Archive for the 'Science Basics' Category

Advice to students writing science essays and answering exams

I’ve just come off the back of marking a quite sizeable pile of exams and coursework for my job. While I have done bits in the past (and earlier this year) this was the first time I had to deal with a large and concerted mass of the two and it allowed me to spot a series of things that irked me. While I am easily irked, the issue is not trivial, good clear writing is essential to communicate your ideas and if you are not doing that right, then this is a problem. It matters not that this is zoology or even biology, in any job or field, precise communication is critical. And not just accuracy but ease of reading – the information can be 100% accurate but if it’s buried in waffle or phrased badly it makes it hard to follow.

I know that I have a fair few regular student readers on here and others find me on occasion so I hope this will be useful. I’m only sorry I wasn’t able to think of this before the last round of exams or this might have been posted in a rather more timely occasion. So, here’s a few things I kept seeing that I’d quite happily never see again. They are all stylistic and people would probably not mark you down for using them, but they are at best, clumsy and inelegant and you want your work to appear astute and well produced. Helping someone to follow the thread of your work and ideas when they are reading their 37th five page long essay on the subject will help your cause.

–       Long and flowery introductions. There is noting wrong at all with a bit of craft to your writing (indeed, it is a good thing) and a little (a little) hyperbole can be good. But having to read a whole half a page before we get anywhere with actual detail is pointless and especially so in an exam. I don’t want, nor need to be told about how magnificent birds are and how they being joy to all who behold them. Write about them.

–       Repeating the question. It if helps you to focus, then feel free to write out the question before answering it. But if the question is “Define the 4 features of X and why their function is important”, don’t write “X has 4 main features, and their functions are important. These are…”. I know there are 4 and they are important, it’s the damned question!

–       The I’s have it. Science is really supposed to be about dispassionate reporting. Don’t talk about yourself. “I think”, “I am saying”, “I will show that”. Even when a question says something like “What do you interpret Smith et al.’s 2004 paper to mean….” you can avoid the first person. Say “It can be shown” or “This can be interpreted to mean”. It’s obviously your interpretation, you are writing it.

–       Don’t describe what you are describing. This seems to go hand-in-hand with the point above. I read far too many things that went “I will now describe the following features of X”. This sentence is pretty much absolutely redundant. Just describe X.

–       An alternative version of this is repeating information in reverse. Where it is pertinent, there’s nothing wrong with reminding the reader of a key point later in the answer. But writing “There are four feature of X” describing them and finishing with “…and these are the four features of X” at the end of the same 2 or 3 sentence paragraph is nonsense. I even saw it done in the same sentence a few times.

–       Try to avoid repetition of phrases. I lost count of people who needing to make similar points over a number of paragraphs would start each section with “Another point / idea / function is…”. About the 4th time you read that it gets very, very boring. Just add a smidge of style. “A further function is”, “The next function to be considered is”, “X is another key function, “In addition, function X”, “Furthermore, X” and so on.

–       Avoid ‘believe’ like the plague. Ideas can be supported, though of, understood to be, have a consensus behind, be agreed upon and others, but not believed. Yes, the vernacular use is one of genera “I accept that” but it really should be kept out of science. It’s even worse when you say it about other people “Smith et al. believe that X…”. Not they don’t, on the balance of the evidence, that’s the hypothesis they support.

–       Unsuitable anthropomorphism or odd terms. Something like an ankylosaur was slow, and heavy, and didn’t move very fast. But to call it ‘ponderous’, ‘clumsy’ or ‘lumbering’ is to give it something close to emotive or descriptive characters that just aren’t suitable for animals.

And finally, on a related note, answer the question. That one really seems to have gone past far too many people.

Problems with advanced publication

Now that the last of the Zhuchangtyrannus stuff is behind me, it’s worth returning to an issue that has in a way affected every aspect of the blogging and media side of things – the fact that what is actually available right now is an uncorrected proof. For those who don’t know, the basic procedure of getting a scientific paper published is that you submit your work to a journal, this goes for review, if it’s seemed suitable the reviews come back to you to make corrections based on them, this is returned to the journal editor and if deemed satisfactory are turned into a ‘proof’ version (i.e. formatted for publication), these come back to you to check and make final tweaks and then go back to the journal for final publication.

