16. Physiology: Coordinated Response
April 14, 2010, 11:05 am
Filed under: Uncategorized

Last week we looked at the organ systems involved in regulation and control of body functions: the nervous, sensory, endocrine and circadian systems. This week, we will cover the organ systems that are regulated and controlled. Again, we will use the zebra-and-lion example to emphasize the way all organ systems work in concert to maintain the optimal internal conditions of the body:

So, if you are a zebra and you hear and see a lion approaching (sensory systems), the brain (nervous system) triggers a stress-response (endocrine system). This is likely to happen during the day, as the biological clock (circadian system) of both animals makes them diurnal, i.e., day-active (as opposed to nocturnal, or night-active animals). If the chase occurred during the night, the lion would run slower and the zebra would take longer to mount a stress-response. Both animals would also be handicapped by lower sensitivity of their sensory systems.

Another name for the stress response is fight-or-flight response. Considering the size, strength and weaponry of the lion, the zebra’s brain is unlikely to make a decision to fight.
Flight, i.e., running away is the best course of action for the zebra.
Zebra’s great speed and the lion’s hunting tactics are a result of a co-evolutionary arms race. Let’s see what is happening in the body of the zebra once it starts running.

Running is movement. In vertebrates, the movement is accomplished by contraction and relaxation of muscles attached to the bones of the internal skeleton. The attachments of muscles to the bones are called tendons (the attachment between one bone and another is called a ligament). By the alternate contraction and relaxation of muscles located on opposite sides of the bone, the bones are moved around the joints, the hooves push against the ground and propel the body forward.

What makes the skeletal muscles contract? Muscles are composed of many muscle cells. Each cell is very long and thin and each cell receives a synaptic connection from a motor neuron. The neurotransmitter at this synapse (called the ‘neuro-muscular junction’) is acetylcholine. Release of acetylcholine into the synaptic cleft and its binding to the receptors on the surface of the muscle cell membrane triggers an influx of calcium into the cell, as well as release of calcium from intercellular stores – the endoplasmatic reticulum.
The muscle cell is divided into segments. The muscle cell is filled with long thin molecules of actin and myosin that run lengthwise along the whole length of the segment. Myosin is the thicker of the two molecules. It contains myosin heads which form cross-bridges by binding to actin filaments. ATP is neccessary for detaching the myosin heads from actin, while calcium is necessary for attaching the heads again – at a new place further down the filament. In this fashion, the two kinds of molecules slide over each other. As they do so, each segment of the muscle cell shortens, thus the whole muscle cell shortens – this is contraction.

So, for the muscles to contract, it is necessary for the muscle cells to be supplied with calcium and with ATP. Calcium is regulated by a number of organs. The intake (absorption) of calcium into the body is controlled by the digestive system. Loss (excretion) of calcium is regulated by the kidney. Calcium is deposited in bones. All three of those processes (absorption in the intestine, excretion into urine, and deposition into bones) is controlled by hormones: parathormone (parathyroid gland), calcitonin (thyroid gland), estradiol (ovary and adrenal cortex) and Vitamin D (a hormone synthesized by skin). If muscle cells lack calcium, parathormone will be released, while calcitonin and estradiol will be inhibited. This will increase absorption from the gut, decrease loss via urine, and release some calcium out of the bones.
The other requirement for muscle contraction is ATP. It is synthetized during breakdown of glucose. The first several steps of the biochemical breakdown of glucose (glucolysis) do not require oxygen and result in production of just a few molecules of ATP. The last several steps of the biochemical breakdown of glucose (Krebs cycle) occur in the mitochondria (of which muscle cells have many), require the presence of oxygen, and result in production of many molecules of ATP.

Thus, in order to synthetize sufficient amounts of ATP needed for contraction, muscle cells need glucose and oxygen. Both are delivered to the muscles via blood, by the circulatory system. Oxygen in blood is bound to the molecule of hemoglobin. Hemoglobin is tightly packed inside red blood cells. In muscles, the concentration of oxygen in red blood cells is greater than in the surrounding tissue, thus hemoglobin releases oxygen which follows its concentration gradient. In lungs, the concentration of oxygen is greater in the air than in the blood, so oxygen enters the blood and binds to hemoglobin. Carbon dioxide does the opposite – it also follows its own concentration gradient, thus leaving the muscle cells and binding hemoglobin in a nearby capillary, then leaving the red blood cells and diffusing into the air in the lungs.

During stress response, epinephrine (from adrenal medulla) and the sympathetic system speed up the heart rate, thus increasing the rate at which blood circulates through the tissues. At the same time, capillaries in the muscle dilate (open up) allowing more blood to perfuse the muscle cells.
Heart is a large muscular organ. All muscle cells in the heart are connected to each other via gap junctions so the electrical potential is spread through the heart very fast. The oxygenated blood from the lungs enters the heart via pulmonary veins into the left atrium (one of the four chambers of the heart). It flows from left atrium into the left ventricle. When the left ventricle is filled, the contraction of the heart expells the blood into aorta – the largest artery of the body. Aorta branches off into many other arteries that take blood into all parts of the body. Smaller and smaller branches of arteries finally end in capillaries.

Capillaries are blood vessels that are bounded only by a very thin single-cell layer with pores, which allows many molecules to leave the bloodstream or enter the bloodstream following their concentration gradients. Oxygen-rich blood enters the capillaries and releases oxygen.

Oxygen-poor blood moves from capillaries into small veins, which join together into large and larger veins and finally into the vena cava. Vena cava enters the heart in the right atrium. From there, O2-poor blood fills the right ventricle. When the heart contracts, the blood is expelled into the pulmonary arteries which take the blood to the lungs where the blood becomes oxygen-rich again.
The frequency and depth of respiration also increase, thus increasing the concentration of oxygen in blood. Furthermore, working muscles produce heat. Higher temperature makes it easier for hemoglobin to release oxygen into the muscle. At the same time, increased ventilation (by intercostal muscles and the diaphragm) of lungs decreases the air temperature in lungs, which makes it easier for hemoglobin to bind oxygen. All this makes more oxygen available to the working muscles.

Still, after only a few seconds of strenous work, the oxygen reserves in the muscle are depleted. The glucose is now broken down only by glucolysis (anaerobically). As a result, the final products of glucose metabolism are not water and carbon dioxide, but lactic acid – the substance that makes tired muscles hurt. The presence of lactic acid decreases the local pH in the muscle, which also makes it easier for the hemoglobin to release addiitonal oxygen into the muscle, but the capacity of blood to bring in more oxygen is overwhelmed by the oxygen need of the working muscle cells.

Where does the muscle get its glucose from? Most of the glucose in the body is stored in the form of glucogen in muscle cells and liver cells. Hormones like glucagon and cortisol trigger the breakdown of glycogen into glucose molecules and release of glucose out of liver into the bloodstream, thus making it available for the muscle to use.

But, where do the glucose stores come from? From food, which is ingested, digested and absorbed by the digestive system.
Digestion of food begins in the mouth, where saliva begins the process of breaking down carbohydrates, along with making the food softer for the action of teeth and tongue in breaking down the food into smaller particles that can be swallowed. The food then goes through the esophagus into the stomach. The stomach is a muscular organ. It secretes hydrochloric acid and many digestive enzymes. The movements of the stomach further turn the food into a liquid. The movements of the stomach, as in many other internal organs, is due to the activity of smooth muscles. Those are much shorter muscle cells which are, unlike skeletal muscles, not under voluntary control. The muscles of the stomach and intestine are inhibited by the sympathetic system, thus digestion slows down during the stress response – the digestive process is too slow to provide glucose to the muscles at a rate needed for escaping the lion, thus the business of digestion (which is quite energy-demanding) is postponed until after the stresful event is over.

Once the food is made completely liquid by the stomach, it passes through the pyloric sphincter into the first portion of the small intestine – the duodenum. Here, the very acidic content of the stomach is neutralized and the pH of the rest of the digestive tract is slightly alkaline. At the beginning of the duodenum, two important organs add their products into the lumen of the intestine – the liver and the pancreas. The liver produces bile which is stored in the gall bladder and secreted into the duodenum. Bile is a mix of salts that act like detergents – breaking down large globules of fats into smaller droplets, thus making fats accessible to enzymes. Pancreas produces a wide range of digestive enzymes which, together with intestinal enzymes, break down different types of food molecules: proteins, carbohydrates, lipids, nucleic acids, various minerals, vitamins, etc.

