloodgroup (antibodies) arise out of minor infections occurring very early in life..."

The cited references are:

Pettenkofer et al. Z. ImmunForsch. 119: 415-429

Springer, GF (1960) Klin. Wschr. 38: 513-514

Unfortunately I have access to neither of these articles, and besides they are presumably written in German.

professors - Are UK faculty salaries in computer science low compared to salaries in United States?

I'm looking at faculty ads for computer science in the UK and noticed that the average salary range seems to be significantly lower compared to the US. Typically, a starting Lecturer ( = Assistent Professor) can expect an annual salary in the range of only 35k - 42k GPD which is in the range of 55k - 66k USD.

On the other hand, if I look at the academic job market in the US, then this would be considered an average PostDoc salary at best, whereas the lower limit for computer science assistant professors seems to be around 80k. Considering that faculty gets this amount for 9 months in the US rather than 12 as in the UK and taking into account the higher income tax rates of the UK, this gap becomes significantly big.

Does the UK system include certain perks that the US system does not have that I'm missing here?

Are there other ways that UK faculty can make up for this quite significant gap?

Answer

You are trying to compare a US salary to a UK salary using the current exchange rate. I do not think this is particularly relevant. Even if you are willing to ignore differences between the UK and US in terms of work/life balance, teaching load, and job security, you probably want to compare the quality of life that a salary buys you and not what would happen if you converted it to USD. The starting salary for a CS lecturer/assistant professor, when converted to USD, is much lower for a UK academic than a US academic, but there are differences between the value of a US and UK salary.

While you say the UK tax rate is higher, that is a huge over simplification. Two random online tax calculators I used gave a US income tax of 24% on an 80,000 USD salary and a UK income tax of 25% on a 42,000 GBP salary. This ignores US state (and possibly city) income tax. The UK VAT of 20% is much higher than typical US sales taxes, but not everything is subject to VAT/sales tax. Even if you can accurately calculate an average total tax liability, you still need to account for purchasing power.

I have work in both the US and UK in comparable cites (not NYC/London) and tend to think that the value of my UK salary is a little lower than value of my US salary. It is worth noting that UK salaries are much more consistent across fields. This means that I make the same as a CS lecturer in the UK, but that in the US I would probably be making 10% less than a CS assistant professor. My guess is that for CS there is a substantial, maybe 15%, hit in quality of life that an academic salary buys.

In the US your starting salary is often your salary until you get tenure/promotion while in the UK you get a larger salary every year. There is a performance based pay raise, that essentially everyone gets, which is generally about 2.5%. This means the gap between the US and UK values gets smaller every year and after 6 years, when one is preparing to be promoted, the gap is pretty small. Further, UK salaries also have a cost of living adjustment. For the past few years this has been about 0.5-2% and less than the inflation, but it wouldn't surprise me if the union negotiates a big salary bump, maybe 10%, in the next few years. This would really close the gap.

It is also worth noting that a US assistant professor is not directly equivalent to a UK lecturer. I think a US assistant professor is often a few years ahead in terms of productivity and experience.

Evolution of the Redundancy of the Genetic Code

In short

Looking at the genetic code, it appears that most redundancy is on the third letter rather than on the first or the second letter of the codon. Why has it evolved this way?

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Longer version

In order to compare the relative redundancy accounted by each letter of the codon, let's assume that that every codon occurs at equal frequency. It is probably wrong but useful for the sake of the calculations. Using observed frequencies of codon usage in a given population would change the following probabilities but the question of why some positions in the codon has more redundancy than some others still hold.

A substitution of the first letter of the codon has a probability of $\frac{1}{2048}≈0.00005$ (Stop codon) to be synonymous. A substitution of the second letter of the codon has a probability $\frac{3}{256}≈0.012$ (nucleobases U and G) to be synonymous. A substitution of the third letter has a probability of exactly $\frac{2}{3}$ to be synonymous.

Probability of a substitution to be synonymous given that it occurred on the...

• First letter: $\frac{1}{2048}≈0.00005$


• Second letter: $\frac{3}{256}≈0.012$


• Third letter: $\frac{2}{3}$

Why are there more redundancy on the third position than on the second (which has more redundancy than the first position) in the codon?

Answer

To fully comprehend the concept of wobble base-pairing we need to consider the nucleotide sequences of the anti-codons in the tRNAs that have to "read" the genetic code when the mRNA is being translated on the ribosome. The nucleotide in the anti-codon's wobble position is, for example, often inosine. Under the rules for wobble base-pairing an Inosine can potentially base-pair with three other nucleotides.

In real terms that means a cell can use less than 63 unique tRNA genes to decode mRNAs carrying messages made of the 63 different "words" (codons).

In an active cell the Ribosome's A-site, where the charged tRNA binds, is occupied by the incorrect tRNA most of the time (based on the law of mass action where any charged tRNA can randomly diffuse into the binding site). With tRNAs that can recognize multiple codons (which is what the wobble hypothesis gets us), any given protein can be translated faster (assuming that correct charged tRNAs are limiting for the polypeptide polymerization reaction).

So those are the practical ramifications of the table that you presented, but the explanation, as for most why based questions about biological evolution, is a retrofit. Natural selection can only work with the materials at hand, and so we can infer that during the period when this genetic code was finalized that the organisms who used it were more successful than the others. And the current code is based on whatever the previous one looked like. "Descent by modification" is the original description.

