A Blog Around The Clock

Welcome to the first experimental issue of the newest science blog carnival – Praxis. Why experimental? Because we still have to see where to set the boundaries. If it is “Life in Academia”, then pretty much everything on science blogs is eligible and the effect is diluted. If we narrow it down to one topic, e.g., Open Access publishing, then there will not be sufficient posts and sufficient interest to keep the carnival alive. We’ll have to define a happy middle. We want people to find each other here – folks that write about the business of science, about publishing and Science 2.0, about survival in the Academia, as we can all learn from each other and help each other. So, we would appreciate your feedback about this so the future hosts (and I hope you will volunteer to be one – just e-mail me) can tighten it up for everyone’s enjoyment.
I have received a number of entries and have added a few more of my own choice. As is often the case with the very first edition of a carnival, old classic posts were eligible so quite a few of those are presented here. Starting with edition #2 next month, only posts written in the interim time will be eligible so get busy writing!
Doing Science
Peter Dawson Buckland: …only limited by imagination.” An interview with Kevin Zelnio:

It’s hard to say. I think it lots of cases there is a culture that teaches young scientists that it is a waste of time. Your time is better-spent writing grants and papers. That is what gets you jobs. Sure, after working all morning, day and night most scientists don’t want to go home and then write about science for free or for few readers whom they do no know. There is no reward structure for communication. Many funding agencies have requirements for “broader impacts”, but a lot of it BS. Some well-known scientists have excellent programs in place. I’m lucky enough to have an advisor who supports communication to a certain degree. He definitely doesn’t approve of me blogging, but we do tours and talks for teachers and grade school students, I judge science fairs, that sort of thing.

Cameron Neylon: A new way of looking at science?:

I’ve spent a long time talking about two things that our LaBLog enables, or rather that it should enable. One is that by changing the way we view the record we can look at our results and materials in a new way. The second is that we want to enable a machine to read the lab book.

Anne-Marie: Belize Update #2:

Lesson 3: I have discovered the wonders of Machete Therapy. If you have anything bothering you, stressing you out, weighing on your mind, just take on 100 m transects of jungle with a machete. It is astoundingly cathartic. Not sure what this says about me? I do hate that we have to leave even a small swath of destruction to do the habitat surveys, but all the data is being put towards conservation research.

Career Choices and Getting Funded
DrugMonkey: NIH Basics: The Study Section:

Let’s start with the NIH study section and how you should go about educating yourself with the information that you need to guide your own grant writing.

Pawel Szczesny: Freelancing science – today and tomorrow:

In response to recent Neil’s comment and questions that repeat in emails, I’ve decided to describe in little more detail my status as a freelancing scientist. However keep in mind that I have no idea about such arrangement outside of Poland, so it is likely that some things may look different in other countries.

Cath@VWXYNot: Finding the alternative within academia:

Hopefully the advice above will help you to make that first step into your new career. But don’t stop now! Your first non-academic position is unlikely to be the amazing dream job that you will do for the rest of your life, but it will expose you to another, broader, range of experiences. For example, as well as the grant writing that is my day-to-day focus, my new job also gets me involved in public relations, website design and intellectual property issues. I haven’t quite figured out which parts I enjoy the most (definitely not intellectual property!), but you can bet that as soon as I do, I’ll start volunteering for more of it.

Alex Palazzo: A way to break out of the pyramid scheme:

One obvious way to prevent such pyramid schemes is to stop the flow of postdocs going up by providing them with career paths at the postdoc level. The result – fewer PIs, more bench scientists, more stability for junior scientists.

Samia: HERRRP ME.:

I could give you all the boring background, but it all boils down to choosing between two labs.

DrugMonkey: Are Stable Research Career Tracks the Solution to “Structural Disequilibria” in the NIH Racket?:

The fact of the matter is that many, many Ph.D. wielding individuals are in the process of serving out such a career. The trouble is that it is not a stable, formal job category. So anyone who makes it to retirement, does so by matter of a series of accidental or lucky steps in joining a lab or labs that can sustain the stable level of funding that is required to maintain very senior Ph.D. level non-PI scientists. This makes this particular ambition a fairly dodgy one.