Next portion of the small intestine is the longest – the jejunum – followed by ileum. In herbivores in general, the small intestine is very long, while in carnivores (e.g, the lion), it is comparatively short. Most of digestion and absorption of nutrients is performed by the small intestine.

The small food molecules absorbed by the intestine are picked up by the hepatic portal system – a system of blood vessels that take the blood to the liver. Liver is the chemical factory of the body – it breaks down toxins as well as foods, builds new molecules out of simpler building blocks and makes those available to the rest of the body by releasing them into the main bloodstream.

Large intestine – the coecum, the colon and the rectum – is primarily involved in reabsorption of water so it is not lost via feces. In some animals, various portions of the digestive tract are enlarged and contain chambers full of bacteria and protista that are capable of breaking down food substances (e.g., cellulose) that the animal itself is incapable of digesting. In ruminants (e.g., cows, sheep, camels, giraffes), it is the stomach that serves this function – it is divided into four large chambers. In horses and zebras, the coecum serves the same function. In humans, coecum is a rudimentary organ – all that is left is the non-functional appendix.

If you paid attention so far, you may have noticed a pattern. During stress response – running in this case – the most important organ system is the system for locomotion – the skeletal muscles. Every other organ system that is involved in providing the muscles with the optimal internal environment for maximal function, i.e., the systems that control calcium, or provide glucose and oxygen to the muscles, are stimulated by the control and regulatory mechanisms. All other systems are inhibited or even completely shut down – they consume precious energy. If the muscles perform their function successfully and the zebra escapes, the normal function of these systems can resume.
However, using up energy by non-essential systems can lead to the zebra not having enough energy for running at the maximum speed for sufficiently long time to evade the lion. Being eaten by the lion is certainly not good for zebra’s homeostasis!
Along with the digestive system, other systems that are inhibited during stress response are the immune system (which we will not cover in this course), the excretory system (kidney) and the reproductive system. Compared to the lion, fighting off bacteria is not so important – this can wait for a couple of minutes. Having to stop to pee is not a good idea while running away from the lion as well. It goes without saying that engaging in reproductive functions is out of question during the flight from the ferocious predator – but the survivors will have the opportunity to breed later, passing on their genes to the next generation – genes that contain information about building the body that is capable of effectively allocating resources in order to escape a lion’s attack.

So, now that you – the zebra – have succesfully run away from the lion, all the functions are coming back to normal – the breathing and heart-rate slow down, the glucose gets redeposited as glucagon in the liver and muscles (under the influence of insulin), the digestion restarts and the immune system re-engages. Let’s now look at the remaining two systems – excretion and reproduction.
The main organ of the excretory system is the kidney. Kidney is built of billions of little tubes called the nephrons. At the beginning of each nephron, a web of capillaries releases much water and other molecules into the nephron. Then, along the length of the nephron, there is exchange between the nephron, the neighboring capillaries and the space between them. Some substances, e.g, glucose, get completely reabsorbed out of the nephron and back into the bloodstream. Toxic and waste materials are actively secreted from the blood into the nephron. Many ions are also exchanged, leading to regulated changes in pH. Finally, most of the water gets reabsorbed as well, under control of antidiuretic hormone and aldosterone. Control of how much water gets excreted in the urine and how much is reabsorbed back into the bloodstream is important not just for preventing water loss, but also in controlling blood pressure. The urine is collected in the urinary bladder and, when it fills up, it is excreted via urethra into the outside environment.
Testis is the main organ of the male reproductive system. Apart from being an endocrine gland – secreting testosterone – this is the site where sperm cells are continuously produced out of their stem cells within long convoluted tubes of the testis. The mature sperm cells – spermatozoids – are collected in the epidydimis on the surface of the testis. At the end of copulation, during orgasm, the sperm cells are ejected via sperm duct (vas deferens) and urethra (housed within the penis) into the female’s vagina. On the way out, the sperm cells are mixed with secretions of three glands – the prostate, the seminal vesicles and the bulbourethral glands whcih provide the optimal environment (e.g, pH, sugars) for the survival of sperm cells in the inhospitable regions of the acidic female genital tract.
In the female, the ovary is the organ which produces hormones estradiol and progesterone. All the egg cells are stored in the ovary before birth, i.e., no new eggs are produced after birth. In every cycle, one of the egg cells matures – it builds around itself a large follicle. Ovulation is the moment at which the follicle bursts and the egg is released into the oviduct. If no fertilization occurs, the egg, together with the lining of the uterus, gets shed out of the body (menstruation). If fertilization does occur in the oviduct, the zygote moves into the uterus and implants itself into its wall. The empty follicle left behind in the ovary turns into the yellow body which secretes progesterone throughout pregnancy. The fertilized egg starts developing. A part of it develops into placenta and the other part into an embryo.


Audesirk, Audesirk and Byers, Biology, 8th edition., Chapters 32, 33, 34, 35 and 40


15. Physiology: Regulation and Control
April 14, 2010, 11:03 am
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It is impossible to cover all organ systems in detail over the course of just two lectures. Thus, we will stick only to the basics. Still, I want to emphasize how much organ systems work together, in concert, to maintain the homeostasis (and rheostasis) of the body. I’d also like to emphasize how fuzzy are the boundaries between organ systems – many organs are, both anatomically and functionally, simultaneously parts of two or more organ systems. So, I will use an example you are familiar with from our study of animal behavior – stress response – to illustrate the unity of the well-coordinated response of all organ systems when faced with a challenge. We will use our old zebra-and-lion example as a roadmap in our exploration of (human, and generally mammalian) physiology:

So, you are a zebra, happily grazing out on the savannah. Suddenly you hear some rustling in the grass. How did you hear it?

The movement of a lion produced oscillations of air. Those oscillations exerted pressure onto the tympanic membrane in your ears. The vibrations of the membrane induced vibrations in three little bones inside the middle ear, which, in turn, induced vibrations of the cochlea in the inner ear.
Cochlea is a long tube wrapped in a spiral. If the pitch of the sound is high (high frequency of oscillations), only the first portion of the cochlea vibrates. With the lowest frequences, even the tip of the cochlea starts vibrating. Cochlea is filled with fluid. Withing this fluid there is a thin membrane transecting the cochlea along its length. When the cochlea vibrates, this membrane also vibrates and those vibrations move the hair-like protrusions on the surface of sensory cells in the cochlea. Those cells send electrical impulses to the brain, where the sound is processed and becomes a conscious sensation – you have heard the lion move.
The perception of the sound makes you look – yes, there is a lion stalking you, about to leap! How do you see the lion? The waves of light reflected from the surface of the lion travel to your eyes, enter through the pupil, pass through the lens and hit the retina in the back of the eye.
Photoreceptors in the eye (rods and cones) contain a pigment – a colored molecule – that changes its 3D structure when hit by light. In the rods, this pigment is called rhodopsin and is used for black-and-white vision. In the rods, there are similar pigments – opsins – which are most sensitive to particular wavelengths of light (colors) and are used to detect color. The change in 3D structure of the pigment starts a cascade of biochemical reactions resulting in the changes in the electrical potential of the cell – this information is then transfered to the next cell, the next cell, and so on, until it reaches the brain, where the information about the shape, color and movement of the objects (lion and the surrounding grass) is processeced and made conscious.
The ear and the eye are examples of the organs of the sensory system. Hearing is one of many mechanical senses – others include touch, pain, balance, stretch receptors in the muscles and tendons, etc. Many animals are capable of hearing sounds that we cannot detect. For instance, bats and some of their insect prey detect the high-pitched ultrasound (a case of a co-evolutionary arms-race). Likewise for dolphins and some of their fish prey. Dogs do, too – that is why we cannot hear the dog whistle. On the other hand, many large animals, e.g., whales, elephants, giraffes, rhinos, crocodiles and perhaps even cows and horses, can detect the deep rumble of the infrasound.

