Outperforming natural photosynthesis

From PhysOrg.com:

“Researchers figure out how to outperform nature's photosynthesis”

“The Proceedings of the National Academy of Sciences (PNAS) last week published a paper titled "Solar hydrogen-producing bionanodevice outperforms natural photosynthesis."

“The authors are Carolyn E. Lubner, Amanda M. Applegate, Philipp Knörzerb, Alexander Ganagoc, Donald A. Bryantc, Thomas Happe and John H. Golbeck.”

“They modified the photosynthetic proteins found in cyanobacteria -- bacteria which gain their energy through photosynthesis.”

Ref: Solar hydrogen-producing bionanodevice outperforms natural photosynthesis PNAS 2011 108 (52) 20988-20991; published ahead of print December 12, 2011, doi:10.1073/pnas.1114660108

Abstract:

Although a number of solar biohydrogen systems employing photosystem I (PSI) have been developed, few attain the electron transfer throughput of oxygenic photosynthesis. We have optimized a biological/organic nanoconstruct that directly tethers F_B, the terminal [4Fe-4S] cluster of PSI from Synechococcus sp. PCC 7002, to the distal [4Fe-4S] cluster of the [FeFe]-hydrogenase (H₂ase) from Clostridium acetobutylicum. On illumination, the PSI–[FeFe]-H₂ase nanoconstruct evolves H₂ at a rate of 2,200 ± 460 μmol mg chlorophyll^-1 h^-1, which is equivalent to 105 ± 22 e^-PSI^-1 s^-1. Cyanobacteria evolve O₂ at a rate of approximately 400 μmol mg chlorophyll^-1 h^-1, which is equivalent to 47 e^-PSI^-1 s^-1, given a PSI to photosystem II ratio of 1.8. The greater than twofold electron throughput by this hybrid biological/organic nanoconstruct over in vivo oxygenic photosynthesis validates the concept of tethering proteins through their redox cofactors to overcome diffusion-based rate limitations on electron transfer.

2010 Report Card for U.S. Science, Engineering, and Technology

From: National Science Board, Science and Engineering Indicators 2010 report.

"The latest edition of Indicators tells us that the state of U.S. science and engineering is strong, but that U.S. dominance of world science and engineering has eroded significantly in recent years, primarily because of rapidly increasing capabilities among East Asian nations, particularly China."

See the OSTP Blog (White House Office of Science and Technology)

Science future, science past

Can you predict the future of science? Can you describe its major accomplishments of the past half century? See what others think:

Decades of future science:
http://cosmiclog.msnbc.msn.com/archive/2009/12/22/2159108.aspx

50 Science Sagas for 50 Years:
http://www.casw.org/casw/article/50-science-sagas-50-years

UK's Royal Institution's Christmas Science Lectures

As a scientist or science enthusiast, you might want to know what they did, the names below, among them scientists, naturalists, inventors, Nobel Prize winners, and Presidents of U.K.'s Royal Institution, all of whom delivered one or more of the Institution?s Christmas science lecture-demonstrations:

"From Michael Faraday to David Attenborough plus adorable lemur ? many eminent figures have delivered Christmas science lectures at the UK's Royal Institution. The organisation has put on 180 series of Christmas lectures since 1825, delivered by a total of 105 lecturers including eight Nobel prizewinners."--

http://www.newscientist.com/gallery/christmas-lectures/1

The names represent selected lecturers in a slide show by NewScientist, the slides showing a photo of the lecturer demonstrating in from an audience, each accompanied by a long side-bar description of the event and biosketch of the lecturer.

The Royal Institution's festive feasts for the mind
http://www.newscientist.com/gallery/christmas-lectures

My favorite: Michael Faraday slide.

Sue Hartley
Susan Greenfield
Charles Taylor
David Attenborough
George Porter
Frank Whittle
Percy Dunsheath
Geoffrey Ingram Taylor
Edward Neville da Costa Andrade
Robert Stawell Ball
Michael Faraday

For info on the 2009 Lecture: http://www.rigb.org/registrationControl?action=home

150th Anniversary Publication Darwin's 'Origin' First Edition

November 24th 2009 marks the 150th anniversary of the publication of the first edition of Charles Darwin's The Origin of Species By Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life - a revolutionary work, hastily completed in response to Alfred Russel Wallace's co-discovery of the principle of 'suvival of the fittest'.

If anyone has a copy of the first edition and would care to share, this blogger would tenderly care for it.