[whoops, sorry about the pedantic voice on the "how selection works" bit, I just looked at your profile and realized you can likely teach me on this subject]

Why is an academic CV not the place to sell?

In a comment, ff524 said this (and got confirmed by scaahu, Nate Eldredge below (not to mention the number of votes)):

Actually, academic CVs are typically not as sales-pitch-y as non-academic CVs. They are usually a very formulaic listing of all the academic things the candidate has done, with no editorializing or embellishment [...]. The "sell" is reserved for other parts of the application.

Why? I know that there are some differences in academia than other environments, but I can't think of a reason why a CV shouldn't be a sale pitch. Sure, we have other metrics to evaluate that, like h-index, but what is so wrong that putting other things (like about me, objectives, other courses, English certification, class standing, etc)? I am asking this question in general, but I also ask it from the new young student standing point in specifically. I know that if you are a novice, LOR are very important. You can say that a CV should be concise and into the point, but a half-page long CV may show that beside that point, you have nothing.

I just wonder what is the harm of making the CV like a sales pitch?

Answer

Largely, it is cultural. So far as I understand it, the idea is that "your record should speak for itself." Of course, you are selling yourself to a degree, by how you choose to put which pieces forward, whether to choose a "selected" versus a "completist" format, etc. The range of acceptable variation, however, is much narrower than for a job resume, and the format is built around showing credibility (in the form of accomplishments) rather than enthusiasm and fit with business goals (which is the goal of a resume).

microbiology - Food safety during roadtrips

I will be moving across the country in the coming weeks, and I have realised that I will likely have leftover perishable food in my apartment before I leave and I was thinking of trying to prepare some of it the night before I leave to bring with me. The trip will take me four days, and I was going to cook (extra thoroughly) hardboiled eggs, pork, bacon and sausages. I might even add some salt or something. And keep all of my packaging as sanitary as possible, eg. straight from pan/pot to sterile ziplock.

The eggs I'm unsure of because of the protective outer layer that is chemically removed during processing. The pork and bacon, I feel like they will be alright if they're eaten first. And I'm not too worried about the sausages because they've been processed and cooked.

I think a visual and olfactory test of the foods before I eat them would be wise - especially if nearing day 4. But, realistically, if I keep the food out of the sun covered up it will probably stay safe to eat, right? Or is this a bad idea?

I think that the food would definitely be safe to eat up until the end of the second day. But, what about any longer than that? How did people back in the old days travel with food?

Edit: Just to clarify my question. I am not asking about whether or not my apartment is sterile. And I'm not asking about whether or not bacteria can multiply. I'm very well aware of these answers.

I'm looking for a realistic estimate on food longevity - not the food-standards enforced onto food manufacturers or restaurants by the FDA/Health Canada.

Answer

The biggest factor in whether bacteria can grow in food is water bio-availability. Most non-sterile methods of preserving food (note that canning IS sterile) utilize this fact. Over salting while curing, adding lots of sugar, and dehydrating (or freeze-drying) all either remove water or remove the ability of the bacteria to utilize the water and hence grow in that medium.

This is the biggest reason that a hamburger from McDonalds can seem to petrify without devolving into an ugly mess. If the burger and bun and condiments dry out, bacteria can't grow on it. Put that same burger in a ziplock bag with a few drops of water and you will have the nastiest mess possible in a few days.

Honey and jams can remain at room temperature for months or years, even after opening despite being "watery", and this is because there is so much sugar in the solution, that all water tightly bound to the sugar molecules, leaving none for the bacteria to use (Note that some yeasts still can). Similarly, because of lack of water, crackers last for years, while bread spoils.

For your question with eggs and bacon, unless it was a hard-boiled egg that was cooked twice as long to ensure pasteurization throughout the yolk and you left the shell on, I wouldn't risk it after a couple of hours. Bacon, once cooked, very little water activity. Fat doesn't count for bacteria propagation, they need water. I take cooked bacon on camping trips all the time. I also take sharp cheeses with me and they are good for days.

Your other option is cooking beans (with seasoning) or something and dehydrating them in the oven on a cookie sheet before you go. Then you just need to add hot water. I do this for camping as well.

Edit: I didn't mention that high salt solutions (see pickling) function outside this paradigm somewhat, in that you are creating such an isotonic concentration in which bacteria membranes lyse. I also didn't mention methods of pickling like kimchee and sauerkraut that use salt to positively select for species of bacteria (that aren't pathogenic to us) that can tolerate that salt concentration (mainly lactobacillus) as well as some yeasts.

Edit2: With a Source about water activity

graduate admissions - Should I include name of potential advisor on my statement of purpose (SOP)

I am currently writing my statement of purpose (SOP) for top graduate schools in engineering majors in US. I am wondering should I include name of my potential advisor on my SOP (Is it a good idea to do that)? The problem is I am thinking if I do not include name of advisor it might be the sign I did not look at his/her research page and I am not very specific about my plan. On the other side, if I include name of potential advisor and my application is not competitive or he/she is not accepting any graduate student this might cause others not to look at my application since they might think I am not interested in their research.

ethics - Is this type of self-plagiarism wrong?

There is an article which contains a section describing preliminary materials, that is, results which have already been published elsewhere and on which the current work is based.

This section is not supposed to contain any new result.

It appears that part of this section (one to two pages) is, up to minor modifications, a copy-paste from another published article.

