When you hear the word "evolution" does "neotony" come to mind?

How many ways can we make a home?  I remember as a child walking through the corridors of the American Museum of Natural History and gawking at the many dioramas which combined realistic painting with artifacts or copies of natural and prehistoric settings.  I saw homes of our ancestors built from mammoth tusks in Siberia.  I saw tepees with animal skin wrapped around a cone of trimmed saplings.  I saw igloos built from blocks of ice or compact snow.  Outside the museum I saw the swank apartments of those who lived on Central Park West and imagined the view of Central Park they enjoyed.  I contrasted that with our own Brooklyn cold water flat with a coal stove in the kitchen.  In books I saw castles and mansions that housed the privileged and log cabins that Presidential candidates promoted as their identification with the underprivileged voter or common man.

 

In a similar way there are many mechanisms by which evolution occurs.  There is natural selection in which adaptive traits survive, thus providing the genetic basis for them that enters a new generation and this in turn changes the gene frequency of the population.  There is the “founder effect” in which a small number of individuals enter a new niche and reproduces rapidly in large numbers to create a population that differs in appearance from its original source.  There are hybrids that undergo a doubling of chromosome number and thus establish a new self-reproducing species. There are developmental mutations that can multiply body parts or organs like wings, limbs, or eyes.  There are other developmental mutations that place organs in different parts of the body producing new variations in a species.  One of my favorites is a process called neotony in which juvenile or embryonic features are carried into adult stages.  In the 1920s such neotonous species were found in salamanders in caves, the fertile adults sporting gills which are normally absorbed in the related species living outside the caves. 

We humans have a neotonous origin from out primate ancestors because we have prolonged child-raising period compared to other primates which are sexually mature and functionally adult in fewer years.  The most recently studied neotonous organisms are the birds that had a dinosaur-like ancestry.  They miniaturized as they shifted from living on land to living in trees and then to the skies as they developed wings for flight.  Their eyes are larger (like an embryo’s) in proportion to their bodies.  We do not reflect as much as we should on these neotonous traits in the evolutionary process, and most of the debates about Creationism and Intelligent design are waged over natural selection which is only one of many ways evolution works. 

COMPARING THE EVOLUTION OF LANGUAGES WITH THE EVOLUTION OF LIFE

     I enjoyed reading Margolit Fox’s new book, The Riddle of the Labyrinth which discusses the decipherment of Linear B in the early 1950s.  The book discusses the major players in the process.  Arthur Evans found the tablets with the unknown script at Knossos in Crete. He tried for 40 years but did not succeed.  Alice Kober figured out what type of language group it was by studying (before computers) the associations and endings of syllables or words.  Michael Ventris finally realized it was an ancient Greek language using a totally different alphabet system.  Each of the contributors was flawed and yet each had some major insight that turned out to be correct. The book raises questions about their personalities and the influence social circumstances had on their careers and personal lives. As I read the book, I thought of the relation to coding, translating languages, and linguistics which does a comparative study of languages including their evolution.  At the same time I thought how this field differs from genetics with its genetic code, role in translating nucleotide sequences into amino acid sequences in proteins, and the evolution of life from a molecular level to an organism and population level. 

     Languages are clearly created by people but they are not intelligently designed by a creator who invented French, Korean, Swahili, or Greek.  Those languages evolved over the years.  When we read 19^th century literature, we find it wordy.  When we read Shakespeare, we need a footnoted copy to figure out the meaning of words and idioms of the past.  Reading Chaucer’s Canterbury Tales is easier in translation than in middle English.  Reading Beowulf is virtually impossible without old English dictionaries or footnotes.  In a similar way genes have evolved by mutations over eons.  Just as there is a social selection of which words  survive and which ones get lost, there is a natural selection for mutational expression which leads to extinction (no progeny) or survival (the adaptive conditions won out). We are not troubled that modern languages did not exist some 3000 years ago but have evolved. Yet those who believe in an intelligent designer for the origin of species cannot imagine how humans can be derived from ape-like ancestors or how mammals could be derived from reptiles or reptiles from amphibians, or amphibians from fish working backwards to the origin of early life forms as bacteria-like or virus-like.  

