Chapter 2 – Orientation for the Bio-Curious  41

operate on binding to intermediate structures in a biochemical reaction. This correct binding

can then trigger subsequent chemical events inside the cell.

The exact mechanism for achieving this is not fully understood but is likely to involve

some conformational change to the receptor upon ligand binding. This conversion of the

original external chemical signal to inner cellular chemical events is an example of signal

transduction. These inner chemical events can then trigger other biological processes and so

in effect represents a means of flowing information from the extracellular environment to the

inside of the cell. There is scope for similar-​shaped molecules outside the cell to compete for

binding with the true ligand, and in fact, this is the basis for the action of many pharmaceut­

ical drugs, which are explicitly designed to “block” receptor binding sites in this way.

There is an increasing evidence now for several different cell types possessing an ability to

also detect nonchemical signals of mechanical origin. In tightly packed populations of cells,

such as in certain tissues and microbial biofilms, the magnitude and direction of mechanical

forces are dependent on spatial localization in the matrix of cells. In other words, mechanical

signals could potentially be utilized as a cellular metric for determining where it is in relation

to other cells. This has relevance to how higher-​order multicellular structures emerge from

smaller discrete cell components, for example, in microbial biofilms and many different types

of animals and plant tissues. As to how such mechanical signals are detected, and ultimately

transduced, is not clear. There is evidence of mechanoreceptors whose conformation appears

to be dependent on local stresses in the vicinity of its localization in the cell membrane. There

is also evidence that mechanical forces on DNA can affect its supercoiling topology in a con­

trolled way.

2.4.3  TRAPPING “NEGATIVE” ENTROPY

A useful thermal physics view of living matter is that this is characterized by pockets of

locally trapped “negative” entropy. The theoretical physicist Erwin Schrödinger wrote a

useful treatment on this (Schrödinger, 1944) discussing how life feeds off negative entropy. By

this, he was really referring to the concept of minimizing free energy to form a stable state,

as opposed to some mysterious quantity of negative entropy per se. Life in essence results in

pockets of locally ordered matter. This appears to be decoupled from the spirit of the second

law of thermodynamics, though note that we cannot consider biological systems to be ther­

mally closed, and instead when we consider the entropy of the whole universe, this will never

decrease due to any biological process. But life can be thought of as being local reductions

of entropy.

How is this achieved? What does “life” actually do to create local order? Ultimately, living

organisms chemically combine carbon with other chemicals to form the various molecular

forms of carbon-​based living matter alluded to previously, all of which have greater order

than their respective reactants. But where does this carbon come from? Organisms can eat

other organisms of course and assimilate their biochemical contents, but somewhere at the

very bottom of the food chain, the carbon has to come from a nonbiological source. This

involves extracting carbon dioxide from the atmosphere by chemically combining it with

water, fueled by energy from the sun, in a process called “photosynthesis,” which occurs in

plants and some microbial organisms.

The first key stage in photosynthesis involves an enzyme called “ribulose-​1,5-​bisphosphate

carboxylase oxygenase” (RuBisCO), which is the most abundant known protein on Earth.

It catalyzes the reaction of carbon dioxide into a precursor of sugars in a process called the

“Calvin cycle,” fueled through ATP hydrolysis. RuBisCO in prokaryotes is often found in

specialized cellular organelles of carboxysomes. The initial absorption of light occurs either

in the cell membrane directly (in photosynthetic cyanobacteria) or invaginated membrane

thylakoids of chloroplasts (in plant eukaryotes) in light-​harvesting complexes, which are

multiprotein machines that operate as antennae to absorb visible light photons in combin­

ation with pigments (e.g., carotenoids and chlorophylls). This results in an effective spatial

funneling of the incident photons through transfer of their energy to surrounding molecules