It just keeps getting worse.
I've decided to compile a list of things that frightens me a bit more about our future as a species on this planet and about the future of the planet itself. I think it's a good coping mechanism. I shall call this list OMG-We're-Doomed!
a) Fertilizer run-off into streams overgrowing algae, messing up the water and causing gender-upsets in fish
To be updated...
Monday, August 4, 2014
The maddening, all-consuming and ultimately pointless act of buying gifts
This must be what it is like for Westerners during Christmas. But for us desis, the gift-buying happens during the once-in-a-blue-moon trip to India.
Over the years, I have developed a system of gift buying. It's not a very efficient one, to be honest. The ideas for gifts start coming a few months before the actual trip. Then, a few weeks later, when I can no longer keep these straight in my head, I write down a list.
As we edge closer to the date of the travel, I realize my hand-written lists are woefully inadequate and I move to Excel spreadsheets. I type down the following: people on my side and on Ram's side that we will meet, categorized by city; gifts that I would like to give; gifts that I have already bought; gifts that need to be bought and the quantities of all these.
When I populate the lists by matching up the gift to the person, that's when the problems start. There will always be about a dozen or so for whom I have not thought of anything at all. And then there will be those teens who used to be mad about a particular thing the last time you saw them, a few years ago, and you buy them something that you think they will treasure. Then, from an offhand comment that someone makes, you realize they are no longer into that thing, that they in fact feel that that particular activity was the stupidest thing they could have indulged in, and that they have moved on to greener pastures, leaving you with a giant-sized cricket bat or multiple pairs of hot-hands hand-painted with scenery by Rembrandt or some such thing (I'm kidding.... really. Even I know not to buy cricket bats in the US!).
Then there are generic gifts that you just buy because you have no clue what to give some people: chocolates, of course; ties, wallets etc.
The hardest gifts to buy are for those uncles whom you haven't met in many years, but for whom you have a soft spot. What might they like, you wonder. Well, what do they do? Watch cricket, drink tea, and umm... well.. that's about it. So all of them get... guess what? Almonds! I figure they can snack on something healthy while watching TV.
Anyway, you buy all this nonsense and go back and give them, hoping that they will find happy homes where they will be treasured. But inwardly you know that most will disappoint, and be thrown aside as junk.
What to do? There's only so many creative gifts one person can think of. And invariably one ends up buying way too many gifts for a particular set of people and not enough for anybody else.
If I have to keep my head and not go mad, I must let go of this attachment, as Buddha would say. I must just get a bunch of gifts that seem nice to me and then, without worrying about consequences, results, fruits of labor or their ultimate fate, release them gently and calmly into the turbulent seas.
Which then brings me to the next problem: how to carry all this within the baggage limit?
*******************************************************************************
Update:
You know what's worse? You lug your luggage (magically made to fit all the hordes of gifts that you bought) and after the inescapably frustrating and long trip, land up in the great desh, and finally get to go... either to your parents' home or to your in-laws' home and with a flourish you open up the gifts and pass them along. Then, because you can't help yourself and because everybody is asking why in the world you had to bring so many pieces of luggage which all weigh a ton, you make the fatal mistake of briefly mentioning the other people for whom you bought gifts.
Uh oh.
Rule #1: let nobody know whom you have bought gifts for.
Because if you, invariably, the response will be: you bought something for them? Why? Don't you know we have not spoken to them for more than a year, ever since they took the inexcusable decision to.... (something.... from not inviting somebody else to some wedding (a big faux pas in Indian weddings when EVERYbody and their neighbors are invited), to not phoning someone when they were in the same town to something minor like not returning some borrowed item).
So suddenly, you've landed yourself in a feud and by taking these gifts, you have claimed friendship with the wrong team.
Over the years, I have developed a system of gift buying. It's not a very efficient one, to be honest. The ideas for gifts start coming a few months before the actual trip. Then, a few weeks later, when I can no longer keep these straight in my head, I write down a list.