In the old days (and by this I mean as little and 5 or so years ago) unless you sent round copies to your colleagues, in general no one would see the paper until it was actually published – physically in paper form in a journal. The gap between returning your proofs and publication was generally weeks and was often months and occasionally years. As such journals soon realised that they were missing out on citations and credit for papers that were basically done and could be viewed as published and with the digital world in full flow, they could put these up in advance.

I see this as generally a good thing. It keeps things moving along and cuts down on the waiting time on work to appear and especially work that everyone already knows about and wants to cite but can’t because the journal is slow. However, many journals have now gone a step further and started putting up the proofs themselves. This is a very bad thing.

First off the more frivolous reasons, it’s annoying. I want the final version, not some pre-version. Journals still charge for these, so there’s a risk you could end up forking out twice for what is essentially the same paper. Similarly, the authors may have reasons for this not appearing before the final version for whatever reason and there’s generally no opt-out. It also makes doing media work hard (like here for me) because the paper kinda is published and kinda isn’t. It’s also a time waster – I fielded a number of e-mails from people asking for apparently ‘missing’ data in the paper which was absent only because of a formatting error, and it was, frankly, a pain as I had to keep trotting out the same reply to lots of people to give them what they wanted and suggest that I wasn’t a complete fool and did put it in there honestly.

More seriously there are taxonomic issues. I think the world’s taxonomists are just ignoring this issue from a practical point of view (which is probably for the best) but I doubt they’re happy. Zhuchengtyrannus is, right now, technically not properly published. The ICZN still require paper copies of papers to make names valid (see the PLoS One discussions of recent years). While I didn’t publish in an online only open-source journal, so far there are no paper copies of this article in libraries so they name doesn’t count. This is stupid and of course genuinely risks that some nefarious person will one day attempt to gazump a real piece of research by simply copying the diagnosis and specimen number, and self publishing a couple of pages of notes and stick them in a few locations and try to steal the name. No one wants this and it does offer unnecessary confusion.

Finally there is the real issue here. Proofs are not really, real. They can be subject to change and these can be profound. I really don’t know of anyone who hasn’t spotted a mistake in a paper they have published and most people would probably tell you there’s an error in most paper they’ve published one way or the other. It can be a simple as a missing comma, a spelling mistake or a mis-citation (I meant Smith et al. 1998 not 1999). I know of people who have spelled major things wrong (including the word ‘Cretaceous’ in the title once). Proofs are your last chance to catch these things and of course add in last minute changes (as I have to do with this one for example). Recently a co-author spotted we had a ‘not’ missing from a sentence in a paper which of course rather changed the meaning of the paragraph at hand!

While some of these (minor and major) will slip through, the vast majority won’t. That’s pretty much the point of the proofs. But if the proofs are already out there, people will see them and might think they are intended. They won’t know you went back and added in a ‘not’: Hey, Smith et al. said this IS true! Surely it’s not true!!!

Now that these are free game and not just seen by authors and editors the cat gets out of the bag in the wrong way. People will read them and cite them. But they will be reading and even citing things you might not officially have said. In the medium and long term the only record will be the real, actual, paper. A colleague told me that some time ago this almost happened to him, someone basically published a paper and in it, refereed to my colleague’s in press work (at the time a proof) and pointed out a significant anomaly in there. In the meantime, said colleague had seen it himself and fixed it. So you now have the bizarre situation that person A has a paper pointing out an error in a paper by person B. Only that error is not in the paper, and actually both papers agree on the point absolutely. This means that if you read both, A looks like a fool and if you only read A’s paper then you think B is. The situation was saved because A was polite and sensible enough to check before he went ahead.

Even so, it seems to me only a matter of time before some major eruption occurs because of these. Someone will get a major roasting in the literature for something they never officially said, or someone will leap on a point to prove their case only to see that data point vanish when the paper is properly published, or someone will be very unscrupulous with a new name or something similar. As such, I utterly hate advanced proofs and I’d love to see them return to whence the came.

Playing the game

I’d been thinking of writing this post when I discovered that the theme I had intended to expand upon was rumbling on itself over on SV-POW. That theme is on amateurs publishing in palaeontology. Yesterday I moaned about poor papers and the effect they can have by generating huge amounts of awkward work for researchers to set the record straight. Here I want to make the point about why, or perhaps how, this happens.

