Cycle 1 - evolution is happening

Cycle 1: Evolution is Happening


Important information from Pre-Lecture 1 Reading:


Definition of Life and Viruses:

  • We struggle to come up with a clear definition of life because its definition must be universal 

  • “The way a discipline defines life is intimately connected to the questions it explores”

  • Whether or not viruses are considered life is still a huge argument (don’t respire or metabolize, but do contain nucleic acid and replicate etc.)


Entity - a wide range of self-replicating and evolving systems 

VS

Organism - forms of life that are made of cells


Key attributes of organisms on earth: displays order, harnesses and utilizes energy, reproduces, responds to stimuli, exhibits homeostasis, grows and develops, evolves.


Viruses

  • Infectious particles

  • 1 or more nucleic acid molecules surrounded by a protein coat (capsid) which may or may not be enclosed within a membrane (envelope) derived from the host cell’s membrane


Virus composition

  • Nucleic genome (can be a single or double strand of DNA or RNA)

  • Viral genomes can range from a few-100 genes

  • All viruses have genes that encode (at least) their coat proteins and proteins involved in transcription (*enveloped viruses have genes for synthesis of envelope proteins and some viral genomes have virus-specific enzymes for nucleic acid replication*

  • Most viruses are helical or polyhedral


Viruses infection rates

  • Viral families end in ‘viridae’

  • Out of the 80 viral families, 21 cause human diseases

  • The effects of viruses range from benign to seriously debilitating or lethal

  • Not all viruses are pathogens, some are beneficial to their hosts

  • Viruses are a vital component of ecosystems, and may be the dominant entity (they affect nutrient cycling through their effects on prokaryotic organisms)

  • Viruses have been a source of genetic material providing? Evolutionary options for cell organisms (may help explain some evolutionary transitions)


How viruses infect host cells

  • Viruses infect animal cells as they would bacteria but both the viral coat and genome enter a host cell

  • Viruses without an envelope bind by their recognition proteins to the plasma membrane and are taken into a host cell via endocytosis

  • A number of animal viruses (like HIV) enter a latent phase, wherein the virus remains in an inactive form while in cell

  • The vast majority of animal viruses are asymptomatic (since causes diseases doesn’t benefit the virus)

  • Pathogenic viruses, however, cause disease in a variety of ways (for example, some cause cell-death when releasing viruses from cell - this can lead to massive cell death, destroying vital tissues (nervous or W/RBC’s))

  • Other viruses release cellular molecules when infected cells breakdown inducing fever and inflammation (influenza)

  • Viruses also alter gene function when inserted into host cells DNA which leads to  cancer and other abnormalities.


How HIV infects a host cell:

  1. Viral particle enters cell

  2. Viral reverse transcriptase that entered the cell in the viral capsid makes a double-stranded DNA copy of the viral RNA genome

  3. Viral-encoded integrase enzymes splices the DNA copy of viral genome into the host DNA. The inserted virus is the provirus. Provirus is dormant and is replicated and passed on as the cell divides. In this state, the virus is hidden from the immune system

  4. When the provirus becomes active, it’s transcribed to produce viral RNA genomes and to produce viral mRNAs, which are translated to produce viral proteins.

  5. Viral proteins assemble into new infective viral particles, which are released from the cell by budding.


Cycle 1: Evolution is Happening


PRE-L2 OUTCOMES:

  • My answers are in blue, questions are in grey and corrections are in red


  1. Why are viruses sometimes considered to be “alive”, and sometimes not?

Viruses are sometimes considered to be alive because they have the ability to replicate and contain a genetic code - features that many biologists consider to be vital descriptions of life. However, viruses do not ‘check all boxes’ so to speak, as while they can replicate and contain a nucleic acid, like living organisms, they do not metabolize or respire and so they are considered to be viral particles or entities, rather than living organisms/life. 

  1. The very basic features of animal viruses and how they infect cells and replicate. You don't have to understand or memorize in great depth here.

Animal viruses are typically polyhedral and contain nucleic acid (either single or double strand of DNA or RNA) bound within a capsid and may be enclosed by a membrane called an envelope. Animal viruses infect host cells by binding to the cell's plasma membrane (using recognition proteins) and entering through endocytosis. Then reverse transcriptase reverse transcribes the virus's genome and splices it into the host cell’s dna (now called a provirus) where it will remain dormant and be passed on from cell-cell during cell division. When the provirus becomes active, it is transcribed and translated into an mRNA and synthesized into viral proteins which come together to form viral particles that will leave the cell through budding and infect other cells.


L1 Notes:


Zoonotic diseases - spread (spill over) to humans from non-human animals

  • 75% of new infectious diseases

  • More likely between closely related species (ie. other primates) ⇒ SIV (simian immunodeficiency virus: has a long history of infecting non-human primates (multiple spillovers to humans (HIV!)

  • Often not harmful in the original host (reservoir) but it's wayy more harmful in the new host


Viruses

  • Have a protein shell w/ nucleic acid genome inside (DNA or RNA, sing. or doub. stranded)

  • Obligate parasites (need to infect cells to make proteins and replicate)


relative to antibiotics (drugs that treat bacterial infections) or antifungals (treat fungal infections), antiviral drugs are harder to design and usually have more serious side effects!


