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"?

Writing into the prefrontal cortex or how to avoid a makeup Class in Calculus

I suspect everbody from Sun Tzu, through Susruta the cosmetic surgeon, via Plato all the way to Goebbels, might have racked their brains on how to control what people think.

But more than control, implying constant and involuntary obedience, I wonder how feasible it might be to transfer what one person has learnt to another. Telepathy is clearly old, and relatively discredited. But I wonder with all the progress made in magnetic resonance imaging (MRI), would it be possible indeed not just to read our thoughts, but to write too?

More on this in a bit. There are apparently clear enough indications that the pre-frontal cortex (PFC) of the brain in Rhesus macaques is capable to showing single cell level changes corresponding to numbers [1]. The blogger who posted this [2] appears to also suggest that simple arithmetic is performed in these monkies. The measurements were made using probes inside the brain to monitor firing of single neurons.

So if we can measure firing when an operation of addition is performed, what would it take to "teach" the brain how to do it. Indeed that raises the same old question, how to we learn. But at a neuronal level.

And then how do we modify this. Is this at the single neuron level? For such simple tasks as addition it appears to be controlled in monkies at the single neuron level. So how about higher mathematical functions? Can we "write" calculus into our brains?

References:

1. Bongard, S. & Nieder, A. (2010). Basic mathematical rules are encoded by primate prefrontal cortex neurons Proc. Nat. Acad. Sci. 10.1073/pnas.0909180107
   
2. http://scienceblogs.com/neurophilosophy/2010/01/single_cells_in_the_monkey_brain_encode_abstract_mathematical_concepts.php

Neuronal model contest

I was again reminded of how much is lacking in modelling biological systems. Neuronal modelling has possibly been one of the earliest fields, along with biochemical kinetics for cellular models. The Hodgkin-Huxley model being a case in point. The contest is a call for models of spike timing prediction at the level of a single neuron- Quantitative Single Neuron Modeling.

Besides the prize of getting it right, there are some other incentives too - CHF 10,000 (swiss francs) for the best performance on 2 of the typically 4 challenges.

Alignment of Polarized Cu Sticks

Some recent exciting research from the IISC Bangalore has experimentally demonstrated the breakdown of the central limit theorem that the sample-sample fluctuation of N particle systems grows as N^1/2. They demonstrate that for non-equilibrium systems the fluctuation can vary as N for N particles.

Interestingly their ordering of the Copper rods only occured in the driven system (between two vibrating plates) when the rods were etched at one end, effectively making them arrow-like. Here are some of the comments from Science:

(FIGURE: Swarms and swirls. In the experiments of Narayan et al., agitated sticks form swarming states that exhibit giant number fluctuations. Similar patterns are observed in fish swarms (top left). Swirls are also observed in systems that are close to jamming, for example, in the motion of bubbles in a sheared foam (right).)

Science 6 July 2007: Vol. 317. no. 5834, pp. 49 - 50 DOI: 10.1126/science.1145113

MATERIALS SCIENCE:
Shape Matters

Martin van Hecke
"Swarming and giant number fluctuations are a hallmark of the alignment displayed by driven collections of nonspherical particles. Theoretical models have been developed to describe swarming and alignment observed in schools of fish, flocks of birds, herds of sheep, or bacterial colonies--often borrowing from equilibrium models for magnetization, which consider the alignment of arrowlike objects. A very simple nonequilibrium model that exhibits cooperative motion arises when these arrows are allowed to propagate (2). In similar models, a collective response to predators and decision-making can arise (3). Toner and Tu first pointed out the giant fluctuations in such models (4).

In these systems, the particles have a preferred direction of propagation--just like real fish and birds. In 2003, Ramaswamy et al. (5) wondered what would happen for "active nematics," liquid crystals in which the particles have an orientation but have identical heads and tails (like the sticks in the present experiment). Their theory predicted that nematic systems also should exhibit giant number fluctuations, and these were recently observed in computer simulations (6).

