Tuesday, November 01, 2016

बांस Bamboo Mast

Bamboo has many legends and sayings associated with it, especially in asian cultures. In hindi (हिंदी) in India we say "Na rehaga baans, na bajegi bansuri", that is there is no hope of hearing sweet reed melodies if the bamboo stops growing. Many chinese charachteristics of strenghth, flexibility and virtue have been attributed by philosophers and poets to bamboo 
(the taller the bamboo grows, the more it bends ~ i.e. truly great people are humble).
From the perspective of the premise of this blog of patterns in nature, Bamboo mast (मास्ट) flowering or the mass synchronized flowering of these plants at the same time, with a long gap (30-120 years) counts with the big mysteries of "snychronization", with an added evolutionary and ecological context. The current ideas suggest a this mass flowering and seeding results in overwhelming the seed eaters by synchronization, giving the plants a survival chance exceeding the normal. Add on to that, bamboos out of sync do not do as well. And in such a context, changes in flowering time can only be integer multiples of the existing period. These integer values can also be reduced to primes by integer factorization (the same thing that lies at the heart of RSA encryption). And add to it, there is the excitement of a plant-biological alarm clock, ticking away. 

Further reading:
1) Synchronization http://www.scholarpedia.org/article/Synchronization
2) Keeley, JE; Keeley, J.E.; W.J. Bond (1999). "Mast flowering and semelparity in bamboos: The bamboo fire cycle hypothesis". American Naturalist. 154 (3): 383–391 https://www.ncbi.nlm.nih.gov/pubmed/10506551
3) Janzen, DH. (1976). "Why Bamboos Wait so Long to Flower". Annual Review of Ecology and Systematics. 7: 347–391. http://www.annualreviews.org/doi/10.1146/annurev.es.07.110176.002023

Monday, March 12, 2012

Cell Like Patterns in the Soil

Some pictures of patterns in non-living matter
The soil near Rameshwaram, possibly near brackish water. The white is probably the deposited salt. The cracking in the soil due to drying. And amazingly regular 'cells' formed in this breakup pattern. Almost appear to have a charachteristic size. Anybody with pointers to theories for this is welcome to comment. Interestingly looking at the size of the cells, it appears to reduce as the front gets closer to water. Something like  a dry state dependent cell-size. Beautiful to look at, and intriguing to think about.
And a nice cellular image to go with that. Seen above an image from Nowark et al. (2009, J. Cell. Biol.) showing a hexagonal geometry in mouse lens fibre cells.
Brings to mind the aphorism "just because things look the same, doesn't mean their underlying causes are the same". And yet.

Wednesday, October 12, 2011

Neuro Concious Tubulin

Microtubules, quantum coherence and conciousness were put together to the best of my knowledge by Sir Roger Penrose in his famous popular book "The Emperor's New Mind". However a not so recent report I came across about a study in the journal Science appears to to put cold water on it.

Charles Seife (2000) Cold Numbers Unmake the Quantum Mind Science Vol. 287 (5454), p791, DOI: 10.1126/science.287.5454.791

Wednesday, May 04, 2011

Diffusion in cells

Diffusion in cells- been teaching the course bio435 - biophysics II or Physical Biology of the Cell or what i really do for a living or...
The fascinating part about diffusion is that it binds both historically and scientifically energy, matter and living-systems. Brown who discovered brownian motion was looking at pollen grains. Einstein who described the relation between macroscopic viscosity and molecular movement is "the physicist".
Using fluorescence recovery after photobleaching, some simple imageJ data extraction and loads of attempts at analyzing the data, we find a few odd things.
A FRAP profile of an E. coli cell expressing GFP

1_ GFP diffuses faster in the E. coli than we can bleach it out.
2_ Reducing the number of bleach pulses doesn't allow any measurable bleaching, i.e. our scanning system is too slow
3_ The recovery kinetics show heavy amounts of imaging-dependent bleaching. Did we not turn down the laser after the bleach?

Saturday, January 01, 2011

The problem(s) with biology and fishy epiphany

Today is a day of epiphany. I bought my first pet fish. And am curious to see how far I get. Hope not to make it into a 10-little indians story (and then there were none). Do we have females and males? Dunno. What species? Orange-Zebrafish.

But the second and more important reason for my feeling of epiphany was facing up to my limited knowledge of biology, and the reasons for which its not my fault.

I enter the aquarium shop knowing well, I know less about fish than the owner. Yet, being a PhD in Biology, I assume I know about general principles of biological life as I have been taught. And when I ask if guppies lay eggs, the man tells me not. So that to me is a contradiction since except for mammalian aquatic organisms like dolphins and whales, fish are "supposed to" lay eggs. So based on smug theoretical knowledge, I wagered a cake. And now after 2 mins of google-research, I find he was right!

Apparently guppy sperm swims up the tubes and fertilizes eggs, which therefore end in live births. Also true of sharks (yes, otherwise the chinese would eat shark egg powder to improve sexual prowess). So apparently Poeciliidae are a genus with high proportion of animals that keep the eggs in their bodies and give live-births [wikipedia].However I was right in one sense that Poeciliidae are oviparous (they produce true eggs). The eggs inside the mother do not get nutrients- package deal, eat what you have inside the egg, no more. However "plitfins and halfbeaks are viviparous [Reference].

So why is it not my fault? The fault lies in the approach to diversity in life. By creating this super structure we have some insights into how animals might be related to each other- habitat (water), egg-layers vs. not, but these are not consistent. And without detailed knowledge of all of the things, we still can't tell what the new animal we come across might be like, without testing in detail. As a theoretical biologist, this is embarassing at the least- if not cause for concern!
More on this.

And the blog is about patterns in living matter. And living matter has patterns and patterns and intersections. And hard to keep apart classifications. So how to we construct laws of living matter, if there is so much "biological variation"?