The other article is from a collaboration of the author of the present paper with other authors. It is cited somewhere in the current article but not as the source of the copied part.

The context and methods of the articles are very similar (hence the need for similar tools), but beside the copied part, the contents and results are different.

In particular, there does not seem to be any plagiarism in the actual novel part of the article in question.

Is this a case of acceptable self-plagiarism?

There are a lot of questions in academia.SE about self-plagiarism but I couldn't make my mind about this case from what I've read.

EDIT: Thank you for all this helpful contributions. As referee for this article, I've chosen the option to ask directly the editor's opinion.

molecular genetics - Why did translation develop a specific codon for initiation?

The translation of mRNA is initiated by a specific methionine-accepting tRNA at a specific initiation codon, usually AUG (complementary to the tRNA anticodon). However translation at suitable (albeit unphysiological) conditions in vitro does not require a specific initiation codon or a specific amino acid, so it is not difficult to envisage an earlier stage in the evolution of the translation apparatus in which this specific initiation system was absent. Instead there might have been random initiation or initiation from the 5′ end of the mRNA.

A specific initiation codon puts constraints on the sequence of the mRNA and adds an unnecessary amino acid to the N-terminus — one that is sometimes unwanted and needs to be removed.

What advantages can one envisage for initiation at a specific internal site, rather than at, say, the 5′ end of the mRNA?

I appreciate it is impossible to prove which factor was actually responsible during evolution, but by soliciting concrete explanations I trust that this question is as valid as the original from which it is derived (see Footnote).

FOOTNOTE

This question has been expanded from one part of a three-part question posted some time ago on “Why is AUG the Initiation Codon?”. This recently resurfaced, and as nobody had answered this particular part, and as it is site policy to ask one question at a time, I decided to remove it from the original and repost it here so it could be considered on its own merits, without the distraction of other questions such as the choice of codon or of methionine over other amino acids. I shall contribute an answer with some thoughts of my own, but, of course, anyone can join in.

human genetics - Skin color explanation?

I do not understand how skin color in humans work, even after taking a basic genetics course and reading some on wikipedia.

From what I understand, skin is color based on multiple genes that control melanin and other products that affect appearance of skin. So then their are multiple alleles for "skin color" and also some of these alleles can be varying in their expression/inheritance? based on the other alleles presence?(epistasis)

So then a black person and a white person could have various skin colors (phenotypes?) And the offspring of these children could then have varying offspring as well?

Diagrams would help me maybe in explaining the concept.

Answer

The genetics of pigmentation is relatively complicated, as the pathway for the pigmentation (regulation of the pigment production, ratio between the melanins, maturation, trafficking and distribution of the melanins from the melanocytes to other cells) is quite long and also subject to different regulations. All the mutations found to date (at least to my knowledge) affect single parts of this long process (so for example MC1R mutations are affecting whether eumelanin is made, while Rab7 and Rab27a is most likely involved in the distribution of the melanosomes). Not all gene functions in this network have been understood so far.

Population studies have shown that the three main ethnic subgroups (west-africans, asians and europeans) have developed independently from a common ancestor with different (and independent) mutations in each arm. See the figure from reference 1 as an illustration, it also shows the genes involved in each arm:

Pigmentation is a protection against UV light, so there is a strong selection against mutations in areas with high UV light (west africa for example). The general theory is that in areas with less UV light the skin got lighter to allow the production of vitamin D (for which you need UV light). If you want to go through the single genes and their influence on pigmentation, please have a look at this Wikipedia page, which gives a good explanation. Also have a look at the references.

References:

1. Unpacking Human Evolution to Find the Genetic Determinants of Human Skin Pigmentation


2. The genetics of pigmentation: from fancy genes to complex traits.


3. Molecular genetics of human pigmentation diversity


4. Human pigmentation genetics: the difference is only skin deep


5. The etiology and molecular genetics of human pigmentation disorders

evolution - Effect of sex-ratio on the effective population size

As stated on this wikipedia article, the effective population size $N_e$ when the sex ratio differs from $\frac{1}{2}$ is

$$N_e = \frac{4N_mN_f}{N_m+N_f}$$

I understand the biased sex-ratio decreases the effective population size and the formula is quite simple. However, I would fail to prove that this formula is right.

Can you demonstrate to me that $N_e = \frac{4N_mN_f}{N_m+N_f}$ is true?

evolution - What are the costs associated with carrying lots of genetic material

What are the costs (if any) associated with carrying lots of genetic material (Big genome size)?

• energy for copying?


• raw material for copying?


• space in the cell?


• Maintenance cost (matter and energy)?


• time to copy is a limiting factor for the minimum generation time?



• Less robustness?


• More likely to evolve a gene that spreads well but has a negative fitness impact on the rest of the genome (selfish gene or outlaw)?

The answer probably depends on the organism. I am interested about any information concerning uni- or multi-cellular eukaryotes, bacteria or viruses.

Do we have any knowledge about how important are these costs or is it pure guesses?

---

^{This post comes in reaction to @AlanBoyd comments on this post.}

Answer

It is generally known that the smaller (or less complex) an organism is, the more "condensed" it's genome is. For example, bacteria (or some eukaryotes) have operons (http://en.wikipedia.org/wiki/Operon) or overlapping genes using different and they don't have introns, which alltogether saves a lot of space.

