Mulitcellular Organisms

Contents

Biological Classifications

Taxonomy is the science of classifying plants, animals, and microorganisms into increasingly broader categories based on shared features. Traditionally, organisms were grouped by physical resemblances, but in recent times other criteria such as genetic matching have also been used. Scientific naming of species emerged in the 1600s, the Swedish naturalist Carl Linnaeus then put it all together in the 1700s. It ended up with seven categories from least specific to most specific (Figure 10-01a, left diagram). An organism's name is designated with entry from the categories of Genus and Species (in Latin). For example, human belongs to the genus Homo (in capital) and the species sapiens - hence Homo sapiens (in italic). However, such naming system is not perfect; it has incited many heated debates among

Figure 10-01a Taxonomy [view large image]

taxonomists for the assignment of certain organism into certain category. The confusion led to new concepts such as the phylogenetic species, which emphasizes shared traits from common ancestor (Figure 10-01a, right diagram). Another scheme involves comparing DNA sequences as shown in Figure 01-02a.

		Biology used to classify living organisms into five kingdoms as shown in Figure 10-01b. They include prokaryotes (no nucleus, no organelles), protista (possess nucleus and organelles), fungi, plants, and animals. The time scale (in billions of years) is referred to the appearance of oldest fossils. Study of DNA variation among different species provides another way to classify them as shown by the tree of life in
Figure 10-01b Five Kingdoms [large image]	Figure 10-02a Tree of Life [view large image]	Figure 10-02a. According to this scheme the common ancestor at the base of the tree gave rise to three branches:

microbes known as archaea (primitive unicellular organisms that live in most extreme environments), bacteria (unicellular organisms without nucleus or cell structure), and eukaryotes (any organism with one or more cells that have visible nucleus and organelles). The lengths of the branches reflect how much the DNA of each lineage has diverged from their common ancestor. They demonstrate that most of life's genetic diversity turns out to be microbial; the entire animal kingdom (shown at the upper right) are just a few twigs at one end of the tree. It is obvious that multicellular organisms such as fungi, plants and animals evolved from unicellular organisms further down the tree. Figure 10-02b expresses pictorally the same kind of division including a

Figure 10-02b Tree of Life, Pictoral [view large image]

hypothetical "Mother of all life" at the very bottom - the "last universal common ancestor" (LUCA).

		Recently, new evidence suggests that the Tree of Life may be more complicated than the version shown in Figure 10-02a. The revised version indicates that early life may not have existed as distinct species; instead they may have traded their genes promiscuously. Life may descend from a huge primordial menagerie rather than from a single common ancestor. Billions of years later, after the three branches split apart, distantly related species still joined
Figure 10-02c Tree of Life, Revised[view large image]	Figure 10-02d Ring of Life [view large image]	together sometimes, as bacteria were swallowed up by other organisms. Two of these fusions - bacteria giving rise to mitochondria and chloroplasts - are shown in the new Tree of Life (Figure 10-02c).

The time scale derived from fossil records is usually calculated from radioactive dating. For example in carbon-14 dating, the fact that the ratio of C14 to C12 is fairly constant (~ 10-12) in living organisms and that C14 is radioactive with a halflife of about 5730 years, would yield the age of the organism since its death (no more accumulation of C14) if we measure the leftover amount of C14 in the sample. The DNA variation (between species) shows only the genetic difference, which can be calibrated with known time difference from fossil records (Figure 10-02e).

Figure 10-02e Fossil and DNA Dating [view large image]

However, this calibration can be extrapolated to the unknown region only if the rate of DNA base substitution (the molecular clock) is constant. Unfortunately, it is found that genes change (mutate) at different rates.

		acid, and a dot indicates the same amino acid as in humans. Figure 10-02g shows the phy-logeny of 20 organisms (including fungi, and many kinds of animals), based on differences in the amino acid sequence of cytochrome-c. The fractional numbers are calculated to best-fit the data with imaginary splitting points. It
Figure 10-02f Amino Acid Replacements [view large image]	Figure 10-02g Phylogeny	corresponds fairly well to the relationships determined from other sources, such as the fossil record.

Cytochrome-c is an electron transporting protein that resides within the inter-membrane space of the mitochondria, where it plays a critical role in the process of oxidative phosphorylation and production of cellular ATP. An increasing amount of interest has been directed toward the role which cytocrome C has been demonstrated to play in apoptotic processes. It consists of 104 amino acids, encoded by 312 nucleotides. Cytochrome-c is a slowly evolving protein. Widely different species have in common a large proportion of the amino acids in their cytochrome-c, which makes possible the study of genetic differences between organisms only remotely related. Other proteins, such as the hemoglobin that evolves more rapidly than cytochrome-c, can be studied in order to establish phylogenictic relationships between closely related species as shown in Figure 10-02h, which also calibrates the time scale of amino acid change for the various proteins.

Figure 10-02h Time Scale Calib.

Evolution of Multicellular Organisms

		Figure 10-03 reconstructs the evolution of the multi- cellular organisms. Water-based life evolved first as illustrated in the bottom half of the picture, land-based life appeared later as shown in the top half.
Figure 10-03 Evolutionary Sequence	[view large image1] [view large image2]

e.g., the pair of cells failed to separate during cell division, or two cells stuck together accidentally. If natural selection favoured this new form, it would survive and prosper. The advantage can be varied. It could be for better dispersal of spore (by a long stalk), for staying in one place (with a root), more efficient feeding, or for confronting predator. One theory suggests that since there is always an open ecological niche for large size organisms, evolution favours bigger size to escape competition with the smaller ones. However, increase in surface area of the cell is always lagging behind increase in volume1, the expanding organism has to go multicellular and to develop specialized cell types (i.e., to move toward greater complexity) to resolve this problem. Figure 10-04b shows the relationship between size and speed of different objects. For living animals, speed is essential for pursuing preys or escaping predators. The broad band in the graph represents the condition on the surface of the Earth where living beings exist in a habitable zone. Note that the largest molecules and the smallest bacteria converge at the point of slowest motion of all of life and of all non-living bodies. It is the realm of Brownian motion where the floating of pollens and some bacteria is supported by

Figure 10-04a Multicellularity [view large image]

the random motion of molecules in the medium. Beyond this size, the animals propel themselves with their internal energy. As the size increases, there will be a myriad of consequences on:

		multicellular is related to the requirement of a single-cell stage in the life cycle. Sexual reproduction2, for meiosis and fertilization can only be achieved in a unicellular stage in eukaryotic organisms. The reason has to do with the way the genetic material is incorporated into chromosomes, and with the separation and recombination (crossover) of the alleles (two versions of the same gene) at meiosis. The fusion of the genes from two parents can only take place in single cell.
Figure 10-04b Size and Speed of Objects [view large image]	Figure 10-04c Multicellular Evolution [view large image]	A scenario for multicellular evolution in six steps starting from choanoflagellates has been proposed in 2009 as shown in Figure 10-04c.

Sexual Life Cycles

This leads to a paradox of cosmic implications: natural selection is simultaneously pushing for a large stage in the life cycle that can compete for food and for a minute single-cell stage that is essential for sexual reproduction. The result is that all multicellular organisms, from small algae and fungi to elephants and human, have a unicellular stage and a large stage of varying dimensions in their life cycle. Figure 10-05 shows the life cycle of animals for which the unicellular stage is the gamete in the form of egg or sperm. This is called the haploid state where a single cell carries n chromosomes after meiosis (cell division that transmits only n chromosomes) The large stage is the diploid state comprised with all the somatic cells in the rest of the body. Those cells carry 2n chromosomes (one from each parent at fertilization) starting from the zygote. They can differentiate into different cell types (performing different function) during mitosis (cell division in which the daughter cells receive the exact chromosome and genetic makeup of the mother cell). [view large image]

Figure 10-05 Life Cycle of Animals

Animal life cycle has the adult (the multicellular form) always in diploid state. However, this is not the case in more primitive species. Figure 10-06 shows the relative importance of the diploid and haploid generations among plants. Mosses are primitive plants, they still require very wet conditions for growth and fertilization. Meiosis produces spores, which germinate into gametophyte (male and female adults in haploid state). The gymnosperms (conifers) and angiosperms (flowering plants) are more advanced; the adult is in diploid state. This evolutionary development seems to indicate that earlier life tried to construct the multicellular body from the simpler cell unit in haploid state. It was switched gradually to the more stable diploid state where two similar copies of the genes are available - a primary and a backup.

Figure 10-06 Life Cycle of

Plants [view large image]

Homeobox Genes

			the front and back ends. Flies and other insects have 8. Mice and other mammals have 4 sets (labeled as HoxA, B, C, D) altogether through duplication totaling 38. The Hox genes are clustered in the chromosome in the exact order as shown. They are expressed in the same order of this spatial sequence, which is also the temporal order of
Figure 10-07a Hox Genes[view large image]	Figure 10-07b Homeodomain [view large image]	Figure 10-08 Early Development	expression. Figure 10-07b presents a magnified view of the homeodo-main within the homeobox protein.

