Why are human wastes yellow?

Why are human wastes yellow?

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Except for the feces, which is more brownish, all the human wastes (urine, earwax, snivel, phlegm, and rheum) are usually yellowish. Why is that? I heard that urine is yellow due to bilirubin(?). What about others?

Why are human wastes yellow? - Biology

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    Welcome to Ask A Biologist. This site has a large collection of biology learning materials that includes stories, games, activities, videos, and a podcast.

    Laboratory Waste Disposal Responsibilities

    Laboratory Personnel

    Laboratory personnel are responsible for managing their activities to eliminate or minimize hazards and to provide a safe working environment for anyone who has a need to enter their laboratory. It is important for laboratory personnel to recognize that other personnel will not be familiar with laboratory activities and may not understand what is being disposed.

    Laboratory personnel must keep floors free of obstructions and hazards to allow Building Services personnel to service the laboratory and clean the floors. Building Services personnel will not pick up sharps from the floor, such as broken glass, glass pipets, plastic pipet tips, glass capillary tubes, razor blades and other related sharps.

    All spills and hazardous materials must be cleaned up by laboratory personnel or, if necessary, with assistance from Environmental Health and Safety personnel. Floors, working surfaces, and equipment must be free of any hazardous residues.

    Building Services Personnel

    Building Services personnel should review the activities and waste practices of each laboratory with laboratory personnel to ensure that everyone understands where and what hazards are present, what services will be provided, and where the wastes are located. Building Services personnel should wear, at a minimum, safety glasses and gloves when working in a laboratory. If you notice a hazardous situation (e.g., spill on floor, hazardous materials in the municipal waste, sharps not properly packaged, etc.) contact your supervisor. The supervisor should discuss the situation with laboratory personnel or leave a discrepancy notice.

    EHS Personnel

    Environmental Health and Safety personnel develop procedures for disposing of wastes that may be hazardous. EHS personnel provide timely removal of hazardous and radioactive waste and provide assistance for the clean-up of hazardous spills, if necessary.

    Laboratory Waste Disposal Procedure Summary

    Make sure the materials placed in the municipal waste are suitable for this type of disposal, especially:

    • Do not place any liquids in the municipal waste.
    • Do not dispose of chemical waste, including stock containers with unused product, in the municipal waste.
    • Empty or rinsed containers must be free of any hazardous residue and be marked "empty."
    • All sharps must be in an appropriate, puncture-resistant container to prevent injuries.
    • If a material can be mistaken as a hazardous, radioactive, or biological waste, but is not, it must be identified as non-hazardous.

    Building Services will dispose of glass if it is cleaned of any hazardous materials and is properly packaged. The total weight must not exceed 40 pounds and the container must be able to be easily and safely handled by Building Services personnel.

    For all other types of waste, make sure the container is appropriately labeled and separated from municipal waste:

    Hazardous waste - manage hazardous wastes in accordance with the Hazardous Materials Management and Disposal Policy and Procedures manual. This type of waste may only be removed by Environmental Health and Safety personnel.

    Radioactive waste - manage radioactive wastes in accordance with the Radiation Safety Manual. This type of waste may only be removed by Environmental Health and Safety personnel.

    Biological waste - manage biological wastes in accordance with the Biohazardous Waste and Sharps Disposal policy.

    Sharps - At U of I a "sharp" is defined as any object which could readily puncture or cut the skin of an individual, including, but not limited to:

    • Needles, syringes, knives, razor blades, lancets, capillary tubes, metal shavings, etc.
    • Glass or plastic pipettes and pipette tips
    • Any broken glass, glass slides, cover slips, plastic, metal, pottery with sharp edges, etc.
    • Anything that could puncture through a garbage bag causing the bag to rupture and spill, or risking injury and exposure to personnel.

    Refer to EHS Guidance Document "Sharps and Pipette Tips Disposal" and the "Sharps Disposal Flow Chart" for more information.

    Other Forms of Waste

    “Pack it in, Pack it out” is a familiar mantra to seasoned wildland visitors. Any user of recreation lands has a responsibility to clean up before he or she leaves. Inspect your campsite and rest areas for trash or spilled foods. Pack out all trash and garbage.

    Plan meals to avoid generating messy, smelly garbage. It is critical to wildlife that we pack out kitchen waste, such as bacon grease and leftovers. Don’t count on a fire to dispose of it. Garbage that is half-burned or buried will still attract animals and make a site unattractive to other visitors.

    Overlooked trash is litter, and litter is not only ugly—it can also be deadly. Plastic bags, cigarette butts, fishing line and other trash can be harmful to our environment when not properly disposed of.

    Carry plastic bags to haul your trash (and maybe someone else’s). Before moving on from a camp or resting place, search the area for micro-trash such as bits of food and trash, including organic litter like orange peels or pistachio shells. Invite the kids in your group to make a game out of scavenging for human sign.


    To wash yourself or your dishes, carry water 200 feet away from streams or lakes. Scatter strained dishwater. Hand sanitizers that don’t require rinsing allow you to wash your hands without worrying about wastewater disposal.

    For dishwashing, use a clean pot or other container to collect water, and take it to a wash site at least 200 feet away from water sources. This lessens trampling of lakeshores, riverbanks and springs, and helps keep soap and other pollutants out of the water. Use hot water, elbow grease, and soap if absolutely necessary. Strain dirty dishwater with a fine mesh strainer before scattering it broadly. Do this well away from camp, especially if bears are a concern. Pack out the contents of the strainer in a plastic bag along with any uneaten leftovers.

    In developed campgrounds, food scraps, mud and odors can accumulate where wastewater is discarded. Contact your campground host for the best disposal practices and other ways to Leave No Trace at your campsite.

    Soaps and Lotions

    Soap, even when it’s biodegradable, can affect the water quality of lakes and streams, so minimize its use. Always wash yourself well away from shorelines (200 feet), and rinse with water carried in a pot or jug. This allows the soil to act as a filter. Where fresh water is scarce, think twice before swimming in creeks or potholes. Lotion, sunscreen, insect repellent and body oils can contaminate these vital water sources.

    Burning Trash Bad for Humans and Global Warming

    When atmospheric scientist Christine Wiedinmyer first went to Ghana in 2011 to investigate air pollution produced by burning different materials &mdash from crop stubble to coal used in stoves &mdash she noticed an unexpected potential source: burning piles of trash.

    Like most residents of developed nations who hadn&rsquot traveled broadly in the developing world, the sight of smoldering rubbish piles, which contain anything from food waste to plastics to electronics, came as a surprise to Wiedinmyer, who works at the National Center for Atmospheric Research in Boulder, Colo.

    &ldquoIt&rsquos just not something that I&rsquove been exposed to,&rdquo she told Climate Central. In the U.S., &ldquowe have waste management. We have people who pick up trash and take it away.&rdquo

    Ghana, Nepal, Mexico and other developing countries often lack the tax bases and infrastructure needed to put such systems into place. So residents and governments often burn piles of their trash in the open removing the garbage from the land but transferring it to the skies. Some 40 percent of the world&rsquos waste may be dealt with in this way.

    Wiedinmyer wondered if this burning waste could be an underappreciated source of air pollutants, from greenhouse gases like carbon dioxide to tiny particles and toxic chemicals that can harm human lungs.

    &ldquoI was curious to see how big that source was,&rdquo she said.

    Wiedinmyer set out to produce the first global estimates of burn-related pollution. The result, detailed in July in the journal Environmental Science & Technology, suggests that burning trash isn&rsquot just bad for human health -- it could pump more greenhouse gases into the atmosphere than had been realized.

    &lsquoFirst Best Guess&rsquo
    Wiedinmyer pored through existing data and inventories and consulted one of the few people already investigating the phenomenon, Bob Yokelson, an atmospheric chemist at the University of Montana in Missoula, who had traveled widely to developing areas and was familiar with the trash burning around homes and villages.

    &ldquoIf you do research or travel in developing worlds, you do see garbage burning in a lot of places,&rdquo he told Climate Central. Working in Indonesia in the 1990s, he said, there was an old man who would come around and gather everyone&rsquos trash, then burn it at the end of the street.

