Aristotle wrestling with the concept of haploid gametes & diploid organisms

He takes on the problems of Pangenesis to boot, 2,100 years before Darwin adopted it as his theory of heredity.

On the Generation of Animals, 722b:

Again, if the semen come from all parts of both parents alike, the result is two animals, for the offspring will have all the parts of both. Wherefore Empedocles seems to say what agrees pretty well with this view (if we are to adopt it), to a certain extent at any rate, but to be wrong if we think otherwise. What he says agrees with it when he declares that there is a sort of tally in the male and female, and that the whole offspring does not come from either, ‘but sundered in the fashion of limbs, some in man’s…’ For why does not the female generate from herself if the semen comes from all parts alike and she has a receptacle ready in the uterus? But, it seems, either it does not come from all the parts, or if it does it is in the way Empedocles says, not the same parts coming from each parent, which is why they need intercourse with each other.

Yet this is impossible…

– Translation by Arthur Platt, from The Basic Works of Aristotle, Richard McKeon, ed., Modern Library (1941).

Random Genome, Naked Genome

On Saturday, my former Center for Genome Sciences colleague Sean Eddy brought up the idea of a Random Genome Project: let’s create a random genome to serve as a null model of genome function. With this random genome, we can determine how much supposedly functional biochemical activity do we expect to see just by chance, and, among other things, we might use a random genome to explore how new functions evolve by “repurposing” (Eddy’s great term) non-functional DNA. In the comments to that post, you can read some discussion of how you might go about making a random genome.

An easier task would be to implement the random genome computationally, an idea I’ve been exploring recently, using a genome-wide binding model along the lines of the one by Wasson and Hartemink.

Why do this? Because we could explore two kinds of null models – the random genome described by Sean Eddy, and the naked genome. Continue reading “Random Genome, Naked Genome”

The truly provocative and disturbing stuff in ENCODE

… at least from my perspective. I’ll now stop ranting about the hype and media coverage of ENOCDE, and extend my compliments to the consortium for an amazingly well-coordinated effort to achieve an impressive level of consistency and quality for such a large consortium. Whatever else you might want to say about the idea of ENCODE, you cannot say that ENCODE was poorly executed.

It’s time to get into the interesting stuff – what’s actually in the papers. Among the results I’ve been most eagerly awaiting to see in print are the DNase hypersensitivity results now published in Thurman et al. (Nature 489, 75–82 (06 September 2012) doi:10.1038/nature11232)

Why is this interesting? Because it raises provocative and possibly disturbing questions regarding how transcription factors navigate and read out information from the genome. Continue reading “The truly provocative and disturbing stuff in ENCODE”

Sunday Science Poem: Mitochondrial Mothers

Despite my experiences of crushing boredom studying cell trafficking pathways in grad school, there was no way I was going to just walk past a book of poems titled Cell Traffic without stopping. In this delightful book, poet Heid E. Erdrich mixes themes of genetics, motherhood, ancestry, and Native American mythology to produce poetry that feels very relevant in a day when we can read information about our ancestry from the text of our DNA.

Today’s Sunday Poem is “Seven Mothers.” The title refers to the seven major, maternally inherited mitochondrial haplogroups popularized by Bryan Sykes in The Seven Daughters of Eve. Since Sykes’ book was published, we have developed a greater ability to use genetic variation in our nuclear DNA to trace our ancestry, and mitochondrial DNA now plays less of a role in our efforts to understand human ancestry than it once did. But it’s hard to beat the impact of mitochondrial maternal ancestry on our imaginations. Continue reading “Sunday Science Poem: Mitochondrial Mothers”

“Lectures on Chemical Reaction Networks”

A classic set of lectures by Martin Feinberg:

The occasion was a semester-long in-gathering of people interested in the behavior of complex chemical systems. At the end of that period there was a large meeting, the proceedings of which were published by Academic Press in a book, “Dynamics and Modeling of Reactive Systems,” edited by W. Stewart, W. H. Ray and C. Conley. My chapter amounted to a summary of some of the things I talk about during the course of the nine lectures.

It was an exciting time, which began when Charles Conley called me at the University of Rochester. He explained the MRC plans for 1979 and asked if I could spend a semester in Wisconsin. He said that they would pay my salary, provided that my salary wasn’t too high. I told him my salary. Conley asked if I could come for a year.

These seem useful, at least based on what I see in this paper: “A Linear Framework for Time-Scale Separation in Nonlinear Biochemical Systems,” Jeremy Gunawardena.