Carl Zimmer reports in the New York Times about a breakthrough in uncovering the early prehistory of the first complex cells. Publishing in the journal Nature, scientists say they have uncovered what might be evidence of an intermediate cell, a “missing link” as Zimmer calls it, that lies somewhere between bacteria — prokaryotes — and the first true eukaryotes, cells with multiple membrane-bound compartments.

This result is to be celebrated, if true, as it would represent a major advance in our knowledge about how such a momentous transition might have taken place. The deeper we go into the most inhospitable environments, the more we uncover ancient holdovers — living fossils, if you will. These organisms live in such inhospitable places perhaps because that is where they first appeared, or perhaps because that is the only place they can still survive and have an advantage against all the other more sophisticated organisms out there.

It’s a little soon to break out the champagne though. What they isolated from the mud deep under the ocean was DNA that has some resemblance to eukaryotes in some features but is missing other features. They haven’t gotten any cells to grow yet, so little more can be said.

Suppose it’s true? Does this mean that “evolution” happened? As always, it depends on what you mean by that word. Evolution in the sense of change over time — from simple to more complex to modern — is certainly possible, in which case we might expect to find such fossil creatures. What remains unanswered, though, is just how such change occurred — whether these evolutionary events could have happened by an unguided process. And I don’t mean guided by natural selection.

To make the transition from prokaryote to eukaryote, from an archaic cell to one with a nucleus, lysosomes, cytoskeleton, mitochondria, and chloroplasts, Golgi apparatus and molecular motors, just to name a few requirements, assumes the appearance of new structures made of new proteins. Getting new proteins from random sequence is quite rare — unless the protein is a simple, highly repetitive sequence with no structure and very little in the way of function, it won’t happen at all.

This kind of result does not explain the very things that call for explanation. What’s needed is a sophisticated, structured protein capable of complex interactions and chemistries. Only one out of 10⁷⁷ random sequences is able to catalyze a sophisticated enzymatic reaction. You could search a very long time to find a target that small.

But suppose a protein magically appeared that performed a true catalytic or structural function. Could it have been co-opted to another function by tweaking? The answer is no, unless the protein had low levels of the new function already, or only four or fewer mutations were required for its conversion. These numbers are based on experimental work and careful modeling of what a bacterial population can achieve in the time available (the age of the universe). So how many proteins have low levels of other functions waiting to be co-opted? One experiment said about 20 percent of metabolic enzymes tested could be substituted by another E. coli gene. That leaves 80 percent with no co-option partner available. That’s no way to build a metabolism.

Real experiments in real laboratories have demonstrated this over and over. I could cite paper after paper about the evolution of proteins but inevitably, if a conversion occurred, it required many more than four mutations, or the mutations were designed by a human mind, or the protein already had a low level of the target function. Many of these papers were billed as success stories, but all fell into the above categories.

I refer you to four papers that explain why this difficulty exists — one on the challenges facing protein evolution, one on the rarity of obtaining of new proteins with a particular function, and two (here and here) on the difficulty of co-opting old proteins to new ones.

I will leave you with two telling comments from Dan Tawfik, a researcher in the field of protein evolution. Speaking of the problem of co-opting proteins to new functions, he said “Nothing evolves unless it already exists,” and as to the rise of proteins in general, he said it is “something close to a miracle.”

Image: Sam Spiro / Dollar Photo Club.