    Yokelson, who is another author of the recent paper, had made some measurements in Mexico of what sort of pollutants were being emitted by trash burning. The U.S. Environmental Protection Agency has catalogued emissions from trash burning in the rural areas of the U.S. But Wiedinmyer found that, on a global scale, &ldquothere wasn&rsquot kind of a consistent story.&rdquo

    To find that story took a lot of digging around and some educated guesswork. Along with data from the few studies like Yokelson&rsquos, Wiedinmyer used guidelines for calculating trash burning emissions produced by the Intergovernmental Panel on Climate Change to determine how much waste was being generated and burned, what exactly was in that waste, and what types of chemicals were likely generated. What she came up with was, as the study describes it, &ldquothe first comprehensive and consistent estimates of the global emissions of greenhouse gases, particulate matter, reactive trace gases, and toxic compounds from open waste burning.&rdquo

    Or, as Wiedinmyer puts it, &ldquoit was my first best guess.&rdquo

    What&rsquos in the Emissions
    What she found was that some 1.1 billion tons of waste, more than 40 percent of the world&rsquos garbage, is burned in open piles, contributing more emissions than is shown in regional and global inventories.

    An estimated 40 to 50 percent of the garbage is made up of carbon by mass, which means that carbon dioxide is the major gas emitted by trash burning. Those emissions are dwarfed by others sources on the global scale, such as cars and power plants, amounting to just 5 percent of total global carbon dioxide emissions. But the carbon dioxide that comes from trash burning can be a significant source in some countries and regions, and it is one not reflected in the official greenhouse gas inventories for those places.

    The more interesting and concerning story to Wiedinmyer are the other pollutants, which accounted for far bigger percentages of global emissions. For example, as much as 29 percent of global anthropogenic emissions of small particulate matter (tiny solid particles and liquid droplets from dust to metals that can penetrate deep into the lungs) come from trash fires, she estimates. About 10 percent of mercury emissions come from open burning, as well as 40 percent of polycyclic aromatic hydrocarbons (PAHs). Such pollution can cause lung and neurological diseases, and have been linked to heart attacks and some cancers.

    &ldquoI was really surprised at the magnitude&rdquo of some of these pollutants coming from trash burning, Wiedinmyer said.

    Just a Starting Point
    Of course, the work is just a starting point, Wiedinmyer and Yokelson said. It shows that the problem of pollution from trash burning is big enough that it warrants further study to try and narrow down the large uncertainties inherent in the study&rsquos estimates.

    &ldquoCan we do better? Can we do more to constrain it?&rdquo Wiedinmyer said.

    More measurements of the kind Yokelson has made are among the biggest holes needed to be filled to get more fine-tuned numbers.

    So, too, is a better understanding of what&rsquos in the trash in different regions, since emissions from organic matter like food are very different than those from plastics. &ldquoThat&rsquos one of the big unknowns,&rdquo Wiedinmyer said. &ldquoWhat&rsquos in the trash?&rdquoWiedinmyer also wants to put her estimates into models of climate and air movement and see if they match up with current air observations. She wants to figure out which populations the pollution might be affecting, and where it is interacting with other pollution sources.

    Overall, it&rsquos an issue &ldquothat I think should get more attention,&rdquo Wiedinmyer said.

    Eri Saikawa, who studies air pollution and its health impacts at Emory University, and wasn&rsquot involved in the new study, plans to use Wiedinmyer&rsquos data in a model to see how it matches observations in China and Southeast Asia, and to see how trash burning might be contributing to the substantial amounts of air pollution there.

    &ldquoWhat they&rsquore interested in is where they can reduce emissions,&rdquo Saikawa said of policymakers she has met with in China. Currently the focus has been on power plants and cars &mdash trash burning hasn&rsquot been part of the conversation.

    Reducing emissions from trash burning isn&rsquot an easy prospect in many areas, though. In Nepal, where Yokelson plans to do further work this year and next, the government is well aware of the problem, but it can&rsquot afford the kind of highly efficient incinerators that would get rid of much of the emissions from trash.

    &ldquoIt&rsquos expensive to get rid of garbage cleanly,&rdquo Yokelson said.

    And it&rsquos not clear how much of an effect reducing this source of pollution would have in different areas.

    But, &ldquoyou need to make a small step to make a big step,&rdquo Saikawa said. &ldquoThis kind of study is very important to figure out what needs&rdquo to be done.

    This article is reproduced with permission from Climate Central. The article was first published on September 2, 2014.


    Andrea Thompson, an associate editor at Scientific American, covers sustainability.

    Biology of the Mouth

    The mouth is the entrance to both the digestive and the respiratory systems. The inside of the mouth is lined with mucous membranes. When healthy, the lining of the mouth (oral mucosa) is reddish pink. The gums (gingivae) are paler pink and fit snugly around the teeth.

    The palate, which is the roof of the mouth, is divided into two parts. The front part has ridges and is hard (hard palate). The back part is relatively smooth and soft (soft palate).

    The moist mucous membranes lining the mouth continue outside, forming the pink and shiny portion of the lips, which meets the skin of the face at the vermilion border. The lip mucosa, although moistened by saliva, is prone to drying.

    The uvula is a narrow muscular structure that hangs at the back of the mouth and can be seen when a person says "Ahh." The uvula hangs from the back of the soft palate, which separates the back of the nose from the back of the mouth. Normally, the uvula hangs vertically.

    The tongue lies on the floor of the mouth and is used to taste and mix food. The tongue is not normally smooth. It is covered with tiny projections (papillae) that contain taste buds, some of which sense the taste of food.

    The sense of taste is relatively simple, distinguishing sweet, sour, salty, bitter, and savory (also called umami, the taste of the flavoring agent monosodium glutamate). These tastes can be detected all over the tongue, but certain areas are more sensitive for each taste. Sweet detectors are located at the tip of the tongue. Salt detectors are located at the front sides of the tongue. Sour detectors are located along the sides of the tongue. Bitter detectors are located on the back one third of the tongue.

    Smell is sensed by olfactory receptors high in the nose. The sense of smell is much more complex than that of taste, distinguishing many subtle variations. The senses of taste and smell work together to enable people to recognize and appreciate flavors (see Overview of Smell and Taste Disorders).

    A View of the Mouth

    The salivary glands produce saliva. There are three major pairs of salivary glands: parotid, submandibular, and sublingual. Besides the major salivary glands, many tiny salivary glands are distributed throughout the mouth. Saliva passes from the glands into the mouth through small tubes (ducts).

    Saliva serves several purposes. Saliva aids in chewing and eating by gathering food into lumps so that food can slide out of the mouth and down the esophagus and by dissolving foods so that they can more easily be tasted. Saliva also coats food particles with digestive enzymes and begins digestion. After food is eaten, the flow of saliva washes away bacteria that can cause tooth decay (cavities) and other disorders. Saliva helps keep the lining of the mouth healthy and prevents loss of minerals from teeth. It not only neutralizes acids produced by bacteria but also contains many substances (such as antibodies and enzymes) that kill bacteria, yeasts, and viruses.

    How Do We Breathe?

    We breathe a lot&mdashroughly 10 times a minute! Have you ever wondered how the process of breathing works so smoothly? Our lungs allow us to inhale the oxygen our body needs, but they do much, much more. They also allow us to get rid of carbon dioxide, the waste product created in the body, and they play a vital role in singing, shouting and even giggling. In this activity you will make a model of a lung and use it to discover how air flows in and out of the lungs with ease.

    All cells in our body need oxygen to create energy efficiently. When the cells create energy, however, they make carbon dioxide. We get oxygen by breathing in fresh air, and we remove carbon dioxide from the body by breathing out stale air. But how does the breathing mechanism work?

    Air flows in via our mouth or nose. The air then follows the windpipe, which splits first into two bronchi: one for each lung. The bronchi then split into smaller and smaller tubes that have tiny air sacs at their end called alveoli. We have millions of alveoli in our lungs! These sacs have thin walls&mdashso thin that oxygen and carbon dioxide can pass through them and enter or leave our blood. The blood transports oxygen to almost every part of the body. The blood also gives the carbon dioxide a ride back to the lungs.

    Lungs take up most of the space in the chest. The 12 pairs of ribs in our ribcage protect the lungs and other organs in our chest cavity, such as our heart.

    Relaxed breathing is a reflex we do not have to think to breathe. During this unforced inhalation our diaphragm&mdashthe dome-shaped muscle between the chest and the abdominal cavity&mdashflattens. This expands the chest cavity and as a result air is drawn in. During exhalation the diaphragm relaxes and the lungs naturally recoil, and air is gently pushed out.