As shown in Figure 10-08, the common feature of animals appeared quite early in development and that specialized features only appeared later. For unknown reason, it seems that in any group of related animals, such as vertebrates, there is a stage in development which is common to all members of the group. This stage is called the phylotypic stage (Figure 10-09a). For vertebrates, it immediately follows gastrulation (about 20 days after fertilization for human) when the main body axis with a very primitive head, and the first few segmented somites, can be seen. Before and after the phyloptypic stage the developmental pathway may be quite different. Thus, ontogeny (development of an individual to maturity) repeats some embryonic features of ancestors in their embryonic development; it does not represent the evolutionary history of an animal as claimed by the German biologist Ernst Haeckel’s biogenetic law, which states that "an animal’s embryonic development recapitulates its evolution".

Figure 10-09a Phylotypic Stage [view large image]

BTW, the somite is one of a series of paired blocks of cells that develop along the back of a vertebrate embryo giving rise to the vertebral column and most of the skeletal muscles.

Evolutionary throwback (atavism or backward evolution) may occur if anything goes awry during embryonic development. Early embryos of many species develop ancestral features. Snake embryos, for example, sprout hind limb buds, as do whale and dolphin embryos, and human embryos have a tail bud. These features usually disappear in later development. But if anything goes wrong in the process, perhaps through a mutation, the ancestral feature may be retained such as the hind limb in the snake. There are many forms of atavism in human including large canines, extra

Figure 10-09b Syndactyly [view large image]

breasts or nipples, polydactyly (extra fingers or toes), and syndactyly (webbed fingers or toes, Figure 10-09b).

The Three Germ Layers and Organs

		The three germ layers (endoderm, mesoderm and ectoderm) encompass the precursors of all structures and organs of the entire body, and are generated by a process called gastrulation (occurs at the early stage of the embryonic development). Body cavities of animals become increasingly more complex as one ascends the evolutionary tree. Ctenophora and Cnidaria are diploblastic (a) and have two thin but well-differentiated tissue layers separated by
Figure 10-10 Body Plans [view large image]	Figure 10-11 Alternate Perspective [view large image]	mesoglea, a gelatinous material that protects the body and lines the gut. Flatworms have three

Advantages of a body cavity (coelom or pseudocoelom):


• Fluid in cavity helps distribute food, wastes, hormones, etc. from one end of animal to the other.
• Better distribution allows animal to grow larger.
• A place to put things, like new organs.
• Hydrostatic skeleton- pressure makes cavity rigid.

		All the vital body organs except for the brain are enclosed within the trunk or torso. The trunk contains two large cavities separated by a muscular sheet called the diaphragm. The upper cavity, known as the thorax or chest cavity, contains the heart and lungs. The lower cavity, called the abdominal cavity, contains the stomach, intestines, liver, and pancreas, which all play a role in digesting food. Also within the trunk are the kidneys and bladder, which are part of the urinary system, and the reproductive organs, which hold the seeds of new human life. Figure 10-12a depicts the front view of the body cavity; while Figure 10-12b shows some inner organs. The three kinds of germ layers have differentiated into more than 350 different kinds of tissues and organs in adults. Table 10-01 is a list of the human organ systems, together with its function, and major
Figure 10-12a Anatomy, Front [view large image]	Figure 10-12b Anatomy, Inside [view large image]	components. All body systems work together; none are independent.

Table 10-01 Human Organ Systems

Stem Cells

		There are 69 cell lines registered with NIH - National Institutes of Health, 15 of these are available for shipment. President Obama signed an executive order on March 9, 2009 to lift the ban under the Stem Cell Policy in the Bush era. He also directed the NIH to develop revised guidelines to ensure that such research "never opens the door to the use of cloning for human
Figure 10-13a Differentiation Pathway [view large image]	Figure 10-13b Stem Cell Cycle [view large image]	reproduction". Legally it is possible that Obama's successor can in turn reverse the Obama executive order. Now back to the stem cell:

Cloning

			There are three types of cloning as depicted in Figures 10-14a, 10-14b, and 10-14c. Media report on cloning in the news usually refers to the type called reproductive cloning. In general, cloning is defined as an asexual process of producing a group of cells or molecular segments or organisms, that are genetically identical descendants of a single parent.
Figure 10-14a DNA Cloning [view large image]	Figure 10-14b Embryo Cloning [view large image]	Figure 10-14c Reproductive Cloning [view large image]

The three types of cloning:


• DNA cloning - As shown in Figure 10-14a the DNA to be cloned is cut into fragments by the restriction enzymes. Such enzymes occur naturally in some bacteria, where they stop viral reproduction by cutting up viral DNA. They restrict the growth of viruses and hence the name. The fragment of DNA is inserted into a vector by DNA ligase, which is another bacterial enzyme that seals any breaks in a DNA molecule. The most common vector is plasmid, which is a small ring of DNA removed from bacteria. Gene splicing is complete when a recombinant DNA (DNA containing fragments from two or more different sources) has been prepared. After the recombined plasmid is taken up by a host cell, cloning is achieved when the host cell and the recombinant DNA of the plasmid reproduce either the cloned gene or a protein product (produced by the gene).
• Embryo cloning - It is also called therapeutic cloning. The goal is to create stem cell for medical purpose. The donor cell is either collected from the blastocyst or oocyte. Blastocyst is extracted from the fertilized egg after it has divided for 5 days, while oocyte is from unfertilized egg (thus by-passing the ethical issue) in the ovaries. These are highly versatile stem cells, which can differentiate into various types of cells. If the nucleus of the stem cell is removed and replaced by the patient's genes, then the various specialized cells produced by the altered stem cell can be transplanted to the patient without the problem of immunological rejection (see Figure 10-14b).
• Reproductive Cloning - The concept behind reproductive cloning seems deceptively simple. By replacing the genetic material of an egg with that of a donated adult cell, it should be possible to create an exact copy of another living creature (see Figure 10-14c). Achieving this goal is another matter. There were lot of failures in mammalian cloning during the 1980s. Cloning of mammals became viable only in early 1990s and was well publicized with the birth of Dolly (the cloned sheep) in 1997. It is found that reproductive cloning is an inefficient and error-prone process. Many cloned embryos are miscarried; others have abnormalities. It is estimated that only 1 to 10 per cent of cloned embryos from adult donor cells develop completely, depending on the species (more complicated organism is harder to clone). It took 277 attempts to clone Dolly the sheep; Carbon Copy, the cloned kitten, came after 86 failures. Only 33 monkey embryos have been created after 738 attempts - and none has produced a live birth.

  Many cloning problems arise because of the key difference between normal fertilization and cloning. A normal fertilized egg contains genetic material from sperm and egg. When united, the genes in them turn on or off in a precise pattern that is in perfect readiness for the development of an embryo. Since clones do not undergo fertilization, this programming does not occur. When the donated adult cell is merged with the egg, the egg tries its best to reprogram - but it doesn't do very well. All the right genes are correctly reprogrammed in only a tiny minority of clones. To succeed in reproductive cloning, scientists need to understand how to reset these genetic instructions.

  Sexual reproduction has evolved for two billion years and is the preferred mode after so many years of natural selection. It increases the rate of adaptive evolution and prevents the accumulation of deleterious (harmful) mutations. Cloning negates these advantages in favour of retaining some special characteristics of an organism. The argument is actually invalid because such characteristics are not determined by the genes alone; they are influenced by external factors such as the developmental environment (for the embryo) as well as subsequent growth and learning (i.e. wiring of the neurons) after birth.

  In the movie "Jurassic Park", dinosaurs are cloned by extracting their DNA stored inside the mosquitoes (preserved in amber), with missing pieces patched up from the modern reptilian version. Scientifically, short segments of DNA has been isolated from 100-million-year-old specimen preserved in ambers - but not in such spectacular scale as presented by Hollywood.

Cell Fate Manipulation

		that it takes close to a month to appear suggests other actors besides transcription factors in setting cell fate. Some of these probable regulators are barely recognized as yet. For instance, the vast majority of all RNA transcripts in mammals may be non-coding such as the
Figure 10-14d Cell Fate [large image]	Figure 10-14e Cell State [large image]	epigenome, suggesting that there's a lot more to learn about regulatory RNAs.

Researchers now know that almost all human cells test the mechanical properties of their microenvironment in the body, and use it to adjust their growth. This is determined by the extracellular matrix, a lattice of proteins and other molecules to which cells in solid tissues anchor themselves. The internal cytoskeleton includes a mesh of fibres made up of actin protein that lines the cell's membrane, plus tough actomyosin bundles in which actin combines with the protein myosin II. These two structures are joined together by integrins (a kind of protein), which span the cell membrane, gripping the actomyosin filaments inside

Figure 10-14f Cell Membrane, Mechanical Structures

the cell and the extracellular matrix on the outside (Figure 10-14f). These structures together response to the push and pull with a lot of flexibility.

	The effect is most obvious in astronauts' bones, which become thinner in the absence of gravity. Tissue stiffness is found to influence the growth or remission of cancer cells. The mechanical effect is most apparent in developing embryo where tissues twist, fold and writhe into the beginnings of adult tissues and organs. Figure 10-14g (left to right) shows
Figure 10-14g Mechanical Effects on Cell Fate	embryonic stem cells grown on soft, medium or rigid matrices start developing into neurons, muscle, and bone cells respectively.

