I have just push live a Network Protocol entitled A method for quantifying phonotaxis in the concave-eared torrent frog which gives details for a method used in the Nature paper Ultrasonic frogs show hyperacute phonotaxis to female courtship calls. And was very pleased by the ideas of “phonotaxis” and “ultrasonic frog”.

You might want to check out this figure from the Nature paper. I wonder what that frog is tying to do to the loudspeaker…

Anyway, it seems that the people the bring us ChemDraw also make some e-mail greeting cards: Mother’s Day cards, Valentine Cards…

Click here to find out more.

I am not sure exactly why I am blogging about this.

Sidetrack: While I am happily married, I do sometimes slightly envy single people – speed dating, for example, sounds like a lot of fun. Anyway, I realised this morning that the closest I come to speed dating is reading a collection of short stories written by different authors.

I am currently reading The Best British Mysteries 2005 and thought that “School Gate Mums” by Murial Gray was most enjoyable. Definitely interested in a second date…

I am especially pleased about:

Chemical Modification

and

Synthetic Chemistry

As these protocols previously did not have a suitable home.

While it is excellent that they are fixing the problems (Hoorah! Keep the updates coming if you are fixing things where “vulnerability can be used to run attacker code and install software, requiring no user interaction beyond normal browsing”.), what worries me slightly is that this in not really a list of “Known Vulnerabilities”: it is really just a list of “Fixed Vulnerabilities”....

We are finally starting the process of moving our content between the old set of categories (which noticibly did not have a suitable home for our chemistry content), to the new set! In this in-between phase, the new categories are being populated, but they do no appear on the category list on our website.

I thought that I would just post these links here so that they exist somewhere!!

Biochemistry and Protein Analysis

Cell and developmental biology

Cell and tissue culture

Chemical Modification

Computational and theoretical biology

Genetic analysis

Genetic Modification

Genomics and proteomics

Imaging

Immunological techniques

Isolation, Purification and Separation

Microbiology and virology

Model organisms

Nanotechnology

Neuroscience

Nucleic Acid Based Molecular Biology

Pharmacology and Toxicology

Plant Biology

Spectroscopy and structural analysis

Synthetic chemistry

The questions that I think we face as individuals or as communities are:

1. Is it important that life, and human life in particular, has meaning?

2. What would constitute meaning in this context?

And it is my opinion that our answers to these questions underpins most of our views on topics as far ranging as “what consitutes cheating in a online Scrabble game?” and “what is the best way to deal with the whole global warming thing – is it even my problem?”. It especially affects whether we see issues as being “black or white” (and hence uncomplicated?), “Shades of grey between blocks of black and white” complicated?), or “shades of grey with no black or white endpoints” (so complicated it is almost better to ignore it and do something else?).

My comments on question 1

Life does not have to have meaning.
Life is meaningless in itself – for it to have it meaning we need to “do effort” to either give it meaning or search for a meaning that satisfies us (which may boil down to the same thing).
A no answer to this question may free many people to be happy and guilt-free.
For a lot of people the idea of life not having meaning is not something that they would be prepared to consider.
A sense that life is meaningless without concomitant happiness might lead some people to self-annihilation in one form or another.
I would prefer that life, and my life in particular, had meaning, but am coming to believe that happiness is more easily achievable (in the same sense that love is more achievable than fairness).

My comments on question 2

There are too many answers to this question!

I cannot even make up my mind about whether meaning is the “motivator” or the “action”.
E.g. 1
God loves me. (Motivator)
I will devote my life to comforting the sick. (Action)

E.g. 2
I am worried about global warming. (Motivator)
I will devote my life to improving the efficiency of solar panels. (Action)

My opinion is that Action is an important part of a meaningful life, but the Motivator needs to be strong enough for us to overcome the necessary “activation energy” (there we are – I have used a scientific term, therefore this is a scientific blog!). A problem, of course, is that this meaning-driven action can take the form of flying into buildings or forcible redistribution of land.

(The “me” in the two examples, is not really me – in case you were wondering. I work at Nature Protocols, and while this is fun, I would have difficulty arguing that doing this constitutes meaning in any Big Serious sense of the word.)

Since Ed Southern developed the Southern Blot, there have been a number of related methods that have been named after compass directions. The two featured articles this week are for south-western (protein-oligonucleotide interactions) and far-western blotting (protein-protein interactions).

Southwestern blotting in investigating transcriptional regulation

Detecting protein–protein interactions by far western blotting

Related Network Protocols

Network Protocols are uploaded by researchers using the protocols.nature.com link. They are usually published within a day or two of being submitted (or as soon as any linked Nature paper appears in PubMed) and form a large portion of the open-access content of our site.

Here are some Network Protocols for “compass-direction” methods:

Northern Blot analysis of mRNA from mammalian polyribosomes

Western blot analysis of sub-cellular fractionated samples using the Odyssey Infrared Imaging System

TH17 cells contribute to uveitis and scleritis and are inhibited by IL-27/STAT1 in the retina (3) Western Blot Analysis

Lunch Box

I have been browsing through the boxes in our protocols (as one does on a Saturday afternoon) and found two that use reagents that you buy at normal shops like greengrocers and butcheries.

Preparation of celery juice extract

Preparation of bovine thymocytes

It is the kind of place where the train station has a rather beautiful canopy of solar panels that power the station lights.

It therefore seems out of place that the station should contain adverts for two really Big, Serious Things that it seems unlikely could be major concerns in this little backwater.

amfAR, The Foundation for AIDS Research

STOP THE TRAFFIK - a global movement against the trafficking of people

I started to wonder: why were these adverts in Woking station? The only reason that I can think of is that someone must think that us commuters have the resources to do something about them.

It also got me to thinking: perhaps my back-of-the-water blog could also be a place where Big, Serious Issues were raised…

(the problem is that Big, Serious Issues are almost always Very Complicated...)

Enzymes can be very useful catalysts in organic synthesis as they tend to have excellent enantio- and regioselectivity. The enzyme used for this reaction is cyclohexanone monooxygenase (CHMO) from A. calcoaceticus. In this method both the starting material and the product are adsorbed on a resin so that neither build up in the reaction medium, and they can be effectively removed once the reaction is complete.

Other related methods described in Nature Protocols are listed here:

One-pot three-enzyme chemoenzymatic approach to the synthesis of sialosides containing natural and non-natural functionalities

Here, an example of an enzyme combination used is: E. coli K-12 sialic acid aldolase, NmCSS, multifunctional P. multocida sialyltransferase and P. damsela 2,6-sialyltransferase

Pyruvate aldolases in chiral carbon–carbon bond formation

The enzyme is 2-Keto-3-deoxy-6-phosphogluconate aldolase (KDPG)

High-throughput screening of activity and enantioselectivity of esterases

In this protocol the objective was to screen esterases (or other hydrolases) produced after random mutagenesis to determine their substrate specificity and enantioselectivity. The idea being to “optimize” enzymes for specific reactions.

