THE LANDSCAPE OF OUR LIVES

      Before most people could even fathom the idea of mapping our genome, before we had the technology to map a cell’s entire epigenome and understand how it bundles DNA to turn genes on and off, the developmental biologist Conrad Waddington was already thinking deeper.

      In 1957, the professor of genetics, from the University of Edinburgh, was trying to understand how an early embryo could possibly be transformed from a collection of undifferentiated cells—each one exactly like the next and with the exact same DNA—to the thousands of different cell types in the human body. Perhaps not coincidentally, Waddington’s ponderings came in the dawning years of the digital revolution, at the same time that Grace Hopper, the mother of computer programming, was laying the foundation for the first widely used computer language, COBOL. In essence, what Waddington was seeking to ascertain was how cells, all running on the same code, could possibly produce different programs.

      There had to be something more than genetics at play: a program that controlled the code.

      Waddington conceived of an “epigenetic landscape,” a three-dimensional relief map that represents the dynamic world in which our genes exist. More than half a century later, Waddington’s landscape remains a useful metaphor to understand why we age.

      On the Waddington map, an embryonic stem cell is represented by a marble at the top of a mountain peak. During embryonic development, the marble rolls down the hill and comes to rest in one of hundreds of different valleys, each representing a different possible cell type in the body. This is called “differentiation.” The epigenome guides the marbles, but it also acts as gravity after the cells come to rest, ensuring that they don’t move back up the slope or hop over into another valley.

      The final resting place is known as the cell’s “fate.” We used to think this was a one-way street, an irreversible path. But in biology there is no such thing as fate. In the last decade, we’ve learned that the marbles in the Waddington landscape aren’t fixed; they have a terrible tendency to move around over time.

      At the molecular level, what’s really going on as the marble rolls down the slope is that different genes are being switched on and off, guided by transcription factors, sirtuins and other enzymes such as DNA methyltransferases (DNMTs) and histone methyltransferases (HMTs), which mark the DNA and its packing proteins with chemical tags that instruct the cell and its descendants to behave in a certain way.

      What’s not generally appreciated, even in scientific circles, is how important the stability of this information is for our long-term health. You see, epigenetics was long the purview of scientists who study the very beginnings of life, not folks like me who are studying the other end of things.

      Once a marble has settled in Waddington’s landscape, it tends to stay there. If all goes well with fertilization, the embryo develops into a fetus, then a baby, then a toddler, then a teenager, then an adult. Things tend to go well in our youth. But the clock is ticking.

      Every time there’s a radical adjustment to the epigenome, say, after DNA damage from the sun or an X-ray, the marbles are jostled—envision a small earthquake that ever so slightly changes the map. Over time, with repeated earthquakes and erosion of the mountains, the marbles are moved up the sides of the slope, toward a new valley. A cell’s identity changes. A skin cell starts behaving differently, turning on genes that were shut off in the womb and were meant to stay off. Now it is 90 percent a skin cell and 10 percent other cell types, all mixed up, with properties of neurons and kidney cells. The cell becomes inept at the things skin cells must do, such as making hair, keeping the skin supple, and healing when injured.

      In my lab we say the cell has ex-differentiated.

      Each cell is succumbing to epigenetic noise. The tissue made up of thousands of cells is becoming a melange, a medley, a miscellaneous set of cells.

      As you’ll recall, the epigenome is inherently unstable because it is analog information—based on an infinite number of possible values—and thus it’s difficult to prevent the accumulation of noise and nearly impossible to duplicate without some information loss. The earthquakes are a fact of life. The landscape is always changing.

      If the epigenome had evolved to be digital rather than analog, the valley walls would be the equivalent of 100 miles high and vertical, and gravity would be superstrong, so the marbles could never jump over into a new valley. Cells would never lose their identity. If we were built this way, we could be healthy for thousands of years, perhaps longer.

      But we are not built this way. Evolution shapes both genomes and epigenomes only enough to ensure sufficient survival to ensure replacement—and perhaps, if we are lucky, just a little bit more—but not immortality. So our valley walls are only slightly sloped, and gravity isn’t that strong. A whale that lives two hundred years has probably evolved steeper valley walls and its cells maintain their identity for twice as long as ours do. Yet even whales don’t live forever.

      I believe the blame lies with M. superstes and the survival circuit. The repeated shuffling of sirtuins and other epigenetic factors away from genes to sites of broken DNA, then back again, while helpful in the short term, is ultimately what causes us to age. Over time, the wrong genes come on at the wrong time and in the wrong place.

      As we saw in the ICE mice, when you disrupt the epigenome by forcing it to deal with DNA breaks, you introduce noise, leading to an erosion of the epigenetic landscape. The mice’s bodies turned into chimeras of misguided, malfunctioning cells.

      THE CHANGING LANDSCAPE OF OUR LIVES. The Waddington landscape is a metaphor for how cells find their identity. Embryonic cells, often depicted as marbles, roll downhill and land in the right valley that dictates their identity. As we age, threats to survival, such as broken DNA, activate the survival circuit and rejigger the epigenome in small ways. Over time, cells progressively move towards adjacent valleys and lose their original identity, eventually transforming into zombielike senescent cells in old tissues.

      That’s

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