The majority of papers don't share their code. However, I sometimes want to reproduce the results, and therefore re-code the experiments to try to reproduce the papers.
Where shall I share the code, findings, comments, and potentially some data sets, put aside from GitHub? Ideally I am looking for a common place where people share the work they have done when reproducing papers.
I am mostly interested in computer science papers.
It is quite common in almost all position opening announcements in academic institutes to demonstrate EXCELLENT teaching capabilities. For instance sentences like below:
Applicants are expected to demonstrate excellent undergraduate and graduate teaching capabilities
But the question is HOW to demonstrate that excellence? Is just listing subjects taught during last couple of years sufficient? I guess we can use teaching statement or teaching philosophy to demonstrate that ability too. But, what type of sentences show that excellence in teaching statement?
I was wondering what the actual reason for death by suffocation is. Obviously it is related to oxygen deprivation. But what is the underlying cause of death?
Answer
Short answer
This is a difficult question to answer. As far as I am aware, asphyxiation results in excitotoxicity, which causes unconsciousness, brain damage and eventually, death.
Background
Asphyxia is a condition of the body that occurs from severely inadequate oxygen supply, or because of excessive carbon dioxide in the body (First Aid and CPR courses). The brain is the organ most sensitive to hypoxia (Medscape). Nerve cells in the brain can survive only up to four minutes without oxygen (First Aid and CPR courses). Consciousness is lost after approximately three minutes (Forensic Pathology). Permanent brain damage begins after approximately 4 minutes without oxygen, and death can occur as soon as 4 to 6 minutes later (Medline). Asphyxial deaths typically involve respiratory arrest with bradycardia / asystole (low heart rate / cardiac arrest) because of the hypoxia-induced dysfunction of the respiratory centers in the brainstem (Forensic Pathology).
Despite the small size of the brain (2% of body weight), it is, however, the largest consumer of total body oxygen (20%) and glucose (25%), which are delivered by 15% of the total cardiac output (Schur & Rigor, 1998).
A lack of oxygen may result in so called hypoxic-ischemic encephalopathy (HIE), i.e., neuronal cell death due to hypoxia. Its pathophysiology is related to the lack of energy because cellular respiration diminishes. This initially causes neurons to stop firing, and eventually in an arrest of cellular functions and cell death. Even sublethal HIE can set in motion a series of toxic reactions that kills injured neurons and even neurons that have not been damaged during the initial insult. Thus, following global brain ischemia, neurons do not die suddenly or all at once. In some of them, damage develops hours or days after the insult. Most neurons undergo necrosis. In some neurons, HIE triggers apoptosis (Neuropathology).
Specifically, energy depletion is believed to result in a failure of the Na+,K+ ATPase, leading to depolarization of the neuronal membrane (Fig. 1). Synaptic function and conductivity cease at this point. Depolarization causes neurons to release glutamate (Glu) into the synaptic cleft. Glu is the most common excitatory neurotransmitter. In small amounts, it is indispensable for neuronal function. In excessive amounts, however, it is neurotoxic. Some Glu receptors, such as the NMDA and AMPA receptors, are non-selective cation-permeable ion channels. Initially, over-activation of these channels causes a passive influx of Cl- (and Na+) into cells causing osmotic (cytotoxic) edema and rapid death (Neuropathology).
Additional structural damage develops hours or even days later as a result of Ca2+ influx into neurons through NMDA and AMPA receptors (Fig. 1). This delayed cell death is caused by an over-activation of NMDA and AMPA receptors by the excessive release of glutamate, which causes massive influx of Ca2+ into neurons. Ca2+ activates catabolic enzymes (proteases, phospholipases, endonucleases), and also NO synthase. NO is a free radical and other free radicals are generated due to the impairment of oxidative phosphorylation. Free radicals and activated catabolic enzymes destroy structural proteins, membrane lipids, nucleic acids, and other cellular contents, causing neuronal necrosis. DNA damage from endonucleases and mitochondrial injury from free radicals trigger apoptosis (Neuropathology). Collectively, these effects are referred to as excitotoxicity (Choi, 1992). When enough brain cells die, the person perishes with them.
Fig. 1. Schematic showing the excititoxic effects of excess glutamate in the brain. Source: Neuropathology.
References
- Choi, J Neurobiol (1992); 23(9): 1261-76
- Schur & Rigor, Dev Neurosci (1998); 20: 348-357
Is glycolysis the beginning part of fermentation, or does fermentation follow glycolysis?
I see conflicting information from different sources
https://honchemistry.wikispaces.com/Lactic+Acid+and+Alcohol+Fermentation+in+Humans
"..Alcohol fermentation follows glycolysis, just like lactic acid fermentation..." <-- So glycolysis is preceding fermentation, not part of fermentation
and
" The Actual Fermentation Part
Glycolysis and fermentation are two separate processes. Glycolysis was explained briefly to give the reader an idea of the events leading up to fermentation and the starting conditions in terms of molecules available for reaction.....Going into the fermentation, the molecules NADH and pyruvic acid are present. " <--- so glycolysis is preceding fermentation, not part of fermentation.
Whereas these two links put glycolysis as part of fermentation, not a preceding stage before fermentation.
"Fermentation and cellular respiration begin the same way, with glycolysis" <-- glycolysis is part of fermentation, not preceding it.
and
http://study.com/academy/lesson/anaerobic-respiration-lactic-acid-alcoholic-fermentation.html
"fermentation, which is a process that anaerobically generates ATP by performing glycolysis..." <-- fermentation includes glycolysis, so glycolysis is part of fermentation, not preceding it.
So, which is it?
Is it a)like khanacademy and study.com, or b)like honchemistry.wikispaces.com
I have heard the idea that glycolysis is independent, in that it can produce some (not much, but some), energy on its own, and it can happen without fermentation or cellular respiration following. Though when would glycolysis occur without fermentation or respiration following? And even if glycolysis is that independent, it may still be at the beginning of respiration and fermentation and not preceding it.
Wikipedia speaks in a contrary way..
https://en.wikipedia.org/wiki/Fermentation
"Before fermentation takes place, one glucose molecule is broken down into two pyruvate molecules. This is known as glycolysis." <-- so glycolysis is preceding fermentation, not part of it.
so the above quote from wikipedia suggests that glycolysis is not the beginning part of fermentation, but a step preceding it
whereas still on the fermentation wikipedia page, it says
"Fermentation is a metabolic process that converts sugar to acids, gases, or alcohol....The first step, glycolysis" <-- so glycolysis is part of fermentation.
Links on respiration are more unambiguous that glycolysis is part of respiration.. the links on fermentation vary a bit on whether glycolysis precedes fermentation or is part of it.
Answer
As @bpedit indicates in his comment, this is a semantic question — i.e. one regarding the meaning and usage of words. I will explain how I and others use these words and why. If you are convinced by my logic you will wish to use them in the same way, if not you are free to use them differently. However there is no ‘universal truth’ here, and if you are student I have no idea what your instructor thinks.
The problem is that ‘fermentation’ and ‘ferment’ (both as a noun and a verb) are old words, predating any understanding of the processes involved. Thus the Oxford English Dictionary quotes a relevant early example of the use of ‘ferment’ as a verb as follows:
1663 Cowley Verses, to Royal Society iv, All their juyce did .. Ferment into a .. refreshing Wine.
From this, it is clear that the idea of the fermentation process is the conversion of some initial compound (the sugar in the ‘juyce’) to some final compound (the alcohol in the wine). This usage is still current in referring to the process of fermentation, for example a Google search brings up a BBC Science educational page which states:
Beer and wine are alcoholic drinks made by fermentation reactions that use yeast to convert sugars into ethanol.
You may or may not be aware that term ‘ferment’ was historically used to mean what we now term yeast, and ‘Zwischenferment’, the obsolete German term for certain enzymes in yeast, is derived from this. So the original concept was merely of some biological conversion effected by yeast, although this has later been extended to bacteria and the idea changed to indicate metabolic processes capable of generating ATP anaerobically.