Vision is a sense that detects radiation in the visible specter. Many animals are capable of seeing light outside of our visible specter. For instance, many insects and birds and some small mammals can see ultraviolet light, while some snakes (e.g., pit vipers like rattlesnakes and boids like pythons) and some insects (e.g., Melanophila beetle and some wasps) can perceive infrared light.

Another type of sense is thermoreception – detection of hot and cold. Chemical senses are attuned to particular molecules. Olfaction (smell) and gustation (taste) are the best known chemical senses. Chemical senses also exist inside of our bodes – they are capable of detecting blood pH, blood levels of oxygen, carbon dioxide, calcium, glucose etc. Finally, some animals are capable of detecting other physical properties of the environment., e.g., the electrical and magnetic fields.

All senses work along the same principles: a stimulus from the external or internal environment is detected by a specialized type of cell. Inside the cell a chemical cascade begins – that is transduction. This changes the properties of the cell – usually its cell membrane potential – which is transmitted from the sensory cell to the neighboring nerve cell, to the next cell, next cell and so on, until it ends in the appropriate area of the nervous system, usually the brain. There, the sum of all stimuli from all the cells of the sensory organ are interpreted (integrated and processed over time) and the neccessary action is triggered. This action can be behavioral (movement), or it can be physiological: maintanance of homeostasis.

The sensory information is processed by the Central Nervous System (CNS): the brain and the spinal cord.
All the nerve cells that take information from the periphery to the CNS are sensory nerves. All the nerves that take the decisions made by the CNS to the effectors – muscles or glands – are motor nerves. The sensory and motor pathways together make Peripheral Nervous System.
The motor pathways are further divided into two domains: somatic nervous system is under voluntary control, while autonomic (vegetative) nervous system is involuntary. Autonomic nervous system has two divisions: sympathetic and parasymphatetic. Symphatetic nervous system is active during stress – it acts on many other organ systems, releasing the energy stores, stimulating organs needed for the response and inhibiting organs of no immediate importance.
Thus, a zebra about to be attacked by a lion is exhibiting stress response. Sympathetic nervous system works to release glucose (energy) stores from the liver, stimulates the organs neccessary for the fast escape – muscles – and all the other systems that are needed for providing the muscles with energy – the circulatory and respiratory systems. At the same time, digestion, immunity, excretion and reproduction are inhibited. Once the zebra successfully evades the lion, sympathetic system gets inhibited and the parasympathetic system is stimulated – it reverses all the effects. The two systems work antagonistically to each other: they always have opposite effects.

But, how does the nervous system work? Let’s look at the nerve cell – the neuron:
A typical neuron has a cell body (soma) which contains the nucleus and other organelles. It has many thin, short processes – dendrites – that bring information from other neighboring cells into the nerve cell, and one large, long process that takes information away from the cell to another cell – the axon.

There is an electrical potential of the cell membrane – the voltage on the inside and the outside of the cell is different. The inside of the neuron is usually around 70mV more negative (-70mV) compared to the outside. This polarization is accomplished by the specialized proetins in the cell membrane – ion channels and ion transporters. Using energy from ATP, they transport sodium out of the cell and potassium into the cell (also chlorine into the cell). As ions can leak through the membrane to some extent, the cell has to constantly use energy to maintain the resting membrane potential.
An electrical impulse coming from another cell will change the membrane potential of a dendrite. This change is usually not sufficiently large to induce the neuron to respond. However, if many such stimuli occur simultaneously they are additive – the neuron sums up all the stimulatory and inhibitory impulses it gest at any given time. If the sum of impulses is large, the change of membrane potential will still be large when it travels across the soma and onto the very beginning of the axon – axon hillock. If the change of the membrane potential at the axon hillock crosses a threshold (around -40mV or so), this induces sodium channels at the axon hillock to open. Sodium rushes in down its concentration gradient. This results in further depolarization of the membrane, which in turn results in opening even more sodium channels which deplorizes the membrane even more – this is a positive feedback loop – until all of the Na-channels are open and the membrane potential is now positive. Reaching this voltage induces the opening of the potassium channels. Potassium rushes out along its concentration gradient. This results in repolarization of the membrane. The whole process – from initial small depolarization, through the fast Na-driven depolarization, subsequent K-driven repolarization resulting in a small overshoot and the return to the normal resting potential – is called an Action Potential which can be graphed like this:
An action potential generated at the axon hillock results in the changes of membrane potential in the neighboring membrane just down the axon where a new action potential is generated which, in turn, results in a depolarization of the mebrane further on down the axon, and so on until the electrical impulse reaches the end of the axon. In vertebrates, special cells called Schwann cells wrap around the axons and serve as isolating tape of sorts. Thus, the action potential instead of spreading gradually down the axon, proceeds in jumps – this makes electrical transmission much faster – something neccessary if the axon is three meters long as in the nerves of the hind leg of a giraffe.

What happens at the end of the axon? There, the change of membrane polarity results in the opening of the calcium channels and calcium rushes in (that is why calcium homeostasis is so important). The end of the axon contains many small packets filled with a neurotransmitter. Infusion of calcium stimulates these packets to fuse with the cell membrane and release the neurotransmitter out of the cell. The chemical ends up in a very small space between the axon ending and the membrane of another cell (e.g., a dendrite of another neuron). The membrane of that other cell has membrane receptors that respond to this neurotransmitter. The activation of the receptors results in the local change of membrane potential. Stimulatory neurotransmitters depolarize the membrane (make it more positive), while inhibitory neurotransmitters hyperpolarize the membrane – make it more negative, thus harder to produce an action potential.
The target of a nerve cell can be another neuron, a muscle cell or a gland. Many glands are endocrine glands – they release their chemical products, hormones, into the bloodstream. Hormones act on distant targets via receptors. While transmission of information in the nervous system is very fast – miliseconds, in the endocrine system it takes seconds, minutes, hours, days, months (pregnancy), even years (puberty) to induce the effect in the target. While transmission within the nervous system is local (cell-to-cell) and over very short distances – the gap within a synapse is measured in Angstroms – the transmission within the endocrine system is over long distances and global – it affects every cell that possesses the right kind of receptors.
Many endocrine glands are regulated during the stress response, and many of them participate in the stress response. The thyroid gland releases thyroxine – a hormone that acts via nuclear receptors. Thyroxine has many fuctions in the body and several of those are involved in the energetics of the body – release of energy from the stores and production of heat in the mitochondria. It also produces calcitonin which is one of the regulators of calcium levels in the blood.

Parathyroid gland is, in humans, embedded inside the thyroid gland. Its hormone, parathormone is the key hormone of calcium homeostasis. Calcitonin and parathormone are antagonists: the former lowers and the latter raises blood calcium. Together, they can fine-tune the calcium levels available to neurons, muscles and heart-cells for their normal function.

Pancreas secretes insulin and glucagon. Insulin removes glucose from blood and stores it in muscle and liver cells. Glucagon has the opposite effect – it releases glucose from its stores and makes it available to cells that are in need of energy, e.g., the muscle cells of a running zebra. Together, these two hormones fine-tune the glucose homeostasis of the body.

Adrenal gland has two layers. In the center is the adrenal medulla. It is a part of the nervous system and it releases epineprhine and norepinephrine (also known as adrenaline and noradrenaline). These are the key hormones of the stress response. They have all the same effects as the sympathetic nervous system, which is not surprising as norepinephrine is the neurotransmitter used by the neurons of the sympathetic system (parasympathetic system uses acetylcholine as a transmitter).

The outside layer is the adrenal cortex. It secretes a lot of hormones. The most important are aldosterone (involved in salt and water balance) and cortisol which is another important stress hormone – it mobilizes glucose from its stores and makes it available for the organs that need it. Sex steroid hormones are also produced in the adrenal cortex. Oversecretion of testosterone may lead to development of some male features in women, e.g., growing a beard.

Ovary and testis secrete sex steroid hormones. Testis secretes testosterone, while ovaries secrete estradiol (an estrogen) and progesterone. Progesterone stimulates the growth of mammary glands and prepares the uterus for pregnancy. Estradiol stimulates the development of female secondary sexual characteristics (e.g., general body shape, patterns of fat deposition and hair growth, growth of breasts) and is involved in monthly preparation for pregnancy.

