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Lecture I. Introduction and General Principles.

Primate phylogeny as imagined by Charles Darwin in 1868. From http://darwin-online.org.uk. Identifier: CUL-DAR80, image 107.

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Biology is the Study of Living Beings.

1. Consist of one or more cells. 2. Contain information allowing them to function and

reproduce, and transmit this information to offspring.

3. Die.

4. Are products of evolution.

In addition, organisms 1. Extract / utilize energy from the environment. 2. Convert chemicals obtained from the environment in-

to biological molecules and / or obtain such molecules directly from the environment.

3. Maintain an internal environment that differs from the

external environment (homeostasis). 4. Respond adaptively (physiologically, behaviorally,

etc.) to changing external conditions.

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Hierarchical Nature of Biological Organization.

1. Biological systems are organized hierarchically.

2. Molecules Cells … Ecosystems Biosphere

3. Larger structures assembled from smaller units. a. Reflected by the disciplinary structure of biology:

Biochemistry, physiology, ecology, etc. However,

b. Recent trend is the increasing use of molecular bi-ology, especially genetics, to frame / answer ques-tions at higher levels of biological organization.

c. Ecological analog is food chain shortening.

Figure 1a. One view of the biological hierarchy.

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Figure 1b. Chain shortening in the study of biological organization. Left. Traditional linear structure. Right. Contemporary efforts to understand biology at all levels in terms of genomes.

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Part I. Physical Law.

Biological Order and Thermodynamics.

1. Conservation of Energy: Energy can be transformed, not created or destroyed.

2. Thermodynamic Systems.

a. Open: Exchange energy

and materials with envt.

b. Isolated: No exchange. 3. Entropy: measures disorder. 4. 2nd Law: Entropy of an iso-

lated system cannot decrease & must increase if work performed – e.g., air conditioners produce heat.

5. An isolated system with maximum entropy is said to

be at thermodynamic equilibrium.

6. Biological systems are not at thermodynamic equilib-rium. They create and maintain order; reduce entropy.

Figure 2. System and en-vironment. Open systems exchange energy and ma-terials with environment; isolated systems, do not.

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Time’s Arrow and Probability.

Figure 3. Two illustrations of the Second Law. Top. Molecules ini-tially confined to a small region of the environment will distribute themselves with the passage of time. Bottom. Disordered states (high entropy) are more probable than ordered states (low entro-py).

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Order and Energy. 1. To impose / maintain order re-

quires energy.

2. Energy can be

a. Used directly by taking ad-vantage of potential gradi-ents – e.g., of temperature, charge, concentration, etc.

b. Stored for later use, e.g., in

the form of high energy compounds such as ATP. c. Difference between a. and b. is that of

i. Using a water wheel to power a flour mill vs.

ii. Using batteries charged with energy from another power source – e.g., coal-fired power plants.

d. Likewise, passive vs. active transport in organisms.

2. Impt: Set-up & maintenance costs inevitably accompa-

ny use of potential gradients, e.g., building the wheel.

Figure 4a. Gravitational potential driving a water wheel.

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Figure 4b. Active and passive fluid transport in plants. Water is transported passively from roots to leaves along gradients of decreasing 𝑯𝟐𝑶 concentration in xylem. Sug-ars are transported both actively and passively.

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Biological Systems are “Open.”

1. Exchange energy & materials with their environment.

2. Plants convert atmospheric

𝐶𝑂2 to sugars via photosyn-

thesis – the energy source is

sunlight.

3. Animals:

a. Eat plants and animals.

b. Use 𝑂2 to convert prod-

ucts of digestion into

high energy molecules that drive other reactions.

4. Energy / material exchange permits local reversal of the 2nd Law and the elabora-tion / maintenance of bio-logical order.

5. By “biological order” is meant

the structural and behav-ioral complexity of living systems.

Figure 5. Two regions of

the universe: is an

open system that ex-changes energy and ma-terials with a surrounding

region, 𝝎. The Second

Law necessitates that reductions of entropy in

necessitate larger in-

creases in the entropy of

. As a result, the entro-

py of the whole, 𝑬 =𝑬𝜶 + 𝑬𝝎, increases.

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6. Biological order achievable only at the cost of in-creased global disorder.

a. Referring to Figure 5, ∆𝐸𝜔 > −∆𝐸𝛼, where ∆𝐸𝛼

and ∆𝐸𝜔 are changes in local and external entro-

py.

b. Alternatively,

𝐸𝛼 ↓ ⇒ (𝐸𝛼 + 𝐸𝜔) ↑.

where (𝐸𝛼 + 𝐸𝜔) is the global entropy, i.e., en-

tropy of the whole. c. Entropic “pollution” an inevitable conse-

quence of the creation / maintenance of islands of order in an increasingly disordered universe i.e., there is no free lunch – e.g., urban “heat is-lands”.

d. Local entropy reduction can also result in the pro-duction of waste products harmful to living sys-tems, i.e., “pollution” in the usual sense of the word, e.g., the great oxygen crisis consequent to the “invention” of photosynthesis.