There are many reasons for that. Available space in the cell is definitely not one if it, however. Energy for copying and maintenance is a good point, but you have to keep in mind how evolution works. Bacteria and unicellular eukaryotes are usually adapted to a very specific environment in which they can reproduce rapidly. This means, they only need a small set of genes, specific for this environment and they have to reproduce very frequent, which means they are very prone to mistakes during DNA-copying. Such a mistake can lead to the death of the cell, which in this case equals the death of the organism.

In higher organisms however, the advantages of a bigger genome outweigh the disadvantages by far. Evolution can happen much faster because and mistake while copying does not necessarily lead to the death of the whole organism. Adaptation to a much greater variety of conditions is also necessary, e.g. when you look at plants: Their genomes are (on avarage) much bigger than the ones we mammals have, because they cannot move if the conditions around them become unpleasent. Instead, they need to find a way to adapt. This means, a big genome is in this case a fitness bonus. More interestingly, plant genoms are highly mutable (http://en.wikipedia.org/wiki/Transposable_element), which was originally thought to be a huge disadvantage.

evolution - Does recombination increase the additive genetic variance for fitness?

On this article, first column, eighth line of the introduction:

By bringing together favourable alleles from different chromosomes, sex and recombination increase the additive genetic variance for fitness [..]

Can you please help me understanding why does recombination increase the additive genetic variance for fitness?

Note: In reaction @mgkrebbs comment, I think that given the subject of this article, when talking about different chromosomes, the authors actually referred exclusively to homologues chromosomes. My question concerns the second part of this sentence anyway: "Why does sex and recombination increase the additive genetic variance for fitness"?

---

Here is another question on the same article

What chemicals and structures control the *direction* of plant growth in leaves, stems and roots?

If you want a specific plant, let's say the snap peas I am growing that I bought at Agway. I noticed that they grow towards the light source through the nearby window. Also I think roots work the same way for water/minerals. also don't various kinds of ants find food conceptually identically?

How much of this is true? Please correct:

• I think analogous to ant colonies, plants will attempt to grow every which way initially, and will only continue growing in directions that give the most/enough light/water/minerals. If a direction is or becomes unfruitful, that section withers. After the initial state the plant will start branching in directions off of locations on still growing sections of plants and that cycle continues until none of the plant can be supported and the whole thing withers (perennials) or slows its metabolism down to the point where it could survive those conditions until they picked up again (such as winter seasonal survival of tree species). Also, it is not as if they decide which direction to go in. that type of decision would forgo going in another direction. And not sure, but I don't think plants have decision capabilities anyways. they grow in directions they grow best.

publications - What does first authorship really mean?

In my field (theoretical computer science), authors of any paper are always listed alphabetically; our papers don't have "first authors". (Well... hardly ever.) In most other disciplines, at least within science and engineering, the ordering of authors is a signal about their relative contributions to the paper, with the first author indicating the most significant contributor. Hiring and promotion committees do give extra weight to "first-author papers" (and sometimes have to be reminded that not all areas have them). As an outsider, I find this practice confusing.

What does first authorship actually mean in your discipline? I understand vaguely that the first author is supposed to be the one who "did the most work", but what counts as "work" in this comparison? Does "most" mean "more than all the other coauthors together" or just "more than any other coauthor"? What happens when the comparison is unclear? How often is "did the most work" the actual truth, versus a cover story for a more complex political decision?

I realize that the precise answer is different for every paper. I'm looking for general guidelines for how an outsider (like me) should interpret first authorship in your field. Pointers to guidelines from journals or professional societies would be especially helpful.

Please give only one answer per discipline.

publications - Can posting to arXiv ruin your reputation?

Arxiv is permanent. So if I publish something now, that I feel is not quite high enough quality for traditional publication, and people leave a bunch of feedback showing issues with my assumptions or methods, am I hurt for life? As I understand it, you can't remove something from arxiv, and people can comment on your work. So, when someone 20 years from now googles my name or domain, they will find the paper and the comments and other undesirables?

At least with traditional publication you have peer review as a filter, which can in part shield you. Is arxiv really this dangerous?

Answer

I think your comment has very important information:

This paper is just that. It presents helpful information but doesn't develop any ideas or utilize the scientific method.

So, it is not crappy, they are not unbacked claims; it is just nothing new. As long as you are aware of it, and it is clear you are not trying to make it look different, it cannot hurt you.

You can think of this paper as a small review or class notes.

The only thing that may hurt your reputation is if it had very serious mistakes, and you don't address them. To be safe, just ask some of your colleagues to review it, even if it is not a thorough one. They should be able to tell you if it is correct, informative, and clear. And by all means, if it is informative, go ahead and publish it.

Also, ArXiv is not only for preprints of papers. For example, I have seen philosophical dissertations on QM very non technical (a second year Physics undergrad should be able to follow), or another about the story of protein folding research in a certain institution.

Edit:

Regarding your comment:

but are arxiv posts considered publications for what you're talking about? i could put my grocery list there if I wanted to, right?

ArXiv is not peer reviewed, so the quality threshold is not so high. You can publish not so technical pieces, or sneak a bad article that looks just fine, they don't count as official publications. But, on the other hand, they are better than nothing. Specially if you are at the beginning of your PhD, when you are not expected to have publications yet, your ArXive papers are an example of your capabilities.

No one will use the sheer number of submitted papers, but if you have some fine pieces (for example, a good, brief review of your field, previous research and terminology), can show you have a promising career for, for example, applying for summer schools or extra funding.