Immobilization of enzymes on heterofunctional epoxy supports

Attaching an enzyme to a solid support is advantageous, because (1) it means that it can easily removed from the reaction medium once the reaction is complete and (2) the immobilised enzyme is pinned into a more rigid conformation making it so that its function is less sensitive to temperature, pH and the presence of organic solvent.

A small but crucial part of that supply chain is the inspection equipment looking for foreign bodies in the food. This aims to ensure the quality of the food dispatched from factory to distributor, supermarket or perhaps another factory higher up the processing chain. There are basically 2 types of inspection equipment:

• Metal detector
• X-ray

Metal detectors work on the principle of electromagnetic induction. This works well for ferrous metals in dry products, but works less well for certain grades of stainless steel or in wet or salty products. X-rays are a more more expensive inspection option. This technique is being increasingly used in the UK due to the limitations of metal detectors. A good X-ray will
be able to detect a small piece of glass in certain products where a metal detector would have no chance of detecting the glass.

An important contaminant in meat products is actually metal from three main sources, the first being obvious but the latter two will surprise a lot of people:

• Metal from the machinery used to process food
• Broken needles
• Lead shot

Whoa! Back up there, you say. Broken needles? Lead shot? How do these get in the food? Good questions and lets deal with them one at a time.

Firstly, since a lot of machinery is used in producing your TV dinner, this implies a lot of screws, bolts, washers, wires, meshes, cutting implements and so on. There may also be contaminants that are part of the product itself, such as the clip on the see-through plastic bag surrounding a loaf of bread – great on the bag, not so great inside the bread. So with all those moving parts, accidents do happen. A bit worrying, true, but logical to make sure a screw hasn’t worked itself loose and fallen into a mince pie.

X-ray image of dog food where one of the clips (found on the ends of the sausage) had found its way inside.

Needles are used on animals a great deal. There are innoculations when the animal is young and then later in their short lives to provide medicine when the animal gets sick. More disturbingly, however, steriods and antibiotics
are used regularly to produce more meat and faster. Pigs commonly squeal and jerk when injected, breaking off the needle which cannot always easily be retrieved.

The next contaminant, lead shot, is perhaps the most surprising of all.
While this is not common in Europe, in the Americas (both North and South) lead shot from game hunters is common. Indeed, the article that inspired this blog is about lead shot in elk. Killing animals is never clean and clinical in the best of environments and killing them in the wild even less so. Even if the hunter does intend to eat the animal, it may happen that the animal escapes after having been shot and only dies later of its wounds.

Even more surprising is lead shot from another source – animals shot not for sport but for thrills. While thankfully not commonplace, there are a significant number of examples of cows, horses (eaten in Argentina and other places) and pigs which have been shot with a non-lethal dose of lead pellets by young hillbillys out for a drunken laugh. When the animal finally does
get to the slaughterhouse, the meat supplier may not even know that the animal has a significant number of lead pellets buried in its body.
Hopefully the metal detectors and X-rays will find these pellets and prevent them from finding their way onto your plate.

Happily, not all aspects of food production are quite so disturbing! On your next trip to the supermarket, when you are about to pick up that cream pastry consider how it got there, smartly packaged next to hundreds of other enticing products. It certainly is food for thought.

Thank you to Alain Dekker for writing the text and supplying the image for this post.

Done using firefox. It obviously did not crash though things did become very slow. :)

Saccharomyces cerevisiae (budding yeast), the yeast of these yeast-extracts, has been used in baking and brewing since the dawn of civilisation.

It is a very useful model organism and was the first eukaryote to have its genome sequenced. It is also one of the key reagents in our latest featured protocol.

Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae
(Authors: Natalay Kouprina & Vladimir Larionov)

There is absolutely no sense in which this constitutes news, but it really is turning into “one of those weeks” where microsoft keeps apologizing to me in these little boxes. The fact that I compulsively send the error reports adds another 5 seconds to each experience. I was uncertain whether there was any point to doing this, really, until my husband directed me to this video:

We Share Your Pain

(you will need sound)

It’s rather old, but I had never seen it before and maybe it is new to you too.

This photo taken near work demonstrates yet again the absolute uselessness of umbrellas in anything stronger than a gently shower.

There seems to have been a flood of questions on the Nature Protocols Discussion Forum!

If you have a moment, please have a look and see if you have any comments or advice to add!

Archaeologists unveil finds in Rome digs

It seems that every time they try to build a third underground line in Rome they discover something irreplacable – this time a 6th century copper factory tops the list.

Perhaps they should (just!) start moving the modern Rome “somewhere else” and let the archeologists and tourists go wild.

Nature Protocols has recently published two protocols that would be useful in research relating to HIV, one of which is currently featured on our homepage (and therefore open access!) showing that we have definitely not forgotten about it.

This is:
Isolation and propagation of HIV-1 on peripheral blood mononuclear cells from the group of Neeltje Kootstra.

The other is for the tetrazolium-based colorimetric assay for the detection of HIV replication inhibitors developed by Erik De Clercq.

This interview with Prof. de Clercq from 1997 might be of interest from a historical perspective…:
Searching for Synergy: An Interview with Erik De Clercq

Last night I attended a talk in Second Life – you remember, the virtual world where Nature has created an island? – by Simon Colton. He was telling us about a new artist called “The Painting Fool”.

He has created (and trained!!) this program which can draw paintings from photographs and even its imagination. From the talk I gather that it has built into it some emotion detection software, so if the person in the photo looks happy, for example, it will draw the picture in brighter colours. He is moving towards the idea that it could be able to generate pictures from its “imagination” using words (such as a newspaper article) as inspiration. I am not completely sure that I am comfortable with computer programs being called “creative”, but it definitely seems very clever and has won an Artificial Intelligence competition!

Here are links to two galleries of its paintings:
Amelie’s Progress
City Series

On a more tangible, smell-the-spraypaint level, I watched a guy painting this portrait of Rolf Harris on the Thames walk near Waterloo Bridge.

He did not tell me his name, but he did give me a postcard with his webaddress. Here is a link to his on-line gallery:
Blam

Yours etc,

Bronwen

Global warming might be working in Woking. From the beginning of February patches of flowering daffodils, crocuses, bluebells and snowdrops have been popping up – all very pretty, but it does feel rather early…

Famous poems rewritten as limericks: I Wandered Lonely As A Cloud

There once was a poet named Will
Who tramped his way over a hill
And was speechless for hours
Over some stupid flowers
This was years before TV, but still.

Taken from LimerickDB

The latest featured Nature Protocol is entitled: Spatially and temporally controlled electroporation of early chick embryos and is for electroporation of expression vectors and morpholino oligonucleotides into the chick embryo epiblast.

It contains some really good videos showing you how to do the experiment, and some look like they are techniques that will be useful for many other studies. The first one shows how to break the shell by tapping the blunt end using coarse forceps, then open a round window, removing any sharp edges.

This really pleased me as it is actually something we did in a development biology practical and brought back memories of when every week brought new methods to learn! I was very enthusiastic about “doing experiments”, but was unfortunately a bit accident prone.