Presenting Data
Scicurious: And Now, a Powerpoint Presentation:

In the afternoon session, I got bored. And in my boredom and jetlag, I have compiled a list. A list of things that you shall NOT do during your big presentation in front of 350 people.

David Ng: The ‘speaking publicly’ list formulized (plus a bit with some clown humour):

The response for the “Things to avoid at all cost when speaking publicly” post was awesome, and so, I’ve tried to formalize the suggestions into a fairly definitive list. The ones that didn’t make it tended to be more debatable, although admittedly, there are few in the list right now that sort of sit on the threshold of that parameter (I’m think about stuff like “winging it” or being “arrogant”).

Coturnix: What makes a memorable poster, or, when should you water your flowers?:

But even apart from one’s own interests, there are some posters that remain forever in one’s memory. I tried to think what was it about those particular posters that made them so memorable to me and to see if any general rules can be drawn out of them.

Sharing and Networking
Cath@VWXYNot: Networking: the basics:

People. People connected to you and to each other. Even if your primary network is quite small, each person in it will connect you to others who you may never have met or even heard of.

Michael Nielsen: The Future of Science:

An ideal collaboration market will enable just such an exchange of questions and ideas. It will bake in metrics of contribution so participants can demonstrate the impact their work is having. Contributions will be archived, timestamped, and signed, so it’s clear who said what, and when. Combined with high quality filtering and search tools, the result will be an open culture of trust which gives scientists a real incentive to outsource problems, and contribute in areas where they have a great comparative advantage. This will change science.

Shirley Wu: Envisioning the scientific community as One Big Lab:

The idea behind One Big Lab is that the scientific community should act as, well, one big lab, sharing resources when it makes sense, and everyone, especially the community as a whole, benefits.

Cameron Neylon: The science exchange:

Turning the funding system on its head is probably not viable and while it makes a nice thought experiment I’m sure there are many reasons why its a terrible idea. What we need to do is find research funders who are serious about increasing their return on investment; not in terms of money, but in terms of results; in terms of science. I think if we can do that, and convince someone of the case for a return on their investment, the rest of the technical problems will be pretty straightforward to crack.

Coturnix: The Scientific Paper: past, present and probable future:

Science has some very conservative elements (in a non-political sense of the term) that will resist change. They will denigrate online contributions unless they are peer-reviewed in a traditional sense and published in a reputable journal in the traditional format of a scientific paper. Some will retire and die out. Others can be reformed. But such reforming takes patience and careful hand-holding.

Pedro Beltrao: Post-publication journals:

No single individual wants to go through all published literature to find the useful information but together we effectively do this. The challenge is how to evaluate specific articles by a combination of metrics to promote them to wider audiences in a way that is not easy to exploit. Kevin Kelly said recently in a Ted Talk that “The price of total personalization is total transparency”. Would this bother scientists ? Lets say that a few science publishers get together with some of these scientific social sites (social networks, bookmarking sites) to mimic the Frontiers model in a larger scale. Users would install a browser plugin that would link their scientific profile and social contacts with their reading activity. The publishers could then use this information to create personal reading hubs for users.

John Wilbanks: On the Erosion of the Public Domain:

The public domain is not contractually constructed. It just is. It cannot be made more free, only less free. And if we start a culture of licensing and enclosing the public domain (stuff that is actually already free, like the human genome) in the name of “freedom” we’re playing a dangerous game.

Jean-Claude Bradley: Open Notebook Science:

It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.

Cameron Neylon: Facebooks for scientists – they’re breeding like rabbits! and An open letter to the developers of Social Network and ‘Web 2.0’ tools for scientists:

I will also be up front and say that I have an agenda on this. I would like to see a portable and agreed data model that would enable people to utilise the best features of all these services without having to rebuild their network within each site. This approach is very much part of the data portability agenda and would probably have profound implications for the design architecture of your site. My feeling, however, is that this would be the most productive architectural approach. It does not mean that I am right of course and I am prepared to be convinced otherwise if the arguments are strong.

