I have copied several paragraphs from our course textbook in my homework, however before starting the section which is from the textbook I have clearly stated that following sections are from textbook (name of book, author, chapter). But I did not put them in quotation marks.
Is that plagiarism?
Should I use software for managing my references? What is the benefit of it? I can write down the references by myself, so I'm not sure what the benefit is.
Answer
You do not need to use reference managers. However, if you use some reference managers like Mendeley then, some of the benefits are obvious:
The pdf of your article is linked to the reference itself.
You can organize references into logical groups (areas, subjects, disciplines, sub-disciplines) by utilizing folders and tags.
You can one-click save articles and organize them from your browser. This is invaluable in saving time on organizing.
You can sync across multiple devices like desktops, laptops and tablets. For instance, Mendeley has an iOS app which does this for you. I use Android so I workaround using Droideley or Scholarley.
You can read your articles inside the reference manager and then do useful things like highlighting and annotations which can then be saved as notes for future reference.
You can export to specific citation styles. This is very useful for someone doing interdisciplinary work. For instance, I have to constantly use the same or similar bibliography using APA style, ACM style, IEEE style.
They are very useful for multiple collaborative platforms. For instance, when collaborating with some computer science colleagues, I generally use LaTeX and Mendeley does a brilliant one-click job of exporting to BibTeX. When I work with social scientists, I generally use MS Word and there is a MS Word plugin for Mendeley which dynamically adds references in-line as well as the full bibliography at the end of the document.
I hope this has been partially useful to you. This is a little Mendeley focused and I am in no certain terms claiming that it is the best or the most useful. However, for me, it certainly has its advantages.
According to this MIT statement of purpose guideline, the statement of purpose seems to be an important part of a PhD application. However, I have also heard that, in the case of MIT, the statement of purpose is only reviewed after the application has been tacitly accepted.
So, how crucial is this part of the application, and what part does it play in the process of graduate admissions at top schools in the US?
Answer
You have to specify which discipline, but for the social sciences the statement of purpose is the most important item in your portfolio.
We also look at grades, GREs, and letters but we scrutinize the statement the most. A good statement can resuscitate a candidate with middling grades, a bad statement can condemn an otherwise good student.
Here is what I feel whenever I find something interesting and feel like pursuing it :
I always end up searching and reading up "Best books to begin A/B/C/D.." instead of actually making myself begin somewhere. This consumes all my energy and I never really start.
Q. Have others faced this ? Q. How do you handle this and actually begin somewhere ?
Any help would be really appreciated.
Background : I am a working professional, with Masters in Computer Science (fascinated with Computer Graphics etc). Its been two years since my masters but I still kind of miss academia, my thesis work and other interesting stuff I did there. My current work is also pretty interesting and partially overlaps with my interest areas. However, other than work, I would really want to continue doing things related to my masters side by side (and MAY BE take up a Phd somewhere down the line). But the never ending feeling of not knowing anything takes over.
Its not that I am being forced to study any of this. Its purely for my personal interests that I want to pursue it.
Update 1 :
Thank you so much everyone for such overwhelming response. I really like several answers and points raised but haven't marked any yet because I am in the process of trying some and would update if something actually works for me. Meanwhile, I also found this talk really helpful :
https://www.ted.com/talks/tim_urban_inside_the_mind_of_a_master_procrastinator
Im getting rejections from my PhD applications and it is rather difficult - emotionally. So, I am doing a 2+3 programme in a non-US country at the moment and I will finish my masters in 4 months or so.
I have consulted my situation with my current advisor and other professors and they said since I have secured 5 year funding here I can just stay for another year or two if I want to. I am tempted but I don't know how it is going to look to admission committees when I apply again to the States for Fall 2015 entry. Should I just leave after my master's? Or should I stay another year? (I think I will learn a lot by just staying another year, I love my supervisor, and I really like the university but it has always been my dream to study in the States and I am definitely re-applying)
When I started my Masters thesis one advice I got for getting good material to read was to subscribe to several journals' alerts system, so that I would get mails with eTOC (electronic Table of Contents).
This was pretty cool then, for months I could stay on top of what's been published out there and was up to date in my own little narrow area. Now almost 3 years later that list of journals have expanded a bit, and the more work I have at the lab more mails that accumulate in my mailbox. What used to be no more than 10 unread mails is now about 900. The output is more than I can handle, what more restrictive method can I implement?
I guess it is pretty clear that this way of following literature is not sustainable in the long run. So I wonder if there are other and perhaps better ways of staying on top of recently published articles?
Please note that I have checked the following two questions prior to asking this one. I do feel though my question differs from these two in its essence.
Answer
During my PhD, I subscribed to the RSS feeds of the journals I would regularly read (started with 6 of them, ended up with a dozen). I would skim through titles of all new articles, and read abstracts of those whose title drew my eye. I then found out that some journals (J. Chem. Phys. in that particular case) offer specific RSS feeds for each of their sections, in addition to the “whole journal” feed. That helped reducing the number of journals I was skimming through.
Now, after the end of my PhD, my research interest are broader, the number of journals I like to watch is larger but my time is more limited. This system didn't work anymore, and I set up a new system, which has worked well for a few years. I use bibliographic databases (SciFinder and Web of Science; but I'm sure Google Scholar and PubMed have the same features) to create publication and citation alerts. Here's what I have set:
Citation alerts for all my own papers: if someöne cites my work, there's a good chance I'll be interested in their paper. This one has two additional “strategic” bonuses: you get to keep an eye on your competition, and you can suggest newer work to other authors when relevant (“hi there, I saw your recent paper citing my 2008 article on X, I thought you might be interested on a new extension of this algorithm that we published this year”).
Publication alerts for major players in the field of interest: I have 10 to 20 of those, watching all papers these people publish.
Citation alerts for some seminal or high-impact papers by others in the field: a good way to see how a new idea is adopted/improved by the community. Those tend to trigger a massive number of cites, so you may want to get rid of them after some time. I have between 5 and 10 of those alerts at a given time.
The only drawback to this method: database updates tend to lag somewhat behind the RSS feeds of the journals themselves, so you get papers that are 2 to 8 weeks old.
In addition, use conferences to stay on top/catch up with the literature:
If you're attending, talk with people… you can also use that opportunity to ask some people (whom you do know well enough):
Have you seen that new technique by the team at MIT? it seems to work really well… I was wondering: what has caught your eye in the recent literature?
I am having troubles understanding the correlation between OD measurements and CFU/ml. What is the conversion factor between the two units, and does this conversion factor somehow compensate for dead cells OD might be reading? (Also lets say the OD is set at the standard 600nm).
I came across yet another infogram, originating from this Nature article, showing the top-40 countries in terms of scientific publications produced for 2011.
The data are based on publications from Thompson Reuters/Web of Science. Similar data are available from Scimago (spanning 1996–2012).
Presented this way, there's some "bias" towards countries with a larger population. I was thus wondering if statistics on the number of scientific publications per capita was available for countries?
... just out of curiosity.
