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Archive for April, 2005

Nanobacteria, an estimate

Thursday, April 21st, 2005

I heard an assertion nanobacteria exist along with some speculation about them and so on. It was news to me and got me wondering if I had missed a discovery announcement, so I ran some numbers:

Consider a large nanobacteria, 30 nm by 100 nm. It has an approximate volume of 7e-23 m3.

How much DNA could this volume contain? Pop up a DNA molecule in Chime and get an estimate of dimensions: 20 bp run for 6.4 nm, so 0.32 nm / bp. The double helix has a radius of 1.3 nm.

Length of DNA with a volume equal to the cell = 7e-23 m3 / [ (1.3 nm)2 x π ] = 1.3e-5 m
Bps = length / bp length = 1.3e-5 m / 0.32 nm = 42 kb of DNA.

A low average bacterial gene length is 300 bp, so a nanobacteria could hold a maximum of 42 kb / 300 bp = 139 genes. The minimum number of genes for an independent living organism is 300 – 500, so a nanobacteria can’t have enough genes. It can’t exist. But let’s run the other numbers, on proteins.

A typical protein is 3 nm, lets call it a cube with a volume of (3 nm)3 = 2.7e-26m3.
A nanobacteria can hold 7e-23m3 / 2.7e-26m3 = 2600 proteins total. Low but not a hard limit on existence.

Now let’s put this together and describe a nanobacteria. 30% of the volume is water and small molecules. Of the remainder, let’s say 2/3 is DNA and 1/3 is protein. The nanobacteria contains enough DNA for 65 genes, and 600 proteins. Which means nanobacteria can’t exist, they are too small. There are quite a few unlikely bits in biology (pretty much every rule in biology has exceptions), so I’ll qualify it and say it is quite unlikely that nanobacteria exist. And to my estimates, add the evidence from projects to mass sequence DNA extracted from the environmental samples–if nanobacteria exist, their DNA would turn up in these projects, and no new phylum of sequences has emerged.

An E. coli by contrast is 1 µ x 3 µ and can hold 600 Mb of DNA and 20 million proteins. It’s genome is actually 4.6 Mb, and the extra space is taken up by a cell wall and protein.

Kernel upgrade

Thursday, April 21st, 2005

Upgraded the kernel on my linux server and it was the easiest thing ever:

yum upgrade kernel-smp

It updated grub and everything! Color me surprised. Linux is getting *so* easy to use.