       One major difference is the time scale of evolution.  For languages it is about 4000 years at most for written languages.  They have the advantage that symbols or words written in stone have survived.  In a similar way there are fossils that go back millions or 100s of millions of years.  They are more difficult to interpret than the languages used since humans began writing their transactions and thoughts. But no one would argue that Jesus spoke English or that the Biblical texts handed down were written in English for Moses to read.   Nor should one readily doubt that the life on earth differs in kind and complexity as we examine more ancient rocks.  The human bones in our graveyards are not found in the rock strata that give us dinosaurs.  Whale bones are not found in the ancient seas that teemed with crinoids.  

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DINOSAURS



Children love dinosaurs. They are extinct relatives and their history was played out long ago so they can’t threaten us. They roamed on earth tens of millions of years ago and most disappeared relatively rapidly some 60 to 70 million years ago, most likely from a collision with a meteor. Most dinosaurs we know from their fossil bones. A few have left imprints of their skin and other remnants behind, including the shells from which they hatched. There is a lot of debate about their physiology, most considering them warm-blooded rather than cold-blooded. There is also debate about their behavior, some arguing they cared for their young after hatching and others arguing for a pattern of dump the eggs and walk away.

The American Museum of Natural History in NY City has recently completed an extensive reorganization of its dinosaur collection and placed them in two of its four connected wings on the origins and variety of the vertebrates. We are vertebrates and belong to the mammals. Our immediate predecessors look more like dinosaurs than mammals. As we enter the first hall of the exhibit we can choose a ten minute film to introduce us to the evolution of vertebrates or a series of paintings that unfold the hundreds of millions of years carved into geological eras. I was immensely pleased by these exhibits. It comes as a shock to see the earliest ancestors of fish, the placoderms, having not teeth but tooth plates, like jagged and irregular chunks of sheet metal that would easily make mince meat of the invertebrate flesh they encountered.

I was surprised to find that sharks came from bony fishes and not the other way around. I marveled at the variety of ways our limbs developed. Some of these early ancestors had up to eight digits to a flipper or foot. The fingers had up to ten phalanges (if you bend your fingers and count, you’ll find three in all except your thumbs). We are surprised that dinosaurs are two or three toed, as if designed by Disney, whose cartoon characters routinely uncrowd their hands with a missing digit.

The exhibits guide us with arrows and mosaic or painted paths, a sort of Yellow Brick Road adventure, as filled with forks and surprises as those Dorothy and her friends took to Oz. I am a passionate museum goer. I don’t develop museum fatigue. I take notes. The students I take with me often wilt and disappear reappearing two hours or so later when we gather to board our bus back to the university. I am used to that and hope a few will read the fine print of the exhibit cards and thrill as I do to see that the curator of the exhibit has demoted reptiles to a cultural term and not of scientific worth. The dinosaurs are part of the saurosids, along with crocodiles, lizards, snakes, turtles, and birds. Birds? Those lovely goldfinches at my feeder? Could they be part and parcel of the saurosids and a bud off the dinosaur branch? It’s controversial, of course, as classifications based on a spotty fossil record often are, but how startling it is to see their two skeletons side by side, reduced to the same size, looking so much like siblings.

