tag:blogger.com,1999:blog-4456348657596914237.comments2024-03-14T09:06:12.900-04:00Eco-Evo Evo-EcoBen Hallerhttp://www.blogger.com/profile/17875404974157070805noreply@blogger.comBlogger594125tag:blogger.com,1999:blog-4456348657596914237.post-68229915021427502322023-05-02T18:47:07.550-04:002023-05-02T18:47:07.550-04:00I am glad to have known Ole Kristian as a colleagu...I am glad to have known Ole Kristian as a colleague - thanks for the beautiful post!Joost Raeymaekershttps://www.blogger.com/profile/11238145495393540939noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-53950408610716748812023-03-07T14:03:44.117-05:002023-03-07T14:03:44.117-05:00Let's take a look at this from another angle. ...Let's take a look at this from another angle. Ken Thompson acknowledges me for providing him the data in his manuscript, but in these public forums states that Dr. Newmaster gave him the data. Interesting, but then Dr. Hebert states in this forum that the study site was my research site at Timmins, but that is also not the truth. Based on this it would appear that neither Ken nor Dr. Hebert know what the truth is. Thus, when viewed in the broader context I am inclined to dismiss the arguments and classify this as a smear campaign rather than a scientific discussion and conclude that Ken couldn't have bungled this one up more if he had tried.Dr. F.W. Bellhttps://www.blogger.com/profile/01921552930782255640noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-32600060334318402412023-02-27T14:44:52.614-05:002023-02-27T14:44:52.614-05:00Thanks for posting, I thought this was very good a...Thanks for posting, I thought this was very good and found it incredibly helpful. Have you received reviewer feedback yet? I'm in Ottawa, and worked with my University on several EDI plans for large-scale grants. All are still out for review...Heather Howleyhttps://www.blogger.com/profile/06263637029000019134noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-42191279695446908472022-12-15T08:14:59.125-05:002022-12-15T08:14:59.125-05:00This is great advice! However, I would also sugge...This is great advice! However, I would also suggest that there are additional ways to structure an introduction to a subject in manuscripts and grants that goes from the big idea to the specific question/problem being addressed. See: https://www.northwestern.edu/climb/resources/written-communication/index.html <br />Combining the two approaches may be optimal. DoughDouglas L Chttps://www.blogger.com/profile/02834407066660774329noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-7593067833225113372022-11-28T01:20:16.754-05:002022-11-28T01:20:16.754-05:00Finally, one thing that I think is key in scientif...Finally, one thing that I think is key in scientific writing is to use the same term for the same concept, consistently. If you write "genetic variation" in one place, "genetic variability" in another, "genetic variance" in a third, and so forth, then the reader is left wondering whether you are deliberately referring to different concepts with those different phrases, or whether you are just using inconsistent terminology. This can be incredibly confusing. In general, it is good not to repeat the same word over and over; vary your vocabulary to avoid being repetitive. Exercise your thesaurus a little. But when it comes to scientific terminology, and particularly for the core scientific concepts that you are referring to over and over, the rule is exactly the opposite: settle on a single term and stick with it.Ben Hallerhttps://www.blogger.com/profile/17875404974157070805noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-73333215534243298372022-11-28T01:02:37.460-05:002022-11-28T01:02:37.460-05:00A point I would add, again in the spirit of "...A point I would add, again in the spirit of "lead the reader by the nose", is: use connecting words that express the relationships between thoughts. These are words like "similarly", "however", "yet", "meanwhile", "regardless", "but", and so forth. Punctuation can also play this role; semicolons, as in this sentence, are particularly useful for expressing that one thought follows upon the heels of another. Another useful punctuation mark for this purpose – if not overused! – is the en-dash, "–". I prefer it to the longer em-dash, "—", because I find the en-dash more readable—but this choice might be dictated by the journal's style guide.Ben Hallerhttps://www.blogger.com/profile/17875404974157070805noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-44297966642255405692022-11-28T00:54:32.794-05:002022-11-28T00:54:32.794-05:00Expanding on #5, I often feel the same way about &...Expanding on #5, I often feel the same way about "as" when used in a sense other than "simultaneously", and "since" when used in a sense other than "in the time after". For example, "As we didn't have enough fish traps, we resorted to nets", or "Since we didn't have enough...". Instead, write "Because we didn't have enough...". Otherwise, the reader has to think about the ambiguity of the different senses of the word. In general, think about whether there is more than one way to read a sentence, and if there is (even if the alternate readings make no sense really), try to rewrite to eliminate the ambiguity. As my mother (a professional editor) used to say, "Lead the reader by the nose".Ben