Posts about open science

Promoting Open Science

As I have written many times in the past we need to take back science from the closed-science journals. Historically journals were useful (before the internet). With the advent of the internet (and its spread) instead of maintaining the mission they started with the journals sought to maximize their profit and their own pay and jobs at the expense of sharing scientific knowledge with the world.

Elsevier — my part in its downfall by Timothy Gowers provides another good look at what can be done to promote science, math and engineering by addressing the damage to that goal being done by closed science publishers.

Recently he announced the launch of Discrete Analysis, a new journal that publishes to arXiv.

Disrupting the subscription journals’ business model for the necessary large-scale transformation to open access from the Max Planck Digital Library provides some good ideas for how to promote science in spite of the closed science journals fighting that goal.

There needs to be a shared understanding that the money currently locked in the journal subscription system must be withdrawn and re-purposed for open access publishing services. The current library acquisition budgets are the ultimate reservoir for enabling the transformation without financial or other risks.

Related: The Architecture of Access to Scientific KnowledgeWhy Copyright Extension is a Very Bad IdeaPublishers Continue to Fight Open Access to Science (2007)Harvard Steps Up Defense Against Abusive Journal Publishers (2012)

Yacouba Sawadogo – The Man Who Stopped the Desert

Quote from the video

Yacouba single-handedly had more impact on the soil conservation in the Sahel than than all the national and international researchers combined.

Dr. Chris Reij, Vrije University of Amsterdam.

As is normally the case making improvements in the real world is challenging and visionaries often face setbacks. Even when they have success that success is threatened by those that want to take the rewards but ignore the lessons. The clip above is a excerpt from the documentary film on his efforts.

Meet Yacouba Sawadogo – The Man Who Stopped the Desert

The simple old farmer’s re-forestation and soil conservation techniques are so effective they’ve helped turn the tide in the fight against the desertification of the harsh lands in northern Burkina Faso.

Over-farming, over-grazing and over population have, over the years, resulted in heavy soil erosion and drying in this landlocked West African nation.

Zai is a very simple and low-cost farming technique. Using a shovel or an axe, small holes are dug into the hard ground and filled with compost. Seeds of trees, millet or sorghum are planted in the compost. The holes catch water during the rainy season, so they are able to retain moisture and nutrients during the dry season.

According to the rules of Zai, Yacouba would prepare the lands in the dry season – exactly the opposite of the local practice. Other farmers and land chiefs laughed at him, but soon realized that he is a genius. In just 20 years, he converted a completely barren area into a thriving 30-acre forest with over 60 species of trees.

Yacouba has chosen not to keep his secrets to himself. Instead, he hosts a workshop at his farm, teaching visitors and bringing people together in a spirit of friendship. “I want the training program to be the starting point for many fruitful exchanges across the region

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Biomass Fueled Power Generator from All Power Labs

All Power Labs produces biomass fueled power generators. They have grown from a open science and engineering foundation to their current position. I really like how they are focused on promoting understanding and encouraging collaboration.

They reject the copyright cartel closed science mindset; which is something I like. Their product takes waste biomass; for example walnut shells, coconut shells, hardwood chips (Oak, Beech), softwood chips (Douglas Fir, Pine). It also takes corn cobs, palm kernel shells and others but there are additional challenges to operation.

Their products use gasification which is most simply thought of as choked combustion or incomplete combustion. It is burning solid fuels like wood or coal without enough air to complete combustion, so the output gas still has combustion potential. The unburned gas is then piped away to burn elsewhere as needed.

The Power Pallet is a complete biomass power generation solution that converts woody biomass into electricity. It costs $29,995 which translates to a cost of $1-$2/watt which is more cost effective that alternatives. They have significant sales in developing markets where power is often problematic. It is specifically not suited to some fuel – wastepaper (could maybe work in pelletized form), municipal waste, coconut husk…

This webcast is the start of a presentation on the history and current state of their efforts (continue to view other clips for the whole presentation):

Related: Ethanol: Science Based Solution or Special Interest WelfareDo It Yourself Solar Furnace for Home HeatingKudzu Biofuel Potential Chart of Wind Power Generation Capacity Globally from 2005 to 2012Turning Trash into Electricity (2006)

Open Source Seeds

I find the current status of government granted patents to be very flawed, including patenting life.

Plant Breeders Release First ‘Open Source Seeds’

A group of scientists and food activists is launching a campaign Thursday to change the rules that govern seeds. They’re releasing 29 new varieties of crops under a new “open source pledge” that’s intended to safeguard the ability of farmers, gardeners and plant breeders to share those seeds freely.

Irwin Goldman, a vegetable breeder at the University of Wisconsin, Madison, helped organize the campaign. It’s an attempt to restore the practice of open sharing that was the rule among plant breeders when he entered the profession more than 20 years ago.

Good for them. This needs to be supported. The crazy practices of seed companies shouldn’t be legal but they pay lots of cash to politicians and the corrupt politicians (which seems to be an awful lot of them) write bad policy and encourage bad regulation.

Even those administrators taking control of universities have subjugated the search for knowledge and improvement to seek monetary gain instead of what the universities used to prioritize. It is a shame and those that have distorted universities so much should be ashamed.

Initial efforts that lead to the bad place we find universities in now were to promote the adoption of university research. To do so they partnered with business in sensible ways. Then administrators saw money was being made and turned the priority into making money and if that meant restricting the benefits to society of university research so be it. This has created universities that have lost ethical foundations and have destroyed a big part of the value universities used to provide society.

