Wednesday, October 18, 2017

Getting creative with molecular biology

Creating something new using concepts you have learned leads to a better understanding of the subject.  Instead of simply remembering the ideas of somebody else, one can actually remember how one used those ideas to create something new. Yet, it is not easy to convince educators about the utility of using visual arts to teach science. A recent review titled "The Role of the Visual Arts in Enhancing the Learning Process" tries to make a case for visual arts in enhancing the learning process.

The class on "Flow of genetic information" that i am currently teaching got a chance to get creative this week. They were given 3 activities to do in the class.

Task 1: Compare DNA replication, Transcription & Translation and create an easy to understand diagram/table.

Task 2: Compare different information flow processes considering as many examples as you can think of

Task 3: Show the hierarchical organization of DNA

  • Use color chalk if needed.
  • Pay special attention to differences between prokaryotes & eukaryotes
Here are the end results:
Task 1

Task 2

Task 3

Thursday, August 24, 2017

Does the central dogma paper have hidden Masonic iconography?

A lot has been written about Freemasonry in recent times. One of the most prominent features of the iconography associated with free masons is the Eye of Providence. The traditional depiction of this involves a triangle or pyramid shape.

If you have read the paper Central Dogma of Molecular Biology by Francis Crick, you might have noticed that the paper is filled with figures that look like above screen grab. It is a triangle and has some circles. This would actually be a very smart way to sneak in Masonic iconography. Was Francis Crick a free mason? It is actually possible, as it has been argued that some of the most powerful and intellectually gifted people have been part of free masonry.

Monday, June 26, 2017

A beetle to be proud of

June is almost over. It has already started raining here in Bhopal. The weather is now at that pleasant optima when it's neither too hot nor too rainy. Wish it could stay like this forever. Humidity is another thing altogether. It is really a pleasure to go out walking in the campus.

You have the frogs making their calls in one place and the beetles roaming in another. See below picture of a beetle we managed to capture.

Wednesday, May 31, 2017

Nautapa - nine hottest days of the season

The end of May is generally the time for Nautapa, the nine hottest days of the season. The term originates from the Hindu astronomical calendar. Here is the sun early in the morning on the 5th day of Nautapa.

Wednesday, May 17, 2017

The Ponds at Georgetown - ducks

The Ponds at Georgetown or simply the ponds is a very pleasant place to live. Here is a picture of few ducks in the pond that is just beside the bus stop (bus #5).

If you zoom-in, at the far end of the pond you can see ducklings swimming. I counted 6 of them in total. While waiting for the bus, I could see a rodent (not sure if it was just a fat rat or some other) trying to swim into the flock and catch one of the ducklings. Probably that was breakfast.

One could imagine this is an advertisement for the place. With great public transportation proximity to the city as well as ypsilanti it is well situated. 

Comparative approaches to study the evolution of nucleotide diversity

Study of diversity at the nucleotide sequence level across the whole genome has provided a useful understanding of numerous processes. However, until recently these studies have been largely focussed within a species but using different populations. This is set to change with the explosion of datasets that are being generated in many species across the globe. We have made our tiny bit of contribution to the use of such an approach with a recent pre-print on bioRxiv "Genome-wide signatures of genetic variation within and between populations - a comparative perspective". 

Many other studies (Singhal et al., Van Doren et al., Ludo et al.) have shown this pattern of correlated landscapes of diversity and divergence. Some have even addressed other questions related to speciation rateshabitat preference as well as their impact on the diversity and divergence landscape. We are also seeing studies in other species groups such as primates and trees. Theoretically oriented groups have also started getting into the nitty gritty of things by trying to understand the patterns better and get into the processes driving them.

The figure-1 (b) from the bioRxiv paper is very interesting as I managed to sneak in the flags of both Germany and Sweden :). We had to cut it in our paper now published with a different title "Genome-wide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa". Our paper even got featured on the Molecular Ecologist blog with a write-up by Arun Sethuraman.

Sunday, April 23, 2017

Abundance of elements on planet earth correlates with year of discovery

We hypothesized that chemical elements that are more abundant and easier to purify in elemental form would be discovered earlier. Obvious evidence for our hypothesis is that heavier elements such as Tennessine have been synthetically created and have been first described as late as the past decade. A better way to evaluate our hypothesis would be to look at all chemical elements discovered till now.

Using the timeline of chemical element discoveries from wikipedia and comparing to the abundance of these elements shows a significant negative correlation (r=-0.27; p-value: 0.0002421). Below figure show the golden age of discovery of chemical elements stretching from 1600 to 2000. Although many of the commonly used metals were well known to the "ancients", a large majority of the elements were discovered within the span of the last 400 years. The negative correlation suggests that less abundant materials were discovered later than the more abundant materials. Rapid discovery of chemical elements overlaps with the timing of the great divergence.

Chemical element abundance vs Year of discovery

Since the abundance of elements on earth is negatively correlated (r=-0.45; p-value: 8.336e-10) with the atomic numbers of the elements, we see a positive correlation (0.53; p-value < 2.2e-16) between the atomic number of elements and when they were discovered. Instead of just using the abundance of elements, a better measure would be the weight of both abundance and ease of extraction.

It would be interesting to see if such correlations would exist on other planets. Would the class of the planet determine the correlation?

The star trek Voyager episode "Emanations" set in the year 2371 (stardate 48623.5), says that 246 elements are known to federation science. This is almost double the number known now. This suggests another age of discovery in the near future. The BBC has an interesting article on what new wonders await us in the outer reaches of the periodic table. However, as yet it is not clear how far the extended periodic table can be extended synthetically and how many of these elements will be found naturally. 

Tuesday, March 7, 2017

Ann Arbor to Chicago union station - a train journey via Amtrack

A train journey from Ann Arbor to Chicago is an easy way to travel. Amtrak runs multiple trains throughout the day on this route which actually starts from Pontiac. The journey of approximately 4 hours can frequently be delayed by upto 30 minutes. Apart from experiencing this first hand, I also overheard a very upset American complaining that this delay had resulted in him reaching 30 minutes late to his job interview. Hopefully, he will still get the job as the interviewer seemed sympathetic to his cause. 

Ann Arbor, Amtrak station, Front entrance in March 2017

The train route meanders down from Ann Arbor through Jackson, Battle creek, Kalamazoo, Niles, and New Buffalo before entering the state of Illinois. After stopping over at Michigan city, it heads into Chicago to stop at the union station.

Kalamazoo is approximately the mid-point (for travelers from Detroit) located 142 miles from Detroit and 138 miles from Chicago. The phrase Timbuktu to Kalamazoo (both real places) commonly used by English speakers to refers to journeys between exotic places. The word is thought to originate from native American's of the Hopewell culture. The journey ends at the historic Union station of Chicago.

Wednesday, January 25, 2017

The sun rises in the east

What you see here is the sun rising. It most definitely is rising in the east.

Let's hope it's not a sunset :) If it was not clear before, let me make myself clear (as if it matters), all views expressed on this blog are my own personal views and don't reflect the views of my employers.