Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source

Richard Lenski set up twelve flasks of E. coli B back in 1988. They were allowed to grow overnight in minimal medium containing 139μM glucose and 1,700 μM citrate. The glucose was the only carbon source that the parent strain could use and it limited growth of the cultures. The citrate was present as a standard chelating agent. The bacteria could not take up citrate and use it as an additional carbon source.

Every day the culture was diluted by transferring one ml to 99 ml of fresh medium (1/100). There were 6.64 generations per day or 2,423 generations per year (slightly more in a leap year).

These cultures were under strong selective pressure. Individual bacteria that could grow faster would out-compete other bacteria in the culture and take over. Lenski expected that each culture would show a variety of different solutions to the selective pressure with many common mutations and many that could be unusual.

Ask a stupid question ... can anyone guess the answer?

I just love the IDiots. They never cease to amaze, and amuse, me. Here's the latest from David Klinghofer at: Intelligent Design as an Orange Flag.

The mention of ID seems to give many writers and commentators what they regard as a green light to blather on without taking a moment to grasp what they're writing about. Denouncing ID is one thing. Denouncing it without comprehending what the phrase refers to, which is amazingly common, is quite another.

I continue to find this amazing. What other subject, both controversial and somewhat recondite, seems to license apparently smart people to write and speak in such an uninformed way?

Gee, I wonder what other subject causes apparently smart people to behave like IDiots? What other subject gives people a green light to blather on when they don't have the slightest clue what they are talking about? Is there another subject that some people denounce without comprehending what it means? Hmmm .....

Can anyone think of such a subject?

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Was Louis Agassiz better in the concrete?

Back in the nineteenth century (i.e. more than one hundred years ago) there was a biologist named Louis Agassiz who didn't like Darwin's radical ideas about evolution. Agassiz, a very famous professor at Harvard, thought that there were major gaps n the fossil record and he lamented the apparent lack of transitional fossils. What he was looking for were fossils of direct ancestors of modern species and not their close cousins.

Stephen Meyer thinks this old debate is still relevant today so he writes it up in Darwin's Doubt as if nobody in the past one hundred years ever thought of an explanation. It fooled Denyse O'Leary (not hard) so she blogged about it today [Louis Agassiz: The selective incompleteness of the fossil record].

This reminds me of a famous photograph of the statue of Louis Agassiz embedded upside down in the courtyard in front of the zoology building at Stanford University. The statue tumbled from its place above the entrance during the San Francisco earthquake of 1906.

According to legend, a passing scientist remarked that,

Louis Agassiz was great in the abstract but not in the concrete.¹

Actually, it would be even better to say that Agassiz looks better in the concrete than in the abstract [see Agassiz in the Concrete and Persecution of Religious Scientists]. By the 1920s (earlier in Europe) Agassiz's reputation had been severely damaged by his willingness to let religious convictions dictate his science.²

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1. The story is apocryphal (a polite word for "false"). The quotation has been attributed to several men, including the President of Stanford, but all have denied it. Nevertheless, it's too good a story to abandon just because it happens to be untrue!

2. Stephen Jay Gould held the Alexander Agassiz Professor of Zoology Chair at Harvard from 1982 until his death in 2002. Alexander Agassiz was Louis Agassiz's son. Alexander served as President of the National Academy of Sciences.

Monday's Molecule #225

Last week's molecule was EF-Tu (elongation factor-thermo unstable). EF-Tu binds to all tRNA molecules in the cell and helps position them in the A-site of the ribosome-mRNA complex during protein synthesis. Its release is coupled to GTP hydrolysis. Eukaryotes contain homologous proteins with different names (e.g. EF-1α). The winner was Jon Nuelle from Texas. The undergraduate winner was Ariel Gershon for the second week in a row.

Today's molecule (below) is an intermediate in a very important pathway that's only found in some species. This is one of those times when you need to supply the common name AND the correct scientific name that specifies the exact molecule shown in the figure.

