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Evolution…a deeper understanding

Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid).

DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits.

The genome is an organism’s complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome.

DNA in the human genome is arranged into 24 distinct chromosomes–physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoining (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences.

Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 20,000-25,000 genes.

Although genes get a lot of attention, it’s the proteins that perform most life functions and even make up the majority of cellular structures. Proteins are large, complex molecules made up of smaller subunits called amino acids. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.

The constellation of all proteins in a cell is called its proteome. Unlike the relatively unchanging genome, the dynamic proteome changes from minute to minute in response to tens of thousands of intra- and extracellular environmental signals. A protein’s chemistry and behaviour are specified by the gene sequence and by the number and identities of other proteins made in the same cell at the same time and with which it associates and reacts. Studies to explore protein structure and activities, known as proteomics, will be the focus of much research for decades to come and will help elucidate the molecular basis of health and disease.

How the Human Compares with Other Organisms

Unlike the human’s seemingly random distribution of gene-rich areas, many other organisms’ genomes are more uniform, with genes evenly spaced throughout.

Humans share most of the same protein families with worms, flies, and plants, but the number of gene family members has expanded in humans, especially in proteins involved in development and immunity.

Although humans appear to have stopped accumulating repeated DNA over 50 million years ago, there seems to be no such decline in rodents. This may account for some of the fundamental differences between hominids and rodents, although gene estimates are similar in these species. Scientists have proposed many theories to explain evolutionary contrasts between humans and other organisms, including those of life span, litter sizes, inbreeding, and genetic drift.

Variations and Mutations

Scientists have identified about 1.4 million locations where single-base DNA differences (SNPs) occur in humans. This information promises to revolutionize the processes of finding chromosomal locations for disease-associated sequences and tracing human history.

The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females. Researchers point to several reasons for the higher mutation rate in the male germline, including the greater number of cell divisions required for sperm formation than for eggs.

Applications, Future Challenges

Deriving meaningful knowledge from the DNA sequence will define research through the coming decades to inform our understanding of biological systems. This enormous task will require the expertise and creativity of tens of thousands of scientists from varied disciplines in both the public and private sectors worldwide.

The draft sequence already is having an impact on finding genes associated with disease. A number of genes have been pinpointed and associated with breast cancer, muscle disease, deafness, and blindness. Additionally, finding the DNA sequences underlying such common diseases as cardiovascular disease, diabetes, arthritis, and cancers is being aided by the human variation maps (SNPs) generated in the HGP in cooperation with the private sector. These genes and SNPs provide focused targets for the development of effective new therapies.

One of the greatest impacts of having the sequence is in enabling an entirely new approach to biological research. In the past, researchers studied one or a few genes at a time. With whole-genome sequences and new high-throughput technologies, they can approach questions systematically and on a grand scale. They can study all the genes in a genome, for example, or all the transcripts in a particular tissue or organ or tumour, or how tens of thousands of genes and proteins work together in interconnected networks to orchestrate the chemistry of life.


Evolutionary arms raceEvolutionary “arms races” result from genetic conflict between human andviral genesWhy do most human genes evolve slowly, while a few are “running on theevolutionary treadmill”? Rapid gene evolution can sometimes be explained bygenetic conflict. A good example is the competition that exists between virusesand their hosts, where each evolves in order to avoid elimination by the other.Evolutionary change resulting from historical viral infections has left a molecular”fossil record” in our DNA sequence. We are using a broad array of techniquesfrom molecular evolution, virology, and comparative genomics to look at humanand primate genes that encode inhibitors of viral infection. Our goal is to learnabout natural strategies that have been successful at beating viruses in the past,and how these might be exploited in the fight against modern viral attacks.

Our lab also studies the process of retroviral integration in hopes that this will

help us understand the deadly reservoir of HIV genomes which integrate into

the chromosomes of infected people. It is this reservoir that makes HIV

essentially incurable once someone has become infected. We have developed

model systems in yeast and human cells to test the implications of evolutionary

innovation on this process.

We are also interested in a systems biology approach to explore how human

genes can change enough to avoid susceptibility to new viruses, yet still

maintain their ability to perform other important cellular functions. We are not

interested in the fine mechanistic details as much as the net effects that

evolutionary change can have on multiple, intertwined biological systems.

http://www.sbs.utexas.edu/sawyer/Sawyer_Lab_Website/Evolutionary_

arms_races_can_result_from_genetic_conflict_between_human_and_viral_

genes.html

The Escape of the Pathogens: an evolutionary arms race

 

Human populations are constantly locked in evolutionary arms races with

pathogens that invade our bodies. We must recognize that these pathogens

(such as the flu virus shown at right) are continuously evolving entities in

order to develop better ways to fight them and control their evolution.

An ounce of prevention…every year?
Recently, the mayor of New York City called upon citizens to get a head start

on one particular evolutionary arms race: “I urge older New Yorkers and others

at risk to protect themselves from flu and pneumonia through a simple and

proven ounce of prevention: immunizations. The time to get immunized is now,

before the peak of the flu season.”1

Many of those New Yorkers had already gotten flu shots the year before and

the year before that, but, perhaps strangely, they were being asked to get

yet another immunization. Why do we need a new flu shot every year? Can’t

modern medicine invent just one vaccine that would do the trick?

Flu viruses evolve rapidly. As they circulate through populations around the

world and switch hosts, flu viruses change so much that our vaccines are

rendered obsolete every year. The flu is a problem for which a solution must

be redesigned and rebuilt every year, like a bridge that gets washed away

every flood season. Only by understanding the flu as an evolving entity can

we understand why our solution to the problem must change every year.

Every day we come into contact with millions of bacteria and viruses. Some

are harmful and others are beneficial, while the rest have no apparent effect

on our health. When harmful microorganisms enter our bodies, a battle ensues.

Rapid reproduction and natural selection
Because bacteria and viruses reproduce rapidly, they evolve rapidly. These

short generation times — some bacteria have a generation time of just 15

minutes — mean that natural selection acts quickly.

In each pathogen generation, new mutations and gene combinations are generated

that then

pass through the selective filter of our drugs and immune response. Over the

course of many pathogen generations (a small fraction of a single human

lifetime), they adapt to our defences, evolving right out from under our

attempts to rid ourselves of them.  But that doesn’t mean that we should

stop trying to win these battles. By understanding these pathogens as

evolving entities, subject to the same processes of evolution that we can

study in fruit flies or the fossil record, we may be able to identify ways to

slow their progress.

Antibiotic resistance: delaying the inevitable

 

Only a few decades ago, antibiotics were considered to be wonder drugs

because they worked so well to cure deadly diseases. Ironically, though,

many antibiotics have become less effective, precisely because they have

worked so well and have been used so often.

Making inroads against infectious disease
The antibiotic era began in 1929 with Alexander Fleming’s observation

that bacteria would not grow near colonies of the mould Penicillium. In the

decades that followed this breakthrough discovery, molecules produced by

fungi and bacteria have been successfully used to combat bacterial diseases

such as tuberculosis and pneumonia. Antibiotics drastically reduced death rates

associated with many infectious diseases.

 

Infectious diseases strike back
The golden age of antibiotics proved to be a short-lived one. During the past

few decades, many strains of bacteria have evolved resistance to antibiotics.

An example of this is Neisseria gonorrhoeae, the bacteria that causes. In the

1960s penicillin and ampicillin were able to control most cases of gonorrhea.

Today, more than 24 percent of gonorrheal bacteria in the U.S. are resistant

to at least one antibiotic, and 98 percent of gonorrheal bacteria in Southeast

Asia are resistant to penicillin. Infectious bacteria are much harder to control

than their predecessors were ten or twenty years ago.

Doctors miss the “good old days,” when the antibiotics they prescribed

consistently cured their patients. However, evolutionary theory suggests

some specific tactics to help slow the rate at which bacteria become resistant

to our drugs.
Evolutionary theory predicted that bacterial resistance would happen. Given

time, heredity, and variation, any living organisms (including bacteria) will

evolve when a selective pressure (like an antibiotic) is introduced. But

evolutionary theory also gives doctors and patients some specific strategies

for delaying even more widespread evolution of antibiotic resistance. These

strategies include:

  • Don’t use antibiotics to treat viral infections.
  • Antibiotics kill bacteria, not viruses. If you take antibiotics for a viral
  •  infection (like a cold or the flu), you will not kill the viruses, but you
  • will introduce a selective pressure on bacteria in your body, inadvertently
  •  selecting for antibiotic-resistant bacteria. Basically, you want your
  • bacteria to be “antibiotic virgins,” so that if they someday get out of
  •  hand and cause an infection that your immune system can’t handle,
  •  they can be killed by a readily available antibiotic.
  • Avoid mild doses of antibiotics over long time periods.
    If an infection needs to be controlled with antibiotics, a short-term,
  •  high-dosage prescription is preferable. This is because you want to
  • kill all of the illness-causing bacteria, leaving no bacterial survivors.
  •  Any bacteria that survive a mild dose are likely to be somewhat resistant.
  •  Basically, if you are going to introduce a selective pressure (antibiotics),
  •  make it so strong that you cause the extinction of the illness-causing
  • bacteria in the host and not their evolution into resistant forms.
  • When treating a bacterial infection with antibiotics, take all your pills.
    Just as mild doses can breed resistance, an incomplete regimen of
  • antibiotics can let bacteria survive and adapt. If you are going to
  •  introduce a selective pressure (antibiotics), make it a really strong
  • one and a long enough one to cause the extinction of the illness-
  • causing bacteria and not their evolution.
  • Use a combination of drugs to treat a bacterial infection.
    If one particular drug doesn’t help with a bacterial infection, you may
  •  be dealing with a resistant strain. Giving a stronger dose of the same
  • antibiotic just increases the strength of the same selective pressure —
  • and may even cause the evolution of a “super-resistant” strain. Instead,
  • you might want to try an entirely different antibiotic that the bacteria
  •  have never encountered before. This new and different selective pressure
  •  might do a better job of causing their extinction, not their evolution.
  • Reduce or eliminate the “preventive” use of antibiotics on livestock and
  • crops.
    Unnecessary use of antibiotics for agricultural and livestock purposes
  • may lead to the evolution of resistant strains. Later, these strains will
  •  not be able to be controlled by antibiotics when it really is necessary.
  • Preventive use of antibiotics on livestock and crops can also introduce
  •  antibiotics into the bodies of the humans who eat them.

Ultimately, recognizing bacteria as evolving entities and understanding their

evolution should help us to control that evolution, allowing us to prolong the

useful lifespan of antibiotics.

 

 

HIV: the ultimate evolver

 

Evolutionary biologists can help uncover clues to new ways to treat or vaccinate

against HIV. These clues emerge from the evolutionary origins of the virus,

how human populations have evolved under pressure from other deadly

pathogens, and how the virus evolves resistance to the drugs we’ve designed.

Controlling the disease may be a matter of controlling the evolution of this

constantly adapting virus.

The human immunodeficiency virus is one of the fastest evolving entities

known. It reproduces sloppily, accumulating lots of mutations when it copies

its genetic material. It also reproduces at a lightning-fast rate — a single virus

can spawn billions of copies in just one day. To fight HIV, we must understand

its evolution within the human body and then ultimately find a way to control its

evolution.

Taking an evolutionary perspective on HIV has led scientists to look in three

new directions in their search for treatments and vaccines:

  • What are the evolutionary origins of HIV?
  • Why are some people resistant to HIV?
  • How can we control HIV’s evolution of resistance to our drugs?

What are the evolutionary origins of HIV?

HIV, like any evolving entity, has been deeply marked by its history. Scientists

studying the evolutionary history of HIV found that it is closely related to other

viruses. Those viruses include SIVs (simian immunodeficiency viruses), which

infect primates, and the more distantly related FIVs (the feline strains), which

infect cats.

However, studies of these related viral lineages showed something surprising:

primates with SIV and wild cats with FIV don’t seem to be harmed by the viruses

they carry. If scientists can figure out how non-human primates and wild cats

are able to live with these viruses, they may learn how to better treat HIV

infections or prevent them altogether.

The diagram shows some of the evolutionary history of HIV as we know it today.

An ancestral virus (bottom) evolved into strains that infected chimpanzees (SIV).

Over time, new strains began to infect humans (HIV).

 Why are some people resistant to HIV?
HIV is by no means the first plague that human populations have weathered.

Many pathogens have deeply affected our evolutionary history. In fact, the

human genome is littered with the remnants of our past battles with pathogens —

and one of these remnants, a mutation to a gene called CCR5, may lead

researchers to a new treatment for HIV.

The mutant CCR5 allele probably began to spread in northern Europe

during the past 700 years when the population was ravaged by a plague. The

mutant CCR5 probably made its bearers resistant to the disease, and so its

frequency increased.

In some parts of Europe today, up to 20% of the population carry at least

one copy of the protective allele. However, the populations of Asia and Africa

were not exposed to the same epidemics; very few Asians and Africans now

carry the allele. Thus, CCR5 is fairly common in northern Europe but its

frequency diminishes as one moves south, and the mutation is rare in the

rest of the world. We now know that the mutant CCR5 allele has an

unexpected side effect: it confers resistance to HIV. Scientists hope that

studying this by-product of past selection will help them develop new

treatments for the HIV epidemic ravaging human populations today.

How can we control HIV’s evolution of resistance to our drugs?


HIV evolves so quickly that it evolves right out from under our treatments.

When a patient begins taking an HIV drug, the drug keeps many of the viruses

from reproducing, but some survive because they happen to have a certain

level of resistance. Because of HIV’s speedy evolution, it responds to selection

pressures quickly: viruses that happen to survive the drug are favoured,

and resistant virus strains evolve within the patient, sometimes in just a

few weeks. However, basic evolutionary theory points out a way that this

evolution of resistant viral strains can be delayed. Patients are prescribed

“drug cocktails” — several different HIV drugs taken together.

When taking any single drug, it is fairly likely that some mutant virus in the

patient might happen to be resistant, survive the onslaught, and spawn a

resistant

lineage.

But the probability that the patient hosts a mutant virus that happens to be

resistant to several different drugs at the same

time is much lower. Although multiple-drug-resistant HIV strains do eventually

evolve, drug cocktails delay their evolution.

An evolutionary trade-off
If a patient is already infected with a drug-resistant HIV strain, basic evolutionary

theory has also pointed out a way to make the drug useful again. Studies of the

evolution of resistance often show that you don’t get something for nothing.

Specifically, it “costs” a pest or pathogen to be resistant to a pesticide or drug.

If you place resistant and non-resistant organisms in head-to-head competition

in the absence of the pesticide or drug, the non-resistant organisms generally win.

Consider a patient who takes a particular drug and winds up with viruses resistant

to the drug. If the patient stops taking the drug for a while, evolutionary theory

predicts that her viral load will evolve back towards a non-resistant strain. If she

then takes very strong doses of the drug, it may be able to halt the replication of

those non-resistant viruses and reduce her viral load to very low levels.

This therapy has shown early, promising results — it may not eliminate HIV, but

it could keep patients’ virus loads low for a long time, slowing progression of the

disease.

Ultimately, understanding the evolutionary history of HIV and its pattern of

evolutionary change may help us control this disease.

Huntington’s Chorea: Evolution and Genetic Disease

Huntington’s chorea is a devastating human genetic disease. A close look at itsgenetic origins and evolutionary history explains its persistence and points toapotential solution to this population-level problem.People who inherit this geneticdisease have an abnormal dominant allele thatdisrupts the function of their nervecells, slowly eroding their control over their bodies and minds and ultimatelyleading to death. In the fishing villageslocated near Lake Maracaibo in Venezuela, there are more people withHuntington’s disease than anywhere else in the world. In some villages, morethan half the people may develop the disease.How is it possible that such a devastating genetic disease is so common in some

populations? Shouldn’t natural selection remove genetic defects from human

populations? Research on the evolutionary genetics of this disease suggests

that there are two main reasons for the persistence of Huntington’s in human

populations: mutation coupled with weak selection.

The diagram shows how the Huntington’s allele is passed down. Since it is the

dominant allele, individuals with just one parent with Huntington’s chorea have

a 50-50 chance of developing the disease themselves.

Mutation
In 1993, a collaborative research group discovered the culprit responsible for

Huntington’s: a stretch of DNA that repeats itself over and over again,

CAGCAGCAGCAG… and so on. People carrying too many CAGs in the

Huntington’s gene (more than about 35 repeats) develop the disease. In

most cases, those affected by Huntington’s inherited a disease-causing allele

from a parent.