Sex and Death

The drawing in Figure 10-15 shows the three stages in the life cycle of organisms with sexual reproduction, human included - birth, growth, and ageing. Death is the final event. The evolution of sex and death is traced in the following. The unicellular bacteria reproduced asexually in a simple process called fission. In this mode of reproduction, a given cell replicates its own DNA and then divides into two perfectly coequal clones of itself, each clonal offspring receiving one copy of the DNA. These cells mature and then repeat the cycle on and on ad infinitum. They are in effect immortal. In reality, they do die as the result of accident or starvation but not the kind of mortality common to all sexually reproduced organisms. A review on the subject of ageing can be found in the appendix. For early single-cell eukaryotes reproducing sexually, sex may involve nothing more than two cells sticking together and swapping portions of their DNA in a process called conjugation. It is then followed by the fission of the participating cells. The new products are genetically different from the parent cells prior to conjugation. As a

Figure 10-15 The Three Ages [view large image]

consequence, the older generation has disappeared - the new generation carrries another set of genes.

Biological Clock

Organisms have evolved to co-ordinate their activities caused by the Earth's rotation, its revolution around the Sun, and the Moon's revolution around the Earth. Table 10-02 is a summary of the various types of biological rhythm. Biological cycles were thought to be passive, driven by environmental cues such as changes in light and temperature. It is only in the late 1990s that an internal-clock more or less independent of external environment was identified at molecular level. Figure 10-16a depicts the daily rhythm of a typical individual. It shows that there is a cyclic variation for most of the biological functions, which attain their high or low point at certain time each day.

Figure 10-16a Circadian Cycle [view large image]

Table 10-02 Types of Biological Rhythms

to the pineal gland. Figure 10-16b shows the mechanism of the circadian clock in the brain. The ganglion cells in the retina of the eye operate independently of the rods and cones, which mediate vision. They track fluctuations in light but are far less responsive to sudden changes or low intensity. That sluggishness befits a circadian system. It would be no good if watching fireworks or going to a movie tripped the mechanism. These cells send information about brightness and duration to the SCN, which then dispatches the information to the parts of the brain and body that control circadian processes. In response to daylight, the SCN emits signals (red arrow) that stop another brain region - the paraventricular nucleus - from producing a message that would ultimately result in melatonin's release by the pineal gland. After dark, however, the SCN releases the brake,

Figure 10-16b Circadian Clock [view large image]

allowing the paraventricular nucleus to relay a "secrete melatonin" signal (green arrows) through neurons in the upper spine and the neck to the pineal gland.

The followings describe the cellular clock mechanism (see Figure 10-17a/b, lower-case for gene, capital for protein):


1. The cycle begins in the cell nucleus, where special initiator genes are in the "on" position (the default).
2. The initiator genes produce the proteins "CYCLE" and "CLOCK". They form a complex and bind to the E-box in the DNA coding the "PER" (period) and "TIM" (timeless) proteins. This process runs continuously until it is inhibited by the "TIM/PER" complex.
3. mRNAs for the proteins PER and TIM are transcribed.
4. The mRNAs move out to the cytoplasm and make the PER and TIM proteins.
5. The "TIM" protein is degraded in the presence of light and so its concentration level is low during the day. This has important implications since it means PER can't accumulate either. It is because PER is degraded by another clock protein "DBT" (double time) when the PER is not bound to the TIM/PER complex. This is the crucial step to delay the cycling, otherwise the oscillatory period would be much less than 24 hours.
6. When the PER and TIM proteins reach a certain concentration in the cytoplasm as day turning to night, they begin to bind in pairs. These PER/TIM complexes have a shape that allows them to enter the nucleus.
7. Once inside the nucleus, the PER/TIM complexes block the operation of the initiator genes so they can no longer activate the clock genes that generate these very proteins in the first place. With the clock genes switched off, the whole process comes to a halt. This is a negative feedback loop, which produces a stable process (a positive feedback loop on the other hand would produces a runaway process).
8. The PER/TIM complexes gradually dissipate in the nucleus, probably eliminated by an enzyme as night turning to day. Once the complexes have vanished, they no longer block the initiator genes, which then switch the clock genes back on, allowing the cycle to start anew. The initiator genes can also be switched back on by the interference of light (photo-entrainment), which destroys the TIM protein and hence the TIM/PER complex. Figure 10-17b shows the timing of the events in 24 hours cycle.

		sometimes weeks to adjust to a sudden shift in day length or time zone. A new schedule of light will slowly reset the SCN clock. But the other clocks may not follow its lead. The body is not only lagging; it is lagging at a dozen different places and hence the phenomenon of "jet lag", which doesn't last, presum-ably because all of those different drummers eventually sync up again. Seasonal rhythms in many animals such
Figure 10-17a Clock Mechanism [view large image]	Figure 10-17b Biological Clock [view large image]	as hibernation, migration, molting and mating may also be regulated by the circadian clock, which is equipped to keep track of the length of days and nights.

		commercial contrivances of Christmas sales and chocolate Easter eggs. However, animals in the wild still depend on the ability to cope with the seasonal change for successful reproduction of progeny by carefully regulating their annual breeding. They have to survive the harsh winter every year with migration or hibernation
Figure 10-17c Daylength [view large image]	Figure 10-17d Migration and Hibernation [view large image]	(Figure 10-17d). Some native birds and mammals in high latitude adopt the strategy of free-running rhythms of sleep and wake allowing them to forage whenever physical conditions are favourable.

	In birds, daylength is detected by deep-brain photoreceptors (DBP) and measured by a circadian clock in the SCN. Daylength information then regulates the activity of GnRH neurons in the hypothalamus. The rest of the process is similar to that for the mammals. The pineal and eye, so important in the circadian system of many birds, are not required for the photoperiodic regulation of reproduction.
Figure 10-17e Regulation of Reproduction [view large image]

Sleep and Dream

		Sleep is another process in the brain that we still have much to learn. We know that while we sleep, we cycle between two very different states. The first is called slow wave sleep characterized by long waves of undulating electrical activity. The second is rapid eye movement (REM) sleep characterized by frantic brain activity that looks very much like wakefulness. It also has very obvious physical signs: the rapid flickering
Figure 10-18 Dreaming Brain [view large image]	Figure 10-19 Peaceful Dream [view large image]	motion of the eyeballs, the near-total muscle paralysis (to prevent from acting out the dreams), and penile erections.

It is found that dreams are associated with REM sleep. During dreaming, the visual cortex is very active (to generate internal imagery), as are the amygdala, thalamus and the brainstem, which fits with the fact that dreams tend to be very visual and emotional. At the same time, the prefrontal and parietal cortices and the posterior cingulate, areas which deal with rational thought and attention, are all very quiet, which tallies with the lack of insight, illogicality and time distortion that characterizes dreams. Although the hippocampus is actively processing long-term memory, the short-term memory region is inactive, which explains why dreamer forgets what just happened (see Figure 10-18).

		feeling floaty" (Figure 10-19) or "there was a feeling of peace". The second type of REM sleep is known as phasic and is characterized by jerky eye movements, spasmodic limb and facial twitching and sudden breathing changes. When volunteers are woken from this sort of REM sleep, they typically describe their dreams as being strongly visual, active and "real". Phasic REM and its accompanying dreams tend to occur later on in the sleeping period.
Figure 10-20a Nightmare [view large image]	Figure 10-20b Data Processing [view large image]	Nightmares are associated with this type of sleep (see Figure 10-20a).

REM sleep appears to have arisen quite early in evolution - worms, insects, reptiles, birds and mammals all do it. Therefore, it must serve a very useful function. There are many theories of sleep function, which fall into four broad classes: restoration and recovery, predator avoidance, energy conservation and information relocation from short-term to long-term memory, (discarding redundant data in the process, Figure 10-20b) similar to

Figure 10-21 Sleep Patterns [view large image]

the transfer of data from disk to tape in the IT (information technology) industry. But not one of them has been confirmed or refuted. Figaure 10-21 shows the sleep patterns (or the lack of it) for a variety of species.

Recent research in 2003 indicates that non-REM sleep may give brain cells a chance to repair themselves, and REM sleep may allow the brain's neuron receptors to recover (regain full sensitivity). It is found that Animals born inmature require more REM sleep. Thus REM sleep may also act as a substitute for the external stimulation that prompts neuronal development in creatures that are mature at brith. Sleep research will identify the brain regions that control REM and non-REM sleep. It will lead to a more comprehensive and satisfying understanding of sleep, its functions, the mechanisms and evolution. It will probably gain insights into exactly what is repaired and rested, why these processes are best done in sleep.

		sleep, when consciousness may be totally obliterated, the brain remains significantly active. There is only a 20% reduction in cerebral blood flow during sleep. Although consciousness is dulled, the brain is still roughly 80% activated and thus capable of robust and elaborate information processing. It is amusing that all these activities occur inside our brain every night but we have only a dim notion of what is going on.
Figure 10-22 Sleep and Dream [view large image]	Figure 10-23 Sleep Cycle [view large image]

Figure 10-22 summarizes the sleep states.


