#140 – LTEE shows evolution in real-time!

The details behind the story of how bacteria mutated in order to grow bigger and better by eating oranges, instead of sugar.

Last week, we talked to a member of the Long-Term Evolution Experiment, Dr. Zachary Blount. He and his colleagues followed 75,000 generations of bacteria competing for a limited food resource — sugar — and described many different kinds of genetic changes in 57 different genes. Creationists and ID-proponents dismiss this as “simply breaking genes.” In this episode, we take a very deep-dive into the story, and show how this is actually a prime example of evolution proceeding through gene duplication, progressive modifications, and the building up of new regulatory pathways and metabolic functions. How it is that well educated anti-evolutionists, especially the biochemists among them, can only see this as destructive and detrimental either says something about them being biased and misled … or deceptive!?

Before we asked Zach to give us the details, we provided some background introductory information:

• evolution often involves duplication of stretches of DNA, followed by modifications which eventually lead to new functions, while leaving the original copy intact. This is NOT “breaking the gene”
• we give a crash course on how bacteria extract energy from glucose (see the color image attached below)
• evolution often happens in three steps:
  • (1) prepare for new function (or “potentiation”) – changes occur which by themselves don’t appear to affect function, but they set the stage for something else
  • (2) get the new function (or “actualization” or “instantiation” – the “something else” suddenly appears as a new function, although usually in a very weak and inefficient form
  • (3) refine the new function – tweaking and optimization

With that introduction in place, we then got deep into the details of this story:

• after 30,000 generations and 16 years, mutant cells had gained the ability to grow on citrate in the presence of oxygen (something that their non-mutated cousins couldn’t do)
• although the LTEE had found many other mutations that occurred in all 12 test-tubes, this one new function only happened in one of the 12 [and this is still true even today!]; this raises raises big questions regarding evolution, and became Zach’s research project (had to test 44 trillion cells to get some of the answers!!!)
• they went back to their “Frozen Fossil Record” (see last week’s post), and learned that mutations happened a year prior which weren’t detectable because the advantage was miniscule. BUT IT WAS THERE!  And it could then be refined (which it did by 33,000 generations)
• some changes enabled the bugs to take up much larger amounts of glucose, but at the “expense” of pooping out acetate, which later became a new food source through a new loophole that connected to citrate
• other changes that “Potentiated” … set the stage to use citrate as a food source
• the “Actualization” step was a duplication of a citrate transporter gene that was put under the regulation of glucose levels (the original copy was left in place and still regulated by oxygen levels … in other words, NOT BROKEN!!); now citrate uptake and metabolism can happen when glucose runs out! Like the Energizer Bunny, these mutant bugs now just keep on going when their non-mutated cousins are slowing down and dying
• ID-proponents, especially their biochemists, should be able to see this as an increase in function, information and complexity, but they PERSIST in dismissing this as “just breaking genes” or asking ignorant questions like: “did they see any examples of entirely new nanomachines?” (again, see last week’s episode) Contrary to the Creationist party line, this is precisely an example of small changes which accumulate and eventually become a new function.
• Evolution may be “clever” and innovative, but often it won’t be elegant; we talked about bizarre and inelegant designs like the anatomy of the recurrent laryngeal nerve, or the biochemistry of a photosynthetic enzyme in plants called rubisco; in the same way, this new re-design of citrate metabolism is also a “clunky” design, but it lets these mutants grow and thrive while their non-mutant cousins go extinct
• the new citrate-using bugs at generation 75,000 are growing better and better on the citrate/succinate microenvironment they’re creating (niche creation), but at the same time, are getting worse at growing on glucose (their ancestral resource). They are becoming a new species … becoming ecologically specialized!

As always, tell us your thoughts on this topic …

Find more information about our guest, Dr. Zachary Blount at his university profile page and his own lab’s web-site. Learn more about the LTEE itself, including descriptions of the team members and lists of their publications, at their webpage. You can also watch a video in which Dr. Blount regales Dr. Richard Lenski on the latter’s 60th birthday, and recounts the whole history of the LTEE.

If you enjoyed this episode, you may also like the mini-series of episodes we did focusing on Intelligent Design and its misrepresentation of science.

Episode image by Andrew Kirkham. Thanks Andrew!

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