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Evolutionary Biology: Deep Time and the Logic of Life

The 4.2-billion-year experiment that produced every living thing — from alkaline vents on a young Earth to the sixth mass extinction. Five scientists guide a journey through deep time, tectonic upheaval, and the molecular evidence that all life shares a single ancestor.

16 Units
2-3 weeks per unit
Curriculum Map

NOT a Memorization Course

This course is organized chronologically through deep time, but each unit builds conceptual frameworks — natural selection, genetic drift, homology, convergence — that make the next chapter comprehensible. The science comes first (Units 1-12). The ethics and the present come after, grounded in 14 units of evidence.

What You Will Learn

The 4.2-Billion-Year Experiment

From alkaline vents to CRISPR — trace the unbroken chain of ancestry connecting every living thing. Nick Lane and Andrew Knoll guide you through the first three billion years most biology courses skip.

Unit 3

Five Extinctions, One Warning

Five times, Earth lost more than 75% of its species. Each time, survivors rebuilt. The sixth is happening now at 100-1,000x the background rate — and it has a known cause.

Unit 8

Your Inner Fish, Your African Genome

Your hiccups trace to a 375-million-year-old neural circuit. Your genetic diversity traces to Africa. Shubin and Tishkoff reveal the deep homology connecting you to every organism that ever lived.

Unit 10

Curated Video Library

6 curated videos to explore — plus 16 more matched to individual units inside the course

The Death of the Dinosaurs: 27 Years Later
55m
lecture
The Death of the Dinosaurs: 27 Years LaterYouTube
University of California Television (UCTV)·Apr 2008(18 years ago)·56K views

Walter Alvarez is the Berkeley geologist who, with his Nobel-laureate physicist father Luis Alvarez, proposed in 1980 that an asteroid impact killed the dinosaurs at the end of the Cretaceous. This 55-minute UCTV lecture is Walter Alvarez looking back at the impact hypothesis 27 years after he and his father proposed it, walking through the original iridium-anomaly evidence, the discovery of the Chicxulub crater that confirmed the prediction, the geophysical models of what the impact's effects would have been, and the broader transformation in earth science that the impact theory's acceptance triggered. For Unit 8 (The Big Five) this is the canonical primary source -- the scientist who proposed the theory, decades later, with the benefit of all the corroborating evidence accumulated since. The pedagogical move that distinguishes Alvarez's lecture from popular treatments: he models how a hypothesis becomes a theory becomes a textbook fact, and what each transition required in terms of independent evidence. For students learning to evaluate scientific arguments, watching the originator narrate that arc is the most valuable possible demonstration of how science actually works.

K-Pg extinctionChicxulub impactiridium anomalymass extinction+1 more
DNA expert Sean Carroll: "Evolutionary Developmental Biology"
1h 12m
lecture
DNA expert Sean Carroll: "Evolutionary Developmental Biology"YouTube
Vanderbilt University·Mar 2009(17 years ago)·21K views

Sean B. Carroll is the molecular biologist whose work on Hox genes and evo-devo (evolutionary developmental biology) is the conceptual bedrock of Unit 6's analysis of the Cambrian explosion and the deep-homology argument that runs through Units 10, 12, and 14. This 72-minute Vanderbilt University lecture is the most rigorous primary-source presentation of the evo-devo framework available on the open internet. Carroll walks through the experimental evidence (the Hox gene clusters that pattern body plans across distantly related species, the fly-wing-to-vertebrate-limb deep homology, the regulatory mutations that transform existing genes into new functions) and shows how this evidence resolved a long-standing puzzle: how could the Cambrian explosion produce so many new body plans so quickly without inventing new genes. The answer -- new ways of regulating old genes -- is the unit's central insight. For a course teaching evolution as a structured argument from evidence, Carroll's lecture models exactly the move from molecular data to conceptual reframing that the course is asking students to internalize.