Answer
Pubs), andPop), and... we get the following (edit: note that the list scrolls down!):
No...Country.......................Pubs/Pop
1....Switzerland...................0.04948049
2....Sweden........................0.03949838
3....Denmark.......................0.03724673
4....Finland.......................0.03512776
5....Iceland.......................0.03384176
6....Netherlands...................0.03266005
7....Norway........................0.03235590
8....Monaco........................0.03153357
9....United Kingdom................0.03034517
10...Australia.....................0.03013565
11...New Zealand...................0.02928470
12...Canada........................0.02848185
13...Israel........................0.02841134
14...Singapore.....................0.02814340
15...Belgium.......................0.02684193
16...Austria.......................0.02538793
17...Slovenia......................0.02456816
18...Liechtenstein.................0.02302488
19...Ireland.......................0.02280205
20...United States.................0.02250084
21...Germany.......................0.02177218
22...France........................0.01953477
23...Spain.........................0.01643973
24...Greece........................0.01601820
25...Italy.........................0.01575377
26...Czech Republic................0.01557232
27...Estonia.......................0.01429077
28...Japan.........................0.01392641
29...Croatia.......................0.01346473
30...Portugal......................0.01319425
31...Luxembourg....................0.01267497
32...Korea.........................0.01157157
33...Hungary.......................0.01128115
34...Greenland.....................0.01071429
35...Cyprus........................0.00913291
36...Poland........................0.00899290
37...Lithuania.....................0.00829172
38...Bermuda.......................0.00745301
39...Faeroe Islands................0.00668606
40...Bulgaria......................0.00620812
41...New Caledonia.................0.00605143
42...Malta.........................0.00601626
43...Grenada.......................0.00528995
44...Palau.........................0.00510745
45...Latvia........................0.00497760
46...Romania.......................0.00432618
47...Kuwait........................0.00423781
48...Barbados......................0.00421932
49...Turkey........................0.00414781
50...Russian Federation............0.00408719
51...Serbia........................0.00399812
52...Chile.........................0.00394931
53...San Marino....................0.00374436
54...Seychelles....................0.00373640
55...Guam..........................0.00360543
56...Tunisia.......................0.00355685
57...French Polynesia..............0.00341107
58...Malaysia......................0.00339218
59...Brunei Darussalam.............0.00326268
60...Armenia.......................0.00315417
61...Jordan........................0.00314134
62...Lebanon.......................0.00309093
63...Puerto Rico...................0.00305665
64...Cayman Islands................0.00297030
65...Argentina.....................0.00288041
66...Qatar.........................0.00282271
67...Uruguay.......................0.00281334
68...Trinidad and Tobago...........0.00279863
69...Macedonia.....................0.00273227
70...Iran..........................0.00265369
71...Belarus.......................0.00262056
72...Oman..........................0.00247495
73...Bahrain.......................0.00247073
74...South Africa..................0.00244784
75...Ukraine.......................0.00241902
76...Brazil........................0.00232119
77...Cuba..........................0.00218313
78...Dominica......................0.00216227
79...Saudi Arabia..................0.00208004
80...United Arab Emirates..........0.00206949
81...American Samoa................0.00204978
82...China.........................0.00198446
83...Montenegro....................0.00175661
84...Fiji..........................0.00174223
85...Botswana......................0.00172363
86...Georgia.......................0.00166009
87...Virgin Islands (U.S.).........0.00164332
88...Tuvalu........................0.00152130
89...Mexico........................0.00137863
90...Costa Rica....................0.00135080
91...Andorra.......................0.00132721
92...Jamaica.......................0.00128646
93...Moldova.......................0.00127910
94...Thailand......................0.00123095
95...Marshall Islands..............0.00119874
96...Bosnia and Herzegovina........0.00116017
97...Egypt.........................0.00110861
98...Mauritius.....................0.00110573
99...Samoa.........................0.00093706
100..Panama........................0.00093654
101..Northern Mariana Islands......0.00091924
102..Gabon.........................0.00091696
103..Venezuela.....................0.00090597
104..Turks and Caicos Islands......0.00089432
105..Vanuatu.......................0.00086952
106..Antigua and Barbuda...........0.00084204
107..Gambia........................0.00084188
108..Morocco.......................0.00083801
109..Azerbaijan....................0.00080366
110..Tonga.........................0.00077186
111..Mongolia......................0.00076525
112..Colombia......................0.00075234
113..Belize........................0.00069432
114..Bahamas.......................0.00069362
115..Algeria.......................0.00066821
116..Namibia.......................0.00064132
117..India.........................0.00060709
118..Swaziland.....................0.00056459
119..Guyana........................0.00053183
120..Albania.......................0.00048797
121..Congo.........................0.00047290
122..Sri Lanka.....................0.00040530
123..Solomon Islands...............0.00040393
124..Maldives......................0.00039889
125..Bhutan........................0.00039767
126..Aruba.........................0.00039069
127..Kenya.........................0.00038740
128..Zimbabwe......................0.00038282
129..Senegal.......................0.00036806
130..Suriname......................0.00035732
131..Cameroon......................0.00034761
132..Kazakhstan....................0.00033660
133..Pakistan......................0.00032448
134..Peru..........................0.00029889
135..Ecuador.......................0.00029486
136..Ghana.........................0.00026906
137..Uzbekistan....................0.00025359
138..Benin.........................0.00025232
139..Bolivia.......................0.00024428
140..Nigeria.......................0.00024256
141..Papua New Guinea..............0.00023985
142..Nepal.........................0.00022093
143..Malawi........................0.00021098
144..Burkina Faso..................0.00020486
145..Uganda........................0.00020330
146..Sao Tome and Principe.........0.00020202
147..Guinea-Bissau.................0.00019536
148..Vietnam.......................0.00018557
149..Zambia........................0.00018529
150..Iraq..........................0.00017914
151..Syrian Arab Republic..........0.00017648
152..Tanzania......................0.00016707
153..Nicaragua.....................0.00016106
154..Lesotho.......................0.00015549
155..Djibouti......................0.00015471
156..Togo..........................0.00015159
157..Equatorial Guinea.............0.00014804
158..Paraguay......................0.00014026
159..Philippines...................0.00013611
160..El Salvador...................0.00012751
161..Bangladesh....................0.00012593
162..Mali..........................0.00011910
163..Kiribati......................0.00011906
164..Tajikistan....................0.00010988
165..Sudan.........................0.00010700
166..Cambodia......................0.00010468
167..Guatemala.....................0.00010131
168..Madagascar....................0.00010097
169..Mauritania....................0.00009194
170..Central African Republic......0.00008817
171..Ethiopia......................0.00008738
172..Honduras......................0.00008720
173..Comoros.......................0.00008223
174..Indonesia.....................0.00008169
175..Rwanda........................0.00007864
176..Yemen.........................0.00007203
177..Niger.........................0.00006895
178..Dominican Republic............0.00006860
179..Eritrea.......................0.00006035
180..Mozambique....................0.00005971
181..Sierra Leone..................0.00005720
182..Haiti.........................0.00004305
183..Turkmenistan..................0.00004156
184..Timor-Leste...................0.00004131
185..Guinea........................0.00003336
186..Burundi.......................0.00002853
187..Liberia.......................0.00002792
188..Chad..........................0.00002249
189..Angola........................0.00002123
190..Myanmar.......................0.00002040
191..Afghanistan...................0.00001626
192..Somalia.......................0.00000589
Countries missed by the join ...