Others may have no family history of the disease, but may have new mutations

which cause Huntington’s.

If a mutation ends up inserting extra CAGs into the Huntington’s gene, new

Huntington’s alleles may be created. Of course it’s also possible for a mutation

to remove CAGs. But research suggests that for Huntington’s, mutation is biased;

additions of CAGs are more likely than losses of CAGs.

Selection
As though that weren’t bad enough, Huntington’s belongs to a class of genetic

diseases that largely escape natural selection. Huntington’s is often “invisible” to

natural selection for a very simple reason: it generally does not affect people

until after they’ve reproduced. In this way, the alleles for late-onset Huntington’s

may evade natural selection, “sneaking” into the next generation, despite its

deleterious effects. Early-onset cases of Huntington’s are rare; these are an

exception, and are strongly selected against.

Persistence
These mechanisms of evolution, mutation and selection, can help us understand

the persistence of Huntington’s in populations. In general, Huntington’s is rare —

30-70 cases per million people in most Western countries — but it is not entirely

eliminated

because selection does a relatively poor job of weeding these alleles out, while

mutation continues creating new ones.

Dr. Nancy Wexler has been studying the remarkably high frequency of

Huntington’s in Lake Maracaibo since the 1970s. She has found that the high

incidence of this disease there is explained by an evolutionary event called the

founder effect.

About 200 years  ago, a single woman who happened to carry the Huntington’s

allele bore 10 children — and today, many residents of Lake Maracaibo trace their

ancestry (and their disease-causing gene) back to this lineage. A simple fluke of history, high-birth rates, and weak selection are responsible for the genetic burden shouldered by this population.

The people of Lake Maracaibo.

Solutions?

Currently, physicians don’t have any cures for Huntington’s disease — there’s no

miracle pill that will stop the progress of the disease. However, understanding the

evolutionary history of the disease — a recurrent mutation that is often “missed” by natural selection — points out a way to reduce the frequency of the disease in the long term: allowing people to make more informed reproductive choices.

Today, genetic testing can identify people who carry a Huntington’s allele long

before the onset of the disease and before they have made their reproductive

choices. The genetic test that identifies the Huntington’s allele works sort of like

DNA fingerprinting. A DNA sample is copied and cut into pieces. The pieces are

then spread out on a gel (see right). The banding pattern can tell researchers

whether a person carries an allele that is likely to cause Huntington’s.

Having this information could allow people to make more-informed reproductive

decisions. For example, at Lake Maracaibo, researchers and health workers have

tried to make contraception available to the local population so that they can make

reproductive choices based on their own family history with the disease. But

whatever people eventually decide to do with this knowledge, a deep understanding of the disease would not be possible without the historical perspective offered by evolution.

Understanding evolution helps us solve biological problems that impact our lives.There are excellent examples of this in the field of medicine. To stay one stepahead of pathogenic diseases, researchers must understand the evolutionarypatterns of disease-causing organisms. To control hereditary diseases in people,researchers study the evolutionary histories of the disease-causing genes. Inthese ways, knowledge of evolution can improve the quality of human life.

http://evolution.berkeley.edu/evolibrary/article/0_0_0/medicine_06

Relevance of evolution: conservation

Given urgent need, limited resources and competing interests, what are our

priorities for conservation, and why? What considerations should be brought to

bear on decisions that affect biodiversity?

Biological systems evolve. Variables change, because evolution is change over

time through descent with modification. So in the field of conservation, history

is a critical part of how we think about the complex issue of conservation.

The case studies in this section focus on how an understanding of evolution can

inform conservation efforts.

In this section we will explore these key questions:

Why is it difficult for a population with few individuals to survive?

How does understanding evolution help us revitalize endangered populations?

How does knowledge of evolutionary history help us make conservation decisions?

Species preservation and population size: when eight is not enough

 

Scientists estimate that about 1000 nesting Kemp’s Ridley sea turtles, 300 right

whales, and 65 northern hairy-nosed wombats survive in the wild, to name just a

few of the world’s endangered species. But what do those numbers mean? Are 65

hairy-nosed wombats enough to save a species teetering on the edge of

extinction? Ignoring evolutionary history, one might answer, “Sure; as long

as they can breed, we only need a few individuals to start a new population.”

But evolutionary theory tells a different story.

According to evolutionary theory, very small populations face two dangers —

inbreeding depression and low genetic variation — that might keep them from

recovering, despite our best efforts to preserve them.

Inbreeding depression

In a small population, mating between relatives are common. This inbreeding

may lower the population’s ability to survive and reproduce, a phenomenon called

inbreeding depression. For example, a population of 40 adders (Vipera berus,

shown at right) experienced inbreeding depression when farming activities in

Sweden isolated them from other adder populations. Higher proportions of stillborn

and deformed offspring were born in the isolated population than in the larger

populations. When researchers introduced adders from other populations — an

example of outbreeding — the isolated population recovered and produced a higher proportion of viable offspring.

The explanation for inbreeding depression lies in the evolutionary history of the

population. Over time, natural selection weeds deleterious alleles out of a

population — when the dominant deleterious alleles are expressed, they lower the

carrier’s fitness, and fewer copies wind up in the next generation. But recessive

deleterious alleles are “hidden” from natural selection by their dominant

non-deleterious counterparts. An individual carrying a single recessive deleterious allele will be healthy and can easily pass the deleterious allele into the next generation.

When the population is large, this is generally not a problem — the population may

carry many recessive deleterious alleles, but they are rarely expressed.

However, when the population becomes small, close relatives end up mating with

one another, and those relatives likely carry the same recessive deleterious alleles. When the relatives mate, the offspring may inherit two copies of the same recessive deleterious allele and suffer the consequences of expressing the deleterious allele

, as shown in the example below. In the case of the Swedish adders, that meant

stillborn offspring and deformities.

For Swedish adders, the solution to the inbreeding depression problem was simple—introduce adders from other populations. But if the northern hairy-nosed wombat suffers from inbreeding depression, there are no other populations that can rescue it.

Understanding the evolutionary history of a population and the likelihood that it

carries recessive deleterious alleles, suggests that we should not allow population

sizes to dip too low in our conservation efforts, or inbreeding depression may

jeopardize the survival of the species.

Low genetic variation Genetic variation is the raw material of evolution. Without genetic variation, apopulation cannot evolve in response to changing environmental variables and,as a result, may face an increased risk of extinction. For example, if a populationis exposed to a new disease, selection will act on genes for resistance to thedisease if they exist in the population. But if they do not exist — if the rightgenetic variation is not present — the population will not evolve and could be wiped out by the disease.As an endangered species dwindles, it loses genetic variation — and even if thespecies rebounds, its level of genetic variation will not. Genetic variation will onlyslowly be restored through the accumulation of mutations over many generations.For this reason, an endangered species with low genetic variation may riskextinction long after its population size has recovered.Evolutionary theory suggests that, for the long-term survival of a species,we need to conserve not just individual members of a species, but also a

species’ ability to evolve in the face of changing environmental variables —

which means conserving individuals and genetic variation.

The risk of extinction or population decline because of low genetic variation is

predicted by evolutionary theory. Scientists have not yet found any absolutely

clear-cut examples of this in endangered species today, but they continue to

investigate the possibility. A case study of the cheetah, which has famously

low genetic variation, suggests the sorts of dangers that are possible. When the

captive felines at an Oregon breeding colony for large cats were exposed to a

potentially deadly virus, it swept through the cheetah population, killing about

50% as a direct or indirect result of the virus — but none of the lions even

developed symptoms.

Decisions, decisions! Using evolution to get the most bang from your

conservation buck

 

Because of limited resources, conservationists must inevitably make a difficult

decision — which ecosystems should we try to preserve? Studying the evolutionary history of the organisms that comprise those ecosystems can help us make decisions that maximize the biodiversity preserved.

By some estimates, we are losing biodiversity at a rate that will halve the number

of species on Earth within the next 100 years.1 There are many reasons for trying

to slow this rate of loss, but it is certain that, no matter what measures we take,

we simply will not be able to save everything. We will have to decide which species and habitats to concentrate our efforts on — and evolutionary history can help us make these

difficult choices.

A “saved” species will not be safe for long if its habitat has been destroyed — so

conservation efforts have increasingly focused on preserving entire ecosystems,

along with the species that comprise them. But how do we decide which ecosystems to preserve? Many scientists argue that we should prioritize ecosystems with the highest biodiversity — and, although there are many other important considerations

involved in making these decisions, phylogenetics provides a useful measure of

biodiversity.

Why would we want to preserve biodiversity anyway?

 

In addition to showing respect for other living organisms on our planet, we

should care about biodiversity because it benefits humans in the following ways:

  • Genes: Wild animals and plants are sources of genes for hybridization
  • and genetic engineering.
  • Biological control agents: Some species of living things help us control
  •  invasive species without the use of poisons.
  • Food sources: Animals, plants, mushrooms, etc.
  • Natural products: Many of the medicines, fertilizers, and pesticides we
  •  use are derived from plants and animals. We also get products such as
  •  oils, adhesives, and silk from natural sources.
  • Environmental services: We rely on plants and animals for important
  •  processes such as soil aeration, fertilization, and pollination.
  • Enjoyment: Biodiversity is often the subject of aesthetic interest.
  • Scientific interest: The diversity of plants and animals inspires scientific
  •  inquiry in many different realms. Evolutionary science, anatomy,
  • physiology, behavior, and ecology are only a few examples.
  • Self-perpetuation: Biologically diverse ecosystems help to preserve their component species, reducing the need for future conservation efforts targeting endangered species.
  • Future potential for even more uses: With new discoveries to come,
  • there will be many more practical reasons to appreciate biodiversity!

An introduction to evolution

 

The definition of biological evolution, simply put, is descent with modification. This

definition encompasses small-scale evolution (changes in gene frequency in a

population from one generation to the next) and large-scale evolution (the

descent of different species from a common ancestor over many generations).

Evolution helps us to understand the history of life.

Biological evolution is not simply a matter of change over time. Lots of things

change over time: trees lose their leaves, mountain ranges rise and erode,

but they aren’t examples of biological evolution because they don’t involve

descent through genetic inheritance. The central idea of biological evolution is

that all life on Earth shares a common ancestor, just as you and your cousins

share a common grandmother.

Through the process of descent with modification, the common ancestor of life

on Earth gave rise to the fantastic diversity that we see documented in the fossil

record and around us today. Evolution means that we’re all distant cousins:

humans and oak trees, hummingbirds and whales.

The history of life: looking at the patternsThe central ideas of evolution arethat life has a history — it has changed overtime — and that different species share common ancestors. Here, you can explorehow evolutionary change and evolutionary relationships are represented in”family trees,” howthese trees are constructed, and how this knowledge affects biologicalclassification.

The family tree

The process of evolution produces a pattern of relationships between species. As

lineages evolve and split and modifications are

inherited, their evolutionary paths diverge. This produces a branching pattern of

evolutionary relationships.

By studying inherited species’ characteristics and other historical evidence, we

can reconstruct evolutionary relationships

and represent them on a “family tree,” called a phylogeny. The phylogeny you

see below represents the basic relationships that tie all life on Earth together.

Download this graphic from the Image library.
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Understanding phylogenies

Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendents of that ancestor. As you move from the root to the tips, you are moving forward in time. When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.

Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.

Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.

Understanding phylogenies A clade is a grouping that includes a common ancestor and all the descendents (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny —all of the organisms on that pruned branch make up a clade.Clades are nested within one another — they form a nested hierarchy. A clademay include many thousands of species or just a few. Some examples of cladesat different levels are marked on the phylogenies below. Notice how clades are nested within larger clades.

So far, we’ve said that the tips of a phylogeny represent descendent lineages. Depending on how many branches of the tree you are including however, the descendents at the tips might be different populations of a species, different species, or different clades, each composed of many species.

Trees, not ladders

  • Several times in the past, biologists have committed themselves to the erroneous idea that life can be organized on a ladder of lower to higher organisms. Similarly, it’s easy to misinterpret phylogenies as implying
  • that some organisms are more “advanced” than others; however, phylogenies don’t imply this at all.

Biologists often put the clade they are most interested in (whether that is bats, bedbugs, or bacteria) on the right side of the phylogeny.

Misconceptions about humans
The points described above cause the most problems when it comes to human evolution. The phylogeny of living species most closely related to us looks like this:

It is important to remember that:

  • Humans did not evolve from chimpanzees. Humans and chimpanzees are evolutionary cousins and share a recent common ancestor that was neither chimpanzee nor human.
  • Humans are not “higher” or “more evolved” than other living lineages. Since our lineages split, humans and chimpanzees have each evolved traits unique to their own lineages.

Building the tree

Like family trees, phylogenetic trees represent patterns of ancestry. However, while families have the opportunity to record their own history as it happens, evolutionary lineages do not — species in nature do not come with pieces of paper showing their family histories. Instead, biologists must reconstruct those histories by collecting and analyzing evidence, which they use to form a hypothesis about how the organisms are related — a phylogeny.

To build a phylogenetic tree such as the one to the right, biologists collect data about the characters of each organism they are interested in. Characters are heritable traits that can be compared across organisms, such as physical characteristics (morphology), genetic sequences, and behavioral traits.

In order to construct the vertebrate phylogeny, we begin by examining representatives of each lineage to learn about their basic morphology, whether or not the lineage has vertebrae, a bony skeleton, four limbs, an amniotic egg, etc.

Homologies and analogies

Since a phylogenetic tree is a hypothesis about evolutionary relationships, we want to use characters that are reliable indicators of common ancestry to build that tree. We use homologous characters — characters in different organisms that are similar because they were inherited from a common ancestor that also had that character. An example of homologous characters is the four limbs of tetrapods. Birds, bats, mice, and crocodiles all have four limbs. Sharks and bony fish do not. The ancestor of tetrapods evolved four limbs, and its descendents have inherited that feature — so the presence of four limbs is a homology.

Not all characters are homologies. For example, birds and bats both have wings, while mice and crocodiles do not. Does that mean that birds and bats are more closely related to one another than to mice and crocodiles? No. When we examine bird wings and bat wings closely, we see that there are some major differences.

Bat wings consist of flaps of skin stretched between the bones of the fingers and arm. Bird wings consist of feathers extending all along the arm. These structural dissimilarities suggest that bird wings and bat wings were not inherited from a common ancestor with wings. This idea is illustrated by the phylogeny below, which is based on a large number of other characters.

Using the tree for classificationBiologists use phylogenetic trees for many purposes, including:

  • Testing hypotheses about evolution
  • Learning about the characteristics of extinct species and ancestral lineages
  • Classifying organisms
  • Using phylogenies as a basis for classification is a relatively new development in biology.

Adding time to the tree

If you wanted to squeeze the 3.5 billion years of the history of life on Earth into a single minute, you would have to wait about 50 seconds for multicellular life to evolve, another four seconds for vertebrates to invade the land, and another four seconds for flowers to evolve — and only in the last 0.002 seconds would “modern” humans arise.

Biologists often represent time on phylogenies by drawing the branch lengths in proportion to the amount of time that has passed since that lineage arose. If the tree of life were drawn in this way, it would have a very long trunk indeed before it reached the first plant and animal branches.

The following phylogeny represents vertebrate evolution — just a small clade on the tree of life. The lengths of the branches have been adjusted to show when lineages split and went extinct.

How we know what happened when

Life began 3.8 billion years ago, and insects diversified 290 million years ago, but the human and chimpanzee lineages diverged only five million years ago. How have scientists figured out the dates of long past evolutionary events? Here are some of the methods and evidence that scientists use to put dates on events:

1. Radiometric dating relies on half-life decay of radioactive elements to allow scientists to date rocks and materials directly.
2. Stratigraphy provides a sequence of events from which relative dates can be extrapolated.
3. Molecular clocks allow scientists to use the amount of genetic divergence between organisms to extrapolate backwards to estimate dates.

Important events in the history of life

A timeline can provide additional information about life’s history not visible on an evolutionary tree. These include major geologic events, climate changes, radiations of organisms into new habitats, changes in ecosystems, changes in continental positions, and widespread extinctions.

Mechanisms: the processes of evolution

Evolution is the process by which modern organisms have descended from ancient ancestors. Evolution is responsible for both the remarkable similarities we see across all life and the amazing diversity of that life — but exactly how does it work?

