When We’re Sixty Four (Thousand)

From the E. coli in the LTEE to the People of the Lab

[To be sung along to this Beatles classic]

 

When we get older, losing our fimbriae,

Many years from now,

Will you still be sending us our thiamine,

Birthday greetings, Erlenmeyer wine?

If we were mutants, crazy and fit,

Would that make you snore?

Will you still feed us, will you still freeze us,

When we’re sixty-four?

 

You’ll be older too,

And if you say the word,

We’ll evolve with you.

 

We could be handy, helping your pubs,

When your grants are gone.

You can write a paper by the fireside,

Weekend days give no time to hide.

Colonies growing, dotting the plates,

Who could ask for more?

Will you still feed us, will you still freeze us,

When we’re sixty-four?

 

Every summer you can buy a freezer when the space gets tight,

If it’s not too dear.

Save our clonal mix,

Plus and minus progeny,

Ara One to Six.

 

Keeping the notebook, pipetting each drop,

Track trajectories.

Indicate precisely what you think will change.

Hypothesize, test, unlimited range.

Give us your data, sequence and store,

Evolving evermore.

Will you still feed us, will you still freeze us,

When we’re sixty-four?

 

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Bacterial Niche Finally Defined

The following scholarly contribution comes from my wife Madeleine Lenski after conversing with her “sister” (my former postdoc) Valeria Souza.

For those with an itch for criteria,

Scratch this: What’s a niche for bacteria?

Don’t take me to task

If I answer “a flask” –

It’s a bitch from warm broth to Siberia.

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January 19, 2016 · 9:08 pm

A Life Well Lived, Part II

This second tribute to my father was written by my son Daniel, who gave me permission to post it here.

~~~ ~~~ ~~~

My dear Grandpa Gerry died yesterday at 91, at home near Seattle with Grandma Ann and three of my aunts by his side. He had a sharp and curious mind undimmed by age, and a kind and sympathetic ear despite his deafness. He enjoyed many years of good health, and I particularly remember his smile after he kept pace with my father during a long walk up a sand dune, in his late 70s.

Grandpa was born and raised in Washington, DC at a time when slabs of ice were delivered in horse-drawn carts, and kids could freely roam the White House grounds and all the embassies, sneak up into the Capitol dome, and surreptitiously feed bubblegum to monkeys through the bars at the National Zoo. I hope the statute of limitations on that particular incident has run out.

As a cryptographer in WW2, Grandpa encoded messages with geared machines weighing hundreds of pounds, surrounded by walls lined with dynamite, yet he also lived long enough to get the hang of touchscreens, to print out this XKCD cartoon and tape it to the side of his iMac, and most importantly to Skype with his great-grandchildren. He got a DNA profile done, and seemed kinda bummed to find out that he was probably not descended from Genghis Khan. In his career as a sociologist he studied religion and technology and critiqued totalitarian governments (topics as important as ever today), wrote several books, and figured out how to edit his own Wikipedia page. I remember more than once in recent years when I stayed up late talking about my life and work at Intel with Grandpa, only to find that he had woken up before me the next morning, brimming with new questions and ideas.

He was an old dog still learning new tricks. On October 30 we went to his favorite restaurant. I drove, but Grandpa pointed out all the shortcuts in the dark. When the waitress came by to take our drink orders, I expected he’d get his usual deer-in-the-headlights look and blurt out “Bud Light,” at which point I’d protest and order him something more interesting. But this time was different. Without missing a beat, Grandpa set down his menu, asked for a Mac and Jack Amber Ale, and turned to me silently with a twinkle in his eye.

~~~ ~~~ ~~~

My son Daniel, me, and my father Gerry in 2012

My son Daniel, me, and my father Gerry in 2012

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A Life Well Lived

My father died peacefully at his home near Seattle this morning, before dawn, at 91 years of age. Gerhard Emmanuel Lenski, Jr. was born (1924) and raised in Washington, DC. His father went by Gerhard, and my father went by “Gerry” (pronounced like Gary) his whole life. My father did his undergraduate and graduate studies at Yale University, with his undergraduate years interrupted by three years of service with the US Army Air Forces during World War II, most of which was spent in England as a cryptographer at a joint USAAF-RAF airbase.