As we edge closer to the date of the travel, I realize my hand-written lists are woefully inadequate and I move to Excel spreadsheets. I type down the following: people on my side and on Ram's side that we will meet, categorized by city; gifts that I would like to give; gifts that I have already bought; gifts that need to be bought and the quantities of all these.
When I populate the lists by matching up the gift to the person, that's when the problems start. There will always be about a dozen or so for whom I have not thought of anything at all. And then there will be those teens who used to be mad about a particular thing the last time you saw them, a few years ago, and you buy them something that you think they will treasure. Then, from an offhand comment that someone makes, you realize they are no longer into that thing, that they in fact feel that that particular activity was the stupidest thing they could have indulged in, and that they have moved on to greener pastures, leaving you with a giant-sized cricket bat or multiple pairs of hot-hands hand-painted with scenery by Rembrandt or some such thing (I'm kidding.... really. Even I know not to buy cricket bats in the US!).
Then there are generic gifts that you just buy because you have no clue what to give some people: chocolates, of course; ties, wallets etc.
The hardest gifts to buy are for those uncles whom you haven't met in many years, but for whom you have a soft spot. What might they like, you wonder. Well, what do they do? Watch cricket, drink tea, and umm... well.. that's about it. So all of them get... guess what? Almonds! I figure they can snack on something healthy while watching TV.
Anyway, you buy all this nonsense and go back and give them, hoping that they will find happy homes where they will be treasured. But inwardly you know that most will disappoint, and be thrown aside as junk.
What to do? There's only so many creative gifts one person can think of. And invariably one ends up buying way too many gifts for a particular set of people and not enough for anybody else.
If I have to keep my head and not go mad, I must let go of this attachment, as Buddha would say. I must just get a bunch of gifts that seem nice to me and then, without worrying about consequences, results, fruits of labor or their ultimate fate, release them gently and calmly into the turbulent seas.
Which then brings me to the next problem: how to carry all this within the baggage limit?
*******************************************************************************
Update:
You know what's worse? You lug your luggage (magically made to fit all the hordes of gifts that you bought) and after the inescapably frustrating and long trip, land up in the great desh, and finally get to go... either to your parents' home or to your in-laws' home and with a flourish you open up the gifts and pass them along. Then, because you can't help yourself and because everybody is asking why in the world you had to bring so many pieces of luggage which all weigh a ton, you make the fatal mistake of briefly mentioning the other people for whom you bought gifts.
Uh oh.
Rule #1: let nobody know whom you have bought gifts for.
Because if you, invariably, the response will be: you bought something for them? Why? Don't you know we have not spoken to them for more than a year, ever since they took the inexcusable decision to.... (something.... from not inviting somebody else to some wedding (a big faux pas in Indian weddings when EVERYbody and their neighbors are invited), to not phoning someone when they were in the same town to something minor like not returning some borrowed item).
So suddenly, you've landed yourself in a feud and by taking these gifts, you have claimed friendship with the wrong team.
Saturday, August 2, 2014
Mitomaniac!
Imagine a negotiation bid that took place billions of years ago. One
bacterial system tells another, "Hey, know what would be really cool? If I
got into you and helped light up your place, get you some energy and in turn,
you protect me from annihilation"
The second bacterial guy scratches its
imaginary head and says, "Well, okay. But you gotta figure out a way to shut
off that energy-making when I don’t need it. I can’t stand the racket you make”
“Deal”
That’s the story of how we got mitochondria within nearly every cell we
possess. And in accordance with the treaty of yore, they reside within the
cells, do all the dirty work and in return, get access to nutrients, protection
from other microbes and harmful chemicals, companionship and love.
And because they weren't total pushovers in that above-mentioned treaty, they got to keep their own DNA. The DNA they have right now is exactly what they need for their primary purpose of energy production. Now, being savvy packers, it might be that they shed some genetic baggage that we don't know much about. But the end result is that we actually carry two pockets of DNA within each of our cells: the check-in baggage that contains the bulk of our DNA stored neatly within the nucleus and our little mitochondrial carry-ons.
