CHAPTER 2
PATTERNS
An Overview of the Basic Concepts of Biology
TO SEE LIFE AS A WHOLE — TO OBSERVE WHAT ALL LIFE HAS IN COMMON — REQUIRES A SHIFT in the way we normally look at things.We must look beyond the individual insect or tree or flower and seek a more panoramic perspective.We need to think as much about process as we do about structure. From this expanded viewpoint, we can see life in terms of patterns and rules. Using these rules, life builds, organizes, recycles, and re-creates itself.
Here we describe sixteen of life’s patterns. Most apply to the smallest organisms and their molecular parts as well as to the most complex of us.We make no claim that our list is definitive.We simply invite the reader to think about life from the standpoint of not just what makes each living thing unique and different, but also what it is that unites us all.
The Sixteen Patterns:
1.	Life Builds from the Bottom Up
2.	Life Assembles Itself into Chains
3.	Life Needs an Inside and an Outside
4.	Life Uses a Few Themes to Generate Many Variations
5.	Life Organizes with Information
6.	Life Encourages Variety by Recombining Information
7.	Life Creates with Mistakes
8.	Life Occurs in Water
9.	Life Runs on Sugar
10.	Life Works in Cycles
11.	Life Recycles Everything It Uses
12.	Life Maintains Itself by Turnover
13.	Life Tends to Optimize Rather Than Maximize
14.	Life Is Opportunistic
15.	Life Competes Within a Cooperative Framework
16.	Life Is Interconnected and Interdependent
2.1	Life Builds from the Bottom Up
The Influence of Small Things
Early debate about evolution centered around the then horrifying notion that humans and apes had a common ancestor. Charles Darwin’s idea (at left) had far more radical implications: Every individual is a colony of smaller individuals (cells), which are in turn made up of smaller nonliving bits. Further, these smaller bits were the first to develop in our evolutionary history. Occasionally these were usefully incorporated into cells, which, over great gulfs of time, assembled into multicellular organisms. Our ancestors were microscopic, wriggling, squirming creatures similar to what we now call bacteria, whose own ancestors were bits of self-replicating molecules.
Before a single plant or animal appeared on the planet, bacteria invented all of life’s essential chemical systems. They transformed the Earth’s atmosphere, developed a way to get energy from the Sun, evolved the first bioelectrical systems, originated sex and locomotion, worked out the genetic machinery, and merged and organized into new and higher collectives. These are ancestors to be proud of !
Given the complexity of the tasks above, we can see why the first multicellular organisms did not appear until the most recent one-eighth of life’s duration on Earth (see page 297). So we exist as “corporate elaborations” — composite communities of cells built out of the accomplishments of our one-celled forebears.
Each living creature must be looked at as a microcosm — a little universe formed of a host of self-propagating organisms, inconceivably minute and as numerous as the stars in the heaven.
Charles Darwin, 1856
Cooperating communities of cells
Small communities of cells — like the taste buds on our tongues — work together as an army of specialists. They create a unique structure, with nerve connections to our brain, that allows us to taste the world around us. (The picture at right represents an enlargement of the human tongue.)
Small things are made of yet smaller things.
The bumps on the surface of our tongues, called papillae, contain our taste buds. These, in turn, are formed of clusters of about fifty cells.
From Bottom Up to Top Down
The building of life from the bottom up (i.e., from single-celled creatures into multicelled creatures) suggests a one-way evolutionary direction — from the simple to the more complex. This, however, is only part of the story. As multicellular creatures evolved, they created new environments for the already existing simpler creatures. For example, the unicellular bacteria residing in the guts of all animals live in a mutually evolving dance with their larger hosts. They provide important benefits, including making the host’s gut inhospitable to disease-causing organisms and producing necessary substances such as vitamins. In some animals, bacteria also secrete powerful digestive enzymes that break down food to prepare it for the host’s own digestive resources. Though the ancestors of these helpful microbes clearly existed before animals, it is highly probable that their hosts contributed to the direction of their later evolution.
This is also the case with parasites, organisms that harm their hosts.They follow a simple rule:“Why make a product yourself when you can easily get it from someone else?” Bacterial and viral parasites, in particular, must have evolved after their hosts. It is likely that many parasites have actually become simpler than their ancestors were.
Finally, consider organisms whose evolution humans have genetically engineered: bacteria that eat oil or attack crop pests. Beyond demonstrating our growing ability to manipulate nature, such creatures exemplify the ongoing worldwide coevolution of micro and macro environments.
Volvox
A spherical colony of many single cells rolls through the water of a pond. Inside the sphere grow daughter colonies, which from time to time break out to spin away on their own.
The colony of cells called Volvox shown above left can be made up of as many as 50,000 individual cells, each with two whip-like propellers (flagella). The cells are held together in a gelatinous sphere, not actually connected to each other as are the cells of your tongue, let’s say, or those of any multicellular organism. Still, the flagella move in a coordinated way to roll the colony through the water, and the colony does seem to have a forward and backward orientation, as well as an inside where new colonies form.
Question.
Why do you suppose such colonies might be more likely to survive and reproduce than might free-living single cells over time? What might be the advantage of a colony’s remaining just a colony, rather than evolving into a multicellular volvox organism?
Answer...
In a fairly calm water environment (where the spheres are likely to remain whole), a colony has an advantage over single cells in that it has daughter colonies that develop in a relatively protected place. Remaining a colony might also be an advantage, because a bite from a predator would just downsize the colony, not kill it.
Virus Attack
The ranks of balloon-shaped objects lined up along the outer edge of this bacterial cell are viruses — bacteriophages (“bacteria-eaters”). About 30 minutes before this picture was taken, they injected all of their DNA into the bacterium. The bacterium’s molecular machinery leapt into action and translated the information in those DNA molecules into new viruses, which you can see bursting through the cell membrane at the lower right. Viruses are so simple that they cannot exist without using another organism’s molecular machinery to reproduce.
A Corporate Elaboration
A sponge is perhaps the simplest “corporate elaboration.” Its cells function as a cooperating group of individuals. Unlike other multicelled creatures, sponges have no true tissues (groups of differentiated cells that work in concert, as in taste buds or muscles), let alone tissues organized into organs. Sponges have eight to ten different types of cells (some of which you can see in the illustration at right), cooperate to maintain constant water flow through the pores, to trap food, to create fibers and mineral structures that maintain the sponge’s shape, and to transport nutrients and wastes.
Probably because of their relative simplicity, sponges regenerate easily: chop a living sponge into pieces and each piece will become a new sponge. Even pressing a live sponge through a fine sieve won’t kill it. Deposited on a culture medium, the tiny fragments will begin to migrate and clump together in mounds that eventually become miniature new sponges.
A colony of a very ancient type of tropical sponge
Notice the tubular, porous structure, ideal for enhancing water flow. Specialized cells with long appendages called flagella create currents that pull nutrient-filled water in from outside and up through pores in the tube. Each individual cell exchanges nutrients and waste with the outside world. The human intestine and trachea (both tubular organs) are also lined with cells that perform a similar kind of absorbing and transporting function.
Doing Science
Autumn, Kellar et al. 2000.
Adhesive force of a single gecko foot-hair.
Nature 405: 681-685.
Imagine a hair one-tenth the diameter of a hair on your head. A gecko lizard has a half-million such hairs on the bottom of each of its four feet. On each of these hairs are from 100 to 1000 still smaller spatula-shaped structures.
Kellar Autumn and collaborators have discovered that these very small structures give the gecko a “leg up” in climbing vertical walls. They have measured inter- molecular forces sealing the gecko’s foot spatulas to the wall surface. In other words, each spatula’s tiny size allows it to press so close to the wall, within a distance comparable to an atom’s diameter, that the molecules of each spatula attract to the molecules of the wall. The intermolecular force generated, multiplied by the millions of spatula structures on each foot, is more than enough to keep the gecko on the wall.
2.2	Life Assembles Itself into Chains
When Difference Becomes Information
At the molecular level, life has adopted the chain as its organizing principle. Chains are made of simple units connected together in long, flexible strands. In an ordinary chain, the links are all the same. In contrast, life’s chains are molecules containing different links. In this respect, the links are the alphabet of life. Letters, in appropriate order, form meaningful words, sentences, paragraphs. Similarly, the sequence of individual links in a chain molecule conveys information.
Chain molecules fall into two main classes: information chains, which store and transmit information, and working chains, which carry out the business of living. Specific lengths of the information chain, called genes, carry the information that becomes specific working chains, called proteins. The two kinds of chains work together in a cooperative loop: information chains provide the genetic prescription or recipe that is translated into working chains; these in turn make it possible to copy the information chains so they may be passed on to the next generation. All of this is explained in much greater detail in Chapters 4 and 5, Information and Machinery.
Life’s Chain Molecules Are of Two Basic Types
Information chains (DNA and RNA) made of four different units (nucleotides)
Working or structural chains (proteins) made of twenty different units (amino acids)
DNA chains naturally twist into a double helix, a shape that protects them and makes them easier to access and duplicate.
According to the sequence of their links, proteins fold into complicated shapes, like the protein on pages 6 and 7. In this way, two-dimensional chains become three-dimensional, functional machinery.
A chain of uniform links is simply a chain — but a chain of different links can carry information:
Morse code is a chain of two different units (dots and dashes),
computer language is also a chain of two units (ones and zeros), and
an English sentence is a chain of twenty-six units (letters).
Two Simple Examples of How Information Requires Difference
Your hand can become an eloquent communication device if you use it to create the letters of American Sign Language (ASL). For the different hand shapes of ASL to qualify as information, they must be recognized by someone else—they must be “read.” As Helen Keller “read” the changing shapes of her tutor’s hand, those shapes become information about the world. And, to be useful over time, information must be stored — placed in memory. For any system to have a memory, it must map differences in the world into coded sequences and keep these secure for later reading. Braille does this: it codes letters into distinct patterns of raised dots impressed on paper or other media.
Folding into Shapes That Work – More About Three-Dimensional Machinery
Information chains (DNA) are translated into working chains (proteins). The shapes that protein chains fold into depend on the multiple interactions among the amino acid molecules that make up the chain. Chemical groups of the amino acids attract each other, making the chain stick together at various points (the black dots in the illustration at right depict the ways that hydrogen bonds can connect one amino acid to another at a distant place on the chain). Once the sequence of amino acids in a chain is dictated by DNA, the shape of a protein inevitably follows. That protein then takes up one of many thousands of different functions in a living organism. It may be the kind of protein that provokes chemical reactions — an enzyme or catalyst.
You can see this kind of invisibly small enzyme at work when you slice into an apple or an avocado— the pristine slice rapidly turns an unappetizing brown as its enzymes cause oxygen in the air to react with the disorganized content of damaged cells to create a molecule that reflects color (a pigment molecule). It turns out that this kind of enzyme, called a polyphenol oxidase, is very ancient and can be found in everything from amoebas to mushrooms to people (where it is responsible for, among other things, suntans and hair and eye color).
Reading Information
Living creatures have incredible capabilities for extracting information from — that is, reading differences in — the world. Monarch butterflies apparently navigate the 1500 miles from Canada to a small area in Mexico by reading differences in the Earth’s magnetic field.
Depending on the sequence of amino acids in the chain, they will bond to other parts of the chain in helices (left) or pleated sheets (right) before they coil into a final shape.
Bats maneuver in darkness using echolocation: responding to differences in the echoes of the high-frequency sounds they emit. Trees “know” when to withdraw the nutrients from their leaves at the approach of winter, in part by reacting to differences in day length.
The ability of widely various creatures to read environmental information has a common source. Embedded in living cells are specialized chain molecules (proteins), which are activated and altered by tiny differences in their surroundings. These complexly coiled proteins act as information receptors and processors, picking up distinctive information from the environmental stream and reporting it to other working proteins for appropriate action. The ultimate information — i.e., the information for making all these information-gathering proteins — is found in DNA.
A cell membrane
Cellular membranes are formed by combining two layers of regimented phospholipid molecules. On the outer row, the water-liking heads face outward toward the watery surroundings.
On the inner row, the water-liking heads face toward the inside of the cell. The two rows effectively isolate the inner environment. Protein pumps, like the one shown at top, move molecules in and out.
Larger “membranes”
Bark safeguards the living part of the trunk of a tree (usually the outermost ring) from insects, disease, and harsh weather.
The atmosphere helps regulate the Earth’s temperature as it protects life from the Sun’s harmful ultraviolet rays and insulates us from the cold vacuum of space.
2.3	Life Needs an Inside and an Outside
Heads Out — Tails In
When danger threatens, musk oxen gather in a circle — heads and horns to the outside, tails to the inside — sheltering their vulnerable calves in the center. This circle of protection is a memorable analogy for one of life’s most fundamental organizing principles — a difference between inside and outside. Life’s chemicals must be kept close together — concentrated — so that they can meet frequently and react readily. To function, the inner environment must maintain a stable level of saltiness, acidity, temperature, etc., different from the outside. These differences are maintained by some form of protective barrier, e.g., a baby’s skin, a clam’s shell, or a cell’s membrane.
The membranes surrounding each of our cells behave something like the threatened musk oxen. The constituent fat molecules have a water-liking head and a fatliking tail. Heads face outside toward the watery environment beyond the cell; tails face inward (above left). Since the inside of a cell also has a watery environment, a second row of fat molecules aligns itself tail-to-tail with the outer layer, heads facing inward (above right).With this protective structure creating an inside and an outside, plus several pumps embedded in the membrane to move materials in and waste out, life can do its work.
Our Debt to Fat
In cells other than bacteria, the cell’s outer surrounding membrane, the plasma membrane, has its counterparts inside the cell. The nucleus is surrounded similarly by a membrane enclosing the DNA, and the machinery for its reading and duplication (Chapter 5). Mitochondria, the bacteria-sized bodies inside cells are membrane-enveloped. And inside them, membranes and associated mobile molecules act as electron conductors in the process of converting sugar to useable chemical energy. Chloroplasts of plants, too, use membrane electron conduction as they convert the energy of sunlight into sugar (Chapter 3).
Throughout cells there are elaborate networks of membranous tubes and channels and conveyor belts which are closely connected with the cell’s elaborate machinery for making protein (Chapter 5). This endoplasmic reticulum serves to convey newly made proteins to their proper locations. Membranes even act like cell mouths.A segment of membrane on the surface of the cell can engulf chunks of material it wants to “eat,” enclose them in membrane, and move the package into the cell. Inside the package, the contents are broken down; the breakdown products are released and then used to build new cell material.
Of course, membranes are barriers too: they keep things that aren’t wanted out of cells.They also bring things that are needed into cells, and they keep them there until they’re used. And they conduct waste material out of cells. These functions are mediated mostly by proteins which sit in the membrane and act as channels or gates.
Many more additional functions of membranes are mediated by proteins lodged snugly into the membrane. Special proteins govern the connections between cells, insuring their coordinated interaction. Proteins that penetrate the full width of the membrane receive signals arriving at the outside of the cell, and by changing their shape, thereby convey a response to the inside of the cell (see pages 218–219).
So these fatty molecules called phospholipids, banding together to shun and preserve ubiquitous water, create for us an inner world in which both water-sustained and water-avoiding chemical events can exist side-by-side to make life possible.
At right are the shapes taken by layers of certain dried protein molecules when they are heated slightly and mixed with water. Notice the double layers in (a) and the complex interior structures in (b). As it turns out, these membranes let certain substances through and repel others.
Question.