Testosterone is very important in the development of a male embryo. Our default condition is female. Lack of sex steroids during development results in the development of a girl (even if the child is genetically male). Secretion of testosterone at a particular moment during development turns female genitals into male genitals and primes many organs, including the brain, to be responsive to the second big surge of testosterone which happens at the onset of puberty. At that time, primed tissues develop in a male-specific way, developing male secondary sexual characteristics (e.g., deep voice, beard, larger muscle mass, growth of genitalia, male-typical behaviors, etc.).

Many other organs also secrete hormones along with their other functions. The heart, kidney, lung, intestine and skin are all also members of the endocrine system. Thymus is an endocrine gland that is involved in the development of the immune system – once the immune system is mature, thymus shrinks and dissappears.

Many of the endocrine glands are themselves controlled by other hormones secreted by the pituitary gland – the Master Gland of the endocrine system. For instance, the anterior portion of the pituitary gland secretes hormones that stimulate the release of thyroxine from the thyroid gland, cortisol from the adrenal cortex, and sex steroids form the gonads. Other hormones secreted by the anterior pituitary are prolactin (stimulates production of milk, amog else) and growth hormone (which stimulates cells to produce autocrine and paracrine hormones which stimulate cell-division). The posterior portion of the pituitary is actually part of the brain – it secretes two hormones: antidiuretic hormone (control of water balance) and oxytocin (stimulates milk let-down and uterine contractions, among other functions).

All these pituitary hormones are, in turn, controlled (either stimulated or inhibited) by hormones/factors secreted by the hypothalamus which is a part of the brain, which makes the brain the biggest and most important endocrine gland of all.

Pineal organ is a part of the brain (thus central nervous system). In all vertebrates except mamals and snakes, it is also a sensory organ – it perceieves light (which easily passes through scales/feathers, skin and skull). In seasonally breeding mammals, it is considered to be a part of the reproductive system. In all vertebrates, it is also an endocrine organ – it secretes a hormone melatonin. In all vertebrates, the pineal organ is an important part of the circadian system – a system that is involved in daily timing of all physiological and behavioral functions in the body. In many species of vertebrates, except mammals, the pineal organ is the Master Clock of the circadian system. In mammals, the master clock is located in the hypothalamus of the brain, in a structure known as the suprachiasmatic nucleus (SCN).

Retina is part of the eye (sensory system), it is part of the brain (nervous system), it also secretes melatonin (endocrine system) and contains a circadian clock (circadian system) in all vertebrates. In some species of birds, the master clock is located in the retina of the eye. The day-night differences in light intensity entrain (synchronize) the circadian system with the cycles in the environment. Those differences in light intensity are perceived by the retina, but not by photoreceptor cells (rods and cones). Instead, a small subset of retinal ganglion cells (proper nerve cells) contains a photopigment melanopsin which changes its 3D structure when exposed to light and sends its signals to the SCN in the brain.
Wherever the master clock may be located (SCN, pineal or retina) in any particular species, its main function is to coordinate the timing of peripheral circadian clocks which are found in every single cell in the body. Genes that code for proteins that are important for the function of a particular tissue (e.g., liver enzymes in liver cells, neurotransmitters in nerve cells, etc.) show a daily rhythm in gene expression. As a result, all biochemical, physiological and behavioral functions exhibit daily (circadian) rhythms, e.g., body temperature, blood pressure, sleep, cognitive abilities, etc. Notable exceptions are functions that have to be kept within a very narrow range of values, e.g., blood pH and blood concentration of calcium.

So, nervous, endocrine, sensory and circadian systems are all involved in control and regulation of other functions inthe body. We will see what happens to all those other functions in the stressed, running zebra next week.


Audesirk, Audesirk and Byers, Biology, 8th edition., Chapters 37, 38 and 39

14. Introduction to Anatomy and Physiology
April 7, 2010, 1:50 pm
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Anatomy is the subdiscipline of biology that studies the structure of the body. It describes (and labels in Latin) the morphology of the body: shape, size, color and position of various body parts, with particular attention to the internal organs, as visible by the naked eye. Histology is a subset of anatomy that describes what can be seen only under the misroscope: how cells are organized into tissues and tissues into organs. (Classical) embryology describes the way tissues and organs change their shape, size, color and position during development.

Anatomy provides the map and the tools for the study of the function of organs in the body. It describes (but does not explain) the structure of the body. Physiology further describes how the body functions, while evolutionary biology provides the explanation of the structure and the function.

While details of human anatomy are essential in the education of physicians and nurses (and animal anatomy for veterinarians), we do not have time, nor do we need to pay too much attention to fine anatomical detail. We will pick up on relevant anatomy as we discuss the function of organs: physiology.

There are traditionally two ways to study (and teach) physiology. The first approach is medical/biochemical. The body is subdivided into organ systems (e.g., respiratory, digestive, circulatory, etc.) and each system is studied separately, starting with the physiology of the whole organism and gradually going down to the level of organs, tissues, cells and molecules, ending with the biochemistry of the physiological function. Only the human body is studied. Often, pathologies and disorders are used to illustrate how organs work – just like fixing a car engine by replacing a broken part helps us understand how the engine normally works, so studying diseases helps us understand how the healthy human body works.

The other approach is ecological/energetic. The physiological functions are divided not by organ system, but by the problem – imposed by the environment – that the body needs to solve in order to survive and reproduce, e.g., the problem of thermoregulation (body temperature), osmoregulation (salt/water balance), locomotion (movement), stress response, etc., each problem utilizing multiple organ systems. Important aspect of this approach is the study of the way the body utilizes energy: is the solution energetically optimal? Individuals that have solved a problem with a more energy-efficient physiological mechanism will be favoured by natural selection – thus this approach is also deeply rooted in an evolutionary context. Finally, this approach is very comparative – study of animals that live in particularly unusual or harsh environments helps us understand the origin and evolution of physiological mechanims both in uhmans and in other animals.

The textbook is unusually good (for an Introductory Biology textbook) in trying to bridge and combine both approaches. Unfortunately, we do not have enough time to cover all of the systems and all of the problems in detail, so we will stick to the first, medical approach and cover just a few of the systems of the human body, but I urge you to read the relevant textbook chapters in order to understand the ecological and evolutionary aspects of physiology as well (not to mention some really cool examples of problem-solving by animal bodies). Hint: use the “Self Test” questions at the end of each chapter and if you answer them correctly, you are ready for the exam.

Let’s start out by looking at a couple of important basic principles that pertain to all of physiology. One such principle is that of scaling, for which you should read the handout that we will discuss in class next time. The second important principle in physiology is the phenomenon of feedback loops: both negative and positive feedback loops.

Negative feedback loop works in a way very similar to the graph we drew when we discussed behavior. The body has a Sensor that monitors the state of the body – the internal environment (as opposed to external environment we talked about when discussing behavior), e.g,. the blood levels of oxygen and carbon dioxide, blood pressure, tension in the muscles, etc. If something in the internal environment changes from the normal, optimal values, the sensor informs the Integrator (usually the nervous system) which initiates action (via an Effector) to bring back the body back to its normal state.

Thus, an event A leads to response B which leads to the countering and elimination of the event A. Almost every function in the body operates like a negative feedback loop. For instance, if a hormone is secreted, along with the functional effect of that hormone, there will also be a trigger of a negative feedback loop that will stop the further secretion of that hormone.

There are very few functions in the body that follow a different pattern – the positive feedback loop. There, an event A leads to response B which leads to re-initiation and intensification of the event A which leads to a stronger response B…and so on, until a treshold is reached or the final goal is accomplished, when everything goes abruptly back to normal.

We will take a look at an example of the positive feedback loop that happens in the nervous system next week. For now, let’s list some other notable positive feedback loops in humans.

First, the blood clotting mechanism is a cascade of biochemical reactions that operates acording to this principle. An injury stimulates production of a molecule that triggers production of another molecule which triggers production of another molecule as well as production of more of the first molecule, and so on, until the injury has completely closed.

