Friday, March 21, 2014

The Kardashev Scale - Great blog post.

Spent some time this morning reading a great blog post by Centauri Dreams about what Kardashev actually meant by Type I, Type II, and Type III civilizations.
See the post here:
http://www.centauri-dreams.org/?p=30255&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+centauri-dreams%2Feepu+%28Centauri+Dreams%29

Centauri Dreams speculates that we should be well past the energy consumption required to categorize us as a Type I civilization, which according to Kardashev was described as:

I – technological level close to the level presently attained on the earth, with energy consumption at ~4 x 1019 erg/sec.


So I did a tiny calculation and indeed, we are WAY beyond the minimum necessary to be a Type I civilization. Total World Energy Consumption (WEC) in 2008 was 15 terawatts, and has increased several percentage points since then. By the way, 4x10^19 erg/sec  = 4 terawatts. So at least in terms of the "literal" definition, we are easily a Type I civilization as our WEC is nearly 4 times that defined by the Kardashev Scale. 

Of course it depends on where this energy comes from, whether we can control it or not, and if we're using it purely for interstellar communication. But since we're using SETI and METI for listening and transmitting signals, plus much of our energy does come from planetary sources (with the exception of solar), I'd say we probably qualify as Type I. What Kardashev meant by "technological level close to the level presently attained on the earth" is a bit weird since it implies earth is more advanced than Type I civilizations. Sort of a bad definition if we're trying to define Earth....

My 2 cents in the half hour I had between experiments.

Tuesday, December 24, 2013

Rant about Bollywood - all are my own opinions.


Let me start be defining what I mean when I use the term “Bollywood”- I use it to refer to the Hindi film industry located in Mumbai, Maharashtra and not any other Indian films. While I have seen a couple of Tamil films, and one could apply the same points I make here to other Indian films, most of the movies I have seen are straight from Bollywood.
There are several reasons why I think Bollywood movies are silly and pointless, these are not difficult to pick up on if you’ve ever watched a Bollywood film. However, aside from the silliness and predictability of the movies, I also think the whole industry and the movies themselves do real harm to the poorest people in the nation.

Bollywood movies are predictable and play off Indian insecurities.
Most Bollywood movies have the SAME EXACT plot – boy meets girl, girl and boy fall in love, there are complications/limitations/disapproving parents, some strife, lots of song and dance, emotional resolution of strife, and boy and girl live happily ever after. All of Bollywood is a Romeo and Juliette rip-off, only now with many more special effects. These movies are designed (yes, designed is the right word and I will explain later) to appeal to India’s need for true love and family approval. Most kids grow up in a strict household with “angry” parents, so all young people can relate to this. Since many marriages in India are still arranged (in rural villages and poorest areas) and pseudo-arranged requiring family approval even in bigger cities, Bollywood movies cater to the average Indian’s dream of finding “true love” and a form of escapism from family control. Maybe not a bad thing, except so many people get so addicted to this rush of feel-good brain chemicals, and that’s one reason 100’s of movies with the SAME PLOT are such a big success. Very few movies address real social concerns, political issues, or anything else meaningful. The movies that do address serious issues are never successful and pretty much amass no earnings or support. Nobody wants to talk about that stuff when they are unhappy and insecure and when there is such blatant escapism to be had.   

Bollywood depicts women as weak and requiring a man.
With very few exceptions, most of Bollywood’s 100+ feature-length films a year depict women as pretty objects in revealing clothing whose personalities have little depth and even less inner strength. Even back in the 40’s and 50’s, when tiny tight shorts weren’t a thing yet, women were seen and treated as objects in the movies, and wore risqué outfits for the age. I have seen hundreds of Bollywood movies, as I used to be a connoisseur. Even if a woman, actually usually a girl, in the movie has a strong personality and can be depicted as headstrong or unique, none of these girls actually resolves the conflict in the storyline by themselves, or with the aid of other strong women. Almost always there is a ‘hero’, a male figure who through various ways (action, emotion, or secret generosity) comes to the rescue and saves the delicate female flower from bad people or from herself. With the exception of perhaps, Mother India (1957, excellent movie), most of Bollywood does not depict true strength and evolution of a woman’s personal self. Okay, so this is partly because India is a patriarchal society in which women have been oppressed, and sure we’re starting to grow out of that. But why the heck is Bollywood still putting out movies like this and intelligent, educated people, still going to see them? Not a single Bollywood movie these days has the main actress fully dressed in something non-sexual. Not a single one!!