Part of the discrepancy in definition may be the emphasis on the end-product of the fermentation — ethanol fermentation, lactic acid fermentation etc. However, it seems clear to me that the fermentation is the whole chain of metabolic events from sugar (or whatever) to alcohol (or whatever); and if glycolysis is part of that process (which it is in this example) then glycolysis is part of the fermentation. (Of course, glycolysis can occur in other circumstances where the product, pyruvate, is oxidised in the tricarboxylic acid cycle, which is not a fermentation process.)
Footnote
The extent to which one can tie oneself in knots with trying to define fermentation is illustrated in the best-selling and well-respected text book, originally written by Lubert Streyer and subsequently maintained by Berg et al. I mention this text both because an older edition is available on-line, and because a book of such value to the publishers is carefully vetted by referees. In the chapter on Glycolysis there is an attempt to define Fermentation:
Fermentation: An ATP-generating process in which organic compounds act as both donors and acceptors of electrons. Fermentation can take place in the absence of O2. Discovered by Louis Pasteur, who described fermentation as “la vie sans l’air” (“life without air”).
So the biochemical lawyers have produced a definition that very few readers will be able to take in at first sight. What is this business about electron donors and acceptors? Well what it means in relation to the fermentation process in which lactic acid is produced (note my legalistic choice of words) is that one organic compound is reduced (glyceraldehyde 3-phosphate) — by NAD+ — and one organic compound is oxidized (pyruvate) — by NADH. And as the production of ATP is included in the definition this means that Berg et al. include glycolysis in this definition of fermentation.
…except that on the same page there is the following statement:
pyruvate is converted, or fermented, into lactic acid in lactic acid fermentation or into ethanol in alcoholic fermentation
So here it seems that the word is being used for the conversion of pyruvate to lactate or ethanol, i.e. it excludes glycolysis.
Pasteur managed to talk about fermentation without being aware of glycolysis or ATP, and it is clear to me that you can write whatever carefully phrased definitions you like, but people are going to continue to use venerable terms like fermentation in whatever way seems natual to them.
In a lab we used distilled water + 3 drops of soap to examine how beetroot would be affected by it. I believe the beetroots membrane denatured and a red pigment leaked from it. However, I cannot explain why this has happened. Can anyone explain the topic question to me?
Answer
@mdperry answered well. If you need some diagrams to help with understanding, this article Should be helpful.
As you surmised, when you add detergent, it is lysing some cells of the beetroot that contain pigment. That pigment then gets released into solution. I've annotated the image below for the micelles that gets formed, except I spelled it wrong :/
As part of their job, professors have to take care of getting funding, prepare classes, advise students, fulfill administrative tasks and attend to various meetings/conferences.
How much time do professors have to carry out research on their own (i.e. excluding the above-mentioned tasks)?
I am especially interested in the field of computer science > machine learning, in the US, in an averaged-size university.
I am mostly looking for studies that try to quantify how much time professors have to carry out research on their own.
Is there any publication venue that makes rejected papers available for download?
I am most interested in the field of computer science, and English-speaking venues.
For example, I want to propose a new algorithm for an existing problem, and I already have published several papers about this topic, they share exactly same background, is it OK for me to copy the "background" and "related work" part from my published paper?
The background contains some already well-studied techniques, in order for the paper to be self-containing, they should be briefly introduced (instead of just being cited).
I don't see the meaning that I have to express the exact same thing in a different way for every new paper
Answer
This is called "text recycling" or even "self-plagiarism" and generally frowned upon by editors. It's better to avoid it as much as possible, even if it results in more work, particularly for non-native speakers of English. Too much overlap can result in rejection or later retraction, where "too much" is at the discretion of the editor. You are also very likely to annoy reviewers if they notice the overlap with your previous publications.
The Committee on Publication Ethics has the following guidelines for journal editors:
When should action be considered?
Text recycling can take many forms, and editors should consider which parts of the text have been recycled. Duplication of data is likely to always be considered serious (and should be dealt with according to the COPE guidelines for duplicate publications [1,2]. Use of similar or identical phrases in methods sections where there are limited ways to describe a common method, however, is not uncommon. In such cases, an element of text recycling is likely to be unavoidable in further publications using the same method. Editors should use their discretion when deciding how much overlap of methods text is acceptable, considering factors such as whether authors have been transparent and stated that the methods have already been described in detail elsewhere and provided a citation. Duplication of background ideas in the introduction may be considered less significant than duplication of the hypothesis, discussion, or conclusions.
When significant overlap is identified between two or more articles, editors should consider taking action. Several factors may need to be taken into account when deciding whether the overlap is considered significant.
Text recycling in a submitted manuscript
Text recycling may be identified in a submitted article by editors or reviewers, or by the use of plagiarism detection software, e.g. CrossCheck. Editors should consider the extent of the overlap when deciding how to act. Where overlap is considered to be minor, authors may be asked to re-write overlapping sections, and cite their previous article(s). More significant overlap may result in rejection of the manuscript. Where the overlap includes data, Editors should handle cases according to the COPE flowchart for dealing with suspected redundant publication in a submitted manuscript [1].
I am a bachelor student at the second year of studies (Physics), but I'm an independent programmer since many more years.
Now, I have some data about an algorithm I've done and I would like to present the results on a research paper - I have a high level of understanding of the theory behind, and some background of theoretical computer science. Is it "reasonable" to write a paper with no titles at all (high school) and without the name of my university maybe? I don't know whether include it or not, since the topic is not related to what I study there.
Answer
You should definitely write it up. There are plenty of good reasons for doing so and no downside. Writing a paper is a good exercise for future paper and report writing, and while you are doing it you are likely to think of new ideas about your research. You will also have to search for similar work that might be suitable for references and you may find something useful there too.
You should also put the paper online somewhere so that it is preserved and available to others who may find it useful. If there is data and/or code that goes with the paper you can use figshare for example. It does not matter if there is not much response to your work, that is common when authors have no background and does not mean it is not good. Someone may pick up on it later when you don't expect it.
You might also want to try to publish in a peer-review journal if you think it is sufficiently original and useful. That might require you to write it up in a specific format such at LaTeX. Again that is all good experience. You will have a much better chance of acceptance in a journal if you can use your university affiliation but you will have to make it clear that you are an undergraduate there to avoid problems and it might be best to check with your tutor. If you search around you may find a suitable journal that is specifically set up to accept work from undergraduates. If you can get it accepted it would look good on your CV whatever you plan to do in the future.
The only circumstance that would make it unwise to publish your work would be if the algorithm is original and of high commercial value and/or patentable in which case you would have to follow a different route to protect your intellectual property. However that is a rare situation.
There are two mechanisms that have been proposed to me.
1) Layering of Schwann cell membrane with conducting fluid between the layers is analogous to several capacitors in series. Since capacitance in series add by the reciprocal rule (as resistors do in parallel), this reduces the total capacitance.
2) The myelin increases the distance between the 'plates' of the capacitor. For parallel plate capacitors $ C = \epsilon A/d$ where d = distance between the plates. Thus increasing the distance reduces the capacitance.
Which of these explanations best applies to myelin, or is it in fact a mixture of both?
Answer
Circuit analogies don't 100% apply to myelin because membranes have complex electrical properties, but both of those explanations work and they are in fact essentially interchangeable: Take a membrane with distance d across the membrane and capacitance c. Then we add some myelin to get a new capacitance C at a new distance D.
If you 4X the distance between plates (D = d * 4), C=c/4 (from the formula you posted as (2) ); if you add 3 extra plates (so now you have a total of 4 plates), C=1/(1/c + 1/c + 1/c + 1/c)=c/4.