Hox genesdeep homologyevo-devoregulatory genes+1 more
Finding our Inner Neanderthal: Evolutionary Geneticist Svante Pääbo's DNA Quest
1h 37m
lecture
Finding our Inner Neanderthal: Evolutionary Geneticist Svante Pääbo's DNA QuestYouTube
National Human Genome Research Institute·May 2014(12 years ago)·233K views

Svante Pääbo won the 2022 Nobel Prize in Physiology or Medicine for sequencing the Neanderthal genome and discovering the Denisovan lineage from a single finger bone, and this 97-minute National Human Genome Research Institute lecture is the most comprehensive primary-source presentation of his work available on the open internet. Pääbo walks through the technical apparatus of ancient DNA recovery (the contamination problems, the fragmentation challenges, the statistical methods for distinguishing endogenous DNA from environmental noise), the substantive findings (every non-African human carries roughly 1-4% Neanderthal DNA, the Denisovan contribution to modern Tibetans, the deep-population structure of African genomes), and the methodological transformation in human evolutionary biology that ancient DNA has produced. For Unit 11 (The African Genome), this is the indispensable primary source -- Pääbo is the founding figure of paleogenomics and his lecture is the most rigorous open-internet treatment of how ancient DNA has rewritten the human evolutionary story. The NIH venue gives the lecture the Q&A texture that makes it pedagogically valuable: research scientists pushing back on specific methodological questions.

ancient DNANeanderthal genomeDenisovanspaleogenomics+1 more
Why is Life the Way it Is? with Nick Lane
34m
lecture
Why is Life the Way it Is? with Nick LaneYouTube
The Royal Institution·Apr 2016(10 years ago)·99K views

Nick Lane is the central biochemical thinker in this course -- his work appears explicitly in Units 1, 2, 3, and 5 -- and this 34-minute Royal Institution lecture is the ideal entry point. Lane walks through the central question of his life's work: why life on Earth has the specific architecture it has (mitochondria-powered eukaryotic complexity emerging exactly once in four billion years, the universal energy currency of ATP, the proton gradients that power every cell), and what those features tell us about whether complex life is a near-inevitable outcome of planetary chemistry or a freak accident that almost did not happen. For a course whose first five units construct exactly this argument from the origin of metabolism through the eukaryotic merger, Lane's lecture is the unifying primary source. The Royal Institution venue matters: this is not a TED talk but a serious academic lecture in front of a scientific audience, with the Q&A preserved. Watch this once before Unit 1 -- the framework Lane lays out becomes the conceptual ground on which the next four units build.

autopoiesisnegative entropyendosymbiosisproton gradient+1 more
Biodiversity Days 2017: E.O. Wilson, "Half-Earth: How to Save the Natural World"
47m
lecture
Biodiversity Days 2017: E.O. Wilson, "Half-Earth: How to Save the Natural World"YouTube
E.O. Wilson Biodiversity Foundation·Sep 2017(8 years ago)·8K views

Edward O. Wilson was the Harvard biologist whose work on biogeography, sociobiology, and conservation defined more of late-twentieth-century evolutionary biology than any other single figure, and the Half-Earth proposal he made in his last decade is the policy capstone of his life's work. This 47-minute Biodiversity Days lecture is the primary source for the proposal: setting aside half the Earth's surface as protected habitat to preserve roughly 85% of species diversity, the empirical argument from species-area relationships (the same theory of island biogeography Wilson and Robert MacArthur developed in the 1960s), and the political and economic arguments for why half is both ecologically necessary and politically achievable. For Unit 13 (The Sixth Extinction) and Unit 16 (Deep Time and Human Responsibility), Wilson's lecture is the moral synthesis the course's empirical chapters build toward. Wilson died in 2021, and this lecture is one of the few full-length primary-source presentations of the Half-Earth framework in his own voice. Watch as the conceptual bridge from the course's analysis of mass extinction to its closing question of human responsibility.

