Talking about old proteins....and DNA organization

Consider bacteria which are, in theory, immortal 


Do they age? [good review article].  


Now there is evidence that as bacteria divide [news report here, and original paper here], the two daughters are not equivalent, one is molecularly younger than the other (can suggest how this is possible before reading the papers?)  

Also, I thought I would remind you of the problem associated with putting ~ 5 million base pairs of DNA into a single bacterial cell.  


In this picture, the bacterial cell (the dark blob in the center) has been opened up to allow its DNA to escape (the thin strands around the cell).  


Pretty amazing, so you can imagine the issues associated with finding a gene in this mess.  


Here is a nice overview article, if you are so inclined.

The value of being random (and dinosaurs migrating)

Apropos of our recent discussions of random processes and gene expression, here is an accessible (and free!) article on how noisy systems can be selected for.

At the same time, here is a piece on how looking at the composition of fossil teeth can lead to a hypothesis of dinosaur migration.  

Chimps and People, major differences after all....

Not withstanding the current absurd levels of political shenanigans, many people thought that there had to be greater differences between humans and other primates than those identified by sequencing the genes encoding various proteins.  Now it appears the differences lie in the regulatory regions, and involve large duplications and deletions of genomic DNA that influence gene expression (and perhaps act in part as a species barrier - you have to wait until the Life cycle section to get this).        Previously this group suggested that the "propensity for cancer in humans versus chimpanzees may have been a by-product of selection for increased brain size in humans."  Ah Well, if true it supports the idea that there is no free lunch (or brain).  (image from Olson & Varki 2003.)

Resurrecting old genes....

This has been an interesting area of research for some time (see the reconstruction of the Sleeping Beauty transposon); it often provokes responses from various pseudoscientific religious fundamentalists.  Here is a recent example, the reconstruction of an ancestral glucocorticoid receptor.  
At Panda's Thumb, P.Z. Meyers (post 1, post2) and Jack Scanlon respond to various distortions of the science.  

The origins of new genes.......

HERE (LINK) is a nature education article on the topic of how new gene originate (in case you want to go beyond biofundamentals).

Then there is a molecular evolution article on the identification of new genes in the primate/human lineage associated with brain function (link HERE).  The surprising observations: i) there are lots of new genes and ii) that are expressed early in neural development.

Here is a nice review of the major mechanisms responsible for Gene Duplication and their subsequent evolution or elimination (link HERE).

Room for optimism and mutations in humans

Turns out that (compared to chimps) people are more drawn to cooperation.  That would explain a lot.  Check it out here.

Also, if you want to read more about mutations in humans, here is a paper by Michael Lynch, which although dense, can can be understood (I believe).  HERE IT IS

How is one to schedule one's future (classes)?

when the rapture may be occurring on the 21st of October; that would be very inconvenient, since we are planning to cover mutations and DNA repair.    If you are an MCDB 1150-03 student, you have to do your highlighting before you leave......

thinking of the molecular nature of life: E. coli

modified from the work of David Goodsell

Fix your genes & shining evolutionary light on genomic dark matter

Now that we are moving into molecular and cellular biology, this becomes a very interesting story.    Here is the original paper....

In addition, using genome sequencing of 29 placental mammals (including a bat and an elephant, and humans, of course), an evolutionary model uncovers some of the previously unknown structure/function relationships within DNA - something that no intelligent design model could even begins to approach.  Check it out:  here

the original paper is here.

Oh no, people......

Down with neomalthusianism? 

And here is an exciting article on mitochondrial evolution (if you are having trouble sleeping!

Fianally, a reference to intracellular parasites
http://www.cell.com/cell-host-microbe/abstract/S1931-3128(09)00181-4

Amazing images....

This year's Nikon small world winners are out (luckily I did not compete, because given how great these images are, I would not have placed!!! )  but the pictures and their subjects are amazing:  link here