Depending on your field, this kind of papers can be extremely useful. For example, in Bioinformatics, most people come from a CS background (programming experts and good Mathematics, but knowing nothing about Biology and Chemistry), Biology (lacking in Algorithmics, Machine Learning, and Statistics), Physics (lots of Maths, but basic knowledge of mostly everything else)... For me, having a quick reference of the basic terminology of other disciplines would save me a lot of time, as I have to look up many simple concepts that would be obvious for, for example, a Chemist undergrad.

phd - Unable to defend and graduate because of advisers fickle mentality

I am an international student at a US university and I have a fantastic, caring and supportive adviser who I find fosters a happy work environment for all his students to grow in.

Here's the drawback to this happily unfolding story:

1. He advises 9 students, 5 of who are PhD students (I am one of them).


2. 4 out of the 5 PhD students are in the final stages of their PhD program (me included).


3. 3 out of these 4 PhD students have families and should have graduated at least about 5-6 months ago but because of "family pressure" they haven't. I don't relate to that because I don't have a family and I want to defend and graduate

My adviser has always had goals that are generally considered unattainable in my group. I had been given 3 weeks to finish my dissertation in 2012 with the dangling carrot that I could defend and then focus on writing papers perhaps.

I met this goal one whole week short of the 3 week goal. However, my advisor has been postponing my defense for a variety of reasons (all of which are true) and is being pulled in several directions at the same time because of an important position in the research area of fuel cells.

So these constant vacillations have led to my defense being pushed to the end of Feb 2013. Now I'm told they don't know when I'll defend.

I find that this is rather unfair and considering that I generally have a good rapport with my advisor I am unsure of how to broach this topic. Why am I so worried? I come from a country where demanding things from your adviser is sinful and gets you kicked out of graduate school.

I'd really like to say that I want to defend and figure out the next step in my life! I am not talking getting a job necessarily but just life in general — get married, have kids, find a job, move to a different place (in no particular order) what have you.

Any advice or similar experience that I can draw from?

Answer

Talk to him (I'm gonna make a template out of that one)

Be professional, stay fact-based, don't say it as a criticism (veiled or not) of him, and you should be in the clear. Say something like:

I wanted to ask you, given your experience on this matter: I had expected that the final period of my PhD, between finishing the thesis and defending, would be quite short. Given that it's not the case, I was wondering: what is, in your expectations, a typical schedule? Am I doing something that hurts my ability to defend sooner? Could I do something to speed the process?

That should open up a dialogue about your expectations, his expectations, your constraints and his, and possibly help unknot the tie you're in.

---

However, you're not giving us much information about the exact nature of the core issue:

he has been postponing my defense for a variety of reasons (all of which are true)

If all the reasons given for postponing the defense are valid (I assume “true” here means “valid”), I don't see why you expect to defend. Do you think he's setting the bar too high? Is it merely a scheduling/timing issue? You say that your thesis is ready, has he gone over it, commented, critiqued, discussed it with you? Is the problem with putting together the committee?

funding - NSF graduate fellowship: how specific should the statement of purpose be?

Several of the students who have come to my group as summer students are planning to submit NSF graduate fellowship applications in the coming weeks. However, one question that I am not sure about is how specific the statement of purpose needs to be.

When I applied for the NSF fellowship (going on fifteen years ago), I had absolutely no clue what I wanted to do as a student, other than it was computational rather than experimental. Therefore, my application was all over the place, talking about three different types of projects I might want to work on as a graduate student (and I ended up choosing none of them in the long run!).

However, I get the impression that today such an essay wouldn't be suitable for the application, and that a more narrowly tailored essay is required. At the same time, there's also the challenge of ensuring that the research problem can be done at the school one has chosen, and not narrowing things so specifically that the student is too "boxed in" or too opaque for a review panel to see the merits of.

So how should students thread the gap between vagueness and specificity in writing these and other fellowship applications?

Answer

I think this is an issue that a lot of students struggle with; at least I did when I applied last year. I was rejected, so probably take what I say with a grain of salt. They say some things on their website that are important to note.

• Keep in mind that NSF does not just seek to fund scientists and engineers; NSF seeks to fund future STEM leaders.


• Use appropriate scientific form (hypothesis, figures, references) in the Graduate Research Statement.


• Instead of elaborate details on theory, focus on the rationale for your studies and the existing literature as it supports your proposed work.

The students that I know that were given the award properly addressed these issues. My proposal did focus on one research idea and that was rewarded with comments on the creativity and feasibility of my proposed idea. One of the critiques I got in my review was "While the applicant does demonstrate an excitement of discovery and should be able to communicate his results to a large audience, ... Broad societal impacts are not evident with respect to encouraging diversity and enabling the participation of underrepresented groups."

The feedback that I got was based on two scores: Intellectual Merit Criterion and Broader Impacts Criterion. I would make sure that your students take both into account. As far as the research proposal goes, I what JeffE said is true. It is an opportunity for the students to show that they are familiar with the current research and are able to come up with an appropriate idea to pursue.

phd - What might the editor do if my supervisor contacts a journal to claim authorship of a paper?

When I was doing my PhD project, I got an idea to solve a different but related problem. However, my supervisor said neither the motivation nor the initial result were interesting, and so he refused to offer me help on this topic. Then, I did a paper on my own with a lot of work afterwards, and submitted it to a high standard journal, and it was accepted.

