Introduction to Physical Anthropology

by Arnie Schoenberg
version: 3/6/19

Figure 64 map of sickle cell allele distribution by Arnie Schoenberg adapted from * Piel, F.B. t al. Global distribution of the sickle cell gene and geographical confirmation of the malaria hypothesis. Nat. Commun. 1:104 doi: 10.1038/ncomms1104 (2010) from * Malaria Atlas Project (CC BY 3.0)

Section 2 Contents

Full Table of Contents

2    intro to biology

2.1    Scale; Human Space; Powers of Ten for Physical Anthropology

2.2    evolutionary theory

2.2.1    history of evolutionary theory, up to Darwin

2.2.1.1    the fixity of species

2.2.1.2    The Great Chain of Being

2.2.1.3    John Ray

2.2.1.4    Carolus Linnaeus

2.2.1.5    Buffon

2.2.1.6    Erasmus Darwin

2.2.1.7    Jean Baptiste Lamarck

2.2.1.8    Georges Cuvier

2.2.1.9   geologists: James Hutton and Charles Lyell

2.2.1.9.1    geological time

2.2.1.9.2    the principle of uniformitarianism

2.2.1.10    Thomas Malthus

2.2.1.11    Mary Anning

2.2.2    Charles Darwin

2.2.2.1    understanding natural selection

2.2.2.1.1    sexual selection

2.2.2.2    Alfred Russel Wallace

2.2.3    beyond Darwin

2.2.3.1    Gregor Mendel

2.2.3.1.1    dominance and recessiveness

2.2.3.1.1    the principle of segregation

2.2.3.1.2    principle of independent assortment

2.2.3.1.3    Punnett squares

2.2.3.1.4    Mendelian traits laboratory

2.2.3.1.4.1   Example: PTC tasting

2.2.3.1.4.2   earwax

2.2.3.1.4.3   mid-phalanx hair

2.2.3.1.4.4   lactase persistence

2.2.3.1.4.5   relative finger length

2.2.3.1.5    ABO blood type

2.2.3.2    population genetics

2.2.3.3    the modern evolutionary synthesis

2.3    forces of evolution

2.3.1    mutation

2.3.2    natural selection

2.3.3    migration

2.3.4    genetic drift

2.4    genetics, cellular biology, and variation

2.4.1    cells

2.4.1.1    organelles

2.4.1.1.1    nucleus

2.4.1.1.1.1   chromosomes

2.4.1.1.2    mitochondria

2.4.1.1.2.1    mtDNA

2.4.1.2    cell division

2.4.1.2.1    mitosis

2.4.1.2.2    meiosis

2.4.1.2.2.1   oogenesis

2.4.1.2.2.2   spermatogenesis

2.4.1.2.3    recombination

2.4.1.2.2.1   crossing over

2.4.1.2.4   non-disjunction

2.4.1.3 fertilization

2.4.2    DNA

2.4.2.1    replication

2.4.2.2    protein synthesis

2.4.2.2.1     polygenic traits

2.3.2.2.2     pleiotropic genes

2.4.2.3    locus → gene → allele

2.4.2.3.1    introns and exons

2.4.3    cells and the source of variation

2.4.4    genetics and ethics

2.4.4.1    identity and ownership

2.4.4.2    stem cells

2.4.4.3    cloning

2.4.4.4     GMOs

2.4.4.5     lateral gene transfer

2.5    summary example: holism in anthropology, sickle cell anemia and malaria

 


 

2 introduction to biology

Physical anthropology is also called biological anthropology. You need to understand the basics of biology before you apply it to humans. We are going to use these ideas as the basis for explaining phenomena in later sections, such as: Why primates scream at each other? How are those two fossils related? Why do people look different from each other? What are people going to look like in a million years? Now is a great time to review your notes from your High School biology class.

Introduction

Physical anthropology is also called biological anthropology. Biology is a broad field that ranges in scale from the microscopic to the geographical. Evolutionary theory is crucial to biology. Charles Darwin's theory of natural selection came from a historical context where many other scientists were contributing to evolutionary theory. Natural selection means that individuals compete for resources and those with the variations that make them more fit to survive in a certain environment tend to survive and reproduce more. Sexual selection is the part of natural selection that focuses on competition for reproduction. Darwin understood the importance of variation.

Gregor Mendel used math to explain how variation is inherited. Population genetics used math to show how inheritance works in large populations. The modern synthesis combined Mendelian genetics and population genetics, to codify evolutionary theory into four forces: mutation, natural selection, migration, and genetic drift.

Inheritance, mutation, and other sources of variation can now be understood through cellular biology and genetics. Humans are made up of cells. Cells have DNA. DNA is the code that directs protein synthesis. Proteins direct the functions of life.

Sickle cell anemia is an example of how the holistic approach of anthropology can use many subfields, mostly from biology, to understand the origins and consequences of an important human disease.

Focus Questions

2.1     scale; human space; powers of ten for physical anthropology

Anthropology is a broad field that incorporates many sub-fields and borrows from many other disciplines, so the space that is relevant to physical anthropology is also vast. It ranges from the atomic particle that causes genetic mutation—the primary cause of evolution—to the plasticity of the human body because of our need to adapt to seasonal changes caused by the elliptical orbit of the planet in the solar system. Anything bigger or smaller is beyond the scope of physical anthropology. Why atomic particles behave the way they do is a question of physics. Whether life exists on other planets is a question of astrobiology. Both are good themes for philosophy and science fiction, but are beyond the scope of this class.

Meters

Common Measurement

Abbreviation

Relevance

10 0

1 meter

1m

space that an individual primate occupies

10 1

10 meters

10m

typical sleeping area of a primate social group

10 2

hectare/ 2.5 acres, football field

100m

typical core area of a primate social group

10 3

10 hectares, 1 kilometer

1km

typical territory of a non-human primate social group

10 4

100 hectares

10km

typical home range of a non-human primate social group

10 5

100 kilometers

100km

typical separation between the unique, learned, cultural behaviors of a non-human primate population

10 6

1,000 kilometers, continent

1000km

typical range of a non-human primate species; range for most of human evolution

10 7

10,000 kilometers, the surface of the planet Earth

100000km

the range of all biological evolution

10 12

1 billion kilometers, 1 terameter

1Tm

the Earth's orbit in the solar system, includes meteors and solar radiation

...

...

...

...

10 0

1 meter

1m

space that an individual primate occupies

10 -1

10 centimeters

10cm

length of a human's opposable thumb

10 -2

1 centimeter

1cm

human ear bones, Anopheles mosquito (malaria vector)

10 -3

1 millimeter

1mm

the height of a cusp on a Y-5 molar

10 -4

100 microns (micrometer)

100µm

typical patch of melanin, width of hair, human egg

10 -5

10 microns

10µm

typical primate cell

10 -6

1 micron

1µm

width of cell nucleus, length of Plasmodium falciparum (causes malaria)

10 -7

100 nanometers

100nm

typical locus, length of a gene

10 -8

10 nanometers

10nm

length of a codon (3 base pairs)

10 -9

1 nanometer

1nm

diameter of DNA helix, size of a base

10 -10

1 Œngstršm

size of an atom (changes in atoms can cause mutations and is used for molecular dating)

Notice that most of the larger ranges are relevant for hominid evolution and primate behavior, the medium sizes are used in osteology and to compare human and hominid variation. The smaller sizes can describe human variation and genetics. Refer back to this chart as we cover those relevant sections.

USE THIS CHART AND WATCH THE MOVIE: POWERS OF TEN:

“Recognize that the very molecules that make up your body, the atoms that construct the molecules, are traceable to the crucibles that were once the centers of high mass stars that exploded their chemically rich guts into the galaxy, enriching pristine gas clouds with the chemistry of life. So that we are all connected to each other biologically, to the earth chemically and to the rest of the universe atomically. That's kinda cool! That makes me smile and I actually feel quite large at the end of that. It's not that we are better than the universe, we are part of the universe. We are in the universe and the universe is in us.”
-Neil deGrasse Tyson

more on scale and measurements: human scale

Imagination Question

When you look in the mirror do you see yourself as a trillion cells, or a trillion, trillion atoms which came from stardust, or a collection of selfish genes, or an individual?

2.2     evolutionary theory

Don't go to a dictionary and look up the definition of "evolution". Most of the definitions are just going to reinforce your confusion. For this class we are using the biological definitions of evolution: the splitting of a lineage into two new species, or the change in allele frequency in a breeding population from one generation to the next. For this class an individual can never evolve in their lifetime, a cell phone operating system can never evolve, only a population or a species can evolve. Darwin understood the problem with the word "evolution" and preferred the phrase "descent with modification", but that obviously never caught on.

Understanding evolutionary theory is crucial for all the chapters that follow. For example, in the paleoanthropology section we will make arguments about how natural selection gave our ancestors advantages in different environments, and we will argue how gene flow kept our recent ancestors from becoming separate species. If you don't learn about the forces of evolution now you won't understand the arguments we're going to make later.

Evolutionary theory is a difficult concept. In the last section we discussed the ideological barriers that extremely dogmatic religious people have that might keep them from understanding evolutionary theory. Another common misconception of evolution is that there is inherently something good about it, that to evolve means to progress. The simple definition of evolution is just "change". It doesn't mean change for the better, or change for the worse, just that a species is different than what it used to be. It's important to separate how a word is used on the street from the very specific definition we are using here in our biological context. The main reason people have problems with a neutral definition of evolution is that we've had thousands of years of cultural baggage that clouds our empiricism. The philosopher Aristotle stressed the importance of finding the essence of a thing, and from this we get the concept of essentialism. People often think of humans as diverging from or progressing towards some ideal form, but these are cultural constructs, not what we empirically see in biology. We carry baggage around that makes simple concepts seem counterintuitive. Understanding the incorrect ideas helps us accept the correct ones.

* Read more about Darwin and design.

2.2.1     history of evolutionary theory, up to Darwin

It helps to understand evolutionary theory if you understand how it "evolved". I put "evolved" in quotes because for this class I want to reserve the word evolution to mean "biological evolution" and not confuse it with historical and cultural changes. There are different ways to study history, and for this section we need to be careful not to fall into the trap of thinking of history as a series of Great Men – important people who change the world through their personal actions. This way of looking at history is very convenient for an introductory class, because you just need to make a handful of flashcards with the names on one side, and what they're famous for on the other. But, try to look beyond the individuals, and imagine the broader movements that were going on at the time these individuals lived.

It helps sometimes to put people and concepts into two columns: did they contribute to evolutionary theory or did they detract from the development of evolutionary theory? But, many historical figures can be put in both columns, depending on their effect on history, and what stage of their life you look at. For example, Linnaeus made amazing strides in biological taxonomy, but opposed evolutionary theory, at least until the end of his life; Lamarck created a great theory of evolution, but it was wrong; Cuvier contributed to our understanding of extinction, but argued against evolution and fixity of species, Lyell argued against biological evolution until after Darwin convinced him; Wallace's evolutionary theory was mixed with quirky spiritualism; Darwin's theory of Natural Selection was revolutionary, but his emphasis on blending made it more likely to ignore important contributions from scientists like Mendel, and gradualism made it harder to accept punctuated equilibrium. Just realize that for an introductory class, we only have time to give you a cardboard cut-out of these fascinating and complex individuals and their historical milieux.

