NCWC-BIO101-Intro to Life Science

Introduction to Biology and the Scientific Method

A. Biology and Life

Biology is the science that studies life. What is life?

Unlike non-living matter, living things exhibit the following properties:

Order: a hierarchical organization (a ‘nested hierarchy’, like Russian dolls). This means that organisms are composed of organs that work together in a systematic manner, the organs are composed of tissues, tissues of cells, cells of organelles, organelles of molecules and molecules of atoms, with the entire organization built in a way that maximizes the internal order, survival and reproduction of the organism.

Crystals exhibit order, but it is not hierarchical, and does not give the crystal a maximal chance of survival and reproduction. In living organisms, the properties of higher levels of organization cannot, unlike in crystals, be explained by the elements at the lower level of organization. Interactions between lower-level elements result in emergent properties at higher levels. For instance, from the order of nucleotides in the DNA we cannot infer how the whole organism looks like or behaves because the sequence does not specify the rules of interactions between the genes, gene-products (proteins), cells during development, and organisms inside their environments.

Sensitivity: response to stimuli in the environment. Even the simplest organisms, like bacteria, are capable of sensing changes in the environment and responding to such changes - they may swim away from or towards areas with higher concentrations of nutrients, salt, oxygen, or levels of illumination. Such responses (e.g., swimming) are active. A seed or a spore, seemingly “dead”, will actively respond to good growing conditions by germinating. A piece of dead matter may expand or even melt at high temperature, but that response is passive - due purely to the laws of physics.

Growth, Development and Reproduction: having a life-cycle. Crystals may grow, but the growth does not change the basic organization of the crystal. On the other hand, growth of an organism is accompanied by reorganization, cell division and cell differentiation. Each organism, at least during some parts of its life cycle, undergoes growth, developmental changes, and production of offspring. The results of reproduction - the offspring - are similar to the parent(s) due to the code inherited via a molecule, either DNA or RNA.

Regulation: All organisms have evolved well-orchestrated biochemical, physiological and behavioral mechanisms that regulate all the organism’s functions, which include finding and ingesting nutrients, processing nutrients and supplying all cells with the end-products of such processing, sequestering and eliminating the by-products of nutrient use. Likewise, every organism has evolved elaborate mechanisms for absorbing, storing, converting, using and dissipating energy - this last criterion may be the most important criterion for testing if something is alive or not, e.g., if one discovers a potentially living form on another planet.

Homeostasis: maintaining relatively constant internal conditions. We will cover this in much detail when we start the unit on human anatomy and physiology.

We will study the details of all five of the above criteria in this course. During the first three lectures, we will look at general properties of living organisms at all levels, from molecules, organelles and cells, through tissues, organs, systems and organisms, to populations, species, communities and ecosystems. During the remainder of the course we will take a look at specific cases: bacteria, protista, fungi, plants and animals, as well as details of the functioning of the human body.

A. Scientific Method and Process

Deductive reasoning applies general principles to predict specific results. Inductive reasoning uses specific observations to construct general principles. Here is a brief description of the steps in the hypothetico-deductive method:

Scientists make observations of processes and events found in nature.

The observations lead to questions: what is this, how does it work, why does it work the way it does? This may necessitate further observations to be made.

The questions are then asked in a form that suggests a possible explanation (hypothesis) for the observations. Scientists try to come up with all possible explanations and pit them against each others as alternative hypotheses.

Using the available knowledge and understanding of the related phenomena, the scientist makes a best guess at which of the alternative hypotheses is most likely to be correct.

Experiments are designed in such a way that one or more hypotheses are tested. This means that the experiment is geared specifically towards rejecting one’s favored hypothesis: it is directly testing if that hypothesis is wrong. If the results are positive, the favored hypothesis is not rejected, but the alternative hypotheses may be rejected. If the results are negative, the favored hypothesis is rejected and one or more of the alternative hypotheses are accepted and further directly tested.

Often, two experiments are conducted at the same time. In one experiment, all the variables are kept constant except one, while the other experiment is called the control experiment, and in that experiment, that variable is left unaltered. The results of the two experiments are compared to each other using statistical methods to determine if the tested variable (the one not kept constant) indeed has an effect on the outcome.

After performing a series of experiments, a paper is written that provides some background information, describes the experimental methods and results, provides the statistical analysis, and draws conclusions from the results. The paper is then submitted for peer review and published in a scientific journal. We will take a look at some real scientific papers later on in the course, so you can see the structure and form of it and be able to find and read such primary literature.

Once all but one alternative hypothesis has been rejected over a series of experiments, the one remaining hypothesis is further tested. The hypothesis, if correct, can be used to make predictions which can be directly tested in subsequent experiments. Predictions provide a way to test the validity of a hypothesis.

As more and more studies are done and the hypothesis gets stronger and stronger (as all possible alternatives get rejected), it grows in its predictive power and it may also grow in its ability to explain a broader range of phenomena. Once a hypothesis reaches the stage at which it is supported with large amounts of evidence after repeated testing, it becomes a theory.

A theory is a body of interconnected concepts most strongly supported by scientific reasoning and experimental evidence. It is a scientific term that is used to denote the scientific concepts that have stood the test of time and are best supported by experimental evidence.

This sense of the word “theory” - the scientific ideas with the greatest certainty that they are correct - is in contrast to the colloquial use of the term, which means almost opposite - lack of certainty (as in “it’s my theory that Secretariat was the greatest American athlete of all times”, or “it’s just a theory - nothing you should trust on its face”). Purveyors of pseudoscience (for financial, religious or political reasons) like to utilize the difference between the two senses of the word, dishonestly implying that a scientific theory they don’t like is uncertain when just the opposite is true.

The strongest theories are those that are supported by a wide variety of kinds of evidence. Theory of evolution is one of the best supported theories of all science not only because it is backed up by mountains of evidence (and no evidence against it), but also because the evidence comes from many different areas of science: paleontology (fossils), biogeography, ecology, mathematical modeling, population and quantitative genetics, comparative genomics, medicine, agricultural breeding, study of animal behavior, comparative anatomy, comparative physiology and comparative embryology.

The way disparate data from quite different areas of science, when put together, all strengthen a single theory, is called consilience. Recently, this word has been misused in popular literature (including a book of the same name) and press to mean quite the opposite - taking the methodology or findings from one discipline and applying it to a variety of other disciplines, e.g., taking the logic of evolution by natural selection and applying it to chemistry, pharmacology, psychology or computer science. That is a worthy endeavor, but it not a correct meaning of the term ‘consilience’.

Sometimes you will see (as opposed to the image on p.5 of your textbook) scientific method schematically depicted like this:

There are two reasons why the Biology textbook does not show a graph like this: a) it is not applicable to biology, and b) it is wrong.

It is wrong because it places “law” above the theory. Actually, the opposite is true - many laws (in physics, for instance) are elements of a greater theory and are parts of the evidence that the theory is correct. Laws are usually mathematical depictions of regular behavior of some aspect of nature. In other words, laws describe nature but do not explain it. Theories explain nature and are thus on the top of the hierarchy of scientific knowledge.

The model above is inapplicable to biology (it was probably drawn by a physicist) because there are no laws in biology. There are rules (like Bergmann-Allen Rule in ecology or Cope’s Rule in evolutionary biology), there are generalizations (e.g., Scaling), there are mathematical models (e.g., in population genetics) and there are Principles (e.g., the Principle of Natural Selection), but there are no laws. Biology deals with processes at much higher levels than does physics, where emergent properties of complex systems introduce a dose of unpredictability. All potential “laws” in biology have many exceptions, or have to be limited to a very small subset of processes, or to a small subset of organisms - they are not exception-less as laws of physics are.

Hypothetico-deductive method described above, while arguably the most powerful part of the scientific method, is not the only one. There is a continuum of scientific “methods” as depicted here (from Brandon 1996):

Collecting the information about all the species of birds and salamanders in the mountains of North Carolina is not a test of hypothesis and is not manipulative (and is not experimental) - yet it is certainly science (place a dot in the bottom right corner of the graph) - it provides important information about the natural world. If patterns emerge from such a survey and prompt new ideas about species distribution, this can then be tested in a more experimental fashion.

Human Genome Project is highly manipulative (and expensive!), yet it is not hypothesis-testing (place a dot in the bottom left corner). Nobody predicted that we would find anything but the four nucleotides known to make up DNA. We had no predictions as what the sequence will be and what would it all mean. Once the work was done, we could use the HGP as a tool for testing new hypotheses, e.g., how many genes do we have, how they are related to the genes of chimps, how diverse are particular gene sequences in human population as a whole, etc.