Where there is DNA, there is genetics. Of course. Mitochondrial genetics is very different from the nuclear genetics that we know and love so well (ha!). For one, ALL the mitochondrial DNA you have within you comes directly from your mom, and nobody else. So you can sequence every person's mitochondrial DNA and trace back your maternal ancestors. And indeed, when people did that, they figured out the entire migratory routes of womankind (yes, you tagged along too, silly males!)
Here's a nice pic showing human migration from the Professor Taboo blog:
Mitochondrial DNA can get mutated, just like the DNA in the nucleus. But unlike the nuclear DNA, mtDNA has no protein complexes, called nucleosomes, enveloping it making it more susceptible to mutations. But on the plus side, there are many mitochondria within each cell. So even if one mitochondrion has mutated DNA, the cell might still function just fine if the rest of the mitos within it are normal. It is all a matter of dosage.
Problems arise when many or most mitochondria end up carrying mutated DNA.
A really cool theory goes like this: Mitochondria accumulate mutations over time. Initially it may be a few mitos that carry mutated DNA, then a few more, and a few more. Even if new mitos are being formed, they arise from mitos that are carrying mutations. So, the new cells in your body are less efficient and more prone to mistakes. Ultimately, new cells may not be produced at all, because there are just too many mutations in the mtDNA. This is what leads to aging and the development of degenerative diseases.
What an interesting concept, no? It forces you to think about your body like a car or a machine. Since mitochondria produce energy, mutations in their DNA can affect the amount of energy each cell produces. As mtDNA mutations accumulate, the efficiency of conversion of food to energy drops off, cell by cell and then organ by organ. It's like an old car that cannot run anymore. It's basic thermodynamics at work: a body needs an energy infusion to keep it running. No more energy, no more running.
As more and more researchers leap on the mito-bandwagon, it is becoming clear that mitochondrial energetics can, at least partially, explain a number of complex diseases or symptoms, including cancer, diabetes, cardiovascular disease and obesity-associated diseases.
Let me conclude this post with another very interesting theory, which goes back to the dosage effect mentioned earlier: different dosages of the same mtDNA mutation can lead to different effects. A small dosage (only a few mutated mitochondria) might lead to a disease like retinitis pigmentosa, leading to blindness in middle-age, a larger dose might lead to blindness at an earlier age, a still larger dose might lead to early death, while at very high dosage, the mutation might cause stillbirths or miscarriages.
What fascinating stuff! Suddenly, a whole new way by which we think about diseases, their pathology and development has opened up. Very different diseases may actually all arise from the same cause!
How does mtDNA get mutated upon different environmental insults like smoking or drinking polluted water? How do mitochondria compensate for their mutated and less efficient brethren? How do nuclear DNA and mtDNA interact, if at all? And finally, what can we do about mtDNA mutations pharmacologically?
Hopefully we find the answers to these and more questions.
Mitochondrial DNA can get mutated, just like the DNA in the nucleus. But unlike the nuclear DNA, mtDNA has no protein complexes, called nucleosomes, enveloping it making it more susceptible to mutations. But on the plus side, there are many mitochondria within each cell. So even if one mitochondrion has mutated DNA, the cell might still function just fine if the rest of the mitos within it are normal. It is all a matter of dosage.
Problems arise when many or most mitochondria end up carrying mutated DNA.
A really cool theory goes like this: Mitochondria accumulate mutations over time. Initially it may be a few mitos that carry mutated DNA, then a few more, and a few more. Even if new mitos are being formed, they arise from mitos that are carrying mutations. So, the new cells in your body are less efficient and more prone to mistakes. Ultimately, new cells may not be produced at all, because there are just too many mutations in the mtDNA. This is what leads to aging and the development of degenerative diseases.
What an interesting concept, no? It forces you to think about your body like a car or a machine. Since mitochondria produce energy, mutations in their DNA can affect the amount of energy each cell produces. As mtDNA mutations accumulate, the efficiency of conversion of food to energy drops off, cell by cell and then organ by organ. It's like an old car that cannot run anymore. It's basic thermodynamics at work: a body needs an energy infusion to keep it running. No more energy, no more running.
