The Illusion of Reality

In 1999, a movie came out which blew everyone’s mind, and still twists our brains today : the Matrix. It described a future where reality is an illusion, a computer-simulated universe in which we thrive. Solipsism with guns in a post-apocalyptic world. But what if I told you… they’re right ? In fact that’s not true, they’re probably completely mistaken. Reality is not a computer-generated dream. Reality is empty. Well… 99,99% empty.

Science basics, matter is made of atoms. Atoms are themselves made of a cloud of electrons orbiting a dense nucleus of protons and neutrons. Separating electrons and the nucleus is just air. Not even air, since air is composed of molecules. This is why I can say that atoms are mostly empty, and therefore matter is mostly empty. We’ve known this for a very long time. Most of us would just give up and say “matter is nothing, so why bother ?”. Most of us, but not scientists. Scientists have twisted and mangled these teensy balls of nothing. They stripped these minuscule objects apart and threw the remains into a 27 kilometers collider to blow them up. They’ve invented machines and probes to witness matter in its very extreme intimacy. In 1951 they invented the Field Ion Microscope and they’ve taken pictures… of individual atoms. Repelled ions looking like clusters of stars or ripples into the nothingness.

So, why bother ? That’s why. Matter is almost empty. But we were here, and we took pictures to prove it.

Picture : Examples of field ion micrographs of (a) iridium, (b) a Pd40Ni40P20 bulk metallic glass, (c) a decorated grain boundary in a neutron-irradiated pressure vessel steel, and (d) 5nm-diameter secondary precipitates in the nickel-based superalloy Alloy 718

M.K. Miller (2000) The Development of Atom Probe Field-Ion Microscopy, Materials Characterization (44):1-2 11-27

Life Inside a Cell

Another week, another type of microscopy. Did you notice how much I like microscopy yet ? Even though, in biology, we have to rely on two major fields, imaging and molecular science. There are things you can’t comprehend in microscopy, just like there are things you can’t see in molecular biology. These are two sides of the exact same coin, and one must juggle between both to try and get some kind of understanding of what’s happening inside the cell. With microscopy, it’s easy to understand why it’s not perfect, why it unfortunately doesn’t hold all the answers. Most of the time, we’ve fixed an instant in time, the cell was living one moment, and was dead the next, stuck forever in what it was doing at the time. Looking into the objective, you can only see what was happening then. And even when doing microscopy on living cells, we mostly have to rely on specific markers, so all of what’s going on around is invisible. Unknown. And that’s without saying that a picture is just that, a picture, and sometimes you’re just baffled by what’s on the screen, just like when you see some abstract piece of art and think “What is this and why in the world is it worth $150,000 ?”

So we might develop wonderful technologies and extravagant techniques, just like the electron microscopy on “unroofed” cells you’re seeing here, we may well go further and further into getting details of what the inside of a cell looks like, we still have a bunch of work until we understand it all.

Still, it looks very, very cool.

Picture credits : Electron Micrographs of Unroofed Cells of D. discoideum, Immunogold Labeled for the Localization of Arp2/3 or the LimEΔcoil ProbeCells in the left panel expressed GFP-p41-Arc, which is marked by anti-GFP antibodies.

The Beauty of Fluorescence

Probably not a very good title, because I love fluorescence very very much, and I find it beautiful very very often. But today I’m going to talk about my favorite dye. 4’,6-diamidino-2-phenylindole or DAPI (cute name, in french we have a song which goes “Pomme de reinette et pomme d’api”, but anyway), is a fluorescent stain which binds to DNA. Therefore it is used in fluorescence microscopy to stain nuclei. It is particularly useful when applying multicolor fluorescent techniques, because the range of greens, yellows and reds sometimes makes it hard to distinguish between cells. DAPI’s blue makes a nice contrast, so we can never get lost.

Did I tell also that it’s the most beautiful thing to see in a microscope ? Because it is, it really is. Sometimes I have to remind myself I’m not looking at Avatar’s version of the night sky.

The Molecular Perspective

Scientific illustration is no easy task. Anyone who’s looked through a microscope and attempted to draw at the same time knows it. Try then to add some information to beauty, as to make the viewer be in awe and learn, and you’ve got a near impossible challenge on your hands. So if you’re familiar with scientific illustration, (or if you’re on Tumblr even,) you’re probably no stranger to David S. Goodsell’s work. Even then, it’s never a waste of time to talk about the best. And David S. Goodsell is certainly one of the best. He’s got the fantastic ability to combine hand-drawn illustration of intricate and complex biological mechanisms, accurate science, wonderful colors and great design, as to remind us that although cells are often represented as spheres full of nothing, they are far from empty.

    To a Skylark - Percy Bysshe Shelley

Data Visualization