Cells Recycle Their Own Garbage

An efficient system involving multiple complex parts
keeps a cell clean, new Darwin-free research reveals

The closer one looks at a biological system, the more wondrous it becomes. That principle has been the rule since Leeuwenhoek‘s eyes widened at the sight of thousands of previously-unknown “animalcules” living in a drop of water. It has only intensified in recent years thanks to super-resolution microscopy and revolutionary techniques for analysis.

Recently Jerry Bergman wrote about a new organelle in the cell that keeps a supply of phosphates available according to need. Now, another system for trash cleanup has been described in more detail than ever before. It involves a molecular nanomachine called the autophagosome. It takes garbage to the cell’s recycle bin: the lysosome.

A look into the heart of cellular waste disposal (Max Planck Institute for Multidisciplinary Sciences, 23 May 2023).

To prevent our body’s cells from overflowing with garbage and to keep them healthy, the waste inside them is constantly being disposed of. This cleaning process is called autophagy. Scientists have now, for the first time, rebuilt the complex nanomachine in the laboratory that starts this process – and it works quite differently from other cellular machines. The researchers’ new insights could help open up new approaches for the treatment of cancer, immune disorders, and neurodegenerative diseases in the future, and possibly even delay aging.

The press release tells how autophagosomes act like trash chutes that collect garbage in the cell and take it to the dumpster, the lysosome (“splitting body”) where the parts—proteins, lipids and carbohydrates get “digested” and recycled. Nothing is ever wasted, therefore; the amino acids from a spent protein can be used again. And when the cell is starving, it can even feast on the garbage. There’s more:

Autophagy also serves another important purpose. It renders harmless viruses and bacteria that successfully bypass the immune system’s defenses and reach the cell plasma. The consequences are correspondingly fatal if the autophagy process is faulty, too slow, or too fast. Neurodegenerative diseases and cancer can develop or disorders of the immune system may occur. Aging processes also appear to accelerate.

“Autophagy is a highly complex process involving many different proteins and protein complexes. We know many of them, but there are still fundamental gaps in our knowledge,” reports Alex Faesen, research group leader at the Max Planck Institute for Multidisciplinary Sciences in Göttingen. “How do the protein components work together? How is the process of autophagy started and stopped? When and where is the autophagosome assembled? That is what we want to find out.”

The process of autophagy [“self-eating”] has been known for a long time, but the nanomachine that does it was somewhat of a black box. One way to understand a machine is to take it apart and try to put it back together. That’s what these scientists did. It was a harder job than they expected: “a mammoth task for the entire research group, taking several years,” they said. Once they had the parts list, they tried to put the machine back together. Once they got the proteins into their complexes (like instruments of a marching band into their sections), the nanomachine assembled itself!

In the next step, the team brought the individual protein complexes together. “The complexes self-assembled into a protein supercomplex, the autophagy initiation complex. In fact, autophagy involves a sophisticated cellular nanomachine – and it works quite differently than previously thought,” the group leader says.

It’s different in that some of the proteins undergo a kind of “metamorphosis” in which they change form, becoming an on/off switch. The term conjures up images of a caterpillar changing into a butterfly. How do the proteins undergo a transformation of form?

But what starts the assembly of the autophagy machine, what starts it and what stops it? The researchers did not find a molecular “on” and “off” switch as in other molecular machines. Instead, the switch uses a highly unusual behavior of proteins: metamorphosis. ” Certain molecules, called ATG13 and ATG101, have the ability to fold in different 3D structures, thereby changing its ability to bind to proteins in the machine. “This protein metamorphosis also gives the go-ahead for the assembly of the autophagy initiation complex at the right time and in the right place,” says Faesen, describing the special features of the nanomachine. Without metamorphosis, the initiation machine does not assemble.

Within 20 minutes, the scientists say, the autophagosome is up and running, collecting trash and delivering it to the lysosome.

The work was published as: Nguyen et al., “Metamorphic proteins at the basis of human autophagy initiation and lipid transfer,” Molecular Cell, 19 May 2023.

This is exemplary scientific work, and especially good because it didn’t wander off into Darwinian storytelling. We often call out evolutionary biologists for that, because they should be ashamed for attributing elegantly engineered biosystems to the Stuff Happens Law. Here, the Max Planck team stayed out of origins, and revealed to the world new fascinating details about happenings going on in our bodies all the time—vital acts at a scale far too small to see without special techniques. The formal paper did not say anything about evolution, either. Bravo; we love good science and are happy to point out good examples like this.

Here were some highlights of their findings:

• • Multiple parts are required for assembly and operation of the machine.
  • These parts have to be at the right place at the right time.
    
  • Some of the parts have to re-fold (metamorphose) into a different shape to switch on assembly.
  • The complex of complexes is a super-complex! That speaks of irreducible complexity.
  • Once assembled, the super-complex machine goes right to work, as if it “knows” what to do.
  • The machine has to work at the right speed: not too slow, and not too fast.
  • When all the parts don’t work right, diseases can occur: cancer, neurogenerative malfunctions, or autoimmune diseases.
  • Recycling is a good thing, illustrated by how our cells keep a clean house.

A lesson from this good example is that Darwinism acts like a ball and chain on good science. Who needs it? It slows down understanding, requiring authors to come up with some kind of story to please the Darwin Party in the Big Science censorship room. Nobody needs that. Just the facts—tell us what you found, and how it works.

Supporters of creation and intelligent design can also use this example to clarify a misunderstood point; in academia, we are not advocating for researchers to praise God within their scientific papers or to pray before experiments, as some critics might allege. Just do everything normally but keep the Darwin narrative gloss out. Readers can make up their own minds about how these things came to be. It should be intuitively obvious to any honest reader that systems this well designed did not just happen.

If you are a follower of Christ, here is one more thing to be grateful for. As you live, work, and sleep, your cellular trash is being recycled throughout the trillions of cells of your body. You don’t even have to think about it. If they weren’t doing their job, you would find out quick: you might get deathly sick or die. As Glicksman and Laufmann emphasize in their book Your Designed Body, there are a thousand ways to die, but only one way to live: that’s for all your body’s systems to be working almost perfectly all the time.

Now that you know, thank your Creator specifically for thinking of everything, including trash collection and recycling in your body’s cells. Maybe what we learned today contains some morals for us, too: Waste not, want not; and: Cleanliness is next to godliness.