ESO 4. Biology and Geology

Topic 1.  Vocabulary: Cellular Reproduction
Genetic material In all cells the genetic material is DNA bound to proteins and organised in chromosomes. Bacteria have one chromosome, while humans have 46 in each cell. Its function is to store, express and transmit to the offspring the instructions that tell how every cell and living being will be self-constructed and how will they work.
Mitosis Cells with more than one chromosome, once they've synthesised a full copy of the whole set of chromosomes, have to carefully organise their division in order to produce two daughter-cells with exactly the same genetic information. Mitosis is the complex process whereby most eukaryotic cells tackle such a task.
Mind Map: Osmosis
Mind Map: Active transport
Mind Map: Enzymes in industry
Topic 2.  Vocabulary: Mendelian Genetics
Locus (pl. loci)A place in a chromosome where a gene resides. Each locus contains the encoded information for a trait, such as "colour of the eyes".
AlleleOr allelomorph gene. Any of a number of the alternative varieties of a gene that reside in the same locus. Each allele contains the encoded information for a quality or a value of a trait, such as "brown colour of the eyes". All the possible alleles for the same locus form a "family of allelomorph genes".
HaploidCell or individual or species with one single set of chromosomes, such as bacteria or the human gametes.
DiploidCell or individual or species with two sets of chromosomes, such as the body cells of humans (and most eukaryotes). Each chromosome of a set is similar to one chromosome of the other set in that they carry exactly the same loci, but they are not identical, as the specific alleles of each locus can be different.
HomologousIn diploid individuals, each pair of chromosomes that carry the same loci. Humans have 22 pairs of homologous chromosomes and one pair (the sex chromosomes) which are partially homologous.
HomozygousOr "pure breed". Diploid individuals are homozygous for a locus when the alleles present in that locus are the same in both homologous chromosomes.
HeterozygousOr "hybrid". Diploid individuals are heterozygous for a locus when the alleles present in that locus are different in each homologous chromosome.
DominanceA type of relationship between two different alleles of the same family whereby one allele (said to be the "dominant" one) cancels out the phenotypic effect of the other (said to be "recessive").
CodominanceA type of relationship between two different alleles of the same family whereby both alleles express their phenotypic effects without blending. This is the case of the alleles for the "A" and "B" human blood types, whose heterozygosis yields an "AB" type.
Incomplete dominanceA type of relationship between two different alleles of the same family whereby the phenotypic effects of each allele are blended in the phenotype. This is the case of the alleles for the red and white colour for the corolla of the flowers of the snapdragon plant, whose heterozygosis yields a pink colour.
Mind Map: First artificial cell
Topic 3.  The Birth of the Theory of Evolution

Before Darwin the general consensus was that species were created independently by some extranatural force, and that they died out without any major change. So, which were the steps needed for a theory of evolution of the biological species to be accepted in the XIX century?

  • Accepting the idea that species can change during their life span.
  • Accepting the idea that species can change so much that they can even generate new species, either by diversification (cladogenesis) or by a global transformation of one whole species (anagenesis).
  • Accepting the idea (that looks like an inevitable result of the previous one) of a common descent, i. e., that all species are related, have a kinship, and they all come from a common ancestor.
  • Accepting the idea that the Earth is old enough for these huge changes to have enough time to occur... so slowly that can't even be perceived during a human life span.
  • And most notably: knowing of any acceptable mechanism by which these types of changes can occur.

Considering that not so long ago, the Anglican bishop James Ussher had stated that the Earth had been created the night preceding 23 October 4004 BC, the idea of an old Earth was, quite possibly, the necessary precondition for all the others to be even borne in mind by anyone. And this revolutionary idea was just there in the right moment, when Darwin started his five years long journey in the Beagle, and was given the first volume of Charles Lyell's Principles of Geology, which set out the idea of masses of land slowly rising or falling over immense periods of time to finally yield the geological features that can be observed in present time. According to Lyell, the Earth was much older than what was thought by that time, probably even millions of years old (some 4,560 years old, to be more precise, and as we know today).

The concept of a gradual change of biological species, now that Darwin knew that there was enough time for it, arose from the observation of different races of tortoises, finches and others, adapted to the particular environments that the Galápagos islands had to offer. And more particularly, to the different nutritional niches available; while some finches had a beak specialised in cracking hard nuts, others were the perfect weapon for chasing insects, etc. And considering that those islands are some 1,200 km away from the continent, it was clear to Darwin that all those finches (or tortoises) had had to come from one (or a few) small group of ancestors that, departing from the mainland, happened to make their way to the islands. The Galápagos finches had evolved on-site, as it was highly unlikely that all those varieties could have possibly reached the islands from the continent, one by one.

