Evolution Evidence and Concepts – Transcript Notes

Evolution Evidence and Concepts – Transcript Notes

Notion of Theory vs Law in Science

• Evolution and natural selection are heavily supported by evidence across multiple lines; they are not treated as “theories” in everyday language, but as well-supported scientific understandings grounded in evidence.
• Scientific theory vs. law:
  • A theory is a well-substantiated explanation of some aspect of the natural world that can incorporate laws, hypotheses, and facts.
  • A law describes observable phenomena that occur consistently under given conditions.
  • Hypotheses can be upgraded to theories as more experiments support them, but a theory is not simply upgraded to a law. Laws describe consistent relationships or rules, often in observable phenomena.
• Mendel’s law (Independent Assortment) is mentioned as a historically foundational principle that may have exceptions in special cases; such exceptions motivate ongoing refinement of our understanding.
• Grounding claims in evidence is emphasized; avoid debating ad hoc or unfounded critiques of macroevolution.

The Fossil Record

• Fossil formation basics:
  • Sedimentary rock layers form over time with older layers beneath newer layers.
  • Dead organisms may be buried by mud, debris, or tar, and minerals replace organic material, producing a rock-shaped fossil.
  • Fossils are preserved remains, not the original organisms; sometimes organic material is recoverable, but usually it is mineralized rock.
• Fossil record limitations:
  • Fossilization is rare; most dead organisms decompose or are consumed.
  • Fossilization bias by habitat; some ecosystems fossilize more readily than others (e.g., tropical rainforests hinder fossil formation due to fast decomposition).
  • No even distribution in habitats or time; the record is incomplete and biased toward certain environments and time windows.
• Transitional fossils (the “holy grail”):
  • Provide snapshots of evolutionary transitions between major groups (e.g., fish to amphibians; dinosaurs to birds; land animals to primates).
  • Examples discussed: Tiktaalik (fish–amphibian transition), Archaeopteryx (dinosaur–bird link), Lucy (Australopithecus) showing closer ancestry to humans than earlier hominids.
  • Fossils are frequently incomplete; often only fragments needed to infer relationships exist, requiring careful extrapolation.
• Why transitional fossils are rare:
  • Timing windows for fossil formation are narrow; where divergence occurs, the opportunity to fossilize is limited.
• How fossils inform phylogeny:
  • Comparative anatomy and structural similarity help identify close relationships and branch points in evolutionary trees.
• Quantitative examples of fossil-based inference:
  • Partial remains (e.g., ankle bones) can yield measurements and ratios to infer homology and relatedness (e.g., linking cetaceans with hippo-like artiodactyls through shared skeletal features).
• Conclusion: fossil evidence supports macroevolution but remains incomplete; new fossils require updating hypotheses and interpretations.

Homology vs. Analogy (Convergence)

• Homologous structures:
  • Derived from a common ancestor and built from the same basic parts; changes reflect different selection pressures but share a developmental blueprint.
  • Examples: tetrapod limbs (humans, bats, whales, moles) built from humerus, radius, ulna, carpals, metacarpals, and phalanges; insect mouthparts and wing adaptations; limb bones of vertebrates.
  • Vestigial structures illustrate retained homology with reduced function (e.g., hind limbs in whales).
• Sequence and structural homology:
  • DNA and protein sequence comparisons illuminate close relationships and common ancestry; they inform branching in phylogenetic trees.
• Analogy and convergent evolution:
  • Analogous structures arise when different lineages independently evolve similar features due to similar selection pressures, not from a shared ancestor.
  • Key difference: homologous structures share developmental origin; analogous structures do not necessarily share developmental pathways.
• Examples of analogy:
  • Eyes: human eye vs. octopus eye perform similar functions but have different developmental wiring; octopus lacks a blind spot due to different retinal organization.
  • Wings: bat (mammal) vs. bird (avians) wings serve flight but have different bone arrangements and tissue supports (bat membranes vs. bird feathers).
  • Hydrodynamic shapes in marine animals (sharks, dolphins, ichthyosaurs) show convergent body designs optimized for speed, despite different vertebrate lineages.
• Implications:
  • Convergent evolution demonstrates similar solutions to similar problems but does not imply a recent common ancestor for the convergent traits.
• Functional vs structural similarity:
  • Even when function is similar (e.g., flight, swimming), the underlying structure and development may differ markedly between lineages.