Email your answer to me at: Monday's Molecule #225. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

Carnival of Evolution #66: The Day of the Doctor

This month's Carnival of Evolution is hosted by none other than John Wilkins. He's a philosopher but don't let that put you off. He blogs at Evolving Thoughts although from time to time he threatens to stop blogging. Encourage John by visiting The Day of the Doctor of Evolution: CoE #66.

The "Doctor" in the title is a reference to Dr. Who. Apparently John watched the first episodes in 1963!! "Who" knew that he was even born in 1963?

I was eight years old in late November 1963. I didn’t pay much attention to the TV news – some guy had been shot or something, and I wasn’t to know that C. S. Lewis had died until much later – but I was instantly taken by the eerie sound of the opening music of a new show. Yes, it was the very first episode of Dr Who, in glorious monochrome! I was a Whovian from the beginning, before it was cool. I’m so hip…

If you can't name the blue thingy on the right then you probably never win trivia games.

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Elizabeth Pennisi writes about Richard Lenski's long-term evolution experiment

Elizabeth Pennisi has written about the long-term evolution experiment of Richard Lenski [The Man Who Bottled Evolution]. The experiment is in it's 25th year and it is entirely appropriate that Science magazine devotes several pages to describing the results. There have been some remarkable discoveries.

But I want to focus on a couple of things that Pennisi says in her article. There has also been a discussion on Panda's Thunb: Lenski’s experiment: 25 years and 58,000 generations. Pennisi writes ...

Lenski's humble E. coli have shown, among other things, how multiple small mutations can prepare the ground for a major change; how new species can arise and diverge; and that Gould was mistaken when he claimed that, given a second chance, evolution would likely take a completely different course. Most recently, the colonies have demonstrated that, contrary to what many biologists thought, evolution never comes to a stop, even in an unchanging environment.

Let's talk about two issues in that paragraph.

Why don't people accept evolution?

Chris Mooney (remember spin framing?) is at it again. This time he writes for Mother Jones: 7 Reasons Why It's Easier for Humans to Believe in God Than Evolution.

Before we look at the seven reasons let's remember the poll from 2005 that surveyed acceptance of evolution in 34 countries. Note that the percentage of the population who reject evolution ("false") is somewhere between 10% and 20% in the countries at the top of the list. About 75% of the people in those countries think that evolution is true.

In the USA the percentage who reject evolution is closer to 40% and only about 40% think that evolution is true. Clearly if we're going to ask why it's easier for humans to believe in god(s) than in evolution then we have to take these differences into account. It seems reasonable, doesn't it, to look for something that the USA, Turkey, and Cyprus have in common that makes people not accept evolution?

What do you think of Brian Pallister's statement?

Brian Pallister is the leader of the Progressive Conservative Party of Manitoba. Here's a statement he made the other day. I'm not particularly offended by what he say about atheists. I think it demonstrates that he is really stupid and probably should have kept his mouth shut but that's actually good for secularism, no? It's pretty clear that he doesn't know any atheists, or, even more likely, none of of the atheists he knows want to tell him that they are nonbelievers.

… I wanted to wish everyone a really really Merry Christmas, Happy Hannukah, all the holiday… all you infidel atheists out there, I want to wish you the very best, also. I don’t know what you celebrate during the holiday season — I myself celebrate the birth of Christ — but it’s your choice, and I respect your choice. If you wish to celebrate nothing and just get together with friends, that’s good, too. All the best.

(I think I understand why his parents gave their farm to his brother. )

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[Hat Tip: Friendly Atheist]

Bill Farrell and Louis C on the Sandwalk

Here's a photo of Bill Farrell ("Doc Bill") and Louis C on the Sandwalk.

They join a distinguished list of people whose visit to the Sandwalk has been recorded here.