However, when Narayan et al. tried to find such fluctuations in experiments, they encountered a surprising hurdle: cylindrical rods, arguably the simplest nematic particles, do not form nematic states and do not exhibit giant fluctuations (7). The authors achieved their present breakthrough only after etching the rods to obtain sticks with thinner ends (see the figure); for unknown reasons, these sticks exhibit nematic order. To complicate matters further, Aranson et al. recently performed similar experiments and observed that weak coupling between the nematic order and spurious in-plane vibrations of the support plate may strongly influence the swirling motion (8). Clearly, swarming is a subtle problem, and the precise nature of the swarming state and the transition to swarming is not yet fully understood.

The experiments of Narayan et al. are part of a bigger story, where nonequilibrium systems of nonspherical particles exhibit surprising behavior: We do not yet understand the consequence of shape. An earlier striking example of this is the finding that, contrary to expectation, M&M candies can be packed more effectively than spheres (9)."

REFERENCES:

1. V. Narayan, S. Ramaswamy, N. Menon, Science 317, 105 (2007).
2. T. Vicsek, A. Czirok, E. Ben-Jacob, I. Cohen, O. Shochet, Phys. Rev. Lett. 75, 1226 (1995).
3. I. D. Couzin, J. Krause, N. R. Franks, S. A. Levin, Nature 433, 513 (2005).
4. J. Toner, Y. Tu, Phys. Rev. E 58, 4828 (1998).
5. S. Ramaswamy, R. A. Simha, J. Toner, Europhys. Lett. 62, 196 (2003).
6. H. Chaté, F. Ginelli, R. Montagne, Phys. Rev. Lett. 96, 180602 (2006).
7. V. Narayan, N. Menon, S. Ramaswamy, J. Stat. Mech. 2006, P01005 (2006).
8. I. S. Aranson, D. Volfson, L. S. Tsimring, Phys. Rev. E 75, 051301 (2007).
9. A. Donev et al., Science 303, 990 (2004).
10. A. J. Liu, S. R. Nagel, Nature 396, 21 (1998).
11. O. Dauchot, G. Marty, G. Biroli, Phys. Rev. Lett. 95, 265701 (2005).
12. A. S. Keys, A. R. Abate, S. C. Glotzer, D. J. Durian, Nature Phys. 3, 260 (2007).
13. W. G. Ellenbroek, E. Somfai, M. van Hecke, W. van Saarloos, Phys. Rev. Lett. 97, 258001 (2006).
14. F. Lechenault, O. Dauchot, G. Biroli, J.-P. Bouchaud; available online at http://arXiv.org/abs/0706.1531v1.

Spring cleaning the WinDisk (win doof auf deutsch)

How do you clean up the installed disk with a Win32 install (other than buying a bigger disk)?
Here are some tips from the trawling of the net.

1. Delete everything inside the Windows Prefetch folder (\\Windows\Prefetch) - you may save a couple of MBs and may also notice that Windows loads faster. (ref1).
2. Clean the cache as follows:
   
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   Cleaning the cache
   
   If you use Internet Explorer, cleaning out the cache is relatively easy. You can do it in a couple of different ways. If you have the browser open, follow these steps:
   
   1. Choose Tools --> Internet Options.
   
   IE displays the Internet Options dialog box.
   
   2. On the General tab, click the Delete Files button.
   
   A warning dialog box offers to delete all your offline content, as well. For most folks, this doesn't matter — they don't browse offline. If you're in the minority that does, select the check box.
   
   3. Click OK.
   
   IE deletes the cache files. Depending on how cluttered your system is, this can take a while.
   
   4. When IE is done deleting cache files, click OK to close the Internet Options dialog box.
   
   You now have a fresh, clean cache, ready once again to be cluttered with new pictures from your Internet road trips.
   
   
   You can also clean out the cache without even opening the browser — just use the Disk Cleanup tool:
   
   1. Choose Start --> All Programs --> Accessories --> System Tools --> Disk Cleanup.
   
   The Disk Cleanup tool starts running. If you have multiple hard drives on your system, you're asked to choose which hard drive to analyze.
   
   2. Pick a hard drive and click OK.
   
   Disk Cleanup looks through your hard drive, calculating how much space it can reclaim. This process may take a while. A dialog box indicates items you can clean.
   