Embryology and Developmental Homology

• Vertebrate embryo basics:
  • All vertebrates share four key embryonic features in early development that distinguish them from other clades: pharyngeal pouches and a post-anal tail are two clear markers; there are two more that characterize vertebrates in early stages.
  • Early-stage embryos of humans, chickens, rats, snakes look similar; gene expression programs later differentiate species.
• Pharyngeal pouches and post-anal tail:
  • Pharyngeal pouches in humans develop into structures such as vocal cords and other throat-associated features; in fish, they develop into gills.
  • Post-anal tail is present in embryos of many vertebrates; in humans, it regresses via apoptosis during development and is not present at maturity.
• Developmental signaling and apoptosis:
  • Controlled cell death (apoptosis) recycles cells during development, shaping final anatomy.
• Implication for evolution:
  • Shared embryonic stages reflect common ancestry; later divergence reflects lineage-specific development beyond the earliest stages.

Molecular Record and the Universal Genetic Language

• Universal genetic code:
  • All life uses the same genetic language: DNA or RNA (A, C, G, T/U) translated through codons (triplets) into amino acids, via the ribosome.
  • Example: the start codon AUG codes for methionine, initiating translation.
  • A few codons code for the same amino acid due to redundancy in the code (degeneracy); this leads to silent mutations where a change in the DNA sequence does not alter the amino acid sequence of the protein.
• Evidence from sequences:
  • Protein sequence homologies often show higher conservation than DNA sequence homologies because of third-base redundancy in codons.
  • Mutations in the third codon position (wobble) can be silent, preserving the protein sequence despite DNA changes.
• Large-scale molecular homology:
  • Regions of high sequence homology between genomes provide strong evidence for common ancestry and historical relatedness (e.g., human vs. chimpanzee chromosome structure).
  • A notable example is human chromosome 2, which appears to be the result of the fusion of two ancestral chromosomes present in other primates (2p and 2q) or an ancestral single chromosome that split in other lineages.
• Practical use of molecular data:
  • DNA sequence comparisons and protein sequence comparisons help construct and revise biogenic trees and infer evolutionary relationships.
• Why molecular data matters:
  • The universality and conservatism of the genetic code across all life form a powerful cumulative argument for a single origin of life and deep common ancestry.

Biogeography and Geographic Contexts

• Biogeography as evidence for evolution:
  • Organisms in the same region tend to be more closely related to each other than to organisms in distant regions, especially when separated by geographical barriers.
  • Geographic barriers (oceans, mountains) limit interbreeding, promoting divergence over time.
• Wallace Line and regional differences:
  • Alfred Russel Wallace observed a biogeographic boundary between Asia and Australia (the Wallace Line) where mammals transition from placentals in Asia to marsupials in Australia and nearby islands.
  • This line reflects historical land connections and subsequent geographic isolation of populations, leading to distinct evolutionary trajectories.
• Marsupials vs placentals:
  • In certain regions (Australia and nearby islands), marsupials dominate; in others (Europe, Asia, the Americas), placentals dominate.
  • Similar ecological roles can occur across continents (e.g., flying squirrels in North America vs sugar gliders in Australia) due to convergent evolution in analogous niches.
• Case studies of biogeographic patterns:
  • Island radiations (e.g., Galapagos finches) show rapid diversification from a common ancestral species into multiple niches adapted to local conditions.
  • Similarities across distant regions often reflect convergent evolution driven by similar ecological pressures rather than direct common ancestry for those traits.

Observed Evolution and Real-time Change

• Direct observation of evolution:
  • Documented rapid changes in populations under strong selection pressures (pesticides, antibiotics) demonstrate evolution in action.
  • Variation within populations allows some individuals to survive, reproduce, and pass on advantageous traits, shifting allele frequencies across generations.
• Selection pressures and pace:
  • Strong, consistent selection can drive rapid changes, especially in organisms with short generation times.
  • Overuse or misuse of antibiotics or pesticides can accelerate resistance development, with public health and ecological consequences if not managed.
• Peppered moths (Britain during industrialization):
  • Pre-industrial era: light-colored moths favored due to lighter tree bark and lichens; dark moths were more visible to birds and less common.
  • Industrialization led to soot-darkened trees, favoring dark-colored moths; later, pollution controls and cleaner environments shifted selection back toward lighter moths.
  • Demonstrates how rapid environmental changes can flip selective advantages and alter population phenotypes.
• Other rapid evolution contexts:
  • Droughts and climatic fluctuations affecting Galapagos-like systems; drought can shift selection pressures across populations, leading to adaptive changes.
• Misconceptions about evolution clarified:
  • Evolution is not goal-oriented; there is no universal drive toward perfection or maximum optimization.
  • Surviving and reproducing is what matters; traits do not become better in an absolute sense, only good enough for the given environment.
  • Extant species are not “peaks” of perfection; many lineages are dead ends or have become maladapted to new conditions over time.

