September 2007 – David Bradley

Smelly alchemist

In the Alchemist chemistry news section over on ChemWeb this week – two smelly discoveries caught my nose. The first points the way to a clearer understanding of how we smell, while the second explains the biochemistry of geosmin, the earthy smell of freshly turned soil and the particular bouquet after rain showers.

We now learn from GATech scientists how a sensor array can weigh up atmospheric or aqueous pollutants and why stirring a dendrimer solution could explain the origins of life. Finally, this week, researchers in California have taken the first steps towards building a gamma-ray laser using a quasi-molecule based on positronium. And, the award mentioned this week goes to the RSC’s Project Prospect team, which received the 2007 ALPSP/Charlesworth Award for Publishing Innovation.

Also, in pharma news this week an interesting development reported in FierceBiotech regarding the issue of whether or not clinical trials are safe. I’ve included it in the comments on the write-up I did on the TGN1412 clinical trial that went disastrously wrong in 2006.

Chemical Blogspace Stats

The Chemical Blogspace Zeitgeist page is an interesting round up of chemical blogs. The ChemSpy blog resides at #9 in the top fifty chemistry blogs (trailed slightly by Sciencebase at #13). That in itself is quite gratifying, but it is the other statistics that make for more entertaining reading. Apparently, ChemSpy has a reading index (Gunning-Fog as it happens, based on the most recent three months posts) equivalent to a scientific journal (index of 14). Reading Sciencebase on the other hand is like picking up a Thomas Pynchon novel. But, at least, the site doesn’t rank alongside
In the Pipeline, The Bioenergy Blog, Cheminfostream, and it’s a puzzle…, which all have a Gunning index of between 17 and 20 and so are apparently equivalent to reading a “Manual for Taiwanese DVD player”. Not my words, Cb’s!

By the way, sites also seemed to be ranked on the basis of their use of InChIs, it’s worth checking out this page to see what molecules are being discussed and to see their structures.

Scrolling down, I learn that Sciencebase is fifth most active blog, while, not unexpectedly, Chemspy is not in the top 20 based on activity (frequency of posting). Once again, Sciencebase features in the top 20 based on wordiness (average posts being around 500 words), while Chemspy’s terse commentary (until today, that is) nestles much further down the tree. The final statistic of interest is the measure of friendliness, which might also be referred to as blog nepotism, or blogotism, to coin a word, just how many times a blog links out to other sites in the chemical blogspace. Again, not unexpectedly, neither Sciencebase nor Chemspy feature in the top 20, basically because my posts tend to be standalone write-ups referencing the primary literature and only occasionally have a need to backlink to other blogs. That said, I’d be interested to know if ChemSpy readers would prefer to see more outbound links to related content elsewhere in the chemical blogspace. Please leave your suggestions in the usual place.

Plain or Vanilla Pheromones

NOW with working links!

The latest issue of chemistry webzine Reactive Reports is now online, in this month’s issue:
Plain or Vanilla Some men smell of vanilla while others smell of urine, but it is not always down to personal hygiene or ice-cream tainted Cologne.

Light Controlled Magic Bullet Targeting diseased tissue directly with the drug to teach it, the so-called magic bullet, came a step closer thanks to work by Senior Lecturer in Pharmaceutics Colin McCoy of Queen’s University Belfast and his colleagues.

Insecticidal Synthesis Professor Steven Ley of Cambridge University and his colleagues over the last two decades have been on a chemical odyssey to make the natural insecticide azadirachtin.

Fire Resistant Paint A way to toughen up the latex particles used to make emulsion paints has been developed by UK chemists.

Caffeine, Painkillers, and Liver Damage

We recently reported on how acetaminophen can slow bone growth. Now, researchers in the US are warning that consuming large amounts of caffeine while taking acetaminophen, the widely used painkiller, could potentially cause liver damage. The combination of painkiller and caffeine is a well-known “morning-after-the-night-before” concoction and is often used to deal with an alcohol hangover, which presumably could compound the potential liver damage still further.

A preliminary laboratory study published in the October 15 issue of Chemical Research in Toxicology explains how this toxic interaction might arise not only through drinking coffee and beverages with added caffeine while taking the painkiller but also from using large quantities of medications that combine caffeine and acetaminophen for the treatment of migraine headaches, menstrual discomfort and other conditions. The preliminary bit of this research refers to the fact that it’s only been demonstrated in bacteria engineered to express the appropriate liver enzymes, though.