Paleontology is somewhere in the middle. It is somewhat manipulative (it takes hard work and a lot of people to do it) and it is somewhat hypothesis-testing (place a dot smack in the middle of the graph). Paleontologists do not dig randomly - they dig in particular places on the planet in particular layers of the sediment, looking for fossils of particular kinds of organisms. For instance, a group recently did an excavation in a particular bed of Late Silurian layer, looking specifically for a fossil of an early tetrapod, i.e., a transitional organism between fully aquatic and fully terrestrial mode of life. They discovered exactly that - a fossil named Tiktaalik whose fins were better suited for walking on land than that of fishes (like mudskippers, catfish and lungsfish), yet not completely evolved for land use as in amphibians.

Sometimes nature provides an experiment that tests a hypothesis (a dot in the top right corner). For instance, a biogeographical model of island succession was tested when the volcano Krakatoa erupted and eliminated all life from the island. The scientists went there and observed which organisms flew in from the mainland, in which order, and how the ecosystem passed through several stages until it reached its mature stage, thus confirming (and somewhat modifying) their hypotheses.

No matter how strongly a theory is supported by empirical evidence, it is always theoretically conceivable that one day, some data will come in that will force the scientists to modify or even eliminate the theory. Even if the scientists are 99.999999999999999999999999999999999% certain that the theory is true, it is philosophically incorrect to say that it is 100% true and to call it the Truth with the capital T. That is why scientists, when interviewed in the media, often sound uncertain and wishy-washy, while some quack or pseudoscientist pronounces his absolute certainty. Audience not educated in the scientific method is likely to swallow the pseudoscience bait, hook and sinker because we, as humans, crave certainty. It takes some scientific training to be able to fully embrace and even love uncertainty. That is why it is difficult for scientific knowledge to counteract financially, religiously and politically motivated assaults on it. However, nature does not care about what we like and wish for: the apples will continue to fall down, the continents will continue to move around the globe (causing earthquakes and volcanic eruptions) and the organisms will continue to evolve whether we like it or not, whether we believe in it or not.

References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 1

Tiktaalik web page

Figure 1 from:
Earth Sciences 10, Lecture 1: Scientific Method by Greg Anderson

Figure 2 from:
Brandon, RN, Does biology have laws? The experimental evidence. PSA 1996, vol. 2, 444–457.

All living organisms are composed of one or more cells - the cell is the unit of organization of Life.

Most cells are very small. Exceptions? Ostrich egg is the largest cell. Nerve cell in a leg of a giraffe may be as long as 3m, but is very thin.

Basic Structure of the Cell

A cell is a small packet or bag of liquid. The liquid is cytoplasm (or cytosol), which is essentially salty water with various organic molecules suspended in it.

The cytoplasm is contained within a cell membrane. Cell membrane is a phospholypid bilayer - this means that it is composed of two layers of tighly packed molecules of fat. Within the membrane, proteins are embedded into the bilipid layer and are more or less free to move around within the membrane. These proteins are important for the communication between the inside and outside of the cell.

You can see a good image here.

On the outside of the membrane, some cells may have additional structures. For instance, many bacterial and plant cells have thick cell walls that confer more rigidity to the cell as well as better defense against mechanical, chemical or biological insults.

Some cells also have hair-like cilia on the surface (e.g., a protist called Silver Slipper), or long whip-like flagella at one end (e.g., sperm cells). Both of these structures allow the cell to move utilizing its own energy.

Inside every cell, there is hereditary material - DNA. Exceptions? Red blood cells which have a membrane and cytoplasm, but no hereditary material.

Differences between prokaryotes and eukaryotes:

Prokaryotes (bacteria) have a cell membrane and cytoplasm and no other organelles.
Eukaryotes (plants, animals, fungi, protista) have a number of different cell organelles.

The nuclear material in Prokaryotes is a single, circular strand of DNA.
The nuclear material in Eukaryotes is organized in multiple chromosomes contained with a nucleus.

Cell Organelles

Eukaryotic cells have organelles. Organelles are subcellular structures that provide internal compartmentalization and other functions.

Nuclues is a large membrane-bound organelle. Its function is to sequester the DNA from the rest of the cell. The nuclear membrane (or nuclear envelope), which is also a phospholipid bilayer, selectively allows molecules to pass between the nucleus and cytoplasm. Inside the nucleus, DNA is organized in chromosomes. A chromosome is a tighly coiled and wound strand of DNA packaged with various proteins (e.g,. histones).

Smooth endoplasmic reticulum is a system of membranes and is involved in carbohydrate and lipid synthesis.

Rough endoplasmic reticulum is a system of membranes that possesses ribosomes. Proteins are synthesized in the rough ER.

Golgi apparatus stores and packages various molecules. When a molecule is needed elsewhere in the cell, a portion of the Golgi membrane closes off and forms a vesicle that can be transported around the cell.

Some eukaryotic organelles contain a little bit of their own DNA: the mitochondria and the chloroplasts. These two organelles used to be intercellular parasites, i.e., different species of bacteria that, over time, became an integral part of a cell.

Chloroplasts are found in plant cells. Photosynthesis is the process that occurs in them.

Mitochondria are found in all Eukaryotic cells. Breakdown of glucose begins in the cytoplasm and ends in the mitochondria, where the final products of the breakdown are ATP, water, CO2 and heat. This process requires oxygen - that is why we breath: to provide the oxygen for the mitochodria and to get rid of carbon dioxide produced in the mitochondria.

ATP (adenosine triphosphate) is the energy currency of the living world. Every cellular process that requires energy gets it from ATP. Thus, mitochondria are sometimes refered to as “factories of the cell”.

The final portion of the process of glucose digestion (the Krebs cycle) is, like any process, not 100% efficient. Errors happen and not every atom of every glucose molecule ends up where it should: in ATP, water or CO2. The result of this inefficiency is production of heat and production of highly reactive small molecules called free radicals (e.g., hydrogen peroxyde, H2O2). Free radicals tend to quickly react with whatever molecule they first encounter upon leaving the mitochondria. Such reactions damage those molecules, be they proteins, lipids, sugars or nucleic acids. The intercellular damage caused by free radicals is one aspect of the process of aging.

Some animals - birds and mammals - have harnessed the heat production by the mitochondria to keep a stable internal temperature. The efficiency of the mitochondrial “machine” is held low under the control of hormones like thyroid hormones. As a result, there is a greater production of free radicals, so warm-blooded animals evolved particularly good mechanisms for neutralizing free radicals and for repairing the damage. If a person keeps a constant low temperature or constant low-grade fever, the first thing the physician will check is the function of the thyroid gland.

The cytoskeleton, composed of filaments and microtubules, anchors the organelles and gives a cell its shape. Microtubules move organelles, including vesicles, within a cell. They also move the membrane-embedded proteins around where they are needed.

References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 5

The DNA code

DNA is a long double-stranded molecule residing inside the nucleus of every cell. It is usually tightly coiled forming chromosomes in which it is protected by proteins.

Each of the two strands of the DNA molecule is a chain of smaller molecules. Each link in the chain is composed of one sugar molecule, one phosphate molecule and one nucleotide molecule. There are four types of nucleotides (or ‘bases’) in the DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). The two strands of DNA are structured in such a way that an adenine on one strand is always attached to a thymine on the other strand, and the guanine of one strand is always bound to cytosine on the other strand. Thus, the two strands of the DNA molecule are mirror-images of each other.

The exact sequence of nucleotides on a DNA strand is the genetic code. The total genetic code of all of the DNA on all the chromosomes is the genome. Each cell in the body has exactly the same chromosomes and exactly the same genome (with some exceptions we will cover later).

A gene is a small portion of the genome - a sequence of nucleotides that is expressed together and codes for a single protein (polypeptide) molecule.

Cell uses the genes to synthetise proteins. This is a two-step process. The first step is transcription in which the sequence of one gene is replicated in an RNA molecule. The second step is translation in which the RNA molecule serves as a code for the formation of an amino-acid chain (a polypeptide).

Transcription

For a gene to be expressed, i.e., translated into RNA, that portion of the DNA has to be uncoiled and freed of the protective proteins. An enzyme, called DNA polymerase, reads the DNA code (the sequence of bases on one of the two strands of the DNA molecule) and builds a single-stranded chain of the RNA molecule. Again, where there is a G in DNA, there will be C in the RNA and vice versa. Instead of thymine, RNA has uracil (U). Wherever in the DNA strand there is an A, there will be a U in the RNA, and wherever there is a T on the DNA molecule, there will be an A in the RNA.

Once the whole gene (100s to 10,000s of bases in a row) is transcribed, the RNA molecule detaches. The RNA (called messenger RNA or mRNA) may be further modified by addition of more A bases at its tail, by addition of other small molecules to some of the nucleotides and by excision of some portions (introns) out of the chain. The removal of introns (the non-coding regions) and putting together the remaining segments - exons - into a single chain again, is called RNA splicing. RNA splicing allows for one gene to code for multiple related kinds of proteins, as alternative patterns of splicing may be controlled by various factors in the cell.

