unnoticeable—an extra D, perhaps, in a chord that doesn’t need that note. Embedded in so many perfectly played notes, hidden among an otherwise flawless chord in an otherwise perfect melody, it’s nothing to worry about. But then, a few minutes later, it happens again. And then, with increasing frequency, again and again and again.
It’s important to remember that there is nothing wrong with the piano. And the pianist is playing most of the notes prescribed by the composer. She’s just also playing some extra notes. Initially, this is just annoying. Over time it becomes unsettling. Eventually it ruins the concerto. Indeed, we’d assume that there was something wrong with the pianist. Someone might even rush onto the stage to make sure she is all right.
Epigenetic noise causes the same kind of chaos. It is driven in large part by highly disruptive insults to the cell, such as broken DNA, as it was in the original survival circuit of M. superstes and in the old yeast cells that lost their fertility. And this, according to the Information Theory of Aging, is why we age. It’s why our hair grays. It’s why our skin wrinkles. It’s why our joints begin to ache. Moreover, it’s why each one of the hallmarks of aging occurs, from stem cell exhaustion and cellular senescence to mitochondrial dysfunction and rapid telomere shortening.
This is, I acknowledge, a bold theory. And the strength of a theory is based on how well it predicts the results of rigorous experiments, often millions of them, the number of phenomena it can explain, and its simplicity. The theory was simple, and it explained a lot. As good scientists, what we had left to do was to try our best to disprove it and see how long it survived.
To get started, Guarente and I had to get our eyes on some yeast DNA.
We used a technique called a Southern blot, a method of separating DNA based on its size and conformation and lighting it up with a radioactive DNA probe. In the first experiment, we noticed something spectacular. Normally, the rDNA of a yeast cell that is made visible by a Southern blot is tightly packed, like a new spool of rope, with a few barely visible wispy loops of supercoiled DNA. But the rDNA of the yeast cells we’d created in our lab—the Werner mutants that seemed to be aging rapidly—were madly unpacking, like a vacuum-sealed bag of yarn that had been ripped open.
LESSONS FROM YEAST CELLS ABOUT WHY WE AGE. In young yeast cells, male and female “mating-type information” (gene A) is kept in the “off” position by the Sir2 enzyme, the first sirtuin (encoded by a descendant of gene B). The highly repetitive ribosomal DNA (rDNA) is unstable, and toxic DNA circles form; these recombine and eventually accumulate to toxic levels in old cells, killing them. In response to DNA circles and the perceived genome instability, Sir2 moves away from silent mating-type genes to help stabilize the genome. Both male and female genes turn on, causing infertility, the main hallmark of yeast aging.
The rDNA was in a state of chaos. The genome, it seemed, was fragmenting. DNA was recombining and amplifying, showing up on the Southern blot as dark spots and wispy circles, depending on how coiled up and twisted they were. We called those loops extrachromosomal ribosomal DNA circles, or ERCs, and they were accumulating as the mutants aged.
If we had indeed induced aging, then we would see this same pattern emerge in yeast cells that had aged normally.
We don’t count the age of a single yeast cell with birthday candles. They simply don’t last that long. Instead, aging in yeast is measured by the number of times a mother cell divides to produce daughter cells. In most cases, a yeast cell gets to about 25 divisions before it dies. That, however, makes obtaining old yeast cells an exceptionally challenging task. Because by the time an average yeast cell expires, it is surrounded by 225, or 33 million, of its descendants.
It took a week of work, a lot of sleepless nights, and a whole lot of caffeinated beverages to collect enough regular old cells. The next day, when I developed the film to visualize the rDNA, what I saw astounded me.17
Just like the mutants, the normal old yeast cells were packed with ERCs.
That was a “Eureka!” moment. Not proof—a good scientist never has proof of anything—but the first substantial confirmation of a theory, the foundation upon which I and others would build more discoveries in the years to come.
The first testable prediction was if we put an ERC into very young yeast cells—and we devised a genetic trick to do that—the ERCs would multiply and distract the sirtuins, and the yeast cells would age prematurely, go sterile, and die young—and they did. We published that work in December 1997 in the scientific journal Cell, and the news broke around the world: “Scientists figured out a cause of aging.”
It was there and then that Matt Kaeberlein, a PhD student at the time, arrived at the lab. His first experiment was to insert an extra copy of SIR2 into the genome of yeast cells to see if it could stabilize the yeast genome and delay aging. When the extra SIR2 was added, ERCs were prevented, and he saw a 30 percent increase in the yeast cells’ lifespan, as we’d been hoping. Our hypothesis seemed to be standing up to scrutiny: the fundamental, upstream cause of sterility and aging in yeast was the inherent instability of the genome.
What emerged from those initial results in yeast, and another decade of pondering and probing mammalian cells, was a completely new way to understand aging, an information theory that would reconcile seemingly disparate factors of aging into one universal model of life and death. It looked like this:
Youth → broken DNA → genome instability → disruption of DNA packaging and gene regulation (the epigenome) → loss of cell identity → cellular senescence → disease → death.
The implications were profound: if we could intervene in any of these steps, we might help people live longer.
But what if we could intervene in all of them? Could we stop aging?
Theories must be tested and tested and tested some more—not just by one scientist but by many. And to that end, I was fortunate to have been put onto a research team that included some of the most brilliant and insightful scientists in the world.
There was Lenny Guarente, our indefatigable mentor. There was also Brian Kennedy, who started the yeast-aging project in Lenny’s lab and has since played a tremendously important role in understanding premature aging diseases and the impact of genes and molecules that increase health and longevity in model organisms. There were Monica Gotta and Susan Gasser at the University of Geneva, who are now some of the most influential researchers in the field of gene regulation; Shin-ichiro Imai, now a professor at Washington University, who discovered that sirtuins are NAD-utilizing enzymes and now does research into how the body controls sirtuins; Kevin Mills, who ran a lab in Maine, then became a cofounder of and chief scientific officer at Cyteir Therapeutics, which develops novel ways to fight cancer and autoimmune diseases; Nicanor Austriaco, who started the project with Brian, now teacher of biology and theology at Providence College, a great combo; Tod Smeal, chief scientific officer of cancer biology at the global pharmaceutical company Eli Lilly; David Lombard, who is now a researcher in the field of aging at the University of Michigan; Matt Kaeberlein, a professor at the University of Washington, who is testing molecules on dog longevity; David McNabb, whose lab at the University of Arkansas has made key and lifesaving discoveries about fungal pathogens; Bradley Johnson, an expert on human aging and cancer at the University of Pennsylvania; and Mala Murthy, a prominent neuroscientist now at Princeton.
Again and again I have been greatly privileged in the matter of those who work around me. And that was never truer than it was in Guarente’s lab at MIT. It was a dream team, and I often felt humbled by the people with whom I was surrounded.
When