Click here for the complete list of videos from this article.

To browse other instructional movies on the Nature Protocols site click here.

I even forget critical bits of information about myself that can be discovered by doing a quick google search for “Bronwen Dekker”.

Today, I was trying to find my very first ever blog to write an answer to the question: Why do you blog?

In so doing I came across this:
Scan Uncovers Thousands of Copycat Scientific Articles

Who would have thought?

The two plants indigenous to South Africa that I looked at were Dioscorea dregeana (a type of yam used medicinally rather than for food) and Avonia rhodesica a tiny succulent. Both of them are used for narcotic purposes (though the yam was used for many other things as well), though I certainly did not find anything terribly exciting in either of them.

A compound that was in every single extract that I made was beta-sitosterol.

This compound was isolated so frequently in our laboratory that the nmr technician claimed that he was able to identify it from the raw NMR data (i.e. before Fourier transformation).

From leafy extracts we would also isolate a black compound which sometimes seemed to have a death grip to glass. NMR spectra showed what looked like a series of aldehyde groups. These would be terribly excting to the naive researcher, but it would turn out to (just) be one of the chlorophylls (the aromatic hydrogens are shifted out there because the porphyrin moiety is very aromatic – is that a meaningful statement?). Don’t get me wrong: chlorophylls are very interesting molecules, they just aren’t new and publishable from a Natural Product Chemistry point of view.

The two active components are warburganal and polygodial and these aldehydes reacted with vanillin to make coloured compounds. I thought that it would be a good idea to stain the bark tissue slides (prepared by slicing the regenerated bark using a vibratome) with vanillin and I got quite a nice effect.

A very simple reaction that I performed numerous times during this study was the direct iodination of a protein with iodine-124.

The reaction takes place in the presence of an oxidising agent which removes electrons from the iodide ion so that you end up doing an electrophilic substition at the position ortho to the hydroxy group on the tyrosine residue.

You have to be slightly paranoid about this oxidising agent as your protein might be sensitive to oxidation itself. It turned out that annexin V was sensitive to stronger oxidising agents (like chloramine T), but seemed to retain its ability to bind to phosphatidylserine if the milder reagent iodogen was used.

We found that the radiolabeled proteins were actually quite stable (to dehalogenation) in vitro – even when incubated in plasma, but in vivo was a whole nother story. It seemed that most of the radioactivity was in the form of iodide ions within about a minute of being injected into mice. This is usually explained by the fact that the iodinated tyrosine residue is sufficiently similar to thryoxin to be deiodinated by the same enzymes. I still think that it dehalogenates amazingly fast to be explained by this alone.

Another moderately mysterious thing that we found was that the radioactive iodide seemed to accumulate not only in the urine, but in the stomach contents. Bear in mind that we injected the radiolabelled protein into the tail vein. At the time, the best explanation that we could come up with that had some support from the literature was that the iodide was somehow passing into the gut through the same channels as the chloride ions of HCl. Another theory is that the mice were injesting their urine. My pet rat, for example, does a behaviour where she wees on me and then proceeds to lick it up – I am sure that she is not the only one!

Analytical chemistry has provided us with many possible ways to deal with quantifying analytes in various matrices. The most common matrix used in forensic toxicology is blood, though during my period working at the Forensic Science Laboratory in Pretoria we analysed vitreous humour, liver, vomit/stomach contents and urine samples routinely. For obvious reasons, it is difficult to get meaningful quantitative information from the latter two, though they can be incredibly useful for obtaining qualitative information.

Here is a photograph of me poised to mince up something meaty:

And a photograph of the exhibits from one of my favourite cases (notice how the clothing has dried onto the bones – this is a common phenomenon if the body has been exposed in dry conditions):

The three problems with the quantitation of analytes from post- (or ante-) -mortem samples that remain clear in my mind are (1) that most drugs or toxins need to be extracted before they can be taken for GC/MS or HPLC (or even ICP) and this process is not perfectly efficient, (2) frequently, the blood concentration of the toxin at the time of death is “low”, meaning that the amount of blood extracted in order to be sure that you do not have a false-negative is non-negligible, and (3) by the time you know which analyte you need to quantify you may not have all that much sample left.

Well, after reading Martin Fenner’s latest blog post, I thought that I might sign up for the Just Science 2008 challenge and try to write a scientific post every day for the next week.

As those of you who routinely read this blog know, I actually do not blog very much about science at all so I think it might be quite an interesting exercise for me. Perhaps I could write about things that are on my CV (or were on my CV in the past, but no longer fit).

1. The honours project on bark regeneration.
2. The MSc in natural product chemistry.
3. Something interesting from working at the Forensic Science Lab.
4. The PhD doing radiolabeling etc for PET imaging of cell death.
5. The post-doc radiolabelling gastrin analogs.

That would be five. The results are obviously hardly new, but there are the odd things that might still be of general interest and maybe I could tie them up with some of the protocols that we have published.

Of course getting hold of the information for some of these is going to be more difficult than for others, but I have just found a pencil-case full of slides for a presentation that I did on the bark regeneration stuff (1995!!) and have taken them along to Jessops to see what they can do about getting them onto a CD for me… These will only be ready on wednesday.

I have also found a box of floppy discs that contain two that are labeled: “ICP results Aug 99” and “Affidavits and letters” dating from the FSL days. I wonder what I could get away with posting. :)

I am (obviously) not going to do this series “in order” – hopefully you won’t mind.

Here are two things that I might do in these situations:
(1) Look through the Network Protocols and add any nice ones to an excel file imaginatively called “Network good ones” in a folder called “Fun Stuff”. If I am in the mood, I might even add the link to an appropriate Wikipedia entry.
(2) Browse through our content – either on-line or the print version to see what interesting things the other people in our team have accepted.

Today, I found a protocol with two videos that I would like to share with you. They show a mouse doing some behaviours… the background music enhances the whole experience, so if you have sound, add it.

Rich spectrum of exploratory and motor behaviors that can be registered in the rodent Suok test

Effects of psychotropic drug lysergic acid diethylamide (LSD) on mouse Suok test behavior

This is the link to the abstract of the protocol by Kalueff et al:

The regular and light–dark Suok tests of anxiety and sensorimotor integration: utility for behavioral characterization in laboratory rodents

Today I went to a talk by Dr Patrick French entitled: “The Return of Syphilis”. It was all about the recent rising incidence of syphilis in the UK after many decades of it being effectively eradicated. The most important things seemed to be that (1) the presence of syphilis sores greatly increases the likelihood of HIV infection and (2) syphilis can be transmitted from a mother to her foetus.

That syphilis is on the increase in the UK is bad, but its incidence here is still not nearly as high as that in, for example, sub-saharan Africa (STD Statistics Worldwide (outdated, but still interesting comparison)). Because syphilis is caused by a rather primitive bacterium, Treponema pallidum , which does not seem to be able to become resistant to antibiotics, it is completely curable with benxathine penicillin if treated early on. It seems therefore that in a more ideal world management and treatment of syphilis would be one of many important items on the checklist for reducing the spread of AIDS. But is this the case now? In very poor communities, what are the most important considerations when dealing with AIDS? How important is the treatment of syphilis (and other related STDs) relative to other considerations?