Chemists studying the properties of phospholipid molecules and of fairly simple protein molecules found that when they were mixed with water, millions of them joined spontaneously to form small bubble-like spheres. When the mixture was shaken, the spheres broke up into even smaller spheres, always self-sealing. To scientists curious about the mystery of how cellular life might have started on our planet, this was an exciting discovery. Why?
Answer...
The discovery provided a possible explanation of how the first cells might have arisen. A fundamental problem in understanding the origin of life is explaining how the vital chemicals might have been confined in a small enough space to promote continuous proximity of reactants. If natural substances like proteins or phospholipids spontaneously create self-sealing spaces, they might, in a primitive soup, have trapped these chemicals inside, allowing them to react and form molecules like nucleotides and proteins.
Earth as Organism
Thinking about life on a much grander scale than that of molecules and cells, some imaginative scientists — James Lovelock and Lynn Margulis were early proponents — have suggested that the Earth itself can be viewed as a life form. In this view, called the Gaia (“Mother Goddess”) hypothesis, the atmosphere, oceans, soils, and living organisms comprise a biosphere — a global self-regulating system that works to maintain its own internal balance (homeostasis) in much the same way a cell or an organism does. Although this hypothesis is hotly contested in the scientific community, viewing the Earth as a life form provides a useful model for thinking about living systems and their need for protective and containing membranes.
Terrestrial vegetation acts as a protective membrane for the land and its living contents. Vegetation absorbs atmospheric CO2 and gives off a great deal of the water vapor, partially responsible for cloud formation and subsequent rainfall. When the membrane of trees and other plant life is removed from a region, water vapor is no longer given off and the surrounding land may become a desert. In coastal areas assured of plentiful rainfall, deforestation (removal of the vegetative membrane) leads to a result just as harmful; once the protective layer of plants and roots is disrupted, erosion is magnified with every rainstorm, and the nutrient layer of topsoil soon is washed away. Eventually little is able to grow or live there.
Earth itself is surrounded by a membrane that is both fragile and tough — the atmosphere. It admits light, vital to the existence of life on this planet, and emits excess infrared radiation (heat) produced by the activities of living things. The atmosphere protects us from the deadly cold of space, from meteorites, and from the Sun’s harmful ultraviolet rays; it also moves and cleanses the air we breathe, and replenishes our fresh water supplies.
When the atmospheric membrane is perturbed (major volcanic eruptions, for instance, can launch particulates into the upper atmosphere), serious climatic changes can occur. After the violently explosive eruption of Krakatau in the South Pacific in 1883, volcanic dust in the stratosphere caused cooler temperatures and spectacular sunsets worldwide. The cooling effect was so great that 1884 was known as the “Year Without a Summer” in much of the Northern Hemisphere.
The Earth’s membrane
This NASA satellite photograph shows the relatively	thin	outer	envelope	(the	Ear th’s atmosphere) that surrounds and protects the planet much like the membrane that surrounds and protects a cell.
Atmospheric perturbation
A recent volcanic eruption seen from the Space Shuttle.
Variations on a theme
The beetle, with some 300,000 separate species (the world’s most numerous order), displays every imaginable color, decorative motif, and proportional distribution of body parts — yet the pattern of relationships that makes beetles is constant.
2.4	Life Uses a Few Themes to Generate Many Variations
The Inward Similarity of Outward Diversity
Life hangs on to what works. At the same time, it explores and tinkers. This restless combination leads to a vast array of unique living creatures based on a considerably smaller number of underlying patterns and rules. For example, when cells divide and grow, they do so in a mere handful of ways. New cells can form concentric rings, as they do in tree trunks and animal teeth. They can form spirals, as in snails’ shells and rams’ horns; radials, as in flowers and starfish; or branches, as in bushes, lungs, and blood vessels. Organisms may display several combinations of these growth patterns, and the scale can vary; but for all life’s diversity, few other growth patterns exist.
Life, in striving for the most economical use of space, borrows mathematical rules. For instance, count the branches coming off a stem for a given number of full turns around the stem, and with surprising consistency the numbers of turns and branches relate to each other as in the series 1 1 2 3 5 8 13 21. . . — the so called Fibonacci series — in which each successive number is the sum of the two preceding it. For example, in a pine cone, there are thirteen scales for every seven turns. Similar patterns occur in the spirals of florets in sunflowers and daisies, the sections of the chambered nautilus, even the branchings of the bronchial tubes in our lungs. Such similarities in pattern give us some insight into how simple rules, used in different contexts, can produce great variety. From few notes, nature creates many symphonies.
Different proportions — the same pattern
Placing these varied fish species within a “stretchable” grid demonstrates that their differences in shape are a matter of proportion. The fundamental pattern is the same.
From d’Arcy Wentworth Thompson, On Growth and Form


Stretching the Grid
All of these fish live in a common fluid — water — and the fluid nature of their environment is one reason for the fea- tures their body structures have in common. However, their environments differ with respect to salinity, plant life, predators, prey, amount of sunlight, type of bot- tom, and many other characteristics. These envi- ronmental diversities are what “stretch the grid.” Predator fish, like pike, are successful if they have a shape that can provide rapid accelera- tion. Grazing fish, like butterfly fish for example, succeed if their shape gives them maneuverability around rocks and corals and allows them to hide from predators.
How a Slime Mold Makes Its Living
A branching growth pattern
A plasmodial slime mold, Physarum polycephalum.
We have already seen that anything living has to have an inside protected from the outside. It’s also true that the shapes living things take over time are indirectly molded by specific survival needs and by the forces of the world outside. Most liv- ing things that are the wrong color or shape or size or have the wrong kind of teeth or breathing apparatus for their environment don’t survive long enough to reproduce. Ones that are better adapted to their environment do reproduce and succeed.
The successful growth pattern in the yellow slime mold shown at left is an adaptation that allows it to absorb food from and exchange gases with the outside. It presents a very large sur- face to the world, and possesses a branching pattern of veins to move materials throughout its volume. The mold lives in a moist, dark, forest underlayer, so it doesn’t need a thick shell or skin to protect it from its environment. In fact, in some sense, the forest underlayer can be thought of as the mold’s “skin.”
A linear growth pattern
Strands of algae—cells divide in only one plane.
Multiple growth patterns
Think of all the different patterns of cell division that created this dragonfly’s shapes.
Patterns of Multiplication
When a cell divides in two, which is how it reproduces itself, the two resulting daughter cells can go their separate ways as unicellular organisms, or they can stick together and function as a multicellular organism. Dividing and adhering cells can occupy space in only four basic ways (right): (1) They can grow in one plane of space, say north-south, creating a single long chain of cells. (2) They can keep extending in that one direction, with occasional offshoots east or west. (3) They can grow consistently in two directions, making a thin sheet of connected cells. (4) Or they can grow in all three spatial planes, adding up and down to east-west and north-south, making chunks, cylinders, and spirals.
The highly complex system of airways of a human lung (a) has a pattern very similar to that of the simpler slime mold. A very different kind of organism, the seaweed Fucus (b), also has a similar pattern.
Adhesion after division
1. Cell division in only one plane.
2. Cell division mostly in one plane; occasionally in others
3. Cell division in two planes regularly
4. Cells divide in all three planes
Question.
Explain the similarity of the patterns you see here in terms of the way each structure sup- plies the needs of the living organism. How are the outsides of these structure adapted to pro- tecting them (or not) from their environment?
Answer...
The branching pattern of airways in the lungs creates a large surface area for air to enter all parts of the lung. That same branching pattern exposes a large area of the seaweed to its fluid environment, allowing it to absorb nutrients and exchange gases. The “outside” of the lungs’ airways is really their interior, and this is covered with cilia and mucus for protection. The seaweed, too, is covered with a kind of mucus, and has tough, leathery skin.
By itself, a sub-robot could never make a complex working part.
For a team of specialists, however, each completing a single step, the task becomes manageable.
2.5	Life Organizes with Information
Making the Parts That Make the Whole
The business of living requires a lot of information. An organism needs to know how to maintain a constant temperature, how to replace worn-out parts, how to defend against invaders, how to get energy out of food, and so on. It has been esti- mated that the information a human being needs for all of his or her functions would fill up 15 encyclopedias. It might be many times greater than that but life has developed a strategy of dealing with this large amount of information: it stores only a certain kind. The nature of this information might be best understood by the fol- lowing analogy: Suppose you decided to build a complex robot requiring millions of individually handcrafted working parts. Presumably, this task would require instruc- tions for the making of each part, plus instructions for the overall assembly, as well as operating instructions. But now imagine that you had another option:You could acquire the instructions to make several thousand tiny sub-robots, each of which knew how to fabricate one stage of one of the parts. And by working collectively, these sub-robots could assemble and operate the entire robot. In other words, an extraordinarily complex robot would result from complicated interactions among many sub-robots, each of which performs a relatively simple task.
This is the kind of information that life stores in its DNA. Sections of DNA — genes — contain no information on maintaining temperature, defending against invaders, decorating a home, choosing a mate, etc. They contain only information on how (and when) to make proteins. The rest is up to the proteins — life’s subrobots.
Enzyme Workers
The cell’s workers — those sub-robots — are protein molecules (in this book, we often show them as the lumpy characters at right). They are able to perform relatively straightforward chemical tasks, like transforming a specific kind of molecule into a slightly altered version. They do this at incredible speeds — thousands of molecules processed per second — without being changed in the process. This kind of protein is called an enzyme — a bio- logical catalyst, or a chemical reaction facilitator. Teams of enzymes work inside cells in a coordinated fashion to convert simple molecules, such as sugar, into the essential building blocks life uses to assemble its own substance: amino acids, nucleotides, fats, etc. Enzymes can also convert cholesterol to hormones such as estrogen and testosterone. They can, with the help of chemical energy, accomplish movement, as in the action of muscle or the transport of substances throughout cells. They can, in sum, by their many coordinated interactions, main- tain a human life!
Muscle action
An enzyme attaches to the myosin molecule, causing the myosin to change shape. The shape change attach- es myosin to the actin molecule and pulls it alongside the myosin, causing a shortening of the actin-myosin complex.
Sweetly Splitting Sugar
A good example of a critically important life task accomplished by a team of enzyme workers is glycolysis (from the Greek for “sweet splitting”). Glycolysis is the breakdown of the six-carbon molecules of glucose to two molecules of the three-carbon pyruvate (shown in the figure top left on the facing page). This process involves ten enzymes, each accomplishing tiny steps, and the end result is the net pro- duction of two energy-rich ATP (adenosine triphosphate) molecules from one sugar molecule. ATP is the energy coinage of life, the molecule that is used by enzyme workers to drive all cellular activity.
Count the enzymes in glycolysis
This picture shows a simplified model of sugar—just its six carbon atoms. The enzyme hexokinase makes the first small change possible, the addition of a phosphate group (here shown as P). In the next tiny step, phosphoglucose isomerase, another enzyme, makes the next phosphate addition possible. Eight more enzymes orchestrate the remaining small chemical changes to glucose that turn it into two three-carbon molecules called pyruvate.
Expanding on ATP
ATP is made of a sugar, three phosphate groups, and a nitrogen base. It looks some- thing like the nucleotide molecules that make up DNA, though it has two extra phos- phate groups attached to it. It is in the bonds that attach those phosphates that the energy that drives glycolysis is stored.
Glycolysis is a way of getting energy from sugar when oxygen is not avail- able. It was used by bacteria-like organisms billions of years before there was free oxygen in the Earth’s atmosphere. Organisms eventually evolved the ability to use oxygen to “burn” the waste product of glycolysis, pyruvate, to produce much larger amounts of ATP. But glycolysis proved to be so useful throughout evolution that it remains a central feature of almost all creatures alive today. You’ll examine this process in much greater detail in Chapter 3, Energy.
Glycolysis is but one example of many very simple parts working together in a coordinated fashion to create complexity. Seemingly impossible tasks are accomplished by doing one small chemical conversion at a time.
You’re a robot designer and you’ve automated an extremely complex machine by designing little sub-robots to do various simple tasks. The problem is that these sub-robots are doing so many simultaneous tasks that they’re getting in each other’s way. If you could build a new feature into some of the sub-robots, they could orchestrate their various tasks and thereby reduce the chaos.
Question.
What new feature would you add? Can you come up with a cellular analogy for this robot design problem?
Answer...
The new feature could be a switch that turns a sub-robot on and off in response to a signal. The switch would be installed in at least one member of every production line or operating team so that it would function only when necessary. Similarly, body cells might reach a point where they were pro- ducing too much pyruvic acid from glucose. The solution to this problem might be another enzyme that reacts to that overload by interfering with the action of the enzyme hexokinase until the amount of pyruvic acid in the cell decreases.
2.6	Life Encourages Variety by Recombining Information
Recombining Instructions
Nature creates new combinations by recombining informa- tion. The earliest life-forms, simple bacteria-like organisms, found a way to inject bits of information (DNA) into each other — a primitive form of sex. Over time, life acquired the ability to exchange ever-larger chunks of information, thus evolving sexual reproduction, which is a more elaborate form of information mixing. Sexual reproduction, in simplest terms, involves lining up two long chains of information from two individuals, randomly cutting them, exchanging the pieces, and then passing a mixed chain to the next generation.
It’s easy to imagine that the longer the chains, the more the possibilities for infor- mation exchange. The number of possibilities is truly staggering. Just with the ten-unit charm bracelet we use here, (each charm represents a gene), there are 1233 possible exchanges. With a chain only two units longer — 12 — there are 4086 pos- sible mixes. And we humans have some 70,000 genes!
It’s important to understand that matching pairs of genes are not always identi- cal. For instance, your gene for the oxygen-carrying hemoglobin protein in your blood may be slightly different from mine. The difference may be trivial, or it can account for poorly function- ing hemoglobin in one of us. All the dif- ferences in our genes account for why each of us is genetically unique. Between any two individuals, about one-third to one-half of all our genes are different in this way.
Some of the matching charms differ in small ways from one another, accounting for the genetic differences between individuals.
Our DNA consists of sequences of genes represented here by charms on a chain. One sequence of charms is from our mother, one from our father. The charms are always in the same order on both chains.
When sperm and egg cells are made, the chains are	...and joined crosswise, each to the opposite strand... brought together, lined up, cut . . .
...making mixed chains. These are now ready to be separated and passed to the next generation.
Choosing chickens
By selecting only chickens with elaborate varieties of head plumage to breed with one another, breeders can quickly vary the appearance of successive generations of these showy chickens.
Having It Your Way with Genes
With generation after generation of information mixing, changes in genes accumulate and the appearance or function of succeeding generations of a living organism can change dramatically. In nature, changes in genes arise from acci- dental alterations — mutations — and from the exchange of genetic information when organisms reproduce. With each alteration of the information that specifies their form and function, creatures become better or worse suited to their environ- ment. The better suited tend to survive and reproduce (to mix and pass on their genes again).
Gene reshuffling creates diversity, causing animals of the same species to come to vary greatly in appearance. Such variation within a species often occurs naturally, but it can be accelerated when genes are purposefully recombined through selective breeding. Throughout history, humans have taken advantage of the possibilities for variation allowed by gene reshuffling to control the characteristics of other animals. Dog breeders do this, for example. All domestic dogs, from Mexican Chihuahua to Great Dane, belong to the same species, though they look radically different. Cats, horses, sheep, and cows have also been manipulated genetically by humans to emphasize certain characteristics that make them more useful or decorative.