Half-Earthbiogeographyspecies-area relationshipbiodiversity conservation+1 more
Andrew Knoll, "A Brief History of Earth: Four Billion Years in Eight Chapters," with Peter Girguis
1h 2m
lecture
Andrew Knoll, "A Brief History of Earth: Four Billion Years in Eight Chapters," with Peter GirguisYouTube
Harvard Science Book Talks and Research Lectures·Apr 2021(5 years ago)·6K views

Andrew Knoll is the Harvard paleobiologist whose work on the early evolution of life and on mass extinctions appears in Units 4, 8, 9, 13, and 16 of this course -- five of the sixteen units rest on his research. This 62-minute Harvard Science Book Talks lecture is the best primary-source overview of the four-billion-year arc the course traces, organized around the eight chapters of his book A Brief History of Earth. Knoll covers the origin of life, the Great Oxygenation Event, the Cambrian explosion, the mass extinctions, the rise of complex ecosystems, and the contemporary biodiversity crisis -- the same conceptual sequence the course follows, in the same chronological order. The pedagogical advantage of pairing the course with this lecture is that students hear the entire arc told once by the scientist whose research informs five separate units, which gives them the integrative frame the course's unit-by-unit structure cannot fully provide. Watch this once near the start of the course (after Unit 1) -- it provides the geological timeline within which everything else makes sense.

deep timeGreat Oxygenation EventCambrian explosionmass extinction+1 more

Explore These Channels

The Royal Institution
~6h

The Royal Institution is the 226-year-old London scientific society whose Friday Evening Discourses have introduced major scientific findings to the public since Faraday. The RI YouTube channel preserves the lecture format -- a single working scientist, an attentive scientific audience, an extended Q&A -- which is exactly the pedagogical format this course requires. Nick Lane has delivered three major RI lectures (origin of life, the Krebs cycle, the vital question) that anchor the course's first five units, and the channel's broader catalog includes Neil Shubin on Tiktaalik, Adam Rutherford on genetics and race, and the major figures in contemporary evolutionary biology. For students who want to follow any unit's primary source deeper, the RI channel is the most rewarding rabbit hole in academic biology on YouTube.

Covers 3 units in this course
PBS Eons
~4h

PBS Eons is the long-form paleontology and deep-time channel that has done more than any other YouTube source to popularize the geological and evolutionary history this course traces. The channel's editorial signature -- 10-15 minute episodes with original animation, primary-research citations in the description, and host scientists who are themselves working paleontologists -- makes it the indispensable wonder-bridge resource for the course's deep-time units (4, 6, 8, 9). Eons' longer-form 'Could You Survive the Cambrian Explosion?' and 'Could You Survive the K-Pg Extinction?' episodes are 45-60 minute deep dives that match the course's pedagogical depth without sacrificing the visual storytelling that makes deep time feel real. For students who find the textual primary sources demanding, Eons is the bridge that makes the conceptual content land before the technical content does.

Covers 4 units in this course
Journey to the Microcosmos
~3h

Journey to the Microcosmos is Hank Green's microscopy channel that pairs phase-contrast microscope footage of living microorganisms with editorial scripts about the evolutionary biology, biochemistry, and ecology of microbial life. The channel's pedagogical contribution to this course is hard to overstate: students reading about cyanobacteria's role in the Great Oxygenation Event or the endosymbiotic origin of mitochondria can watch the actual living organisms whose ancestors performed those evolutionary feats. The channel's 'Complicated Legacy of Lynn Margulis' episode is the most thoughtful short-form treatment of Margulis's career available -- it covers both her endosymbiotic theory's vindication and her later embrace of fringe positions, modeling the kind of nuanced engagement with scientific reputation the course's Unit 5 framing requires. For Units 4 and 5 specifically, Journey to the Microcosmos provides the visual texture that makes the theoretical content feel embodied.

Covers 2 units in this course
University of California Television (UCTV)
~4h

University of California Television is the public-affairs and lecture channel of the UC system, and it is one of the most underused academic-lecture archives on YouTube. For this course, UCTV hosts the Walter Alvarez 'Death of the Dinosaurs: 27 Years Later' showcase lecture, the Neil Shubin 'Your Inner Fish: Conversations with History' interview that anchors Unit 10, and the UC San Diego CARTA series with Sarah Tishkoff on local human adaptation. The channel's editorial discipline -- full-length lectures with intact Q&A, no superimposed editorial overlay, transcripts available -- matches the course's pedagogical contract. UCTV is also the channel that hosts the Nobel-laureate lecture archives from UC Berkeley, UCSF, and UCSD, which makes it the most efficient single source for primary-research presentations from the West Coast biology and earth science faculties.

