Public Articles
Lessons on Sharing from Bacteria
A recent article in Nature Communications \cite{Benomar_2015} is extremely informative.
Like many good studies, it takes assumed fixtures or mainstays of a field (in this case isolated culturing in microbiology), flips them in some way, and arrives at novel observations and conclusions.
Bacteria have usually been studied in single culture in rich media or in specific starvation conditions. These studies have contributed to understanding and characterizing their metabolism. However, they coexist in nature with other microorganisms and form consortia in which they interact to build an advanced society that drives key biogeochemical cycles.
Briefly, the authors showed co-cultured bacteria (i.e. two different species from the same environment were grown together) formed physical connections with each other to allow one species to harness the other’s unique metabolic chemistry when the former could not survive under the given starvation conditions. In turn, the donor species growth was elevated compared to isolation due to accessing it’s partners’ own metabolites.
The researchers got some great pictures.
Working on a Ph.D.? There may not be an academic job for you at the end of the tunnel.
This blog post is part of a series called Is Academia Broken? This is the second in the series and it discusses the overabundance of PhDs compared to the number of available academic openings. The first blog post, on the perils of doing interdisciplinary research early in your career, can be found here.
Disseminate Better
So you actually want your research read...
Every year in science, tech, and medicine, on the order of 2 million papers are published.
That’s a lot of papers.
To remain current with their field, physicians must read about 20 papers a day. Given the growing “scourge” of cross-disciplinary science and the interconnectivity of life, our world, and everything, 20 papers honestly seems low.
How, then, is an average journal article only read by 10 people, or only 20% of cited papers actually read?
Maybe it has to do with the overextension of researchers (see Alberto’s post above for massive discipline-spanning course lists).
Or maybe it has to do with the way papers are presented. They’re long, in archaic formats, and only accessible with a background in the given discipline (and, critically, freedom from paywalls).
Why can’t we - scientists/communicators of knowledge/sharers of discoveries - agree to write clearly, concisely, and for broad impact and appeal?
Many universities and other research institutions have press offices that interface with the public for just this reason. This is critical, as institutions’ research and resources help attract more funding and, nobly, should be shared with the world.
The problem?
You, as the person who did the research, probably know it better!
And you (hopefully) won’t oversell it!
High Impact Research in Lower Impact Packages
In recent coverage of a massive meta-analysis of the Google Scholar archives, the top-ten “elite” journals are compared to “the rest” in several broad disciplines.
For papers published from 1995 to 2013, there was a 64% average increase of top-1000 cited papers coming out of non-elite journals (here, “elite” = top-ten most-cited journals for a given category; “non-elite” = the rest). Lest you worry these represent the only cited articles in non-elite journals: the total share of citations going to non-elite articles rose from 27% to 47% over the same period.
Part of the reason for this sudden shift is digitization. In the conclusion to the paper the team responsible for Google Scholar (released 10 years ago in November 2014) state:
Now that finding and reading relevant articles in non-elite journals is about as easy as finding and reading articles in elite journals, researchers are increasingly building on and citing work published everywhere.
With the introduction of exactingly searchable databases, the playing field is indeed leveling for access and awareness of all tiers of journals, splashy-high-impact or otherwise. This naturally leads to faster and more efficient scientific endeavors. (Imagine getting even closer, accessing new developments and discoveries in near-real-time. If you think the rate of progress in science is dizzying now...)
Not mentioned, however, is the fact fields have grown more specialized, and publishers have responded by producing more specialty-specific journals. This may in part account for the increased share of non-elite citations: the publication of a groundbreaking article in a lower impact specialty journal will become a necessary citation in many subsequent papers in that and related fields. Another interesting point to consider in future studies is how open access journals measure up in citation rate.
It has also been documented that high impact, elite journals have higher rates of retraction \cite{Fang_2011}. Do the high impact works from non-elite journals show comparable rates of retraction? Given their high impact, many of the same explanations high impact journals give for higher retraction rates should still apply (i.e. increased exposure and thus increased scrutiny).
Regardless, it is clear that new considerations must be made and changes are underway with respect to academic publications. Hopefully scientists return to their roots of open discourse and dissemination of their data so we can get further, faster, together.
Academia: a view from the bottom
This post is part of a series called Is Academia Broken? It relates the experiences of Jeff, Authorea’s Community coordinator, and weighing the options on pursuing a PhD. Be sure to check out Alberto’s first blog post, on the perils of early career interdisciplinary research, and his second, on the overabundance of PhDs and dearth of academic positions.
