Key Concepts:

Anatomy of the gene: what genes are.

• Parallel between atom, bit and gene.
  • Irreducible building blocks that are part of larger, hierarchically organized wholes.
• Importance of finding organizing principles:
  • Understanding the smallest part is crucial to understanding the whole.
    [Necessary, but not sufficient; there are severe limits to reductionism]
  • Allows you to go from explanation to control and manipulation (of the gene).
• Genes, chromosomes, DNA and the genome.
  • Chromosomes: each human cell contains 23 chromosomes pairs (23 from each parent).
  • Genes: each chromosome carries long strands of genes (in total, about 21-23k genes).
  • DNA: each gene is made of a chemical called DNA (4 bases and a backbone, 3 billion base pairs).
  • Genome: the entire set of genetic instructions is termed the genome (gene + chromosome).
• Trying to understand the nature of heredity: how does like beget like.
  • What is the logic behind heredity, behind organization in biology?
  • All chaotic and complex phenomena are the result of highly organized natural laws.
  • Aristotle (350 BC): heredity is about the transition of information.
    • Message (semen) becomes material (body), then becomes message again (semen), etc.
    • Cycle: information begets form begets information, etc.
  • Darwin (1859): nature is a process of cause and effect, not static.
    • You can understand the present/future by examining the past (origin).
      • Asks the question: how does nature evolve, how does information transfer and transform.
      • The answer is survival of the fittest: variation, competition, selection, reproduction.
    • For evolution to work and produce stable, but adaptable organisms, you need both change (variation through mutation) and stability (transmission through reproduction).
    • Darwin can’t answer the question of “blending”: what keeps variation from being constantly watered down and diluted over time (for instance, all birds slowly become the same blended color).
  • Mendel (1865): variance is based on unitary, distinct traits.
    • Explains the lack of “blending” for some traits.
    • Every trait is determined by an independent, indivisible particle of information.
    • Heredity involves the passage of these discrete pieces of information.
    • Discrete units of information = genes (coined in 1905 by Bateson).
  • Morgan & Muller (1908): genes likely physically linked and carried on chromosomes.
    • “Maleness” determined by unique factor:
      • Y chromosome only present in male embryos.
    • Proposed that all genes may be carried on chromosomes.
    • Some phenotypes always appear together (in fruit flies), suggested genes are physically linked together.
      • Genes don’t travel independently, they move in packs.
      • The tightness of the physical traits predicts the physical proximity of genes on chromosomes.
• The idea of the gene predated its actual physical discovery.
  • What we know about genes at this point is only that they:
    • Are packages of information with an unknown chemical and physical nature.
    • Can become mutated and thereby specify alternative traits.
    • Tend to be chemically or physically linked to each other.
    • Are located at the chromosomes.
• The idea of genes offers a potential solution to the central problem of information in biology:
  • Every biological activity requires decoding of coded instructions (ie, needs information).
    • How do living things arise (genesis)?
    • How do species look the way they look (evolution, variation)?
    • How does a single cell create a living thing and how do cells function (living)?
  • What is the nature of instruction and how is this information passed on (heredity)?
• Questions that are being answered: how do species look the way they look?
  • How can discrete particles of information (genes) give rise to smooth, continuous variations in a population (height, etc.)?
    • Answer lies in math.
    • The combinatorial power of (many) genes and environmental interacting creates a vast amount of potential outcomes (smooth curve).
  • How are certain traits selected for over time?
    • Distinction of genotype (genetic composition) and phenotypes (physical features).
    • Theory: genotype + environment + chance + time = phenotype (physical features).
    • Genes that produce physical features that are the best fit with their environment, survive, reproduce and become over-represented.
    • The engine of evolution is the ongoing matching of features and environment.
  • Why are species distinct and separate?
    • For a new species to arise, some factor must make interbreeding impossible.
    • If two populations become sufficiently varied, genetic incompatibility may arise.
• These theories deal mostly with issues of genes travelling vertically (reproduction, parent to child).
• Throughout the process of vertical transfer, genes remain invisible (chemically).
• Transformation: the horizontal transfer of genes:
  • Genes can be transmitted between two organisms without any form of reproduction.
  • Happens rarely in mammals, but often in bacteria.
  • If genes are physical molecules with chemical properties, what are should these properties be?
    • Possess some regularity: to allow for copying and transmission.
    • Capable of irregularity: to explain variation, diversity.
    • Compact: carry vast amount of information, but also neatly packaged into a cell.
• Life in general is a special type of chemistry:
  • Cells depend on chemical reactions to live.
  • Organisms continue to exist because of chemical reactions that are “barely possible”.
    • If there is too much reactivity, we “combust”.
    • If there is too little reactivity, we die.
    • We live on the edge of “chemical entropy”.
• Two chemical candidates for the gene are identified: they are proteins or nucleic acids.
  • Chromatin (chromosomes) is the biological structure where genes reside.
    • It is made of two types of chemicals: proteins and nucleic acids.
  • Proteins enable the “barely possible” chemical reactions necessary for living.
    • Nearly every cellular function (metabolism, respiration, division, etc.) requires proteins.
    • Proteins speed up some and slow down other reactions, just enough to be compatible with living.
  • Nucleic acids are the dark, unknown horses.
    • Early 1920s: discovery of DNA and RNA (both nucleic acids).
      • Both DNA and RNA are long chains made of four components (DNA: A, G, C and T; the bases), strung together along a backbone.
      • Initially thought to be too monotonous to be the carrier of genetic information.
    • Early 1940s: isolation and confirmation of DNA as carrier of genetic information (Avery).
• Knowing the chemistry, what is the physical form of the gene molecule?
  • In life, physics enables chemistry, which enables physiology, which enables biology:
    • The physical structure of a molecule enables its chemical nature.
    • The chemical nature enables its physiological function.
    • The physiology ultimately permits biological activity.
    • [Levels of information, emergence of complexity]
• So what is the form, the structure of DNA?
  • We know the chemistry (bases and backbone), but not the physics.
  • How is it linked to the physiological function of the gene (to transmit information)?
  • How are the four bases attached to a backbone of sugars and phosphates?
  • Watson and Crick (1953) discover the double stranded helix structure of DNA, linking form and function.

