Ethics of scraping "public" data sources to obtain email addresses

I am wondering whether the following research practice is ethical.

A software engineering researcher downloads source code repositories from Github, a large source of publicly available open source code. The researcher searches the git commit logs to find email addresses of software developers who have committed to a project, and uses these email addresses to send them an email asking them to participate in a survey. If the recipient clicks on the link to the survey, the survey contains an appropriate briefing and obtains informed consent. The researcher follows all institutional and legal requirements related to human subjects research. The researcher limits the number of emails sent to only the number of participants they think they will need to test their hypotheses. However, at least one recipient of this email is annoyed that the researcher obtained their email address in this fashion and sent them unsolicited email.

Is this an ethical research practice? In particular, what would be the relevant ethical principles or ethical framework for analyzing this question? I've read a bunch of papers and backgrounders on ethics in human subject research and in engineering research, but they seem focused on other issues. Are there accepted norms or guidelines relating to this sort of situation? Has it been considered in other fields, such as the social sciences?

A possible argument that the practice is ethical: The data source is publicly available, and the email addresses were collected from this publicly available data. Developers chose to make their software repository publicly available, and they should assume that any information contained in it are public. Developers who don't want to be contacted could have configured their git client specially to use a different email address. The research will benefit our understanding of the science of software development. Subjects have an opportunity to decide whether or not to participate in the survey. Participant confidentiality will be protected, and all responses will be treated anonymously. The research complies with all legal and compliance requirements. From a legal perspective, the emails are not "spam", since the unsolicited email was not sent for a commercial purpose.

A possible argument that the practice is unethical: Software developers probably would not expect someone to scrape email addresses from the git commit logs. Their email address might be contained in a publicly available data set, but some developers might expect/consider the information private, or at least not public and free for unrestricted use. Some developers might object that it is one thing to use email addresses that are publicly listed on their Github profile page, but it is another thing to extract private email addresses that are provided as part of their git configuration, and that their understanding of social norms is that the email addresses automatically inserted into the commit logs by their git client were not intended for this purpose. Some software developers might object to having an unwanted email message in their inbox or find the practices "creepy".

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Please note: I am not asking about IRBs, legal requirements, or compliance. I am super-familiar with those considerations. Assume that the researcher has complied faithfully with all of those requirements that are applicable in their country. I'm not asking about that aspect. In my view, researchers have an independent obligation to conduct research in an ethical manner, and to exercise their own judgement in avoiding unethical behavior, even if is legally permitted or approved by an IRB.

genetics - Understanding a Chromosomal formula in a karytope analysis

I am reading a medical reporting results of a karyotype analysis. On it it is written:

Chromosomal formula

46,XX,del(7)(q11q36)[12]/46,XX[13]

I understand that 46 is the number of chromosomes, XX refers to the pair of sexual chromosomes, del(7)(q11q36) means a deletion on the long arm of chromosome 7 spanning the bands 11 to 36.

What do [12] and [13] mean?

Answer

Cytogenetic nomenclature is standardized in the International System for Human Cytogenetic Nomenclature. Unfortunately it is not free and my institution does not have access. However, looking at a preview of the 2013 version in Google Books, it would seem that the number in square brackets is the number of cells scored with that karyotype.

species identification - What are these tiny creatures swimming around my aquarium?

I was checking out my aquarium today, and decided to scoop out a water sample and take a look at it more closely. What I discovered were numerous, very, very tiny white worms (?) swimming around in the water.

The worms hover around 1 mm or smaller, almost invisible to the naked eye, with some exceptional specimens reaching nearly 2 mm in length. They swim very fluently, not by wiggling or waving their bodies around, but simply, effortlessly gliding through the water.

I checked them out under a microscope, and recorded some videos. I apologize in advance for the lackluster quality, as I'm not working with expensive equipment here. It took me hours to locate the worms under the microscope, made no easier by how surprisingly fast they are.

Here's a picture:

When I first saw this, I wasn't sure I was looking at the right thing. As you can see in this video, it appears to stay rooted at the tail, while wiggling its head (?) around in various directions. Its most notable characteristic is the two ball-like structures on the front of its body. I have a feeling that those structures will be key here.

This next part was very poorly recorded, but boy did it surprise me when I saw it. Eventually, the worm stretched forward, its head seemingly morphing into three parts (video):

Finally, here's one more clip showing off how fast they can be when they want to (I swear it's not even sped up!). I wasn't able to get it back under the microscope at this point.

Does anyone know what these are, or at least what kinds of worms they might be related to (with respect to the ball-like structures on its head)?

For a little extra background, I found these in my native tank sourced with creatures caught in southern Alberta. The tank contains some longnose dace, which have been a source of concern due to heavy flashing (scratching) ever since I caught them. It makes me wonder if these worms are related, such as some kind of parasite. I'm happy to have them if they're some harmless detritus worm-- any members of the cleanup crew are welcome-- but if they're something to be worried about, I'd prefer to know.

Answer

Hard to tell because of the poor picture/video quality, but almost immediately the body shape, distinct "face", size and behavior made me think of a small invertebrate animal called a rotifer (Phylum Rotifera).

^{Rotifer eating protists. Photo Credit: Jacqueline Ronson, 2016}

There are about 2000 species occurring worldwide within this primarily freshwater phylum, each of which is fairly simple anatomically. Their name (which means "wheel bearer") comes from the two crowns of quick-moving cilia they possess on their heads:

^{Source: Gifer}

These cilia attempt to push food posteriorly toward the rotifer's back-set "mouth" (which is actually a modified pharyn called a mastax:

^{Photo Credit: Jean-Marie Cavanihac}

Rotifers are small (always < 2 mm) and so eat small planktonic and protist prey. From UC Berkeley:

As rotifers are microscopic animals, their diet must consist of matter small enough to fit through their tiny mouths during filter feeding. Rotifers are primarily omnivorous, but some species have been known to be cannibalistic. The diet of rotifers most commonly consists of dead or decomposing organic materials, as well as unicellular algae and other phytoplankton that are primary producers in aquatic communities.

As for body shape:

Although all Rotifer species are bilateral animals, they vary quite a bit in body shape. Box-like shaped rotifers are referred to as being loricate, while more flexible worm-shaped species are considered to be illoricate.

^{Photo Credit: Juan Carlos Fonseca Mata}

Regarding sometimes staying "rooted at the tail" as the OP observed:

Some rotifers are found usually free-swimming, while others "glue" down their posterior "toes" to anchor themselves to some substrate or debris. Again from UC Berkeley:

The final region of the rotifer body is the foot; this foot ends in a "toe" containing a cement gland with which the rotifer may attach itself to objects in the water and sift food at its leisure.

^{Source: Starr et al. 2013 (Cengage Learning)}

See here for further "fun facts!"

species identification - Can you help me identify this "thing"?

I found these "things" by chance on my wild strawberries which I grow in my organic garden. Basically, some strawberries are completely covered with them.

They're transparent, they have dots equally aligned and they don't move. I've tried searching for transparent slugs and worms and also faeces but to no avail.

molecular genetics - Are the number of base pairs in a given chromosome same between different individuals?

This is a basic question but I couldn't find an answer through a web search; hopefully this is the right place to ask. Is the number of base pairs in a particular chromosome the same in all individuals? For example if I take an X-chromosome from two random humans would I count exactly 155,270,560 base pairs in both cases? or are there mutations that would make one longer than the other? If they're not exactly the same, what's the range in length variation?

Answer

Welcome to Biology.SE.

if I take an X-chromosome from two random humans would I count exactly 155,270,560 base pairs in both cases

No, you would probably not find the exact same number of base pairs because mutations do no only change one nucleotide to another (what we call a substitution) but sometimes add or delete few (or sometimes many) nucleotides.

note, btw that you don't need to take two different individuals, you can just consider the two X chromosomes of a female (or any other pair of chromsom in any gender) and find this difference in the length of chromosomes.

what's the range in length variation?

Good question (+1)!

Telomere issue

Before I start, I want to make clear that I consider the length of those chromosomes at the moment of conception. Chromosomes will vary in length during the lifetime due to telomere reduction. I will not consider this in the following calculations. Also, some mutations directly introduce (or delete) a large number of nucleotides (transposable elements for example), I am not considering those mutations here, assuming they are rare in comparison to to single insertions and single deletions (this assumption might not hold!). So please really take the following with a grain of salt.