READ DENNIS O'NEIL'S INTRO

2.2.1.1     the fixity of species

In this modern world, we are so used to change that it's hard not be ethnocentric and imagine a time when things were pretty much the same as it was for your grandparents, and you expected things to be pretty much the same for your grandkids. Imagine growing up and liking the same music as your great-grandparents. Most religions around the world are conservative. God creates a world and some people to interact with it. And the reasoning often goes that if your deity is all-powerful, His creations would be perfect and He wouldn't need to keep tinkering with them. When people looked around at all the living creatures on the planet, they assumed that everything was stuck the way they saw it. This concept is called the fixity of species, and "fixity" in this case refers to being in a fixed position; unchanging.

Evolutionary theory is diametrically opposed to the fixity of species.

2.2.1.2     The Great Chain of Being

The Great Chain of Being incorporates the concept of the fixity of species but ranks life into better or worse, noble animals like eagles and lions go towards the top, slimy animals like worms and eels go down to the bottom. Noah's Ark usually boards the same way, first-class passengers first. When applied to humans, the Great Chain of Being has always functioned to perpetuate political oppression such as racism, sexism, and classism. The dominance of the Great Chain of Being in Eurasian philosophy makes it hard at first for many students to accept the complete absence of any system of ranking or progress in evolutionary theory.

 hierarchical tree that ranks life

Figure 15 1579 drawing of the Great Chain of Being by Didacus Valades from the Rhetorica Christiana. (Public Domain)

2.2.1.3     John Ray

Figure 16 Rev. John Ray © Bridwell Library Special Collections, Perkins School of Theology, Southern Methodist University

John Ray (1627-1705) is important to us because he invented the concept of the species (the word "species" is one of those Latin words that doesn't change between the singular and plural; "one species, two species"). Species are the most fundamental way of grouping life forms. You might ask how a book entitled "The Wisdom of God Manifested in the Works of Creation" could contribute to evolutionary theory but a common theme in all science is how scientists get some things right and some things wrong.

Figure 17 "The word 'species' always has an 's' on the end" by Dr. Arnie Schoenberg 2018, derived from, but not sponsored by, © 2016 Dr. Seuss Enterprises, L.P. and Oceanside Media (fair use)

In Ray's book History of plants he grapples with how to group the varieties of life, and he comes up with a concept that is still useful today – individuals that can reproduce are from the same species:

no surer criterion for determining species has occurred to me than the distinguishing features that perpetuate themselves in propagation from seed. Thus, no matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as to distinguish a speciesÉ Animals likewise that differ specifically preserve their distinct species permanently; one species never springs from the seed of another nor vice versa * [Ray 1686; Ray 1686]

A species is something that exists over time and is capable of perpetuating itself, and variations within a single species occur. Notice at the end of the quote how he insists on the fixity of species, and denies speciation, but we still use Ray's species concept today.

The definition of species in the * Endangered Species Act is what most biologists today call a population.

2.2.1.4     Carolus Linnaeus

Linnaeus is the father of taxonomy. Taxonomy was different from the Great Chain of Being because instead of grouping animals into Biblical categories, Linnaeus grouped them by biological characteristics: how they give birth, what they eat, aging, exterior movement, internal propulsion of fluids, diseases, death, glands, skin, and the shape of the inner ear (Foucault 1970). This list is very arbitrary compared to how today we compare the DNA of a species to classify it, but Linnaeus' taxonomy was radically different from the more poetic groupings of his time. Linnaeus was able to distinguish bats from birds and flying fish, and snakes from eels and worms. His taxonomy changed over his lifetime and has been an important concern of biology to this day.

His approach to classifying humans codified scientific blunders regarding race that have continued over two centuries.

READ THIS  INTRODUCTION TO LINNAEUS

Figure 18 1760 Hoppius based on Linnaeus, left to right: Troglodytes, Lucifer/Homo caudatus, Satyr, Pygmie (public domain)

Figure 19 from Linnaeus's 6th edition of Systema Naturae 1748 (Public Domain)

* Briefly scan Linnaeus' system of nature 1740

* Skim the pages on humans from this 1757 version

2.2.1.5     Buffon

George Louis Leclerc, Comte de Buffon wrote about how life changes according to the environment but didn't explain how.

2.2.1.6     Erasmus Darwin

Erasmus Darwin was the grandfather of Charles Darwin and his poetic writing about how life forms might change influenced his grandson, Charles.

* if you like prose, skim his chapter on generation

2.2.1.7     Jean-Baptiste Lamarck

Lamarck is known for his theory of Acquired Characteristics, also called the Use-Disuse theory. The theory goes that the physical traits you change during your lifetime get passed on to your kids. So if you believe in Lamarck's theory then you would expect Arnold Schwarzenegger's babies to be born with lots of muscles.

Arnold Schwarzenegger

Figure 20 http://www.bodybuilding.com/fun/arnold-schwarzenegger-blueprint-trainer-mass-training.html (permission pending)

Description:https://www.advancedphotoshop.co.uk/users/2598/thm1024/docubaby.jpg

Figure 21  "Baby" by Tobias Hellstršm © 2008

Of course, Lamarck was wrong. Physical characteristics acquired during an individual's lifetime are not transferred to its offspring (with a few epigenetic counterexamples). We'll show why he was wrong in the section on cellular biology. The reason Lamarck's theory sounds so plausible is because culture is transmitted this way; what you learn during your lifetime can be taught to your children. But biological inheritance has very specific mechanical processes that we can now see in a microscope. You have to give Lamarck credit for coming up with an elegant theory of evolution. It has been disproven, but it was still a great theory for its time. Understanding why Lamarck was wrong will help you understand natural selection.

LOOK AT THE CLASSIC EXAMPLE OF GIRAFFES

SKIM THIS BIOGRAPHY OF LAMARK

2.2.1.8    Georges Cuvier

Cuvier is important to evolutionary theory in promoting the concept of extinction. He saw fossils of animals no longer on the planet, such as giant elephants, and he correctly explained their disappearance as extinction, the big elephants just died out.

Figure 22 The jaw of an Indian elephant and the fossil Jaw of a mammoth from Cuvier's 1798–99 paper on living and fossil elephants (public domain)

His views on extinction contributed to evolutionary theory but his attempts to reconcile geology with The Bible did not. Cuvier is also known for his theory of Catastrophism: extinctions in the fossil record are only because of sudden changes in the environment, such as world wide floods, like Noah's flood.

2.2.1.9     geologists: James Hutton and Charles Lyell

Geology has always had a profound impact on evolutionary theory. Most of the scientists of the 18th and 19th Centuries called themselves "naturalists" and didn't distinguish between fields such as geology and biology. James Hutton and Charles Lyell were two of the most important scientists to use empirical observations to guide theories of how the Earth arose and became what we see today. Their two main contributions to evolutionary theory are the concept of geological time and the principle of uniformitarianism.

Geology is important to biological anthropology in many ways, such as dating and environmental context in paleoanthropology. In archaeology, Lyell's Law of Superposition is crucial – the deeper you dig, the older things are.

2.2.1.9.1 geological time

How long are you going to live? 50 years? 100 years? The length of time that you can perceive is limited by your own biological expiration date. The neat thing about geology is you start thinking like a rock. Imagine 1,000 years passing, 10,000 years, 100,000 years, 1,000,000 (a million) years, 1,000,000,000 (a billion) yearsÉ Lyell proved that the Earth is old, that rocks have been around for a long time. This was important to biologists and paleontologists because it showed that fossils are very old too. If life has been around for billions of years we can more easily accept that drastic changes could happen over that long a time span. Geological and astronomical time is sometimes called Deep time, and it is one of those very disturbing nonhuman concepts that science often forces us to think about.

* Bishop Ussher dates the world at 4004 BC.  

explore our current understanding of geological time

2.2.1.9.2 the principle of uniformitarianism

What happened in the past continues to happen today. Most cosmologies around the world have some concept of a mythical past, where different laws of nature applied. Lyell demonstrated that huge geological formations can be explained by the same simple forces that we see today, such as erosion, wind, earth moved by earthquakes. We can explain something as awesome as the Grand Canyon with two simple processes that can be seen today: uplifting and erosion.

In biology, we can find simple processes that differentiate me from a banana slug. Both, the biological and the geological require huge quantities of time.

* skim the 1830-3 Table of Contents of Lyell's Principle of Geology (10 pages)

2.2.1.10  Thomas Malthus

Malthus studied demography, how populations change. Overpopulation creates competition for limited resources. This idea of competition within a population is similar to the idea of competition within a species, and creates change. According to Malthus, humans can increase their population faster than they can increase their food supply. Having more people than food leads to starvation and competition for limited resources.

For example, imagine that Octamom has 8 daughters who each have 8 daughters who each have 8 daughters who each have 8 daughters, and in 5 generations you have a population of around 32,000. When Octamom works a plot of land she can produce one bushel of food per month, with her daughters helping she can produce 2 bushels, with her grandkids helping, 3 bushels, but by the time her great-great-grandkids have exhausted the nutrients in the soil, and run out of fertilizer made from non-renewable resources, her descendants are back to producing about 3 bushels a month, except it's like a Mad Max dystopia with thousands fighting over those few bushels, and most starving to death.

Darwin took Malthus' very specific observations of how humans compete for limited resources and generalized them to the broader field of biology.

2.2.1.11  Mary Anning

Mary Anning was the most famous fossilists of 19th century. A fossilist is someone who gathers fossils. A fossil is the imprint of a biological form, and we will come back to fossil in the sections on paleontology and paleoanthropology. Fossils represent biological data. If we go back to section 1.1 and consider the scientific method, it's important to remember that hypotheses are based on empirical observations, things we can see with our own senses. With a phenomenon like gravity you see the apple falling from the tree, but seeing evolution is more difficult. What many of the evolutionary thinkers of the 19th century got to see were the fossils collected by Mary Anning.

* Watch this puppet show of Mary Anning's life

Imagination Questions

2.2.2     Charles Darwin

One of the most profound impacts Darwin had was to change how we ordered life, from a ladder (like the Great Chain of Being) to a tree.

Figure 23 Some researchers believed life developed in a linear fashion, from simple to more complex forms (left). Darwin compared the emergence of new species to the branching of a tree (right). by * The University of California Museum of Paleontology, Berkeley and the Regents of the University of California © 2018

READ DENNIS O'NEIL'S DARWIN AND NATURAL SELECTION

sketch of tree and interpretation

Figure 24 from Charles Darwin's 1837 private notebook “Notebook B on the transmutation of species,” 1837–1838 (public domain)

The sketch above is Darwin's main Eureka! moment and contribution to evolutionary theory. He shows how species (1) evolves into species A, B, C, and D, and everything in-between goes extinct: "I think ... Case must be that one generation then should be as many living as now. To do this and to have many species in same genus (as is) requires extinction. Thus between A & B immense gap of relation. C & B the finest gradation, B & D rather greater distinction. Thus genera would be formed.—bearing relation [next page] to ancient types with several extinct forms."