While in Chicago over the Christmas period, I visited the Adler Planetarium. Despite the fact that I almost always prefer to be outside rather in an museum, I learnt one or two things here that pleased me.

The most important was that I learnt how to find “Orion”. I realise that most of you are able to identify any number of constellations, but you must remember how it felt to “find” your first one – I am filled with delight every time I see it now.

As it happens, in the early evening you can also see taurus at the moment (if you are in the Northern hemisphere).

I have taken this image from Utah Skies

She swallowed the cow to catch the dog …
She swallowed the dog to catch the cat …
She swallowed the cat to catch the bird …
She swallowed the bird to catch the spider…
That wiggled and jiggled and tickled inside her.
She swallowed the spider to catch the fly.
I don’t know why she swallowed that fly—
Perhaps she’ll die.

I am finally un-jetlagged after returning from my holiday in Champaign-Chicago. While I had a lovely holiday (Chicago is a very beautiful city to walk around in), I found traveling even more of a drag than normal. Planes were delayed because of fog and thunderstorms; and they ran out of vegetarian meal options before reaching our seats (and yes we had requested these in advance).

On returning home, we found that the train fares back here in London have increased. What with the fact that there are seldom enough seats for everybody and the almost daily delays caused by congestion at Waterloo, I find myself asking what we are actually paying for. And the answer is: “to travel through space and time—and sometimes quite a lot of the latter”.

Yours etc.

Bronwen

Caption: This images shows cultured HUVECs where the centre cell was injected with Lucifer Yellow (LY) fluorescent dye and left for 1minute. The spread of LY from the central cell to the neighbouring cells demonstrate a functional direct communication channel via gap junctions between HUVECs.
Contributed by Chiuhui Mary Wang.

The New Featured Protocol

This week’s new featured protocol comes from Professor Kenneth Peterson at the University of Kansas Medical Center. The protocol describes a method for preparing intact yeast artificial chromosome (YAC) DNA for the transgenesis of mice. Large capacity cloning vectors such as YACs are useful as they enable the entire locus and all its flanking cis-regulatory elements to be included in the construct, however, physical shearing of the DNA must be avoided during purification and microinjection in order to obtain animals bearing full-length transgenes. This method uses pulsed field gel electrophoresis to separate YAC DNA from yeast chromosomal DNA and then employs a second dimension electrophoresis to concentrate the YAC DNA. Maintenance of the YAC in an agarose gel matrix until the final steps before microinjection avoids damage to the DNA, then the matrix-embedded YAC DNA is enzymatically digested to produce a solution that can be microinjected.

Preparation of intact yeast artificial chromosome DNA for transgenesis of mice

Thank you to Hannah Clark our resident expert for supplying the text for this section.

News from the Protocols Network

My happiness index increased to almost-maximum earlier this week when the new Protocols Network submission page went live. You can check it out here:

protocols.nature.com

Happy New Year etc

Well, it is almost the end of the year, and I think that this will be the last post on my blog in 2007. I am off to Chicago for Christmas to visit with a friend and am looking forward to it despite being ever so slightly apprehensive about the coldness!

Enjoy the festivities and best wishes for 2008!

Caption: Budding yeast expressing Clathrin Heavy Chain-RFP (Chc1-RFP) and Actin Binding Protein 1-GFP (Abp1-GFP), imaged by conventional fluorescence microscopy.
Contributors:Tom Newpher, Robin P. Smith, Vance P. Lemmon, Sandra K. Lemmon

The New Featured Protocol

Pecunia non olet, or, in English, money does not smell. This Latin expression, which was apparently coined by Roman emperor Vespasian to defend his decision to reinstate a ‘urine tax’ on the use of public toilets, has since been translated in countless languages and repeated ad nauseam, to use another Latin expression, in who knows how many contexts, usually to justify (or refer to) practices of dubious moral rectitude.

If money may not smell however, Nature Protocols can now confirm that poached ivory does indeed do so (well, figuratively at least). The newest featured protocol in our website, Isolation of DNA from small amounts of elephant ivory by Celia Mailand & Samuel Wasser details the extraction of genetic material from poached ivory with the aim of assigning the samples’ geographic origin through an independently developed gene-frequency map. A relatively small sample of ivory can therefore be used to trace back the area of Africa where the late rightful owner of the tusk was native of.

I first read an article referring to this approach in the London’s Guardian, and I knew right then I had to try and get Professor Wasser to write for us. He immediately accepted my invitation but had eventually to ask for an extension of the submission deadline. He had in fact to work on the testimony on maintaining the international ivory ban he was about to give to CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora), an international agreement between governments members of the World Conservation Union (IUCN). HOW COOL IS THIS GUY?

Anyway, although, given the circumstances, it was perfectly fine to delay the submission of the manuscript, this procrastination also meant that I sadly had to pass on to Hannah the processing/peer reviewing/editing of this article, as I was going on a few weeks’ leave of absence just around that time.

So going back to the Pecunia non olet thread, the lamentable dearth of squeamishness often observed when it comes to the looking into the origins of riches has of course less to do with the availability of adequate ‘noses’ than it does with general political will. I hope that by publishing this protocol, and now featuring it (making it thus accessible for free temporarily), Nature Protocols will be able to make its contribution to the struggle against the illegal ivory trade. The more scientists know about this protocol, the harder it is for people whose will is less than good to ignore its implications.

GO ELEPHANTS!!!

Thank you to Baldo Lucchese our resident expert for supplying the text for this section.

Do you know the answer?

Do you know anything about treating cells with the enzymes heparanase III and chondroitinase ABC for investigating heparan sulphate proteoglycans?

If you do, perhaps you will be able to answer this question on our discussion forum.

End of year party

Last night was Nature’s end of year party – the theme was “Alter-Ego” or “Hats and Wigs”. After some drinks at our offices in London we went to a club near Piccadilly Circus. The Protocols Team, placing a higher priority on food than on drink, quickly nipped to a cafe for a bite of something more substantial than the promised canapes. We had a really good time, but faded quite a while before the closing time of 3 a.m.

Here are some photos of the Nature Protocols team.

Katharine, Dot, Baldo and Hannah.

Li Kim and Me.

Caption: The image shows cultured Human Umbilical Vein Endothelial Cells (HUVEC) stained for phalloidine (green), gap junction protein connexin (red) and nuclei (blue).
HUVECs is a cell type commonly used in studies related to vascular biology.
Author: Chiuhui Mary Wang
Here is a link to a related protocol.
‘A protocol for isolation and culture of human umbilical vein endothelial cells’

The new featured protocols

These describe Marc Hellerstein’s lab’s methods for mearuring cell proliferation using heavy water. Cells are grown in medium containing ²H₂O (D₂O) and the incorporation of deuterium into purine nucleotides is detected by GC/MS. Pretty cool stuff.