Importantly, myelin also increases the membrane resistance, and because myelin is typically very thick compared to a normal membrane (~10nm for one layer vs. 500-2500nm for myelin), you can almost consider myelination to increase resistance to infinity (compared to the axial resistance of cytoplasm) and the capacitance to zero.
See this page for some more info.
Note that the reason these explanations are interchangeable is that there is effectively no distance between the added plates in series and no difference in capacitance for each individual capacitor/piece of membrane (for example, see this page).
If a hermaphrodite animal (like slug, snail, etc) finds a partner they can mate immediately.
If another animal with "normal" reproduction (lets say a mouse) finds a partner they can only mate if they have the opposite gender.
So it seems logical that the hermaphrodite way of reproduction is more successful than the "normal" way.
But it is not, as far as I know all higher developed species are using the standard way of reproduction (male and female).
Why? What are the disadvantages of hermaphroditism?
Answer
Firstly I'll clarify that you are talking about simultaneous hermaphrodites rather than sequential hermaphrodites (1st one sex, then the other e.g. the limpet Patella vulgata).
It is perhaps easiest to address the question by countering it and asking why dioecy (2 sex systems/2 gonochoric types e.g. male and female) is better? As you have pointed out there are obvious advantages to being a hermaphroditic species such as more chance of mating - more likely to provide an advantage at very low population densities where interactions are infrequent.
There are two key disadvantages of hermaphroditism which I will briefly cover but have been discussed in this paper and probably other costs.
The first is energy costs. Maintaining the capacity to produce male and female gametes will be more costly than maintaining one. This gives the hermaphrodite a fitness disadvantage because energy is rarely an infinite resource. Therefore at higher population densities, when mating opportunities are not rare, the gonochoric individuals will have a higher fitness because they have more energy. Monogamy is also analogous to rare encounters but true monogamy is rare (1 partner for life).
The second disadvantage of hermaphroditism is self fertilisation. This will cause an increase in homozygosity and lead to inbreeding depression (reduced fitness).
So you are right to some extent...
the hermaphrodite way of reproduction is more successful than the "normal" way.
...but the conditions which give rise to an hermaphroditic advantage are restricting. Overall, the above costs, combined with the obvious complexity of evolving the ability to produce male and female gametes, the ability to both fertilise and be fertilised, pregnancy and birth, and mating systems, mean that it is often more beneficial to be a dioecious species. Thus dioecy evolves.
EDIT: Question Raised by @Single_Digit
I have been pondering this question for a while and I get what RG255 is saying. I'm just not sure I entirely buy it. Take earthworms, for example. They are simultaneous true hermaphrodites (as far as I understand). The anatomy doesn't have to be that complex*. They simply have two genital openings (one for eggs and one for sperm) and they line up in a "69" (excuse the vulgarity) position. This should, in theory, minimize the inbreeding depression. However, it doesn't eliminate the maintenance of two sets of reproductive systems. But most organisms are not internally fertilized mammals with wildly complicated systems of internalized embryonic care. Most species lay a pile of eggs that a male squirts sperm on or squirt eggs while the male squirt sperm and then they hope for the best.
I would think the advantages of simultaneous parenting (after all, many MANY species' males don't provide much in the way of child care) and its fitness advantage would vastly outweigh the burden of a second set of reproductive organs.
With that said, I don't have a better explanation, but I find the question a very interesting one. The linked article is pay-walled, aside from the abstract, but I still disagree with some of its tenets. To me true hermaphroditism should be very common (I realize it isn't) in species that don't need two parents to raise offspring, but do benefit from some (as in one parent's) parental care. I recognize that it would do little to help species that merely dump gametes and leave because specialization of one reproductive system would likely do the job better and both genders equally contribute under that type of system.
So, RG255 convince me! Clearly there are good reasons, since gender (or asexual repr) is the norm, but I need more/better evidence.
- Yes I realize they would need separate internal anatomies for each type of gamete, but still...
My response:
You have presented one example of hermaphroditism and used that as evidence that all species should be hermaphrodites. Earthworms are small slow creatures living in soil, I don't imagine they have high rates of encounter, and therefore low rates of encountering the opposite sex, therefore hermaphroditism would be favoured as discussed above.
Further, you say most species are external fertilisers (do you have a reference for this?) and therefore it is not costly be a hermaphrodite. I don't see your logic there, the cost is not necessarily to do with the cost of bearing child, producing & maintaining the gonads and gametes is also a costly process. I would argue that this is extremely complex. This is not just on a morphological level but also physiological: in non-hermaphroditic species the sexes have very different, and often, conflicting gene expression and hormone production patterns. Hermaphrodites would not be able to optimize to the fulfilling both the male and female roles.
Finally, you pointed out that the worms do not inbreed. Inbreeding avoidance does not have to be the cause of the hermaphroditism persisting, if the environment/other factors favour hermaphroditism. I never said that both were simultaneously necessary.
I hope this clarifies it for you, if not please expand as to why, I am on here because I want to help people understand biology properly!
Further response from @single_digit:
Well fair enough about my external fertilizers comment. I don't have a reference, but I was thinking all multicellular life and I'd have to imagine that when you factor in plants, that external fertilization is relatively the norm (as is hermaphrodism (dioecy) for the plants). As to earthworms, I disagree about your description of them. Their densities are actually pretty high, so I'd wager they encounter each other frequently, so I'm not sure where that leaves them in terms of pressures for hermaphroditism. Your point on the physiologic/hormonal issues of maintaining the systems is one I haven't previously considered. I honestly don't have any clue as to how daunting (or simple) that is, but I'd imagine that the sophistication of the systems would play a pretty key role. Makes me wonder how much this has been researched in true hermaprhodites. I suppose the main thing I keep coming back to is the overwhelming disadvantage gender has in terms of potential to create offspring. Males in many (most?) species essentially act as little more than sperm donors, thus half the individuals have effectively zero fitness. That just seems like an overwhelming advantage for hermaphrodites.
My Response
Why do you consider half of the individuals to have zero fitness? Fitness is widely accepted as the number of offspring a parent produces because this is directly related to number of copies of their genes passed to the next generation. Sperm donor type males achieve increased fitness by mating as do females - with out the male they would never be fertilized. The key disadvantage of dioecy is the halved (assuming equal sex ratio) frequency of potential encounters that could lead to mating. The general disadvantages of hermaphroditism are inbreeding depression and high cost & complexity.
Single_digit:
Zero fitness isn't exactly correct, but if we look at parental care as conveying a survival advantage for K selected species, and huge numbers of offspring conveying an advantage for r-selected species (obviously the type of env affects this) does a deadbeat dad really optimize for either of these? Passing on genes is fine, but if offspring survival is low, does it matter? Does it simply boil down to the maintenance of two repr systems plus decreased fitness from inbreeding vs the increased reproductive success from extra child care? Or is there more?
My response:
r/K selection theory has generally been disregarded in the evolutionary biology community due to the substantial evidence against it so it is unhelpful to think of selection in this way. As long as the 2 sexes strategy is more successful at passing on genes than a hermaphroditic strategy it will (should) prevail. Dioecy will be more successful if the hermaphroditism introduces to much cost through production and maintenance of sexual organs/gamete and inbreeding whilst not attaining substantial gains from higher potential mating frequency.
@Single_Digit
Interesting about r/K selection. I hadn't heard that. Do you have any links? I'd be curious to learn more there. I incorrectly earlier made a comment about dioecy where I meant monecy. But this seems to beg the question, why is monecy/hermaphroditism so much more prevalent in plants? Obviously there are different survival pressures, but I'd think the same basic principles would apply as in animals, but the condition seems to be far more common than in animals.
My Response
I seem to remeber there being a reason in plants, don't have time to look it up right now. The work about r/K selection was Reznick/Stearns/Charlesworth. Reznicks is the most recent and more overview type paper - best place to start: http://www2.hawaii.edu/~taylor/z652/Reznicketal.pdf
I'd be interested in tools helping to organize thoughts and ideas, especially in a non-linear way (i.e. not as most existing note taking tools, working with lists and bullets, but rather as a post-it application). Ideally, something like the tool they use in Minority Reports would be cool (without the fancy-touch thingy), but an important point would be the ability to visually connect different ideas/notes together.