Of course, health experts have warned for many years that excess alcohol coupled with acetaminophen could cause liver damage and in the worst-case scenario even death. This is the first time that a potentially harmful interaction with the painkiller and caffeine has been reported, and even if it has only been demonstrated to harmful to bacteria you might err on the side of caution and go cafe lite next time you’re popping those pills to quench a hangover.

What is the Structure of Taxol

I’m a bit confused, I had assumed that the complete stereochemistry of the anticancer drug Taxol (paclitaxel) had been assigned years ago, presumably at the point when its first total synthesis was performed if not before. I’ve written about the compound several times, in particular reporting that first total synthesis of the compound in the UK paper, The Daily Telegraph.

However, it seems there is ambiguity spreading across the net. Most notably, ChemSpider’s Tony Williams tells me (and has blogged about it), there is a potential discrepancy in the structure of Taxol given in Wikipedia.

Now, I know for a fact that Wikipedian chemist Martin Walker (see my recent interview with him in Reactive Reports) who is a member of the ChemSpider advisory board will already be on the case to double check and check again the structure in Wikipedia.

Aside from the politics of open access information and data, it is crucial that services like ChemSpider and Wikipedia give their users the correct structure for any given compound. There must be dozens of synthetic organic chemists who have carried out full stereochemical assignments on Taxol and know for certain the correct structure. Perhaps it’s time we had a referendum so that the winning structure could be posted to Wikipedia and other information repositories.

Science Helps Dig Up Your Genetic Family Tree

Genetic algorithm

My wife’s mother is very keen to trace her family tree and has dug up roots as far back as the early 18th century with possible hints at some ancestors dating back to the late 1600s. She has quite a rare and locally focused maiden name, so it has been a little easier for her than it would be for someone in England called Smith. Personally, I gave up any notion of trying to find my ancestors as my name, while not incredibly common is not rare, meaning as it does “broad field” and so is quite widespread in its various forms.

However, a group of computer scientists, mathematicians, and biologists from around the world have developed a new computer algorithm that could help anyone trace their genetic ancestry in minutes without any prior knowledge of their background. This will not, of course, help you find great, great, great grandfather Bartholemew or whoever, but it could provide important insights into your genetic heritage and the true origins of your germ line.

The new program is unique in that it searches for specific DNA markers, single nucleotide polymorphisms, or SNPs (pronounced snips), using nothing more than a DNA DNA sample collected by simple cheek swab. The researchers, led by Petros Drineas of Rensselaer Polytechnic Institute, New York, used genetic data from previous studies to perform and confirm their research, including the new HapMap database, which scientists are using to find variations in the human genome.

“The program will be a valuable tool for understanding our genetic ancestry and targeting drugs and other medical treatments because it might be possible that these can affect people of different ancestry in very different ways,” explains Drineas. The program will also help us understand our unique backgrounds and assist historians and anthropologists in studying the origins of different populations as well as how our global society evolved.

So, while it may not help mother-in-law find her great, great, great, great grandfather and add the final twigs to her individual family tree, the new program (details in Plos Genetics) could lead to a wider understanding our wider genetic heritage, which could lead to the keenly sought personalized medicine. If researchers can uncover the minute genetic details that set each of us apart, biomedical research and treatments can be better customized for each individual, Drineas adds.

Sciencebase archives and artefacts

Sharp-eyed readers may have spotted that, once established, Sciencebase moved on from a simplistic static site to a CMS-driven blog. As such, some of the pages (with a small p as opposed to a WordPress big P) don’t have the acoutrements of the CMS. This isn’t deliberate, it’s an artefact of the way I set up Sciencebase way-back when.

Here are a few that have already made the grade, hopping from an early edition of Elemental Discoveries (the proto-Sciencebase ezine) to the fully fledged CMS – Touch Wood – A Guide to Viagra Louts, the story of Viagra, The Real Butterfly Effect, how the physical structure of butterfly wings is helping technologists create new optically functional materials, and Scientific Stereotypes, in which I discussed children’s perception of scientists and whether or not that perception matters to science.

There are dozens more feature articles in the Sciencebase archives outside the blog system, which you can access using the Science Articles link in the menu above.