This is barely legible, confusing, and poorly written, so please don't use this as an example of anything you want to turn in for my class. Darwin's genius comes from translating this sketch into a 500 page bestseller by 1859, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, which thoroughly explained Natural Selection and supported it with voluminous evidence. We remember Charles Darwin's not for the Aha! moment in 1837, but for the two decades of work he did afterwards to finish On the Origin of Species by 1859. The media tends to sensationalize scientific discovery (e.g. Isaac Newton gets hit by an apple and suddenly understands the mathematical equation that describes gravity), but for most scientists, it's more about hard work.

Figure 25 On the Origin of Species by Charles Darwin 1859. Photo by Wellcome Collection CC-BY-4.0

Open Charles DARWIN'S 1859 ON THE ORIGIN OF SPECIES BY MEANS OF NATURAL SELECTION, OR THE PRESERVATION OF FAVOURED RACES IN THE STRUGGLE FOR LIFE.; READ THE THE DESCRIPTION OF THE CHAPTERS CAREFULLY (Page V to Page X), then skim the rest for a few minutes

* a more readable version of On the Origin of Species, or this ebook, and more of Darwin's writtings,

Darwin had an unremarkable personal life. He wasn't a great student, he didn't have strong philosophical, political, or religious views.

* Good summary of Darwin's personal life

Darwin did not use evolution to promote atheism, or to maintain that no concept of God could ever be squared with the structure of nature. Rather, he argued that nature's factuality, as read withing the magisterium of science, cannot resolve, or even specify, the existence or character of God, the ultimate meaning of life the proper foundations of morality, or any other question with the different magisterium of religion. [Gould 1999]

He wasn't oblivious to the social consequences of his findings, and was reluctant to publish.

*watch Creation: a pretty good Hollywood movie about Darwin's personal and ethical problems; the story of how the movie was censored in the US says a lot about how this is still an important political issue.

Figure 26 Creation movie poster 2009 (fair use)

2.2.2.1     understanding natural selection

Figure 27 "Evolution is no different than your family tree … except over a much longer period of time." by M.F. Bonnan/Florida Citizens for Science © 2010

A classic example of natural selection is the industrial melanism of the peppered moth. The same species of moth has black moths and white moths which can interbreed. When they land on white tree bark, the black moths tend to be eaten, and they become rare. Because of industrial pollution, the bark turned black, and now the white moths became rare. They cleaned up the pollution, the bark became lighter, the white moths survived more than the black moths. There are a few problems with the research but it is still a great example of how evolution works.

a dark and light moth on a dark tree trunk

Figure 28 Which moth is most likely to survive a hungry bird? from "The Role of Photographs and Films in Kettlewell's Popularizations of the Phenomenon of Industrial Melanism" by Rudge, D.W. Science & Education (2003) 12: 261.

"Peppered Moths: Natural Selection in Black and White"

Figure 29 * a video game that simulates Kettlewell's research by Craig Tevis © 2003 (permission pending)

* Scientists may have found the gene that determines the color change of the moths.

Unfortunately, very few of us have grown up on a farm, so it's hard for us to understand where Darwin got the phrase "natural selection" from. We don't ever use the phrase "unnatural selection" but that's what human selection is. After every harvest the farmer notices the tastiest, biggest, or most fruitful plants and keeps their seeds until next season to plant, and animal breeders mate their best stock together. The farmers and breeders are selecting desirable characteristics and increasing the chance that they will be passed on to the next generation. From this process of selection we get all the food we eat today and an amazing range of domesticated pets.

Big and little dog 1

Figure 30 "Big and Little Dog" By Ellen Levy Finch CC-BY-SA-3.0

We see In the archaeological record of Mesoamerica how teosinte was selected over thousands of years and became corn.

AppleMark

Figure 31 Mesoamerican farmers selected for a gradual accumulation of mutations to get from teosinte to maize, photos by Hugh Iltis (left) and John Doebley (right), © * The Doebley Lab, Department of Genetics, University of Wisconsin-Madison

Part of Darwin's genius was to recognize that the process farmers and animal breeders use to change a species, was also a natural phenomenon, that competition in an environment of limited resources would select those individuals who were more fit for that environment, and he coined the phrase "natural selection"

.

When we use the word "fit", don't think of 24-Hour Fitness, think of square peg fits into square hole, round peg fits into round hole. Some individuals fit into an ecosystem or an environment better than others.

Figure 32 Fitness by Yoel Ben-Avraham, Flickr (Permission Pending)

*Article on genes and dog size

2.2.2.1.1    sexual selection

Darwin didn't stop with natural selection, he continued to expand evolutionary theory throughout his lifetime. Darwin avoided a few difficult ideas in The Origin of Species and left them for his 1871 work:* THE DESCENT OF MAN, AND SELECTION IN RELATION TO SEX. This book tackled both a difficult scientific question – sexual selection, and a difficult social question – the origins of humans. And within the book, Darwin left his most controversial chapters at the very end:* Part II Sexual selection of man (316-84) and General summary and conclusion (385-405).

Peacocks gave Darwin a headache. Natural selection implies that tasty defenseless birds are more likely to survive and reproduce if they are camouflaged and avoid predators. But, selection is more than just surviving, you need to mate to pass your genes on to the next generation. If you are so hidden that the opposite sex can't find you, the camouflage strategy backfires. Male peacocks are flamboyant to attract female penhens. Peahens are drab and camouflaged to avoid predators, just as chicks of both sexes are drab. The balance between survival and reproduction led to an exact timing where male chicks become flamboyant at the same time as they're ready to reproduce. Darwin expanded natural selection to include sexual selection, and it became a useful explanation for some of the weirdest shapes, patterns, and behaviors in biology. Sexual selection has been to explain why humans have big butts.

Description: Minnie:Users:Arnie:Desktop:City:Graphics:FemaleChickPeacock_1686.JPG

Figure 32 "Peahen and chick" by Arnie Schoenberg (CC BY-NC 4.0)

Description: Minnie:Users:Arnie:Desktop:City:Graphics:MalePeacock_1709.JPG

Figure 33 "Peacock" by Arnie Schoenberg (CC BY-NC 4.0)

But, what especially bothered Darwin, and the male chauvinist scientists of his time, was the idea that the female was responsible for choosing the mate and driving evolution. When people try to apply their cultural beliefs to the natural world they more often then not end up with trite metaphors. Human culture is something very different from nature. Be very careful when comparing sexual differences in other animals to human gender.

2.2.2.2     Alfred Russel Wallace

Wallace was almost famous, but Darwin published before him.

READ DENNIS O'NEIL'S DARWIN AND NATURAL SELECTION

WATCH THE 'THE ANIMATED LIFE OF A.R. WALLACE'

* Skim Wallace's early, 1855, article on evolutionary theory: On the Law Which Has Regulated the Introduction of New Species, skip to the end and read the comments by Bernard Michaux who argued that Wallace probably believed in something close to natural selection because his article contains all the important themes of Darwinism: "gradualism, utility, adaptation to different environments, allopatric speciation, imperfection of the fossil record" (Michaux 2000).

Imagination Question

1) Natural Selection
In the novel Cryptonomicon, Neal Stephenson presents the origin of his protagonist as a series of survivors:

Like every other creature on the face of the earth, [he] was, by birthright, a stupendous badass, albeit in the somewhat narrow technical sense that he could trace his ancestry back up a long line of slightly less highly evolved stupendous badasses to that first self-replicating gizmo—which, given the number and variety of its descendants, might justifiably be described as the most stupendous badass of all time. Everyone and everything that wasn't a stupendous badass was dead.

In the movie Beast of the Southern Wild, the teacher describes a mythical predator depicted in the Lascaux cave paintings as

a fierce, mean creature that walked the face of the earth back when we all lived in caves. They would gobble the cave-babies down right in front of their cave-parents. And the cavemen couldn't do nothing about it, because they were too poor, too stupid, too small.
Who up in here think the caveman was sitting around crying like a bunch of pussies? Y'all gotta think about that.
Any day now, the fabric of the universe is coming unraveled. Ice caps gonna melt, water's gonna rise, and everything south of the levee is going under. Y'all better learn how to survive now.

Do you think of yourself as a badass? Do you give your ancestors credit for making you what you are? Do the hardships your ancestors overcame inspire you to overcome the problems of the future?

2) Money talks

A) If Wallace's family had more money, evolutionary theory might have gone down a different path. Wallace was more spiritual than Darwin. Jonathan Marks defines "Atheistic Darwinism" as the use of Darwin to support atheism (2011:57-9). Maybe the backlash against evolutionary theory would have been less with Wallace at the helm?

B) The fictional protagonist of Elizabeth Gilbert's novel The Signature of All Things comes up with a "theory of competitive alteration" almost identical to Darwin and Wallace, through the same methods of empirical research and world travel, but she never publishes it, mostly because of her gender. How does power influence science?

3) Great Chain of Being

Below is a tongue-and-cheek reference to the Great Chain of Being from Margaret Atwood's novel Life Before Man:

Auntie Muriel is unambiguous about most things. Her few moments of hesitation have to do with the members of her own family. She isn't sure where they fit into the Great Chain of Being. She's quite certain of her own place, however. First comes God. Then comes Auntie Muriel and the Queen, with Auntie Muriel having a slight edge. Then come about five members of the Timothy Eaton Memorial Church, which Auntie Muriel attends. After this there is a large gap. Then white, non-Jewish Canadians, Englishmen, and white, non-Jewish Americans, in that order. Then there's another large gap, followed by all other human beings on a descending scale, graded according to skin color and religion. Then cockroaches, clothes moths, silverfish and germs, which are about the only forms of animal life with which Auntie Muriel has ever had any contact. Then all sexual organs, except those of flowers. [Atwood 1979]

There has always been implicit racism in the Great Chain of Being; social inequalities were created by God. But there are broader questions. Why do humans feel the need to rank things? Why do we make top ten lists? Facebook started as a facial ranking network, Hot or Not. The grade you get in this class is basically part of a ranking system for employers and other schools. The difference in salaries between full-time and part-time faculty separates professors into two socioeconomic classes.

In the primate behavior section coming up, we'll see other primates similarly obsessed with dominance hierarchies. Perhaps ranking is human nature?

2.2.3     Beyond Darwin

Science doesn't stop with a founder. Creationists blame Darwin for evolutionary theory, but most biologists wouldn't call themselves "Darwinists", any more than most physicists wouldn't call themselves "Newtonists." Natural selection is just one factor of evolutionary theory. People know much more about evolution today than they did during Darwin's time. That doesn't mean that Darwin was wrong, just that science has progressed.