Ethan Zuckerman: The complexity of sharing scientific databases:

Under US law, pretty much anything you write down is copyrighted. Scrawl an original note on a napkin and it’s protected until 70 years after your death. Facts, however, are another matter – they can’t be copyrighted. So while trivial but creative scribblings are copyrighted, unless you choose to release them into the public domain, the information painstakingly discovered about the human genome – DNA sequences, for instance – aren’t. But the containers they’re stored in – the databases they’re held in – can be copyrighted.

Deepak Singh: The commons and the anticommons:

I am not quite sure I agree with the entire premise. While in certain areas, I do believe in the tragedy of the commons, that is not true for the fundamental scientific data talked about on this blog. The only tragedy that can occur there is not allowing people to use the underlying data to not just innovate, but also learn. What we do with the discoveries we make, perhaps a new drug, an innovative idea on how we can leverage nature’s blueprint, is where we need to develop “property rights”, but we should not forget the anticommons when we do so.

Chad Orzel: Peer Review Does Not Define Science:

Peer review is an important part of the modern scientific establishment, but peer review is not the core of science. Holding peer review as the only standard for what counts as doing science is a step toward making a scientific guild system, which is something we absolutely do not want.

Dr. Free-Ride: Peer review and science and Objectivity and other people:

What’s the point of the peer review process? The goal is to figure out what we agree upon and to filter out the influence of subjective preference as much as possible. Which parts of how the world seems to me are due to the world, and which are due to my subjective preferences? The parts we tend to agree on might be the best candidates for the features of our experience that correspond to real features of the world.

Getting Published
Jonathan Eisen: Why I am ashamed to have a paper in Science:

So I just had a paper published in Science last week. In many ways, it has all the makings of one of those papers I should be really proud of….

Rock Doctor: Publish well or perish??:

The long and short of it is that it is no longer good enough to do good research and publish, now you must publish properly or you may become so much chattel alongside the academic road.

Pawel Szczesny: By any measure I’m average at most:

Reputation-wise I’m going to be in the middle unless I will make something extraordinary. But honestly to make a scientific breakthrough the last thing I need is a number describing quality of my thinking.

Coturnix: On my last scientific paper, I was both a stunt-man and the make-up artist:

But now, when science has become such a collaborative enterprise and single-author papers are becoming a rarity, when a 12-author paper turns no heads and 100-author papers are showing up more and more, it has become necessary to put some order in the question of authorship.

The Publishing Business
Bill Hooker: The Future of Science is Open, Part 1: Open Access, The Future of Science is Open, Part 2: Open Science and The Future of Science is Open, Part 3: An Open Science World:

I’ve never had an idea that couldn’t be improved by sharing it with as many people as possible — and I don’t think anyone else has, either. That’s why I have become interested in the various “Open” movements making increasing inroads into the practice of modern science.

Richard Akerman: My article on peer review for Nature:

One of my main concerns is that Wisdom of Crowds is sometimes oversold, in the way that Service-Oriented Architecture (SOA) is. Just put together a system, sprinkle some magic Wisdom of Crowds dust on it, and hey presto, the system is continuously improved by everyone who uses it.

Frank Norman: Who needs information skills?:

In my early days as a librarian I envied the information wizards who performed online literature searches – they had mastered the arcane system commands and database indexing and could react quickly to adjust their search as results came through. Then I became a wizard myself and enjoyed being able to pull bibliographic rabbits out of digital hats. When disintermediation hit, searching moved from the esoteric to the commonplace. Everyone could have a go at it and they did.

Bjoern Brembs: Journals – the dinosaurs of scientific communication:

Today’s system of scientific journals started as a way to effectively use a scarce resource, printed paper. Soon thereafter, the publishers realized there were big bucks to be made and increased the number of journals to today’s approx. 24,000. Today, there is no technical reason any more why you couldn’t have all the 2.5 million papers science puts out every year in a single database. It doesn’t take an Einstein to realize that PLoS One is currently the only contender in the race for who will provide this database. For all the involved, it is equally clear what the many advantages of such a database would be. Consequently, traditional publishers are rightfully concerned that their customerbase is slowly dissappearing.

Kevin Zelnio: Free Access to Internet Resources Helps Conservation:

There were several conclusions drawn about plant conservation, but here is a tidbit about how free access to information helped in assessing conservation status.