    We can also breathe more forcefully. When we exercise, sing loudly or otherwise need or want more air or oxygen we can exert force to breathe more deeply. We use various muscles to increase chest volume more dramatically. In the same way as in relaxed breathing the expansion of the chest cavity draws air in so the lungs fill up. The relaxation of the chest cavity pushes air out. Muscles can also force the chest cavity to contract even further, pushing even more air out. Because the expansions and contractions are larger in this case a bigger volume of air flows in and out of our lungs, and our body gets a larger supply of oxygen or we have more air to create sound.

    • Disposable empty transparent bottle (10&ndash16 fluid ounces) made of hard plastic (such as a sports drink bottle)
    • Ruler
    • Two balloons (8-inch balloons work well)
    • Utility knife (have an adult help and use caution when using the knife)
    • Adult helper
    • Scissors
    • Drinking straw (optional)
    • Modeling clay (optional)
    • Tape (optional)
    • Additional balloon (optional)


    • Ask an adult to cut the plastic bottle. Cut off the bottle's bottom so that when a balloon hangs inside the bottle from the spout there is about 1/3 to 3/4 of an inch of empty space below the balloon.
    • Place the cut bottle down on the wide opening. Lower a balloon into the bottle until only part of the balloon's neck sticks out. Fold the neck of the balloon over the top of the bottle. The balloon represents a lung.
    • Turn the bottle over (keeping the balloon inside) so the bottle top rests on the table. In the next steps you will create and add the diaphragm to your model.
    • Make a knot in the neck of the second balloon. At the opposite side of this balloon cut off about a third of the balloon so you are left with a wide opening.
    • Stretch the wide opening of the cut balloon over the wide opening of the bottle. Pull the edges of the balloon far enough up the bottle so the balloon surface is gently stretched. Make sure that the knot is on the outside and located near the middle of the bottle opening.
    • Like an inflated balloon our lungs are full of air. We have two lungs, which are enclosed in the ribcage and protected by 24 ribs. When you breathe in, air flows into your lungs. When you breathe out, air flows out of your lungs. The balloon inside the bottle is like one of your lungs. The bottle is like your ribcage.
    • Hold the bottle so you can see the balloon inside (representing the lung). Gently pull down on the knot. What happens to the balloon inside the bottle?
    • Let the knot come back to its neutral position and then gently push it in. What happens to the balloon inside the bottle now?
    • Repeat these steps a few times. Does this resemble breathing? Why?
    • Which part resembles breathing in and which part resembles breathing out?
    • If your model is working well, air will rush into the balloon when you pull the knot outward and flow out when you push the knot inward. Why do you think this happens?
    • When we breathe in a relaxed way our diaphragm&mdashthe muscle that separates the chest cavity from the abdominal cavity&mdashmoves to expand and contract the chest cavity. How is that similar to what you do with your model?
    • Push and pull the knot a few more times. Using the model can you find which movement of the diaphragmcreates inhalation and which creates exhalation?
    • Feel your ribs and breathe in deeply then exhale. Can you feel your ribcage expand and fall back?
    • The center of our diaphragm moves more when we take deep breaths: up to four inches! In the model you made, the ribcage (the plastic bottle) is fixed, but you can move the "diaphragm" more by pulling the knot farther and pushing it in more. Try it out. How does that change the volume of air that flows in and out of the lung balloon?
    • Extra: Add a windpipe to your model. To do this take the balloon out of the bottle and slip its neck over a straw secure the balloon to the straw with tape. Hang the balloon&mdashand a short section of the straw&mdashin the bottle's neck, and use clay to hold it in place. Make sure the clay makes an airtight seal around the straw and the bottle neck. No change is needed to the second balloon that closes off the bottom of the bottle. Can you see which part models the windpipe?
    • Extra: A cough is the body forcefully expelling air to get rid of something that caused irritation. During a cough you breathe in relatively deeply but instead of air flowing out while the chest cavity contracts, your throat closes, and air builds up in the lungs. When the throat opens the chest contracts even more and air flows out in a forceful way. Can you mimic a cough with your model?
    • Extra: Find a way to create a model that includes a windpipe that splits into two bronchi, each with a lung attached. The model with a windpipe and one lung is a good start. How can you add a second lung? Can you find a reason why having two lungs is beneficial for us?

    Observations and Results
    When you pulled the knot back, the space inside the bottle increased and your balloon probably filled up with air. In the same way, when the diaphragm in our body pulls back, the chest cavity increases and air flows into our lungs, and we inhale.

    When you pushed the knot in, the space inside the bottle decreased, and the balloon probably deflated. In the same way, when the diaphragm relaxes the chest cavity decreases, and air is pushed out of the lungs, and we exhale.

    When you pulled and pushed the knot further the balloon inflated and deflated more. This mirrors what happens when a bigger volume of air is displaced when we breathe more deeply.

    This dynamic works because of air pressure, a measure of how hard air presses against objects. Air pressure increases when you decrease the amount of space the air has&mdashand decreases when you give air more space. Close a flimsy empty plastic bottle and try to compress it. It is difficult! The air inside pushes back. Open the bottle, and try to compress the bottle again. It is much easier. The air presses back with a much reduced force. Unless something blocks the movement, air will move from areas of high pressure to areas where the pressure is lower, and this is what happens when air rushes in or out of the lungs. When the chest cavity expands there is more space around your lungs. In this condition the lungs can expand, making it a low-pressure area, and air rushes in to balance out the difference in pressure. Then to breathe out the chest cavity and lungs shrink. This raises the air pressure in your lungs, and the air rushes back out.

    This activity brought to you in partnership with Science Buddies

    Liver Anatomy

    The liver is a reddish-brown organ that is located below the diaphragm and superior to other abdominal cavity organs such as the stomach, kidneys, gallbladder, and intestines. The most prominent feature of the liver is its larger right lobe and smaller left lobe. These two main lobes are separated by a band of connective tissue. Each liver lobe is internally composed of thousands of smaller units called lobules. Lobules are small liver segments containing arteries, veins, sinusoids, bile ducts, and liver cells.

    Liver tissue is composed of two main types of cells. Hepatocytes are the most numerous type of liver cells. These epithelial cells are responsible for most of the functions performed by the liver. Kupffer cells are immune cells that are also found in the liver. They are thought to be a type of macrophage that rids the body of pathogens and old red blood cells.

    The liver also contains numerous bile ducts, which drain bile produced by the liver into larger hepatic ducts. These ducts join to form the common hepatic duct. The cystic duct extending from the gallbladder joins the common hepatic duct to form the common bile duct. Bile from the liver and gallbladder drain into the common bile duct and are delivered to the upper portion of the small intestines (duodenum). Bile is a dark greenish or yellow fluid produced by the liver and stored in the gallbladder. It aids in the digestion of fats and helps eliminate toxic wastes.

    The history of biological warfare

    During the past century, more than 500 million people died of infectious diseases. Several tens of thousands of these deaths were due to the deliberate release of pathogens or toxins, mostly by the Japanese during their attacks on China during the Second World War. Two international treaties outlawed biological weapons in 1925 and 1972, but they have largely failed to stop countries from conducting offensive weapons research and large-scale production of biological weapons. And as our knowledge of the biology of disease-causing agents—viruses, bacteria and toxins—increases, it is legitimate to fear that modified pathogens could constitute devastating agents for biological warfare. To put these future threats into perspective, I discuss in this article the history of biological warfare and terrorism.

    During the [Second World War], the Japanese army poisoned more than 1,000 water wells in Chinese villages to study cholera and typhus outbreaks

    Man has used poisons for assassination purposes ever since the dawn of civilization, not only against individual enemies but also occasionally against armies ( Table 1 ). However, the foundation of microbiology by Louis Pasteur and Robert Koch offered new prospects for those interested in biological weapons because it allowed agents to be chosen and designed on a rational basis. These dangers were soon recognized, and resulted in two international declarations—in 1874 in Brussels and in 1899 in The Hague—that prohibited the use of poisoned weapons. However, although these, as well as later treaties, were all made in good faith, they contained no means of control, and so failed to prevent interested parties from developing and using biological weapons. The German army was the first to use weapons of mass destruction, both biological and chemical, during the First World War, although their attacks with biological weapons were on a rather small scale and were not particularly successful: covert operations using both anthrax and glanders ( Table 2 ) attempted to infect animals directly or to contaminate animal feed in several of their enemy countries (Wheelis, 1999). After the war, with no lasting peace established, as well as false and alarming intelligence reports, various European countries instigated their own biological warfare programmes, long before the onset of the Second World War (Geissler & Moon, 1999).

