Composting Chitosan Cat-litter Composite

Spectroscopy Now

That has to be the oddest blog headline I’ve come up with this week, but it’s not in fact that esoteric once you get down to it. Basically, researchers in China have created a new material based on dolomite (porous kitty litter material) and the crab shell derivative chitosan.

The new composite material not only absorbs water it can release an NPK (nitrogen, phosphorus, potassium) fertiliser over a prolonged period for use in agriculture and horticulture. Advantages are, improved irrigation efficiency and less run off into waterways together with improved crop yields. More on this, in my SpectroscopyNOW column this week and you get a chance to see a photo of my kitty too. What more could you want? Other than links to the rest of this week’s news in SpecNOW, of course.

In NMR news, a brainy approach to using microNMR coils could allow scientists to probe the activity of cerebral compounds, such as choline, without having to worry about NMR’s relatively low sensitivity. In the X-ray ezine, I report on how British scientists have demonstrated that it is possible to predict the crystal structures of small organic molecules using software, winning them accolades at this year’s Blind Test in Crystal Structure Prediction, organised by the University of Cambridge and hosted by the Cambridge Crystallographic Data Centre.

Finally, new informatics evidence suggests that the land-bridge which is currently the Bering Strait was the sole route into the Americas for humans tens of thousands of years.

Male Semen is Redundant

Male sperm

You’ve seen the kind of thing: “Warehouse Razed to the Ground in Fire”, as if razing didn’t already mean the building was levelled. Worse, “Balloon Ascends Up into the Air”, ascending down is very difficult, simultaneously, at the same time, if not impossible; so too is descending up.

However, the award for the most redundantly tautological headline of the year has to go to Scientific American for Male Semen Makes HIV More Potent, that’s male semen as opposed to the female variety, is it? It’s an important discovery, nevertheless that a chemical constituent of semen affects the immune system facilitating viral infection.

Scientific American is probably not the first and original nor the ultimate and last publication to use this phrase though. DoctorNDTV ran a story with the title: Male semen loss concerns and risky sexual behaviour. Then there’s a research paper in the Journal of Avian Biology that discusses bacteria found in the “male semen” of red-winged blackbirds. Even the venerable and well-respected New Scientist recently published an item on insect courtship and egg laying. Apparently, the trigger for egg laying “is a small protein called sex peptide (SP) in the male’s semen.” Again, the word male, while perhaps making the sentence smoother, is totally redundant and not needed.

A search for the phrase “male semen” on PubMed produced not hits, although “male sperm” came up several times in various journals. So as not to appear sexist, I also did the equivalent searches for “female semen” and “female sperm” and quite surprisingly got several PubMed hits. One paper on mythology mentions how at one time in human history a godly being or other supernatural entity was thought to intervene in the merging of male and female semen to bring about conception. Not quite a modern biomedical reference point, then. The phrase “female sperm” gave absolutely no hits, unsurprisingly.

Maybe the clue as to why these various publications qualify the word semen lies in those papers discussing the mythology of reproduction. A quick Google shows that there are many references to religious and proto-religious texts that discuss both male and female semen as if they were both real. Perhaps by qualifying semen as male in modern writing, rather than simply discussing semen, there is some referential nod to humanity’s misconstrued understanding of reproduction. But, modern understanding of reproductive biology defines semen as a product of the male reproductive organs that acts as a transport medium for sperm, so, like I said, it’s redundant.

I asked linguistic guru Steven Pinker of Harvard University, whose book The Stuff of Thought I reviewed on Sciencebase recently, about this apparent paradox. Pinker told me that he suspects that, “the cause is not a nod to the ancients, but a desire to call the reader’s attention to the fact that it’s
the naturally occurring fluid that encourages the potency of the virus, not some externally administered product.

“Semen Makes HIV More Potent implies to me,” he said, “that adding semen increases the potency, rather than that the HIV exploits the properties of the semen it finds itself in.” He adds that it is peculiar that this may be the case. “Odd that the redundancy should do that,” he told me, “but somehow I think it does.”