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THE INVENTIONS OF LIFE ARE LARGELY MOLECULAR

We identify human cultural evolution with basic ideas like the domestication of animals and plants, the invention of the city, the invention of written languages, and the invention of the Golden Rule. We then lead our way to the advocacy of universal human rights in this past century. Each early event helped humanity to prepare for later events. Perhaps in this first century of the third millennium we may see new inventions that make us more respectful and appreciative of human diversity. We might find ways of settling differences without a resort to violence, terrorism, or war. Let us hope we find ways to celebrate and use our common human talents to solve the many problems likely to emerge in the years ahead. I thought a similar approach could be applied to the evolution of life. What were the great inventions of nature that made our present life in all its diversity possible? Here is my list of those great events:
• The formation of complex organic molecules from simple ones by natural processes leading to amino acids, nitrogenous bases, sugars, and simple lipids.
• The invention of chains of nucleotides forming RNA molecules and their capacity to replicate their sequences.
• The invention of chains of nucleotides forming DNA molecules and their capacity to replicate their sequences.
• The invention of the genetic code
• The invention of virus-like systems using proteins to protect their nucleic acid.
• The formation of aggregates providing mutual benefit and acting as cell-like organisms.
• The formation of bacteria-like cells.
• The invention of photosynthesis.
• The invention of abundant energy production by using oxygen to react with small organic molecules.
• The invention of eukaryotic cells having a separate nucleus to house its DNA.
• The invention of meiosis to provide efficient sexual reproduction and genetic diversity.
• The invention of cell adhesives to make colonies of cells.
• The invention of differentiation to make different tissue types possible in a single organism.
• The invention of body plans to make our phyla possible.
• The invention of the kidneys and lungs to make the shift from water to land animals possible.
• The invention of a centralized nervous system and the sense organs to inform it.
• The invention of learning and teaching to by-pass inherited instincts to respond faster to changing environments.
• The invention of self-awareness to make human cultural evolution possible.

As these great inventions are resolved by the end of this century, arguing against evolution by attacking the fossil record will be like arguing today that the earth is the center of the universe and angels push the sun, moon, and planets in circular orbits around us.

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HOW DOES EVOLUTION WORK AT THE LEVEL OF THE GENE?


When Darwin worked out the evidence for a past evolution of life and presented a theory of natural selection to account for that evolution, he did not have the advantage of a theory of heredity. That would not enter evolutionary studies for another 35 to 50 years. What Darwin described were things he saw which we call phenotypes. My hazel eyes and full head of hair at age 77 are phenotypes. It would take a genetic analysis to reveal the genes involved in those two phenotypes and today that is largely done at a molecular level, the actual genes being isolated, sequenced, and their functions worked out in the cells where they are expressed. For most of the traits Darwin studied, he assumed that change was very gradual to bring about increases in size, change in intensities of color, developing visual acuity, or other biological functions necessary for survival. In the late 1890s most biologists thought such factors involved in character formation were numerous each with a slight effect and things like height would be a consequence of these numerous factors sorting themselves out into bell-shaped curves. It was the prevailing idea from the 1920s to the 1970s for measuring human intelligence with IQ tests.

What was surprising to me at the 74th Cold Spring Harbor laboratory Symposium on evolution that ended in early June 2009 was how different we interpret such changes in appearance today. Instead of thousands of barely observable changes that distinguish a dachshund from a wolf only about a dozen major genes are involved. Similarly the difference between an eyeless albino cave fish and one that has full sight and pigmentation is also due to a dozen or so genes. In both cases one can deconstruct the recent and bring it back to the past by genetic breeding in only a fraction of a human life time. I was discussing this with my former student, Ron Sederoff at the meeting when Jim Watson joined us and said, “What this conference has shown is that gradualism is dead”. Sederoff and I continued our discussion and we agreed that small numerous changes leading to domestic breeds of animals and plants were not true. But there are traits like coat color in cereal grains and human skin color where about five pairs of genes can distribute color in bell-shaped curve. Such quantitative traits, like the beak size and shape of finches in the Galapagos may depend on a similar small number of factors that form such bell-shaped curves. What is exciting about the analysis of domesticated forms or the evolutionary changes in cave fish where no human intervention was involved, is the small number of genetic changes that led to the “degeneration” of the eyes and coat color of the fish and the small number of changes that led to the development of more acute sensing of pressure in the dark cavern waters they live in.

What this illustrated to me is the fallacy we often fall into of assuming that what we see (the phenotype) corresponds to our imagined mechanism of how it came to be (the genotype). Genotypes are resolved by breeding analysis or by molecular analysis of the genes involved. The wonderful thing about science is that analysis and experimentation are far superior to doctrine and logic as guides to the past, whether that doctrine is “creationism” in any of its forms or “Darwinian gradualism” in any of its premolecular forms.

