Archive July 2010

Loops to tie a knot in proteins? Grant Jacobs Jul 30


Most proteins fold onto themselves without forming knots. A minority form a ’topologically entangled conformation’, a knot.

Proteins are strings of amino acids, chained together one after the other.

(Source: WIkimedia Commons.)

(Source: WIkimedia Commons.)

The properties of proteins depends on their specific three-dimensional fold, how the chain of amino acids are arranged in space.

When proteins are first made by reading the RNA copy of a gene, the order of the adjacent triplets of RNA bases (letters of the RNA code) specify a specific order of amino acids, one amino for each particular triplet of bases.

This initial chain of amino acids is just that, a linear chain.

Proteins fold through the physical properties of the particular sequence of amino acids making up the protein inducing a particular collapsing of the protein on itself in water.

For the vast majority of proteins this collapsing on itself does not involves a portion of the chain threading itself through another portion of the chain to form a knot.

Intuitively this makes sense; self-knotting of a protein chain would be more finicky that simply placing portions of chain adjacent to other portions of the chain.

A few proteins, however, manage to pull off this self-knotting feat.

Being able to accurately predict the folding of a protein from it’s amino acid sequence, to solve the ’protein folding problem’ would open door to designer enzymes and vastly increase our understanding of life through having available the detailed chemical arrangement of proteins in 3-D.

In this cartoon of a protein, the grey tubes represent loops connecting the more compact helical and ribbon (red arrow) regions of this small portion of a protein (Source: Wikimedia Commons.)

In this cartoon of a protein, the grey tubes represent loops connecting the more compact helical and ribbon (red arrow) regions of this small portion of a protein (Source: Wikimedia Commons.)

Examining knotted proteins, with their potentially more finicky folding requirements, might be another way to explore the detailed basis protein folding.

What features might guide self-knotting in proteins and can they teach us something about how proteins fold?

European computational biologists compared proteins that form knots and those that do not, looking for features that might be associated with knot formation.

For the most part the amino acid sequence of the proteins did not distinguish knotted proteins from those without knots.

Comparing the 3-D structures of proteins, in particular those with similar overall folds but with one case being knotted and the other not, their work suggested particular loops on the surface of some the proteins examined are a feature common to knotted proteins not found in unknotted proteins.

These might be, in their words, ’knot-promoting’ loops, in some way these loops may be aiding the chain in threading through itself.

(Source, Fig 1 of Reference.)

(Source, Fig 1 of Potestio et al, see References.)

I’ve no doubt that researchers will now look very closely at these particular protein loops and see if they do in fact promote the formation of a protein knot.


Potestio, R., Micheletti, C., & Orland, H. (2010). Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops PLoS Computational Biology, 6 (7) DOI: 10.1371/journal.pcbi.1000864

Other articles in Code for life:

Rex and The Wrong Trousers – uncanny resemblance?

Making the most of lousy book reviews on Amazon

Consumer brain-computer interface

Developing bioinformatics methods: by who and how

Testing common ancestry to all modern-day life

Rex and The Wrong Trousers – uncanny resemblance? Grant Jacobs Jul 29

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(Source: Rex Bionics publicity material.)

(Source: Rex Bionics publicity material.)

The Wrong Trousers:

(© Aardman / Wallace & Gromit Ltd 1993. Used with permission. [Thanks!])

(© Aardman / Wallace & Gromit Ltd 1993. Used with permission.)

Now, imagine if someone fiddled with Rex, added wireless remote control and …*


* For the confused Rex is a recently-announced assistive device for paraplegics and The Wrong Trousers is a Aardman / Wallace and Gromit claymation movie featuring a pair of robotic trousers. If you haven’t seen the movie, I can recommend for ‘kids’ of all ages. (It has reviewed extremely well, for example getting a 100% fresh rating at Rotten Tomatoes.)

My thanks to Bob O’H, whose comment suggested this (see Walking with Rex). I’m still kicking myself for not having thought of it for myself.