    Table 1

    1155Emperor Barbarossa poisons water wells with human bodies, Tortona, Italy
    1346Mongols catapult bodies of plague victims over the city walls of Caffa, Crimean Peninsula
    1495Spanish mix wine with blood of leprosy patients to sell to their French foes, Naples, Italy
    1650Polish fire saliva from rabid dogs towards their enemies
    1675First deal between German and French forces not to use 'poison bullets'
    1763British distribute blankets from smallpox patients to native Americans
    1797Napoleon floods the plains around Mantua, Italy, to enhance the spread of malaria
    1863Confederates sell clothing from yellow fever and smallpox patients to Union troops, USA

    It is not clear whether any of these attacks caused the spread of disease. In Caffa, the plague might have spread naturally because of the unhygienic conditions in the beleaguered city. Similarly, the smallpox epidemic among Indians could have been caused by contact with settlers. In addition, yellow fever is spread only by infected mosquitoes. During their conquest of South America, the Spanish might also have used smallpox as a weapon. Nevertheless, the unintentional spread of diseases among native Americans killed about 90% of the pre-columbian population (McNeill, 1976).

    Table 2

    DiseasePathogenAbused 1
    Category A (major public health hazards)  
    AnthraxBacillus antracis (B)First World War
      Second World War
      Soviet Union, 1979
      Japan, 1995
      USA, 2001
    BotulismClostridium botulinum (T)
    Haemorrhagic feverMarburg virus (V)Soviet bioweapons programme
     Ebola virus (V)
     Arenaviruses (V)
    PlagueYersinia pestis (B)Fourteenth-century Europe
      Second World War
    SmallpoxVariola major (V)Eighteenth-century N. America
    TularemiaFrancisella tularensis (B)Second World War
    Category B (public health hazards)  
    BrucellosisBrucella (B)
    CholeraVibrio cholerae (B)Second World War
    EncephalitisAlphaviruses (V)Second World War
    Food poisoningSalmonella, Shigella (B)Second World War
      USA, 1990s
    GlandersBurkholderia mallei (B)First World War
      Second World War
    PsittacosisChlamydia psittaci (B)
    Q feverCoxiella burnetti (B)
    TyphusRickettsia prowazekii (B)Second World War
    Various toxic syndromesVarious bacteriaSecond World War

    Category C includes emerging pathogens and pathogens that are made more pathogenic by genetic engineering, including hantavirus, Nipah virus, tick-borne encephalitis and haemorrhagic fever viruses, yellow fever virus and multidrug-resistant bacteria.

    1 Does not include time and place of production, but only indicates where agents were applied and probably resulted in casualties, in war, in research or as a terror agent. B, bacterium P, parasite T, toxin V, virus.

    In North America, it was not the government but a dedicated individual who initiated a bioweapons research programme. Sir Frederick Banting, the Nobel-Prize-winning discoverer of insulin, created what could be called the first private biological weapon research centre in 1940, with the help of corporate sponsors (Avery, 1999 Regis, 1999). Soon afterwards, the US government was also pressed to perform such research by their British allies who, along with the French, feared a German attack with biological weapons (Moon, 1999, Regis, 1999), even though the Nazis apparently never seriously considered using biological weapons (Geissler, 1999). However, the Japanese embarked on a largescale programme to develop biological weapons during the Second World War (Harris, 1992, 1999, 2002) and eventually used them in their conquest of China. Indeed, alarm bells should have rung as early as 1939, when the Japanese legally, and then illegally, attempted to obtain yellow fever virus from the Rockefeller Institute in New York (Harris, 2002).

    The father of the Japanese biological weapons programme, the radical nationalist Shiro Ishii, thought that such weapons would constitute formidable tools to further Japan's imperialistic plans. He started his research in 1930 at the Tokyo Army Medical School and later became head of Japan's bioweapon programme during the Second World War (Harris, 1992, 1999, 2002). At its height, the programme employed more than 5,000 people, and killed as many as 600 prisoners a year in human experiments in just one of its 26 centres. The Japanese tested at least 25 different disease-causing agents on prisoners and unsuspecting civilians. During the war, the Japanese army poisoned more than 1,000 water wells in Chinese villages to study cholera and typhus outbreaks. Japanese planes dropped plague-infested fleas over Chinese cities or distributed them by means of saboteurs in rice fields and along roads. Some of the epidemics they caused persisted for years and continued to kill more than 30,000 people in 1947, long after the Japanese had surrendered (Harris, 1992, 2002). Ishii's troops also used some of their agents against the Soviet army, but it is unclear as to whether the casualties on both sides were caused by this deliberate spread of disease or by natural infections (Harris, 1999). After the war, the Soviets convicted some of the Japanese biowarfare researchers for war crimes, but the USA granted freedom to all researchers in exchange for information on their human experiments. In this way, war criminals once more became respected citizens, and some went on to found pharmaceutical companies. Ishii's successor, Masaji Kitano, even published postwar research articles on human experiments, replacing 'human' with 'monkey' when referring to the experiments in wartime China (Harris, 1992, 2002).

    Although some US scientists thought the Japanese information insightful, it is now largely assumed that it was of no real help to the US biological warfare programme projects. These started in 1941 on a small scale, but increased during the war to include more than 5,000 people by 1945. The main effort focused on developing capabilities to counter a Japanese attack with biological weapons, but documents indicate that the US government also discussed the offensive use of anti-crop weapons (Bernstein, 1987). Soon after the war, the US military started open-air tests, exposing test animals, human volunteers and unsuspecting civilians to both pathogenic and non-pathogenic microbes (Cole, 1988 Regis, 1999). A release of bacteria from naval vessels off

    . nobody really knows what the Russians are working on today and what happened to the weapons they produced

    the coasts of Virginia and San Francisco infected many people, including about 800,000 people in the Bay area alone. Bacterial aerosols were released at more than 200 sites, including bus stations and airports. The most infamous test was the 1966 contamination of the New York metro system with Bacillus globigii— a non-infectious bacterium used to simulate the release of anthrax—to study the spread of the pathogen in a big city. But with the opposition to the Vietnam War growing and the realization that biological weapons could soon become the poor man's nuclear bomb, President Nixon decided to abandon offensive biological weapons research and signed the Biological and Toxin Weapons Convention (BTWC) in 1972, an improvement on the 1925 Geneva Protocol. Although the latter disallowed only the use of chemical or biological weapons, the BTWC also prohibits research on biological weapons. However, the BTWC does not include means for verification, and it is somewhat ironic that the US administration let the verification protocol fail in 2002, particularly in view of the Soviet bioweapons project, which not only was a clear breach of the BTWC, but also remained undetected for years.

    Even though they had just signed the BTWC, the Soviet Union established Biopreparat, a gigantic biowarfare project that, at its height, employed more than 50,000 people in various research and production centres (Alibek & Handelman, 1999). The size and scope of the Soviet Union's efforts were truly staggering: they produced and stockpiled tons of anthrax bacilli and smallpox virus, some for use in intercontinental ballistic missiles, and engineered multidrug-resistant bacteria, including plague. They worked on haemorrhagic fever viruses, some of the deadliest pathogens that humankind has encountered. When virologist Nikolai Ustinov died after injecting himself with the deadly Marburg virus, his colleagues, with the mad logic and enthusiasm of bioweapon developers, re-isolated the virus from his body and found that it had mutated into a more virulent form than the one that Ustinov had used. And few took any notice, even when accidents happened. In 1971, smallpox broke out in the Kazakh city of Aralsk and killed three of the ten people that were infected. It is speculated that they were infected from a bioweapons research centre on a small island in the Aral Sea (Enserink, 2002). In the same area, on other occasions, several fishermen and a researcher died from plague and glanders, respectively (Miller et al., 2002). In 1979, the Soviet secret police orchestrated a large cover-up to explain an outbreak of anthrax in Sverdlovsk, now Ekaterinburg, Russia, with poisoned meat from anthrax-contaminated animals sold on the black market. It was eventually revealed to have been due to an accident in a bioweapons factory, where a clogged air filter was removed but not replaced between shifts ( Fig. 1 ) (Meselson et al., 1994 Alibek & Handelman, 1999).