Childbirth is another example of the positive feedback loop. When the baby is ready to go out (and there’s no stopping it at this point!), it releases a hormone that triggers the first contraction of the uterus. The contraction of the uterus pushes the baby out a little. That movement of the baby stretches the wall of the uterus. The wall of the uterus contains stretch receptors which send signals to the brain. In response to the signal, the brain (actually the posterior portion of the pituitary gland, which is an outgrowth of the brain) releases hormone oxytocin. Oxytocin gets into the bloodstream and reaches the uterus triggering the next contraction which, in turn, moves the baby which further stretches the wall of the uterus, which results in more release of oxytocin…and so on, until the baby is expelled, when everything returns to normal.

Next example of the positive feedback loop is also related to babies – nursing. When the infant is hungry, mother brings its mouth to the nipple of the breast. When the baby latches onto the nipple and tries to suck, this stimulates the receptors in the nipple which notify the brain. The brain releases hormone oxytocin from the posterior pituitary gland. Oxytocin gets into the bloodstream and stumulates the mammary gland to release milk (not to synthetize milk – it is already stored in the breats). Release of milk at the nipple stimulates the baby to start suckling vigorously, which stimulates the receptors in the nipple even more, so there is even more oxytocin released from the pituitary and even more milk is released by the mammary gland, and so on, until the baby is satiated and unlatches from the breast, when everything goes back to normal.

Next example of the positive feedback loop is also related to babies, but nine months earlier. Copulation – yes, having sex – is an example of a positive feedback loop, both in females and in males. Initial stimulation of the genitals stimulates the touch receptors which notify the brain which, in turn, stimulates continuation (and gradual speeding up) of movement, which provides further tactile stimulation, and so on, until the orgasm, after which everything goes back to normal (afterglow nothwithstanding).

The last example also applies to the nether regions of the body. Micturition (urination) is also a positive feedback loop. The wall of the urinary bladder is built in such a way that there are several layers of cells. As the bladder fills up, the wall stretches and these cells move around until the wall is only a single cell thick. At this point, urination is inevitable (cannot be stopped by voluntary control). Beginning of the urination starts the movement of the cells back from single-layer state to multi-layer state. This contracts the bladder further which forces urine out even more which contracts the wall of the bladder even more, and so on until the bladder is completely empty again and everything goes back to normal.

The concept of feedback loops is essential for the understanding of the principle of homeostasis. Homeostatic mechanisms ensure that the internal environment remains constant and all the parameters are kept at their optimal levels (e.g,. temperature, pH, salt/water balance, etc) over time. If a change in the environment (e.g., exposure to heat or cold) results in the change of internal body temperature, this is sensed by thermoreceptors in the body. This triggers corrective mechanisms: if the body is overheated, the capillaries in the skin expand and radiate heat and the sweat gland release sweat; if the body is too cold, the capillaries in the skin contract, the muscles start shivering, the hairs stand up (goosebumps), and the thyroid hormones are released, resulting in opening of poers in the membranes of mitochondria in the muscles, thus reducing the effciency of the break-down of glucose to water and carbon-dioxide, thus producing excess heat. Either way, the body temperature will be returned to its optimal level (around 37 degrees Celsius), which is called the set-point for body temperature. Each aspect of the internal environment has its own set-point which is defended by homeostatic mechanisms.

While essentially correct, there is a problem with the concept of homeostasis. One of the problems with the term “homeostasis” is linguistic: the very term homeostasis is misleading. “Homeo” means ‘similar, same’ and “stasis” means ‘stability’. Thus, the word homeostasis (coined by Walter Cannon in the early 20th century) suggests strong and absolute constancy. Imagine that you were told to draw a graphical representation of the concept of homeostasis in 10 seconds. Without sufficient time to think, you would probably draw something like this:
The main characteristic of this graph is that the set-point is constant over time. But that is not how it works in the real world. The graph above is correct only if the time-scale (on the X-axis) spans only seconds to minutes. If it is expanded to hours, days or years, the graph would be erroneous – the line would not be straight and horizontal any more. The set point changes in a predictable and well-controlled manner. For instance, the set-point for testosterone levels in the blood in human males over the course of a lifetime may look like this:
That would be an example of developmental control of a set-point. At each point in time, that set-point is defended by homeostatic mechanisms, but the set-point value is itself controlled by other physiological processes. Another example of controlled change of a set-point may look like this:
This would be an example of an oscillatory control of a set-point. In the early 1980s, Nicholas Mrosovsky coined a new term to replace ‘homeostasis’ and specifically to denote controlled changes in set-points of all biochemical, physiological and behavioral values – rheostasis.

Almost every aspect of physiology (and behavior) exhibits rheostasis, both developmental and oscillatory (daily and/or yearly rhtyhms). Some notable exceptions are blood pH (which has to be kept within very narrow range 7.35-7.45) and blood levels of Calcium. If pH or Calcium levels move too far away from the optimal value, cells in the body (most notably nerve cells, muscles and heart cells) cannot function properly and the body is in danger of immediate death.


Audesirk, Audesirk and Byers, Biology, 8th edition., Chapter 31.

Additional Readings:

“Medicine Needs Evolution” by Nesse, Stearns and Omenn (

13.What Creatures Do: Animal Behavior
April 5, 2010, 1:03 pm
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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 integrator (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 swerve 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 integrator. The state can be modified by hormones, hunger, tiredness, libido, general energy levels, etc. The integrator (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).


Audesirk, Audesirk and Byers, Biology, 8th edition., Chapter 25

12.Organisms In Time and Space: Ecology
April 5, 2010, 1:01 pm
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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.


Audesirk, Audesirk and Byers, Biology, 8th edition., Chapters 26, 27, 28 and 29

11. Current Biological Diversity
March 24, 2010, 10:48 am
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In the first two parts of this lecture we tackled the Origin of Life and Biological Diversity and the mechanisms of the Evolution of Biological Diversity. Now, we’ll take a look at what those mechanisms have produced so far – the current state of diversity on our planet.

The Three Domains

The organisms living on Earth today are broadly divided into three large domains: Bacteria, Archaea and Eukarya (Protista, Plants, Fungi and Animals). Our understanding of the relationship between the three domains is undergoing big changes right now. The old divisions have been based on morphological and biochemical differences, but recent genetic data are forcing us to rethink and revise the way we think about the three Domains.


It was thought before that Bacteria arose first, that Archaea evolved from a branch off of bacterial line, while the first Eukarya (protists) evolved through the process of endosymbiosis: small bacteria and archaea finding permanent homes within the cell of larger bacteria and forming organelles. It was thought that bacteria were always simple, that Archaea are somewhet more complex, and that Eukarya are the most complex.

Neither Bacteria nor Archaea possess any organelles or subcellular compartments. The chemistry of cell walls is strikingly different between the two groups. The genes of Archaea, like Eukaryia, have introns. Until recently, it was thought that bacterial genes have no introns, however remnants of bacterial introns have been recently discovered, suggesting that Bacteria used to have introns in the past but have secondarily lost them – becoming simpler over the 3.6 billions of evolution. The enzymes involved in transcription of DNA in Archaea are much more similar to the equivalent enzymes in Eukarya than those in Bacteria.

Molecular data, as well as what we know from evolutionary theory how population size affects the strength of natural selection, a new picture has emerged. The earliest Bacteria were simple, hugging the Left Wall of Complexity. While their population sizes were still small, Bacteria evolved greater and greater complexity, leaving the left wall somewhat, evolving more complex genomes, more complex mechanisms of DNA transcription (including introns), and perhaps even some organelles. Likewise, the Archaea split off of Bacteria (or perhaps they even appeared first) and evolved much greater complexity in parallel with the Bacteria. Eukarya also split off of Bacterial tree early on and evolved its own complexity. Thus there were three groups simultaneously evolving greater and greater complexity.


Then, Bacteria and Archaea grew up in population sizes. Instead of small pockets somewhere in the ocean, now bacteria and archaea occupied every spot on Earth in huge numbers. Large population size makes natural selection very strong. Greater complexity is not fit, thus it is selected against. Thus, the originally complex bacteria and archaea became simpler over time – they turned into lean, mean evolving machines that we see today – the dominant life forms on our planet throughout its history. They lost introns, they lost organelles, and lost many complicated enzymatic pathways, each species reducing its genome and strongly specializing for one particular niche.

