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At Quanta Magazine: By Losing Genes, Life Often Evolved More Complexity

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Viviane Callier writes:

Two surprising analyses that appeared in Nature Ecology & Evolution early this year have hammered home just how inessential genes can be, and how creatively evolution can deal with losing them. By analyzing hundreds of genomes from across the animal kingdom, researchers in Spain and the United Kingdom showed that a startling degree of gene loss pervades the tree of life.

Their results suggest that even early animals had relatively complex genomes because of an unprecedented spurt of gene duplication early in life’s history. Later, as lineages of animals evolved into different phyla with distinct body plans, many of their genes began to disappear, and gene loss continued to be a major factor in evolution thereafter. In fact, the loss of genes seems to have helped many groups of organisms split away from their ancestors and triumph over new environmental challenges.

Recognition that gene loss has been important to evolution throughout the animal kingdom opens new doors for research. 

Use It or Lose It

Gene losses in evolution may sound like damaging events, since genes confer the traits that make life and health possible. It’s true that if individuals lose a genuinely essential gene, they may die or fail to flourish, and natural selection will weed them out of the population. But in reality, the majority of gene losses during evolution are likely to be neutral, with no fitness consequences for the organism, says Michael Hiller, an evolutionary genomicist at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany.

The reason is that evolutionary gene losses often occur after some change in the environment or behaviors makes a gene less necessary. If a key nutrient or vitamin suddenly becomes more available, for example, the biosynthetic pathways for making it may become dispensable, and mutations or other genetic accidents may make those pathways disappear. Losses can also occur after a chance gene duplication, when the superfluous copy degenerates, since selection no longer preserves it.

Plants offer abundant examples of this “use it or lose it” strategy, because many plant species have undergone whole genome duplications followed by waves of gene loss, explains Lydia Gramzow, a plant biologist at the Friedrich Schiller University Jena. Sometimes the duplicate copies persist for many millions of years before being lost, for reasons that Gramzow and Thießen are still investigating.

Photograph of a pair of dolphins swimming at the ocean’s surface.
The Miscellanista

One of the best examples of adaptive gene loss in animals can be seen in cetaceans (the order of aquatic mammals including whales and dolphins), which have lost 85 protein-coding genes seen in other mammals, as Hiller reported last year. Many of these losses are probably neutral, but some seem linked to diving-related adaptations, like the narrowing of blood vessels during diving. One of the lost genes, KLK8, is interesting because it is involved in the development both of sweat glands in the skin and of the hippocampus in the brain; cetaceans lost it during their transition from land back to water. The loss of this gene is linked to the development of a thicker epidermis and the loss of hair (hair is not adaptive in aquatic environments, where it creates drag and does not preserve body heat as it does in terrestrial animals).

Note: The statement, “hair is not adaptive in aquatic environments, where it creates drag and does not preserve body heat as it does in terrestrial animals,” explains why river otters are so slow and cumbersome and seem so poorly designed to be able to thrive in water.”

The article goes on with other examples, and states:

The different solutions to metabolic or developmental puzzles that evolution has achieved by subtracting key genes could do more than reveal new biological insights; they could inspire new biomedical interventions for human disease.

Complete article available at Quanta.

I’ll first take issue with the title of the Quanta article – genes involve complex specified information; the loss of genes, even unused ones, constitutes a loss of information and complexity, not an evolution of new complexity. To see this, just imagine continuing the process of gene loss: how much complexity would an organism have if it lost all of its genes? The unanswered question in the article is, “How did the genes develop in the first place?” We know from probability analysis that it couldn’t have happened by chance within the limited spacetime of our universe.

4 Replies to “At Quanta Magazine: By Losing Genes, Life Often Evolved More Complexity

  1. 1
    chuckdarwin says:

    So much for “devolution.” And then the knee jerk riposte:

    [J]ust imagine continuing the process of gene loss: how much complexity would an organism have if it lost all of its genes? The unanswered question in the article is, “How did the genes develop in the first place?”

    Seriously, if it lost all of its genes? And of course, the research wasn’t designed to explore where genes come in the first place. So why gratuitously throw that in? The point of evolution is not the preservation of “information and complexity,” it is adaptation to the environment. I think this is a fundamental misunderstanding that plagues folks who insist on a strict linearity in the process of evolution. If loss or deletion of a gene aids adaptation, natural selection has done its job.

    Otters are one of my favorite animals. However, unlike dolphins, porpoises and whales they do not spend 24/7 in the ocean, plumbing its frigid depths and traveling thousands of miles to and from breeding grounds. I have a hard time imagining an otter migrating from the North Pacific or Bering Sea to Lanai or Cabo and back while feeding its young. They’d be like little sitting ducks in the open ocean. Otters are terrestrial animals that are phenomenal short distance swimmers. Otters partially hunt fish, but they also have a significant diet of birds and small mammals. They live in cairns and other types of dens on land where their young are born and live until they are adept swimmers. In the winter, in particular, they need all the hair they can get…….

  2. 2
    jerry says:

    Two surprising analyses that appeared in Nature Ecology & Evolution early this year have hammered home just how inessential genes can be, and how creatively evolution can deal with losing them

    It should be

    have hammered home just how inessential some genes can be, and how creatively evolution can deal with losing them

    This is what Michael Behe’s book is all about.

    However, not all genes can be discarded. Many are essential for the complex systems a body needs to survive. The basic argument that not all genes are necessary to survive is obvious. It’s a non-sequitur to argue that no gene is necessary or many genes are not necessary.

  3. 3
    relatd says:

    Another incredibly bad article. Incredibly bad. No logic.

    “Their results suggest that even early animals had relatively complex genomes because of an unprecedented spurt of gene duplication early in life’s history. Later, as lineages of animals evolved into different phyla with distinct body plans, many of their genes began to disappear, and gene loss continued to be a major factor in evolution thereafter.”

    Early animals had relatively complex genomes. This is 100% against the idea that early animals were primitive and that relatively modern animals are more complex – for no particular reason. Evolution has no goal or foresight but it went from “early” animals with more genes to more complex/better modern animals. So much for small, gradual – accidental – changes leading to more complex animals.

    “…unprecedented spurt of gene duplication early in life’s history.” A disembodied thing called “evolution” just decided on a spurt of gene duplication, as if it was planning on the future.

    Not credible. Not credible at all.

  4. 4
    hnorman42 says:

    There may be cases where improving fitness can be accomplished by loss of complexity but in no way does that demonstrate the creative power of natural selection. That demonstrates the destructive power of selection. — And devolution can be by design. It’s just that design will be undetectable there.

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