Darwin often gets blamed for Social Darwinism, the political ideology that extends "survival of the fittest" to justify exploiting the poor, but Darwin didn't come up with this phrase nor did he apply Natural Selection to human society. Social Darwinism was invented and promoted by others such as Herbert Spencer, Thomas Huxley, and Francis Galton. Charles Darwin objected to the application of his biological model to human social structure, and he definitely would have objected to the "Darwin Project" battle royale game, and "Darwin Awards" given out in his name.

Figure 34 Darwin Awards (permission pending)

So far, our overly broad unifying theories that try to justify Social Darwinism haven't ammounted to much more than interesting metaphors, so please try to separate nature from nurture: biology from culture.

2.2.3.1     Gregor Mendel

Even though neither Darwin nor Mendel knew about how heredity worked at the cellular level, it's almost impossible to talk about the consequences of their work without referring to what we know now. So we will introduce a few terms in this section that are anachronistic, and we'll wait to explain them in depth until the section on cellular biology.

Figure 35 Gregor Mendel from * "On Tenderness: What Genetics Godfather Gregor Mendel Teaches Us about the Heart of Science" by Maria Popova, 2013 (permission pending)

The genius of Mendel is how he used mathematics to show how inheritance worked.

 

Figure 36 Mendel counted peas, courtesy of the Mendelianum, ©Moravian Museum Brno.

2.2.3.1.1    dominance and recessiveness

Remember that Gregor Mendel (1822-1884) didn't know about DNA when he did his experiments, he didn't see meiosis in the microscope, he wasn't directly involved in the debates over evolution, but he found one of the sources of variation that Darwin's theory of natural selection relies on, and he discovered two important principles that are the foundation of genetics: The Principle of Segregation and The Principle of Independent Assortment. Darwin knew that variation was crucial to his theory, but he didn't know the source of variation.

The pea plant has variation. Some seeds are smooth, some wrinkled; some yellow, some green. Some pods are inflated, some constricted; some green, some yellow. Some flowers are purple, some white; some along the stem, some at the top. Some stems are tall, some are short. Mendel was careful to exclude other kinds of variation: how some plants are eaten by snails, some don't get enough water, some too much sun, some are cooked in soup, some peas are overcooked, some shot through straws. Mendel ignored all these things that happen to peas and only paid attention to this first set of variations, the either/or inherent characteristics that can be seen.

Mendel was rediscovered around 1900. Theories of inheritance at the time of Mendel focused on blending, for example, one parent with extremely dark skin and one parent with extremely light skin have a child who is neither very light, nor very dark, but a color that is in between the extremes. But when Mendel bred purple flowers with white flowers, he got only purple flowers, and then when he bred those purple flowers together, in the next generation he got mostly purple but some white ones. The white flower trait disappeared and then came back. The purple color dominated the white one, but the recessive white color was not gone for ever, it came back in a later generation. If you cross a purple flower with a white flower, Darwin would have expected a whitish-purple flower. What happened to the blending?

If you don't remember from your high-school biology class, here are some basics that we got from Mendel:

2.2.3.1.1    The Principle of Segregation

     Good science can come from unlikely sources. Mendel would momentarily escape from the duties of a monk in a cold monastery.

   Mendel frequently took sanctuary in the little two-room building nestled into a corner of the monastery courtyard right up against the brewery next door. It gave him not only blessed warmth but also the space to engage in his scientific pursuits -- which would, he believed, prove important enough in time to earn him a place in the annals of horticulture. He had filled the glasshouse's long tables with pots of pea plants, each carefully labeled as to seed source and variety. His immediate goal was to breed these peas, thirty-four different seed types in all, after allowing them to self-fertilize for two full years. In the speeded-up growing seasons of the glasshouse, two years of growing meant perhaps six full generations -- enough to assure Mendel that the seeds were indeed what they appeared to be. [Marantz Henig 2000:14]


     Mendel isolated and bred different pea plants together and observed the characteristics of their offspring, and what really amazes me is that he counted them--and looking at the numbers he noticed patterns, and used simple math to work out the ratios of different traits.

First, he crossed true breeding plants (P) to get heterozygous plants, called hybrids (F1), and then he crossed those hybrids with each other (F1 x F1 = F2) and counted:

Expt 1: Form of seed. –– From 253 hybrids 7,324 seeds
were obtained in the second trial year. Among
them were 5,474 round or roundish ones and
1,850 angular wrinkled ones. Therefrom the ratio
2.96:1 is deduced.

Expt 2: Color of albumen. –– 258 plants yielded 8,023
seeds, 6,022 yellow, and 2,001 green; their ratio,
therefore, is as 3.01:1.

[...]

Expt. 3: Color of the seed–coats. –– Among 929 plants,
705 bore violet–red flowers and gray–brown seed–
coats; 224 had white flowers and white seed–
coats, giving the proportion 3.15:1.

Expt. 4: Form of pods. –– Of 1,181 plants, 882 had them
simply inflated, and in 299 they were constricted.
Resulting ratio, 2.95:1.

[...]

Expt. 5: Color of the unripe pods. –– The number of trial
plants was 580, of which 428 had green pods and
152 yellow ones. Consequently these stand in the
ratio of 2.82:1.

Expt. 6: Position of flowers. –– Among 858 cases 651 had
inflorescences axial and 207 terminal. Ratio,
3.14:1.

Expt. 7: Length of stem. –– Out of 1,064 plants, in 787
cases the stem was long, and in 277 short. Hence a
mutual ratio of 2.84:1. In this experiment the
dwarfed plants were carefully lifted and
transferred to a special bed. This precaution was
necessary, as otherwise they would have perished
through being overgrown by their tall relatives.
Even in their quite young state they can be easily
picked out by their compact growth and thick
dark–green foliage. [Mendel 1865]

Notice that the ratios of the F2 generation work out to about 3:1 which means that three plants have the dominant phenotype for every one plant that has the recessive phenotype. Mendel showed that each trait (seed color, seed shape, pod shape, pod color, flower color, flower position, stem length) is determined by a pair of characters, and they get them from their parents, one from the pollen cell and one from the egg cell, which come together to form the embryo. When the pollen and egg cells are made, these two characters are "segregated" so each egg and pollen cell has only one character. In genetics we now call these traits, genes, and the pair of characters is called a pair of alleles. From cellular biology, we now know that the segregation of alleles during the production of eggs and sperm is called meiosis. We'll come back to this in the sections on genetics and cellular biology.

2.2.3.1.2    the Principle of Independent Assortment

If you take true breeding plants with two different traits, like form of seed and color of seed-coat, cross them together, you first get all of the dominant trait. Then if you cross those new versions again, you get some interesting numbers 9:3:3:1 The numbers reveal that there's no connection between the traits; the traits are independently assorted. We can now explain this with cellular biology because the two traits are on different chromosomes.

2.2.3.1.3    Punnett squares

A Punnett square is a grid or matrix that represents the outcomes of different combinations. They are often presented as proofs of Mendel's Principle of Segregation and Principle of Independent Assortment, but Punnett squares came after Mendel, and I think it's important to understand the steps Mendel went through in his research: empirical observations of pea plant variations, breeding true-breeding plants, crossing specific traits, getting weird results, counting them, working out simple ratios, explaining the ratios as biological Principles as to how the peas (and all life, including humans) reproduce and transmit the information using traits from parent to offspring. Punnett squares are graphic representations of sexual reproduction: all the possible sperm are one axis, all the possible eggs on the other, and in the middle are all the possible combinations of fertilization ­– the individual zygotes (fertilized egg) who develop into fetuses, babies, and then adults. About a hundred years after Mendel's experiment we got to look in a microscope to confirm Mendel's mathematics and we continue to explore Mendelian traits in humans.

Read: "Mendelian laws apply to human beings"

Here is an example using Tay-Sachs disease. The * HEXA gene on chromosome 15 makes part of an enzyme that is important for maintaining your central nervous system. If you have one or two normal alleles, you're OK, but if both your alleles have a Tay-Sachs mutation, then you'll have different neurological problems usually starting as an infant. If you are a genetic counselor and a couple comes to you planning to have kids, and they are both carriers (heterozygotes), you want to be able to tell them what is the chance their baby will have Tay-Sachs. If we assign symbols to alleles, "t" = a Tay-Sachs mutation, and "T" = normal HEXA allele, then we can diagram the possible outcomes of fertilization.

 

T

t

T

TT

Tt

t

Tt

tt

Statistically, 25% of their children will be normal (TT), 50% of their children will be carriers (Tt), and 25% of their children will be born with Tay-Sachs (tt). This principle works with most recessive diseases.

Autosomal recessive EN

Figure 37 "Autosomal Recessive" by By Aymleung from Wikimedia Commons (CC BY-SA 3.0)

If it's a dominant trait then there are no cariers, only one parent needs a single copy to be affected, and half the kids will get the trait.

Autosomal dominant - en

Figure 38 "Autosomal Dominant" by Français : Domaina from Wikimedia Commons (CC BY-SA 3.0)


2.2.3.1.4    MENDELIAN TRAITS LABORATORY

Your phenotype results from the interaction of your genotype and the environment. Most traits are polygenic, meaning several genes contribute to how they are expressed. Even though your genes guide your development, the environment where you grow up influences how those genes are expressed. The combination of polygenic and environmental influence leads to an amazing variety of individuals. However, humans have a small number traits that are readily observable because they are: 1) Mendelian (determined by a single gene) so their expression is on/off, 2) tend not to be effected by the environment, 3) have high enough allele frequencies that someone in the class probably expresses them, and 4) are visible without genetic testing.

For each of the traits described below (PTC tasting, cerumen, mid-phalanx hair, lactase persistence, relative finger length), your assignment is to: 1) record your phenotype, 2) assign letters to represent the alleles of the gene, and 3) list your possible genotypes according to Mendel. Describe each of your phenotypes in a complete sentence: "I can ____.", "I cannot ___."; "I have ____.", "I don't have ____." Include only the trait that you express. Mendelian genetics assigns letters or combinations of letters to represent alleles. For two-allele genes, often a single letter is used, the capital letter for the dominant allele and the lowercase letter for the recessive allele. For a two-allele gene, you can have three possible genotypes: heterozygous, homozygous dominant, and homozygous recessive. Depending on your phenotype, you may have more than one possible genotype that leads to the phenotype that you observed. [text adapted from Mendelian Traits Laboratory; missing source]

2.2.3.1.4.1    Example: PTC tasting

PTC, or phenylthiocarbamide, is a human-made chemical. While the majority of people find PTC to have a bitter taste, many find this substance tasteless. To discover your phenotype, chew a strip of filter paper that has been soaked in a concentrated solution of PTC. The ability to taste PTC is inherited as a dominant. There are some studies that compare tasting PTC to tasting broccoli. There are several genes and environmental influence involved but "PTC tasting is largely determined by a single gene, TAS2R8, with two common alleles, and the allele for tasting is mostly dominant over the allele for non-tasting" (McDonald 2012).

You would write:

PTC Tasting


My phenotype: Broccoli tastes bitter to me, and I can taste PTC.


Alleles: B= the allele that codes for tasting PTC; b= the allele that codes for not tasting PTC

My possible genotypes: BB or Bb

or depending on your phenotype you might write:

PTC Tasting


My phenotype: Broccoli tastes good to me, and I can't taste PTC.

