An engineered minimal cell evolves to escape the negative consequences of genome streamlining.
IU Biology news: Artificial cells demonstrate that "life finds a way."
Published: Jul 5, 2023
“Listen, if there's one thing the history of evolution has taught us is that life will not be contained. Life breaks free. It expands to new territories, and it crashes through barriers painfully, maybe even dangerously, but . . . life finds a way,” said Ian Malcolm, Jeff Goldblum's character in Jurassic Park, the 1993 science fiction film about a park with living dinosaurs.
You won't find any Velociraptors lurking around evolutionary biologist Jay T. Lennon's lab; however, Lennon, a professor in the College of Arts and Sciences Department of Biology at Indiana University Bloomington, and his colleagues have found that life does indeed find a way. Lennon's research team has been studying a synthetically constructed minimal cell that has been stripped of all but its essential genes. The team found that the streamlined cell can evolve just as fast as a normal cell—demonstrating the capacity for organisms to adapt, even with an unnatural genome that would seemingly provide little flexibility.
“It appears there’s something about life that’s really robust,” says Lennon. “We can simplify it down to just the bare essentials, but that doesn’t stop evolution from going to work.”
For their study, Lennon’s team used the synthetic organism, Mycoplasma mycoides JCVI-syn3B—a minimized version of the bacterium M. mycoides commonly found in the guts of goats and similar animals.
Over millennia, the parasitic bacterium has naturally lost many of its genes as it evolved to depend on its host for nutrition. Researchers at the J. Craig Venter Institute in California took this one step further. In 2016, they eliminated 45 percent of the 901 genes from the natural M. mycoides genome—reducing it to the smallest set of genes required for autonomous cellular life. At 493 genes, the minimal genome of M. mycoides JCVI-syn3B is the smallest of any known free-living organism. In comparison, many animal and plant genomes contain more than 20,000 genes.
In principle, the simplest organism would have no functional redundancies and possess only the minimum number of genes essential for life. Any mutation in such an organism could lethally disrupt one or more cellular functions, placing constraints on evolution. Organisms with streamlined genomes have fewer targets upon which positive selection can act, thus limiting opportunities for adaptation.
Although M. mycoides JCVI-syn3B could grow and divide in laboratory conditions, Lennon and colleagues wanted to know how a minimal cell would respond to the forces of evolution over time, particularly given the limited raw materials upon which natural selection could operate as well as the uncharacterized input of new mutations.
“Every single gene in its genome is essential,” says Lennon in reference to M. mycoides JCVI-syn3B. “One could hypothesize that there is no wiggle room for mutations, which could constrain its potential to evolve.”
The researchers established that M. mycoides JCVI-syn3B, in fact, has an exceptionally high mutation rate. They then grew it in the lab where it was allowed to evolve freely for 300 days, equivalent to 2000 bacterial generations or about 40,000 years of human evolution.
The next step was to set up experiments to determine how the minimal cells that had evolved for 300 days performed in comparison to the original, non-minimal M. mycoides as well as to a strain of minimal cells that hadn't evolved for 300 days. In the comparison tests, the researchers put equal amounts of the strains being assessed together in a test tube. The strain better suited to its environment became the more common strain.
They found that the non-minimal version of the bacterium easily outcompeted the unevolved minimal version. The minimal bacterium that had evolved for 300 days, however, did much better, effectively recovering all of the fitness that it had lost due to genome streamlining. The researchers identified the genes that changed the most during evolution. Some of these genes were involved in constructing the surface of the cell, while the functions of several others remain unknown.
Details about the study can be found in a paper recently featured in Nature. Roy Z. Moger-Reischer, a Ph.D. student in the Lennon lab at the time of the study, is first author on the paper.
Understanding how organisms with simplified genomes overcome evolutionary challenges has important implications for long-standing problems in biology—including the treatment of clinical pathogens, the persistence of host-associated endosymbionts, the refinement of engineered microorganisms, and the origin of life itself. The research done by Lennon and his team demonstrates the power of natural selection to rapidly optimize fitness in the simplest autonomous organism, with implications for the evolution of cellular complexity. In other words, it shows that life finds a way.
Evolution is the single most important concept in all of biology.
By: Fallacy Man
Published: Aug 31, 2015
Evolution is the single most important concept in all of biology. It is absolutely vital for understanding both the history of life on earth and why our modern organisms have their current traits and behaviors. Nevertheless, it is also one of the most misunderstood concepts in modern science. Much of the confusion stems from creationists’ faulty arguments, but even those who accept evolution often don’t really understand it. Therefore, I am going to describe and debunk ten of the most common myths and misconceptions about evolution.