Fundamental to the process is genetic variation upon which selective forces can act in order for evolution to occur. This section examines the mechanisms of evolution focusing on:

  • Descent and the genetic differences that are heritable and passed on to the next generation;
  • Mutation, migration (gene flow), genetic drift, and natural selection as mechanisms of change;
  • The importance of genetic variation;
  • The random nature of genetic drift and the effects of a reduction in genetic variation;
  • How variation, differential reproduction, and heredity result in evolution by natural selection; and
  • How different species can affect each other’s evolution through coevolution.

Descent with modification

We’ve defined evolution as descent with modification from a common ancestor, but exactly what has been modified? Evolution only occurs when there is a change in gene frequency within a population over time. These genetic differences are heritable and can be passed on to the next generation — which is what really matters in evolution: long term change.

Compare these two examples of change in beetle populations. Which one is an example of evolution?

1. Beetles on a diet
Imagine a year or two of drought in which there are few plants that these beetles can eat.
All the beetles have the same chances of survival and reproduction, but because of food restrictions, the beetles in the population are a little smaller than the preceding generation of beetles.
2. Beetles of a different colour
Most of the beetles in the population (say 90%) have the genes for bright green coloration and a few of them (10%) have a gene that makes them browner.
Some number of generations later, things has changed: brown beetles are more common than they used to be and make up 70% of the population.

Which example illustrates descent with modification — a change in gene frequency over time?

The difference in weight in example 1 came about because of environmental influences — the low food supply — not because of a change in the frequency of genes. Therefore, example 1 is not evolution. Because the small body size in this population was not genetically determined, this generation of small-bodied beetles will produce beetles that will grow to normal size if they have a normal food supply.

The changing colour in example 2 is definitely evolution: these two generations of the same population are genetically different. But how did it happen?

Mechanisms of changeEach of these four processes is a basic mechanism of evolutionary change.

Mutation
A mutation could cause parents with genes for bright green coloration to have offspring with a gene for brown coloration. That would make genes for brown coloration more frequent in the population than they were before the mutation.
Migration
Some individuals from a population of brown beetles might have joined a population of green beetles. That would make genes for brown coloration more frequent in the green beetle population than they were before the brown beetles migrated into it.Genetic drift
Imagine that in one generation, two brown beetles happened to have four offspring survive to reproduce. Several green beetles were killed when someone stepped on them and had no offspring. The next generation would have a few more brown beetles than the previous generation — but just by chance. These chance changes from generation to generation are known as genetic drift.
Natural selection
Imagine that green beetles are easier for birds to spot (and hence, eat). Brown beetles are a little more likely to survive to produce offspring. They pass their genes for brown coloration on to their offspring. So in the next generation, brown beetles are more common than in the previous generation.

All of these mechanisms can cause changes in the frequencies of genes in populations, and so all of them are mechanisms of evolutionary change. However, natural selection and genetic drift cannot operate unless there is genetic variation — that is, unless some individuals are genetically different from others. If the population of beetles were 100% green, selection and drift would not have any effect because their genetic make-up could not change.

So, what are the sources of genetic variation?

Without genetic variation, some of the basic mechanisms of evolutionary change cannot operate.

There are three primary sources of genetic variation, which we will learn more about:

  • Mutations are changes in the DNA. A single mutation can have a large effect, but in many cases, evolutionary change is based on the accumulation of many mutations.
  • Gene flow is any movement of genes from one population to another and is an important source of genetic variation.
  • Sex can introduce new gene combinations into a population. This genetic shuffling is another important source of genetic variation.

Mutations

Mutation is a change in DNA, the hereditary material of life. An organism’s DNA affects how it looks, how it behaves, and its physiology — all aspects of its life. So a change in an organism’s DNA can cause changes in all aspects of its life.

Mutations are random

Mutations can be beneficial, neutral, or harmful for the organism, but mutations do not “try” to supply what the organism “needs.” In this respect, mutations are random — whether a particular mutation happens or not is unrelated to how useful that mutation would be.

Not all mutations matter to evolution
Since all cells in our body contain DNA, there are lots of places for mutations to occur; however, not all mutations matter for evolution. Somatic mutations occur in non-reproductive cells and won’t be passed onto offspring.

The only mutations that matter to large-scale evolution are those that can be passed on to offspring. These occur in reproductive cells like eggs and sperm and are called germ line mutations.

A single mutation caused this cat’s ears to curl backwards slightly.
Some really important phenotypic changes, like DDT resistance in insects are sometimes caused by single mutations. A single mutation can also have strong negative effects for the organism. Mutations that cause the death of an organism are called lethals — and it doesn’t get more negative than that.

There are some sorts of changes that a single mutation, or even a lot of mutations, could not cause. Neither mutations nor wishful thinking will make pigs have wings; only pop culture could have created Teenage Mutant Ninja Turtles — mutations could not have done it.

The causes of mutations

Mutations happen for several reasons.

DNA fails to copy accurately
Most of the mutations that we think matter to evolution are “naturally-occurring.” For example, when a cell divides, it makes a copy of its DNA —

and sometimes the copy is not quite perfect. That small difference from the original DNA sequence is a mutation.

External influences can create mutations
Mutations can also be caused by exposure to specific chemicals or radiation. These agents cause the DNA to break down. This is not necessarily unnatural — even in the most isolated and pristine environments, DNA breaks down. Nevertheless, when the cell repairs the DNA, it might not do a perfect job of the repair. So the cell would end up with DNA slightly different than the original DNA and hence, a mutation.

Gene flow

Gene flow — also called migration — is any movement of genes from one population to another. Gene flow includes lots of different kinds of events, such as pollen being blown to a new destination or people moving to new cities or countries. If genes are carried to a population where those genes previously did not exist, gene flow can be a very important source of genetic variation. In the graphic below, the gene for brown coloration moves from one population to another.

Sex and genetic shuffling

Sex can introduce new gene combinations into a population and is an  important source of genetic variation.

You probably know from experience that siblings are not genetically identical to their parents or to each other (except, of course, for identical twins). That’s because when organisms reproduce sexually, some genetic “shuffling” occurs, bringing together new combinations of genes. For example, you might have bushy eyebrows and a big nose since your mom had genes associated with bushy eyebrows and your dad had genes associated with a big nose. These combinations can be good, bad, or neutral. If your spouse is wild about the bushy eyebrows/big nose combination, you were lucky and hit on a winning combination!

This shuffling is important for evolution because it can introduce new combinations of genes every generation. However, it can also break up “good” combinations of genes.

Natural selection at work

Scientists have worked out many examples of natural selection, one of the basic mechanisms of evolution.

Any coffee table book about natural history will overwhelm you with full-page glossies depicting amazing adaptations produced by natural selection, such as the examples below.

Orchids fool wasps into ‘mating’ with them

Katydids have camouflage to look like leaves

Non-poisonous king snakes mimic poisonous coral snakes

Behaviour can also be shaped by natural selection. Behaviours such as birds’ mating rituals, bees’ wiggle dance, and humans’ capacity to learn language also have genetic components and are subject to natural selection. The male blue-footed booby, exaggerates his foot movements to attract a mate.

In some cases, we can directly observe natural selection. Very convincing data show that the shape of finches’ beaks on the Galapagos Islands has tracked weather patterns: after droughts, the finch population has deeper, stronger beaks that let them eat tougher seeds.

In other cases, human activity has led to environmental changes that have caused populations to evolve through natural selection. A striking example is that of the population of dark moths in the 19th century in England, which rose and fell in parallel to industrial pollution. These changes can often be observed and documented.

What about fitness?Biologists use the word fitness to describe how good a particular genotype is at leaving offspring in the next generation relative to how good other genotypes are at it. So if brown beetles consistently leave more offspring than green beetles because of their colour, you’d say that the brown beetles had a higher fitness.Of course, fitness is a relative thing. A genotype’s fitness depends on the environment in which the organism lives. The fittest genotype during an ice age, for example, is probably not the fittest genotype once the ice age is over.Fitness is a handy concept because it lumps everything that matters to natural selection (survival, mate-finding, reproduction) into one idea. The fittest individual is not necessarily the strongest, fastest, or biggest. A genotype’s fitness includesits ability to survive, find a mate, produce offspring — and ultimately leave its genes in the next generation.

It might be tempting to think of natural selection acting exclusively on survival ability — but, as the concept of fitness shows, that’s only half the story. When natural selection acts on mate-finding and reproductive behavior, biologists call it sexual selection.

Sexual selectionSexual selection is a “special case” of natural selection. Sexual selection acts on an organism’s ability to obtain (often by any means necessary!) or successfully copulate with a mate.Selection makes many organisms go to extreme lengths for sex: peacocks maintain elaborate tails,elephant seals fight over territories, fruit flies perform dances, and some species deliver persuasive gifts.After all, what female Mormon cricket could resist the gift of a juicy sperm-packet? Going to even more extreme lengths, the male red back spider literally flings itself into the jaws of death in order to mate successfully.

Sexual selection is often powerful enough to produce features that are harmful to the individual’s survival. For example, extravagant and colourful tail feathers or fins are likely to attract predators as well as interested members of the opposite sex.

It’s clear why sexual selection is so powerful when you consider what happens to the genes of an individual who lives to a ripe old age but never got to mate: no offspring means no genes in the next generation, which means that all those genes for living to a ripe old age don’t get passed on to anyone! That individual’s fitness is zero.

Selection is a two-way street. Sexual selection usually works in two ways, although in some cases we do see sex role reversals:

Male competition
Males compete for access to females, the amount of time spent mating with females, and even whose sperm gets to fertilize her eggs. For example, male damsel flies scrub rival sperm out of the female reproductive tract when mating.
Females choose which males to mate with, how long to mate, and even whose sperm will fertilize her eggs. Some females can eject sperm from an undesirable mate.

Artificial selection

Long before Darwin and Wallace, farmers and breeders were using the idea of selection to cause major changes in the features of their plants and animals over the course of decades. Farmers and breeders allowed only the plants and animals with desirable characteristics to reproduce, causing the evolution of farm stock. This process is called artificial selection because people (instead of nature) select what organisms get to reproduce.

As shown below, farmers have cultivated numerous popular crops from the wild mustard, by artificially selecting for certain attributes.

These common vegetables were cultivated from forms of wild mustard. This is evolution through artificial selection.

Adaptation

An adaptation is a feature that is common in a population because it provides some improved function. Adaptations are well fitted to their function and are produced by natural selection.

Adaptations can take many forms: a behaviour that allows better evasion of predators, a protein that functions better at body temperature, or an anatomical feature that allows the organism to access a valuable new resource — all of these might be adaptations. Many of the things that impress us most in nature are thought to be adaptations.

Fish species that live in completely dark caves have vestigial, non-functional eyes. When their sighted ancestors ended up living in caves, there was no longer any natural selection that maintained the function of the fishes’ eyes. So, fish with better sight no longer out-competed fish with worse sight. Today, these fish still have eyes — but they are not functional and are not an adaptation; they are just the by-products of the fishes’ evolutionary history.So what’s not an adaptation? The answer: a lot of things. One example is vestigial structures. A vestigial structure is a feature that was an adaptation for the organism’s ancestor, but that evolved to be non-functional because the organism’s environment changed.

Misconceptions about natural selection

Because natural selection can produce amazing adaptations, it’s tempting to think of it as an all-powerful force, urging organisms on, constantly pushing them in the direction of progress — but this is not what natural selection is like at all.

First, natural selection is not all-powerful; it does not produce perfection. If your genes are “good enough,” you’ll get some offspring into the next generation — you don’t have to be perfect. This should be pretty clear just by looking at the populations around us: people may have genes for genetic diseases, plants may not have the genes to survive a drought, and a predator may not be quite fast enough to catch her prey every time she is hungry. No population or organism is perfectly adapted.

Second, it’s more accurate to think of natural selection as a process rather than as a guiding hand. Natural selection is the simple result of variation, differential reproduction, and heredity — it is mindless and mechanistic. It has no goals; it’s not striving to produce “progress” or a balanced ecosystem.

  Coevolution

The term coevolution is used to describe cases where two (or more) species reciprocally affect each other’s evolution. So for example, an evolutionary change in the morphology of a plant, might affect the morphology of an herbivore that eats the plant, which in turn might affect the evolution of the plant, which might affect the evolution of the herbivore…and so on.

Coevolution is likely to happen when different species have close ecological interactions with one another. These ecological relationships include:

  • Predator/prey and parasite/host
  • Competitive species
  • Mutualistic species

Plants and insects represent a classic case of coevolution — one that is often, but not always, mutualistic. Many plants and their pollinators are so reliant on one another and their relationships are so exclusive that biologists have good reason to think that the “match” between the two is the result of a coevolutionary process.

But we can see exclusive “matches” between plants and insects even when pollination is not involved. Some Central American Acacia species have hollow thorns and pores at the bases of their leaves that secrete nectar (see image at right). These hollow thorns are the exclusive nest-site of some species of ant that drink the nectar. But the ants are not just taking advantage of the plant — they also defend their acacia plant against herbivores.

This system is probably the product of coevolution: the plants would not have evolved hollow thorns or nectar pores unless their evolution had been affected by the ants, and the ants would not have evolved herbivore defense behaviours unless their evolution had been affected by the plants.


What are species anyway, and how do new ones evolve?
 

Here, you can explore different ways to define a species and learn about the various processes through which speciation can occur. This section also addresses the topics of co speciation — when two lineages split in concert with one another — and modes of speciation that are specific to plants.

Defining a species

A species is often defined as a group of individuals that actually or potentially interbreed in nature. In this sense, a species is the biggest gene pool possible under natural conditions.

For example, these happy face spiders look different, but since they can interbreed, they are considered the same species: Theridion grallator.

That definition of a species might seem cut and dried, but it is not — in nature, there are lots of places where it is difficult to apply this definition. For example, many bacteria reproduce mainly asexually.

Also, many plants, and some animals, form hybrids in nature. Hooded crows and carrion crows look different, and largely mate within their own groups — but in some areas, they hybridize. Should they be considered the same species or separate species?

If two lineages of oak look quite different, but occasionally form hybrids with each other, should we count them as different species? There are lots of other places where the boundary of a species is blurred. It’s not so surprising that these blurry places exist — after all, the idea of a species is something that we humans invented for our own convenience!

The big issues

All available evidence supports the central conclusions of evolutionary theory, that life on Earth has evolved and that species share common ancestors. Biologists are not arguing about these conclusions. But they are trying to figure out how evolution happens, and that’s not an easy job. It involves collecting data, proposing hypotheses, creating models, and evaluating other scientists’ work. These are all activities that we can, and should, hold up to our checklist and ask the question: are they doing science?

All sciences ask questions about the natural world, propose explanations in terms of natural processes, and evaluate these explanations using evidence from the natural world. Evolutionary biology is no exception. Darwin’s basic conception of evolutionary change and diversification (illustrated with a page from his notebook at left) explains many observations in terms of natural processes and is supported by evidence from the natural world.

Some of the questions that evolutionary biologists are trying to answer include:

  • Does evolution tend to proceed slowly and steadily or in quick jumps?
  • Why are some clades very diverse and some unusually sparse?
  • How does evolution produce new and complex features?
  • Are there trends in evolution, and if so, what processes generate them?
The pace of evolutionDoes evolution occur in rapid bursts or gradually? This question is difficult to answer because we can’t replay the past with a stopwatch in hand. However, we can try to figure out what patterns we’d expect to observe inthe fossil record if evolution did happen in bursts, or if evolution happenedgradually. Then we can check these predictions against what we observe.What should we observe in the fossil record if evolution is slow and steady?
If evolution is slow and steady, we’d expect to see the entire transition, fromancestor to descendent, displayed as transitional forms over a long period of timein thefossil record.In fact, we see many examples of transitional forms in the fossil record. Forexample, to the right we show just a few steps in the evolution of whales fromland-dwelling mammals, highlighting the transition of the walking forelimb to the flipper.

Transitional forms in whale evolution

What would we observe in the fossil record if evolution happens in “quick” jumps (perhaps fewer than 100,000 years for significant change)?
If evolution happens in “quick” jumps, we’d expect to see big changes happen

quickly in the fossil record, with little transition between ancestor and descendent.

In the above example, we see the descendent preserved in a layer directly after

the ancestor, showing a big change in a short time, with no transitional forms.

When evolution is rapid, transitional forms may not be preserved, even if fossils

are laid down at regular intervals. We see many examples of this “quick” jumps pattern in the fossil record.

Does a jump in the fossil record necessarily mean that evolution has happened in

a “quick” jump?
We expect to see a jump in the fossil record if evolution has occurred as a “quick” jump, but a jump in the fossil record can also be explained by irregular fossil preservation.

