Category: Technology

Tech Talk – Miscellaneous discussion of gadgets, industry, computer science, social media, AI

Medline on Facebook

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

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

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

Science Blogs, Favourites of 2007

Science OPML

In an effort to keep Sciencebase bubbling along during the holiday season, I figured a quickie post listing some of my favourite science blogs from this year might be interesting. Blogs come and go, of course, and my newsreader account is in constant flux with new blogs that catch my attention briefly getting pole position and then dropping off.

However, I remembered that there is a quicker way for you to grab a recent snapshot of my feed favourites and that is with my newsfeed OPML file (right-click and save the link with an “.opml” extension. You can then import it into any compatible news aggregator, offline (Snarfer) or online (Google Reader) with minimal fuss. Or use an OPML editor to edit it, it’s entirely up to you. My science OPML file is up to date, relatively speaking, although I may have added or removed a few feeds from my own aggregator in the last few days. Anyway, it’s as good as it gets at this time of year.

Meanwhile, a growing list of blogs with a genetics, DNA, and health theme can be found on the DNA Network. At the time of writing, my good friends Ricardo Vidal and Hsien-Hsien Lei are busy creating a new website for the Network that will feed on all the RSS files from the member blogs (I should admit, Sciencebase is a member of the Network). It’s difficult to single out any of the other blogs in the DNANetwork for specific attention, Ricardo and Hsien’s are superb, and so are many of the others. So. once you’ve trawled through my science OPML, do check out the DNA Network too.

Ten Computing Tips | Data Recovery

Faster Firefox

Seeing as the holiday season is fast approaching, I thought I’d offer an extra post covering some of the browsing and blogging tips and tricks I run on the Significant Figures site at Sciencetext.com. On that site I used to mainly discuss inappropriate unit conversions, sloppy statistical use, and dodgy typos in the media and still do occasionally.

For instance, there was a lot of press on the comet bigger than the sun issue recently, which interconverted miles and kilometres with astoundingly high improvements in significant figures. Then there was the discussion of how much does Santa Claus weigh…

But, like I say, mostly it’s tips on how to get the most from your web browser, improve security, and boost your blog’s performance. It acts as my personal lab book for all kinds of hacks, so I always have an online reminder of tweaks in case I lose track of how I fixed a particular problem. To follow are some of the most commonly accessed pages on the site, hopefully one or two of them will strike a chords and be of use to Sciencebase readers:

So, there you go, if you plan to use any of these, please backup any important data files first to avoid the need for data recovery and don’t blame me if it all goes horribly wrong, you use them at your own risk. I would be interested to hear how you get on if you do apply any of my hacks.

Male Semen is Redundant

Male sperm

You’ve seen the kind of thing: “Warehouse Razed to the Ground in Fire”, as if razing didn’t already mean the building was levelled. Worse, “Balloon Ascends Up into the Air”, ascending down is very difficult, simultaneously, at the same time, if not impossible; so too is descending up.

However, the award for the most redundantly tautological headline of the year has to go to Scientific American for Male Semen Makes HIV More Potent, that’s male semen as opposed to the female variety, is it? It’s an important discovery, nevertheless that a chemical constituent of semen affects the immune system facilitating viral infection.

Scientific American is probably not the first and original nor the ultimate and last publication to use this phrase though. DoctorNDTV ran a story with the title: Male semen loss concerns and risky sexual behaviour. Then there’s a research paper in the Journal of Avian Biology that discusses bacteria found in the “male semen” of red-winged blackbirds. Even the venerable and well-respected New Scientist recently published an item on insect courtship and egg laying. Apparently, the trigger for egg laying “is a small protein called sex peptide (SP) in the male’s semen.” Again, the word male, while perhaps making the sentence smoother, is totally redundant and not needed.

A search for the phrase “male semen” on PubMed produced not hits, although “male sperm” came up several times in various journals. So as not to appear sexist, I also did the equivalent searches for “female semen” and “female sperm” and quite surprisingly got several PubMed hits. One paper on mythology mentions how at one time in human history a godly being or other supernatural entity was thought to intervene in the merging of male and female semen to bring about conception. Not quite a modern biomedical reference point, then. The phrase “female sperm” gave absolutely no hits, unsurprisingly.

Maybe the clue as to why these various publications qualify the word semen lies in those papers discussing the mythology of reproduction. A quick Google shows that there are many references to religious and proto-religious texts that discuss both male and female semen as if they were both real. Perhaps by qualifying semen as male in modern writing, rather than simply discussing semen, there is some referential nod to humanity’s misconstrued understanding of reproduction. But, modern understanding of reproductive biology defines semen as a product of the male reproductive organs that acts as a transport medium for sperm, so, like I said, it’s redundant.

I asked linguistic guru Steven Pinker of Harvard University, whose book The Stuff of Thought I reviewed on Sciencebase recently, about this apparent paradox. Pinker told me that he suspects that, “the cause is not a nod to the ancients, but a desire to call the reader’s attention to the fact that it’s
the naturally occurring fluid that encourages the potency of the virus, not some externally administered product.