EDIT: Maybe to make things more explicit, I have a visual memory, and it helps me a lot having a graphical disposition to classify things (like important things at the top-right, urgent ones on the middle-left, etc). Basically, I'd like to find my messy desk on my screen :)
Answer
For nice graphical note editing/drawing:
If you get the hang on it, you probably could use http://prezi.com/
Your notes would look great, and you can always zoom in and out, if you want to add details.
For sharing your notes everywhere (web/smartphone):
Actually springpad is no longer available..
see http://www.springpadit.com, another nice option for taking notes: - Take your notes on the go (clients for most smartphones). - Edit your notes and analyse them, on the web. - You can tag and label your notes, so you have some non-linear flexibility as well.
Forgive me if this is not the right place to ask pedagogical questions, but it seemed the most appropriate.
I am a TA for a programming/CS course. This is my first time teaching recitation and I'm not really sure what the best approach is. What I've been doing is covering what the professor asked me to, with a mix of lecturing (which I don't really like as I feel the students get enough of that) and me solving problems on the board with their help (which is OK but it's usually the same students answering the questions).
I can think of several different methods of recitation:
Can anyone provide insight for which of these ideas are most effective?
Further information: It's a summer course, so the pace is pretty fast. Furthermore there are three recitations a week, each an hour and a half. It's the second CS course, so it's mostly programming (data structures and safe code) with a bit of theory thrown in.
I had an amazing time at my REU (Research Experiences for Undergraduates) last summer. I would really love to do another one this year.
Problem is, I am about to graduate, so I will technically not be an undergraduate this summer. I do intend to continue my education in graduate school in the Fall, and have been admitted somewhere.
I've been told that I should just kick back and relax this summer so that I'm fully unwound for grad school, but I don't have any money to travel, all my friends will have left for their grad school already, and there's really nothing that would stress me out more than sitting around and doing nothing for three months. I love to travel, make new friends, and learn cool stuff, so I think doing another REU would actually be the perfect way for me to unwind.
At my last REU, we had a student who had graduated that year and was about to go into a Master's program. It was rumored that she had omitted/lied about this on her application and the admissions people just didn't look into it carefully. I don't know if this is true, though. It seems possible that the program staff simply felt her application was strong enough to warrant making an exception - after all, she wasn't going to grad school yet.
Is it possible to be admitted to a mathematics REU the summer between undergrad and graduate school?
If not, would offering to go without pay (for only room and board) make any difference? What about REUs in physics, or compsci, or other sciences which might want somebody with a math background?
Answer
I quote from the NSF REU guideline (emphasis mine):
Eligible Student Participants: Undergraduate student participants supported with NSF funds in either REU Supplements or REU Sites must be U.S. citizens, U.S. nationals, or permanent residents of the United States. An undergraduate student is a student who is enrolled in a degree program (part-time or full-time) leading to a baccalaureate or associate degree. Students who are transferring from one college or university to another and are enrolled at neither institution during the intervening summer may participate. High school graduates who have been accepted at an undergraduate institution but who have not yet started their undergraduate study are also eligible to participate. Students who have received their bachelor's degrees and are no longer enrolled as undergraduates are generally not eligible to participate. For REU Sites, a significant fraction of the student participants should come from outside the host institution or organization. Some NSF directorates encourage inclusion in the REU program of K-12 teachers of science, technology, engineering, and mathematics. Please contact the appropriate disciplinary program officer for guidance. Within the framework of the basic eligibility guidelines outlined here, most REU Sites and Supplements further define recruitment and selection criteria, based on the nature of the particular research and other factors.
So this means that (a) your host will not be able to receive funding for you from the NSF if s/he accepts you into the program (b) on the other hand if you and/or the PI of the grant is able to secure funding otherwise, there's generally no rule saying that a student in your position cannot be involved in research in some way.
You will need to individually contact the REUs you are interested to find out whether they'd be willing to grant you the leeway.
My question is simple. Why is a virus considered a microbe? Considering a microbe is considered to be a "living" unit of life, which viruses are not.
Answer
What is a microbe?
A microbe (or microorganism) is a microscopic organism. Anything that is considered alive and that is small enough is called a microbe.
Note that this definition has two issues.
Is a virus a microbe?
A virus IS and IS NOT alive depending on the definition. Note btw, that the definition of what is alive is not a matter of Biology but a matter of Philosophy. Most of the time, viruses are considered as not being alive. It is important to understand that the definition of life has absolutely no impact on biology and is nothing but a question of nomenclature.
If you want to call a virus a living thing, then yes, viruses are microbes. As stated on the wiki article:
Some microbiologists also classify viruses (and viroids) as microorganisms, but others consider these as nonliving.
You can find a discussion of why viruses are generally considered as not being alive here.
Unit of life
The concept of "unit of life" has not much meaning in biology and, to my experience, is most often used as a nice image for teaching young students what a cell is. Most of the time that I heard of "unit of life" (mostly when I was in secondary school and eventually high school) was used to describe a single cell making up a multicellular individual such as a cell of your blood for example and not a unicellular individual.
The problem I've always had with evolution is the actual lack of variation between animals. More specifically, the lack of observable gradual change between species.
Take for example the hammerhead shark. It obviously has a strong connection with a normal shark, but where's the "half-hammerhead" shark? Where's the species that only has a SLIGHTLY wider head?
I really doubt that a single mutation on a normal shark resulted in a head shaped like that, it had to happen gradually. Right? As far as I understand, evolution works by random mutation in a child being somehow slightly beneficial to that animal so it get's to live longer and reproduce more, eventually resulting in it's genetic material in dominating the inferior ones before it. But if it was for whatever reason beneficial to have a slightly wider head, why don't all the sharks have slightly wider heads now? On the other hand, if it wasn't beneficial, how come the hammerhead still exists?
Furthermore, I feel like some characteristics of a certain animal can't really have gradual benefits. There's a lizard that shoots blood out of it's eyes. The original ancestor certainly didn't, and I'm sure that if it's child only bled slightly from it's eyes it wouldn't really help if much in life. So for it to actually become beneficial, it seems to me that there had to be a ton of lizards that had a disadvantage of bleeding slightly. In fact, there had to be so many that they evolved even further in the same direction and kept doing that until they bled so much it's an actual benefit (sorry for this turning so gross). So why did the inbetweeners survive long enough to evolve even more, and why did they THEN die out?
Answer
More specifically, the lack of observable gradual change between species.
Most significant phenotype differences occur over several thousand generations, which means several thousand years on up. While we certainly can create experiments where a controlled form of evolution occurs within a very small time-frame, I'm going to assume that you're not interested in closed laboratory experiments given the nature of your question.
It obviously has a strong connection with a normal shark, but where's the "half-hammerhead" shark? Where's the species that only has a SLIGHTLY wider head?
The data below does answer you question, but in reverse. Hammerheads are much older than most of their relatives; so their cousins have actually grown smaller heads... but there are certainly intermediates.
From Andrew Martin (1993 - mtDNA data) via Elasmo-research.org:
*The circles represent the head-width vs. body-length ratio.
Martin's conclusion: "...the hammer appeared rather suddenly and fully formed, and was later optimized along different lines to suit various selection pressures."
I really doubt that a single mutation on a normal shark resulted in a head shaped like that, it had to happen gradually. Right?
Not necessarily. Single Nucleotide Polymorphisms (a.k.a. - "SNPs" - a change in one nucleotide) can have pretty wide-ranging effects.
The vast majority of humans, for instance, are lactose intolerant in adulthood. However, lactose tolerance evolved twice from two different SNPs in two different human populations: One European and one African. One gene. One regulatory mechanism change. Massive benefits (essentially opening up a whole new resource in adulthood).
