A Small Correction

Since transferring the LTEE to Jeff Barrick’s lab at UT-Austin in 2022, we’ve been going over the old lab notebooks, making sure everything looks good. It turns out, though, that I made a small error when I started the LTEE back in 1988. I thought that transferring 10 ml into 10 ml was a hundred-fold dilution because there’s a 0 right there after each of the 1s, and 100 has two zeros. QED: a hundred-fold dilution. Right?

Well, it turns out I was a bit off. That’s only a two-fold dilution because, apparently, the correct way to do the math is 10 / (10 + 10) = 1/2. Who knew? New math, I guess. Anyhow, everyone in the lab thought I had figured it out, since I was the perfesser, and they just kept doing the same thing all these years. So instead of 75,000 generations, it was only something like 11,250 when we sent the stupid amazing LTEE to Taxes. Oh well, still a big number.

We also discovered another tiny error. You know, I always thought some sucker hard-working student came in and did the transfers on weekends and holidays. I never quite knew who it was, but I figured someone did the unpaid work transfers. Well, it turns out, not so much. OK, never. Fridays were ok at 40%, and Mondays were even better at 53%. On Tuesdays, we maxed out at 73%. Not bad! We trailed off a tad at 59% and 47% on Wednesdays and Thursdays.

Anyhow, after correcting for these tiny oversights, the LTEE had gone past 4,300 generations before we sent it down to Taxes. Speaking of Taxes, I hope I don’t get audited again this year. But I hear you can stall if you’re a big shot. Being a PI qualifies, right?

The LTEE Returns to MSU

You will remember that the LTEE moved to Jeff Barrick’s lab at UT-Austin this past June. My understanding was that things were going pretty well down there, and that the generations were clicking along nicely.

Well, guess what just came in the mail today? Boxes upon boxes of frozen samples, and 12 tiny flasks sealed with parafilm and packed in bubble wrap. And a hand-written note from Jeff, with a picture enclosed.  The note reads:

Hi Rich,

This LTEE of yours is just too much work. Day in and day out for almost a year, we’ve transferred the 12 lines to fresh medium, just like you said we should. But when we look at the cells under the microscope, they’re still just little bacteria – not even a decent yeast cell among them, much less a worm or something more interesting.

And all I have to show for it is a broken arm from doing all that pipetting, after everyone else quit. So, I’m sending back all those boxes and boxes of frozen samples that you foisted on sent us last year, along with the 12 lines as of when I last transferred them, maybe a week or two ago. I’m not sure of the exact number of generations, because we lost count a while back. But I’m pretty sure it started with a 7.

Good luck continuing this fool’s errand the LTEE back in your lab. Maybe you’ll eventually see something interesting, but I doubt it.

Jeff

So, there you have it. The LTEE has returned to MSU. I hope Devin is ready to do the next few hundred daily transfers!           

[Jeff, with cast, and Emmanuel celebrate sending the LTEE back to MSU] 

A Change in Plans

Back in February, I wrote about our plan to move the LTEE from here at MSU to Jeff Barrick’s lab at UT-Austin later this year. 

Well, Jeff told me he’s had a change of heart. When he explained to his lab team that the lines required daily transfers that included weekends and holidays, everyone went totally berserk and threatened to resign then and there. And if that happened, Jeff would have to do all the transfers himself, 365 days a year. 

Jeff is a hard worker … or at least he used to be. But he’s a professor now. Like me, I’ll bet he doesn’t even know where the pipette tips and clean flasks are stored in his lab, much less how to make the culture medium from all those jars of chemicals with strange names. 

With that painful possibility in mind, Jeff called me up, and he said we’d have to keep the LTEE going here. I was kind of annoyed because I was in the middle of doing Wordle, and for some reason it wouldn’t accept “ecoli” as a guess. But despite all that, I said ok to Jeff.

So yesterday, when I told the people in my lab that we’d have to keep doing the transfers until I found another sucker lab to take over, everyone here went totally berserk and threatened to resign on the spot. To calm everyone down, I had to promise that today we’d stop the LTEE, empty out the freezers, and autoclave all of the samples.

But that’s no big deal, because we’ve already learned more than any other secular lab in the world about why evolution never does anything interesting. After all, the little buggers are still just bacteria, despite a possible glimpse of something slightly more interesting around this time last year.