“Semen Makes HIV More Potent implies to me,” he said, “that adding semen increases the potency, rather than that the HIV exploits the properties of the semen it finds itself in.” He adds that it is peculiar that this may be the case. “Odd that the redundancy should do that,” he told me, “but somehow I think it does.”

Intriguingly, after I contacted Pinker, I saw that the journal Nature, as opposed to the popular science magazine, Scientific American, had covered the same story. In Nature, however, their piece was entitled – Semen boosts HIV transmission. So, for some reason they felt semen does not need a masculine qualification of any kind. The tautology of the phrase “male semen” may seem trivial, but it is an important issue.

8 Squeezes for Your iPhone Battery

Battery life (Image courtesy of BatteryUniversity.com)

If you’ve just bought an iPhone, you’re probably expecting many happy years of battery power. Well, not so fast. Laptop batteries are very similar to rechargeable batteries in other devices, they wear out. I’ve had my current laptop for about 18 months and in the last few weeks I’ve noticed that I’m not getting quite the battery life from it that I was when I first bought it. I used to be able to run for about 3 hours doing wordprocessing, email, and web browsing even on a wireless connection. Lately, however, the lithium battery seems to run down within an hour or so, which is a real pain when I’m offsite.

I checked out Battery University to see if there is anything I can do to get my battery life back to normal. Apparently, there isn’t, and as a chemist, I should have known that (it’s all about crystallization of the components and such). It turns out that I basically broke all the rules concerning lithium battery use. Here’s a quick run down of what you should and shouldn’t do to help maintain the health of any lithium battery whether in a laptop, iPhone (other hybrid devices are available):

  1. Avoid frequent full discharges; regular partial discharges and an occasional full discharge are better. Lithium batteries have no charge “memory”, unlike NiCd batteries, so frequent recharging does no harm.
  2. Carry out a deliberate full discharge once every 30 charges, you can do this by simply running the battery down in the equipment (if you have power management enabled switch it off temporarily and make sure you are not running any critical software). An advantage of this approach is that it helps calibrate the battery fuel gauge and avoids premature hybernation.
  3. Keep the lithium-ion battery cool. Heat is a killer for batteries. Don’t leave your device in a hot car or window ledge, don’t use a laptop on your lap (how’s that for irony), above about 45 Celsius, a lithium will wear out very quickly.
  4. If you’re running on fixed power, think about removing the battery from a laptop to reduce the impact of internal heat. Of course, you lose the mobility advantage of the battery and also the safety should your mains power go down.
  5. Don’t buy spare lithium-ion batteries to use later on. Even when not in use a lithium battery will age.
  6. If you do have a spare lithium-ion battery, use one most of the time and keep the other wrapped in a hermetically sealed plastic box or bag in the refrigerator, but do not freeze your battery.
  7. If you have to store your battery or device, make sure it’s charged to about 40% before leaving it for extended periods.
  8. If you’ve just bought a new device, follow this advice and pop back in a year or so to let me know how you got on. After 12 months any lithium battery no matter how well looked after may lose up to 20% of its charging capacity but if you’ve lost more than that, then you probably broke the Battery University rules.

This post was originally destined for my blogging and browsing tips site Significant Figures, for more of the same and different again, check out the Sig Figs site at sciencetext.com

Open Access Scientific Publishing

Imperial College’s Bob MacCallum runs an interesting site called Compare Stuff, which I’ve reviewed on various occasions elsewhere. Recently, he started blogging about some of the interesting results that emerge when you compare search engine hit rates for different terms against each other. One of the most interesting comparisons was run using the terms “open access” versus “journal”.

The results produce an intriguing chart in which there appear to be far more mentions of bioinformatics in the context of the term journal and open access compared with, say, maths, astronomy, or psychology. As MacCallum is bioinformaticist he says that this makes sense as many of the leading figures in the open access movement come from this field. However, physicists and computer scientists have been enormously active, if less vocal, about OA, so it is odd that those two fields do not show up quite so sharpy. What about open access chemistry, you say? Hmmmm.

Give MacCallum’s Compare Stuff site a try, it’s quite amazing what charts you can make. I just tried Organic versus Inorganic in the context of “emotions”. It looks like organic and inorganic are equally stressful but leave few people anxious, scared, lonely, happy, jealous, angry or sad.

Revealing Invisible Science

Revealing the Invisible Web with CCReSD

The notion of the Invisible Web created quite a buzz, long before Google even had just one “oo” let alone half a dozen. The phrase alluded to the putatively millions of additional web pages, essentially hidden from view behind database scripts – fascinating product catalogues, riveting company backend data, and, scientific databases.

Scientific databases, you say, invisible?

Of course! You probably think of the databases with which you are personally familiar as being directly accessible and that there is nothing hidden about their contents at all. Much of the search functionality of countless scientific databases will work perfectly well regardless of your IP address, irrespective of whether you have logged in, and from almost anywhere in the world. Some are closed off to non-subscribers or those outside a particular campus or organisation, of course, but many are not. So, by what stretch of the imagination might they be described as hidden, or worse, invisible?