Science and scientific research is open to everyone. It is supposed to be open to everyone, if you have an idea or some research and can back it up with evidence, you should be able to demonstrate it in some form of public forum. Now researchers prefer peer-reviwed journals as this does result in some basic weeding out of poor practice (mistakes in methods, data collection etc. etc.) and ensures that people are likely to find your work and able to publish replies and so on. However, any book, magazine or journal should be OK in theory.

In practice it is another matter of course, because of this very openness. By opening ourselves to any work of any form then we risk the presence of poor work: inclusiveness at the expense of quality control. The simple fact is that we want everyone to participate in the game of research we really don’t set rules and simply expect (or perhaps rather, hope) that people follow the protocols that most of us do. It is those who want to play the game, and indeed are joining in, that have not bothered to learn the rules, or don’t know they are there, or deliberately snub them, that cause the problem. Since we don’t enforce those rules by say deliberately setting prescedent that only peer-review counts, or can’t in the private games outside of peer-reviewed journals, then all manner of problems surface and are allowed to surface.

Ignorance can always be forgiven, but it generally takes at least some decent form of basic knowledge of the process of both science and scientific publication to even try. Thus one cannot help but suspect that in many cases, perhaps most, or even the great majority, the reason the rules are circumvented is a combination of laziness, overconfidence or deceit. Such poor papers are being produced by those who want to take part in the game, to be seen to be taking part in the game, but are simply not playing by the rules.

Unless science makes a concerted effort to shift the rules or enforce them in a different way (and I think it neither will, nor should) we will have to put up with these issues. But it would help a great deal if these people would both realise what they are doing and the problems they are causing. The game would be more enjoyable and go faster without these intrusions and that should be possible. It is great that anyone, everyone, can get involved in real science, but there is a significant difference between doing it right, and just doing it. Sadly there are far too many people who seem not to get this, but one hopes things will improve.

And while we are on the subject…

While I’m wimbling about science reporting, here’s, for me, an encapsulation of two key issues. First go and read this. Now I’m all in favour of people selling science and being cool and an opportunity to sell the merits of footprints is great. But the piece has got it all backwards.

“The Polish discovery reveals that the ancestors of all birds were small, light and four-footed”. No. We knew that already. If we didn’t know that already we would not be abel to work out what the footprints belonged to. This merely shows that these animals were present at the time these tracks dat from. This is a pretty big misstep – the sun does not come up because it gets light in the morning, but the other way round.

This should be pretty obvious from the paper and, well, common sense. You need the skeleton to match to the footprint or an odd print is just an odd print.

The second problem is the fact that this is an editorial in the Guardian. These, if any, are the best of the Uk newspapers for science reporting (home as they are to George Moinbot, Bad Science, the Lay Scientist) and others. I would hope for and expect better of them. If they can’t even run their own pieces past their own experts for error then one must wonder a little at how luck rather than intent might have played a part in getting as good a team as they have assembled. No one is perfect of course, but such simple errors belie the amount of work there is still to do to even the best up to scratch on some basics.


The science network

A good scientist knows what he knows and knows what he does not know. He has a good idea of his strengths and weaknesses and his areas of expertise and ignorance.

I know I know pterosaurs and theropods quite well, sauropods less well, ornithischians much less well and so on. I have a good handle on systematics and taxonomy and behaviour, but not on taphonomy or morphometrics. However, crucially, I also know people who are good at the things I’m not good at and are not good at the things I am good at. There are also people who are real specialists and can use a method or know a group better than almost anyone else alive, or generalists (which I’m certainly closer to) who can do a fair range of things quite well and link the other stuff together. Together we have breadth and depth.

This is important for two different reasons. Firstly it allows us to cover both a wide range of fields and get deep into them, without us all tripping over each other’s work. People can specialise or generalise and science will move forward as a result. More importantly though, it allows us to cross check and revise our collective work and have confidence in what we are doing across the whole of science, even, or perhaps particularly, when we have little or no understanding of that field individually.

I really do not know very much about astrophysics (big surprise). But I know a couple of people who do. I know the training they go through, I know the colleagues they have who check and review their work (peer review) and examine their ideas in the literature (through papers). I also know that those people are also cross-examined and checked by still other people and so on. It would be enormously time consuming, but I bet I can find a chain of co-authors and collaborators that links me to my collegiate astrophysicists. I have collaborators in geology and biology and some of them will have collaborators who are chemists and biochemists and physicists right up to guys working on star formation. At every point each person will have anywhere from a handful to dozens or even hundreds of collaborators, and dozens or hundreds or even thousands more who are reading and reviewing and replying to their papers. They have enough expertise to analyse each link in the chain, and perhaps one or two links either side of it, even if they can’t begin to handle either end.

