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Sunday evening reading: factoid, articles & video Grant Jacobs Aug 08

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To round out my Sunday splurge, a motley collection of articles and factoids.

The British Library goes down eight stories (four levels) underground. Should that be high-rise or low-rise? It occurs to me that this is a place where if you asked the librarian to bring up a book from the basement, they’d ask back “which one?” (The article containing the comment that lead me to this factoid, ruminates on the future of the printed book.)

BL-basement-stacks

(Source: Wikimedia Commons.)

(Source: Wikimedia Commons.)

There’s an excellent article and ensuring discussion at Panda’s Thumb if the concept of phyla should be dropped. (Taxonomists divide life into a hierarchal series of divisions. Phyla is one of the higher levels, between below Kingdom and above Class; see illustration to the right.)

The New Yorker is running a long and moving story, Letting go: What should medicine do when it can’t save your life? (Tender souls: handkerchief warning.)

As companion to Embargo Watch — with articles about embargo breaches — from the same author (Ivan Oransky) we now have Retraction Watch. He elaborates his reasons for founding this blog in his opening article. I can imagine some who wish that their retraction would not attract too much attention will be quietly cursing this development.

Frequent readers of my blog will know I’m a fan of historical accounts of science, both for their entertainment value and for the understanding of science’s origins that they bring. Caroline Rance at The Quack Doctor has an article ‘Like a half-felled cow’ – a case of arsenic poisoning in Victorian Scotland, which gives an account of treatment of cancer by an unlicensed practitioner in 1868 that went badly wrong. Her account features the quote “…being like a ‘half-felled cow’. Foam issued from her mouth, and she roared most unnaturally.” These narrative-style excerpts fill the accounts of older science, and are part of the fun of reading them.

Max-Perutz-and-the-secret-of-life

If you read the article you’ll see that even 150 years ago people were concerned at unlicensed practitioners, which has resonance with local issues. If you think this account if horrific, one vivid illustration on a site with historical images that I previously wrote about was of a woman dressed in rags, pulling teeth from a hanged man dangling from his gallows. It was a blunt and stark reminder of one perhaps better forgotten corner of life in earlier times.

Janet Stemwedel takes a look at professionalism and the Hippocratic Oath with her usual well thought-out style, pointing out in the end that professionalism is pragmatic too.

Stephen Curry has an account of the mechanics, if you will, of how haemoglobin works in A molecule of life and death, which features Chitty Chitty Bang Bang and animations of haemoglobin doing it’s thing, presented as videos. (It reminds me that I still haven’t gotten around to reading my copy of Georgina Ferry’s account of Max Perutz’s life and reviewing it… sigh.)

Finally, on YouTube is a promotion of Mary Roach’s newest book, Packing for Mars: The Curious Life of Science in the Void using a light-hearted personal hygiene angle:

YouTube Preview Image


Other articles on Code for life:

Preserving endangered species – of gut microbes

Epigenetics and 3-D gene structure

An history of ancient science in less than ten minutes and A brief history of science, part 2

Mid-week links and a milestone

Consumer brain-computer interface Grant Jacobs Jul 25

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As you read this blog article, your brain is processing what it sees on the screen. The devices you interact with the computer are most likely a keyboard, mouse or trackpad.

Imagine instead thinking about what you want the computer to do and the computer responding to that.

Tan Le from Australian company emotiv in the TED lecture below presents what could be described as a commercial mind-reading device.

The headset can be purchased for $US299.

I was writing the other day that science fiction looks ahead to where the future might go. Who’s for picking more of this to be part of it?

YouTube Preview Image

This is not the only mind-computer interface on the market; Wikipedia’s Comparison of consumer computer-brain interface devices page is one starting point to learning about competitor’s efforts.

Emotiv also has a Facebook page, where you might learn more about what they are doing. (Their latest post reports that interest in the TED lecture overwhelmed their web server.)

I would love to hear the experiences of anyone who has used any of these devices. It must be a remarkable experience when you first instruct a computer to do something directly with your brain.


Other articles on Code for life:

Walking with Rex (robotic legs for paraplegics)

iPads for the disabled (Perhaps a useful counterpoint to this post)

Temperature-induced hearing loss (Temporary loss of hearing during fevers or higher temperatures)

Describe your fantasy institute (The features of your ideal research institute are…?)

Basic fluid science on the space station (Video of simple, but intriguing science on the space station)

Vitalism ideology in chiropractic advertising Grant Jacobs Jul 25

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A dissection of an advertisement in which a local chiropractor tries to make vitalism sound credible

It’s been a very long time since I have taken the local chiropractor to task over one of his advertisements. I’m not able to give a full dose of Respectful Insolence in Orac’s inimitable style, but the chiropractor’s latest effort is begging to be deconstructed.

(Source: Wikimedia Commons.)

(Source: Wikimedia Commons.)