Unlike DNA, the mRNA molecule is capable of exiting the nucleus through the pores in the nuclear membrane. It enters the endoplasmatic reticulum and attaches itself to one of the membranes in the rough ER.

Translation

Three types of RNA are involved in the translation process: mRNA which carries the code for the gene, rRNA which aids in the formation of the ribosome, and tRNA which brings individual amino-acids to the ribosome. Translation is controlled by various enzymes that recognize specific nucleotide sequences.

The genetic code (nucleotide sequence of a gene) translates into a polypeptide (amino-acid sequence of a protein) in a 3-to-1 fashion. Three nuclotides in a row code for one amino-acid. There are a total of 20 amino-acids used to build all proteins in our bodies. Some amino-acids are coded by a single triplet code, or codon. Other amino-acids may be coded by several different RNA sequences. There is also a START sequence (coding for fMet) and a STOP sequence that does not code for any amino-acid. The genetic code is (almost) universal. Except for a few microorganisms, all of life uses the same genetic code.

When the ribosome is assembled around a molecule of mRNA, the translation begins with the reading of the first triplet. Small tRNA molecules bring in the individual amino-acids and attach them to the mRNA, as well as to each other, forming a chain of amino-acids. When a stop signal is reached, the entire complex disassociates. The ribosome, the mRNA, the tRNAs and the enzymes are then either degraded or re-used for another translational event.

Protein synthesis - post-translational modifications

Translation of the DNA/RNA code into a sequence of amino-acids is just the beginning of the process of protein synthesis.

The exact sequence of amino-acids in a polypeptide chain is the primary structure of the protein.

As different amino-acids are molecules of somewhat different shapes, sizes and electrical polarities, they react with each other. The attractive and repulsive forces between amino-acids cause the chain to fold in various ways. The three-dimensional shape of the polypeptide chain due to the chemical properties of its component amino-acids is called the secondary structure of the protein.

Enzymes called chaperonins further modify the three-dimensional structure of the protein by folding it in particular ways. The 3D structure of a protein is its most important property as the functionality of a protein depends on its shape - it can react with other molecules only if the two molecules fit into each other like a key and a lock. The 3D structure of the fully folded protein is its tertiary structure.

Prions, the causes of such diseases as Mad Cow Disease, Scabies and Kreutzfeld-Jacob disease, are proteins. The primary and secondary structure of the prion is almost identical to the normally expressed proteins in our brain cells, but the tertiary structure is different - they are folded into different shapes. When a prion enters a healthy brain cell, it is capable of denaturing (unwinding) the native protein and then reshaping it in the same shape as the prion. Thus one prion molecule makes two - those two go on and make four, those four make eight, and so on, until the whole brain is just one liquifiied spongy mass.

Another aspect of the tertiary structure of the protein is addition of small molecules to the chain. For instance, phosphate groups may be attached to the protein (giving it additional energy). Also, short chains of sugars are usually bound to the tail-end of the protein. These sugar chains serve as “ZIP-code tags” for the protein, informing carrier molecules exactly where in the cell this protein needs to be carried to (usually within vesicles that bud off the RER or the Golgi apparatus). The elements of the cytoskeleton are used as conduits (”elevators and escalators”) to shuttle proteins to where in the cell they are needed.

Many proteins are composed of more than one polypeptide chain. For instance, hemoglobin is formed by binding together four subunits. Each subunit also has a heme molecule attached to it, and an ion of iron attached to the heme (this iron is where oxygen binds to hemogolobin). This larger, more complex structure of the protein is its quaternary structure.

See animations:
Transcription
Translation

References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 3, 14 and 15.

Cell-cell interactions

Cells do not exist in complete isolation. For a coordinated function of cells in a tissue, tissues in an organ, organs in a system and systems in the body, cells need to be able to communicate with each other. Each cell should be capable of sending chemical signals to other cells and of receiving chemical signals from oter cells, as well as signals (chemical or other) from its immediate environment.

Cell membrane is a double layer of molecules of fat. Some small chemical messengers are capable of passing through the membrane. Most ions and most molecules cannot pass through the membrane, thus the information between the inside and the outside of the cell is mediated by proteins embedded in the membrane.

Membrane proteins serve various functions. For instance, such proteins form tight junctions that serve to glue neighboring cells together and prevent passage of substances between the two cells. Other surface proteins are involved in cell-cell recognition, which is important for the immune response. Other membrane proteins serve functions in communication between the inside of the cell and the cell’s immediate environment.

How does a cell send a signal?

A cell can communicate signals to other cells in various ways. Autocrine signaling is a way for a cell to alter its own extracellular environment, which in turn affects the way the cell functions. The cell secretes chemicals outside of its membrane and the presence of those chemicals on the outside modifies the behavior of that same cell. This process is important for growth.

Paracrine signaling is a way for a cell to affect the behavior of neighboring cells by secreting chemicals into the common intercellular space. This is an important process during embryonic development.

Endocrine signaling utilizes hormones. A cell secretes chemicals into the bloodstream. Those chemicals affect the behavior of distant target cells. We will go into more details of autocrine, paracrine and endocrine signaling later on, when we tackle the human endocrine system.

Direct signaling is a transfer of ions or small molecules from one cell to its neighbor through pores in the membrane. Those pores are built out of membrane proteins and are called gap junctions. This is the fastest mode of cell-cell communication and is found in places where extremely fast and well-coordinated activity of cells in needed. An example of this process can be found in the heart. The muscle cells in the heart communicate with each other via gap junctions which allows all heart cells to contract almost simultaneously.

Finally, synaptic signaling is found in the nervous system. It is a highly specific and localized type of paracrine signalling between two nerve cells or between a nerve cell and a muscle cell. We will go into details of synaptic signaling when we cover the human nervous system.

How does a cell receive a signal?

Some small molecules are capable of entering the cell through the plasma membrane. Nitrous oxide is one example. Upon entering the cell, it activates an enzyme.

Some small hormones also enter the cell directly, by passing through the membrane. Examples are steroid hormones, thyroid hormones and melatonin. Once inside the cell, they bind cytoplasmic or nuclear receptors. The hormone-receptors complex enters the nucleus and binds to a particular sequence on the DNA. Binding dislodges a protein that inhibits the expression of the gene at that segment, so the gene begins to be transcribed and translated. Thus, a new protein appears in the cell and assumes its normal function within it (or gets secreted). The action of nuclear receptors is slow, as it takes some hours for the whole process to occur. The effect is long-lasting (or even permanent) and changes the properties of the cell. This type of process is important in development, differentiation and maturation of cells, e.g., gametes (eggs and sperm cells).

There are three types of cell surface receptors: membrane enzymes, ion channels, and transmembrane receptors.

When a signaling chemical binds to the membrane enzyme protein on the outside of the cell, this triggers a change in the 3D conformation of that protein, which, in turn, triggers a chemical reaction on the inside of the cell.

When a signaling molecule binds to an ion channel on the outside of the cell, this triggers the change of the 3D conformation of the protein and the channel opens, allowing the ions to move in or out of the cell following their electrical gradients and thus altering the polarization of the cell membrane. Some ion channels respond to non-chemical stimuli in the same way, including changes in electrical charge or mechanical disturbance of the membrane.

G protein-linked receptors are seven-pass transmembrane proteins. This means that the polypeptide chain traverses the membrane seven times. When a chemical - a hormone or a pharmaceutical agent - binds to the receptor on the outside of the cell, this triggers a series of chemical reactions, including the movement and binding of the G-protein, transformation of GTP into GDP and activation of second messengers. Second messengers (e.g., cyclic AMP) start a cascade of enzymatic reactions leading to the cellular response. This signaling method is quite fast and, more importantly, it amplifies the signal. Binding of a single hormone molecule quickly results in thousands of molecules of second messengers acting on even more molecules of enzymes and so on. Thus, the response to a small stimulus can be very large. We will go into details of G-protein-mediated signaling when we tackle the endocrine and the sensory systems.

References:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 7.

In the first lecture, we covered the way science works and especially how the scientific method applies to biology. Then, we looked at the structure of the cell, building a map of the cell - knowing what processes happen where in the cell, e.g., the production of energy-rich ATP molecules in the mitochondria.

In the third part of the lecture, we took a closer look at the way DNA code gets transcribed into RNA in the nucleus, and the RNA code translated into protein structure in the rough endoplasmatic reticulum. Finally, we looked at several different ways that cells communicate with each other and with the environment, thus modifying cell function.

All of that information will be important in this lecture, as we cover the ways cells divide, how cell-division, starting with a fertilized cell, builds an embryo, how genetic code (genotype) influences the observable and measurable traits (phenotype) and, finally, how do these processes affect the genetic composition of the populations of organisms of the same species - the process of evolution.