That panorama was clearly speaking about gradual transmutation of those animals by adaptation to different environments (species can change), and with it, Darwin's mechanism of evolutionary change had started to develop.

But was that slow and gradual change powerful enough to produce new species, or were all those differently adapted finches simple varieties of the same species? Friends are to come to the rescue when needed, and so it was with Darwin's mate John Gould, an ornithologist, who announced that the specimens of finches that Darwin brought back to England after his trip belonged, in fact, to three different species. In Darwin's mind, that meant that gradual adaptation to the environment can actually produce new species.

Finally, how do species get to adapt to each one of the many specific environments that Nature provides? How can a population gradually reach its ecological niche, one that allows it to survive and thrive for generations? That was the last and greatest obstacle to overcome, and recent History showed that clearly. Jean-Baptiste de Lamarck had already come up with similar thoughts to Darwin's a couple of decades before the Beagle departed: species evolve, and do it by gradual adaptation to their environment. But Lamarck could never demonstrate that acquired-on-life traits can be passed on to the offspring, and we know nowadays that that just can't happen: the genes of your eggs or sperms will not change because of you dying your hair. And this is how Lamarck passed to History as an unsuccessful attempt to explain the how and the why of the evolutionary process.

But not Darwin. It turns out that among the many different types of individuals that are randomly produced every generation in every species, some happen to be better suited to their environment than others: the former feed better, grow faster, survive longer and as a result... reproduce more than the latter. And as the traits that make them the fittest were inherited, they will also pass those traits to their children. As a final result, those traits will be more present in the next generation than those that conferred a lesser success. This was what Darwin (and Alfred R. Wallace) elucidated, and that's why everyone is now celebrating his 200th anniversary. Or almost everyone.

Topic 3.  Main Evolutionary Ideas in Linné, Lamarck and Darwin
1Species can change gradually over their lifetime.NYY
2Species change by means of a progressive improvement in their adaptation to the environment.n/aYY
3Species can change so much that each one of them can transmute into a new different species (anagenesis).n/aYY
4Species can also change in a way that one species can give birth to several new descendent species by branching off (cladogenesis).n/aNY
5All species are thus related and come from a common ancestor.n/aNY
6Evolutionary change by progressive adaptation to the environment happens because every living being has an innate tendency to improve its adaptation to the environment, and so organs are developed or atrophied during life as needed.n/aYN
7Acquired-on-life changes (such as the atrophy or development of organs) are inherited.n/aYN
8Evolutionary change by progressive adaptation to the environment happens because the fittest leave a greater offspring.n/aNY
9The traits that confer a greater fitness were inherited from the parents, and so they can be passed on to the children.n/aNY
N.B.: 4 and 5 go together as 5 is the result of 4; 6 and 7 go together and make Lamarck's idea of the mechanism of evolutionary change; 8 and 9 go together and make Darwin's idea of the mechanism of evolutionary change.
N.B.: Carl von Linné (= Carl Linnaeus) is best known for having developed the binomial (= binominal) nomenclature of the species, by which all species have an official scientific name, called binary name or binomen because it is made of two latinised words. Thus the "wolf" is called "lobo" in Spanish or "loup" in French, but may be also called "Canis lupus" all throughout the world. The binomen is made of the genus name ("Canis") and an specific name ("lupus").
Topic 3.  How Does Natural Selection Work?

Natural Selection is all about a central event: some individuals reproduce more than others. And this has a cause and a result. Step by step:

  • There are many different types of individuals in any biological population. We all can see that. And it is due to mutation and recombination. Mutation increases the number of possible alleles for every loci throughout time, and even creates new loci, or gets rid of loci or alleles. But in the long run mutation tends to increase the number of genes (either alleles or loci) for every species. Mutation takes place mostly due to errors during the duplication of DNA prior to cell division. Also, the recombination of loci during meiosis multiplies the number of different possible gametes that any individual can produce.
  • Different types of individuals interact differently with their environment. Some of them are stronger, faster, bigger, smarter... and so some of them grow faster and reach fertility sooner, hide better from predators and manage to sort the threats out better, are more efficient absorbing nutrients or chasing the prey, are more convincing when looking for someone of the opposite sex to mate...
  • The individuals that have more successful interactions with their environment leave a greater offspring. No way it can be otherwise. If you reach fertility faster, survive longer, and your nutritional efficiency leaves you more free time, chances are that you are going to have a greater reproductive success.
  • Many of the traits that make these individuals more successful are inherited. Although in some species (us!) some "rules for success in Life" can be learned, capability for learning is itself an inherited trait. And, although your genes don't determine the weight that you'll have when you are 25, they do determine a certain range or weights you are likely to fall within.
  • The alleles of the individuals with a greater reproductive success will be present with a higher frequency in the next generation, and vice versa. As a result, the phenotypic traits coded by the successful alleles will be more present in the next generation, and this noticeable phenotypic change improves the overall fitness of the population gradually, generation after generation.

