“I don’t think there will be a return journey, Mr. Frodo”: how thermodynamic irreversibility makes life flourish

Understanding the origin of life is one of the most enduring and fundamental scientific challenges there is. Of all branches of science, physics is probably not the first place one would think to go to for enlightenment. Life seems too complicated and multi-layered to be captured by the simplistic frameworks of physics. Today’s paper tackles a small part of understanding the origin of life – the physics of self-replication.

Plants detect gravity by going with the (granular) flow

Plants need to know the direction of gravitational pull in order to grow their roots downward and their stems upward. This information is crucial whether the plant grows in your garden, on a cliffside, or even on the International Space Station [1]. While it’s been said that it took a falling apple for Newton to figure out how gravity works, our photosynthetic friends use a more intricate microscale sensor to detect gravity. This sensor consists of starchy granules called statoliths which can be found on the bottom of specialized cells called statocytes.

Who needs polymer physics when you can get worms drunk instead?

If you speak to a soft matter physicist these days, within a few minutes the term “active matter” is bound to come up. A material is considered “active” when it burns energy to produce work, just like all sorts of molecular motors, proteins, and enzymes do inside your body. In this study, the scientists are focusing specifically on active polymers. These are long molecules which can burn energy to do physical work. Much of biological active matter is in the form of polymers (DNA or actin-myosin systems for example), and understanding them better would give direct insight into biophysics of all kinds. But polymers are microscopic objects with complex interactions, making them difficult to manipulate directly. To make matters worse, physicists have yet to fundamentally understand the behaviors of active materials, since they do not fit into our existing theories of so-called “passive” systems. In this study, Deblais and colleagues decided to entirely circumvent this problem by working with a much larger and easier-to-study system that behaves similarly to a polymer solution: a mixture of squirming worms in water.

Lifehack: How to pack two meters of chromatin into your cell’s nucleus, knot-free!

The entirety of our genetic information is encoded in our DNA. In our cells, it wraps together with proteins to form a flexible fiber about 2 metres long known as chromatin. Despite its length, each cell in our body keeps a copy of our chromatin in its nucleus, which is only about 10 microns across. For scale, if the nucleus was the size of a basketball, its chromatin would be about 90 miles long. How can it all fit in there? To make matters worse, the cell needs chromatin to be easily accessible for reading and copying, so it can’t be all tangled up. It’s not surprising then that scientists have been puzzled as to how this packing problem can be reliably solved in every cell. The solution is to pack the chromatin in a specific way, and research suggests that this may be in the form of a “fractal globule”.

Fold and Unfold

Animation of GFP unfolding

For the most part of biology, it is form that follows function. Proteins are a perfect example of this — they are made of a sequence of amino acids (the protein building units), which are synthesized by the ribosome. Once synthesized, the long strings of amino acids fold up into a particular 3D shape or conformational state. Proteins take less than a thousandth of a second to attain their preferred conformational state (called “native state”) that — if nothing goes wrong — ends up being the same for a given sequence. This process is called protein folding. Explaining how a protein finds its folding preference out of all possible ways in such a short time is a longstanding problem in biology.

Sticky light switches: Should I stay or should I go?

“One day it’s fine and next it’s…” red? Microscopic algae depend on photosynthesis, so they follow light. Previous research has shown that their swimming is directed towards white light but not to red light. New work shows that light-activated stickiness allows microscopic algae to switch between different movement methods.

Dividing Liquid Droplets as Protocells

In the beginning there was… what, exactly? Uncovering the origins of life is a notoriously difficult problem. When a researcher looks at a cell today, they sees the highly-polished end product of millennia of evolution-driven engineering. In today’s paper, David Zwicker, Rabea Seyboldt, and their colleagues construct a relatively simple theoretical model for how liquid droplets can behave in remarkably life-life ways.

Knotty DNA

Try taking out your earphones from your pocket and, in all probability, you’ll find knots and entanglements between the ends. As it turns out, this knotting effect is not limited to macroscopic objects, but occurs on the nanoscale as well. A DNA molecule that carries the genetic information of a living organism is actually a long string-like polymer, so you can imagine that it would also get tangled up just like the cords of your earphones. In today’s paper, Calin Plesa and his colleagues at TU Delft are able to observe and measure these knots in DNA strands and uncover behaviour which has not been observed before.