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evolutio,ERNST HAECKEL: THE MOST HATED GERMAN SCIENTIST DESERVES A BETTER REPUTATION.

The most hated name from the 1870s to the 1940s by those who despised an evolution of life was not Charles Darwin but Ernst Haeckel (1834-1919). Haeckel was a German biologist who published hundreds of articles and about two dozen books. Some of his books were popularizations of science and they were translated into many languages so most of the world learned about evolution not by reading Darwin (whose books were intended for scholarly readers and not the general public).

I read a recent biography of Haeckel by Robert J. Richards The Tragic Sense of Life: Ernst Haeckel and the Struggle over Evolutionary Thought (2008) and I learned a lot about German science in the 1800s. It was strongly influenced by the poet Goethe (whose Faust we know) who was trained as a scientist (he made his living as a mining engineer). Goethe helped launch the Romantic Movement in both the arts and sciences. Like Spinoza, he saw God in nature and this tinged German science with views of vitalism (animated matter). Haeckel started out that way but in 1864 he read the first German translation of Darwin’s Origin of Species and this enabled him to classify hundreds of marine protozoa called radiolarians (they have exquisitely beautiful shells but are single celled organisms). Using natural selection, Haeckel constructed a phylogenetic tree of their descent. He also coined three new terms –ecology (the study of organism in their environments), phylogeny (the study of a diverse group of organisms organized by their relatedness), and ontogeny (the study of life cycles, especially the embryological process that begins as a single fertilized egg).

Haeckel abandoned religion after his wife, whom he adored, died on his birthday, 18 months after their marriage, probably of an ectopic pregnancy. He felt a god who kills good people does not deserve to be worshipped and he became an atheist (he called his outlook monism) – only the world of matter existed; the supernatural being our own wish fulfillment. His popular books aggressively promoted both his evolutionary and atheistic views. Darwin avoided all mention of religion and tried hard to avoid a confrontation with those offended by his evolutionary views. This is why Haeckel was more hated than Darwin in the late nineteenth and early twentieth century.

Richards’ biography restores Haeckel’s good name. Haeckel was accused of fraud (in his illustrations used in popular science books), of being an academic lightweight, and of assisting German racism and anti-Semitism that led to Nazism, and of stultifying the progress of science (especially embryology). All of these are studied at great length by Richards, using primary sources, and all of them he shows to be false or distorted by his critics. Haeckel paid a price for his efforts to popularize science and his monist philosophy. Most of his contributions are now forgotten – he was the first (in 1866) to suggest heredity resided in the nucleus of the cell; he was the first to popularize the use of phylogenetic trees to depict the relations of species; and he was the first (in the 1870s) to develop experimental embryology (which two of his students extended some 20 years later)

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A ROSE IS A ROSE IS A PRODUCT OF FIVE GENES NECESSARY FOR FLOWER DEVELOPMENT

Few things irritate those in the humanities more than the efforts of science to reduce the metaphorical, complex, and beloved through the reductionism of experimental analysis. The image of scientists plucking sepals, petals, stamens, carpels, and ovules from a flower is debasing to the aesthetic sense of a rose. One thinks of Charles Dickens’ horror in Hard Times, when a student defines a horse as a “gramniferous quadruped” to the teacher’s (appropriately named Gradgrind) delighted but sterile soul. But such studies lead to medical cures, commercial applications in horticulture, new varieties to delight the eye, new scents to bring ecstatic responses, and many an amorous kiss when flowers are delivered from one lover to another. For scientists it is the understanding that trumps all of these otherwise desirable uses of new knowledge. Why new knowledge is so threatening is difficult to understand because every scientist I know who has made a discovery will describe the thrill as akin to writing a novel, composing a poem, working out a dance routine, composing music, or painting a landscape. Think of the pleasure it must be to wrestle one more unknown from nature.