Intriguingly, after I contacted Pinker, I saw that the journal Nature, as opposed to the popular science magazine, Scientific American, had covered the same story. In Nature, however, their piece was entitled – Semen boosts HIV transmission. So, for some reason they felt semen does not need a masculine qualification of any kind. The tautology of the phrase “male semen” may seem trivial, but it is an important issue.

David Bradley Abbreviated

I wrote a rather vainglorious post on my Significant Figures site last week – entitled David Bradley: Killer, Lover, Player Puller, it was basically an excuse to do a bit of personal branding but also highlighted the fact that there are so many other David Bradleys out there, including dozens of professors, photographers, a porn star, actors and tractors, and worst of all at least one lawyer.

One of my virtual friends on StumbleUpon, spostareduro, picked up on this article saying it was a great idea for branding. In an email chat though she asked “Do you know how nifty it is to have initials that stand for Data Base.” Obviously, I was aware of this…it was part of the underlying psychology of morphing Elemental Discoveries into Sciencebase when I registered this website’s domain in 1999. However, it got me thinking about what else my initials (I’ve no middle name so, they’re plain old DB) stood for, so here’s a brief list.

  • Data Base – as already mentioned, a database is usually thought of as a structured file containing information accessible with a computer, whether or not I or Sciencebase fit into that definition I couldn’t possibly say.
  • dB – decibels – a useful logarithmic unit for power in acoustics, physics, and electronics. An increase of 10 dB represents a ten times increase in power. Normal conversation bubbles along at 60 dB for instance, a rock concert, at 120 dB, is 1,000,000,000,000,000,000 times louder, which might just explain why so many aging rock stars suffer hearing loss.
  • db (pronounced dee-bee) – is, according to the Urban Dictionary, the ultimate power word, used for expressing absolutely any emotion at all. Of course, in its inimitable style, the Urban Dictionary also has a whole slew of more offensive definitions, which I am not citing here as a matter of principle.
  • In chemistry, my native tongue, DB is both 4-(2,4-dichlorophenoxy)butanoic acid di-n-butyramide.
  • Classiest automotive abbreviation has to be Daimler Benz, unless you add a digit and mention the Aston Martin DB9, obviously, maybe when Sciencebase has a few more dB income I could start saving for one.
  • Sticking with the classy Germans, there is also Deutsche Bahn, the German railway company.
  • And by sheer coincidence, or maybe not the next DB is also German – www.db.com – Deutsche Bank, obviously.
  • Db – dubnium, very heavy element.
  • If you really want more DB’s than you could shake a stick at…check out the wiki entry for DB

UPDATE: Been messing around with name again and have created a page called David Bradley Actor just for fun.

Some time after this, I created a logo based around dB/ figuratively a decibel meter dial.

Cholesterol Hearing Test

Cholesterol Structure

Levels of cholesterol in the membranes of hair cells in the inner ear can affect your hearing according to an article in the Journal of Biological Chemistry. There are two types of sensory hair cells in the inner ear called the inner and outer hair cells. It is the outer hair cells that are affected by cholesterol levels and produce the inaudible sounds in the ear canal.

SOURCE: Baylor College of Medicine

Could Warm Feet Save the World?

Warm feet - photo by spiralz

Wind turbines, photovoltaic power cells, wave energy, porous hydrogen storage composites for fuel cells, carbon sequestration, nuclear, even the idea of damming the Red Sea for a massive hydroelectric power plant are among the high-tech approaches being developed in the battle to reduce our collective size 9 carbon footprints to mere tiptoes.

Saving energy and reducing emissions does not have to be about high tech and macro engineering. The developed world is unlikely ever to give up its dependence on personal motor transport, frequent and pointless air travel, patio heaters, high-definition DVDs, hot and cold running water, and countless other energy-intensive luxuries unless someone actually physical pulls the power plug.