Population not found for following countries mentioned w/publications:
Anguilla
Bouvet Island
British Indian Ocean Territory
Cape Verde
Christmas Island
Cocos (Keeling) Islands
Cook Islands
Côte d'Ivoire
Democratic Republic Congo
Falkland Islands (Malvinas)
Federated States of Micronesia
French Guiana
French Southern Territories
Gibraltar
Guadeloupe
Heard Island and McDonald Islands
Hong Kong
Kyrgyzstan
Laos
Libyan Arab Jamahiriya
Macao
Martinique
Mayotte
Montserrat
Nauru
Netherlands Antilles
Niue
Norfolk Island
North Korea
Palestine
Reunion
Saint Helena
Saint Kitts and Nevis
Saint Lucia
Saint Pierre and Miquelon
Saint Vincent and The Grenadines
Slovakia
South Georgia and The South Sandwich Islands
Svalbard and Jan Mayen
Taiwan
Tokelau
United States Minor Outlying Islands
Vatican City State
Virgin Islands (British)
Wallis and Futuna
Western Sahara
Publications not found for following countries mentioned w/populations:
Cabo Verde
Cote d'Ivoire
Curacao
Hong Kong SAR
Isle of Man
Kosovo
Kyrgyz Republic
Lao PDR
Libya
Macao SAR
Micronesia
Sint Maarten (Dutch part)
Slovak Republic
South Sudan
St. Kitts and Nevis
St. Lucia
St. Martin (French part)
St. Vincent and the Grenadines
West Bank and Gaza
I did a bunch of code projects like implement a algorithm or use the code from a paper on a different dataset. These may not be unique (they may be, but I am not sure). I wouldn't say that these projects have the best efficiency/accuracy for a particular problem. But these are stuff that I was just messing around with and got some interesting outputs. I maintain a blog about all these activities that I do. These projects are related to machine learning, a subject in which I am interested in pursuing a MS degree.
Should I mention these blog posts in my SOP?
My SOP is a research statement, and these are not entirely research projects, but they do reflect my interest in machine learning. Would mentioning these projects benefit me in any way?
If you do recommend that I mention them, how should go about that?
Answer
Yes. You could mention it in your SOP and/or in your CV.
I have received some applications from students in which they mentioned a technical blog, and so far it has always left a positive impression. In my opinion, keeping such a blog demonstrates:
Is it homogeneous or did they converge? Did we both evolve from warm-blooded reptiles that are extinct maybe?
Answer
Welcome to Biology.SE.
Did you say warm-blooded?
The term warm-blood is very unclear. The correct terms are endo-, exo-, poikilo- and homeo- therm. In short…
Source of heat
Variation in inside temperature
Any combination of these two axes exist. For example: If the temperature in the environment never varies you can be homeotherm without needing to be endotherm. A fun example also are the large dinosaurs that are thought to be homeotherms because their metabolism produce some heat and they are so large that they remain warm thanks to this heat source. However, they were probably not able to regulate actively their temperature. Therefore, I would tend to qualify dinosaurs as homeo-exo-therm but I wouldn't be surprised if someone prefers to call large dinosaur homeo-endo-therm individuals. Hope that makes sense to you.
By warm-blooded I will assume you meant endotherm.
MRCA of mammals and birds (and other things)
The Most Recent Common Ancestor (MRCA) lived 301.7 millions years ago (see on tolweb and on OneZoom). This MRCA was exotherm. In consequence, birds and mammals endothermy are an example of convergent evolution (even if they are not using exactly the same mechanisms).
References to go further into the evolution of endothermy in birds and mammals
I'm TAing a class that uses Piazza (an online student forum), in addition to the traditional office hours. A student made a (private) post, where he uploaded a MATLAB figure and asked whether it is correct. The figure is what the first question of the homework assignment asks for.
Am I supposed to tell him whether his answer is correct/wrong? Especially over an online forum?
I don't think so, because that would be giving out the solution. How do I reply without sounding "mean"? Do I tell him to come to office hours instead?
(It's my first time TAing ever...)
Answer
Welcome to the most standard "trick" students use to get answers out of professors/TAs :).
My answer is as a professor, but I think the basic principle works for TAs as well. What I usually do is turn the question back to them. Something like:
S: Is this answer correct ?
Me: Well, what do you think ?
now things can go in different ways:
case 1: S says "well I'm not sure". In which case you can say, "well how might you go about verifying that your answer is correct" ? this might then lead to a discussion of how to check answers without you having to commit to commenting on their particular answer.
case 2: S says "Well I think it's correct". Then you can say "Ok then :). I understand that you think it's correct" and leave it at that.
They might persist and say "can you tell me if you think it's correct". At which point you can say "No, but how would you go about checking its correctness" taking you back to case 1 and the "methodology" of checking.
The underlying pedagogical point is this: you don't want students checking answer correctness with you ahead of time because
a) learning to check your own answers is an important part of learning. It allows you to diagnose problems and identify the correct path to an answer.
b) it's unfair to those who don't ask, and it's a waste of your time
c) using this socratic approach allows you to assess how they are approaching the problem, and allows you to guide them in their approach, rather than spoonfeeding a prescribed answer. Everyone approaches problems differently.
p.s Students often also ask for hints. The material I teach is usually mathematical, so they're asking for hints for a proof. There you have some more leeway, but the trick is to draw them out into explaining their thought process, and then trying to gently nudge them without revealing the answer. It takes some practice and a lot of Socratic dialogue.
Is there any scientific evidence that in humans males are taller than females? And if so, what is the reason that they are taller (please include genes or hormones that accounts for human growth and how they are affected in males and females)?
Answer
Are males taller than females?
Best data I could find come from the Statistical Abstract of the United States (1999) > Section 3. Here is a table reporting the percentage of the male and female population which height is lower than a given threshold
Note that this data collection was done among students in US universities and is therefore not representative of the whole world or even the whole country.
Does height follow a bimodal distribution?
A difference in height between males and females is often used as a classical example in introductory statistic class to exemplify a bimodal distribution as seen in this picture
and on these (a priori fake) data
However, Schilling et al. 2002 argued that while the difference in mean height between the sexes is real, this difference is too small relative to the variance in height within each sex to be clearly depicted on a graph.
Note that I found this non-peer-reviewed paper which shows real data that display a truly bimodal distribution of height.
Genetics of height
The question why are they taller? is very broad. I will just focus to give you some hints about the genetics of height in humans. First, you want to make sure you understand the concept of heritability.
Evoy and Vissher 2009 report a heritability coefficient of 0.8. This estimate is impressively high - only a few phenotypic traits have such high heritability. They also review articles discussing that 50 loci are correlated with variation in height (actually, today, more than 500 loci are known to contribute to height, see the link in AlexDeLarge's comment to this answer). However, these loci are not sufficient to explain the whole heritability observed (common missing heritability issue). Yang et al. 2010 provide evidence that the remaining heritability is due to incomplete linkage disequilibrium between causal variants and loci of weak effects. In short, height is a highly polygenic trait.
Related post
You should have a look at Is there a genetic reason explaining the difference of the height of male and female? for more information.
I'm in literature and applying for a tenure-track position. One of my job applications is asking for "evidence of effective teaching methods" as one of the documents I am to submit.
Does anyone have any idea of what this should be?
Research to date has given me very little. My usual go-to sources for job application information and help have not had anything to address this sort of thing.
Sure, there are teaching philosophies and teaching statements, both of which I've written in the past.
Evidence of teaching ability, in my field at least, includes your teaching evaluations and letters, your teaching philosophy, and a few syllabi relevant to the job search at hand. But, there is no clear-cut answer to that one either. And it varies a lot, depending on who you ask.