In his most recent advertisement (see lower right, page 5) he is selling that vitalism is not only credible (it’s not), but also implying it’s increasingly gaining acceptance (which it certainly isn’t and isn’t going to any time soon).

What’s strikes me isn’t the vitalism angle, it’s that the reasoning used reminds me very much of creationists trying to dismiss the theory of evolution.

Let’s back up a little and start at the beginning.

He starts by asserting — not demonstrating or questioning, asserting — that vitalism exists:

The first chiropractors called this special nature of the body its “Innate Intelligence […]

Note how this slips in an assertion “this special nature of the body”: vitalism is assumed to be true from the onset.

It resembles something I’ve often seen in creationist arguments: founding assumptions that assert or imply at the onset what they want to prove true, making their whole argument fallacious.

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Friday photo, links and video (16th July 2010) Grant Jacobs Jul 16

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The end-of-the-week round-up of those open tabs…

But first the photo of the week, the rings of Saturn in the distance behind Lutetia photographed in Rosetta’s flyby of Lutetia. For more details see the Rosetta blog.

(Source: The Planetary Society blog.)

(Source: The Planetary Society blog.)

OK, now those links:

And a video, from NASA, Interstellar Clouds And Dark Nebulae (great viewing):

YouTube Preview Image
Other articles in Code for life:

What famous writer do you write like?

Describe your fantasy institute

Honey’s anti-bacterial properties found?

Temperature-induced hearing loss

Boney lumps, linkage analysis and whole genome sequencing

Temperature-induced hearing loss Grant Jacobs Jul 14

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Two recent studies independently report mutations in the otoferlin (OTOF) gene are the cause of a rare temporary hearing loss caused by a high body temperature.

Ear-120px

I have a hearing loss, and if I spot research on deafness when updating papers for my own research (see Footnote of previous post) I often take a peek.

Tonight I learnt that some people have deafness that is dependent on their body temperature, with a high temperature (say, a fever) inducing deafness. They recover some time after their body temperature has returned to normal.

In some ways it’s quite quirky, but knowing how molecules interact I can imagine how this might be possible.

The study I ran into was a Chinese study examining a collection of 73 Han Chinese patients with auditory neuropathy*. During this study, they uncovered a case of temperature-dependent hearing loss:

However, his hearing was affected by a slight change of body temperature. His mother found that his hearing in the morning is generally better than in the afternoon, and temperature measurements showed that his body temperature in the afternoon was generally 0.1-0.6 Π [˚C?] higher than that in the morning.

They tested his hearing loss, raising his body temperature during an extended hospital visit and found that

When his body temperature rose above 36.5°C, the boy’s hearing loss was severe (70-80dB HL) and this symptom could last for a whole day.

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Science bite: Longevity gene study has flaws? Grant Jacobs Jul 08

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A quick heads’s up* that a recent genetic study on longevity may need further work.

Last week Science published a paper reporting a genome-wide association study (GWAS) for genes for long life, which was widely covered in the media (e.g. in the Guardian). Almost immediately some scientists queried aspects of the work, as is usual in science. Being a well-publicised work, these queries have wider reach than for other research papers.

Harry Patch at 105** (Source: Wikimedia Commons)

Harry Patch at 109** (Source: Wikimedia Commons) Wikipedia writes: “Harry Patch, known as "the Last Tommy", was a British supercentenarian, and the last surviving soldier to have fought in the trenches of the First World War.”

Newsweek has an article by Mary Carmichael that does a good job of explaining some of the issues.

Rather than repeat the main issues Carmichael points out in condensed form here, I encourage readers to read the original.

Daniel MacArthur writing at Genetic Future adds that the high-scoring SNPs (single-nucleotide polymorphisms) have no near neighbours with similarly high scores, a pattern which is more typical of spurious peaks (i.e. noise rather than signal). This should invite checking if these are noise or signal, or if there is a wider problem.

I have a similar opinion, based on experience using markers in linkage analysis. Markers lie along the chromosome, one after the other. If you plot the linkage score for each marker and are looking for regions that are candidates to be linked to the disease you are studying, ideally you want table mountain-shaped peaks, with several adjacent markers having a high score, rather than Matterhorn-shaped peaks (Aspiring-shaped for New Zealanders), with only a single high-scoring marker.

Having several independent markers indicating an association gives more confidence that the association is likely to be real.

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Boney lumps, linkage analysis and whole genome sequencing Grant Jacobs Jul 06

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We all have our lumps, the quirky features we develop with time.

Some of these are bone spurs, extra growths of bone.

These can be caused from damage to joints, like the lumpy joints seen in elderly people with arthritis. Bone spurs from differing causes can develop in many parts of the body, spine, toes, heel and hands.

Most bone spurs are associated with damage and old age, but some have genetic origins.