Let's make some messy calculations

In classical theoretical population genetics, we tend to consider mostly substitutions. But I can maybe try to make some extrapolation out of this work if you allow me to make some strong assumptions, use poor estimates of actual true values and using some non-rigorous mathematics! This is going to be ugly and not extremely trustful $\ddot \smile $.

Not explaining why this is true (it is a result coming from Coalescent Theory), the expected number of pairwise differences between two neutral sequences for a diploid population is $E[\pi] = 4\cdot N\cdot \mu$ (quite an impressively simple result), where $N$ is the population size (assuming panmictic population) and $\mu$ is the mutation rate for the whole sequence. Assuming a constant per site mutation rate of $\mu_s = 10^{-9}$. Knowing the length of the sequence of interest (chromosom X) $L ≈ 1.55 \cdot 10^8 $, the mutation rate for the whole sequence is $\mu = L\cdot \mu_s = 0.155$. Let's consider a population size of $N = 5 \cdot 10^7$ (the equations assume a panmictic population so I just took some value that felt more or less reasonable to me much smaller than the actual worldwide population size). Therefore the total number of substitutions should be $E[\pi] = 4 \cdot 5 \cdot 10^7 \cdot 0.155 ≈ 10^7$.

Now, let's assume that only a fraction of $\frac{1}{100}$ of the mutations bring variation in the number of nucleotides, we might want consider the value $\frac{1}{100} \cdot 10^7 = 10^3$. And because a mutation that deletes a nucleotide from a long sequence will rather diminish the number of variant in sequence length that increasing it, let's say that will divide this number by 10!... so I'd say that two typical X chromosome would differ in length by about 100 nucleotides.

I am sure that with some work one can come up with more rigorous calculations and a more accurate expectation. Intuitively, the result of 100 nucleotides doesn't sound totally crazy (it is not 1 nor 10^6 at least).

Also, one could probably use available sequence data to estimate this value.

entomology - Why do flies "rub" their front legs when resting?

I've noted that every time a house fly is resting on a surface, it appears to "rub" or "scrub" its front legs in a repetitive movement. And they do it continuously. Why?

Answer

Flies rubbing their legs are cleaning themselves. They can also often be seen rubbing their back legs often. Additionally, flies also often clean their wings, compound eyes and bodily bristles. Legs and wings are used as a primary means of locomotion and means of escape. Eyes and bristles are sensory organs and hence also essential for their survival.

Below a picture of a tachinid fly showing the bristles and compound eyes:

The eyes need to be clean as they are essential for the detection of visual stimuli. The bristles, as a commenter rightfully stated, contain chemoreceptors reminiscent of receptors on the human tongue that sense sweet and bitter tastes. These taste receptors alert the fly for sweet (food) and bitter (poisons) substances. Hence, cleaning of the legs may not only serve hygienic purposes, but may well be important for keeping the bristles and hence the associated sensory organs clean and free of prior encountered substances.

What education does one need to be called "Professor" in the United States of America?

What education does one need to be called "Professor" in the United States of America? A woman with a law degree in a junior college paralegal program insists on being called professor at a local community college. She is the only one in the whole school that does this. Is this normal?

evolution - What measures are commonly used for the complexity of an organism?

I'm aware of measures like number of distinct cell types being used as a measurement of complexity in biology, for example in the G-value paradox. But this doesn't really help for unicellular organisms. Is it possible to define a unit of complexity to make comparisons between different organisms?

Answer

This is a very interesting question. Not sure if there is any way to answer without specifying a definition for complexity.

It is clear that everything is made of only the same few elements, so complexity must involve more than that. Do the number and position of identical molecules matter? If so, size matters and we would label a large jelly-fish as more complex than a cat and the air in a large hot-air ballon as more complex than any single living organism (assuming it is bigger).

I think it is clear that this is not what is meant by biological complexity. Molecules acting identically should not count multiple times; the number of different molecules matters more than the mere number of molecules. But are immune cells really more complex simply because of a relatively minor difference that allows them to generate a wide variety of genetic variants?

What about the variable coat color of a calico cat. Does the complex and non-repeatable (even with cloning) pattern mean it is complex, or does the fact that a simple genetic process underlies it mean it is simple.

The difference in complexity of different representation of the same thing is a classic problem in information theory (see Kolmogorov complexity). The ratio of the circumference of a circle to its diameter requires an infinite number of decimal digits to describe, but it is just a single geometric concept and it can be represented with one or two characters, as pi or π. This applies to the problem of using phenotypes to measure complexity -- the language and definitions we use to describe or to differentiate phenotypes determines what is complex and what is simple.

Moving beyond a simple static snapshot case, biological complexity involves time-dependent evolution. The "game of life" demonstrates how simple rules + initial conditions yield apparent complex behaviors, and the beauty of fractals arises the same way. Many apparently complex organisms grow from small seeds plus time-evolved exposure to simple things like water and light and CO₂. Are trees only as complex as the seed they grow from?

Finally, what about higher order complexity? One human brain is very similar in general makeup to another, but the concepts and memories stored seem complex and very different. Comparing the complexity of stored information between two people is the whole complexity problem over again.

It seems to me that complexity can only be cleanly measured within a specific context, and then only relatively. One can measure the relative genomic complexity of two organism as the edit distance between the alphabetic sequences representing their genomes. The relative regulatory complexity can be measured as mentioned above by @user1682. Each of these says something about an organisms complexity. But what if organism A has higher genomic complexity and organism B has higher regulatory complexity? It might be possible to derive something like a principle component "basis set" from several of these kinds of measurements using a training set and a list of organisms with predefined complexity values. Applying this "standard" scoring metric to another organism would allow ranking it on a "standard" scale, but it would be difficult to generate and obtain consensus on the initial "expert" ranked organism scale. Such a standard might have some value, but is not really theoretically satisfying in that it describe an organisms complexity in the same way that the average of a small sample describes the distribution of a large population.

legal issues - Legality of downloading books from websites such as Library Genesis

I am an international student who will be joining a graduate program at a US university starting Fall '18. In my home country, I have used such websites as Library Genesis and BookFi to download textbooks, from such publishers as Springer etc., which are otherwise either not available or available at exorbitantly high prices in my home country.

Is it legal or illegal for graduate students to download books from such websites? Would I get into any trouble if I download textbooks from such websites either from my personal computer or from a university-owned computer?

career path - How to measure achievement in a field where large collaborations are normal?

In some fields of research, huge collaborations are the norm. This is especially true in experimental high-energy physics.

Say I'm evaluating someone's resume, and that person is transitioning out of one of these fields into something else, such as a career in industry or teaching. I'm not a specialist in that field, and I'm not familiar with current research in it except at a very broad level. How do I tell whether this person was any good at what they did? I can do a literature search on the person's name, but that will just pop up a bunch of papers where the list of authors looks like this: "The XYZ Collaboration: A. Aarons, J. Abelson, ... [183 additional authors not shown]"

conflict of interest - Should you recuse yourself from the hiring committee if you have had a past romantic relationship with an applicant?

If you are on a hiring committee and find out that one of the applicants is someone you have had a past romantic relationship with, should you recuse yourself?

nutrition - Where can you find the quantities of each amino acid of a particular protein or food?

Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information?

Is there a freely accessible database online with these statistics? Or, one that contains something for each protein from which this could be derived? (and if so how?)

Answer

There's a fantastic database available from the United States Department of Agriculture that includes almost 9,000 common foods, including their nutritional information. This database is searchable and available from the USDA Agricultural Research Service. Here is a link for the online searchable database.

Within the database you are able to search for a number of parameters; including, food composition, water content, individual amino acid content, fatty acid and total fat content, vitamins, minerals, phytonutrients, and more! One of the nice things is that you can ask it to rank the foods in order of nutrient composition. For example, ranking all the foods in the database in order of protein content or a specific amino acid (or whatever else you're interested in).

It's a great database, especially for researchers that need a database of trusted nutrient data.