Covers 3 units in this course

Course Modules

Module 1: Origins — The First Three Billion Years

Lane + Knoll
1
45-60 minutes
The Desire for Perfect Equivalence
In 1868, Thomas Huxley told a packed Edinburgh audience that protoplasm was the 'physical basis of life' — that mind, feeling, and will were nothing more than molecular motion. He was half right. This unit traces the centuries-long attempt to reduce life to chemistry, from vitalism's mysterious 'life force' to Schrödinger's negative entropy to the radical insight of autopoiesis: life is not a thing. It is a process that continuously produces itself.
  • •Trace the historical debate between vitalism and mechanism and explain why neither fully captured what makes life distinctive
  • •Explain Schrödinger's concept of negative entropy and its significance for molecular biology
  • •Define autopoiesis and distinguish it from simpler forms of self-organization
  • +1 more objectives
Start learning
2
45-60 minutes
The Engine at the Bottom of the Sea
In the year 2000, a research vessel stumbled upon a ghostly forest of white mineral towers rising from the Atlantic seafloor, 700 meters below the surface. The towers were warm, alkaline, and saturated with hydrogen gas. The chemistry inside them bore an eerie resemblance to the chemistry inside living cells. This unit follows the evidence from the bottom of the ocean to the origin of life itself.
  • •Distinguish between black smoker and alkaline hydrothermal vent environments and explain why alkaline vents are more plausible settings for the origin of life
  • •Explain Lane and Martin's alkaline vent hypothesis for the origin of metabolism
  • •Compare 'metabolism first' and 'genetics first' hypotheses for the origin of life and evaluate the evidence for each
  • +1 more objectives
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3
45-60 minutes
LUCA — The Last Universal Common Ancestor
Every living thing on Earth — every bacterium, every fungus, every plant, every animal, every archaeon thriving in boiling acid — uses the same genetic code, the same 20 amino acids, the same ATP, and the same ribosomal machinery for translating genes into proteins. This extraordinary uniformity points backward, through four billion years, to a single ancestral population. This unit reconstructs what we can know about that ancestor — and how we know it.
  • •Explain what LUCA represents and why it is understood as a population rather than an individual organism
  • •Describe Carl Woese's discovery of the three domains of life and explain why it was initially rejected
  • •Distinguish between vertical inheritance and horizontal gene transfer, and explain why the 'tree of life' is more accurately a web
  • +1 more objectives
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4
45-60 minutes
The Great Oxygenation Event
About 2.4 billion years ago, a group of microbes called cyanobacteria evolved a trick no organism had ever managed: they learned to split water molecules using sunlight, releasing oxygen as a waste product. For the anaerobic world that had existed for over a billion years, this was not a gift. It was a catastrophe — the first mass extinction, written in rust-red bands of iron oxide that stripe ancient rocks around the world.
  • •Explain why the evolution of oxygenic photosynthesis was a catastrophic event for most existing life on Earth
  • •Interpret banded iron formations and other geological evidence as records of atmospheric oxygenation
  • •Describe the Snowball Earth hypothesis and evaluate the evidence connecting it to the Great Oxygenation Event
  • +1 more objectives
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Module 2: Complexity, Catastrophe, and the Cambrian

