How life works

Following from Philip Ball's How Life Works. Certain fundamental themes that life runs on. (From the Preface). A good functional designer or a coder or a coding-language designer or a platform designer will see a lot here to learn from and aspire to in their work.

Key themes and principles:

a) Complexity & Redundancy:

"I once heard Nature’s former biology editor say very wisely that in biology the answer is always “yes.” (One might argue that it is in fact “yes, but. . . .”) By this she meant that there are many different ways that a process can happen—that a signal can be transmitted within a cell, that a gene can be switched on or off, that cells can assemble into a particular structure. Traditionally this feature has often been  regarded as a kind of fail-safe mechanism: because interactions between one molecule and another can’t always be guaranteed to happen, evolution has provided backups. But in fact we’ll see that the logic of biological redundancy is often of a different kind: there is a fuzziness to the system, so that different combinations of interactions can have the same result, and a particular combination can have different outcomes depending on the context. This, it seems, is a better way to get things done in a microworld beset by randomness, noise, and chance fluctuations."

Perhaps here that any kind of FOMO is just ill-founded. What needs to be will find a way to be. As someone said, rue not, what you lose comes back to you in perhaps a different form.

b) Modularity:

"Life never has to start from scratch. Evolution works with what is already there, even if this means redirecting it to new ends. We might (with great caution!) compare it to an electronic engineer who uses preexisting circuit components like diodes and resistors, and standard circuit elements such as oscillators and memory units, to create new devices. Thus life possesses a modular structure. This is most obvious in the way large organisms like us are assemblies of cells, as well as sharing common structures such as hearts and eyes. Modularity is an efficient way to build, since it relies on components that have already been tried and tested and permits the modification or replacement of one part more or less independently from the others."

Begin where you are, with what you have.

c) Robustness:

"Life’s resilience is remarkable. After a summer of terrible drought that saw all of England turn yellow-brown, it has taken only a few heavy rain showers for the green to start reappearing. Life is not invulnerable, but it is extraordinarily good at finding ways through adversity (which the world supplies in dismaying abundance). We will never have adequately explained life until we can understand where its robustness comes from. No doubt the aforementioned redundancy is a part of that, but robustness features in many contexts: in the way most embryos grow into the “right” shape, wounds heal, infections are suppressed, and more broadly, life on Earth has sustained its continuity for close to four

billion years."

d) Canalization:

"Life is what physicists might call a “high-dimensional system,” which is their fancy way of saying that there’s a lot going on. In just a single cell, the number of possible interactions between different molecules is astronomical—and there are around 37 trillion cells in our bodies. Such a system can only hope to be stable if, out of all this complexity, only a limited number of collective ways of being may emerge. The number of possible distinct states that our cells adopt is far, far smaller than the number of ways one cell could conceivably differ in detail from another. Likewise, there are only a limited number of tissues and body shapes that may emerge from the development of an embryo. In 1942 the biologist Conrad Waddington called this drastic narrowing of outcomes canalization. The organism may switch between a small number of well-defined possible states, but can’t exist in arbitrary states in between them, rather as a ball in a rugged landscape must roll to the bottom of one valley or another. We’ll see that this is true also of health and disease: there are many causes of illness, but their manifestations at the physiological and symptomatic levels are often strikingly similar."

e) Multilevel, mutlidirectional, and hierarchical organization:

"To understand how life works, there is no single place to look. You will never find all the explanations at (speaking both metaphorically and literally) a single level of magnification. What is more, each level in the hierarchy of life’s organization has its own rules, which are not sensitive to the fine details of those below. They have a  kind of autonomy. At the same time, influences can propagate through these levels in both directions: changes in the activity of  genes can affect the behaviors of whole cells and organisms, and vice versa."