Within the database you can search by nutrient or by food, whichever you are curious about. For example, as you mention in the question, I entered potato and in the second screen shot below you can see the listing of all the nutrients in the potato. These are listed as % weight per 100g of potatoes - with or without the skin.

To get to the amino acid content breakdown, click on Full Report (All Nutrients) at the top.

genetics - How is eye color in humans inherited?

In high school we studied the inheritance of eye color, as it was explained to us in the most simple way: blue eye color is a recessive, monogenic, autosomal trait. Now I know that it is a bit more complicated than that; there are several genes which determine the inheritance of eye color. That's as far as I my knowledge goes.

Which are these genes and what do they encode for? How is the eye color trait inherited? Provided that a man with blue eyes and a woman with brown eyes have a child, can the probability of their child to have blue eyes be calculated?

evolution - When does weak selection produce qualitatively different results from strong selection?

In evolutionary game theory, it is typical to model organisms as having a base fitness that is modified slightly by the game interaction. The ratio of the game effect versus the base fitness determines the strength of selection, with weak selection meaning the game modifies overall fitness only slightly, and strong selection meaning that the game payoff is a big part of the overall fitness of the organism.

Most analytic models like to assume weak selection because it allows the authors to Taylor expand the selection function and linearize it by dropping terms that are higher order in the stength of selection. However, it is unclear that results derived for weak selection would necessarily hold under strong selection. Are there mathematical (or computational) models where weak and strong selection produce qualitatively different results? If not, is there an argument as to why weak and strong selection should produce the same results?

I've also seen this discussion come up outside of evolutionary game theory, in a more general biological setting. In particular, with respect to inclusive fitness. The take away message I got was that in the regime of weak selection relatedness means what you expect it to mean, but for strong selection the concept becomes very slippery and counter-intuitive. What does inclusive fitness theory tell us about going from weak to strong selection? Again, I prefer arguments supported by clean mathematical or computational models over ones based on intuition and words alone.

biochemistry - What can cause the bloating in high protein diet of Whey proteins?

I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins. Liver does breaks those proteins to branched chain amino acids (BCAA), which can cause this swelling.

However, I am not sure if this is the reason. It may be the carbohydrates which are broken to enable this BCAA synthesis. If you take the protein diet with carbohydrates, there seem to be less swelling. So apparently easier energy for BCAA synthesis.

The combination of proteins, carbohydrates and lipids seem to be important. Creatine should also be mentioned. Fat burner thing is also important here, I think.

What can cause the swelling of gastrointestinal system after high protein diet of Whey proteins?

Answer

The cause of the swelling is lack of lymphatic carriage capability of proteins to the muscles, because of systemic conditions affecting the circulation of proteins through your lymphatic system. There will be edema extracellularly because of insufficient carriage of proteins through lymphatic system.

My schematic drawing about the fluid movement between these spaces

I started to think why some people do not observe so much swelling. I discussed with a few and come to conclusion that the main difference between those people who did not have noticeable swelling was that that they did lymphatic system massage by maximising abdominal breathing after taking whey proteins (before training and after training). I think it sounds sensible to some extent. Those people also included lymphatic system massage in their recovery after training. One video here Lymphatic Drainage for Abdomen and Trunk. So another reason what may cause the swelling is insufficient drainage of lymphatic system.

The swelling does not happen to the same extent in all people. Some people swell much after one intake of protein drink. Some people also do not have to do lymphatic massage.

My conjecture: The reason to this is most probably one glue-gene-group. Those people who have this genome have other systemic diseases that causes the lymphatic drainage have high proportion of proteins already:

• for instance, uncontrolled asthma patients, who are circulating lysed DNAs of lymphocytes from small bronchial tree through the lymphatic circulation

Lymphatic circulation is the system which circulates the proteins to the muscles. After absorption from the digestive tract, lymphatic circulation carries proteins systemically. However, since there is already a high proportion of proteins, lymphatic circulation cannot take much more proteins to carry. Our body has to remove toxic wastes before it can build new materials. Catabolism then conquers anabolism in some situations.

thesis - Is copying equations plagiarism?

I defended my master thesis successfully yesterday. Everything in my master thesis was written by me and there is no problem. However I'm a bit skeptical about one thing. So in my thesis I have a part that explains a very well known model. To explain the model you basically need to calculate the gradient of some function, and calculating the gradient is basically lengthy and spans many subsections. So there are many papers and I believe even books that show how to calculate the gradient step by step. So I found one paper and I read it and understood it and understood how the gradient of the function is derived. Next I compared the calculations in the paper to other books and I found that they are very similar.

Since I'm introducing the model in my thesis I had to explain how to calculate the gradient. I explain everything in my own words. However when I wrote the equations they look almost like a copy from the paper!! Since I had the same understanding, so the calculations just almost look the same. So I was really confused what to do about this. Since I want to include the derivation of gradient in my thesis and it looks almost the same from the paper. So I was wondering if this is plagiarism! Since I was skeptical, I checked that the equations also look somehow almost the same from other papers. So to make sure that I don't be held for any kind of plagiarism and credit the authors, I mention at the beginning of the section that starts to explain the model is that my following explanations are based on the explanation given in the paper, where I learned about the model. Calculating the gradient is kinda lengthy and spans couple subsections, so in the subsections I assumed that since I credited the authors at the beginning then I didn't credit them again later for the other derivations of the gradient.

Now my question, is what I did correct?! I mean they were only the derivations of the gradient, so they were equations and I can't just "rephrase" them!

I remember once asking one postdoc that I'm using a lot of equations from one paper and he said that I just need to credit the authors that I'm using the same notation, which what I did. However, when I look at the formulas I feel somehow uncomfortable, because they look like a copy from that paper. Should I be worried?!

I really tried to credit the authors and I cited the papers in many places where I was explaining the models. But only the look of those large chunks of equations seems like copying.

As I said earlier I defended my thesis today, so I just hope that I didn't do anything wrong with that because I really worked hard for my thesis and every single word is mine.

P.S what I know is that copying common knowledge is not plagiarism. So this was my assumption behind the calculation of the gradient. Because the derivation of the gradient is not a contribution and the derivation is done in many papers. (like the gradient of the log-likelihood of logistic regression).

So in short, suppose that calculation of the gradient of the log-likelihood of logistic regression is very lengthy in general. And I just copied the equations from a paper that does the derivation. However when I motivated Logistic regression in my thesis I said that my explanations in the next subsections are based on the explanation in the paper where I copied the equations from. Is that okay?

Answer

Mathematical equations are not normally considered subject to plagiarism, since there are only so many ways they can be written, and because they represent ideas rather than material that can be "stolen" without proper attribution.

So long as you cite the material you are drawing from, and explain the equations in your own words, you should be fine.

PhD Admissions Importance: Research vs. Grades

I have read and been told that research is the single most important factor for applying for PhD programs in STEM fields. But, I also hear that GPA and GRE scores are the first cutting point for adcoms.

What is actually more important, grades or research? Will committees look at applicants with low GPAs?

In my scenario, I have a ~3.4 GPA overall, ~3.7 in Major (CS). This is not stellar. But what I do have is 1 first-author conference publication (Best Paper Award at conference) and 1 first-author journal publication as a Junior, with more other work/papers in progress. And my GREs are 158V/170Q/4.5W.

I'm very interested in top schools, but I'm worried my GPA will hold me back.

Will admissions throw away my application at sight of my GPA? Or will they take the time to review my whole application?

Answer

Graduate admissions committees should, in principle, be able to review all of the applications they receive in full; this is not like undergraduate admissions, where a small team may be responsible for 10,000 or 20,000 applications. That said, some of the larger graduate departments may receive several hundred applications per year, and it may be necessary to do a preliminary screening before deciding which applications will be examined in further detail. However, what gets through such a screen can vary strongly from school to school and department to department. For instance, if you're at a school whose alumni regularly go on to graduate schools and have a track record of success, that can also be a "plus" factor. If you're near the top of your class, that can also mitigate "weak" grades somewhat (because it indicates that your school resists grade inflation).

I would hope that graduate admissions flag applications with publications listed, but it depends on whether or not the database reports that summarize applications actually can do a screen for the presence of publications.