As for my own pedagogical experience, I would imagine this could include some sample assignments? Perhaps a narrative of what innovative teaching methods I've used in the past, perhaps some student comments from evaluations that speak to methodology in particular?
But, I'm really guessing here, and I was hoping someone who has dealt with this particular item in job applications would have some idea of what this might be.
Thanks for the suggestions on how to clarify the question.
Answer
From the perspective of someone who has been on a search committee this would normally mean your teaching evaluations -- either as a TA or as the instructor on record. Any teaching awards you might have won in this regard would also count
But we also recognize that not everyone has had TA/IOR experience. So it could also include:
This question is deliberately broadly worded so as to not exclude people who haven't had to teach. You can include a cover sheet to this item category (i.e., when you upload your PDFs you include or prepend a cover sheet) that notes how you have interpreted this and let the committee know that you are willing to send more material if requested.
Why is this material requested? After the search committee makes its decision, your file goes to the Provost's office. The Provost will want to see "evidence of teaching effectiveness" as well as "evidence of research" as part of the portfolio. It's simpler for the committee if you can make this case for them ahead of time.
Question
What exactly is the definition of a scientific publication or journal?
Background
What fueled this question in particular is the current rise of predatory publishers. Jeffrey Beall had a list published online of suspected predatory publishers, but his blog has very recently been discontinued (cached copy, 11 Jan 2017). Speculations of this disappearance include threats and political motivations.
Anyway, predatory publishers are characterized by any or all of the following:
For more backgrounds on predatory publishers see the wiki page.
Now still these predatory publishers profile themselves as being scientific publishers, e.g., Scientific Research and Austin Publishing Group.
Access these links at your own risk. I would not call this class of journals scientific, as pretty much any author willing to pay a few grand can make it in there.
So what makes a scientific journal scientific? How exactly is this defined? I long thought a peer review process guarantees scientificness, but it can be faked or even absent, yet publishers claim to be scientific.
Where this question becomes particularly relevant is in the role of teaching - when I tell students only to use 'scientific literature' then what is it exactly? Would it be more a matter of what it is not?
Answer
There is no general definition for scientific journal. The Wikipedia definition is as vague as reality is. This is because there is no clear definition of scientific. It is a case-by-case distinction - not only for journals, but also for individual articles in a journal or one method described in an article. Additionally, scientific and predatory are not mutually exclusive.
Your instruction to your students to only use scientific literature is the key to the answer to your question: What is scientific and what is not depends on the concrete content of an article or the applied method. To distinguish between these two is the first step towards scientific thinking.
An answer on a list of predatory publishers can be found in this question here.
There are a lot of questions here on what predatory journals are, and how to tell if a journal is one or not.
Are there known cases where a journal has "switched" camps, or where substantial evidence has been presented that they have? That is, has it ever occurred where:
For example, if someone has claimed, "The Podunk University Journal of Advanced Best Practices in Intermediate Spline Reticulation used to be a low-impact but serious journal, but after Podunk U was rocked by a cheating scandal in 2003 and there was a gradual movement away from Spline Reticulation toward Spline Retransmogrification from about 2005 to 2010 with a corresponding drop in the number of serious papers on Spline Reticulation being submitted, they started becoming a 'pay for play' publication and nowadays mostly publish incomprehensible screed written by rich patrons who want to increase their publication count.", that would count.
As the definition of a "predatory" journal is somewhat vague and based on professional judgments rather than 100% objective criteria, I would consider any of the following to "count" as a determination that a journal is or is not "predatory":
I submitted a paper to a journal five months ago. The status of the paper was 'With Editor' for the first three months. After three months from my submission, I sent the journal a polite enquiry about my submission. I did not receive any reply, however, the status of the paper changed from 'With Editor' to 'Under Review' less than 24 hours after I sent my enquiry.
It has been two more months now, and I still have not received anything back. What should I do? I am assuming that the editor has forgotten about my paper, then when he or she received the reminder, sent it to a few people for review. In which case, I was going to wait another month, then enquire about my paper again. Is this too conservative? I would love to get a reply, as this paper is part of my forthcoming PhD thesis which I'm about to submit soon.
My Ph.D. research is related to both computer-science and economics. I collaborate with researchers in both these disciplines, and naturally submit papers to journals of both disciplines. Now, while looking for an academic job, I find out that departments count only the publications published in journals of their own discipline. This is true both in the acceptance decision and in the tenure decision. So, whether I go to CS or to economics department, in expectation, I have only half the number of counted publications of a one-discipline researcher. What can I do about it?
Is this true that an two-disciplinary researcher should work twice as hard to attain the same career status as a one-discipline one?
Answer
I find out that departments count only the publications published in journals of their own discipline. This is true both in the acceptance decision and in the tenure decision.
While it's certainly possible that some departments would adopt a foolish policy of this sort, which is effectively tantamount to a decision not to have any interdisciplinary researchers, I think it's also possible that you are misunderstanding what the statement that "departments count only the publications published in journals of their own discipline" means. When interpreted in the right way, this statement may be a lot less troubling than you might think.
Specifically, the way promotion decisions typically work for researchers who have a joint appointment in two departments is that each of the departments does its own review of the researcher's work, and the input from both departments is then reviewed by a higher campus committee and taken into account to reach a final decision. Moreover, each of the departments doing the review knows full well that it has only partial "ownership" of the candidate's time. So, to take an example that I am familiar with, a researcher who has a 50% partial appointment in a math department and a 50% partial appointment in a biology department will have published some mixture of math papers, biology papers, and papers that are about both math and biology. Now, it is true that in its review, the math department will "count only the publications published in journals of its own discipline", in the sense that the math department doesn't have the expertise to evaluate work in disciplines other than math and will only be seriously looking at the math papers. But the math department also knows that the researcher only has a 50% appointment in math, so all its expectations regarding the amount of math research the researcher should have produced will be weighted accordingly. The biology department will apply similar reasoning. The end result would be that if the researcher is overall as productive as a typical single-discipline researcher, the promotion review will have a successful outcome. (In fact, because of the existence of papers that can be appreciated by both departments, there can even be some amount of double-counting that may lead each of the departments to conclude that you are producing more research than they were expecting you to produce -- this will probably be a weak effect, but note that it will work in your favor rather than against you!)
I would encourage you to ask at any department where you are considering applying for a job whether the above interpretation of the promotion process is a faithful description of their approach to evaluating the work of interdisciplinary researchers like yourself.
With that being said, I should add that from my observations I find it very true that interdisciplinary researchers have to work a little bit harder than everyone else. Being a member of two departments is a big headache: you have twice as many colleagues to get to know and to get along with; twice as many administrative processes to get used to, department-wide emails to receive and respond to, etc.; and, most importantly, when you come up for promotion you need to find a way to effectively communicate your research to two groups of people with very different backgrounds and research cultures. Perhaps there will indeed be times when you feel you need to work twice as hard as everyone else, but as a general rule saying that you need to work twice as hard all the time is a wild exaggeration -- as others have noted, this is both physically impossible and a highly illogical expectation, considering the fact that I strongly doubt you are paid twice as much as other researchers.
Finally, on the positive side, you should remember that working in two disciplines can often also be twice as much fun!
I am an undergraduate student starting my second year. Last semester, I took part in a research project and earned co-authorship of their paper, which got recently published.