Mitosis

The only way to build a cell is by dividing an existing cell into two. As the genome (the complete sequence of the DNA) is an essential part of a cell, it is neccessary for the DNA to be duplicated prior to cell division.

In Eukaryotic cells, chromosomes are structures composed mostly of DNA and protein. DNA is a long double-stranded chain-like molecule. Some portions of the DNA are permanently coiled and covered with protective proteins to prevent DNA expression (transcription). Other parts can be unraveled so transcription can occur.

The number of chromosomes is different in different species. Human cells possess 23 pairs of chromosomes. Prior to cell division each chromosome replicates producing two identical sister chromosomes - each eventually landing in one of the daughter cells.

The process of DNA replication - the way all of the DNA code of the mother cell duplicates and one copy goes into each daughter cell - is the most important aspect of cell division. It is wonderfully described in your handout and depicted in the animation. Other cell organelles also divide and split into two daughter cells. Once the process of DNA replication is over, the new portion of the cell membrane gets built transecting the cell and dividing all the genetic material into two cellular compartments, leading the cell to split into two cells.
Meiosis

Meiosis is a special case of cell division. While mitosis results in division of all types of cells in the body, meiosis results in the formation of sex cells - the gametes: eggs and sperm. Mitosis is a one-step process: one cell divides into two. Meiosis is a two-step process: one cell divides into two, then each daughter immediately divides again into two, resulting in four grand-daughter cells.

Each cell in the body has two copies of the entire DNA - one copy received from the mother, the other from the father. Fertilization (fusion of an egg and a sperm) would double the chromosome number in each generation if the egg and sperm cells had the duplicate copy. Meiosis ensures that gametes have only one copy of the genome - a mix of maternal and paternal sequences. Such a cell is called a haploid cell.

Once the egg and a sperm fuse, the resulting zygote (fertilized egg) again contains double dose of the DNA and is called a diploid cell. Thus the resultant zygote inherits genetic material from both its father and its mother. All the cells in the body except for the gametes are diploid. Sexual reproduction produces offspring that are genetically different from either parent.

DNA Replication

DNA replication is a complex process of duplication of the DNA involving many enzymes. It is the first and the most important process in cell division. Please read the handout (BREAKFAST OF CHAMPIONS DOES REPLICATION by David Ng) to appreciate the complexity of the process, but you do not need to memorize any of the enzymes for the exams. Also, it will help your understanding of the process if you watch this animation.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 11, 12 and 14.

Further reading:

THE CELL CYCLE: A UNIVERSAL CELLULAR DIVISION PROGRAM By David Secko

There are about 210 types of human cells, e.g., nerve cells, muscle cells, skin cells, blood cells, etc. Wikipedia has a nice comprehensive listing of all the types of human cells.

What makes one cell type different from the other cell types? After all, each cell in the body has exactly the same genome (the entire DNA sequence). How do different cells grow to look so different and to perform such different functions? And how do they get to be that way, out of homogenous (single cell type) early embryonic cells that are produced by cell division of the zygote (the fertilized egg)?

The difference between cell types is in the pattern of gene expression, i.e., which genes are turned on and which genes are turned off. Genes that code for enzymes involved in detoxification are transribed in lver cells, but there is not need for them to be expressed in muscle cells or neurons. Genes that code for proteins that are involved in muscle contraction need not be transcribed in white blood cells. The patterns of gene expression are specific to cell types and are directly resposible for the differences between morphologies and functions of different cells.

How do different cell types decide which genes to turn on or off? This is the result of processes occuring during embryonic development.

The zygote (fertilized egg) appears to be a sphere. It may look homogenous, i.e., with no up and down, left or right. However, this is not so. The point of entry of the sperm cell into the egg may provide polarity for the cell in some organisms. In others, mother may deposit mRNAs or proteins in one particular part of the egg cell. In yet others, the immediate environment of the egg (e.g., the uterine lining, or the surface of the soil) may define polarity of the cell.

When the zygote divides, first into 2, then 4, 8, 16 and more cells, some of those daughter cells are on one pole (e.g., containing maternal chemicals) and the others on the other pole (e.g., not containing maternal chemicals). Presence of chemicals (or other influences) starts altering the decisions as to which genes will be turned on or off.

As some of the genes in some of the cells turn on, they may code for proteins that slowly diffuse through the developing early embryo. Low, medium and high concentrations of those chemicals are found in diferent areas of the embryo depending on the distance from the cell that produces that chemical.

Other cells respond to the concentration of that chemical by turning particular genes on or off (in a manner similar to the effects of steroid hormones acting via nuclear receptors, described last week). Thus the position (location) of a cell in the early embryo largely determines what cell type it will become in the end of the process of the embryonic development.

The process of altering the pattern of gene expression and thus becoming a cell of a particular type is called cell differentiation.

The zygote is a totipotent cell - its daughter cells can become any cell type. As the development proceeds, some of the cells become pluripotent - they can become many, but not all cell types. Later on, the specificity narrows down further and a particular stem cell can turn into only a very limited number of cell types, e.g., a few types of blood cells, but not bone or brain cells or anything else. That is why embryonic stem cell research is much more promising than the adult stem cell research.

The mechanism by which diffusible chemicals synthesized by one embryonic cell induces differentiation of other cells in the embryo is called induction. Turning genes on and off allows the cells to produce proteins that are neccessary for the changes in the way those cells look and function. For instance, development of the retina induces the development of the lens and cornea of the eye. The substance secreted by the developing retina can only diffuse a short distance and affect the neighboring cells, which become other parts of the eye.

During embryonic development, some cells migrate. For instance, cells of the neural crest migrate throughout the embryo and, depending on their new “neighborhood” differentiate into pigment cells, cells of the adrenal medula, etc.

Finally, many aspects of the embryo are shaped by programmed cell death - apoptosis. For instance, early on in development our hands look like paddles or flippers. But, the cells of our fingers induce the cell death of the cells between the fingers. Similarly, we initially develop more brain cells than we need. Those brain cells that establish connections with other nerve cells, muscles, or glands, survive. Other brain cells die.

Sometimes just parts of cells die off. For instance, many more synapses are formed than needed between neurons and other neurons, muscles and glands. Those synapses that are used remain and get stronger, the other synapses detach, and the axons shrivel and die. Which brain cells and which of their synapses survive depends on their activity. Those that are involved in correct processing of sensory information or in coordinated motor activity are retained. Thus, both sensory and motor aspects of the nervous system need to be practiced and tested early on. That is why embryos move, for instance - testing their motor coordination. That is why sensory deprivation in the early childhood is detrimental to the proper development of the child.

The details of embryonic development and mechanisms of cell differentiation differ between plants, fungi, protists, and various invertebrate and vertebrate animals. We will look at some examples of those, as well as some important developmental genes (e.g., homeotic genes) in future handouts/discussions, and will revisit the human development later in the course.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 18 and 19.

One often hears news reports about discoveries of a “gene for X”, e.g., gene for alcoholism, gene for homosexuality, gene for breast cancer, etc. This is an incorrect way of thinking about genes, as it implies a one-to-one mapping between genes and traits.

This misunderstanding stems from historical precedents. The very first genes were discovered decades ago with quite primitive technology. Thus, the only genes that could be discovered were those with large, dramatic effects on the traits. For instance, a small mutation (change in the sequence of nucleotides) in the gene that codes for RNA that codes for one of the four elements of the hemoglobin protein results in sickle-cell anemia. The red blood cells are, as a result, mishapen and the ability of red blood cells to carry sufficient oxygen to the cells is diminished.

Due to such dramatic effects of small mutations, it was believed at the time that each gene codes for a particular trait. Today, it is possible to measure miniscule effects of multiple genes and it is well understood that the “one gene/one trait” paradigm is largely incorrect. Most traits are affected by many genes, and most genes are involved in the development of multiple traits.

A genome is all the genetic information of an individual. Each cell in the body contains the complete genome. Genomes (i.e., DNA sequences) differ slightly between individuals of the same species, and a little bit more between genomes of closely related species, yet even more between distantly related species.

Exact DNA sequence of an individual is its genotype. The collection of all observable and measurable traits of that individual is phenotype.

If every position and every function of every cell in our bodies was genetically determined, we would need trillions of genes to specify all that information. Yet, we have only about 30,000 genes. All of our genes are very similar to the equivalent genes of chimpanzees, yet we are obviously very different in anatomy, physiology and behavior from chimpanzees. Furthermore, we share many of the same genes with fish, insects and even plants, yet the differences in phenotypes are enormous.

Thus, it follows logically that the metaphor of the genome as a blueprint for building a body is wrong. It is not which genes you have, but how those genes interact with each other during development that makes you different from another individual of the same species, or from a salmon or a cabbage.