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Building Biological Order. 1. Erwin Schrödinger: author

of famous (but not entirely original) attempt to account for the existence of biological order in physical terms.

2. Order from disorder:

a. Local reversal of the 2nd Law.

b. I.e., energy used to cre-ate complex structures and sustain non-random behavior – see above.

3. Order from order.

a. Use of already organized materials, e.g. glucose and essential amino acids.

b. Encoding the information necessary for life in an “aperiodic crystal”.

Figure 6. Erwin Schrö-dinger, celebrated con-tributor to quantum me-chanics, spent WWII in Ireland. His 1943 lec-tures at the University of Dublin were later pub-lished as What is Life?

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4. Schrödinger’s sources of order leave unspecified a. How reversal of the 2nd law leads to structural /

behavioral complexity.

b. How organisms use information encoded in the aperiodic crystal.

5. We now know that DNA (in some cases RNA) encodes

the information for synthesizing proteins, but, a. The genome in no way a blueprint for embryonic

development.

b. Likewise, there is no road map for organismal development post partem / hatching.

6. What needs to be added to Schrödinger’s account are

a. Emergent properties: Aggregates have proper-

ties not shared by their components.

b. Self-organization: Local (equivalently micro-

scopic) interactions ⟹ global (equivalently mac-roscopic) patterns.

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Emergent Properties.

1. What one observes at any level of organization conse-quent in part to what transpires at lower levels.

2. I.e., Aggregate / macroscopic, behavior often de-termined by behavior at the microscopic level.

3. Macroscopic attributes that do not exist at the micro-

scopic level, called “emergent properties”.

4. Physics: A gas has temperature & pressure.

a. Consequent to molecular motion.

b. Its constituent molecules do not, they have ve-locity, mass & position.

5. Biology: Cognition.

a. Consequent to neuronal activity.

b. Brains think; neurons (nerve cells) do not, they just fire (or not) – more precisely, they exist in dif-ferent states: Excitable; Firing; Refractory.

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Figure 7a. Macroscopic vs. microscopic properties of a gas. Deri-

vation of the gas law, 𝑷𝑽 = 𝒏𝑹𝑻, from molecular motion was argu-ably the triumph of 19th century physics. Recall: momentum = mass

× velocity.

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Self–Organization and Pattern Formation.

1. Physical: Bénard cell formation – directly induced by temperature gradients.

Figure 7b. Top Left, Right. Imposing a temperature gradient on a fluid can organize random molecular motion into Bénard cells. Top Center. Cell formation at temperature, 𝑻 = 𝒕𝒄 exemplifies a bifur-cation, i.e., a qualitative change in behavior in response to a small change in the value of a parameter, this case the temperature dif-ferential. Bottom. Cell formation corresponds to the onset of con-vection whereby the rate of heat transfer through the fluid increas-es. With further increases in the temperature gradient, the motion becomes turbulent, and the cells break down. Think boiling water.

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2. Bénard cells in nature have important ecological and evolutionary consequences.

Figure 7c. Convection cells in the earth’s atmosphere (above) and interior (right) are driven by temperature differentials. The former account for global variations in winds and rainfall; the latter, for crustal spreading and subduction.

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3. Honey bee Nest Construction. a. No single bee can assess the entire hive. Colony-

wide properties result from local interactions among individuals with limited information.

b. At the microscopic level, one has individual bees, their innate preferences and tasks. Latter include

i. Depositing and / or removing nectar and pol-

len into or out of cells.

ii. Feeding the brood (larval bees). b. At the macroscopic

level, one has proper-ties of the hive: i. Pollen, nectar &

brood distribution.

ii. Honeycomb cells –

the hexagon shape of which is conse-quent to worker decision, in addition to pure-ly physical forces (Nazzi, 2016).

Figure 7c. Brood, nectar and pollen in a domestic bee hive (Camazine et al., 1990).

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Self-organization Rules for Honey Bees: No Bee has a Blueprint.

1. Queen lays in cells with an initial preference for nest center; subsequently lays in empty cells close to exist-ing brood (= developing larvae).

2. Returning pollen gatherers disgorge pollen into cells chosen at random.

3. Returning nectar gatherers unload nectar to house bees at hive entrance which instinctively move up the comb before regurgitating into empty cells.

4. Nurse bees preferentially remove pollen and nectar from cells close to the brood, thereby creating nearby empty cells into which the queen lays more eggs.

5. Results: a. In the area of developing brood: Nectar/Pollen

cells Empty cells Brood cells.

b. In other areas, Empty cells Nectar cells (above brood) and Pollen cells (mostly below brood).

c. Nectar above pollen cells because house bees

move up the comb while pollen gatherers do not.

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Animal Development.

1. A step-wise process (Figure

8a).

2. Entails successive differenti-

ation of initially totipotent

cells (Figures 8b).

