Janaki Ammal Correspondence with Cobb Blanchard - Part 1

Have managed to photograph all the correspondence involving Janaki Ammal from the Bentley archives. So i have around 150 pages worth of material to read through and discuss. So, this is going to be spread over numerous blog posts with my own comments and observations. Finally, i hope to put all this information together to paint a picture of Janaki Ammal as seen through these letters.

The first letter i am going to talk about is dated December 24th, 1931 from the Department of Botany, the Presidency college Madras. It is addressed to Frieda Cobb Blanchard, who along with Harley Harris Bartlett worked on evening primrose research. Cobb, earned her doctorate in 1920 while studying Mendelian inheritance in certain strains of Oenothera. This letter is written by Janaki Ammal, after she has returned to India and has taken up a position as a Research Fellow at the Presidency college.

The letter begins by thanking Cobb Blanchard for the data about her Egg plant cultures sent along with the letter. Then she inquires about the little girls (Cobb's daughters). As a Indian, i can appreciate the similarity of life back in 1930's to what we have now when she writes "I led a very gypsy life in Malabar visiting all the members of the E.K clan and being introduced to all the new arrivals". Its hard for me to decipher if this sentence reflects some amusement on her part at having to visit so many members of her Clan.

She writes "I have just fitted up a small cytological lab." Her teachers in Botany, Prof. Tyson and Dr Ekambaram are keen that they perform cytological studies. She is also supposed to guide 3 boys working for their Msc and give a few lectures in Cytology.

Apart from this position, she is also in contact with a Sugar cane expert at the agricultural station in Coimbatore who wants her help in studying the cytology of Indian sugar canes. In November she visited this cane station and fixed (for cytological examination) some material. She also talks about how life in Madras is very interesting and that they are having the "All India Women's Educational Conference". Most of the delegates are being house at the Queen Marry college where she is at that time. Its probably worth noting that the All India Women's Conference was formally registered in 1930. However, i did not find mention of this event in Madras in their history.

The 37's: How i came to find more information about Janaki Ammal

"Rust" - high levels of ferric oxide, led star trek voyager to a old automobile floating through space. They find even more evidence of human objects on a planet, halfway across the universe in the delta quadrant. True to their nature of exploration, they follow these pieces to find the 37. "The 37" are actually earth humans that were "abducted by aliens" in the 20th century and transported to the delta quadrant. Some of the progeny of these individuals manage to overthrow the alien masters and establish a human civilization in the far off Delta quadrant. While i could begin to wonder if a population from such a small group of people would have enough diversity to sustain a whole new earth, it has to be pointed out that the aliens have abducted very different people, a world war 2 Japanese soldier, a African-American farmer and even Amelia Earhart.

Yes, the first female aviator to fly solo across the Atlantic ocean who disappeared leaving behind numerous theories about what happened. This episode of star trek is a fitting tribute to Amelia and her legacy of inspiring generations of men and women that followed. Another lady who was active during the same time, traveled half way across the world, was a scientist of repute, Janaki Ammal. Apart from various academic achievements, a Padma Shri award has been conferred on her by the government of India. Her story is one of pioneering inspiration and grit.

Recently, while walking past the Rackham graduate school (Janaki Ammal was a Barbour scholar at University of Michigan) i was somehow reminded of her. After some digging around,  i came to know that the Bentley archives has maintained some of the correspondence involving her. Hopefully, i will be able to share the details of the contents and discuss some of interesting parts on this blog. The archive managers were super-helpful in finding the material and some of the digitized photographs. Given below are two of the photographs which include Janaki Ammal.


She is rather easy to spot as she is the only Indian lady in both pictures, even without the writing below the second picture.
 

My hope is to be get hold of the 15 – 20 letters worth of correspondence between Dr. Janaki Ammal and the Blanchard family in Box 5 of the Matthaei Botanical Gardens records and some additional correspondence in Box 11 of the University Herbarium records. It will be especially interesting to read about her experiences during the second world war.

LTEE - E.coli and long term evolution - Lenski and his E coli

The E.coli long-term evolution experiment is an experiment started in 1988, which has been continued for more than 65,000 generations now. Changes in fitness, evolution of new phenotypes and the associated changes in the genome have been monitored for 12 initially identical populations that have now diverged. We recently discussed the analysis of a dataset spanning 50,000 generations that showed an abundance of non-synonymous over synonymous changes. Even after 50,000 generations "beneficial" (non-synonymous) changes outnumber the synonymous changes. 

Re-plotting the data provided in the paper, we see a clear pattern of non-synonymous/synonymous >1 for the non-mutator populations with a peak at around 20,000 generations, followed by a decline. The point mutator populations have the opposite pattern with more synonymous changes than non-synonymous changes. 

The plot below shows a clear difference in the rate of accumulation of mutations between the "mutator" and non-mutator strains. Both these patterns are noted in the paper and are used to make say "Our experimental results thus support a selectionist view of molecular evolution, complementing indirect evidence based on comparative genomics in bacteria, Drosophila and humans. Of course, the LTEE may differ from many natural populations in important respects including its low mutation rate, the absence of sex or horizontal gene transfer, and a stable environment. As we showed, high mutation rates tend to obscure the role of selection in molecular evolution."

Just to pretend that i found something new in the data, i plot the G-score (which is used to assess the degree of parallelism between clones) across the genome. In the below figure, it looks like we have a cluster of high G-scores between 3,248,576 and 3,481,685. This cluster has 7 of the 15 highest G-score genes reported in the Table-1. Although not consecutive genes, this pattern does seem a bit striking.

