Feb 242014
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Life on earth is a tremendously complex process and, independent of whether one believes in one god or the other or not, evidence accumulates that this complexity originates from an evolutionary process. [1-3] According to the dogma of molecular biology DNA is to be transcribed into messenger RNA, a rather transient active copy, which is translated into proteins by using transfer RNAs (tRNA) as adaptors. [4] This dogma states that proteins are the only class of macromolecules that carry out catalytic functions. But how could such a complex system have evolved from a ‘primordial soup’? A significant modification of the central dogma of molecular biology was caused by the Nobel prize winning discovery of RNAs that are capable to catalyze biochemical reactions without the need of a protein component [5, 6] , giving rise to a theory of molecular evolution based on an RNA world. [7, 8] But even if you go for the RNA world hypothesis the initial question is only transferred from proteins to RNA: How could large, complex RNAs evolve from the vast ocean? This question leads to

The concentration problem:

Any kind of (bio) chemical reaction can only proceed to high yield if the concentration of starting material is high and best yields are achieved when the products either catalyze further reactions or when product and starting material get separated, resulting in a constant pull due to the continuing disruption of any equilibrium. Alas the concentration of organic molecules in the primordial ocean is thought to be similar to the one in the cotemporary ocean, which means too low to support life. [9]

The Contemporary solution to the concentration problem:

In contemporary life forms the concentration problem is solved by compartmentalization: Bacteria and
Archaea are equipped with a cell membrane that forms there outer hull, while Eukarya possess even additional sub compartments. Consequently the first life forms, so-called protocells, would consist of an outer membrane and an informational and functional biopolymer, i. e. RNA. [10] It could be shown that fatty acids (the ‘ancestors’ of present phospholipids) can self-assemble into lipid membranes and thereby form compartments that are capable to internalize new nucleic acid building blocks (nucleotides), while retaining the copied biopolymer. [11]

Thermophoresis as a possible primordial solution of the concentration problem:

This ‘membrane first’ approach would introduce an additional quite unlikely event in the schedule that would ultimately result in the evolution of life. As with basically any unlikely event there of course exists a competing theory, which in this case relies on inorganic compartmentalization as the cradle of life. [12] Several years ago Baaske et al. proposed an especially elegant approach to inorganic compartmentalization in the RNA world: The authors applied their recently developed theory of thermophoresis in aqueous solutions [13] in simulations on nucleotide diffusion in pore systems of hydrothermal vents at the bottom of the sea. [14] Thermophoresis describes movement of molecules in a temperature gradient: Heat of a specific source (here a hydrothermal vent) dissipates in solution and the resulting temperature gradient facilitates molecule accumulation or depletion in the heat source, depending on the nature of the molecule investigated. [15] The pore system of the vent would not only supply compartmentalization is this scenario but a whole network of compartments that are connected by thermophoresis.
The result of the simulations of Basske et al. was: By an interplay of solvent transport by convection and thermophoresis single nucleotides could be accumulated more than 10 8 -fold, while polynucleotides were concentrated even more, depending on their length and the pore geometry. [14] The authors note that their model already supplies a setting of temperature oscillation like it is used in exponential DNA amplification by the Polymerase Chain Reaction (PCR). Herewith a possible mechanism of mono- and polymer concentration was developed but an important question remained: It was unclear whether any self-replication of nucleic acids would be possible in the hydrothermal pore system. Obermayer et al. could address this question by a theoretical approach [15] , while Mast et al. succeeded recently in addressing this system experimentally in a DNA system. [16]
It seems like the thermophoresis model is indeed capable to compete with other model of evolution and we can be looking forward to the studies to come.

Felix Spenkuch

[1] J. E. Barrick et al., Nature 2009, 461, 1243-1247.
[2] D. Brawand et al., Nature 2011, 478, 343-348.
[3] F. C. Jones et al., Nature 2012 484, 55-61.
[4] F. Crick, Nature 1970, 227, 561-563.
[5] C. Guerrier-Takada, K. Gardiner, T. Marsh, N. Pace, S. Altman, Cell 35, 3, 1983, 849–857.
[6] K. K. Kruger et al., Cell 1982, 31, 1, 147-157.
[7] W. Gilbert, Nature 1986, 319, 618.
[8] G. F. Joyce, Nature 1989, 338, 217-224.
[9]E. V. Koonin Proc Natl Acad Sci USA 2007, 104, 9105-9106.
[10]J. P. Schrum et al. Cold Spring Harb Perspect Biol 2010, 2, a002212.
[11]Mansy et al. Nature 2008, 454, 122-5.
[12]S. E. McGlynn et al., Phil. Trans. R. Soc. A 2012, 37, 1969, 3007-3022.
[13] S. Duhr, and D. Braun, Proc Natl Acad Sci USA 2006, 104, 22, 9346-51.
[14] P. Baaske, F. M. Weinert, S. Duhr, K. H. Lemke, M. J. Rusell and D. Braun,s Proc Natl Acad Sci USA 2007, 104, 22, 9346-51.
[15] B. Obermayer, H. Krammer, D. Braun and U. Gerland PRL 2011, 107, 018101-1-4.
[16]C. B. Mast et al. , Proc Natl Acad Sci USA 2013, 110, 20, 8030-5.