You can access the full text by going to:
Measurement of cell proliferation by heavy water labeling
Measurement of very low rates of cell proliferation by heavy water labeling of DNA and gas chromatography/pyrolysis/isotope ratio–mass spectrometric analysis

Some random news

Odyssey Press produces the print version of Nature Protocols and they have won a prize for “their printing quality and craftmanship in the production of Volume 2 Number 7” in the 2007 New England Regional Awards of Excellence gala.

Ask Aunty Bron

What is the difference between a Network Protocol and a Nature Protocol?

On the Nature Protocols site there are two types of content: Protocols that are peer-reviewed, edited and laid out by a production team (Nature Protocols).
Protocols that can be made available on the internet very soon after the author has uploaded them (Network Protocols).

Nature Protocols are listed in PubMed and you need a site-license to access them.
Network Protocols are freely available to everyone.

Both have DOIs and are cited as Nature Protocols.

They are listed separately on the category pages (e.g. Structural Analysis) and their appearance is alo quite different. Perhaps have a look at these two examples to see what I mean:

A Nature Protocol: ‘Purification of naturally occurring peptides by reversed-phase HPLC’
A Network Protocols on a similar subject: ‘Determination of neopterin and biopterin by liquid chromatography’

On a bleak day in the late Seventies I was sitting in an upper floor classroom of my old school. It was cold outside, with a blanket of snow on the ground, and there was a gusting wind that moaned and rattled at the windows. I was certainly glad of my grey-coloured school jumper that day, for I never felt overly warm in those exposed rooms in the upper parts of that block.

As if in response to the wintry conditions outside, the teacher of that particular class gave us a discourse on the subject of the previous Ice Age. There was some talk of mammoths and great glaciers, and of men dressed in furs crossing large areas that were seas frozen over and covered in ice. She also gave us some indication as to when the last Ice Age had been – namely, about ten thousand years ago – and went on to suggest the next one was due any time. Indeed, she even suggested the bitter winters of the last few years may represent the onset of this putative new Ice Age; with that statement came a warning we as children might have to get used to a world turning steadily colder during the course of our lives.

It was not a particularly cheering thought, as I trudged my way home through the snow that day, to consider our climate becoming harsher. Certainly, the teacher had been right about the winters of the early Seventies, I could appreciate that. Our town was set in the hills of the Pennines and I was quite used to seeing snow thick and heavy and lasting for weeks. Whilst great for the sledge, this was not so great for the school bus, which sometimes could not attempt the steep and meandering roads of my estate in such weather. The lingering snow could make life difficult in the vale; the bitter cold had its impact on the vulnerable and the elderly; services became disrupted; roads in and out of the valley were often rendered treacherous or closed.

But with the onset of the Eighties those hard winters I remember as a boy seemed to fade away; and as I progressed onwards through my education I never heard that impending Ice Age mentioned again. In fact, as the years have rolled by the very opposite thing has been much considered. From the Eighties until now the planet has gradually become warmer. There are various ways to go about explaining why this has happened; there are plenty of models and predictions concerned with where this warming might end, some with more spectacular results that others; and for sure in current times this issue is much tangled up in politics, money and the media spotlight. Is global warming natural or are we causing it? For all the noise and spin, this question is still to be satisfactorily answered.

Geological ages come in the context of thousands or millions of years. I am not yet forty, yet I have been around long enough to hear people talk quite seriously both of an impending Ice Age and now, more recently, of looming catastrophic events related to warming.

Richard Shaw, Hadfield

This one in last month’s JACS is just adorable:

It is for the article ‘A Simple Molecular Machine Operated by Photoinduced Proton Transfer’
by Silvi et al.

Caption: Mouse Dorsal Root Ganglion (DRG) culture stained for tubulin and imaged by confocal microscopy

Contributors: Robin P. Smith, Vance P. Lemmon

The new featured article

Why are there (only) twenty natural amino acids to build proteins from? Even though not based on a rigorously true statement (there are actually a few other rare amino acids besides the ‘canonical’ twenty), it is a nevertheless intriguing question. What’s so cool about twenty anyway? Twenty is certainly NOT one of the accepted symbolic numbers. Twenty is not nearly as cool and suggestive as say one, three, seven, thirteen, seventeen (Friday the 17th is the day of wretched luck in Italian lore, as opposed to the more common Friday the 13th), 666… Twenty does sound kind of square and uninteresting in comparison, doesn’t it? It’s a relatively small integer, yet pathetically far from being a prime number. The small symbolic numbers that most reverberate in lore all seem to be prime for some reason. Does anyone know the reason for this apparent preference? Any guesses?

What if we had more than twenty amino acid building blocks to assemble proteins from? Would we get super-proteins that would enable even Arnold Schwartzenegger to learn to act finally? Or big time CEOs get a sense of humor? How about a protein that would get Zinedine Zidane to finally admit his behavior was unforgivable? (By the way, 2006, what a number). Or would we just get a warning from Mother Nature not to get ahead of ourselves, with the new cyborg proteins proving a complete waste of perfectly good time? Well, many scientists have asked that question, and some have tried to give answers. Arguably the most accomplished and famous researcher in this field is Professor Peter Schultz of the Scripps Research Institute in La Jolla, California.

The newest featured protocol in Nature Protocols homepage has as its main author Professor Jason Chin, himself an ex-member of Schultz’s research lab (which I presume he joined as a post-doc). The protocol covers a procedure to achieve insertion of un-natural amino acids in proteins ‘expressed’ (produced) in eukaryotic cells (human cells are eukaryotic for instance). It details in particular the generation and genetic selection in yeast (yes, they’re eukaryotic organisms too) of a library of (mutated) enzymes that are ultimately able to insert site-specifically un-natural amino acids in proteins in response to the so-called amber stop codon that the researchers purposefully ‘add’ the protein’s codifying gene. For the record, the test un-natural amino acid referred to in the protocol is O-methyltyrosine. Pretty cool and thought-provoking stuff, I can assure you.

Alas in the protocol you won’t find too much along the lines of philosophical considerations on the significance of the number twenty when it comes to proteins, but if you are looking for somewhere to start in such a quest, this is as good a place to start as any. Well, at least we at Nature Protocols think so…

Thank you to Baldo Lucchese our resident expert and Great Dane for supplying the text for this section.

The Discussion Forum

We have recently had very helpful replies to questions posted a few weeks ago! Perhaps you have been waiting to find out the answers as well.

The one about the comet assay

The one about affinity purification of anti-peptide rabbit polyclonal antibodies

Ask Aunty Bron

What is the impact factor of Nature Protocols?

This is a very good question, and one that we get asked quite frequently. The short answer is that we don’t have an impact factor yet.

The slightly longer answer involves answering another question: “What is an impact factor?”

Impact Factor = (the total number of citations in indexed journals that a journal receives for articles published in the year after “the year of interest”) / (the number of citable articles published by the journal in “the year of interest”)

This means that a journal needs to be more than two years old to have an impact factor. Nature Protocols launched in June 2006.