Significant differences in phenotypes (the physical appearance of something) can require more gene mutations, or not. It depends on where the mutation is in the genome and what the gene does.
But if it was for whatever reason beneficial to have a slightly wider head, why don't all the sharks have slightly wider heads now?
The simple answer is because either there wasn't enough selective pressure that the rest of the shark phenotypes succumbed to that the hammerhead avoided, or that the hammerhead design doesn't give enough of an advantage to completely dominate the gene pool. An alternate, but more abstract answer, is that there simply hasn't been enough time for the hammerhead design to dominate the shark phenotype. Remember, evolution works by generations - not years. It would take unknown thousands of generations for a weakly-advantageous design to dominate an entire niche - if it ever would.
Also, it is worth it to point out that evolution doesn't only select for advantageous mutations. Mutations that aren't very detrimental can still exist within a population as long as the detriment doesn't prevent resource exploitation and offspring production. Think Huntington's Disease which severely restricts a person's survivability, but only after their mid-30's (in general) - plenty of time for the person to have sex and raise a kid into semi-adulthood. It is a genetic defect which sticks around only because it allows humans to reproduce before it seriously affects them.
The original ancestor certainly didn't, and I'm sure that if it's child only bled slightly from it's eyes it wouldn't really help if much in life.
Maybe, maybe not. Maybe it shot something else before blood, and then a mutation caused it to shoot blood instead - but the overall effect (deterring predators) was the same so it doesn't really matter.
You're correct that some traits might appear very awkward if they had evolved gradually, but the question then becomes: Did they evolve gradually? Sometimes we simply do not know.
So why did the inbetweeners survive long enough to evolve even more, and why did they THEN die out?
Like I said above, just because a trait is detrimental doesn't necessarily mean it will be eliminated. As long as the being can survive long enough to reproduce successfully with the trait, the trait might not be eliminated for a very, very long time- if ever.
As for in-betweeners dying out - it's difficult to think of it like that. You're talking bout LCAs ("Last Common Ancestors") of extant (currently-living) species. While some LCAs just die out for some reason or another, it's more common that the LCA simply continued to evolve and become a genetic relative due to some sort of isolation.
Think of it like the in-betweeners coming to a fork in the road. Some choose right, some choose left. There isn't anybody left behind - merely two populations that are changing over time that were once one group until they don't really mate between each other anymore (or can't). Heck, even Biologists have trouble deciding at what point a population is considered a different "species" because of discoveries in the last 50 years - so right now a firm answer like "It takes 15% of the genome to change for a new species to emerge" isn't possible as it doesn't really work like that.
We'll get to it eventually, but for the time-being, it might be easier to say that everything currently living on Earth is an in-betweener of something else in the future. Everything in its current iteration will eventually die off, but not before something else emerges from our offspring which may or may not be significantly different from us due to however many genetic mutations our offspring have from us. It could be one that opens up a whole new realm of possibilities (like lactose tolerance) or an accumulation due to selective pressures (like Phoemelanin production and pale skin in humans [Redheads] to produce more Vitamin D3 at higher latitudes).
Is there any research/study/survey/... that tried to estimate how much it would cost to remove paper pay-walls so that all existing research papers are made publicly available free of charge?
E.g. France paid Elsevier 172 million EUR (mirror) so that 476 universities and medical center can have legal access to 2000 journals for five years. I wonder how much it would cost to buy the access to all papers so that anyone can access then.
In mathematical scientific papers, which section would I detail pseudo code or sample source code? Would that be included in an Appendices section or above under Methods?
Answer
If it is both Long and Required, then perhaps you are writing overly detailed pseudocode. I know the formal pseudocode I learnt in high school was detailed to the point of being executable -- which defeats the purpose of pseudo-code -- if it can be written clearly in a language that is in common use in your area (E.g. R for statisticians, Matlab for signals engineers) you can just write it in that language and avoid any ambiguity.
If on the other hand it is short and not required, it can go anywhere (Possibly even in a footnote). Though its still not required.
A common pattern, I've seen a few times is to have pseudocode, or just textual descriptions of the algorithm in the main text. Then an implementation in a real programming language in an appendix; And/Or a footnote linking to the authors website/github where it can be downloaded
I'm a PhD student, and my advisor published what appears to be the theoretical frame I came up with for my dissertation as a standalone paper with some other people (not me). It seems (to me, though who knows) like I was going to make a reasonably important contribution to my subfield, so I'm even more cut up than maybe I would have been. And now I have to finish my dissertation as other people are now using this theoretical frame on data similar to mine. There is also, of course, a small chance that my advisor came up with the same idea as me, but it smells wrong, since we don't work in quite the same area. (My feeling that something is wrong is bolstered by knowing that he very definitely screwed me over in another incident.) How do I handle this? Do I have to cite his paper? I cannot switch advisors --my department is small, so there isn't someone else who can advise me in it. I'm also too close to done. I have no desire to fight; I only want to survive, preferably with some of my dignity intact (i.e., some way not to cite my advisor's paper). I'd be grateful for comments from folks who are well along in their careers in academia, since I think part of my problem here is really not understanding academic culture.
Context: I did a masters in another subfield before starting my phd; my idea is basically drawing a common set of ideas from the master's subfield into the new subfield (where they are almost never used); I cited all of these things in my dissertation proposal, which I turned in before my advisor's paper came out, and which my committee read. The tricky thing is that I could still see my advisor saying the idea came from him - which is false and unlikely, since again, they don't know my other subfield. But still, I am terrified as well as angry.
I began working on a paper during my undergraduate degree in the summer of 2014. I continued to work on the same paper into summer 2015, at which time I graduated and moved to a different university to pursue a graduate degree. However, all experiments failed and my collaborators and I were unable to produce any meaningful results. In fall 2015, while enrolled in graduate studies at the second university, I realized that the question at the centre of this paper could be answered using a completely different method. I contacted my collaborators and we have been able to produce some great results.
Now I am writing the paper and wondering what I should list as my affiliation, since the project was begun at one university but overhauled and completed at another. I see four options:
What is standard practice in a situation like this, where work is begun in one lab but completed in another? Does the re-design of the project from the second university complicate the issue?
Answer
Most journals understand that such complexities exist, and will allow you to list multiple institutions, so all four of your options are certainly viable.
That said, given that you have done much of your work on the paper while at your new institution, your new institution should certainly be listed as an affiliation, which means that you should be using either your option #2 (new only) or #3 (both institutions).
That leaves the question of whether the old institution should be listed or not. From what I have seen, the customs on this tend to vary by field and also by institution: you can probably make a reasonable argument for either listing or not listing the old institution. I would thus recommend talking with your co-authors to see what their feelings on the matter are, particularly if you have some co-authors from the old institution on the paper, who are the ones most likely to be upset if your judgement disagrees with theirs (in either direction).
Inspired by the question Is it acceptable to write a reference letter for yourself?
I have a related but somewhat different question: Given no choice, is it acceptable to write a recommendation letter for self?
This question is based on real cases. In non-English speaking countries, many professors don't know how to write good recommendation letters in English. The professor may know how to write papers in English in his field. But, when writing recommendation letters, he has limited vocabulary to write about his students. In other words, his English is not proficient. To make the matter worse, some professors may only be able to write simple English sentences. The professor may tell the student the contents of the letter in his native language and ask the student to translate it into English and then signs it.
The student may want somebody else to write the letter because he does not want the professor to do this unethical thing. But, the professor just happens to be his advisor (undergraduate or master). The student may want to suggest that his professor ask the professor's colleagues for help to write the letter. The professor may say no. Therefore, the student writes the recommendation letter for himself by translating the professor's draft in their native language into English.
Is it acceptable? If not, what should the student do?
Answer
Thanks for asking this question.