    Anthrax as a biological weapon. Light (A) and electron (B) micrographs of anthrax bacilli, reproduced from the Centers of Disease Control Public Health Image Library. The map (C) shows six villages in which animals died after anthrax spores were released from a bioweapons factory in Sverdlovsk, USSR, in 1979. Settled areas are shown in grey, roads in white, lakes in blue and the calculated contours of constant dosage of anthrax spores in black. At least 66 people died after the accident. (Reprinted with permission from Meselson et al., 1994 © (1994) American Association for the Advancement of Science.)

    The most striking feature of the Soviet programme was that it remained secret for such a long time. During the Second World War, the Soviets used a simple trick to check whether US researchers were occupied with secret research: they monitored whether American physicists were publishing their results. Indeed, they were not, and the conclusion was, correctly, that the US was busy building a nuclear bomb (Rhodes, 1988, pp. 327 and 501). The same trick could have revealed the Soviet bioweapons programme much earlier ( Fig. 2 ). With the collapse of the Soviet Union, most of these programmes were halted and the research centres abandoned or converted for civilian use. Nevertheless, nobody really knows what the Russians are working on today and what happened to the weapons they produced. Western security experts now fear that some stocks of biological weapons might not have been destroyed and have instead fallen into other hands (Alibek & Handelman, 1999 Miller et al., 2002). According to US intelligence, South Africa, Israel, Iraq and several other countries have developed or still are developing biological weapons (Zilinskas, 1997 Leitenberg, 2001).

    Detecting biological warfare research. A comparison of the number of publications from two Russian scientists. L. Sandakchiev (black bars) was involved, as the head of the Vector Institute for viral research, in the Soviet project to produce smallpox as an offensive biological weapon. V. Krylov (white bars) was not. Note the decrease in publications by Sandakchiev compared with those by Krylov. The data were compiled from citations from a PubMed search for the researchers on 15 August 2002.

    Apart from state-sponsored biowarfare programmes, individuals and non-governmental groups have also gained access to potentially dangerous microorganisms, and some have used them (Purver, 2002). A few examples include the spread of hepatitis, parasitic infections, severe diarrhoea and gastroenteritis. The latter occurred when a religious sect tried to poison a whole community by spreading Salmonella in salad bars to interfere with a local election (Török et al., 1997 Miller et al., 2002). The sect, which ran a hospital on its grounds, obtained the bacterial strain from a commercial supplier. Similarly, a right-wing laboratory technician tried to get hold of the plague bacterium from the American Tissue Culture Collection, and was only discovered after he complained that the procedure took too long (Cole, 1996). These examples clearly indicate that organized groups or individuals with sufficient determination can obtain dangerous biological agents. All that is required is a request to 'colleagues' at scientific institutions, who share their published materials with the rest of the community (Breithaupt, 2000). The relative ease with which this can be done explains why the numerous hoaxes in the USA after the anthrax mailings had to be taken seriously, thus causing an estimated economic loss of US $100 million (Leitenberg, 2001).

    These examples clearly indicate that organized groups or individuals with sufficient determination can obtain dangerous biological agents

    Another religious cult, in Japan, proved both the ease and the difficulties of using biological weapons. In 1995, the Aum Shinrikyo cult used Sarin gas in the Tokyo subway, killing 12 train passengers and injuring more than 5,000 (Cole, 1996). Before these attacks, the sect had also tried, on several occasions, to distribute (non-infectious) anthrax within the city with no success. It was obviously easy for the sect members to produce the spores but much harder to disseminate them (Atlas, 2001 Leitenberg, 2001). The still unidentified culprits of the 2001 anthrax attacks in the USA were more successful, sending contaminated letters that eventually killed five people and, potentially even more seriously, caused an upsurge in demand for antibiotics, resulting in over-use and thus contributing to drug resistance (Atlas, 2001 Leitenberg, 2001 Miller et al., 2002).

    One interesting aspect of biological warfare is the accusations made by the parties involved, either as excuses for their actions or to justify their political

    Cuba frequently accused the USA of using biological warfare

    goals. Many of these allegations, although later shown to be wrong, have been exploited either as propaganda or as a pretext for war, as recently seen in the case of Iraq. It is clearly essential to draw the line between fiction and reality, particularly if, on the basis of such evidence, politicians call for a 'pre-emptive' war or allocate billions of dollars to research projects. Examples of such incorrect allegations include a British report before the Second World War that German secret agents were experimenting with bacteria in the Paris and London subways, using harmless species to test their dissemination through the transport system (Regis, 1999 Leitenberg, 2001). Although this claim was never substantiated, it might have had a role in promoting British research on anthrax in Porton Down and on Gruinard Island. During the Korean War, the Chinese, North Koreans and Soviets accused the USA of deploying biological weapons of various kinds. This is now seen as wartime propaganda, but the secret deal between the USA and Japanese bioweapons researchers did not help to diffuse these allegations (Moon, 1992). Later, the USA accused the Vietnamese of dropping fungal toxins on the US Hmong allies in Laos. However, it was found that the yellow rain associated with the reported variety of syndromes was simply bee faeces ( Fig. 3 Seeley et al., 1985). The problem with such allegations is that they develop a life of their own, no matter how unbelievable they are. For example, the conspiracy theory that HIV is a biological weapon is still alive in some people's minds. Depending on whom one asks, KGB or CIA scientists developed HIV to damage the USA or to destabilize Cuba, respectively. Conversely, in 1997, Cuba was the first country to officially file a complaint under Article 5 of the BTWC, accusing the USA of releasing a plant pathogen (Leitenberg, 2001). Although this was never proven, the USA did indeed look into biological agents to kill Fidel Castro and Frederik Lumumba of the Democratic Republic of Congo (Miller et al., 2002).

    Hmong refugees from Laos, who collaborated with the American armed forces during the Vietnam War, accused the Soviet Union of attacking them with biological or chemical weapons. However, the alleged toxin warfare agent known as yellow rain matches perfectly the yellow spots of bee faeces on leaves in the forest of the Khao Yai National Park in Thailand. (Image reprinted with permission from Seeley et al., 1985 © (1985) M. Meselson, Harvard University).

    We are witnessing a renewed interest in biological warfare and terrorism owing to several factors, including the discovery that Iraq has been developing biological weapons (Zilinskas, 1997), several bestselling novels describing biological attacks, and the anthrax letters after the terrorist attacks on 11 September 2001. As history tells us, virtually no nation with the ability to develop weapons of mass destruction has abstained from doing so. And the Soviet project shows that international treaties are basically useless unless an effective verification procedure is in place. Unfortunately, the same knowledge that is needed to develop drugs and vaccines against pathogens has the potential to be abused for the development of biological weapons ( Fig. 4 Finkel, 2001). Thus, some critics have suggested that information about potentially harmful pathogens should not be made public but rather put into the hands of 'appropriate representatives' (Danchin, 2002 Wallerstein, 2002). A recent report on anti-crop agents was already self-censored before publication, and journal editors now recommend special scrutiny for sensitive papers (Mervis & Stokstad, 2002 Cozzavelli, 2003 Malakoff, 2003). Whether or not such measures are useful deterrents might be questionable, because the application of available knowledge is clearly enough to kill. An opposing view calls for the imperative publication of information about the development of biological weapons to give scientists, politicians and the interested public all the necessary information to determine a potential threat and devise countermeasures.

    . virtually no nation with the ability to develop weapons of mass destruction has abstained from doing so

    Intimate interactions of hosts and pathogens. (A) The face of a smallpox victim in Accra, Ghana, 1967. (Photograph from the Center of Disease Control's Public Health Image Library.) (B) A poxvirus-infected cell is shown to illustrate just one of the many intricate ways in which pathogens can interact with, abuse or mimic their hosts. The virus is shown in red, the actin skeleton of the cell in green. Emerging viruses rearrange actin into tail-like structures that push them into neighbouring cells. (Image by F. Frischknecht and M. Way, reprinted with permission from the Journal of General Virology.)

    The current debate about biological weapons is certainly important in raising awareness and increasing our preparedness to counter a potential attack. It could also prevent an overreaction such as that caused in response to the anthrax letters mailed in the USA. However, contrasting the speculative nature of biological attacks with the grim reality of the millions of people who still die each year from preventable infections, we might ask ourselves just how many resources we can afford to allocate in preparation for a hypothetical human-inflicted disaster.