My supervisor knew this, and he commanded me to add his name to the paper, otherwise he would write to the editor. I asked him what his contribution was. He had nothing to say, but insisted he had spent time to discuss the result with me.

So, if he writes to the editor, what would happen? Or if the paper has been published, then he has nothing to do with it? I am pretty much sure he can almost show nothing about the evidence of the contribution.

biochemistry - Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head?

The oxygen anion in the phosphate group is likely to be bonded with a hydrogen cation and thus forming a hydroxyl.

When the phosphate group is condensed with glycerol to make a phospholipid, is the hydroxyl from the glycerol molecule taken or the hydroxyl from the phosphate group taken?

I believe it's related to the difference of electronegativity of oxygen and phosphorus which causes unequal sharing of electrons between atoms, thus making a hydroxyl from one side easier to get taken off than the hydroxyl from the other side is.

reproducible research - How to proceed when the baseline (state-of-the-art) published results claim much better performance than I can reproduce?

I am graduate student, to finish my degree I need to build methods outperform what is already there. An issue that I came across with, is that two papers reported way (I mean more than 20%) more than what resulted from my reimplementation. This could be due to two reasons:

1. 
   

   I missed something during the implementation. Which is what I have been telling myself. For months, I tried all possible combinations and possible paths. One of the methods is straightforward. Still, I could not reach their claimed performance.

   
   

   I contacted the corresponding authors, and no one replied. So I tried to contact the other authors.

   
   

   The first paper, the author replied and sent me the code. He/she told me to keep all details ”confidential”. Well, it turns out they they are not using the data they claim in their the paper, of course their results are different than my reimplementation. And my implementation was correct.

   
   
   

   The second paper author also replied and they didn’t send me the code because they say it is easy to implement, but confirmed that what I did is correct still I couldn’t understand why such difference.

   
   

   Both papers are published in <2 impact factor journals. Their web servers are not working.

   
   


2. 
   

   They are not honest.

   
   

Now I am stuck, my method does outperform my reimplementation of their methods but not what they claim. The first paper I can’t say anything because “it is confidential” the second paper I can only confirm that I correctly implemented their method for the most part (based on my chat with the authors)

I know that I probably could not publish on this part of my work, because who is going to believe a young scientist who just started her way? But not sure how the committee are going to believe me. What can I say or do? Please help me

journals - What is the difference between SCI and SCIE?

I knew that the difference between SCI (Science Citation Index) and SCIE (Science Citation Index Expanded) is that SCI has a list of top quality journals, while SCIE includes more than the former.

I found a link that seems to support this previous statement. However, I can't find any official information on this regard.

Does someone has some official links to what the difference is? if any.

Answer

From Thomson Reuters:

... the evaluation of and acceptance of a journal for the SCI or the SCIE is essentially the same with ONE major difference. The only difference is the storage media. SCI is only available on CD/DVD format; however, SCIE is available online.

mathematics - How do I tell my current research advisor I want to work in a related field with another professor?

I am currently an undergraduate student looking to work on a senior thesis. Over the course of the past summer and sporadically throughout the Fall semester, I worked with a professor in extremal graph theory. There has been some (from my point of view) subtext between us that I would continue this work into my senior year, though this was never explicitly said.

However, I want to pursue something more algebraic, and have been in contact throughout the Fall semester with a professor working in algebraic graph theory.

How do I tell my current research advisor I want to work in a related field with another professor?

Answer

Just tell him. Be polite. You're over-thinking this.

career path - Are employments in universities affiliated (or named) with a specific religion restricted to people with the same religion?

I just saw an ad in mathjobs.org about an opening in a Catholic university, see here. I am not christian. So I was wondering to be eligible for employment in a university or college affiliated with a specific religion, should the applicant have the same religion, or other people from other religions (or even non-religious people) are eligible to apply as well?

Answer

In my experience, the answer is usually no but occasionally yes.

Note: This answer is specific to the United States.

Most employers in the US are forbidden by law from discriminating on the basis of religion; they have to give equal consideration to candidates of any religion or no religion, and generally they will avoid asking about religion at all. This includes non-denominational academic employers.

However, religiously affiliated employers (such as churches, religious charities etc), are exempt from this rule, and may use religion as a criterion for employment if they so choose. This includes religiously affiliated academic institutions. Each such institution will have its own policy on whether they consider religion and what the criteria are. These policies will usually be mentioned in job postings.

In my experience, most intentionally choose to not consider religion as a factor, usually giving the justification of creating an inclusive community. These may be institutions that were founded by a church and may still receive funding from them, but operate mainly as a secular institution, accepting students and faculty without regard to religion. Job postings will often indicate this with phrases like "equal opportunity employer". They may have a "mission statement" with religious wording, and a tradition of religious activities on campus (such as regular church services), but nobody is obligated to participate.

There are others which choose to be more overtly religious. They may accept students and faculty only if their religious beliefs align with those of the institution. These are more likely to have formal religious activities on campus, and sometimes strict moral conduct codes. Their job postings often ask explicitly about the applicant's spiritual beliefs.

The institution's name is not always a good indicator of where they fall in this spectrum.

As one example, Nebraska Wesleyan University describes itself as:

an academic community dedicated to intellectual and personal growth within the context of a liberal arts education and in an environment of Christian concern.