Your specific case, however, is unfortunately in the "no man's land"—not a clear "read no matter what," but also not an automatic "throw away," either. It is probable that you will have a tough time if you look only at "top 5" or "top 10" departments, but you should be able to get considered by many good programs.

Real time PCR normalization algorithm

When performing normalization of real time PCR results, I found two ways of doing it:

1. 
   

   In my lab they follow the next layout: $\text{Efficiency}^{-(CT\ _{\large\text{interest gene}} - CT _{\large\text{ housekeeping}})}$ each time controls with controls and treatments with treatments. Then they divide the all values (treated and controls) each with controls.

   
   


2. 
   
   

   On the other hand I found another way to normalize that follows this steps: $\text{Efficiency}^{(CT_{\large\text{control}} - CT_{\large\text{treated}})}$. Then you make the same for the normalizing gene and divide the first by the last.

   
   

The values obtained are similar but not exact. Also I noticed that first algorithm gives rather different values for most diluted when performing a standard curve. Which is correct?

Answer

First step is the calculation of efficiency, denoted by lets say $E_{gene}$. See this post for calculation of primer efficiency.

So the fold change for that gene will be calculated by $E_{gene}^{-\Delta Ct_{gene}}$

Where:

$\Delta Ct = Ct^{treated} -Ct^{control}$

But these Ct values are not normalized. For normalization, you take some reference gene which need not be a housekeeping gene. Reference gene should chosen such that it is not affected by the treatment. In some cases usual housekeeping genes can also get affected for e.g. in treatments affecting cell cycle or differentiation. In such cases you should use a spike-in (an artificial RNA bearing low resemblance with any known gene).

You can either normalize the fold change (Case A) or find fold change of the normalized expression (Case B).

Means the same mathematically.

Case A:

$E_{gene}^{-\Delta Ct_{gene}} / E_{ref}^{-\Delta Ct_{ref}}$

Case B:

$\large\frac{[E_{gene}^{-Ct^{treated}_{gene}}]/[E_{ref}^{-Ct^{treated}_{ref}}]} {[E_{gene}^{-Ct^{control}_{gene}}]/[E_{ref}^{-Ct^{control}_{ref}}]}$

You can rearrange the numerator and denominator to get Case A from Case B. I'm not sure how you are ending up getting different values. Recheck once. It may be because of numerical approximation errors.

Case A looks much neater; so it is best to calculate that way :)

phd - Is it necessary to have a background in philosophy in order to get a position in logic in philosophy departments?

What the title asks.

Apparently there are some professors in departments of philosophy working on logic or semantics (e.g. William Starr or Nino Cocchiarella [retired]). Does one need to know the "real philosophy" to get such kinds of positions in departments of philosophy? Or does one only need to know logic/semantics (and not, say, treatises of Plato)? And does one have to have a PhD in philosophy, or does a PhD in math or linguistic suffice?

teaching - Should one offer to take over a lecture that the lecturer is struggling to teach?

Once upon a time in a lecture I attended, the lecturer had clearly not fully understood the material and was struggling to explain it. I was a student, but very knowledgeable about the topic, and had taught it many times in informal settings, so I felt silly just listening.

In the interest of the other attendees' learning, I considered offering to take over the lecture. However, I stopped myself, out of concern that the lecturer might feel humiliated, or think I'm questioning their authority more generally.

In such a situation, is it appropriate for a student to offer to teach a topic? What about other teaching staff who are attending? How would one politely suggest it, or otherwise deal with the situation?

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Related questions: From a student's perspective: offering alternative viewpoints on lecture content, handling unintelligible lecturers and handling lecturers who just read from the book. From a lecturer's perspective: teaching a class you've never taken.

Answer

Perhaps the best approach would be to ask leading questions that helps the lecturer head in the right direction. Or, offer an answer to a question that wasn't going well.

I've taught classes (especially ones that use complex libraries, such as parts of a game engine, that I wasn't a seasoned expert with), and have had students who had more experience with a specific topic chime in to the discussion with details I didn't know. It was great. I've also had students who were aggressive and conveyed arrogance and had them derail the class by setting up a me vs them dynamic. Not so great.

The most important thing is classroom dynamics: let the lecturer retain control (ie. facilitate the discussion) but you actively participate. The lecturer should be there to create a learning environment, not bestow knowledge on the class. You can make it clear you know the topic, and let them have you participate as much as they are comfortable.

Asking to "take over" would not go over well; offering your knowledge on bits and pieces and nudging the lecturer in the right direction through questions would be better.

pathology - Why are antibiotics prescribed with a viral infection like a cold?

I've heard both ways; people going to the doctor for a cold and then getting a prescription for antibiotics and those that go to the doctor and told they have ride it out because it's a viral infection. Do antibiotics really help in true cases of a viral cold?

Answer

In general antibiotics don't help with viruses. However, sometimes a bacterial infection may follow a cold virus, so there might be some scenarios in which antibiotics would be needed. However in many cases it could be due to people demanding antibiotics from their doctor.

You can read more here (CDC site): http://www.cdc.gov/Features/getsmart/

publications - Active or Passive Voice in International research journal, within the field of microorganism?

I have been composing the International journal for microbiology research. I learn that research journal should consist of active voice not passive, but I find that the previous researchers for related subject mainly used passive voice. How should I consider?

• 
  
  

  Examples:

  
  
  
  
  1. 
     

     This genus is characterized by two types of conidia called α–conidia (fusiform) and β–conidia (filiform). [I think it is valid. Please correct me if I could change it to active voice]

     
     
  
  
  2. 
     

     Diaporthe sp was reported causing dieback of rooibos (Aspalathus linearis) (Van Rensburg et al. 2006)
     [Van R et al 2006 reported Diaporthe caused dieback of rooibos (Aspalathus l.)?]

     
     
  
  
  3. 
     
     

     A novel Phomopsis sp was reported as a weed (Carthamus lanatus) pathogen and may be used as a biocontrol agent (Ash et al. 2010). [Ash et al. 2010 clarified that a novel Phomopsis sp as a weed (Carthamus lanatus) pathogen may be used as a biocontrol agent?]

     
     
  
  
  
  

*** Note - 9/4/2013: Thank you so much, I appreciate the clarity from everyone.

I also did online research and learn this (may it help those who have the similar problem):

"Many writers are torn between whether they should write the paper in the active or passive voice. In the former, the subject performs the action; in the latter, the subject receives the action. Too much use of the active voice has the tendency to make the text monotonous because of too many first-person references. On the other hand, overuse of the passive voice can cause the tone of the paper to be dry, boring and even pompous. To ensure that the text is more lively and readable, it is best to try and strike a balance. Consider the following example:

We used eosin-methylene blue agar plates for the preliminary isolation of P. aeruginosa. The bacteria were Gram-negative bacilli, and motile. The results for oxidase and catalase activities were negative. Additional experiments showed that the bacteria did not ferment glucose, galactose, maltose or lactose (Table 2). Based on these results, we concluded that the organism had an oxidative metabolism.

Try translating this in to an entirely passive or active tone. You’ll notice that the creative mix of both voices makes this narrative not only lively and engaging but also states the results in a clear, confident and unambiguous manner."

preprint - What are the pros and cons of submitting same paper to more than one open repository?

What if I submit a same preprint to several open access repositories, e.g. arxiv, vixra, philica etc.?

I guess doing so would give to a paper more visibility. But would it be a bad practice? Would it be unethical? Scientific community would complain or blacklist me? Is there any copyright issues, or other notes that I should know? What do you advice?

I know it's unethical to submit a paper to more than a journal (or maybe conferences), but here I want to know about preprints and open repositories.

Answer

From the viewpoint of the repository (although, I am speaking primarily from the viewpoint of a university institutional repository), it would not be considered unethical or undesirable for authors to submit their work to more than one repository. Open repositories are built to increase access to the products of research and creativity, by making works publicly and freely available online. Submitting work to more than one repository is another way for an author to increase accessibility to his/her work.

The only copyright issue present would lie in the relationship between the author and the publisher that published the author's article. Most journals allow authors to deposit pre-prints of their work, that do not contain any edits or revisions from the publication process, in open repositories. Others allow authors to deposit pre-prints of their work that have been revised to show the revisions made in the publication process, and a few journals will allow authors to deposit the final publisher's version of the article. Some publishers will want their authors to wait a few months after publication before making their works accessible through open repositories.