Larry Moran
PZ Myers
John Wilkins
Ryan Gregory
The God Delusion
Cody
John Hawks
Michael Barton
Seanna Watson
Steve Watson
Michael Richards
Jeffrey Shallit
Chris DiCarlo
Bill Farrell and Louis C

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Answering ten questions from the IDiots

On this American Thanksgiving Day, David Klinghoffer gives thanks for Richard Dawkins and Jerry Coyne [Thank Goodness for Richard Dawkins]. He says ...

... we're also grateful for guys like Richard Dawkins and Jerry Coyne who provide a rich source of unintended comedy. See, for example, our colleague Dr. Michael Egnor's always entertaining mining of Coyne's writings.*

* Admittedly we'd be even more pleased to have a worthy opponent on the Darwin side of the debate who did not run from a fight every time but answered our best arguments and evidence in a lucid, trenchant and informative style.

Well, I gotta tell you, David, that I'll be eternally grateful to the Discovery Institute for sending us Dr. Michael Egnor. It's the gift that just keeps on giving, and giving, and giving ....

Natural selection may not lead to evolution?

I recently discovered a new book called The Princeton Guide to Evolution. It looks pretty authoritative so I ordered a copy.

There are excerpts online. The first chapter is "What Is Evolution?" by Jonathan Losos. I'm not very impressed with his answer but I was shocked to read the following passage.

The logic behind natural selection is unassailable. If some trait variant is causally related to greater reproductive success, then more members of the population will have that variant in the next generation; continued over many generations, such selection can greatly change the constitution of a population.

But there is a catch. Natural selection can occur without leading to evolution if differences among individuals are not genetically based. For natural selection to cause evolutionary change, trait variants must be transmitted from parent to offspring; if that is the case, then offspring will resemble their parents and the trait variants possessed by the parents that produce the most offspring will increase in frequency in the next generation.

However, offspring do not always resemble their parents. In some cases, individuals vary phenotypically not because they are different genetically, but because they experienced different environments during growth (this is the “nurture” part of the nature versus nurture debate; see chapters III.10 and VII.1). If, in fact, variation in a population is not genetically based, then selection will have no evolutionary consequence; individuals surviving and producing many offspring will not differ genetically from those that fail to prosper, and as a result, the gene pool of the population will not change. Nonetheless, much of the phenotypic variation within a population is, in fact, genetically based; consequently, natural selection often does lead to evolutionary change.

I never heard to this idea before (that natural selection may not lead to evolution). I thought that natural selection was DEFINED as a change in the frequency of alleles in a population due to selection. Doesn't it have to have a genetic component?

Does this mean that natural selection may not lead to adaptation? Or, does it mean that adaptation isn't necessarily evolution?

The chapters are written by an impressive group of authors (Jonathan Losos is the editor-in-chief). It must represent the current consensus among evolutionary biologists. I'm surprised that I never heard of this definition of natural selection.

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Monday's Molecule #224

Last week's molecule was the second messenger, phosphatidylinositol 4,5-bisphosphate or PIP₂. The winner is Dean Bruce. The undergraduate winner is Ariel Gershon [Monday's Molecule #223].

Today's molecule is a protein (purple). It's one of the most abundant proteins in E. coli because it's bound to almost all tRNA molecules in the cell. Name the protein (complete name, not just initials).

Email your answer to me at: Monday's Molecule #224. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

What is bioethics? Is Margaret Somerville a bioethicist or a Roman Catholic apologist?

I had an interesting conversation with a student the other day. She's studying "bioethics" at the University of Toronto. This is a program run by the Deptment of Philosophy.

I asked her to define "bioethics" and she couldn't. To her credit, she immediately recognized that this wasn't right. If she's taking an entire program in bioethics she ought to be able to explain what it was all about. She was then joined by her friend, who is also majoring in bioethics. My colleague, Chris DiCarlo also joined us. He's a philosopher writing a book on ethics.

We described a scenario where I wanted to end my life and Chris was willing to help me. Neither of us have an "ethical" problem with that decision. So why is assisted suicide thought to be a problem for bioethics? If some people don't want to participate in euthanasia then nobody is going to make them? Where's the problem?