• A "Wake" state including stages 1 and 2 has been added in the Diagram. The actual sleep cycle involves only the NREM (in brown color), and the REM (in green).
• Behaviour - Changes in position can occur during waking and in concert with phase changes of the sleep cycle. Two different mechanisms account for sleep immobility. The first is disfacilitation (during stages 1- 4 of NREM sleep). The second is inhibition (during REM sleep). During dreams, we imagine that we move, but we do not.
• Awake - Waking (in the present context) is the phase during which the body prepares for sleep. All people fall asleep with tense muscles, their eyes moving erratically. Then, normally, as a person becomes sleepier, the body begins to slow down. Muscles begin to relax, and eye movement slows to a roll.
• Sleep can be divided into five stages. Although the signals for transition between the five stages of sleep are mysterious, it is important to notice that these stages are discretely independent of one another, each marked by subtle changes in bodily function and each part of a predictable cycle whose intervals are observable. Sleep stages are monitored and examined clinically with polysomnography, which provides data regarding electrical states of the muscle (electromyo-gram - EMG), the brain (electroencephalogram - EEG), and eye movement (electrooculogram - EOG) during sleep.
  
  
  1. Stage 1 - This is a stage of drowsiness. Polysomnography shows a 50% reduction in activity between wakefulness and stage 1 sleep. The eyes are closed during Stage 1 sleep, but if aroused from it, a person may feel as if he or she has not slept. Stage 1 may last for five to 15 minutes.
  2. Stage 2 - Stage 2 is a period of light sleep during which polysomnographic readings show random fluctuation. These waves indicate spontaneous periods of muscle tone mixed with periods of muscle relaxation. The heart rate slows down, and body temperature becomes lower. At this point, the body prepares to enter deep sleep.
  3. Stage 3 - This stage is known as slow-wave, or delta, sleep. During slow-wave sleep the EMG records slow waves of relatively high amplitude, indicating a pattern of deep sleep and rhythmic continuity.
  4. Stage 4 - This stage is similar to Stage 3 but more intense. The period of non-REM sleep (NREM) is comprised of stages 1 - 4 and lasts from 90 to 120 minutes. In addition, stage 2 and 3 repeat backwards before REM sleep is attained. Therefore, a normal sleep cycle has this pattern: stage 1, 2, 3, 4, 3, 2, REM. Usually, REM sleep occurs 90 minutes after the onset of sleep.
  5. REM - REM sleep is distinguishable from NREM sleep by changes in physiological states, including its characteristic rapid eye movements. However, polysomnograms show wave patterns in REM to be similar to Stage 1 sleep. In REM sleep, heart rate and respiration speed up and become erratic, while the face, fingers, and legs may twitch. Intense dreaming occurs during REM sleep as a result of heightened cerebral activity, but paralysis occurs simultaneously in the major voluntary muscle groups. Because REM is a mixture of encephalic (brain) states of excitement and muscular immobility, it is sometimes called paradoxical sleep. The first period of REM typically lasts 10 minutes, with each recurring REM stage lengthening, and the final one lasting an hour. The percentage of REM sleep is highest during infancy and early childhood, drops off during adolescence and young adulthood, and decreases further in older age.
  A sleep cycle (see Figure 10-23) comprises five stages of sleep, including their repetition. The first cycle, which ends after the completion of the first REM stage, usually lasts for 100 minutes. Each subsequent cycle lasts longer, as its respective REM stage extends. So a person may complete five cycles in a typical night's sleep.
• Sample tracings of three variables used to distinguish the state are also shown in Figure 10-22: The EMG tracings are highest during waking, intermediate during NREM sleep and lowest during REM sleep. The EEG and EOG are both activated during waking and REM, but inactivated during NREM sleep. Each sample shown is approximately 20 seconds long.
• The three bottom rows in Figure 10-22 describe other subjective and objective state variables such as sensation, perception, thought, and movement.

Meditation

		slightly higher frequency range than the Delta (sleeping) state (see Figure 10-21). The state is on the border line between consciousness and sleeping. The anterior cingulate gyrus becomes underactive in meditation (see Figure 10-25). As shown in Table 10-03, the cingulate gyrus concentrates on internal stimuli, and contains the feeling of self. Curiously, this is the same area that becomes underactive in hypnosis (when the identity of self dissolved) and Schizophrenia (when own thoughts are confused with outside voices). Thus it doesn't seem to be accidental that in
Figure 10-24 Meditation [view large image]	Figure 10-25 Meditating Brain [view large image]	meditation, the sense of boundaries is lost and it induces a feeling of "at one" (union) with the universe.

Meditation, nearly as old as humanity, has always been part of Eastern religions. Starting from 2nd century A.D. meditation became important part of Christian practice until early 1500s when Martin Luther disapproved mysticism. Jewish and Muslim meditations have established around 1000 A.D. Meditation was used as a medium to communicate with the higher being(s). Actually, the brain is playing trick on the practitioners by producing various illusions. Now the West is rediscovering the benefits of meditation. In its most modern forms, it has dropped the mantra bit that has the subject memorize a secret phrase or syllable; instead it only requires focusing on a sound or breathing. In fact, just closing the eyes in a quiet place (to block sensory inputs) and relaxing the mind (to minimize internal processing) would attain the same result without much ado.

Consciousness

Consciousness is usually defined as the part of the human mind8 that is aware of the feeling, thoughts and surroundings. Actually there is no simple, agreed-upon definition of consciousness. A more detailed definition(s) will be discussed later. Most of the philosophical discussions of consciousness arose from the mind-body issues posed by Rene' Descartes in the 17th century. He asked: Is the mind, or consciousness, independent of matter? Is consciousness physical or non-physical? It is now recognized that the phenomena by which we define consciousness are correlated with certain configurations of activity in certain nervous systems and not with others. Most neural activity doesn't generate consciousness, even in the supremely conscious human brain. Moreover, the activities that do generate consciousness do not produce it by accident or in a happenstance manner. Consciously processed events in the nervous system have a very clear physical signature, in the form of characteristic brain activity. There is good empirical evidence that consciously registered events leave distinct traces in the brain and are processed in special ways within the brain's networks. Techniques such as EEG, f MRI, and PET provide information about the relationship between mental tasks and the collective activities of groups of many millions of

Figure 10-26 Correlation of

Brain Activities and Mental Tasks [view large image]

Sigmund Freud, the founder of psychoanalysis, compared the human mind to an iceberg. The tip above the water represents consciousness, and the vast region below the surface symbolizes the unconscious mind. This subconscious mind is the sum total of our past experiences. What we feel, think, or do forms the basis of our experience. These experiences are stored in the form of subtle impressions in our subconscious mind. These impressions interact with one another and create tendencies. The resultant of these tendencies determines our character (see Figure 10-27a). However, if the unconsicous drives (the id) might prompt behavior that would be incompatible with our civilized conception of ourselves, the action would be suppressed by the conscious mind (the ego). This Freudian concept has been fallen out of favour by 1950s. Better understanding of brain chemistry gradually replaced his model with a biological explanation of how the mind arises from neuronal activity. But since mid 1990s, attempts to piece together diverse neurological findings have validated the general sketch Freud made almost a century ago.

Figure 10-27a Consciousness [view large image]

The lower diagram in Figure 10-27a identifies some Freudian terminologies with the modern anatomy of the human brain.

Figure 10-27b presents a modern view of the conscious. It divides the conscious and subconscious thought into four divisions (controllers). While the Pavlovian controller is the brain's autopilot, the other three control systems (see more detail in the diagrams, and brain components) combine both kind of thought to achieve the best possible outcome depending on the level of uncertainty about the situation you are in. In this model, subconscious and conscious thoughts are more like equal partners than competitors. The two work together to evaluate all the available information whether consciously or subconsciously perceived. Our behaviour is often driven by more than one of the four controllers. This is especially true when we are learning something new where the balance between ignorance and experience changes. Importantly, the subconscious isn't the dumb cousin of the conscious, but rather a cousin with different skills.

Figure 10-27b Conscious Controllers [view large image]

The state of consciousness can be divided into three levels:


• The most basis state is that of being conscious and of not being conscious. The site of consciousness seems to be in or around the thalamus, or it should at least involve interactions between the thalamic and cortical systems.
• A background state is an over all state of consciousness such as being awake, being asleep, dreaming, being under hypnosis, and so on. It includes a range of normal and of "altered" states.
• Specific states of consciousness are the fine-grained states of subjective experience. Such states might include the experience of a particular visual image, of a particular sound pattern, of a detailed stream of conscious thought, and so on. A detailed visual experience, for example, might include the experience of certain shapes and colors, of specific arrangements of objects, of various relative distances and depths, and so on. Much of the most interesting work on "Neural Correlates of Consciousness" (NCC) is concerned with states like these. NCC usually probes neural activity deep down into the cellular level.

The three classes of consciousness definition:



		The first is the definition of consciousness as a state. Most mammals, and many non-mammalian species as well, have this aspect of conscious capacity. All mammals alternate between states that can be labeled as asleep, awake, and alert. Several species of mammals even seem to dream as we do and show rapid eye movements and brain waves that resemble our own during certain phases of asleep. Most mammals also show daytime variation in arousal; i.e., they alternate between what we
Figure 10-28a Consciousness Circuit [view large image]	Figure 10-28b Thalamic Nuclei [view large image]	call active, vigilant, and wide-awake states and those that are passive, unfocused, and marked by a reduced level of activity.