Diversity in clades

Imagine that you’ve travelled back in time to around 350 million years ago, give or take 50 million years. Your goal is to check out the cool insects living at this point in time. You see a lot of little insects that look like modern silverfish — no big deal.

But something interesting and significant is happening that you can’t see — a lineage has split into two. One of these newly isolated lineages will eventually give rise to about 400 extant species that look a lot like the ancient insects you see. But the other lineage will give rise to millions of extant insect species, the bulk of animal life on Earth today. Why is there such a big difference in diversity between these two lineages? After all, they were indistinguishable 350 million years ago…

Being in the right place at the right time is a reason that one clade might be more diverse than another.

Looking at complexity

Life is full of grand complications, such as aerodynamic wings, multi-part organs like eyes, and intricate chemical pathways. When faced with such complexity, both opponents and proponents of evolution, Darwin included, have asked the question: how could it evolve?

Science does not sweep such difficult questions under the rug, but takes them up as interesting areas for research. The difficulty is as follows.

Since many of these complex traits seem to be adaptive, they are likely to have evolved in small steps through natural selection. That is, intermediate forms of the adaptation must have evolved before evolution arrived at a fully-fledged wing, chemical pathway, or eye. But what good is half a wing or only a few of the elements of an eyeball? The intermediate forms of these adaptations may not seem adaptive — so how could they be produced by natural selection?

There are several ways such complex novelties may evolve:

Advantageous intermediates: It’s possible that those intermediate stages actually were advantageous, even if not in an obvious way. What good is “half an eye?” A simple eye with just a few of the components of a complex eye could still sense light and dark, like eyespots on simple flatworms do. This ability might have been advantageous for an organism with no vision at all and could have evolved through natural selection.

A Planaria flatworm with its light-sensitive eyespots.

Co-opting

The intermediate stages of a complex feature might have served a different purpose than the fully-fledged adaptation serves. What good is “half a wing?” Even if it’s not good for flying, it might be good for something else. The evolution of the very first feathers might have had nothing to do with flight and everything to do with insulation or display. Natural selection is an excellent thief, taking features that evolved in one context and using them for new functions.

Trends in evolution

An evolutionary trend can be either directional change within a single lineage or parallel change across lineages, in other words, several lineages undergoing the same sort of change. However, not just any change counts as a trend. After all, if the weather gets warmer one day, you wouldn’t call it a warming trend; warming would have to go on for some length of time before you’d call it a trend. Biologists think about evolutionary trends in the same way — there has to be something about the change that suggests that it’s not just a random fluctuation before it counts as a “trend.”

For example, titanotheres (a cool, extinct clade related to modern horses and rhinos) exhibit an evolutionary trend. Titanotheres had bony protuberances extending from their noses. The sequence of fossil skulls from these animals shows that evolutionary changes in the size of these “horns” were not random; instead, changes were biased in the direction of increasing horn size. And in fact, several different titanothere lineages experienced the same sort of change in horn size.

The titanothere reconstructions shown here range from about 55 mya (A) to 35 mya (D).The cause of this trend is not obvious. It may be a by-product of selection for increasing body size, and/or it may be a result of selection on horn size directly: big-horned individuals may have had an advantage in “butting” contests for females, as in sheep and goats.

HUMANZEES AND VESTIGIALITY…PROOF OF OUR EVOLUTION

The humanzee (also known as the Chuman or Manpanzee) is a hypothetical chimpanzee/human hybrid. Chimpanzees and humans are closely related (95% of their DNA sequence, and 99% of coding DNA sequences are in common), leading to contested speculation that a hybrid is possible, though no specimen has ever been confirmed.

In spite of the usual convention of portmanteau words to describe hybrids, there is no consensus as to which word to use, though “chuman” or “humanzee” are used in popular speech. Hybrids are named according to the convention first part of sire’s name + second part of dam’s name (except where the result is unwieldy). For geneticists, “Chuman” therefore refers to a hybrid of male chimpanzee and female human, while “Humanzee” or “manpanzee” refers to a hybrid of male human and female chimpanzee.

Humans have one fewer pair of chromosomes than other apes, since the ape chromosomes 2 and 4 have fused into a large chromosome (which contains remnants of the centromere and telomeres of the ancestral 2 and 4) in humans. Having different numbers of chromosomes is not an absolute barrier to hybridization. Similar mismatches are relatively common in existing species, a phenomenon known as chromosomal polymorphism.

The genetic structure of all the great apes is similar. Chromosomes 6, 13, 19, 21, 22, and X are structurally the same in all great apes. 3, 11, 14, 15, 18, and 20 match between gorillas, chimpanzees, and humans. Chimps and humans match on 1, 2p, 2q, 5, 7–10, 12, 16, and Y as well. Some older references will include Y as a match between gorillas, chimps, and humans, but chimpanzees (including bonobos) and humans have recently been found to share a large transposition from chromosome 1 to Y that is not found in other apes.

This level of chromosomal similarity is roughly equivalent to that found in equines. Interfertility of horses and donkeys is common; although sterility of the offspring (mules) is nearly universal (around 60 exceptions have been recorded in the whole of human history).

In the 1920s the Soviet biologist Ilya Ivanovich Ivanov carried out a series of experiments to create a human/non human ape hybrid. At first working with human sperm and chimpanzee females, none of his attempts created a pregnancy. In 1929 he organized a set of experiments involving non human ape sperm and human volunteers, but was delayed by the death of his last orang-utan. The next year he fell under political criticism from the Soviet government and was sentenced to exile in the Kazakh SSR; he worked there at the Kazakh Veterinary-Zootechnical Institute and died of a stroke two years later.

In 1977, researcher J. Michael Bedford discovered that human sperm could penetrate the protective outer membranes of a gibbon egg. Bedford’s paper also stated that human spermatozoa would not even attach to the zona surface of non-hominoid primates (baboon, rhesus monkey, and squirrel monkey), concluding that although the specificity of human spermatozoa is not confined to man alone, it probably is restricted to the Hominoidea.

In 2006, research suggested that after the last common ancestor of humans and chimpanzees diverged into two distinct lineages, inter-lineage sex was still sufficiently common that it produced fertile hybrids for around 1.2 million years after the initial split.

However, despite speculation, no case of a human-chimpanzee cross has ever been confirmed to exist.

There have been no scientifically verified specimens of a human/ape hybrid, although a performing chimp named Oliver was popularized during the 1970s as a possible Chuman/Humanzee. Genetictests conducted at the University of Chicago concluded that, despite Oliver’s somewhat unusual appearance and behavior, he was a normal chimpanzee; he had the same number of chromosomes as normal chimpanzees. The “hybrid” claims were possibly a promotional gimmick. Despite the general scientific dismissal of these claims, it is evident that some of popular culture clings to Oliver’s representational legacy. The decades long speculation about Oliver’s origins and the possibility that he was a human-chimp hybrid have led to numerous references, even in current popular culture. Many of these are satirical in nature or at least intended to be humorous.

Looking back millions of years into early human history, current research into human evolution tends to confirm that in some cases, interspecies sexual activity may have been a key part of human evolution. Analysis of the species’ genes in 2006 provides evidence that after humans had started to diverge from chimps, interspecies mating between “proto-human” and “proto-chimps” nonetheless occurred regularly enough to change certain genes in the new gene pool:

A new comparison of the human and chimp genomes suggests that after the two lineages separated, they may have begun interbreeding… A principal finding is that the X chromosomes of humans and chimps appear to have diverged about 1.2 million years more recently than the other chromosomes.

The research suggests that

There were in fact two splits between the human and chimp lineages, with the first being followed by interbreeding between the two populations and then a second split. The suggestion of hybridization has startled paleoanthropologists, who nonetheless are ‘treating the new genetic data seriously.

http://en.wikipedia.org/wiki/Humanzee#The_Ivanov_experiments

Great Ape Project

The Great Ape Project (GAP), founded in 1994, is an international organization of primatologists, anthropologists, ethicists, and other experts who advocate a United Nations Declaration of the Rights of Great Apes that would confer basic legal rights on non-human great apes: chimpanzees, bonobos, gorillas, and orang-utans. The rights suggested are the right to life, the protection of individual liberty, and the prohibition of torture. The organization also monitors individual great ape activity in the United States through a census program. Once rights are established, GAP would demand the release of great apes from captivity; currently 3,100 are held in the U.S., including 1,280 in biomedical research.

The book of the same name, edited by philosophers Paola Cavalieri and Peter Singer, features contributions from thirty-four authors, including Jane Goodall and Richard Dawkins, who have submitted articles voicing their support for the project. The authors write that human beings are intelligent animals with a varied social, emotional, and cognitive life. If great apes also display such attributes, the authors argue, they deserve the same consideration humans extend to members of their own species.

The book highlights findings that support the capacity of great apes to possess rationality and self-consciousness, and the ability to be aware of themselves as distinct entities with a past and future. Documented conversations (in sign languages) with individual great apes are the basis for these findings. Other subjects addressed within the book include the division placed between humans and great apes, great apes as persons, progress in gaining rights for the severely mentally retarded (once an overlooked minority), and the situation of great apes in the world today.

Their biological similarity with humans is also the key to the traits for which they are valuable as research subjects. For example, testing of monoclonal antibody treatments cannot be done in species less similar to humans than chimpanzees. Because the antibodies do not elicit immune responses in chimpanzees, they persist in the blood as they do in humans, and their effects can be evaluated. In monkeys and other non-apes, the antibodies are rapidly cleared from the bloodstream. Monoclonal antibody treatments are being developed for cancer; autoimmune diseases such as rheumatoid arthritis, lupus erythematosis, multiple sclerosis, psoriasis, and Crohn’s disease; and asthma. Chimpanzees also contain unique advantages in evaluating new Hepatitis B and C vaccines, and treatments for malaria, again because of the similarity in their response to these antigens to humans.

The Great Ape Project is campaigning to have the United Nations endorse a Declaration on Great Apes. This would extend what the project calls the “community of equals” to chimpanzees, bonobos, gorillas and orang-utans. The declaration seeks to extend to non-human great apes the protection of three basic interests: the right to life, the protection of individual liberty, and the prohibition of torture.

Right to life

The declaration states that members of the community of equals, which includes humans, may not be killed except in certain strictly defined circumstances such as self-defense or abortion.

Protection of individual liberty

The declaration states that members of the community of equals are not to be deprived of their liberty, and are entitled to immediate release where there has been no form of due process. Under the proposed declaration, the detention of great apes who have not been convicted of any crime or who are not criminally liable should be permitted only where it can be shown that the detention is in their own interests or is necessary to protect the public. The declaration says there must be a right of appeal, either directly or through an advocate, to a judicial tribunal.

Prohibition of torture

The declaration prohibits the torture, defined as the deliberate infliction of severe pain, on any great ape, whether wantonly or because of a perceived benefit to others. Under International Human Rights Law this is a jus cogens principle and under all major human rights documents it cannot at any time be derogated by any State.

http://en.wikipedia.org/wiki/Great_Ape_Project

Parahuman

A parahuman or para-human is a term used to describe a human-animal hybrid or chimera. Scientists have done extensive research into the mixing of genes or cells from different species, e.g. adding human (and other animal) genes to bacteria and farm animals to mass-produce insulin and spider silkproteins, and introducing human cells into mouse embryos.

Parahumans have been referred to as “human-animal hybrids” in a vernacular sense that also encompasses human-animal chimeras. The term parahuman is not used in scientific publications. The term is sometimes used to sensationalize research that involves mixing biological materials from humans and other species. It was used in a National Geographic article to describe an experiment in 2003, during which Chinese scientists at the Shanghai Second Medical University successfully fused human cells with rabbit eggs. According to Daily Mail, as of 2011, more than 150 human-animal hybrid embryos were created in British laboratories since the Human Fertilisation and Embryology Act 2008.

There are several reasons for which parahumans or chimeras might be created. The current forms of chimera exist for medical and industrial purposes, e.g., production of drugs and of organs suitable for organ transplantation. Other experiments aim to reveal knowledge about the function of the human body, e.g., by creating mice with a human-like immune system to study AIDS or with a brain incorporating human nerve cells. Restrictions on cloning and stem cell research have made chimera research an attractive alternative.

If a line of parahumans could be created using germline engineering, if they also bred true, and if they were different enough from ordinary humans to be unable to breed with us, then they would qualify as a species. Parahumans created using only somatic genetic engineering would have human children. Another key difference is that a germ-line parahuman would have to be modified before birth, while a somatic parahuman could be an adult human who chooses to be modified. Which one is more ethical is a matter of debate. An argument for the former is that no harm is done to a person born with modified genes because the person would have had no control over their genes in the first place. An argument for the latter being more ethical is that the changes would be made with informed consent.

There is no scientific field of parahuman research. Ethical, moral, and legal issues of parahuman research are speculative extensions of existing issues that arise in actual research.

In contrast, some transhumanists see this technology as one of many ways to overcome fundamental human limitations, such as disease and aging, and point out the many potential commercial and medical benefits. The debate can also be seen in terms of individual freedom to use germinal choice technology or reprogenetics.

Other ethical issues (shared with genetic engineering in general) involve the legal and moral status of a hybrid individual or race, whether the decision-making power over its creation should lie with governments or individuals, whether a distinction should be drawn between strictly medical treatments (restoring lost function) and those enhancing humans above some “normal” standard, whethermedical ethics allow doctors to offer parahuman-related treatments, and whether xenotransplantation poses risks of cross-species disease transfer.

The developmental biologist Stuart Newman applied for a patent on a human-nonhuman chimera in 1997 as a challenge to the U.S. Patent and Trademark Office and the U.S. Congress on the patentability of organisms.

http://en.wikipedia.org/wiki/Parahuman

Human vestigiality

In the context of human evolution, human vestigiality involves those characters (such as organs or behaviours) occurring in the human species that are considered vestigial—in other words having lost all or most of their original function through evolution. Although structures usually called “vestigial” often appear functionless, a vestigial structure may retain lesser functions or develop minor new ones. In some cases, structures once identified as vestigal simply had an unrecognized function

Vestigial characteristics occur throughout nature, one example being the vestigial hind limbs of whales and snakes. Many human characteristics are also vestigial in other primates and related animals. The following characteristics have been or still are considered vestigial in humans.

In 1893, Robert Wiedersheim published a book on human anatomy and its relevance to man’s evolutionary history. This book contained a list of 86 human organs that he considered vestigial, or as Wiedersheim himself clarified “Organs having become wholly or in part functionless, some appearing in the Embryo alone, others present during Life constantly or inconstantly.

Anatomy

Appendix

The vermiform appendix is a vestige of the cecum, an organ that would have been used to digest cellulose by humans’ herbivorous ancestors. Analogous organs in other animals similar to humans continue to perform that function, whereas other meat-eating animals may have similarly diminished appendices. In line with the possibility of vestigial organs developing new functions, some research suggests that the appendix may guard against the loss of symbiotic bacteria that aid indigestion.

Coccyx

The coccyx, or tailbone, is the remnant of a lost tail. All mammals have a tail at one point in their development; in humans, it is present for a period of 4 weeks, during stages 14 to 22 of human embryogenesis. This tail is most prominent in human embryos 31–35 days old. The tailbone, located at the end of the spine, has lost its original function in assisting balance and mobility, though it still serves some secondary functions, such as being an attachment point for muscles, which explains why it has not degraded further.

In rare cases congenital defect results in a short tail-like structure being present at birth. Twenty-three cases of human babies born with such a structure have been reported in the medical literature since 1884.

Wisdom teeth

Wisdom teeth are vestigial third molars that human ancestors used to help in grinding down plant tissue. The common postulation is that the skulls of human ancestors had larger jaws with more teeth, which were possibly used to help chew down foliage to compensate for a lack of ability to efficiently digest the cellulose that makes up a plant cell wall. As human diets changed, smaller jaws were selected by evolution, yet the third molars, or “wisdom teeth,” still commonly develop in human mouths. Currently, wisdom teeth have become useless and even harmful to the extent where surgical procedures are often done to remove them.

Interesting comparison between human and macaque monkey ear

The ears of a Macaque monkey, and most other monkeys, have far more developed muscles than those of humans and therefore have the capability to move their ears to better hear potential threats. Humans and other primates such as the orang-utan and chimpanzee however have ear muscles that are minimally developed and non-functional, yet still large enough to be identifiable. A muscle attached to the ear that cannot move the ear, for whatever reason, can no longer be said to have any biological function. In humans there is variability in these muscles, such that some people are able to move their ears in various directions, and it has been said that it may be possible for others to gain such movement by repeated trials. In such primates the inability to move the ear is compensated mainly by the ability to turn the head on a horizontal plane, an ability which is not common to most monkeys—a function once provided by one structure is now replaced by another.