The interesting thing that I found today, was that Wikipedia has got entries for “numbers”. Check out the entry for 3.

Try some of your favourite numbers by putting the digits, e.g. 34, in the search box.

After struggling for ages to think of anything interesting to say about goats, there was a breakthrough this afternoon when Dot told me about a recent HSBC advert that featured goats grazing in a tree!

Here is a link to the advert

In trying to find this video, I came across another person who had a problem with the goat-sheep continuum.

It also reminded me of the whole business of donating money to, for example, Oxfam to buy, for example, goats for someone in the third world instead of buying presents for your family and friends.

If this is your type of thing (or this is the first you have heard of it), here are two websites that might be of interest:
Oxfam unwrapped
A bbc story

While I think that it is an excellent idea to donate money to these causes, and that most Christmas presents are a waste of time/space/money/resources/etc, it seems a bit odd that we would need to pretend that such a donation is a Christmas present for one of our friends or relatives.

She swallowed the goat to catch the dog …
She swallowed the dog to catch the cat.
She swallowed the cat to catch the bird …
She swallowed the bird to catch the spider
That wriggled and jiggled and wiggled inside her.
She swallowed the spider to catch the fly.
But I dunno why she swallowed that fly
Perhaps she’ll die.

Thank you to Naomi and Dot for providing goat photos

4 jobs you’ve had:
1. Part-time piano teacher at a junior school
2. Part-time chemistry/biochemistry tutor/demonstrator.
3. Forensic analyst (toxicology).
4. Radiochemistry post-doc-type thing.

4 movies you could watch over & over (and I have):
1. Groundhog Day
2. Notting Hill
3. Mary Poppins
4. Contact

(these are not necessarily my favourites or those that I think are objectively the best – they are the equivalent of comfort-food)

4 places you’ve lived:
1. East London, South Africa
2. Durban, South Africa
3. Pretoria, South Africa
4. Manchester, England

4 TV shows you love to watch (I don’t own a TV so these are ones that I own the DVDs for):
1. Friends
2. David Attenborough “Life of…”
3. Frasier
4. The World at War

4 places you’ve been on holiday:
1. Norway (Oslo, Flam, Bergen…)
2. Israel (most of the south…)
3. Italy (Naples, Pompeii, Capri…)
4. US (New York, Grand Canyon, Big Bear mountain…)

4 websites you visit daily:
1. Nature Network
2. Facebook
3. Google
4. Wikipedia

4 of your favorite foods:
1. Mushroom risotto (from Pret)
2. Mushroom pizza (from M2)
3. Cinnamon and raison bagel, very toasted with a little bit of butter (my local coffee shop)
4. Cappuccino (from Pret or local coffee shop)

4 places you’d rather be:
1. Ein gedi (Israel – except in summer)
2. Flam (Normay – but only in summer)
3. Edale (Peak District, UK - except when raining)
4. Happily ever after.

4 lucky people to tag (Nature Network people, help spread the meme bloggy joy):
1. Brian
2. Richard
3. Nicolau
4. Andrew

Caption: Spectral karyotype of a polyploid human tumor cell
Authors: Carrie Viars, Steve Goodison, and George McNamara
See this protocol for more information on SKY hybridization.

The new featured article

Recently, I went to a talk on patents in Second Nature by Sue Scott. An interesting insight from this talk was that it is not always in a company’s interests to file a patent. For example, if Coca-cola had patented their recipe for Coke, they would not have been able to keep it a secret!

The newly featured protocol is for using Scirus to search these very mysterious legal documents for scientific information.

The new Network Protocols

This week, I would like to highlight a Network Protocol where a question has been asked and, recently, answered using the commenting functionality.

A simple and rapid method for RNA isolation from plant tissues with high phenolic compounds and polysaccharides

Ask Aunty Bron

What is this question-in-a-cloud thing all about?

On our homepage, this box links to our Discussion Forum on the Nature Network. This is a good place to ask all sorts of methods-related questions like:
“What is the best method to achieve…?”
“I have been doing ‘this method’, but getting unexpected results. Can anybody help?”

If you are the technical-guru in your lab, perhaps you would like to check it out to see if you have any useful tips that you can give. You don’t even need to wait for a question, you could share your tip (perhaps with a photo) by joining up and creating a new post.

For those of you who are more like me, your story might go something more like this: “You really should not try to attach an Ehrlenmeyer flask to a rotavap. I tried it and it imploded…”

While we at Nature Protocols agree on almost everything of importance, there are a few topics that will always stimulate heated debate. One of these I have already hinted at: What colour is, e.g., the Piccadilly line? (we see colours differently). Another is: Which are better: cats or dogs?

While I am always on the cat side of this discussion, I have to acknowledge that dogs are more useful to human beings than cats are. They guide blind people, can be trained to detect drugs, help in hunting for food, and pull sleighs. We even sent dogs into space for us to see whether human space flight might be possible!

Here is a picture of Leika the space-dog who, on the 3rd of November 1957, was the first recorded living creature from Earth to enter orbit:

She swallowed the dog to catch the cat …
She swallowed the cat to catch the bird …
She swallowed the bird to catch the spider
That wiggled and jiggled and tickled inside her.
She swallowed the spider to catch the fly.
I don’t know why she swallowed that fly—
Perhaps she’ll die.

Thank you to Katharine for letting me use her dog photo.
The photo of Leika was lifted from Wikipedia

Inevitably mistakes creep into this process, can you spot the mistake on the current homepage?

The new featured protocol

The latest featured article, which means that it is freely available, is for a fast walking method for single-tube transposon mapping. This is a method of flanking sequence retrieval that has been applied to map the insertion of transposons. It is based on the original Universal Fast Walking (UFW) method that was published by the authors in their 2002 ‘Gene’ paper

However, in this protocol, the original method can also be enhanced by the use of agarase, to allow composite nucleotide sequences to be unscrambled. This protocol would also be applicable to general genome walking and cDNA walking, as well as viral and other insertional element mapping.

Finally, on an entirely unrelated and unscientific note, I think that a UFW protocol is very timely, as I seem to have found myself Universally Fast Walking home from the station every day this week in order to combat the effects of the drop in temperature we have suffered! On the upside, the weather has provided some beautiful sunsets here at work…

[Thank you to Hannah, our resident expert, for supplying the text for this section.]

The new image

This was supplied by L. A. Donaldson, L. Grace, and L. Holland.

Can you guess what it is?

The new Network Protocols

This week, I would like to highlight a series of Network Protocols uploaded by the Raghava group. These are bioinformatics methods for predicting whether or not a peptide is antibacterial,
a protein is mitochondrial,
a protein is likely to be allergenic,
and a protein is likely to bind to MHC class II molecules.

Ask Aunty Bron

What is the difference between Nature Methods and Nature Protocols?

This is a really good question! There are two important differences:
(1) Nature Methods publishes primary research, that is, methods that are new and have not been published before, while Nature Protocols publishes (hopefully) reliable methods that have already been used to generate results in primary research papers. Most of Nature Protocols’ content is commissioned.
(2) Nature Methods are formatted as a normal article, while in Nature Protocols, the procedure is written as a series of number steps in the active tense.