After receiving his Ph.D. in 1950, my father joined the Department of Sociology at the University of Michigan, where he rose through the faculty ranks. In 1963, he moved to the University of North Carolina, where he was Alumni Distinguished Professor and served as department chair for several years. He retired in 1992. He wrote several important books including “The Religious Factor: A Sociological Study of Religion’s Impact on Politics, Economics, and Family Life” (1961), “Power and Privilege: A Theory of Social Stratification” (1966), “Ecological-Evolutionary Theory: Principles and Applications” (2005), and “Human Societies: An Introduction to Macrosociology” (1970), now in its 12th edition (2014). He served as vice president of the American Sociological Association, and as president of the Southern Sociological Society. His honors included a Guggenheim Fellowship, election to the American Academy of Arts and Sciences, and a Career of Distinguished Scholarship Award from the American Sociological Association.

In 1948, my father married my mother, the former Jean Cappelmann, a poet, and they had 4 children. They were active together in working for civil rights and against the Vietnam War. They were married for 45 years before my mother passed away in 1994. In 1996, my father married the former Ann Blalock, who was a close family friend and whose late husband Hubert “Tad” Blalock, had been a colleague of my father’s at both the University of Michigan and the University of North Carolina.

After moving to the Seattle area, my father enjoyed visiting northwest sites and cities including the Olympic National Park, Mount Baker, Portland (where my son lives), and Victoria; cheering on the Seahawks and Mariners; watching the ships on the Puget Sound; and talking with his children and grandchildren, always full of questions and ideas about technology and life.

My father was beloved by family and friends for his storytelling and humor – who can forget the story about the time he and a childhood friend gave their chewing gum to monkeys at the National Zoo? – as well as his deep knowledge of and appreciation for human history.

My father was fortunate to have lived a good and full life for 91 years, and I was very lucky to have him for almost six decades. I was also lucky to spend Thanksgiving with him, and we had the chance to share many stories that spanned his life—from baseball trivia to meeting his newest great-grandson in my father’s first-ever Skype.

Dad and Me on Dad's 90th

My father and me on his 90th birthday

ADDITION 1: Click here for a picture of my father from his days at UNC.

ADDITION 2: My son Daniel wrote a wonderful tribute to his Grandpa here.

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Representing Science to My Representative

My research is funded by the National Science Foundation, including the BEACON Center for the Study of Evolution in Action. BEACON is one of a dozen or so NSF Science and Technology Centers. Today, our Representative in the US Congress, Mike Bishop, came to BEACON for 40 minutes to discuss our center—what we do, what impacts our work has, and so forth.

It was something of a “fire hose” for Mr. Bishop, with several presenters trying to convey a lot of information very quickly.  However, he was engaged and asked thoughtful questions.  I think he left with an understanding of the importance of scientific and engineering research, including how fundamental curiosity-driven research can lead to applications.

I had 10 minutes to show him my lab and explain what we do and why.  When I make a short presentation like this one, I often write out a version in advance.  I don’t read it or memorize it by any means. However, writing it out helps get my thoughts in order—removing details that aren’t important, ordering ideas into a narrative, reminding me of what I most want to convey.