Human eye – Nictitating membrane

The plica semilunaris is a small fold of tissue on the inside corner of the eye. It is the vestigial remnant of the nictitating membrane (the “third eyelid”) which is present in other animals such as birds, reptiles, and fish. It is rare in mammals, mainly found in monotremes and marsupials. Its associated muscles are also vestigial. The plica semilunaris of Africans and Indigenous Australians are slightly larger than in other peoples. Only one species of primate, the Calabar Angwantibo, is known to have a functioning nictitating membrane.

Sensory

Although the sense of smell or olfaction is highly important for many animals in avoiding predators, finding food, and other functions, it is far less essential to human survival, as humans have for the most part no predators, and obtain food mostly by agriculture. There is great variation in olfactory sensitivity from person to person, which is common in vestigial characteristics. It has been observed that native South Americans, American Natives, and African peoples have a highly developed sense of smell, such that they may be able to identify others in the dark by their odour alone. This does not mean that having any olfactory ability at all is vestigial, for example it may save a person from inhaling toxic fumes. A characteristic may degenerate despite being of some use if there is very little or no selection pressure on the genes associated with it.

Behavioural

Humans also bear some vestigial behaviors and reflexes. For example, the formation of goose bumps in humans under stress is a vestigial reflex; a possible function in human evolutionary ancestors was to raise the body’s hair, making the ancestor appear larger and scaring off predators. Raising the hair is also used to trap an extra layer of air, keeping an animal warm. Due to the diminished amount of hair in humans, the reflex formation of goose bumps when cold is also vestigial.

The palmar grasp reflex is supported to be a vestigial behavior in human infants. When placing a finger or object to the palm of an infant, it will securely grasp it. This grasp is found to be rather strong. Some infants—37% according to a 1932 study—are able to support their own weight from a rod; although there is no way they can cling to their mother. The grasp is also evident in the feet too. When a baby is sitting down, its prehensile feet assume a curled-in posture, much like what is observed in an adult chimp. An ancestral primate would have had sufficient body hair to which an infant could cling unlike modern humans, thus allowing its mother to escape from danger, such as climbing up a tree in the presence of a predator without having to occupy her hands holding her baby.

http://en.wikipedia.org/wiki/Human_vestigiality

Is evolution progressive?
This is not an easy question to answer. From a plant’s perspective, the best measure of progress might be photosynthetic ability; from a spider’s it might be the efficiency of a venom delivery system.

The problem is that we humans are hung up on ourselves. We often define progress in a way that hinges on our view of ourselves, a way that relies on intellect, culture, or emotion. But that definition is anthropocentric.

It is tempting to see evolution as a grand progressive ladder with Homo sapiens emerging at the top. But evolution produces a tree, not a ladder — and we are just one of many leaves on the tree.

http://evolution.berkeley.edu/evolibrary/article/evo_01

Origin of language

The origin of language concerns the onset in prehistory of human language — whether gestural or spoken. There are numerous hypotheses about how, why, when and where it happened, but all are speculative because the relevant developments occurred so early in human prehistory and have left no direct historical traces; nor are comparable processes observable today.

The time range in question extends from the separation of Homo (2.3 to 2.4 million years ago) and Pan (5 to 6 million years ago) to the emergence of full behavioral modernity some 50,000 years ago.

The evolution of spoken human language requires the development of the vocal tract used for speech production and the cognitive abilities required to understand and produce linguistic utterances. Some debate surrounds the time line, sequence and order of developments associated with this.

It is mostly undisputed that pre-human australopithecines did not have communication systems significantly different from those found in great apes in general, but scholarly opinions vary as to the developments since the appearance of Homo some 2.5 million years ago. Some scholars assume the development of primitive language-like systems (proto-language) as early as Homo habilis, while others place the development of primitive symbolic communication only with Homo erectus (1.8 million years ago) and the development of language proper with Homo sapiens less than 100,000 years ago.

 Biological foundations for human speech

The descended larynx was formerly viewed as a structure unique to the human vocal tract and essential to the development of speech and language. However, it has been found in other species, including some aquatic mammals and large deer (e.g. Red Deer), and the larynx has been observed to descend during vocalizations in dogs, goats, and alligators. In humans, the descended larynx extends the length of the vocal tract and expands the variety of sounds humans can produce. Some scholars claim that the ubiquity of nonverbal communication in humans stands as evidence of the non-essentiality of the descended larynx to the development of language.

The descended larynx has non-linguistic functions as well, possibly exaggerating the apparent size of an animal (through vocalizations with lower than expected pitch). Thus, although it plays an important role in speech production, expanding the variety of sounds humans can produce, it may not have evolved specifically for this purpose, as has been suggested by Jeffrey Laitman, and as per Hauser, Chomsky, and Fitch (2002), could be an example of preadaptation.

The control capabilities of human tongue should also be considered. As a result of higher intelligence, the human brain can control its organs and peripherals more precisely. Therefore, the tongue is more creative to curve, bend, stop and throw the sound waves produced by larynx.

Language origin hypotheses – Gestural theory

The gestural theory states that human language developed from gestures that were used for simple communication.

Two types of evidence support this theory.

  1. Gestural language and vocal language depend on similar neural systems. The regions on the cortex that are responsible for mouth and hand movements border each other.
  2. Nonhuman primates can use gestures or symbols for at least primitive communication, and some of their gestures resemble those of humans, such as the “begging posture”, with the hands stretched out, which humans share with chimpanzees.

Research has found strong support for the idea that verbal language and sign language depend on similar neural structures. Patients who used sign language, and who suffered from a left-hemisphere lesion, showed the same disorders with their sign language as vocal patients did with their spoken language. Other researchers found that the same left-hemisphere brain regions were active during sign language as during the use of vocal or written language.

The important question for gestural theories is why there was a shift to vocalization. There are three likely explanations:

  1. Our ancestors started to use more and more tools, meaning that their hands were occupied and could not be used for gesturing.
  2. Gesturing requires that the communicating individuals can see each other. There are many situations in which individuals need to communicate even without visual contact, for instance when a predator is closing in on somebody who is up in a tree picking fruit.
  3. The need to co-operate effectively with others in order to survive. A command issued by a tribal leader to ‘find’ ‘stones’ to ‘repel’ attacking ‘wolves’ would create teamwork and a much more powerful, co-ordinate response.

Humans still use hand and facial gestures when they speak, especially when people meet who have no language in common. There are also, of course, a great number of sign languages still in existence, commonly associated with Deaf communities; it is important to note that these signed languages are equal in complexity, sophistication, and expressive power, to any spoken language—the cognitive functions are similar and the parts of the brain used are similar. The main difference is that the “phonemes” are produced on the outside of the body, articulated with hands, body, and facial expression, rather than inside the body articulated with tongue, teeth, lips, and breathing.

Critics of gestural theory note that it is difficult to name serious reasons why the initial pitch-based vocal communication (which is present in primates) would be abandoned in favor of the much less effective non-vocal, gestural communication. Other challenges to the “gesture-first” theory have been presented by researchers in psycholinguistics, including David McNeill.

Self-domesticated ape theory

According to a study investigating the song differences between white-rumped Munias and its domesticated counterpart (Bengalese finch), the wild munias use a highly stereotyped song, whereas the domesticated ones sing a highly unconstrained song. Considering that song syntactical complexity is subject to female preference in the Bengalese finch, it is likely that maternal resource allocation strategies play a role in song evolution. In the field of bird vocalization, brains capable of producing only an innate song have very simple neural pathways: the primary forebrain motor center, called the robust nucleus of arcopallium (RA), connects to midbrain vocal outputs which in turn project to brainstem motor nuclei. By contrast, in brains capable of learning songs, the RA receives input from numerous additional forebrain regions, including those involved in learning and social experience. Control over song generation has become less constrained, more distributed, and more flexible.

When compared with other primates, whose communication system is restricted to a highly stereotypic repertoire of hoots and calls, humans have very few pre specified vocalizations, extant examples being laughter and sobbing. Moreover, these remaining innate vocalizations are generated by restricted neuronal pathways, whereas language is generated by a highly distributed system involving numerous regions of the human brain.

Evolutionary timeline – Primate language

Not much is known about great ape communication in the wild. The anatomical structure of their larynxes does not enable apes to make many of the sounds that modern humans do. In captivity, apes have been taught rudimentary sign language and the use of lexigrams—symbols that do not graphically resemble their corresponding words—on computer keyboards. Some apes, such as Kanzi, have been able to learn and use hundreds of lexigrams.

The Broca’s and Wernicke’s areas in the primate brain are responsible for controlling the muscles of the face, tongue, mouth, and larynx, as well as recognizing sounds. Primates are known to make “vocal calls,” and these calls are generated by circuits in the brainstem and limbic system. However, modern brain scans of chattering chimpanzees prove that they use Brocas area to chatter and there is evidence that monkeys hearing monkey chatter use the same brain regions as humans hearing speech.

In the wild, the communication of vervet monkeys has been the most extensively studied. They are known to make up to ten different vocalizations. Many of these are used to warn other members of the group about approaching predators. They include a “leopard call”, a “snake call”, and an “eagle call”. Each call triggers a different defensive strategy in the monkeys that hear the call and scientists were able to elicit predictable responses from the monkeys using loudspeakers and prerecorded sounds. Other vocalizations may be used for identification. If an infant monkey calls, its mother turns toward it, but other vervet mothers turn instead toward that infant’s mother to see what she will do.

Similarly, researchers have demonstrated that chimpanzees (in captivity) use different “words” in reference to different foods. They recorded vocalizations that chimps made in reference, for example, to grapes, and then other chimps pointed at pictures of grapes when they heard the recorded sound.

Early Homo

Regarding articulation, there is considerable speculation about the language capabilities of early Homo (2.5 to 0.8 million years ago). Anatomically, some scholars believe features of bipedalism which developed in australopithecines around 3.5 million years ago would have brought changes to the skull, allowing for a more L-shaped vocal tract. The shape of the tract and a larynx positioned relatively low in the neck are necessary prerequisites for many of the sounds humans make, particularly vowels. Other scholars believe that, based on the position of the larynx, not even Neanderthals had the anatomy necessary to produce the full range of sounds modern humans make.

The term proto-language, as defined by linguist Derek Bickerton, is a primitive form of communication lacking:

  • a fully developed syntax
  • Tense, aspect, auxiliary verbs, etc.
  • a closed-class (i.e. non-lexical) vocabulary

That is, a stage in the evolution of language somewhere between great ape language and fully developed modern human language. Bickerton places the first emergence of such a proto-language with the earliest appearance of Homo, and associates its appearance with the pressure of behavioral adaptation to the niche construction of scavenging faced by Homo habilis.

Anatomical features such as the L-shaped vocal tract have been continuously evolving, as opposed to appearing suddenly. Hence it is most likely that Homo habilis and Homo erectus during the Lower Pleistocene had some form of communication intermediate between that of modern humans and that of other primates.

 Homo neanderthalensis

The discovery in 2007 of a Neanderthal hyoid bone suggests that Neanderthals may have been anatomically capable of producing sounds similar to modern humans. The hypoglossal nerve, which passes through the canal, controls the movements of the tongue and its size is said to reflect speech abilities. Hominids that lived earlier than 300,000 years ago had hypoglossal canals more akin to those of chimpanzees than of humans.

However, although Neanderthals may have been anatomically able to speak, Richard G. Klein in 2004 doubted that they possessed a fully modern language. He largely bases his doubts on the fossil record of archaic humans and their stone tool kit. For 2 million years following the emergence of Homo habilis, the stone tool technology of hominids changed very little. Klein, who has worked extensively on ancient stone tools, describes the crude stone tool kit of archaic humans as impossible to break down into categories based on their function, and reports that Neanderthals seem to have had little concern for the final form of their tools. Klein argues that the Neanderthal brain may have not reached the level of complexity required for modern speech, even if the physical apparatus for speech production was well-developed. The issue of the Neanderthal’s level of cultural and technological sophistication remains a controversial one.

Homo sapiens

Anatomically modern humans first appear in the fossil record 195,000 years ago in Ethiopia. But while they were modern anatomically, the archaeological evidence available leaves little indication that they behaved any differently from the earlier Homo heidelbergensis. They retained the same Acheulean stone tools and hunted less efficiently than did modern humans of the Late Pleistocene. The transition to the more sophisticated Mousterian takes place only about 120,000 years ago, and is shared by both H. sapiens and H. neanderthalensis.

The development of fully modern behavior in H. sapiens, not shared by H. neanderthalensis or any other variety of Homo, is dated to some 70,000 to 50,000 years ago. The development of more sophisticated tools, for the first time constructed out of more than one material (e.g. bone or antler) and sortable into different categories of function (such as projectile points, engraving tools, knife blades, and drilling and piercing tools) are often taken as proof for the presence of fully developed language, assumed to be necessary for the teaching of the processes of manufacture to offspring.

The greatest step in language evolution would have been the progression from primitive, pidgin-like communication to a creole-like language with all the grammar and syntax of modern languages. Some scholars believe that this step could only have been accomplished with some biological change to the brain, such as a mutation. It has been suggested that a gene such as FOXP2 may have undergone a mutation allowing humans to communicate. However, recent genetic studies have shown that Neandertals shared the same FOXP2 allele with H. sapiens. It hence does not have a mutation unique to H. sapiens. Instead, it indicates this genetic change predates the Neandertal – H. sapiens split. There is still considerable debate as to whether language developed gradually over thousands of years or whether it appeared suddenly.

The Broca’s and Wernicke’s areas of the primate brain also appear in the human brain, the first area being involved in many cognitive and perceptual tasks, the latter lending to language skills. The same circuits discussed in the primates’ brain stem and limbic system control non-verbal sounds in humans (laughing, crying, etc.), which suggests that the human language center is a modification of neural circuits common to all primates. This modification and its skill for linguistic communication seem to be unique to humans, which imply that the language organ derived after the human lineage split from the primate (chimps and bonobos) lineage. Plainly stated, spoken language is a modification of the larynx that is unique to humans.

According to the Out of Africa hypothesis, around 50,000 years ago a group of humans left Africa and proceeded to inhabit the rest of the world, including Australia and the Americas, which had never been populated by archaic hominids. Some scientists believe that Homo sapiens did not leave Africa before that, because they had not yet attained modern cognition and language, and consequently lacked the skills or the numbers required to migrate. However, given the fact that Homo erectus managed to leave the continent much earlier (without extensive use of language, sophisticated tools, or anatomical modernity), the reasons why anatomically modern humans remained in Africa for such a long period remain unclear.

Communication, speech and language

Many scientists make a distinction between speech and language. They believe that language (as a context for communication, and primarily as a cognitive ability to form concepts and communicate them) was developed earlier in human evolution, and speech (one of the forms of communication) was developed much later. The presence of speech (without language) is also possible in some cases of human mental retardation or learning disabilities (like Specific Language Impairment) and is also known in the animal kingdom. For instance, talking birds are able to imitate human speech with varying ability. However, this ability to mimic human sounds is very different from the acquisition of syntax. Likewise, the production of speech sounds is not necessary for language use, as evidenced by modern sign languages, which use manual symbols and facial grammar as a basis for language rather than speech.

It has been  suggested that the key feature of human language is the ability to ask questions. Some animals (notably bonobos and chimpanzees), who learned to communicate with their human trainers (using mostly visual forms of communication), demonstrated that they have the ability to correctly respond to complex questions and requests, but they failed to ask even the simplest questions themselves. Conversely, human children are able to ask their first questions (using only question intonation) at the babbling period of their development, long before they start using syntactic structures. It is crucially important that although babies from different cultures acquire native languages from their social environment, all languages of the world without exception – tonal, non-tonal, into national and accented – use similar rising “question intonation” for yes-no questions. This fact is a strong proof of the universality of question intonation. It should also be noted that arbitrary expressions of joyful excitement, regardless of the language or nationality of the speaker, generally have falling intonation and this may also be universal.