Bill Hooker: An Open Access partisan’s view of ‘Electronic Publication and the Narrowing of Science and Scholarship’:

In fact, the comparison between print and online access is barely even possible when considering Open Access information. The same considerations of cost — who can afford to read what — apply to commercial print and online publications, but free online information has essentially no print ancestor or equivalent. Few if any scholarly journals were ever free in print, so there’s a huge difference between conversion from commercial print to commercial online on the one hand, and from commercial print to Open Access on the other.

Coturnix: Historical OA:

In discussions of Open Access, we always focus on brand new papers and how to make them freely available for readers around the world as well as for people who want to mine and reanalyse the data using robots. But we almost never discuss the need to make the old stuff available. Yet we often lament that nobody reads or cites anything older than five years. Spending several years reading everything published in the field in the 20th century up until about 1995 (as well as some 19th century stuff) helped me greatly in my own research. It would help others, I’m sure, especially those who are now revisiting old questions with new techniques. How are the classical papers going to be made available for today’s students?

Science Communication and Education
John Hawks: How to blog, get tenure and prosper: Starting the blog, Graduate students and blogging and How to blog, get tenure and prosper: A very useful engine:

Science is ultimately a social activity that progresses toward greater understanding. Blogging is also a social activity, which can serve the ends of science, if you apply your expertise. What is more, by incorporating the content management paradigm into your workflow, you can maintain a blog with very minimal work.

Maddox2: Advice on Freelance Science Writing:

I know some of these seem like no-brainers, and I hope I haven’t offended anyone. If I did, I apologize in advance 🙂 But as I said, I have had freelance writers violate every single one of the points above at one point or another…so maybe they’re not as no-brainer as we’d like to think.

Coturnix: Scientists are Excellent Communicators (‘Sizzle’ follow-up):

Or should we just leave the MSM to rot and die, and put our efforts into new media, the kind in which there is no intermediate (who may believe that he-said-she-said journalism is the way to go) but the communication is many-to-many with instant feedback? Because in such an environment scientists are experts and seen as authorities and listened to and believed.

Abel Pharmboy: Is organic chemistry still relevant in the pre-medical curriculum?:

An old professor bud of mine compared professional education to building a retaining wall. One first digs a trench and put several layers of pilings in the whole which are then covered up. No one sees them, but they are the foundation upon which the rest of the wall stands. How easy is it then to decide what pilings are needed for success in today’s physicians?

Panthera studentessa: Reducing research culture shock in undergrads:

Research is so fundamental to a science education that I don’t know why we aren’t being taught how to do it much earlier. Our brains are filled with facts about what other people have already discovered, but many of us aren’t learning how to make our own discoveries as well. Instead of learning to know and regurgitate the right answer, maybe we should be learning how to figure it out on our own.

Jennifer Rohn: In which I am utterly Fooed:

The chaotic nature of the entire event was equally evident in the session I helped organize with SF novelist John Gilbey and pseudoscience basher Ben Goldacre called ‘Seducing the Public with Science. (Ben wanted to call it ‘Pimping Science’ or ‘Seducing the Pubic’ but was gently overruled.) Someone spontaneously decided to summarize the unfolding discussion on the white board and, as you can see from the figure above, what it lacked in coherence it made up for in raw enthusiasm.

Academic Atmosphere
Zuska: Locking the Barn Door:

You are a university president. You naturally wish to avoid scandal and negative publicity during your administration. The time to make it mandatory for all faculty and staff to undergo training in how to avoid sexual harassment is:
A: When you take office, or shortly thereafter.
B: After one of your professors is caught emailing female students a quid pro quo: A’s if they would expose their breasts and allow him to fondle them.

Anna Kushnir: Horror Stories, of the Scientific Variety:

A few questions came to mind after listening to these stories (they weren’t really delivered as stories. More like ranty monologues with shaking hands and dangerously-tilted wine glasses). The first question had too many expletives to reproduce here. The second was, “How do you do that?” How do you scoop people you see on a daily basis? I understand that the funding crisis really is, at this point, a crisis. I understand that jobs are painfully difficult to come by. What I don’t understand is when and where ethics and common decency slip out the door.