Protocol manuscripts are also structured slightly differently: The headings are Abstract, Introduction, Materials (Reagents, Equipment, Reagent Setup and Equipment Setup), Procedure, Timing, Troubleshooting, and Anticipated Results.

There are also cute little callouts.

Editorial Blooper

The invitation for the currently featured protocol, written by Professor William M. Gelbart from the Department of Molecular and Cellular Biology, Harvard University, was originally sent to William M. Gelbart, Professor of Chemistry at UCLA… who gracefully declined.

It is at this point in the rhyme that we realise that this is not a true story: A small bird maybe, but a cat… that is a bit hard to swallow.

This animal worshiped by the ancients was part of one of the most famous thought experiments . The idea of cats hovering between life and death waiting for you to open the box before going either way is probably just as unlikely as the old lady in the rhyme, but there is something about cats that is definitely mysterious… Here is a photo of Henry’s pet by way of example.

Cats have also given their name to the three-dimensional x-ray image, which led me to wondering whether cats ever had CAT scans. There are a few cases where cats have been used as model organisms for diseases where CAT scans are used as part of the diagnosis, but actually it turns out that if your pet insurance covers it, that these scans are also used for diagnostic purposes in veterinary medicine as described in this recent article in the Telegraph:

Give your pet cover a CAT scan

In writing this post, I found out that recently, a cat named Cinnamon had its DNA encoded as part of the Cat Genome Project.

I especially liked the acronym: GARField (Genome Annotation Resource Fields)!

She swallowed the cat to catch the bird …
She swallowed the bird to catch the spider
That wiggled and jiggled and tickled inside her.
She swallowed the spider to catch the fly.
I don’t know why she swallowed that fly—
Perhaps she’ll die.

Thank you to Hannah and Henry for providing the photos for this blog post.

While I was on holiday in Eilat a few years ago, I met some ladies who very enthusiasticaly invited me to a talk on migrating birds. Apparently, Eilat is a very popular tourist destination for birdwatchers and, not having anything else to do that evening, I went along. While my Hebrew was absolutely definitely not up to following the talk (my ornithology-relevant vocabulary being limited to “ציפור” (bird)) there were some really impressive slides of flocks of birds as well as of the results of birds hitting aircraft.

A combination of the fact that Israel has in the order of 500 million migrating birds flying over it in Spring and Autumn, and that Israel has a fairly active airforce, means that bird-plane collisions were an inevitable part of Air Force life. Yossi Leshem’s then did a study of the migration routes of birds, and was able to recommend areas that should be avoided during the peak migration seasons which reduced the number of collisions by about 75 %.

A quick internet search this afternoon yielded two other bits of bird-plane trivia:
In response to concerns for aircraft safety due to the presence of birds at the Zagreb airport, trained birds of prey were introduced to chase them away. This worked.
Birds and air traffic safety on Zagreb airport

Appropriately arranged lights on aircraft can decrease the chance of collision – the birds fly so as to avoid the planes.
Reactions of Migrating Birds to Lights and Aircraft

And: No I don’t know what type of bird is in the photograph

She swallowed the bird to catch the spider
That wiggled and jiggled and tickled inside her.

I don’t know about anywhere else in the country, but Woking is teeming with spiders at the moment. Dew is coating their webs in the mornings and later in the day you can watch them waiting for dozy insects to get trapped.

I have noticed recently, that the world wide web also seems to be full of spiders. The chemical forums, for example, lists the number of spiders that are present on their site:

So what are these spiders?

As far as I can tell they are computer programs that are used to browse webpages making lists of the hyperlinks that they contain. These new hyperlinks are then added recursively to the list of webpages that the program needs to visit. This process then forms a very large index of webpages that can be used by search engines to retrieve information.

Wikipedia writes about these spiders under the heading Web Crawler.

“Spider” has also come up in the names of two web applications that I have been introduced to while doing my job at Nature Protocols:

ChemSpider – Database of chemical structures
SPIDER – System for Processing Image Data from Electron microscopy and Related fields

She swallowed the spider to catch the fly.
I don’t know why she swallowed that fly—
Perhaps she’ll die.

Another possible subset of people are those that are more interested in watching flies than in commenting on… well anything for that matter. And today I have an offering for this group of people.

The latest addition to our featured protocols is:
‘A method for quantifying aggression in male Drosophila melanogaster’.

It even contains a movie!

Repeated orientation of the attacking male prior to the first attack.

According to our in-house expert, it is more politically (and ethically!) correct to study aggression in flies than it is to put two men in a confined space and watch them fight for attention over a page 3 model!!

As usual I seem to be writing the postcard after returning home. I had a lovely time with Alex in Belgium and am still in quite a relaxed frame of mind. The closest I came to doing anything scientific was to taste test as many different species of truffles and waffles as possible.

Alex and I always have plenty to talk about. The most interesting thing that she told me this weekend was to do with cows. Apparently, most cows in Europe are conceived by artificial insemination and delivered by Caesarian section. So maybe making cloned cows in not such a big step after all… This is getting too weird for me. Perhaps I should become a vegetarian.

Yours etc.

Bronwen

Grote Markt in the chocolate window, Mechelen

“After this Protocol was published, I discovered an article on mice observed in large outdoor enclosures in the USA. The authors observed a behavior they termed “burrow cleaning”. During March and April (i.e. spring) many burrows were found with enlarged holes and considerable debris and/or grass deposited at burrow entrances.
This behaviour seems very like “burrowing” as seen in the laboratory. Thus the latter may be based on “spring cleaning” behaviour. It is tempting to speculate that in humans, delaying or cancelling the spring cleaning could be one early sign of a neurodegenerative disorder.

Reference:
Schmid-Holmes, S., Drickamer, L.C., Robinson, A.S. & Gillie, L.L. Burrows and burrow-cleaning
behaviour of house mice. Am. Mid. Nat. 146, 53-62 (2001).”

This pleased me.

Anyway, am off on holiday for a few days. Will try to send a postcard, but like most postcards it will probably arrive a week after my return.

In my opinion, the most amazing thing about flies is that when they are determined they can keep up. You are walking along and the fly is buzzing around your head, and no matter how quickly you walk it manages to match your pace. For the most part, though, the flies that I see are resting. They are gorging on pollen, poo or pudding, or just resting on a leaf or a wall.

I am not sure where the phrase “I’d like to be a fly on the wall” comes from, but it describes our desire to know what goes on in situations where we are not present. This desire is surprisingly strong: there is always someone who listens at keyholes in an Agatha Christie mystery, and sufficient numbers of people watch “Big Brother” on TV for them to make series after series.

I have been wondering for quite a long time really, why more people don’t comment on papers in for example Nature Protocols and Nature Precedings. I have proposed theories and hypotheses, and read other very similar theories and hypotheses, but today I am going to propose another one (new for me, but almost definitely not new in the absolute sense):

People are waiting, like flies on the wall, to see what everyone else is going to do.