From the Unconscious to the Conscious

Here, a quote from:

Gazzaniga MS. (2008) Human: The Science Behind What Makes Us Unique. HarperCollins. ISBN 978-0-06-089288-3.

"How the brain drives our thoughts and actions has remained elusive. Among the many unknowns is the great mystery of how a thought moves from the depths of the unconscious to become conscious."

Any thoughts? Through memos?

Interesting View of Science Writing

I thought you might resonate with something science writer, Natalie Angier, wrote in her Introduction to The Canon: A Whirligig Tour of the Beautiful Basics of Science (Houghton Mifflin Co., Boston . New York, 2007, isbn-13:978-0-618-24295-5):

"..the time had arrived for writing, the painful process, as the neuroscientist Susan Hockfield so pointedly put it, of transforming three-dimensional, parallel-processed experience into two-dimensional, linear narrative. "It's worse than squaring a circle," she said. "It's squaring a sphere.""

3-D to 2-D. Parallel to linear processing.

Hits the mark, doesn't it?

The Wisdom of Many in One Mind

Herzog SM, Hertwig R. The wisdom of many in one mind: improving individual judgments with dialectical bootstrapping. Psychol Sci 2009;20:231-7.

Abstract: (paragraphed for easier readability)

The "wisdom of crowds" in making judgments about the future or other unknown events is well established. The average quantitative estimate of a group of individuals is consistently more accurate than the typical estimate, and is sometimes even the best estimate.

Although individuals' estimates may be riddled with errors, averaging them boosts accuracy because both systematic and random errors tend to cancel out across individuals.

We propose exploiting the power of averaging to improve estimates generated by a single person by using an approach we call dialectical bootstrapping. Specifically, it should be possible to reduce a person's error by averaging his or her first estimate with a second one that harks back to somewhat different knowledge.

We derive conditions under which dialectical bootstrapping fosters accuracy and provide an empirical demonstration that its benefits go beyond reliability gains. A single mind can thus simulate the wisdom of many

My Comment:

I will try to explain the method in a subsequent post.

Seeking Comments on Draft Version of Article Entitled ''Life''

See Life/Draft on the online 2nd generation Wikipedia, Citizendium. Seeking comments, suggestions, collaborators, etc., on an article I have been developing on the question, "What is Life". Comment here or email me directly (Anthony_Sebastian@msn.com).

Forget to Remember

Jonah Lehrer (Proust Was a Neuroscientist; How We Decide) discusses the virtue of forgetting in a 2007 post on his blog, The Frontal Cortex. Think what you would experience if you remembered every perception, every recollection of every perception and thought. If you think such a non-fadeable photographic mind a consummation devoutly to be wished, read Lehrer's post, and the comments it received.

The Gardeners' Gopher Problem

My gardener friends complain endlessly about gophers eating and damaging their plants. They also recount their histories of tactics to defeat the furry little geniuses, all failures.

My thought: Build a small robot to wander the gopher tunnels, detecting and eliminating the furry little geniuses. Perhaps deploy a number of such robots per plot, each at different tunnel location, to cover all escape routes.

Seems to me if one can build a robot to vacuum one's carpets, one should have little trouble building one to solve the gopher problem.

Research and imagination needed for design specifications.

Will President Obama's Administration Address the Fundamental Problems Resulting from Global Exponential Population Growth

One test of President Obama's wisdom consists in a measure of the extent to which he recognizes that preventive measures often can trump curative measures, and not just in programs to prevent the most common devastating human diseases, which conceivably cost less than treating after the fact.

Questions that might arise in substantially reduce the rate of human population growth:

• Given the amount of Earth's sustainable/renewable resources, and other related factors, what can we conclude about an optimal population cap for Earth?
• Have we already exceeded that cap?
• If so, how can we redress the situation?
• If not, how can we ensure we do not exceed that cap?

For the most part, prevention of human disease requires human lifestyle changes, and an infrastructure that supports, not thwarts, its achievement. Prevention of human disease and disease of the Earth may require a similar approach.

Did Earth’s Genetic Raw Materials Arrive From Extraterrestrial Sources?