Retrovirus - any of a family of RNA viruses that have reverse transcriptase (enabling them capable of making a complementary DNA copy of the viral DNA (which is then integrated into a host cell’s DNA))















  1. A virion fuses with a host cell

  2. Viral RT (reverse transcriptase) reverse transcribes viral RNA to double stranded DNA

  3. Viral integrase splices viral DNA into host DNA

  4. Viral DNA gets transcribed, translated and then forms new virions.                                       



AZT - is a drug/nucleoside analog-shaped almost like thymine (T). It was used  to treat HIV by disrupting RT when reverse transcribing viral RNA. However, after a couple of weeks-months, RT was able to adapt to the AZT due to a random mutation. 

⇓

Evolution of AZT 

  • Mutations led to variation in AZT-resistance

  • AZT-resistance passed from ‘parents’ to ‘offspring’ 

  • Not all virions reproduce

  • When AZT is present, the AZT resistant forms are more likely to reproduce than others (AZT-susceptible)

  • Viral population changes over time 








BIG IDEA:


VARIATION + NON RANDOM SURVIVAL = EVOLUTION THROUGH NATURAL SELECTION


⇒ “mutation proposes, selection disposes”


  • New genetic variants (mutations) are constantly occurring regardless of the environment

  • The environment (in this case, presence vs. absence of AZT) affects which variants become more common, NOT which variants occur 

  • This is because the variants that are more suited to their environment, will have a  greater chance of survival and be able to reproduce, thereby increasing that variants population


L1 summary: 

  • Evolution can be very fast

  • Even non-living things can evolve 

  • Viral evolution involves themes such as: evolutionary history, mutation and variation, natural selection and humans as an evolutionary force.


L1 OUTCOMES:

  • My answers are in blue, questions are in grey and corrections are in red


  1. How are viruses similar to cellular life and how are they different?


  1. Explain the evolutionary origins of HIV and why treating viral diseases are different then antibacterial or fungal?

 

  1. How did HIV evolve resistance to drugs we use to treat it and why is the effectiveness of any new antiviral drugs likely to decrease overtime? 

 

  1. What are the principles underlying evolution by natural selection: heritable variation, non-random reproduction or survival, change in genotype of a population?

 

  1. How does the viral mutation rate affect the likelihood of developing a long term effective vaccine, or developing long term effective antiviral drugs?


Important information from Pre-Lecture 2 Reading:

FINISH


Misconceptions about evolutionary theory and processes

  1. Evolution is a theory about the origin of life: Evolutionary theory focuses primarily on how life changes after it originated, not on how life began.

  2. Evolution occurs randomly: While mutation is random, natural selection, a key mechanism of evolution, is non-random, leading to adaptations that suit organisms to their environments.

  3. Evolution results in progress: Evolution does not always lead to progress or "better" organisms; traits beneficial in one environment may not be advantageous in another, and not all evolutionary changes are adaptive.

  4. Individual organisms evolve in a single lifespan: Evolution happens across populations over many generations, not within an individual’s lifetime.

  5. Evolution only happens slowly: Evolution can occur both gradually and rapidly, depending on factors like environmental changes and population size.

  6. Humans cannot influence evolution: Human activities, such as environmental changes and medical practices, can drive evolutionary changes in other species.

  7. Genetic drift only occurs in small populations: Genetic drift happens in all populations, but its effects are more pronounced in smaller populations.

  8. Humans are not evolving: Humans are still evolving, but the selective pressures have changed due to advances in technology and medicine.

  9. Species are distinct, easily recognized entities: The concept of species is not always clear-cut, as it can be difficult to apply to organisms like bacteria or those that hybridize.


Misconceptions about natural selection and adaptation

  1. Natural selection involves organisms trying to adapt: Organisms do not "try" to adapt; natural selection works through random mutations that provide survival advantages, not through conscious effort.

  2. Natural selection gives organisms what they need: Natural selection does not provide organisms with what they need; it acts on existing genetic variation, and if the right variation isn't present, the species may not survive.

  3. Humans can't negatively impact ecosystems because species will evolve what they need: Natural selection doesn't guarantee survival; species lacking the necessary genetic variation may go extinct when faced with rapid environmental changes caused by humans.

  4. Natural selection acts for the good of the species: Natural selection favors traits that benefit individuals, not the species as a whole. Altruism can evolve if it benefits the individual's relatives or if there is some form of repayment.

  5. The fittest organisms are the strongest, healthiest, fastest, or largest: Evolutionary fitness refers to an organism’s ability to reproduce and pass on its genes, not its physical strength or size.

  6. Natural selection is about survival of the very fittest: It's more about survival of the "fit enough" — many individuals survive and reproduce, not just the strongest or "best" ones.

  7. Natural selection produces organisms perfectly suited to their environments: Natural selection is limited by trade-offs, historical constraints, and other factors, so organisms are not perfectly adapted.