Myth 1: Evolution is just a theory
This is arguably the most common myth about evolution, and it is probably creationists’ most well worn trope. It is also a fundamental misunderstanding of how science works. I’ve explained this in more detail before, but briefly, evolution is both fact and theory depending on exactly what we are talking about. The idea that all modern organisms (including humans) evolved from a single celled organism over a period of millions of years is a scientific fact. It has been confirmed by the fossil record, genetics, biogeography, etc. Like it or not, it’s a fact, but there is also a theory component. You see, theories explain facts. So, the theory of evolution by natural selection states that natural selection has been the dominant mechanism causing species to evolve. In other words, it is a fact the evolution occurred, and the theory of evolution by natural selection explains how that evolution occurred. Indeed, it is a common misconception that Charles Darwin came up with the idea of evolution. In reality, many scientists before him thought that organisms evolved, but they couldn’t figure out how or why they evolved. So, what Darwin (along with Alfred Russel Wallace) did that was so extraordinary, was to provide a mechanism that drove evolutionary change (i.e., natural selection).
Finally, it is worth noting that theories are actually among our highest forms of scientific certainty. They have been rigorously tested and consistently make accurate predictions. So gravity (i.e., the theory of universal gravity), the idea that all matter is made of atoms (i.e., atomic theory), the idea that all living things are made of cells (i.e., cell theory), the idea that bacteria make you sick (i.e., the germ theory of disease), etc. are all “just theories.”
Myth 2: We evolved from monkeys/apes
We did not evolve from modern apes, but we share a common ancestor with them. In other words, if we back the clock up a few million years, we will find an ape-like ancestor whose populations split, and different groups went down different evolutionary paths. One group evolved into us, and another group evolved into chimps. So we and chimps share a great, great, great…great grandparent who went extinct a few million years ago, but we did not evolve from chimps, monkeys, or modern apes.
Myth 3: Evolution conflicts with the second law of thermodynamics
People often describe the second law of thermodynamics as, “the disorder of a system always increases,” which leads people to erroneously claim that evolution violates the second law because it says that overtime life becomes more organized. The problem is that the above definition is a terrible one which misrepresents the law and overlooks several key components.
The best way to understand the second law is in conjunction with the first law. The first law (also known as the law of the conservation of energy) states that energy cannot be created or destroyed, but it can change forms (e.g., it can go from potential energy to kinetic energy). The second law then describes the natural flow of energy within a system (i.e., the direction in which the changes take place). Both of these are dealing with energy states, and taken together, they say that a system cannot go from a low energy state to a high energy state without the input of additional energy. The classic example of this is a diving board. Someone standing on a tall diving board is in a higher energy state (i.e., they have more potential energy) than someone standing at the bottom of the ladder. So, to a physicist, the person at the bottom is more “disorganized” than the person at the top, because the person at the top has more potential energy. In technical terms, this concept of disorganization is known as entropy, and the person at the top of the board would have less entropy than the person at the bottom.
Notice, these laws do not state that it is impossible for systems to go from a low energy state to a high energy state. Rather, they say that the transition cannot take place without the input of additional energy. In other words, it is completely possible for the person at the bottom of the ladder to climb up onto the board and reach a higher energy state (i.e., become more organized/have less entropy), but doing so requires an input of energy (i.e., they have to use energy to move their muscles and climb the ladder). Another way to describe this is to say that a closed system cannot become more organized, at least in the long term (a closed system is one that receives no energy from outside sources). These laws do not, however, state that an open system cannot become more organized (an open system is one that does receive energy from outside sources).
Now, let’s apply all of that to evolution. The earth is most definitely an open system. It is constantly receiving energy from the sun. In fact, the sun drives nearly all life on earth. So, since the earth is an open system, there is no conflict between evolution and the thermodynamics. Let me use an example to prove that. I think we can all agree that a tree is more organized (has a higher energy state) than a seed. So, if thermodynamics worked the way that creationists claim, it should be impossible for a seed to grow into a tree, but it clearly is possible for seeds to grow. Why? Quite simply, because the earth is an open system. Even so, it is entirely possible for life to become more organized because organisms are constantly receiving energy from the sun (or from food which grew because of energy from the sun). So there is no conflict between evolution and thermodynamics.
Note: Myth#3 was edited on 5-Sept-15
Myth 4: We haven’t found any “missing links”
Odontochelys is a transitional fossil between turtles and their lizard like ancestors, complete with partially formed shell. Image via Chun et al. 2008.
