chapter 1: Science and the Question of our Origins

how long has life been around on earth

3.5 billion years of Earth’s 4.5-billion-year existence

Science

a “way of knowing”—that is, a way of determining what to accept as true.

empiricism

external testing of ideas, to check whether an assertion is supported or contradicted by observations

data

observations

Biology

the branch of science that has to do with the empirical investigation of life.

inductive reasoning

argues for a conclusion that makes sense but is not at all certain to be correct. even if the premises (assumptions, assertions) are indeed true, the conclusion still might not be.

parsimonious

simple, straightforward (like the most obvious explanation but could also not be true)

deductive reasoning

if the premises are true, then the conclusion must be also; there is no logical way around it.

theory

broadly encompassing explanation that pulls together and makes sense of a wide variety of observations. provide a framework of understanding for the various facts of a discipline

Cosmology

the big bang theory

Physics

atomic theory, thermodynamic theory, string theory, quantum theory, the theory of relativity, and the theory of gravity

Geology

the theory of plate tectonics

Biology

cell theory, endosymbiotic theory, germ theory, and the theory of evolution

hypothesis

A possible explanation

observation

A piece of information (data)

conclusion

An outcome or finding; new knowledge/understanding

Theory

A framework of understanding that explains (accounts for) a multitude of facts

Life

biochemical system that has the ability to grow, respond to stimuli, and reproduce.

organism

a complete, self-perpetuating biochemical system, a single whole living thing, made up of 1 or more cells

cell

smallest system that is unquestionably capable of meeting all three of the basic criteria for life

Living systems use energy to

drive change (as in the biochemical reactions of cells, the physiological functioning of organs, or the exchange of goods with the environment)

energy =

ability to grow/work, power to carry out life processes.

information =

provides the instructions for how to carry out life processes (primarily stored in DNA) direct and control life changes

The particular nucleotide base pair sequences that are present in these molecules give organisms their

particular features, or phenotypes

gene

sequences of DNA that code for heritable characteristics (phenotypes); encode RNA, proteins, or regulatory sequences (regions that control the expression of genes, by binding to regulatory molecules) codes for a single complete outcome

allele

A particular version / nucleotide sequence of a given gene (particular versions of a gene (5’6 & 5’10); arise by genetic mutation (alterations of the original gene sequence) and code for the different varieties of a characteristic (different traits)

Evolution

scientific theory that explains where the different species (particular kinds) of life have come from. It posits that the great diversity of life that exists today has been produced through a process of descent with modification

descent with modification

new species arise from ancestral species due to changes that arise within them over generations

what year was the theory of evolution by means of natural selection outlined by Charles Darwin and Alfred Russel Wallace

1858

when was On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life by Charles Darwin published?

1859

when was Watson and Crick’s discovery of the structure of DNA

1953

population

All the members of a species that inhabit the same area at the same time

An Essay on the Principle of Population, Thomas Malthus publish year

1798

variation within a species

due to small differences in the DNA sequences of their genes

inheritance of the different variations

due to the passing of genes from parents to offspring—from one generation to the next

selection

certain variants are consistently passed on more successfully than others, such that they become more common over time in a nonrandom way

variation is…

random

selection is…

nonrandom

selection is caused by…

anything in the environment that imposes a systematic bias on reproduction

convergent evolution

Similar selective pressures tend to produce species with similar adaptations

disparate selective pressures

different or distinct environmental forces that push populations to evolve different kinds of physical forms and biological solutions

traits are

determined by the particular sequences of nucleotides in DNA (aka alleles)

mutations

A heritable change in DNA sequence that occurs due to copy errors during DNA replication or direct alteration by external agents; these errors result in new alleles and, with enough change, whole new kinds of genes

Chromosome

a single large, complete molecule of DNA

genotype

the particular combination of alleles an organism carries for a given gene; this combination determines the particular physical trait

Homozygous genotype

the alleles in the individual’s genotype are the same (i.e., the individual only carries and will pass on one particular version of the gene)

Heterozygous genotype

the alleles in the individual’s genotype are different (i.e., the individual carries and may pass on multiple variants of the gene)

Gene family

a group of genes that code for different characteristics but remain similar to each other in sequence and sometimes function; arise by more extensive mutation of an original gene sequence to the point that the genes in the family have fundamentally different outcomes or responsibilities