In light of recent strong comments I have made on closely related issues elsewhere, let me say that I think that getting a letter translated from one language to another is an absolutely kosher academic practice. The classy thing to do would be to also include the original (e.g. how do you know that the readers will not speak that language?) and also indicate who the translator was.
However, the translator should not be the student. That is a problem because:
(i) It is an obvious conflict of interest.
(ii) Recommendation letters are often meant to be confidential, and this violates confidentiality.
If you absolutely cannot get anyone other than the student to translate the letter then you should clearly indicate "translated by the student" and expect to have your honesty applauded and the letter largely dismissed.
I must say that my heart opens up for a student who is living in a context where there is no qualified third party to translate a letter into English. I have been to academic departments in several non-anglophone countries and never encountered such a situation...but of course I have not been everywhere, nor to a random sampling, nor to any academic department in a "third world" country. That's a tough situation. Translating the letter yourself does not seem like the best answer.
Let me also say the following: if you are a non-anglophone student whose English skills are far superior to those of the faculty at your university [and assuming that you are applying to anglophone graduate programs, of course!], then you might try to cultivate relationships with anglophone professors elsewhere in the world. Twenty years ago that would have been preposterous advice, but due to the proliferation of mathematical interaction via the internet, it seems very viable today. For instance there is a small but positive number of students with whom I have had sufficiently substantial interaction on MathOverflow and (more often) math.SE so that I would be glad to write them a strong recommendation letter. If you are a math student, you can always try writing to any professor and having mathematical interactions with them. They are not obligated to respond (I certainly do not always respond...), but they often do (I often do...) especially if you show them something truly promising.
[At some point in the previous paragraph I forgot that I was supposed to be writing for a general academic audience rather than an academic mathematical audience. But since I am not sure how far my advice extends outside of mathematics, I will leave the m-word in.]
Among US students applying to US graduate programs, it is increasingly frequent for at least one of three recommendation letters to come from the director of a summer undergraduate research experience (REU) than a faculty member at the university. Such letters are not necessarily the most penetrating -- they read very similarly, perhaps because of the implicit motivation to paint one's summer research experience in a positive light -- but they often get the job done, i.e., they lead to admissions.
Let me also say that a letter of recommendation for graduate admission is not always the most important part of the application. If I get an application from a university that I have not heard of, and letters from faculty that I have not heard of and whose reputations I do not know, I can only take the letters so seriously no matter what they say. (And it is quite true that not everyone knows how to write a good "American-style recommendation letter". This does not necessarily get counted against the student; it just doesn't get counted for them.) If you are coming from an "obscure program" then your goal is to convince the readers of the applications that your training is equal to (or superior than!) the training that students in more familiar programs get. So it can be helpful to include very specific information about coursework: e.g. not just the title of the course and the course grade but the textbooks used. If you wrote a paper which does not make any research contribution but shows a solid understanding of graduate-level material, by all means include that as part of the application. Also be sure to take all the applicable standardized tests and do your best on them (and don't cheat on them!!).
Someday, as strange as it feels to me right now, I might be asked to review an article for publication. A while ago my advisor and I were talking about this, and it hit me that I don't really know how to be a good reviewer, beyond the basics:
Respond timely to things,
Make your report clear and detailed,
Have actually read the paper,
Etc.
Beyond this, though, I'm completely in the dark. So I'd like to ask:
What's some good advice for a first-time reviewer?
My field is math, but I'm really interested in general advice (although advice specific to math, or another field, would also be interesting and useful).
I'd like to make this question "community wiki" or analogous, but I can't seem to figure out how - if someone can do so, please do, and then I will delete this paragraph.
Sometimes men wake up with an erection in the morning. Why does this happen?
Answer
Sometimes men wake up with an erection in the morning. Why does this happen?
Shortly speaking: REM (Rapid Eye Movement) is one phase of sleep. During this phase, we dream and some of our neurotransmitters are shut off. This include norepinephrine, which is involved in controlling erections. Norepinephrine prevents blood from entering the penis (preventing the erection). In absence of norepinephrine—during REM phase norepinephrine is absent—blood enters the penis, leading to an erection. This phenomenon is called nocturnal penile tumescence. Such erections typically occur 3 to 5 times a night. A related question concerning similar erections in women can be found here.
High pressure in the bladder may also lead to a "reflex erection". This erection allows for preventing uncontrolled urination. The drawback is that when in the morning one has an erection and can't wait to pee it might get hard to accurately target the toilets!
This video is also a nice and easy source of information on the subject.
Is it bad?
(Reading my "note" below, you have edited your post to get rid of this question, thank you)
It is perfectly healthy you don't have to worry about that. These erections are even thought of as contributing to penile health. At the opposite end of the spectrum, the absence of erections during the nights are an index of Erectile Dysfunction (E.D.).
Note
Be aware that medical questions are often considered off-topic on this site. Asking "is it bad?" turns your question into a medical one. Health-related questions (but not personal health) should be asked on health.SE
Recently, I submitted an article and got a response from a reviewer that I cited 6 of my own articles out of 44. The reviewer said that it’s a cheap act of self promotion.
The reviewer didn’t say I cited senselessly, rather he complained about the citation of my own work. How to respond in this given situation?
I happened to find a PhD project that would align with my past experience really well. I would like to contact the professor responsible for the project. How brief should I be in my first email?
In addition to introducing myself and referring to the position, I would like to ask at least two questions about the project, and mention that I have been working on a similar project.
Is that enough? How would I finish the email then in a proper way? Just something like
If you are not too busy, I hope you could discuss the matter further. Attached is my CV.
or something entirely else?
I have a very good publication record, have received big prizes, lot of experience, etc. in my pocket but I guess I should not repeat that in the email, since it is in the CV?
This is a follow-up question to Open versus Blind reviewing process, and is somehow related to What happens to the reviews that people write for journal articles after they're sent back to the author?
However, my question does not concern the reviews I receive for the papers I submit, but concerns the reviews I write for papers I have been assigned. Since the whole process is done under confidentiality, it is not clear who owns the copyright on a review I wrote, and what does the review include.
For instance, let us assume that X is member of a PC of a conference Y, and assigns to me a review of a paper Z, written by A and B (assuming it's not a double-blind). Can I publish on my blog: "Here is my review for Y, asked by X, on the paper Z, written by A and B"?
I think that there are two points here:
EDIT: There is been several comments/answer wondering why I would like to publish a review I wrote. To give a bit of background of this question, I believe that the current reviewing system, created when the academic community was small and there was no Internet (i.e. no easy access to information), might not be the best, although clearly working. This is for me a very interesting debate, but somehow out of the scope the Q&A format of Academia SE, which is why I tried to focus on my question on whether it was possible to do so, not if it was the best thing to do in the current system (and just to be clear, I don't plan to do it, but I just like to know what are my options). Anyway, thanks for the answers bringing a different light on this debate.
EDIT 2: After seeing the update in Jeff's answer, I just realised that I didn't make it explicit that I was talking about reviews after the reviewing process. Jeff says that it's ok if the paper is accepted, and although I clearly understand the argument of why I shouldn't publish a review of a rejected paper, the question still holds: by publishing a review of a rejected paper, I publish the information that these authors submitted this paper to this conf/journal, which is supposed to be confidential between the authors and the editors. Would I break any rule by doing so?
Answer
The standard rule in my community is that once I finish reviewing a paper, I'm supposed to pretend that I don't know the paper exists. In particular, I am not supposed to use any insights I gained by reading that paper in my own research. I am not supposed to reveal the results to my colleagues. Some venues ask that I destroy any copies of the paper I'm reviewing, along with any programs or data I used to verify the paper's results. This embargo lifts only when the paper is finally published, but I am never supposed to reveal my identity to the authors, even indirectly.
Under those rules, publishing reviews is completely unethical. Maybe it would be okay if I had the explicit permission of both the authors and the editor, but I would expect most authors and reviewers to vehemently object. I would feel weird even asking.