 Theory of mind

Simon Baron-Cohen argues that theory of mind must have preceded language use, based on evidence of use of the following characteristics as much as 40,000 years ago: intentional communication, repairing failed communication, teaching, intentional persuasion, intentional deception, building shared plans and goals, intentional sharing of focus or topic, and pretending. Moreover, Baron-Cohen argues that many primates show some, but not all, of these abilities. Call and Tomasello’s research on chimpanzees supports this, in that individual chimps seem to understand that other chimps have awareness, knowledge, and intention, but do not seem to understand false beliefs. Many primates show some tendencies toward a theory of mind, but not a full one as humans have. Ultimately, there is some consensus within the field that a theory of mind is necessary for language use. Thus, the development of a full theory of mind in humans was a necessary precursor to full language use.

 Scenarios for language evolution

All human populations possess language. This includes populations, such as the Tasmanians and the Andamanese, who may have been isolated from the Old World continents for as long as 40,000 years.

Linguistic monogenesis is the hypothesis that there was a single proto-language, sometimes called Proto-Human, from which all other vocal languages spoken by humans descend. (This does not apply to sign languages, which are known to arise independently rather frequently.)

According to the Out of Africa hypothesis, all humans alive today are descended from Mitochondrial Eve, a woman estimated to have lived in Africa some 150,000 years ago. This raises the possibility that the Proto-Human language could date to approximately that period. There are also claims of a population bottleneck, notably the Toba catastrophe theory, which postulates human population at one point some 70,000 years ago was as low as 15,000 or even 2,000 individuals. If it did indeed transpire, such a bottleneck would be an excellent candidate for the date of Proto-Human, which also illustrates the fact that Proto-Human would not necessarily date to the first emergence of language.

The multiregional hypothesis would entail that modern language evolved independently on all the continents, a proposition considered implausible by proponents of monogenesis.

http://en.wikipedia.org/wiki/Origin_of_language

The Proto-Indo-European language (PIE) is the reconstructed common ancestor of the Indo-European languages, spoken by the Proto-Indo-Europeans. The existence of such a language has been accepted by linguists for over a century, and reconstruction is far advanced and quite detailed.

Scholars estimate that PIE may have been spoken as a single language (before divergence began) around 3700 BC, though estimates by different authorities can vary by more than a millennium. The most popular hypothesis for the origin and spread of the language is the Kurgan hypothesis, which postulates an origin in the Pontic-Caspian steppe of Eastern Europe and Western Asia. In modern times the existence of the language was first postulated in the 18th century by Sir William Jones, who observed the similarities between Sanskrit, Ancient Greek, and Latin. By the early 1900s well-defined descriptions of PIE had been developed that are still accepted today (with some refinements).

PIE is known to have had a complex system of morphology that included inflections (suffixing of roots, as in who, whom, whose), and ablaut (vowel alterations, as in sing, sang, sung). Nouns used a sophisticated system of declension and verbs used a similarly sophisticated system of conjugation.

As there is no written evidence of Proto-Indo-European, all knowledge of the language is derived by reconstruction from later languages using linguistic techniques such as the comparative method and the method of internal reconstruction. Relationships to other language families, including the Uralic languages, have been proposed though all such suggestions remain controversial.

http://en.wikipedia.org/wiki/Proto-Indo-European_language

Social evolution…the building block of civilization

Consciousness

Consciousness is a term that refers to a variety of aspects of the relationship between the mind and the world with which it interacts. It has been defined as: subjectivity; awareness; the ability to experience feelings; wakefulness; having a sense of selfhood; or the executive control system of the mind. Despite the difficulty of definition, many philosophers believe that there is a broadly shared underlying intuition about what consciousness is.

Philosophers since the time of Descartes and Locke have struggled to comprehend the nature of consciousness and pin down its essential properties. Issues of concern in the philosophy of consciousness include whether the concept is fundamentally valid; whether consciousness can ever be explained mechanistically; whether non-human consciousness exists and if so how it can be recognized; how consciousness relates to language; and whether it may ever be possible for computers to achieve a conscious state. Perhaps the thorniest issue is whether consciousness can be understood in a way that does not require a dualistic distinction between mental and physical entities.

At one time consciousness was viewed with skepticism by many scientists, but in recent years it has been a significant topic of research in psychology and neuroscience. The primary focus is on understanding what it means biologically and psychologically for information to be present in consciousness—that is, on determining the neural and psychological correlates of consciousness.

The earliest English language uses of “conscious” and “consciousness” date back, however, to the 1500s. The English word “conscious” originally derived from the Latin conscious (con- “together” + scire “to know”), but the Latin word did not have the same meaning as our word — it meant knowing with, in other words having joint or common knowledge with another.

Consciousness is the ownership of perceptions, thoughts, and feelings; awareness. The term is impossible to define except in terms that are unintelligible without a grasp of what consciousness means. Many fall into the trap of equating consciousness with self-consciousness—to be conscious it is only necessary to be aware of the external world. Consciousness is a fascinating but elusive phenomenon: it is impossible to specify what it is, what it does, or why it has evolved. Nothing worth reading has been written on it.

Is consciousness a valid concept? A majority of philosophers have felt that the word consciousness names a genuine entity, but some who belong to the physicality and behaviorist schools have not been convinced. Many scientists have also been skeptical. The most compelling argument for the existence of consciousness is that the vast majority of mankind has an overwhelming intuition that there truly is such a thing.

Many philosophers and scientists have been unhappy about the difficulty of producing a definition that does not involve circularity or fuzziness. The neuroscientist Antonio Damasio, for example, calls consciousness “the feeling of what happens”, and defines it as “an organism’s awareness of its own self and its surroundings”. These formulations seem intuitively reasonable, but they are difficult to apply to specific situations.

How does it relate to the physical world? Mind–body problem

Inputs are passed by the sensory organs to the pineal gland and from there to the immaterial spirit. The first influential philosopher to discuss this question specifically was Descartes, and the answer he gave is known as Cartesian dualism. Descartes proposed that consciousness resides within an immaterial domain he called res cogitans (the realm of thought), in contrast to the domain of material things which he called res extensa (the realm of extension). He suggested that the interaction between these two domains occurs inside the brain, perhaps in a small midline structure called the pineal gland.

Several physicists have argued that classical physics is intrinsically incapable of explaining the holistic aspects of consciousness, but that quantum theory provides the missing ingredients. Several theorists have therefore proposed quantum mind (QM) theories of consciousness; the most notable theories falling into this category include the Holonomic brain theory of Karl H. Pribram and David Bohm, and the Orch-OR theory formulated by Stuart Hameroff and Roger Penrose.

Which came first? Consciousness or language?

How does it relate to language? In humans, the clearest visible indication of consciousness is the ability to use language. Medical assessments of consciousness rely heavily on an ability to respond to questions and commands, and in scientific studies of consciousness, the usual criterion for awareness is verbal report (that is, subjects are deemed to be aware if they say that they are). Thus there is a strong connection between consciousness and language at a practical level. Philosophers differ, however, on whether language is essential to consciousness or merely the most powerful tool for assessing it.

Descartes believed that language and consciousness are bound tightly together. He thought that many of the behaviors humans share with other animals could be explained by physical processes such as reflexes, but that language could not be: he took the fact that animals lack language to be an indication that they lack access to res cogitans, the realm of thought. Others have reached similar conclusions, though sometimes for different reasons. Julian Jaynes argued in The Origin of Consciousness in the Breakdown of the Bicameral Mind that for consciousness to arise, language needs to have reached a fairly high level of complexity. Merlin Donald also argued for a critical dependence of consciousness on the ability to use symbols in a sophisticated way.

Those are, however, minority views. If language is essential, then speechless humans (infants, feral children, aphasics, etc.) could not be said to be conscious, a conclusion that the majority of philosophers have resisted. The implication that only humans, and not other animals, are conscious is also widely resisted by theorists such as evolutionary psychologists, as well as by animal rights activists.

How can we know whether non-human animals are conscious?

Am I conscious? The topic of animal consciousness is beset by a number of difficulties. It poses the problem of other minds in an especially severe form, because animals, lacking language, cannot tell us about their experiences. Also, it is difficult to reason objectively about the question, because a denial that an animal is conscious is often taken to imply that it does not feel, its life has no value, and that harming it is not morally wrong. Descartes, for example, has sometimes been blamed for mistreatment of animals due to the fact that he believed only humans have a non-physical mind. Most people have a strong intuition that some animals, such as dogs, are conscious, while others, such as insects, are not; but the sources of this intuition are not obvious.

Philosophers who consider subjective experience the essence of consciousness also generally believe, as a correlate, that the existence and nature of animal consciousness can never rigorously be known. Thomas Nagel spelled out this point of view in an influential essay titled What Is it Like to Be a Bat? He said that an organism is conscious “if and only if there is something that it is like to be that organism — something it is like for the organism”; and he argued that no matter how much we know about an animal’s brain and behavior, we can never really put ourselves into the mind of the animal and experience its world in the way it does itself. Other thinkers, such as Douglas Hofstadter, dismiss this argument as incoherent. Several psychologists and ethologists have argued for the existence of animal consciousness by describing a range of behaviors that appear to show animals holding beliefs about things they cannot directly perceive.

Another approach applies specifically to the study of self-consciousness, that is, the ability to distinguish oneself from others. In the 1970s Gordon Gallup developed an operational test for self-awareness, known as the mirror test. The test examines whether animals are able to differentiate between seeing themselves in a mirror versus seeing other animals. The classic example involves placing a spot of coloring on the skin or fur near the individual’s forehead and seeing if they attempt to remove it or at least touch the spot, thus indicating that they recognize that the individual they are seeing in the mirror is themselves. Humans (older than 18 months) and other great apes, bottlenose dolphins, pigeons, and elephants have all been observed to pass this test. The test is usually carried out with an identical ‘spot’ being placed elsewhere on the head with a non-visible material as a control, to assure the subject is not responding to the touch stimuli of the spot’s presence.

States of consciousness

There are some states in which consciousness seems to be abolished, including sleep, coma, and death. There are also a variety of circumstances that can change the relationship between the mind and the world in less drastic ways, producing what are known as altered states of consciousness. Some altered states occur naturally; others can be produced by drugs or brain damage.

The two most widely accepted altered states are sleep and dreaming. Although dream sleep and non-dream sleep appear very similar to an outside observer, each is associated with a distinct pattern of brain activity, metabolic activity, and eye movement; each is also associated with a distinct pattern of experience and cognition. During ordinary non-dream sleep, people who are awakened report only vague and sketchy thoughts, and their experiences do not cohere into a continuous narrative. During dream sleep, in contrast, people who are awakened report rich and detailed experiences in which events form a continuous progression, which may however be interrupted by bizarre or fantastic intrusions. Thought processes during the dream state frequently show a high level of irrationality. Both dream and non-dream states are associated with severe disruption of memory: it usually disappears in seconds during the non-dream state and in minutes after awakening from a dream unless actively refreshed.

A variety of psychoactive drugs have notable effects on consciousness. These range from a simple dulling of awareness produced by sedatives, to increases in the intensity of sensory qualities produced by stimulants, cannabis, or most notably by the class of drugs known as psychedelics. LSD, mescaline, psilocybin, and others in this group can produce major distortions of perception, including hallucinations; some users even describe their drug-induced experiences as mystical or spiritual in quality. The brain mechanisms underlying these effects are not well understood, but there is substantial evidence that alterations in the brain system that uses the chemical neurotransmitter serotonin play an essential role.

There has been some research into physiological changes in yogis and people who practice various techniques of meditation. Recent research with brain waves during meditation has shown a distinct difference between those corresponding to ordinary relaxation and those corresponding to meditation. It is disputed, however, whether there is enough evidence to count these as physiologically distinct states of consciousness.

http://en.wikipedia.org/wiki/Consciousness

The science of sleep

We spend a third of our lives doing it.

Napoleon, Florence Nightingale and Margaret Thatcher got by on four hours a night.

Thomas Edison claimed it was waste of time.

Why do we sleep?

So why do we sleep? This is a question that has baffled scientists for centuries and the answer is no one is really sure

. Some believe that sleep gives the body a chance to recuperate from the day’s activities but in reality, the amount of

energy saved by sleeping for even eight hours is miniscule – about 50 kCal, the same amount of energy in a piece of toast.

We have to sleep because it is essential to maintaining normal levels of cognitive skills such as speech, memory,

Innovative and flexible thinking. In other words, sleep plays a significant role in brain development.

What would happen if we didn’t sleep?

A good way to understand the role of sleep is to look at what would happen if we didn’t sleep.

Lack of sleep has serious effects on our brain’s ability to function. If you’ve ever pulled an all-nighter, you’ll be

familiar with the following after-effects: grumpiness, grogginess, irritability and forgetfulness. After just one night

without sleep, concentration becomes more difficult and attention span shortens considerably.

Research also shows that sleep-deprived individuals often have difficulty in responding to rapidly changing situations

and making rational judgements. In real life situations, the consequences are grave and lack of sleep is said to have been

be a contributory factor to a number of international disasters such as Exxon Valdez, Chernobyl, Three Mile Island

and the Challenger shuttle explosion.

Sleep deprivation not only has a major impact on cognitive functioning but also on emotional and physical health.

Disorders such as sleep apnoea which result in excessive daytime sleepiness have been linked to stress and high

blood pressure. Research has also suggested that sleep loss may increase the risk of obesity because chemicals

and hormones that play a key role in controlling appetite and weight gain are released during sleep.

What happens when we sleep? What happens every time we get a bit of shut eye?

 

Sleep occurs in a recurring cycle of 90 to 110 minutes and is divided into two categories: non-REM (which is further

split into four stages) and REM sleep.

Non-REM sleep

 Stage one: Light Sleep

During the first stage of sleep, we’re half awake and half asleep. Our muscle activity slows down and slight twitching

may occur. This is a period of light sleep, meaning we can be awakened easily at this stage.

Stage two: True Sleep

Within ten minutes of light sleep, we enter stage two, which lasts around 20 minutes. The breathing

Pattern and heart rate start to slow down. This period accounts for the largest part of human sleep.

Stages three and four: Deep Sleep

During stage three, the brain begins to produce delta waves, a type of wave that is large

(high amplitude) and slow (low frequency). Breathing and heart rate are at their lowest levels.

Stage four is characterised by rhythmic breathing and limited muscle activity. If we are awakened

during deep sleep we do not adjust immediately and often feel groggy and disoriented for several

minutes after waking up. Some children experience bed-wetting, night terrors, or sleepwalking during this stage.

The first rapid eye movement (REM) period usually begins about 70 to 90 minutes after we fall asleep.

We have around three to five REM episodes a night. Although we are not conscious, the brain is very active –

often more so than when we are awake. This is the period when most dreams occur. Our eyes dart around

(hence the name), our breathing rate and blood pressure rise. However, our bodies are effectively paralysed,

said to be nature’s way of preventing us from acting out our dreams. After REM sleep, the whole cycle begins again.

How much sleep is required?

There is no set amount of time that everyone needs to sleep, since it varies from person to person.

Results from the sleep profiler indicate that people like to sleep anywhere between 5 and 11 hours,

with the average being 7.75 hours.

Jim Horne from Loughborough University’s Sleep Research Centre has a simple answer though:

“The amount of sleep we require is what we need not to be sleepy in the daytime.”

Even animals require varied amounts of sleep: With continued lack of sufficient sleep, the part of the brain that

controls language, memory, planning and sense of time is severely affected, practically shutting down. In fact, 17

hours of sustained wakefulness leads to a decrease in performance equivalent to a blood alcohol level of 0.05%

(two glasses of wine). This is the legal drink driving limit in the UK.

The current world record for the longest period without sleep is 11 days, set by Randy Gardner in 1965

Four days into the research, he began hallucinating. This was followed by a delusion where he thought he

was a famous footballer. Surprisingly, Randy was actually functioning quite well at the end of his research

and he could still beat the scientist at pinball.

http://www.bbc.co.uk/science/humanbody/sleep/articles/whatissleep.shtml

Eight hours of sleep a day seems like a colossal waste of time, doesn’t it?

After all, in the hectic world we live in,those precious hours could be put to use responding to all those e-mails or

hitting the spa. So why do we need so much sleep?

Dr. Neil B. Kavey, director of the Sleep Disorders Center at Columbia-Presbyterian Medical Center in New York City,

offers some clues: We don’t fully understand the importance of sleep. What we do know is that sleep is an anabolic, or

building, process. And we think it restores the body’s energy supplies that have been depleted through the day’s activities.