However, when adding names from our anonymous submission to the camera-ready version, the primary author misspelled my first name(Garret instead of Garrett). Because this was a fairly minor edit, I didn't notice it until a few weeks after it had been fully published.
I've already asked the advising professor about it and he said that it wasn't anything to worry about, and that I should create an account on Google scholar and manually add the paper to my account. I've done this, but is there anything else I should do? How bad is this, or is it actually fairly minor?
I was reading Cellular and Molecular Immunology By Abul K. Abbas, Andrew H. H. Lichtman, Shiv Pillai and stumbled upon the following excerpt $-$
In every individual there are millions of different clones of B-cells,each producing antibody molecules with the same antigen binding site and different in this site from the antibodies produced by other clones.
What are these clones of B-cells, one producing monoclonal antibodies and the other polyclonal antibodies?
Answer
When you read further you'll get it. Basically, when the antibody expressed on a B-cell recognizes an antigen, then the B-cell divides and expands its population to produce more antibodies (through plasma cells). This process is called clonal expansion.
I recently had a university student (my ex) expelled from my undergrad university when he was found responsible for physical abuse and sexual misconduct. How would this expulsion affect his future educational career?
How would the expulsion affect him if he tried to apply to law school?
I suspect anybody who's a professor knows this story: you meet someone new in a social setting and it comes up that you're a professor. The inevitable next question is, "oh, what do you teach?"
It's a perfectly reasonable question, and one simple answer is: well, tell them what you teach! But the question also implicitly suggests that professors do nothing but teach, and to answer it directly feels like you're only reinforcing that perception. It also does nothing to steer the conversation toward your other passions, like doing research and writing grants.
Q: How do you answer this question without being rude, while still painting a more representative picture of what a professor actually does?
Answer
I usually get assigned to teach ____________ (e.g. introductory biology classes), but actually, most of my work at the university involves research in the area of ____________.
PhD students usually go through a specific topic in depth for several years: understand it and contribute to its literature. Some topics are multidiscipline by nature. Thus, while studying, students may find nice contribution opportunities in not-directly related areas to their research problem.
is it better to be goal-driven (i.e focus on the thesis problem alone) or opportunity-driven (i.e spend your PhD in different problems you encounter in this topic)?
I recently submitted applications for tenure track positions to several US universities via their online job systems (https://jobs.xxx.edu/).
Last week I got a feedback from one of the schools that my application would no longer be considered. However, a week later, the status of my application on the portal is still "under review".
This raises a question for me: after the department has decided to reject the application, how soon is the status in the online system updated?
I want to know that because I have not received a feedback from the other schools I applied, and am wondering if it's possible that the department has already decided to reject but the portal was not updated?
Answer
Academic jobs are a nightmare from the HR perspective. While the posting might be on the jobs portal, the files themselves initially go to the hiring department which comes up with a long and then medium list that they then do some preliminary screening before ending up with a short list for on-site interviews. This can take several months.
The search committee then comes up with a ranked list with some candidates "above the line" and some "below the line" that the department votes on. This list -- which may have one, two, or three people that the department thinks are hireable (or in some cases, none, if the search fails). This list then goes to the provost, equal opportunity, and numerous other sundry university committees before getting approved (or not) and sent back down the line. This can take several more months.
So we are now 4-6 (or 6-8) months into the search. The search can have several results:
In other words, there are many reasons why a job posting might still remain open even one or two years after the initial posting. Departments are hesitant to finally close files unless they are absolutely positive that they are never, ever getting that slot back again -- or that the person who accepted the offer really is going to show up on August 1st.
On ResearchGate, if you upload something like a thesis, and then it says publish resources, does this mean the thesis becomes properly published in the sense of the usual requirements of journals that there be no prior publication of the submitted work?
I ask because I’m drafting thesis chapters into journal articles and did not choose to publish the thesis as a whole work in order to do so, so I want to make sure that by clicking publish resources I am not actually publishing the copy I’ve uploaded, I’m just making it publicly available? Does this mean it becomes published despite it not technically being a published work? (If so, I’ll just remove the copy I uploaded).
Answer
The problem is less ResearchGate and more your field. As far as I know, ResearchGate, unlike Academia.edu, does not claim copyright or commercial license for your uploads; and they refer to their upload service as more self-archiving than anything else. That said, different fields and different publishers have different attitudes toward what it means to be prior publications.
In Mathematics (my field), for example, almost certainly no journal will count uploads to pre-print repositories or online social media or your own webpage as prior publication.
In fields like Medicine and some subfield of Biology, the rules are much stricter, where sometimes too-detailed conference posters can count as prior publication when it comes to journal submissions. Wikipedia has a listing which shows, e.g., journals of the American Society for Microbiology having this type of strict pre-publication rule.
So the only general advice for your question is: consult the website of the journal to which you intend to submit your articles.
If you are interviewing for faculty positions, how can you find out whether a particular work environment would likely be toxic? (Either generally toxic, or particularly bad for you as a {woman, early career researcher, researcher in a particular subfield, etc.})
Can such environments be avoided?
Can you ask about this during a visit or interview? Who should you ask (faculty, deans, students) and what should you ask that might elicit the relevant information?
Are there other ways to detect a toxic environment, besides for asking people who know to be on their best behavior for you?
This has been discussed here, here, and here for prospective PhD students, but not for faculty candidates (as far as I know). I believe the answers will be different for faculty candidates - for one thing, PhD students are likely to be honest when telling a prospective student about their advisor; faculty members talking to a candidate about their colleagues, not so much. Also, the interview/visit procedure is different for faculty candidates, as are some of the relevant indicators of toxicity.
[Source: I read this question on FemaleScienceProfessor]
Answer
What I found useful was to be very watchful of how the interviewers act towards each other. Typically some sort of meal is part of an on-campus interview and you will be eating with several of the faculty members. If they can't make it through the meal without doing something objectionable you probably have a toxic environment. The funny thing is that they know to act properly towards you but will still forget to do so to their colleagues even though you are right there.
As an example there was one such dinner where I was pressured into drinking alcohol the night before the real part of the interview and the junior (and female) faculty member who was present was the target of most of the jokes from the senior male faculty members. Both of these details did not help their chances of getting me to accept their offer. Fortunately I had another offer to take instead.
This is by no means going to catch every situation you want to get away from but the general idea is to watch their behavior. In larger departments where the jerks are kept away from the candidates you may have to be more active in searching for these issues. I was mostly interviewing in small departments where I was able to meet everyone.
Can one cite a comparison table in a relevant work in his own paper without asking the jounal or authors permission if the source has been explicitly stated (e.g. A comparson of X and Y in Z conditions [32])? For those writing survey papers sometimes they cite tables, diagrams and algorithms from different papers do they explicit permission from every one of them?
Edit: I have included dummy illustrations of original table and referenced for more clarity (Note that in the papers there are six columns. I reduced it to five. Thanks in advance
Answer
Unless the paper you are citing it from has been licensed under something like a creative commons license, you most likely need permission.* The good news is, if you're citing from a reputable publisher and publishing with a reputable publisher, this should be easy and free. Below is a screenshot of, as an example, a recently published article from JACS, note the highlighted "Rights and Permissions" link.
Clicking this link will take you to the Copyright Clearance Centre. Follow the on-screen instructions to register your request and receive your license. Most of the major journal publishers and learned societies have a reciprocal agreement that allows content to be reproduced between their journals free of charge.