Artificial Selection as a Window into Evolution

• Artificial selection vs natural selection:
  • Humans select and breed for particular traits (e.g., crop plants, domesticated animals, fancy pigeons).
  • This can produce dramatic changes quickly, but the resulting traits aren’t necessarily advantageous in the wild context; many human-desired traits would be maladaptive in natural settings.
• Implications for understanding evolution:
  • Artificial selection illustrates that selection pressures can be strong and directional, reshaping populations rapidly without inventing new genetic material from scratch.
  • When artificial selection stops, natural selection often reasserts itself, potentially restoring traits that are advantageous in the wild.
• Examples:
  • Domesticated dog breeds, corn (maize) from wild ancestors, selective pigeon varieties.
  • The idea that traits produced by human preferences are not guaranteed to be adaptive in natural environments if released back into the wild.

View of Design, Intelligently Designed vs Natural Design

• Evolution as non-teleological:
  • The lecture challenges the idea that natural history is goal-directed toward a perfect design.
  • Some biological traits appear suboptimal (e.g., human heart’s plan of supply) if imagined as “designed,” suggesting design is not a necessary explanation.
• Heart anatomy example:
  • Coronary arteries supply the heart; a blockage can cause ischemia and heart attack, with bypass and stents available as medical interventions.
  • If one could redesign from scratch, redundancy might be added (multiple arteries supplying the heart) to avoid catastrophic failure.
• Epiglottis and choking:
  • The shared tube system for eating and breathing can cause choking; a completely separate airway pathway would be a cleaner design, but such a variant is not found in ancestral populations.
• Takeaway:
  • Imperfect or non-optimally designed features can arise from historical constraints, trade-offs, and path dependencies in evolution, rather than deliberate engineering.

Case Study Context: Rock Pocket Mice and Valley of Fire

• Case study setup:
  • Focus on Rock Pocket mice in the American Southwest, notably across lava flows and altered landscapes (e.g., New Mexico’s Valley of Fire).
  • Eruption events created lava flows (~1000 years ago) covering large areas (~40 miles long) with dark rock.
• Evolutionary angle:
  • Coloration of rock-dwelling mice likely undergoes selection based on background matching to lava rock, influencing predation risk by visually hunting predators.
  • This case will be revisited in future lectures, offering a practical example of natural selection and adaptation in a real landscape.

Common Misconceptions and Clarifications (Wrap-up)

• Evolution is not a guided ascent to perfection; it’s a trial-and-error process constrained by existing variation and environment.
• The fossil and molecular records together provide converging lines of evidence for common ancestry, while also leaving gaps that require careful interpretation and revision.
• Vestigial structures are informative about ancestry and development, even if their current function is diminished or repurposed.
• Observed evolution is powerful evidence but does not imply a predetermined endpoint; the balance of costs and benefits governs trait persistence.
• The universal genetic code and molecular homologies are among the strongest pillars of the common-ancestry narrative, underscoring a deep shared history of life on Earth.

Key Concepts at a Glance (LaTeX-ready ideas)

• Codon-to-amino-acid mapping (example):
  ext{AUG}
  ightarrow ext{Met}
• Codon degeneracy and silent mutations:
  ext{DNA codon changes at third position may be silent: coding }
  ightarrow ext{unchanged amino acid}
• Human chromosome 2 fusion hypothesis:
  2p + 2q
  ightarrow ext{chr. 2 (human)}, ext{ vs. two separate chromosomes in other primates}
• Universal genetic language as evidence for common ancestry:
  ext{DNA/RNA codons (triplets) → amino acids; all life shares this language}
• Wallace Line and biogeographic zones: isolation leads to divergent radiations (marsupials vs placentals)
• Peppered moth explanation in industrial Britain: selection shifts with environmental change
• Vestigial examples: goosebumps, appendix, whale hind limbs

Quick glossary (for review)

• Vestigial: a structure that has lost or changed its original function through evolution but remains in the organism.
• Homology: similarity due to shared ancestry and development.
• Analogy/Convergence: similarity due to similar function and selective pressures, not common ancestry.
• Apoptosis: programmed cell death used during development to shape anatomy.
• Polarity of fossil record: biases toward certain habitats, ages, and preservational conditions.
• Silent mutation: a nucleotide change that does not alter the amino acid sequence of a protein.
• Adaptive radiation: rapid diversification of a lineage into a variety of ecological niches.