    12.2 Characteristics and Traits

    By the end of this section, you will be able to do the following:

    • Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems
    • Develop a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross
    • Explain the purpose and methods of a test cross
    • Identify non-Mendelian inheritance patterns such as incomplete dominance, codominance, recessive lethals, multiple alleles, and sex linkage

    Physical characteristics are expressed through genes carried on chromosomes. The genetic makeup of peas consists of two similar, or homologous, copies of each chromosome, one from each parent. Each pair of homologous chromosomes has the same linear order of genes. In other words, peas are diploid organisms in that they have two copies of each chromosome. The same is true for many other plants and for virtually all animals. Diploid organisms produce haploid gametes, which contain one copy of each homologous chromosome that unite at fertilization to create a diploid zygote.

    For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not encode the same version of that characteristic. Gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles . Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for any given gene in a natural population.

    Phenotypes and Genotypes

    Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype . An organism’s underlying genetic makeup, consisting of both physically visible and non-expressed alleles, is called its genotype . Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. When true-breeding plants in which one parent had yellow pods and one had green pods were cross-fertilized, all of the F1 hybrid offspring had yellow pods. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow pods. However, we know that the allele donated by the parent with green pods was not simply lost because it reappeared in some of the F2 offspring. Therefore, the F1 plants must have been genotypically different from the parent with yellow pods.

    The P1 plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are homozygous at a given gene, or locus, have two identical alleles for that gene on their homologous chromosomes. Mendel’s parental pea plants always bred true because both of the gametes produced carried the same trait. When P1 plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning that their genotype reflected that they had different alleles for the gene being examined.

    Dominant and Recessive Alleles

    Our discussion of homozygous and heterozygous organisms brings us to why the F1 heterozygous offspring were identical to one of the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor the recessive allele was referred to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosome pairs. For a gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical (that is, they will have different genotypes but the same phenotype). The recessive allele will only be observed in homozygous recessive individuals (Table 12.4).

    Dominant Traits Recessive Traits
    Achondroplasia Albinism
    Brachydactyly Cystic fibrosis
    Huntington’s disease Duchenne muscular dystrophy
    Marfan syndrome Galactosemia
    Neurofibromatosis Phenylketonuria
    Widow’s peak Sickle-cell anemia
    Wooly hair Tay-Sachs disease

    Several conventions exist for referring to genes and alleles. For the purposes of this chapter, we will abbreviate genes using the first letter of the gene’s corresponding dominant trait. For example, violet is the dominant trait for a pea plant’s flower color, so the flower-color gene would be abbreviated as V (note that it is customary to italicize gene designations). Furthermore, we will use uppercase and lowercase letters to represent dominant and recessive alleles, respectively. Therefore, we would refer to the genotype of a homozygous dominant pea plant with violet flowers as VV, a homozygous recessive pea plant with white flowers as vv, and a heterozygous pea plant with violet flowers as Vv.

    The Punnett Square Approach for a Monohybrid Cross

    When fertilization occurs between two true-breeding parents that differ in only one characteristic, the process is called a monohybrid cross, and the resulting offspring are monohybrids. Mendel performed seven monohybrid crosses involving contrasting traits for each characteristic. On the basis of his results in F1 and F2 generations, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely.

    To demonstrate a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green pea seeds. The dominant seed color is yellow therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with green seeds, respectively. A Punnett square , devised by the British geneticist Reginald Punnett, can be drawn that applies the rules of probability to predict the possible outcomes of a genetic cross or mating and their expected frequencies. To prepare a Punnett square, all possible combinations of the parental alleles are listed along the top (for one parent) and side (for the other parent) of a grid, representing their meiotic segregation into haploid gametes. Then the combinations of egg and sperm are made in the boxes in the table to show which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg, that could result from this mating. Because each possibility is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant or recessive) is known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible. All offspring are Yy and have yellow seeds (Figure 12.4).

    A self-cross of one of the Yy heterozygous offspring can be represented in a 2 × 2 Punnett square because each parent can donate one of two different alleles. Therefore, the offspring can potentially have one of four allele combinations: YY, Yy, yY, or yy (Figure 12.4). Notice that there are two ways to obtain the Yy genotype: a Y from the egg and a y from the sperm, or a y from the egg and a Y from the sperm. Both of these possibilities must be counted. Recall that Mendel’s pea-plant characteristics behaved in the same way in reciprocal crosses. Therefore, the two possible heterozygous combinations produce offspring that are genotypically and phenotypically identical despite their dominant and recessive alleles deriving from different parents. They are grouped together. Because fertilization is a random event, we expect each combination to be equally likely and for the offspring to exhibit a ratio of YY:Yy:yy genotypes of 1:2:1 (Figure 12.4). Furthermore, because the YY and Yy offspring have yellow seeds and are phenotypically identical, applying the sum rule of probability, we expect the offspring to exhibit a phenotypic ratio of 3 yellow:1 green. Indeed, working with large sample sizes, Mendel observed approximately this ratio in every F2 generation resulting from crosses for individual traits.

    Mendel validated these results by performing an F3 cross in which he self-crossed the dominant- and recessive-expressing F2 plants. When he self-crossed the plants expressing green seeds, all of the offspring had green seeds, confirming that all green seeds had homozygous genotypes of yy. When he self-crossed the F2 plants expressing yellow seeds, he found that one-third of the plants bred true, and two-thirds of the plants segregated at a 3:1 ratio of yellow:green seeds. In this case, the true-breeding plants had homozygous (YY) genotypes, whereas the segregating plants corresponded to the heterozygous (Yy) genotype. When these plants self-fertilized, the outcome was just like the F1 self-fertilizing cross.

    The Test Cross Distinguishes the Dominant Phenotype

    Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross , this technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F1 offspring will be heterozygotes expressing the dominant trait (Figure 12.5). Alternatively, if the dominant expressing organism is a heterozygote, the F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes (Figure 12.5). The test cross further validates Mendel’s postulate that pairs of unit factors segregate equally.

    Visual Connection

    In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the round pea parent plant is homozygous dominant or heterozygous? If the round pea parent plant is heterozygous, what is the probability that a random sample of 3 progeny peas will all be round?

    Many human diseases are genetically inherited. A healthy person in a family in which some members suffer from a recessive genetic disorder may want to know if he or she has the disease-causing gene and what risk exists of passing the disorder on to his or her offspring. Of course, doing a test cross in humans is unethical and impractical. Instead, geneticists use pedigree analysis to study the inheritance pattern of human genetic diseases (Figure 12.6).

    Visual Connection

    What are the genotypes of the individuals labeled 1, 2, and 3?

    Alternatives to Dominance and Recessiveness

    Mendel’s experiments with pea plants suggested that: (1) two “units” or alleles exist for every gene (2) alleles maintain their integrity in each generation (no blending) and (3) in the presence of the dominant allele, the recessive allele is hidden and makes no contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals. Such heterozygous individuals are sometimes referred to as “carriers.” Further genetic studies in other plants and animals have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism. If Mendel had chosen an experimental system that exhibited these genetic complexities, it’s possible that he would not have understood what his results meant.

    Incomplete Dominance

    Mendel’s results, that traits are inherited as dominant and recessive pairs, contradicted the view at that time that offspring exhibited a blend of their parents’ traits. However, the heterozygote phenotype occasionally does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus (Figure 12.7), a cross between a homozygous parent with white flowers (C W C W ) and a homozygous parent with red flowers (C R C R ) will produce offspring with pink flowers (C R C W ). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance , denoting the expression of two contrasting alleles such that the individual displays an intermediate phenotype. The allele for red flowers is incompletely dominant over the allele for white flowers. However, the results of a heterozygote self-cross can still be predicted, just as with Mendelian dominant and recessive crosses. In this case, the genotypic ratio would be 1 C R C R :2 C R C W :1 C W C W , and the phenotypic ratio would be 1:2:1 for red:pink:white.


    A variation on incomplete dominance is codominance , in which both alleles for the same characteristic are simultaneously expressed in the heterozygote. An example of codominance is the MN blood groups of humans. The M and N alleles are expressed in the form of an M or N antigen present on the surface of red blood cells. Homozygotes (L M L M and L N L N ) express either the M or the N allele, and heterozygotes (L M L N ) express both alleles equally. In a self-cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct. However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies.

    Multiple Alleles

    Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple alleles may exist at the population level such that many combinations of two alleles are observed. Note that when many alleles exist for the same gene, the convention is to denote the most common phenotype or genotype among wild animals as the wild type (often abbreviated “+”) this is considered the standard or norm. All other phenotypes or genotypes are considered variants of this standard, meaning that they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele.