Sleep is also the time when the body does most of its repair work; muscle tissue is rebuilt and restored. We know,

for example, that growth hormone is secreted during sleep. This hormone is important for growth in children, but

is also important throughout adulthood in rebuilding tissues. Think of the body as a car. No car can keep going and going

and going without a tune-up or oil change. If it’s not tuned, the car may keep running, but not as smoothly as it did when

it was maintained properly. You can think of sleep as your body’s daily tune-up.

Human beings can function without a full tune-up, but they will be in a state of relative sleep deprivation

and won’t be able to work or to think as well as they do when they are fully rested. It’s like an engine that

gets only four out of eight spark plugs replaced and then runs sluggishly.

Sleep is also a time for restoring mental energy. We spend all day thinking and creating, and that uses up our energy

stores.

It is interesting that in dream sleep the brain is actually very active. And this is where things get really theoretical.

We’re not really sure exactly what dreams accomplish. Some experts believe that dreaming is actually some king of

clearing-out process. More sleep researchers think that dreams serve the function of helping to reorganize and store

psychological information taken in during the day.

Not enough ZZZ’s

One of the ways we have of understanding why we need to sleep so much is to look at what happens

if we don’t get enough sleep. It affects our personalities and our sense of humour. We may become

irritable and less tolerant. Parents of small children often tell me that when they’re tired they get irritated

at the antics of children that might amuse them if they were properly rested. Lack of sleep clearly affects our

thinking, or cognitive, processes. A sleep-deprived brain is truly running on four rather than eight cylinders.

If we’re trying to be creative, the motor doesn’t work as well. We can perform calculations, but not as quickly.

We’re much more likely to make errors. It’s because the brain’s engine hasn’t been replenished.

Sleep deprivation also affects us physically. Our coordination suffers. We lose our ability to do things with agility.

Sleep improves muscle tone and skin appearance. With adequate sleep athletes run better, swim better and lift

more weight. We also see differences in immune responses depending on how much someone sleeps.

The amount of sleep a person needs will vary from individual to individual. But most people require around eight

hours. No one really knows how humans evolved to sleep an average of eight straight hours each night. Factors

that influence human sleep patterns probably include our physical size, muscle mass, brain size and the ability

to think.

http://www.msnbc.msn.com/id/3076707/ns/technology_and_science-

science/t/why-do-we-need-so-much-sleep/

What are dreams? What is their purpose?

This is a vast an unknown area of study. Scientists understand the mind in only small ways. They can detect how

particular parts of the brain work on different tasks. But they are far from understanding the bigger picture of how

it all pulls together.

Perhaps dreams are the minds way of balancing the two central parts of the brain the Id and the EGO. What people must understand is that the brain is not one but two computers. The left brain and the right brain are completely separate. That is why we as humans are very successful.

The Left brain – the left side of the brain deals with rational thought and conscious logical problems. It is good at math and other mathematical type problem solving. It is also very much in charge of communication and so is in charge of our command of language.

The right brain – the right side of the brain is the unconscious mind. It provides imagination and magical intuition. The left side adds up numbers very well – but the right side can step back and say – Is it actually worth adding them up? What’s the point? So the unconscious provides an overview.

Are dreams are the way by which these two vast computers the conscious and the unconscious are linked? As someone who knows a bit about computers linking computers together is no simple task.

This is absolutely essential to our success as a human. We need to process information in order to survive. But the two brains must work harmoniously together if we are to succeed.  The brain must have some mechanism for sorting out which of the two super brains it should take account of – the left or the right?

http://www.unclesirbobby.org.uk/what.php

Sleep in non-human animals refers to how the behavioral and physiological state of sleep, mainly characterized by reversible unconsciousness, non-responsiveness to external stimuli, and motor passivity, appears in different categories of animals

Sleep can follow a physiological or behavioural definition. In the physiological sense, sleep is a state characterized by reversible unconsciousness, special brainwave patterns, sporadic eye movement, loss of muscle tone (possibly with some exceptions; see below regarding the sleep of birds and of aquatic mammals), and a compensatory increase following deprivation of the state. In the behavioral sense, sleep is characterized by non-responsiveness to external stimuli, the adoption of a typical posture, and the occupation of a sheltered site, all of which is usually repeated on a 24-hour basis. The physiological definition applies well to birds and mammals, but in other animals (whose brain is not as complex), the behavioural definition is more often used. In very simple animals, behavioral definitions of sleep are the only ones possible, and even then the behavioral repertoire of the animal may not be extensive enough to allow distinction between sleep and wakefulness.

Sleep in different species

Sleep in invertebrates

Caenorhabditis elegans is the most primitive organism in which sleep-like states have been observed.

Sleep as a phenomenon appears to have very old evolutionary roots. Here, a lethargus phase occurs in short periods preceding each moult, a fact which may indicate that sleep primitively is connected to developmental processes.

The electrophysiological study of sleep in small invertebrates is complicated. However, even such simple animals as fruit flies appear to sleep, and systematic disturbance of that state leads to cognitive disabilities. There are several methods of measuring cognitive functions in fruit flies. A common method is to let the flies choose whether they want to fly through a tunnel that leads to a light source, or through a dark tunnel. Normally, flies are attracted to light. But if sugar is placed in the end of the dark tunnel, and something the flies dislike is placed in the end of the light tunnel, the flies will eventually learn to fly towards darkness rather than light. Flies deprived of sleep require a longer time to learn this and also forget it more quickly. If an arthropod is experimentally kept awake longer than it is used to, then its coming rest period will be prolonged. In cockroaches that rest period is characterized by the antennae being folded down and by a decreased sensitivity to external stimuli. Sleep has been described in crayfish, too, characterized by passivity and increased thresholds for sensory stimuli as well as changes in the EEG pattern, markedly differing from the patterns found in crayfish when they are awake.

Sleep in fish and reptiles

Sleep in fishes is not extensively studied. Some species that always live in shoals or that swim continuously (because of a need for ram ventilation of the gills, for example) are suspected never to sleep. There is also doubt about certain blind species that live in caves. Other fish seem to sleep, however. For example, zebra fish, tilapia,  brown bullhead, and sharks become motionless and unresponsive at night (or by day, in the case of the swell shark); Spanish hogfish and blue-headed wrasse can even be lifted by hand all the way to the surface without evoking a response. A 1961 observational study of approximately 200 species in European public aquaria reported many cases of apparent sleep. On the other hand, sleep patterns are easily disrupted and may even disappear during periods of migration, spawning, and parental care.

Sleeping African Dwarf Fischer’s Chameleon

 A Komodo dragon sleeping.

In Reptiles , the electrical activity in the brain has been registered when the animals have been asleep. However, the EEG pattern in reptilian sleep differs from what is seen in mammals and other animals. In reptiles, sleep time increases following sleep, and stronger stimuli are needed to awaken the animals when they have been deprived of sleep as compared to when they have slept normally. This suggests that the sleep which follows deprivation is compensatory deeper.

Sleep in birds

A sleeping Cockatiel

There are significant similarities between sleep in birds and sleep in mammals, which is one of the reasons for the idea that sleep in higher animals with its division into REM and NREM sleep has evolved together with warm-bloodedness. Birds compensate for sleep loss in a manner similar to mammals, by deeper or more intense SWS (slow-wave sleep).

Birds have both REM and NREM sleep, and the EEG patterns of both have similarities to those of mammals. Different birds sleep different amounts, but the associations seen in mammals between sleep and variables such as body mass, brain mass, relative brain mass, basal metabolism and other factors (see below) are not found in birds. The only clear explanatory factor for the variations in sleep amounts for birds of different species is that birds who sleep in environments where they are exposed to predators have less deep sleep than birds sleeping in more protected environments.

A flamingo with at least one cerebral hemisphere awake

A peculiarity that birds share with aquatic mammals, and possibly also with certain species of lizards (opinions differ about that last point), is the ability for uni hemispheric sleep. That is the ability to sleep with one cerebral hemisphere at a time, while the other hemisphere is awake. When only one hemisphere is sleeping, only the contra lateral eye will be shut; that is, when the right hemisphere is asleep the left eye will be shut, and vice versa. The distribution of sleep between the two hemispheres and the amount of uni hemispheric sleep are determined both by which part of the brain has been the most active during the previous period of wake—that part will sleep the deepest—and it is also determined by the risk of attacks from predators. Ducks near the perimeter of the flock are likely to be the ones that first will detect predator attacks. These ducks have significantly more uni hemispheric sleep than those who sleep in the middle of the flock, and they react to threatening stimuli seen by the open eye.

Opinions partly differ about sleep in migratory birds. The controversy is mainly about whether they can sleep while flying or not. Theoretically, certain types of sleep could be possible while flying, but technical difficulties preclude the recording of brain activity in birds while they are flying.

Sleep in mammals

Sleep duration

Flying foxes, asleep

Different animals sleep different amounts. Some animals, such as bats, sleep 18–20 hours per day, while others, including giraffes, sleep only 3–4 hours per day. There can be big differences even between closely related species. There can also be differences between laboratory and field studies: for example, researchers in 1983 reported that captive sloths slept nearly 16 hours a day, but in 2008, when miniature neurophysiologic recorders were developed that could be affixed to wild animals, sloths in nature were found to sleep only 9.6 hours a day.

Sleeping polar bears

As for birds, the main rule for mammals (with certain exceptions, see below) is that they have two essentially different stages of sleep: REM and NREM sleep (see above). An animal’s feeding habits are associated with its sleep length. The daily need for sleep is highest in carnivores, lower in omnivores and lowest in herbivores. Humans do not sleep unusually much or unusually little compared to other animals, but we sleep less than many other omnivores. Many herbivores, like Ruminantia (such as cattle), spend much of their wake time in a state of drowsiness, which perhaps could partly explain their relatively low need for sleep. In herbivores, a direct correlation is apparent between body mass and sleep length; big animals sleep more than smaller ones. This correlation is thought to explain about 25% of the difference in sleep amount between different animals. Also, the length of a particular sleep cycle is associated with the size of the animal; on average, bigger animals will have sleep cycles of longer durations than smaller animals. Sleep amount is also coupled to factors like basal metabolism, brain mass and relative brain mass.

Mammals born with well-developed regulatory systems, such as the horse and giraffe, tend to have less REM sleep than the species which are less developed at birth, such as cats and rats. This appears to echo the greater need for REM sleep among newborns than among adults in most mammal species.

Comparative average sleep periods for various mammals in captivity over 24 hours have been given as: horses – 2.9 hours; elephants – 3 plus; cows – 4.0; giraffes – 4.5 hours; humans – 8.0; rabbits – 8.4; chimpanzees – 9.7; Red foxes – 9.8; dogs – 10.1; House mice – 12.5; cats – 12.5; lions – 13.5; platypuses – 14; chipmunks – 15; Giant armadillos – 18.1; and Little brown bats – 19.9 hours. Reasons given for the wide variations include the fact that mammals “that nap in hiding, like bats or rodents tend to have longer, deeper snoozes than those on constant alert.” Lions, which have little fear of predators also, have relatively long sleep periods, while elephants have to eat most of the time to support their huge bodies. Little brown bats conserve their energy except for the few hours each night when their insect prey are available and platypuses eat a high energy crustacean diet and, therefore, probably don’t need to spend as much time awake as many other mammals.

Sleep in monotremes

Since monotremes, egg-laying mammals are considered to represent one of the evolutionarily oldest groups of mammals – they have been subject to special interest in the study of mammalian sleep. As early studies of these animals could not find clear evidence for REM sleep, it was initially assumed that such sleep did not exist in monotremes but developed after the monotremes left the rest of the mammals and became a separate, distinct group. However, EEG registrations of the brain stem in monotremes show a firing pattern that is quite similar to the patterns seen in REM sleep in higher mammals. In fact, the largest amount of REM sleep known in any animal is found in the platypus. The average sleep time in a 24-hour period of a platypus is said to be as long as 14 hours. This may be because of their high-calorie crustacean diet.

Sleep in aquatic mammals

Northern sea pup with adult female and male, the largest of the eared seals. Habitat: the northern Pacific

Among others, seals and whales belong to the aquatic mammals. Seals are grouped in earless seals and eared seals, which have solved the problem of sleeping in water differently. Eared seals, like whales, show uni hemispheric sleep. The sleeping half of the brain does not awaken when they surface to breathe. When one half of a seal’s brain shows slow-wave sleep, the flippers and whiskers on its opposite side are immobile. While in the water, these seals have almost no REM sleep and may go a week or two without it. As soon as they move onto land they switch to bilateral REM sleep and NREM sleep comparable to land mammals, surprising researchers with their lack of “recovery sleep” after missing so much REM.

Cap fur seal, asleep in a zoo

Earless seals sleep bi hemispherical like most mammals, under water, hanging at the water surface or on land. They hold their breath while sleeping under water, and wake up regularly to surface and breathe. They can also hang with their nostrils above water and in that position have REM sleep, but they do not have REM sleep underwater.

REM sleep has been observed in the pilot whale, a species of dolphin. Whales do not seem to have REM sleep, nor do they seem to have any problems because of this. One reason REM sleep might be difficult in marine settings is the fact that REM sleep causes muscular atony; that is to say, a functional paralysis of skeletal muscles that can be difficult to combine with the need to breathe regularly.

Uni hemispheric sleep

Uni hemispheric sleep refers to sleeping with only a single cerebral hemisphere. The phenomenon has been observed in birds and aquatic mammals, as well as in several reptilian species (the latter being disputed: many reptiles behave in a way which could be construed as uni hemispheric sleeping, but EEG studies have given contradictory results). Reasons for the development of uni hemispheric sleep are likely that it enables the sleeping animal to receive stimuli – threats, for instance – from its environment, and that it enables the animal to fly or periodically surface to breathe when immersed in water. Only NREM sleep exists uni hemi spherically, and there seems to exist a continuum in uni hemispheric sleep regarding the differences in the hemispheres: in animals exhibiting uni hemispheric sleep, conditions range from one hemisphere being in deep sleep with the other hemisphere being awake to one hemisphere sleeping lightly with the other hemisphere being awake. If one hemisphere is selectively deprived of sleep in an animal exhibiting uni hemispheric sleep (one hemisphere is allowed to sleep freely but the other is awoken whenever it falls asleep), the amount of deep sleep will selectively increase in the hemisphere that was deprived of sleep when both hemispheres are allowed to sleep freely.

The neurobiological background for uni hemispheric sleep is still unclear. In experiments on cats, where the connection between the left and the right halves of the brain stem is severed, the brain hemispheres show a desynchronized EEG where the two hemispheres can sleep independently of each other. In these cats, the states where one hemisphere slept NREM and the other was awake, as well as one hemisphere sleeping NREM with the other state sleeping REM were observed. Interestingly, the cats were never seen to sleep REM sleep with one hemisphere while the other hemisphere was awake. This is in accordance with the fact that REM sleep, as far as is currently known, is not uni hemispheric

The fact that uni hemispheric sleep exists has been used as an argument for the necessity of sleep. It appears that no animal has developed an ability to go without sleep altogether.

Sleep in hibernating animals

Animals that hibernate are in a state of torpor, differing from sleep. Hibernation markedly reduces the need for sleep, but does not remove it. Hibernating animals end their hibernation a couple of times during the winter so that they can sleep.

http://en.wikipedia.org/wiki/Sleep_(non-human)

THE MYSTERY OF SLEEP
The question of the process and function of sleep throughout the animal kingdom is truly fascinating. Sleep occurs in animals as different as humans and flies. It’s obviously important: our bodies keep track of lost minutes of sleep and then try to make them up. The need for sleep can become irresistible even in the face of death, with many car accidents each year due to drowsy drivers. When completely deprived of sleep for too long, we sicken and die. We still don’t fully understand why sleep is so important – but we do know that it is a very active state. Contrary to previous assumptions, the brain is not resting- some nerve cells in our brains fire 5 to 10 times more frequently during certain sleep stages than during wakefulness.

As you probably suspect, most of what we know about sleep comes from studying mammals- but sleep probably is common to most of the animal kingdom. It sort of depends on how you define sleep. In the most broad terms we tend to say that sleep must have these four behavioural characteristics 1) minimal movement; 2) a typical sleep posture (e.g., for humans, lying down; for bats, hanging upside down); 3) reduced responsiveness to external stimulation (moderate noises don’t awaken you); and 4) quick reversibility of reduced responsiveness to relatively intense stimulation (distinguishing sleep from other states like death or coma). Certainly these have been observed in insects, frogs, reptiles, birds and of course mammals like us. When studying mammals or birds, we can more specifically define sleep and subdivide it into various classes by looking at brainwave patterns (EEG) and muscle activity patterns (EMG, EOG). These stages are called stage I-IV sleep and REM (rapid eye movement) sleep. Normally, animals progress through the stages of sleep in an orderly pattern of alternating REM and non-REM sleep. When you look at sleep according to these brainwave patterns instead of just the observed behaviours, things get pretty interesting! Some animals can sleep with eyes open, while moving, or with only half the brain at a time. Below, I’ve listed some of the wide variations in the style (posture) and the amount of total sleep, and the amount of REM sleep found among different animals.