Speciation and divergence at the level of the transcriptome, genetic editing and microRNA

Eviatar Nevo has studied speciation in the "Evolution Canyon" to understand the process of evolution at different scales. In a recent paper from his group, sympatric speciation as a model for the origin of species is investigated using Spalax galili as a model system. Their hypothesis is that the phenotypic differences between the Chalk and Basalt dwelling populations have their respective phenotypes due to changes in DNA mutations (SNP's) or differences in DNA/RNA editing.

".. comprehensively screened the basalt and chalk genomes and transcriptomes for DNA and RNA editing and identified both differential DNA and RNA editing." They identify a few candidate genes that differ in the level of editing. While this does not establish a causal link, it is extremely interesting to think of non-SNP traits as potential markers. They also focus on microRNA and differences in codon usage preferences.

This picture shows the face of a spalax species. The entire clade consists of numerous species and has been the focus of intense study over the years. Blind mole rats have been the focus of numerous studies that have looked at how eye and eye proteins function.
  

The Pursuit of Happiness or Happyness

Most people want to be happy. Except for the rare idiosyncratic individual the world really is a place filled with people who are in the pursuit of happiness. Happiness is a weird and sometimes illusive thing. The movie about The Pursuit of Happiness does a good job of capturing the illusive nature of Happyness.

Would eating the Gumbo make you happy? It has a history as much as Thomas Jefferson does, or may be even more.

 

How about modelling the evolution of directed graphs along a phylogeny? Would it make any difference what those directed graphs represent? They could be anything really, a map of the brain (connectome), parasite transmission networks, protein protein interaction networks or simply a simulation.  

In the end we are still only chasing after it.

Who has found it?

The unlikeliest of people have found it.  No it has nothing to do with Pittsburg skyline and everything to do with the mind.

Dolphins, crows and apes - as clever as it gets

Dolphins, just like crows & apes are very smart. In some way they represent the pinnacle of the independent evolution of intelligence in species that dwell in the oceans, fly in the sky and walk on land respectively. What can the brains of these distinct yet similar taxa tell us about intelligence? Will they be able to provide crucial insight needed to understand intelligence, thought and the brain? How can they guide artificial intelligence research?

All these may seem far fetched questions for another day. However, we are not too far away. A study published in the year 2013, "Large-scale network organization in the avian forebrain: a connectivity matrix and theoretical analysis" was able to generate a preliminary map of a avian forebrain. Work in this field is progressing at an incredible pace. It might be worth noting that one of the co-authors Murray Shanahan is actually a Professor of Cognitive Robotics and has written the book "The Technological Singularity". So the fields are not so far apart after all. 

Few months ago, while writing up my PhD thesis "Speciation genomics: A perspective from vertebrate systems" i began to realize how intricately linked the world is. One needs to understand the evolutionary genetics of phenotypic traits to be able understand speciation and adaptation. This understanding of genetics will play an important role someday in the future to look at traits like "intelligence". We may infact be able to unravel the great mysteries of the brain and its evolution. 

Understanding the brain, its evolution and genetics definitely have their own merits. The next step into the world of artificial intelligence and culture actually seems exciting at this point. What kind of morality would different machine cultures create? Would speciation "co-evolve" with culture in artificial systems as much as it seems to in the natural world?

Ensembl Perl API to get all intron lengths in Human genom

The below script will get all stable id's from Ensembl and prints out the intron lengths for each transcript of every gene. Along with intron length, the flanking exon id's are also printed. One can get the upstream and downstream intron length for each exon using the output.

The output would look like this:
Gene Id                     Transcript Id            Previous Exon          Next Exon               Intron length
ENSG00000084674 ENST00000233242 ENSE00000932268 ENSE00000932269 717 ENSG00000084674 ENST00000233242 ENSE00000932269 ENSE00000932270 2338 ENSG00000084674 ENST00000233242 ENSE00000932270 ENSE00000932271 112 ENSG00000084674 ENST00000233242 ENSE00000932271 ENSE00000719046 1100 ENSG00000084674 ENST00000233242 ENSE00000719046 ENSE00000718984 261 ENSG00000084674 ENST00000233242 ENSE00000718984 ENSE00000932272 863 ENSG00000084674 ENST00000233242 ENSE00000932272 ENSE00000932273 1663 ENSG00000084674 ENST00000233242 ENSE00000932273 ENSE00000718481 1240 ENSG00000084674 ENST00000233242 ENSE00000718481 ENSE00000542194 482

 #!/usr/bin/perl  
 use strict;  
 use warnings;  
 use Bio::EnsEMBL::Registry;  
 use Bio::SeqIO;  
 use Getopt::Long;  
 my $registry = 'Bio::EnsEMBL::Registry';  
 ## Load the databases into the registry  
 $registry->load_registry_from_db(  
  -host => 'ensembldb.ensembl.org',  
  -user => 'anonymous'  
 );  
 ## Get the gene adaptor for human  
     my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );  
     # Fetch my gene of interest usning ensemble ID  
     my @gene_ids = @{$gene_adaptor->list_stable_ids()};  
 foreach my $geneid(@gene_ids){  
 #print "$geneid\n";  
 my $gene = $gene_adaptor->fetch_by_stable_id($geneid);  
  foreach my $transcript (@{ $gene->get_all_Transcripts }) {  
   foreach my $intron (@{ $transcript->get_all_Introns }) {  
   print $gene->stable_id,"\t",$transcript->stable_id,"\t",$intron->prev_Exon->stable_id,"\t",$intron->next_Exon->stable_id,"\t",$intron->length,"\n";  
   }  
  }  
 }