Mechanisms of evolutionary saltation

 kw: book reviews, nonfiction, evolution, development, evo-devo, dna, molecular biology

It took Stephen Jay Gould twenty years to write The Structure of Evolutionary Theory. It will take me longer than that to read it. I bought a copy when it was released in 2002, and I am only one-third of the way through it. I intend to read it all.

You may know that Dr. Gould is one originator of the hypothesis of Punctuated Equilibrium: fossils show that species tend to persist almost unchanged for periods of a million years to tens of millions of years, and then undergo rapid change, during which new species arise quickly. His book discusses this matter, and much more, in a historical context. I probably haven't come to the "good bits" yet. But others have, and scientists continue to discover new aspects of genetics and evolution, so I read widely in the field.

A stellar new volume is Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA, by Neil Shubin, a researcher and professor of Organismal Biology and Anatomy. His book outlines certain events in the history of evolutionary thought and genetic discovery, with an emphasis on a seminal thought expressed by one of his mentors, "Things didn't start when you think they did."

For example, he discusses wings and flight. Flight arose at least four times, in insects, pterosaurs (reptiles), bats (mammals), and birds. In each case, wings didn't appear all at once, but we find that earlier tissues and structures with different functions were co-opted to become wings, in a rather short time span. Furthermore, by digging into the genetics of wing development, he and others have found that the precursors to wings have similar origins in these very different types of animals. I can't do justice to an explanation of this. The book's discussion is brief yet illuminating. Bottom line: structures that could later become wings were developed long ago, for other purposes, and only millions of years later did the new function of "catching air" arise, requiring comparatively modest further development.

Another example every school child of my generation learned (do they still?): lungs developed from flotation bladders in fish. Whether the bladder developed a connection to the mouth by accident or for another reason, once that occurred, the already-existing practice many fish had of gulping air when the oxygen supply in the water was low, when combined with a new place to put that air, allowed these fish to survive better. Also, fins in some fish species were modified with "lobes", and these precursors of legs were used to move along the bottom of a lake or stream. "Walking" in this way keeps the animal below the worst of currents that it wants to move against; only later were the "legs" used to move onto and across the land, and eventually they were strengthened into legs strong enough to support amphibian bodies.

The pace of evolutionary development was very slow long ago, but has been accelerated over time with various developments. The first living things were like bacteria, or perhaps their cousins, the archaea. These together are called prokaryotes ("before the nucleus"): a prokaryote cell's DNA is a loosely-wound loop that runs throughout the interior of the cell. After a half billion years of gradual proliferation, some prokaryotes developed photosynthesis. Before that all life was chemosynthetic, using processes such as robbing sulfur from metal sulfides for energy. There are several kinds of photosynthesis; only one, initially, used CO2 and water to produce sugar, with oxygen (O2) as a waste product. Today's cyanobacteria (also called blue-green algae) are descended from O2-producing bacteria that arose about 3,500 million years ago.

At first, all the excess oxygen was used up by oxidizing sulfides into oxides and sulfates. This slowed down after another billion years, and oxygen began accumulating into the atmosphere. From 2,500 million to 1,500 million years ago, during the "boring billion", O2 slowly increased to about 2%. Then things began to change more rapidly. About that time, or perhaps a few hundred million years earlier, more complex cells developed. The DNA was encapsulated inside its own membrane, and at least two events of engulfment happened. Most probably the first "guests" invited into a larger cell (or they were invaders that were subdued and enslaved) were cyanobacteria, which were put to work turning air into sugar, while being kept safe inside the cell. Now they are called chloroplasts. Almost immediately, the second event was the capture of certain small, energy-efficient bacteria that probably looked a lot like E. coli. These became mitochondria. These larger, compound types of cell are called eukaryotes ("good nucleus"). A discussion of this process on pp 195-6 seems to imply that plants have chloroplasts but not mitochondria; not so, they have both. They need both!