I’m sure I was not as clear or coherent as the text that follows.  I offer it here because it conveys the points I tried to make in the few minutes that I had as a representative of science speaking with a representative of the people.

~~~~~~~~~~~

I want to show you one of the experiments in my lab.  We call it the long-term evolution experiment. It’s an unusual experiment because it’s been running for over 27 years.  And we keep it going because it’s been a scientific goldmine leading to new discoveries about how bacteria change over time.

It’s important that we understand bacteria and how they evolve for many reasons. Bacteria are best known because some of them can cause dangerous infections. But many of them protect us against infections—if our guts were not filled with harmless bacteria, then the dangerous ones would have a much easier time getting established in our bodies. Some bacteria also provide nitrogen to plants and perform other essential functions in the environment, including degrading some of the wastes that we produce.  And some bacteria are the workhorses of biotechnology.

To give one example of why bacterial evolution is so important:  If bacteria didn’t evolve, we would have defeated nearly all the pathogenic bacteria on Earth with antibiotics.  But they do evolve and become resistant to our drugs, and so the pharmaceutical industry has to spend billions of dollars trying to keep up with the evolving bacteria and viruses by developing new drugs to treat infections.

It’s possible to see evolution-in-action in bacteria, like we do here, for several reasons.

  • Their populations are huge.  The number of bacteria in just one of these little flasks is comparable to number of people in the United States.
  • They grow really fast.  Every day, there are about 7 generations of bacteria in each of the flasks.  So each day we see the great-great-great-great-great grandkids, so to speak, of the bacteria that were in our flasks yesterday. After 27 years, the experiment has run for over 63,000 generations.
  • And one more important thing about bacteria. We can freeze them and bring them back to life, and so we’ve got a frozen fossil record of the experiment.

When I started the experiment in 1988, there was no human genome project, and not even a single bacterial genome had been sequenced.  Now we go into our freezers and sequence the bacterial genomes to see how their DNA is changing over time.

The work we’ve done in this curiosity-driven experiment has inspired others who are using similar ideas and approaches to understand the rates and mechanisms of how bacteria evolve.

I’ll give two quick examples that show how our NSF-supported fundamental science gets translated into applications that are important for security and health.

First, you remember the anthrax letter attacks on Congress that occurred right after the 9/11 attacks. In the first few days after the anthrax attacks, I was contacted by the Defense Threat Reduction Agency for advice on how to identify the source of the strain used in that bioterrorism, and how to distinguish it from other related strains. And in the months that followed, I was asked for and provided advice to the FBI and other agencies investigating the attacks. Tracking the source of microbes in outbreaks—whether natural or terroristic in origin—requires understanding how they change over time.

Second, my colleague Prof. Martha Mulks studies bacteria that colonize the lungs of people with cystic fibrosis (CF).  There are about 30,000 people with this disease in the US alone.  It’s an inherited disease that makes people susceptible to lung infections and, unfortunately, those infections kill many kids and young adults with CF.  Some of the bacteria that infect the diseased lungs are not pathogens to most of us—they’re bacteria that live in soil and on plants, but when they get into the lungs of CF patients they evolve and adapt to that new environment. They also evolve resistance to the antibiotics that are meant to get rid of them. How exactly the various bacteria change to become better adapted to the CF lung environment is not known. Luckily, though, Martha Mulks and other foresighted scientists and clinicians have kept frozen samples of these bacteria over the years—just like we’ve done with the long-term experiment I described a moment ago. Now the BEACON Center is supporting work by a graduate student, Elizabeth Baird, who will analyze the DNA from old and new samples and apply some of the same approaches and methods that we’ve used and developed for the laboratory experiment to see how the bacteria have changed—how they have become resistant to antibiotics and otherwise adapted to the environment of the lungs of people who suffer from cystic fibrosis.

The bottom line is that the fundamental, curiosity-driven research that the National Science Foundation supports is also an engine for future applications—often ones that we may not even have dreamed of—as well as a training ground for the talented and dedicated young people who you can see working all around us in this lab and throughout the BEACON Center.

~~~~~~~~~~~

Rep. Mike Bishop (MI-08) and me in the lab.  [Photo: Danielle Whitaker, MSU.]

Rep Mike Bishop and me in lab, 14 Oct 2015

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Lucky in Life, Prologue

I’ve been meaning to write for a long time about the role of chance … luck … whatever you want to call it … in life, from the grand sweep of evolution to our individual existence.