Alleles: B= the allele that codes for tasting PTC; b= the allele that codes for not tasting PTC

My possible genotypes: bb only

Now try to follow this example for the traits below:
2.2.3.1.4.2    EARWAX

Earwax, or cerumen, occurs in two basic forms. The dry form is gray and brittle while the wet form is brown and sticky. The dry form is inherited as a recessive. The gene is located on * chromosome 16

Figure 39 "Mimikaki -- Japanese Ear Picks" © 2014 Dr. Timothy C. Hain (http://www.dizziness-and-balance.com/disorders/hearing/images/mimi2.jpg)

Figure 40 "Cotton swab" by Aney. Wikimedia Commons (CC BY-SA 3.0)

2.2.3.1.4.3    MID-PHALANX HAIR

Look at the middle segment (phalanx) of your fingers. Note the presence or absence of hair. Complete absence of hair reflects a homozygous recessive genotype. Note that some types of work may wear the hair away.

2.2.3.1.4.4    LACTASE PERSISTENCE

The ability to digest milk as an adult is a dominant trait. This is good example of biocultural evolution: a biological trait intertwined with cultural factors (how people produce food).

* more info at Wikipedia

2.2.3.1.4.5    RELATIVE FINGER LENGTH

Lay your right hand on a piece of lined paper with the fingers perpendicular to the lines. Note the relative lengths of the second (index) and fourth (ring) fingers. There are three possible situations: the second finger is longer than the fourth, the second finger is shorter than the fourth, or the second finger is the same length as the fourth.

Individuals who are homozygous for the allele for short index finger have a shorter index finger. Individuals who are homozygous for the allele for long index fingers have longer index finger. Individuals whose index and ring fingers are equal length are heterozygous. However, this is not a true Mendelian trait because the expressions of the two alleles in the heterozygous individual show that this trait is influenced by at least one other gene on the 23rd chromosome. Heterozygous males express an index finger that is equal to or shorter than the ring finger. But heterozygous females will have an index finger that is equal or longer than the ring finger.

Because this is a sex-linked trait, your relevant phenotype should also include whether you are male or female.

Figure 41 "Index finger longer than ring finger" by Arnie Schoenberg, adapted from "Gaye Holud and Mehendi" by Russell eee from Wikimedia Commons (CC BY-SA 4.0)

IS YOUR RING FINGER LONGER THAN YOUR INDEX FINGER?               

If so, you're up to three times more likely to develop arthritis of the knee than women whose ring fingers are the same length as or shorter than their pointers. The British scientists who discovered the link speculate that it may have to do with hormones. This finger pattern is more common in women with low estrogen levels. Another clue: Men are more likely to have longer ring fingers, but for them, there's less of an arthritis link.
 [Good Housekeeping 2008:37]

Figure 42  Male and female hand prints. © Roberto Ontanon Peredo, Dean Snow

* article on cave art and relative finger length


2.2.3.1.5    ABO Blood type

READ DENNIS O'NEIL ON HUMAN BLOOD

ABO is a mostly Mendelian trait because both the A and B alleles are dominant to O allele. It's not a true Mendelian trait because the A and B alleles are co-dominant to each other, and this is how you can get type AB blood.

Try not to confuse the letters (ABO) with the positive/negative (+ -). The ABO blood type is determined by the pair of alleles on a gene located on the ninth chromosome. The Rhesus factor (Rh+, Rh-) is determined by a different pair of alleles on a different gene located on the first chromosome. So when someone says your blood type is "A positive", they're actually talking about two different blood types on two different chromosomes. Because they are on different chromosomes they are assorted independently during meiosis. Mendel's Principle of Independent Assortment demonstrated how this works before we knew about chromosomes.

Figure 43 "Antibody" by Fvasconcellos via Wikimedia (Public Domain)

Figure 44 ABO blood group system by InvictaHOG via Wikimedia (Public domain)

Try to shift your thinking from Dominant means good/strong/prevalent, and Recessive means bad/weak/rare. Recessive just means it takes two alleles to expressive the trait. Dominant means you can have 2, or just 1 allele to express the trait. Don't conflate dominance with fitness. Dominance has to do with Mendel and inheritance, fitness is from Darwin's theory of natural selection.

REVIEW DENNIS O'NEIL'S MENDELIAN GENETICS

* Skim Mendel, Gregor. 1865. "Experiments in Plant Hybridization"

* Play around with the Online Mendelian Inheritance in Man database. Try typing in the name of a disease, or body part into the search engine, and follow the link.

Vocabulary

2.2.3.2      population genetics

By the 1920s, a new definition of evolution became popular: "a change in allele frequency". We're looking at how many people have a trait in one generation and how it might change in the next generation.

To translate a Punnett square into math, just replace the sperm and eggs with variables that represent allele frequencies, and you get a pretty simple algebraic equation, that can be used to study how populations change over time. It was discovered independently in 1908 by two scientists: Hardy and Weinberg.

 

p

q

p

pp

pq

q

pq

qq

A frequency is just another word for a percentage except we write it as a decimal e.g.  = .5 is the same thing as saying 50% are p, or that half the alleles are p. This implies that the other half are q, because with a two-allele gene, the percentages have to add up to 100% (the frequencies add up to 1.00), so

p + q = 1

we can square both sides to get:

(p+q)2 = p2 + 2pq + q2 = 1

Now compare this to the Punnett square: pp is p2, qq is q2, and the two pq are 2pq. The p2 and q2 represents the frequencies of the homozygotes and 2pq represents the frequency of the heterozygote. So you can take a population, count the total alleles, and count the phenotypes of the individuals and compare them to see if anything looks weird. Mathematically, you expect the numbers to work out, and when they don't, you know some kind of evolution is occurring.

Figure 45 How the allele frequencies are supposed to work without evolution; the null hypothesis by Johnuniq via Wikimedia (CC BY-SA 3.0 or GFDL)

READ THE DENNIS O'NEIL INTRO TO THE HARDY-WEINBERG EQUATION.

Figure 46 "Simple overview of Hardy-Weinberg equilibrium in a hypothetical beetle population" by Angelahartsock via Wikimedia (CC0)

* a Hardy-Weinberg puzzle (do one and two)

* and here is a longer introduction to Population Genetics, if the math freaks you out, just skim to later sections.

2.2.3.3     the modern evolutionary synthesis

By the 1920s, evolutionary theory had synthesized the macroevolution of Darwin, with the microevolution of Mendel and population genetics, and came up a short list of factors that cause evolution. They tested populations with the Hardy-Weinberg equation, and when they failed to get a null hypothesis, they started trying to figure out which of the four forces of evolution caused the change in allele frequency: mutation, natural selection, genetic drift, and migration. The theories have been refined in the last hundred years, the four forces of evolution is still a useful way to think of evolution.

Vocabulary for 2.2

2.3     forces of evolution

One of the elegant things about evolutionary theory is it can describe phenomena on both the small scale and the large scale. We can use these same forces to explain microevolution ­– the change of an allele frequency of a population of the same species from one generation to the next; and we can use them to explain macroevolution ­– the change of one species into another species over long periods of time. This is similar to the way the theory of gravity can be used to describe the motion of molecular particles or large galaxies.

We use the word "force" to refer to a process that drives change, but thinking about evolution as a set of forces can be dangerous because it's easy to fall into the trap of thinking of evolution as a directional agent, pushing organisms towards an ultimate goal.

2.3.1     mutation

Mutation is the prime mover, the creator of all new alleles. We'll learn more about how mutations happen in the section on cellular biology.

* article on carcinogenic traditional medicine, notice the kinds of mutations this plant causes

2.3.2     natural selection

Review the last section on Darwin.

READ DENNIS O'NEIL'S DESCRIPTION OF NATURAL SELECTION WITH AN EMPHASIS ON POPULATION GENETICS.

2.3.3     migration

Migration (also called "gene flow") is where someone physically moves alleles from one population to another. When people move from one population to another they pack all 23 pairs of chromosomes inside the nuclei of their cells, and bring it all with them. If this changes the allele frequency of either population then it is by definition a kind of evolution. It can bring new alleles to a population that hadn't had that mutation recently, or just bring or remove a significant quantity of a certain allele to change the frequency of either population.

The individual doesn't actually have to migrate to the new population, they can just leave or pick up a few alleles. The stereotype that sailors have kids in every port, is probably better represented by today by the traveling businessman, soldier on leave, sexual tourist, or the sex trafficked. Migration is the geographic movement of alleles from one population to another.

We'll come back to migration in future sections as an important point in understanding human origins and human variation. It is why there is only one species of hominid on the planet today.

* article on coywolves and other hybrids which can be understood as a kind of gene flow and loosening of the species concept.

2.3.4     genetic drift

     Random genetic drift, or genetic drift, is about statistics. The "drift" part has nothing to do with geographical movement (that would be migration/gene flow), what drifts is the allele frequency, like when you look at a graph of a complex system changing over time, and from a distance it looks like a straight line, but as you zoom in, the line becomes jagged, jumping up and down; the smaller your field of view, the more drastic the changes become.

A good way to understand genetic drift is to plan two trips to Viejas Casino, the first with $1,000,000,000 and the second with $100. Sit down at the cheapest table or slot machine you can find and start playing. For your first trip, your money will go up a little ($1,000,000,135) and down a little (down a little more because the House sets the odds $999,999,564) but after a few hours, you'll get bored and go home with around $1,000,000,000. Ok now go back with $100, your money will go up a little ($135) and down a little ( $64), then up a little ($68), then down a little ($24) then up a little ($26) then down a little ($4) then up a little ($6) then down... whoops! no more money ($0), time to go home broke. The analogy here has to do with population size and alleles. Every generation alleles are shuffled and with a huge population statistically the allele frequency will stay pretty much the same, but with a small population, the random fluctuations are more drastic, and allele frequencies can drop to zero. If an allele frequency drops to zero, the game's over, and it's gone from the gene pool.

Here's a statistics exercise called the Gambler's Fallacy that also shows the difference between flipping a few coins and flipping a thousand coins.

     A bottleneck is where the population shrinks to the point where lots of alleles drop out like this. The founder's effect is where a small group of people move to a new area and start a new population. The new population may grow quickly, but even though the number of people grows, if there is no other force of evolution, the allele frequencies of the new population is determined by the small number of founders who might happen to not represent the population they left. There's no way a small number of people can represent the diversity of a large population. In statistics this is known as sampling error. When comparing the old and new population, they have different allele frequencies, so by definition, evolution has occurred, and we attribute this kind of evolution to genetic drift.

READ DENNIS O'NEIL'S SMALL POPULATION SIZE EFFECTS

READ STANFORD'S ENCYCLOPEDIA OF PHILOSOPHY: RANDOM DRIFT

The "drift" in genetic drift comes from statistics, called * stochastic drift. Stochastic just means "random", so stochastic drift is a fancy way to say that random stuff tends to happen with a small sample size.

vocabulary for 2.3

2.4     genetics, cellular biology, and variation

Figure 47 "Cells of similar structure organise themselves into different tissues, each of which carry out specific functions." from Levels of Complexity by Vivien Martineau © 2014

By the middle of the 20th century, microscopes were good enough to actually see the "characters" that Mendel discovered, and by the end of the turn of this century, an outline of the human genome was completed, and now new alleles are discovered daily, and some even intentionally created.