Horticulturalists have been very selective in plant breeding, as well. U.S. grain crops, with their large seeds and huge yields, would be unrecognizable to ancient farmers. The flowers in almost every garden today are mostly selectively bred strains that didn’t exist a century ago, and the same is true for most of the fruits and vegetables you eat.
The decorative chickens you see above are widely varying descendants of much plainer ancestral chickens. At Plimoth Plantation in Massachusetts, agricultural scientists are selectively breeding highly specialized modern chicken species to try to produce ones with the characteristics of their seventeenth-century ancestors — a kind of reverse selective breeding.
Question.
What characteristics would the scientists try to achieve, given the environmental challenges to the original Plimoth chickens?
Answer...
The traits that would be selected for are likely to be muted colors, ability to thrive on sparse food, hardiness to cold and damp, quickness, and good vision.
Question.
Who is engineering organ- isms, and why? It is impor- tant to note that there is a lot of controversy sur- rounding genetically engi- neers organisms and crop plants. What might be some of the objections to their use?
Answer...
This one is up to you.
Taking Gene Mixing into Our Own Hands
Since the mid-1970s we have been able to accomplish an entirely new kind of purposeful gene transfer, almost unimaginable before the discovery of the structure and function of DNA and proteins. We have learned to take specific lengths of DNA (genes from one organism) and insert them into another, in some cases turn- ing that other organism into a “factory” for making specific proteins. The first such successful gene transfers were accomplished in 1979, when the genes that describe two human proteins, insulin and human growth hormone, were inserted into bacte- ria. These “genetically engineered” bacteria multiplied, producing large amounts of the two proteins. Now these proteins and others useful to humans are produced industrially in huge fermenter tanks that can hold thousands of gallons of bacterial cultures.
The same idea lies behind the genetic engineering of new food plants such as the New Leaf potato. With an inserted gene from a bacterium (Bacillus thuringiensis), this plant makes its own “natural” pesticide. The bacterial gene produces a protein that is toxic almost exclusively to the plant’s principal predator, the potato beetle. Along with the rest of the plant’s DNA, the gene for the toxin is reproduced in every cell of the potato plant as it grows, protecting it from being eaten by the beetles. Thus it is unnecessary to spray the potato plants with insecticides that might kill other, more benign insects.
Rice is a major food staple in the developing world, where hundreds of millions of people suffer from vitamin A and iron deficiencies. Lack of vita- min A leaves people susceptible to disease and progressive blindness. Lack of iron affects even more people and causes anemia, as well as playing havoc with the immune system. Recently, a new strain of rice has been engi- neered that includes bacterial genes for producing beta-carotene, a protein that the human body converts into vitamin A.This golden-grained rice also has genes that promote the accumulation of iron. Thus, people who eat this grain get, at one bite, their staple food and a vital vitamin and mineral supplement.
Mixed-up corn
Here you can see the progressively larger edible seeds of selectively bred corn plants. The wild form, called teosinte, is on the left of the picture.
Doing Science
Wen-Jing Hu et al. 1999. Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nature Biotechnology 17: 808-812.
Dr. Hu and his colleagues report in this paper that they have genetically engineered aspen trees to make them into more useful and faster-growing paper producers. (Aspen trees’ structural cellulose chains are used to make paper, and the lignin molecules that “glue” the chains together gum up the papermaking process.)
Hu’s research demonstrates a way to block the gene that produces an enzyme that aspen cells use to make lignin. The genetically engineered trees end up with half as much lignin in proportion to cellulose as normal aspens have.
With a lower proportion of lignin to cellulose, aspen trees are not only more easily and cheaply made into paper — the process uses less energy and fewer chemicals — they also grow faster. The lower proportion of lignin also makes it more practical to use these trees to produce ethanol and other biofuels.
Size and surface
Wrinkles and bumps allowed the elephant’s ancestors to get big- ger. Increasing surface area by creating hills and valleys also allowed organs such as intestines (see page 68), lungs, and brains to increase their functional capacity while con- fined within a limited body space.
2.7	Life Creates with Mistakes
Accidents Ensure Novelty
When individual cells reproduce, they first make a copy of the information they carry in their DNA. Usually this copy is exact, so the information is transmitted per- fectly to the next generation. But every so often, cellular mechanisms make errors in nucleotide sequences — sometimes by only a tiny bit. Miscopying even a single nucleotide in a gene, like dialing a single wrong digit in a phone number, alters the gene sequence (see page 28) and therefore changes the piece of information being transmitted.The altered information may have no effect, or may show up in the off- spring as a defect. But every once in a while, it shows up as an improvement — something that makes the offspring better adapted for survival than its parents.
As an example, take the elephant. Scientists speculate that its early ancestors were small and smooth-skinned. Imagine a copying error in the distant past that jumbled the instructions for the elephant’s skin cells, making them assemble into wrinkly and bumpy patterns. It happens that wrinkly skin provides more surface area than smooth skin, a fact of geometry that came in handy for the elephant. Large animals generally have a problem with overheating. A wrinkled skin exposes more surface to the air or water and thereby cools the animal more efficiently. Thus wrinkled skin helped make it possible for the elephant to grow larger and to enjoy the advantages that come with increased size.
As you come to appreciate the evolutionary role of copying errors, it is apparent that calling them “mistakes” oversimplifies. We may, in a larger context, view them as nature’s way of introducing randomness, an essential feature of all creative processes.
A mistake for one organism can be an advantage for another.
Albinism, a defect in pigmentation, occasionally shows up in many kinds of plants and animals. Most albinos find themselves at a disadvantage in life, since they don’t blend into their surroundings, and albino offspring in many species do not survive infancy. Snowy white polar bears, ptarmigans, arctic foxes, and snowshoe hares, however, owe their camouflaging white coloring (and their very existence) to their albino ancestors.


Nature is, above all, profligate. Don’t believe them when they tell you how economical and thrifty nature is . . . Extravagance! Nature will try anything once. This is what the sign of the insect says. No form is too gruesome, no behavior too grotesque. If you’re dealing with organic compounds, then let them combine. If it works, if it quickens, set it clacking in the grass; there’s always room for one more; you ain’t so handsome yourself. This is a spendthrift economy; though nothing is lost, all is spent.
Annie Dillard, A Pilgrim at Tinker Creek, 1999
Mutations — Good or Bad?
Consider this paradox. The genes of all organisms have evolved to their present state through mutations — random changes in life’s information chains (DNA). Mutations have gotten us here. At the same time, a few of these mutations produce effects that are detrimental to the organism that inherits them. There are over 4000 known genetic diseases that are attributable to defects in a single gene. Huntington’s disease, Down’s syndrome, and sickle cell disease are examples of the harmful effects of mutated genes. Like a fine Swiss watch, perfected over centuries, an organism does not tolerate change easily. Modifications are likely to make it work less well, rather than better. Thus, it’s not surprising that life has evolved mechanisms to limit mutations. Cells have effective machinery for monitoring their DNA, finding errors and correcting them. So the mutation rate — the rate at which inherited, uncorrected changes accumulate in the genes of living creatures — is kept to a minimum.
There’s an important distinction to be made between the mutations that occur in the trillions of cells that make up the body and those that occur in the special cells that become sperm and egg cells. Mutations in body cells affect only the individual who sustains them. Mutations in sperm and egg cells, on the other hand, are passed on to another generation so a mutation rate substantially higher than the current one would compromise the future of the entire species.
Mutations are generally caused by: (1) mistakes made by the DNA duplicating machinery when cells divide, (2) X-rays or UV and cosmic radiation impinging on DNA, or (3) certain toxic chemicals interacting with DNA. Viewed more broadly, a mutation could be considered to be any change in DNA, such as a mistake in duplication resulting in extra genes or the acquisition of genes from a virus. It is important to realize, however, that although a small change in a gene can affect a critical function of a protein, many changes in genes affect non-crucial parts of a protein, and therefore have no noticeable effect. These neutral differences in protein can accumulate over time to produce the variations that we detect by gene sequencing (see pages 168-169). It might seem ironic that genetic mutation, the effects of which can be disease or malformation, is also the source of evolutionary creativity. When the venerable and trustworthy Swiss watch underwent the substitution of a quartz crystal for its spring, it made a quantum leap forward in timekeeping. So it is with genes. A mutation that allowed cells to stick together opened the door for all multicellular organisms. Such a change might have arisen when the gene for a receptor molecule in a single cell’s membrane mutated and instead produced a protein that recognized and bound firmly to a receptor molecule on another cell. Proteins called adherens act in just this way.
Sticky proteins
Cells stick together by adherens proteins at places on their membranes called desmosomes.
Housekeeping mutation?
The lens of the eye, as seen by a scanning electron microscope.
Mutations affecting the gene for an ordinary housekeeping protein may have resulted in the transparent tissue that forms the lens of the eye. That protein, called lactate dehydrogenase, has been involved in cellular energy production for millenia. It is structurally identical to lens proteins called crystallins, which stack like lumber inside lens cells.The crucial genetic event in the past was probably a change that allowed large quantities of the housekeeping protein to be made. Somehow, cells packed with an excess of the transparent protein provided a simple organism of the past with the ability to detect and respond to light. An advantage that made that organism survive and reproduce better than other, non-mutant types led, step by step, to the eye.
Whether a Mistake Is Good or Bad May Depend on Where You Are
Among humans, one genetic mistake shows up as sickle cell disease, a painful and debilitating hereditary condition. When depleted of oxygen (deoxygenated), normal human red blood cells retain their familiar round shape. In sickle cell disease, some of the deoxygenated red blood cells become elongated and curved in shape (like the tool called a sickle). When this happens, the sickle cells begin to clog blood vessels, and inflammation and tissue destruction occur. All of this damage is the result of a small change in the gene for the oxygen-carrying protein hemoglobin.
Interestingly, however, the sickle cell condition provides some protection against malaria, a blood parasite. Sickle cell disease is very common in equatorial Africa, where malaria is endemic. Scientists speculate that the disease, which might have been expected to remain uncommon because it decreases its victim’s chances for survival and reproduction, is common precisely because it protects against malaria, a serious killer in Africa. A person who is homozygous for sickle cell disease, meaning that the defective gene was inherited from both parents, usually dies at a young age; one who is heterozygous, or inherits the gene from only one parent, suffers a much milder form of the disease and thus lives long enough to enjoy its protective effects against malaria, and to pass the gene on to descendants. This offers a good example of how a beneficial trait that evolved in one environment (tropical Africa) may prove detrimental in another environment (temperate America and Europe).
Normal and sickled red blood cells
These are scanning electron micrographs of a normal red blood cell (top) and of a cell with just one incorrect amino acid in its hemoglobin protein (see that protein on page 17).
2.8	Life Occurs in Water
The All-Purpose Molecule
Of all the molecules of life, none is so omnipresent as water. Our cells are 70 percent water. Life began in water. When our ancestors arose from the sea to become land dwellers, we brought water along with us, within our cells and bathing them. Most of the essential molecules of life dissolve and transport easily in water.
Water participates in all kinds of chemical reactions. Bounded by water-insoluble membranes, cells owe their shape and rigidity to water. Water provides an inexhaustible supply of the hydrogen ions needed for converting the Sun’s energy into chemical energy.
What is it about water that makes it so special? The key is its polarity. Composed of a single oxygen atom sharing electrons with two hydrogen atoms like a head wearing a pair of Mickey Mouse ears — a water molecule looks quite ordinary. While the molecule’s overall electric charge is neutral, the oxygen tends to pull negatively charged electrons toward it, leaving the hydrogen “ears” slightly positively charged relative to the more negative oxygen “head.”
This means that an ear of one water molecule will form weak bonds with the head of another and vice versa, so that water molecules continuously stick and unstick to each other, thus forming dynamic, evanescent lattices. This self-embracing quality of water accounts for its tendency to remain liquid when most other substances with molecules its size are gases.
Most of life’s important molecules are readily soluble in water: they tend to form weak bonds with water as easily as water bonds with itself. The random motion of all molecules, and their tendency to spread out evenly in a solution ensures that, once dissolved, they rapidly diffuse throughout the body’s watery environment. Luckily for us, water also has the unusual
property of expanding when it freezes, so that the less dense ice floats. This provides an insulating layer that prevents further freezing of our lakes, rivers, and oceans. If water were like most natural materials, whose solid state is denser than their liquid state, ice would sink, and bodies of water in colder climates would freeze solid, making life untenable.
The most abundant fluid on Earth is, happily, the one most suited for encouraging living chemistry.
...this polarity enables water to form lattices, giving it an optimum viscosity and surface tension.
Water’s specialness is due to its molecular structure. The two hydrogens (Mickey’s ears) have a positive charge, the oxygen, a negative charge...
The Just-rightness of Water
Water is by far the most plentiful chemical constituent of living creatures; it is the medium in which life came into being on our planet; and it is a pervasive part of the environment in which we now find ourselves. That molecules consisting of nothing more than an oxygen atom bonded to two hydrogen atoms could be so essential to sustaining life seems hard to believe, but water has some surprising properties that make it optimally suited to its role. 1) Its tendency, already mentioned, to become lighter (less dense) as it approaches freezing, and even lighter when it crystallizes as ice. (2) Its relatively high heat conductivity as a liquid but poorer conductivity as ice or snow. (3) Its thermal capacity — the fact that it takes a lot of energy to change its temperatures. (4) Its high surface tension — cohesiveness or sticktogetherness (illustrated at left). (5) Its capacity to remain liquid over a wide range of temperatures. (6) Its relatively low viscosity — low resistance to flow and consequent ease with which substances diffuse through it. And finally (7) its activity as an almost universal solvent.
This unusual collection of properties has a number of consequences for our environment: Water is preserved on the Earth’s surface (it doesn’t fly off into space), and even in the coldest climates remains liquid under an insulating layer of ice and snow.	Consider the impact water has on rocks. Water has, for billions of years, crept into crevices of rocks (high surface tension), cracked them (when water froze and expanded), ground them up (in glaciers), dissolved their minerals, and carried these minerals to the sea in streams and rivers where they became essential constituents of living things.
Water contributes importantly to the general environment because of its resistance to temperature change; water vaporizes as the temperature rises (absorbing heat energy) and condenses as the temperature falls (releasing heat energy). If water’s density weren’t close to that of the creatures floating in it, they would sink to the dark cold of the bottom or rise to the surface where they would be more readily exposed to the damaging effects of ultraviolet light.
Within and among living cells, water’s optimum viscosity protects delicate structures from the sheering forces of shape-change and motion — it acts as a kind of lubricant. Evaporation of water from the leaves of plants and trees constantly pulls water upward — water’s surface tension makes this possible. In multicellular creatures, where a circulatory system is needed to move materials to all cells, and to conduct away waste and heat, water’s low viscosity ensures that tiny-diameter capillaries will conduct it and its dissolved chemicals to and from the remotest parts of the body. It is especially interesting that the viscosity of watery fluids containing cells (such as blood) drops as the pressure forcing it through a vessel rises, making the distribution of materials even easier.
It is hard to imagine a more perfect environment for life. This is why scientists searching for clues to the existence of life elsewhere (as on the Moon or Mars) keep a sharp eye out for evidence of past and present collections of liquid water.
Surface tension
The forces between the water molecules (shown above) are strong enough to support the weight of this water strider on the surface of a pond.
Water molecules’ tendency to stick together means that water disrupted by dissolved salts on one side of a membrane will attract water molecules from the other side of the membrane to dilute the salt solution — a tendency called osmotic pressure.
