Notes to self re: the chicken genome

• no [SINEs] have been active in the chicken genome for the last ~50Myr.
  
• there is a detectable signal in orthologous splice site comparisons beyond the consensus derived from comparing non-orthologous splice sites (PDF). [E]ither some subtle classes of splice site sequences are conserved beyond the generic consensus that can only be observed at the bird–mammal evolutionary distance, or that there is a significant but weak conservation in mammalian introns that is not detectable in mammalian–bird alignments
• introns of ion channel genes are particularly enriched for conserved sequences, in agreement with reports that such introns contain RNA-editing targets
• Sequences expressed in the chicken brain ... are more conserved than testis-expressed sequences
• 43% of the chicken genes are present in 1:1:1 orthology relationships for [human:fugu:chicken]
  
• 72% (7,606) of chicken–human 1:1 orthologues also possess a single orthologue in [fugu]
• Genes absent from chicken. Genes encoding vomeronasal receptors, casein milk proteins, salivary-associated proteins (statherin and histatins) and enamel proteins seem to be absent from the chicken: from within both the EST sets and the genome. This is unlikely to result from imperfections in the chicken genome assembly because it preserves orthologues of closely linked (syntenic) mammalian genes.
• gene density shows a strong negative association with chromosome length
• ... a strong correlation between the length of a gene and the size of the chromosome in which it is found, an effect that is determined largely by variation in intron size
• Intron length in the chicken correlates negatively with recombination ..., G+C content ..., and gene density ..., as has been reported previously for other genomes
• The synteny maps confirm ... that the human genome is closer to the chicken than to
  rodents in terms of chromosomal organization of genes
• only 2.5% of the human sequence aligned with chicken [44% protein-coding, 25% intronic ; 31% intergenic]
  

Since when is hybridization not based on sequence?

Yet another trivial objection to an interesting study:

"A non-sequence-based method for studying copy number variation that avoids this limitation of draft sequencing is array-based comparative genomic hybridization".

I thought hybridization is indeed based on sequence. Perhaps the authors meant that the method does not require knowledge of the sequence.

Gene copy number variation spanning 60 million years of human and primate evolution.
Dumas et al. Genome Research, September 2007.

the limits of time compression

Paul "PZ" Myers writes,

"In development, time is often at a premium, though: In some lineages, the evolutionary pressure is on accelerating the rate of development to increase the rate of reproduction. The clock can be adjusted to run faster and faster, but there are limits: Increasing the rate can increase errors, as well, negating the advantages of speed with failures in successful completion in development. Molecules and cells can only respond so fast to fluctuations in the levels of regulatory genes without the whole process smearing into incoherence."

becoming a scientist, Smolin about Einstein

In the book Curious Minds: How a Child Becomes a Scientist, Lee Smolin writes about reading Einstein's essay "Autobiographical Notes":

"One of [Einstein's] ideas that appealed to me was that by becoming a scientist you could transcend the pain and uncertainty of ordinary life. By grasping the laws of nature, you connected with an aspect of the world more permanent and beautiful than the short striving of human life."

As if the practice of science were certain and painless...

Species whose genomes should be sequenced

1. The giant sequoia.

What allows this tree to grow for thousands of years?

2. The capybara.

This is the largest rodent. How did it become the largest rodent?

3. The donkey and the mule.

Why can a horse and donkey reproduce, and why is their offspring infertile? (Prediction: ultraconserved sequences will hold one key to the answer.)

4. The wolf and the fox.

What makes them so clever? When did canines develop the ability to learn human words?

5. The lion, tiger, leopard, panther, jaguar, cheetah, etc.

Because they're such great creatures, because they're endangered, and in the interest of comparative genomics. For example, why don't cats understand human words?