We could easily do a whole class on this section, but you should focus on trying to understand the mechanisms of human variation, which we'll be dealing with for the rest of the class. What is the cause of human variation? How does it happen at the cellular level? Darwin knew that variation was essential for the functioning of natural selection, but he had no clue how it worked. Mendel's research in heredity suggested principles of simple variation, but failed to explain 90% of what you see in life. In order to understand where most of variation comes from you need a microscope, and understand basic cellular biology and genetics.

I find it helpful to get an overview of the scale of human variation. How big is the thing we're talking about? Go back and watch the 10 minute Powers of Ten movie, and focus on the cellular section.

Figure 48 "Multiscale models of the human body targeting complex processes span many time and length scales of biological organization" by Filippo Castiglione, Francesco Pappalardo, Carlo Bianca, Giulia Russo, Santo Motta. "Modeling Biology Spanning Different Scales: An Open Challenge ," BioMed Research International doi:10.1155/2014/902545 (CC BY 3.0)

Even the pictures can get confusing until you get a sense of how everything fits together. The same chromosomes can look different at different stages. During protein synthesis it's hanging loose, and during cell division it's all wound up like a dreadlock.

 

Figure 49 Scale of the Chromosome by Arnie Schoenberg adapted from Guillaume Paumier, Philip Ronan, NIH, Artur Jan Fija?kowski, Jerome Walker, Michael David Jones, Tyler Heal, Mariana Ruiz, Science Primer (National Center for Biotechnology Information), Liquid_2003, Arne Nordmann & The Tango! Desktop Project via Wikimedia (CC BY-SA 2.5)

Here's another graphic that goes from small to big and mentions a few of the functions of chromosomes at different stages:

Figure 50 Chromatin Structures By Richard Wheeler via Wikipedia (GFDL or CC-BY-SA-3.0)

A pair of sister chromatids and centromere and a pair of homologous chromosomes are about the same size; you get two chromatids because of DNA replication in preparation for cell division; you get two homologous chromosomes because of fertilization, one from Dad, and one from Mom.

All cells arise from pre-existing cells.

2.4.1     cells

You are made up of about a trillion cells. Cell size can vary drastically, but ova are big and sperm are small.

Each cell has organelles inside them. A very important organelle is the nucleus. Inside the nucleus are your chromosomes. Your chromosomes direct protein synthesis, which determine how the cells interact with each other, and how you as an individual function.  

2.4.1.1     organelles

The ribosomes manufacture proteins. The mitochondria convert and store energy so the cell can use it. There are many others, but these are the most important to understanding human variation.

2.4.1.1.1    nucleus

The nucleus contains the DNA, and is metaphorically like the brain of the cell.

2.4.1.1.1.1    chromosomes

There are 23 pairs of chromosomes inside the nucleus of most human cells for most of the time. They come in pairs because as Mendel discovered, you get one from your dad and one from your mom. There are two kinds of chromosomes: autosomes and sex chromosomes. The 22 pairs of autosomes are named for auto which means "self"; they're the chromosomes that stay with yourself. They are numbered from biggest to smallest. The last pair, the sex chromosomes, are named because they tend to determine the sex of an individual.

A genome is an entire set of genes.

Different species have different number of chromosomes. Humans have 23 pairs, other apes have 24 pairs, hermit crabs have 127 pairs. Compare humans to a table of different species according to their number of chromosomes

The number of chromosomes doesn't make much difference; you can store the same data on a small number of larger chromosomes, or a large number of smaller chromosomes. For a computer analogy, think of how when you format a hard drive into different sectors: it might have the same memory capacity regardless of the number of chromosomes.

2.4.1.1.2    mitochondria

Mitochondria are the power plants of the cell, and they have their own separate DNA. The history of how mitochondria came to be is fascinating. We think they used to be independent living creatures swimming around, until 2 billion years ago, an ancestor of eukaryotic cells swallowed one, but instead of digesting it, that mitochondrion survived and began a symbiotic relationship with the host cell, reproducing inside the host's cytoplasm and being passed on to the next generation as the cell divided.

2.4.1.1.3    mtDNA

Mitochondrial DNA (mtDNA) can be used for genealogy and for dating the migrations of pre-historic populations.

Mitochondria are like cells within cells. Because, our cell's DNA is in the nucleus, and the mitochondrion in the cytoplasm, the mitochondrial DNA (mtDNA) was separated from the nuclear DNA of the host cell during reproduction. When sexual reproduction began, the eggs were bigger and they were almost always the source of mitochondria for the zygote. This means that you get your mtDNA from your mom, and it is inherited through matrilineal descent. Your mtDNA come:

from your great-great-great-great-great-great grandmother,

to your great-great-great-great-great grandmother,

to your great-great-great-great grandmother,

to your great-great-great grandm¿ther,

to your great-great grandm¿ther,

to your great grandm¿ther,

to your grandm¿ther,

to your m¿ther,

to y¿u.


And because of matrilineal descent, if your great-great-great grandmother had a mutation (o→¿) in the mtDNA of an egg, that mutation would be passed down to all of the descendants of that egg, and you would share the mutation with your mom, and your siblings, all those aunts and uncles, and fourth cousins on your great-great-great grandmother's side. The mutations in mtDNA accumulate and become markers to show ancestry, as well as demonstrate the evolutionary forces of migration and genetic drift. Because mitochondria are so simple, they have almost no functional variation – they either work or they don't – and without variation, natural selection doesn't happen. When you control for natural selection, the rate of neutral mutations of mtDNA becomes like a constant (one or two mutations every half-a-dozen millennia), and you can count how many different mutations two individuals have, and approximate how many generations ago they had a common ancestor. And by comparing large samples of indigenous populations, you can approximate where the mutation took place. We can correlate the genetic "when" and "where" with archaeological and historical data to test fascinating hypotheses of how humans moved across the globe.

*National Geographic's Genographic Project

*skim Wikipedia: Mitochondria

* Mitochondrial diseases

2.4.1.2     cell division

explore Sex cells have one set of chromosomes; body cells have two.

2.4.1.2.1    mitosis

Mitosis is the production of body cells for growth and healing. In mitosis, cells copy their chromosome and copy themselves, so that each daughter cell has the same number of chromosomes as the parent cell. Variations in the body cells can continue to be copied through mitosis (e.g. cancer), but the variations will not be passed down to the next generation.

mitosis gif

Figure 51 "Mitosis in Pig Kidney Epithelial Cells" by Nikon © 2018

WATCH AN 8 SECOND MITOSIS MOVIE (try manually moving the cursor to see it slowly)

2.4.1.2.2    meiosis

Meiosis is the production of gametes for sexual reproduction. In meiosis, cells copy themselves twice, but only copy their chromosomes once, so each of the viable daughter cells ends up with half the number of chromosomes as the parent cell. Individuals get the full number of chromosomes when two gametes combine during fertilization. Variations in gametes will be passed on the next generation. This is why when you get an x-ray, they put a lead blanket over your gametes – to block the radiation, and decrease birth defects.

WATCH A QUICK MEIOSIS MOVIE

2.4.1.2.2.1    oogenesis

Oogenesis makes ova or eggs.

2.4.1.2.2.2    spermatogenesis

Spermatogenesis makes sperm.

2.4.1.2.3    recombination

Meiosis is important because it increases variation by recombining your parents' genetic information.

Your genetic information comes in a small number of little packets, called chromosomes, and they were passed down from grandparent to parent to child. They come in pairs. One from one parent, one from the other. Meiosis splits the pairs, and shuffles them randomly so for example you might get one of your 3rd chromosomes from your paternal grandmother and one of your 4th chromosomes from your maternal grandfather.

Below is my genome with an approximation of my ancestry. If you know what to look for you can see which chromosomes came from my Mom and which from my Dad. My maternal grandparents were mostly descended from Britain and Ireland, and show up as light and dark blue on this chart. My paternal grandparents were mostly descended from Ashkenazim and show up as dark green. So for the first chromosome pair, the top one came from Dad and the bottom one from Mom. For chromosome pair 22, the top one is from Mom and the bottom one from Dad. For the sex chromosomes I got the Y from my Dad, and the single X from my Mom.

If I had my grandparents' DNA, I could figure out whether the X chromosome that I got from my Mom, came from my maternal grandmother or my maternal grandfather. I definitely know that my Y chromosome came from my paternal grandfather. Each of my 46 chromosomes came from some great, great, great, ... grand-parent up in my family tree.

chart comparing chromosomes

Figure 52 Arnie Schoenberg's 23&me ancestry report, 3/29/18. © 23andMe, Inc. 2007-2017

2.4.1.2.3.1    crossing over

Notice that that most of the chromosomes above aren't solid colors. The interspersed segments come from crossing over. During meiosis the homologous chromosomes are brought very close to each other. Because they are the same chromosome and have the same genes, pieces of one chromosome can "cross-over" to the one next to it.

Recombination includes the shuffling of chromosomes that you're getting from each parent, and a specific kind of recombination, called crossing over, where the chromosomes themselves can change, and genes can cross over from one grandparent's chromosome to another's. The discrete packages of chromosomes don't stay the same every generation, they open up and traits move from one to another.

2.4.1.2.4    non-disjunction

While meiosis sorts and delivers the packets of genetic information we call chromosomes, one part of the process where variation can occur is that meiosis can deliver an extra packet, and we call this non-disjunction.

During meiosis the homologous chromosomes are brought together, and then pulled apart, but sometimes they aren't pulled apart hard enough and they stick to each other, and both chromosomes are pulled into one gamete, and the other gamete gets none. This is called non-disjunction; the junction between homologous chromosomes that is usually broken during meiosis is not. Having the wrong number of chromosomes is usually lethal, and the fertilized egg just doesn't reproduce, and you just don't get pregnant that month. Many people survive and do fine with more or fewer than 46 chromosomes. Chromosomes are numbered by size, so non-disjunction with higher numbered chromosomes tends to be less lethal. Down syndrome is also called Trisomy 21, having three of the somatic chromosome number 21.

READ THE DOWN SYNDROME ASSOCIATION OF SAN DIEGO, DOWN SYNDROME FACTS

* new treatments for people with Down syndrome

2.4.1.3 fertilization

A random sample of half the chromosomes from your mom, and half from your dad, come together to make you.

Figure 52a "No, the sperm doesn't penetrate the egg..." by Arnie Schoenberg adapted from Biology by Gary Calkins 1917 (CC BY-NC 4.0)

* Emily Martin's 1991 article The Egg and the Sperm: How Science Has Constructed a Romance Based on Stereotypical Male-Female Roles

2.4.2     DNA

Deoxyribonucleic Acid is the chemical name for DNA we use to talk about its chemical structure. It comes in packages, called chromosomes which we can see in the microscope when it's all natted up as big dreadlocks inside the cell nucleus, when the cell is about to divide.