3. As in the case of the much simpler case of bee nest

organization, there is no master plan.

Figure 8b. By the 8-cell stage, echinoderm embryos have dif-ferentiated with regard to animal and vegetable poles (top and bottom), and totipotency has been lost.

Figure 8a. Stages in starfish development.

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4. Instead, organs are produced by sequential interac-

tion of developing tissues.

5. At the genetic level – cell specialization is mediated by

differential gene expression.

6. Multiple genes form cascades. At each step, genes

code for transcription factors1 that control the synthe-

sis of other factors acting on the next set of genes.

1 Transcription factors are proteins that bind to specific sequences of DNA, thereby controlling the transcription of information from DNA to RNA.

Figure 8c. Reciprocal tissue induction in vertebrate eye development: a. The expanding optic vesicle induces lens local thickening (lens placode formation). b. Devel-oping lens determines size of the optic cup and c. induc-es formation of the cornea.

.

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Necessity of Evolution.

1. Repair mechanisms notwithstanding, the 2nd Law ne-cessitates death.

2. This is because repair mechanisms themselves break down2, thereby requiring secondary mechanisms, which themselves break down, etc.

3. Thus, the only way to live on is via one’s offspring. 4. But reproduction necessitates duplicating the heredi-

tary material, which, per #2 above, => copy errors. 5. By definition, copy errors are heritable, i.e., it is

the hereditary material, and hence, the information it encodes, that is altered.

6. Some copy errors necessarily affect reproductive

succes and parental survival.

7. In short, evolution by natural selection necessitated by the 2nd Law.

2 Hence the accumulation of DNA lesions with age and “age related com-promise of repair” (Lombard et al. 2005).

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Part II. Genes, Epigenetic Marks and Cells.

Molecular Biology’s Central Dogma.

1. Nucleic acids (principally DNA) are Schrödinger’s aperiodic crystals.

2. Central dogma: Infor-

mation flows from nucle-ic acids to proteins but (generally) not back.

3. Information passed

a. To DNA, e.g., when cells divide.

b. To proteins in a two-step process.

i. Transcription:

DNA → RNA.

ii. Translation:

RNA → protein. Figure 9a. Central dogma of molecular biology.

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4. DNA Structure.

a. Chains consist of sugar-phosphate backbone linked to nucleobases: adenine (A), cytosine (C), guanine (G), thymine (T).

b. Chains held together by H-

bonds between the bases.

c. In m-RNA; uracil (U) replac-es thymine (T).

5. Triplet code.

a. Each 3 base codon

specifies an amino acid or other func-tion, e.g., STOP.

b. Each gene consists

of many codons.

6. Triplet code ~ univer-sal & degenerate, i.e., n to 1, where 𝑛 > 1.

Figure 9b. Structure of DNA. Phosphate groups connect adjacent sugar molecules at so-called 3’ and 5’ positions.

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7. Genetic diversity is amplified both before and after mRNA → protein translation.

Figure 9c. Protein diversity exceeds genetic diversity by a fac-tor of at least 40. Most of the increase is post-translational, i.e., is consequent to reactions that modify proteins after their pro-duction at the ribosome. Figure from “Overview of Post-Translational Modifications (PTMs)” Thermo-Fisher Scientific.

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Figure 9d. Historical note: Schrö-dinger’s “aperiodic crystal traces to the work of Nikolai Kol’tsov [1872-1940], who in 1935 pro-posed the existence of a double stranded hereditary molecule that replicates semiconservatively. From V. Soyfer’s (2001) review, we read that “Each chromosome, in accordance with Koltsov’s hypothesis, consists of two chromatids, each of which is composed of one double-stranded giant hereditary molecule, in which every gene is repre-sented by its own symbol. During cell division, each strand is used as a tem-plate for the synthesis of its mirror copy or replica, so that the lineage can be preserved in hereditary records …”

Kol’tsov’s hypothesis confirmed by Watson and Crick in 1953. Ac-cording to his wife Kol’tsov was murdered by the NKVD (later the KGB) in 1940 for endorsing views (eugenics / Mendelian genetics) deemed fascistic by the Soviet government. Figure from Kol’tsov (1935) via Soyfer (2001).

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Exceptions to the Central Dogma.

1. RNA RNA (RNA viruses).

2. RNA DNA (Retroviruses).

3. Protein Protein (Prions).

a. PrP (prion protein)

abundant in nerv-

ous systems –

b. Appears to prevent demyelination via ox-idative stress.

c. Misfolded PrP does not protect.

d. Abnormal protein acts as a template that causes the normal form to re-fold.

e. Result: protein to protein information trans-

fer causing cerebral cortex degeneration and fatal neurodegenerative diseases, e.g., mad

cow disease, Creutzfeldt–Jakob syndrome.

Figure 10. Cortical degenera-tion and spongiform pathology in prion-induced disease.

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Beyond Base Pair Sequences: I. 1. DNA more than an information repository.

2. Especially in eukaryotes, DNA part of a complicated system whereby genes are expressed and proteins produced on an as needed basis.

