Portrait of a molecule

Last night I was reading a new book which claimed that we’ve never seen atoms or molecules. The point the author was making is that in evolutionary biology you don’t need to actually see evolution happening, you can infer it — just as we can confidently infer the existence of atoms and molecules.  The point is correct, but the example is not.

We can actually see atoms and molecules.  This morning I awoke to find out that a really spiffy molecule has been visualized using a new type of microscope.

It’s pentacene, with 22 carbons and 14 hydrogens.  The molecule consists of five fused benzene rings, and is used, among other things, in solar panels.

IBM researchers in Switzerland imaged the molecule using a sophisticated new technology that includes a single molecule of carbon monoxide as an imaging device.


Fig. 1.  Image of pentacene from the atomic force microscope

The AFM [atomic force microscope] uses a sharp metal tip that acts like a tuning fork to measure the tiny forces between the tip and the molecule. This requires great precision as the tip moves within a nanometer of the sample.

‘Above the skeleton of the molecular backbone (of the pentacene) you get a different detuning than above the surface the molecule is lying on,’ Mr Gross said.

This detuning is then measured and converted into an image.

To stop the tip from absorbing the pentacene molecule, the researchers replaced the metal with a single molecule of carbon monoxide. This was found to be more stable and created weaker electrostatic attractions with the pentacene, creating a higher resolution image.

Here’s the conventional molecular representation of pentacene:


Fig. 2. Pentacene as you might have seen it in O-chem

And, as I say in WEIT, we’ve been able to visualize atoms ever since the scanning tunnelling microscope was created in 1981. (Its inventors got a Nobel Prize five years later.)

Here’s a bunch of atoms, looking like little balls:


Fig. 3 : A photograph of about 500 atoms of Niobium (41) and Selenium (34) neatly arranged at the surface of a crystal (darker atoms are simply lying lower in the surface).


  1. newenglandbob
    Posted August 30, 2009 at 6:43 am | Permalink

    That is strange that I can not see god in there anywhere, just the 22 carbon and 14 hydrogen atoms. Do I need to pray harder to see more?


  2. Drew Smith
    Posted August 30, 2009 at 7:04 am | Permalink

    Actually, I think the original author’s example is still valid. When we refer to typical “seeing”, we are referring to the everyday process by which photons from some light source bounce off an object and into our eyes, where our brains infer the existence of the object. (So even normal “seeing” involves some measure of inference.)

    In the case of the atoms and molecules given above, the statement “[t]his detuning is then measured and converted into an image” tells us that there are additional steps required to produce the photons that reach our eyes. Inference is involved at each step, so overall more inference is involved.

    These additional steps or levels of inference are perfectly valid, but they are less direct than when we “see” the typical object in our surroundings. And I think the same can be said regarding evolution.

  3. Thanny
    Posted August 30, 2009 at 7:48 am | Permalink

    Let’s not forget this:


  4. Torbjörn Larsson, OM
    Posted August 30, 2009 at 10:53 am | Permalink

    When we refer to typical “seeing”, we are referring to the everyday process by which photons from some light source bounce off an object and into our eyes, where our brains infer the existence of the object. (So even normal “seeing” involves some measure of inference.)

    Yes, but that is still incomplete. If this was enough then those who complain would be satisfied with seeing any surface or colored liquid/gas at any time. (In fact, they would probably be satisfied with any optical phenomena involving atoms or ions besides direct scattering, such as luminescence and so on.)

    What they seem to want is an image of identifiable objects. As an analogy, people was cheering when the first images of exoplanets where released, obtained from light filtered and processed but showing such an image. This was accepted as “direct” evidence as opposed to “indirect” methods, say transit light curves from stars.

    Never mind that those images was a few pixels wide because of diffraction from a point source less than a pixel wide. (And never mind that awesome indirect small scale thermal maps of exoplanets had been acquired well before.)

    We have such images also, from individual ions blinking in ion traps, since the -90s I believe.

    In the future we may obtain resolved images of planets by using long baseline interferometry. By the new and terrific power of negative refraction index material it seems to be possible to continue the trend starting by other methods to achieve image resolutions well below the wavelength of EM radiation used. I wouldn’t currently bet against the possibility of one day similarly resolve atoms with light.

  5. Posted August 30, 2009 at 9:02 pm | Permalink

    With the detail given by a carbon monoxide molecule, I wonder what detail we might get with a hydrogen molecule tip.

  6. Roscoe Holcolm
    Posted September 20, 2012 at 8:26 pm | Permalink

    Well…at least no one responded with some obscure meaningless bible verse that was translated in multiple layers and copied and recopied by hand hundreds of times over 2,000 years.

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