On the other hand, Eukarya did not grow in numbers as much. The population sizes remained small, thus the selection against complexity was relaxed – the eukaryotes were free to evolve away from the Left Wall. They increased in complexity, engulfing other microorganisms that later became mitochondria and chloroplasts.

Thus, though we, for egocentric reasons, like to think of greater complexity as being better than being simple, the Big Story of the evolution of life on Earth is that of simplification. Natural selection harshly eliminated organisms that experimented with greater complexity – the Eukarya being the exception: an evolutionary accident that happened due to their existence in small, isolated populations in which selection against complexity is relaxed.



Bacteria are small, single-celled organisms with no internal structures or organelles. Bacteria may have cell walls on the surface of their cell membranes, and may have evolved cilia or flagella for locomotion. The DNA is usually organized in a single circular chromosome. Some bacteria congregate into collonies or chains, while in other species each cell lives on its own.

In the laboratory, bacteria can be easily separated into two major groups by the way their cell walls get stained by a particular stain into Gram positive (purple stain) and Gram negative (red stain) bacteria. By shape, bacteria are divided into cocci (spherical cells), bacilli (rod-like shapes) and spirilli (thread-like or worm-like cells).

Bacteria are capable of sensing their environment and responding to it – i.e., they are capable of exhibiting behavior. Bacteria are also capable of communicating with each other – for instance, they can sense how many of them are present in a particular place and they can all change their behavior once the poulation size reaches a sertain treshold – this kind of sensing is called quorum sensing.

Many bacteria are serious pathogens of plants and animals (including humans). Others are important decomposers of dead plants and animals, thus playing important roles in the ecology of the planet. Yet others are symbionts – living in mutualistic relationships with other organisms, e.g., with plants and animals.

The inside of out digestive tract provides a home for numerous microorganisms. The best way to think about out “intestinal flora” is in terms of an ecosystem. We acquire it at the moment of birth and build it up with the bacteria we get from the environment – mostly from our parents. The bacterial populations in the intestine go through stages of building an ecosystem, similarly to the secondary succession. If, due to disease or due to use of potent antibiotics, the balance of the ecosystem is disrupted, it may recover through phases akin to primary succession.

Experiments with completely internally sterile animals (mostly pigs and rabbits) demonstrated that we rely on our intestinal bacteria for some of our normal functions, e.g., digestion of some food components, including vitamins. In many ways, after millions of years of evolution, our internal bacteria have become an essential part of who we are, and there is now a push for sequencing the complete genome of our becterial flora and to include that information in the Human Genome. The composition of the bacterial ecosystem in out guts can affect the way we respond to disease, or even if we are going to get fat or not, thus there is much recent research on individual variation of the intestinal flora between human individuals, so-called “poo print” (yes, scientists do have a sense of humor).

Deinococcus radiodurans is one famous Bacterium. It thrives inside nuclear reactors. Of course, our reactors are a very recent innovations, so the scientists were puzzled for a long time as to what natural environment selected these organisms to be able to survive in such a harsh environment. It turns out that dehydration (drying-out) has the same effects on the DNA as does radioactivity – fragmenting and tearing-up of pieces of the DNA molecule. Deinococcus evolved especially fast and accurate mechanisms for DNA repair. Bioengineering projects are underway to genetically engineer these Archaea in such a way that they can be used to clean up radioactive spills and digest nuclear waste.


Archaea may have been the first life forms on the Earth. Today, they tend to occupy niches that no other organisms can. Thus, they are found living inside the rocks miles under the surface, they are found in extremely cold and extremely hot environments, in very salty, very acidic and very alkaline envrionments as well. The hot water of the Old Faithful geiser in Yellowstone national park are inhabited by a species of Archaea. They are difficult to study as they die in normal conditions in the laboratory – room temperature, neutral pH etc.

Though some Archaea have been found to live inside our bodies, not a single one has, so far, been indentified as a pathogen. Only very recently (i.e., last few weeks) has it been shown that one archaean does have an effect on our health – not as a pathogen but as an enabler. It can migrate into roots of our teeth and set up colonies there. It then changes the environment in the tooth in such a way that it becomes conducive to the immigration and reproduction of a pathogenic bacterium than can then attack the tooth.


Protists are an artificial group of organisms – every eukaryote that cannot be classified as a plant, a fungus or an animal is placed in this category. Thus, the number of species of protists is very large and the diversity of shapes, sizes and types of metabolism is enormous.

Some protists are microscopic unicellular organisms, like the Silver Slipper (Paramecium), while others are multicellular and quite large (e.g, sea kelp). Some protists, e.g., cellular slime molds, have a single-celled and a multi-celled phase of their life-cycle.


Even some of the unicellular protists can be quite large – an Acetabularia (‘mermaid’s wineglass’, see picture) cell is about 5 cm long, thus perfectly visible to the human eye. Most protists reproduce regularly by asexual processes, e.g., fission or budding, utilizing sexual reproduction (e.g., conjugation, which is gene-swapping) only in times of stress. Some protists are surrounded only by a plasma membrane, while some others form shells of silica (glass) around themselves. Some protists have flagella or cilia, while some others move by pseudopodia (false legs – ameboid movement).

Traditionally, protists have been artificially subdivided into three basic groups according to their metabolism: protists capable of photosynthesis (autotrophs) are called Algae, heterotrophs are called Protozoa, while the absorbers are Fungus-like protists. According to morphology, protists have been divided into about 15 phyla, grouped into six major groups. New molecular techniques are thoroughly changing the taxonomy and systematics of Protista. One group, the Green Algae, has recently been moved out of Protista and into the Kingdom Plantae. Another group, the Choanoflaggelata, has been moved to the Kingdom Animalia as they are most closely related to sponges.

Some protists are parasites that cause human diseases. Most well-known of those are Plasmodium (malaria), various species of Trypanosoma (sleeping sickness, leischmaniasis and Chagas Disease) and Giardia (Hiker’s Diarrhea). Dinoflagellates live on the surface of the ocean and are almost as important for absorption of CO2 and production of O2 as are forests on land.


Plants are terrestrial, multicellular organisms capable of photosynthesis (though some species have secondarily moved back into the aquatic environment or lost the ability to photosynthetize). There are about 300,000 species of plants on Earth today. They are divided into two broad categories: non-vascular and vascular plants. Mosses, liverworths and some other smaller groups are non-vascular plants. All other plants are vascular, meaning that they possess systems of tubes and canals that are used to transports water and nutrients from root to stem and leaves, and from leaves back to the root. Those tubes and canals are called phloem and xylem.

Of the vascular plants, some reproduce by forming spores, while others produce seed. Seedless vascular plants that produce spores are, among others, ferns and horsetails. Seeds are produced by two large groups: Gymnosperms (e.g., conifers) and Angiosperms (flowering plants).

An important evolutionary trend in plants was a gradual reduction of the haploid portion of the life-cycle (gametophyte) and simultaneous rise to dominance of the diploid portion – the sporophyte. In mosses, for instance, almost all of the plant is haploid, except for the diploid spores developing at the very tip of the stem. In flowering plants, e.g., trees, almost all of the plant’s cells are diploid (just like in us), while the flowers contain male and female gametes (pollen and egg).


Fungi can be unicellular (e.g., some yeasts and molds) or multicellular (e.g, mushrooms). Molecular data show that fungi are more closely related to animals than plants. Fungi are heterotrophs that obtain nutrients from the soil by secreting enzymes into the substrate and absorbing the digested materials. They cannot photosynthetize. Fungi are composed of hyphae, which are thin long filaments. A mass of hyphae is called the mycelium which can build large structures like mushrooms. Spores are the means of reproduction and are formed by sexual or asexual processes.

Fungi tend to enter into symbiotic relationships with other organisms. Some of those relationships are parasitic, as in our own fungal diseases. Other relationships are mutualistic, e.g., lychens, mycorrhizae and endophytes. Lichens are a mutualistic association between a fungus and a photosynthesizer, usually a green algae. Mycorrhizae form mutualistic associations between the fungi and plant roots (e.g., alfalfa). Endophytes are plants that have fungi living inside them in intercellular spaces and may provide protection against herbivores by producing toxins.


