Popular Science Discoveries This Year

Happy New Year 2008

No science blog would be fulfilling its annual duties if it didn’t provide an end of year round up of what’s been hot and what’s been not in the past year. So, I activated Alex King’s excellent Popularity Contest plugin (new version out now) to find out what Sciencebase readers have been reading the most on the site over the last 365.256363051 or so days. So, here’s the top ten.

  1. Potato powered mp3 player – a video spoof on lighting a bulb with a lemon battery, don’t try this at home!
  2. How does salt affect the boiling point of water – a perennial question in science class.
  3. Obesity gene – is hereditary to blame for overweight?
  4. The secret of Newton’s laws explained with Lego – If only Newton had been made of plastic. Enjoy the falling apples.
  5. Chemistry News – Regular round up of chemical discoveries
  6. Sniffing out our sense of smell – Olfactory inlet
  7. Christmas rose and hellebrigenin – Christmas chemicals
  8. People caught pubic lice from gorillas – Ewwww, gross!
  9. Egg in a bottle – Yes, air pressure alone is enough to force a hard-boiled egg without its shell into a bottle
  10. Viagra and steroids – Drug testing and elder Congressmen

Not included in this list are archive articles from the legacy version of Sciencebase, which used to go under the name of Elemental Discoveries, you can check out a stack more popular science writing via the archive index page.

All the best for 2008!

Science Blogs, Favourites of 2007

Science OPML

In an effort to keep Sciencebase bubbling along during the holiday season, I figured a quickie post listing some of my favourite science blogs from this year might be interesting. Blogs come and go, of course, and my newsreader account is in constant flux with new blogs that catch my attention briefly getting pole position and then dropping off.

However, I remembered that there is a quicker way for you to grab a recent snapshot of my feed favourites and that is with my newsfeed OPML file (right-click and save the link with an “.opml” extension. You can then import it into any compatible news aggregator, offline (Snarfer) or online (Google Reader) with minimal fuss. Or use an OPML editor to edit it, it’s entirely up to you. My science OPML file is up to date, relatively speaking, although I may have added or removed a few feeds from my own aggregator in the last few days. Anyway, it’s as good as it gets at this time of year.

Meanwhile, a growing list of blogs with a genetics, DNA, and health theme can be found on the DNA Network. At the time of writing, my good friends Ricardo Vidal and Hsien-Hsien Lei are busy creating a new website for the Network that will feed on all the RSS files from the member blogs (I should admit, Sciencebase is a member of the Network). It’s difficult to single out any of the other blogs in the DNANetwork for specific attention, Ricardo and Hsien’s are superb, and so are many of the others. So. once you’ve trawled through my science OPML, do check out the DNA Network too.

Chemistry’s Sun Rises in the East

Andrew Sun Chemistry Blogger

Many of you will know chemist Andrew Sun from his On the Road blog and from his occasional but insightful comments on the Sciencebase site. I recently interviewed him for the Reactive Reports chemistry webzine and you can read the result there in the current issue. I edited his answers to fit the magazine for length and housestyle but I’ve reproduced his full answers to one or two poignant questions here exclusively for Sciencebase readers.

How do you think being a chemist in China differs from working in “The West”?

I don’t know very much how people doing chemistry in the west. I get an impression from videos of lab work posted online. But one difference I am very sure is that we do not have enough money and we do have a poor academic system. Most students still have to pay tuition at the MS stage. The campus scholarship can only pay for a dinner with your friends, and we have far fewer, or no, third-party scholarships here). In the PhD phase public subsidies can still hardly cover the cost of living. Bosses (supervisors) cannot be too nice to their students because they are also running out of money. To apply for more funds and get promoted in a badly designed academic system they have to publish enough papers in high quality journals. They have to publish more in less time so they need more unpaid PhD students working harder.