Question.
One of these fish lives in the ocean; the other lives in fresh water. The labels describe each fish’s water loss or gain and how it regulates the movement of water across its cell membranes. Which one of the fish must live in the ocean? What significance does the amount of urine production have?
Answer...
The fish on the right does not drink water, but still gains water through its cell membranes (osmotic water gain). Its exterior environment must be less salty than the interior environment of its cells; it is a freshwater fish. High urine production is a way of concentrating salts in body cells to keep the internal environment from becoming as dilute as the exterior environment.
Water Organizes and Orients Other Molecules
Almost immeasurably tiny and opposing electric charges accumulate on the single oxygen and two hydrogen atoms of a water molecule. The attractions and repulsions set up by these electric charges create an environment for life. Water molecules cling to one another’s oppositely charged ends, and so influence one another’s orientation in space.They also attract or repel and therefore orient other kinds of charged molecules.This interplay between electrical attraction and repulsion sets the scene for the development of molecular containers (cells) that maintain an inner and an outer environment.
The molecules (called phospholipids, see page 32), that make up most of a cell membrane have one charged end.The instant such molecules are in the presence of water, they orient their charged (phospho-) end toward the hydrogens of the water molecules.The fatty (lipid) tails of the molecules are not charged at all, and so tend to stay away from any water molecules. This hydrophilic (“water-liking”) and hydrophobic (“water-shunning”) molecular behavior provides a clue to how bilayered spheres might first have formed.
How salt dissolves in water
Table salt crystals are composed of oppositely charged sodium and chloride atoms (called ions). In water, the negative chloride ion attracts the positively charged end of water molecules, and the positive sodium ion attracts the negatively charged end. These attractive forces are strong enough to pull the salt crystals apart. Notice how the dissolved salt components can now diffuse quickly through the water.
Bilayered sphere formation
When a layer of phospholipid molecules like this one on the water’s surface is agitated by wind, spheres with water droplets inside can form, and when the sphere drops back to the surface, the fat-liking ends of the molecules on its outside join with those extending from the water surface to create bilayered spheres.
Plants produce and store sugar for their own consumption. Animals eat the plants or prey on those that do. Bacteria consume the bodies of all. Thus sugar percolates throughout life.
Glucose, life’s key sugar molecule, is broken down — metabolized — by living cells, and its parts used to make life’s essential molecules.
2.9	Life Runs on Sugar
A Molecule to Burn
Sugars are simple, energy-packed chains of three to seven carbon atoms festooned with hydrogens and oxygens. Life’s central sugar is glucose. It is the fuel that drives the engine of life and the basic material from which much of life is constructed. Each year, plants, marine algae, and certain kinds of bacteria convert 100 billion tons of atmospheric carbon dioxide (CO2) and hydrogens extracted from water (H2O) into sugar — using energy from sunlight in a process called photosynthesis. The by-product of this massive conversion is oxygen.
Plants, algae, bacteria and animals all “burn” sugar. That is, inside their cells they transform the energy in sugar’s chemical bonds into an especially potent form of chemical energy — ATP. In this living combustion process, called respiration, sugar’s carbons and oxygens are discarded as CO2 and its hydrogens are linked to oxygen from the air and discarded as H2O. Thus the very substance of life materializes from air and finds its way back to air. The constantly generated ATP powers all life’s work, such as moving, breathing, and laughing. Sugar also serves as the starting material for the assembly of the simple molecules — amino acids and nucleotides — from which large molecules are assembled.
Several hundred million years ago, the rate of photosynthesis was greater than respiration, and enormous quantities of the remains of trees, plants, animals, and bacteria were buried deep in the earth, subjected to intense heat and pressure, and transformed into coal, petroleum, and natural gas. Much of this material was initially chains of sugar molecules — cellulose and other related chain molecules. So sugar reemerges as the basic ingredient of the fuels that drive the engines of civilization.
Each year terrestrial and marine plants make enough glucose to fill a freight train 30 million miles long.
2.10	Life Works in Cycles
A steam engine
The engine’s main wheel is turned by steam. A belt from the wheel causes the governor — a spinning ball system — to rotate. The faster the wheel turns, the faster the governor’s shaft turns, the farther outward fly the balls. This lifts the disk, raising the lever, and closes the steam input line, slowing the engine.
Circular Control
In the simplified steam engine above, a fire heats water, making steam, which activates a piston, which turns the engine’s drive wheel, which spins the governor, which controls the steam supply. Such a three-component loop passes information from part to part so that the engine is able to self-correct by way of the governor.
A similar self-correcting system comes into play when a protein makes a chemical product. Each protein performs a simple task (e.g., adds a part) in assembly-line fashion. The circular arrangement allows the initial protein to keep track of the overall output. As products either pile up or become scarce, it adjusts the speed of the overall operation. Chapter 6, Feedback, discusses how it does this.
A Circular Flow of Information
Life loves loops. Most biological processes, even those with very complicated pathways, wind up back where they started. The circulation of blood, the nervous system’s sensing and responding, menstruation, migration, mating, energy production and consumption, the cycle of birth and death — all loop back for a new start.
Loops tame uncontrolled events. One-way processes, given sufficient energy and materials, tend to “run away,” to go faster and faster unless they are inhibited or restrained. The steam engine with a governor illustrates the principle: As steam pressure rises, the engine goes faster. The governor, consisting of two rotating arms that lift higher as its shaft spins faster, progressively reduces the steam input; the engine slows; the governor slows; the steam input increases; the engine speeds up. Thus information courses around the circuit to produce action in the opposite direction.The system self-corrects; the parts self-adjust. If such self-generated restraints and inducements occur in small steps, the overall system appears to maintain itself in a steady state.
Every biological circuit, whether a sequence of proteins in the act of consuming a sugar molecule or a complex ecosystem exchanging material and energy, exhibits selfcorrecting tendencies like those of the steam engine.
Information flows around the circuit and feeds back to the starting point, making necessary adjustments along the way. It’s easier to understand how molecular systems assemble into complicated, apparently purposeful organisms when we look at events in terms of multilayered loops of control and creation — and substitute the term “self-correcting” for “purposeful.”
Doing Science
A large number of valuable scientific hypotheses were inspired by the Industrial Revolution (including the governor on steam engines).
T. H. Huxley (1825–1895), a British anatomist, describes an early reductionist approach to understanding biological processes in just such terms. (Huxley was the first and one of the strongest supporters of Darwin’s theory of evolution by natural selection and was often called “Darwin’s bulldog.”
After men acquired a rough and general knowledge of the animals about them, the next thing which engaged their interest was the discovery in these animals of arrangements by which results, of a kind similar to those which their own ingenuity effects through mechanical contrivances, are brought about. They observed that animals perform various actions; and, when they looked into the disposition and the powers of the parts by which these actions are performed, they found that these parts presented the characters of an apparatus, or piece of mechanism, the action of which could be deduced from the properties and connections of its constituents, just as the striking of a clock can be deduced from the properties and connections of its weights and wheels.
T. H. Huxley, The Crayfish, 1880
Self-correcting maneuvers
As an owl tracks a fleeing mouse, she quickly translates the mouse’s zigzags into movements of her wings and tail. The owl gets her dinner by maintaining a feedback loop between her eyes, brain, wing and tail muscles, and the mouse’s movements.

CHAPTER 1
SETTING THE STAGE
IMAGINE YOU ARE WALKING ALONG A DESERTED BEACH AND YOU COME UPON THE CARCASS OF a whale. Time and tide and carrion birds have taken much of the flesh. Your first reaction might be a compassionate recognition of kinship. You might be curious about what happened — what was this whale’s story?
As you examine the skeleton, a pattern strikes you. In each of the whale’s front fins, the bones are arranged in three sections, with one bone in the section closest to the body, two parallel bones in the middle section, and five radiating branches of smaller bones in a more complex outer section. In fact, the bones of a whale’s fin look very much like those of a human arm and hand. The proportions differ, but the pattern is remarkably similar.
How is it that a whale has arms like yours? And why does a whale have finger bones when it doesn’t have fingers? Does this mean we’re related to whales? Could it be that this limb pattern has been around longer than either whales . . . or humans?
1.1	A Singular Theme
When we muse about life, what impresses us is its diversity — the sheer variety of organisms everywhere we look. Televi- sion programs and books about nature tend to celebrate the astonishing multiplicity of ways that life has adapted to our planet. This book’s theme is different: It celebrates unity. It focuses on the things common to all forms of life, everywhere on Earth.
Those homologous, or common, patterns in the bones of the human arm and the whale fin and, for that matter, in the bones of a bird’s wing and a bat’s wing, and even in the fossil remains of creatures that lived millions of years ago — are the first visible signs of unity. And the deeper we explore, the more signs we discover.
Every living being is either a cell or is made of cells: tiny, animate entities that gather fuel and building materials, produce usable energy, and grow and duplicate.
1.2	Thinking Small
Much of this book takes place inside the cell. If you are unfamiliar with this microscopic landscape, understanding just how small and how numerous molecules are requires a considerable stretch of the imagi- nation.
The great Scottish mathematician and physicist Lord Kelvin said:“Suppose that you could mark the molecules in a glass of water; then pour the contents of the glass into the ocean and stir the latter thor- oughly so as to distribute the marked molecules uniformly throughout the seven seas; if then you took a glass of water anywhere out of the ocean, you would find in it about a hundred of your marked molecules.”
Size and speed are related. Generally, the smaller an object is, the faster it can move. Water molecules, and all the other thousand or so kinds of molecules you have within you, swim about at stupendous speeds, flashing past each other and bumping into each other every millionth of a millionth of a second.
Life depends upon these frequent and vigorous collisions. It becomes a little easier to grasp the speed of the life-sustaining chemical transformations that constantly occur inside your cells (at the rate of thousands of events per second) when you realize that the participants move and collide millions of times faster.
When we think about parts of the body, we tend to think of organs: lungs, heart, brain, etc. The next step down in size brings us to the cells of which those parts are made. That drop in size is immense. Human cells are about ten times smaller than the point of a pin, and your body is composed of 5 trillion of them. With- in each cell are multitudes of atoms, molecules, and structures made of molecules — the principal characters in our story.
As we introduce them, the picture above might help you to grasp their relative sizes.
Imagine you are standing on a pier. In one hand, you hold a BB — its size will represent an atom. In the other hand, you hold a marble — analogous to a simple molecule. Next to you is a cat — a chain molecule. Parked nearby is a tractor-trailer truck — a molecular structure. Tied up at the pier is an ocean liner — a cell. The pierisonthecoastof NorthAmerica—thewholecontinentbeinganalogousinsizetoahumanbeing.
On the following four pages we present a visual guide for distinguishing small things. Notice that four separate scales are necessary for spanning the range of size from atom to cell (a 200,000-fold jump in size).
From Atoms to Cells — Comparative Sizes
Scale 1. Atoms and Molecules
Magnified 50 Million Times
Atoms are the elemental units of which everything in the universe, living and non-living, is made. Atomic diameters range from one to a few hundred millionths of an inch.
Molecules are atoms bonded together. Much of life depends on three tiny molecules that have 2 to 3 atoms apiece: carbon dioxide (CO2), the ultimate source of life’s carbon atoms; oxygen (O2), the gas crucial to energy generation in most life forms; and water (H2O), the sea inside our cells in which life’s machinery is bathed, and which aids chemical events inside our cells.
Roughly one thousand different kinds of slightly larger mole- cules made of 10 to 35 atoms are also found inside cells.These small molecules are either food (fuel) or building materials, or molecules that have been or will be food or building materials. We call all these simple molecules.The important ones in this book are sugars, nucleotides, and amino acids.
Throughout this book we depict nucleotides and amino acids as shown above. This best illustrates their function.
Scale 2. Chain Molecules
Magnified 10 Million Times
The vital working parts inside cells are chain molecules — very long strings of many simple molecules linked to one another.The most numerous of the chain molecules are proteins, which consist of 300 to 400 or more amino
acids strung end to end. Each protein molecule — there are thousands of different kinds — has a special job to do in the cell. Cells also contain many varieties of ribonucleic acid (RNA), which can have tens of thousands of linked nucleotides, and deoxyribonucleic acid (DNA), which can have millions of nucleotides.
Scale 3. Molecular Structures
Magnified 1 Million Times
Chain molecules can fit together forming complex architectural arrangements — called molecular structures — inside cells.These complex molecules are the cell’s infrastructure, the equivalent of its roads, tunnels, power plants, factories, and libraries. Shown here are a ribosome, the cell’s protein-making factory, and a bit of a mitochondrion, the cell’s energy generator.
Scale 4. A Cell
Magnified 10 Thousand Times
An animal cell, like this one, has a nucleus, which contains most of its DNA.The nucleus is surrounded by the cytoplasm, where most of the cell’s active processes occur. An average plant cell is about three times larger than an animal cell.
Robert Hooke — discovering a new world
Hooke was so enchanted by the new world of tiny things that he studied and observed anything and everything he could. Among his Descriptions of Minute Bodies Made by Magnifying Glasses With Observations and Inquiries Thereupon, recorded in 1665, were these snowflake structures at four different magnifications.
1.3	Using Microscopy to Explore the Cell and Beyond
Focus on the Minuscule
All the pictures you see on pages 6 and 7 of atoms, molecules, chain molecules, molecular structures — including a bit of a mitochondrion — depict things that until this century were invisible and thus unknown to us. It was not until the mid 1600s that the first evidence of the existence of things smaller than the unaided eyes could see was gathered.
In the 1660s, Robert Hooke was the first to report using a magnifying lens to systematically study the microscopic world (see above). It was he who first applied the term “cell” to each of the densely packed chambers he saw in a thin slice of cork. As he carefully drew each one, he was reminded of monks’ cubicles — otherwise known as cells. This was the first documented microscopic observation of what we now know to be the basic structural unit of living things.
During the next three centuries, many improvements were made to the basic microscope (called the light microscope), and people were able to observe a previous- ly unexplored universe of microstructures and microorganisms. Cells and many details of their surfaces and interiors, bacteria and their moving parts, and millions of other tiny living things are vividly observable under a light microscope. But the light microscope has its limits. To get a closer view, a new technolo- gy had to be created. To communicate the sizes of the minuscule things observed, a new system of measurement had to be devised.
All the units we use for measuring the sizes of these minuscule structures are subdivisions of a meter — the standard unit of length used in the metric system (or International System of Units). A centimeter is 1 hundredth of a meter (10-2), a millimeter is 1 thousandth (10-3), a micrometer is 1 millionth (10-6), and a nanometer — the unit we use on pages 7 and 8 — is 1 billionth of a meter (10-9).
I wish [that man], before entering into larger studies of nature . . . [would] look on himself and get to know the proportions between nature and man . . . let him behold the tiniest things he knows of. Let a mite show him in the smallness of his body parts incomparably smaller legs with joints, veins in the legs, blood in the veins, humours in the blood, vapors in the drops, which dividing to the smallest things, he wears out his imaginative powers. . . . Blaise Pascal, Pensées, 1669
Magnified to the max
This is a strand of bacterial DNA magnified using current technology — a scanning electron microscope. Magnify- ing a 12-inch length of string this much would yield an image twelve miles long. We can see that DNA is a long molecule, but we get no information about the details of its structure.
