Protein Homology Network, data visualization by Alex Adai, Institute for Cellular and Molecular Biology – University of Texas, 2002

“The network summarizes the results of aprox. 92 billion pairwise amino acid sequence alignments between 289,069 proteins from 90 genomes. The final network is composed of 27,325 connected sets summing to 7,940,873 edges. An edge is colored blue if it connectes 2 proteins from the same species, and red if it connects 2 proteins from 2 different species. If that information is not available the edges are colored based on layout hierarchy.”

via Visual Complexity

When it comes to atoms, language can be used only as in poetry. The poet too, is not nearly so concerned with describing facts as with creating images.

Niels Bohr 

In his first meeting with Werner Heisenberg in early summer 1920, in response to questions on the nature of language, as reported in Discussions about Language (1933); quoted in Defense Implications of International Indeterminacy (1972) by Robert J. Pranger, p. 11, and Theorizing Modernism : Essays in Critical Theory (1993) by Steve Giles, p. 28

The atoms come into my brain, dance a dance, and then go out — there are always new atoms, but always doing the same dance, remembering what the dance was yesterday.

Quote in context:

“For instance, the scientific article may say, “The radioactive phosphorus content of the cerebrum of the rat decreases to one-half in a period of two weeks.” Now what does that mean? It means that the phosphorus that is in the brain of a rat — and also in mine, and yours — is not the same phosphorus as it was two weeks ago. It means the atoms that are in the brain are being replaced: the ones that were there before have gone away. So what is this mind of ours: what are these atoms with consciousness? Last week’s potatoes! They now can remember what was going on in my mind a year ago — a mind which has long ago been replaced. To note that the thing I call my individuality is only a pattern or dance, that is what it means when one discovers how long it takes for the atoms of the brain to be replaced by other atoms. The atoms come into my brain, dance a dance, and then go out — there are always new atoms, but always doing the same dance, remembering what the dance was yesterday.”

Richard Feynman, “The Value of Science” (speech at NAS meeting, 1955)
reprinted in The Pleasure of Finding Things Out: The Best Short
Works of Richard P. Feynman
 (Jeffrey Robbins, ed., 1999)

For every atom belonging to me as good belongs to you.

Quote in context: 

I CELEBRATE myself, and sing myself,

And what I assume you shall assume,

For every atom belonging to me as good belongs to you.”

— Walt Whitman, “Song of Myself,”  Leaves of Grass (1891)

Did you know that the phrase “and sing myself” didn’t appear in the 1855 version?


From The Earth Story Facebook:

While it certainly looks as though someone has taken a great deal of paint to these hills, these colours in fact formed naturally.
This unique geological formation is known as the Zhangye Danxia landform, found in southern China. It was formed by sediments laid down in a low-elevation fault basin during the Cretaceous period, which then experienced uplift due to their position on top of various fault zones. The various colours are a result of the erosion of the thick-bedded red sandstone and conglomerate: from running water erosion, biological effect, chemical precipitation and organic staining.

Caption: “Intercalation induces structural distortions. Left: unchanged DNA strand. Right: DNA strand intercalated at three locations (black areas).”

“In chemistryintercalation is the reversible inclusion of a molecule (or group) between two other molecules (or groups). Examples include DNA intercalation and graphite intercalation compounds.”

From the Wikipedia article on “Intercalation

(img source)

I don’t know what to call this pattern, but I like it!

Image 1: “The Maze” by Debralee Wiseberg (link and another gallery)… I think it’s corroded metal?

Image 2: 2,2-(Bipyridine)(Naphthalene)-fusion melt (25x)

Herb Comess. Honorable Mention, 1994 Nikon Small World Photomicrography Competition (link)


Exotic Fractals


These images look like exotic phyto-plankton, but in fact they are boundary of different Julia sets.  Julia sets are mathematical fractals. The same pattern repeats infinitely in smaller and smaller detail. Following the same simple rules repeatedly, these amazing patterns are formed.

Fathom the Universe

Source and image credit:


Dude! That top one totally looks like a dendrimer! Will post more about dendrimers soon…

Bucky Ball Pendant by Shannon Henry (image source)

More info on buckminsterfullerene

Pendant from Polymath Design Lab, and similar ones are available at their Etsy store, although I don’t see this particular wooden version (or is it leather?).

They have other cool designs too!


In the image above we see two spheres of the same size, shape, and material being dropped into water. The left sphere has almost no splash, whereas the one on the right has a spectacular curtain-like splash. Why the big difference? It all comes down to the surface treatments. The glass sphere on the left is hydrophilic, but the right one has been treated to be hydrophobic. As a result, the water-fearing molecules of that sphere push the water away, allowing air to be entrained below the water’s surface instead. This creates a big splash that’s absent when the water moves smoothly around the hydrophilic sphere. (Photo credit: L. Bocquet et al.)

Image 1: B-factor plot for 1AV1 truncated human apolipoprotein A-I


Caption: “B-factor plot of 1AV1, refined at 4 Å using the PMB B-factor patch for isotropic B-factor restraints. Note that even the side-chain b-factors are well-behaved, and that the molecular motions are modeled more accurately by these individual B-factors than they could be by a series of group B-factors.”

What is a B-factor plot? I don’t know, but these folks say: “Blue means helix, red means strand and green means turns and random coil.”

Image 2: Another view of 1AV1 structure

Source and more info:

What is apolipoprotein A1? According to Wikipedia, it’s “the major protein component of high density lipoprotein (HDL) in plasma” i.e. the good cholesterol. It helps clear fats! Good job, apo A-I!

“First direct observation of the orbital structure of an excited hydrogen atom”!


Original article: Stodolna et al. 2013. “Hydrogen Atoms under Magnification: Direct Observation of the Nodal Structure of Stark States.” Phys. Rev. Lett. 110, 213001 DOI: 10.1103/PhysRevLett.110.213001

Covalent bonds made visible!

“The chemical rearrangement of oligo-(phenylene-1,2-ethynylenes) as seen in the microscope image (top) and the stick diagram of the molecular structure. Photo: de Oteyza et al.”


Original article:
de Oteyza et al. 2013. “Direct Imaging of Covalent Bond Structure in Single-Molecule Chemical Reactions.” Science. Vol. 340 no. 6139 pp. 1434-1437 DOI: 10.1126/science.1238187

Visualizing bond-length differences in a single molecule (hexabenzocoronene) using atomic force microscopy
Image from:

Source article:
Gross et al. 2012. “Bond-Order Discrimination by Atomic Force Microscopy.” Science. Vol. 337 no. 6100 pp. 1326-1329. DOI: 10.1126/science.1225621