Try not to confuse the doubling-thing in DNA and chromosomes because there are four very different kinds of doubling that happen at different times and scales, listed here from big to small:

First, the biggest scale of doubling is the pairing up of duplicated homologous chromosomes at the beginning of meiosis (metaphase I), but this doesn't last long. Karyotype pictures are often taken during this phase, so you see what looks like four chromosomes for each of the 23.

Second, for most of cell's life it has two of each of the 23 chromosomes, in what are called homologous pairs. The pair comes from fertilization, you get one from your mom and one from your dad; this is what Mendel was studying. Another pairing at this same scale is the duplicated sister chromatids after replication, and before the beginning of meiosis mentioned above.

Third, if you compare the upper and lower part of each of the 23 in a karyotype, you see the sister chromatids are joined in the center by a centromere, and the upper and lower parts of each side are called arms. The centromere is never exactly in the middle, so every chromosome has a shorter arm, p (for petit), and the longer arm, q. So, the X chromosome was named because after replication it has two sister chromatids joined in the middle by a centromere, and it looks like an "X", a dot with four arms.

Fourth, the smallest scale of doubling is at the structural level: the complementary strands of DNA wound together in a double helix. So if you have an A on one side, you have a T on the other; if you have a G on one side, you have a C on the other. These complementary strands are like the two sides of a zipper that come apart for protein synthesis and replication.

2.4.2.1     replication

DNA likes to make copies of itself.

2.4.2.2     protein synthesis

There are two main stages in protein synthesis: transcription and translation. It starts in the nucleus with transcription, where enzymes take the message from the DNA and transcribes it into messenger RNA (mRNA). The mRNA takes the message out of the nucleus into the cytoplasm to the ribosome.

Translation occurs when the ribosome reads the message and puts the right amino acids in the right order. The ribosome needs help to gather and place the amino acids and uses transfer RNA (tRNA). The tRNA has an amazing property that a combination of three bases (codon) will stick to a particular amino acid, and as the ribosome reads the message from the mRNA it uses the tRNA to transfer the correct amino acid in the correct order to make a protein.

After protein synthesis, the protein can leave the cell and do whatever it needs to do to keep the individual alive.

Check out this groovy example of hippy science from Stanford University in 1971: protein synthesis reenactment (the trip kicks-in at around 3:13)

A gene is a discrete sequence of DNA nucleotides.

Often one gene makes one protein, but not always. The expression of genes is influenced by the environment. Some proteins require many genes. Some genes produce more than one protein.

2.4.2.2.1     polygenic traits

Polygenic traits are determined by a combination of many genes. For example, the hemoglobin protein takes 4 genes (6 for fetuses) and we'll look at a tiny change in one of the four genes that causes sickle cell anemia.

2.3.2.2.2     pleiotropic genes

Pleiotropy is where a single gene can effect multiple traits.

2.4.2.3     locus > gene > allele

The words locus, gene, and allele can be very confusing, especially since people (including myself) get lazy and use them interchangeably, but technically they are distinct and you may as well get in the good habit of using them correctly. Locus has the same root as "location", and it refers to a place on a chromosome where a string of bases will fit. If that string of bases codes for a protein (a functional product), then that spot is also a gene. But in many cases, there can be variations as to what bases fit in that same spot, and each of those possible variations is called a different allele, and often codes for different proteins and change the organism. In summary, if a locus does something it's a gene, all the different versions of the gene are alleles.

2.4.2.3.1    introns and exons

One of the ways to increase variation is where genes modify other genes, and there are many stages of protein synthesis when that can happen, one of them being during transcription where parts of the code are cut out.

Read S-cool's description of introns and exons.

The RNA message is sometimes edited.

Some DNA does not encode proteins.

* article "Exon Skipping: Borrowing from Nature to Treat Rare Genetic Diseases"

2.4.2.3.2 codons

DNA words are three letters long.

2.4.3     cells and the source of variation

The origin of all variation is mutation. Mutations can occur at many different scales. The smallest is the Single Nucleotide Polymorphism (SNP, called a "snip") that changes a single base.

If we think of meiosis as sorting and delivering genetic information to our kids in packets that we call chromosomes, there are many parts of the process where variation can occur, including: 1) meiosis shuffles the packets of information in recombination as Mendel proved in his Principle of Independent Assortment, 2) meiosis moves traits from packet to packet in crossing over, and 3) meiosis can deliver an extra packet in non-disjunction.

Another possibility is that two different packages can stick together, like the chromosomal shifting that fused the greater ape chromosome 2a and 2b, into Homo sapiens chromosome 2. The same genes are there, just on one chromosome instead of two. These big changes are important for macroevolution (speciation), and makes it impossible for humans to reproduce with other apes (apologies to Jerry Springer and the Weekly World News).

The use of the word recombination can be confusing because most of the recombination that makes you different from your siblings is Mendel's principle of independent assortment, the shuffling of chromosomes, but there is also a type of recombination called crossing over that is a very different specific process on a smaller scale where genes jump between homologous chromosomes. Also, recombination is technically not a separate force of evolution, it's an aspect of all of them.

Because this is an introduction we have skipped many other processes that influence variation, such as genes that don't produce proteins directly, but just effect other genes that do. But, most genes make proteins, so let's get the basics down first.

for another review read Dennis O'Neil's description of mutation and recombination

* Single Nucleotide Polymorphisms (SNiPs)

* Some viruses store genetic information in RNA.

* Genetic disorders

imagination Activities

Follow the instructions on this video, and take a selfie with your own DNA.
For each cell, how many membranes does the soap have to break down to release the DNA?

check out the National Society of Genetic Counselors, the American Board of Genetic Counselors, and the UC Irvine program, and the KGI program

Imagination questions

The Human Genome Project is federally funded. Do you think it's worth it?

Take a few minutes to explore the human genome with MapViewer at the National Center for Biotechnology Information. How is exploring our genome different from exploring unknown jungles, or the bottom of the sea, or outer space?

Figure 55 By Guillaume Paumier, Philip Ronan, NIH, Artur Jan Fija?kowski, Jerome Walker, Michael David Jones, Tyler Heal, Mariana Ruiz, Science Primer (National Center for Biotechnology Information), Liquid_2003, Arne Nordmann & The Tango! Desktop Project via Wikimedia (CC BY-SA 2.5)

What of humans is mechanistic? Where does free-will exist?

What is a person? A bunch of cells. Each individual is made up of about a trillion cells (1,000,000,000,000). Most of those cells have 46 chromosomes. Each chromosome has about a million and a half base pairs, and the human karyotype has about 3.2 billion base pairs total. The information in the 3,200,000,000 base pairs makes sure the 1,000,000,000,000 cells all work together. 3.2 billion seems like a lot of base pairs, but if you take computer memory as a metaphor it's not that much. If you think of a base pair like something between a bit and a byte, then all the genetic information fits on a 3.2 gigabyte (3.2 GB) thumbdrive. It's like the basic install of a video editing program. Not something you could attach to an email, but it wouldn't take that long to download. So what makes people so complicated, if their code is so small?

Here's an introduction to chimerism, the idea most of us are conjoined twins to a small extent. Does this change how you think of yourself?

2.4.4     genetics and ethics

Remember that the anthropological imagination avoids scientism: putting science on a pedestal protected from all criticism, and valuing science and scientific knowledge above people. Anthropology is the science of humans, so there is no way to avoid humanistic questions. The field of genetics has grown in a political context where world economic systems have loosened many ethical guidelines. It's like the wild, wild, west.

2.4.4.1         identity and ownership

If you think the government reading your emails is bad, think of having scientists steal your genetic code without your consent and owning you in your afterlife.

*Read an update on Henrietta Lacks' genome

* New HBO movie:

One of the great things about Obamacare is that it headed-off a growing problem of insurance companies using genetic information as a way to screen out members with a propensity for expensive medical conditions.

Our reliance on genetics in forensic anthropology (using anthropology for legal, usually police, situations) can lead to problems such as this case which seems straight out of the Jerry Springer show: * Man Fails Paternity Test Because Unborn Twin Is The Biological Father Of His Son

2.4.4.2     stem cells

Stem cells are undifferentiated, that means they divide and grow into many different kinds of cells. When you think of yourself as a trillion cells, once upon a time, you used to be one cell: a tiny, cute, little zygote (what happened!??!!). Stem cells are leftover from that transition from one cell to billions of cells. They are great for medicine because if you are missing cells in your body, you tell the stem cells to become them.

The controversy was much worse a decade ago when the major source of stem cells was aborted fetuses, but today, they can be harvested from your own baby teeth, your blood, even from your leftover liposuction.

* article on stem cell therapy for Crohn's disease

* article on stem cell therapy for diabetes, protein synthesis is how a cell produces insulin

2.4.4.3     cloning

Figure 56 "Science can tell you how to clone a Tyrannosaurus rex. Humanities can tell you why this might be a bad idea." © Image Courtesy of the University of Utah College of Humanities

To me, human cloning is no big deal. We're already dealing with the ethical issues that cloning raises.

Genetically identical humans? It's what we get with identical (monozygotic) twins, when the zygote divides and then separates into two embryos who become two individuals. They may be identical genetically, but variations in how they interact with their environment will make them physically distinct, and most importantly, their different cultural experiences will make them different people.

Exploiting people to harvest their organs? The demand for kidneys has led to transplant tourism and black markets in places like India and the Philippines, and a legal kidney market exists in Iran. The 1% are already playing God and cannibalizing the bodies of the 99%.

[Full disclosure: my tolerance for cloning may be biased because I am currently raising several clones of my own of various ages on a secret organic ranch in Eastern Nevada which I plan to use to for parts as I get older. Here's a home video of my favorite "Little Arnie", AS0983-2342, getting in shape for his transplant surgery.]

2.4.4.4     GMOs

Skim a description of CRISPR-Cas9 technology

I think recombinant DNA, or genetically modified organisms (GMOs) are a bit scarier... Will it kill you to eat them? No! Are they poisonous? No! Are they toxic? No! Will they make you sick? No! Should you try to avoid them? Yeah, it's probably a good idea to eat as much locally-grown organic produce as as you can afford. You would think it would be totally safe to type out a string of base pairs on a computer, to make a gene, which codes for a protein, which determines the exact phenotype (physical structure) of what you put in your mouth. But life is never that simple; there are other variables that cause variation, we know from evolution that all species tends to change, and science exists in a social context.

GMO food is part of a dysfunctional agricultural system, which can be described as mono-crop, agribusiness, industrial, petroleum based, and unsustainable. GMOs have mostly added to the problems. I present a highly unlikely nightmare scenario about HGT below, but the nightmare is already here: Monsanto's Roundup® ready crops have promoted the increased use of herbicides, patented seeds mean farmers have to buy them every year, inserting pesticide genes into crops kills butterflies and beneficial insects along with the pests. GMOs are part of a larger broken system, and the profit motive encourages people to live in denial, counting on scientists to discover some magic GMO solution to all our problems. Organic produce may seem expensive in the supermarket, but industrial agricultural passes on an environmental debt to the next generation.