• A second class of definition takes an architectural approach, whereby consciousness is considered as the central processor located at the top of the control hierarchy. Its physical counterpart is distributed across several subsystems of anatomical structures. These subsystems are identified to be the various thalamic nuclei located in the thalamus (see Figure 10-28a). Figure 10-28b shows the actual location of some thalamus nuclei. They are the mediator between the unconscious atuonomic functions in the brain stem and conscious awareness - the higher mental activities in the forebrain. This conceptual organization brings cognition, emotion, and action under a unified command. Consciousness would correspond to the active state of this command center in the thalamus. For instance, when suddenly you feel the need for a drink. This "need" is the thalamus, on behalf of its autonomic subsystem, breaking through into your conscious awareness and modifying your behavior to meet your body's basic needs.
  
  
  Here's how it works:
  
  
  • Inputs arrive in the thalamus as nerve signals. They may be from the senses, especially sight, taste, and touch; from the limbic system or recticular formation in the brain itself (about basic need and drives); and from internal organs such as the heart and intestines. It is also influenced by hormones circulating in the blood, and by concentrations of glucose, sodium, and other substances in the blood passing through it and in the cerebrospinal fluid just above it. Inside the thalamus are several pairs of relatively discrete nuclei. Some tasks of the thalamus are assigned to a specific pair; others seem to be spread through several areas which communicate by nerve fibers so that they can work together as a single "center" for one main role.
  • The thalamus sends outputs as nerve signals to the motor (muscle controlling) parts of the midbrain, the limbic system, and the various autonomic centers in the brain stem that control processes such as heartbeat, blood pressure, and urine production, as well as the glands producing saliva, sweat, and digestive juices. It also produces hormones - such as the antidiuretic hormone (ADH) - which are passed to the pituitary.


The late Francis Crick (1916-2004) believed that the command center is in the claustrum instead of the thalamus. The claustrum is a thin sheet of grey matter that resides parallel to and below part of the cortex. It is present in all mammals, but it has been little studied and its function is not known. What is known, however, is that there are two-way connections between the claustrum and most, if not all, parts of the cortex as well as subcortical structures involved in emotion. It is likened to the conductor of an orchestra, who is responsible for binding the performances by individual musicians into an integrated whole that can be much more than the sum of its parts. The neuroanatomical connections of the claustrum, then, just match with the "conductor" required to bind together the various disparate components of the conscious experience represented in many different brain regions.


• The third definition of consciousness takes a human-centered view of cognition and has more to do with enlightenment, or illumination, than with mere attention. This is the representational approach, in which consciousness is made dependent upon our human capacity for symbolization. Language is one example of representing something in symbolic form, which expands the power of storing knowledge and information enormously both in space and time (in the forms of books, CD-ROMs, and libraries, ...). This definition relates consciousness exclusively to mental process in the cortex of a human brain.
  
  Recent research indicates that consciousness is involved only in activities stemming from the associative regions of the cortex. These regions are found in the neocortex, which consists of four lobes: the occipital, patietal, temporal and frontal. The associative cortex is involved with the conscious perception and identity of one's own body; in the planning of movement, spatial perception, orientation and imagination; and in spatial alertness. The development of consciousness seems to be largely reliant on the numerous nerve cells in the cortex being linked to each others. The cortex's high number of connections vastly exceeds the number of points of entry and exit. This arrangement means that the cortex communicates with itsef more than with the sensory organs and motor apparatus.



• Recently in 2007, it is suggested that all the above are "red herrings". Consciousness does not depend on language as babies, and many animals are not insensate robots. Nor can consciousness be equated with self-awareness. At times we have all lost ourselves in music, exercise or sensual pleasure, but that is different from being knocked out cold. Even the central control architecture is an illusion. Consciousness turns out to consist of a maelstrom of events distributed across the brain. These events compete for attention, and as one process out-shouts the others, the brain rationalizes the outcome after the fact and concocts the impression that a single self was in charge all along.

Modern explanation of consciousness is based on "neural correlate", which assumes:


• The subjective content associated with a conscious sensation does exist and has its physical basis in the brain.
• All the different aspects of consciousness (smelling, pain, visual awareness, self-consciousness, and so on) employ a basic mechanism.
• Consciousness is a property of the human brain, a highly evolved system. It therefore must have a useful function to perform, e.g., to produce the best current interpretation of the environment and to make it available to the parts of the brain which contemplate, plan and execute voluntary motor outputs (including language).
• At least some animal species posses some aspects of consciousness.

a unique way. Different coalitions activate to represent different stimuli from the senses (Figure 10-28c). The Quantitative model maintains that neurons across the brain fire in synchrony and prevail until a second stimulus prompts a different assembly to arise. Various assemblies coalesce and disband moment to moment, while incorporating feedback from the body. Stronger external stimuli engage larger number of neurons and trigger higher degree of consciousness (Figure 10-28c). These models have not addressed the all-important middle

Figure 10-28c NCC Models [view large image]

step of how a phenomenon causes an experience. They have not explained how consciousness arise, i.e., how physiological events in the brain translate into what is experienced as consciousness (dubbed as the "hard problem").

By implanting electrodes in the brains of 10 volunteers with drug-resistant epilepsy, a study in 2009 reports that the signature of consciousness involves:
1. During the first 30 milliseconds of the experiment, brain activity involving the non-conscious and conscious tasks was very similar, indicating that the process of consciousness had not kicked in.
2. There is an increase in the voltage levels of the signals in the brains after the first 30 milliseconds.
3. The frequency and phase of neurons firing in different parts of the brain become synchronize.
4. Some of these synchronized signals appear to be triggering others.
5. This study suggests that consciousness has no single seat. It is more a question of dynamics than of local activity.

Fungi

		The oldest fossils of fungi date back 460 million years ago. New knowledge on evolutionary lineage shows that they are more closely related to animals than plants. The first vascular plant fossils (dated back to about 400 million years ago) have petried mycorrhizae - indicating that plants and fungi moved onto land together. Mycorrhizae are the roots of fungus, which lives in plant roots where it provides the plant with minerals and the plant gives organic nutrients in return.
Figure 10-29 Bread Mold Life Cycle [view large image]	Figure 10-30 Fungi [view large image]

Fungi lack chloroplasts, as do animals. Thus the process of photosynthesis, which is very common and important in plant life because it serves as their source for food, is absent. Fungi obtain food by heterotrophic process. They secrete enzymes into the nutritive materials. These exoenzymes degrade those substances to which they are adapted, and the resulting compounds must be absorbed through the wall of the cell while leaving the residues (wastes) outside.

The bodies of all fungi, except unicellular yeast, are made up of filaments called hyphae. A hypha is an elongated cylinder containing a mass of cytoplasm and many haploid nuclei, which may or may not be separated by cross wall. A collection of hyphae is called a mycelium.

Fungi reproduce in accordance with the haplontic life cycle as shown in Figure 10-29. This figure shows the life cycle of the black bread mold. Asexually, a mycelium gives rise to spore-producing sporangia. Sexually, the tip ends of hyphae from opposite mating strains can fuse, giving a zygote, the only diploid portion of the cycle. After a period of dormancy, meiosis is followed by germination of the zygospore and production of a sporangium. Windblown spores, an adaptation to land, produce mycelia.

There are many different types of fungi as shown in Figure 10-30. There are sac fungi with saclike cells to store the spores; some have shape like a cup. Yeasts are sac fungi that do not form fruiting bodies; they carry out the fermentation: "glucose => carbon dioxide + alcohol" for either baking or production of wines and beers. The blue-green molds (notably penicillium) are also sac fungi; they are used to provide flavor in cheeses and to produce antibiotic penicillin. Club fungi include the mushroom, which store the spores in the gills under the cap. Some mushrooms are poisonous while other types of fungi cause diseases such as althlete's foot and vaginal infection.

Plants

		7000 species of green algae living today. They include microscopic, unicellular forms like chlorella and chlamydomonas; colonial forms like the filamentous spirogyra; and multicellular forms like ulva, the sea lettuce. Although some of the multicellular forms are large, they never develop more than a few differentiated types of cells and their
Figure 10-31 Plant Evolution [view large image]	Figure 10-32 Plant Reproduction [view large image]	fertilized eggs do not develop into an embryo.

About 400 million years ago, plants began to establish themselves on land. The animals soon followed. The following table compares the aquatic and land environments and the kind of adjustments the organisms had to make in order to live on land.

Table 10-04 Water and Land Environments Comparison

Plants are photosynthetic organisms with the following characteristics:


• Plants contain chlorophylls; they store reserve food as starch and have cellulose cell walls. Animals store reserve food as glycogen and do not have cellulose cell walls.
• Plants lack the power of motion or locomotion by means of contracting fibers.
• Plants are multicellular and have cells specialized to from tissues and organs.
• Plants have a life cycle that is identified as alternation of generations (see Figure 10-06).
• Plants have sex organs with an outer layer of nonreproductive cells that can prevent desiccation of gametes
  (see Figure 10-32).
• Plants protect the developing diploid embryo from drying out by providing it with water and nutrients within the female reproductive structure (see Figure 10-32).