In short, Natural Selection takes place through the following sequence of events:

  1. Variation due to mutation and recombination.
  2. Differential fitness.
  3. Differential reproduction.
  4. Heritability of phenotypic traits.
  5. Change in the frequencies of the alleles of a population.
  6. Overall phenotypic change in a population.
Topic 3.  The Formation of New Species

The formation of new species or speciation is one of the main outcomes of the evolution of Life, the opposite to extinction, and the most visible result of adaptation.

Sexually reproducing species (virtually all that exist, except prokaryotes) are defined as those groups of individuals that can leave fertile offspring by sexual reproduction, and thus share a common gene pool: the genome of species. This is so because sexual reproduction can be considered as a way to produce new combinations of genes (new genotypes) by means of sharing half of the genes of each one of the two partners. Sexual reproduction is a bit like dealing sets of, say, five cards after having shuffled the deck. In the analogy, each card would be a gene, each set of five cards the genotype of a new individual, and the deck of cards is the genome of the species.

The members of the same species also share the same ecological niche, this is, they dwell on the same habitat, they feed the same way, they prefer a similar amount of humidity or sunlight, the are prey to the same predators, etc.

If two individuals of opposite sex that can leave fertile offspring by sexual reproduction belong to the same species, then, speciation must be the process by which two populations, that originally belonged to the same species, split apart and, after a time of adaptation to different environments (or ecological niches), evolve differently to the end that eventually they become unable to leave fertile offspring by sexual reproduction. This end point of speciation is called reproductive isolation.

This process can take place by different ways. Sometimes the appearance a new geographical barrier is the decisive event. That is the case of the Galápagos tortoises, presumably descendants of a common ancestor, that after colonising the different islands of the archipelago, the sea between the islands posed an almost invincible obstacle for them to meet and mate. This way, the different populations settled down in the different islands, couldn't share a common gene pool anymore, and natural selection made them to evolve differently by improving their adaptation to each particular island. Eventually, they changed so much that if individuals of these different populations happened to meet due to the sea currents or the action of men, they were so different that they would not able to leave fertile offspring by sexual reproduction. Those different populations were now different species.

But speciation does not always need huge geographic barriers. In the case of Galápagos finches, different species appeared in the same islands because when this virgin territory was colonised by their ancestors, a variety of ecological niches were at their disposal, and while some of the finches specialised in feeding off insects, other preferred grains, and so forth. They shared a common habitat, but occupied different places in it and performed different ecological roles. The enhancement of that specialisation (the improvement of their adaptation) to each specific ecological niche by means of natural selection did the rest, and, like the tortoises, with time enough took them to be so different that one day they were reproductively isolated.

But how different two individuals of the opposite sex have to be, to be reproductively isolated? The answer is: either...

  • So different that the male wouldn't be able to fertilise the female, because...
    • They don't attract each other sexually anymore: courting does not work for them;
    • Their genitals have become incompatible;
    • The sperms are unable to make their way towards the egg, in the case of mammals;
    • etc.
  • Or so different that even if the male can fertilise the female, they can't leave fertile offspring, because...
    • The zygote can't divide by mitosis (consider a sperm with 23 chromosomes and an egg with 24: this makes a total diploid number of 47, which is odd, and mitosis cannot take place with an odd number of chromosomes);
    • The embryo degenerates soon;
    • The children are weak and die before sexual maturity;
    • The offspring is sterile, as in the case of the mules;
    • etc.
Topic 4.  Fossils
What are fossils?

Fossils are the petrified remains of the living beings from the past or of their vital traces. They are studied by the science of the Paleontology.

Fossils are commonly found in sediments or sedimentary rocks (limestone, sandstone, mudstone, shale), typically as a result of the burial of the remains of a living being within a layer of sediments. Heavy metamorphism and the extreme temperatures of the magmas (> 700ºC) are likely to destroy any remain or trace of a living being, and so fossils are not found in heavily metamorphosed rocks (schist, gneiss) or igneous rocks (granite, diorite). Only sedimentary rocks that have undergone a gentle metamorphism, such as slates, are likely to contain fossils.