The term “missing link” is a misnomer because they aren’t missing. We have hundreds of fossils that clearly represent transitions between two groups of organisms. Creationists invariably claim that these fossils are simply uniquely created organisms that happen to look like transitions, but this is a clear and enormous ad hoc fallacy because evolution predicted the existence of these fossils. If, for example, I asked you to describe what an intermediate between a turtle and its lizard-like ancestor would look like, you would inevitably describe a creature with half the features of a lizard and half the features of a turtle (e.g., a partially formed shell, a turtle like skull that still retains lizard like teeth, a somewhat specialized neck, etc.). Well guess what, that’s exactly what we see in the fossil record with species like Odontochelys and Pappochelys which have some lizard features and some turtle features. Similarly, if I asked you to describe an intermediate between a dinosaur and a bird, you would probably describe a featured dinosaur with partially formed wings and some skeletal modifications like an enlarged breastbone, but which still retains some dinosaur features like teeth. Indeed, the creature that you are imagining closely matches fossils like Archaeopteryx, Confuciusornis, and Jeholornis. The same is true for the transition for fish to amphibians, amphibians to reptiles, reptiles to mammals, etc.
In each of those cases, we have multiple fossils that are exactly what we would expect if evolution was true, and the only way that you would reject the notion that these are intermediates is if you were already convinced that intermediates don’t exist. This is the fundamental problem with creationism (and a big part of why it is pseudoscience). Creationists have determined ahead of time that no intermediates exist, so no matter how perfect a transitional fossil may be, they will always claim that it is just a unique species that happens to look like a transitional (I explained this in much more detail here and you can find a good list of intermediates here [yes, I know Wikipedia isn’t a good source, but this list is actually quite useful and you can use it as a starting point to look up the details of specific fossils in more reputable sources]).
Myth 5: Evolution isn’t science because it hasn’t been observed/repeated
First, we have to specify what we mean by “evolution.” You see, evolution on a small scale has been observed numerous times. Bacteria evolving resistance to antibiotics is the most well-known example of this, but there are many others. For example, we have been able to observe finches on the Galapagos evolve and change their beak sizes in response to droughts (Grant and Grant 2002). We have even been able to observe entirely new species form (lots of good sources here).
Nevertheless, when most people make this claim, there are generally referring to evolution over a long period of time. In other words, they are saying that we have not observed or repeated something like a relative of the T. rex evolving into a chicken. First, it is important to realize that there is no real difference between “microevolution” and “macroevolution.” Macroevolution is just an accumulation of microevolutionary steps. So if evolution on a small scale occurs (as has been observed and experimentally demonstrated) then ipso facto, evolution on a large scale occurs. One inevitably leads to the other (more details here).
Finally, the idea that we have to directly observe something and repeat the event itself in order for it to be science is a fundamental misunderstanding of science. Most science is not based on direct observation of the actual event of interest. Rather, we observe clues that are left behind by the event, and we infer information about the event from them. For example, no one has directly observed two hydrogen atoms joining an oxygen atom to form a water molecule, but we know that it happens because we can conduct chemistry experiments which give observable results that we can use to infer the sharing of electrons that lets those atoms combine. Similarly, we constantly solve crimes without either observing or repeating them because there are clues left behind that we can use to infer who committed the crime (this is known as forensic science). Even so, we do not need to observe a dinosaur evolving into a bird to know that it happened because there are clues left behind in the fossils, DNA, etc., which we use to infer evolution. There is nothing unscientific about that, and, in fact, it is how most science works. We make predictions like, “if and only if birds evolved from reptiles, then birds should share more DNA with reptiles than any other group.” We then test those predictions, and when they consistently come true, we conclude that our hypothesis is most likely correct. That is the scientific method at its finest (I explained this in more detail here).
Myth 6: Individuals evolve
Populations evolve not individuals. Evolution is just a change in the genetic composition of a population over time, so, since individuals cannot change their genetic composition, they cannot evolve. For example, if a drought comes along and destroys all seed-bearing plants except for ones with very large seeds, an individual bird with a small bill cannot evolve in response to that drought. In other words, it cannot change its genetic makeup and alter its bill size to eat the large seeds. In biological terms, it cannot adapt. As a result, the birds that have small bills will get less food and produce less offspring than the birds with large bills. This means that there will be more genes for large bills in the next generation. So the population will evolve and adapt to the drought, but the individuals will not evolve.