Special thanks to Aardman / Wallace & Gromit for permission to use their image.

(Updated to add a little information for those likely to be confused.)

Other posts on Code for life:

Walking with Rex

Consumer brain-computer interface

Mid-week links and a milestone

Minorities, disabilities and scientists

What do you want in a Head-of-Department? Grant Jacobs Jul 28


Office with speaking tubes (Source: Wikimedia Commons.)

Office with speaking tubes (Source: Wikimedia Commons.)

While skimming a long comment thread elsewhere, I noted Austin Elliott pointing readers to an article, The HoD Delusion (warning: large PDF file) in Physiology News, written by an anonymous (recovering) head of department.

It opens with an anecdote about being a Head of Department (HoD), then examines what the writer considers are the issues facing a incumbent HoD. The opening passage reads,

“It is frequently said, though I forget who started it, that managing academics is like herding cats. My experience, as both cat owner and Head of Department (HoD), suggests that this is grossly unfair to cats; our feline friends tend not to discuss their destination at length, let alone all the ins and outs of if, why, and how they want to go there; nor do they resist change with nearly as much enthusiasm as academics.

Over several years I have realized that becoming a HoD, rather than cat-herding, is more like becoming a parent — for the following three reasons in particular. First, you take it on in addition to your other jobs; second, nothing really prepares you for the reality; and third, you undertake its major responsibilities and possible consequences with little — if any — appropriate training.”

Think of this blog post as a call to both walk in their shoes for a little bit, and to discuss what you think HoDs should do – and not do. Comments from current or previous HoDs are particularly welcome.

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Mid-week links and a milestone Grant Jacobs Jul 27

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I have too many interesting articles to read and too little time to write… here a few articles I can recommend, and a milestone. Of sorts.

  • Holt milestone (Source: Wikimedia Commons.)

    Holt milestone (Source: Wikimedia Commons.)

    It’s officially sex week over at the Loom. Given Carl Zimmer is one of several science writers who also blog that last year brought us far more than we really needed to know about duck penises, so this is worrying. He starts out with fungal sex; reading between the lines viruses may turn up somewhere along the way. (You’ll have to ask him if he is going to include Aves.)

  • Science writer Deborah Blum, who blogs at Speakeasy Science, has a piece in Slate, The Raw Milk Deal, about the health issues of drinking raw milk. New Zealanders, being the big milk drinkers we are, might want to compare an American science writer’s perspective.
  • Ben Goldacre has put up a podcast of the British government’s response to homeopathy, a topic I’ve frequently written about in the past. It’s long (30 mins), so try this when you have time.
  • Dave Munger writes about plagiarism, science writing and blogging, including what happened to Brian Switek’s article. I fairly regularly get posts copied by the robot plagiarists that he mentions in passing. (These copy posts in their entirety onto websites set up to show off advertising.) I’ve also had an advocacy group copy an article wholesale, which I was less impressed with. (I let them know that I didn’t approve in my comments but got no reply. Read the rest of this entry »

Who has the most bioinformatics scientists? Grant Jacobs Jul 27

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Every day I receive a number of marketing emails, including those advertising research databases.

Today I received one from a regular source* that offered this table as an example of it’s contents:

Top 10 Countries for Bioinformatics Research (ranked by number of senior Bioinformatics researchers)

United States Of America (44,561)

Japan (4,269)

Germany (4,076)

United Kingdom (3,901)

France (2,677)

Canada (2,262)

Italy (1,833)

Australia (1,022)

Spain (999)

China (991)

New Zealand is indicated to have 125 senior bioinformatics scientists.

Read the rest of this entry »

Making the most of lousy book reviews on Amazon Grant Jacobs Jul 26


Here I join in with Jennifer Ouellette in ranting about lousy book reviews on Amazon (or the like), and add a consolation for writers that some of us put them to positive use.