The physiology of the gene: how do genes work.

• Knowing the physics and chemistry of the gene, how do they enable the gene’s function?
  • How do DNA bases translate into physical features? What links genotype and phenotype? What is the gene’s action?
  • Beadle & Tatum (1941): a gene “acts” by directing the building of proteins.
    • A gene carries instructions, the code, to build proteins.
    • These proteins then proceed to perform all the cellular functions.
      • A protein is created from 20 simple chemicals (amino acids).
      • The shape of a protein relates to its specific function in a cell.
• First: DNA provides instruction to build RNA (transcription)
  • DNA first copies its genetic information into that of a complementary RNA molecule.
    • Similar to DNA: RNA has four bases (A, G, C and U – DNA’s “T” is substituted for a “U”).
  • RNA moves from the nucleus to the cytosol.
  • This process allows for multiple copies of the gene to be in circulation and for the number of copies to be decreased and increased on demand.
• Then RNA provides instructions to build proteins.
  • The sequence of the bases in the genetic code specifies the genetic information.
  • The genetic code occurs in triplets: three bases specify one amino acid in a protein.
• Universal flow of information through living systems:
  • DNA – RNA – proteins.
• Knowing how the gene acts generally, what enables a gene’s specific “selective action”?
  • How and when do the properties implicit in genes become explicit in different cells? How are they turned on and off?
• DNA regulation:
  • A gene possesses not only information about what to build, but also when and where.
  • Regulatory sequence:
    • Every gene has an “on” and “off” switch, a regulatory DNA sequence, triggered by what goes on in the environment.
      • When “on”, genes produce RNA.
      • When “off”, genes stop producing RNA.
      • This allows it to regulate the production of (the amount of) RNA.
  • Proteins act as regulatory sensors, turning genes on and off.
    • DNA contains the information for the development and maintenance of organisms.
    • But, proteins actualize the information inside the DNA/gene.
    • Proteins “conduct” the genome.
    • Cyclical and iterative process: a gene encodes a message that builds a protein that regulates a gene that encodes a message, etc.
  • The combination of regulatory sequences and protein-encoding sequences defines a gene.
    • The genome contains not only the blueprint, but also the program for controlled execution.
• DNA replication:
  • DNA is replicated when DNA copies itself (strands separate and new strands are formed).
  • Regulated by a specific enzyme to avoid rogue copying:
    • DNA polymerase: the enzyme that allows DNA to replicate.
• DNA recombination:
  • One of two mechanisms for generating genetic diversity:
    • Mutation: occurs when DNA is damaged (chemicals, copying error).
    • Recombination: swapping of genetic information between (male and female) chromosomes (when sperm and egg are combined).