Journals rely on the quality and originality of the articles they publish to build reputation. As most journals charge subscription fees, the originality of their articles is important. Open repositories do not operate on this model, so the ethics of publishing in journal do not translate to depositing your work in an open repository. Most repositories require their authors to sign a non-exclusive distribution license to deposit their work, which allows the repository to make the work accessible online. As a non-exclusive license, authors retain the right to submit their work to journals, other publications and other repositories.

Different open repositories have different functions. Institutional repositories capture the research and creative outputs of their host institutions. Subject-based repositories capture the the work being done in a specific field. Because repositories exist for different reasons, I would see no problem in submitting your work to multiple repositories.

graduate admissions - Value of having done applied math research when applying to PhD programs in pure math

I will be a second year math under-grad in September, and currently doing an internship at applied math research institute. Most probably, I will come up with a research paper at the end of the internship.

However, my interest after my bachelors is to do PhD in pure math from a top math school.My question is this:

Would the admission committee consider my current research since it is in applied math?

In addition, if anyone can suggest me some ideas on how can I bridge the gap between my paper in applied math and my interest in analysis, I would be extremely grateful.

P.S.: Here is a related but different question also of mine.

Answer

Would the admission committee consider my current research since it is in applied math?

Certainly. In my experience, nobody cares at all whether an applicant's research experience is directly related to their proposed specialty in graduate school. There are several points to keep in mind:

1. 
   

   There are only a limited number of research opportunities available for undergraduates, so finding one on your very favorite topic may not be possible. Nobody would hold this against you.

   
   


2. 
   

   Some topics just aren't accessible to undergraduates in the first place (e.g., motivic cohomology).

   
   


3. 
   

   Most applicants don't really know what they will write their dissertations on, even if they think they do. Many will change their minds a year or two into grad school.

   
   


4. 
   
   

   Undergraduate research in mathematics is generally not as deep as grad student research, and the specific things you learn are not crucial. Instead, the point is to see whether you have an aptitude for research and whether you enjoy it. For those purposes, the precise topic doesn't really matter. (Unless, of course, there's only one thing in the world that you would like to study, but I would consider that sort of narrowness to be a problem itself.)

   
   

industry - Why don't professors start companies?

Why don't more professors attempt to use the knowledge gained during the course of their research work by starting a company and commercializing their findings?

I'm asking this question per this comment.

Answer

This question seems to be based on a misconception, namely that professors start companies substantially less frequently than they could or should.

The vast majority of professors, even in fairly applied areas like computer science (compared with literature, say), are simply not in a position to start companies based on their research. You need a viable business plan, and they don't grow on trees. Specifically, even really profound research with many practical applications usually just doesn't have obvious commercial potential as a stand-alone business, since it won't be clear how to monetize it. Of course, there are exceptions, and plenty of important businesses were started by faculty, but only a small fraction of professors could do this successfully.

Here's another way of looking at it. There's no reason why a business based on a professor's research needs to be founded by the professor. If you see someone with great ideas, you can buy the rights to the ideas and found your own company. If professors were missing a lot of wonderful opportunities to found companies, then you'd expect entrepreneurs to step in and do it, but that doesn't happen very often either.

Ultimately, this is why we have academic research. The stuff that leads to obvious business plans could easily be funded by industry. By contrast, one of the reasons why academia includes research is to make sure work that can't easily be sold doesn't get neglected.

graduate school - What percentage of phds in math actually get a tenure track academic job?

I'm interested in knowing what percentage of math phds actually succeed in landing a tenure track academic job?

Also, does a phd from AMS Group 1 guarantees you an academic job in top universities? If not what other factors come in to role to play?

mathematics - How do professors view a student who has good grades but always asks stupid questions?

I am planning to apply for Ph.D programs in mathematics in U.S. and I am thinking about which professors I should ask for letters of recommendations from. In order to get "strong" letters, I need to determine which professors believe I am really strong.

Although I do well in most of my classes (I am always trying to get full marks on my homework and tests), I do have a "bad" habit of asking stupid questions frequently. I can see from the faces of professors that they dislike students who always ask stupid questions, while welcoming students to ask questions. (If you are a professor and don't think this is the case, please let me know...I really appreciate it.) I feel like professors prefer the questions that will make them have a better understanding about the subject instead of the questions that they will waste their time on.

What do professors think of a student who has good grades but always asks stupid questions? Should I expect good letters from them? Or I should go to the professors whom I seldom ask questions (but still do well in their classes)?

Answer

Students often have a highly distorted perception of themselves with respect to the feelings of their professors. The differential in both power and experience between student and professor is just so large that it's quite common for a student to confuse the very distinct attributes of professorial attitude, personal affection, and intellectual respect.

As such, I would suggest that you really don't know what your professors think of you until you ask them. Maybe you are reading them correctly, but maybe not: many professors are quite pleased to have a student who carefully advocates to improve their understanding of material, even if they might wish to be getting on with the lecture in the moment.

My recommendation is to tell the professor you're thinking of applying to Ph.D. programs and ask them something like:

Do you think that you would be able to write a strong letter of recommendation for me?

The "strong" is important here, because that's what will get you the honest opinion of whether the professor thinks well of you or not, and you don't want letters that are not strong.

teaching - Are learning by reading from a textbook compared to listening to lectures different roads to same goal

I have seen few people who learn better(or mostly) by reading textbooks themselves in private as that gives them more time to think back and forth about the material. While there are other students who are quick at grasping things transmitted orally like in a lecture and despise reading it through books. Few of the former even have this habit of not being able to learn at all sitting in a class as lesser time is devoted to discussion on a particular topic and the lecturer tries best to move to the next topic as quickly as possible(not always though). So should those who like to learn on their own through books be guilty for not attending classes(mandatory like in bachelors or masters programs) since they are anyway not going to assimilate much and it will be waste of time?

Can an acknowledgement section of a thesis contain names of music bands?

Can I add some music bands in the acknowledgement section of my bachelor thesis? I used to listen these bands during all my 3-year long studies and during all the writing of my thesis, so I think they helped me quite a lot.

Answer

The only two unwritten rules of thesis acknowledgment sections are as follows:

1. 
   

   Thank your advisor. (Preferably first. Yes, even before God if you're religious.)

   
   


2. 
   

   Don't say anything outright offensive.

   
   

Other than that, go nuts!

genetics - How does the size of insert affects the rate of Homologous Recombination in yeast?

When performing genetic knockouts in yeast using homologous recombination to replace a target gene sequence via a vector DNA, does the region between the flanking regions in the vector have to be the same length as the site of recombination in the host cell's gene?

neuroscience - Why do neurons have a negative resting potential?

Neurons expend the majority of their energy powering ion pumps to maintain the chemical gradients that power their electrical activity. To have a negative resting potential, neurons leak potassium across the membrane, which seems like a terrible waste of energy to me. I would like to know what benefit a neuron receives in exchange for this seemingly unnecessary metabolic load.

I am not asking how the resting potential is achieved. I am also not interested in the trivial answer: that the voltage-gated channels are configured to require a transition across the -40mV or so threshold in order to fire an action potential. It seems to me that this threshold is arbitrary; if there was no advantage to maintaining this gradient then neurons would have evolved to avoid it.

Any ideas? Or better yet, pointers to places where this has already been answered?

My best guess so far looks like this: The total range of available voltages is more-or-less fixed from -90 to +50mV. We want to avoid getting too close to either end, since the channels become less effective near their reversal potentials, so maybe the effective range is more like -70 to +30 (to go outside that range, we must sacrifice speed). Within that 100mV range, we leave the bottom 30mV or so for EPSP integration, and the other 60mV for action potentials. Now, if the resting potential was 0mV, the available dynamic range for integration and spiking would be much smaller which probably translates to making the output noisier.

Answer

Essentially all animal cells maintain an ionic balance causing a resting potential of about -70 mV in order to maintain their internal environment including pH, ion concentrations, osmotic pressure and volume. (Lodish, Molecular Cell Biology) Neurons developed from existing types of cells and it's unlikely that the cost of maintaining resting potential in the neuron could have driven evolution of an entire alternative system to provide the homeostasis supported by the existing system.

