Why god is so fond of beetles?

Beetles form insect order Coleoptera, which is very rich in diversity. JBS Haldane's quote "that god has an inordinate fondness for beetles" is used to portray this rather astonishing fact. Various experiments have been done to identify the reason for the larger diversity found in beetles. 

Reasons such as host specificity driven speciation, specifically herbivory and angiosperm evolution in particular is suspected.While this study has contradicted this line of reasoning based on large scale phylogenies.

Higher survival capabilities of the beetle lineages has been attributed to their pre-Cretaceous origins. Was this diversity a result of an adaptive radiation that has been sustained by further diversification into a variety of niches? Does the beetle have a better ability to adapt? What makes it more adaptable?

Do the reasons for the diversification come from predators and defense mechanisms that beetles had to develop to escape these predators. In fact beetles use mimicry, chemical defenses, strong mandibles or horns or spines to deter predators.

Sex chromosomes of beetles have interesting biology and could play a role in the generating diversity.Frequent changes in sex determination mechanisms as has been seen in many insect groups could be important.

Could the genome shed some light on the reasons? The genome of the red flour beetle (Tribolium castaneum) has been sequenced. Presence of genes involved in detoxification, development, cell-cell communication and various other genes involved in ability to interact with diverse environments might explain the extraordinary ability of the beetles to adapt.

On the contrary Haldane was a self professed atheist who thought that "My practice as a scientist is atheistic. That is to say, when I set up an experiment I assume no god, angel or devil is going to interfere with its course... I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world.". So may be he was making a more complicated point which we mere mortals have failed to comprehend?

Cold dog Stockholm Sweden

The lion statue in Stockholm although not famous is known to people who visit the palace. The cold dog with rags drapped around it is almost not seen squatting in a corner.

Cold dog Stockholm, Sweden

Even though its not as majestic as the lion or one of the kings who ruled Sweden, its amazing in its own way. The rags which look so realistic are made out of metal, but on the first look very realistic. It is at home in the cold winters but even in the summer it is not out of place.

Get duplicate fasta sequences

ALLPATHS-LG had the DEDUP option turned off by default prior to release 42726. So this bit of code identifies exact duplicates either on the same or negative strand. Many of my runs had 30 to 60 Kb of sequence that was duplicated with almost equal amounts on both strands.

 #!/usr/bin/perl  
 use warnings;  
 # Input parameters  
 open FASTA, $ARGV[0] or die $!;  
 my $seqst_temp="";  
 my $seqs = {GENENAME =>my $genename,LEN =>my $qcom};  
 while($line = <FASTA>){  
 if($line=~ /^>/){  
 if($header){  
 if(exists $seqs{$seqst_temp}{GENENAME}){print "$seqs{$seqst_temp}{GENENAME}\t$header\t$seqs{$seqst_temp}{LEN}\n";}  
 $rseqst_temp = $seqst_temp;  
 $rseqst_temp=revcomp($rseqst_temp);  
 if(exists $seqs{$rseqst_temp}{GENENAME}){print "$seqs{$rseqst_temp}{GENENAME}\t$header\t$seqs{$rseqst_temp}{LEN}\treverse\n";}  
 $seqs{$seqst_temp}{GENENAME}=$header;  
 $seqs{$seqst_temp}{LEN}=length $seqst_temp;  
 }  
 chomp $line;  
 $header="";  
 $header=$line;  
 $seqst_temp="";  
 $rseqst_temp="";  
 }  
 else{  
 $line =~ s/[\n\t\f\r_0-9\s]//g;  
 $seqst_temp .= $line;  
 }  
 }#end of while loop  
 if($header){  
 if(exists $seqs{$seqst_temp}{GENENAME}){print "$seqs{$seqst_temp}{GENENAME}\t$header\t$seqs{$seqst_temp}{LEN}\n";}  
 $rseqst_temp = $seqst_temp;  
 $rseqst_temp=revcomp($rseqst_temp);  
 if(exists $seqs{$rseqst_temp}{GENENAME}){print "$seqs{$rseqst_temp}{GENENAME}\t$header\t$seqs{$rseqst_temp}{LEN}\treverse\n";}  
 $seqs{$seqst_temp}{GENENAME}=$header;  
 $seqs{$seqst_temp}{LEN}=length $seqst_temp;  
 }  
 close FASTA;  
 sub revcomp{  
     my $input = shift;  
     my $revcomp = reverse($input);  
     $revcomp =~ tr/ACGTacgt/TGCAtgca/;  
     return $revcomp;  
 }  

Although this does the job, its ugly in having the same bit of code used twice, once within the loop and once after the while loop. May be the end of file can be handled more elegantly.