Single-celled eukaryotes are still with us, most familiarly in the form of protozoa such as Amoeba and Paramecium. Some time before 1,000 million years ago, molecular mechanisms that were being used to attach to a substrate or to food particles before "swallowing" them, were re-purposed to allow cells to cling together. In the book a lovely discussion of choanoflagellates discusses how this works. The earliest multi-cellular creatures, whether they were proto-plants (with chloroplasts) or proto-animals, had a variety of shapes, but mostly looked quilt-like or mat-like. Some time around 600 million years ago an organizing principle arose. To introduce it, we must look into segmentation.

The prototype of segmented animals is the earthworm. You can see the segments, a lot of them. We vertebrates are segmented also. Our spine expresses the segmentation. Not all animals are segmented; in fact most phyla are not, but all have some kind of body plan. The Homeobox, or HOX, genes are controllers of body plan development. Every animal species has them. The HOX genes are organizers, and represent a kind of meta-control. The simple idea that we have "a gene" for this or that is a big distortion. Even in a simple animal such as a 1mm nematode, there are HOX genes that make the difference between front and rear and so forth. The more complicated sets of HOX genes found in more complex animals arose from reduplication.

Reduplication is a big theme in genetics. The added sets of HOX genes we need are an example. Mutation isn't a matter of creating a new, complex function out of whole cloth. It proceeds by various errors of copying, which will usually just kill the animal, but occasionally are at least mostly harmless, and over time, the odd bit can gain a new function. The most common mutations are single-point changes, such as from an A to a G in the genetic code. But whole segments can be duplicated, particularly during the "crossover" that occurs during the production of eggs and sperm. If an extra set of HOX genes is produced, one set can go its merry way, controlling the body's development, while the other set is modified and can lead to an extra function or body part or even whole section. Again, this isn't usually good for the animal, but it can be.

Segmentation arose by reduplication. In some cases, many identical segments were produced (earthworm). In others, the segments became specialized. The HOX genes control all this. The illustration, from this article at Socratic.org, compares the HOM genes (as they are called for insects) with the multiple sets of HOX genes in humans and mice. The segmentation of the insect's body is emphasized in the drawing.

It may seem strange that we share this organizing principle with fruit flies, mice and everything else. From an evolutionary perspective, it makes sense. The system works, and we can see that it works, for it has produced millions of species of animal.

Now to the matter of saltation, as in this review's title. Saltation is a dirty word to most evolutionists. It has come to mean things like a rabbit suddenly "evolving" into a dog or a horse. That's ludicrous.

In a proper sense, saltation means "jumping", and the concept (if not the term) had to be coped with once Barbara McClintock discovered jumping genes in corn. They have since been found in every species, and certain kinds of them form much of the "junk DNA" found between the genes in our genome. But others have been put to use, and HOX may be an example.

Just by the way, there's a lot less "junk" in our DNA than early reports claimed. Just 2% of it codes for proteins. An additional 2% (perhaps much more) consists of regulatory sequences that control when and how the genes make those proteins, a further 8-10% consists of deactivated viruses, which form a "library" of stuff gathered from everywhere, that can be re-purposed. Some is apparently second- and third-level regulatory stuff. About 2/3 is "palindromic repeats" (such as AATTGCACGTTAA) that consist of head-to-toe copies of "stuff", which at the moment, is at least useful for landmarks used by CRISPER/CAS gene editing.

All these things, and many more discussed in the book, are mechanisms for more rapid evolutionary change, compared to waiting for single-letter mutations to accumulate. Even over millions of years, that process is dreadfully slow. The beauty of these mechanisms, still being discovered, is that they allow big changes to occur without disaster.

The Earth would seem quite full of many species, were there only a few tens of thousands of them. It is astonishing that there are millions! I work in the "shell room" of a museum, and every time I open a cabinet I see something new, just among the mollusks! That room contains specimens for more than 20,000 species...of seashell! Nearly 100,000 are known. It seems that life, having figured out how to spin out new kinds of creatures, is still ramping up. While we may be driving thousands of species to extinction, it is likely that new species are arising even faster. If we attain wisdom enough to let nature alone and "live lightly", we may see even more variety in the multiplicity of life in the future.