Shubin + Hughes
5
45-60 minutes
The Merger
For two billion years, life on Earth was microbial, single-celled, and simple. Then, roughly 1.8 billion years ago, an archaeon swallowed a bacterium — and neither died. That singular event, which appears to have happened exactly once, produced the mitochondrion and made all complex life possible. Nick Lane argues this merger was so improbable that its occurrence on Earth may be the rarest event in the history of the universe.
  • •Explain why prokaryotic cells face an energy ceiling that limits their complexity
  • •Describe the endosymbiotic origin of mitochondria and evaluate the evidence supporting it
  • •Analyze why the merger between an archaeon and a bacterium appears to have happened only once in four billion years
  • +1 more objectives
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6
45-60 minutes
The Cambrian Explosion and the Genetic Toolkit
540 million years ago, every major animal body plan appeared in a geological instant — roughly 25 million years. The Cambrian explosion was not driven by the invention of new genes but by new ways of using old ones. The same Hox genes that pattern a fruit fly's body segments also pattern your spine. What changed was regulation, not raw material — and that insight reshaped our understanding of how evolution innovates.
  • •Describe the Cambrian explosion and explain why the rapid appearance of major animal body plans poses a challenge to gradualist evolutionary thinking
  • •Explain the role of Hox genes in body plan development and the significance of their conservation across distantly related species
  • •Distinguish between evolving new genes and evolving new ways to regulate existing genes, and explain why this distinction matters
  • +1 more objectives
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7
45-60 minutes
Moving Continents, Moving Species
Identical fossils of the seed fern Glossopteris appear on every southern continent — South America, Africa, India, Antarctica, Australia. Either these continents were once joined, or seed ferns swam the Atlantic. Alfred Wegener proposed the former in 1912 and was dismissed for half a century. The story of continental drift and biogeography reveals how the movement of tectonic plates has shaped the distribution of every species on Earth.
  • •Explain how biogeographic patterns provided critical evidence for both evolution and continental drift
  • •Describe Wallace's Line and explain why biogeographic boundaries persist even when continents are geographically close
  • •Analyze why the scientific establishment rejected Wegener's continental drift hypothesis for fifty years despite strong evidence
  • +1 more objectives
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8
60-75 minutes
The Big Five — Mass Extinctions as Engines of Change
Five times in the last 540 million years, Earth lost more than 75% of its species in a geological instant. Volcanic eruptions that lasted millions of years. An asteroid the size of Manhattan. Ocean chemistry flipping to lethal. Each catastrophe was devastating beyond human comprehension — and each was followed by an explosion of new life forms that filled the emptied world. Mass extinction is not the opposite of evolution. It is evolution's most brutal instrument of renovation.
  • •Identify the five major mass extinctions in Earth's history, including their approximate dates, probable causes, and magnitude of species loss
  • •Explain why mass extinctions are not simply destructive events but serve as preconditions for subsequent evolutionary radiations
  • •Analyze the relationship between extinction magnitude and frequency using Raup's kill curve framework
  • +1 more objectives
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Module 3: The Age of Innovation

Shubin + Tishkoff
9
45-60 minutes
After the Dying — Adaptive Radiation
Sixty-six million years ago, a rock the size of Manhattan hit the Yucatan Peninsula and killed three-quarters of all species on Earth. The survivors — small, nocturnal, insect-eating mammals among them — did not fill the old dinosaur-shaped holes. They invented entirely new ways of being alive. This unit examines adaptive radiation: the explosive diversification that follows ecological catastrophe.
  • •Define adaptive radiation and explain the ecological conditions that trigger it
  • •Analyze how mass extinctions create opportunities for surviving lineages to diversify
  • •Evaluate Gould's contingency thesis and its implications for the predictability of evolution
  • +1 more objectives
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10
45-60 minutes
Your Inner Fish — Deep Homology
In 2004, paleontologist Neil Shubin found what he was looking for in the Canadian Arctic: a 375-million-year-old fish with wrists, a neck, and primitive lungs. Tiktaalik roseae is a transitional fossil — part fish, part tetrapod — and its anatomy is still visible in your body. Your hiccups, your hernias, your aching knees are all the legacy of a fish that crawled.
  • •Explain how Tiktaalik was predicted by evolutionary theory and found using geological reasoning
  • •Define deep homology and describe how shared developmental genes connect vertebrate body plans across 375 million years
  • •Identify specific human anatomical features that are legacies of our fish ancestry
  • +1 more objectives
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11
45-60 minutes
The African Genome
Africa holds more human genetic diversity than the rest of the world combined. Every non-African human on Earth descends from a small group that left the continent roughly 70,000 years ago — carrying only a fraction of Africa's genetic heritage. The visible differences between human populations are recent, superficial adaptations layered atop a shared African foundation. Genomics has demolished the concept of biological race while revealing a human story far more interesting than any racial taxonomy could contain.
  • •Explain why Africa contains more human genetic diversity than the rest of the world combined
  • •Describe the out-of-Africa bottleneck and its consequences for global patterns of human genetic variation
  • •Distinguish between clinal (gradual) genetic variation and categorical racial classification, using genomic evidence
  • +1 more objectives
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12
45-60 minutes
Co-evolution and the Arms Race
Darwin predicted that somewhere in Madagascar, a moth must exist with a tongue long enough to reach the nectar at the bottom of a 30-centimeter orchid. He was right — the moth was discovered 40 years later. Co-evolution is evolution's conversation: species shaping each other across millions of years, locked in arms races that produce cheetah speed, immune system complexity, and antibiotic resistance. It is also evolution's most dangerous lesson for public health.
  • •Define co-evolution and distinguish between antagonistic and mutualistic co-evolutionary relationships
  • •Explain the Red Queen hypothesis and apply it to predator-prey, parasite-host, and pathogen-immune system interactions
  • •Analyze how co-evolutionary dynamics drive antibiotic resistance and evaluate the public health implications
  • +1 more objectives
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Module 4: Evidence, Ethics, and the Sixth Extinction