Does it only become a bioethical problem if some people want to impose their views on others? In this case, the people who are personally opposed to euthansia want to pass a law preventing me from ending my life with the help of my friend. Our students were puzzled by this discussion. Even though they have taken many courses on bioethics, nobody had ever raised this issue. Isn't that strange? You would think that any program run by a Department of Philosophy would emphasize critical thinking. Sadly, this turns out to be rare whenever the topic of bioethics comes up.

You simply won't believe what the IDiots are saying now!

Do you remember Vincent Joseph Torley (vjtorley)? He's the IDiot with a Ph.D. (2007) from the Department of Philosophy at the University of Melbourne (Australia). That's a legitimate university. Apparently Vincent Torley went off the rails sometime after 2007.

Here's his latest post on Uncommon Descent: Does scientific knowledge presuppose God? A reply to Carroll, Coyne, Dawkins and Loftus.

The scientific enterprise stands or falls on the legitimacy of making inductive inferences, from cases of which we have experience to cases of which we have no experience. The aim of this post will be to show that there can be no scientific knowledge if there is no God, and that there is no way of justifying inductive inference on a systematic basis, in the absence of God.

BLAH, BLAH, BLAH, etc. etc. etc.

I alluded above to the troubling fact that even if we assume that objects somehow instantiate rules, there remains the epistemic problem of knowing whether we’ve chosen the right model, or identified the right mathematical equation (i.e. laws of Nature) for characterizing the rules that define a certain kind of object – be it a tiny electron or a star, like the sun. But if we make the two assumptions about God which I referred to in the preceding section – that God wants to make intelligent beings, and that God wants these intelligent beings to reason their way to God’s existence – then we can infer that the rules which are embodied by objects in the natural world must be tailor-made to fit the minds of intelligent beings that are capable of contemplating their Creator. In other words, the universe is designed to be knowable by us. Hence we don’t need to concern ourselves with the theoretical possibility that the rules which characterize things might be too complicated even in principle for us to grasp.

God, then, is the ultimate Guarantor that science can work.

Well, that does it for me. Either I stop being a scientist or I have to become a believer in God in order to continue doing science.

Tough choice. Let me get back to you on that one ... anyone want a job as a professor of biochemistry?

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God Only Knows by The Beach Boys

The Pet Sounds album by The Beach Boys was released in 1966. The album ranks in the top ten of almost everyone's list of best albums (English/American culture). It's #2 on Rolling Stone's list of the 500 Greatest Albums of All Tine.

I wasn't a big fan of the album but I adored God only knows, and I still do.¹ It's one of my top ten favorite songs. The song ranks at #25 in Rolling Stone's 500 Greatest Songs of All Time. Paul McCartney, who played for another popular group in the 1960s, says that God Only Knows is his favorite song of all time.

The music was written by Brian Wilson² and the lyrics are by Tony Asher. I don't know very much about music so you'll have to read the Wikipedia article to appreciate why so many people admire Brian Wilson. Carl Wilson, Brian's younger brother, sings the song.

The video is from Good Timin': Live at Knebworth England 1980. It's one of the rare occasions after 1965 when all six Beach Boys (Brian Wilson, Dennis Wilson, Carl Wilson, Mike Love, Al Jardine and Bruce Johnston) are together. I think it's the only video where Brian Wilson is playing on God Only Knows. (That's him on the piano.)

I never saw a live performance of the original Beach Boys but I've seen the Mike Love version twice.

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1. Some atheists will never like this song because it mentions God. That sort of thing doesn't bother me. I can still sing God Save the Queen and the Canadian national anthem without batting an eyelash. There are much more important things to fret about.

2. I just read in the Wikipedia article that he was inspired by the Lovin' Spoonful song You Didn't Have to Be So Nice. That song is also one of my personal favorites but I never twigged to the similarity until now.