Pod, poddy, podd

Apple has got ever so touchy about websites using the term podcast more liberally than its claims to trademark registration would allow. Cease and desist letters have been sent to the likes of Mypodder and Podcastready by the company, according to reports in Wired and The Register.

There are, of course, some bloggers that claim that the term podcast actually has nothing to do with Apple’s brand of mp3 player and that it originates in the phrase “publish-on-demand”-cast. Yeah, right!

Nevertheless, there is no mention of Apple in the dictionary.com definition of podcast: “a Web-based audio broadcast via an RSS feed, accessed by subscription over the Internet” or “to deliver a Web-based audio broadcast via an RSS feed over the Internet to subscribers”. Moreover, despite the term having an obvious etymology in a bastardisation of iPod and broadcast, neither an iPod nor over-the-air broadcasting is need to make or listen to a podcast.

Mark Ramsey of Hear 2.0 reckons it’s time we ditched the term podcast anyway, too few people “get it” he says, and the word should be changed to “audiomag” or something similar. This assertion is made despite the fact that the Ricky Gervais Show is mentioned in the Guiness Book of Records as the most popular podcast, presumably that will change soon with the launch of Sciencebase’s very own Geordie Boffin Podcast. Well, we can all dream, can’t we?

Bizarrely as ever, The Register includes a list of podified words in its report: antipodean, cephalopod, chiropodist, monkeypod, podgy and uropod. They overlooked arthropod, podiatrist, peapod, monopod…some of which point to the fact that pod, the prefix, has its etymology in the Greek word for foot. Maybe it’s time to give it the boot and go with Ramsey’s suggestion, or better still, we could rename them “blogcasts”, no doubt that would open yet another can of bad applies as the trademark owner of that term would more than likely kick up a fuss too.

Top Ten Hot Biologists

Purely in the interests of science, I headed over to flickr to see if I could find a snap of a particular biologist I was writing about today. Couldn’t find a single one, but all the faces that came up got me thinking that perhaps it would be fun and waste a few minutes when I should be working to pull together a list of the top biological totty. So, here it is a whirlwind tour of the world of biologists, in no particular order and no one vetted particularly closely.

Female biologists in action

  • Ninoka
  • Heather
  • Louise and friends
  • Susan
  • Claire
  • Alicia
  • Cerbu
  • Neguin
  • Elinay
  • Beck

For the sake of completeness, and to avoid accusations of sexism, I also gathered together ten male biologists in the field who also featured on flickr.

  • Glyn
  • John
  • Geoff
  • James
  • Dan
  • Alan
  • Bruce
  • Stan
  • Jeff
  • Chuck

I’ll leave it to Sciencebase readers to decide which if any should be in either top ten list. One thing to note, facial hair is common among biologists (but only in the second list).

Tomorrow, physicists on Pixsy.com and then chemists on myspace

Ironically small

An incredibly small item in Saturday’s Times announced that a Voluntary Reporting Scheme – established by DEFRA – in the UK to record and assess the risks posed by nanoparticles has been created. Scientists have welcomed the announcement, apparently. More likely, they are rather peeved that yet another layer of bureacracy has been added to their workload.

According to the paper, “Little is known of the potential risk to health by the creation through nanoengineering of altered particles.” No doubt, UK tabloids and scaremongers will jump on any future pronouncements as an admission of guilt once the first minute risks are revealed. Forgetting, of course, the enormous risks we face every day simply cross the road or jumping in our nanoparticulate-pumping cars.

Interestingly, there is a get out clause for scientists who may wish to peel back that bureacratic layer. The scheme is entirely voluntary!

So, if you’re an “evil scientist” intent on creating a doomsday scenario on a very, very small scale, then you needn’t worry about being risk assessed, just don’t add your research to the database.

Geordie Boffin Science Podcast – #1

UPDATE: I recorded just six episodes, but time pressure and deadlines at the time meant its untimely demise, I may resurrect the Podcast at some point, but I think it would be much better served if I did it as a chats type discussion on science news with colleagues rather than it simply being me reading out the latest blog post.

Geordie Boffin Podcast

Welcome to the first Geordie Boffin Podcast from David Bradley. This irregular and irreverent podcast will bring you audible reporting from the sciences. For most Sciencebase readers this will most likely be your first chance to hear my dulcet tones (and those of my wife) as well as a little effected guitar playing for the intro!

You can play the sound file by using the media player built-in to this post, download the mp3 and stick it on your iPod.

Check out our information sheet for more about the Geordie Boffin Podcast, and for some definitions, in case you’re wondering what any of those three terms actually mean!