3. This allows for efficient

a. Execution of recurrent activities e.g. cell division. b. Response to external stimuli, proteins, hormones,

etc.,

i. During development – e.g., cell differ-entiation, tissue for-mation, etc.

ii. Response to envir-onmental stress.

4. Note: In eukaryotes, trans-

cription but one of several levels at which gene ex-pression regulated.

Figure 11. Regulation of gene expression in eukary-otes by intron removal one of several mechanisms.

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Eukaryote Chromatin.

Figure 12. Top. The basic unit of eukaryotic chromatin is the nu-cleosome. Nucleosomes consist of core histones (proteins) to which DNA is attached by another histone called H1 (blue). Bot-tom. The nucleosomes may be coiled into larger fibers. Coiled DNA is less likely to be transcribed than uncoiled DNA.

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Chromatin Remodeling.

Figure 13. Middle. Schematic. Histone acetyl transferase (HAT) enzymes attach acetyl groups (O=C-CH3) to histone tails, thereby causing chromatin to open and promoting transcription. Opening of the DNA is called “decondensation.” Acetylation is reversed by his-tone deacetylase (HDAC) enzymes that remove acetyl groups from the histone tails. Top and Bottom. Electron micrographs of con-densed and de-condensed chromatin.

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Beyond Base Pair Sequences II: Epigenetics. 1. DNA expression is regulated during development.

Mechanisms include a. DNA methylation (addition of CH3 to cytosine). b. Histone tail methylation, acetylation.

2. Methylation of DNA and histones silences gene ex-

pression by tightening histone-DNA binding.

3. Acetylation of histones promotes gene expression by loosening histone-DNA binding.

4. Methylation of histone tails tightens or loosens coiling, i.e., represses or promotes gene expression. 3

5. Thus: Methylation (DNA)↓; Methylation (Histones)

↓or↑; Acetylation (Histones)↑.

6. Differences in epigenetic control of development

can lead to profound phenotypic differentiation in ge-netically similar groups – e.g., among primates.

7. Both hyper- and hypo- methylation cause cancer.

a. Too much silences tumor suppressor genes. b. Too little activates oncogenes.

3 The response depends on which histones are methylated.

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Figure 14. Epigenetic “marks” regulate DNA expression. Principal marks are methylation of cytosine in “CpG” (cytosine-phosphate-guanine) dinucleotides and methylation or acetylation of histone “tails” that comprise the chromatin.

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Primordial Germ Cells (PGCs) 1. Give rise to egg and sperm cells. 2. Sequestered early during development. 3. Most, but not all epigenetic marks, erased. Nec-

essary for totipotency.

Figure 15. Three primordial germ cell (PGC) loci, Vm2r29, Sfi1, …, that escape demethylation (left) and one that doesn’t (right). Circles represent unmethylated (open) and methylated (filled) CpG linkages. Vertical axis labels, E10.5 ,,, , refer to embryonic age in days. From Hacket et al. (2013) who suggest that the preservation of epigenetic marks during development a possible mechanism for transgenerational epigenetic inheritance.” Dazl, a locus that doesn’t escape demethylation is shown at the right for comparison.

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A Resurrected Heresy.

1. The idea that environmental conditions can induce heritable adaptive change a. Generally associated with Jean Baptiste La-

marck, Darwin’s best known predecessor,

b. Even though it was widely accepted by naturalists of the day including Darwin himself.

c. Today, “Lamarckism”, aka “the Lamarckian here-sy”, as this belief sometimes called, rejected.

d. Exception is changing gene frequencies, with new

mutations being random with regard to need.

2. But –

3. Exposure to novel environmental conditions can sometimes induce epigenetic modifications affecting gene expression that a. Are transmissible to offspring.

b. Induce adaptive phenotypic responses.

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4. A recent and particularly compelling example is fear conditioning in mice.4 a. Male mice trained to

associate specific odors with mild elec-tric shocks.

b. Their naïve de-scendants displayed heightened sensi-tivity to odorants (chemicals producing odors in question).

c. In one case, the known odorant receptor (a pro-tein) up-regulated., i.e., gene expression ↑.

d. Consequent to hypomethylation (reduced methylation) of the gene in question. Remember DNA methylation reduces gene expression.

e. Base sequence unaltered.

4Diaz, B, G. and K. J. Ressler. 2014. Parental olfactory experience influ-ences behavior and neural structure in subsequent generations.. Nature Neuroscience.17: 89-96.

Figure 16a. Newspaper an-nouncement of evidence for the epigenetic inheritance of fear.

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5. Environmentally-induced methylation / demethylation

of small regulatory RNA molecules another possi-ble source of epigenetic inheritance. These molecules a. Modulate gene stability, transcription, transla-

tion.

b. Are passed from parent to offspring both mater-nally and paternally, i.e., in eggs and sperm.

Figure 16b. Epigenetic inheritance of fear. Data from the original article.