Bollywood is corrupt and kills national development.
Yes, while millions of people STARVE to death in India, Bollywood actors, directors, producers, make BILLIONS of rupees. I know there is corruption in every country, to some extent (although very little in Scandinavian countries), but the Bollywood industry is really very bad. Acting is hereditary apparently, because all rich famous actors and their sons and granddaughters have bought their way into the industry, not only at their own expense, but at considerable expense to striving new actors and actresses. Producers and directors will happily buy into the influence of old film families, by passing any new artistic talent in the industry. Bollywood movies and music are also the only “art” in the country. It ignores thousands of years of real Indian art and music. Bollywood is more politics than art, in that it’s in the business of campaigning for itself and making money. It kills real art in the nation, I don’t know any independent Indian artists. Really sad since in the past, India has a rich ancient history of the most amazing art and sculpture, classical music and classical dance, none of that is promoted by Bollywood.

Bollywood is selling a dream to the poor – the “mind-rape” of a nation.
How do you keep the poorest of poor masses happy while you wallow in your millions? By giving them a dream and selling them hope. This is where my original comment that Bollywood is the mind-rape of a nation applies, and that Bollywood films are designed. The same repeated plot, the catchy happy music, the “good guy/underdog always wins”, the inevitable girl gets guy happy endings – these are all designed. These appeal to unhappy masses whose situation is so unfathomable to Western sensibilities. Most people in India live their entire lives in poverty or extreme poverty (according to Western standards) where clean, running water and reliable electricity are an issue. Bollywood sells a dream to those in villages or slums, in poverty or oppression. Surveys show that these poor people will pay several rupees to go see a Bollywood movie even if they could use those rupees for much needed food, fuel, etc. They are basically buying a dream rather than rising up to be educated and strive for more. Bollywood is a form of oppression in my mind, keeping the people at the bottom happy with dreams and distractions, rather than using those billions to educate, motivate, or truly inspire a nation.

Ok, I’m done ranting. Bear in mind these are mostly my opinions based on what I see and hear from Indian people (in America and in India) regarding Bollywood, and how obsessed people from all walks of life are about those movies. I know India is a developing democracy and is doing some amazing things recently like sending a mission to orbit Mars. When you have 1.4 billion people, some are bound to become technologically educated. The fact remains that the true measure of a society’s personal advancement is its treatment of the poor and needy, its independent art and music, its social progressiveness, and in my opinion Bollywood has distracted Indians from those important things for far too long.  

Wednesday, June 5, 2013

Moving forward with sequence analysis.

Had to take a hiatus again for an interview and such-what. I hope it went well!
So I am continuing with the QIIME struggle.Today I am doing the split_libraries.py command.
I typed in for my Lake sequences:
split_libraries.py -m Lakes_Map_reverse_primer1.txt -f lakes454.fna -q lakes454.qual -b hamming_8 -o split_library_output_revprimers/ -z truncate_only

This code takes the Lakes 454 fasta sequences (with barcode, and forward and reverse primers) and splits them into a file with just the sequences with their names. The output folder gives you 3 files. The first is the .fna output file with the sequences and names mentioned. The log file is a summary of the sequences. The histogram file tells you how many sequences are within the lengths (peak) before and after processing. Look at where the majority of sequences are after processing and choose a range around those. Then run the split libraries again specifying a minimum and maximum length.

The number of written sequences should always be less than the number of input sequences.
The –b hamming_8 part of the script specifies that the barcode sequence is 8 bp long. 
The –z part indicates that you want the primer sequences taken off if they are detected.
The script takes between 15-20 minutes to run on my slow ass computer with a default of 200 minimum and 1000 maximum nt’s per read. The tighter this range, the less noise or non-specific amplification of primers you will have.

The forward (27 F) and reverse primers (519 F) should be amplifying a product around 492 bp long.


QUESTIONS I have:
The split libraries output gives me a log file and I have questions about it. Why are there sequences with an identifiable barcode but no detectable reverse primer? Why is there a list of “Total valid barcodes that are not in mapping file”? Should these be in the final written .fna file, or are they just sequences that could be barcodes that the script picks up?

I redid this (on original files, notice the change in name of output folder) to shorten the product range: 
split_libraries.py -m Lakes_Map_reverse_primer1.txt -f lakes454.fna -q lakes454.qual -b hamming_8 -l 410 -L 490 -o split_library_output_revprimers_Run2/ -z truncate_only


The -l lets me set a minimum for base pairs, and -L lets me set a maximum. I chose this range using the histograms.txt file generated by the first run. I based by range upon where the peak length was for maximum number of sequences, and around that peak to get a big fraction of total sequences. But I was still pretty stringent. This gave me a file with the quality controlled sequences. 
Enough for today!