Chemical structure lookup service

The NCI CADD Group headed by Marc Nicklaus and colleagues has just launched the Chemical Structure Lookup Service (CSLS). This web-based system allows one you to locate chemical structures in over 70 different public and commercial data sources. Stored within the system is information on over 30 million chemical structures and it provides a simple search interface for looking up chemicals by specific structure as well as by parent structure, and by various identifiers.

There are two mirror sites: http://cactus.nci.nih.gov/lookup/ and http://cholla.chemnavigator.com/lookup/

Smells like Godzilla

I once interviewed renowned odor theorist Luca Turin who described one particular group of chemicals as being the “the Godzilla of smells”. He added that “You can’t believe how awful they smell…They make you vomit your guts out instantly.” Thankfully, I never came across them when I worked in a lab, but I’m sure he’s right.

Of course, the reason that I never happened upon these compounds during my lab days is that they have such an offensive odor that mosts chemists side-step them when designing their syntheses. That’s a shame though because they have several distinct benefits missing from the properties list of other ingredients.

Now, Michael Pirrung and Subir Ghorai, of the University of California at Riverside have found a way to make a new family of isonitriles. Their approach uses low-risk starting materials and they work well in the kinds of chemical synthesis reactions in which existing compounds are not quite so good. But, more to the point, these isonitriles don’t make you vomit. Instead, that have rather pleasant odors of soy, malt, natural rubber, mild cherry and even caramel, according to the team.

A bad smell is usually an indication that something won’t be too good to eat though. A mild cherry and caramel reaction sounds almost tasty, but I would seriously not recommend making it a lab-time snack.

More on isonitriles in the latest issue of JACS.

Cheating agents

Sciencebase visitors commonly search the site for specific chemicals they’re interested in. Of course, I’d always recommend hoping over to Chemspy.com for structures, MSDS and other information. You can search PubChem, ChemFinder, ChemRefer, ChemIndustry and several other chem sites via the ChemSpy toolbox (bottom right, homepage, enter your keywords and click the database of choice)

Anyway, yesterday someone was looking for 2,4,6-tri(2-pyridyl)-1,3,5-triazine, so I did a quick search myself to see where the interest in this compound lay. Lots of search results came back, but one in particular caught my eye, this claw-like molecule is apparently a “cheating agent”, at least according to a patent that came up on an esp@cenet search. Now, unless the compound in question has gained some novel yet devious physiological properties, I’d have to assume they missed the “l” and that it’s actually a chelating agent that can grab on to metal ions with more than one of its own items with a claw-like grip, in fact. I could be wrong…

Why Does Natural Selection Take So Long

In an item on The Register about why natural selection takes so long to get results, Dr Stephen Juan, an anthropologist at the University of Sydney makes several statements that seem to me to be at odds with evolutionary theory.

“Most mutations do not help the species survive.”

This is true in one sense, but natural selection doesn’t act on species, all it does is remove individuals from the gene pool that are no longer best adapted for a particular environment. If a mutation in an individual’s DNA mean it is better adapted to a changing environment then it will pass the “new” gene(s) on to its offspring who will then have the trait and the viability in that environment to reproduce and so on.

“A species and an environment exist in balance with each other.”

Do they? Perhaps, but only in the sense that should either one change radically then we will no longer observe a balance. Moreover, several mutations over several generations that allow individuals to cope with a changing environment leads to species diversity.

“Populations simply adapt to their current surroundings and to changes in those surroundings.”

No they don’t. Individuals either survive the new surroundings and pass on their genes to their offspring or they don’t. Usually, only those best adapted to new environmental conditions survive to do so. Populations may display synergetic effects between individuals but this is not the same as a population adapting.

“They do not necessarily become better in any absolute sense over time.”

There is no such thing as “better” or “worse” evolutionarily speaking. An individual either survives and passes on its genes or it does not. If those genes endow the offspring with the ability to survive and pass the genes on again then the genes survive. If they don’t they are lost. Evolution is littered with dead-ends but every single living thing on the planet has ancestors that were capable of reproducing.

Random search beats algorithms

Search EnginesSearch engines spend huge amounts of money fine-tuning their search algorithms, but a report in the journal Complexus suggests that they might be wasting their time. Lörincz and colleagues argue that random results provide just as many positive hits on a given subject as even the sharpest algorithm available. You can read my interpretation of their findings in this article on search engines.

Reposted with link correction.

Giant planet makes metallic water

Can planetary giants make metallic water? That’s a question answered theoretically by US scientists in this week’s Alchemist, we also learn why mussels are not as happy as clams thanks to Prozac, what makes organic semiconductors light up and the possibility of powering your mp3 player with your beach umbrella. Also in this week’s news distillate, uranium-munching bacteria have the mettle to construct nanoscopic platinum particles. Finally, digestion on a grand scale could be releasing five times as much methane into the atmosphere above Siberian lakes.

The latest chemistry news from ChemWeb.