Sep 032013
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Currently the gray days of autumn seem to be right around the corner and the water pouring from the sky is much too cold to be enjoyable. So most people just want to get through the rain to some dry place. Our instinct tells us to run as fast as we can to avoid getting wet. But is this intuition correct? Do you really get less wet if you run at your maximum speed?

The short answer is no. But as always the long answer is more complicated and while this might not be cutting edge research in physics it presents a useful training problem for undergraduates and has thus been discussed in the literature. So naturally different answers can be found depending on the assumptions the authors made.

The first assumption one has to make is the shape of the body that is moving in the rain. While it is usually assumed that this does not influence the general answer a recent paper showed that it actually does [1]. Borrowing methods from electrodynamics more complex body shapes could be addressed in this paper and the value of the optimal velocity was compared. That is if an optimal velocity even exists, i.e. it is not the best strategy to run as fast as you can.

Not surprisingly the answer does not only depend on the shape of the body but also on the direction from which the rain is coming. If the rain is coming straight from the back, for example, an optimal velocity always exists and its value does not even dependent on the body shape. For other direction the answers vary and no general rules seem to exist.

Another restriction that may apply is the assumption of a rigid body motion. While it is convenient to calculate a rigid cylinder floating effortlessly through the rain humans are not rigid, especially while running. No attempt has so far been made to include this into the models.

So if the rain is not coming straight from the back you might need to do some further calculations to figure out what the best speed is for your body shape and running style. But as a final tip make sure that you do the calculation in a nice and dry place and only then venture out into the rain. If the weather catches you off guard, just take your chances and run to the next cover.


Stephan Koehler


Read more:

[1] F. Bocci, Whether or not to run in the rain , Eur. J. Phys. 33 (2012) 1321–1332

Dec 312012
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“Science is what scientists do, and there are as many scientific methods as there are individual scientists.”
— Percy W. Bridgman

To the public, ‘science’ is primarily an abstract authority in questions of knowledge. Mostly, contact with this authority is limited to the products of scientific work, while the inner workings of science usually remain hidden behind the walls of research institutions, laboratories, and offices. What do people actually do when they ‘do science’? The actual day-to-day work behind the scenes is most often not nearly as organized and systematic as the finished products in academic journals and by far not as glamorous as contemporary scientific mega-conferences may suggest. Doing science is first and foremost a mere form of labor, a mundane but complex practice, a way of going about things and getting things done which depends on the right time, place, people or mood to produce scientific knowledge. For this issue of JUnQ, we asked scholars from various disciplines to share their experiences and views upon the labor of science and invited them to reflect upon and give us an insight in their daily work as a scientist or scientific writer. What does ‘good’ scientific labor mean to those who do it? What, in their eyes, makes for ‘good’ (enough?) scientific work?

Read more: Scientific Labor

Oct 212012
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During our chemical education in school, most of us heard of noble gases just as elements that are completely unreactive. Furthermore they are quite scarce, thus, there is no need for further mentioning them. They cannot be of much use anyway.

In fact, most of us use noble gases in our everyday life, e.g. they are essential in fluorescent lamps. And the heavier noble gases could even be brought to reaction by chemists. Still the chemistry of those elements is not of much interest outside the scientific community. But it was found out that one of those gases – xenon – shows a decreasing concentration in the earth’s atmosphere.

Detektor.fm asked Andreas Neidlinger, Editor of the Journal of Unsolved Questions “How did all the xenon vanish?”.

Listen to the podcast here.

For further information, please refer to:

May 092012
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Every morning it’s the same: A few drops of coffee end up on your table. And once they dry, they form ring-shaped stains. But why? This problem is related to the question how to build tomorrow’s communication systems.

Some of you might remember your grandma’s coffee pot, which had a sponge attached to the spout. This was done to avoid coffee stains. These stains – black on the outside, white on the inside and always round in shape – are also interesting for science, especially for nanotechnology.

Physicists might use the coffee stains as a model to design better communication systems in the future. This is why the question of the month reads:

“Why does coffee always form ring-shaped stains and not a chaotic splash?”

Detektor.fm asked Leonie Anna Mueck, Editor of the Journal of Unsolved Questions.

Listen to the podcast here.

Read more about self-assembly in colloidal dispersions here: A. Marin et al. “Order-to-disorder transition in ring-shaped colloidal stains”, Phys. Rev. Lett. 107, 085502 (2011)

Feb 092012
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This is not an unusual situation: You just took a painkiller against the first indications of an evolving cold and before dozing away you bothered to read the patient information sheet – and a few hours later your head is about to explode, you feel dizzy and dumb, exactly as was mentioned among the possible side effects.