f) Combinatorial logic

"It has been estimated that humans can discriminate between around one trillion odors. Quite what that number means is open to debate, but it is clearly very much larger than the mere four hundred different “receptor” molecules in our olfactory system: there is evidently not a separate molecular detector for each smell. The different odor sensations must arise from different patterns of activation of this relatively small set of receptors. That is, the smell signals our brains receive are combinatorial. Think, for comparison, of how just three light sources (red, green, and blue-violet) in visual display screens can create a whole gamut of colors through differences in their relative brightness. Molecular signals that are combinatorial, rather than relying on unique molecules to supply different outputs, are widely used in biology, probably because they are economical in component parts, versatile, adaptable, and insensitive to random noise: all of them attributes that serve life well."

g) Self-organization in dynamic landscapes

"Many things are possible in life, but not everything. Evolution does not select from an infinite  palette: there are specific patterns and shapes in space and time that arise out of the complex and dynamic interactions between the components of biological systems, much as there are common features of cities or animal communities, or of crystal structures or galaxies. Think of it rather like rain falling on a landscape: the water itself is not programmed to flow in any particular direction, but the shape of the landscape causes it to gather in some places and to move away from others. The language of landscapes, basins, and channels is often useful in biology."

h) Agency and Purpose

"Agency and Purpose is becoming something of a buzzword in some biological circles, especially those concerned with processes of cognition. The trouble is, no one seems able to agree on what it means. Intuitively, we might suspect that what distinguishes living organisms from nonliving matter is this notion of agency: they can manipulate their environments, and themselves, to achieve some goal. This makes agency inextricably linked to ideas about purpose. That is probably why the problem of agency has been (absurdly) neglected for so long in the life sciences, where questions of purpose have long been shunned as quasi-mystical teleology, perhaps only one step away from the dreaded concept of intelligent design. The result of this neglect and avoidance is that we can end up skirting around the most characteristic feature of all life. I propose that the time has come to embrace it—and that there is nothing to fear in doing so."

Perhaps thoughts: Life seems to follow the path of linear programming for optimum efficiency given the constraints of time, space and resources. Its objective function seems to be propagation, or life forward. To that objective everything seems to be aligned and seems to find lightening paths or optimum solutions in its particular local time-space geography. Dynamic optimum solutions, shifting as conditions shift.

i) Causal Power: 

"One of the biggest obstacles to understanding how life really works has been a failure to get to grips with causation. It’s a hard problem, not least because causation is a vexed topic in its own right; philosophers still argue about it. We already know from daily experience how difficult it is to decide what counts as a cause of a phenomenon. Are the words appearing on my screen being caused by the impacts of my fingers on the keyboard, by electrical pulses within my computer’s silicon chips, or by the more abstract agency of my thoughts and feelings? But these questions are not intractable, and we do have some conceptual and mathematical tools for handling them. Too often, causation in biology, as

indeed in the world in general, has been assumed to start “at the bottom” and filter up—so

that, for instance, characteristics at the level of an organism’s traits are deemed to be “caused” by genes. As we’ll see, we can gain a better understanding of how life works, and how to intervene in it effectively, when we take a more sophisticated view of biological causation."

Perhaps, perhaps in modern times, one can look at emergence rather than cause. Emergence seems to encompass more of the chain of causes that leads to particular effects. Rough-thoughts. People even say time is emergent, so is consciousness. Human life seems to be such a big sum of so many smaller parts, that anything that is, is an emergence.

***

And, for the temptation to regard a cell as a machine, he says the idea cannot be transferred linearly because the physical laws operating at molecular level are very different from physical laws operating at our level.

We should not expect the principles of our own machinery to translate in a straightforward way to the molecular scale, where the roles and even the nature of phenomena such as viscosity, friction, rigidity, and adhesion are very different. As philosopher of science Daniel Nicholson has said, "Owing to their minuscule size, cells and their macromolecular components are subject to drastically different physical conditions compared with macroscopic physical objects like machines, and . . . using machine metaphors to explain microscopic phenomena is consequently more likely to obscure and deceive than it is to elucidate and enlighten."