All Five
13
45-60 minutes
The Sixth Extinction
Current extinction rates are 100 to 1,000 times the background rate. The same evidentiary framework that identified the Big Five mass extinctions — applied with equal rigor to the present — yields an unambiguous conclusion: we are inside a mass extinction event. The difference is that this time, the cause knows what it is doing.
  • •Apply the analytical framework of mass extinction events to present-day biodiversity data and explain why current losses qualify as a mass extinction event
  • •Distinguish between background extinction rate and current observed rates using quantitative evidence
  • •Explain shifting baseline syndrome and how it makes the sixth extinction harder to perceive than the previous five
  • +1 more objectives
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14
45-60 minutes
Reading the Code — CRISPR and Conservation Genomics
CRISPR-Cas9 lets us rewrite the genetic code that evolution spent 4 billion years composing. De-extinction, ancient DNA, disease-resistant corals, gene drives that rewrite wild populations. The technology exists. The question it forces is not whether we can intervene in evolution — we already are — but whether we can do so wisely.
  • •Explain the mechanism of CRISPR-Cas9 gene editing and its origin as a bacterial immune system
  • •Evaluate three applications of conservation genomics — genetic rescue, disease resistance engineering, and de-extinction — including their limitations
  • •Analyze the ecological and ethical implications of gene drives as a conservation tool
  • +1 more objectives
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15
45-60 minutes
The Dangerous Metaphor
Herbert Spencer coined 'survival of the fittest' before Darwin published — and applied it not to finches but to human societies. The phrase launched Social Darwinism, the eugenics movement, and forced sterilization programs that touched 60,000 Americans. This unit is deliberately placed after 14 units of real evolutionary biology, so students can identify exactly where the distortion departs from the science.
  • •Distinguish Herbert Spencer's 'survival of the fittest' from Darwin's theory of natural selection, identifying the precise points of departure
  • •Trace the historical path from Social Darwinism to the American eugenics movement and its influence on Nazi racial policy
  • •Explain Lewontin's 1972 finding about genetic variation and its implications for the concept of biological race
  • +1 more objectives
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16
45-60 minutes
Deep Time and Human Responsibility
4.2 billion years of unbroken ancestry. Every one of your ancestors survived — every catastrophe, every mass extinction, every shift in climate and chemistry. You are the first species capable of understanding that history and altering life's trajectory. This capstone unit asks the only question that matters now: what do you do with that knowledge?
  • •Synthesize the major themes of the course — from the origin of life to the sixth extinction — into a coherent narrative of life's 4.2-billion-year trajectory
  • •Explain the concept of the Anthropocene and evaluate the evidence for designating it as a formal geological epoch
  • •Articulate what it means to be the first species capable of understanding and altering its own evolutionary history
  • +1 more objectives
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An open educational resource. Primary voices: Neil Shubin (Your Inner Fish), Nick Lane (The Vital Question), Andrew Knoll (A Brief History of Earth), Sally Hughes, and Sarah Tishkoff.