In the 1970s two laboratories independently isolated three (now there are five) genes associated with floral development. They gave them the generic letters A, B, and C (now D and E have been added) and they called their theory the ABC theory of floral development. That’s easier to remember than to call it the Coen-Meyerowitz theory. If you look at a flower and (shudder) strip it of its components, the outermost will be the sepals, which are usually leaf-like. Then come the gorgeous colored petals. Next come the male organs or stamens; then innermost is the female organ or carpel with its inner treasure, the ovules. All have gene E. Sepals add an A. Petals have A and B as well as the E. Stamens dump the A and replace its function by turning on gene C. The carpel turns off the B and that leaves C and E. The ovules add the D function and that makes them CDE. Scientists can mutate any of these five genes and make abnormal flowers lacking one or more of these structures or putting the wrong component in the ring of structures we call a flower. It’s possible to convert hermaphroditic plants into two sex plants, one bearing stamens and the other bearing the carpels.

Molecular botany is having a great time identifying genes for flower scent formation, flower color, and making plants to order for different climates. The horticulture business generates 50 billion dollars a year so they are quite happy to hire molecular biologists to develop new varieties. They are also identifying and synthesizing the thousands of plant scents and floral pigments. There are genes for petal number, petal shape, and petal texture. For many of these botanists, it is like selecting fabrics to make quilts or dresses. It is like an artist’s palate of colors squeezed from tubes. We love seeing the gorgeous carmine used to paint a rose, but we would be aghast when told that is produced by scraping off thousands of scale insects from a cactus and crushing them to a powder to make the carmine dye. Sometimes we prefer not be in the kitchen to see how gourmet food is made. We prefer the mouth-watering fantasy of a gorgeous cut of T-bone steak and not the sight of a gutted carcass from which it comes.

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SOME INSIGHTS INTO THE ORIGIN OF MULTICELLULAR ANIMALS

Most animals that you have encountered are worms, insects, snails, clams, fish, lizards, snakes, amphibians, birds, or your fellow mammals. Some of you may have gone scuba diving and increased your repertoire of animals including corals, jellyfish, tunicates, and sponges. The least complicated in body plan of all these animals belongs to the sponges. They have only a few cell types. One of these, known as collar cells, have a filament (called a flagellum) that whips around inside a fringe-like collar attached to the cell. The flagellum sweeps up bacteria and smaller protozoa and digests them inside the cell. Very similar to these specialized cells of the sponges are protozoan single cells called choanoflagellates (a very fancy name for collared cells). When I was a graduate student at Indiana University taking a course in invertebrate zoology, I imagined that these choanoflagellates might have been ancestors of sponges in a distant evolutionary past.

In 2008 a team of California scientists coordinated by Nicole King and Daniel Rokhsar published a DNA analysis of a species of choanoflagellates, Monosiga brevicollis. It has about 9200 genes, which is about one half what most multicellular animals have (we have 23,000 genes in a sperm or egg). Monosiga has split genes, like humans, but its genes have slightly fewer “junk DNA” insertions (an average of 6.6 per gene compared to 7.7 in our genes). What were more interesting were the functions of some of Monosiga’s genes. They had several associated with cell adhesion (what makes cells stick to one another as they do in our muscles or skin), cell recognition, and immunological defense. Before King and Rokhsar’s work, these genes were thought to be unique to multicellular animals and missing in single celled protozoa.

The authors compared Monosiga’s genes with genomes of other plants, animals, and fungi. They found that of 24 genes associated with multicelled animals, only 3 were shared in fungi and plants, but Monosiga shared 16 of them. This is a striking association that suggests many of the components for animal evolution were present in protozoa like Monosiga. Very likely around 600 million years ago, an era called the Precambrian, the first gathering of cells by adhesion took place and by the Cambrian era the proliferation of animal types appeared in the fossil record. Future studies of the 125 known species of choanoflagellates and related protozoa and simple animal forms may reveal the way these different body plans came into being.

The difference between my vague suspicions some fifty years ago and the molecular and biochemical analysis possible today is stunning. Evolution studies are now providing models of how cellular processes, embryonic processes, and genetic processes participate in bringing about an evolution that predates the fossilized skeletal remains of more advanced forms of animals first appearing about 500 million years ago.