Hallerhttps://www.blogger.com/profile/17875404974157070805noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-29775863778242540462022-08-02T23:29:20.836-04:002022-08-02T23:29:20.836-04:00Nice. Redundancy, man. It's mechanical engin...Nice. Redundancy, man. It's mechanical engineering.Ben Hallerhttps://www.blogger.com/profile/17875404974157070805noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-27537762892164235492022-08-02T14:42:12.689-04:002022-08-02T14:42:12.689-04:00Yes - those introductions!Yes - those introductions!Andrew Hendryhttps://www.blogger.com/profile/03653724437118653645noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-78278296589737016952022-08-02T14:41:45.156-04:002022-08-02T14:41:45.156-04:00COVID shook up everything. Mostly bad. Maybe some ...COVID shook up everything. Mostly bad. Maybe some good.Andrew Hendryhttps://www.blogger.com/profile/03653724437118653645noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-31516938143975901522022-07-21T08:31:12.697-04:002022-07-21T08:31:12.697-04:00This makes good sense. Maybe it would have been w...This makes good sense. Maybe it would have been worthwhile to continue with those other systems as long as you had continuity, because there is so much value to a continuous dataset; but once continuity is broken, that strongly increases the incentive to shift strategies. And the stickleback work is so cool; I recently saw Katie give a talk about the new work with the post-rotenone stickleback introductions, and that project sounds really exciting.Ben Hallerhttps://www.blogger.com/profile/17875404974157070805noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-75441373835185914702022-07-21T03:19:09.829-04:002022-07-21T03:19:09.829-04:00Really insightful Andrew. You are not alone. How m...Really insightful Andrew. You are not alone. How many others are feeling the same? I know I am. In this ever ratcheting climate of field research logistics something's got to give. Many fieldstations are suffering from underuse since their heydays decades ago and the efforts to maintain multiple field programs is just overwhelming. I wonder what the long term COVID effects will be on natural field sciences as researchers streamline their programs. Hans Larssonhttps://www.blogger.com/profile/13716626635965458510noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-90440333793517020262022-06-08T07:11:07.901-04:002022-06-08T07:11:07.901-04:00This comment has been removed by the author.Chris Leonardhttps://www.blogger.com/profile/09692988042787256294noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-40930271815225251102022-06-08T07:10:31.527-04:002022-06-08T07:10:31.527-04:00I'd be happy to elaborate more on this, but I ...I'd be happy to elaborate more on this, but I was involved in launching a product for journal editors which took the heavy lifting out of this procedure. We indexed preprints from publicly available servers, did some concept extraction on each one, and used these concepts to match preprints to journals (each journal had its own semantic fingerprint based on concepts from manuscripts it has published in the last 3 years). We even evaluated language and reference recency to help further refine this - and editors simply picked the preprints they wanted to invite to submit to their journal. We even allowed automated sending of email invitations somewhat following the example in this blog post.<br />However, we had seriously underestimated the number or proportion of preprints which had already been submitted to a journal by the time they are available on the preprint server. it seems the explosion in popularity of preprints is at least partially down to the fact that people are happier submitting to a journal and preprint server *at the same time*. This is different to how preprints were envisioned to be used when arXiv was set up. <br />This problem needs to be fixed before preprints can be thought to be a serious source of submissions for journals. Happy to hear any thoughts on how this could be done.Chris Leonardhttps://www.blogger.com/profile/09692988042787256294noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-34784551606702182982022-06-04T18:53:40.680-04:002022-06-04T18:53:40.680-04:00Thanks for these remarks. I'm a philosopher o...Thanks for these remarks. I'm a philosopher of science, and for me, being able to read the source code that was used in paper is often invaluable--for example for understanding how scientists use relationships between probabilities in simulations, statistical methods, and biological processes. This is is a little bit like being a student or a postdoc--so my point is related to F2--but I'm often asking different questions than scientists would ask. I know I'm not part of the usual target audience for scientific papers, however. Perhaps another benefit of providing code is like the benefit of potentially irrelevant methods information ("we fed the rabbits with Purina Kibble #5"); you never know what might turn out to make a difference. Some library routines turn out to have bugs later.mars0ihttps://www.blogger.com/profile/05791487029413606315noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-67829196675318018422022-04-11T15:53:23.745-04:002022-04-11T15:53:23.745-04:00The post above sounds like a rant (and it is, a bi...The post above sounds like a rant (and it is, a bit), but I do generally like the idea of scouting, I just think the idea (and