Category: Web 2.0

April 18, 2011

A button for Tastefulword’s Readable Script

For some time now, I’ve been wanting a Firefox UI button for Gabriel Coarna’s extremely useful Readable Bookmarklet/Script which makes the web “reading-friendly” by cutting out all the flashy ads and colors.

Only, I don’t like bookmarklets, they take up too much space. Fortunately you can use existing Firefox extensions to turn this bookmarklet into a Firefox UI button.

THE SIMPLE WAY WITH A DEFAULT STYLE

Install the CustomButtons extension.

Then click here to install the button. Click OK and this is will setup my style for the button. Skip to points 3 and 4 in the Custom Way below.

THE CUSTOM WAY

If you want to put in a custom style, go to Readabale’s setup page and customize your style.

1. Right click the Readable Bookmarklet and select “Copy Link Location”.

2. Then click here and select EDIT. Go to the “Code” tab and paste the copied text into quotes after loadURI(“ ”). Hit OK.

3. Right Click anywhere on the toolbars and select “Customize”. You should see the Readable button.

4. Drag where you want and enjoy.

February 10, 2010

Reigning in Evolution

Life is diverse. There is no doubting that. In fact, the diversity has led many to believe that the possibilities offered by the seed of complex interactions, several thousand genes and their myriad products are so large, that we shouldn’t really be surprised at just about anything we see in the biosphere.

Adding a little bit of spicy strangeness along those lines, is the phenomenon of ‘convergent evolution’. This is one of those not-so-rare cases when species that aren’t very similar or closely related , turn out to have a feature that is strikingly, almost awe-inspiringly, similar. Wikipedia has a pithy list of examples of convergent evolution, my favorite one being the case of the human eye, and the Octopus eye. See how similar* they look, even though Cephalopods(them) and Vertebrates(us) diverged in evolution millions of years ago, before any eyes of similar nature were invented by the ubiquitous tinkering of evolution.

There are many explanations for why convergent evolution might occur, but they are circumstantial at best, speculative at worst and usually not very convincing. If you are a biologist, you will know that finding out the truth in such cases is intensive enough to just suffice ourselves with Orgel’s Second rule “Evolution is cleverer than you are”, and leave it at that.

But it’s starting to turn out, that while evolution may be a clever tinkerer, there aren't too many ways to skin a cat. A couple of papers published in the last few weeks show that while evolution may create similar characteristics in unrelated organisms, it tends to use the same mechanism at the molecular level to do so. Chan et al report in Science, that sticklebacks in different isolated populations tend to lose a feature of their anatomy: the pelvic girdle, by the same molecular event – the loss of a genetic regulatory element called the Pitx1 enhancer. Now you may say that these are the same species, and not nearly as spectacular as the Octopus-Human comparison, but remember that these populations do not interbreed, and not all populations have sticklebacks lose their pelvic girdle. It is pretty astounding that three populations who lose their pelvic girdle do so in the same manner – by eliminating Pitx1.

More exciting was a paper published in PloS Genetics by Counterman et al. , who examine the genes that produce the color in Heliconius butterflies. In contrast to the earlier paper, Counterman et al. study populations of a species of butterfly called the Small Postman (H.erato), that is a Muellerian mimic of its poisonous relative , the Postman butterfly (H.melpomene). The idea is that birds know that the Postman butterfly is poisonous , and will not eat it. H.erato will try to mimic the appearance of the its toxic cousin, so that birds leave it alone in a case of mistaken identity. Both H.erato and H.melpomene are poisonous, and have independently evolved similar appearances despite having diverged millions of years ago. The mimicry is a huge benefit to both species, since it ensures that predators have one thing firmly entrenched in their collective memory – if it looks like Postman butterfly, do not eat it .

[The author of the paper has educated me about the nature of interaction between these two species. See comments for details].

Heliconicus melponeme Heliconicus erato

Of course, the various populations of H.erato are not all equal, some seem to be better make-up artists and look much more like their miasmatic relative. Counterman et al. perform a population genetic analysis of these, and find, to their surprise that all of them show a dependence on only one site (locus) in the genome of these butterflies.

