Biology with Firefox

Firefox-using molecular biologist kinda person? Then, you should check out BioFox (thanks for Bertalan Meskó of ScienceRoll for the tip off).

Code bioFOX integrates various bioinformatics tools into the Firefox web browser, allowing users to analyse genes without all the hassle of retrieving data from NCBI or Swiss-Prot and can then manipulate the information via various tasks including: Translation of a nucleotide sequence, blast search (For eg. blastn, blastp etc.) of the desired nucleotide/protein sequence, calculation of properties (like PI, charge, molecular weight, AT/GC content etc.) of a protein/nucleotide sequence, conversion between formats (Genbank, Fasta, Swiss-Prot etc.), and prediction of sequence for sub-cellular localization (PREDOTAR, TargetP, pSORT etc).

Maybe chemical connector Tony Williams is reading this and thinking…How might a Firefox Plugin be used to provide chemists with similar levels of information manipulation and functionality via their databases, such as ChemSpider?

Medline on Facebook

For those who care about such things as online social networking, and if you’re reading this blog, I assume that could be you, there is now a Facebook application available that allows you to cite your journal publications (provided they are listed in PubMed).

You can add the Medline Application (yes, I realize PubMed and Medline are not synonymous, but that’s the name the authors used) – by following this link.

I’ve added a few of my publications from Science, Nature RDD, Drug Discovery Today and PNAS, they’re listed towards the bottom of my profile below my Flickr gallery.

Chemical Language Translated

Gold Book Logo

During my time at the Royal Society of Chemistry (do I sometimes make it sound like a prison sentence?), I watched in awe as my old mucker Andrew Wilkinson helped reformulate the IUPAC book of chemical definitions commonly known as the Gold Book. That mighty auric tome is online and searchable with a click these days. And is as useful as ever to chemists looking for a quick description for a jargon word.

Take chiral, for instance: “Having the property of chirality“. Hmmm. So, look up chiral: “The geometric property of a rigid object (or spatial arrangement of points or atoms) of being non-superposable on its mirror image; such an object has no symmetry elements of the second kind.” Such a crisp and easily comprehended definition. Not.

Obviously, there is a need for technical definitions, but somtimes such definition simply complicate something that could be just as easily described often with a single word. Chiral = handed. (The clue’s in the word itself, which comes from the Greek for hand and I’m pretty sure the scientist who coined the term did so to save us all the trouble of talking about non-superimposable mirror image objects (you know, like hands and gloves?). Indeed, many a chemistry student would grasp the concept much faster and many a lay reader of a scientific paper would understand if such terms were explained in parallel with their simpler analogue. So, for all you non-chemists, here’s a Boxing Day list together with links to their technical definitions if you need the fully Monty,

  • Chiral – handed
  • Hydrophobic – water hating
  • Hydrophilic – water loving
  • Micelle – microscopic bubble
  • Cyclodextrin – starch rings
  • Mass – how much stuff
  • Isotope – same element, different mass
  • Bond – a link between atoms
  • Organic – made with carbon
  • Inorganic – made without carbon
  • Lipid – Oily or fatty natural molecule
  • Morphology – shape
  • Half life – Time taken for value to half
  • Second Life – Virtual meeting place

Obviously, these simple definitions gloss over the finer details, but isn’t that the point of a glossary? “Professionals often face difficulties explaining these terms to lay people because they are too aware of the exactness of the concept, emphasizing both the morphological and functional aspects,” says chemist Andrew Sun, recently interviewed in Reactive Reports. There are many more I use in writing for a non-technical audience, but some jargon words are quite stubborn. Are there any good, simple definitions for the following?

  • Polymer
  • Sublime
  • Catalyst

A Billion Light Years from Home

Cosmic death star (Credit: NASA et al)

Have you ever come across this kind of description of an astronomical event:

“…astronomers have witnessed a supermassive black hole blasting its galactic neighbor with a deadly beam of energy…Both galaxies are situated about 1.4 billion light-years away from Earth…The offending galaxy probably began assaulting its companion about 1 million years ago…”

How can that be? asks Sciencebase reader Adam Azman. If the event is at a distance of 1.4 billion light years from Earth it will have had to have started its journey from that point in space to reach us 1.4 billion years ago, yet, the article tells us the event only began 1 million years ago? It seems quite paradoxical, but according to Dave Mosher, author of the article Galaxy Blasts Neighbor with Deadly Jet, the explanation is quite simple and essentially glosses over Einstein’s theory of relativity to help astronomers talk about the times and distances as if there were a fixed universal frame of reference.

“Most astronomers,” Mosher told Sciencebase, “refer to time relative to Earth when they say something happened. E.g. as an observer on Earth 1 million years ago, the event would have just been getting started. They avoid stating it happened 1.401 billion years ago because of the quirkiness of relativity…in other words, just because light appears to be 1.401 billion years old doesn’t mean it actually is… there’s too much fudge factor to be certain. It’s more accurate AND precise to say the light reached Earth 1 million years ago.” He admits that the issue sometimes “fries his brain”, and told Sciencebase that he is “really going to start putting an explanatory graph in my stories from now on… there’s no way around it.”

Meanwhile, Azman, a chemistry student at the University of North Carolina Chapel Hill, had also done some digging of his own and had spoken to Bryan Preston, a political blogger who often writes about cosmological matters. Preston’s explanation is close to that of Mosher, “The ‘million years ago’ bit is a reference to ‘as seen from earth’ – if we’d had a Hubble telescope a million years ago, we could have seen this event begin,” he says, “But the event actually happened 1.4 billion years ago and it took the light that long to get to us to see it in the first place.”

Preston adds that, “if we’d been technologically advanced a million years ago, we’d have used that technology to see the start of the Death Star’s bombardment of its neighbor. To have seen it all happening when it actually happened, we’d have had to be at the scene, 1.4 billion light years away from Earth.”

These timelines can be confusing and are a constant source of letters to the editor for popular science publications and space websites. “For instance,” adds Preston, “we name supernovae by the year they were observed to have blown up, hence SN1987A. But that star was 100,000 light years away, so it actually blew up 100,000 years ago, but we just saw it blow up in 1987 because it took the light 100,000 years to get here.”

It’s all relative, you see?