But even under less stringent reviewing rules, I think posting reviews is a very bad idea. Criticism is best given privately. One of the purposes of anonymous reviewing is to give authors brutally honest feedback on their work. Referees can offer direct criticism without worrying that it will harm the authors, and authors are more willing to hear that criticism because they know it will never be public.
Yes, that means authors sometimes get credit for ideas that I suggest in referee reports. (Most authors are nice and thank the anonymous referee.) On the other hand, several referees have offered suggestions that have significantly improved my papers, so it all comes out in the wash.
Update: I should add that these ethical constraints attach only to reviews of unpublished papers being considered for publication. Once a paper is actually published, everyone is free, if not encouraged, to publish their own reviews of the published version.
The standard protocol for a person experiencing chest pains is to chew a 300mg aspirin tablet, the argument being that chewing rather than swallowing the tablet results in the aspirin entering the blood stream faster.
From a biological standpoint, why is this the case? Given that the stomach and GI tract are specialised tissues to allow for maximum diffusion, why would it be faster to pass aspirin across the gums (bucaal administration?) tongue and cheeks which are not specialised for this purpose?
It is not just a special case for aspirin either, as HypostopTM/GlucogelTM (acute treatment for hypoglycaemic shock, essentially concentrated sugar) is applied directly to the gums or cheek with a similar argument that in critical situations it is faster.
The only suggestion I could find was very vague from the "Merck Manual":
The stomach has a relatively large epithelial surface, but its thick mucous layer and short transit time limit absorption Which I assume could mean that it is the reduced absorption rate in the stomach that makes the oral membranes faster, yet it also says that the delay in the stomach is brief.
I'd be really interested to know the biology behind this!
Answer
There are several issues here:
1) Any mucous membrane is a specialized tissue for absorption.
Mucous membranes are indeed not so good for passive diffusion, that makes them absolutely perfect tools for active absorption of certain substances, almost independently from the membrane type. To provide some examples: many drugs like cocaine are inhaled and absorbed in nasal cavities, whereas the rectum is also known and favorite delivery way for medicines.
Generally the absorption force of the mucous membrane is dependent upon how well it is vasculated, for after going through the basal membrane the substance directly enters the blood flow and quickly travels away, thus the concentration gradient on both sides of the basal membrane -- the main barrier in mucosa -- remains relatively high.
See Bhat P. 1995. The limiting role of mucus in drug absorption: Drug permeation through mucus solution for an experimental model for this statement.
2) Mouth mucosa can absorb many substances.
There is a special term called "oral absorption" to describe the rapid drug absorption into blood flow from the mouth cavity. The mucous membrane is not specialized here, but small molecules are able to permeate here through all barriers.
3) Advantages of oral absorption.
There are some:
The mucous membrane in the mouth cavity is very highly vascularized. The whole mouth can be seen as a bundle of skeletal muscles and every muscle requires a lot of energy and oxygen, therefore they have one of the highest vascularity rates, having much less distance between single capillaries.
Blood flow is higher in the mouth cavity walls than in other inner organs. This is mostly because muscle contractions (during chewing) lead to increased propulsion of blood through capillaries and small vessels here.
Any substance that enters blood flow here bypasses the hepatic-portal system. This means that the substance does not have to wait until it is filtered by our liver, it is immediately distributed through the whole body.
There are special reflexes from oral mucosa to inner organs. Even not so important in case of aspirin, this is very important for some placebo drugs like methyl valerate (known as "Validol" in many countries) used a lot for treating angina pectoris whose only action is to activate the cold receptors in mouth and thereby leading to reflectory dilating of cardiac vessels.
This is why many drugs, like for example loperamid, are administered only as sub-lingual tablets. And this also explains why in emergency medicine many remedies are injected directly into the tongue.
I really wish this question only contained the title and tags, but the website forces me to write some text.
Answer
The answer depends on whether you want to know in the common sense or in the modern scientific sense. The phrasing of the question suggests you want to know in the common sense, but the choice of the phylogenetics tag indicates you want a scientific answer.
In modern biology, the term lobe-finned fish would be formally taken as (an imprecise) convenient term for the clade Sarcopterygii. Presuming you are not an alien or computer but are human, yes, you are a lobe-finned fish (a member of the class Sarcopterygii).
In the common sense, no, you are not a fish, lobe-finned or otherwise. This would also be the answer under the old tradition of zoological taxonomy, which was based on taximetrics (measurement of an organism's form) rather on the modern phylogenetic (evolutionary relationship) basis for biological taxonomy.
One of my advisor's students asked me how frequently I have meetings with him. And since at that time we had very few meetings I replied:
"We have a very few meetings and the advisor does not allocate time to me."
The advisor heard it and has started retaliating by reducing those few meetings to zero and complaining about me to other faculty, etc. Do you have suggestions about what I should do now?
TL;DR: Young graduate student in his first year of a PhD program who has lost a passion for the academic world. Seriously considering quitting but don't know what to do. Science background. Would love some advice from anyone.
So, as the title says I'm thinking about leaving my Doctoral program. I'll give you the rundown of my situation. I'll be withholding specifics to try and keep anonymity, but I'll try and give the best information as I can. This will likely be very long.
My background
I'm 21-25, with a Science background, B.Sc in Physics. Took a year off between Undergrad and Grad school and worked full time as a research scientist. Theoretical background (most of my work has consisted of modelling). Strong quantitative and computer skills. Excel in presentation/project focused environments.
General Information
I am currently finishing the second semester of my first year in a PhD program at a top tier US school in an engineering program. I have a full scholarship that pays for all of my tuition and a living stipend (typical graduate student stipend ~$1800 a month after taxes, so quite enough to live off of). I'm not a US citizen (from Canada), so I'm here on a student VISA, so if I decide to stop I have 2 weeks to leave the country. I cannot hold any other employment in the US while here on my VISA. My PhD consists of ~1.5 years of combined coursework and research, followed by a qualifier at the end of that period (research based), then into your thesis (doesn't have to be related to what your qualifier research was on).
Current Academic Situation
As I said, I am currently finishing my second semester. I came first semester ready to start a new life...(first time moving away from home- did my undergrad where I was born). I did very well first semester (3.9/4.0 GPA) and research was on track (mostly lit. review). By the end of first semester however, I noticed that I was losing interest very quickly in both my coursework and research - it started to become very hard to get myself through to work on a daily basis. Went home Christmas break for a few weeks and came back to start my second semester and immediately noticed a big change. I started to struggle in my classes and fall behind on research. It wasn't that the material was too difficult, I just had no motivation to do it. No excuses here - just didn't really want to do it so I didn't. I reached the end of the semester and realized just how far behind I was. I am likely going to hit ~C average this semester (A last) and am drastically behind on research. I had weekly-biweekly meetings with my supervisor all semester, but I sort of hid just how bad things were going. Had a long meeting last week where I basically came clean on everything (said I was struggling in classes, behind on research) and the supervisor was very supportive. The supervisor believed in my potential and suggested I speak to a school counsellor and emphasized that this kind of thing was common for doctoral students.
Personal situation/feelings
I come from a family where both my parents have PhDs. Although my parents have always been supportive and open to my life, I feel as though they would be very disappointed if I quit and this pressure is very real to me. I have tried to have the conversation with them and their attitude is mostly: "just put your head down and work through it, it's just a phase". Quite frankly most people seem to think it's a "phase" when I tell them. Outside of school my life is great. I'm not unhappy or depressed, I have hobbies, friends, I work out - it's just school that makes me feel this way. I just don't like the academic world at all any more. I HATE classes (always have) and where in the past research has been the saving grace keeping me interested in school, it now is losing a lot of it's appeal.