Are we alone in the Universe? The emergence of life
Previous “Drake Equation” – Next “Fermi Paradox”
We are thinking creatures living on a planet orbiting a pretty common star in a pretty common galaxy. Our home planet has been around for about 4.5 billion years, while the Universe is about 13.7 billion years old. We just learned that there are about 1 000 000 000 000 000 000 000 = 1021 planets potentially similar to the Earth in the cosmos, a number larger than the amount of grains of sand found on every beach and every desert on Earth. Are we alone? To answer this question in 1961 scientist Frank Drake formulated his famous equation, which I discussed in the previous post of this series. The Drake equation calculates the number N of communicative civilizations in our Galaxy. In its 2015 form it reads:
N ≈ 2 fl fi fc L
Are we alone in the Universe?
In this short post series I try to tackle one of the biggest questions out there: Are we alone? The reasoning leads to some radical implications for the very near future of humankind. Read till the end and feel free to comment as you go. Hopefully this will spark interesting discussions.
Habitable Planets How many habitable planets exist in the Universe?
The Drake Equation How to estimate the number of technological civilizations in our Galaxy?
Astrobiology Is biological life common in the Universe?
The Fermi Paradox Is intelligent life common in the Universe? And if yes, does it last?
Interactive Drake Equation Use your own intuition to calculate the chance of being alone or not
From academia to founding a startup: five tips.
Thinking of leaving academia to become an entrepreneur? Here’s five tips to improve your chances to succeed.
Open Science Takes Major Leap Forward: Authorea Releases Unprecedented Details of Ebola Study.
and 4 collaborators
NEW YORK – Last June, a dedicated global team of Ebola researchers began an ambitious project to track the virus using large-scale genome sequencing. Their research, which was written on the research platform Authorea and published June 18 in the journal Cell \cite{26091036}, reveals critical information about how the virus traveled and mutated over seven months of the recent Ebola outbreak.
Today Authorea is pleased to announce that the working draft, data, workflows, and full edit history of the paper are available to the public for free on Authorea.
This is the first time that such complete details have ever been released for a scientific paper. This release provides unprecedented transparency and detail, empowering students and researchers to review every change and edit to every word during the writing of this landmark research paper, using Authorea’s “History” feature.
“When we planned this study, our team decided to make our work as open and transparent as possible, and writing the paper on Authorea is part of that,” said co-lead author Daniel Park. “We felt a moral imperative to put everything out there, especially in this kind of emergency situation.”
“Authorea was founded to make researchers’ day-to-day tasks easier,” says Authorea co-founder and Harvard Research Associate Alberto Pepe. “We realized we were wasting time emailing around documents and data. So we built a website where everyone could write and edit in the same place.”
But Authorea also supports a bigger goal: making science more open. The platform is free to use for open research. “We encourage scientists to publish their entire research process: writing, data, and discussion,” said Dr. Pepe. “The default stance is often to be closed, and we encourage more openness and transparency.”
Researchers in life sciences and other fields often withhold their raw data for months before and even after publishing, according to recent surveys. This practice has questionable utility, as it slows the pace of research, makes it less reproducible, and erodes public trust in science.
“Open access saves lives,” said Professor Peter Suber from the Harvard Office for Scholarly Communication and the Harvard Open Access Project, which were not involved with the Cell Ebola study. “Research saves lives, and when access is unaffordable or delayed, the access barriers put lives at risk. This is especially true in a crisis like Ebola where time is of the essence.”
Sharing and Caring. In the Open.
and 3 collaborators
Friday June 26, 2016.
Today is a great day for human rights.
The Supreme Court of the United States has ruled that the Constitution guarantees a right to same-sex marriage. This decision reflects a shift in American public opinion: according to recent polls, 60% of Americans now support same-sex marriage.
As a company devoted to promoting openness and collaboration, Authorea feels strongly this is an important step in the right direction.
Obviously, sharing the ups and downs of life with another person is an immensely more important and complex task than writing a collaborative paper. Yet if we can draw a parallel, we might say that a useful measure of the progress of a society, and humankind in general, is its ability to share and care openly, together.
That’s the way to unlock society’s true potential, and foster creativity and love.
Happy writing.
Happy loving.
Authorea
A “Modern Scientist” Manifesto
Science is going through a rapid phase of transformation. Two important trends are emerging:
Research is becoming more complex, requiring larger collaborations and bigger experiments.
Science and technology increasingly affect modern society.
The first trend is easy to understand. Let’s think of the cumulative knowledge of humankind as a sphere. Scientists work at the surface and try to “push the boundary”. Discovery increases the volume of knowledge. As the sphere’s volume grows, so does its surface area. Therefore an ever increasing number of researchers is required to tessellate the expanding cutting-edge of science. Moreover, contrary to a few hundred years ago when the sphere of knowledge was so small that a single polymath could master large chunks of it, nowadays no human can understand the details of more than a few research topics. To capture the bigger picture and understand very complex research questions, collaborative efforts combining together a number of highly specific expertises are required.