Land plants first developed as mosses living in moist places. These are fairly simple plants that do produce a number of differentiated cell types and whose fertilized egg grows into a distinct embryo. However, they don't have vascular tissue⁹ (xylem and phloem) to transport water and minerals from their roots up to their leaves. Ferns and horsetails are primitive vascular plants. They still require a wet environment for fertilization to take place. Swamps in the Carboniferous era are believed to have contained fernlike foliage in great abundance.

As suggested in Table 10-04, land dwelling organisms should be able to support themselves against gravity and to protect their reproductive units from desiccation. These requirements are fulfilled by the vascular tissues and embryo sporophytes in gymnosperms (naked seed) and angiosperms (capsuled seed). Figure 10-32 shows the reproductive cycle of the flowering plants. The first stage of sexual reproduction is pollination. This is the transfer of pollen from the stamen to the stigma. When pollen is carried from the stamen to the stigma of the same plant, the process is called self-pollination. When pollen is carried to the stigma of another plant, it is called cross-collination. Most plants have developed ways of avoiding self-pollination because it reduces genetic variation. When a grain of pollen lands on a stigma, a tube, called a pollen tube, grows from the sigma down into the overy. The male gametes in the pollen pass down this tube and meet the ovule. The fusion results in the formation of a seed which contains a plant embryo. The ovary ripens to form the friut around the seed. In order to prevent overcrowding and competition for space, light, and water, seeds and fruits are carried away from the parent plant by wind, animal or explosion. Further details of plants living through the geological periods from Cambrain to the present are described in "Evolution of Micro-organisms and Plants". More details about the living plants can be found in "Anatomy of Plants".

Animals

Animals are believed to have arisen from protozoans ("first animals" in Greek), which were in existence way back in the Archaean period about 3 billion years ago. These unicellular organisms evolved to multicelluar organisms called metazoa over 600 million years ago. Primitive metazoa can be grouped in three basic categories: sponge-like animals, cnidarians, and worms. The sponges, and cnidarians, are the most primitive with about 11 specialized cell types. Worms and higher metazoa have approximately 55 specialized cells. Sponges are the simplest grade of multi-celled animals. In general, sponges have open-topped, sack-like bodies which are fixed to the sea floor. Water is pulled through pores in the body, and food is filtered out; rest of the water exits from the opening. The cnidarians include corals, hydras, sea anemones, and jellyfish. Their basic body plan is also a sack-like form, but at one end there is a mouth/anus, which can be opened and closed, and tentacles which direct food to the mouth.

Figure 10-33 Animal Evolution [view large image]

Figure 10-33 shows animal diversification over the age. All this diversity stems from successive branchings, starting from a single bacterium-like ancestor. Each branching event is called a speciation: a breeding population splits into two, and they go their separately evolving ways. Among sexually reproducing species, speciation is said to have occurred when the two gene pools have separated so far that they can no longer interbreed. Speciation begins by accident, but natural selection operates in a non-random way. When separation has reached the stage where there is no interbreeding even without a geographical barrier, we have the origin of a new species.

Further details of animals evolving through the geological periods from Cambrain to the present are described in an appendix - Age of Animals. The living animals are described in the Anatomy of Animals.

What Makes Us Human?

The question of "What makes us human?" has been pondered by philosophers and others since time immemorial. The answer is usually implied in the charateristics of humans. We can draw up a list of differences: bodily differences such as the plantigrade (flat to the floor) foot, opposable thumbs, bipedal gait and big brains; mental differences in intelligence, speech, imagination, tool manufacture and use, fire and cooking; and

Figure 10-34a Human and other Primates [view large image]

social differences in culture, religion, music, art, reason, use of medicine, social learning and the formation of social groups. Such list would separate us more or less from the other animals (Figure 10-34a). Figure 10-34b shows the steps leading to human starting from 6 million years ago with the split of the chimp and human lineages.

Figure 10-34b Becoming Human [view large image]

Gene	Mutation in Human	Function
AMY1	More copies	Digestion of starch
ASPM	Several bursts of change	Brain size
DUF1220	Lot of duplicated copies	High cognitive function
FOXP2	In 2 locations of the amino-acid sequence	Speech and Language
HAR1	Substantial change	Fetal brain tissue development
HAR2	Second most changes (after HAR1)	Wrist and thumb development
LCT	Mutation on chromosome 2	Digestion of milk sugar in adulthood
MYH16	Tiny mutation	Affecting jaw muscle leading to smaller jaw
TRIM5	Single base change	For combating the PtERV1 virus

Table 10-05 Gene Mutations in Human

A new study has found the strongest evidence yet in the brain's right prefrontal cortex that sets humans apart from other primates. This is the site where we understand the mental processes of others - the basis of our socialization and what makes us human. It gives rise to our capacity to feel empathy, sympathy, understand humor and when others are being ironic, sarcastic or even deceptive. It is the cumulative result of 300,000 years of tool-making evolution, which requires the ordering of sequences and the hierarchical assembly of the same components into different configurations (to make tools of different functions). As makers of single-component tools, we progressed at a remarkably slow pace starting about 2.5 million years ago. But with the appearance of composite tools, near-modern brain size anatomy and perhaps of grammatical language 300,000 years ago, the pace quickened exponentially.

Figure 10-35a Human-like Consciousness in Other Animals [view large image]

We became long-range planners and grammatical speakers. Eventually, we possess all the prefrontal capacities - working memory, our sense of self, and theorizing about other people's minds. The so-called intentionality now constitutes the essential ingredient for the new

With the publication of the draft DNA sequence of the chimpanzee genome in the summer of 2005, more data are now available for understanding human biology and evolution. Although the human and chimpanzee genomes are very similar, there are about 35 million nucleotide differences, 5 million indels (insertions or deletions) and many chromosomal rearrangements to take into account. Most of these changes will have no significant biological effect, so identification of the genomic differences underlying such characteristics of "humanness" as large cranial capacity, bipedalism and advanced brain development remains a very difficult task. Given the short time since the human-chimpanzee split, it is likely that a few mutations of large effect are responsible for part of the current physical (phenotypic) differences that separate humans from chimpanzees and other great apes.

Figure 10-35b Gene Evolution [view large image]

There are three prevailing hypotheses to account for the evolution of "humanness traits" (Figure 10-35b):


1. Protein evolution - Natural selection is commonly thought to operate mainly at the protein level. For this reason, nucleotide changes in protein-coding regions are usually classified into two groups: "synonymous changes" K_S (which do not cause any change in amino-acid) and "non-synonymous changes" K_A (which do cause amino-acid changes). It is found that protein-coding regions with K_A/K_S > 1 (which means a lot of non-synonymous changes) are not involved in processes related to supposed humanness traits. They are mostly related to host-pathogen interaction, immunity and reproduction. Such pattern is also found in rats, mice and other mammals. However, some regions with small K_A/K_S may actually have produced dramatic consequence. For example, two amino-acid changes alone in the highly conserved FOXP2 protein (a gene-transcription factor) might have contributed to the human capacity for speech.
2. Less -is-more - This hypothesis posits that loss-of-function changes relative to the "prototypical ape" traits are characteristic of certain humanness traits - for example, lack of body hair, preservation of some juvenile traits into adulthood and expansion of the cranium. Such loss-of-function changes could be caused by non-synonymous substitutions, indels, loss of coding regions and deletions of entire genes. The comparisons to the chimpanzee have unveiled 53 human genes with disruptive indels in the coding regions, and genes in this category may be associated with intriguing phenotypes. Small indels could plausibly be major contributors to human-chimpanzee phenotypic differences, especially given that these mutations can also influence the two other hypotheses for the evolution of humanness (see triple overlapped area at the center of Figure 10-35b).
3. Gene-regulatory evolution - There is a long-standing hypothesis that the phenotypic differences between humans and chimpanzees primarily arise from changes in gene-regulatory regions - the promoter regions. The current analyses do not address this issue in detail, because it is still notoriously difficult to identify such regions. This hypothesis is the hardest to test, yet it may be the most promising one.

The draft sequence of the chimpanzee and macaque genomes released in 2006 enables scientists to compare chimp, human and monkey DNA to search out signals that seem unique to people. Followings are some initial findings:


• It is found that one gene contains a protein-coding domain that is repeated 212 times in people, compared with 37 repeats in chimps, 30 in macaques and one in mice and rats. This protein domain is active in human brain cells and other tissues. Genomic study of the patients with brain dysfunctions found that of the 290 cases with unexplained mental retardation, one patient had a deletion in the same region of the relevant gene.
• Mutating the relevant genes in mice indicates that they could enlarge mouse brains by inducing fetal mice to over-express the regulatory chemical -catenin. That suggested the chemical might regulate pathways that control human brain size.
• By comparing the human and chimp genomes, one gene is found to evolve rapidly during the transition from chimps to people. This gene is expressed at 7 - 19 weeks of human fetal development, when neurons are know to be forming and moving throughout the brain.

Future of the Human Race

		Figures 10-36 and 10-37 show two world models among many others, which were built specifically to investigate five major trends of global concern - accelerating industrialization, rapid population growth, widespread malnutrition, depletion of nonrenewable resources, and a deteriorating environment. Like every other model, they are imperfect, oversimplified, and unfinished. The model uses feedback loop similar to the logistic equation to trace the development of the eight variables as labeled without scales in the diagrams. The
Figure 10-36 World Model, Standard [view large image]	Figure 10-37 World Model, Controlled [view large image]	horizontal time scale is also vague because the model just indicates the general behavior, the numerical values are not as significant as some critic would like to ascribe.