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Cell Theory.

1. If we exclude viruses, cells the basic structural and physiological units of life.

2. Can exist as independent organisms (most prokaryotes) or serve as building blocks of multicellular organisms (mostly eukaryotes).

3. Cells from cells – Francesco Redi’s maggot ex-

periment (Figure 17) overthrew persistent theo-ries of spontaneous generation.

4. Complete set of genetic information replicated /

transmitted during cell division.

5. Differentiation consequent to differential gene ex-pression as previously noted.

6. What about viruses? Generally considered non-life.

a. Lack structure of even the simplest cells.

b. However, like cellular life, viruses evolve.

c. So-called “giant viruses” (Lecture II.4) may be de-generate descendants of more complex entities.

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Disproof of Spontaneous Generation.

Figure 17. Experiments that disproved the theory of spontaneous generation (abiosis). Top. Francesco Redi (1626-1697) showed that maggots come from fly eggs. Bottom. Louis Pasteur (1822-1895) demonstrated that microorganisms come from the air. These experiments were later used to counter the idea of continuing abiot-ic origination, i.e., from non-life, of life’s simplest forms as imagined by Lamarck and others. Important Note: These experiments do not disprove spontaneous generation of life in environments that no longer exist or in exotic environments such as deep-sea trenches.

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Not all Cells the Same.

1. E.g., prokaryotes vs. eu-karyotes.

2. If cells derive solely from

cells, both cell structure and the number of cell types must change within and between generations.

3. Within generations (de-

velopment): multicellular organisms begin life as a single “totipotent” cell, which subsequently di-vides. Thereafter,

a. Cells differentiate;

b. Totipotency lost.5

4. Between generations, i.e., over evolutionary time, new cell types arise.

5 Hence the interest in stem cells for the treatment of degenerative disease.

Figure 18a. Pro- and eu-karyotes compared sche-matically.

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Figure 18b. Derivation of different classes of mammalian blood cells from totipotent stem cells, here labelled hemo-cytoblasts), in the bone marrow. Erythrocytes (red blood cells) and thrombocytes (platelets) lack nuclei. Leukocytes (white blood cells) do not.

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Part III. Evolution.

The Pattern.

1. If species related solely by ancestry, a tree of life the result.

2. Species (more accurate-

ly phylogenetic lineages)

a. Change with time (anagenesis).

b. Give rise to new spe-cies by splitting (cla-dogenesis).

3. Lineages can also fuse

consequent to a. Hybridization.

b. Symbiogenesis – see Part IV below.

4. And they swap genes – lateral gene transfer (LGT).

Figure 19. Amniote evolution as a branching tree. Shared deived characters, so-called “synapomorphies”, (embryonic sac, hind limb under body, etc.) are shown as slices.

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Natural Selection (NS): Conventionally be-lieved to be the Principal Evolutionary Driver.6 1. Superior individuals out-

compete inferior ones.

2. NS requires:

a. Excess biotic po-tential – more off-spring than survive.

b. Heritable variation in traits affect fitness.

3. For the present, define

fitness as per individu-al rate of increase, of a lineage of organisms or genes – i.e.,

𝐹𝑖𝑡𝑛𝑒𝑠𝑠 ≈(𝑏𝑖𝑟𝑡ℎ𝑠 − 𝑑𝑒𝑎𝑡ℎ𝑠) 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙⁄

𝑡𝑖𝑚𝑒 (1)

6 The discovery of NS, more precisely, its application to the “species prob-lem”, is generally credited to Charles Darwin and A. R. Wallace who inde-pendently concluded that adaptive evolutionary change would result.

Figure 20. Substitution of a superior mutant as imagined by Darwin and Wallace.

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4. Previously, mutations of small phenotypic effect, e.g., single base pair substitutions were believed to be the “stuff” of evolution.

5. In fact. genes that regulate development (large ef-fects), turn out to be as, if not more, important – see, for example, the chickenosaurus video.

6. Developmental regu-

lation undercuts the case for Darwinian grad-ualism – i.e., the idea that evolution proceeds by small steps.

7. More generally, equating

evolution with changing gene frequencies

a. Of small or large effect

b. Becomes untenable to the extent that environ-mentally-induced epigenetic change is adap-tive and common.

Figure 21. Paleontologist Jack Horner hopes to recreate “non-avian” dinosaurs by manipulat-ing development of their avian descendants.

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Fitness.

1. Criterion of evolutionary “superiority.” 2. Can be defined as the relative contributions of dif-

ferent individuals (genes) to future generations per Eq. 1.

a. But what do we mean by “future generations”?

b. After all, > 99% of all species go extinct.

c. And if environment is changing, so also are rela-tive degrees of superiority / inferiority.

3. Also, populations can’t be collapsed into a single

number – individuals differ according to age, sex, eco-logical circumstance, etc.