However, for millions of people in the developing world, who may not even be aware of the problems we face with iPhone tariffs, double booked business flights, and lost Facebook friends, life is hard at a much more fundamental level. Aside from poverty, unreliable water supply, malnutrition and disease, even very basic needs are not met, such as keeping warm and dry in freezing mountain villages with no access to heated spa pools and acrylic nail extensions, and wireless internet access to refresh the contents of your Kindle.

D. Buddhi of the Thermal Energy Storage Laboratory at Devi Ahilya University in Indore, India, Atul Sharma of the Department of Mechanical Engineering at Kun Shan University, Tainan, Taiwan, ROC, and S.D. Sharma of UAE Innovations Center in Ras Al Khaimah, UAE have turned to a perennial problem of those without the comforts of central heating and doubly glazed windows – keeping one’s feet warm.

The researchers have designed and tested three foot warmers that can store up solar energy during sunshine hours and then be used during cold evenings as a sustainable alternative to electric heaters. The optimum temperature, the team found in their trials, was just above body temperature. With this in mind, commercial grade lauric acid (which has a melting point 42.2 Celsius and a latent heat of fusion of 181 kilojoules per kilogram was used as the latent heat storage material in their PCM (phase change material) designs. Basically, the material inside melts in the sun and then once the sun goes down the material begins to solidify giving off enough latent heat as it does so to raise the temperature of the container to about 40 Celsius.

They carried out experiments (details are reported in the International Journal of Global Energy Issues) during a winter season to study how well the PCM units performed in the sunny but cold winter climate of northern India. The devices could easily reduce reliance on costly 1 kilowatt electric heaters for keeping the legs and feet warm; and although PCM units do not have the benefit of creating circulating warm air in a room, much of that energy is wasted anyway.

So, could a solar-powered foot warmer save the planet? Perhaps not, at least not until those in the developed world abandon their predilection for vehicle climate control and optical mice. However, alongside other simplified technologies such as solar cookers, arsenic-removing water filters, and clockwork radios, they could at least make a significant difference to the cost of living of people in the poorer parts of the world without compromising their quality of life. Moreover, those in frozen climes will at least be able to keep their feet warm while pondering shag pile carpets and remote control storm shutters.

WiChempedia Coming Soon

It seems it’s now public knowledge that WiChempedia is on its way thanks to Tony Williams at ChemSpider and his colleagues.

“Over the past few weeks I have had a few discussions with a member of the ChemSpider Advisory group regarding a concept to create WiChempedia. I’ve enjoyed these conversations with Alex Tropsha (professor and Chair in the Division of Medicinal Chemistry and Natural Products in the School of Pharmacy, UNC-Chapel Hill),” says Williams in his latest blog post.

Over the past few weeks Williams and his colleagues have been looking at the quality of data on Wikipedia and trying to figure out the best way to mash ChemSpider’s efforts with those of the WP:CHEM team. “Our intention is to deliver wiki-capabilities in ChemSpider and to use the Open Content associated with chemicals and drugs on Wikipedia inside the system,” Williams says, without, he adds, reinventing the wheel or offending the Wikipedians.

“My intention as we work through downloading the data and to check, validate and correct what is sitting on Wikipedia directly for benefit to the community,” adds Williams.

Volcanoes, Moons, Pearls, and Alchemy

Moon (Photo by David Bradley)

This month’s physical sciences Spotlight over on the Intute site turns on oceanic plans, lunar volcanoes, and pearl necklaces:

Infertile Global Warming Plan – Plans to fertilize the oceans with iron or other nutrients in order to absorb atmospheric carbon dioxide and so ward off global warming are not viable according to a report from researchers at Stanford and Oregon State Universities.

Buckyball Pearl Necklace – A new type of polymer material made by stringing together the tiny football-shaped fullerene molecules has been synthesised by chemists in Spain. Under the microscope, the material resembles a string of pearls.