However, they also say:

Nebraska Wesleyan University provides equal educational opportunities to all qualified persons in all areas of university operation, including education and decisions regarding faculty appointment, promotion or tenure, without regard to race, religion, age, sex, creed, color, disability, marital status, national or ethnic origin or sexual orientation.

At the other extreme, Dordt College included this wording in a recent job posting:

The Mathematics, Statistics and Computer Science department at Dordt College has a history of preparing students for graduate school, industry and K-12 education. This preparation is infused with an unashamedly Reformed Christian worldview, in order to prepare students to be global citizens in God’s service. [...]

We look forward to receiving applications from candidates who wish to join us in [...] teaching mathematics from a Christian perspective in the context of educating the whole person.

Qualified persons committed to a Reformed, Biblical perspective and educational philosophy are encouraged to send a letter of interest and curriculum vitae/resume [...]

Generally, institutions that will only consider applicants of a certain religion will make this clear at the outset. However, even if not, you will have to decide if the religious environment (or lack thereof) on a particular institution's campus will be comfortable for you. This is an appropriate topic to ask about during an interview.

evolution - What is the minimum eye?

What is the minimum eye which confers some evolutionary advantage?

By minimum I mean anything less than this has no advantage whatsoever and therefore is not favored by natural selection.

By eye, I mean not just a light sensor but also infrastructure which converts the light stimulus into an advantageous response.

Ideally would like a clear unambiguous before/after case especially on the infrastructure between the mutated protein and the cell's response mechanism which translates this into a survival advantage.

(I assume Opsin proteins floating around the cytoplasm by themselves confers no advantage without some kind of other infrastructure)

please also provide an estimate of the number of coordinated DNA base pairs which needed to change to confer this advantage so that a proper probability estimate can be done.

genetics - How is gene expression estimated?

I'm reading this fantastic article on estimating body time: Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles and one of the things that is not very clear to me is how the researchers estimated which genes are expressed and which ones are not:

Total RNA was prepared by using Trizol reagent (GIBCO􏱾BRL). cDNA synthesis and cRNA labeling reactions were performed as described (5). Affymetrix high- density oligonucleotide arrays (Murine Genome Array U74A, Version 1.0, measuring 9,977 independent transcripts) were hybridized, stained, and washed according to the Technical Manual (Affymetrix). Affymetrix software was used to deter- mine the average difference (AD) between perfectly matched probes and single-base-pair-mismatched probes. The AD of each probe was then scaled globally so that the total AD of each microarray was equal. The resulting AD values reflect the abundance of a given mRNA relative to the total RNA popu- lation and were used in all subsequent analyses

I'm not sure if I'm reading this correctly - did the researchers look at all RNA available in the cells and calculated the levels of messenger RNA produced by expressed genes? if not, how can the level of expression of a gene be estimated?

Answer

The technique described here is called microarray. Your question has given me an opportunity to put forth one of my opinions about certain problems of gene expression studies.

Gene expression is a measure of the activity of any gene. If the gene performs its activity in the form of a protein, then its expression should be a measure of the protein. If a gene makes a non-coding RNA then its expression is a measure of the RNA concentration.

[You can omit the cases of post-translational modification because of signal transduction. They are highly expressed and transiently but frequently used. ]

Like your example there are many studies which use mRNA concentration as a proxy for protein activity. This proxy works in many cases because transcriptional gene regulation is more frequently used mechanism for imparting stable changes. But the best strategy would always be to measure the proteins also.

Apart from microarray there are several techniques to measure RNA concentration:

• RNA sequencing (high throughput)


• Real-Time PCR (medium throughput)


• Northern Blotting (Low throughput, semi-quantitative)

Many techniques exist for measuring proteins also:

• Mass spectrometry (high throughput)


• ELISA (Low throughput, quantitative)


• Western blotting (Low throughput, semi-quantitative)

Usually the "proxy method" is used because protein quantification is comparatively more difficult. Antibody based techniques like ELISA and Western blotting have problems of cross comparison of proteins because of the variability of the antibody binding efficiency.

computer science - Parameter quantifying the number of publications expected from a good researcher

Is there any such notion of parameter that quantifies the number of journal articles someone has to publish to be a good researcher or to obtain his tenure?

For instance, how many publications per year is considered to be a good performance

• for a PhD student


• for a non-tenured university teacher

in computer science?

publications - Can you publish studies based on confidential customer data that comes from private companies?

I am working on a project in biostatistics involving some private companies. Specifically, these companies share data about their customers with us and we try to apply our algorithm to this data. The good part is that both the algorithm and the application are very new, and seem to work quite well. Unfortunately we can not publish this data in paper or conferences, as it is privately owned.

• What is the typical way to proceed in this case?


• Does the fact that it is not possible to publish the data implies in general that also results based on this data are also unpublishable?

publications - Should I publish a given unit of work in more smaller papers or fewer larger papers?

Having just spoke with my advisor, and speaking on occasion with other professors, I have come to the impression that one should not "subpublish." Let me say what I mean. I'm a 3rd year graduate student right now, and the professors I talk to seem to say that it is not a good idea to publish many small papers along the way to a result: that is, holding fixed the total mathematical content across N papers, it is best if N is minimized. I was trying to understand why. My advisor cited the reason of "reputation" and I have invented my own reason that perhaps there is an upfront cost to the process of writing and submitting a paper so that although effort per length may be constant, it is to my advantage to pay the upfront cost as few times as possible. (Finding a referee is the only upfront cost that comes to mind, but keep in mind I've never done this before.)