Animals are multicellular heterotrophs (they do not photosynthetize). They exhibit embryonic development and mostly reproduce sexually. One of the important characteristics of animals is movement. While microorganisms (bacteria, archaea and small protists) can move, large organisms (large protists, plants and fungi) cannot – they are sessile (attached to the substrate). Animals are large organisms that are capable of active movement: swimming, crawling, walking, running, jumping or flying. While some animals are also sessile, at least one phase of their life-cycle (e.g., a larva) is capable of active movement.

Some of the major transitions in the evolution of animals are evolution of tissues, evolution of symmetry (first radial, later bilateral), evolution of pseudocoelom and coelom, the difference between Protostomes and Deuterostomes, and the evolution of segmentation.

There are about 37 phyla of animals. Animals can be divided into two sub-Kingdoms: Parazoans and Eumetazoans. Parazoans are choanoflagellates and sponges. They do not have tissues – their cells are randomly organized. A sponge can be pushed through a sieve and all cells get detached from each other during the process, yet they will reconnect and form an intact sponge afterwards. Sponges move by reorganization of the whole body – cells move over each other (pulling the silicate spicules along) and can move as much as 6mm per day. All other animals are Eumetazoans – their cells are organized within proper tissues.

Parazoans also have no body symmetry. Some phyla of animals (e.g, Cnidaria) have radial symmetry – they are called Radiata. Most phyla of animals – the Bilateria – have bilateral symmetry: the left and the right side of the body are mirror images of each other. In bilaterally symmetrical animals, there is early embryonic determination not juts of up-down axis, but also of front-back axis. Bilateral symmetry gives the animal direction – it moves in one direction, the sensory organs and the mouth tend to be in front, while excretion and reproduction are relegated to the back of the animal.

Early during development, the cells of the spherical embryo (gastrula) organize into layers. Some animals (Diploblasts) have only two layers: ectoderm on the outside and endoderm on the inside. Most animals (Triploblasts) have evolved a third layer in between – the mesoderm. Ectoderm gives rise to the skin and nervous system. Endoderm gives rise to the intestine and lungs, among else. Mesoderm gives rise to muscles and many other internal organs. Usually, Radiata are Diploblasts, while Bilateria are Triploblasts.

In more primitive animals, there is no internal body cavity (e.g., flatworms). In others, a cavity forms during the development between the endoderm and mesoderm – it is called pseudocoelom (e.g., nematodes). In most animals, a proper coelom develops between two layers of mesoderm. Our abdominal and chest cavities are parts of our coelom.

In most phyla of animals, the early embryo divides by spiral cleavage. The blastopore – an opening into the cavity of the blastula- eventually becomes the mouth. These animals are called Protostomes. Protostomes are further divided into two groups: in one group animals grow by adding body mass (e.g., annelids, molluscs and flatworms), while others grow by molting (e.g., nematodes and arthoropods).

In Echinodermata and Chordata, the embryo divides by radial cleavage. The blastopore becomes the anus. These animals are Deuterostomes.

Three large phyla of animals – Annelida, Arthropoda and Chordata evolved segmentation, using Hox genes to drive the development of each segment.

You will HAVE to read the three relevant animal chapters in the textbook to learn more about the following phyla: sponges, cnidarians, annelids, molluscs, arthropods and chordates.


Phylum Chordata is the one we are most interested in for egocentric reasons – because we are chordates. The phylum consists of some invertebrate groups and the Vertebrata (all other animal phyla are also Invertebrata). The invertebrate chordates are hemichordates (acorn worms), tunicates (Urochordata – sea squirts) and cephalochordates (e.g., the lancelet – Amphioxus, see picture). The larvae of invertebrate chordates are very similar to the larvae of echinoderms, both groups are also Deuterostomes, and recent molecular data confirm close relationship between chordates and echinoderms as well.

All chordates have, at least at some point during the development, a notochord. The early chordates were aquatic animals. Hagfish and lampreys are two of the most primitive groups of vertebrates. Before the molecular analysis was performed, these two groups were clumped into a single group of Jawless Fish (Agnatha), but have since been split into two separate classes.

‘Fish’ is the lay term for several different groups of aquatic vertebrates. The most important classes are cartilagenous fish (Chondrichthyes, e.g., sharks, rays and sturgeons), lobe-finned fish (Sarcopterygii, e.g., gars) and ray-finned fish (Actinopterygii – most fish that you can think of). The latter two of those are also sometimes lumped together and called the bony fish (Teleostei). Chrossopterygii, a once-prominent group of lobe-finned fish that survives today with only one living species (Coelacanth, or Latimeria), is the group that gave rise to ancient amphibians – the first vertebrates to invade the land (check out the Tiktaalik website for more information).

Amphibians are frogs, toads, salamanders and cecilians. At least one portion of the life-cycle – reproduction and early development – is dependent on water. They have legs for locomotion and lungs for respiration on land.

Reptilia are a large and diverse class of vertebrates. They include lizards, snakes, tuataras, turtles, tortoises and crocodilians. They have scaly skins that allows them to survive in arid environments. They have evolved an amniotic egg – an egg that contains nutrien-rich yolk and is contained within a leathery shell. Thus, reproduction and development are not dependent on water. Many reptiles live in deserts.

A now-extinct group of ancient reptiles (therapsyds) gave rise to mammals (class Mammalia) about 220 million years ago. The early mammals were quite large carnivores. However, during the 150 million year reign of the Dinosaurs (another extinct group of reptiles) mammals were constrained to a very small niche – that of nocturnal burrowing insectivores. Only after the demise of Dinosaurs (65 million years ago) could mammals embark on a fast evolutionary radiation that produced groups we know now.

Birds and mammals are endotherms – they can control (and keep constant) their body temperature by producing the heat in organs like muscles and liver. This is a metabolically expensive strategy that requires these animals to eat very frequently, but gives them speed and stamina and allows these animals to live in every part of the Earth, incuding polar regions. Other vertebrate classes are ectotherms – they gain their heat from the environment and, if they are cold, they are slow and sluggish.

As it is very difficult for large bodies to lose heat, large reptiles (like dinosaurs), once heated, can retain their body temperature for long periods of time – they are effectively warm-blooded. Some reptiles, notably pythons and iguanas, are capable of producing some of the heat internally. While they cannot keep a constant body temperature, they are capable of some degree of thermoregulation (e.g., becoming somewhat warmer than the external environment). By shivering their muscles, pythons raise their body temperature above ambient and use this heat to incubate their eggs.

There are about 4500 species of mammals, organized into 19 orders. The defining characteristics of mammals are milk ­producing glands and hair.

Monotremes (platypus and echidna) are egg-laying mammals. Their mammary glands are not completely evolved yet – the young lick the milk of off mothers hair.

Marsupials are the pouched mammals (e.g., kangaroo, koala, opossum). The immature newborn offspring crawls up into the pouch and lives inside it until they are large enough to fend for themselves.

Placental mammals (the remaining 17 orders) have a placenta that nourishes their embryos during development. The new molecular data, coupled with a number of exciting newly-discovered fossils, are changing our understanding of genealogical relationships between different orders of mammals, including our new knowledge about the evolution of whales, the relationship between elephants and hyraxes, between Carnivores and Pinnipedieans (seals, etc.) and between rodents and rabbits.

The most recent vertebrate class – the birds (Aves) – evolved out of a branch of Dinosaurs. There are 28 orders of bird in 166 families. Two primary characteristics distinguish birds from reptiles: feathers and flight skeleton. Their feathers are modified reptile scales. Feathers are obviously important for flight, but also insulate as birds are endotherms.


Audesirk, Audesirk and Byers, Biology, 8th edition., Chapters 19, 20, 21, 22, 23 and 24.

Additional Readings:

New ideas about early evolution of life

10. Evolution of Biological Diversity
March 24, 2010, 10:39 am
Filed under: Uncategorized

In the previous segment of the lecture, we looked at the Origin of Life and the beginnings of the evolution of biological diversity. Now we move to explanations of the mechanisms by which diversity arises.