If an open access article has been licensed under a Creative Commons (or similar) license, you do not need to follow this process, you can just use it under the terms of that license (typically this means that you'd need to include the reference it was taken from and "copyright [year] by [publisher or authors], used under cc-[type]" in the figure caption).
Do be careful with non-commercial use though - if you work in a university, you count as non-commercial, but the publisher probably counts as commercial. So you can't usually rely on a non-commercial permission for republishing in a journal.
*Data itself isn't copyrightable, but the table is. Exactly where the line is drawn (e.g. if you re-typeset a basically identical table) I don't know. But getting permission, in most cases, should be trivial. So there's no reason not to do it.
I was preparing to submit a manuscript to a journal when I made a fatal realization: the journal publishes everything as open access and the author(s)/institution/funding agency must cover the cost ($500). This was a solo side project that I undertook on my own time with no co-authors nor outside funding. I was not expecting to publish this as open access as I was unaware of this policy. In fact, when I initially targeted this journal I thought that some articles were open access and others were not. Upon further inspection this is not the case. I'm clearly at fault for not being diligent enough about the journal's policies.
Now this situation would not be such a big deal except that
Am I crazy for wanting to just submit the paper and pay the open access fee out of pocket? $500 does not seem exorbitant compared to other journals' fees. Unrelated to my current situation, a few weeks ago I spoke with my advisor about creative ways to fund open access, but he stated that our university does not have options for funding - this must come through grants. It doesn't seem right asking him to cover the fees as he was not involved in the project and is not a co-author.
In this question, @ff524 suggests seeking funding through PLOS or a fee waiver through the journal/publisher. Other questions on Academia SE result in answers suggesting that authors request funds through the university, library, etc. When is it appropriate to ask for a waiver and/or seek funding from an outside source? Prior to submission, during submission, or after a paper is accepted? It seems like a massive waste of time to seek funding from multiple sources only to have a paper be rejected outright. At the same time, it would seem like withholding relevant information to wait until after a paper is accepted to ask for a fee waiver.
Answer
I don't think you're crazy at all. From a purely economic point of view, although $500 sounds like a lot of money, it is quite insignificant (in a US context) compared both to your future earnings once you graduate, and to the present potential earnings you are foregoing by attending graduate school in the first place instead of working at a "real job". Thus, if you truly think that paying the fee will help you get on with your other research projects and graduate faster and/or with a more impressive publication record, then, assuming you can afford to pay the fee without sacrificing other important or crucial things at least, it seems to me that paying the fee is a reasonable decision.
With that said, I think a note of caution is also in order. My main concern is that a good proportion of the journals that charge open access publication fees are predatory journals, and given that you are a graduate student and new to publishing, there is a risk that the journal you are considering publishing in could be one of those. I would therefore suggest not paying any fee until you have made absolutely certain, by consulting your advisor or other experienced researchers, that the journal in question is a reputable one and that publishing in it will actually further your career and goals. Good luck!
If someone scores quite high on the GRE, how and where would they list it? Or would they even list it at all?
Answer
Copying my comment:
I don't think you should. I can't recall ever seeing test scores listed on a CV. Nobody really cares about GRE scores except graduate admissions committees, and they get the scores straight from ETS anyway.
I am currently on the academic job market, and scheduling on-campus interviews with institutions that might want to hire me.
Suppose I am invited to an on-campus interview at the University of X, and must travel there by air. They handle travel on a reimbursement basis: I buy the plane ticket, and then they reimburse me.
However, the interview is a few weeks away. Since the job market sometimes moves fast, there is a chance that by the time of the scheduled interview, I may have already accepted another offer (say from the University of Y). Of course I should then decline the interview at X, but I would have already bought the plane ticket.
How should I plan for this contingency?
I could buy a refundable ticket to X. However, these are normally several times the price of a non-refundable ticket, and if I do end up traveling to X, they might balk at reimbursing me for such an expensive fare.
I could buy a non-refundable ticket to X. If I end up not going there, I could ask X to reimburse me for the cost of the ticket (or at least the "change fee" charged by the airline to let me use the ticket's value for a future flight). However, I suspect they will be reluctant to reimburse me for a trip I'm not making, and might refuse to do so altogether, in which case I am out-of-pocket.
I could wait until the last minute to buy a non-refundable ticket for X. But it may still be expensive for them (or may exceed their limits), and the most convenient flights may be sold out.
I could contact University of X and ask them for guidance. I'm a bit hesitant to do this, as I am afraid that if I bring up the possibility that I might accept another position, they might think I am not seriously interested in theirs.
Is there a standard way to handle this situation?
This is in the United States, if it matters.
How do we differenciate between catabolic and anabolic reactions?
According to my researches;
Catabolic Reactions
Catabolic reactions (also called “catabolism”) break down larger, more complex molecules into smaller molecules and release energy in the process. The smaller end products of a catabolic reaction may be released as waste or they may be fed into other reactions. The energy that is released by catabolic reactions can be captured and used in many ways. Some of the energy is released as heat and increases the temperature of the cell. Sometimes the energy is stored in the chemical bonds of another molecule. And sometimes it can be used to do work, such as movement of cellular machinery to power the active transport of materials across cell membranes. Catabolic reactions are central to biological processes such as cellular respiration and the digestion of food molecules.
Anabolic Reactions
Anabolic reactions (also referred to as "anabolism") use energy to build more complex molecules from relatively simple raw materials. “Anabolic” and “catabolic” sound similar but are opposites. To remember the difference, it may help to think about how “anabolic steroids” promote the buildup of muscle mass. All of the complex molecules of life — carbohydrates, lipids, proteins, nucleic acids — are generated by anabolic reactions. Anabolic reactions are central to processes like photosynthesis, protein synthesis, and DNA replication.
Here are my questions
Is there water in every chemical reaction?
Do i just need to look at water ($H_{2}O$)?
Regards
Answer
Starting of with the basics, reactions are the breaking of bonds in the reactants and the forming of bonds in the products.
To answer your questions about water, there is not always H2O present, although most of the times there is water. You are referring to the hydrolysis and dehydration synthesis reactions, in which water is added or removed, to break down and combine molecules, respectively.
Catabolic reactions are more defined as the net release of energy in the reaction. They break down bigger molecules to smaller molecules. There is a need for energy input to begin the reaction and break the bonds of the reactants, however, the release of energy when the bonds of the products form are far greater, resulting in a net release of energy.
Anabolic reactions are essentially the opposite, where smaller molecules are combined and built up to larger macromolecules, many times with the removal of H2O. This results in a net decrease in free energy, as energy is absorbed/stored in the larger molecule. Energy inputted to break bonds of the reactants are far greater than the small energy released as bonds form.
As you will learn soon, these reactions can be characterized by exergonic/exothermic, and endergonic/endothermic reactions. They can be considered synonymous in many cases.
This was a conversation I was having with a colleague earlier today. He was offered a postdoctoral position and doesn't want to move after that. It's a very highly regarded university so it's understandable that he doesn't want to leave, but it made me wonder how common this is. Do postdocs frequently advance in the ranks at the same university or is it still the norm to go to school A for PhD, school B for postdoc, and school C for professorship?
I'm currently a Master's student in my final year and I want to start a Ph.D. next year. I really like doing research (one of my papers got published in a fairly reputable journal), but I more or less dislike the teaching aspect that comes with the Ph.D. title. Is there any alternative way to do research, outside of industry, and not be obligated to teach?