 How genes build, maintain, repair and reproduce humans

• Genesis: how do genes make a whole organism grow out of a single cell.
• First three phases: axis determination, segment formation, and organ building:
  • The egg cell inside the womb is placed asymmetrically.
  • This causes certain proteins to be present in higher or lower concentrations in certain parts of the cell.
  • High versus low concentration activates different genes that determine the head-tail axis.
  • After this, mapmaker genes are activated that split the body into segments.
  • The next step is master-regulatory genes controlling the development of segments, organs, structures.
• Next step, the process of cell differentiation:
  • Invariance: most cells arise and develop in a precise and stereotypical manner.
  • Programmed death: regulated, controlled, programmed cell deletion.
  • Natural ambiguity: within severe constraints, the fate of some cells (under influence of neighboring cells) can change.
• Human physiology is the complexity that emerges when genes and proteins interact over time:
  • Most genes do not behave like one-to-one blueprints for proteins.
  • Interactive and cyclical processes among large numbers of genes and proteins.
  • Varying concentrations of proteins switch on or off varying numbers of genes, which then create varying amounts of other proteins, etc.

DNA cloning – the writing of genes

• Use of viruses to smuggle foreign DNA into a human cell:
  • In viruses, genes are not stretched out on chromosomes, but strung into a circle of DNA.
  • Once inside a human cell, the virus becomes a linear string that attaches itself to a chromosome.
  • Need an enzyme to cut open the virus’ genome circle and paste in foreign DNA.
• Use of bacteria to contribute enzymes that cut and paste:
  • Restriction enzymes: recognize unique DNA sequences and cut at a specific site.
  • Ligase: enzyme that stitches two pieces of broken DNA together.
• Provides the basis for artificial “recombination” (as opposed to natural recombination).
  • Labeled “recombinant DNA” (basis of drug production).
  • If recombination takes place inside bacterial cells, allows for bacterial cell rapid replication (and drug production).

DNA sequencing – the reading of genes

• The sequence (of base pairs) carries the meaning of the genetic code.
• Most genes are split into parts and modules that can be mixed and matched to create a vast range of “messages”:
  • Exons (message DNA) and introns (the “stuffer” fragments).

DNA sequencing and cloning allows for manipulation of genes

• Based on specific process – reverse transcriptase:
  • If you want to reproduce a function, look for the protein that triggers that function.
  • Then look for the RNA that produces that protein.
    • Build libraries of RNA that are active in each cell.
    • Look for differences in active RNA.
  • Then use that RNA to reproduce DNA.
• Potential to look for genes related to diseases, regulatory processes in the body, etc.
• Marks the start of the use of technology to manipulate genes.
  • Medicine: production of proteins from recombinant DNA (for instance, insulin).

DNA and disease

• Mutations in one gene can cause different types of disease in different types of organs.
• Reverse also true: different genes can influence one aspect of physiology.
• Certain genes only activate (disease) phenotypes upon environmental triggers or chance.
• Misunderstandings about  mutation:
  • Mutation, ie genetic diversity, is the natural state.
  • Mutation is relative: a variation from what is normal (called: “wild type”).
  • We are all mutants.
  • Whether or not a mutation is “good” or “bad” is not absolute.
  • It depends on the match between the genetic mutation and the current environment.
    • The definition of disease: a variation that is mismatched with its environment.
• Problem of detection – the need for a genome map:
  • There are 3 billion base pairs, some diseases are linked to only a handful of them.
  • Process of isolating genes linked to disease time consuming and inefficient.
    • Linkage analysis: use other traits paired with disease to locate part of the gene.
    • Requires zooming in on ever smaller fragments to isolate single DNA fragment.
  • Need to map the genome to be more efficient in locating specific disease related genes.
  • Genome map also needed to identify and understand multi-gene diseases.

