Making Science More Open Access

Michael Eisen over at his blog it is NOT junk wrote a post about a talk he gave recently asking for a more open science. It was primarily directed at tenured faculty, and focused on increasing access, reducing the importance of impact factors and fixing the peer-review system.

He mentioned the six tenants of what he called The Mission Bay Manifesto, and how if the faculty together agree to this then substantive change is possible:

(1) We will make everything we write immediate freely available as soon as it is finished using “preprint” servers like,, or the equivalent. 

(2) No paper we write, or data or tools we produce, will ever, for even one second, be placed behind a paywall where they are inaccessible to even one scientists, teacher, student, health care provider, patient or interested member of the public. 

(3) We will never refer to journal titles when discussing my work in talks, on my CV, in job or grant application, or any other context. We will provide only a title, a list of authors and publicly available link for all of my papers on CVs, job and grant applications.

(4) We will evaluate the work of other scientists based exclusively on the quality of their work, not on where they have published it. We will never refer to journal titles or use journal titles as a proxy for quality when evaluating the work of other scientists in any context.

(5) We will abandon the slow, cumbersome and distorting practice of pre-publication peer review and exclusively engage in open post-publication peer review as an author and reviewer (e.g. as practiced by journals like F1000 Research, The Winnower and others, or review sites like PubPeer). 

(6) We will join with my colleagues and collectively make our stance on these issues public, and will follow this pledge without fail so that our students, postdocs and other trainees who are still building their careers do not suffer while we work to fix a broken system we have created and allowed to fester.


Interesting tenants well worth considering! Check it out!

Why isn’t the Mars rover heading towards the liquid water? MICROBES

As I’m sure you noticed, NASA has found liquid water on Mars! Given that here on Earth we have found life in some fairly inhospitable places, this renews hope for Martian life!

Many people have wondered, why aren’t we sending the Curiosity Rover right on over to check it out? I mean what is that little guy doing up there that is more important than LIFE!

There are two reasons:

  1. The rover doesn’t move very far very fast. Even with the lack of traffic, it would take about a year to cover the 150km to get to our new putative Martian fountain of life.
  2. Microbes

Even though anything that leaves Earth for space exploration is scrubbed thoroughly to remove any potential bacterial contaminates, there can still be some hitchhikers. So we won’t send the rover over to investigate, just in case we end up seeding Mars with Earth Microbes. Read about it over at NPR.


Please note, this renews my interest in pursuing a career in microbial ecology. So that I can go study the microbial ecology ON MARS.


How to spot a fraud

Carl Sagan was a vocal proponent of science, among many many other things. One of his great legacies are a series of spectacular popular science books.

A recent post over at Brain Pickings recounts a chapter from Sagan’s The Demon-Haunted World: Science as a Candle in the Dark entitled “The Fine Art of Baloney Detection”. In this chapter Sagan reflects on the many frauds that claim to be fact, or science.  Rather than attempt to defraud each fraud individually, Sagan gave us a the tools to arm ourselves against being deceived by fraud, allowing us to grow and defraud liars ourselves.

He called it a “baloney detection kit”, and by adopting the kit we are able to shield ourselves against deliberate manipulation. Below I have listed nine of these tools (or read all about all of them here):


  1. Wherever possible there must be independent confirmation of the “facts.”
  2. Encourage substantive debate on the evidence by knowledgeable proponents of all points of view.
  3. Arguments from authority carry little weight — “authorities” have made mistakes in the past. They will do so again in the future. Perhaps a better way to say it is that in science there are no authorities; at most, there are experts.
  4. Spin more than one hypothesis. If there’s something to be explained, think of all the different ways in which it could be explained. Then think of tests by which you might systematically disprove each of the alternatives. What survives, the hypothesis that resists disproof in this Darwinian selection among “multiple working hypotheses,” has a much better chance of being the right answer than if you had simply run with the first idea that caught your fancy.
  5. Try not to get overly attached to a hypothesis just because it’s yours. It’s only a way station in the pursuit of knowledge. Ask yourself why you like the idea. Compare it fairly with the alternatives. See if you can find reasons for rejecting it. If you don’t, others will.
  6. Quantify. If whatever it is you’re explaining has some measure, some numerical quantity attached to it, you’ll be much better able to discriminate among competing hypotheses. What is vague and qualitative is open to many explanations. Of course there are truths to be sought in the many qualitative issues we are obliged to confront, but finding them is more challenging.
  7. If there’s a chain of argument, every link in the chain must work (including the premise) — not just most of them.
  8. Occam’s Razor. This convenient rule-of-thumb urges us when faced with two hypotheses that explain the data equally well to choose the simpler.
  9. Always ask whether the hypothesis can be, at least in principle, falsified. Propositions that are untestable, unfalsifiable are not worth much. Consider the grand idea that our Universe and everything in it is just an elementary particle — an electron, say — in a much bigger Cosmos. But if we can never acquire information from outside our Universe, is not the idea incapable of disproof? You must be able to check assertions out. Inveterate skeptics must be given the chance to follow your reasoning, to duplicate your experiments and see if they get the same result.


Thanks Dr. Sagan, we are forever grateful!

Sharks are not as deadly as selfies

So far this year, sharks have killed fewer people than selfies. Read about it here.

This could be a post about how we as a society are far too afraid of sharks.

But given that this year alone taking a selfie with a bison has caused injury, and Waterton Canyon park in Colorado closed because too many people were taking selfies with bears, maybe this should be a post about safety protocols while taking selfies.

But it turns out someone has done that already…

How about instead, I once again direct your attention to trying to take a selfie with a more innocuous organism!



Pigpen actually resembles… everyone you know

You know Pig-Pen? That adorable little guy from the Peanuts cartoons who has a cloud of dirt perpetually surround him? Well, it turns out he looks a lot like everyone you know.

We may not be walking around in a cloud of dirt, but it turns out, we are all walking around in a cloud of microorganisms. That we are spewing out. Into the air around us. Constantly.

The field of microbiology has been finding microbes inside and on top of us for years now (thank you advances in sequencing), this is the the first time it has been demonstrated that we are spewing microbes into the air around us.

Read about it over at NPR.

Or read the original article over at PeerJ.


A Postdoc is an Expression of Love for the Pursuit of Knowledge

One of our contributors just published an EXCELLENT article about what it means to be a postdoc.

How do you explain this position to non-academics? What is it exactly that you are doing? And when are you going to be able to get a financially secure long term job (it is not looking good out there…)

Jeremy also explains what his postdoc has looked like so far, and what he plans (hopes) to do in the future. And he ends his piece with one of my new favorite quotes about the postdoc:

“But I like what I do in academic research, and I think it’s worth doing. If nothing else, a postdoc should be an expression of love for the pursuit of knowledge. Times being what they are, it must also be an expression of hope. ”




Good News! Biologists aren’t replaceable

Self-driving cars, online “fem bots” and auto piloted planes.

As technology gets better, more and more jobs are taken by automation/robots (awesome video about it here).

But I come bearing good news! According to an interactive website over at the BBC, biologists have a fairly low risk of becoming automated. Good news for the job market!

Read about it here, or just play with all the different positions and how they know what will and will not become automated.