Genome

the entire regular set of chromosomes carried by an organism; its complete genetic blueprint, including all of its genes and non-coding DNA sequences

genetic drift

A shift in allele frequencies that occurs in a population just due to random chance

what is the ultimate source of diversity

Genetic mutation

genetic recombination

mixes the various alleles into a greater variety of potentially winning combinations in individuals. different combinations within individuals, thereby generating even more options to work with. occurs when organisms share DNA in some way

vertical gene transfer

passing genes from parent to offspring

s**ual reproduction

each offspring inherits a mix of alleles from two parents

prokaryotic

organisms that lack a nucleus or other membrane-bound organelles inside their cells

how do prokaryotes diversify

by mutation with horizontal gene transfer

eukaryotes

organisms made of cells that do have organelles

when does vertical gene transfer happen in eukaryotes

as a consequence of DNA being transferred by viral infections

a**ual reproduction happens in

prokaryotes and eukaryotes

a**ual reproduction

produces offspring that are (outside of any mutation) an exact copy of the parent, by the parent passing on its full complement of chromosomes = NO genetic recombination

s**ual reproduction happens in

eukaryotes

s**ual reproduction

produces offspring that are a genetic mix of two parents, by each parent passing on half its full complement of chromosome = the offspring are genetically recombined

Horizontal gene transfer

transfer of bits of DNA from one organism to another = sharing of genetic “apps”

Conjugation happens in..

prokaryotes

Transformation happens in…

most prokaryotes and a few eukaryotes

Conjugation

small circular molecules of DNA called plasmids are deliberately passed directly from one cell to another via a tube called a pilus

Transformation

When an organism dies or breaks apart, fragments of its DNA may "spill" into the environment. Other organisms nearby can then take up these fragments & incorporate them into their own DNA

Transduction

fragments of DNA are carried from one organism to another by a virus

Organisms with a higher incidence of mutation and shorter generation times have the ability to evolve more

rapidly

Slower reproducing organisms with more accurate DNA copying systems have the ability to evolve

slower

Bacteria has generations as short as

tens of minutes

Greater selection

has the effect of eliminating mutations that arise thereby suppressing genetic diversity

why do different genes within a species typically exhibit different rates of evolution, and these rates may change over time

differences in the selection pressures they experience after mutations occur. some genes are more consequential to the survival of the organism than others.

the more fundamentally important a feature is to an organism’s basic development, operation, and survival…

the less the genes that code for it tend to tolerate any variation, and the more highly conserved (unchanged) their sequences tend to remain through time

punctuated equilibrium

an evolutionary model characterized by long periods of stability where little change occurs within a group, interrupted by great bursts of relatively rapid change

when do punctuated equilibrium leaps occur

new genetic innovations, environmental options, or environmental changes

evolution occurs

whenever the distribution of alleles changes in a population over time (generations) for any reason, whether it be the selective forces of the environment or just the whims of chance

Darwinian Revolution

Charles Darwin & Alfred Russel Wallace provided natural selection as the mechanism to explain how species change over generations. By grounding this theory in evidence, transformed biology from a collection of isolated facts into an integrated science where evolution serves as the fundamental unifying theory of life

abiogenesis

the scientific hypothesis that life originally arose from nonliving matter through natural chemical processes

It is thought that in order for life to form, these early environments must include four key ingredients that could together potentially produce the first very simple cell:

an aquatic environment, a membrane bubble, a way to concentrate the molecules of life, and a self-replicating biomolecule

Living things today are what % water by mass

~60-90%

membranes of cells today are mostly made of

lipids

ribozymes

exhibit catalytic activity, they have the functional ability to drive chemical reactions. both store genetic information and perform the work of driving cellular processes

Hydrothermal vents

found in areas of the sea floor where minerals boil up from the Earth’s interior and mix with seawater above. supply a rich and complex stew of chemicals

what do experiments suggest that hydrothermal vents could produce

fatty acids, which could form bubbles that trap mixtures of chemicals within thereby producing primitive cell precursors or protocells

protocells

primitive cell precursor. essentially are fatty acid bubbles that naturally form and trap a mixture of chemicals inside, creating a self-contained environment

In the hydrothermal vent hypothesis, what two specific biological processes may have been supported by varying environmental conditions?

Uptake and concentration of molecules (which allowed the protocell to grow) and Lengthening or copying of internal genetic molecules (which allowed the protocell to store and replicate information)

Growth of the protocells could have occurred by

fusion with additional free fatty acids, with those that had grown very large being broken into smaller ones by turbulence thereby achieving reproduction.

Homologous structures

structures that share a common evolutionary origin, even if their functions are now different: they derived from the same starting point by descent with modification.

Analogous structures

structures that have the same function, but evolved entirely independently of each other, as an example of convergent evolution: the phenomenon in which similar selective pressures produce similar outcomes in different species.

Vestigial structures

structures that still exist in a species even though they are not particularly useful anymore, essentially representing relics of evolution: they have so little function anymore as to be rather superfluous, making sense only as remnants of the past.