publishing in general) could make use of some more sensible policies.Dacehttps://www.blogger.com/profile/17432988016546917519noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-10070344352517363132022-04-11T14:54:05.117-04:002022-04-11T14:54:05.117-04:00" it is frustrating to authors to receive a s..." it is frustrating to authors to receive a solicitation for a preprint that must be extensively reformatted prior to submission. "<br /><br />I would be livid if I were invited to submit a specific paper only to be told that I must rewrite/reformat it. In my opinion, journals often emphasize the wrong formatting at the wrong stage. The first stage of review should be strictly about the science, who cares if you didn't format your sections properly. The second step, peer review, I would argue should simply remove any identifying information; _maybe_ insist on small formatting changes (like choice of font).<br /><br />Now, I understand the counterargument: that certain authors might format in certain ways and therefore compromise the anonymity, but chances are, if you are so familiar with a field of work that you are being asked to review a paper, you are probably familiar with the research groups in the field and what they study. I can't imagine someone would recognize a specific group based on the formatting of their preprints alone. If a preprint is already publicly available, then the chances of anonymity being compromised is already high.<br /><br />I may be a bit biased as I recently submitted a paper, and a journal made me:<br />1. Trim 3 pages<br />2. Convert all images to grey scale<br />3. Move all figures and tables to a separate document<br />4. Move the bibliography to a separate document<br />5. Change the overall layout (two-column, add line numbers, specified margin, and font etc.)<br /><br />And after all that, they decided it wasn't appropriate topic for the journal and rejected it without sending it for review.<br /><br />As for whether to "flag" an invited paper, I think this would be mandatory, for exactly the reasons stated, but also because if a scout is inviting the wrong sort of papers, there should be a mechanism that the editors can have to try to evaluate why/how this paper was submitted. Flagging the paper also gives the scout an opportunity to clarify why the paper was invited. Whether or not reviewers should be able to see the flag: I would lean towards no, as it might bias their opinion.Dacehttps://www.blogger.com/profile/17432988016546917519noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-34352898799000137272022-03-22T11:18:07.546-04:002022-03-22T11:18:07.546-04:00Thanks Amanda for a wonderfully written journey th...Thanks Amanda for a wonderfully written journey through the reality of doing science...and the power of collaboration and lateral thinking- I hope The Art of the Pivot is found by aspiring scientists everywhere. Anonymoushttps://www.blogger.com/profile/05761449200548712145noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-76338868090811343662022-03-02T11:15:17.592-05:002022-03-02T11:15:17.592-05:00I think it is fine to promote our own students dis...I think it is fine to promote our own students disproportionately, but in doing so I see no need to "claim" them. This applies mostly to PAST trainees - not current ones. For instance, I tend to retweet posts of my former students - without adding to those posts that they are my "former student."Andrew Hendryhttps://www.blogger.com/profile/03653724437118653645noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-58639239794712523212022-02-24T20:29:26.702-05:002022-02-24T20:29:26.702-05:00Surely, by the same logic, you should make sure to...Surely, by the same logic, you should make sure to mention/congratulate everyone equally, regardless of whether they're your trainee or not? After all, if your mentions and congratulations disproportionately go towards your own trainees, other people are going to realize that, even if you avoid use of phrases like "my student" or "my postdoc". Dr. Foxhttps://www.blogger.com/profile/02948439373673427525noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-18049447592290596782021-12-09T09:06:24.341-05:002021-12-09T09:06:24.341-05:00One basic but very important question/consideratio...One basic but very important question/consideration is what about Stochastic models. They cannot/should not be expected to produce the exact same result when run again. In the Rationale it is mentioned the code should provide the exact same results if someone downloads the data and runs the code on their computer. Many of the important modelling approaches employed by ecologists (i.e. MCMC) are stochastic, therefore the resulting output is expected to change with each run. Is there consideration for the inherent randomness encapsulated by stochastic models, surely some guidance or clarification is warranted to explain when someone provides code for their stochastic model, another user should not expect the exact same result. Anonymoushttps://www.blogger.com/profile/03205694489667739761noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-87622885620915073292021-10-20T02:15:51.663-04:002021-10-20T02:15:51.663-04:00A very astute and forward-looking analysis of the ...A very astute and forward-looking analysis of the rotten publication system we have to deal with today. Indeed, scientific *societies* have missed the opportunity of using *social* media to reinvent themselves, just as our scholarly communities in general seem to have buried their heads in the proverbial sand since about 1995, pretending that everything that happens around the ivory tower doesn't concern us. Now we will have to pay the price for this digital hibernation. Many have mentioned the parallel to the climate crisis, where humanity has been similarly oblivious to the numerous opportunities to obtain change for cheap.