Month: July 2005

US Patent 6,907,350

Fed up with -omics (you know what I mean, genomics, proteomic, metabonomics etc etc etc etc ad infinitum…….?)

Well, a recent US patent from Japanese chemists seeks to create yet more. They claim to have coined the term “chene” meaning a chemical substance (what was wrong with chemical or compound I don’t know), and that we can now look forward to chenomics – the study of the interactions of chenes with biological systems.

What annoys me about their choice of word is that they’ve hybridised chemical and gene to make chene (obviously), but I would have thought the natural successor to the word chemical would be a cheme (a la Dawkins’ “memes”).

The word chene could have a bright side though, if science writers and journalists were to adopt it, we might be able to stave off some of that rampant chemophobia that litters the media these days.

Imagine the headlines: “Explosion at chene plant leads to thousands evacuated”, “Chene spillage closes freezes traffic into DC”, “Chene sensitivity causes eczema”….it would obfuscate the underlying public relations problem nicely…or maybe not.

Chemistry Magazine (September 1946)

A chemistry magazine from 1946 has made its debut on ebay. Is this the first item of chemical historical interest to appear I wonder? It’s certainly not something I would have thought to look out for, but the seller emailed me the link: Chemistry Magazine (September 1946) [link now excised], so I thought I’d give it a plug.

The issue discusses radioactive poison warfare, making Germany self-supporting, and the chemical industry on the west coast. It could be a contents list from a current issue of C&EN for all we know. Plus ca change.

Facial

My wife uses a facial toner from a famous UK store that claims to have “Plant extracts at levels that really work” and is obviously marketing at the cynically savvy consumer who has realised “homeopathic levels” are a nonsense. That’s all well and good, but the list of ingredients in this product still looks to be pretty much a standard set of cosmetic chemicals to me – “Aqua, butylene glycol, alcohol denat., glycerin, polysorbate 20…and at last…Equisetum arvense, then phenoxyethanol, lactic acid, glycolic acid, parfum, citric acid, dipropylene glycol, malic acid, sodium citrate and tartaric acid…

…that plant extract is from the noxious weed field horsetail. Is this really something you’d want to be rubbing on your skin at “levels that really work”? I better warn my wife.

ID Theft

Is it just me, or does it strike anyone else as odd, that at a time when we’re being warned about bank security, phishing and identity theft, that my bank asked me to send a completed credit card application with all my personal details and a signature together with my driving licence or birth certificate and a utilities bill through the post? Haven’t they got the electronic means to verify my identity?

Doubly odd is the fact that all our utilities are paid for through electronic funds transfer and we only get an email receipt, which could easily be changed! So, how will a copy of a utilities bill help them confirm who I am anyway?

PubChem – Making Chemical Information Open

A Eurekalert report discusses the topic of PubChem, a database I mentioned last year in a Nature news item.

This time, the issue is more contentious than an announcement of how useful such a database might be as certain toes in the profit-making-not-for-profit sector have been trod on.

According to my good friends Peter Murray-Rust and Henry Rzepa, an XML-based approach to the communication of chemical information in the biomedical literature would prevent the loss of crucial information and facilitate the re-use of data – and would be easily achievable using existing open tools and resources. They have published a commentary article in the Open Access journal BMC Bioinformatics arguing that it is time chemistry followed in the footsteps of bioinformatics and structural biology and moved towards the creation of an open semantic web facilitating access to chemical information.

PMR of the University of Cambridge, John Mitchell and Henry Rzepa of Imperial College London argue using three case studies that conventional methods such as cutting-and-pasting chemical information are time-consuming and introduce errors. The authors argue in favour of an open XML architecture linking to connection tables or open databases such as PubChem, to identify chemical compounds mentioned in the biomedical literature. Their article thus provides additional support for open chemical databases like PubChem, which is currently at the centre of a legal battle between the NIH and the American Chemical Society (ACS).

The chemists explain that an open XML-based architecture would provide a cost-effective and user-friendly way to publish chemical information.

Google Search: umberleevabull

Google really is rather clever, isn’t it. As a jape I used the “word”, umberleevabull in a chat to a friend. Try a search on that word and Google recognises that you really meant unbelievable: Google Search: umberleevabull.