As more and more researchers leap on the mito-bandwagon, it is becoming clear that mitochondrial energetics can, at least partially, explain a number of complex diseases or symptoms, including cancer, diabetes, cardiovascular disease and obesity-associated diseases.
Let me conclude this post with another very interesting theory, which goes back to the dosage effect mentioned earlier: different dosages of the same mtDNA mutation can lead to different effects. A small dosage (only a few mutated mitochondria) might lead to a disease like retinitis pigmentosa, leading to blindness in middle-age, a larger dose might lead to blindness at an earlier age, a still larger dose might lead to early death, while at very high dosage, the mutation might cause stillbirths or miscarriages.
What fascinating stuff! Suddenly, a whole new way by which we think about diseases, their pathology and development has opened up. Very different diseases may actually all arise from the same cause!
How does mtDNA get mutated upon different environmental insults like smoking or drinking polluted water? How do mitochondria compensate for their mutated and less efficient brethren? How do nuclear DNA and mtDNA interact, if at all? And finally, what can we do about mtDNA mutations pharmacologically?
Hopefully we find the answers to these and more questions.
Wednesday, July 30, 2014
Doom Gloom
I don't think I'm especially prone to thoughts about mortality and death, but these past few weeks have agitated my composure badly. What with the airplane tragedy in Ukraine, the escalating and baseless war in Gaza, our ever-increasing population, the disappearing ice cap in the Arctic, the high levels of animal and plant extinction in South Asia (including India) and (this is kind of a non-sequiter, perhaps) the ridiculous schooling system in the US, I sometimes feel like it was a big mistake to bring my kids into this world.
What a drama-queen statement to make, one might say. But think about it. When has there been a time in our history when things have been quite so bad politically, environmentally, economically, and morally, all at the same time? When has there ever been such a vast disparity between people, when have we failed to understand each other less, when have we been so eager to start or prolong wars, when have we been less tolerant of one another?
This is the sort of hyperventilating dialogue that sends people into nursing homes for nervous breakdowns, but I can't imagine anybody denying that things are looking kind of bad for us Earthlings.
Tuesday, June 24, 2014
Wildflowers near my lab
On the properties of the two abandoned houses near the Pitt genomics core lab on Forbes between Halket and Craft, I found:
a) Chicorium intybus. Chicory! The same chicory that's used as a coffee additive/alternative!
a) Chicorium intybus. Chicory! The same chicory that's used as a coffee additive/alternative!
b) Oxalis stricta. Yellow woodsorrel. It's much too beautiful and fragile a plant to be named ox-anything!
c) Achillea mellifolium. Yarrow. I've been reading about this for a while and its medicinal properties are stupendous. It can be used as a pain reliever, to stop bleeding, and as an insect repellent. I need to grow some in the garden!
d) Taraxacum officinale. Dandelions! Yet another flower whose scientific name woefully falls short of describing the flower. Who doesn't know dandelions?
e) Many more whose names I haven't yet figured out.
Wednesday, June 18, 2014
Oh my F-ing God
I want to be able to make a circular heat map. Like this:
To do this, I need to install a software called Circos, which runs on Perl.
But thankfully, for Perl-morons like me, there are detailed instructions on how to use the thing.
First thing to do, obviously, is to download and install the thing. So I try doing that, and I get an error like this:
*** REQUIRED MODULE IS MISSING ***
You are missing the Perl module Clone. Use CPAN to install it as described in this tutorial
http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules
Okay, I think. Let me get this Clone then.
So I get the module and try to install that, only to get an error message like this:
bash: make: command not found
I try to find this "make". I try > man make and >which make and >locate make, all to no avail.
Fine. I think I can circumvent make and go directly to CPAN and install the thing. I do so, and I get the message
Going to write /Users/shridharv2/.cpan/Metadata
Clone is up to date (0.37).
Hurray! NOW maybe I can get cracking. But no:
*** REQUIRED MODULE IS MISSING ***
You are missing the Perl module Clone. Use CPAN to install it as described in this tutorial
Okay...I go back to the Circos troubleshooting page and hunt this out:
So get this: To install any software that runs on Perl (and I assume there must be tons of those softwares, since Perl has been around for a gazillion years), you need some component. But the software which has the component itself messes up Perl.