There was a historic period in agronomy known as the* "Green Revolution" where scientists developed super crops to feed the world. But for many it was a technocratic disaster that increased overall starvation. Hopefully, we can learn lessons from the Green Revolution and avoid potential disasters with our current GMO revolution. If you step back and look at the causes of starvation: unequal distribution and overpopulation are as significant as insufficient production; it's not so much that we need more food, it's that we're greedy and there are too many of us. It's too bad we can't just genetically modify humans to share more. GMOs can help feed the world for a few years, but they won't address our Super Size Me culture.

Figure 57 from Hard Boiled © 2017 Geof Darrow, Dave Stewart, and Frank Miller, published by Dark Horse Comics

We look at hackers today as some kind of noble outlaw or social bandit, but we need to keep asking ourselves: what are our limits? how far we are willing to go to hack ourselves and the code that makes us who we are? Gene hacking is the latest in a long history of tropes about mad scientists with hubris. Classic stories include: the Jewish golems, the alchemists of the Middle Ages, Mary Percy Shelly's Frankenstein; or, the Modern Prometheus. Some of my recent favorites include the Larry Fessenden 1991 movie The Telling, and Margaret Atwood's 2003 novel Oryx and Crake. Another trope related to hubris and the rapidly expanding technology of genetic modification is the chaos theory idea from Jurassic Park, or what I like to call the Homer Simpson effect ­– shit happens. No matter how good the plan is, genes can move around out of our control, and I think this next section is even scarier:

2.4.4.5     gene transfer

Lateral gene transfer (LGT), also called horizontal gene transfer, is where genes move from one individual to another in a way that is completely different from how parents pass their genes on to their kids. LGT is distinguished from the kind of up-and-down verticalness of heredity that we represent with a family tree, where genes are passed down from one generation to the next. With LGT the genes move sideways within a generation. It's important that you understand the classic Standard Evolutionary Theory of Darwin, Mendel, and the Modern Synthesis, because that's how things work 99.999999% percent of the time, and LGT is an extremely rare exception. Some evolutionary scientists have advocated including LGT research into an Extended Evolutionary Synthesis, others say that the old paradigm works fine. Some consider LGT to be a kind of gene flow, but classic gene flow happens within the same species through migration. LGT is about genes that can be moved from one nucleus to another in ways other than meiosis and fertilization. And, the individuals don't even have to be from the same species. Humans have learned to do this intentionally as shown in the previous section on GMOs, but it can also happen naturally.

I think the scariest thing about all the genetic engineering going on today is the potential combination of GMOs and LGT. Nature has dealt with LGT for billions of years and you can expect that we've evolved to deal with whatever genes are floating around in the environment. When you create a new gene, you can test how it will influence a certain organism in the laboratory, but when you release the gene into the environment, there is no way to test every possible combination of that gene inserted into every other species. So for example, you make a gene that allows leaf cells to produces their own pesticide and you put it in corn. Fine, the corn is great, no bugs, no need to spray pesticides. But, what happens if that gene moves to bacteria that live in your stomach. Whoops! Now you don't have to bother drinking pesticide, because you're producing it in your stomach already. This scenario is very speculative; it hasn't happened and there is very tiny chance that it actually will. But since we already have sustainable food producing systems that have worked for thousands of years, why take chances?

On the bright side, LGT does make a great back-story for horror movies.

*You are what you eat; a good introduction to LGT

* A recent editorial about "GMOs, Herbicides, and Public Health"

*An article on genomic infection.

*scare tactics: Genetic Roulette movie trailer

*good rebuttal to Genetic Roulette

* article on Monsanto suing farmers for saving seeds


* article on human embryo editing

* website for the FDA's Cellular, Tissue, and Gene Therapies Advisory Committee

* an article on human babies with two mothers and a father (a mitochondrial donor) or just two mothers, which the FDA is considering

Imagination Questions

Imagination Actions

GMOs

Using what you've learned, find a recent campaign calling for the labeling of genetically modified foods (e.g. Just Label It), and write a letter to the appropriate policymaker, arguing for, or against, the legislation/action.

Vocabulary

2.5     summary example: holism in anthropology, sickle cell anemia, and malaria

READ THE SECTION CALLED "SELECTION AGAINST BOTH HOMOZYGOTES" FROM DENNIS O'NEIL NATURAL SELECTION

Anthropology is holistic because it covers many branches of knowledge. To understand sickle cell anemia we need look at the smallest change in a base pair, and at the global migration of alleles. We need to look two thousand years back in time to a transition from hunter-gatherers to horticulturalists, to the racial discrimination of the 20th Century. We apply the knowledge to the most deadly disease on the planet, and to mixology.

Mutation starts the process. In the sperm or egg on the 11th chromosome, at the 17th nucleotide of the gene for the beta chain of hemoglobin, there is a point mutation where an A is replaced by a T, which changes the codon GAG (for glutamic acid) to GTG (which encodes valine). Thus the 6th amino acid in the chain becomes valine instead of glutamic acid. The beautiful architecture of the hemoglobin molecule collapses, as if you took the capstone off of an arch, and the red blood cell takes on a sickle-shape. The sickled cells get caught in blood vessels and don't carry oxygen as well.

Figure 58 a part of the normal and mutated DNA strand, resulting change in mRNA and amino acid sequence by Thomas Samuel for ACC-BioinnovationLab, 2015 (CC BY-SA 4.0)

Figure 59 normal red blood cells and a sickle cell to the left, by Arnie Schoenberg derived from Janice Haney Carr, OpenStax, College Anatomy & Physiology, 18.3 * Erythrocytes, 2013 (CC-BY-4.0)

Figure 60 Figure A shows normal red blood cells flowing freely in a blood vessel. The inset image shows a cross-section of a normal red blood cell with normal hemoglobin. Figure B shows abnormal, sickled red blood cells blocking blood flow in a blood vessel. The inset image shows a cross-section of a sickle cell with abnormal (sickle) hemoglobin forming abnormal strands. National Institute of Health * Sickle Cell Disease (public domain)

* skim the medical literature on sickle cell anemia and click on the location to get a sense of what a gene is

This new allele is called the S allele, and as a Mendelian trait, you get one from each parent.

AA=normal hemoglobin
AS=sickle cell trait, sickle cell carrier
SS=sickle cell anemia

The allele frequency of any Single Nucleotide Polymorphism (SNP) is about 1 in 100,000, so you might expect the allele frequency of the S allele to stay at that rate: S=0.00001 But in some places the frequency of the S allele gets as high as 1 in 5, or S=0.2 When population geneticists see changes in allele frequencies they know that evolution is occurring, and the connection to malaria makes it clear that this is a case of natural selection.

The sickled cells are bad for blood flow and carrying oxygen, but they are good because they protect you from the parasites which cause malaria.

Malaria is an infectious disease caused by the parasite, Plasmodium falciparum, and is carried by mosquitoes, and easily spread. One little parasite gets into one of your red blood cells, reproduces 30,000 times, pops the cell, and then go on to infect thousands of other cells, which then go on to infect thousands more, until you are really sick.

Figure 61 Electron micrograph of red blood cells, one infected with Plasmodium falciparum which forms protrusions called 'knobs' on the surface of its host red blood cell, by Rick Fairhurst and Jordan Zuspann, National Institute of Allergy and Infectious Diseases, National Institutes of Health (CC BY-NC 2.0)

)

Figure 62 Life Cycle of the Malaria Parasite by National Institutes of Health 2009 (Public Domain)

But, when the parasite infects a sickle-shaped cell, there is less room to reproduce, and it doesn't pop the cell, so it's not spread. Sickle cell anemia is bad, but it gives you immunity to malaria.

Natural selection acts on the mutation to change its allele frequency.

Fetuses produce a special kind of hemoglobin (HbF) that helps pull mom's oxygen across the placenta. Once born, the fetuses normally stop producing HbF, but some adults inherit a gene that tells their body to persist in producing fetal hemoglobin all their lives. The correlation between people with blood diseases like sickle cell anemia and hereditary persistence of fetal hemoglobin suggests that natural selection may have selected for the persistence of fetal blood to mitigate the effects of sickle cell anemia. Malaria makes it advantageous to have sickle cells, and then sickle cells makes it advantageous to have the hereditary persistence of fetal hemoglobin.

Sickle cell anemia is an example of biocultural evolution because human cultural activity was the cause of people's genetic change. People in West Africa developed a new subsistence practice that produced more food by clearing land and planting crops. But it also created open spaces for mosquitoes to breed, and higher population densities that made it easier for malaria to spread. As malaria became endemic it became more advantageous to have the S allele.

Figure 63 distribution of malaria by Hay SI, Guerra CA, Gething PW, Patil AP, Tatem AJ, Noor AM, et al. (2009) A World Malaria Map: Plasmodium falciparum Endemicity in 2007. PLoS Med 6(3): e1000048. https://doi.org/10.1371/journal.pmed.1000048. from * Malaria Atlas Project (CC BY 3.0)

Figure 64 map of sickle cell allele distribution by Arnie Schoenberg adapted from * Piel, F.B. t al. Global distribution of the sickle cell gene and geographical confirmation of the malaria hypothesis. Nat. Commun. 1:104 doi: 10.1038/ncomms1104 (2010) from * Malaria Atlas Project (CC BY 3.0)

Other cultural factors range from racism to mixology. Because of racism, and the misconception of sickle cell anemia as a racial disease, the US military initially prohibited African-Americans from flying planes fearing that all African-Americans would suffer sickling events at high altitudes. British Colonialists lacking malaria resistance turned to the bark of a tree from South America called quinine, and they preferred to drink this bitter tonic with gin for good measure. Unfortunately, because of natural selection, most malaria parasites are now resistant to quinine, and drinking gin & tonics in the tropics is more likely to cause dehydration than prevent malaria.

Figure 64a "The gathering and drying of cinchona bark in a Peruvian forest." Wood engraving, by C. Leplante, c. 1867, after Faguet. Wellcome Images (CC BY 4.0)

Figure 64b Qualaquin® is made from quinine. FDA Medication Guide (public domain)

* history of the gin and tonic

The holistic approach of anthropology allows us to understand sickle cell anemia through a wide range of disciplines including archaeological research on sites in West Africa, the genetics of humans, plasmodium parasites, and mosquitoes, racism in the US, and even mixology.

Figure 65 Mosquitos are the world's deadliest animals by Bill Gates © Copyright The Gates Notes, LLC

* The Center for Disease Control About Malaria

* exploring the use of fetal hemoglobin as a treatment for sickle cell anemia

* a 360º VR 3D video on malaria, and how to prevent it

* a CRISPR mosquito update

Imagination Question

Figure 66 "Spray to kill Malaria mosquitoes hide in your home" Office for Emergency Management. 1943-5 (Public Domain)

Figure 67 mosquito net by Max Pixel (CC0)

Imagination Actions

Vocabulary for 2.4


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