Note that the depolarization of the membrane at any particular place during an impulse is very short so the impact of the ion flows have only limited effect on the cell's overall internal environment beyond requiring adjustment by ion pumps for the losses involved. It also is not obvious how the wave-like characteristic of a nerve impulse could be generated if the membrane did not carry a nonzero potential; there would be no stored energy (in the form of ion gradients) available to make the pulse swiftly spread across the membrane.

Another point to consider is that the perhaps 15% of a neuron's energy spent on replacing leaking ions may have some hidden usefulness. This paper suggests that neurons may actually be set up to leak at a rate higher than they would if it were minimized.

teaching - What to do about students who ask for help too often?

For my writing courses, about 5% of students will come to me prior to deadlines asking for help with their paper. I see no problem advising students, as I often similarly came for help when I was an undergraduate. Recently, though, I found an increase in students who apparently just want to abuse this:

• Students will bring me some plagiarized work, showing it to me early, as a sort of test if I will notice. It seems difficult to punish plagiarism when the paper is not yet submitted.



• Students will bring in papers again and again, with little changes put in at each stage, hoping their minimal effort each time will be sufficient to reach their goal of a "D".

I've tried stopping students, but then they are angry when they see the "F" that they hoped I would help them get away from. While most of these students are probably just incredibly lazy, there is a chance that some among them are genuinely trying to improve, but just struggling a great deal, and I can't see it.

How might I go about blocking such abuses?

PhD Research under guide/advisor of a different department

I am a physics undergrad, who is also interested in pure mathematics. I am not very sure what I want to pursue for my PhD. Though I have specific interests in each of the two, and also inter-linked interests, in general I am very confused. My question is it legally and practically allowed for you to chose a guide from another department different than that which you are affiliated to? If not, can someone from another department become a co-guide? In particular, I am looking for laws and practices in the US and Europe (may differ from country to country).

Answer

Yes.

At least in the US, it is quite common for PhD students enrolled in department X to be advised by faculty in department Y, either alone or with a co-advisor in department X. Off the top of my head, I can think of PhD students in my (computer science) department who are advised or co-advised by faculty in electrical engineering, mathematics, and industrial engineering. Similarly, faculty in my department who advise PhD students in mathematics, electrical engineering, mechanical engineering, and biology.

That said, if you enroll in the PhD program in department X, you will have to satisfy the degree requirements (courses, comprehensive/qualifying exams, etc.) for department X, even if your advisor and your eventual research interests are in department Y.

publications - Why is manuscript review in mathematics taking so long (over 8 months)?

I submitted my paper on mathematics to a journal 8 months ago but I have no received any reports or comments yet. I sent an email to the editor asking him about the manuscript, he just replied that it is still under review. What shall I do?

ethics - What else can I do if a journal editor ignores my report of plagiarism?

I am now drafting a complaint letter to the editor-in-chief of a technical journal, against an act of plagiarism committed by a famous researcher in my field. This researcher is apparently aware of my original work, written three years prior to his/her work. I've been having trouble with two of my own submissions to the same journal. I suspect this researcher may have intentionally sabotaged my review process by either offering unfair comments or delay the review process, while his/her own submission got revised, accepted and published in a whirlwind. Ironically, this researcher did actually cite my only published work, a conference paper, and at the same time pretended that he/she didn't know that I did it, and helped him/herself to do it all over again.

I am somehow confident about the objectiveness of the editor-in-chief, although it might be that the AE is also involved in this misconduct. But in case my complaint is unfortunately ignored, what can I do to defend myself?

Can I directly contact the superior of this researcher's institution to bring up the complaint again, hoping to have a different result?

---

Added later: for those who is unclear about what I mean and downvoted my question, please compare the difference between:

Reference [xxx] already did it. The result shown here can be found in [xxx].

and

Reference [xxx] mentioned it. But it is really me that first give the result.

---

Added much later: someone suggests that this might be an insufficient attribution. If you were in my place, what will you do then?

Suppose I am this famous researcher and I found out a nobody is not giving me sufficient attribution, will the situation be completely different?

---

Added much much later: Many thanks for all the comments and replies. I have drafted my letter of inquiry very carefully after taking the many suggestions given to me. Nevertheless I am prepared to eat the shxt...fool me once, shame on you; fool me twice...

Now I think it is not true that the "game" is rigged for me just because I am a Chinese...if I received my education in one of the top universities in Europe or in the states, I would have a much lower chance of knowing people like this researcher in the first place...now it sounds like it is still because I am a Chinese...damn this life played with hard mode...

Answer

Given your addendum, what you are talking about is not plagiarism. It might be a case of insufficient attribution, but without seeing the papers and knowing the field it is impossible to tell.

You are guaranteed to fail in your efforts, and to make yourself look bad in the process, if you accuse this famous researcher of the wrong transgression simply because you don't know the difference between plagiarism and insufficient attribution.

As an aside, the fact that you don't know this difference makes me question whether you are able to objectively judge whether or not the researcher in question has violated the norms of your field. I'd strongly advise seeking advice from a trusted senior mentor before doing anything.

GRE Score Advice: Should I retake?

I took the GRE in April and recently received my score. I placed in the 88th percentile, which is respectable but far from impressive. I am hoping to get into a top 25 math grad school for a PhD in pure math. I don't think my score is representative of my mastery of the undergraduate curriculum as I barely prepared for the exam.

I didn't prepare as much as I should have and now am worried about whether I should study over the summer and take it again next year. I have an REU this summer which will eat up eight weeks and would like to get a start on my senior thesis afterwards. As such, my question is:

As far as graduate school admissions are concerned, is it worth it to take the time out of more interesting pursuits to prepare for retaking the GRE next year?

united states - Professor falsely accusing me of cheating in a class he does not teach, two months after end of the class. What precautions should I take?

I'm a domestic student in the US. Despite my poor English, it's my first language.

In May 2019, I finished a class on web development. My final submission was a simple but fully functional web app. The professor of the that class seemed happy with my work (and the work of my classmates) and gave positive feedback. No one was accused of plagiarism. It was a small class with only five people, we all know each other fairly well and I don't think anyone cheated. I know I certainly didn't.

This summer I am taking another class, which is co-taught by Prof X, who has made it clear that he thinks I am an idiot. Prof X is also one of the co-chairs of my program.

Last week, I asked Prof X a question. He scoffed at me and asked me how I completed the web-development class if I didn't already know the answer to the question. I told him I had completed it just fine. Then he told me I couldn't possibly have completed the final project. I told him I did. I asked him the question again. Then he asked me what my grade was in the web development class. I got an A, so I told him that. Normally I wouldn't get into it but I was happy with the grade. I was not able to get an answer to my question.

This week I found out that Prof X is starting a formal university disciplinary process against me.

I didn't cheat and I can prove it. I have all the code I wrote for the project and it's in my GitHub in a private repo so it was all version-controlled. I also have the presentations I gave to the class that show the work in progress. The web-development class's professor would vouch for me if needed, I'm sure of that.

While I think this is likely to blow over and not result in any problems for me, what are some precautions I should take just in case?

---

Bringing info from OP's self-answer below up into the question:

@MichaelKay - "my guess would be that you wrote the code and got it working despite not understanding some fundamental concept of WHY it worked; and the Prof, having a more theoretical mind-set than yours, can't imagine the possibility that people can get code working without understanding the theory."

I accept that I may not understand some fundamental concepts of why it worked. However, Prof X is not a computer science professor and by his own admission is not a programmer. The class I'm taking this summer is in psychology and that is the area of research of Prof X.

"It would help to know exactly what the question was."

Sure, without going into too much detail about the coursework, I had asked for help with my presenting skills. My question did not have anything to do with programming. The class I'm taking this summer is in psychology, no programming involved.

Prof X has never criticized my coding skills, only my ability to pass the web development class based on my question about giving presentations.