Sure, there’s no-one out there (I suspect) who knows as much as I do about a couple of specimens I’ve worked on, but there are people who know nearly as much, and who know more about other close specimens, and know more about the methods I used to test them. This constant cross checking and evaluation means that we can have real confidence in our results and methods. I may not know how the stats package on my computer runs an analysis I want to use, but I do know that the mechanics have been written and tested by software engineers, I know the stats concepts have been produced by mathematicians and the methods have been verified by others. There are biologists with enough maths background to check the principles behind it and the appropriateness of the methods and the correctness of the results and so on. I know the taxonomy of the group at hand is right because enough taxonomists have checked the principles used to erect the species and specialists on the clade have looked at the anatomy and ecology and confirmed the species are distinct and so on. They may not know each other or even recognise each other’s work (I suspect you could really confuse a mathematician with a graptolite and some whale baleen), but it all fits together.

In this sense then, scientists are not so much a group of individuals as a cohesive whole. There are, obviously, errors made (occasionally profound ones) but this colossal network of research ideas and analysis does produce a singular, and generally very reliable, whole. I may not understand astrophysics, but I recognise and trust the methods used to generate the data, the analyses and the people behind it. So can you.

A good article on science…

in a national newspaper. Makes a nice change, though of course, it is written by a scientist, so perhaps it’s less of a surprise.

Still, this is well worth a read on the subject of scepticism and self-correction in science.

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The complete ‘how to’ guide for young researchers (so far)

It seems that recently some of my various ‘how to’ posts have been found by various search engines and readers and since I don’t have much to write about today and that these are, I think, some of the most important and beast things I have written, it seemed a pertinent time to resurrect them under a single banner for any more recent followers who have yet to0 find them. For those who have missed out, I wrote an extended series of posts covering all the basic skills of research such as writing and reviewing papers, giving talks, editing work and so on. These I hope have been and will continue to be of use to students and young graduates trying to break into science or generally improve their skills during their education, so here I have bundled them all up into one single slot to make it more accessible and easier to link to as well as hopefully bring this to the attention of new Musings readers.

Basic advice to young researchers

How to complete a PhD

How to get hold of papers

How to write a paper (and get it published)

How to contribute to a paper

How to review a paper

How to edit a volume of papers

How to write a conference abstract

Things to do at a meeting

How to give a talk

How to make a scientific poster

How to arrange a meeting

A ‘how to’ summary (contains various updates and links to other sites)

And finally don’t forget the ‘science basics‘ section on here which contains all of these and more.

Do make use of these and feel free to pass them on to your colleagues / friends / students and do add comments to help keep them thorough and up-to-date. The feedback I have had on these has been very good, so I’m happy to be confident that they are doing some good.

More advice

Mike Taylor has a great write-up over at SV-POW! on chosing where to publish your academic research papers. It’s worth a good read through when you have time and covers a lot of ground that I never did when writing about how to get a paper published as part of my ‘famous’ and ‘successful’ how-to series.

Avoiding abstracts

imgp2670As most, if not all, of you will know scientific meeting abstracts can make up an important part of scientific research. For those that are unaware, well formal scientific meetings, researchers who are attending send off short abstracts of their work that they will present at the meeting (if you have not seen one before a quick google will give you a good idea). Usually this is just a couple of hundred words describing the very basics of the work, though occasionally you get longer ones with reference lists and even figures. This means that in advance of the meeting and the talk itself you have an idea of what is being discussed which helps understand the presentation itself. If it’s a big meeting where you can’t attend every talk, then the abstract can help you decide which talks you want to see (or avoid) and afterwards you have a record of who said what about what subject. In theroy at least, and that is the problem.
Continue reading ‘Avoiding abstracts’

Getting hold of papers

Over at the Open Source Paleontologist there is an excellent article about getting hold of research papers (primarily PDFs, but also other sources). It’s well worth a read as he lists various sources for PDFs and ways of searching for them online. There are a few on there I didn’t know about so it’s well worth a look.