According to a report from a European and American collaborative group of scientists interested in Earth and Planetary science, analysis of a meteorite suggests that organic compounds involved in the chemical reactions that produce the purines and pyrimidines that make up DNA and RNA may have already been present in the early solar system, reaching Earth through meteor bombardments and other contacts with extraterrestrial sources. The abstract of the article by astrobiologist Zita Martin and colleagues, reads as follows:

"Carbon-rich meteorites, carbonaceous chondrites, contain many biologically relevant organic molecules and delivered prebiotic material to the young Earth. We present compound-specific carbon isotope data indicating that measured purine and pyrimidine compounds are indigenous components of the Murchison meteorite. Carbon isotope ratios for uracil and xanthine of δ13C=+44.5‰ and +37.7‰, respectively, indicate a non-terrestrial origin for these compounds. These new results demonstrate that organic compounds, which are components of the genetic code in modern biochemistry, were already present in the early solar system and may have played a key role in life's origin."

See: Martins Z, Botta O, Fogel ML et al. Extraterrestrial nucleobases in the Murchison meteorite. Earth and Planetary Science Letters 2008;270:130-6.

http://www.sciencedirect.com/science/article/B6V61-4S3G406-1/1/eb630b2a66119aa41767b7be4b697c44

Speaking of Life

To see life, look here:

http://en.citizendium.org/wiki/Life

Citizendium's latest version of its answer to the perennial question:

What is life?

Many other interesting free encyclopedia articles at Citizendium:

http://en.citizendium.org

The Ride of Life

News from the Cardiff Centre for Astrobiology

The Earth moves in many different patterns concurrently. It rotates on an axis, it wobbles its rotation on that axis, it revolves around the sun, it moves with the sun and its system of planets through space in the Milky Way galaxy, and moves with the galaxy's spinning and hurtling away from some and toward other galaxies.

In addition to those patterns, along with the solar system, the Earth bounces alternating bi-directionally through the plane of the galaxy. The denser parts of the galaxy's plane has huge gravitational masses that dislodge comets from their paths, some of which impact Earth. The bounce-throughs occur every 35-40 million years, in keeping with Earth's 36 million year interval of increased comet impacts. Several of Earth's mass extinctions coincide, too.

The researchers who "discovered", in a computational simulation, the bouncing solar system ride, speculate that the bombardments might strew some of Earth's microorganisms through the galaxy, perhaps seeding life elsewhere. Or introducing new life. Perhaps other solar systems do likewise. Imagine, a galactic-wide primordial soup! An alphabet soup spelling 'mother'.

See story at:

http://www.cardiff.ac.uk/news/articles/did-the-solar-system-bounce-finish-the-dinosaurs.html

Did the solar system 'bounce' finish the dinosaurs?

Designer Evolution

Suppose you wanted to direct the evolution of molecular systems that behaved according to parameters you set. By whatever means you implement that, you must have a method for directing evolution of individual molecules toward desired functional properties, since the system must have the appropriate parts to generate its functionality. In that case, you must have a molecule generating factory for the component parts. Starting with enormous numbers of generators of different efficiency/capacity, and limiting the substrate precursors of the desired molecules, iteratively in rapid succession, and imposing the parameters defining the desired functional molecule, natural selection will favor preservation of the high-capacity, fast-reacting, efficient generators that yield the targeted molecule.

 

That process admits of automation on a chip, as demonstrated by Brian M. Paegel and Gerald F. Joyce, in the Departments of Chemistry and Molecular Biology, of the Scripps Research Institute, La Jolla, California, and in the Skaggs Institute for Chemical Biology, of the Scripps Research Institute, La Jolla, California, both in the U.S.

 

The procedure produces a continuous stream of real-time data, giving the experimenter a record of the evolutionary course in terms of population size and heterogeneity, and growth conditions, including availability of limiting resources. Each microchip contains multiple microfluidic circuits independently addressable. The method costs modestly, so the process makes Darwinian evolution readily accessable. As easy almost as implementing the evolution of the system on a computer.

 

Darwinian Evolution on a Chip. Paegel BM, Joyce GF. PLoS Biology Vol. 6, No. 4, e85 doi:10.1371/journal.pbio.0060085

Chip-Based Designer Molecular Evolution

Suppose you wanted to direct the evolution of molecular systems that behaved according to parameters you set. By whatever means you implement that, you must have a method for directing evolution of individual molecules toward desired functional properties, since the system must have the appropriate parts to generate its functionality. In that case, you must have a molecule generating factory for the component parts. Starting with enormous numbers of generators of different efficiency/capacity, and limiting the substrate precursors of the desired molecules, iteratively in rapid succession, and imposing the parameters defining the desired functional molecule, natural selection will favor preservation of the high-capacity, fast-reacting, efficient generators that yield the targeted molecule.