But, how do genes interact with each other? Genes code for proteins. Some proteins interact with other proteins. Some proteins regulate the transcription or replication of DNA. Other proteins are enzymes that modify other chemicals. Yet other proteins are structural, i.e., become parts of membranes and other structures.

A slight difference in the DNA sequence will have an effect on the sequence of RNA and the sequence of the resulting protein, affecting the primary, secondary and tertiary structure of that protein. The changes in 3D shape of the protein will affect its efficiency in performing its function.

For instance, if two proteins interact with each other, and in order to do so need to bind each other, and they bind because their shapes fit into each other like lock and key, then change of shape of one protein is going to alter the efficiency of binding of the two. Changes in shapes of both proteins can either slow down or speed up the reaction. Change of rate of that one reaction in the cell will have effects on some other reaction in the cell, including the way the cell reacts to the signals from the outside.

Thus genes, proteins, other chemicals inside the cell, intercellular interactions and the external environment ALL affect the trait. Most importantly, as the traits are built during development, it is the interactions between all these players at all levels of organizations during development that determine the final phenotype of the organism.

The importance of the environment can be seen from the phenomenon of the norm of reaction. The same genotype, when raised in different environments results in different phenotypes. Furthermore, different genotypes respond to the same environmental changes differently from each other. One genotype may produce a taller plant at higher elevation while a slightly different genotype may respond quite the opposite: producing a shorter plant at higher elevations.

So, if genes do not code for traits, and the genome is not a blueprint, what is the best way to think about the genome and the genotype/phenotype mapping? I have given you handouts (see below) with four different alternative metaphors, at least one of which, I hope, will feel clear and memorable to each student. I will now give you a fifth such metaphor, one of my own:

Imagine that a cell is an airplane factory. It buys raw materials and sells finished airplains. How does it do so? The proteins are the factory workers. Some of them import the materials, others are involved in the sale of airplanes. Some guard the factory from thieves, while others cook and serve food in the factory cafeteria.

But the most important proteins of this cell are those that assemble the parts of airplanes. When they need a part, e.g., a propeller, they go to the storeroom (nucleus) and check the Catalogue Of Parts (the DNA), and press the button to place an order for a particular part. Other proteins (storeroom managers) go inside and find the correct part and send it to the assembly floor (endoplasmatic reticulum).

But, protein workers are themselves robots assembled out of parts right there in the same factory, and the instructions for their assembly are also in the Catalogue of Parts (DNA) in the nucleus.

Handouts:

How do you wear your genes? by Richard Dawkins.
An analogy for the genome by Richard Harter.
It’s not just the genes, it’s the links between them by Paul Myers
PZ Myers’ Own Original, Cosmic, and Eccentric Analogy for How the Genome Works -OR- High Geekology by Paul Myers

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 17.3 and 21.

Evolution

Imagine a small meadow. And imagine in that meadow ten insects. Also imagine that the ten insects are quite large and that the meadow has only so much flowers, food and space to sustain these ten individuals and not any more. Also imagine that the genomes of those ten insects are identical, except for one individual: that one has a mutation in one gene (due to an error in DNA replication, or due to crossing-over during meiosis). That mutation, during development led to the induction of the production of more mitochondria in each muscle cell.

Normally, that mutation is not obvious - the insect flitters from flower to flower just like anyone else. However, if the situation arises, the mutant individual is just a tiny little bit faster because the additional mitochondria in muscles allow it to switch from aerobic to anaerobic sources of energy later than in other individuals. Thus, the “normal” individuals can fly one yard in one second, while the mutant can fly one yard plus one inch in one second.

Now imagine that, over some time period, a bird comes by the meadow four times. Each time, the bird chases the insects and catches the one that is the closest to her. Which individual is, statistically speaking, least likely to get caught and eaten? The mutant, as the little extra speed may give it just enough edge in comparison to other individuals. This comparative “extra edge” is called increased fitness.

After four insects have been eaten, six remain - three males and three females. They pair up, mate, lay eggs and die. Each pair lays, let’s say eight eggs, which all hatch, proceed normally through the larval development and become adults. This makes a total of 24 insects in a meadow that can support only ten individuals. At the same time, the bird has laid eggs, the eggs hatched and the hatchlings sometimes come to the meadow to hunt.

Let’s look at the genetics of this population for a moment. Two pairs of “normal” insects produced a total of 16 offspring, all of them “normal”. The offspring of one “normal” and one “mutant” each got one of the chromosomes from the mother, the other one from the father. All of them will have the mutation on one, and not on the other chromosome. Let’s say that having a mutation on only one chromosome adds a half-inch to the yard-per-second flaying speed. The full mutant is homozygous for this mutation. The half mutant is heterozygous for this mutation. The heterozygous individuals are still relatively more fit than the “normals”. As the hatchling birds hunt down the insects and cut down the population to ten individuals, the half-mutants are more likely to be present in the remaining population than the non-mutants.

Let’s call the “normal” variant of the gene A and the “mutant” variant of the same gene a. A and a are alleles of the same gene.

In the next generation, some normals will breed with normals, producing normal offspring. Some half-mutants will mate with normals and produce a mix of normals and half-mutants. Some half-mutants will mate with some half-mutants and the resulting eight offspring will consist of 2 normals (AA), two mutants (aa), and four semi-mutants (Aa).

As the a allele confers relative fitness to its carriers, this allele will spread through the population over several generations and either completely eliminate allele A, or attain some stable balanced ratio in the population.

When one compares the genetic composition of this population over generations, one notices that it changes over time, from preponderance of A in the first generation, through a series of intermediate stages, to the preponderance of a in the last generation.

The change of genetic composition of a population over multiple generations is called evolution. That sentence is the most commonly used definition of evolution.

The process that favored one allele over the other, resulting in evolution of flight speed in these insects, is called natural selection.

The environment - the carrying capacity of the meadow plus the bird predators - was the selecting agent. The process that turns a genetic change (mutation) into a trait that can affect fitness of the whole organism is development. Thus, one can also define evolution as “change of development by ecology”.

For evolution to proceed, the trait must vary in a population, one of the variants has to confer greater fitness than the other variants, there has to be a limit on the fecundity (how many offspring can survive in each generation) leading to differential rate of reproduction, and the trait has to be heritable, i.e., the offspring have to be more like parents in respect to that trait than like other individuals in the population. The inheritance is usually, though not always, conferred by the genome (the DNA sequence).

The example we used is quite unrealistic. Populations are much more likely to number in thousands or millions than just ten individuals. Thus, instead of a few generations, it may take thousands or millions of generations for a new allele to sweep through the population. In annually breeding organisms, this means thousands to millions of years. In slow-breeding animals, like elephants, it will take even longer. In fast reproducers, like bacteria, this may only take several months or years, as in evolution of antibiotic resistance in bacteria or evolution of pesticide resistance in agricultural pests.

Another way that the example was unrealistic was the assumption that all the individuals were genetically identical to each other except for that one mutation in that one gene. In reality, there will be variation (two or more alleles) in every gene, and new mutations show up all the time. Some mutations decrease fitness, some are neutral and some increase fitness. Some alleles affect fitness depending on which other alleles of other genes are present in the same individuals, or depending on the environment it finds itself in at a particular time, as in the norm of reaction phenomenon. Due to this, some combinations of alleles may tend to move from one generation to the next together.

Finally, in many organisms, genes can be transmitted horizontally - not from parent to offpspring but directly from one individual to another. This most often happens in bacteria, where individual bacteria may excahge bits and pieces of their DNA. Likewise, viruses are carriers of DNA sequences from one organism to another as well. Some of the sequences in our genome are of bacterial origin, transmitted some time in the past by viruses, and now fully integrated into our genome and even assuming an indispensible function. For instance, HERV genes are originally viral genes that are now parts of our genome and are neccessary for the development of the placenta.

Thus, in the real world, the situation is more complicated than in our example. Still, the proportions of various alleles of many genes are constantly changing - evolution occurs all the time.

Let’s now assume that our insects live in a much larger area and that there are millions of them. The frequences of various alleles fluctuate all the time, and there is quite a lot of genetic variation contained in the population. Natural selection may work on preserving the average phenotype as its fitness is high and outliers at each end have lower fitness. This is called stabilizing selection.

As the climate slowly changes, or other aspects of the environment change, the relative frequences of alleles of various genes will track those changes. New conditions may, for instance select for larger body size. The largest individuals tend to leave most offspring, while the smallest individuals, on average, put the least of their genes into the next generation. The selection for large body size is an example of directed selection.

In some cases, selection may favor the extremes, but not the middle. Fast fliers may be selected for because they can escape the birds. The slowest fliers may be selected because they mostly walk or crawl and are thus not easily spotted by birds. They are also fit, but via a different strategy. The medium-speed fliers are selected against. This is an example of discruptive selection, forming two different morphs of the same species.