 Genome map: sequencing the genome:

• Starts with sequencing the genome of the worm and fruit fly
• C. elegans:
  • 18,891 genes.
  • 36% of its genes encode for proteins the same as humans.
  • 10,000 genes are unique to worms.
  • 90% of the genome is dedicated to organism building.
• Fruit fly:
  • 13,000 genes.
  • More complex organism than worm, fewer genes.
• Complexity is not achieved by the number of genes, but by the organization of them.
  [in other words, network structure is key]
• Venter & Collins (2000): successfully sequence the whole human genome.

 Genomics and Identity:

• Cross over from using genes to analyze pathologies to understand “normalcy”.
• Use genetics to investigate human history:
  • Mutations accumulate in populations over generations.
  • Section of a population with the most mutations is likely the oldest section.
    • Provided genes have not blended recently.
    • So, you need to analyze genes that don’t recombine during reproduction.
    • Use mitochondrial DNA: part of the egg, you only get it from your mother.
• What we learnt about human history from genetics:
  • Young (200k years) and homogenous (the diversity of the human genome is small).
  • Originated from a narrow slice of sub-Saharan Africa.
  • Started to leave Africa about 100k ago.
  • Only one female lineage for mitochondrial DNA (there is a mitochondrial Eve).
• What we learnt about race from genetics:
  • Humans are largely similar in genetic terms, but with enough variation to have diversity.
  • Based on this diversity, you can form clusters of variations and features and label the categories, for instance “race”.
    • The choice of features and traits (identity) used to categorize tends to be cultural, social and political.
  • Genetic differences in general traits within these groups tend to be larger (85-90% of variations) than genetic differences between such groups (about 7% of variations).
    • Most variation antedates the separation into continents.
    • Too little time for the accumulation of substantial divergence.
  • We are culturally inclined to magnify differences, even if they are relatively minor.
    • What is normal becomes superior, what is rarer becomes inferior.
    • Human need to categorize and superimpose other attributes.
  • Using genetics is a one way street only:
    • You can use the genome to derive a person’s general ancestry.
    • You can’t use a person’s general ancestry to predict its genome (and associated traits).

 Genomics and sex/gender:

• Big picture: males and females are anatomically and physiologically different.
  • These differences are specified by genes.
  • These differences influence an individual’s identity.
• Sex, gender, identity:
  • Sex: the anatomic and physiological aspects of male versus female bodies.
  • Gender: the psychic, social and cultural roles that individuals assume.
  • Identity: an individual’s sense of self.
• XX versus XY:
  • Sex chromosome: XX (female) versus XY (male).
    • Sperm carries 50% only X and 50% only Y chromosomes, combining with the egg’s X.
  • On the Y chromosome:
    • Unpaired: there is no duplicate copy, like other chromosomes.
    • Therefore, mutations on it can’t be fixed and are vulnerable to damage.
    • Over time, it has shrunk and is now the smallest chromosome.
    • Genes for important traits have shuttled away to other chromosomes.
    • It may disappear completely over time.
    • A single gene on it activates the “male pathway”.
  • [Side note: purpose of “sex”: not reproduction (it would be easier for cells just to make duplicate copies), but recombination: produce variation to protect the species.]
• Sex is determined by a single gene.
• Gender and identity are more complex:
  • Influenced by the interaction over time of genes, culture, environment, etc.
• Generally, nature and nurture are not abstract and absolute:
  • Iterative interaction over time (as opposed to nature vs nurture).
  • At the top (or at the start), nature works forcefully (ie, master genes for this or that).
  • From there on, iterative interactions between nature and nurture follow.

