The corpus of science - a biophysical perspective

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A month ago, Tim Jones posted the following video on his blog, featuring a montage of drawings people had made on the subject of what is important to them in science, along with their audio commentaries.

Once published, the post generated quite some interest in online communities of scientists, artists and others, and so he decided he would open up his experiment and invite others to follow, subject to a few rules. Some people have already submitted their contributions, which he has started putting together. This post is my attempt to join the party.

To me, one of the most important aspects of science is that it provides the means to investigate,  describe and manipulate the relationships between elements of matter across scales in space and time. This is as fundamental as it sounds, and the intricacies of this relationship become especially apparent in biological systems, which form the core of my research.

Life is organized at many different spatial scales, from single molecules to the whole biosphere of our planet and quite possibly beyond. As a biophysicist, I am interested in the forces and energies that shape biological systems. These are different at each level of organization — the forces sufficient to move a molecule around the air in our room are simply too weak to lift us off our chairs to float along, but the chemical reactions the molecule may cause in our nose, and the physiological or cognitive reactions of our body to them, may well end up generating the mechanical forces necessary to leave the room.

To investigate structures and processes at the different levels, level-specific tools are thus necessary, as well as some means to adapt their perspective to the level of interest. I like to call these two tools Methodenkarussell and Organisationsebenenfahrstuhl, respectively (rough translations: methodological merry-go-round and lift between organizational levels). Typical examples for the latter aspect would be microscope and telescope, which help us travel between the scale of the human eye and things that are much smaller or larger than that. At each of these scales, usually several methods exist (or are being developed, or sometimes only wished for) that allow to address a particular question: To investigate red blood cells, for example, you can use microscopes based on visible or infrared light, on ultrasound or electron beams, or you can subject them to all kinds of spectroscopy, e.g. electrorotation.

Pipet rack

Most methods combine both aspects to some extent — the pipets in this rack, for instance (photographed this afternoon with a little help from a friend who has them in the lab), can all be used to transfer microliter amounts of aqueous liquids, but they perform best at different quantitites within that range. Scientific disciplines overlap in a similar way — while biologists use microscopes (many would do) to investigate a specific type of cell they grow, physicists might use cells (many would do) to test the specific type of microscope they build.

As a biophysicist, I lived in both camps but lately more in the second one, which also provided the basis for my piece of the puzzle. I let you have a closer look at it before I am going to explain my thoughts below.

EvoMRI

What we see here is a grid of squares arranged in ten rows and ten columns, with the last row sticking out from the previous ones, and with the top left and the bottom right squares being somewhat peculiar too. Let's start on the top left where we have an unfertilized oocyte of the South African Clawed Frog, Xenopus laevis, imaged by means of Magnetic Resonance Microscopy — my pet peeve in the microscope family. The image was acquired as a preparatory step in a study targeted at sampling the chemistry of the (living) cell while it was taking up a drug. The cell's nucleus as well as the outer cell membrane are clearly visible, as is a gradient in image brightness that reflects the asymmetric distribution of water (concentrated on the top, the so-called animal pole) and fat (concentrated at the bottom, the so-called vegetal pole) within the oocyte.

Magnetic Resonance is an atom-level equivalent of name-shouting in a crowd — if someone happens to shout a popular name like "Daniel" in a crowd, some of those Daniels who heard it will probably turn around to see what is up. When they figured they are not the one that was targeted, they will return to what they did before. Magnetic Resonance does something very similar with atomic nuclei — it shouts (by means of radio waves) a name popular for atomic nuclei in that oocyte (1H, for hydrogen), and some of those turn in response to the signal, and return a little later. It is this turning and returning that is translated into signal intensity, with the brightness influenced by the number of 1H nuclei in that pixel, and by how easily they can turn, i.e. how strongly they are engaged with their environment, like their binding partner or some luggage they carry (this way, 1H nuclei in water and fat, can be distinguished). Of course, the way we shout will also influence the results. This is apparent, for instance, in the alternating light-dark pattern at the top and bottom of these squares, which reflects the way the radio coil was wound around the water-filled glass tube in which the embryo developed. Basically no method is entirely free of artifacts of this sort — that is certainly another important point about science, worth remembering when interpreting data or reading the interpretations of others. For the record, the colour table for the images represents a false colour scheme simply translated from the image intensity in each pixel, and the diameter of the oocyte is about 1.2mm.

The remaining squares of the upper nine rows contain similarly acquired images from a fertilized oocyte that developed into a tadpole during the two days that the experiment lasted. In the first three rows, single cells can still be seen dividing, but after some more divisions, only movements involving large numbers of cells remain visible. Finally, the tadpole and the yolk sac (in dark) appear, shortly before hatching. The whole image sequence is available as a video online, embedded below.

The next row bridges across temporal scales — from years (the growth rings, similar to those in trees) to decades (the piece was collected hundred years ago in today's Tanzania) to about 150 million years (the age of the fossil, which was found along with dinosaur remains). It depicts a belemnite, i.e. a fossil relative of today's squids, and the different image squares do not correspond to developmental time but represent cross-sections of the fossil in intervals of about 1mm, taken from a longer image sequence that is also available as a video online and embedded below. The unit length of each of these squares is about 1.5cm.

What do the fossil and the developing embryo have in common? First, evolutionary and developmental biology have recently ended their many decades of divorce and are undergoing a phase of synthesis under the new umbrella of evolutionary developmental biology, or evo-devo for short. In this respect, it is certainly of note if a method is capable of imaging these two very different kinds of biological systems and that the major signal contribution in both cases comes from water. As a sidenote, evo-devo had an early peak over a century ago here in Jena when Ernst Haeckel wrote his Welträtsel just a few hundred meters away from where I am typing these lines now.

The societal context in which science is embedded is addressed in the bottom-right square. It depicts one slice of the belemnite image series that I just described. I had used it as a profile image on some online social networks, basically because I wish to further explore the potential of Magnetic Resonance techniques for comparative evolutionary investigations. One of these online forums is Twitter, where I am EvoMRI and by which I got to know about Tim Jones' corpse of science initiative. As a signal of support for the protesters against the Iranian election fraud, many users of the platform changed their avatar to something greenish, and so did I. In the following weeks, the protests in Iran were almost muted by harsh actions of governmental forces, while the news elsewhere in the world had soon moved on. I kept the image green so far, and since Tim Jones required entries to be signed, I think this little symbol of protest against injustice is a good way to do it.

License: Text, image and MRI videos CC-BY, Corpse video © Tim Jones.

ResearchBlogging.orgLEE, S., CHO, J., MIETCHEN, D., KIM, Y., HONG, K., LEE, C., KANG, D., PARK, K., CHOI, B., & CHEONG, C. (2006). Subcellular In Vivo 1H MR Spectroscopy of Xenopus laevis Oocytes Biophysical Journal, 90 (5), 1797-1803 DOI: 10.1529/biophysj.105.073502

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