Two quick things I will add here (which I also left in a comment on the site) are quite important to this area of scientific research (both for amateurs and professionals). First off, while Andy mentions them, there are increasing numbers of ‘PDF collections’ online, with indices of whole rafts of papers based around subjects (ones for theropods, pterosaurs and ankylosaurs are out there) or people (Marsh is done and Cope I believe is in progress) and more and more researchers are making their papers availbale online on homepages and lab pages (Mike Benton for example has most of his papers, going back to the 70’s, available to download). In other words, in addition to open source journals and google there are huge stores of research inforamtion available online to anyone with a computer and two minutes worth of ‘googling’. Which brings me to my second point.

Why must I (and plenty of other people) put up with the endless requests for papers from people? If you want a copy of *my* papers, then fine, I’ll more than happily send on a PDF or hardcopy if I can. I want people to read my research and cite my papers. That’s a fundamental part of my job and all to the good. What I don’t like is the constant barrage of requests made by people all over the web for every single paper that comes out. This is especially seen on blogs where someone reports on a paper and instantly half a dozen people request copies of the PDF (and this is the same on mailing lists too, with constant requests for papers followed up by loads of other guys asking for a copy once the cry has gone up). It is probably freely available online and if not, the authors will happily send you a copy if you e-mail them.

It is, I feel, discourteous to expect researchers to spend their time randomly e-mailing copies of papers to anyone who asks when they have nothing to do with the paper. Yes it is their chocie to blog about it and spead the news in the first place, but that is in itself a service, and asking for all kinds of ‘extras’ constantly is an unfair use of their time. It will take you as long to e-mail the original author and ask for a copy of the paper as it will to put in a comment on the blog asking for someone to mail the paper to you, who has nothing to do with the work, and is already giving up his time to tell you about it in the first place. It’s especially true of the non-professionals who understandably don’t necessarily have access to all the journals etc. but enough professionals are guilty of the same thing and that’s not an excuse to harry people for reprints and PDFs.

I know some people are good about going this extra mile for service, and yes obviously not every paper is easily available online, or for that matter the contact details of the author (though increasingly that is less and less of an excuse) but it IS a pain. I feel mean when I don’t dig them out myself and send them on because, well, I am a nice guy, but it is (in my opinion) unthinking and unnecessary to expect people to just send out these things when they have real work to do. The act of unthinkingly asking (or even demanding) papers becuase you want to read them is not right. So if you are one of those “I must have it now, please send it to me” types, do stop and think for a minute. You have google. You have online archives. You can contact the authors. You can, and this may be shock, wait a few days before you read it, it won’t kill you – so calm down and look properly online first. If you must contact someone, contact a close research assocaite of the author who is likely to have a copy (a common co-author, his students, or someone who works in a simialr field) who is likely to have it. Send them a short and polite e-mail asking for a copy. Don’t just bang down a bunch of comments on blog threads or e-mail half the palaeo community asking for it.

This is something that rarely affects me personally I admit (apart from when I have my inbox filled with people requesting some new fish paper via the Vert Pal mailing list) and I am not sure how much it bothers others but is I think an important piece of netiquette that people need to think about. Do your own work, and don’t expect others to do it for you. And if you have to ask, ask nicely and ask the right people. Authors are delighted to know people are interested in and reading their papers and it helps them keep track of who is doing what and how their work is recieved, so just ask them.

More hows and whys

I’m basically in transit for the next day or so heading back to Beijing after a thoroughly enjoyable trip to the UK and Germany. In order to keep things ticking over while I am in the air (or in airport lounges) and recovering from jet lag and the time difference, here are a few other things for you all to read. I have put this in Science Basics as these fit nicely with that theme.

First off, here is a review on how to review or critique a paper by those good people at Nature.

Similarly, there is advice from Science on writing papers (though it is very brief and general) via River Continua.

More generally Matt Wedel has a big series of posts on general science communication between scientists and how new ideas are often generated and discussed. It’s a nice take on a rarely discussed area should be of interest to young academics and the general public alike. I’m not if he is finished yet, but he has so far produced four parts to the series. Read them here, and here, and here and here.

A ‘how to’ summary.

This latest week-long series of posts on ‘how to’ do various things (combined with other earlier ones) seems to have generated a few comments (overwhelmingly positive, I am pleased to see) and have been read by a great many people (hits over the last week in general, and for the specific posts have been way above my normal averages). Between these points and few other things that have cropped up, it seemed well worth adding a short off the cuff summary to what all of this has been about and what I tried to achieve with these posts (and I hope to have more in the future). Continue reading ‘A ‘how to’ summary.’

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