Although traits can be inherited by non-DNA ways, and DNA sequence does not neccessarily translate directly onto the traits, in the long term the differences between species tend to be recorded in the genome. Thus, differences between genomes of different species are most important differences between them. How do differences between genomes arise? There are six major (and some minor) ways this happens:

Mutations are small changes in the sequences of DNA. Some of the changes are just substitutions of one nucleotide with another, others are deletions, insertions and duplications of single nucleotides or small strings of nucleotides within a gene, or within a non-coding regulatory sequence. Such small changes may alter the function of the gene-product (protein) which may translate into changes in traits which may be selected for by natural or sexual selection.

Gene duplication occurs quite often due to errors in DNA replication during cell division, or due to errors in ‘crossing-over’ phase of meiosis. Instead of a single copy of a gene, the offspring have two copies of that same gene. As long as one copy remains unaltered and functions properly, the other gene is free to mutate (i.e., there will stabilizing selection on the first copy, and no selection for the preservation of the sequence of the second copy). The second gene may transiently become non-functional, but as it keep mutating it may beging coding for a completely novel protein which will start interacting with other molecules in the cell. If this new interaction confers increased fitness on the organism, this new gene sequence will become selected for and fine-tuned by natural (or sexual) selection for its new function.

Chromosome duplication may also occur due to errors in DNA replication during cell division. Instead of just one gene being duplicated, a large number of genes now exist in two copies, each pair of copies consisting of one copy that is preserved by stabilizing selection and another copy that is free to mutate and thus potentially evolve novel traits.

Genome duplication has occured many times, especially in plants. The whole genome doubles, i.e., all of the chromosomes are duplicated. The resulting state is called polyploidy. This provides a very large amount of genetic material for natural selection to tinker with and, over time, produce novel traits.

Rearrangement of segments of the DNA along the same chromosome, or between chromosomes, places different genes that were once far from each other into closer proximity. Thus, genes that were previously quite independent from each other may now be expressed together or may start influencing each other’s expression. Thus, the genes become linked together (or unlinked from each other), restructuring the batteries of genes that work together in a common function. This may free some genes to evolve independently, while tying some genes together and thus constraining the direction in which development of traits may evolve.

Lateral transfer (sometimes called ‘horizontal transfer’) is an exchange of DNA sequences between individuals of the same species or of different species. While vertical transfer moves genes from parents to offspring, lateral transfer moves genes between unrelated individuals. Such transfer is very common in microorganisms. Some species of Bacteria, Archaea and Protista routinely engage in gene swapping, which results in increase of genetic diversity of the species and thus provides raw material for evolution to build new traits. Gene swapping between organisms of different species may transfer a complete function from one species to another. Sometimes viruses act as carriers of genes from one species to another. For instance, a virus may take a piece of a bacterial genome and later insert it into a genome of a plant or a mammal. Some key genes involved in the development of the placenta originated as bacterial genes inserted into early mammalian genomes via viruses.

One important thing to bear in mind is that evolution has to ensure the survival of the individual at all stages of its life-cycle, not just the adult. Thus, evolution of new traits can occur only if it does not disrupt the viability of eggs, larvae, immature adults and mature adults.

Another important thing to keep in mind is that traits arise through embryonic and post-embryonic development. Thus, evolution of traits is really evolution of development. Evolution of genomes, thus, is not evolution of random grab-bags of many genes, but evolution of complexes of genes involved in development of particular traits.

A product of a gene is a protein. A protein that is capable of binding to DNA and thus regulating the expression of other genes is called a transcription factor. When bound to a gene, a transcription factor may induce its expression, block its expression, or increase or decrease the rate of its expression. The patterns of gene expression are key to embryonic development and cell differentiation, so it is not surprising that transcription factors play a large role in evolution of new traits via development.

A novel pattern of gene expression may arise in two ways. First, by mutation of a transcription factor (so-called trans-factors), it changes which genes it affects and the way it affects them. Second, by mutations in regulatory regions (so-called cis-factors) of the target genes, the transcription factors may or may not bind to them, or a different transcription factor may bind to them, or the effect of the binding on transcription of the gene may change.

Most important genes in evolution of development are transcription factors. Often, they work in batteries (or complexes or toolkits), where one gene induces transcription of the second gene which in turn induces transcription of the third gene, and so on. Such batteries tend to be strongly preserved in many species of living organisms, though the genes that act as final targets of action of such complexes differ between species. Such complexes may determine what is up and what is down in an early embryo, or what is forward and what is bakward in an embryo. Such complexes are used over and over in evolution to produce protruding structures, like limbs. Another such complex has been used in 40 different groups of animals for the construction of 40 quite different types of eyes.

Possibly the most important such complex in animals is the complex of Hox genes that regulates segmentation. Most animals are segmented. While this is obvious in earthworms where all segments look alike, in many other animals segments are formed in the early embryo and each segment then develops unique structures on it. Thus, an insect will develop jaws and antennae on its head segment, wings and legs on its thoracic segment, and reproductive structures and stings on its abdominal segment. You will need to carefully read the handout “A Brief Overview of Hox Genes” ( and be able to define Homeotic genes, Homeobox (DNA sequence), Homeodomain (protein structure) and Hox genes. Interestingly, non-segmented Cnidarians (corals and jellyfish) do not have true Hox genes, though they do have scatterings of Hox-like genes, which may be evolutionary precusors of true Hox genes.

Thus, evolution of diversity can be thought of in terms of changes in the way developmental toolkits are applied in each species. The same toolkits are used over and over for development of similar traits. The sequences of the genes within the toolkits will vary somewhat between species, and the sequences of genes that are final targets of action of toolkits will vary much more.

Thus, with quite a limited number of genetic toolkits, nature can develop a myriad different forms, from cabbages and sponges to honeybees and humans. This also explains why we do not need more than 30,000 genes to develop a human, as well as why our genome is about 99% identital to the chimpanzee genome. It is not the sequence of genes, but the combinatorics of the way the genes are turned on and off during the development that results in the final phenotype.

The common theme, then, is that evolution keeps tinkering with the same genetic toolkits over and over again. It is not neccessary to evolve thousands of completely new genes in order to have a new species spring up out of its ancestral species. A little tweak in developmental patterns of gene expression is all that is needed. The same genes may be expressed at a different place in the embryo in two different species (heterotopy), or may be expressed at a different time during development (heterochrony), or may result in expression of other final-target genes (heterotypy). Such changes account for most of the evolution of diversity of life on Earth.

Of course, such changes take a long time. It took about 3.6 billion years for life to evolve from the first primitive bacteria-like cells to the current diversity of millions of species of Bacteria, Archaea, Protista, Fungi, Plants and Animals. Our brains have never before needed to be able to comprehend such vastness of time. We do qute well with durations of seconds, minutes, hours and days. We are pretty good at mentally picturing the duration of weeks, months and years. A decade is probably the longest duration of time that our brains can correctly imagine. Already our perception of a century is distorted. Perception of a thousand years is impossible for human brains. Now try to imagine how long 10,000 years is? Any luck? Now try 100,000. How about 1.000,000 years? Add another zero and try comprehending 10.000,000 years. Multiply by ten again and try 100.000,000 years. Now try 1,000.000,000 years. Now try four times more – 4 billion years.

It is not surprising that some people, unable to comprehend 4 billion years, just plainly refuse to acknowledge that this amount of time actually passed and stick to a shorter, emotionally more pleasing yet incorrect number of about 6,000 years for the age of the Universe. Such people, of course, cannot believe that evolution actually happened, although mountains of evidence show us not just that it happened, but exactly how it happened. You can see exactly what happened when if you take your time and do this animation. You’ll notice how the whole of human history is too short to be visible on a line representing billions of years. Given such enormous amount of time, the evolution of amazing diversity of life is not surprising. Actually, if such diversity did not arise – that would be a surprise.


Audesirk, Audesirk and Byers, Biology, 8th edition., Chapter 18

Watch Animation:



A Brief Overview of Hox Genes
Bat Development
How To Make A Bat

Additional Readings:

Jellyfish Lack True Hox Genes