<br />Björn BrembsUnknownhttps://www.blogger.com/profile/08407252791464596913noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-2440555462690057842021-06-16T20:48:02.921-04:002021-06-16T20:48:02.921-04:00I dunno, actually. All of this adds overhead; it ...I dunno, actually. All of this adds overhead; it will slow down your work, and so you'll get less done during the time you have left to live. It also requires frequent reviewing and updating; it's not a one-time task, but *continuous* overhead. It would often be unnecessary overhead; sudden, accidental death can certainly happen, but my guess is that the majority of scientists will have at least some warning of their impending death (if not retirement plans!), and will be able to put their affairs in order when that time comes. And it's depressing, demoralizing, and fear-inducing, which also has costs in terms of stress, productivity, etc. And I suspect most of these details – who the mentorship of a student passes on to, say – will get worked out just fine when the time comes, and trying to pre-plan it won't really add much. Life is unpredictable; you might plan that student A will move on to supervisor B in the event of your death, but when you die, maybe supervisor B is busy, or on sabbatical, or themselves deceased, or maybe new faculty member C has just joined the department, needs new lab members, and is a better fit for the student anyway. Can such things really be planned? I'd say there are a few key things that *are* worth making sure of: most notably, that somebody else has your passwords and can get in to your machine, your GitHub, your Dropbox, etc., to access your files. Beyond that, I'm maybe a bit skeptical that this really makes sense. (But happy to hear counterarguments!)Ben Hallerhttps://www.blogger.com/profile/17875404974157070805noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-74886375566064688602021-05-19T13:26:52.101-04:002021-05-19T13:26:52.101-04:00I'm not Dan but am an editor-in-chief of a jou...I'm not Dan but am an editor-in-chief of a journal and have dealt with retractions, so can I have a go at your questions?<br /><br />1. "What are the journals going to do?" No editor or reviewer could have been expected to catch the well-hidden data fabrications within individual papers by Pruitt. I don't think anyone involved in the prepublication peer review of those papers was at fault or has earned any kind of warning. I think the lessons are that postpublication peer review is important and necessary, and that obligatory data sharing in public repositories is a necessary step toward postpublication review that's open and transparent. <br /><br />2. "Why would someone do this? This culture of publication-at-any-cost, is deeply troubling." I agree the first question is important, and the second statement may be true, but I don't think they necessarily have anything to do with each other in this case. Indeed, this is letting Pruitt off the hook with a Twinkie-style defense. There have always been incentives to cut corners, cherry-pick results, or fake data, but the vast majority of researchers don't do these things. I don't think Twinkies made Pruitt do it. Hoping the report by McMaster will tell us more.Anonymoushttps://www.blogger.com/profile/11633706023670019209noreply@blogger.comtag:blogger.com,1999:blog-4456348657596914237.post-89081921626190988592021-05-19T00:31:42.583-04:002021-05-19T00:31:42.583-04:00Dear Dan,
Thank you for a detailed account of the...Dear Dan, <br />Thank you for a detailed account of the whole incident. There are a lot of learning lessons here, for researchers of every age. I have two questions:<br /><br />1. What's your take on the review process from this incident? How to make it stronger so that the problematic manuscripts don't pass through the gaps? Where does the buck stop in such cases? Without blaming anyone who was involved in the reviewing and publishing process, how can we make the process more resilient? More specifically, should the reviewers and associate/handling editors of those particular manuscript be gently warned? What are the journals going to do? Have such talks have been happening in the closed-door meetings? <br /><br />2. If the data were fabricated, what does it say about the culture of scientific research? The 'why' question is important. Why would someone do this? This culture of publication-at-any-cost, is deeply troubling. The culture of more and higher of everything -- grants, impact factor, publications, chairs, committees -- could be toxic. How does/should the fraternity deal with that? In the end, are we going to rely merely on an individual's scientific integrity or can we create better structures to avoid these falls?<br /><br />I am an early career scientist. You can understand my worries and dismay seeing this case.Ahttps://www.blogger.com/profile/07325146951316044741noreply@blogger.com