    An example of multiple alleles is coat color in rabbits (Figure 12.8). Here, four alleles exist for the c gene. The wild-type version, C + C + , is expressed as brown fur. The chinchilla phenotype, c ch c ch , is expressed as black-tipped white fur. The Himalayan phenotype, c h c h , has black fur on the extremities and white fur elsewhere. Finally, the albino, or “colorless” phenotype, cc, is expressed as white fur. In cases of multiple alleles, dominance hierarchies can exist. In this case, the wild-type allele is dominant over all the others, chinchilla is incompletely dominant over Himalayan and albino, and Himalayan is dominant over albino. This hierarchy, or allelic series, was revealed by observing the phenotypes of each possible heterozygote offspring.

    The complete dominance of a wild-type phenotype over all other mutants often occurs as an effect of “dosage” of a specific gene product, such that the wild-type allele supplies the correct amount of gene product whereas the mutant alleles cannot. For the allelic series in rabbits, the wild-type allele may supply a given dosage of fur pigment, whereas the mutants supply a lesser dosage or none at all. Interestingly, the Himalayan phenotype is the result of an allele that produces a temperature-sensitive gene product that only produces pigment in the cooler extremities of the rabbit’s body.

    Alternatively, one mutant allele can be dominant over all other phenotypes, including the wild type. This may occur when the mutant allele somehow interferes with the genetic message so that even a heterozygote with one wild-type allele copy expresses the mutant phenotype. One way in which the mutant allele can interfere is by enhancing the function of the wild-type gene product or changing its distribution in the body. One example of this is the Antennapedia mutation in Drosophila (Figure 12.9). In this case, the mutant allele expands the distribution of the gene product, and as a result, the Antennapedia heterozygote develops legs on its head where its antennae should be.

    Evolution Connection

    Multiple Alleles Confer Drug Resistance in the Malaria Parasite

    Malaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae (Figure 12.10a), and is characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the most common causative agents of malaria, and P. falciparum is the most deadly (Figure 12.10b). When promptly and correctly treated, P. falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region.

    In Southeast Asia, Africa, and South America, P. falciparum has developed resistance to the anti-malarial drugs chloroquine, mefloquine, and sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life stage in which it is infectious to humans, has evolved multiple drug-resistant mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance are associated with each of these alleles. Being haploid, P. falciparum needs only one drug-resistant allele to express this trait.

    In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene are localized to different geographic regions. This is a common evolutionary phenomenon that occurs because drug-resistant mutants arise in a population and interbreed with other P. falciparum isolates in close proximity. Sulfadoxine-resistant parasites cause considerable human hardship in regions where this drug is widely used as an over-the-counter malaria remedy. As is common with pathogens that multiply to large numbers within an infection cycle, P. falciparum evolves relatively rapidly (over a decade or so) in response to the selective pressure of commonly used anti-malarial drugs. For this reason, scientists must constantly work to develop new drugs or drug combinations to combat the worldwide malaria burden. 2

    X-Linked Traits

    In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes. The sex chromosomes are one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes . In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains many fewer genes. When a gene being examined is present on the X chromosome, but not on the Y chromosome, it is said to be X-linked .

    Eye color in Drosophila was one of the first X-linked traits to be identified. Thomas Hunt Morgan mapped this trait to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies, the wild-type eye color is red (X W ) and it is dominant to white eye color (X w ) (Figure 12.11). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous , because they have only one allele for any X-linked characteristic. Hemizygosity makes the descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack a second allele copy on the Y chromosome that is, their genotype can only be X W Y or X w Y. In contrast, females have two allele copies of this gene and can be X W X W , X W X w , or X w X w .

    In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the female in the P1 generation. With regard to Drosophila eye color, when the P1 male expresses the white-eye phenotype and the female is homozygous red-eyed, all members of the F1 generation exhibit red eyes (Figure 12.12). The F1 females are heterozygous (X W X w ), and the males are all X W Y, having received their X chromosome from the homozygous dominant P1 female and their Y chromosome from the P1 male. A subsequent cross between the X W X w female and the X W Y male would produce only red-eyed females (with X W X W or X W X w genotypes) and both red- and white-eyed males (with X W Y or X w Y genotypes). Now, consider a cross between a homozygous white-eyed female and a male with red eyes. The F1 generation would exhibit only heterozygous red-eyed females (X W X w ) and only white-eyed males (X w Y). Half of the F2 females would be red-eyed (X W X w ) and half would be white-eyed (X w X w ). Similarly, half of the F2 males would be red-eyed (X W Y) and half would be white-eyed (X w Y).

    Visual Connection

    What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color?

    Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked trait, she will pass the trait on to 100 percent of her offspring. Her male offspring are, therefore, destined to express the trait, as they will inherit their father's Y chromosome. In humans, the alleles for certain conditions (some forms of color blindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters therefore, recessive X-linked traits appear more frequently in males than females.

    In some groups of organisms with sex chromosomes, the sex with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in which they are hemizygous.

    Human Sex-linked Disorders

    Sex-linkage studies in Morgan’s laboratory provided the fundamentals for understanding X-linked recessive disorders in humans, which include red-green color blindness, and Types A and B hemophilia. Because human males need to inherit only one recessive mutant X allele to be affected, X-linked disorders are disproportionately observed in males. Females must inherit recessive X-linked alleles from both of their parents in order to express the trait. When they inherit one recessive X-linked mutant allele and one dominant X-linked wild-type allele, they are carriers of the trait and are typically unaffected. Carrier females can manifest mild forms of the trait due to the inactivation of the dominant allele located on one of the X chromosomes. However, female carriers can contribute the trait to their sons, resulting in the son exhibiting the trait, or they can contribute the recessive allele to their daughters, resulting in the daughters being carriers of the trait (Figure 12.13). Although some Y-linked recessive disorders exist, typically they are associated with infertility in males and are therefore not transmitted to subsequent generations.

    Link to Learning

    Watch this video to learn more about sex-linked traits.


    A large proportion of genes in an individual’s genome are essential for survival. Occasionally, a nonfunctional allele for an essential gene can arise by mutation and be transmitted in a population as long as individuals with this allele also have a wild-type, functional copy. The wild-type allele functions at a capacity sufficient to sustain life and is therefore considered to be dominant over the nonfunctional allele. However, consider two heterozygous parents that have a genotype of wild-type/nonfunctional mutant for a hypothetical essential gene. In one quarter of their offspring, we would expect to observe individuals that are homozygous recessive for the nonfunctional allele. Because the gene is essential, these individuals might fail to develop past fertilization, die in utero, or die later in life, depending on what life stage requires this gene. An inheritance pattern in which an allele is only lethal in the homozygous form and in which the heterozygote may be normal or have some altered nonlethal phenotype is referred to as recessive lethal .

    For crosses between heterozygous individuals with a recessive lethal allele that causes death before birth when homozygous, only wild-type homozygotes and heterozygotes would be observed. The genotypic ratio would therefore be 2:1. In other instances, the recessive lethal allele might also exhibit a dominant (but not lethal) phenotype in the heterozygote. For instance, the recessive lethal Curly allele in Drosophila affects wing shape in the heterozygote form but is lethal in the homozygote.

    A single copy of the wild-type allele is not always sufficient for normal functioning or even survival. The dominant lethal inheritance pattern is one in which an allele is lethal both in the homozygote and the heterozygote this allele can only be transmitted if the lethality phenotype occurs after reproductive age. Individuals with mutations that result in dominant lethal alleles fail to survive even in the heterozygote form. Dominant lethal alleles are very rare because, as you might expect, the allele only lasts one generation and is not transmitted. However, just as the recessive lethal allele might not immediately manifest the phenotype of death, dominant lethal alleles also might not be expressed until adulthood. Once the individual reaches reproductive age, the allele may be unknowingly passed on, resulting in a delayed death in both generations. An example of this in humans is Huntington’s disease, in which the nervous system gradually wastes away (Figure 12.14). People who are heterozygous for the dominant Huntington allele (Hh) will inevitably develop the fatal disease. However, the onset of Huntington’s disease may not occur until age 40, at which point the afflicted persons may have already passed the allele to 50 percent of their offspring.

    Agar Cell Diffusion

    All biological cells require the transport of materials across the plasma membrane into and out of the cell. By infusing cubes of agar with a pH indicator, and then soaking the treated cubes in vinegar, you can model how diffusion occurs in cells. Then, by observing cubes of different sizes, you can discover why larger cells might need extra help to transport materials.