If those two morphs tend to, on average, be more likely to find each other and mate with each other within a morph than between two morphs, this may lead to splitting the species into two species - this is called sympatric speciation. As the gene flow between the two groups declines, more and more mutations/alleles will be found only in one morph and not the other. Those genes will also be under the influence of selection, and the selecting environment is different between crawlers and fliers. Soon enough, the individuals belonging to the two groups will not even recognize each other as belonging to the same species. Even if they recognize each other, they may not like each other (”mate-choice”) enough to mate. Even if they mate, their eggs may not be fertile. Even if their eggs are fertile, the resulting offspring may not be fertile (hybrids, like mules for instance). If, for whatever reason, two related populations do not, will not or cannot interbreed, they have became separate species - speciation occured.

Imagine now that a small cohort of about ten individuals got blown away by wind from the mainland to a nearby island. The mainland population is huge. The island population is tiny. The ability of any mutation or any allele to spread fast through the population is much greater in a small group. The selective pressures are also different.

It may be better for the island insects to be small and for the mainland insects to be large, perhaps due to the types of flowers or kinds of predators that are present. The mainland insects may be selected for high flying speed because of bird predation. The island insects may not have any bird predators, but, those individuals who are the best fliers are most likely to be swept off the island by wind and drown in the ocean, never placing their genes into the next generation. Thus, they are selected not to fly, even to lose their wings.

If, after a number of generations, those two populations again get into contact - e.g., a land bridge gradually arises, or another cohort of mainland insects floats on a log onto the island, the two populations will not recognize each other as the same species (or not like each other enough to mate, or not having fertile eggs or offspring). Thus, they have also become reproductively isolated, thus, by definition, they have become two separate species. Speciation occured. This type of speciation, where a geographic barrier separates two parts of a population preventing gene flow between them is called allopatric speciation, and is much better documented and much less controversial than sympatric speciation.

Billions of such speciation events, meaning branching of species into two or more species, resulted in the evolution of all species of organisms on Earth from a single common ancestor (a very primitive bacterium) over a period of more than 3.5 billion years.

Read:
Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 13, 21, 22, 23 and 24.

Watch animation:
Evolution

Further readings:
Understanding Evolution
What is Evolution?
Introduction to Evolutionary Biology
Evolution FAQs
Index to Creationist Claims
Talk Design Articles
Talk Reason
Transitions

Imagine that you are a zebra, grazing in the savannah. Suddenly, you smell a lion. A moment later, you hear a lion approaching and, out of the corner of your eye, you see the lion running towards you.

What happens next? You start running away, of course. How does that happen? Your brain receieved information from your sensory organs, processed that information and made a decision to puruse a particular action. That decision is relayed to the muscles that do the actual running.

In short, that is behavior and it can be schematically depicted like this:

Environment———> Sensor ———-> Integrator———> Effector

Here, the change in the environment (appearance of a lion) is perceived by the sensors (eyes, nose, ears), processed by the effector (the brain) and results in the activity of the effectors (muscles).

But, it is usually not that simple. The flow chart, as depicted, may be accurate when describing behavior of a bacterium, a protist, a fungus or a plant. A molecule in the cell membrane of a bacterium may sense nutrients, toxins or light. This information is processed by the cell as a whole, and as a result, the cilia or flagella move the bacterium in an appropriate direction.

Specialized cells in the shoot-tips or root-tips may detect up and down, or the position of the Sun, and guide growth in an appropriate direction (shoots up, roots down). Sunflowers and some other plants track the position of the Sun throughout the day. Many plants open and close their flowers or leaves at particular times of day. Some flowers, e.g, Venus flytrap and some orchids, can move even faster in order to capture insects.

Pilobolus, a fungus (seen as fine white fuzz on manure), shoots its spores towards the Sun at a particular angle at a particular time of day. Those are all simple behaviors involving a single sensor, a single integrator and a single effector in a simple unidirectional flow of information.

Once we get to animals with central nervous systems, things get a little bit more complicated. There are often multiple sensors. In the zebra example, the changes in environment are detected by three separate sensors: for vision, audition and olfaction. Effectors are many muscles, working in a highly coordinated manner.

Sensors located in the muscles feed the information about their activity back to the integrator. Integrator feeds back to the sensors as well - raising the sensitivity of the sensory organs, including vision, hearing, smell and the tactile sense (touch), while reducing the sensitivity of other sensors, e.g., for pain. The subjective perception of the rate of passage of time slows down, allowing for more fine-grained sensation and faster decision-making by the integrator.

Furthermore, the integrator will stimulate secretion of the hormones which, in turn, may increase the ability of effectors (muscles) to do their work. Integrator will also raise the activity of other organ systems that are important in allowing muscles to perform at their maximal level, e.g., circulatory and respiratory systems that bring oxygen and energy to the muscles.

At the same time, the brain temporarily shuts down the activity of organ systems not neccessary for short-term survival, but which may take the valuable energy away from the muscles. Thus, the digestive, immune, excretory and reproductive systems are inhibited.

As the zebra runs away, the act of running results in subsequent changes in the environment, which are again detected by the sensors. The integrator makes decisions to suddenly sverve if the lion gets closer, or to buck and kick if the lion gets very close, or to stop and find the safest route back to the herd if the lion has abandoned the chase.

All the changes described in the zebra example above are elements of the stress response, which is an excellent example of a complex behavior. There are multiple sensors, multiple effectors, various modifications of the body’s physiology, and several kinds of information feedbacks involved. Behavioral biology studies all aspects of it.

In addition, it is not just the activity itself, but also the propensity for such activity that is studied by behavioral biology. Probability of a behavior happening depends on the motivation, or the state of the effector. The state can be modified by hormones, hunger, tiredness, libido, general energy levels, etc. The effector (e.g, the brain) also possesses timing mechanims (clocks and celandars) which make some behaviors much more likely during the day or during the night, some more likely during spring or summer, others more likely during fall or winter.

What Is Behavior?

It is difficult to define behavior without resorting to just listing examples of various kinds of behaviors, but let’s try to define it anyway: Behavior is a change in body’s position, shape or color, or a change in potential for such change, in response to changes in the external or internal environment. Behavior is endogenously generated (i.e., if I move your arm - that is not your behavior, it’s mine), purposive (meant to achieve a goal), and is an evolved adaptation that contributes to survival or reproduction, thus increases one’s fitness (which is obvious in the case of the fleeing zebra).

How to study behavior?

The most informative and profitable way to study behavior is an integrative approach. This means that the behavior under study is approached at all levels of organization (from molecules to ecosystems) and from four different angles. The first angle is Mechanism, which denotes study of the physiology underlying behavior. Most of the analysis of the zebra’s behavior described above focused on this aspect - the physiology of the sensory, neural, muscular and other systems and the way they work together to produce the behavior.

The second one is Ontogeny, the study of embryonic and post-embryonic development of the behavior - how does an individual acquire the behavior, how much is the behavior inherited vs. learned, at what time in one’s life cycle can the behavior be learned or expressed, at what times of day or year are the behaviors most likely to be expressed, etc.

These first two angles - mechanism and ontogeny - are sometimes called Proximate Causes of behavior and are designed to ask and answer the “How” questions of behavior (how does it work, how does it develop). The next two are called Ultimate Causes of behavior and are designed to ask and answer the “Why” questions (why behave in such way).

History is the third approach. It studies the evolutionary history of a behavioral trait, usually by employing the comparative method, i.e., comparison of a number of related species, trying to discover if the behavior is common in all of them, in which case it is present due to the deep phylogenetic history, or of it most reliably varies with the type of environment the species lives in, suggesting that the behavior is a recent adaptation for a particular way of life. Finally, the fourth approach is Function. It tests the hypothesis that the behavior in question increases the animal’s fitness, aids in survival and/or reproduction, and has evolved for that function - is it an adaptation.

Recently a fifth question has been added to this list. Animal cognition asks “Can animals think?” Here, careful use of some unusual (and quite controversial) methods, including anecdotes, introspection and anthropomorphism, aids in the development of testable hypotheses about the inner worlds of animals.

No other area of biology is as integrative as behavioral biology. It is possible for a biochemist to ignore ecology or for an ecologist to ignore biochemistry (though at the risk of performing irrelevant research), but a behavioral biologist cannot ignore any aspect of the biology of the species under study. This makes the study of behavior the glue that holds all of biology together. This makes behavioral biology difficult to do, as one needs to have strong background in many areas of biology, technical expertise in a broad range of laboratory and field techniques, and lots of time to follow up on the literature in a number of related fields.

Only a few - the best - behavioral biologists are capable of exploring every aspect of a behavior at all levels. Mostly, the problem is divided among a number of laboratories around the world, each researcher using a slightly different approach and different techniques. The laboratories then communicate with each other via formal channels - the publications in scientific journals - and via informal channels - conferences and personal communication. Thus, a big picture is slowly being built out of its smaller parts, each piece of research being informed by all other pieces of research.