Different models can be constructed easily by changing the value of parameters in the computer programs. The followings summarizes the essential features in these models:


• Doubling the resource reserves in 1900 or assuming "unlimited" nuclear power do not change the outcome as the growth in other variables are stopped by rising pollution.
• World model with "unlimited" resources and pollution controls allow population and industry to grow until the limit of arable land is reached. Food per capita declines, and industrial growth is also slowed as capital is diverted to food production. Population decline is delayed for about 30 years.
• The combination of "unlimited" resources, pollution controls, and increased agricultural productivity removes so many constraints to growth that population and industry reach very high levels. Although each unit of industrial production generates much less pollution, total production rises enough to create a pollution crisis that brings an end to growth.
• Instead of an increase in food production, an increase in birth control effectiveness is tested as a policy to avert the food problem. It shows that population continues to grow, but more slowly. Nevertheless, the food crisis is postponed for only a decade or two.
• Figure 10-37 is a world model with "unlimited" resources, pollution controls, increased agricultural productivity, and "perfect" birth control. The result is a temporary achievement of a constant population with a world average income per capita that reaches nearly the present US level. Finally, though, industrial growth is halted, and the death rate rises as resources are depleted, pollution accumulates, and food production declines. Population decline is delayed for about 50 years.

It has been shown that positive feedback loops operating without any constraints generate exponential growth. In the world system two positive feedback loops are dominant now, producing exponential growth of population and of industrial capital. In any stabilized system there must be constraints acting as feedback loops to stop exponential growth. The growth stopping pressures from negative feedback loops are already being felt in many parts of human society. Another response to the problems created by growth would be to weaken the positive feedback loops that are generating the growth. Such solution involves growth-regulating policies, which generates a "better" behavior mode. Figure 10-38 shows a world model with regulating policies to produce an equilibrium state sustainable far into the future.

Figure 10-38 World Model, Stabilized [view large image]

The policies that produced the stabilized world model are:


1. Population is stabilized by setting the birth rate equal to the death rate in 1975. Industrial capital is allowed to increase naturally until 1990, after which it, too, is stabilized, by setting the investment rate equal to the depreciation rate.
2. To avoid a nonrenewable resource shortage, resource consumption per unit of industrial output is reduced to 1/4 of its 1970 value.
3. To further reduce resource depletion and pollution, the economic preferences of society are shifted more toward services such as education and health facilities and less toward factory-produced material goods.
4. Pollution generation per unit of industrial and agricultural output is reduced to 1/4 of its 1970 value.
5. To avoid food shortage, capital is diverted to food production even if such an investment would be considered "uneconomic".
6. This policy alters the use of agricultural capital to make soil enrichment and preservation. It implies, for example, use of capital to compost urban organic wastes and return them to the land.
7. To counteract the drains on industrial capital resulting from the above-mentioned policies, the average lifetime of industrial capital in increased, implying better design for durability and repair and less discarding because of obsolescence. This policy also tends to reduce resource depletion and pollution.

The conclusions of The Limis to Growth:


1. If the present growth trends in world population, industrialization, pollution, food production, and resource depletion continue unchanged, the limits to growth on this planet will be reached sometime within the next 100 years. The most probable result will be a rather sudden and uncontrollable decline in both population and industrial capacity.
2. It is possible to alter these growth trends and to establish a condition of ecological and economic stability that is sustainable far into the future.
3. If the world's people decide to strive for this second outcome rather the first, the sooner they begin working to attain it, the greater will be their chances of success. That is, the sooner the better.

		breaking up and shrinking at an alarming rate of about 7% every decade since the 1970s. The images in Figure 10-39b compare the annual sea ice minimum in 1979 and 2003. The same picture also shows satellite images of a big chunk of ice shelf
Figure 10-39a Global Warming [view large image]	Figure 10-39b Arctic Ice, Disappearing [large image]	breaking up from the Ellesmere Island in the Canadian Arctic at the end of 2006. In addition to warming up the atmosphere, we are also guilty of plundering the sea and polluting the land. In view of

On February 2007, the IPCC (Intergovernmental Panel on Climate Change) released some climate change statistics through a very rigorous process, which excludes researches deemed controversial (such as the slowing down of the North Atlantic Gulf Stream), not fully quantified (e.g., the breaking up of Antarctic ice sheet), or not yet incorporated into climate models (discarding the real-world evidence of 88 cm per century for worst-case sea level rise):

		The atmosphere is warming up 0.13oC each decade in the last 50 years. Annual CO2 growth rate during 1995-2005 is at 1.9 ppm/year (see more in Figure 10-39c). The oceans have warmed to a depth of 3 km since 1961 absorbing more than 80% of the heat added to the climate system. Thus, even if there is no CO2 emission, this heat reservoir would continue to warm up the atmosphere by 0.1oC per decade. Sea level rises 1 - 2 cm in each decade during the 20th century. The amount of man-made heating entering the
Figure 10-39c CO2 Emission [view large image]	Figure 10-39d Man-made Heating [view large image]	Earth's climate system is more than 10 times of the radiation from the Sun (see Figure 10-39d). The certainty is 90% that we are to blame.

The harmful effects of global warming on daily life are already showing up, and within a couple of decades hundreds of millions of people won't have enough water. At the same time, tens of millions of others will be flooded out of their homes each year as the Earth reels from rising temperatures and sea levels. Tropical diseases like malaria will spread. By 2050, polar bears will mostly be found in zoos, their habitats gone. Pests like fire ants will thrive. For a time, food will be plentiful because of the longer growing season in northern regions. But by 2080, hundreds of millions of people could face starvation, according to the report, which is still being revised. The warming trend will likely deliver an ice-free Arctic and a 30% drop in rainfall in many subtropical region. Meanwhile, higher latitudes will get wet wetter as the air warms and storm tracks move, and hurricanes will become more intense. See details in the IPCC website. See also the "Climate Change" site provided by the Nature magazine.

Even if parts of the region have not been consumed by desertification, floods, drought or extreme weather will render such areas uninhabitable. Monsoon rains may lead to greening (reforestation) of a small portion of the tropic. Some coastal area and islands will be lost to rising sea levels (assuming a 2-meter rise). Human population will re-settle into the polar and sub-polar regions, which become food-growing zones. The abandoned tropical regions will be utilized to produce solar, geothermal, and wind energy. Human population will decline by the billions if the changeover process is not well managed.

Figure 10-39e A Warmer World [view large image]

Human survival depends very much on whether the CO2 level can be reduced to 280 ppm (to the 1900 level as shown in Figure 10-39c). The natural reglation by marine animals turning CO2 into calcium carbonate shells does not work any more because the man-made increase has risen 14000 times as fast as the average of the past 610000 years.

		10-41) was particularly critical; after the larger trees were harvested, nothing was left to make the seagoing canoes needed for voyaging to other sources of food and material. A common thread in the catastrophic collapse of past civilizations is a tendency to impose self-inflicted environmental degration, and unwise responses to societal problems such as using war as an instrument to resolve
Figure 10-40 Mayan Civili- zation [view large image]	Figure 10-41 Deforestation [view large image]	disputes, which mostly involve the sharing of resources - it is mostly about oil in this epoch of civilization.

Natural selection -- This is the path for human evolution millions of years in the past. As human population migrated to different kinds of environments in the last 2 million years, it developed into different races with different body types, eye folds, skin colors, and curliness of hair. These groups retained just enough connections with one another to avoid evolving into separate species. With the globe fairly well covered, one might expect that the time of evolving was pretty much finished. It turns out not to be the case. Genetic studies reveal that more than 300 regions on the human genome showed evidence of recent changes mostly related to improve people's chance of surviving and reproducing. Examples included resistance to diseases, changes in skin pigmentation in African; hair follicles among Asians, and more competent sperm (because our species is not exactly monogamous).

Figure 10-42 Evolution of Human Race in Future [view large image]

Un-natural selection -- This is related to the changes in living conditions brought about by agriculture and cities. For example, few people in China and Africa can digest fresh milk into adulthood, whereas almost everyone in Sweden and Denmark or North America can. This ability presumably arose as an adaptation of dairy farming.

Coexistence with Machine -- In this modern age, we are already very much dependent on machines. As much as we build them to meet our needs, we have structured our own lives and behavior to meet theirs. As machines become ever more complex and interconnected, we will be forced to try to accommodate them. Darwinian evolution may be a victim of its own

success, unable to keep up with non-Darwinian processes that it has spawned. Our technological prowess threatens to swamp the old ways that evolution works. One view maintains that past record of success gives us good grounds for thinking that coevolution (biological and technological) will continue to lead in desirable directions. A darker view envisions that various mechanical / electronic components will eventually link up together to create a being superseding human kind.

Figure 10-43 Coexistence with machine

Figure 10-43 presents the two views of human-machine coexistence. The picture on the left shows a harmonious relationship with robot and human dancing together, while the one on the right portrays a rather intimidating computer system such as the HAL 9000 in "2001: A Space Odyssey".