@Bey - This isn't a major research university, it's a medium-sized state school. Prof X is not a department chair, he is one of the co-chairs of my program specifically, not the whole department. I can't drop the course as it is past the drop date now. But regardless, Prof X is one of three professors teaching this class and the other two seem to think highly of me so far, so I am less concerned about the grading.

nutrition - Has there ever been an attempt to create nutritionally tailored food for adult human consumption?

For all domestic animals, and for all animals kept in laboratory, complete and precise composition of perfect food is figured out (cat food, dog food, cattle, rats, laboratory monkeys and apes) -- which contains precise composition of carbs, fats, proteins, aminoacids, minerals and vitamins. Everything is known. Convenient dry cat/dog food contains exactly that. Animals are healthy on this food.

The composition is also known for human babies. This is manufactured as "baby formula". Everything baby's organism needs to be healthy (and to grow).

How let's take human adults.

Was ever attempt made to create "dry human 'dog-food'"? This sounds stupid, but there are emergency situation in which such food can come very useful.

So my question is, is there anything special in human biology that prevents creation of complete "dry human food" that contains everything our organism needs to be healthy ?

Or it was created but tasted so disgusting that nobody would eat it ?

Or it actually exist somewhere ? Just curious.

graduate school - Doing a PhD with significant external time obligations (e.g., marriage)

Graduate school has a reputation for being a tremendous time-sink. I'm currently married with kids, and I have a fairly busy extracurricular schedule. Is it common for married people - or anyone, actually, with significant external time constraints - to not finish their graduate work, specifically due to conflicting obligations?

Answer

I've seen it work both ways: some people realize that they have a limited amount of time to work as a result of their external commitments, and therefore make themselves super-productive during the hours they are able to do research. I think, to some extent, that most of the people with severe external obligations fall into this class.

For a sizable minority, however, the balancing act proves too difficult—although this is often a function of a mismatch in expectations between the advisor and the graduate student. If you believe this could be a problem for you, you should definitely talk with your advisor; if the outcome is unsatisfactory, you should also consider speaking with your thesis committee and the "graduate officer" of your department.

In general, I think that if you are a productive graduate student, your advisor would be willing to work out suitable accommodations for your schedule.

Is there an optimum time to leave between writing and self-proofreading?

Having read a number of guides on tips to do when proofreading as well as some questions on this website. They all refer to leaving some time between writing and proofreading. This time can vary from 5 minutes as per Purdue online writing lab

Even a five-minute break is productive because it will help you get some distance from what you have written.

to

Put the paper aside for a few hours, days, or weeks. The writing centre-UNC

My question is has there been any scientific work/papers done that gives a result on an optimum time to leave between writing and self-proofreading?

Answer

It appears a number of factors come into this, such as what point proofreading should be done, familiarity with the text and length of time away from it.

According to Jane Cogie, Kim Strain and Sharon Lorinskas

It is important also that editing [proofreading] be done at the appropriate stage of the writing process, that is, as the last step, after issues of organization, coherence, and flow have been addressed.

In a study, The generation effect in reading and proofreading, the authors Meredyth Daneman and Murray Stainton conducted the following experiments in which;

Subjects spent 30 minutes composing an essay on student life; after a 20 minute interval (Experiment 1) or a two week interval (Experiment 2) they proofread their own essay, another subject's essay after being familiarized on an error-free version of it, or another subject's essay without the benefit of a preview. Experiment 1 showed that subjects were less able to detect errors (e.g., The best part of student like is socializing.) in self-generated essays than in unfamiliar other-generated essays; on the other hand, they were better able to detect errors in familiar other-generated essays that in unfamiliar ones. Experiment 2 showed that the disadvantage for proofreading self-generated text is likely a by-product of extreme familiarity rather than any special quality of self-generated knowledge per se

Commenting on the above study, Maura Pilotti, and Martin Chodorow (doi:10.1007/s11145-007-9110-x) state that;

The difficulty experienced by proofreaders with their own writing occurred even though the proofreaders were warned that errors had been added to their writing prior to proofreading. Interestingly, the impairment uncovered by Daneman and Stainton turned into an advantage after a delay of 2 weeks between writing and proofreading. The researchers argued that the ‘‘excessive’’ familiarity afforded by one’s own text, which is likely to decline over time, is detrimental to proofreading because it promotes a less thorough processing of written material.

It would appear from the above that 20 minutes is too short a period, and that something like two weeks is more optimum, but if possible leave it as long as possible.

publications - Publishing in PNAS

I am curious about how competitive is publishing a paper in the United States' Proceedings of the National Academy of Sciences (PNAS) in comparison to leading journals in a field. Is PNAS on the same level as Science? Thoughts will be appreciated, but factual materials (i.e., links to research studies or other information on the topic) even more so. Do they consider/publish survey papers?

Additionally, I am interested in answers to the following related question. PNAS defines itself as a multi-disciplinary outlet, while my brief review of their editorial board left me with an impression of a strict field-based classification. Then, the question is: how one would submit a multi-disciplinary paper, in particular within information systems field of study, considering such classification?

The paper that I have in mind is a survey paper (or similar, i.e., position paper), based on my dissertation (its literature review, that is). The paper would cover the following domains: Economic Sciences (via ecosystems), Engineering Sciences (via software engineering), Social and Political Sciences (via ecosystems), Computer and Information Sciences (via software engineering).

Final question: does PNAS accept submissions from unaffiliated (independent) researchers?

molecular biology - Can forensic DNA analysis be used to generate a visual approximation of a suspect?

In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I realize the term reasonable is subjective, so characteristics, such as skin color, hair color/texture, approx height, eye color, freckles, etc. I came across this article a few years ago, but the company that made the test went bust in 2009. It could detect race (how accurately?). I seem to recall reading an article a few years ago stating that "soon" we'd be able to get an approximation of appearance from a DNA sample that was better than a sketch artist could provide, though I can't recall now where I read it.

job search - What is the recommended option for a faculty applicant after accepting an offer and getting another better offer?

As universities provide short deadlines for faculty position offers, applicants can accept an offer-1 (verbally or by signing a contract) and which is not the best. What is the recommended option if a late and a better offer-2 arrives after accepting offer-1?

• Reject offer-2 and stay with offer-1.


• Reject offer-1 and accept offer-2.


• Accept and delay offer-2 for a year or two if possible, and work for a year or two with University-1.



• other options?

Answer

This situation should not actually arise if you are handling your faculty job search properly. If you accept an offer, you should withdraw all your remaining job applications. Otherwise either you are wasting their time in considering you for a position you won't accept, or you were insincere in accepting the previous offer. If you aren't comfortable withdrawing your other applications, then you aren't comfortable accepting the job. You can negotiate on this point, for example by telling them that another job would solve your two-body problem and you hope they can wait on a final decision until you hear about that job, but there's no guarantee that they will agree.

The basic ethical principle here is honesty: you shouldn't give someone a decision they understand to be final without actually meaning it. By default, job acceptances are considered binding decisions in the parts of academia I'm familiar with (certainly in mathematics in the U.S.), so you can't just assume that of course they knew you might change your mind. If you have any reservations or conditions, you should make them explicit before accepting the position. This can't hurt you if nobody really considered the decision to be final in the first place, and it will avoid unethical behavior if they did.

Even though this shouldn't happen, people do occasionally get themselves into this situation. If you unilaterally rescind your initial acceptance and take the other position instead, you face almost no legal risk, since nobody's going to try suing over this. However, you can hurt your reputation, which is a serious danger.

Instead, the way you should handle it is by careful discussions. Typically, University 2 will let you defer their offer for at least a year, since otherwise they look like jerks for trying to steal you away from University 1 after you already accepted an offer. (Another possibility is that University 2 had no idea you had already accepted and will rescind their offer upon learning this.) Then you approach University 1 and apologize profusely for inadvertently creating a terribly awkward situation. You explain that you are willing to come to University 1 and fulfill your obligations, but you have an offer from University 2 and you would very likely leave after a year to go there, so you wonder whether there is any chance they would release you from your acceptance. If they agree, then you are ethically free to accept University 2's offer immediately. (University 1 still won't be happy with you, so you shouldn't do this unless it really matters to you, but asking them for permission is much better than just announcing you aren't coming.) If University 1 insists that they need you next year, then you defer University 2's offer and show up at University 1.

