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The New Yorker Takes “A Journey to the Center of Our Cells”

Casey Luskin
Image credit: David S. Goodsell, RCSB Protein Data Bank. doi: 10.2210/rcsb_pdb/goodsell-gallery-042.

When I first started writing for Evolution News back in 2005, we were overwhelmed with media outlets misreporting on intelligent design and evolution. This was in fact one of the original reasons for launching Evolution News — to fact-check and critique media coverage. Every once in a while, however, it’s nice to highlight media stories that do a good job of covering science. 

A recent article in The New Yorker, “A Journey to the Center of our Cells,” says hardly anything about evolution and it says nothing about intelligent design. There’s no evidence that the article’s author or the scientists he interviews are sympathetic to ID. But it provides new insights into the complexity of the cell — insights that unwittingly pose a challenge to theories of a fully natural chemical origin of life. 

The article explains that biologists are beginning to “grasp the strangeness of the zone [inside the cell], bigger than atoms but smaller than cells, in which the machinery of life exists,” further noting that “It’s proteins that run the cellular world, by sparking chemical reactions, sending signals, and self-assembling into biological machines.” 

A Problem for Biologists

But there’s a problem that biologists have long pondered — how do proteins find other proteins within the cell that they are supposed to interact with and combine with to form these “biological machines” or perform necessary biochemical reactions? The article explains that the solution was thought to be random Brownian motion in cells, where molecules suspended in a liquid medium undergo random motions within a contained space, and eventually find their counterparts. Here’s how the article puts it:

For decades, biologists had assumed that activity in the cytoplasm was essentially random; the cellular world churned with such dramatic speed that the right proteins would eventually bump into one another.

Brownian motion was thought to guarantee that within a reasonable time, proteins and other biochemical molecules would find their requisite chemical partners and interact or self-assemble to produce whatever structure or pathway was needed. But new discoveries have changed this way of thinking. Again, from the article: 

But it turned out that some molecules in the cytoplasm weren’t randomly circulating. They were swirling in ways that brought related parties together. Suppose an important reaction involved five proteins out of ten thousand; the five tended to hang around one another, loosely attracted. (They sometimes had floppy regions that exerted a mutual pull, and which had been missed in images made of the proteins when they were in crystallized form.) Brangwynne and others found that, under the right conditions, groups of proteins could “phase separate,” like bubbles of oil in a salad dressing, forming structures. For decades, researchers had known that complex biochemical reactions tended to happen faster in living cells than in test tubes. Now they knew why: the lava-lamp-like conditions inside a living cell allow chemicals to take advantage of subtle attractive forces more efficiently than is possible in the looser and more uniform environment of a tube or a dish. We’ve long imagined a spark of life — but it could be the physical structure of cytoplasm that’s the key.

The “Humpty Dumpty Problem” 

The physical structure of the cytoplasm is of course an important aspect of the cell which exists outside of the DNA. It’s a form of initial structural conditions which effectively carry extra-genetic information that is key to cellular organization and cellular function. According to The New Yorker piece, it’s also key to understanding the enigma of what biologists have called the “Humpty Dumpty problem.” 

This concept was summarized in the textbook The Design of Life, where biologist Jonathan Wells and mathematician William Dembski write about a real experiment testing the idea of the unguided, chance assembly of a cell. First, a living cell is placed into a test tube filled with the appropriate nutrients. Then the cell is poked with a sterile needle so that its contents spill out into the solution. The test tube now contains all the materials needed for life — not just the amino acids, but the fully assembled proteins. Nevertheless, even with all the right materials present, the cell cannot reassemble itself. As Wells puts it in the textbook, origin-of-life researchers “have been spectacularly unsuccessful in putting Humpty-Dumpty back together again.”

The New Yorker article also references failures to resolve the Humpty Dumpty problem, and explains how the lack of a physical structure of the cytoplasm in the “popped cell” helps explain why researchers could never reassemble a cell into a functioning whole, even when all the necessary “parts” were seemingly present: 

This new understanding has begun to open doors. In 2017, Glass helped found the Build-a-Cell consortium — a steering committee for hundreds of labs that are trying to build a working cell from scratch. Researchers in the consortium began combining nonliving parts — proteins, ribosomes, RNA, and other molecular constructions — into membranes that resembled cells, hoping that the mixture would come to life by expressing genes, doing metabolic work, and eventually dividing. Drew Endy, a professor of bioengineering at Stanford who is one of Glass’s co-founders, described the group as trying to solve the Humpty Dumpty problem: could the parts add up to a whole? Such artificial cells could be used as living factories for the production of biofuels or drugs, or as hyperefficient sites of artificial photosynthesis. But although the right parts are there, none have crossed the border from nonliving to living. Endy’s group was experimenting with slightly different ingredients; if that failed, the problem might be in how they’re physically arranged. [Emphasis added.]

In other words, you could never simply generate a cell by having the right parts present. You also need a properly shaped cytoskeleton that can arrange those parts in a manner that allows reactions and pathways to proceed in a manner that keeps the cell alive. 

Lip Service to Evolution

The New Yorker article pays lip service to evolution, stating: “The human body contains brain cells and fingernail cells, blood cells and muscle cells, and dozens of species of single-celled bacteria. Each has been shaped to fit its niche by aeons of evolution.” But this idea is inconsistent with the implications of the report that it’s not just the parts that are needed for a cell to exist. Of course the parts are needed — they are necessary, but not sufficient for a living cell. Some organization apart from those parts is also needed. Thus, what this article nicely points out is that the parts must also be organized properly into a physical arrangement where the “physical structure of cytoplasm” ensures that the right molecules find one-another to foster cellular reactions that the cell needs. 

The importance of the physical architecture to the viability of any cell adds an elegant dimension of irreducible complexity to cellular operations and a major obstacle to natural, unguided chemical models for the origin of life.