The totality of fossils and their placement in the rocks containing them constitute the fossil record. This placement may be as important as the fossil itself, because it can give a lot of information about the way and the type of ecosystem in which the fossilised organism lived. For instance, if a fossil is found within a conglomerate, which is a rock formed from the sediments deposited by a river, we'll know that it is one of a land organism. Or if an unknown fossil is found in the same rock where we also find fossils of seashells, it will probably be the fossil of a marine living being.

The fossil record is gappy and uneven. It is gappy because fossilisation is a rare event that happens sporadically and irregularly, depending heavily on the environmental conditions in the moment when a living being dies. If a land animal dies in a place that undergoes a landslide a short time after its death, most likely it will be well preserved inside the sediments. But if it dies in a place where strong winds, or heavy river flow or marine currents drag its corpse for a long time before it is left in a quiet place to be buried as sediments are deposited, chances are that the corpse will be destroyed by those currents, and the scavengers, detritivores and decomposers during the long time that it took before it was buried. And it is uneven because not all species have the same chances to leave any kind of fossil remain. As a start, hard structures (bones, teeth, shells) are commonly necessary, because soft tissues decay rapidly when the scavengers and decomposers (chiefly invertebrates, bacteria and fungi) start to predate on them. Organisms such as jellyfish or worms have really low possibilities to leave body fossils; traces such as imprints or burrows in the sediments are amongst their very few chances to leave a sign of their existence.