Crazy shit. Why can't these software developers get their acts together? Is it SO freaking difficult to put a "make" command where I can find the damn thing without having to pull my hair out?
And why in the world would ANYbody think it's a good idea to remove "make"? Doesn't the name itself sound like it might be something important?
**************************************************************
Update: to get "make", you have to create yourself an ID claiming you're an Apple developer, then hunt out and download the right version of X-code command line, to install which you require admin permission. Then, you can get hold of "Make" and install Clone.
But does that mean you can finally use Circos? No! Because now your Mac OS Lion 10.x has a bug that doesn't allow your permission to use the main program, for which you now have to go to each individual file and change the permission settings.
**************************************************************
Update 2: Still haven't been able to use Circos because of the above-mentioned permission problems. Am waiting for some bright spark of inspiration to strike me soon...
To do this, I need to install a software called Circos, which runs on Perl.
But thankfully, for Perl-morons like me, there are detailed instructions on how to use the thing.
First thing to do, obviously, is to download and install the thing. So I try doing that, and I get an error like this:
*** REQUIRED MODULE IS MISSING ***
You are missing the Perl module Clone. Use CPAN to install it as described in this tutorial
http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules
Okay, I think. Let me get this Clone then.
So I get the module and try to install that, only to get an error message like this:
bash: make: command not found
I try to find this "make". I try > man make and >which make and >locate make, all to no avail.
Fine. I think I can circumvent make and go directly to CPAN and install the thing. I do so, and I get the message
Going to write /Users/shridharv2/.cpan/Metadata
Clone is up to date (0.37).
Hurray! NOW maybe I can get cracking. But no:
*** REQUIRED MODULE IS MISSING ***
You are missing the Perl module Clone. Use CPAN to install it as described in this tutorial
Okay...I go back to the Circos troubleshooting page and hunt this out:
So get this: To install any software that runs on Perl (and I assume there must be tons of those softwares, since Perl has been around for a gazillion years), you need some component. But the software which has the component itself messes up Perl.
Crazy shit. Why can't these software developers get their acts together? Is it SO freaking difficult to put a "make" command where I can find the damn thing without having to pull my hair out?
And why in the world would ANYbody think it's a good idea to remove "make"? Doesn't the name itself sound like it might be something important?
**************************************************************
Update: to get "make", you have to create yourself an ID claiming you're an Apple developer, then hunt out and download the right version of X-code command line, to install which you require admin permission. Then, you can get hold of "Make" and install Clone.
But does that mean you can finally use Circos? No! Because now your Mac OS Lion 10.x has a bug that doesn't allow your permission to use the main program, for which you now have to go to each individual file and change the permission settings.
**************************************************************
Update 2: Still haven't been able to use Circos because of the above-mentioned permission problems. Am waiting for some bright spark of inspiration to strike me soon...
Wednesday, June 11, 2014
Blech!
So, some time ago, I had bumped into JY at the salad bar in the cafeteria and she was looking for the balsamic vinaigrette. JY is one of my role models: she's a mom with two kids, a kick-ass scientist and very straight-forward and very friendly. I gave her the one I normally use, which is in one of those big plastic bottles next to Ranch, Italian etc. She literally shuddered and said, "Oh God, I am morally opposed to any dressing that has sugar and high fructose corn syrup. I'm looking for the smaller glass bottle".
I'd been pondering this for a while and so yesterday I thought I too should be ultra-healthy (forget the fact that I'm eating a salad for lunch! Instead of French fries!), and shunned the plastic bottle and hunted for the small glass bottle which just has vinegar with some grape juice in it. I liberally doused my salad in the stuff and with a feeling of extreme virtue, tried to eat it.
It was AWFUL! Oh. My. God! My whole lunch was spoiled because of that excessively healthy nonsense.
I'm going to stick with the unhealthy dressing from now on.
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