I got a 4.0 out of 5.0 on my teaching evaluations. The average grade in my department is a 4.5. Should I put this on my CV/resume?
For reference, I am a PhD student and this is the first class I've taught.
I recently came across a friend who is applying for a PhD in my lab. He happens to be from Brazil, on an F-1 visa. He was told by my advisor that his citizenship status affects the sources of funding available to support his work. I was always under an impression that the principal investigator applies for research grants and funding does not depend on visa status (if any) of the students under his guidance. Was I wrong in making this assumption?
I am curious about how much more a child can be alike to one parent than the other. If a child were to inherit all the alleles that are shared between both parents from one parent, but inherit all alleles from the other parent which the first parent doesn't possess, wouldn't this make the child genetically more uniquely similar to the second parent?
This question would be aided by understanding of how many alleles on average a person already shares with another person. Taking into account regional areas probably yield more similar people, I would imagine the average couple would share more than two randomly chosen people on the planet.
Answer
I will attempt to answer the question. Allele is defined, in simple terms, variation of a given gene, e.g. through deletions, SNPs etc. Humans are diploid organisms, meaning we have two sets of chromosomes, one from mother and one from father. Now since we have two sister chromosome, we can only have (share) two alleles of a given gene (one from mother and one from father) unless there are multiple copies of a gene or chromosome, which is mostly observed in disease conditions but that's not what we are talking about. Now since every humans have SNPs at roughly 1 every 1000 base pair, there are genetic variations between sequences of genes between humans, although there are some hot spots, which are more varied and some genes are very highly conserved due to their critical function such as cytochrome C. This just means that parents of the child you are describing (if not related to each other) are not likely to share the exact same, sequence wise, genetic code for a given gene selected at random.
The inheritance of a given allele of a gene on a chromosome happens through independent assortment (a process which happens maternally and paternally), meaning a child (offspring/zygote) would get one copy of a gene/allele (from the possible two that each parent themselves have) from maternal and one copy from paternal side at random. This is one source of genetic variation in a zygote. The other source of genetic variation is gene cross-over (through homologous recombination) meaning bits of the maternal or paternal chromosomes swap at gamete stage before the gametes are fused together to form a zygote, which makes the offspring unique and no offspring alike (except MZ twins but thats another discussion). This overall means that you can inherit a maximum of two alleles of a given gene (assuming again the parents of the child are not closely related) and even then the sequence of the offspring genes are not likely to be exactly the same as their parents, which makes every human unique. But saying that, you have a much higher gene sequence match to your parents than any other non-related human selected at random.
One thing worth noting here is that mitochondrial genes, are inherited exclusively from you mother (through the egg) and males inherit the Y chromosomes paternally so there are circumstances I guess you could say you inherit certain gene/alleles paternally or maternally.
What I speculate you might be thinking about is how many homologues (similar versions) of a given genes humans have and I think the average in the human genome is 3 but do check this! Flies (Drosophila) tends to have one, which is why its such a great model organism to study genetics and genetic interactions with as you do not tend to get redundancies.
I hope this answers your question
I am an undergraduate student who got into a voluntary internship for a year in my department.
Without going into much detail, I'm a trainee in the lab where programming lessons are held with lots of computers available for the students(Teaching Lab).
The main problem of concern is that my supervisor, who also happens to be the administrator of the lab, does not seem to believe in my abilities and underestimates my intelligence, which I can't understand why.
When I signed up for the internship I submitted my resume, followed by a short interview from the university. I can say I got the job easily mainly due to my background.
I was hoping that I was going to work on something productive, like a research project. On the contrary, my supervisor seems to be very lazy and constantly assigns chores to me (cleaning, being his personal mailman on the university etc).
At the start since he found out I was bored he suggested to study some basic HTML (Fact is, I worked as a professional web developer some time ago!). If I reply that the tasks he sets for me are easy, he gets mad and tries to get me wrong so that he can show that I have no idea what I'm talking about.
Professors who knew me before and visited the lab asked my supervisor to offer me some motivation for extended bibliography and some more productive learning. He answered that if I have the right foundations then we can negotiate for something more productive! (Yet, he only has one paper, published 20 years ago).
What are your opinions on this? I was about to withdraw due to boredom but I only have some months left. Should I talk to a professor about this topic? Am I expecting too much or am overqualified?
Answer
I don't say this lightly, but given everything you've said: I think you should probably quit the internship, or at least present the prospect of that to your supervisor.
Some key points:
1) You say it's a "voluntary internship". Well, all academic internships are voluntary (I hope!), so I think what you mean is that you are a volunteer, i.e., unpaid. [Added: I just looked this up, and apparently this phrase is quite common in parts of the anglophone world outside of North America. Sorry.]
2) You wrote
I was hoping that I was going to work on something productive, like a research project.
That is a very reasonable expectation for a volunteer internship. However, the parameters of the job seem to be very different:
I'm a trainee in the lab where programming lessons are held with lots of computers available for the students.
But that doesn't sound research-related at all: it sounds like you're in a teaching lab, not a research lab. If you were actually doing the training, you'd be some kind of TA...without pay. Unfortunately:
On the contrary, my supervisor...constantly assigns chores to me (cleaning, being his personal mailman on the university etc).
Having to clean up a laboratory space after using it is very reasonable. In my branch of the academic world at least (North America), cleaning up after other people is a paid job, not part of an internship. Similarly, mail delivery is the sort of thing for which someone is usually paid an hourly wage. If you are doing some of this and some of something else, it might be okay if the something else were especially attractive and rewarding. But given that you're not, it sounds to me that you're simply being exploited. Certainly I would feel that way if I were you.
Yet, he only has one paper, published 20 years ago.
Yikes. So the professor is probably not even research-active, or at least not to the level necessary for it to be plausible that he is the head of some kind of research team. He is not a good choice to supervise your research. In view of everything else you've said, I'm afraid that it seems likely that the business about your having a "proper foundation" -- especially in the context of his willful ignorance of the skills that you already have -- is just an excuse.
I would go to this professor and say that there's been a misunderstanding. You thought you were getting involved in a research internship, and as it hasn't panned out that way, you'd like to give notice. If he wants to change your mind, have him mention not just the prospect of future research "when you're ready", but actually nail down research that you can get started on right away.
It would also be good to speak to at least one of the other faculty members you've mentioned. I don't know where in the world you're writing from, so it's possible that your local academic culture is very different from mine. But unless you find out that it would be a big bridge-burning mistake to quit your internship, I think you should be angling for that outcome.
Among the various indices for academic productivity/impact in the respective field, which is most accepted one?
You can see some productivity measures, used in academia, here and here
This question is inspired by the comment here and should not be confused with this
Clarification: The word accepted meant to be taken as accepted in the respective field of activity, for various requirements, say appointments, career advancements, selection for awards, invitation as an examiner, editor, reviewer etc. These measures might not have much impact on the general public, and that is not being asked.
Answer
There is no accepted numerical measure for an individual's academic productivity. The available measures can sometimes be useful, but they all have serious weaknesses and many detractors. In particular, there is no widely accepted or safe choice: if you make any public use of a productivity measure, many people will react angrily, no matter which measure you choose (and their anger may well be justified).