Unburleaverbull!

(Doesn’t recognise that one though, hah!)

Footnote: Actually, it now does recognize that last spelling and once again suggests Unbelievable. I presume they have some sort of algo in place that automatically updates the database when someone uses the misspelled word and lets Google correct them. Very, very clever.

Happy Birthday mp3

On July 14th, 1995, the mp3 was born!

Its the tenth anniversary since the Fraunhofer Institute for Integrated Circuits IIS researchers who came up with the mp3 sound compression format decided mp3 was a much easier name to remember than “ISO standard IS 11172-3 MPEG Audio Layer 3”.

Thank goodness they did. Can you imagine the anchor guys trying to get their collective tongues around that mouthful every time they reported on the advent of music file sharing and the emergence of the portable digital music player over the last decade.

With a great lack of foresight, however, the Fraunhofer team suggested that their audio codec, first developed in 1992, would be far “too complex for practical application”. This less than famous proclamation won’t go down in history like Bill Gates’ alleged questioning of the need for a PC to have more 640 kilobytes of RAM. But, no one living in this century could fail to appreciate the omnipresence of ISO standard IS 11172-3 MPEG Audio Layer 3 today. Unless they’ve only ever heard of iTunes and bypassed Napster, WinMX, Gnutella, Kazaa, Grokster, eDonkey, Torrents, etc etc…

Of course, in defence of the Fraunhofer guys it has to be mentioned that they moved on a long while ago and came up with mpeg4…

By the way, if you’re one of the many readers who hit this page looking for the kids party song, try this link to search Google for the happy birthday mp3.

Red eye removal

red eye removal

A neat way to remove the old red eye problem when you’ve taken a portrait with your camera’s built-in flash and the subject was staring right at the camera, is to paint it away. Unfortunately, this can be less than realistic because the catchlight and other details in the eye are lost.

Instead, of simply blasting black into the eye, use a
soft brush set to ‘color’ mode and set the brush color to black. Then carefully paint over the red-eye area to remove it. This desaturates the area you painted over without loss of detail in the eye. You might want to then use the “burn” tool to darken the pupil a little more to produce an even better result.

The catchlights in the eye and any other gradations are retained with this red eye removal technique – results in a much more natural look than those automatic red eye removal tools in iPhoto and other programs.

Sometimes the red eye flash back from the retina spills over into the iris too. You hopefully know what colour your subject’s eyes are normally so set the foreground colour to that hue rather than black (if you have a photo of them without red-eye use the dropper tool to grab the color) and with a soft and suitably sized brush set to “color” mode once more, paint over the iris area with this color. Results may vary and you may want to use masks and layers and all that other stuff to help you get the most natural and authentic look. Obviously, none of this is automatic, but then who wants automatic photography?

I’m proud to say that this tip was featured in Geoff Lawrence’s flash photography tutorial from whom we’ve borrowed the thumbnail of the red-eye girl above.

Citrus Compound Cuts Cholesterol

It’s old news now, but a recent visitor to Sciencebase hit the site searching for citrus PMFs, so here’s a link to the information they were probably after: Compound found in the peel of citrus fruit can potentially lower cholesterol more effectively than some prescription drugs, at least if you’re a hamster.

According to multiple media reports, “US scientists fattened up hamsters on a high-cholesterol diet, and then fed them compounds found in tangerine and orange peel. They found the compounds significantly lowered the animals’ levels of LDL cholesterol – which is associated with heart disease.”

The compounds in question are a kind of antioxidant known as polymethoxylated flavones (PMFs).

Diagnose-it-Yourself

Almost every minor symptom seems to be tied to a deficiency in some mineral or micro-nutrient or other, according to the Body Language site. I’ll leave visitors to check into the affiliations of the website, in case they’re simply touting supplements, although I don’t think they are.

Meanwhile, a taster, as it were:

Muscle cramps, calf tenderness, hypertension? – Magnesium

Wheezy after fruit/veg/wine? – Molybdenum

Stretch marks? – Zinc

Vitiligo/premature grey hair? – PABA and magnesium