China pours the world’s second largest bucket of money into science according to statistics, but one should also consider the fact that no NMR machines, no TEM, SEM, AFM sets, neither other instruments, are manufactured in China. Bosses have to buy these from abroad (CNY 1.00=USD 0.13=EUR 0.10, plus taxes) – and regain the cost by charging several hundred per sample for characterization requests. (Cryo-TEM, which is widely used in the study of soft matter, cost CNY 2000 per sample here!) Money thus goes two ways to both buying the instruments needed and to paying the usage fees.

In addition we have a weak chemical industry here which cannot provide qualified reagents. So to conduct a delicate synthesis with less failures in less time, one trick is to buy your reagents from Alfa Aesar, Sigma Aldrich, etc. who charge your boss more. Not to mention the local glassware – we cannot find any tight ground glass joint from local manufacturers. Oftentimes PhD are forced to manipulate impure reagents in a leaky glove box, with minimal budgets to test their products for sure, yet still having to publish in journals with high impact factors.

As such PhD students in China are a depressed group and we hear of suicides among PhD chemists from time to time (in one case the poor guy synthesised a few milligrams of potassium cyanide and…). That’s why now lesser MS grad students are moving on to a PhD. In fact most of the MS students aren’t truly working for science; they are only working for the degree which could mean a slightly better salary than a BS degree in the job market. So most MS students go to find a job once they get their degrees, and yet a large number pursue their career of science abroad. So we have the brain drain problem – obviously the above mentioned situation in China is not attractive enough of them to come back in the future.

However I’m still hopeful because everything is getting better, not worse. Therefore I chose to stay in China during my PhD period.

What more can chemists around the world do to work towards a global chemical community? How might certain more restrictive governments be persuaded of the benefits of such international collaborations?

First it is important for them, both the chemists and the governments, to realize the benefits of international collaborations; not only why, but practically how. Currently with limited communication, for example, a US scientist can hardly know why he/she should cooperate with a Chinese scientist for a project. More communication and understanding between chemists from different countries are needed to start any collaboration. The growing online chemistry community could provide such chances. But currently Chinese chemists who actively participate in the online community are rare; I know no one else except me.

Governments might consider much more, for example the ‘leakage’ of knowledge or secrets. However I believe the advantage of collaboration can outweigh the shortcomings which can be overcome by carefully designed policies and contracts. I guess the Chinese government should welcome global collaborations because we are currently much weaker and have a lot to learn from others. But currently the extent of this is much smaller than I’d hope for. There is still much to change.

For more Reactive Profiles, grab the site’s chemistry interview feed.

Don’t Poison Your Dog This Holiday

Theobromine structure

‘Twas the night before Christmas, when all through the house
Not a creature was stirring, not even a mouse

Well, that may not be quite true, do you know what your dog is doing right now? What about the cat? They’re not rummaging through the presents under the tree are they? You didn’t leave any luxury plain or dark chocolates under there did you? If you did, you could wake up to a quite horrible surprise when Christmas morning comes around. Chocolate makes pets ill! That’s the important seasonal warning being delivered by vets everywhere.

Poisonous chocolatesSo, what’s the problem? Surely a little chocolate snack in the night isn’t going to harm good-old Fido? Well, our vet begs to differ and so do the veterinary toxicology sheets for the chocoholics’ favourite fast-food. Man’s best friend, and several other animals, you see lack a particular liver enzyme that their owners do possess, that breaks down a toxin found naturally in chocolate – theobromine.

Theobromine has nothing to do with the element bromine, rather it is a bitter alkaloid from the seed of the cacao tree, known scientifically as Theobroma. The basic chemical skeleton is a xanthine unit, same one on which several other more well-known natural chemicals are based. The stimulant caffeine (from coffee beans) is a xanthine, for instance, so too is theophylline (found in tea and used in treating COPD and asthma).

Non-chocolate Labrador

Lacking the enzymes to metabolize theobromine leaves dogs exposed to the toxic action of the compound, which can cause vomiting, diarrhoea, hyperactivity, tremors, seizures, abnormal heart rhythms, and in extreme cases death.