  8. All traits of organisms are adaptations: Not all traits are adaptive; some are by-products of other traits or the result of historical accidents with no adaptive purpose.


PRE-L2 OUTCOMES:

  • My answers are in blue, questions are in grey and corrections are in red


  1. What are examples of "scala natura" thinking, and why is this type of classification not compatible with modern evolutionary theory?


  1. What are examples of evidence that supports the idea of descent with modification from a common ancestor?


  1. What are examples of homologous traits?


  1. How has our understanding of evolution changed since Darwin's time?


  1. Why are mutations important to evolution?


  1. What are some misconceptions about evolution and natural selection, and why are they incorrect?

There are many so I'll just list a few:


L2 Notes:


“Humans evolved from earlier species of animals”


Evolution ⇒ remains controversial with the general public

  • Species change over time 

  • Humans have descended from other animals

  • These ideas conflict with some belief systems and creation stories


Belief system - set of principles or beliefs which together form the basis of a religion, philosophy or moral code


Belief - conviction or acceptance that certain things are true or real, faith


⇑ not intended to be tested or rely on evidence ⇑


VS


Scientific theory - a coherent set of testable hypotheses that try to explain facts about the natural world (logical)

⇒ must be TESTABLE and FALSIFIABLE; if falsified, change the theory ] some possible observation or experimental finding could prove the theory (or hypothesis to be wrong)


“AZT-resistant forms of HIV will increase in frequency if a patient is taking AZT. These forms will NOT increase in frequency if the patient is not taking AZT”


VS


“Positive thinking can cure cancer, if you try hard enough” 

⇒ if cancer keeps spreading, you can argue that they didn’t try hard enough, therefore this is a belief since it is not testable/falsifiable



What is the theory of evolution? - descent with modification from a common ancestor


  1. Evolution happens 

  • Allele frequencies in a population change from one generation to the next


  1. All life is related through common ancestry


  1. Speciation: lineages diverge into daughter lineages 


KEYNOTE:


Evolution is not transformational, but VARIATIONAL!

⇓

Individuals do not ‘evolve; within a lifetime; populations evolve one generation to the next



Gradualism and transitional forms - takes many generations to produce large changes; some transitional forms may be found in the fossil record


Selection generates many adaptations and explains much evolutionary change (but not all!)


Correcting common evolutionary-theory misconceptions: 

  • Humans are related to chimps. NOT descended

  • No living species are ‘more highly evolved’ than any other living species

  • Mutations are not directed towards the needs of the organism (because mutations are RANDOM!)

  • Selections results in adaptation but not perfection


Major Evolutionary Theory Insights:

  • Life on earth today has evolved gradually

  • Life originated from one entity; perhaps a self-replicating molecule, that existed over 4 billion years ago

  • That changed over time, giving rise to cells and continuing to change in different ways and diverging into new and diverse forms of life which continue to evolve


L1 OUTCOMES:

  • My answers are in blue, questions are in grey and corrections are in red


  1. What are the characteristics of a scientific theory? Differences between scientific theories and belief systems? How can scientific theories be tested, potentially falsified, and updated?

Scientific theories are logical and must be both testable and falsifiable. Belief systems on the other hand, are not testable or falsifiable and they are not intended to rely on evidence unlike scientific theories. 


  1. What are the major components of modern evolutionary theory: change through time, common ancestry, speciation, variational rather than transformational, gradualism, role of selection?


Change through time: Evolution takes many many years and spans across many generations of a species/organism.


Common ancestry: it is believed that all life today is related by a common ancestry that originated 4 billion years ago as the first living specimen.


Gradualism: Mutations happen gradually over long periods of time from generation to generation. 


Variational rather than transformational: Evolution is not transformational, but variational. So rather than a linear process that evolves species from one generation to the next, it is more like many trials and errors resulting from random mutations that create a myriad of different variations of an organism from a common ancestor. 


Role of selection: natural selection plays a large part in how species evolve. While selection itself is not responsible for the genetic mutations that occur in organisms, it is responsible for the survival of the organisms that have gained beneficial adaptations that better suit it to its environment. 


  1. What are misconceptions about the theory of evolution, and why are they incorrect?

  • Evolutionary theory aims to describe how life has evolved since its origin; it does not seek to explain the origin. 

  • Beneficial mutations that lead to a species adaptation are just random mutations that occurred in an organism that lead to a higher chance of survival and therefore reproduction in that organism, they are not intentional but rather purely random.

  • (Significant?) Evolution takes many years and spans across many generations, it does not happen from one generation to the next (this concept is called gradualism)

  • Evolution is variational and so rather then going from one form of the organism to the next, there are multiple variations of the same organism alive at one time, however, only the adaptations that make surviving in that species given environment ‘easier’, will be passed on as those will be the organisms that survive and reproduce therefore passing on those beneficial traits to their offspring. 


  1. How do various real or hypothetical observations might support, undermine or revise components of evolutionary theory?

Some possible observation or experimental finding could prove the theory (or hypothesis to be wrong)