Related: Open-Source Biotech (2006)Scientists Say Biotechnology Seed Companies Prevent Research (2009)The A to Z Guide to Political Interference in ScienceArduino: Open Source Programmable HardwareMoney Is Corrupting Our Political Process

Goats Excel at Learning and Remembering a Complex Tasks

I like research showing animals using intelligence that seems advanced, for example: Crow Using a Sequence of Three ToolsInsightful Problem Solving in an Asian ElephantBird-brains smarter than your average apeTropical Lizards Can Solve Novel Problems and Remember the SolutionsPigeon Solves Box and Banana Problem.

I also like open access science, and this has both: Goats excel at learning and remembering a highly novel cognitive task

The majority of trained goats (9/12) successfully learned the task quickly; on average, within 12 trials. After intervals of up to 10 months, they solved the task within two minutes, indicating excellent long-term memory. The goats did not learn the task faster after observing a demonstrator than if they did not have that opportunity. This indicates that they learned through individual rather than social learning.”

The individual learning abilities and long-term memory of goats highlighted in our study suggest that domestication has not affected goat physical cognition. However, these cognitive abilities contrast with the apparent lack of social learning, suggesting that relatively intelligent species do not always preferentially learn socially. We propose that goat cognition, and maybe more generally ungulate cognition, is mainly driven by the need to forage efficiently in harsh environments and feed on plants that are difficult to access and to process, more than by the computational demands of sociality. Our results could also explain why goats are so successful at colonizing new environments.

The experiment was done with domesticated goats. I also learned this from the article, which I didn’t know before:

Domestication is known to strongly affect brain size. Consistent reductions in brain size relative to body size, as well as in brain size parts, have occurred in many domestic species.

Related: Orangutan Attempts to Hunt Fish with SpearFriday Fun: Bird Using Bait to FishPhoto of Fish Using a Rock to Open a Clam

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Nobel Prize Winner Criticizes Role of Popular Science Journals in the Scientific Process

Randy Schekman, 2013 Nobel Prize winner in physiology or medicine has written another critique of the mainstream, closed-science journals. How journals like Nature, Cell and Science are damaging science

Mine is a professional world that achieves great things for humanity. But it is disfigured by inappropriate incentives. The prevailing structures of personal reputation and career advancement mean the biggest rewards often follow the flashiest work, not the best. Those of us who follow these incentives are being entirely rational – I have followed them myself – but we do not always best serve our profession’s interests, let alone those of humanity and society.

We all know what distorting incentives have done to finance and banking. The incentives my colleagues face are not huge bonuses, but the professional rewards that accompany publication in prestigious journals – chiefly Nature, Cell and Science.

There is a better way, through the new breed of open-access journals that are free for anybody to read, and have no expensive subscriptions to promote. Born on the web, they can accept all papers that meet quality standards, with no artificial caps. Many are edited by working scientists, who can assess the worth of papers without regard for citations. As I know from my editorship of eLife, an open access journal funded by the Wellcome Trust, the Howard Hughes Medical Institute and the Max Planck Society, they are publishing world-class science every week.

Just as Wall Street needs to break the hold of the bonus culture, which drives risk-taking that is rational for individuals but damaging to the financial system, so science must break the tyranny of the luxury journals. The result will be better research that better serves science and society.

Very well said. The closed access journal culture is damaging science in numerous ways. We need to stop supporting those organizations and instead support organizations focused more on promoting great scientific work for the good of society.

Related: Fields Medalist Tim Gowers Takes Action To Stop Cooperating with Anti-Open Science CartelScience Journal Publishers Stay StupidHarvard Steps Up Defense Against Abusive Journal PublishersThe Future of Scholarly Publication (2005)The Trouble with Incentives: They WorkWhen Performance-related Pay BackfiresRewarding Risky Behavior

Huge Human Population Boom 40,000 to 50,000 Years Ago

Interesting open access paper on looking at the Y-chromosome to explore our ancestry: A calibrated human Y-chromosomal phylogeny based on resequencing. I can’t understand all the details but the basic idea isn’t that complicated. It is interesting to see these details as are the conclusions that can be drawn: that we had a big explosion of human population o 41,000–52,000 years ago.

This population explosion occurred, between the first expansion of modern humans out of Africa 60,000 to 70,000 years ago and the Neolithic expansions of people in several parts of the world starting 10,000 years ago.

“We think this second, previously unknown population boom, may have occurred as humans adapted to their new environment after the first out-of-Africa expansion,” says Dr Qasim Ayub, lead author from the Wellcome Trust Sanger institute. “We think that when humans moved from the horn of Africa to Asia, Australia and eventually Europe, they remained in small groups by the coasts. It took them tens of thousands of years to adapt to the mountainous, forested surroundings on the inner continents. However, once their genetic makeup was suited to these new environments, the population increased extremely rapidly as the groups travelled inland and took advantage of the abundance of space and food.”

The work highlights how it is now possible to obtain new biological insights from existing DNA sequencing data sets, and the value of sharing data. The majority of the DNA information used for this study was obtained from freely-available online data-sets.

This is the first time researchers have used the information from large-scale DNA sequencing to create an accurate family tree of the Y chromosome, from which the inferences about human population history could be made.

Full press release

Related: Laser Tool Creates “blueprints” of Archeology SitesHHMI on Science 2.0: Information RevolutionScientists crack 40-year-old DNA puzzle

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