So, with that in mind let me show you some examples of commenting-on-articles in action.

Examples from Nature Protocols:
Preparation of organotypic hippocampal slice cultures: interface method
Production of neuron-preferential lentiviral vectors

Examples from Nature Precedings:
Open Notebook Science Using Blogs and Wikis
Molecular Static and Dynamic Analyses reveal Flaw in Murine Model used by US FDA to Detect Drug Carcinogenicity

This does not mean that it was not a positive experience – in fact I would recommend doing it for at least one week (preferably a week when your work-load is not too high!).

Thank you for reading, commenting and for otherwise being encouraging.

I was going to write a post about my observations and thoughts about the blogging experience. And it was going to be long. But I started typing up my notes, got fed up and did something else completely. Outside.

The starting materials:

(1)

(2)

For those of you who have been following the blogs this week, you may have noticed that there has been a discussion of radiation on Brian’s blog.

For my last post on this beautiful friday afternoon I am going to let you know that not only are there gamma-waves, radio-waves and micro-waves, but there are also very low frequency sound waves.

They are completely inaudible (to us), but apparently increase the likelihood that people will have a ‘paranormal experience’.

Proof of beautiful London weather

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For the rest of the month, all of the protocols from Volume 2 of Nature Protocols are freely available!

To whet your appetite here are three that were added today:

Reprogramming the amino-acid substrate specificity of orthogonal aminoacyl-tRNA synthetases to expand the genetic code of eukaryotic cells

Protocol for preparing proteins with improved solubility by co-expressing with molecular chaperones in Escherichia coli

DMS footprinting of structured RNAs and RNA–protein complexes

One of the really neat features of our site is that you can comment on the protocols. So, if you have a question for the author, or an additional tip that makes the protocol work better in your hands, why not write one?!

........................

Last night I went to a talk on the relevance of Spiritualism in Society today. It is is the second event hosted by Skeptics in the Pub that I have attended thanks to a posting on the London Events calendar (Thank you Li-Kim!).

Emma-Louise Rhodes spoke about the history of spiritualism from its “invention” by the Kate and Margaret Fox in 1848 to the Psychic Sisters service available at Selfridges.

There were many interesting ideas both in the talk and in the discussion afterwards:

a) Because I don’t have a TV, I was surprised at the number of programs e.g. Crossing Over, Sixth Sense and Most Haunted
b) Apparently there are more than 350 Spiritualist Churches in the UK
c) There is Fraudulent Mediums Act which replaced the Witches Act (1735)
d) Materialisations seemed to stop occurring after the advent of infrared photography

While exploiting people’s weakness and grief is a horrible, horrible thing to do; who else is taking people’s grief seriously? For how long are we sympathetic, before we start using words like “counselor”, “analyst”, “anti-depressants”?

On a lighter note: One of the “sceptics in the pub” suggested that there might be a similar gathering “on the other side” called “Spirits in the Pub” who were similarly dissing the mediums; and perhaps we should form an alliance with this group to ensure that they are more effectively able to communicate with their loved ones.

........................

When I first came to England in 2001, I met a lady who told me that she worked for a company called Amazon, an internet mail-order bookstore. At the time, I thought: “this is a really cool idea, but I don’t think that I will ever actually buy anything off the internet”, an example from a long list of things that “I would never do” that have ended up being part of my life.

Being in the UK, I always order my books from amazon.co.uk so had not looked at the amazon.com site until I clicked on the link in Brian Clegg’s comment on my Sunday post. The content on the two sites is actually quite different!!

Let us have a look at the entries for Stephen Hawking’s “A Brief History of Time” as an example:
On the UK site
On the US site

The US site seems to have a lot of added features so if you would like to use amazon as an information source or as a “discussion forum” it might be worthwhile for those of us on this side of the Atlantic to dip into it.

It even has tagging!!

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Firefox is currently my favourite web browser. It is a bit slower than Internet Explorer, but on a reasonably fast computer you won’t notice the difference.

The beauty of Firefox is in the Add-ons, and the Add-on that convinced me to change from Internet Explorer was Screengrab. The reason for this is that I take a lot of screenshots, either to describe things on our website that I would like changed or to create a version of a website that prints out exactly as it is shown on the screen. This Screen Grab tool allows you to do this, and saves the image as png file – the resolution is beautiful and it it is small in kilobyte terms.

Another cool thing for those of you who use del.icio.us is that there are a variety of related Add-ons available – the one that I use is for a sidebar that looks like this:

Notice that it is more-or-less the same as Bookmarks, except it is neatly sorted into the tags that you chose in del.icio.us.

Adding RSS feeds using Firefox and iGoogle is easy-peasy and you can generate you own little homepage with the things that are of most interest to you.

Perhaps you can WOW me with you favourite Firefox addons, or perhaps there is yet another browser worth trying. :)

Let’s assume for argument’s sake that (1) I was the type of person to got to an Alternative Medicine Practitioner (AMP) and (2) it was important to me that the AMP had had some sort of formal tertiary education or training.

If the AMP’s business card read: “Holistic healer Extraordinaire B.Sc.”, what would I want that BSc to be in? Would I be unreasonable to be sceptical about her healing powers if she had a BSc in geology or applied mathematics?

The first thing that I would like to say is that in order for it to be credible, it must definitely not be a “soft option”: I don’t want someone who is in this, because they failed medical school. The person must have been taught what ailments are absolutely definitely better treated by “conventional medicine” – it would be stupid e.g. to die of something that could be cured using antibiotics. And they must had done a first aid course/refresher course recently – dying in an AMPs consulting room would just be too humiliating.

I would want the person to have learned about clinical trials and have the tools to understand the results in medical journals. One of the criticisms regarding alternative medicine relates to the pausity of “positive” clinical trial data. This might mean that the treatments don’t stand up to too much scrutiny, but it also might mean that people have yet to find good solutions to the “unique” problems e.g. the difficulty in getting good “placebos” for acupuncture treatments.

There are a lot of conventional science courses that exist that would be appropriate in an Alternative Medicine BSc. e.g. Anatomy, Physiology, Chemistry, Statistics, Clinical Biochemistry. That is, it could be a real BSc. There are a few special subjects that this person might need to do that are not in a normal BSc, like ethics, legal considerations and the history and of course the practice of their specialty, but I could envision a curriculum requiring an extra year of study plus a year of “supervised practical experience” that I would still consider deserving of the title BSc and fulfilling the requirement of preparing the person for practicing their chosen profession.

The question of whether a person needs a BSc to comfort a patient through a difficult period of their life which is producing psychosomatic symptoms is obviously a different thing completely.

To make up for a largely sedentary lifestyle during the week, I like to get a reasonable amount of exercise over the weekend and usually go swimming on Saturday and Sunday afternoons.

Recently a friend of mine told me that he always swam 2 km (crawl or freestyle depending on your vocabulary) and then stated the length of time that it took him to do this. I was intrigued. How long would it take ME to swim 2 km?

Interestingly, the “biggest” problem with answering this question is ensuring tha