The light microscope, which works by magnifying and focusing the image formed when light passes through an object, cannot distinguish objects smaller or closer together than the shortest wavelength of visible light. (Visible light is just that — the light we can see, and its shortest wavelength is small indeed — about 200 nanometers or nm)*. A protein molecule, like the one shown at different scales in all the drawings on pages 6 and 7, is only about 4 nm, and so is not visible through a light microscope). The transmission electron microscope and the scanning electron micro- scope use a beam of electrons controlled by electromagnetic fields. With such a micro-scope it is possible to see details of cell surfaces and interiors invisible with a light microscope and to discern at least the rough shapes of large molecular structures such as ribosomes.
Comparing Sizes
The scanning electron micrograph at right shows part of the inside of a cell, including a piece of a mitochondrion (marked M) and a portion of a Golgi body (marked G). The scale line is 1000 nanometers, or 1 micrometer. The mito- chondrion is about the size of the common bacterial cells (E. coli) that live in our intestines. Ribosomes (25 nm) and indi- vidual proteins (25 nm) are far smaller, almost invisibly so, even to the most powerful microscopes. We can only visual- ize the details of these complex, interlaced chains of mole- cules through the mathematical power of computer models, using data from X-ray diffraction (see page 13).
*See page 106 for more about light.
It’s a small world
A magnified pin point with a population of E. coli bacteria.
A 3-D interior
This view allows us to see many of the cell’s molecular structures, or organelles.
The cell’s nucleus
The rounded shape in the upper left of this micrograph is the nucleus of a cell; it is covered by outer and inner nuclear membranes (ONM and INM) and surrounded by cytoplasm, in which float various organelles. PM (plasma membrane) marks the double membrane that envelopes all of the cell’s contents.
“Faith” is a fine invention When Gentlemen can see — But Microscopes are prudent In an Emergency
Emily Dickinson (1830–1886)
How many bacteria can live on the point of a pin? Quite a few. The rod-shaped bacteria in the picture (top right), each a single cell, are about the size of the mito- chondrion you saw on the preceding page, anywhere from 1000 to 1500 nanome- ters long. A typical animal cell is much larger; its nucleus (the library) — a portion of which you see above left in a cell broken open by freezing and then fracturing it — is roughly ten times larger in diameter than the bacterium.
Another view of the cell (above right) on a similar scale of magnification, but using a different magnification technique, shows part of the nucleus (N), and more of the cytoplasm’s contents, such as Golgi bodies (protein-packaging factories, G) and vesicles (V).
The smallest living cells are about 1 micrometer, or 1 millionth of a meter, in size. Among the largest cells is Acetabularia, an algal cell that can reach 10 centime- ters in length (see page 189). Some animal nerve cells are incredibly long, reaching from the spinal cord to the foot, although they are so thin that you would still need a microscope to see them.
Using X-ray Diffraction
Not only do microscopes allow us to “picture the invisible,” they allow us to see them in their natural “landscape,” in relation to the other structures around them. If we want to go deeper and study the structural details of the individual protein mole- cules that do the cell’s work and are critical parts of cellular structures, we must resort to a different approach. First, we must “isolate” the protein molecules — free them of all of the associated materials that surround them. The protein molecules are crystal- lized, so that they stack regularly in a three-dimensional lattice. Then, we apply X- ray crystallography, which allows us to “see” the molecules at a wavelength of a few tenths of a nanometer (close to the diameter of a hydrogen atom!). This technique contributed to Watson and Crick’s discovery of the double helix structure of DNA and Perutz and Kendrew’s description of the structure of the blood protein hemo- globin — Nobel-Prize-winning achievements.
X-rays, like visible light (and the microwaves in your oven, for that matter), are a form of electromagnetic radiation (see page 106), but their wavelength is much smaller: 0.1 nm. If a beam of X-rays is focused on a crystallized protein, most of the rays pass through, but some are deflected, or scattered, when they hit the atoms. The deflected X-rays will produce a diffraction pattern — a pattern of exposure spots on a photographic film placed behind the protein sample. Regularly repeating atoms in the crystal structure deflect the X-rays at certain angles, creating, on the film, spots whose density and spacing correspond to the density and spacing of the atoms.
Collaboration among many scientists has combined information from X-ray dif- fraction,electronmicroscopy,andothertechnologies. Thisinformation,enteredinto enormous data banks, is the basis for accurate computer models of various, amazingly complicated protein molecules. Now we truly can visualize the invisible.
Light diffracted by DNA
In this diffraction pattern of DNA captured by Rosalind Franklin and deciphered by James Watson and Francis Crick (see page 157), the distance between spots forming the X indicates the distance between turns of the DNA’s helix. The X is a reliable indicator of a helical (corkscrew-like) molecular shape.
1.4	Parts and Wholes
It’s useful to think of life’s organization in levels, from the simple to the complex: atoms, simple mole- cules, chain molecules, molecular structures, cells — and onward and upward to organs, organisms, popula- tions, communities, and ecosystems. A higher level includes everything in the levels below it, as shown by the Russian nesting dolls above.
Scientists find that knowing a lot about a lower level produces useful explanations of what’s happening at the next higher level. To understand how your car works, you must know something about cylinders and spark plugs and fuel injection and how they interact.
This way of getting to understand the whole by learning about its parts, called reductionism, has pro- duced in the last several decades an explosion of knowledge about what genes are and how they work, and how living processes are energized, informed, operated, and controlled. They are the “what” and “how” questions we take up in this book.
When we ask why things are the way they are we need to see things from the outside, and in relation- ship to others and to the surroundings. For example, why do birds have different beaks? To discover the answer, we need to study not just the birds themselves but the food they eat and where they live. “Why” questions address patterns of connection in both space and time. They relate particularly to evolution — a subject touched on throughout Chapter 2, Patterns, and explained in depth in Chapter 8, Evolution.
Biochemists and molecular biologists tend to see themselves as reductionists, while naturalists and ecol- ogists tend to take a holistic view. But, in fact, every scientist must shift his or her gaze regularly from the parts to the whole — from the trees to the forest — and back again.
We recommend that you try to be similarly fluid so that you can move back and forth with us as we shift from the tiny micro world to the larger macro world and back again.
1.5	The Way Science Works
“Why” questions have been posed ever since humans have had conscious brains, and over the course of the last 300 years or so, observant, curious people scattered everywhere on Earth have, in common, devised averifiable,self-correctingsystemforansweringthesequestions. Wecallthatsystemat- ic asking of questions and search for answers science.
Science is, in essence, organized curiosity. It is initiated by careful observation and nurtured by wonder, creativity, and skepticism. While the overall pattern of a scientific inquiry is common to scientific work, each individual explorer lays out his or her own itinerary into the unknown: observes an interesting event or phenomenon, identifies a particular aspect of it that can be stated as a problem, produces a hypothesis (an imag- ined scenario) that explains the event, and when possible, tests the hypothesis by exper- iment. In science “one endlessly play[s] at setting up a fragment of the universe which the experiment . . . rudely correct[s]” (François Jacob). The process is a wholly natural and active extension of the one we all use intuitively, from birth, to build our picture of reality.
The hypotheses scientists come up with generally lend themselves to predictive statements: If I do this, that should happen. If a prediction is borne out by experiment or observation — if the predicted event happens — this outcome builds confidence in the hypothesis but cannot prove it right (since better information or new experimen- tal techniques may come along later and indicate that it’s wrong). Thus, good hypotheses are often those that suggest ways in which they can be proved false. If a hypothesis offers no way to prove itself false, it is not useful scientifically. The conclusions scientists arrive at after extensive observa- tion or after experimentally testing many hypotheses are statements that have a greater or lesser probability of reflecting reality; they are never certainties. They gain strength as ongoing tests and accumulating evi- dence continue either to verify them or to prove reasonable alternative hypotheses to be false. And the better the conclusions fit with those of other experimental approaches to the same problem, the surer we are they’re right. The possibility that some of our most cherished truths may someday turn out to be false can never be ruled out. “In the growing cathedral of science, many crumbling stones at the growing points are replaced, and the more important their position, the sooner the defect is disclosed” (B. D. Davis).
Hypotheses that are disproved by experiments have value, of course. They are signposts telling others where not to go. In science, an idea becomes substance only if it fits into a dynamic accumulating body of knowledge, a progression of understanding. Each new piece of work must fit into the bigger picture — the published work of other scientists. It is inspected, tested, tentatively accepted, modified, perhaps discarded. In the march of scientific discovery the artisans of experimentation blend into history like the builders of the great cathedrals. Scientists would have to have more than their fair share of egotism to avoid acknowledging their own expendability. This reality, as well as teaching us how little we know and how difficult what we do know was to come by, makes science a profoundly humbling experience.
Observation of and wonder at the workings of nature are what initiate “why” questions.These activities are not the sole province of scientists. In fact, they begin in childhood and are more or less developed in all of us.Throughout this book you will find observations of nature by novelists, poets, amateur scientists, and painters, done in their own ways. Science joins art as another branch on the tree of observation and wonder.
The Ultracentrifuge
Developing tools (like the microscope) that help us to visualize, measure and define the invisible world around us is one very active and imaginative aspect of the scientific process. Biology adapts the tools of other sciences and of industry to its own purposes.
Dr.T. Svedberg, at the University of Uppsala, Sweden, was trying to find a way to make the protein molecules he was studying settle out of the solution they were floating in. Learning of work done in England in the 1880s in fluid dynamics that used a very fast-spinning centrifuge (from the Latin for “flee from the center”) to increase the gravitational pull on objects in solution, he seized on this idea to devel- op an entirely new way of separating and comparing the sizes of cell components and biological molecules — the ultracentrifuge.
Over the succeeding 75 years, the ultracentrifuge has proved to be one of the most useful tools of cell biology and biochemistry. It is basically a rotor that spins tubes containing materials from broken cells at speeds of up to 80,000 rpm — exert- ing a force of as much as 500,000 times that of gravity!
Cells are first broken open by any of several means: by grinding in a glass tube and rotating pestle, by treatment with ultrasound, or by osmotic shock. These proce- dures are carried out in the cold in solutions resembling those in the interior of cells. The result is a sort of rich organic soup (referred to as a homogenate) in which most of the cells’ organelles remain intact and functional.
The most common use of the ultracentrifuge is to prepare large quantities of cell components for use in biochemical laboratory experiments. The homogenate is centrifuged first at low speed (typically at 1000 times gravity for 10 minutes). This brings whole unbroken cells, clumps of membranes, and nuclei to the bottom of the tube in the form of a “pellet.” The fluid above this pellet, the supernatant, is poured into a second tube and centrifuged at 20,000 times gravity for 20 minutes, produc- ing a pellet of mitochondria. Next, the supernatant above the mitochondria, centrifuged at 80,000 times gravity for an hour, yields a pellet of microsomes (ribosomes attached to mem- branes). Finally, very high-speed centrifugation (150,000 times gravity for 3 hours) yields free ribosomes and large molecules.
Velocity sedimentation provides a finer degree of separa- tion. Here, large molecules like the chain molecules on page 7— proteins, DNA, and RNA — are centrifuged through increasing concentrations of sugar (sucrose), where they sepa- rate into bands according to their size. The rate of sedimenta- tion (the S value, named after Svedberg) is a standard way of describing the size of large molecules.
This tiny tissue section of liver cells, blood cells, and con- nective tissues would be ground up into “organic soup” and centrifuged to separate out the various cellular components.
1.6	The Way Life Works — The Basic Idea
In exploring life’s unity, we set out to connect the world of molecules with the world you can see around you.
Our central characters in this story are two chain molecules: One carries the information,theotherdoesthework. Toputthingssimply,youmightsaythatlifeis played out in the interaction between these two players — DNA and protein, whose relationship can be seen as that between information and machinery.
A computer-created model
A model of the oxygen- carrying protein hemoglobin, a chain molecule contained in all of our red blood cells. Each tiny sphere represents an atom of carbon, nitrogen, hydrogen, or iron. The atoms are bonded together in amino acid molecules, which in turn are strung together into chain molecules, which fold and twist into very specific three-dimensional molecular structures — in this case called globular proteins — of which four then join to form a multiple-chain molecule.
Picturing the Invisible
Objects the size of atoms, simple molecules, and even DNA and proteins, are truly invisible because, even with the aid of the highest-magnifying microscope, our eyes can’t see them. Although as you have learned scientists do have other powerful ways of finding out what very small things “look” like (see the computer model above), nobody really sees details of molecular structures exactly. Thus we have taken liberties in picturing our principal molecular characters in ways that convey clearly what they do.
We depict DNA as a kind of extended Tinker-Toy structure that readily assem- bles and pulls apart. Proteins — the working molecules of life — are pictured as somewhat human-like little characters. This distinguishes them — things that act — from other molecules, things that are acted upon. We don’t imply that proteins are like people in any other ways — except, perhaps, for a certain obsessive tendency to do the same things over and over again. The protein’s affable but blank expression should convey the idea.
Your Itinerary — A Map of This Book
The next chapter — Patterns — offers a panorama of some of life’s key features designed to focus your thinking and whet your appetite. Many of the questions it raises will be answered by the time you’ve finished the book.
Life is sustained by the conversion of sunlight into energy. The story of this flow is the subject of Chapter 3, Energy.
You may find it useful, in starting out, to think of Information, the subject of Chapter 4, as a primer on the “know-how” for life, written out in the chemical language of DNA, and stashed inside each cell of a living organism. Information, in turn, codes for life’s Machinery, discussed in Chapter 5 — protein molecules that do all life’s jobs, including constructing themselves.
Energy, information, and machinery would lead nowhere without some means by which cells can regulate rates of chemical reactions, minimize waste, promote efficiency, and ensure that multiple interlocking processes work harmoniously together to promote the welfare of the whole. This is the role of life’s system for coordination and control — which we call Feedback, the focus of Chapter 6.
All the above has to do with what individual cells need to live and function. Chapter 7, Community, examines principles governing how cells interact with each other in multicellular organisms and, particularly, how a single cell — a fertilized egg — becomes a multicellular individual.
Having examined the “what” and the “how” of life, we consider the “why”: Why are living things the way they are? As information passes from generation to generation over vast stretches of time, it changes and, inevitably, modi- fies life’s machinery. That machinery, the means by which every organism makes contact with the surrounding world, determinestheorganism’sfateand,consequently,thefateoftheinformationwithinit. Chapter8addressesthetheme that knits all of biology together into a comprehensible whole — Evolution.
Some of the Things You Learned About in Chapter 1
atoms 6 carbon dioxide (CO2) 6 cells 4, 6–9 chain molecules 7 deoxyribonucleic acid (DNA) 7 diversity 3 experiments 15 hemoglobin 17 holism 14 homology 3 hypotheses 15 measuring tiny things 7, 10 molecules 6 molecular structures (ribosome, mitochondrion) 7, 8–11
nanometer (nm) 7–9 nucleotides, amino acids, and sugars 6 nucleus 8, 12 oxygen (O2) 6 proteins 6, 17 reductionism 14 ribonucleic acid (RNA) 7 science 15 simple molecules 6 the ultracentrifuge 16 unity 3 visible light 11
Questions About the Ideas in Chapter 1
1.	The theme of this book is expressed on the first page — uncovering the unity in diversity. In light of what you have read in this chapter, what does this phrase mean to you?
2.	Come up with an example of unity in diversity from your own surroundings. 3.	As you observe the photographs and illustrations in this chapter, what “why” questions can you come up with? Alternatively, look around, outdoors or in, and come up with some “why” questions.