   3. Make sure the Temporary Internet Files option is selected.
   
   Temporary Internet files translates to what's stored in the cache. You can also pick other things to clean up, if desired.
   
   4. Click OK.
   
   Disk Cleanup displays a dialog box asking if you want to proceed.
   
   Depending on what you asked Disk Cleanup to do, the actual cleanup can take a few minutes to complete. Cleaning out cache files this way takes no longer than cleaning from within the browser.
   Finding the cache
   
   Most people never worry about where their browser stores its cache files. Microsoft recognizes this and doesn't make a big deal of advertising where the cache is located. You can locate the cache by displaying the Internet Options dialog box (in the browser, click Tools --> Internet Options) and then clicking Settings. The resulting Settings dialog box indicates where the cache is located (next to Current Location in the middle of the dialog box).
   
   As you examine the path name, notice that it's associated with the current user. If your computer is shared by multiple users, Windows creates a cache folder for each.
   
   Another interesting tidbit is that Microsoft hides the cache folder. It doesn't hide it in the Settings dialog box, but it does hide it if you try to get to the folder yourself.
   
   To see how this works, open a My Computer window for the C: drive. Double-click the Documents and Settings folder, then your account name. If you don't see a Local Settings folder in the account folder, even though the Settings dialog box says you should, don't worry. The reason is that the Local Settings folder is configured as a hidden folder; it doesn't show up when normally viewing folders.
   
   To see the hidden folder, follow these steps:
   
   1. In the folder window, choose Tools --> Folder Options.
   
   Windows displays the Folder Options dialog box.
   
   2. In the Advanced Settings area on the View tab, select the Show Hidden Files and Folders option.
   
   3. While you're at it, deselect the Hide Extensions for Known File Types and also the Hide Protected Operating System Files options.
   
   (You might have to scroll down the list to see these options.) Deselecting these two options ensures that you see as much information as possible; with more information, you can make better decisions in the long run.
   
   4. Click OK.
   
   As the Folder Options dialog box disappears, the information in the account folder is updated. You can now see the Local Settings folder, but the folder icon should appear a little more washed out than other icons. This indicates that the folder is normally hidden. You can still double-click it and then double-click the Temporary Internet Files folder to see what's in your cache.
   Changing the cache size
   
   Internet Explorer makes a point of ensuring that your cache never gets too big. In some respects, the cache is similar to the Recycle Bin — when its maximum size is attained, it starts deleting the oldest files to make room for the new files.
   
   The problem is that the cache is often set much larger than it needs to be. The Settings dialog box has a control that indicates the amount of disk space to use for the cache. By default, Internet Explorer allocates 10 percent of your disk to its cache folder. This doesn't mean the folder automatically uses that much space, just that IE keeps storing files in the cache (without deleting any of them) until that 10 percent mark is reached.
   
   Think about that for a moment — most computers these days come with at least a 20-, 40-, or 60GB hard drive. If all that space is allocated to a single drive and IE uses that drive for its temporary files, you can easily set a maximum cache size to 2-, 4-, or 6GB. Wow. If the average image downloaded from a Web site is approximately 10K, IE could store anywhere from 200,000 to 600,000 images on your system without deleting anything. Talk about clutter! When hard drives were smaller, the 10 percent rule made more sense.
   
   
   You can lower the cache size by following these steps:
   
   1. In the browser, choose Tools --> Internet Options.
   
   The Internet Options dialog box appears.
   
   2. On the General tab, click the Settings button.
   
   The Settings dialog box appears.
   
   3. Adjust the cache size via the Amount of Disk Space to Use slider or by typing a number in the text box.
   
   You shouldn't hesitate to lower the cache space to 75MB. If you have a high-speed Internet connection, lower it even more — perhaps to 35MB or 40MB.
   
   By making this simple adjustment, you save lots of hard drive space for better uses and won't hurt the overall performance of Internet Explorer.
   (ref2)
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References:

1. Don't Prefetch
2. How dummies cleanup cache no catches here