4. Moreover, reproduction and survival often depend on

the other genes / individuals. Thus, fitness of gene 𝑎1 in species A partly determined by

a. Frequencies of genes 𝑎2, 𝑎3, …, (also in A).

b. Frequencies of genes 𝑏1, 𝑏2, … in species B; by

those of 𝑐1, 𝑐2, … in species C, etc.

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Fitness in Red Clover (Trifolium pratense).

1. Pollinated by bumblebees: a. Long floral tube prevents

smaller bees from get-ting to the nectar.

b. Advantage of long tubes:

i. Attract large bees

that can carry more pollen than small.

ii. Depends on abun-

dance of large bees.

2. Darwin (1859, pp. 73-74) suggested that bumblebee abundance depends on the numbers of village cats. a. Field mice destroy bumble bee nests.

b. Cats kill field mice.

c. => more bumblebees.

d. => greater fitness of flowers with long tubes.

Figure 22. Bumblebee on red clover. Small bees ig-nore the flowers because their tongues are too short to reach the nectar at the bottom of the tube.

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3. Hence local abundance of cats affects the relative fit-ness of plants with long and short tubed flowers.

a. More cats should select for long tubes.

b. Fewer cats should select for floral modifica-tions that obviate the need for bumblebees.

4. An example of complex fitness dependence.

Figure 23. Darwin’s example of complex ecological interactions. By their negative effect on field mice, which destroy bumblebee nests, village cats promote (dashed blue line) the pollination and hence the abundance of red clover. They also affect clover evolution by increasing the fitness of plants with long tubed flowers that can only be pollinated by large insects.

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1. Individual vs. Group Selection.

1. Except in special circumstances, traits do not evolve to benefit whole populations or species – a common misunderstanding.

2. To the contrary, selection on individuals can act to the detriment of a population.

3. Example: Predators can evolve to extinction – i.e., absent countervailing forces, improved predatory pro-ficiency (and reduced prey abundance) always select-ed for.

a. As prey numbers decline, selection for greater

predator proficiency will increase, with resultant vanishing food supply and predator extinction.

b. Unless there are trade-offs and / or alternative

food species.

4. Outstanding Problem: The evolution of altruism (increasing the fitness of conspecifics at one’s own ex-pense) remains difficult to account for – see ex-cerpts (linked to Announcements) from May (2009) for discussion.

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Artificial Selection (AS).

1. Darwin viewed AS analogous to NS; argued that NS was a “true cause” analogous in its effect to gravity.

2. Wallace viewed domestic breeds as “monstrosities” that cannot survive in nature,

3. These views are not incompatible.

4. Breeds of domestic dogs exemplify the extent to which

heritable variations can be selected for. But, most in-ter-fertile. Not different (See Lecture II.3).

Figure 24. “Real” dog (left) and “rodent” dogs (right) share a common wolf-like ancestor. Both shown in their native habitats,

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Figure 25. Simplified canine phylogeny.

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Explaining Adaptation.

1. How complex structures such as the eye evolve?

2. Before Darwin, accepted answer was Design – so-called “teleological argument”7.

3. Most contemporary biologists disagree: adaptation the

result of variation plus selection (V+S).

4. V+S modulated / obscured by

a. Developmental correlations;

b. Trade-offs: what’s good for one thing, bad for another.

c. Non-adaptive change due to sampling error;

d. Infrequent events – e.g., Chicxulub impact. 5. Even if one accepts V+S as the entire story,

a. Characterizing past selection uncertain.

b. Inferring why characters have evolved difficult.

7 The belief that adaptation reflects Divine Wisdom and Beneficence.

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The Giraffe’s Neck: Changing Explanations.

1. Traditional View: Long necks allow individuals to forage high up in the canopy.

2. But,

a. Giraffes often for-

age lower down.

b. Males use their necks to fight with each other.

c. Male necks larger,

more heavily mus-cled than female necks.

3. New Hypothesis: Long

neck evolved in response to sexual selection, i.e., males contesting for females.

Figure 33. Giraffe feeding on acacia leaves with head fully extended. Below this level, the tree has been stripped bare. Note the 18” tongue.

Figure 34. Foraging height frequency diagrams for male / female giraffes.

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4. Anatomical evidence equivocal.

a. Male giraffe skull heavily armored. Consistent with sex-ual selection.

b. Skull-neck joint al-

lows complete ex-tension of the head (Fig. 35). Consistent with foraging hy-pothesis.

c. Hypotheses not mu-

tually exclusive.

5. In fact, more recent data (Fig. 36)

a. Supports selection

for more massive skulls in males.

b. But not for longer

necks.

Figure 35. Skull of a male gi-raffe in section. Note promi-nent frontal (FS) and parietal (PS) air sinuses within which struts support the skull roof thereby impeding transmis-sion of blows from above to the brain and nasal cavities. The enlarged occipital con-dyle (OC) permits backwards rotation of the head so as to bring the anterior-posterior axis of the skull in line with the neck, thereby permitting full extension of the head. Reproduced from Owen, 1866. On the Anatomy of Vertebrates. II. Birds and Mammals. Longman, Green and Co. London.