Volcanoes of the Moon – Even though astronauts have set foot on the Moon, analysed its surface and brought samples back to Earth, we do not yet fully understand the Moon’s origins nor how it has evolved during the last few billion years since its formation. New clues have now emerged from a study of the Moon’s past volcanic activity that suggest that volcanic activity began 4.35 billion years ago (+/- 0.15billion), a relatively short time after the formation of our planet’s biggest satellite.

And, in ChemWeb’s The Alchemist newsletter: Small-scale chemistry with a variety of applications that could improve not only healthcare but the environment has led to the Small Times innovation award going to Louisiana Tech’s Yuri Lvov, The Alchemist hears this week. Also in chemistry news, old anticancer drugs could be repurposed for treating genetic blood disorders sickle-cell anemia and beta-thalassemia.

A barrel of fun is to be had analyzing wine barrels for dioxins and polyaromatic hydrocarbons, while laser light has been found to switch vanadia films from reflective to transparent without heating, a possible boon for optoelectronics applications. Finally, in this week’s Alchemical selection, holy double-helical nanorings of DNA with single-stranded gaps have been engineered by German scientists while US researchers have demonstrated that pouring millions of dollars and tons of iron into the oceans may not have the desired effect on reducing atmospheric carbon dioxide levels after all.

Googling for Genes

Those clever people at Harvard are using Google‘s API to allow users to search for gene sequence fragments on the Web in combination with a text query. You’re limited to 1000 searches per day and have to enter your own API key to get the maximum benefit. But. that’s probably enough to be going on with.

From the site: Query Gene is distinctive because it is not limited to a single database. Instead it captures genetic information across the net using Google. It works by taking a gene sequence in combination with other search terms, finds similar sequences using NCBI’s MegaBlast, retrieves the descriptions of those matching genes from NCBI’s Entrez Nucleotide database, and performs a series of Google searches using the combination of your original search terms and each gene description. The percent sequence identity is indicated alongside each match: this indicates how much of your queried sequence is contained in the sequence it matches.

You might want to find out what disease states are associated with a specific nucleotide sequence. No problem. Paste in the sequence and enter a text phrase, such as “genetic disease associated with” and up pop the results. Well, actually, they didn’t with the test I tried, but that could be down to my browser configuration. I got “Sorry, we are under maintenance: Please try again in a few weeks”.

A sample sequence is given here. If someone else could confirm or refute the maintanance outage for ChemSpy readers that would be very helpful.

Sciencebase Top Ten Molecules of 2007

Graphene

Everyone loves a list. (Don’t they?) Well, as we’re approaching the end of the year and some of us are well into the panto and party season already, I thought it would be a good idea to run down a hit parade of this year’s molecules. So, here’s the Sciencebase Top Ten Molecules of 2007:

  • 10 – Graphene – chicken wire carbon sheets hit the headlines this year and will continue to do so as researchers learn more about this unique material’s optical and electrical properties. One day, carbon may even replace silicon as the elemental of choice in computing.
  • 9 – Helium – at the time of writing physicists in Canada had taken an important step towards understanding supersolidity in helium, stretching it a bit to include this in a list of molecules. This new state of matter forms at very low temperature and under extreme pressure and now it has been found that cooling makes supersolid helium even stiffer.
  • 8 – DNA – deoxyribonucleic acid, and more specifically, the deoxyribonucleic acid that resides in every cell of genomics pioneer Craig Venter. The J Craig Venter Institute claims that this “Independent sequence and assembly of the six billion base pairs from the genome of one person ushers in the era of individualized genome-based medicine”.
  • 7 – Water – Good old H2O continues to confound those scientists hoping to explain its anomalous properties, as supplies of the fresh stuff will dwindle as the century moves on, it’s heartening to know that close to absolute zero, water exists in yet another phase.
  • 6 – Ethanol – a seasonal favourite, of course, the active ingredient in so many beverages. As with a certain other molecule in this Top Ten, this year there has been a lot of hot breath resulting from various and conflicting health studies on the effects of ethanol on human health, expectant mothers and their unborn children, and others. So…raise your glasses to ethanol!
  • 5 – Rotaxane – 140 years ago, Scottish physicist James Clerk Maxwell devised a thought experiment that might help scientists break the law. An entirely legal, molecular version of Maxwell’s Demon made its debut this year, thanks to chemists at Edinburgh University.
  • 4 – Azadirachtin – After decades of trying and countless post-doc and grad students have come and gone Steve Ley at Cambridge University finally published a total synthesis for the natural insecticide azadirachtin.
  • 3 – Epothilone – could the anticancer drugs produced by soil microbes finally have come of age with the announcement from pharma giant Bristol Myers Squibb that it has obtained approval in the US for semi-synthetic analogue of epothilone B against drug-resistant metastatic breast cancer.
  • 2 – Carbon dioxide – this year, there has been more hot air produced around this greenhouse gas and climate change than I care to cite.
  • 1 – Hydrogen sulfide – yet another small molecule with a big impact. Scientists recently discovered that H2S could be the key to longevity, at least if you’re a nematode worm. A study published in PNAS in December demonstrated that the “rotten egg” molecule increases heat tolerance and lifespan in the molecular biologist’s favourite, Caenorhabditis elegans
  • Well, those are my choices, I deliberately avoided looking at Science to see what they’d come up with for their Molecule of the Year, before I put this post together. If anyone has their own Top Ten or even just a Number 1 let me know.

Youtube for Scientists

Youtube for scientists

Regular readers will know that I have a penchant for posting science videos every now and then. I’ve written about vids on how to explain Newton’s laws with Lego, A spoof sweet potato battery to power your mp3 player, Einstein meets Hendrix, and desktop hockey with one of the most water-repellent materials ever invented from chemists at Queen’s University Belfast. Youtube has long since been oustripped as the place to go for science-related videos, there are dozens of sites that specialise in science videos:

Science Hack, for instance, showcases hundreds of videos every one of which has been screened by a scientist to verify its accuracy and quality. Typical searches include Hubble, Space, Sulfur Hexafluoride, Psychology, and the site has its own Facebook app if you’re feeling supra-uber-geekish. Indeed, I’ve used the Science Hack Facebook app on my own Facebook pages.

Science press release repository Science Daily also has its own dedicated video channel. At the time of writing, top video posts included “Engineers Measure Blood Alcohol Content With Spectroscopy”, “Cardiac Electrophysiologists Make MRIs Safe For People With Pacemakers”, and “Engineers Build Automated Parking Garage”.

Often referred to as Youtube for scientists, SciVee.com doesn’t really have any more of a claim to such a title as any of the other science vid sites listed here, but it is good, carrying an intriguingly entitled video called “Ten Simple Rules for Making Good Oral”, which turns out to be about presentations rather than anything else.

AthenaWeb has also been given that Youtube for geeks label (like there could be anything more geeky than using Youtube in the first place) by various bloggers. I’m pretty sure AthenaWeb has gone through at least a couple of launches, but it looks pretty fresh today and offers a Top 5 science videos, which include an exploration of nanotechnology and one on apoptosis, or cell death.

Then, if you want to limit yourself to one science guy, there’s Robert Krampf who has a stack of science experiments he records to video, in fact one or two of his videos have featured on Sciencebase in the past, including Save a balloon with water.

Finally, in this brief round-up, there is Youtube itself, which is the archetypal Youtube for Scientists. Just follow a search for science to bring up a goodly number of science vids.

There are many other science video directories (including VideoJug’s environment section, the public relations offices at various companies, universities, and other organisations often include videos with their output. If you know of any gathering place or the next Youtube for scientists, let me know by putting the link in the comments frame below.