Types of behaviors

Foraging behavior involves finding, catching, handling and ingesting food. It includes the formation and use of feeding territories, learning the hunting techniques, the physiology of hunger, as well as behavioral strategies for avoiding becoming prey.

Animal movement includes, most prominently, long-distance migration including the neural mechanisms of spatial orientation and navigation.

Communication is the ability of animals to communicate information to each other (within and betwen species) via several sensory channels (or modalities). Those modalities include vision (including infrared, ultraviolet and polarized light, as well as thermoreception), sound (including ultrasound, infrasound and substrate vibrations), chemical signals (smells, pheromones, taste), touch and electrical signals (as in electrical fish).

Reproductive behaviors encompass a broad range of behaviors. Mate-finding, male-male competition, mate-choice and courtship are behaviors involved in securing a mate. Mating behavior ensures fertilization. Nesting and parenting behaviors are meant to ensure the survival of the offspring.

Reproductive behaviors are important elements of evolutionary change. Many phenotypic traits are a result not of natural selection, but of sexual selection, where a trait is selected not by the physical environment but by potential mates. Traits favored by the individuals of the opposite sex tend to be more likely to be passed on to the next generation in that population. This leads to the evolution of exaggerated traits (e.g., the peacock’s tail) and to differences between sexes (e.g., in many bird species the male is brightly colored while the female looks drab).

Mate choice can, potentially, be involved in sympatric speciation, if different individuals in the population favor different traits in their mates, so the gene flow between the two groups gets progressively smaller with each generation. This kind of mating is called assortative mating (as opposed to random mating, where each individual is equally likely to mate with each individual of the opposite sex).

The most common types of mating systems are monogamy, polygyny, and polyandry. A good example of polygyny is the elephant seal in which only one male (after defeating all the other males in one-on-one fights) mates with all the females in his territory.

Polyandry is found only a little less often - one female mates with multiple males over the course of a breeding season, resulting in her offspring being of mixed paternity (i.e., different eggs were fertilized by different males). This has been studied mostly in frogs.

Monogamy is the rarest form of mating strategy in the animal kingdom. A distinction is made between social monogamy and sexual monogamy. Many animals that form breeding pairs, including most species of birds, are engaged in social monogamy - the male and the female build the nest together, mate and raise the chicks together. However, DNA fingerprinting has shown that a small proportion of the eggs is invariably fertilized by a different male - a fleshy neighbor who may not be a good “husband” and “father”, but whose size, bright colors or powerful song indicate other genetic qualities. Thus, some of the progeny of the same female will be fleshy sons, some will be “good husband” sons and some will be daughters - the female is hedging her bets about the production of grandoffspring.

Humans are not officially classified as monogamous animals - though human polygamy (both polygyny and polyandry) tends to be in the form of serial monogamy, i.e., sticking monogamously with one partner for a particular length of time, then changing the partner. Social norms have strongly opposed, but did not eradicate human non-monogamy. Increased life-span, invention of reliable contraception, and economic independence of women are making it more and more difficult to supress the non-monogamous tendencies in humans, as seen from statistics for divorce (around 50%), re-marrying, and cheating (around 60% of both men and women) that have held quite steady over the past 50 years or so.

Social behaviors involve relationships between individuals of the same species. Some animals tend to live alone, each individual defending a territory, and a male and a female meeting only briefly during the mating season. Other animals tend to live in smaller or larger groups. Some animals change their social structure seasonally - for instance, European quail live in coveys (10-12 birds) during the winter), in huge flocks during spring and fall migrations, and in breeding pairs during summer.

Within groups, there is often a hierarchy of individuals - the so-called “pecking order”. The social hirearchy is established through aggression, often in form of ritualized displays. In many species, the ritualized aggressive behaviors are so-called “fixed-action patterns“, i.e., a strongly heritable order of particular movements. Mating behaviors are also often fixed-action patterns.

In some species, the mating fixed-action patterns are also used for aggressive encounters. In some cases, when a male mounts another male utlizing a typical mating pattern, this is actually a display of social dominance. However, in other species, a male mounting a male is actually homosexual behavior, evolved not to determine social hirearchy, but quite the opposite, to increase social coherence within the group (”making friends”). In pygmy chimps (bonobos), everyone in a troup mates with everyone else in the troup, regardles of gender. This makes the troup socially cohesive (which helps in group’s defense if attacked by another troup).

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapter 52.

Ecology is the study of relationships of organisms with one another and their environment. Organisms are organized in populations, communities, ecosystems, biomes and the biosphere.

A population of organisms is a sum of all individuals of a single species living in one area at one time.

Individuals in a population can occupy space in three basic patterns: clumped spacing, random spacing and uniform spacing.

Metapopulations are collections of populations of the same species spread over a greater geographic area. There is some migration (ths gene-flow) between populations. Larger populations are sources and smaller populations are sinks of individuals within a metapopulation.

Population size is determined by four general factors: natality, mortality, immigration and emigration.

Natality depends on a number of factors: the proportion of the population that are at a reproductive age (as opposed to pre-reproductive and post-reproductive), proportion of the reproductively mature individuals that get to reproduce, sex-ratio of the reproductives, the mating system, the fertility of individuals (sometimes affected by parasites), the fecundity (number of offspring per female), the maturation rate (the amount of time needed for an individual to attaint sexual maturity), and longevity (amount of time an individual can live after reproducing).

Mortality is affected by bad weather, predation, parasitism and infectious diseases. It depends on the mortality of pre-reproductive stages (from eggs and embryos, through larva and juveniles), mortality of reproductive stages, and mortality of post-reproductive stages (often from disease or aging).

A population can, theoretically, grow exponentially indefinitely. However, in the real world, the growth is limited by the amount of space, food (energy) and predators. Thus, the population size often plateaus at an optimal number - the carrying capacity of that population.

Some organisms produce a large number of progeny, most of which do not make it to maturity. This is r-strategy. The population size of such species often fluctuates in boom-and-bust patterns.

Other organisms produce a small number of progeny and make a heavy investment into parenting and protecting each offspring, This is K-strategy. The population size of such species grows more slowly and tends to stabilize around the carrying capacity.

All populations show small year-to-year fluctuations of population sizes around the optimum number. Some species, however, exhibit regular oscillations in population sizes. Such oscillations often involve populations of two different species, usually a predator and its prey, the most famous example being that of the snowshoe hare and the lynx.

Correct prediction of future changes in a population size is essential for the assessment of the populations viability and for its protection.

A biological community is a collection of all individuals of all species in a particular area. Those species interact with each other in various ways, and have evolved adaptations to life in each others’ presence.

Niche is a term that describes a life-role, or job-description, or one species’ position in the community. An example may be a large herbivore, a nocturnal burrowing seed-eater, a seasonal fruit-eater, etc.

Within one community only one species can occupy any particular niche. If two species share some of their niche, they are in competition with each other. If two species occupy an identical niche, they cannot coexist - one of the species will be forced to move out or go extinct.

If two species compete for the same resource (food, territory, etc.), one will utilize the resource better than the other. Competitive exclusion is a process in which one species drives another species out of the community.

Complete exclusion is not inevitable. The competition between two species can be reduced by natural selection, i.e., one of the species will be forced to assume a slightly different niche. For instant, two species can geographically partition the territory, e.g., one living at higher altitude than the other on the same mountain-side. Two species can also temporally partition the niches, for instance one remaining active at night and the other becoming active during the day.

Predation is one of the most important interaction between species in a community. Predation often causes evolutionary arms-races between predators and prey. For instance, by killing the slowest zebras, lions select for greater speed in zebras. Greater speed in zebras selects for greater speed in lions.

The most interesting examples of evolutionary arms-races between pairs of enemies are those in which the prey is dangerous to the predator, often by being toxic or venomous. For example, garter snakes and tiger salamanders on the West coast are involved in one such arms-race. Prey - the salamander - secrete tetrodotoxin from its skin. This toxin paralyzes the snake. Locally, some snakes have evolved an ability to tolerate the toxin, but the side-effect of such evolution is that these snakes are slow and sluggish - themselves more vulnerable to predation by birds.

Ground squirrels (prey) in the Western deserts have evolved immunity to rattlesnake venom, so the rattlesnakes (predators) are becoming more venomous. Similarly, and in the same area, desert mice have evolved immunity to the toxin of their prey - the scorpions, resulting in increasing toxicity of the scorpion venom in that region (but not in areas where these two species do not overlap). A Death’s-head sphynx moth steals honey from beehives and has evolved partial immunity to honey-bee venom.

