Wednesday, May 27, 2020

Profiles in Scientific Creativity ~ A Review of Some Assembly Required

Thwarted in her desire to major in genetics at Cornell University because the major was closed to women at the time, Barbara McClintock (1902-1992) turned to horticulture, one of the university's acceptable distaff majors.  She made the most of this sexism,studying the genetics of corn and, in 1983, won a Nobel Prize for a key finding from that work.  Corn was a fortuitous focus of study:  each kernel on an ear is an embryo, thus providing a multiplicity of opportunities (about 1,000 per ear) to explore the functioning of genes.  Amid this wealth of genetically distinct embryos, McClintock found an area of the corn genome in which the chromosomes were fractured and, most tellingly, she saw that this area (a gene) with its chromosomal disjuncture moved around from place to place on the genome across generations.  When this gene landed in the midst of another gene that influenced the pigment of a kernel, the color pattern was disrupted.  But, if subsequently the gene with the breakpoint moved out of the pigment gene, the original color pattern was restored.  There is, she demonstrated, a startling degree of dynamism in the corn genome.

It was subsequently learned that these so-called “jumping genes” are ubiquitous, existing in all species, and as they move they copy themselves.  Indeed, nearly three-quarters of the human genome consists of such genes.  The picture that emerges is that of a genome marked by struggle between the jumpers and the genome writ large, a struggle to keep the jumpers within bounds possibly creating beneficial changes, and prevent them from doing grievous harm to the host organism.  Certainly, this was not the picture that science had painted previously of the genome.

McClintock's personal and professional story is told briefly in Some Assembly Required:  Decoding Four Billion Years of Life, from Ancient Fossils to DNA (2020), a new book by paleontologist and evolutionary biologist Neil Shubin.   Of McClintock's discovery of genes that leap around the genome, Shubin writes, "This single insight was one of the great ideas in the history of genetics:  the genome is not static - genes can jump from place to place."  (p. 142)  Beyond just the identification of jumping genes, there has been a revolution in our understanding of how DNA and the genetic landscape function, a revolution that has profound implications for evolutionary biology, explaining how genetic changes that natural selection works with arise in the first place.  Shubin, in this new volume, offers an accessible, well-crafted introduction to the discovery and implications of these game-changing advances in our knowledge.

He structures his book entirely upon a scaffolding of well-crafted vignettes about individual scientists, offering glimpses into both personal history and scientific work.  An engaging construct that works.  The scientists are often wonderfully quirky and complex, working with myriad organisms - from sea squirts to corn to amphipods (little beach sand creatures).  Particularly in the early years, these scientists often did their study of gene functions with low-tech implements, refashioning and using whatever they have available (think MacGyver), and applying creative thinking to hypothesize from what they found.  The stories that Shubin has brought together offer a view of the scientific process that shows how much grit, luck, and creative insight are actually involved, and how nonlinear it is.  Shubin characterizes the process these scientists followed as mirroring in many ways how changes occur in the genome.

St. George Jackson Mivart (1827-1900), an irascible character to be sure, is the first scientist Shubin introduces to us.  Mivart isn't in the book because he had some critical insight or made a crucial discovery.  Rather, he’s a reagent, here because of the reaction he elicited from Charles Darwin (1809-1882).  Mivart, accepting of evolution though he was, published a volume skewering the evolutionary gradualism that Darwin espoused in On the Origin of Species.  Mivart argued that truly major changes in organisms could not occur through incremental changes whose initial steps would have no evolutionary value, but had to come about in leaps, appearing whole cloth and setting organisms on new and different paths.  As Shubin notes, the problem Mivart identified is what paleontologist Stephen Jay Gould (1941-2002) labelled the "2% of a wing problem."  In other words, what good is just a small portion of a wing?  Shubin writes that Darwin responded to Mivart in the 6th edition of On the Origin of Species, adding a new chapter, which utterly disposed of Mivart's objection and the 2% problem.  His core argument came in just five words.  He asserted that evolution of physical attributes might occur "by a change of function," one of the foundational ideas in evolutionary biology.  The use we ascribe to a physical feature need not be the use for which it originally arose.  In an incipient stage, such a feature might have served perfectly well some other purpose.  The evolution of feathers is an iconic example.  The current thinking is that feathers first emerged for thermoregulation and only later, more fully developed, were shifted in use to flight.  Indeed, repurposing is a hallmark activity within living creatures’ genomes.

Over the course of the book with its accounts of individual scientists and their discoveries, Shubin describes some of the key ways that evolutionary change occurs in living organisms.  Among them are:

Biological features can be shifted from their original uses to new ones – The example of feathers was just cited.  Shubin outlines how overarching this process is within genomes from the simplest single-celled organisms to more complex multicellular ones.  For example, the genomes of those unicellular taxa contain the very genes that, in many celled animals, create the proteins central to building their bodies, but here they are being used for different purposes.  “Microbes adapting to their world developed the chemical precursors that animals later used to make bodies.  Multicellular life is possible only because new combinations of molecules were repurposed from there original function in single-celled life.  The great inventions that made bodies possible predate the origin of bodies themselves.”  (p. 206)

Features can serve more than one purpose – A dual-use example are swim bladders in fish.  Yes, they ultimately evolved to become our lungs, but in fish they have served either as a means to control buoyancy or as lungs to breathe, or, in some taxa, both.

An unused feature can be reemployed for a new use – Only about two percent of the human genome is made of genes, much of the rest has been labelled "junk" because it appears to just sit around doing nothing.  That said, it shouldn't be considered "garbage" because it contains evolutionary potential, and, given the dynamism in the genome (for instance, think "jumping genes"), some portions of it may be switched on at some point in the future.

Alteration of the timing of events in the development of living organisms from larva to adult fuels evolution – The versifying (literally) scientist Walter Garstang (1868-1949) demonstrated, with salamanders, that small chemical changes can trigger fluctuations in the pace of development of an organism or its endpoint, a process that can have major consequences, including setting in motion the transition from invertebrate to vertebrate life.

Organisms can evolve by coopting, utilizing, and incorporating other entities – For instance, perhaps ten percent of the human genome consists of dead viruses, some such viruses have critical functions for us, including the fashioning of memory.  Lynn Margulis (1938-2011) recognized the similarities between certain organelles in the nucleus of the cells in complex organisms, and bacteria and blue-green algae.  She argued, quite correctly, but against great resistance, that these organelles were in fact the descendants of bacteria and algae that had been coopted and put to use in cells long ago.

These among the aspects of genetic change in living organisms that generate the variations upon which natural selection works.  In a previous book, Your Inner Fish:  A Journey Into the 3.5-Billion-Year History of the Human Body (2008), Shubin described the morphological features of humans that had evolved over the millennia from those found in fish.  The present volume is a companion to that earlier book, describing how those changes might have occurred, delineating the genesis and the genetics of key changes in the genome needed for life to make significant changes, including the transition from fish to land dweller (e.g., changing fin to fingers).
Having mentioned Your Inner Fish, I feel the need to observe in conclusion that, for all of its virtues (and there are many), Some Assembly Required pales in comparison to that earlier volume which changed forever how I view the human body, and is one of the most persuasive arguments yet advanced against creationism.
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