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6. Conclusions:

a. Initial acceptance of select sexual selection hy-

pothesis premature – scientists traveling in herds.

b. Alternative adaptive scenarios not necessarily mu-tually exclusive.

c. There are always explanations alternative to

current utility. Among them –

i. Adaptation to past circumstances – e.g., seeds

formerly dispersed by large mammals now ex-tinct (Figure 37).

ii. Developmental constraints, i.e., correlated change among seemingly unrelated characters.

Figure 36. Neck length and head mass plotted against body mass for male and female giraffes. Only head mass is proportionately larger in males. From Mitchell et al. 2009. J. Zool. 278: 281–286.

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Figure 37. Giant ground sloth and foot-long beans of the pink shower tree, Cassia grandis. Livestock introduced into Central America by Spanish settlers now substitute for ex-tinct giant sloths and elephant-like gomphotheres as dis-persal agents.

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Correlated Characters: Fox Farm Experiment.

1. Forty year Russian breeding experiment.

2. The only character selected for was tameness, a behavioral trait.

3. Nonetheless, some half dozen morphological

traits, many found in domestic animals, in-creased in frequency.

Figure 38. Selection for tameness in foxes. The animal at the left was not permitted to breed. The animal at the right (fear, but no viciousness) was. Its descendants show no negative emotional responses to humans. Note the differ-ences in coat color.

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Characteristic

Animals per 100,000 with Trait

Increase in Frequency

Domesticated Population

Non-Domesticated

Population (Per cent)

Loss of Pig-mentation

12,400 710 1,646

Brown Mottling 450 86 423

Gray Hairs 500 100 400

Floppy Ears 230 170 35

Short Tail 140 2 6,900

Tail Rolled in Circle

9,400 830 1,033

1. From Trutt, L. N. 1999. Early canid domestication: The Farm-

Fox Experiment. American Scientist. 87: 160-169.

Changes Following Selection for Tameness in Foxes1

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Figure 39. Cute kit. The evolutionary importance of corre-lated characters is underscored by forty years of fox breeding experiments. Although tameness was the only character selected for, numerous other changes were ob-served. These included increased incidence of floppy ears, and piebald color pattern (patches of different color), and smaller skulls, characters observed in other domesti-cated species. Shown here is a human-friendly juvenile in-teracting with a caregiver.

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Part IV. Systematics and the History of Life.

Linnaean System: Kingdom, phylum, etc.

1. Additional taxa e.g., subspecies, sometimes often

added. Modern humans – H. s. sapiens; Neanderthals – H. s. neanderthalensis; domestic goat – C. h. hircus.

2. Linnaean system predates evolution. Linnaeus be-

lieved most species created in their present form.8 3. Contemporary systematics imagines all species de-

scended from a single original form – tree of life.

8 Linnaeus also recognized what would later be called “true varieties” as “products of Nature”. In so doing, he initiated a 200+ year journey from Spe-cial Creation to evolution.

The Linnaean Classification

Kingdom Animalia Phylum Chordata

Class Mammalia Order Primates Artiodactyla

Family Hominidae Bovidae Genus Homo Capra

Species sapiens hircus

Comm. Name Man Goat

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How Many Kingdoms? 1. Historically two: Animalia and Plantae – both of

which included single cell organisms, i.e., protists. 2. Fungi – because they have cell walls – were believed

to be plants that had lost their chloroplasts and there-fore placed in Plantae.

3. With discovery of bacteria, prokaryotes (no nucleus)

were distinguished from eukaryotes (nucleus plus oth-er organelles), and

4. Two kingdoms replaced by five:

a. Monera (prokaryotes) b. Protista (unicellular eukaryotes) c. Plantae d. Fungi e. Animalia

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Three Domain Scheme. 1. Introduces “domains” (category above kingdoms).

a. Bacteria (= eubacteria) b. Archaea (= archaebacteria) c. Eukarya (= eukaryotes)

2. Based on analysis of ribosomal RNA.

Figure 40. Three domain scheme as shown in many textbooks.

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Simplified Version.

Figure 41. Simplified version of the three domain scheme. Note that Eukarya and Archaea are represented as having a more re-cent common ancestor (red circle) than either with Bacteria. “Common Ancestor To all life today” refers to the most recent common ancestor of contemporary life.

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Three Domains vs. Five Kingdoms.

Figure 42. Five kingdom (a) and three domain (b) classifications compared. Monera is divided into Bac-teria and Archaea. Fungi, Eukarya unites Fungi, Plan-tae and Animalia.

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But –

1. Eukaryotes may have resulted from the fusion of an archaebacterium (Archaea) and a eubacterium (Bacte-ria), a process called symbiogenesis.

2. If yes, the “tree” metaphor fails at its base.

3. Which it also does at the branch tips consequent to

hybridization, of which there is lots – especially in plants.

Figure 43. Symbiogenic origin of eukaryotes as proposed by Lynn Margulis. “UCA” stands for “universal common ancestor.”