Many plants have evolved thorns or toxic chemicals to ward off their enemies - the herbivores. Monarch butterflies are capable of feeding on milkweed despite this plant’s toxic content. Moreover, the Monarchs store the noxious chemical they extracted from milkweed and that chemical makes the butterflies distasteful to their own predators.

The shape and color of the prey often evolves to protect from predation. Warning coloration, usually in very bright colors, informs the predators that the prey is dangerous. Aposomatic coloration is one commonly found kind of warning coloration - the black and yellow stripes on the bodies of many bees and wasps are almost a universal code for dangerous venomous stings.

Cryptic coloration, or camouflage, on the other hand, allows an animal to blend in with its surroundings. Many insect look like twigs, leaves or flowers, effectively hiding them from the eyes of predators. Some animals have evolved behavioral color-change, e.g., chameleons, some species of cuttlefish and the flounder.

Batesian mimicry is a phenomenon in which non-toxic species evolve to resemble a toxic species. Thus, some butterflies look very similar to Monarch butterflies and some defenseless flies and ants have aposomatic coloration.

Mullerian mimicry is a phenomenon in which two or more dangerous species evolve to look alike. This is “safety in numbers” strategy as a predator who tastes and spits out one of them, will learn to avoid all of them in the future.

Co-evolution does not occur only between enemies. It can also occur between species that positively affect each other. The best example is co-evolution of flowers and insect pollinators.

Symbiosis is a relationship between organisms that are not direct enemies (e.g,. predator and prey) to each other. Commensalism, mutualism and parasitism are forms of symbiosis.

In commensalism, one partner benefits, while the other one is not affected at all. For instance, birds building nests in a tree do not in any way affect the fitness of the tree.

Mutualism benefits both partners. The best known examples are lichens, mycorrhizae, and legumes. Birds that clean the skin or teeth of crocodiles, hippos or rhinos are protected by their hosts.

Parasitism is detrimental to one of the partners. Parasites that are too dangerous, i.e., those that kill their host, are not successful since they also die without leaving offspring. Thus, parasites evolve to be minimally harmful to their hosts. The same logic goes for infectious agents - the disease should help propagate the microorganism (e.g, by causing sneezing, diarrhea, etc.) without killing the host.

The organisms that make up ecosystems change over time as the physical and biological structure of the ecosystem changes. Right now, one of the effects of global warming is that some species migrate and others do not. Thus, old ecosystems break down and new ones are formed. The ecosystems are in a process of remodelling. During that process, many species are expected to go extinct.

When an ecosystem is disturbed to some extent, but not completely eradicated, the remodelling process that follows is called primary succession.

When an ecosystem is completely wiped out (e.g,. a volcanic eruption on an island), secondary succession occurs, with a predictable order in which species can recolonize the space. One species prepares the ground (quite literally) for the next one. The process may start with bacteria, lichens and molds, continuing with mosses, fungi, ferns and some insects, etc, finally ending with trees, birds and large mammals. The final structure of the ecosystem is quite stable over time - this is a mature ecosystem.

Read:

Peter H. Raven, George B. Johnson, Jonathan B. Losos, and Susan R. Singer, Biology (7th edition), McGraw-Hill Co. NY, Chapters 53-57.

Adaptation vs. Diversity

Biology is concerned with answering two Big Questions: how to explain the adaptation of organisms to their environments and how to explain the diversity of life on Earth.

Much of the course content so far engaged the question of the origin and evolution of adaptation, and much of the remainder of the course will also look at particular adaptations of humans and other vertebrates. This is the only lecture specifically targeting the question of diversity.

The way this material is usually taught is to go over long lists of organisms and tabulate their characters, how the members of one group are similar to each other and different from members of other groups. We, in our course, will try a different approach, i.e., not just describing, but also explaining diversity - how it comes about.

If you think about it, knowing what we learned so far about the way evolution works, the origin of adaptation and the origin of diversity are deeply intertwined: as local populations evolve adaptations to their current local environments, they become more and more different from each other until the species splits into two or more new species. Thus, evolution of adaptations to local conditions leads to proliferation of new species, thus to the increase in overall diversity of life on the planet.

Origin of Life

One can postulate four ways the life on Earth came about: a) it was created - poof! - out of nothing by an intelligent being, e.g., God; b) it was created - poof! - out of nothing by an intelligent being, e.g., space aliens, either on Earth or elsewhere, then brought to Earth; c) it spontaneously arose elsewhere in the Universe and was brought to Earth by comets and meteors; and d) it spontaneously arose out of chemical reactions in the ancient seas in the presence of the ancient atmosphere.

Science is incapable of addressing the first notion - being untestable and unfalsifiable (impossible to prove that it is wrong), it is properly outside of the realm of science and within the domain of religion.

The first three notions also just move the goalposts one step further - how did life (including God and/or Aliens) arise elsewhere in the Universe? Thus, scientists focus only on the one remaining testable hypothesis - the one about spontaneous and gradual generation of life out of non-life, a process called abiogenesis. The scientific study of abiogenesis cannot say and does not attempt to say, anything about existence of God or Aliens. It only attempts to figure out how life could have arisen on its own, sometime between 3 and 4 billion years ago.

All of life on Earth descends from a single common ancestor. It is quite possible that life initially arose multiple times, but as soon as one life form became established and competitive enough, all the other instances of spontaneous generation of life were outcompeted and did not leave progeny.

It is difficult to study the origin of life as molecules do not leave fossils. They do leave chemical traces, though, so we know a lot about the chemistry of the ancient oceans, soil and atmosphere. Thus, we know under what conditions and what available materials (and energy) life first arose. By replicating such conditions in the laboratory, we can study the details of how life might have evolved out of non-life.

The study of the origin of life is a lively and exciting area of biology, perhaps because so little has yet been settled with great certainty. There are a number of competing hypotheses promoted by various research groups. Those hypotheses can be classified into groups: RNA First, Protein First, RNA-Protein First and Bubbles First.

RNA is a molecule that can be replicated and thus can serve as the original hereditary material (DNA is too large and complex even for some of today’s viruses, let alone for the first simple organisms). RNA is also capable of catalytic activity - promoting and speeding up reactions between other molecules, as well as replicating itself. Thus, RNA is the best candidate for the first molecule of life. Still, it is not capable of everything that life needs, so a few simple polypeptides (and those are really easy to synthetize in a flask mimicking the original Earth conditions) were probably involved from the very beginning. For those reactions to occur, they had to be separated from the remaining ocean - thus some kind of “cell membrane”, like a soap bubble, was also neccessary for the origin and early evolution of life.

Those early “cells” competed against each other. Those that, through chemical evolution, managed to become good enough at remaining stable for a decent amount of time, capable of acquiring the energy from the environment, and capable of dividing into two “daughter cells” outcompeted the others - chemical evolution turned into biological evolution. As they changed through trial and error, some cells gradually got better at “living” and outcompeted all others. One best competitor of the early living world is the common ancestor of all of the subsequent life on Earth, including us.

Directionality of Evolution

There are two common misconceptions about evolution. First is the idea that evolution tends towards perfection. But, always remember that evolution favors individuals who are slightly better optimized to current local conditions than other individuals of the same species, i.e., what wins is the relative fitness, not absolute fitness (i.e., perfection). In other words, you have to be capable of surviving and reproducing in your current environment and be just a tad little bit better at it than your conspecifics - there is no need to be perfectly adapted.

The second common misconception about evolution is that it has a tendency to generate greater complexity. Originally, right after the initial origin of life on Earth, evolution did produce greater complexity, but only because there was no way to become any more simple than the first organisms already were. There is a “left wall” of complexity in the living world, i.e. there is a minimum complexity that is neccessary for something to be deemed alive.

Thus, initially, the only direction evolution could take was away from the left wall (red dot), i.e., becoming more complex. But once reasonable complex organisms evolved, they were not snuggled against the left wall any more (yellow dot). Adaptation to current local conditions can equally promote simplification as it does complexification of the organism in question. In other words, as populations evolve, the members of the populations are equally likely to become simpler than they are to become more complex.

Actually, as we know from the world of man-made machines, there is such a thing as being too complex (blue dot). Over-complicated machines break down much more easily and are more difficult to maintain and repair. Likewise, organisms of great complexity are often not as fit as their simpler relatives - their genomes are so large that the error rate is greater and cell division is more difficult. Cells can “go wild” and turn into cancer. Also, with so many interacting parts, it is more difficult for complicated organisms to evolve new adaptations as the development of the whole complex system has to change and adapt to such changes.

Thus, simplification is as often seen in evolution as is acquisition of greater complexity. Just think of parasites - they are all simplified versions of their free-living relatives - no need for eyes, other sensory organs or means of locomotion if one spends one’s life attached to the lining of the host’s intestine, sucking in nutrients and growing billions of eggs.

Measuring Diversity - Taxonomy and Sys