But you really shouldn't let yourself get further faculty offers after you've already accepted a job. You might be able to get away with it once by explaining that you accidentally forgot to withdraw your other applications, but you really don't want to develop a reputation over time as someone who deliberately manipulates the system in unethical ways.

biotechnology - Selection of recombinant host by color selection method

In recombinant DNA tech, To select a recombinant host from non-recombinants, we have different types of techniques available.

The one I'm talking about is the color selection method with the use of 2 markers(one antibiotic resistant gene for eg. Ampicillin, and the other Z-gene). We use Z-gene as the reporter gene. We use vectorless E. Coli as the host cell here.

Now, when we add add Ampicillin to the petri dish containing all of the variants (transformants and non-transformants), - the non-transformants will die. The transformants survive.

Now, we add X- gal to the replica of this petri dish, and we see some of the colonies turning blue due to the action of the enzyme β- galactosidase, which in turn is produced by the intact Z-gene in the plasmid. That means our blue colonies are the non-recombinant ones.

My question is-

The medium taken in the petri dish should contain glucose too , shouldn't it? Otherwise the recombinants would too give the colour reaction (X-gal is a homolog of lactose) due to the Z-gene present in their chromosomal DNA (operon concept).

The question maybe silly since it's kind of obvious we have to supply basic necessities for the growth of bacteria(which obioviously is glucose).

Just wanted to confirm in case we don't have glucose available ! =p

Answer

The Z gene you are talking about should be lacZ that encodes the $\beta-$galactosidase, which is made from $\alpha$ and $\omega$ peptides. Neither peptide is functional by itself.

$\beta-$galactosidase will cleave the glycosidic bond in X-gal and form galactose and 5-bromo-4-chloro-3-hydroxyindole. The latter product then dimerizes and oxidizes to 5,5'-dibromo-4,4'-dichloro-indigo, an intense blue product that is easy to identify and quantify.

Next, you should check out the genotype of your bacterial strain because they typically have only the $\omega$-peptide encoded in its genome. Thus, the enzymatic activity of the $\beta-$galactosidase is only recovered when the $\alpha$-peptide is in the environment, and the process is called $\alpha$-complementation.

Two commonly used strains for cloning and expression in E. coli are Dh5$\alpha$ and TOP10.

The genotype for Dh5a is like this:

F– Φ80lacZΔM15 Δ(lacZYA-argF) U169 recA1 endA1 hsdR17 (rK–, mK+) phoA supE44 λ– thi-1 gyrA96 relA1

Here, lacZΔM15 indicates that the M15 segment is lost from lacZ, and the mutant protein will only have the $\omega$-peptide.

The genotype for TOP10 is like this:

F– mcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara leu) 7697 galU galK rpsL (StrR) endA1 nupG

Again, you will notice lacZΔM15, which is still a non-functional peptide segment after all.

Finally, to your question. Even if the there is no glucose as primary energy source in the medium and only X-gal is present, the operon of your host bacteria(I suppose it's E. coli) cannot produce the functional $\beta-$galactosidase on its own. Moreover, the recombinants, with the vector sequence encoding the $\alpha$-peptide disrupted, will not exhibit $\alpha$-complementation. No color reaction then! :D

Reference:
1.Genotypes of Invitrogen™ competent cells - TOP10, retrieved from: https://www.thermofisher.com/cn/zh/home/life-science/cloning/competent-cells-for-transformation/chemically-competent/top10f-genotypes.html.
2.Genotypes of Invitrogen™ competent cells - DH5a, retrieved from: https://www.thermofisher.com/us/en/home/life-science/cloning/competent-cells-for-transformation/chemically-competent/dh5alpha-genotypes.html.

3. Langley, K. E.; Villarejo, M. R.; Fowler, A. V.; Zamenhof, P. J.; Zabin, I. (1975). "Molecular basis of beta-galactosidase alpha-complementation". Proceedings of the National Academy of Sciences of the United States of America. 72 (4): 1254–1257. doi:10.1073/pnas.72.4.1254. PMC 432510 Freely accessible. PMID 1093175. 4.

First RNA polymerase-mRNA

We know that RNA polymerase produces mRNA by reading DNA strand. Which enzyme produces the first RNA polymerase if other RNA polymerases are synthesized in the same way like other enzymes(proteins) ?

anatomy - Evolution of long necks in giraffes

In this question, the OP uses giraffe necks as a supportive example of evolution. Is the mechanism described in this post accurate? At some point, I thought I remember hearing that giraffes did not evolve long necks to reach higher food resources, but instead longer, stronger necks gave some sort of mating advantage (male competition perhaps?).

Is there a consensus in the scientific community as to evolutionary mechanism(s) that contributed most to the evolution of long necks in giraffes?

Answer

There seems to consensus that it is not competition for tall food. Giraffes actually often feed on resources that are lower than their maximum possible height. See:

Simmons, R. E. & Scheepers, L. 1996. Winning by a Neck: Sexual Selection in the Evolution of Giraffe. The American Naturalist 148: 771–786

This paper put forth the idea that sexual selection is the reason behind long necks. The idea is that longer necked males are dominant. But this theory has also been questioned. See:

G. Mitchell, S. J. Van Sittert, J. D. Skinner. 2009.Sexual selection is not the origin of long necks in giraffes. Journal of Zoology 278, Issue 4: 281–286

So in the end there's no clear consensus. Some papers have returned to the theory of competition for research in the past few years.To put it simply, no there is no consensus.

My PhD seems daunting and overbearing. How shall I regain motivation and interest?

EDIT: I should clarify this is not the first draft of my PhD, it's the first draft of my upgrade document to go from MPhil to PhD.

I have been working on my PhD for about two years now, it is a six year part-time program. I have a very good relationship with all my supervisors and they are very supportive. I am fortunate to be part of a good university which is open-minded and free-thinking. I also have attracted the interest of a well-known external academic who is an authority within the field and who wants to be involved. I am very lucky.

The problem is that I am just not that interested or convinced by my research [chiefly its significance]. I have to submit my upgrade document [MPhil > PhD] in about five week's time, and the viva is a week after that. I have written a draft document which is 12,000 words and my main supervisor has written a lot of comments which are suggestions for improvements. The issue is that I do not feel that interested or compelled to work through them.

I am under the impression that my supervisor is not that convinced by my research, even though she keeps saying she has no concerns. I feel my research is too vague, too broad but also too overbearing. It incorporates three disciplines [at the advice of one of my supervisors], disciplines A B and C. Discipline A I am not that interested in - I was for my master's but now I find it quite tedious but it is quite an important part of the whole. It is a well-worn discipline and feels rather old and stale to me now. Discipline B is quite new and interesting, I have published within this discipline. Disipline C is very new and up-and-coming. I find it quite exciting and my supervisor has written the least amount of comments about it in my draft paper, which I take to mean she has the least amount of complaints about it [she has a lot of comments to make about dispclines A/B]. She has also said that discpline C is a 'key' part of the PhD.

I do not know what to do. I am really not that interested and the whole thing seems so daunting. My PhD focuses on A and B mostly with C being only a feature, but I am wondering whether I should switch things round entirely and make it more about C. I feel I will not really be able to convince my panel about the significance of my research in the viva if I am not excited about it or convinced myself. In my master's I was always keen to research and write, now I am not, but I know I would be if the topic were carried out a bit differently.

What shall I do, how shall I regain interest? My PhD seems rather fluffy and not sharp enough. Additionally, I am daunted by the scope of the whole thing: it seems too large to work through and 'bigger' than me. I am kind of at a loss for what to do.

Answer

What you are going through is common among graduate students. I had it back when I was doing my M.Sc. and then my Ph.D. Now my students have it from time to time. The other answers offer good advice but they might apply to different phases of a Ph.D. journey.

So here is my advice. Don't burn the bridge behind you. You've come all the way, so you might as well get your Ph.D. Ph.D. is not just a dissertation, but a journey. All the people you meet, all the new books and papers you read, all the new tools and skills you learn, they all contribute to making you a better person/researcher. From your question, I understand that you could be satisfied with those things. Even though you are not satisfied with your dissertation, you have all the time after your Ph.D. to pursue other interesting fields.