By doing more intensive analysis on this locus, they are able to determine that in fact, it is only one gene – kinesin, that seems to make most of the difference between a good mimic , and a bad one. Once more, the appearance and nature of a rather complex trait, is shown to be linked to a rather small region of DNA. If you want to look like the Postman butterfly it seems, you need to mess with the Kinesin gene.

In the light of these findings, a hint of a molecular explanation for convergent evolution begins to emerge. As the authors of either paper suggest, there may be evolutionary hotspots in our genome for a given trait. Whenever natural selection pressures the species into changing the trait, it is this genomic hotspot that feels the brunt. At the molecular level, evolution seems to be much more constrained than the medley of phenotypic outcomes lead us to believe.

I wouldn’t be surprised if one day we found that the developmental genes or regulatory programs that make an octopus eye and a human eye are more akin than their tentacles and our hairy heads seem to suggest.

*Note : It is interesting that despite the compelling similarity, the eyes are not completely identical. The retina of the Octopus eye actually has the reverse order of cell layers , when compared to the Human eye. This actually makes the Octopus eye somewhat better, since its optic nerve does not have to penetrate the retina – thus, an Octopus eye has no blind spot! Morever, because its photoreceptors have no obstrcutive cell layer (unlike us), it probably has a higher sensitivity to light as well.

References

Chan, Y., Marks, M., Jones, F., Villarreal, G., Shapiro, M., Brady, S., Southwick, A., Absher, D., Grimwood, J., Schmutz, J., Myers, R., Petrov, D., Jonsson, B., Schluter, D., Bell, M., & Kingsley, D. (2009). Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer Science, 327 (5963), 302-305 DOI: 10.1126/science.1182213

Counterman, B., Araujo-Perez, F., Hines, H., Baxter, S., Morrison, C., Lindstrom, D., Papa, R., Ferguson, L., Joron, M., ffrench-Constant, R., Smith, C., Nielsen, D., Chen, R., Jiggins, C., Reed, R., Halder, G., Mallet, J., & McMillan, W. (2010). Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato PLoS Genetics, 6 (2) DOI: 10.1371/journal.pgen.1000796

February 3, 2010

Passive Sensationalism

You see, this is why you begin to mistrust journalists. The passive sensationalism is, ironically blatant. I am referring to an article in the Indian Express .

Before I begin I’ll reproduce the article here….

China considered India ‘bottomless pit’ for foreign aid

Agencies Tags : Jawaharlal Nehru, Richard Nixon, Indira Gandhi

Posted: Sunday , Jan 24, 2010 at 1217 hrs

New Delhi:

While former Prime Minister Jawaharlal Nehru coined the famous slogan ‘Hindi Chini Bhai Bhai’, China considered him ‘discourteous’ and India to be ‘bottomless pit’ for foreign aid.

It also held the view that it was a ‘pity’ that late prime minister Indira Gandhi "has also taken as her legacy the philosophy of her father embodied in the book Discovery of India," which China believes revealed his idea of a great Indian empire encompassing Malaysia, Ceylon among others.

The comments were made by former Chinese Prime Minister Chou En Lai to former American President Richard Nixon, who famously called Gandhi a ‘bitch’ and a ‘witch’ while his National Security Adviser Henry Kissinger called Indians ‘bastards’.

The comments are now a part of the book ‘Nixon, Indira and India: Politics and Beyond’ written by a senior journalist Kalyani Shankar.

What this article is actually talking about, is a Cold-War-era conversation between a United States president and a Chinese Prime Minister, about India. India was all buddy-buddy with the Soviet Union at this time, much to the dismay of the US, and of course, China had already gone to war with India over territorial ambitions. In effect, these two political figures were talking about their counterparts in what they essentially considered to be a hostile country. It is rather tame language when talking about someone you think is your enemy, no?

Yet, this article (and that is it in its entirety) , provides only the juiciest tit-bits, without any context whatsoever – no doubt to rile up the sentiments of those Indians who read it upon seeing their leaders being insulted.

Of course, this is excellent promotion for the upcoming book, although if Mr.Shankar has a shred of decency as a political writer, he will want to give the journalist a piece of his mind, and I hope that includes some expletives.

October 28, 2009

Twitter finally on the Phishing Target list

Update 00:30 Oct 29 2009 : I reported the website to Phishtank and the website should now be blocked on all modern browsers. Tested on Safari 4 and Firefox 3.5. Move along now, nothing to see.