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Even if eukaryotic nucleus, endoplasmic reticulum (ER),

etc., originated in eukaryotes absent symbiogenesis, 1. Mitochondria and chloroplasts of symbiogenic origin.

2. Lateral gene transfer (LGT) common among pro-

karyotes.

3. And between domains – e.g., bacteria copping venom genes from black widow spiders.

4. Consequence: Gene trees and species trees not necessarily the same.

Figure 44. Three domain scheme modified to include symbiogenic origin of mitochondria & chloroplasts. Omitted is hybridization at branch tips, gene flow between domains & possible symbiogenic origin of eukaryotes.

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Trans-domain gene exchange in Wolbachia, a bacterium that parasitizes arthropods.

Figure 45a. “Models of lateral DNA transfer between eukaryotes and bacteriophages. (a) The eukaryotic cell can harbor multiple microbes capable of horizontal gene transfer. Genetic transfers between eukary-otes and bacteriophages can, in theory, occur (b) directly between eu-karyotic chromosomes and phage genomes; (c) indirectly between eu-karyotic and Wolbachia chromosomes; or (d) indirectly between eukary-otic chromosomes and an intermediary.” Figure and caption from Bor-denstein and Bordenstein. 2016. Nature Communications | 7:13155 | DOI: 10.1038/ncomms13155

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Figure 45b. One of the eukaryotic genes in Wolbachia phage WO codes for venom produced by black widow spiders. The venom may facilitate phage dispersal by punching holes in the plasma membrane of the eukar-yotic cell, parasitized by the host bacterium.

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Part V. On the Nature of Scientific Inquiry.

Science as the Modeler’s Art.

1. Models are simplified representations of reality.

a. Mathematical, pictorial or verbal.

b. Reduce real world complexity to “essentials.”

2. All theories are models, and they must be falsi-fiable at least in principle if they are to be con-sidered scientific.

a. Mechanistic assumptions => testable predic-

tions.

b. Model falsification results if

i. Observation ≠ prediction.

ii. Assumptions prove wrong / inappropriate.

2. Models can be falsified, not proved.

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Figure 46. The “scientific” / hypothetico-deductive method. Obser-vations, along with intuition, experience and God knows what else, inform hypothesis formulation. Hypothesis-induced predictions are then compared with observations. Falsification (hypothesis-observation mismatch) necessitates hypothesis revision

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Hard Cores and Protective Belts. 1. Falsifiability often claimed to distinguish scientific

conclusions from other forms of opinion. But –

2. In practice, it is useful to distinguish between

a. The “hard core” (HC) to which scientists cling, and

b. The “protective belt” (PB) of auxiliary hypothe-ses (AHs), the reformulation of which permits HC survival in the face of anomalous observations.

3. Example. As discussed in Lecture II.2,

a. Natural selection theory widely rejected as a plau-

sible evolutionary mechanism in late 19th century.

b. Nonetheless, paleontological evidence increasingly supported common descent – the HC.

c. Alternative mechanisms, including resurrection of

Lamarck proposed in its place – AH adjustment.

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Wiggling the Elephant’s Trunk.

1. Revising AHs to accommodate new information is not equivalent to confirming a theory’s predictions.

a. What results is a new model.

b. Which itself must then be subjected to at-

tempted falsification.

2. Increasing computing power a blessing & a curse.

a. Makes possible all-but-the-kitchen-sink simu-

lations that can’t be analyzed mathematically.

b. One can only perform numerical experiments.

c. Increased imprecision an inescapable con-sequence of adding variables and parameters, each of which must then be estimated.

d. Worse, some parameters only estimable by

fitting data to a priori assumptions.

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Figure 48. Computer performance (past and projected)

vs. time. A megaflop is 106 floating point (non-integer

math) operations per second; a gigaflop, 109 operations, etc. (McGuffie & Henderson-Sellers, 2005).

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What Makes a Good Theory?

1. Mechanistic plausibility / internal consistency.

2. Non-trivial, ideally quantitative, predictions.

3. Accounts for multiple phenomena, especially those

a. Initially considered unrelated to the problem of interest.

b. Unknown or deemed hostile to the theory when first formulated.

c. Vestigial organs an example.

i. Unexpected if species created by God.

ii. Expected if new species descended from old.

“To every thoughtful naturalist the question must arise,

What are these [rudiments] for? What have they to do with the great laws of creation? … If each species has been created … without any necessary relations with pre-existing species, what do these … apparent imperfections mean”? … [But] if … the great law which has regulated

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the peopling of the earth … is, that … no new creature shall be formed widely differing from anything before exist-ing; … then these rudimentary organs are necessary, and

are an essential part of the system of Nature.” [Wallace

(1855), pp. 195-196]

Remember: Nature

1. Supremely indifferent to human proclivity.

2. “Always bats last.” – Stephen J. Gould (1999)

Figure 49. Non-functional cetacean femur and pelvis.