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Footnotes

¹Since the volume increases (as ~ length³) faster than the surface area (as ~ length²), a single cell cannot enlarge its size indefinitely. It has a limit beyond which the surface area is not capable of absorbing enough nutrition (including oxygen) and draining off excessive waste.

²Sexual reproducation endows genetic variations and replaces damaged genes. Cloning negates these evolutionary advantages by skipping the haploid phase of the life cycle (see Figure 10-05). Dolly, the world's first cloned sheep has died on February, 2003 at the age of 6 after a veterinary examination confirmed the lung disease. Sheep can live to 11 or 12 years of age and lung infections are common in older sheep, particularly those housed inside. She has developed other old age symptoms such as arthritis, a condition usually expected in older animals. Research in 1999 suggested that Dolly might be susceptible to premature ageing -- a possibility raised after a study of her genetics.

³A gene is defined to be a section of DNA that transcribes a protein. The gene expression (transcription) is initiateed by binding the transcription factor (such as the homeodomain) to the beginning section of the gene called the promoter.

⁴Protein is produced from DNA via the transcription/translation process. The base (nucleotide) Thymine (T) becomes Uracil (U) in the transcription from DNA to RNA. Three bases translate into one amino acid according to the genetic code. The amino acids link together to form a protein.

⁵Male germ cells (sperms) are produced continuously in the testes throughout life. About 50,000 female germ cells (eggs) are prepared in the ovaries of the female embryo 12 days after fertilization. It is reported in 2004 that stem cells for oocytes (immature female reproductive cells) are found within the ovaries of mice in contrary to traditional believe.

⁶Even though if cellular damage by external causes can be avoided, an inherent problem is bound to arise by internal metabolism. The metabolic pathway in mitochondria relies on the transportaton of free electrons, which eventually attach to oxygen and are normally neutralized by hydrogen ion to form water. This is usually referred to as respiration. Sometimes the process breaks down, the electrons do not attach to the oxygen and instead, attach to other oxygen species. Specific molecules, each carrying a wayward electron, were created. They are call free radicals (such as hydroxyl, superoxide and peroxide - collectively called reactive oxygen species or ROS). These free radicals are highly reactive and can do tremendous damage to the cell. The ROS can indiscriminately damage anything that gets in their way - proteins, fats, RNA, and DNA. The effect is cumulative and a serious problem will occur if ROS numbers get too high. Not surprisingly, the cell has responded to this threat by creating various enzymes that bind to free-radicals and inactivate them. Collectively, molecules that destroy free radicals are called anti-oxidants. Aging is probably the result of the breakdown in the cellular safety nets - not enough anti-oxidants are produced naturally. In addition, modern life has enormously increased the number of toxic free-radicals introduced into our bodies every day from the surrounding environment. The most significant sources of excess free-radicals are dietary or environmental. Dietary sources are usually fats, either rancid or hydrogenated fats, and fats that have been heated to high temperatures during cooking. Environmental pollutants include automobile exhaust, cigarette smoke and numerous other chemicals, physical exercise, stress, and radiation. To increase the defence against these ROS, it is suggested that consumption of special kinds of foods, herbs, and dietary supplements (including vitamins C and E, beta carotene and selenium) will scavenge excess free-radicals and provide raw materials necessary for the body to produce antioxidant enzymes. Recently, it is observed that the most efficient way to delay aging is through caloric restriction. It is found that by reducing 30 - 40 percent the calories in an animal's diet, results in healthy and long-lived mice and rats. It seems that the animals have switched their metabolism from a pro-growth mode to a pro-repair mode. The latest research tries to manuplate the level of the IGF-1 (insulin-like growth factor-1) protein so that people can maintain the pro-repair mode without diet restriction.

⁷The biofeedback technique uses electronics to detect and amplify internal body activities too subtle for normal awareness. One of such methods is the galvanic skin resistance (GSR). It utilizes the fact that skin resistance increases in a calm and relaxed state; it goes the other way at tensing up even slightly. The difference is a reflection of variations in the sweat gland activity and pore size, both of which are controlled by the autonomic nervous system. When the fingers are placed on the sensing plates of the GSR device, the tone lowers with progressive relaxation. The objective is to relax by learning how to diminish the tone of the GSR device to the lowest point possible.

⁸Mind is defined as the mental activity, which includes both conscious and unconscious processes, thus mind has a broader meaning than consciousness.

⁹Vascular tissue is made up of two parts: xylem and phloem. Xylem carries water and minerals up the plant. Phloem carries dissolved foods such as glucose around the plant. Transpiration is the evaporation of water out of the plant, through pores in the leaves called stomato. As transpiration takes place, water is forced up the stem xylem and into the leaves, to replace the water that is lost.

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References:

• Five Kingdoms, Details -- http://waynesword.palomar.edu/trfeb98.htm
• Five Kingdoms, Short Table -- http://curie.uncg.edu/~esmith/kingdom.html
• Evolutionary Tree -- http://www.phy.auckland.ac.nz/old/354sc/html/p6_p8.html
• Multicellular Organisms, Origin -- http://www.devbio.com/chap22/link2203.shtml
• Sexual Life Cycle -- http://bama.ua.edu/~ksuberkp/bsc114/Lectures/B14meios.htm
• Sexual Life Cycle, Plants -- http://www-plb.ucdavis.edu/courses/f98/bis1a/LifeCycl.htm
• Slime Moulds -- http://www.this-magic-sea.com/COMCELL.HTM
• Homeobox Genes -- http://homeobox.biosci.ki.se/
• Body Plans, Animals -- http://www.bio.indiana.edu/courses/L111-Bever/class%20notes/OCT22-24Protists_to_Animals.htm
• Stem Cells -- http://www.nih.gov/news/stemcell/primer.htm
• Embryonic Stem Cell Policy (US) -- http://www.bioethics.gov/background/es_moralfoundations.html
• Sex and Death -- http://www.dhushara.com/book/sci/sexdeth.htm
• Biological Clock -- http://cal.man.ac.uk/student_projects/1999/sanders/home1.htm
• Clock of Ages -- New Scientist, vol. 178, issue 2391 - 19 April 2003, page 26. (Reprint)
• Cloning, Facts about -- http://www.ornl.gov/TechResources/Human_Genome/elsi/cloning.html#intro
• History of the Earth -- http://www.bio.miami.edu/tom/bil160/bil160goods/09_platetec.html
• Paleontology -- http://www.awesomelibrary.org/Classroom/Science/Paleontology/Paleontology.html
• Life on Earth -- http://www.palaeos.com/Default.htm
• Cambrian Explosion -- http://biocrs.biomed.brown.edu/Books/Chapters/Ch%2019/Fossil-Embryos/Time-Cambrian.html
• Animal Kingdom -- http://www.swishweb.com/Animal_Kingdom/
• Animal Evolution, Slide Show -- http://www.uwinnipeg.ca/~simmons/Chap3298/sld001.htm
• Animal Phyla, Present Day -- http://www.sidwell.edu/us/science/vlb5/Labs/Classification_Lab/Eukarya/Animalia/
• Becoming Human, Interactive Documentary -- http://www.becominghuman.org/
• Human Origins and Evolution in Africa -- http://www.indiana.edu/~origins/
• New Look at Human Evolution -- Scientific American, Special Edition, 2003
• Evolution of the Brain -- http://primatesociety.com/Into/survival/timeline/timeline.html
• Anatomy of the Human Brain -- http://sprojects.mmi.mcgill.ca/brain/contents.htm
• Overview of the Brain -- http://brain.web-us.com/brain/aboutthebrain.htm
• Biology of Consciousness -- http://www.colorado.edu/Honors/honr4000-882dubin/projects/sujatha/index.html
• Neural Correlates of Consciousness -- http://www.u.arizona.edu/~chalmers/papers/ncc2.html
• Sleep and Dream -- http://faculty.washington.edu/chudler/sleep.html
• Sleep and Dream -- http://hcs.harvard.edu/~husn/BRAIN/vol1/sleep.html>

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Index

Ageing Allelic pairs Aminals Antioxidant Archaea Archaeopteryx Axon Bacteria Basal layer Biofeedback Biological clock Biological classifications Body Cavity (Coelom) Bone marrow Bony Fish Brain Brain waves Burgess Shale Cambrian Period cAMP Carboniferous Period Cloning Conjugation Consciousness Cretaceous Period Dendrites Devonian Period Dinosaurs Diploid Dream Ectoderm Embryo Embryonic development Endoderm Eukaryotes Evolution of multicellular organisms Evolutionary Tree Five Kingdoms Free radical Fungi Gamete Gametophyte Germ cells

Haploid Hemocoelic (blood) space Homeobox genes Homo Sapiens Sapiens Homeodomain Human organ systems Immortal Jurassic Period K-T Boundary Meditation Meiosis Mesoderm Micronucleus Mitosis Multicellurity Multipotent cells Neurons Ordovician Period Permian Period Plants Pluripotent cells Prokaryotes Protista Pseudoplasmodium Quaternary Period Retinoic acid Sex and death Sexual life cycles Silurian Period Sleep Slime moulds Somatic cells Sorocarp Spores Stem cells Tertiary Periods Three germ layers Tomography (CAT, PET, MRI) Totipotent cells Triassic Period Turing equation Vascular Tissue Zygote

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