Figure 1A from Sobreira et al. (see References)

Figure 1A from Sobreira et al. (see Reference)

Metachondromatosis is a rare disorder that affects bone growth, where benign bone tumours produce lumps, mostly on the hands and feet.*

These lumps develop in children, with some of them reducing or resolving over time, others persisting.

Nara Sobreira and her colleagues set out to find genes that might cause this disease using a new approach that exploits sequencing of the whole genome of one patient.

Genetic changes that cause a disease can be as small a changing a single base in the roughly three billion bases in our DNA.

We have many, many differences that make us unique.

The art of locating the cause of a genetic disease is to determine which of those many changes from a lot of DNA is the one that has a role in causing the disease.

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Friday round-up: zombies, cats, embargoes, XMRV papers Grant Jacobs Jul 02

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Zombie-eyed polydactyl kitten (Source: Wikimedia Commons.)

Zombie-eyed* polydactyl kitten (Source: Wikimedia Commons.)

Scienceblogs has gone zombie. There are zombie articles coming out all over the place… A good starting point is the list PZ Myers has put together. (He fingers Scicurious as the original vector. She is happy about the Zombie Menace…) More seriously, this is a good effort on the part of the scienceblogs community. (A cynic would say that they’d do anything to promote their lot. Even turn to the living dead.)

An internet search following a discussion reveals that scibling Alison Campbell has a first. If you search Google Images for ‘cat with thumbs’, the first hit is… her blog. This is, of course, a feeble excuse to justify my posting a LOLcat picture. Or two. (Hey, I’m even admitting to it.) Check Alison’s old blog post for a one-two hit of LOLcat pictures.

On Embargoes. Director the British Science Media Centre, Fiona Fox, has a few words about embargoes. (Jonathan Leake gets particular mention.) I have to admit I have have mixed views on embargoes. Readers here will know that I have previously introduced Embargo Watch, a blog entirely devoted to embargo leaks. Included there is Leake’s view of the embargo system. (I’d welcome thoughts on embargoes in the comments.)

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XMRV prompts media thought: ask for the “state of play” Grant Jacobs Jun 29

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Previously I considered that media might ask experts what is known rather than their opinion.*

XMRV (Source: Singh Laboratory, University of Utah.)

XMRV (Source: Singh Laboratory, University of Utah.)

The fuss about the potential link between XMRV and CFS over the past few months has reminded me of the need for coverage to present what the current state of play is.

One of the more frustrating things for scientists to watch is media reports jumping in too soon,** reporting each new finding in an unresolved story as if it were the last word.

It portrays each research paper as definitive on their own. Research papers are in effect an argument for a case, a case that might potentially later prove wrong.

“Instant” blow-by-blow accounts portray science as a progression of abrupt discoveries, rather than an accumulation of smaller pieces from many different sources that lead to larger conclusions over time. It is true that occasionally there are genuinely startling findings that fly in the face of most of what was known in an area, but these are rare; much more usual are additions to what is known.

Sometimes research findings are contradicted by later studies.

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Friday reading – Legionnaires’ Disease, human ash sculptures, and more Grant Jacobs Jun 18

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As a science blogger my web browser gets full of open tabs holding articles I’d like to read, but haven’t time to do more than skim. Weeding out the good but not good enough to leave you with the better of these, I give you with this reading list:

Legionnaires’ Disease occurs in New Zealand occasionally. Pump Handle’s blog post reports that a The European Journal of Epidemiology research paper concludes that perhaps ~20% of cases in England and Wales can be linked with car windscreen wiper fluid, not a source most of us would think of.

(Source: via BoingBoing.)

(Source: BoingBoing; artist: Wieki Somers.)

Immortalise yourself as a 3-D sculpture using your ashes? BoingBoing has a short post pointing to Dutch artist Wieki Somers’ work. (Click on ‘Consume or…’) An example is shown to the right. (HT: @JenLucPiquant)

The New York Review — that home of good book reviews — now has blogs, good ones too. (HT: Neuron Culture.)

Lancet editor sacked. The Scientist outlines some of the back story to why a senior editor at top medical journal The Lancet has been sacked.

Save research funding: close alternative medicine centres? PZ Myers passes on a money-saving idea for the NIH: close the centres investigating “alternative” remedies. (Potential saving: $US240 million.)

Measuring science and scientists. Nature News has put up a round-up of their articles and editorials on science metrics. (Not all the linked entries are open access, unfortunately, but some are. It’s a pity that they don’t indicate which are (are not) so if you aren’t a subscriber you get to find out by trial and error!)

Open Access 101. NCAR Magazine has an article looking into Open Access in some depth.

As always, comments welcome…! (Encouraged, in fact!)


Other posts on Code for life:

Oliver Sacks on Hallucinations

In good health or not? – “natural health” advertising in newspapers, magazines

Conspiring against science

What is your relationship with your research notebook?

That Ben Goldacre fuss