4.	Why bother to connect the “world of molecules” with the world you can see around you?
5.	What are homologous patterns? What does the existence of homologous patterns tell us about pos- sible relationships among apparently dissimilar living creatures?
6.	If you were the person standing on the dock in the picture on page 4, would you be closer in size to a simple molecule, a chain molecule, a cell, or a molecular structure?
7.	Three tiny molecules (2 to 3 atoms apiece) found in abundance on Earth, are essential to life. What are they?
8.	Three larger molecules (10 to 35 atoms apiece) are the building blocks for life’s energy, information, and machinery systems. What are they?
9.	Which of the following best captures the meaning of the nest of dolls on page 14? (a) Everything fits into compartments. (b) A higher level includes everything in the levels below it. (c) The bigger the object, the more complicated its parts.
10.	Look carefully at the skeletal forelimbs of the frog, lizard, cat, and whale. See if you can identify and label the homologous bones in each. Describe some of the useful differences among these structures that make them well suited for the environment and needs of that organism. Can you hypothesize as to why the thickness of the bones of the cat and the whale differ so much? What might be one explanation for the structural differences between the cat’s forelimb and the lizard’s?
11.	Unity and diversity frequently go hand-in-hand even with ordinary household objects. Choose two completely different types of chairs with which you are familiar, and describe how they are the same, and yet different. Find the one single unifying element for all chairs, then show how multiple varia- tions can be made using different types of chair components (wood, stone, metal, plastic, bamboo) arranged in different ways.
12.	To understand cellular fractionation, answer the following questions based on the size, weight, and density of a substance: Gold sinks to bottom of a prospector’s pan, while dirt particles remain sus- pended in water — Why? Why does the nucleus separate out and sediment on the bottom of the tube in a low-speed centrifuge run, while membrane vesicles (smaller, sealed pieces of membrane) require much faster speeds (higher gravitational forces) to form a pellet on the bottom?
References and Great Reading
Alberts, B., D. Bray, J. Lewis, M. Raff, K. Roberts, J.D.Watson. 1994. Molecular Biology of the Cell, 3e. New York & London: Garland Publishing, Inc.
Bozzola, John L., and Lonnie D. Russell. 1999. Electron Microscopy, 2e. Sudbury, MA: Jones and Bartlett Publishers.
Bronowski, Jacob. 1973. The Ascent of Man. Boston: Little, Brown and Company.
Davis, B. D. 2000. The Scientist’s World. Microbiology and Molecular Biology Reviews, 1-12. Robin, Harry. 1992. The Scientific Image, From Cave to Computer.
NewYork: Harry N. Abrams.
Strickberger, Monroe. 1999. Evolution, 3e. Sudbury, MA: Jones and Bartlett Publishers.
Svedberg,T., and R. Fähraeus. 1926.A new direct method for the determination of the molecular weight of the proteins. J. Am. Chem. Soc. 48: 430-438.
For more questions and links to web resources, go to
WEB Connection
www.jbpub.com/connections

A continuing feedback loop keeps the micro environment of this pond clean and nurturing for all kinds of organisms (a). Aquatic plants photosynthesize and provide food and oxygen for aquatic animals, which produce carbon dioxide as waste, and eventually die, providing further nutrients for microbes and plant life. When too many nutrients are pumped into such an environment from fertilizer used on crops or lawns, an uncontrolled event occurs; the loop is interrupted. In response to the nutrients, huge numbers of plants grow (b), far more than the animal life can process. The plants die and fall to the bottom. In decomposing, the plants use up all of the water’s dissolved oxygen.
Question.
What would be the overall effect of too little oxygen in the water? How could the interrupted loop be reestablished?
Answer...
With too little oxygen, fish and other aquatic animals suffocate. Their decomposition uses up even more oxygen. Limiting nutrients such as phosphorus and nitrogen that enhance plant growth and/or aerating the water to introduce more oxygen would help reestablish the pond’s balanced ecology.
Fever as a Feedback Loop
Fever is the body’s biological response to viral and bacterial infection. Proteins called pyrogens, produced by the invading organisms and by the body’s own white blood cell defense system, cause an area in the brain called the hypothalamus to “reset” the body’s temperature higher. This reset signal constricts the blood vessels and causes shivers (which produce heat internally). The body’s core temperature rises to the new set point, and the higher temperature either kills the invaders outright or stimulates the body’s immune system to dispatch them.
When the invaders have been destroyed, pyrogen levels drop. The body responds by dilating the blood vessels and sweating profusely. Evaporation of water from the skin surface cools the body, bringing its temperature back to normal. This is a classic feedback loop — a self-correction par excellence.
Big eaters
Here is another part of the feedback loop that suppresses infection. The green invading bacteria are engulfed by large white blood cells called macrophages (“big eaters”). The bacteria and the macrophages produce pyrogens and other proteins that cause immature white blood cells to mature into macrophages that can engulf more bacteria. This cycle continues as long as there are bacteria to trigger it.
Macrophages attack bacteria	Macrophage engulfs bacterium and displays parts on surface
Proteins secreted
Specific immune response initiated
Body temperature rises
Monocytes triggered by proteins to mature into macrophages
Interfering with Self-Adjusting Systems
The elaborate anatomical loop you see below — the human gas transport and exchange mechanism (the respiratory and circulatory systems) — has many feedback functions: It regulates the blood’s oxygen and carbon dioxide levels, helps maintain blood’s acid-base balance, and helps protect us from airborne toxins and disease.
Biological circuits like this one exist in a delicate balance with their extracellular environments. If something coming from outside interferes with the functioning of one part of the loop, the system will call for greater input from other parts of the loop — heavier breathing, faster heart rate, and so on.
The gas transport loop works effectively if the body’s gaseous environment remains within certain limits — for example, if the lungs take in normal atmospheric gases (mainly oxygen, nitrogen, and carbon dioxide). Add an uncontrolled event to the mix — carbon monoxide, sulfur oxides, nitrogen oxides, or ozone (produced by cars, power plants, factories, home heating and air conditioning systems, and cigarettes), and blood chemistry goes awry, along with the respiratory system’s cellular functioning.
Breathing as a feedback loop
This is how we exchange gases with the environment: Oxygen, absorbed by alveoli in the lungs, enters the bloodstream and travels to body tissues. CO2, the product of respiration, diffuses into the blood from tissue cells, travels to the alveoli, and is exhaled.
The pollution connection
This graph is a dramatic display of the relationship between an episode of high air pollution in New York City in 1962. In — sulfur dioxide levels rose from 0.2 ppm to 0.8-0.9 ppm, and immediately the numbers of nasal infections, colds, coughs, pharyngeal infections, eye irritation, and headaches all rose dramatically. [Redrawn from J.R. McCarroll et al., Health and the Urban Environment: Health Profiles versus Environmental Pollutants in American Journal of Public Health 56 (1966): 266-275.]
For every molecule that the living world makes or uses...
...there exists an enzyme somewhere to break it down.
2.11	Life Recycles Everything It Uses
A Circular Flow of Materials
We humans are unique among animals; we leave behind us a trail of accumulating, unusable products. Everywhere else in the living world, intake and output are balanced, and one organism’s waste is another’s food or building materials. Waste from a cow circulates from bacteria to soil, to earthworms, to grass, and back to the cow. Crabs need calcium, which they normally get from the ocean, to build their shells. Land crabs, lacking an ocean source, extract calcium from their own shells before discarding them during molting. Hermit crabs save energy by moving into shells cast off by other species, trading up when the shell gets too small. At the molecular level, key atoms pass from molecule to molecule in a succession of small steps. The end product of one process becomes the starting point of another, the whole train of events bending around into a circle. One creature’s “exhale” becomes another’s “inhale.” Oxygen, dumped by plants as a by-product of photosynthesis, becomes an essential key to combustion in animals’ respiration. The carbon dioxide waste that animals exhale is taken up by plants for sugar-making. From the standpoint of the whole ecosystem, these interchanges occur so smoothly that the distinction between production and consumption, and between waste and nutrient, disappears.
Each generation of living things depends on the chemicals released by the generations that have preceded it.
In a continuous cycle, plants and animals exchange the chemicals necessary for energy and building materials.
Carbon exchange
Carbon atoms are the basic structural units of the molecules that compose the cellular structures of all living organisms. The purple arrows show how, by photosynthesis and respiration, carbon circulates through organisms and their environments. The carbon of long-dead organisms may be stored for millions of years in limestone (the remains of shellfish) or in oil and coal deposits (the remains of other living things). Eventually, even that carbon is used as fertilizer, or burned and released to the atmosphere as carbon dioxide, once more becoming part of life’s carbon loop.
Ultimate Recycling
When things die, they don’t go to waste. Death is a natural process for recycling life’s raw materials. Life lets nothing go to waste. The carcass of a bison, left behind first by wolves and then by coyotes and crows, continues to be digested and broken down by insects, bacteria, and fungi. When each of these organisms dies, it decomposes as well. Every living thing has other (often many) living entities that feed on it, and one organism’s waste products are another organism’s source of nutrients or shelter.
Cremation is simply combustion (burning), which turns the complex molecules that make up a living organism into simpler ones such as water and carbon dioxide gas. Thus the body’s carbon, hydrogen, oxygen, nitrogen, calcium, and phosphorus atoms return to the atmosphere and the soil. Burial in an embalmed state, in a lined coffin, slows down the decomposition process for hundreds of years, and mummification can slow it for thousands. Eventually, though, every organism returns to the earth or atmosphere as a dispersal of atoms and molecules.
Every atom in your body is unimaginably old, dating back to the origin of the universe. However, during their last few billion years spent here on Earth, your atoms have cycled through a great many mineral and organic forms, over and over again. At one time or another, they may have been part of the atmosphere or the Amazon River, diatoms or dinosaurs, rocks or rabbits, trees or trilobites. This is ultimate recycling.
Wood recyclers
Fungi and bacteria are hard at work decomposing the intricately complex molecular structures of these fallen trees.
Ferreting Out the Final Facts
Along with bacteria, fungi and insects are among the natural world’s most persistent and enthusiastic recyclers. For at least a century, our growing understanding of their diverse and predictable habits of decomposing once-living organisms has played an important role in establishing the time and (in some cases) place of death of a human or other organism. Forensic entomologists study the succession of insect types that find, lay eggs on, and eat dead organisms. By observing the kind of insect feeding on a dead animal, and the larval or pupal stage its offspring have reached (many insects go through four or five different developmental stages), they can tell how long the organism has been dead. For instance, one of the first kinds of insects that detects and arrives to colonize a dead vertebrate animal is the blowfly. The fly will lay eggs on a dead body within two days. The egg then hatches to form, in succession, three larval stages and two pupal stages before the adult emerges. Each of these stages takes a predictable length of time to develop, so the time since the flies’ arrival can be determined, and from this the time of death. The insect species found on a body can also tell the trained observer where the body has been kept, whether it has been moved from its original position, and whether or not it has been frozen.
In recycling a body, the insects also ingest any drugs or poisons the once-living organism may have used or been given. This recycled body chemistry thus can become useful evidence of drug use or poisoning, even when the body itself is too far decomposed for testing. Even DNA can be retrieved from the digestive tracts of blood-sucking insects, and used to identify a specific person’s presence at a specific location during a specific time period.
“... I think your [victims] were killed during the day, or at least the bodies were exposed during daylight hours for a while before burial. I found larviposition by Sarcophaga bullata.... Indeed, I also suspect that the bodies were exposed outside, at least for a short period.The Sarcophagidae aren’t quite as willing to enter buildings as some other groups.”
Kathy Reichs, Déj`a Dead, 1999
National Briefs
Oregon
Forest fungus called the largest organism
CORVALLIS — U.S. Forest Service researchers report that a fungus that has been weaving its way through the roots of trees for an estimated 2400 years has become the largest living organism ever found. The fruiting bodies of Armillaria ostoyae are linked by an underground network extending a length of 3.5 miles and burrowing as deep as 10 feet underground.
Protein mechanics
Keeping a living system in a state of high organization necessitates the continuous building and destroying of its parts.
Cell turnover
Whole cells also turn over; i.e., they have a short or long life, die, and get replaced by new ones.
Cells that rarely turn over — neurons
Cells that turn over in days or weeks — liver, intestine, skin
2.12	Life Maintains Itself by Turnover
Put It Together — Take It Apart
Consider the following dilemma. To exist, life requires organization. Organization requires energy. Life’s complex molecules have lots of energy in the bonds that hold them together, but these bonds don’t hold together indefinitely. They tend to fall apart — dissipate. Now, a system that is unstable when it’s organized has a problem. How can it avoid inevitable breakdown? Living systems have answered this question with an ingenious strategy. Day in and day out, round the clock, organisms routinely take apart their own perfectly good working molecules and then reassemble them. Each day about 7 percent of your own molecules are “turned over.” That means virtually 100 percent have “turned over” in about two weeks. In this way, no molecule lingers in your system long enough to “unintentionally” dissipate.
Turnover also provides flexibility. A change in the environment often calls for a switch in proteins. New proteins can be made from disassembled old ones.
In turnover we can sense life’s continuous “flow-through” of energy. A highinformation/high-energy state must be dynamically maintained by the ceaseless building and destroying, ordering and disordering, of life’s parts.
Skin renewal
The bottom layer of these skin cells is fed by tiny blood vessels looping up from larger vessels, providing a constant supply of raw materials.
Parts Renewal
Living cells’ ongoing turnover requires a constant supply of raw materials and the energy to assemble them. The energy, originally supplied by the Sun and trapped in plants’ molecular bonds by photosynthesis, enters your body in the form of food.That food provides most of the raw materials for synthesizing new proteins and other components of cells. Other raw materials come from the breakdown of these same complex molecules.
In some parts of the body, existing cells reproduce themselves by division. Your skin (or dermis) constantly replenishes itself, for instance, by shedding its surface layer (the epidermal cells). The cells at the base of the dermis (the basal cells) divide; as new cells are formed at the bottom and old ones are shed at the top, the cell layers advance toward the surface and their eventual death. In fact, the surface of your entire body is covered with dead cells, forming a protective layer for the living cells beneath. What are they protecting you from? Ultraviolet radiation, chemicals, dehydration, hydration, and abrasion. Living animal cells would die rather quickly in the presence of any of these.
You have another dermal layer lining your gut (digestive tract) from mouth to anus. Your gut is effectively a tube that runs right through your body. Food goes in one end and is processed, and waste is expelled from the other end. The processing involves acids and enzymes that break down food substances into smaller molecules, and the dermal layer lining the gut protects your other cells from these digestive acids and enzymes. Each section of the gut is lined with specialized cells that variously protect, secrete chemicals, or absorb nutrients after food has been digested. The basal cells of the gut’s dermal layer also divide continuously and the surface cells are scraped and sloughed off with the rest of the waste.
In animals, many cells turn over (i.e., are born and die) but not most nerve cells (including those in the brain associated with longterm memory).
Question.
Speculate on why nerve cells rarely turn over.
Answer...
One plausible theory is that nerve cells’ function — including memory — depend on patterns of connections with other nerve cells. These connections develop over time. Cell death and replacement could break existing connections, thereby disrupting memory and other functions.
Blood cells, both red and white, originate in the marrow — the soft fatty tissue in the hollows of large bones. In the marrow, stem cells divide continuously, producing a constant supply of blood cells. A single drop of human blood typically contains 5 to 6 million red blood cells, and 5 to 10 thousand white blood cells. Extra blood cells are stored in the spleen, and old ones are broken down in the liver — a constant turnover.