This is just a quick post to warn people that Twitter messages are being used for phishing people's Twitter passwords.

I recieved a "Direct Message" on Twitter from @AccessDNA that went as follows :

"hi. this you on here? http://blogger.djhxkcs.com " (Warning! Do not enter details on the linked page)

Of course, out of curiosity I visited the link , and waiting for me was a page that looked exactly like Twitter's Sign in page – except that it was posting the information to a different address , and would thus send any details I entered to some database. In time, I would expect my Twitter account to be usurped.

Watch out for suspicious messages and pay attention to the address, secure-connection icons and such, people.

October 1, 2009

Wave Mania

I woke up today to Wavemania hitting the tubes. Google apparently decided to send out 100,000 invites to their chosen lot. Obviously , I am not one of their chosen lot – since a quick check of my inbox revealed no invitation.

Twitter however was buzzing, and Google was bombarded with searches for “Google Wave invites”, as evidenced by the spike in the graph below.

Search for “google wave invites“

I tried foraging for some invites, but I quickly gave up. Mainly because, with only a hundred thousand invites, some chaps even thought of selling them on eBay, fetching as much as $70. Obviously, anyone who now had an invite was not going to let it go to the masses just like that.

So, much as I would like to try Wave to explore its uses in scientific communication, I think I will sit this one out – when Google decides to make it public.

March 10, 2009

Using Ubiquity+Readability Project

The Readability Experiment lets you restyle web pages for better reading. They offer “Bookmarklets” that one can click to re-style a given webpage so that it is easier to read.

Ubiquity is an “intelligent” command-line and natural language parser for Firefox. Its hard to explain because of its ubiquitous features( everything from Twitter posts to Maps and email), so I’ll leave that to the excellent screencast on their site.

I thought it would be cool to have a Ubiquity command that uses the Readability project and fixes your web-based reading material. Turns out, its easy to have it, and the results are very satisfactory to me.

The screenshot shows how a cumbersome page can be viewed cleanly using Ubiquity.

Ubiquity can be downloaded from Mozilla Labs . Once Ubiquity is installed , Ctrl+Space (be default) opens the Ubiquity panel.

For an easier method to start using the Readability command , just visit this page , and in the bar where Firefox tells you it has found Ubiquity commands, click “Subscribe”.

You can manually add the command to Ubiquity as well. To install custom commands such as this one : type command-editor in Ubiquity, which will take you to your custom command editor page.

March 6, 2009

A Better Gmail (in Firefox only)

UPDATE 4th July 2009 : Due to lack of time and the fact that similar and much better scripts have been written, I recommend everyone install the Gadget-supported Gmail (ad-less and wide) script.

I myself use this script now, and it is done much better. The author also commits to updating the script periodically.

Cheers and thanks for the support !

UPDATE : While I myself do not use the ThreadLinks box (New, Expand all etc.) and don’t miss it, a couple of users have written in asking that it be implemented. Iain was kind enough to point me to jtulloch’s version, which used the Gmail API to put the Threadlinks box into the left-side nav-pane.

I’ve arrived at a quick and absolutely dumb solution, which is to simply merge jtulloch’s script with mine , thus nuking ads in a fell-swoop while retaining the ThreadLinks box using his code.

So to all those who’d like to use the ThreadLinks box , you can download a newer version of the script here.

The older version is still available for people who don’t want to mess with their navPane.

I love Gmail, I hate ads. I use Gmail for syndicating all my email. It is perfectly legitimate of Google to expect some revenue; but when they put ads in a space that they allot to me as personal (such as my inbox when reading an email), it irks me to no end.

So I whipped up a small script that will remove advertisements in the message reading pane and widen the concerned pane to take up the full area that was intended for it. You will need the Greasemonkey extension for Firefox, to use this script.

You can obtain Greasemonkey here .

After installing Greasemonkey, click here to install the Remove Gmail Ads and Widen Message view script, for a cleaner Gmail.

You can also right-click the link and choose to see the source.