2. VARIATION IN TOTAL SLEEP TIME IN MAMMALS

Mammal Total Daily Sleep Time (in hours)
Giraffe 1.9
Roe deer 3.09
Asiatic elephant 3.1
Pilot whale 5.3
Human 8.0
Baboon 9.4
Domestic cat 12.5
Laboratory rat 13.0
Lion 13.5
Bats 19.9

One theory proposes that how much an animal sleeps is largely determined by its status as prey or predator-that prey animals sleep less because they might get attacked. But it’s not clear that sleep increases vulnerability to predation, since the victims of predators are generally the very young, the sick, and the old, even when they are wide awake. A contrasting theory suggests that a major function of sleep is to protect animals from predation-to keep them out of harm’s way when they have satisfied their need for food etc. However, this doesn’t explain the unrelenting need to sleep even upon risk of death, or the pressure to retrieve “lost” sleep.

There seems to be a correlation between body size and the amount of sleep: small mammals tend to sleep more than large ones. But there are exceptions; some large animals (e.g., lions and tigers) sleep 14-16 hours per day, and dogs and cats sleep 10-12 hours, while some small animals (e.g., moles) sleep only 8 hours. The reason for the relationship between sleep have something to do with energy conservation, which is a bigger problem for small mammals (which carry little fat) than for larger ones. Sleep might help conserve energy, especially in smaller mammals which are in almost continuous danger of depleting their energy resources, by providing long periods of lowered metabolic activity to save energy. However, the metabolic rate during sleep is only about 10% lower than during quiet wakefulness, so one might wonder why mammals don’t simply rest, rather than sleep- there is clearly more to sleep than energy maintenance and avoiding predators.

3. Variation in sleep style/ posture/time of day

Humans Sleep in night, wake in the day (diurnal)
Mice Sleep in day, wake at night (nocturnal)
Some rodents and insects Sleep in night and day, wake at dawn and dusk (crepuscular)
Moles/rabbits Sleep in burrows
Zebras Sleep in the open
Cows Sleep with eyes open
Horses Sleep standing
Leopards Sleep on tree limb
Bats Sleep upside down
Seals/ Hippos Sleep underwater (part of the time)
Dolphins/porpoises Sleep with one half of the brain at a time to allow breathing while swimming/sleeping
Ducks/pigeons Sleep with one half of the brain while keeping one eye on predators
Migratory birds Sleep while flying across the ocean
Fruit flies/some fish Sleep-like rest periods with decreased movement, and altered threshold for stimuli.

4. Variation in rem/ non-rem sleep among animals

we’re familiar with the different states of being awake like running, eating, quietly resting, daydreaming, and studying. In sleep, there are also different states. Different types of brainwave activity are characteristic of the different stages of sleep. REM sleep is a sleep state where dreaming is most common, the eyes move wildly, and the body is totally limp (loss of muscle “tone”). Not only do all mammals sleep, but as a rule, they experience cyclical alternation between non-REM and REM sleep. An outstanding exception to this pattern is the echidna (spiny anteater-a small Australian monotreme), which is a mammal that bears its young from eggs, as birds and reptiles do. Echidnas have no REM sleep, only non-REM sleep. This is amazing since other mammals will die when totally deprived of just the REM type of sleep. Like mammals, birds have cycles of non-REM and REM sleep, but with some differences. One of the most striking differences is that both non-REM and REM sleep episodes are quite short in birds; their non-REM sleep episodes average only about 2 1/2 minutes, and REM sleep episodes only9 seconds. In contrast, non-REM and REM episodes in humans are much longer. At the start of the night, we have non-rem sleep for about 90 minutes followed by 8-10 minutes of REM. The REM episodes get longer through the night and by early morning, the non-REM episodes are about 10 minutes followed by 90 minutes of REM. Another difference is that most birds do not “go limp”(lose muscle tone) during REM sleep as mammals do, which is understandable, since many birds sleep while standing or perching. Although birds are thought to have evolved from reptiles, REM sleep has not been detected in reptiles and lower animals. This may be due to the fact that their brain structures are simpler. However we do know that a new neurotransmitter “HCRT” (hypocretin/ orexin) is important to sleep state control. Deficiency of HCRT causes the sleep disorder Narcolepsy in humans, and seems to particularly impact REM sleep. We know now that this neurotransmitter is present in animals as distant as frogs, and fish so it must also be in reptiles. Therefore, there are a couple of possibilities: perhaps REM sleep evolved independently in birds and mammals, to fulfil a function essential to more complex brains. Or perhaps part of the basis of REM sleep arose early in evolution, but we only recognize it in higher animals. The field of hypocretin/orexin research is moving really fast right now. We hope that understanding the molecules involved will help us to understand the function and process of sleep in animals as well as humans. 

http://www.madsci.org/posts/archives/2000-08/965504574.Zo.r.html

Do Thoughts have mass?

If so, can they influence the real world using the laws of physics? This is what Noetic scientists are trying to answer.

Noetic Sciences explores how on a quantum level we are affected and affect the world. This is a fascinating area of science and seeks to answer fundamental questions like – do thoughts have mass? / do thoughts have weight? / do thoughts have matter? So fascinating is this field that it is being used in bestseller books and movies. Just look at the new Dan Brown Book – The lost Symbol.

The Theory that thoughts have mass goes as follows: When a person thinks of something this brain activity is made up of electrical impulses. This Brain activity (electrical Impulses – or anything else) is then measured using ultra sensitive devices that measure minute changes in mass. Many People believe that they have proved thoughts have Mass in line with Einstein’s theories.

Can Thoughts having weight then influence the Real World?

Many people around the world have come across unexplained phenomenon. E.g. I’m sure we have all heard of the lady who had an inoperable cancerous tumor – she focused on imagining it getting smaller and smaller every day until it eventually disappeared. Did her thoughts impact the tumor and make her healthy? Such thought healing is referred to as Quantum Healing and is explained by the theory that thoughts have matter.

It is this same theory that says thoughts (which have mass or weight) can therefore have a real impact on the world. Something with mass can alter the real world! It is the underlying fundamental force in the universe we live in, the Theory of Relativity.

http://slotseeker.com/do-thoughts-have-mass/

Social Evolution

We have loosely used the informal concept of the “organism” as a distinct kind of living entity. We must recognize that this distinction is largely arbitrary and only useful in limited domains. A number of examples, such as viruses, beehives, slime molds, and other symbiotic and parasitic relationships threaten to blur the distinction between the living organism and the community as the elemental living system.

Yet if we assume the existence of distinct organisms, then the hierarchy of neural evolution is marked by a series of metasystem transitions within organisms. But at the same time, metasystem transitions also occur which bring organisms together in groups. Some simple examples include breeding populations and the dynamics of fish schools and bird flocks. When these group controls are very strong, some of the more marked transitions (e.g. the development of multicellular organisms) result.

But when the group controls are considerably weaker, we have the existence of societies of organisms. The most integrated form of such societies can be found in the social insects: ants, bees and termites. Human society is much less strongly integrated but much more complex. Higher-level societies are usually marked by culture, which can be defined simply as models which are inherited between organisms in a non-genetic manner. We can define such non-genetic information, when carried between people, as memes. Memes, similar to genes, undergo a variation and selection type of evolution, characterized by mutations and recombination of ideas, and by their spreading and selective reproduction or retention.

As outlined in our discussion of cognitive evolution, thought can be understood as the ability to control the production, reproduction and association of memes in the minds of humans. What follows is the possibility of evolution at the memetic level. The emergence of human thought marks the appearance of a new mechanism of evolution: conscious human effort instead of natural selection. The variation and selection necessary for the increase of complexity of the organization of matter now takes place in the human brain; it becomes inseparable from the willed act of the human being.

Thus the emergence of human intelligence and memetic evolution precipitated a further, currently ongoing, Metasystem Transition, which is the integration of people into human societies. Human societies are qualitatively different from societies of animals because of the ability of the human being to create (not just use) language. Language serves two functions: communication between individuals and modeling of reality. These two functions are, on the level of social integration, analogous to those of the nervous system on the level of integration of cells into a multicellular organism. The body of a society is the bodies of all people plus the things made by them. Its “physiology” is the culture of society.

Using the material of language, people make new symbolic models of reality (scientific theories, in particular) such as never existed as neural models given us by nature. Language is, as it were, an extension of the human brain. Moreover, it is a unitary common extension of the brains of all members of society. It is a collective model of reality that all members of society labor to improve, and one that preserves the experience of preceding generations.

http://pespmc1.vub.ac.be/SOCEVOL.html

What is the Human Genome Project?

Begun formally in 1990, the U.S. Human Genome Project was a 13-year effort coordinated by the U.S. Department of Energy and the National Institutes of Health. The project originally was planned to last 15 years, but rapid technological advances accelerated the completion date to 2003. Project goals

  • Identify all the approximately 20,000-25,000 genes in human DNA,
  • Determine the sequences of the 3 billion chemical base pairs that make up human DNA,
  • Store this information in databases,
  • Improve tools for data analysis,
  • Transfer related technologies to the private sector, and
  • Address the ethical, legal, and social issues (ELSI) that may arise from the project.

To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse.

What’s a genome? And why is it important?

genome is the entire DNA in an organism, including its genes. Genes carry information for making all the proteins required by all organisms. These proteins determine, among other things, how the organism looks, how well its body metabolizes food or fights infection, and sometimes even how it behaves.

DNA is made up of four similar chemicals (called bases and abbreviated A, T, C, and G) that are repeated millions or billions of times throughout a genome. The human genome, for example, has 3 billion pairs of bases.

The particular order of As, Ts, Cs, and Gs is extremely important. The order underlies all of life’s diversity, even dictating whether an organism is human or another species such as yeast, rice, or fruit fly, all of which have their own genomes and are themselves the focus of genome projects. Because all organisms are related through similarities in DNA sequences, insights gained from nonhuman genomes often lead to new knowledge about human biology.

What are some practical benefits to learning about DNA?

Knowledge about the effects of DNA variations among individuals can lead to revolutionary new ways to diagnose, treat, and someday prevent the thousands of disorders that affect us. Besides providing clues to understanding human biology, learning about nonhuman organisms’ DNA sequences can lead to an understanding of their natural capabilities that can be applied toward solving challenges in health care, agriculture, energy production, environmental remediation, and carbon sequestration.

Rapid progress in genome science and a glimpse into its potential applications have spurred observers to predict that biology will be the foremost science of the 21st century. Technology and resources generated by the Human Genome Project and other genomics research are already having a major impact on research across the life sciences.Some current and potential applications of genome research include

  • Molecular medicine
  • Energy sources and environmental applications
  • Risk assessment
  • Bio archaeology, anthropology, evolution, and human migration
  • DNA forensics (identification)
  • Agriculture, livestock breeding, and bio processing

 

Molecular Medicine

 

  • Improved diagnosis of disease
  • Earlier detection of genetic predispositions to disease
  • Rational drug design
  • Gene therapy and control systems for drugs

Technology and resources promoted by the Human Genome Project are starting to have profound impacts on biomedical research and promise to revolutionize the wider spectrum of biological research and clinical medicine. Increasingly detailed genome maps have aided researchers seeking genes associated with dozens of genetic conditions, including myotonic dystrophy, fragile X syndrome, neurofibromatosis types 1 and 2, inherited colon cancer, Alzheimer’s disease, and familial breast cancer.

On the horizon is a new era of molecular medicine characterized less by treating symptoms and more by looking to the most fundamental causes of disease. Rapid and more specific diagnostic tests will make possible earlier treatment of countless maladies.

Energy and Environmental Applications

 

  • Use microbial genomics research to create new energy sources (bio fuels)
  • Use microbial genomics research to develop environmental monitoring techniques to detect pollutants
  • Use microbial genomics research for safe, efficient environmental remediation
  • Use microbial genomics research for carbon sequestration

In 1994, taking advantage of new capabilities developed by the genome project, DOE initiated the Microbial Genome Program to sequence the genomes of bacteria useful in energy production, environmental remediation, toxic waste reduction, and industrial processing.

Despite our reliance on the inhabitants of the microbial world, we know little of their number or their nature: estimates are that less than 0.01% of all microbes have been cultivated and characterized. Microbial genome sequencing will help lay a foundation for knowledge that will ultimately benefit human health and the environment. The economy will benefit from further industrial applications of microbial capabilities.

Bio manufacturing will use nontoxic chemicals and enzymes to reduce the cost and improve the efficiency of industrial processes. Microbial enzymes have been used to bleach paper pulp, stone wash denim, remove lipstick from glassware, break down starch in brewing, and coagulate milk protein for cheese production. In the health arena, microbial sequences may help researchers find new human genes and shed light on the disease-producing properties of pathogens.

Risk Assessment

  • It assess health damage and risks caused by radiation exposure, including low-dose exposures
  • It assess health damage and risks caused by exposure to mutagenic chemicals and cancer-causing toxins
  • Reduce the likelihood of heritable mutations

Understanding the human genome will have an enormous impact on the ability to assess risks posed to individuals by exposure to toxic agents. Scientists know that genetic differences make some people more susceptible and others more resistant to such agents. Far more work must be done to determine the genetic basis of such variability. This knowledge will directly address DOE’s long-term mission to understand the effects of low-level exposures to radiation and other energy-related agents, especially in terms of cancer risk.

Bio archaeology, Anthropology, Evolution, and Human Migration

  • Study evolution through germ line mutations in lineages
  • Study migration of different population groups based on female genetic inheritance
  • Study mutations on the Y chromosome to trace lineage and migration of males
  • Compare breakpoints in the evolution of mutations with ages of populations and historical events

Understanding genomics will help us understand human evolution and the common biology we share with all of life. Comparative genomics between humans and other organisms such as mice already has led to similar genes associated with diseases and traits. Further comparative studies will help determine the yet-unknown function of thousands of other genes.

Comparing the DNA sequences of entire genomes of different microbes will provide new insights about relationships among the three kingdoms of life: archaebacteria, eukaryotes, and prokaryotes.

DNA Forensics (Identification)

  • Identify potential suspects whose DNA may match evidence left at crime scenes
  • Exonerate persons wrongly accused of crimes
  • Identify crime and catastrophe victims
  • Establish paternity and other family relationships
  • Identify endangered and protected species as an aid to wildlife officials (could be used for prosecuting poachers)
  • Detect bacteria and other organisms that may pollute air, water, soil, and food
  • Match organ donors with recipients in transplant programs
  • Determine pedigree for seed or livestock breeds
  • Authenticate consumables such as caviar and wine

Any type of organism can be identified by examination of DNA sequences unique to that species. Identifying individuals is less precise, although when DNA sequencing technologies progress further, direct characterization of very large DNA segments, and possibly even whole genomes, will become feasible and practical and will allow precise individual identification.

To identify individuals, forensic scientists scan about 10 DNA regions that vary from person to person and use the data to create a DNA profile of that individual (sometimes called a DNA fingerprint). There is an extremely small chance that another person has the same DNA profile for a particular set of regions.

Agriculture, Livestock Breeding, and Bio processing

  • Disease-, insect-, and drought-resistant crops
  • Healthier, more productive, disease-resistant farm animals
  • More nutritious produce
  • Bio pesticides
  • Edible vaccines incorporated into food products
  • New environmental cleanup uses for plants like tobacco

Understanding plant and animal genomes will allow us to create stronger, more disease-resistant plants and animals, reducing the costs of agriculture and providing consumers with more nutritious, pesticide-free foods. Already growers are using bioengineered seeds to grow insect- and drought-resistant crops that require little or no pesticide. Farmers have been able to increase outputs and reduce waste because their crops and herds are healthier.

Alternate uses for crops such as tobacco have been found. One researcher has genetically engineered tobacco plants in his laboratory to produce a bacterial enzyme that breaks down explosives such as TNT and dinitroglycerin. Waste that would take centuries to break down in the soil can be cleaned up by simply growing these special plants in the polluted area.

http://www.ornl.gov/sci/techresources/Human_Genome/project/about.shtml

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2 Comments

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