Provided with enough nourishment, your body can produce a sufficient supply of skin, gut, and blood cells. Usually the new cell is an exact copy of the old one. As you know, though, mistakes can happen when any of your cells divide. For example, too much sunlight can damage the DNA of skin cells, resulting in abnormal cells. They lack the protein that tells them when to stop reproducing. When these abnormal cells divide, they often do so too fast, piling up into tumors.
A single abnormal cell...
...becomes a tumor.
When a human liver is damaged in an accident and part of it has to be removed surgically, the remaining portion grows rapidly, producing a full-sized liver in a week or so. Experiments show that, normally, most of the liver’s substance is being regularly broken down and rebuilt (i.e., its big molecules are turning over inside its cells). Also, in the early stages of regeneration, the liver begins to increase in mass, without any increase in the rate of production of new cells.
Question.
How can cellular mass increase without a pickup in the rate of production?
Answer...
If there are increasing numbers of liver cells and the rate of production has not increased, it must be that fewer liver cells are being broken down.
The value of science remains unsung; ours it not yet a scientific age. Perhaps one reason for this is that you have to know how to read the music. A scientific article, for instance, might say something like this:“The radioactive phosphorus content of the cerebrum of the rat decreases to onehalf in a period of two weeks.” Now, what does that mean? It means that the phosphorus in the brain of a rat (and also in mine and yours) is not the same phosphorus that was there two weeks ago. All the atoms that are in the brain are being replaced, and the ones that were there before have gone away. So what is this mind? What are these atoms with consciousness? Last week’s potatoes! Which now can remember what was going on in your mind a year ago — a mind that we long ago replaced.When we discover how long it takes for the atoms of the brain to be replaced by other atoms, we come to realize that the thing I call my individuality is only a pattern or dance. These atoms come into my brain, dance a dance, and then go out, always new atoms but always performing the same dance, remembering what the dance was yesterday.
Richard Feynman, The Value of Science, 2000

2.13	Life Tends to Optimize Rather Than Maximize
When Less Is Better
To optimize means to achieve just the right amount — a value in the middle range between too much and too little. Too much or too little sugar in the blood will kill. Everyone needs calcium and iron, but too much is toxic. The rule of optimization generally holds true for minerals, vitamins, and other nutrients the body requires, as well as for behaviors such as exercise and sleep.
At the molecular level, life operates elaborate signaling and management systems to maintain optimum levels. Certain proteins have the ability to regulate precisely concentrations of essential chemicals, shutting down production when optimum quantities have been reached, starting up again when concentrations fall below critical levels.
At the level of the organism, optimizing is an intricate dance involving many interacting parts and values. Deer antlers require an optimum mix of strength, shock absorption, weight, and growing ability (since they must be regrown every year). A change in any one of these variables might adversely affect the others. Something that might make the antlers stronger, like a higher mineral content, might also make them heavier or unable to grow quickly enough. Thus, maximizing any single value (i.e., pushing it to the extreme) tends to reduce flexibility in the overall system, so that it may not be able to adapt to adverse environmental change.
Maximizing can be seen as a form of addiction, in that more leads to more. Occasionally, over generations, an organism may drift from optimizing to maximizing, from adaptation to addiction. The peacock’s tail has been cited as an example of the maximizing of one variable trait. If female peacocks choose males who display the most luxuriant tail feathers, the next generation of peacocks will have a greater representation of “big tail” genes. If this process continues unabated, each generation will have a larger average tail size until the tails reach the upper limit of physical practicality. A tail can only grow so large in relation to body size before it impedes a bird’s ability to get around. Likewise, a redwood tree can only grow so tall without toppling over; a walrus’s tusks can grow only so long without overstraining the animal’s neck muscles.
Every once in a while, a sudden change in the environment can catch a species that has drifted too far into maximization and push it into extinction. More often, as the costs of maximization rise, the species self-corrects. Larger-tailed peacocks may be unable to run as fast or hide as well. Because these peacocks are more vulnerable to predators, the survival advantage shifts back toward their smaller-tailed rivals. Thus, life persistently tends toward optimal balance, illustrating one of nature’s cardinal rules:“Too much of a good thing is not necessarily a good thing.”
There is, however, one value that life can be said to maximize. Every organism has as its most elemental goal the transfer of its genetic information to the next generation. In this sense, all optimizing of function aims at this ultimate maximization — the survival of DNA.
ELKS,WHELKS,AND THEIR ILK The monarchs of the Irish bogs Succumbed to neither men nor dogs But (most ecologists agree) To calcium deficiency. They scoured the base-deficient peat For antlers and old shells to eat Around the Celtic countryside And finding all too few, they died. Then mourn the passing of the elks But not the wisdom of the whelks That roam the shore — their native heath — With silver-indurated teeth. And bore to death their mollusc friends, Who come to sad, unsuccored ends. Without the need for extra lime The whelks survive to modern time. Thus ungulate and gastropod, And all that live by sea or sod, Are doomed to be or not to be By biogeochemistry.
Ralph A. Lewin, The Biology of Algae and Diverse Other Verses, 1987
Maximizing to extinction?
The odd positioning (facing forward) and sheer massiveness (up to twelve feet across) of the Irish elk’s antlers suggest they were used for display to attract females, rather than for combat. But in the face of major environmental change — “oversized” antlers might well have contributed to the disappearance of this species.
With all hair removed, the bodies of a gibbon and a human are remarkably similar. Humans have adapted successfully to far more environments than have gibbons.
Question.
How is the gibbon maximized compared to the human? How might the human’s optimal body structure explain its success in adapting?
Answer...
The gibbon’s arms, hands and legs are optimized only for living in and moving through treetops — outside a forest these traits would be maximized, and a gibbon would be largely helpless and easy prey for fast ground-based predators. Also, the use of the hands for locomotion interferes with their usefulness as a tool for manipulation of objects in the environment. The human, on the other hand, while not specialized for a single environment, can climb trees if necessary, run across open land, climb mountains, and use tools to modify the environment.
Being Adaptable Pays Off
In times of crisis, the most specialized (maximized) organisms tend to become extinct; the most adaptable (least specialized) survive. Specialization always has a price: loss of adaptability. In stable times, maximization sometimes works; in changing times, optimization rules.
Over the course of life’s evolution on Earth, there have been periods of major global climate change and mass extinctions. Geologists have devised a time scale based on the sedimentary rock and fossil records. Two of the most famous documented mass extinctions came at the end of the Permian period, approximately 250 million years ago, and at the end of the Cretaceous period, 65 million years ago. It is estimated that more than 90 percent of marine animals and a large percentage of land animals became extinct at the end of the Permian. The Cretaceous extinction, most famous for the demise of the dinosaurs, saw the number of species decline by perhaps 50 percent.
What survived? The least specialized, most adaptable organisms. In other words, the optimized plants and animals capable of living in altered environments, adapting to changes in climate, air or water composition, and diets. Following a mass extinction, adaptive radiation (the evolution of many different species from a few ancestors) occurs on a large scale as life rushes to fill the vacated niches of vanished species.
Some of the most spectacular fossils are those of maximized species, such as the largest dinosaurs, the saber-toothed tiger, the woolly mammoth, and the Irish elk pictured on the previous page. But maximization is not confined to large animals. Certain plant species (many orchids, for example) depend entirely on a single species of insect for pollination. The two, plant and insect, are said to have coevolved. The disappearance of the one is likely to lead to the extinction of the other.
Certain aphids demonstrate a sort of optimization. One species (pea aphids) produces individuals of two colors, red and green. Both colors exist together, feeding on the same plants (peas and other legumes). The pea aphids have two main predators, ladybugs and parasitic wasps. The ladybugs primarily eat the red aphids, presumably because they’re easier to see. The wasps more often lay eggs in the green aphids, perhaps because eggs laid in the red individuals get eaten before maturity. The dual coloration appears to be an optimization strategy, permitting more individuals to survive in the presence of either predator.
An exclusive orchid
Only certain insects can find their way into this orchid’s distinctive blossom, and the orchid’s pollen is deposited on very specific parts of such an insect. When the insect visits the next orchid, pollen is rubbed directly onto the plant’s reproductive part, the stigma.
Optimizing from the Bottom Up
Just as life has to organize from the bottom up, so must it optimize its parts from individual cells on up through cellular communities to whole organism. Individual, free-living cells and the ones that make up multicellular living things are almost all microscopically small, as you saw in the first chapter, and most are similar in size. There is an important reason for the size limit on most cells: in order to function they must constantly take in useful materials from their environment and dispose of waste materials to the environment. The only way they do this is through the cell membrane, and the materials have to get where they’re going pretty quickly to do their jobs. Since most molecules move through a cell simply by being bumped around by other molecules, they don’t move very fast.
If you look at the picture (above right) of the difference in surface to volume ratio between a larger and a smaller object, it becomes pretty clear that the smaller the cell, the larger the proportion of area it has to move molecules in and out, and the shorter distance they have to travel once inside. A diameter of one to ten thousand nm seems to be an optimal size for an animal cell, and most of them fall within this range. Larger cells need to be very long and thin, or have very convoluted surfaces (the same adaptation as the elephant’s skin), or devise more elaborate mechanisms for moving molecules. You’ll read more about this in Chapter 5, Machinery.
An exclusive orchid
Antler growth and extinction of Irish elk. RonA.Moen, JohnPastor, andYosefCohen. Evolutionary Ecology Research, 1999, 1: 235-239.
Adult male Irish elk grew antlers that averaged 40 kg (88 lbs) in weight, the largest antlers of any of the deer species, alive or dead. Fossil remains of the elk tell us that they all died out over a relatively short period of time. They were all gone about 100 years after a major and continued temperature drop forced a change in their environment, and diet — from mineral-rich willow and spruce to less mineral-dense tundra plants.
In this paper, Ron Moen and his colleagues hypothesize that the amount of minerals required to grow antlers yearly was so great that when the elks’ food supply changed to a less mineral-dense forage, they were unable to get enough minerals from their food to support building both skeleton and antlers. The investigators devised a computer model that compared the known nutritional and mineral needs of the modern moose to those of a simulated Irish elk. The simulated Irish elk depleted the mineral reserves in its skeleton to support antler growth during the summer but was able to replenish those reserves in the fall, when antlers were shed after the mating season. Thus, the bigger its antlers, the more likely the elk was to suffer from temporary osteoporosis. With climate and vegetation change, the Irish elk were less and less able to replenish their skeletal minerals, leading to either permanent osteoporosis or reduced antler growth, either of which would interfere with the elk’s reproductive success, and with the long-term survival of the herd. The authors conclude: “Sexual selection pressures for larger antlers and larger body size were opposed by selection pressures for smaller antlers and smaller body size imposed by environmental change. We suggest that the inability to balance these opposing selection pressures in the face of rapid environmental change contributed to extinction of the Irish elk 10,600 years [ago].”
2.14	Life Is Opportunistic
Making the Most of What Is
A rotting tree on the forest floor may look like life at a dead end. In actuality, it marks the beginning of an explosive new stage — more varied and bustling than when the tree was alive. Early on, mosses and lichens establish themselves on the decaying surface. Carpenter ants, beetles, and termites initiate a succession of invasions by tunneling through the rotting wood. Fungi, roots, and microbes follow these paths. They in turn become food for grazing insects. Spiders feed on the grazers. Roots of seedling trees and shrubs take hold in the emerging humus as moles and shrews burrow through the soft wood to feed on the newly grown mushrooms and truffles.
The “living dead” tree illustrates not only life’s tenacity, but also life’s universal tendency to “make do” with whatever is available in its surroundings. Because of this tendency, life flourishes even in the world’s harshestplaces. InAfrica’sNamibDesert,surfacetemperaturessoarto150°F, and rain may not fall for three or four years at a stretch. Few plants can survive, yet just under the barren sand live a host of insects, spiders, and reptiles — even several types of mammal. The smallest creatures get moisture from wisps of fog and nutrients from tiny bits of plant and animal detritus blowing across the sands. The larger creatures live on the smaller.
In the arctic ice, 100-year-old lichens grow in temperatures of –11 °F. Some antarctic fish have a natural antifreeze running through their blood vessels, enabling them to thrive where others would perish. Tubeworms live in darkness 8000 feet underwater, depending on minerals streaming from hot water vents on the ocean floor. The world’s champion adapters, fast breeding generations of bacteria, can adapt to virtually any environment — from near-boiling sulfur springs to the acid guts of termites. And so on.
Together, over time, the genetic code and the protein structure of all living things permit a marvelous flexibility. Hence, life forms are opportunists. Generations of opportunists don’t wait around for the right conditions. They adapt to what is, and they make use of whatever they find around them.
Self-burial
To avoid winter’s harsh dry winds, the mescaxl cactus withdraws completely into the ground.
Growing toward darkness
In order to find a tree to climb, the monstera vine must first grow toward darkness. Once it reaches a trunk, it switches strategies and grows toward light.
Adapted to fire
Resin in the seedbearing cone of the lodgepole pine prevents the scales from opening. Fire not only melts the resin and releases the seed, it also leaves a fertile bed of ashes in which the seedling can take root.
An invitation to sex
With the right odor, pattern, and degree of hairiness, the bee orchid entices the male bee into an attempt at copulation. The bee leaves, covered with pollen, to be enticed by another bee orchid.
Living stones
Lithops are plants that look like stones, which helps them avoid being eaten by foraging animals.
Hollow leaves
Moisture condenses on the inside of the pitcher plant’s leaves and is then carried directly to the roots, which need to be kept wet because they are exposed to the air.
Like rotting meat
With an evil smell, the Rafflesia plant encourages pollination by flies.
2.15	Life Competes Within a Cooperative Framework
Strategies for “Fitting In”
1. Every creature acts in its own interests.
2. The living world works through cooperation.
These two statements may appear to be contradictory; they are not. Creatures are self-interested but not self-destructive. Selfish behavior, pushed to the extreme, usually has unpleasant costs. A dominant animal engaging in too-frequent combat may sustain injuries. A parasite may kill its host and have nowhere to go. These self-defeating strategies generally get weeded out by evolution, so that in the long run most organisms tend to adopt some form of “getting along.”
Being eaten may not feel much like getting along, but in fact when predators take only the smallest, weakest, or most unhealthy of their prey species, they leave the fittest members to survive and reproduce. We can recognize this as being competitive at the individual level, cooperative at the group level. (Although we don’t suggest that creatures generally think in terms of the group.)
Noncompetitors
Although these different species of wading birds feed side by side, they might as well be on separate planets. Each eats a different diet with its unique bill. The fact that each species occupies its own special niche may be taken as evidence for nature’s tendency to “get along.”
Plants and animals evolved from predator/prey truces among bacteria. The ancestors of chloroplasts and mitochondria (the sugar-making and sugar-burning components of plant and animal cells, respectively) originally acted as small predators, invading larger bacteria. They exploited but did not destroy their host. Such “restrained predation” is a recurring theme in evolution, and in it we see the beginnings of cooperation. In time, the host developed a tolerance for the invaders, and each began to share the other’s metabolized products. Eventually they became fullfledged symbionts — i.e., essential to each other’s survival. This progressive cooperation set the stage for all higher life forms. The lesson, as biologist Lewis Thomas has stated, is not “Nice guys finish last,” but rather “Nice guys last longer.”
Ritualized aggression
Animals compete to establish dominance. Such fights rarely result in serious injury and frequently involve only “displays.” This can be seen as cooperative behavior.