February 15, 2009

Why Scientists won’t use Twitter…

Twitter doesn’t need an introduction. The microblogging service is widely popular, and most Twitter users swear by its wonderful utility. It is a “Social Commons”, as one enthusiastic web junkie put it. But a few months into using Twitter, I realised that there are very few scientists – and I mean natural scientists, on Twitter. For instance, at the time of writing this post, the Twitter account science had 2,247 followers , while some popular individuals have followers 10-fold that number.

It seemed perplexing – science today is collaborative, everything depends on communication and sharing ideas , it seems perfect for scientists to share information fast, on a on on one basis if required or tweet to the community. Don’t get me wrong there are plenty of tech-twitter services that discuss the latest gadgetry to hit the markets, but none that discuss the fundamental subjects – the quartet now known as STEM – Science Technology Engineering and Mathematics. So I pondered on the reasons, using my own department as a small study group to try and ascertain why scientists don’t seem to use Twitter, despite the hype.

Here’s a list of reasons I came up with :

1. The Twitter Reputation : Some might say allusion to little bird sounds is cute, hip – but it also gives Twitter the image of something frivolous, not really useful , and part of the MySpace/Facebook category (collectively chided as being a narcissistic phenomenon a.k.a MyFace). Most scientists hold the impression that Twitter is a social network – a place where one wastes time, and real discussions happen only on mailing lists and forums.

2. The Social Activation Barrier : It isn’t just a stereotype. Scientists are substantially asocial – feeling more at home dwelling on the workings of their pet problem rather than interested in what other people are thinking about. Of course, scientists have a tinge of megalomania, and generally will assume that anyone who hasn’t earned credibility with brilliant ideas or research is not really worth listening to. This does not mean they are impolite to lay men, but they rarely take laymen seriously. It is not a reflection of personality , merely a result of the widespread examples of utter silliness among laymen (Intelligent design? ), poor understanding of how the natural world works on the part of laymen and the stringent standards that scientists are used to apply to themselves and their peers (oh, is my megalomania showing here? ).

3. Email vs. Twitter : Scientists will talk of course to experts in their field , but the preferred method of communication is email. Scientific discussions tend to involve lot of fact-stating and elaboration of theories, and the 140 character limit is simply ill-suited for this purpose. Email is also private, let’s you communicate with people you know are interested and stays as a permanent record. Even if Twitter does some of those things, but it doesn’t top email when it comes to communication. So why change?

4. Privacy (read ‘Secrecy’) : The data and models a scientist generates and the insight they provide is the usually the culmination of a long arduous process. In most cases, it represents years of sacrifices, blood and sweat (of the researcher, metaphorically and his lab rats, literally). As such , the culture of Twitter , which is to openly pass out information is entirely antithetical to the culture of science. Scientists will protect their data from all eyes until it can be represented to the public through a legitimate medium. Only a peer-reviewed journal or a patent is a legitimate medium , by the way, Twitter is not. It is a vicious circle. Twitter is not a legitimate source because of Point 1-3…and Points 1-3 would be rectified if Twitter was considered a legitimate source.

5. Science Media : Speaking of legitimate publication media, the science publishing industry hasn’t quite taken to Twitter. Although some journals (Science , for example) offer podcasts and other “Web 2.0” methods of disbursing information, the core process of publishing science remains tied to the Print/Paper method. All other methods are , in the psychology of a typical scientist simply “Pop-Sci” offerings – the real technical stuff is in the ‘Paper’. Discussions and debates also proceed through a process of writing to the Corresponding Author over email or the Editor of the Journal , who then publishes it and so on. A painfully slow process , I might add, especially in this day and age.

Unfortunately, the above points are also applicable to other “Web 2.0 “ Science resources. Social Networks for scientists (see ResearchGate, Nature Networks) have received only lukewarm reception even when backed by a highly rated research journal – and the few who register are mostly graduate students. Serious scientists still don’t seem to care. I, personally, appreciate the enormous potential of services like Twitter to encourage dialogue between scientists, and to act as a fast information highway. To be fair, there are isolated cases of scientists actually using these resources ( OpenWetWare ). But until the culture of science undergoes a paradigm shift, I am afraid Twitter and its brethren will remain excluded from the scientific community, to be the subject of blog posts by individuals have who taken to it, and to be ignored by the institutions.

Technorati Tags: science,twitter,stem,web 2.0