Basically, I feel no passion or drive for what I am doing any more. This for me is a huge problem. I'm not the kind of person who lacks passion in life. Quite the opposite in fact - I will just about kill myself trying for things I love to do/want. I have incredible drive when I want something, but when I don't...I don't. Right now I have no such drive for school. I have a long term long distance relationship with someone from home that is incredibly happy and stable. They visited here many times since I moved and we are doing great. I would be lying if I said it wasn't a factor in me wanting to quit. I hate being away and If I moved back home, we would likely move in together almost immediately. Moving here is a lot more complicated because unless we are married (probably too soon), a work/student visa is needed to be here on a permanent basis, and that would severely limit options available. The relationship has been incredibly supportive and is very aware of my current situation and has maintained a very neutral stance, trying to play devils advocate wherever possible and trying to make sure it doesn't influence the decision. I should state that I am pretty sure if I had to choose between school and the relationship, I would choose the relationship immediately with no regrets.
Basically I have just reached a point where I find myself doing just about anything else but school work. I'll get groceries, clean the apartment, watch TV etc... before doing any work. I'm trying to stick around for a couple of months for the summer (to see if not having classes changes anything) but since talking to my supervisor I'm already having doubts about even that. At this point, I feel like moving home and getting any job would make me happier than what I am doing.
Financial situation
I have a few thousand dollars in the bank (enough to get me home /move out etc...) and zero debt. If I move back home, I can likely live with my parents for the first month to get back, then I'd be looking for a job and moving in with my partner. I realize having no debt puts me ahead of a lot of people and I'm not particularly concerned about the situation financially - I'm very lucky to have what I have and am aware of this.
So what's the deal? I know I have this amazing opportunity. I'm at a top tier school on a full scholarship. I wake up every day and get to work with the top minds in my field doing important research. I'm doing something a very small % of the population ever gets a chance at and yet still I have no motivation to do it. I'm not sure if I'm doing it for me any more, or I'm doing it so I don't let down other people in my life. My parents, mentors, friends, all the people who keep telling me how amazing this opportunity is. The more I look back, the more I realize that Grad school was what I did because I basically just didn't have another plan.
What would I like to do
I'd love to find a job. I don't need to make a lot of money to be happy - I live off of 22k a year right now and am perfectly comfortable. Money isn't a major motivator for me. (Obviously more money isn't bad, but it isn't important in what I do, I only want to make enough to not be very worried about my financial situation). Working in the financial sector, doing quantitative risk analysis, banking, DoD, just about anything sounds more appealing than school to me. I know I'm smart and I've got a strong quantitative background combined with very good personal skills. I'm great with people and one of the things I HATE about the academic world is how under-used that part of my skill set feels.
I have no idea what to do. I want to quit, but I haven't. Maybe I shouldn't? I've been looking into options, but quite frankly I'd much prefer to have some kind of plan before quitting - at the very least this pays my living right now. I'd love advice from anyone. Someone who's been in this situation, someone who hasn't It doesn't matter.
I know that what I am doing does not make me happy. But I don't know what will. Please help.
(Thanks for anyone who took the time to look at this. I really appreciate your time and input)
I am in my first semester of a computer engineering PhD in the USA. At my University during your first year they will pay for your expenses to attend, up to $1000.00, for a conference. Every year after that they will pay your expenses if you get a paper accepted.
I am wondering how others look at/find conferences that they feel are worth the monetary and time commitment for what they provide. My areas of interest are embedded systems, computer architecture, and security. I have found many conferences but am unsure of how I should vet the quality of these.
What criteria do others use when looking at conferences and judging their relevance to the area they address? What opinion or otherwise do people have of academic conferences vs industry type conferences vs enthusiast type conferences?
Does one parent transmit more DNA to the offspring than the other one? Or do both parents always transmit the same amount of genetic material to their offspring?
In other words, can a baby be provided with a gene from the mother without an "opposite gene" from the father?
I am a physics Master's student. I have good grades, with CGPA above 9(/10)(However, all courses in my university are graded on a curve so the actual marks are significantly lower than 90%). This has been my marks throughout my undergraduate and graduate courses and I was happy because this was above average. Also, my summer projects in UG were usually computational and any difficulty I had in theoretical aspects I attributed it to my inexperience in advanced Physics.
However, recently I have started to work on pure theoretical project and while reading for the project I realized that I consistently miss some details from each topic. I understand the general idea, can re-derive most of the equations(with some effort) however when I discuss things with my professor or when I read further topics I realize that I have missed certain key-details. This is exactly similar to the case of me missing a few key questions in my exams and getting that 9 grade point instead of 10(or at-least I think so). I was not worried about this before but now I realize that there is some flaw in the way I study (but I do not know what).
Since I want to apply for Physics PhD I realized that I will need to have solid concepts and it would be best to correct my mistakes but I do not know how or even what could be the reason for my imperfect understanding.
Any direct suggestion would help or even certain general guidelines on what I can do.
Things I've tried recently -
1) I've started to written down almost everything I read. This is slightly laborious but is certainly helping. It also helps me to gloss over the things I read previously when I come back the next day.
2) I completely avoid smartphone when I'm library/study room so that I won't get distracted. Not sure if it helps me solve the above problem but certainly helps me study better in general.
3) I've tried to read the topics from several sources. The books I am reading is somewhat like a collection of research papers and hence does not have a exercises. So I though reading from various sources might help get better ideas but it's not really helping because most other sources are too high level as an introductory text. But this will probably help me in cases where it's practical to do this.
4) Somewhat similar to point (1)- I am trying reread, whenever I can, what I've done until that point. But not sure how much this will help me in filling the gaps.
Answer
I will give a separate answer for textbooks and for scholarly papers. The difference is that textbooks normally come with exercises to help solidify the understanding of the material.
For a scholarly work in a technical field, however, a proven method is to read the paper three times, but with a different focus each time.
The first reading is something like a deep skim. You are looking for an overall, not a detailed, understanding at that point. Take notes as you go, but don't just try to copy things. The notes should capture the main points of the paper. What was the methodology, what are the main conclusions. But also take notes about what you don't get from this reading.
Wait bit, a day or so, before the next reading so that the ideas have a chance to settle in your mind.
The second reading is deep. Here you are trying to follow the arguments of the paper in detail. Use the notes from the first reading to guide you. Think about how the paper extends the field. Think about what it does that is new and interesting. Take notes also. The notes include those things you don't yet understand. Different colored note cards are very useful for different kinds of notes.
The third reading, again after a short wait, is to solidify the second, if needed, but also to look for ways that the paper can be extended. What future research does the paper suggest, explicitly or implicitly. Again, refer to your older notes and take new ones.
Then, after the third reading, summarize your notes. What is most interesting about the paper? What is incorrect in it? What are the important things to retain?
Note that not every paper requires this deep understanding, but those that relate to your own research probably do.
For textbooks, you can do the above, but it may not be necessary for two reasons. First, a scholarly paper is directed at a small group of specialists and you may not yet have the skill and experience to understand it quickly, but the textbook is supposed to be written for people still learning. So, it should be more accessible, using more complete arguments, say. But you can also, intersperse your readings with the exercises. Ideally you should be able to do every exercise in the book. (There are exceptions, in which research problems are hidden in the "exercises", but these are rare.) If you don't have an obvious solution to an exercise, seek feedback on your attempt. Even if you don't have time to do every exercise, you should read them. Think about how you would attack that exercise.
Time is obviously an issue if you adopt/adapt this method. One way to handle that is to make sure that you don't waste time, not that you spend longer hours. If you take notes on notecards and paper then you aren't tied to your desk. If you have periods of inactivity, say on a long commute by bus, make sure that you always have a copy of the current paper and a few note cards. Even if there are only a few moments, waiting in a line to buy coffee, you can review your note cards and jot down a few ideas if they come.
There is a learning theory behind all this. Deep learning requires reinforcement. You don't "learn" something by reading or seeing it once. Feedback from exercises is also an important element, but harder to get for papers. One way to do that is to read a paper as part of a study group and have a discussion after, say, the second reading. Discussions with the professor for students can also work if it is available.