Well, do you know precisely what is contained in the close to 1000 terabytes of information in the National Climatic Data Centre? What about your favourite literature database? What about PubMed or ChemSpider? Or, any of dozens and dozens of other databases hidden by virtue of their very nature from conventional search engines. Obviously, specific users will have a relatively detailed perspective of the contents of a particular database, but what about cross-disciplines or, perish the thought, lay outsiders who may need to access information quickly without spending hours, days, weeks, attempting to find the right database and then attempting to figure out what is in it?

Yih-Ling Hedley and Anne James of the Faculty of Engineering and Computing at Coventry University, and Muhammad Younas of the Department of Computing at Oxford Brookes University, Oxford, England, point out that invisible web databases dynamically generate results in response to users’ queries. And, therein lies the rub. Search engines, which traditionally crawl, spider and index, the web, see only the front-end search page when they visit a site acting as a user interface for a database, in general. This means that the actual keywords associated with the data within those databases is not accessed, because it is dynamically generated by real users, and is not rendered by the search engine robots

Nevertheless, Hedley and colleagues say, “The categorisation of such databases into a category scheme has been widely employed in information searches,” but with only limited success. Now, the team has developed and tested a Concept-based Categorisation over Refined Sampled Documents (CCReSD) approach that effectively handles information extraction, summarisation and categorisation of such databases. Unlike a conventional search engine, CCReSD behaves in some ways like a real live user and detects and extracts query-related information from sampled documents of databases.

The result is that the system can generate a table of keyword terms and their frequencies to summarise database contents. The team explains that their system also generates descriptions of concepts from their coverage and specificity given in a category scheme.

Okay, sounds useful, CCReSD is basically a database savvy search engine spider that can create an index from otherwise hidden web resources by spoofing the behaviour of a genuine human user of that database. Aside from the potential breaching of database terms & conditions that forbid automated accesses, this could be a potentially very useful tool for technical subjects that have many, many hidden databases.

The team tested their system on the Help Site database (computer manuals on a system with multiple templates), CHID (a healthcare database with a single template) and the general database-driven site Wired News (single template). They found that it could extract relevant information from sampled documents and generate terms and frequencies with improved accuracy on previous approaches.

The team discusses CCReSD in detail in the Int J High Performance Computing Networking, 2007, 5, 24-33

Video Lecture Search and Natural Language

A new speech and language search engine that could help you find particular subjects discussed in a video lecture, has been developed by MIT scientists in the Computer Science and Artificial Intelligence Laboratory. Regina Barzilay, James Glass and their colleagues say the web-based technology currently allows students and others to search hundreds of MIT lectures for key topics.

“Our goal is to develop a speech and language technology that will help educators provide structure to these video recordings, so it’s easier for students to access the material,” explains Glass. More than 200 MIT lectures are now available at http://web.sls.csail.mit.edu/lectures/ but there is no reason to think that the system could not be scaled to even the most puerile of Youtube video at some point in the future.

Meanwhile, a Cambridge, UK, company has gone into private beta with its natural language search engine. TrueKnowledge is discussed in more detail in an article entitled “What time is it at Google Headquarters?”, which is exactly the kind of question it can help you answer.

Facing up to Facebook

Facing up to Facebook

Sciencebase readers who scroll all the way down to the footer of any page on the site will most likely have spotted a clutch of new icons in a section I call Geeky Fun Stuff. I never thought of myself as an ubergeek until recently, but I guess it all adds up: big science fan, science degree, science writing as a career, fan of the more technical kinds of music, Rush, Peter Gabriel, Pink Floyd, that kind of stuff, oh and the The Dickies (I jest), and running a blog with literally thousands, well not thousands, dozens of plugins, that you spend far too much time tweaking.

And, part of being an ubergeek is stepping out of denial and facing up to one’s Facebook presence, the installation of Scrabulous, South Park character creator, and of course, the creation of one’s own niche group (science writers, 167 members and growing, by the way).

Once you’re up on Facebook, there’s no reason not to have a Twitter and a Pownce account too, as well as providing readers with direct access to your StumbleUpon and del.icio.us pages (see the footer). But, of course, those of you who reached the footer already know all this. To top it all, I guess fessing up to ubergeekicity also involves giving bits of your blog odd names, such as Elemental Discoveries, and Geeky Bits.

It probably also involves including links to a collection of my subscribed feeds known as an OPML file, worrying about how many subscribers the site has, and spending inordinate amounts of time running a science podcast that’s available on iTunes but doesn’t involve me laying down my Geordie accent in an mp3.

So, if you’ve haven’t been down under on Sciencebase, now is your chance, there is lots happening at the foot of this page. Feel free to “friend” me via any of those icons of web 2.0 but only if you want a self-professed ubergeek in your virtual circle.

Never Divide by Zero

There is nothing like a Lego movie to cheer up an overcast day, and it has been a long time since I posted the Newton’s Laws Explained with Lego movie. So let’s get metaphysical and find out what happens when you square infinity or when a bug in the totalityofexistence leads to a universal divide by zero.

I assume everyone spotted that the time – 10:21 – at 1’13” into the movie doesn’t change, it’s still 10:21 at 2’20” in…nice touch or continuity error…or just a lack of another 2 sticker for the Lego clock.