New York Open Science Meetup: Are we alone in the Universe?
and 1 collaborator
There is on average one planet orbiting every star in the Universe. Our Galaxy (the Milky Way) is an immense disk of gas and stars with a diameter of about 100 000 light years, hosting about 100 billion stars and, therefore, also about 100 billion planets. Take a deep breath. Now, it turns out the Milky Way is just one of 100 billion galaxies that populate our Universe, a colossal expanding stretch of spacetime with an age of 13.7 billion years. The math is trivial: There are about 10 000 000 000 000 000 000 000 = 1022 planets out there. This number is extremely large. Apparently larger than the number of grains of sand found in every beach and every desert on Earth. But how many of these planets host life? And in particular, how many planets host intelligent life we might be able to communicate with?
RSVP and join us for our second official New York Open Science Meetup. Check this blog post series if you wanna know more.
This event is supported by Authorea.com, Minds.com and the Bitcoin Center NYC.
Authorea Newsletter - July 2015: Full LaTeX, Templates, and Ebola on Authorea
and 1 collaborator
If you find Authorea useful, please help support it: send us feedback, invite colleagues to sign up, or buy a subscription.
Keep up the good work! Best regards,
A Tufte-styled scientific article.
A central problem in convex algebra is the extension of left-smooth functions. Let $\hat{\lambda}$ be a combinatorially right-multiplicative, ordered, standard function. We show that ℓI, Λ ∋ 𝒴u, 𝔳 and that there exists a Taylor and positive definite sub-algebraically projective triangle. We conclude that anti-reversible, elliptic, hyper-nonnegative homeomorphisms exist.
Authorea demos new Rich Text editor at the NY Tech Meetup
and 1 collaborator
We’re pleased to announce that Authorea will do the first public demo of our new Rich Text editor – Authorea for Word users! – at the New York Tech Meetup tomorrow, September 9, at 7pm.
You can buy a ticket here: http://www.meetup.com/ny-tech/events/220016163/
The presentation will feature our co-founders Nate and Alberto and chief scientific officer Matteo all together on stage, with the Authorea team cheering in the audience. If you live in NYC and want to meet the folks behind Authorea, this is a great opportunity!
The Meetup is held at the NYU Skirball Center for the Performing Arts.
Authorea on Xconomy
Measuring Open Science
and 4 collaborators
“Open science commonly refers to efforts to make the output of publicly funded research more widely accessible in digital format to the scientific community, the business sector, or society more generally” writes the Organisation for Economic Cooperation and Development (OECD) in its newly released study “Making Open Science a Reality”.
In the digital age the role of tools like Authorea is to increase the efficiency of research as well of its diffusion. The benefits of open science identified by the OECD are multiple:
Reducing duplication costs in collecting, creating, transferring and reusing data and scientific material; allowing more research from the same data; and multiplying opportunities for domestic and global participation in the research process.
The greater scrutiny offered by open science allows a more accurate verification of research results.
Increased access to research results (in the forms of both publications and data) can foster spillovers not only to scientific systems but also innovation systems more broadly. (Firms and individuals may use and reuse scientific outputs to produce new products and services.)
Open science also allows the closer involvement and participation of citizens.
Physicists can code
how did you guys manage to build the codebase for Authorea since you're all physicists?
Library of Words
This blog post describes the rationale and motivation behind the Library of Words, a digital collection of pages filled with every possible combination of 320 words.
Concinnitas: The Art of the Equation
and 3 collaborators
San Francisco, CA – On view at Crown Point Press is an exhibition of etchings by scientists and mathematicians, September 4 - October 27, 2015.
We came across this set of beautiful etchings on Artsy depicting mathematical equations. We decided to reproduce them on Authorea, using our equation editor and some LaTeX. Here’s the result.
Authorea Raises a new round of funding to Advance Open, Reproducible, Data-Driven Research
Authorea is rapidly growing in fields outside of the hard sciences, such as genomics, environmental science, and computational biology. For example, in June 2015, a dedicated global team of epidemiology researchers began an ambitious project to track the Ebola virus using large-scale genome sequencing. Their groundbreaking research, written on Authorea, was published in the journal Cell and covered by the New York Times. The Authorea version of their article is the only place where readers can peruse the history, workflows, and research data connected with the study. Authorea is poised to shake up the stale academic publishing industry via an online platform that encourages data sharing, and a more open and transparent dissemination of research results complete with all the data sources necessary to reproduce them. Authorea plans to use the proceeds of this funding to encourage more open, data-driven research of this kind.
Introducing real time chat for user support
and 1 collaborator
Authorea goes to Paris
and 1 collaborator
Great news! We're happy to announce that Authorea is one of the winners of the NYC-Paris Business Exchange competition. We'll be opening an Authorea office in Paris in March 2016. C'est génial!