Biology and Evolution

Recently I requested Dan Graur’s book (“Molecular and Genome Evolution”) through interlibrary loan (ILL). Little did I realize that I took away the only copy available in the US university libraries. For proof, I attach this request slip hidden inside. My copy came from Reed College, which is not far from where I live, but look where else it went to. The request slip shows that someone from Harvard University borrowed the same copy through ILL. Given the distance between Harvard (east coast) and Reed College (west coast), I came to the conclusion that no other copy was available in any library in between.

I recently picked up the latest “Campbell Biology” (11th edition) after reading two excellent books on genome evolution, namely “The Origins of Genome Architecture” by Michael Lynch and “Molecular and Genome Evolution” by Dan Graur. Descriptions of the later two are posted for our expert members.

Clarification to those easily offended - the title of this post refers to the Swedish word ‘genomfart’, meaning “place of passage” or “the way forward”. More relevant to our blog, it is the last chapter of Michael Lynch’s 2007 book - “The Origins of Genome Architecture”. I enjoy Lynch’s papers on genome architecture, but must admit that his catchy chapter title compelled me to request his book from the library. So, if you are click-baited into this blog post, I am in a similar boat.

A new preprint titled “Legacy Data Confounds Genomics Studies” is recently posted in biorxiv. It shows that the researchers using data from 1000-genome project need to be cautious about garbage-in-garbage-out effect (technical term: batch effect) leading to spurious discoveries.

We are continuing our discussion of eukaryotic genome evolution based on Dan Graur’s “Molecular and Genome Evolution”. In this post, we present a number of puzzling observations in various eukaryotic genomes. The title of each section also includes the page number of Graur’s book, where the observation is reported.

We are continuing our discussion of eukaryotic genome evolution based on Dan Graur’s “Molecular and Genome Evolution”. In this post, we look at two key measures - genome size and gene size.

In the previous post, I wrote about the book “Molecular and Genome Evolution” by Dan Graur. It contains thirteen chapters as shown below. Chapters 7-11 may be considered the heart of the book, where Graur discusses how the genomes evolve and how new genes come into existence. Among those, the chapters 6-8 present three mechanisms for genome evolution, namely DNA duplication, molecular tinkering and mobile elements. Subsequently, chapters 10 and 11 discuss evolutionary aspects of the prokaryotic and the eukaryotic genomes respectively.

Over the last two weeks, I have been reading Dan Graur’s book titled “Molecular and Genome Evolution”. This is a fantastic book that everyone should read before starting to work on any genome-related project. For the benefit of our readers, I will share some comments in this short post. If time permits, I will later follow up with a longer post on the book.

Our readers interested in DNA ancestry will surely enjoy a new paper from Eran Elhaik and collaborators that came out in Genome Biology and Evolution. Also, I have something exciting for those curious about ancestry research. I am open-sourcing my own DNA genotyping data along with complete analysis steps. More on that in the following post. The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine

‘Ancient’ Bene Israel Jews and late-arrived Baghdadi Jews in India started the Bollywood movie industry. Many famous early Indian actresses also came from these communities. This is not common knowledge in India, because those actresses took Muslim (Firoza Begum) or Hindu (Sulochana, Pramila) screen names.

Prior to 1960s, most computers were analog computers.

Previous segment - Organoids and the Coming Medical Revolution (i)

Among all biomolecules within the cell, tRNAs got the least respect. Their supposed importance ended right after the ‘adaptors’ related to entries in the genetic code table were identified (mid-60s). Since then, the attention shifted to more complex RNAs like the rRNAs.

Among various biotechnology inventions of the last few years with potential to revolutionize medicine, nothing excites us more than growing of three- dimensional human organoids on matrigel. Therefore, we plan to devote a number of posts on this topic to keep our readers aware of the practices, potentials and challenges.

How did life originate on earth? What chemical properties of living objects make them different from the non-living objects? Where did the genome come from in the first place? How was life before the emergence of the genetic code? Why does the genetic code have that specific form? What biochemical advantages do the proteins get by having methionine as their first amino acid? How did the metabolic pathway evolve to its current form? How did bacteria, archaea and eukaryotes evolve into distinct kingdoms? How did multi- cellularity evolve? How did our ability to hear and smell evolve? Where did the adaptive immune system come from?

Venter’s group published a new paper on minimal genome.

This is another fascinating paper showing how little we know about the most basic questions, including ‘symmetry-breaking’ during animal development.

We earlier covered the population genetics work of Dr. Eran Elhaik in “New Study Sheds Light on the Origin of the European Jewish Population”. The paper gained ‘controversial’ status for not supporting the previous claims of common origin of all Jews promoted by Harry Ostrer. Elhaik argued that the Ostrer used flawed methodology to derive his claim.

Zerohedge reported -

Here is a challenge. Guess the author’s name before looking at this new arxiv paper.