COURSE OVERVIEW:

Organisms are physicochemical systems whose history matters. Their history, shaped evolutionary processes over the course of billions of years, resulted in their current structure and behaviors.

Even processes as amazing as dreaming and laughing are based on natural systems, and so can be studied scientifically.

We can think of cells as the atoms of life, the smallest living units. The Cell Theory holds that all cells are derived from pre-existing cells. It does not speak to where the original cells came from. The simplest organisms consist of single cells. Social evolutionary processes have produced cells that cooperate in various ways.

Sexual reproduction, multicellular organisms, multi-organismic communities and ecosystems are the result of social evolutionary processes.

Organisms are non-equilibrium, homeostatic, and adaptive self-replicating systems.

Genetic information, stored in the nucleotide sequence of DNA molecules, has accumulated over time through evolutionary processes acting on molecular level noise (variation).

Based on the fossil record and cellular and molecular-level similarities, it appears that all organisms now living on earth are derived from a common ancestor, known as the"last universal common ancestor" (LUCA), which lived between 3.5 to 3.8 x 10⁹ years ago.

Since then, cells (and organisms) have been formed from pre-existing cells (and organisms), through an unbroken chain of life. Turns out that every cell in your body can trace its ancestory back about 3,500,000,000 years. This is just one of many strange scientific conclusions [link].

The diversity of organisms has been generated by various evolutionary mechanisms that include gene and genome duplication, gene reorganization, mutation, selection, and random (non-selective) processes.

Different types of organisms, known as species, are defined as different by their "reproductive isolation" from one another.

It is estimated that there are > 1,500,000 (1.5 x 10⁶) types of living organisms, of which ~750,000 are insects, ~250,000 are plants, and ~41,000 are vertebrates (">" means greater than, "~" means "approximately").

The number of distinct microbial species remains difficult to determined accurately, in part because of the ubiquity of what is known as "horizontal gene transfer" and the lack of sexual reproduction in such organisms (we will return to these topics later in the course).

While there are currently millions of different types of organisms, over the course of Earth's history there have been even more. Most types of organisms that have existed no longer do, they are extinct. To be extinct means that they have no living descendants.

Today there are organisms that range in size from less than 0.000001 (10^-6) meters (1 µm) to more than 30 meters long, a range of over 10⁷ fold.

Organisms range from those consisting of a single-cell, known generically as microbes, to multicellular plants and animals that can contain over 10¹³ distinct cells.

A particular type of organism can live independently or in communities, and different types of organisms live together in ecosystems. For example, microbes often live together in biofilms. Within a biofilm, organisms can cooperate or compete (or both) with one another in complex and evolving ways. In fact, some organisms are so co-dependent that we have yet to discover how to grow them in isolation from one another.

Right now, there are many microbes living within your gut, and together with you, they form an "enteric" ecosystem [link].

The simplest form of multicellular organisms are colonies of related cells, held together in loose aggregates. In these simple colonial organisms, all cells can reproduce.

A major innovation in the history of life was the appearance of true multicellular organisms. Multicellular organisms are social organisms, different types of cells carry out different functions and only a small subset of cells, known as germ cells, give rise to the next generation of organisms. Other cells, known as somatic cells, form the body of the organism, and perform specific roles, but all somatic cells die when the organism dies. Social evolution involves what is known as "inclusive fitness".

In a multicellular organism, control of cellular behavior is critical and complex. For example, when somatic cells begin to divide in an uncontrolled (anti-social) manner, the result is cancer. To guard against anti-social behavior, multicellular organisms (and social groups) use various strategies.

Inclusive fitness has allowed evolution to produce social organisms, like humans, in which a range of interactions are critical for reproductive success. Evolutionary mechanisms can produce eusocial organisms, where individuals act as a part of super-organism; bee hives and naked mole rat colonies behave in this way. In eusocial organisms, only a limited subset of organisms reproduce to form the next generation, like the germ line of a multicellular organism [link][link].

Organisms interact with one another and their physical environment to form ecosystems. These interactions take many forms, including predator-prey, host-pathogen, and various forms of interdependence: parasitism, symbiosis and mutualism).

In an ecosystem, organisms have to deal with the impacts of other organisms on their physical environment.

The most dramatic life-based environmental impact to date has been the generation of molecular oxygen (O₂) as a waste product of one form of photosynthesis. O₂ is highly reactive. Its accumulation transformed the conditions under which most organisms lived, and they either had to adapt or find an environment in which O₂ was not present.

While a catastrophe for some, the appearance of O₂ was an opportunity for others; it made possible the emergence of large, active multicellular organisms, such as ourselves.

In analogy with computers, all cells use a version of the same basic operating system.

They store genetic information in molecules of deoxyribonucleic acid (DNA). To use this information it must be first transferred into a molecule of ribonucleic acid (RNA). The DNA-dependent synthesis of RNA is known as transcription.

RNA molecules have a number of roles in cells, one of which is to direct the synthesis of proteins - this process of RNA-directed protein synthesis is known as translation. Translation iscatalystcomposed of RNAs and proteins, the ribosome.

With each new cell formed, DNA is replicated and the "daughter"cell receives a copy - a copy is also retained by the mother cell.

DNA is not completely stable and replication is not error free; changes in the DNA (mutations) occur, although most are repaired.

With minor (explicable) variations, all organisms use the same universal code that links DNA sequences to protein sequences.

Many of the chemical reactions used to capture energy, to build and disassemble macromolecules (e.g. proteins and nucleic acids), are common to all cells. Cells share a common central metabolism.

Cells have a boundary layer, a plasma membrane, that separates their insides (called cytoplasm) from the external world.
This membrane is composed of a lipid bilayer and embedded and associated proteins.

The Theory of Evolution:

Because DNA is not completely stable, and because errors can occur during its replication, changes in DNA (mutations) occur and are passed on to daughter cells.

Mutations can have a range of effects on the organism that inherits them, from little or none to death. Over time, different organisms will have different genotypes (DNA molecules) that lead to different phenotypes (different behaviors, physical characteristics, etc).

Because of their phenotypic differences, some organisms reproduce more successfully than others. Which organisms reproduce most successfully will be determined in part by interactions with their environment (which includes other organisms).

Over many generations the differential reproductive success of individuals will lead to changes in the frequency of specific genotypes within a population. This in turn will lead to changes in phenotypes,the population will evolve.

Over time, evolution responds to changes in a population's environment, as well as changes within the population which influence reproductive success.

A population that fails to adapt rapidly enough to changes in its environment may disappear, it will become extinct.

Populations can also divide and adapt to different environments, a process that over time leads to reproductive isolation between populations, this produces new types or species of organisms.