So, what are the first signs of chocolate poisoning, what’s the lethal toxic dose, and what should you do if you think your dog has been at the chocolatier’s produce? Well, the first signs of chocolate poisoning are vomiting and diarrhoea, increased frequency of urination, and nausea. A toxic dose that will cause symptoms is about 100-150 milligrams of theobromine per kilogram of body weight, toxic dose could be approximately 250 and 500 mg/kg. A kilogram of milk chocolate will contain about 2 grams of theobromine. So a greedy, little dog is at greater risk of a serious digestive upset than a big gluttonous dog if he or she snaffles a 250 g bar of milk chocolate.

There is no direct way to treat chocolate poisoning in dogs, although inducing vomiting if the animal is caught “brown-pawed” (best left to the vet) is probably a good idea. A dog that has eaten a lot of chocolate will almost certainly require hospitalisation for at least the four days while the theobromine is naturally excreted (It takes about 17 hours for a dog to excrete half of the theobromine in its system, which means this toxin will reach vital organs repeatedly via the blood stream). But, who needs that, or worse, at Christmas? As they say: a gram of prevention is worth a kilo of cure.

For lovers of cats (small, domestic, big, wild) keep the aspirin out of reach. It’s deadly poisonous to felines.

December Chemical Discoveries

In addition to my interview with Chinese chemist Andrew Sun, mentioned earlier this week, the December issue of Reactive Reports features the pick of chemistry news

DNA nanorings DNA Nanorings  A simple approach to making rigid DNA nanorings with tailor-made functionality has been developed by Michael Famulok and his team at the University of Bonn, Germany.

Sunshine superpower Sunshine Superpower  In the depths of the Northern winter, as we approach the shortest day of the year, what could be more welcome than a little sunshine news.

ACS chemical discoveries of 2007 Five Firsts in Chemistry  With 2007 rapidly coming to an end, the inevitable lists are popping up. Not wishing to be left out this holiday season, the American Chemical Society has compiled a Top 5 from its own publications. Oh, and by the way, Sciencebase didn’t want to be left off the wish list either, so I did a Top Ten Molecules of 2007 item just recently.

Ten Computing Tips | Data Recovery

Faster Firefox

Seeing as the holiday season is fast approaching, I thought I’d offer an extra post covering some of the browsing and blogging tips and tricks I run on the Significant Figures site at Sciencetext.com. On that site I used to mainly discuss inappropriate unit conversions, sloppy statistical use, and dodgy typos in the media and still do occasionally.

For instance, there was a lot of press on the comet bigger than the sun issue recently, which interconverted miles and kilometres with astoundingly high improvements in significant figures. Then there was the discussion of how much does Santa Claus weigh

But, like I say, mostly it’s tips on how to get the most from your web browser, improve security, and boost your blog’s performance. It acts as my personal lab book for all kinds of hacks, so I always have an online reminder of tweaks in case I lose track of how I fixed a particular problem. To follow are some of the most commonly accessed pages on the site, hopefully one or two of them will strike a chords and be of use to Sciencebase readers:

So, there you go, if you plan to use any of these, please backup any important data files first to avoid the need for data recovery and don’t blame me if it all goes horribly wrong, you use them at your own risk. I would be interested to hear how you get on if you do apply any of my hacks.

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.

雷竞技官网 Abbreviated

I wrote a rather vainglorious post on my Significant Figures site last week – entitled 雷竞技官网 : 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 雷竞技官网 s 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.

    Deutsche Bahn AG

  • 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.
  • Then there’s DoonesBury, okay, that’s just a D not a DB, but cartoon archives often use “db” to denote the Doonesbury folder. The classic situational scientist episode is a must for anyone struggling with ID and climate change skeptics.
  • 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 雷竞技官网 Actor just for fun.

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