 

That process admits of automation on a chip, as demonstrated by Brian M. Paegel and Gerald F. Joyce, in the Departments of Chemistry and Molecular Biology, of the Scripps Research Institute, La Jolla, California, and in the Skaggs Institute for Chemical Biology, of the Scripps Research Institute, La Jolla, California, both in the U.S.

 

The procedure produces a continuous stream of real-time data, giving the experimenter a record of the evolutionary course in terms of population size and heterogeneity, and growth conditions, including availability of limiting resources. Each microchip contains multiple microfluidic circuits independently addressable. The method costs modestly, so the process makes Darwinian evolution readily accessible. As easy almost as implementing the evolution of the system on a computer.

Darwinian Evolution on a Chip. Paegel BM, Joyce GF. PLoS Biology Vol. 6, No. 4, e85 doi:10.1371/journal.pbio.0060085

Citizendium Grows

Citizendium, the online wiki encyclopedia guided, monitored, and much written by credentialed knowledge professionals as editors, keeps growing. It now has over 3800 articles, with many 'subpages'. Check it out here.

Biologists might find interesting the many articles guided by the Biology workgroup. See for example

Biology and Biology/Draft

Life and Life/Draft

The '/Draft' articles are working copies destined to update the main article.

Then go to the list of all biology articles, here.

As a wiki, Citizendium welcomes contributions (new articles, edits of existing articles) from the general public and knowledge professionals, all under gentle guidance by Citizendium's editors.

Questions?

Monkeys Learn Their Numbers

Diester I,Nieder A (2007) Semantic Associations between Signs and Numerical Categories in the Prefrontal Cortex. PLoS Biol 5(11): e294 doi:10.1371/journal.pbio.0050294

From the Abstract:

• The utilization of symbols such as words and numbers as mental tools endows humans with unrivalled cognitive flexibility.
  
• In the number domain, a fundamental first step for the acquisition of numerical symbols is the semantic association of signs with cardinalities.
  
• We explored the primitives of such a semantic mapping process by recording single-cell activity in the monkey prefrontal and parietal cortices, brain structures critically involved in numerical cognition.
  
• Monkeys were trained to associate visual shapes with varying numbers of items in a matching task.
  
• After this long-term learning process, we found that the responses of many prefrontal neurons to the visual shapes reflected the associated numerical value in a behaviorally relevant way.
  
• In contrast, such association neurons were rarely found in the parietal lobe.
  
• These findings suggest a cardinal [probably no pun intended] role of the prefrontal cortex in establishing semantic associations between signs and abstract categories, a cognitive precursor that may ultimately give rise to symbolic thinking in linguistic humans.
  

Author Summary:

We use symbols, such as numbers, as mental tools for abstract and precise representations. Humans share with animals a language-independent system for representing numerical quantity, but number symbols are learned during childhood. A first step in the acquisition of number symbols constitutes an association of signs with specific numerical values of sets. To investigate the single-neuron mechanisms of semantic association, we simulated such a mapping process in rhesus monkeys by training them to associate the visual shapes of Arabic numerals with the numerosity of multiple-dot displays. We found that many individual neurons in the prefrontal cortex, but only a few in the posterior parietal cortex, responded in a tuned fashion to the same numerical values of dot sets and associated shapes. We called these neurons association neurons since they establish an associational link between shapes and numerical categories. The distribution of these association neurons across prefrontal and parietal areas resembles activation patterns in children and suggests a precursor of our symbol system in monkeys.

Copyright: © 2007 Diester and Nieder. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Citizendium Seeking Expert Contributors to Science Articles

From Citizendium's Main Page:

"The Citizendium (sit-ih-ZEN-dee-um), a "citizens' compendium of everything," is an experimental new wiki project. The project, started by a co-founder of Wikipedia, aims to improve on that model by adding "gentle expert oversight" and requiring contributors to use their real names."

I like Citizendium because of the expert-guidance of collaboratively written science articles -- the feeling of confidence that gives in reading an article. I like the opportunity to edit articles in progress when I have something to contribute. I like the opportunity to start new articles from scratch and develop them offline before posting and giving other experts the opportunity to comment and edit. I like the fact that 'approved' articles have an accompanying 'draft' version to continue working on, eventually to replace the earlier 'approved' version -- science does not stand still.

"Share your knowledge. It's a way to achieve immortality." --Attributed to Dalai Lama