Over at Cocktail Party Physics, Jennifer Ouelette reviews samples of the worst reviews of some recent popular science books at Amazon and concludes that

The lesson to be gleaned from all this, for all those who’ve written books, or are contemplating doing so, is this: just as you can never really believe your own publicity, so, too, you should never take what reviewers – especially of the anonymous variety on Amazon – say to heart.

So true.

newton and the counterfeiter

I’d like to add a consolation thought for writers (and publishers) that not all is lost.

Some of us put those terrible reviews to positive use, using the reviewer’s errors figure out what the book is not.

This might seem dead obvious, and in some ways it is, but there is a slight bit of subtlety here.

A ‘classic’ mistake I’ve seen (year after year…) is buyers of, say, computer programming literature who have bought a reference book thinking it to be a textbook then score the book poorly complaining that the reference book didn’t teach the subject, it ‘only’ provided the material in drier form to be looked up if you already knew the basics.

Of course: that’s what computer reference books are for.*

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Consumer brain-computer interface Grant Jacobs Jul 25


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


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.

Read the rest of this entry »

Beyond Preaching to the Choir Grant Jacobs Jul 21


Thoughts on publishing in journals outside your immediate speciality that might use your work, and on articles reporting developments in related fields.

This brief stream-of-concious* post is inspired by librarian Bonnie J. M. Swoger’s post that takes it’s lead from Stevens’ research article Beyond Preaching to the Choir: Information Literacy, Faculty Outreach, and Disciplinary Journals (DOI: 10.1016/j.acalib.2006.08.009).

Swoger argues that librarians should make some effort to target their message to the users of their services, and not only publish in what I guess we could call librarianship journals.

In a similar way, I have always liked the notion of publishing some (note all!) bioinformatics or computational research articles that are of direct use to researchers in general biological journals that the users of the methods or knowledge might read them, rather than have them buried in the specialist bioinformatics journals.

You might publish a new method for aligning genomes and it’s ’web server in a genomics journal, rather than a bioinformatics journal, with the aim of reaching the potential users directly.

Maybe it’s just my perception, but too many journals exclude bringing in news from related fields.

You could view this as a general problem within science, the communication between disciplines is typically poor and there are relatively few proactive efforts to overcome it.

It’s accepted that it’s the scientists’ job to search around the literature. I like reading widely myself, but it’s also a luxury few have the time for really; most barely have time to keep up with their own niche.

Read the rest of this entry »

Blogimmuniqué: Tracking the science blogosphere Grant Jacobs Jul 20


Introducing a new section on my blog that lists other science blogs and more departures from the US-based scienceblogs collective.

A blog tracking list The main reason I am writing this quick post is to introduce a new section on my blog. If you look at the lower portion of the banner you can see a series of links to pages. Today there is one more. In this screen shot I’ve highlighted the link to draw your attention to it:


I want to emphasis that this list of blogs is not just for those blogs that were formerly part of scienceblogs; it is for all science blogs, anywhere. The current exodus from scienceblogs is merely the ’inspiration’, if you want to call it that, that has promoted me to start this.

This will take some time to develop – I’m only one man and I have a busy day job! – but the first dozen or so blogs are already on the list. If there are others you’d like to suggest that I consider adding, let me know.

Today departures The exodus over at Scienceblogs continues, with Bora Zivkovic, ’PalMD’ and Deborah Blum’s blogs all on the move. Orac, of Respectful Insolence is left pondering.

Bora Zikovic’s long farewell post is an interesting account of both his personal development as a science blogger and science blogging as a whole. It’s worth reading. (If you can find the time, it is long!) Deborah Blum has built her’s around a Tennyson poem.

David Dobbs summarised Bora’s post on twitter thusly: BoraZ summary: Blogs have matured. Ecosystem changing. Exciting times ahead, add: Serious blogging is Media; ethics follow

Other articles on Code for life:

Scientific article download costs

Temperature-induced hearing loss

Boney lumps, linkage analysis and whole genome sequencing

Royal Society publishing free to read, 1665 – today

What is your relationship with your research notebook?

Book sales, frumpy readers, and mental rotation of book titles

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