Types of fossils
  • Body fossils are the petrified remains of living beings from the past, and are produced by the substitution of the biomolecules that pertained to the deceased organism by mineral substances that precipitate from the groundwater that circulates through the sediments in which the corpse is buried. This requires a rapid burial of the organism following its death; otherwise, it will be soon destroyed, as explained above. Other times the remains can be destroyed once covered by sediments, but leaving an organism-shaped hole in the rock: this is called an external mould. If this hole is later filled with other minerals, it is called a cast. An internal mould is formed when sediments or minerals fill the internal cavity of an organism, such as the shell of a bivalve or the skull of a vertebrate.
  • Trace fossils are the physical remains of the vital activity of living beings from the past, and are produced by their movement (trackways left by trilobites, footprints from hominans), their reproduction (eggs of dinosaurs), their nutrition (coprolites, gastrolites, holes drilled in the shells of the prey), and other living habits (burrows, root cavities, stromatolites...). The oldest physical fossils on Earth fall into this category. They are stromatolites, and the oldest might be the 3.5 by old found in Warrawoona, Australia. Stromatolites are layered rocks generated by communities of microorganisms, usually dominated by cyanobacteria, which produced the precipitation of mineral substances dissolved in the seawater, generating layers of sediments that stacked one on top of another creating a stratified biogenic rock.
  • Biochemical fossils are the biochemical remains of the vital activity of living beings from the past. The best examples are carbon-rich rocks (such as the stromatolites) or minerals (such as graphite granules) that have more 12C than usual and less 13C than normal. As the CO2 molecules with 12C weigh 44 u instead of the 45 u of a molecule of CO2 with 13C, the former move faster (they are called "light CO2") than the latter, and have more chances to randomly reach the places of a living being capable of capturing them. This way a plant captures light CO2 in a greater proportion than it is found in the atmosphere, and so the fossilised remains of a plant will contain 12C in a greater proportion than it is found in the atmosphere. The oldest fossils on Earth might be 3.8 by old graphite granules found in Isua, Greenland, that contain a greater than normal proportion of 12C.
Topic 4.  Main Geochronologic Units
EonEraPeriodStart date (m.y.)
Hadean  4,570
Archaean  4,000
Proterozoic  2,500
Topic 4.  Earth's Timeline
Geological eventsTime (m.y.)Biological events
· The Big Bang: the origin of time, space, matter and energy, all formed from one single point. The Universe is expanding ever since.13,700 
· The Sun, formed from a giant cloud of gas and dust (a nebula), ignites and becomes a young star.
· The nebula starts taking a flat shape and forms the protoplanetary disk or accretion disc that revolves around the young Sun.
· The Earth and all rocky matter in the current Solar System start forming by accretion: the accumulation of matter in increasingly bigger nuclei due to the pull of gravity.
· The Earth's atmosphere initially lacks oxygen.
· Theia, a planet of the size of Mars, collides with the Earth, which causes a massive ejection of matter into orbit around the Earth, which will finally coalesce to form the Moon.4,530 
· Zircons found in Australia are the oldest known minerals.4,400 
· The surface of the Earth cools enough for the crust to solidify and the first continents ("shells") form. The atmosphere and the oceans form.4,100 
· The Acasta gneisses, in Canada, are the oldest known rocks.4,030 
· The inner planets receive the continuous impact of meteors, which probably boiled the oceans away and killed off any form of Life that could have developed.≤ 3,850 
 3,800· First possible fossils: chemical imprints of Life in graphite granules found in the oldest known rocks with a sedimentary origin, in Greenland.
· The first living beings were similar to prokaryotes, and obtained the carbon from CO2 and the energy from inorganic substances such as H2S, that could have been obtained from the thermal vents that are found in the undersea tectonic boundaries.
 3,430· First possible physical fossils: possible biogenic stromatolites found in Australia. These are layered rocks created by a multispecific community of microorganisms dominated by cyanobacteria.
· The concentration of oxygen starts to rise in the Hydrosphere and the Atmosphere, which is the most critical ecological change in the History of Earth, killing off most prokaryotes (which were anaerobic) and paving the road for the evolution of all the aerobic forms of life, including plants and animals.2,400 
 2,100· Eukaryotic cells appear, probably derived from prokaryotes engulfing others via phagocytosis.
· Supercontinent Columbia.1,700 
 1,200· Sexual reproduction appears, increasing the rate of evolutionary change.
· First multicellular organisms appear as colonies of cells with some kind of division of labour.
· Supercontinent Rodinia.1,000 
· Ice age: Snowball Earth.750 
· Supercontinent Pannotia.580· Ediacara biota: first complex multicellular organisms.
 540· Cambrian explosion: most modern types of animals appear, including trilobites, ancestors of modern arthropods.
 500· First vertebrates (fish).
· First land plants.
· First land fungi.
· First land arthropods.
 380· Amphibians, first four-limbed tetrapods, evolved from fish, start colonising the continents.
· Fern forests start to dominate the land.
· Supercontinent Pangaea starts forming.300 
 250· A massive extinction at the end of the Permian eliminates 95% of living species.
 230· Dinosaurs appear.
· Seed plant (gymnosperms) forests start to dominate the land.
· Supercontinent Pangaea starts breaking up.180 
 130· Rise of angiosperms (flowering plants).
 66· A massive extinction at the end of the Cretaceous, possibly caused by a 10 km across meteorite that left the crater of Chicxulub, in Mexico, eliminates about half of all animal species, including all dinosaurs (except the ancestors of modern birds) and ammonites.
· Mammals will take advantage of this event and will diversify rapidly, occupy most ecological niches left by dinosaurs, and become the dominant vertebrates on land.
 6-7· Hominans (biped primates) appear in Africa, maybe with Sahelanthropus tchadensis (-7my) or Orrorin tugenensis (-6my).
 2.5· Humans (Homo habilis) appear in Africa.
 0.2· Modern humans (Homo sapiens) appear in Africa.
 0· With a human population approaching 7 billion, the impact of humanity is felt in all corners of the globe. Overfishing, anthropogenic climate change, industrialisation, intensive agriculture, clearance of rain forests and other activities contribute to a dramatically rising extinction rate.
Mind Map: Events after fertilisation
Mind Map: The Nitrogen cycle
Presentation: We are eating up our world
Topic 8.  Vocabulary
Geological agentAny agent able to alter the surface of our planet.
External geological agentGeological agents powered by the Sun or the Earth's gravity: the water flows (streams, torrents, rivers, glaciers), the sea, the wind, the atmospheric phenomena (rainfall, thunderstorms, cyclones), the temperature variations or the living beings.
Weathering / ErosionWeathering is the decomposition of rocks, soils and their minerals through the action of some of the external geological agents. It is called erosion when the decomposing agent also transports the resulting fragments away.
ClastsThey are the resulting rock grains of the weathering process. They are classified upon their size as follows: clay (< 0.004 mm), silt (< 0.06 mm), sand (< 2 mm), gravel (< 6 cm), cobbles (< 25 cm) and boulders (> 25 cm).
Frost shatteringOr freeze-thaw weathering. It's a kind of physical weathering usually produced by the expansion of the water filling the cracks in the rocks of the mountain areas where the daily temperature variation is around 0°C. The nightly pieces (wedges) of ice thus formed exert a pressure in the cracks called ice-wedging.
GullyLandform that resembles a series of sharp and very short channels carved by intermittent running water, usually by streams, and typically formed on deforestated hillsides.
RavineDeep, narrow and short channel with steep sides, carved by intermittent running water, usually by torrents. Bigger than gullies and smaller than valleys.
Canyon / GorgeAn extreme type of V-shaped valley: narrow, deep and with very steep sides (cliffs), carved by running water, usually by rivers. If the sides are stepped, reflecting alternating rock resistances, it is called a canyon; otherwise it is a gorge.

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