    Tools and Materials

    • Agar-agar powder
    • Digital scale
    • Graduated cylinder
    • Water
    • Whisk or fork
    • Microwaveable bowl or container at least 500ml in volume
    • Microwave (not shown)
    • Hot pad or oven mitt
    • Heat-safe surface
    • pH indicator, such as bromothymol blue or phenolphthalein
    • Ammonia
    • Small glass baking pan or cube-shaped silicone ice-cube molds
    • Clear plastic metric ruler
    • Sharp knife
    • Clear container for immersing agar cubes
    • Vinegar
    • Calculator
    • Pencil and notepaper
    • Spoon
    • White paper or plate
    • Timers


    1. Measure out 1.6 g of agar-agar and 200 ml water. Mix them together with a whisk or fork in a large microwave-safe bowl.
    2. Heat the solution in the microwave on high for 30 seconds. Remove to a heat-safe surface using a hot pad or oven mitts, stir, and return to the microwave for 30 seconds. Repeat this process until the mixture boils. (Keep your eye on it as it can boil over very easily!) When done, remove the container, and set it on a trivet or other heat-safe surface.
    3. Choose ONE pH indictor to work with (either bromothymol blue or phenolphthalein) and add a few drops of it to the agar solution. ​If you’re using bromothymol blue, add enough indicator so that the mixture turns blue. If it has a greenish hue, add ammonia a drop at a time until it is blue (see photo below). If you're using phenolphthalein, add enough indicator so that the mixture turns pale pink. Add ammonia drop by drop until the mixture turns (and remains) a bright pink color (see photo below).

    To Do and Notice

    Place a few millileters of the pH indicator into a small container (either bromothymol blue or phenolphthalein). Using a dropper, add a few drops of vinegar. What do you notice?

    As an acid, vinegar has a large number of hydrogen ions. When the hydrogen ions come into contact with the pH indicator, the solution changes color.

    Fill a clear container with vinegar to a 3-cm depth. Place one agar cube of each size in the vinegar, making sure the blocks are submerged. The untreated blocks (one of each size) will be used for comparison. What do you think will happen to each cube?

    Determine the surface area and volume of each cube. To find the surface area, multiply the length of a side of the cube by the width of a side of the cube. This will give you the area of one face of the cube. Multiply this number by 6 (the number of faces on a cube) to determine the total surface area. To find the volume, multiply the length of the cube by its width by its height. Then determine the surface-area-to-volume ratios by dividing the surface area by the volume for each cube.

    How will you know if hydrogen ions are moving into the cube? How long do you think it will take the hydrogen ions to diffuse fully into each of the cubes? Why? How would you be able to tell when the vinegar has fully penetrated the cube?

    After 5 minutes, remove the cubes from the vinegar with a plastic spoon, and place them on white paper or on a white plate. Compare the treated cubes to the untreated cubes and observe any color changes.

    How much vinegar has been absorbed by each treated cube? One way to measure this is to calculate the percentage of the volume of the cube that has been penetrated by the vinegar. (Hint: It may be easier to first consider the volume that has not been penetrated by the vinegar—the portion that has not yet changed color.) Do you want to adjust any of your predictions for the diffusion times? What are your new predictions?

    Carefully return all of the treated cubes to the vinegar. Continue checking the vinegar-soaked cubes every 5 minutes by removing them to determine the percentage of the cube that has been penetrated by the vinegar. Continue this process until the vinegar has fully penetrated the cubes. Make a note of the time when this occurs.

    What do you notice about the percentage of penetration for each of the cubes at the different time intervals? What relationships do you notice between surface area, volume, surface-area-to-volume ratio, and percentage penetration? What does this say about diffusion as an object gets larger?

    What’s Going On?

    Biological cells can only survive if materials can move in and out of them. In this Snack, you used cubes of agar to visualize how diffusion changes depending on the size of the object taking up the material.

    Diffusion occurs when molecules in an area of higher concentration move to an area of lower concentration. As hydrogen ions from the vinegar move into the agar cube, the color of the cube changes allowing you to see how far they have diffused. While random molecular motion will cause individual molecules and ions to continue moving back and forth between the cube and the vinegar solution, the overall concentrations will remain in equilibrium, with equal concentrations inside and outside the agar cube.

    How did you find the percentage of the cube that was penetrated by the hydrogen ions at the various time intervals? One way to do this is to start with the volume of the cube that has not been penetrated—in other words, the part in the center that has not yet changed color. To determine the volume of this inner cube, measure the length of this inner cube and multiply it by the width and height. Subtract this from the original volume of the cube and you obtain the volume of the cube that has been penetrated. By dividing this number by the original volume and multiplying by 100%, you can determine the percentage penetration for each cube.

    You may have noticed that the bigger the vinegar-soaked cube gets, the time it takes for additional vinegar to diffuse into the cube also increases—but not in a linear fashion. In other words, if the cube dimensions are doubled, the time it takes for the hydrogen ions to completely diffuse in more than doubles. When you triple the size, the time to diffuse MUCH more than triples. Why would this happen?

    As the size of an object increases, the volume also increases, but by more than you might think. For example, when the cube doubles from a length of 1 cm to a length of 2 cm, the surface area increase by a factor of four, going from 6 cm 2 (1 cm x 1 cm x 6 sides) to 24 cm 2 (2 cm x 2 cm x 6 sides). The volume, though, increases by a factor of eight, increasing from 1 cm 3 (1cm x 1 cm x 1 cm) to 8 cm 3 (2 cm x 2 cm x 2 cm).

    Because the volume is increasing at a greater factor than the surface area, the surface-area-to-volume ratio decreases. As the cube size increases, the surface-area-to-volume ratio decreases (click to enlarge the table below). The vinegar can only enter the cube through its surface, so as that ratio decreases, the time it takes for diffusion to occur throughout the whole volume increases significantly.

    Anything that comes into a cell (such as oxygen and food) or goes out of it (such as waste) must travel across the cell membrane. As cells grow larger, the ratio of surface area to volume decreases dramatically, just like in your agar cubes. Larger cells must still transport materials across their membranes, but have a larger volume to supply and a proportionately smaller surface area through which to do so.

    Bacterial cells are fairly small and have a comparatively larger surface-area-to-volume ratio. Eukaryotic cells, such as those in plants and animals, are much larger, but have additional structures to help them conduct the required amount of transport across membranes. A series of membrane-bound structures continuous with the plasma membrane, such as the endoplasmic reticulum, provide additional surface area inside the cell, allowing sufficient transport to occur. Even with these strategies, though, there are upper limits to cell size.

    Going Further

    While this Snack investigates how the size of an agar cube impacts diffusion, the shape of each cube remains consistent. Biological cells, however, come in different shapes. To see how different shapes of “cells” affect diffusion rates, try various shapes of agar solids. Ice-cube molds can be found in spherical and rod shapes in addition to cubes. How does the shape impact the surface-area-to-volume ratios?

    Teaching Tips

    This Snack fits well into a series of investigations on osmosis and diffusion. The Naked Egg Snack will allow students to explore how concentration gradients power movement of materials into and out of cells. The Cellular Soap Opera Snack will help students consider the types of materials that move through cell membranes.

    To help students better understand the concepts of surface area, volume, and surface-area-to-volume ratio, have them build models with plastic centimeter cubes. Physical models can help make these ideas more concrete. Students can also graph class data to better understand the mathematical relationships involved.

    If there’s not enough time within a class period for the largest cubes to be fully penetrated by the hydrogen ions present in the vinegar, students can make note of the percentage of the cube that has been penetrated by the vinegar and use that data to extrapolate a result. Alternatively, students in the following period may be able to note the time for the previous class.

    Agar-agar comes as a powder and can be purchased online or at markets featuring Asian foods. Unflavored gelatin can be used as a substitute, but is more difficult to handle. To make cubes from gelatin, add boiling water (25% less than the amount recommended on the package) to the gelatin powder, stir, and refrigerate overnight. You may need to experiment with the ratio of water to gelatin to achieve the perfect consistency.

    Cabbage juice can be used as an inexpensive alternative to commercial pH indicator solutions. To make cabbage juice indicator, pour boiling water over chopped red cabbage and let it sit for 10 minutes. Strain out the cabbage, and use the remaining purple water to mix with the agar powder.