Can someone expand upon how reputation is relevant here i.e. for fixed mathematical content why it looks bad to come out with many small papers? Are there also benefits to the community or the knowledge pool that I'm trying to expand however slightly by writing such papers if it all comes at once in one big paper? One would think that if I "subpublish" that actually since my results become available more immediately that it would benefit the community if I did so. The only person it would seem to possibly hurt is me if I were to get scooped.

Are there other ways in which upfront costs to the whole process of publishing may happen?

I am interested in all my questions in both advantages and disadvantages to me, and also to those who would use my work.

Answer

To address the reputation aspect:

Think about a typical reader of your papers. Most likely they will only look at one paper you have written. Unless you impress them with that one paper the likelihood of them reading anything else you have written depends on whether that first paper convinces them it is worth their time to read another. So the more content that is in each of your papers the more impressed the reader will be with you. If the first paper of yours someone reads has a small amount of mathematical content then they probably won't expect too much from any of your other papers.

In your formulation the ideal N may not always be 1, but each paper should actually have something worthwhile in its own right to say. You shouldn't expect someone to read more than one paper to get to only one meaningful idea.

A side comment, the author does not find referees. The editor does. Sometimes the author may suggest candidates but the editor or the suggested referee can always say no.

Is it sensible to do two PhD's simultaneously?

I have finished my master's degree in Physics (Radiation and Health Physics Option) with distinction, but I want a PhD in Medical Physics. My university does not offer that pathway and other universities are insisting I do a M.Phil. for a year before they will consider me for PhD candidacy I really do not have the energy and time to concentrate on the M.Phil. right now and I fear I might not make the desired grade.

I have an offer to do a Ph.D. in my area of specialization (Radiation and Health) and I need to make a decision on this. I am thinking of accepting both offers and in case I don't get the desired grade to move over to PhD in medical physics, so I can still have my PhD in Radiation and Health Physics and not lose both ways.

human biology - Why do we sleep?

While we do know that the human body is regulated by a circadian clock that keeps humans on a sleep/wake cycle, we don’t really know why. Sleep is the time when our bodies repair tissues and perform other maintenance activities, and we spend nearly a third of our lives snoozing. Some other organisms don’t need to sleep at all, so why do we?

etiquette - What is the best way to deal with cranks?

Imagine you are minding your own business when you receive an email from someone who claims to have discovered the Answer to the Ultimate Question of Life, the Universe, and Everything. He provides some "details" about his theory, then says he wants to meet you and / or arrange a time for a phone conservation to discuss it. What should you do?

The only thing I've seen is this 1983 article by Underwood Dudley about what to do when the trisector comes. Dudley says not to examine the trisector's proof, and also not to direct the trisector to the proof that trisection is impossible. Instead one should send computer-generated results showing that the trisection is imperfect. Problem with this is that it only works for questions that can be attacked by computers - there was a recent question here on Academia SE challenging conservation of angular momentum which this won't work for.

What are some general guidelines for dealing with these situations?

Edit: ignoring an email is easy, but what if the crank calls or visits in person?

Answer

This happens far less frequently than inappropriate requests for postdocs that have absolutely nothing to do with your area, invitations to participate in conferences that have nothing to do with you, invitations to serve as section editor on predatory journals, .....

Handle them all the same. Use your delete button.

A call or visit is harder to deal with. A polite "... very interesting, but I don't have the time to follow up on this" might get you off the hook. If the person shows up at your door more than once, I recommend calling security.

mathematics - Is someone who solely contributes negative feedback to a paper considered an author?

Say person A and person B are collaborating on a mathematics paper. It goes like this: person A repeatedly suggests proofs, and person B repeatedly finds flaws in them. Over time, this process culminates in a correct proof.

Does person B deserve to be an author on this paper? One might argue that the final paper would not have existed without B, so they deserve authorship. On the other hand, they did not actually contribute anything in the final work - each successive proof was generated by A alone.

Wikipedia says that the development of RSA went something like this: "Rivest and Shamir, as computer scientists, proposed many potential functions while Adleman, as a mathematician, was responsible for finding their weaknesses," until Rivest hit on the final answer. But that might be overly reductive, and I don't know of any other examples.

(As a final note, I'm not A or B in this scenario - I'm just curious.)

Answer

To moderate Yemon Choi's comment: yes. Your first assertion is that A and B are collaborating, which means they should be co-authors, unless one actively backs out.

For a mathematical project, it's easy to have lots of ideas but not enough time to pursue them all to see which (if any) work. If someone can shoot down ideas and tell you they definitely (or with high likelihood) won't work, this can help put you on the right track. So in your situation I would say B was instrumental in finding a correct solution.

(In a somewhat different abstract scenario where B dismisses some approaches to a problem that A suggests, and B does not otherwise actively work on the project, it may depends on the situation and they should have a discussion about whether B is a co-author or not. And some people will have different opinions about the same situation, e.g. RS versus A in the RSA example.)

In general in a mathematical collaboration, if there's one key idea it's unlikely that both collaborators arrive at it together. Maybe through discussion they enhance each other's understanding of the problem, and then one will have the key idea and the other will encourage/validate it. That doesn't mean was the other person was unnecessary, even if you can't pinpoint parts of the final paper as being "their contribution."

(And if collaborations became competitive to the point of dropping co-authors just because the didn't see the final solution first, who would want to collaborate?)