Patience Finally Rewarded in the LTEE

The LTEE has run for over 33 years and more than 74,000 generations. But we had almost nothing to show for all the hard work, until something fantastic happened last night.

Until last night, only one of the 12 lines had done anything even vaguely interesting: It figured out how to consume citrate—lemonade, basically. And it took them years to do even that simple trick.

And as some incredibly astute commentators have pointed out, even those citrate-eaters are still bacteria, just as they were when I started the experiment in 1988.

In fact, they’ve been bacteria for over 6000 years, according to the calculations of James (Jimmy the Bishop) Ussher, who placed the start of the creation at “the entrance of the night preceding the 23rd day of October [in] the year before Christ 4004.”   

It’s too bad that Ussher didn’t just make it Saint Patrick’s Day. That way, we would at least all remember to celebrate that pretty special day. After all, Ussher was an Irish Primate.

Well, speaking of primates, guess what Devin discovered in one of the LTEE flasks when he went to do the transfers this morning?  Monkeys!  Yes, monkeys!!

Not quite the primate sort of monkeys, though.  No, these were Sea-Monkeys!

With hindsight, I should have realized that with a liquid culture medium, we would evolve aquatic animals, not terrestrial ones. Maybe if we put some of those little plastic trees inside the flasks we could evolve real monkeys. 

Time to restart the LTEE, this virus be damned

The LTEE ran for over 32 years and more than 73,000 generations, without missing a beat. Then this stupid coronavirus came along and made me shut down the lab and stop the experiment. Well, I think it’s high time for everyone to return to the lab and get back to work.

We’ve wasted a hell of a lot of time here.  The LTEE lines were frozen on March 9th.  That’s 23 days ago, for crying out loud.  Do you know how many generations have been lost?  With 100-fold daily dilution and regrowth, that’s ~6.7 generations per day.  So we’ve already lost over 150 generations. And with 12 populations that’s a net loss of more than 1,800 generations.

Another way of looking at it is that each population produces around half a billion new cells each day.  So that’s 23 x 12 x 500,000,000 cells that went missing. You get the picture, that’s a sh*t-load (a technical term for those of us who study E. coli) of baby bacteria that never got born!

I’ve gotten in enough trouble already with a certain crowd for our claim to have observed evolution. If they find out we’ve denied these adorable baby bacteria their existence, there’s no telling what letters they might send me.

Plus, speaking as a scientist, I have this premonition that something really big would have happened during those missing generations. I’ve been expecting them to evolve the ability to produce palladium from citrate. They could then use the palladium for cold fusion, which would surely get some attention. Stupid virus!

Heigh-ho, heigh-ho, it’s back to work I go.  I sure hope you have a nice day at home.

Oh, never mind

 

 

Closing up shop

UPDATED to add incredible breaking news from Prof. Neil Shubin at the University of Chicago!

The LTEE has been running for more than 31 years and over 71,000 generations. It’s time to close up shop, as of today.

It’s been a hell of a lot of work, and we have almost nothing to show for it. As some brilliant commentators have noted around the web, the creatures in the flasks are still just bacteria—creatures, just as they were created.

If you read the first LTEE paper*, you’ll see we predicted the bacteria should become yeast by about 5,000 generations, nematodes at 15,000 generations or so, and fruit flies by 30,000 generations, maybe 35,000 at the outside.

After that, we’d have to stop the experiment anyhow, because we wouldn’t be able to freeze and bring them back alive any longer.

Plus, we’d have to get IRB approval for human experimentation if we ran it much past 50,000 generations.

Well, we’ve given the LTEE all this time, and still … they’re just bacteria. Same old same old.  I guess we’ve proven that Charles Darwin was wrong after all.

As an astute reviewer pointed out when we submitted that first paper, “I feel like a professor giving a poor grade to a good student …” I should’ve listened and quit way back then. It would’ve saved everyone a lot of time and effort.

Now it’s going to be a hell of a lot of work next week emptying the freezers and autoclaving all those samples.

Anyone need some old flasks?

UPDATE: It seems that I’m not the only scientist who was fooled by that Charles Darwin fellow.  Even Prof. Neil Shubin seems to have fallen hook, line, and sinker for the theory of evolution.  

*Lenski, R. E., M. R. Rose, S. C. Simpson, and S. C. Tadler. 1991. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. American Naturalist 138: 1315-1341.