In most cases this is not just coincidence but the so-called nocebo effect, which can be considered the “evil twin” of the placebo effect.

The nocebo effect makes us sick instead of miraculously healing our illness. Because just as a patient can feel better after taking a placebo, the awareness of possible side effects alone can have a negative effect on a patient’s health. What is this nocebo effect all about?

This is the question of the month and will be answered by Tobias Boll, editor of the Journal of Unsolved Questions.

Listen to the podcast on detektor.fm here

Dec 082011
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Is Green Chemistry more than a marketing term? Probably so. Green Chemistry may lead to a renunciation of the traditional production processes in chemical industry. But what is behind this concept?

Christmas time is cookie time. Of course, cookies should taste of vanilla. There are two possibilities for this purpose: The use of natural vanilla, which is very expensive, or the use of artificial vanilla, which is manufactured from crude oil by chemical industry. Wouldn’t it be nice if there were a method to produce vanilla in an eco-friendly, but simple way?

This is an example for what green chemistry is supposed to accomplish. It deals with the question how modern chemical production processes can be designed sustainably.

The unsolved question of the month is: How can this be achieved? What has already been attempted?

Detektor.fm asked Thomas Jagau, editor of the Journal of Unsolved Questions, for an answer.

You can listen to the podcast here.

Nov 122011
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Darwin’s theory says: Only the fittest survives. But why some species live in a communities, in which reproduction is a privilege of only a few members, can seemingly not be explained by the theory of evolution.

A prominent example for division of labour are the honey bees. In their colony, the work is minutely divided. Nutrition is procured by the group and the offspring is jointly nursed. But parenthood is the privilege of the queen bee, all other females are infertile.

The technical term for this behaviour is eusociality. Somehow the renouncement of reproduction makes sense in terms of evolution for certain communities and certain species.

We would like to know, why this is the case and thus ask the question of the month: “How is the theory of evolution compatible with eusociality?”

Detektor.fm asked Thomas Jagau, editor of the Journal of Unsolved Questions, for an answer.

You can listen to the podcast here.

Nov 122011
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For a long time their was no satisfactory explanation to why fireflies glow. A new model from quantum mechanics could solve this problem – and casually save us from loads of labwork.

The warm season is slowly ceasing and thus we also have to bid farewell to the fireflies. When they swirl around and glow on a lukewarm summer evening, everybody is fascinated.

Meanwhile it is more or less clear, why they show this behaviour – and as with a lot of strange phenomena it has to do with reproduction. The fireflies want to attract potential partners. But how exactly they glow has not been answered by physics and chemistry yet. But now a new method could bring light into this darkness.

Within the firefly moving electrons cause the lightwaves to be emitted. But thereby a so called “quantum mechanical many-body problem” is encountered. The cause is that the particles are not independent from each other in their arrangement.  If one particle changes its position, all other particles adjust accordingly. It is very difficult to calculate these processes, physicists usually approximate them by averaging. Usually the electrons are then described as being too close to each other – and thus the movement of one electron does not depend on the movement of another electron in the correct way.

Loren Greenman and David Maziotti have not come up with a new model to describe the electrons’ movement. Since it is more exact than older models it could soon provide a tool for solving chemical problems with the computer instead with expensive and laborious experiments in the lab.

Fireflies and quantum mechanics – what does the behaviour of electrons have to do with a light phenomenon on summer evenings? This is detekor.fm‘s Question of the Month. Detektor.fm posed this question to Leonie Mueck, editor of the Journal of Unsolved Questions.

Listen to the podcast here.

Sep 072011
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Image by Arz

We are surrounded by colours. You only have to peek outside the window and to see a red tiled roof, the yellow sun, the green grass, or the blue sky. But although our way of naming colours seems unshakable: the grass is not green in all languages and the sea is not always depicted as blue.

There are languages, Japanese for example, that traditionall do not distinguish between blue and green, or Welsh, whose speakers use the same word for the colour of the see, of grass, and of silver. The opposite phenomenon is also known. Spanish strictly distinhuishes between “celeste” (light blue) and “azul” (dark blue)

Listening to languages around the world quickly shows you that names for colours vary dramatically. But also the number of base colours that have a distinct name, red or yellow for example, differs among the languages. We wanted to know why and thus ask the open question of the month: “Why do some languages not distinguish between blue and green?”

The woman, who can give at least a few answers to this question, is Leonie Anna Mueck. She is a Ph. D. student and co-founder of the Journal of Unsolved Questions.

Listen to the podcast (in German):

Warum unterscheiden manche Sprachen nicht zwischen gruen und blau?

Read more in “Through the language glass” by Guy Deutscher (ISBN 9780434016907)