A World From Dust (Plus): This is Water, Part 2: Water Swims Around Worms

 

Ever looked in the wrong place for something? It happens to scientists all the time.

It happened in a previous post, where it was noted that very different animals swim with the same motion through water, because they have evolved to converge on an identical, efficient movement through the fluid. The eye is drawn to the animal, but the common denominator and the explanation is found in the water surrounding the animal. The properties of the water shape the movement of the animal, and evolution is just the method of search for the movement of greatest efficiency.

This flips what you expect on its head. If you want to understand how an animal swims through water, you look at the animal, not the water, right? Wrong. It's more accurate to say the water is swimming around the animal, as it guides the animal and shapes its movements.

This is shown even more clearly in another paper, a recent PNAS study titled "Propensity of undulatory swimmers, such as worms, to go against the flow." Worms swimming near a surface turn against the flow, and the question is why and how they do this.

The eye is drawn to the worm. Maybe it has a sensor, "sees" the wall, and turns, right? Wrong. The flow field in the water turns the worm. In the sense, the worm is as passive as a leaf flowing in the river -- an undulating leaf, perhaps, but the water is the active agent and the cause here. Because the water causes the turning, this turning happens in widely different organisms. As the study puts it, there is no involvement of the worm's nervous system, and the turning of the worm "results from purely mechanical interactions."

As Adrian Bejan puts it when describing the similarities among flying animals, where the fluid that shapes the movements is the air, but the idea is the same:

"It is the inanimate fluid in the wake of the leading body that organizes itself. It does so using no brain power whatsoever, so that it may travel and spread itself the fastest through the stationary fluid." p. 240, Shape and Structure

This is air, and this is water. Each flows where it wills. Even when you don't see it, it shapes complex behavior into an efficient and predictable biology.

Book Review: Incomplete Nature by Terrence Deacon

It's been half a decade since I read a science book that inspired me this much. (The previous one was The Chemistry of Evolution by Williams and da Silva, and I've just written a full book inspired by that one.)* Deacon has built a dynamical theory of how things happen. By itself, that sounds kind of abstract, but he applies it to two mysteries that preoccupy my time: the origin of life and the workings of consciousness, or in short, evolution and mind.

The theory does appear to offer a possible ways forward on the first front, although I'm not as sure about the second, but that's not my primary area and I'm fascinated by the chemical possibilities. Deacon's take on physical chemistry and the nature of energy is solid enough and unique enough that I'm considering how to teach it in my physical chemistry course. Much better than I could do on neuroscience (Deacon's primary area), that's for sure.

As Deacon admits, this book is only a sketch, albeit a 545-page sketch. I could have used more. Since dynamical processes have particular structures, I could have used more figures to clarify some of Deacon's terms and "levels" of dynamics. Although the evolution and mind subjects are interrelated, I think we could have gotten one book on evolution and a second book on mind, and that would have left room to explore more side roads and give more examples. But I'm intrigued enough to come up with examples on my own.

The biggest ally left unenlisted may be theology. Apophatic theology involves double negatives and absential qualities like Deacon's work. Again, this is an open door for others to walk through. I think there's fruitful progress to be made in taking Deacon's ideas seriously and then using those as a basis for natural theology (a la McGrath, not a la Paley, of course!).

In sum, this is a book that I've only begun to soak in. It already makes the short list of "10 most influential books" in my life.


* Deacon and RJP Williams do both emphasize constraints, so much so that I'm already seeing new things by juxtaposing the two. My first public reflection on Williams was a lecture titled "The Chemical Constraints on Creation" no less!

A World From Dust (Plus): How Oxygen Stress Steers a Protein

This is part of a series of posts expanding and updating the book A World From Dust: How the Periodic Table Shaped Life. This post involves biochemical concepts such as protein structure.

Complex I of the respiratory chain is one of the crucial enzymes that ultimately helps you use the oxygen you breathe. It is the first funnel through which electrons are poured on their path to combining with oxygen. Part of this funnel is shaped by oxygen's unique chemical properties.

Enzymes like Complex I, called hydrogenases, first show up around Chapter 6 of A World From Dust, well before oxygen fills the atmosphere in Chapter 8.  Still, if any oxygen is around at all, they are shaped by it, because they must avoid oxygen's negative power. Oxygen reacts with stray electrons to form Reactive Oxygen Species (ROS) that shatter the insides of a cell.

If a hydrogenase drops too many electrons out of its "funnel", they are picked up by oxygen and make havoc-wreaking ROS inside the cell. Avoiding the negative consequences of oxygen shapes life as much as running toward the positive consequences of oxygen's energy.

This was shown in the recent study "Reactive Oxygen Species Production by Escherichia coli Respiratory Complex I" in Biochemistry. This study is built on a previous experiment in that increased the amount of electron-carrying "electron boxes" inside the cell called NADPH. Normally Complex I only gathers electrons from the NADH electron box through its funnel, but when there's high amounts of NADPH, it will evolve to accept NADPH as well. It does so precisely at the green sticks at the bottom of this figure:

(Figure provided in supplemental materials to the paper cited above)

 

The orange sticks are NADH, and the green sticks are placed exactly where the "P" is that makes NADPH different from NADH. If this enzyme is to bind NADPH, those green sticks must get out of the way. In the previous experiment, they did, evolving to alanine (A) and glycine (G).

 

The key to the new paper is where the green sticks didn't evolve to. Other green sticks still bind NADPH just as well as alanine and glycine. In particular, histidine (H) and glutamine (Q) were not observed, although they interact well with the P in NADPH and can even increase binding. So why were these perfectly capable mutations not observed?

 

The answer provided in this new paper is that, with histidine and glutamine, too many electrons fall off the NADPH, out of the funnel, and onto oxygen, making too many Reactive Oxygen Species (ROS). Because these are dangerous to the cell, the protein does not evolve in that direction, but rather evolves in the direction of alanine and glycine.

 

This can be summarized as the letters for these particular positions. In the "word" that is the enzyme, at this one position, we don't see "H" or "Q", but we do see "A" and "G", not because the enzyme works better with those two letters, but because the whole cell works better with those two letters.

 

Instead of four possibilities, evolution chooses two, and in this very small way, it is constrained by the need to avoid oxygen stress. This is a biochemical example of two important points of the book:

 

1.) Because of oxygen's chemical tendency to form ROS, the protein has fewer options at that position than it would otherwise. (It is constrained by oxygen's chemistry.)

 

2.) To understand why it's restricted, we must account for the oxygen stress on the whole cell, not just the efficiency of the one enzyme or the NADPH-binding properties of the one residue. (We must look at the higher level of the cell biology rather than the lower level of the biochemistry; the higher level constrains the lower.)

 

To cite the central metaphor motivating the book, if this tiny motif in the "tape of life" were replayed, we would still "hear" A and G, not H and Q. There is freedom for the system to select A or G, but not H or Q. The possibilities are constrained by the double-edged sword of oxygen stress, and the river flows in one direction, but not the other.