From predation to cooperation
A parasitic mitochondrion invades a larger bacterium.
Many generations later, invader and host begin to share metabolized products.
After many more generations, they’ve come to need each other.
Question.
Why did the opposing sides during trench warfare in World War I refrain from shelling each other’s meal wagons?
Answer...
The restraint derived from mutual self-interest. If one side left the other’s meal wagons alone, the other side would tend to reciprocate and so both would get to eat. This is a good example of how cooperation can evolve — even among mortal enemies.
Shrimps’ Selfish Cooperation
In the June 6, 1997 issue of Nature, J. Emmett Duffy reported his observations of several different colonies of Caribbean snapping shrimp. He found that all of the shrimp in a single colony (they live inside sponges) are closely related — descendants of a single mother, or “queen,”andasinglefather. Theshrimparefiercedefendersoftheircoloniesandwillchase off or kill any intruders from other colonies. Duffy set up some small experimental colonies in his lab and discovered that the shrimp welcomed former members of their own colony, even when space and food were in short supply. This welcoming behavior might seem to be foolish at first, but it is a beautiful example of combined self-interest and cooperation. Purely individualistic self-interest might dictate that any intruder would use up precious resources and should be killed or chased off. The longer-term interest of the colony, though, would consider any shrimp with the same DNA just as valuable for carrying on the life of the colony. Thus, the welcoming behavior is in the interest of the colony’s survival.
Wormy Opportunists
In the absolute darkness of the ocean bottom, no photosynthesis can occur. Even so, dense communities of gigantic tube worms, mussels, and clams cluster around towering hot water vents on the ocean floor. These communities are something of a mystery. There are absolutely no plants here. What do these creatures use for food? Why are they found only near the hot water vents?
It seems that the answer lies in the relationship between bacteria and the molecules dissolved in the hot sea water. As sea water seeps into the ocean floor in places where hot magma from the Earth’s interior is close to the surface, it dissolves subterranean minerals such as iron, calcium, sulfur and copper. These minerals then rise with the heated water through the vents in the ocean floor. They provide food and energy (in the form of the bonds in molecules of hydrogen sulfide gas) for enormous communities of bacteria that live on the inner surfaces of the vents. Just as the chloroplasts in plants use solar energy to turn carbon dioxide and hydrogen into sugar, these bacteria use the chemical energy in hydrogen sulfide molecules to make sugar. The tube worms, mussels, and clams filter these bacteria out of the sea water, ingest them, and use their sugars as nourishment. There would be no opportunistic animals in this dark biosphere without the opportunistic bacteria.
Making the Most of Toxic Waste
Bacteria, among the most versatile and opportunistic of living things, can populate what may seem to be impossible environments and can turn many kinds of chemical bonds into energy for themselves. Using a lot of creative imagination, we human beings are learning to cooperate with bacteria to address many of our environmental cleanup problems.
The Savannah River nuclear materials site in Georgia has been contaminated for 50 years with the toxic solvents triand tetrachloroethylene (or TCE).	TCE is so toxic that five gallons of it can contaminate up to a billion gallons of groundwater, and TCE molecules are very stable, unlikely to break down into harmless component molecules without outside help. Certain bacterial proteins, though, can do the degrading job, specifically those of bacteria that use the bonds in methane (natural gas) molecules to supply their energy needs. These methanotrophs (“methaneeaters”) were already living in the contaminated Savannah River site soil and were very slowly breaking down the TCE molecules when their preferred methane wasn’t sufficiently abundant.
To the creative minds of the cleanup crew at Savannah River came the idea of taking advantage of the methanotrophs’ food preference. They figured that more methanogens would mean faster TCE degradation, so they ran pipes through the soil that bubbled out a constant supply of bacterial nourishment — methane and oxygen. The bacterial population burgeoned, and then, when the supply of methane was lowered, this huge population turned to the resident TCE molecules, breaking them down into harmless component molecules. The cleanup was a success, and it took months instead of years.
An extremophile swimming pool
Organisms that live in conditions at the extremes of temperature, acidity, alkalinity, or salinity are called extremophiles. This 75 oC alkaline spring in Yellowstone National Park is a congenial home for the mat of bacteria in the foreground.
Any competition here?
Electron microscopic views of Mars meteorite ALH84001 found in Antarctica in 1984 showed these 20 nm long tubular shapes, which suggested the possibility of microorganismic life on Mars. (See page 7 for comparative sizes.)
Question.
What might be one strong argument against the possibility of these shapes being microorganisms?
Answer...
Looking at the sizes of the molecules on page 7, it seems clear that 20 nm is too small a space to include all of the basic chemical machinery of life.
Nudibranchs are born defenseless but acquire a protective toxin by eating poisonous anemone tentacles and incorporating them into their skin as spines.
Parrot fish nibble away at the reef while grazing on algae. In the process they excrete calcium as a fine sand. Each fish produces thirty pounds of sand per year, playing an important role in building beaches.
Pink algae use the reef as a secure place to grow. At the same time, they contribute mightily to holding the reef together by secreting a limey “glue.”
Crabs encourage sponges to grow on their backs. A good sponge growth discourages octopuses from eating the crab.
Sea squirts carry tiny creatures called nephromyces in their kidneylike organs. Inside the nephromyces live special bacteria. Both the nephromyces and the bacteria appear to be useful in recycling nitrogen for the sea squirt.
Reef-building coral polyps harbor tiny algae within their cells. The algae promote the coral’s growth and receive carbon dioxide and nutrients in exchange.
Cleaner fish live safely in the mouths and gills of larger fish, removing parasites.
2.16	Life Is Interconnected and Interdependent
A Network of Interactions
The stony coral, a pea-sized animal that resembles a miniature flower, might easily go unnoticed were it not for the tiny limestone cup it secretes for its home site. As the multiplying coral add on their cups, they form vast apartment complexes — the largest life-made structures on earth. Pink algae, taking hold in the crannies, “mortar in” the loose and broken sections with a limey secretion of their own. Turtle grass, sea fans, sponges, and mollusks attach themselves to the reef surface. Moray eels take up residence in the dark crevices. Starfish arrive to feed on the coral, and triton conches feed on the starfish. Hundreds of species of fish — some grazers, some predators — move in, along with crabs, octopus, shrimp, and sea urchins. Competitive and cooperative relationships emerge.
Damselfish flit with complete immunity among the poisonous tentacles of the large sea anemones. Crabs place sponges on their backs where they grow and act as a protection from octopuses. Cleaner fish and shrimp remove parasites from predator fish and eels, even entering their gills and mouths with complete safety. Algae live comfortably inside the coral’s cells, and large sponges offer housing to thousands of minute creatures.
Lookatthecoralreefasamultilevel,integratedsystem. Ultimately,everythingin the reef connects with everything else. The survival of the reef shark is closely tied to the survival of the coral polyp, even though the two may have no direct contact and no particular awareness of each other. What survives and evolves are patterns of organization — the organism plus its strategies for making a living and for fitting in. Any successful change of strategy by one organism will create arippleofadjustmentsinthereefcommunity. Calledcoevolution,this is the kind of creative force at work everywhere life has taken hold.
Small Creatures, Big Effects
New evidence points to the astonishing role that life, particularly microscopic life, has played in establishing and maintaining the Earth’s atmosphere, temperature, and climate. Life has acted both as a stabilizing force, dampening the effects of solar fluctuations and volcanic activity, and as a creative force, setting the stage for new and more complex organisms.
For example, estimates of the Sun’s energy output in life’s earliest phase suggest that the Earth would have frozen over but for the small amounts of ammonia released by primitive bacteria. These were simple creatures that thrived in a lowoxygen environment. Later, photosynthetic bacteria and other organisms secreted enough oxygen into the atmosphere to create an environment in which aerobic (oxygen-breathing) creatures, including the first animals, evolved.
Since the Earth’s beginning, the Sun has been getting hotter. At the same time, volcanoes have been adding carbon dioxide to the atmosphere, contributing to the atmosphere’s ability to absorb energy from the Sun (the well-known greenhouse effect). Although the Earth’s temperature would be expected to rise steadily, this has not happened very fast — until the widespread burning of fossil fuels in this century. Instead, average temperature has remained relatively constant, primarily because, over eons, microbes have steadily and dramatically reduced the amount of carbon dioxide in the air to its current level of 0.03 percent. Tiny plants, as they grow and die,“nibble away” rocks and trap carbon dioxide in the soil. There, it dissolves in water and washes eventually into the sea where it is used by marine life to build shells. Ocean algae also trap large quantities of carbon dioxide as they photosynthesize, which finds its way into marine shells (as calcium carbonate) and ends up on the ocean floor, ultimately becoming limestone and chalk.
And what about water? Planets such as Mars and Venus have lost all of their surface liquid water, probably because certain elements such as iron bonded with the water’s oxygen to form oxides. The leftover hydrogen was too light to be held by the planet’s gravity and was lost to space. On Earth, microbes prevented this loss of hydrogen by taking volcanic hydrogen sulfide, extracting the hydrogen for energy, and excreting the sulfur as pellets. Also, photosynthetic organisms kept producing water as they make ATP — enough for the Earth to retain its oceans, and thus, provide an environment for the further evolution of life.
A recent and plausible theory proposes that microorganisms are responsible for cloud formation over the oceans. Cloud formation is aided by the presence of tiny particles. Marine algae emit vast quantities of sulfide particles, which serve as “seeds” for cloud condensation. The creation of clouds over oceans covering two-thirds of the Earth’s surface significantly affects the global climate.
So microscopic forms of life have worldwide physical and chemical effects — they create much of their own environment.
Surface differences
The surface differences of Earth and its moon, as seen by the Galileo spacecraft, show the vast difference that bacterial life has made to the surface of our planet.
This photo of Mars’ surface was taken in 1997 during the Pathfinder landing. This mission confirmed that Mars had once been covered by large amounts of liquid water, but so far there is no undisputed evidence that there has been life on the planet.
And it is strange thing that most of the feeling we call religious, most of the mystical outcrying which is one of the most prized and used and desired reactions of our species, is really the understanding and the attempt to say that man is related to the whole thing, related inextricably to all reality, known and knowable. This is a simple thing to say, but a profound feeling of it made a Jesus, a St. Augustine, a Roger Bacon, a Charles Darwin, an Einstein. Each of them in his own tempo and with his own voice discovered and reaffirmed with astonishment the knowledge that all things are one thing and that one thing is all things — a plankton, a shimmering phosphorescence on the sea and the spinning planets and an expanding universe, all bound together by the elastic string of time.
— John Steinbeck, Log from the Sea of Cortez, 1958
All mammals’ skeletons are said to be fundamentally alike (homologous). These pictures show a horse’s hind leg and a human leg. The two different legs appear to bend in the opposite direction.
Question.
Does this suggest a lack of homology, or is there some other explanation?
Answer...
Appearances are deceiving. A horse’s hind leg bends forward at its knee, just as the human leg does. However, the proportions of the various leg bones differ — the horse actually stands on its toe.
Some of the Things You Learned About in Chapter 2
adaptability 72 American Sign Language 30 atmosphere 35 bacteria 24 biosphere 35 catalysts 42–43 cell turnover 67,68 cellular membranes 32–34 chain molecules 28, 30–31 colonies of cells 27 deforestation 35
diffusion 52, 54 DNA and RNA 28–30 enzymes 42–43 evolution 24 feedback loops 58-61 flagella 26 Gaia hypothesis 35 genes 28, 44–47 mating 44 multicellular organisms 24 mutations 49-51 osmotic pressure 55 parasites 26, 75
polarity 52 phospholipid molecules 32–34, 55 protein gates 34 proteins 28, 30–31, 40, 42-43 recycling 62-65 solubility 54, 55 sperm and egg 44–45 sugars 57 tissues 26 unity in diversity 36–39 viruses 26
Questions About the Ideas in Chapter 2
1.	What is the fundamental feature of information?
2.	What is the smallest number of units required to make a code?
3.	Given that cells both contain and are surrounded by a watery environment, what special features must membranes have to enclose their contents?
4.	Name at least three features that all the beetles on pages 34-35 have in common.
5.	How does the expression “similarity precedes difference” apply to the beetles on pages 34-35?
6.	If you were to take all of the beetles on page 34 out of the widely diverse environments in which they actually live and place each, with a mate, on a rosebush with red blooms in the middle of a garden full of sharp-eyed songbirds, which of the beetles do you think would live to produce offspring? Which would be among the first to be eaten by the birds? Describe what the population of beetles might look like three years from now.
7.	How are proteins like tiny robots?
8.	Genes do not contain information for seeing, breathing, thinking, defending the body against invaders, and so on.	What information do genes contain, then, that allows us to do all these things?
9.	In what sense is error essential to the creation of new forms of life?
10.	The molecules of CO2 (carbon dioxide) and CH4 (methane) are about the size of H2O (water) molecules, but unlike water, carbon dioxide and methane are gases at room temperature.	What accounts for the ability of water to remain liquid at room temperature?
11.	All biological systems are “self-correcting.”	What is meant by this?
12.	Which of the following exhibit self-corrective behavior: An autopilot, a stopwatch, a thermostat, car’s cruise control mechanism, an automatic teller machine?
13.	Give some examples of “cycles” of life.
14.	What is meant by “turnover”?	Give examples of two levels of turnover in living systems.
15.	Why do biological systems turn over?
16.	In nature, too much of a good thing is not necessarily a good thing. Why?
17. Weedsgrowingupthroughcracksinthesidewalk,moldcoveringbreadleftouttoolong,and birds nesting in the eaves of a barn are all examples of what tendency of life?
18.	How might mitochondria have evolved from bacteria?
19.	Give an example of coevolution.
20.	Animals regulate their temperature partially by the amount of surface area they have to dissipate internally generated heat. What features of the elephant on page 48 are likely to be useful in temperature regulation? What features of the polar bear serve the same purpose? Explain how we humans regulate our surface area and thus, help control our temperature.
References and Great Reading
Alters, Sandra. 2000. Biology, Understanding Life 3e. Sudbury: Jones and Bartlett Publishers.
Autumn, K. et al. 2000. Adhesive force of a single gecko foot-hair. Nature 405: 681–685.
Darnell, J., H. Lodish, and D. Baltimore. Molecular Biology of the Cell. NewYork. Scientific American Books, Inc. 1986.
Evans, C., 1996. The Casebook of Forensic Detection, How Science Solved 100 of the World’s Most Baffling Crimes. New York: John Wiley & Sons, Inc.
Feyman, Richard. 2000. The Pleasure of Finding Things Out. Cambridge: Helix Perseus Books. Huxley,T.H.,1880. TheCrayfish. AnIntroductiontotheStudyofZoology.NewYork:D.Appleton and Company. Lewin, Ralph A. 1987. The Biology of Algae and Diverse Other Verses. California: Boxwood Press.
Moen, Ron A., et.al. 1999. Antler growth and extinction of Irish elk. Evolutionary Ecology Research 1: 235–249.
Needham, C., M. Hoagland, McPherson, and B. Dodson. 2000. Intimate Strangers; Unseen Life on Earth. Washington: ASM Press.
Reichs,Kathy.1999.Déj`a Dead.NewYork:Pocket Books. McGee, Harold. 1990. The Curious Cook, More Kitchen Science and Lore. San Francisco: North Point Press.
Wen-Jing Hu et al. 1999. Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nature Biotechnology 17: 808-812.
WEB Connection
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