Well, just this morning, I came pretty close to demise by random genetic drift. Almost every weekday, I walk to and from work at Michigan State University. It’s a pleasant walk through pretty neighborhoods and the beautifully landscaped MSU campus.

Today was not much different from most other days. It had been sprinkling lightly, but no wind or anything out of the unusual.

I walked the route I usually take, crossing the streets by habit in more or less the same spots every time, I guess. The only moderately big road I cross is Grand River Avenue, where it intersects with Bogue Street. No problem on Grand River.

I walk down Bogue on the east side or the west side of the street depending on the traffic light, where cars are, on whimsy I guess. I was walking on the east side, though I would have to cross over to the west to get to the building where I work.

At this point in my walk, I’d guess that’s the side I’m still on maybe 80% of the time. Lucky today was one of those days. I heard a loud crack on the other side of the street. A tree limb snapped and crashed hard on the sidewalk.

Maybe half a second from snap to crash? And the limb was big and bifurcating, with two main branches, each maybe a foot in diameter. It came down straight, square and hard against the sidewalk. Even if you had an instant to react, it wouldn’t be clear which way to run to avoid one branch and not get smacked by the other.

I wasn’t the only lucky one. No one was there to get hit. A student was walking toward the spot, maybe 100 feet away. I called out something like “That was crazy, lucky you weren’t there.” He nodded and crossed to my side of the street.

It was only in walking the next couple hundred feet that I realized I had been lucky, too, to be walking this morning on the east side and not the west side of the road.

Indeed, each of us is incredibly lucky just to be here—the product of billions of generations of parents who were not only fit enough to survive and reproduce, but also lucky enough to have escaped the random drift of life and death.

The sidewalk

The break

[Both photos: Richard E. Lenski.]

Added November 1:  The second tree to come after me this autumn … or maybe I should say this fall.  This one was much smaller but fell just a few steps behind me on my morning run!

Me and tree 2

[Photo: Madeleine Lenski]

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63,000 Strong

Ever wonder about those big numbers posted in a window in that tall building on the east side of Farm Lane, across from the entrance to the MSU Dairy Store?

Right now, the digits read 63000. That’s the number of generations in an experiment that’s been running in my lab for over a quarter century.

We call it the LTEE, which stands for the Long-Term Evolution Experiment. There are 12 populations of E. coli bacteria in the experiment, and they all started from the same strain.

Every day—weekends and holidays included—a member of my team takes 1% of the cells in each population and puts them in a flask with fresh food. Over the next 24 hours, the population grows 100-fold and then runs out of food. These dilutions and renewals go on day after day, week after week, month after month, year after year, decade after decade. I hope the experiment will continue long after I’m gone, so that someday someone can write “and century after century.”

Bacteria grow by binary fission: 1 cell makes 2 cells, 2 cells make 4, 4 make 8, etc. So the 100-fold growth in the fresh medium represents about 6.6 doublings, or generations, every day. (There’ve been some interruptions since the LTEE began in 1988, but not many.)

Now consider a bacterial cell that gets a mutation in its DNA that lets it acquire more food and grow a little faster. That cell will leave more descendants than its competitors—that’s adaptation by natural selection. Over time, the bacteria are becoming stronger and fitter in their flask-worlds.

By watching the 12 populations evolve, we can answer questions about the dynamics and repeatability of evolution in a group of organisms—bacteria—that are essential for life on Earth as well as important players in health and disease. We measure the growth rates of the bacteria, we sequence their DNA, and we see just how much evolution can achieve even in short order.

Oh, about the sign. Zachary Blount is a talented postdoc who works on this project, and he likes to have fun with science. He put up the window display which, if you look closely, has a picture of Charles Darwin on the left, “The E. coli Long-Term Evolution Experiment” over the number, and “Generations and Counting” to the right. Every 1,000 generations or so, Zack updates the sign.

63K window

[Photo credit: Zachary D. Blount]

Note:   This piece first appeared at eastlansing.org after an invitation from Alice Dreger to explain the numbers in the window to our community.

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