Sunil: Postdoc personalities:

Postdocs come in all shapes, sizes and characters, but there are a few character types you want to avoid hanging out with (even if you are one of them), in order to remain sane and content. Surprisingly, like most normal people, postdocs too fit into some characteristic groups (including those you want to avoid). So here are some of the classes of postdocs whom I do my best to avoid (and hope never to become).

Rhea Miller: Vow to never become Jaded…:

I really only notice these attributes in young scientists, i.e. graduate students and post-docs. Does this mean that the Jaded ones eventually give-up, get use to it, change their prospectives, or do they hide that inner Jaded color as they progress?? Or maybe it’s just that grad students/postdocs can’t seem to see the light at the end of the tunnel until they get there??

Special topic of the month: Animal Research
DrugMonkey: Animals in Research: The conversation begins, Animals in Research: IACUC Oversight and Animals in Research: Guide for the Care and Use of Laboratory Animals:

This brings me to what may be a personal view. I believe that everyone that works with research animals has not merely the right, but rather the obligation to report situations that appear to compromise the health and welfare of the research animals.

Dr. Free-Ride: When the tactics become the message:

Maybe some of the groups involved in firebombing and other violent attacks used to have a point worth taking seriously. At this point, their violent tactics have become their message.

Orac: Animal rights terrorists firebomb a researcher’s house:

Also, comparing animal rights terrorists with civil rights advocates in the 1950s and 1960s is an insult to the memory of those nonviolent protesters who, sometimes at great personal risk, spoke out against injustice. Vlasak’s cowardly little band of animal rights terrorists are far more akin to the Ku Klux Klan and white power rangers who used violence to try to stop the civil rights marchers. They’re far more akin to the criminals who bombed the 16th Street Baptist Church in 1963 and other thugs who tried to stop the civil rights movement through violence and terrorism. They are scum.

Abel Pharmboy: Escalating lunacy:

Yes, Capt Clark, a logic transplant would indeed be necessary.

Matt Springer: Defending Science:

But as far as I can tell, there’s only one research subject that has a real chance of getting a scientist murdered.

Scicurious: Animal Research:

Animal research is a necessary part of medical progress. But that doesn’t give us the right to go cutting into any animal we like. There are strict rules in place to ensure that the animals we use are treated in the best possible way. The researchers I work with are incredibly compassionate people, but there is also a practical reason. A suffering animal is not going to give you good data, and an animal that is not healthy can show a different reaction to a drug. It is in the best interest of science that the animals we use be well treated.

Acmegirl: Support the People Who Do Animal Research:

I don’t work with animals. But I have done so in the past, and I can honestly say that it is not like what you see in the movies. There is training, protocols to be evaluated, logs, etc. A researcher doesn’t just have cages and tanks with random animals hanging around for them to tinker with for no good reason than a whim. Everything is planned, regulated and overseen.

drdrA: Firebombings and such:

Drugmonkey has a nice post up about this topic- and well, since I actually teach a couple of hours on the ethical use of animals in research to graduate students in biomedical sciences, medical students and sometimes undergraduates, I thought I would add my two cents worth as well. First, there is a very useful chapter about this very subject in a book entitled ‘Scientific Integrity’ by Francis Macrina… I believe that the operative section is chapter 6- ‘Use of Animals in Biomedical Experimentation’, much of what I have written below is taken from this chapter. I would like to have students leave my class with a basic understanding in a couple of areas.

Sandra Porter: Support animal research, save lives, Book review: ‘The Animal Research War’, Handling research animals: taking courses and learning how to be kind and More thoughts on animal research: Pets and wild animals benefit, too:

What do these cases have to do with animal research? In the United States, animal vaccines are regulated by the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS), Center for Veterinary Biologics (CVB). Like the vaccines produced for humans, the vaccines produced for animals must be pure, potent, safe, and they must work. This means that all the vaccines that are given to your pets, agricultural animals, and wild animals were tested on lab animals to make sure that the vaccines are safe and that they work.

The next edition of Praxis will alight on Life v. 3.0 blog on 15th of September, 2008, so get writing and submit your posts.