Tuesday, May 28, 2013

Bioinformatics or Bust!

Ok, so that was more than a day’s hiatus I took from the QIIME tutorial, but I had a hooding ceremony to attend! My folks just left Sunday, it was a great visit :)

Today I also sent my dissertation to my committee… and immediately after discovered additional formatting errors after battling formatting issues for a week. LeSigh.

Back to the QIIME tutorial using the VirtualBox and Ubuntu interface. Today I learned the following:

1. How to convert a .sff file to .fna file in fasta format via QIIME 
(http://qiime.org/scripts/process_sff.html). It’s easy. Basically in your terminal window, make sure you’re in the directory (cd) that the .sff file is. Then use the command

process_sff.py -i lakes454.sff

That will convert the input file (-i) named lakes454.sff, which is what 454 pyrosequencing gives you, to outputs lakes454.fna and lakes454.qual. The .fna is fasta format of all the 454 sequences. There is also a .qual file that is generated, which tells you about the quality of the bases/sequences. A full description can be found here under “Quality Scores” http://qiime.org/tutorials/tutorial.html

Also to get info about a script (.py) type in
process_sff.py –h

This will bring up the help file. It tells you all the inputs and outputs you will get. You can also type in
process_sff.py

By itself and get general info about what this script does.

2. Making a mapping file. BY HAND. Yes, I’ve been given the sample name, barcode sequences, forward primer, and reverse primer in a .txt file… but not in the format required by QIIME. So, to do it by hand, I am following the instructions here:

It’s not horrible… okay yes it was. I named the file Lakes_Map1.txt. Started it in Excel with each heading as a separate column. Then copied and pasted the samples IDs and barcodes in the appropriate columns, etc. Tried to save as tab-delimited .txt file, and Excelt added double quotations to the .txt file.

I deleted all the double quotations by hand in the .txt file (Gatta be a better way to do this but all I could find online were Excel macros and I don’t use those yet) itself and saved it again.
I then checked my mapping file to see if there were any formatting errors in it using the command:

check_id_map.py -m Lakes_Map1.txt -o Lakes_output

This generated a new folder entitled Lakes_output with some files in it. The .html file tells you where the errors are and the _corrected.txt file tries to correct them for you. I deleted the …. That were inserted where the errors in my file were and resaved the file as Lakes_Map1.txt (deleted all the old ones). And redid the check_id_map.py command. This time there were no errors. Yay!

So this is as far as I got today. Not bad! I’m also using the QIIME tutorial files they give to try the new commands first and then using the Lakes data given to me by a co-worker to try these things on REAL data. I feel that’s the only way I am going to learn this process. Today’s bioinformatics “workout” took about 2.25 hours with all the errors and doing stuff by hand.

Signing off for today. Time for a real physical workout.

Monday, May 20, 2013

My journey onward

This week I am being "Hooded". Basically that means I wear some robes (rented) and my mentor and the Dean of my college say a few words about me at the doctoral ceremony. My parents are coming to Delaware from Colorado because they wanted to take pictures...
My actual defense is June 11th.
I'll be happy to see my parents this weekend, regardless.

Why am I not more excited to be getting my doctorate after 27 years of academia (since I started preschool at age 4 in India)? I'm not sure... I think it's because of the following:
1. impending sense of DOOM due to the collapse of the American economy
2. impending sense of DOOM because science doesn't seem to matter to most people
3. impending sense of DOOM due to not having a job lined up yet
4. impending sense of DOOM because I don't know bioinformatics.

So what can I do about this sense of DOOM? Well, probably nothing about number 1 or 2 short term. Number 3 I am applying for everything which interests me, so I'm bound to get lucky sometime.
Number 4 is obvious, teach myself bioinformatics.
It's a painful process, though, since it requires expertise in computers, scripting/programming, understanding many openly available programs and data-harvesting sites, and lots of time.
Today I made some progress in this! I am trying to teach myself Qiime (pronounced chime apparently), and I am using their free tutorial to do so. It took me hours to just download and install the VirtualBox and get it running. Make space on my hard drive by backing-up/deleting old pictures. I had to figure out how to turn on virtualization technology in the BIOS of my laptop. Finally get to typing in commands and have Qiime do things for me using their example files.

All I did today was check to make sure the mapping file was properly formatted. Generally you get a file like this from 454 sequencing of 16S rRNAs. The program gave me a corrected file which looks good. YAY.
I will continue with this tomorrow. For now I have to go and format my dissertation. It must be sent to the committee on Monday next week.