Added in edit: In my experience, citation and publication counts are sometimes mentioned in letters of recommendation, but just as a crude numerical measure, rather than with any serious importance attached to them; most letters do not mention them. (I've never seen an h-index mentioned in a letter or job application, but perhaps it is more common in physics.) Hiring committee members occasionally impose minimal numerical standards, but just to rule out inappropriate cases ("we won't consider anyone for a tenure-track job unless they have at least two publications", say). In the departments I'm familiar with, nobody uses them to choose between serious candidates. Like Dan C says, they just aren't that useful: they add a small amount of information, with a lot of noise and even systematic bias.
Archiving of papers and projects is very important for most of the people, and everyone has a method of it.
I, personally, try to have different folders for different papers. In the folder of each paper, in addition to my manuscript, I keep my simulation files, experimental data, program codes, etc, in different subfolders. Also, I try to keep track of my revisions on the paper, reviewer comments, my response to reviewers in different subfolders. My method has the advantage of all the related material for a paper are together, and I can quickly track the whole process from initial submission to the final proofreading. However, this usually leads to duplicated files.
I work with both my office desktop and my personal Laptop. I transfer my files between these systems by a flash memory. I agree maybe cloud technology is a better choice in this age, but I postponed it because of my poor internet connection at home.
I am curious to know how others approach to archive their works. I also hope to find some methods more efficient than mine, or get some tips to improve my method.
Edit at 2 Apr 13: Thanks to these great answers, it is almost a month that I use Git for my version control. Also, I manage my repositories in the Bitbucket, which gives me unlimited storage for unlimited number of projects.
Answer
I have a similar approach with folders, with two additions:
Everything goes into a revision control system. In my case, I've got some things in Subversion repositories, and others in Mecurial repositories (I've also dabbled with Git, but haven't made the final transition). The benefits of revision control are that you can always go back to a previous version, you won't have old versions littering your folders, and sharing with collaborators is relatively easy. This should take care of your duplicated-file problem.
I also use Dropbox extensively, in order to have my files available on any computer at any time. Dropbox provides a modicum of version control (30 days worth), but it should not replace a proper revision control system. It does provide a cloud-based backup of your work.
Finally, regardless of how you're keeping your work arranged, make sure you keep an off-site backup (e.g., via Dropbox or personally-controlled media).
I am rather disappointed by the existing research in my area of interest. There is a big disconnect between the solutions practitioners need and what researchers look at.
Can I publish short here-is-an-idea paper (e.g. “Proposed Solution for X” or “(new) Model for Y”) well before having any means of providing some proof?
I am reading Charlesworth et al. 1997. They talk about diversity within and between allelic classes.
Nucleotide diversities ($π$) at each neutral site were estimated from the mean of $2 \sum z_t (1-z_t)$, over replicated introductions at the site of single variants, where zt is the frequency of the neutral variant at time t, and summation is over all times until either fixation or loss occurs.
The total genetic diversity at the neutral sites ($π_T$) was also decomposed into that within and between allelic classes at the polymorphic locus. Diversity within allelic classes, which will be written here as $π_A$, was estimated from the mean of $2 \sum \left( x_t(1-x_t)+y_t)(1-y_t) \right)$ where $x_t$ and $y_t$ are the frequencies of the neutral variant within the first and second allelic classes, respectively. Diversity between allelic classes with respect to the polymorphic locus was calculated as the difference between the total diversity values and $π_A$
Note that the parentheses don't match up but this this is what is written in the paper!
Why am I confused about this text?
I am confused about the term allelic class. I first think there is anything fancy in here and I think we can simply replace the term "allelic class" by "allele". but then when I saw the equation for $\pi_A$ I realize that the frequency of the two allelic classes does not necessarily adds to 1 (even though we consider only two allelic classes).
I also got also a little confused about the difference between $\pi$ and $\pi_T$ but I think that they just used two notations for the same think ($\pi = \pi_T$)
In population genetics's jargon, diversity just mean expected heterozygosity. $\pi_T$ makes sense to me. It is just the average heterozygosity $\left(2 z(1-z)\right)$ calculated over all time steps. Maybe a more intuitive to put it would to integrate rather than summing over time rather than time steps.
Question
I can read the equation for $\pi_A$ but I fail to get any intuition behind what it means. For example, I have no idea why it should be called within-allelic class diversity. Where does $2(x(1-x)+y)(1-y)$ come from? My whole issue might boil down to the definition of allelic class.
EDIT
The term allelic class is defined in Innan and Tajima (1997)
Suppose that there are two nucleotides, say A and T, in a particular site. Then, we can divide DNA sequences into two classes: one class includes sequences with A and the other includes sequences with T in this site. We call such a class an allelic class
(Slatkin 1996 might help as well).
I am still not quite sure what the within allelic class variance. Maybe it is: Take the most common sequence in the considered allelic class. For each, sequence, calculate the number of pairwise differences to the most common sequence and square this value. Sum over all sequence and divide by the number of sequences. In math form it would be: $\frac{1}{2N}\sum_i^{2N} (D_i)^2$, where $N$ is the population size and $D_i$ is the number of pairwise difference between the sequence $i$ and the most common sequence in the considered allelic class. Does it sound right to you?
Answer
From the way I have read what you have written z(1-z) translated into a sentence would be the frequency of the neutral variant (z) times the frequency of all other possible variants (1 - z) at the particular time t.
Nucleotide diversity is then the average of 2 times the sum of all of the frequencies of neutral variants (z) times the the frequency of all other possible variants (1-z) for all of the time periods until either there is no longer a change in the sequence or the allele is lost (which can happen over evolutionary time, especially if the allelic class is a deleterious variant, or the heterozygous allele provides enough expression to mask).
To me, this sounds like the result will be the probability of the neutral variant existing over time, which should be a number between 0 and 1. If z was 1, that would imply that the neutral variant is always the case, so the frequency of other variants is 0 making 2* 1(1-1) = 0 which makes sense to me as that would mean there is no nucleotide diversity. That sequence is always that sequence and so there is no sequence diversity.
As this looks like it is dealing with frequency distributions I think that total genetic diversity is implying the probability of all of the different allelic classes that make up an allele. So if you have class one which has the frequency of x and a class two with a frequency of y it sounds like the overall diversity would be the probability of the neutral variant of x and the probability of the neutral variant y.
Generally, when you are looking at the probability of multiple events, you would multiply the probability of one event times the probability of the other event. As a result, I am inclined to say that the Nucleotide diversity within classes πA is 2 times the average of the sum of the frequency of x times the frequency of y, or 2∑ x(1-x)(1-y) + y(1-y) or factored 2∑ (x(1-x) + y)(1-y) or in words the Within Class Diversity (πA) is 2 times the average of the frequency of x as the neutral variant times the frequency of all other variants when x is the neutral variant times the frequency of all other variants when y is the neutral variant plus the frequency of y as the neutral variant times the frequency of all other variants when y is the neutral variant.
I think that the reason that this might be done is that, for reasons of selective pressure, x might be favored, so those times that the variant is y, some of those variants (possibly all of them) will be x, so by multiplying the within class diversity of x by the frequency of all of the variants when the class is y implies that there will be less diversity within class than if you just added the frequency probabilities together.
One thing I would do is to do a search to see if there was a correction published to this article, as there was a mistake in the formula. That might help to clarify. Also note, I could be wrong in my assessment as I do not have access to the actual paper you have referenced.
Best of luck in working this out.