MD5 file list checker

This program reads a file with filenames with correct path and MD5 values separated by a tab character and checks if the MD5 is correct or not.

#!/usr/bin/perl
use strict;
use Digest::MD5 qw(md5_base64);

open MD5, $ARGV[0] or die $!;
my $line="";
while($line = ){
chomp $line;
my @files=split(/[ \t]+/,$line);
open(FILE, $files[1]) or die "Can't find file $files[1]\n";
my $digobj = Digest::MD5->new;
$digobj->addfile(*FILE);
$digest = $digobj->hexdigest;
close(FILE);
if($digest!~m/$files[0]/){print "Md5 does not match for file:" . $files[1];}
else{
print "Md5 match for file:$files[1]\n";
print $digest ."\n" . $files[0] . "\n";
}
}

It would make sense to have MD5 checks integrated into the OS and have a MD5 list in each folder. May be it will get added into the code of various programs like ftp, sftp or even ordinary copy and mv.

Sort fasta file

Many programs like GATK require the fasta files to be sorted before use. Here is a rather simple script for the job:

 #!/usr/bin/perl  
 open FASTA, $ARGV[0] or die $!;  
 my $temp="";  
 my $seqs = {SEQ =>my $fheader};  
 my $sortemp="";  
 while($line = <FASTA> ){  
 if($line=~ /^>/){  
 if($header){$seqs{$header}{SEQ}=$temp;}  
 chomp $line;  
 $header="";  
 $line =~ s/[\s]/_/g;  
 $header=$line;  
 $temp="";  
 }  
 else{$line =~ s/[\n\t\f\r_0-9\s]//g;$temp .= $line;}  
 }#end of while loop  
 if($header){$seqs{$header}{SEQ}=$temp;}  
 close FASTA;  
 foreach $sortemp (sort keys %seqs) {  
 print "$sortemp\n";  
 print "$seqs{$sortemp}{SEQ}\n";  
 }  

However, you can find more elegant solutions that use Bioperl at Wolf/Takebayashi lab.

Why you cannot give Feedback to the LS?

The recent Anna Hazare movement has been opposed by many. Intellectuals like Nandan Nilekani among many others wanted the use better ways to comment or provide feedback to the parliament.

I wonder if Mr Nilekani has ever tried using the feedback form on the parliament of India website. The website which is designed and hosted by National Informatics Centre has a very interesting feature indeed :)

It has excellent code which makes sure that feedback can never be submitted. If you don't believe me you can try it yourself. As soon as you type anything in the feedback form the javascript onkey event calls the validate function. This function is supposed to replace all special characters. However, the brilliant person who designed this included the ^ (caret) character in the "myC" array that lists all special characters. This results in all possible characters being matched by the Regular expression. Hence, anything thats typed into the feedback form gets deleted.

If this is the situation in a website that can be easily verified by anybody with access to the internet. We can only imagine what happens to the feedback which actually manages to reach the Politicians after manging to escape the caret.

English? Inglish? Or watever this is!!

Recently, i found this(See picture) stamped on a bill from westside. It says, "No Exchange on Sale Merchandise". My first thought was it meant "No Exchange on Sold Merchandise". Would this qualify for Inglish? May be the BBC would find it interesting enough to publish? A similar collection of images about chinglish was published few years ago.

The English may find that their language is being ruined. But is that the price that must be paid to be an international language? How much can a language be stretched and modified before it stops being itself?

After further thought, it seemed that it actually meant "No Exchange on merchandise which is on 'Sale(Being sold at a lower price)' ". May be it is self evident as a measure to save on print space.