Myth 7: Evolution has a direction or goal
People often talk about evolution “trying to accomplish” something, or they may describe primates and other mammals as being “more evolved” than other animals, but statements like that are extremely problematic because they inherently imply that evolution has a direction or goal, which it doesn’t. Biologist often like to say that, “evolution is blind.” All that evolution can do is adapt an organism for its current environment and way of life (I’m talking specifically about evolution by natural selection here). Evolution has no foresight, and it is completely incapable of predicting what will be useful in the future, so a trait that has been selected for thousands of generations may suddenly become harmful if the environment changes.
Because evolution just adapts organisms to their current environment and way of life, it doesn’t really make sense to describe one species as “more evolved” than the other. For example, a monkey is not “more evolved” than the fly that gets its moisture from the monkey’s poop. The monkey is certainly more complex, but it’s not really more evolved because both the monkey and the fly are extremely well suited to their way of life. If you try to say that the monkey is more evolved than the fly, then you are implying that evolution has a direction, which it doesn’t.
Finally, this explains the common creationist criticism that certain species have “evolved backwards” (e.g., penguins lost the ability to fly, whales went back into the ocean, etc.). This again assumes that evolution has a direction or goal, when in reality, it’s just adapting organisms to their current environment. So, at one point in time, flight was useful so evolution selected for it and produced flying birds, but as those birds invaded the antarctic, the ability to fly was not as important as the ability to swim and stay warm, so evolution selected against adaptations for flight and produced penguins.
Myth 8: Some systems are too complex to evolve
This is one of the oldest criticisms of evolution, and it has recently resurfaced under the moniker “irreducible complexity.” The basic idea is that some systems are too complex to evolve because they aren’t functional until all of the parts are in place. For example, an eye that is missing a single piece no longer sees, and a bacterial flagellum that is missing a single protein can no longer act as a flagellum. So the argument claims that these systems could not have evolved because there would have been steps that served no useful function, and nature could not have selected for those steps. The problem is that this argument ignores the fact that evolution is blind. Traits don’t need to function for some ultimate final product in order to be selected for. Rather, if they provide any useful function at all, nature will select them. Indeed, no one has ever been able to find a truly irreducible system, and we have evolutionary pathways that explain how complex systems evolve. For example, an early precursor of the eye would have simply involved a few light sensitive cells (much like some flatworms have). They don’t function as an eye, but they still function, so nature will select for them. Similarly, the proteins that make up a flagellum all serve other functions in the cell, and we have even figured out a step-wise series of events that would form a flagellum with each step serving a useful function for the cell, even though only the final step actually serves as a flagellum. So there is just no truth to the notion that some systems are too complex to evolve (I explained this in more detail here).
Myth 9: Evolution describes the formation of the universe/the first cell
I often hear people argue that, “evolution isn’t true because blah, blah, blah…big bang” or some nonsense about how we haven’t figured out how the first cell formed. Beyond the specific issues with those arguments (which I won’t go into here), those arguments are totally irrelevant to evolution. The big bang theory deals with the formation of the universe, and abiogenesis deals with the formation of life. Evolution only comes into play after life formed. So, even if you managed to disprove the big bang or disprove abiogenesis, you would not have in any way shape or form disproved evolution. Indeed, there are some people who think that God created the first cell, then let evolution take its course. In other words, they reject abiogenesis but accept evolution (to be clear though, there is no good scientific reason to reject abiogenesis or the big bang).
Myth 10: Evolution is faith based
To anyone who makes this claim, I would like to know which part exactly you think is faith based. As I explained in #5, the fact that we did not directly observe millions of years of evolution doesn’t disqualify it as science. In fact, evolution is one of the most well supported ideas in all of science, and if you actually read Origin of the Species it is packed with evidence. Further, Darwin was an exceptional scientist and made clear predictions about what future researchers should find if his theory was correct. For example, he explicitly stated that we should find intermediate fossils, and we have (see #4). Think about that for a second. Evolution predicted the existence of organisms decades before we found them. That is an utterly incredible feat. Similarly, evolution predicted a strong agreement between the fossil record and genetics, and, once again, its predictions have come true with remarkable consistency. So if you are going to claim that evolution is based on faith, I want to know precisely what part of it you think is faith based, because there is no aspect of it which I cannot back up with empirical data.
Finally, it is worth noting that, contrary to popular perception, evolution is not inherently atheistic. Darwin was not an atheist and there are scientists who both accept evolution and believe in God. Evolution is not based on faith, and it doesn’t stem from a philosophical or religious desire to reject God. Rather, it is a scientific fact which is supported by an insurmountable mountain of evidence.
The best thing about understanding evolution and rejecting magical bullshit is realising you’re part of - not separate from - the natural world around you.