Healthy PubMed Searching

This post is more in the bio camp than the chemo field, but may be of interest both to chemists with a life sciences investment and/or hypochondriacs in your lab.

The Healia health portal has added a specially designed PubMed/Medline search to their site that helps consumers retrieve abstracts of scientific articles published in biomedical journals in a more user-friendly way than the standard PubMed search. The system still searches the National Library of Medicine’s (NLM) PubMed/Medline dataset, which includes more than 17 million abstracts and citations from approximately 5000 biomedical journals published since the 1950s. One of the unique capabilities of the additional Healia Clinical Trials Search is that you can restrict searches geographically and map locations of study sites.

It is possible to filter a search to Professionals, Females, Males, Kids, Teens, Seniors, African Heritage, Asian Heritage, Hispanic Heritage, Native Peoples and a few other categories.

What Will You Make with Your 3D Printer

3D Printer

Fancy a new vase or some unbreakable crockery for that camping trip, but haven’t got time to go shopping? What about a replacement for the broken spoke on your spectacles or an individually designed heads for your golf clubs? Or, how about a scale model of that new sports car your kids designed or a mini objet d’art created from photos of a Henry Moore sculpture? The possibilities for 3D printing are limited only by your imagination and what someone could come up with in a 3D drawing package or with CAD software.

3D printing, rapid prototyping, as it is often known, is not new. I first heard about 3D printing sometime in late 1980s while still a student. However, these devices, which have featured in TV shows such as CSI, could soon be coming to a workshop near you and may represent the biggest shift in commerce and manufacturing in decades. The Fab@Home wiki has more information on the technology, but 3D printing, essentially, turns a digitized representation of a solid object, which you might download, email, or create, into a real solid object. It using a vat of uncooked starting material (plastic, metal or alloy) and a laser, or other device, controlled by computer holding the digitized information to build up the object layer by layer.

There are numerous commercial 3D printers, known in some circles as fabbers, being used by the military for creating battle components in the field, in design studios for prototyping, and more recently for creating just about anything you care to name. However, once the killer app emerges, these machines will quickly enter the mainstream.

There are several videos of 3D printers in action on Youtube. But, I was brainstorming with my wife today, while walking the dog, to see if we could think of that killer app…clothes, disposable diapers or nappies, plastic paperclips, teacups, and buckets, were my first few suggestions. But, I blush to tell you what her first suggestion was…sex toys. Moreover, it’s our silicon wedding anniversary today, and all I could think was that she was trying to tell me something.

But, then it occurred to me, how 3D printing might rapidly move into the mainstream, and no, I’m not thinking of rubbery objects for the bedroom, but virtual gifts!

With the advent of social networking and web 2.0 communities there are often occasions when you might wish to reward or surprise someone you meet or interact with in such virtual spaces. Being sent a link to an interesting site, image, or music file as a gift is nice. But, what if you could send someone a solid object without actually having to buy it, package it up (discretely in some cases), and ship it out? A 3D printer suddenly becomes a way to spread the lurv in polymer resin. And, if you’re getting really close to that certain someone you met online, then you could always take on my wife’s original idea, and spread more than a little lurv, although I don’t a 3D printer exists yet that can produce 1.5 volt batteries.

What will you make with your 3D printer?

Diagnosing Disease With a CD Player

Years ago, I wrote about the lab-on-a-CD concept (actually it was in the September 2001 issue of Reactive Reports). Now, it seems the use of CD-ROMs and DVDs and the hardware used to play these popular audio and video compact discs (CDs) is coming of age in terms of home health monitoring and laboratory-based testing. Spanish scientists say CD technology could be adapted for tests ranging from the measurement of environmental toxins to at-home disease diagnosis.

Angel Maquieira and colleagues at Valencia Polytechnic University, Spain, have developed a CD with an immunoassay surface coating that can detect three pesticides, 2,4,5-TP, chlorpyrifos, and metolachlor, when samples are placed on the disc. By spinning the disc in a CD player the standard laser light can “read” the chemistry of the bound pesticides and a computer interpret the changes in laser intensity to identify them.

“The obtained results show the enormous prospective of compact discs in combination with CD players for multiresidue and drug discovery applications,” the researchers say. They are now improving sensitivity and versatility.

More information in the journal Analytical Chemistry