 Genomics and self, behavior, sexuality:

• Genes play a role in influencing sexuality, but we know very little about genetic determinants.
  • For instance, despite many attempts, no single “gay” gene has been discovered.
• Inherited differences in genes influence many aspects of “normalcy” in varying degrees.
  • Strong and binary influence: simple, master-switch type genes at the top of a developmental hierarchy (ie, maleness vs femaleness).
  • Weak influence: if they act further down the chain (likelihoods, continuous outcomes).

 Epigenetics: from predisposition to disposition:

• The “last mile”: genes provide probabilities, but can’t predict certain outcomes.
  • Until now: genetics focused on shared traits in population to understand pathologies.
  • Now: investigate variations in individuals to understand human form and function.
• Can be answered by looking at these questions:
  • Why do identical twins growing up together become different over time?
  • What causes the difference if both twins are identically predisposed?
• Generally, genes perform a balancing act of stability and adaptability by switching on and off:
  • Balance between intrinsic, pre-determined genes react and chance, external influences.
• But if genes can switch on and off, why are certain outcomes fixed over time?
  • Why do embryonic cells irreversibly turn into specific cell types over time?
  • How are genetic fragments switched on or off indeterminately?
• Waddington (1950): epigenetics.
  • Cells somehow carry a mark above (epi) their genes.
    • A constant imprint of the cell’s history and identity.
  • The attachment of small molecules to DNA was correlated to a gene switching off.
    • Small molecules: methyl and histone tags.
  • This system of silencing and reactivation (through chemical tags) persists in time.
    • Tags can be added, erased, amplified, etc.
    • In response to cues from a cell or its environment.
  • The chemical tags can be changed, but not easily.
    • For instance, cell differentiation (from embryonic to specific cells) is largely irreversible.
  • Over time, every genome acquires its own, unique epigenome.
    • If nurture has an influence, it’s by leaving its marks on nature.
  • The epigenetic system, by selective de-activation, allows the genome to function.
    • Cells devoid of epigenetic selective repression and reactivation would be overwhelmed and could not function.
  • Ultimate purpose of epigenetics is to establish the individuality of a specific cell.
    • Individuality of the larger organism may be unintended consequence.
  • Epigenetic marks are not carried forward across generations.
    • Epigenetic marks are (almost always) erased in sperms and eggs.

Human genetics

• Two fundamental elements:
  • Genetic diagnosis: predicting future fate from genes (reading the genome).
  • Genetic alteration: intentional changing of the genes (writing the genome).
• Genetic diagnosis:
  • Pre-emptive diagnosis of (probable) illnesses.
  • Creating a backward catalog of genetic disorders:
    • Knowing that the syndrome has materialized, catalogue the mutant genes.
  • Lacking a forward catalog:
    • If someone has the mutant gene, what are the chances of developing the syndrome (function of penetrance and expressivity).
  • Limitations:
    • Genes may cause multiple phenotypes, some “good”, some “bad”.
    • Complex systems:
      • Difficult to analyze vast amount s of (interacting) individual genes.
      • Impact of chance and environment over time.
    • Requires a lot more computing power to be efficient.
• Genetic alteration:
  • Stem cells versus embryonic stem cells:
    • Stem cells (SC):
      • Can renew themselves.
      • Can give rise to limited number of other cell types.
      • Reside in particular organs and tissues
      • Change in SC does not alter the human genome (across generations).
    • Embryonic stem cells (ESC).
      • Arise from an organism’s embryo.
      • Pluripotent: can give rise to every cell type.
      • Can be isolated from the embryo and grown (in a petri dish).
      • Change in ESC affects the germ line, the human genome permanently.
      • Changes in ESC can be easily and selective made (in mice…).
  • Gene/foreign DNA therapy
    • Using viruses or foreign DNA to deliver genes into a cells’ genetic material.
    • Unreliable, inefficient and imprecise.
  • CIRSPR/Cas9: genome editing
    • Doudna & Charpentier (2012): programmed gene cutting and repairing.
    • For now, technique is still cumbersome and inefficient.