Ecology of Deep-Sea Hydrothermal Vents

Organic Evolution

Please discuss the pre-biotic conditions on planet earth. Why did it take approximately one half billion years before the earliest bacteria-like life evolved? Why did the formation of oxygen by photosynthesizers make such a difference on the planet? Specifically, why does it appear that the aerobic metabolic pathway is a mirror image of the photosynthetic pathway? What would have happened to this system if oxygen had been present on earth 4 billion years ago?

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Scientists believe that about 5 million years ago, the Solar System was filled with a plethora of hot gases and dust, swirling around a hot core. They think that once the core approached about 1 million degrees, the physics and chemical properties caused the gases to coalesce, forming the sun. During this time, there were millions and millions of asteroids. As these asteroids collided with one other, some combined and as their mass increased, gravity pulled more and more particles and debris in, and the planetoids became larger and larger until the planets of the solar system were formed. This was a process known as accreation, and over hundreds of millions of years, the solar system formed — the continual bombarding of asteroids changing the planets, forming the rings of Saturn, and the landscapes of others, including the moons — which were just smaller planetoids caught in the gravitational pull of the planet (Palmer, 2003).

The constant bombardment of these asteroids did two things: first, it released an enormous amount of energy onto the earth’s crust, causing it to melt in places. Second, by opening up chasms, radioactivity was released and caused mega-volcanoes to release molten rock and gases, which in turn reacted to even more of the asteroid bombardment. H2) was released from the meteorites and the crust, rising as a gas into the atmosphere, where it combined with CO2 and other cases, and formed dense clouds above the earth. The clouds acted as a kind of reflective shield above the planet, keeping solar heat from penetrating to the surface and evaporating any residual moisture. With this shield, a primitive atmosphere was formed, further protecting the planet from continual bombardment at the previous levels. Thus, with fewer impacts, a dense cloud shield, and the combination of gases, the earth began to cool a bit and rain pelted down cooling the molten rock from the volcanoes, thus creating lakes and the great oceans. A combination of heat, water, and wind then began to soften and eventually cause more of the geologic features familiar today (Fortey, 1999).

For years, scientists through that the early Earth had a reducing atmosphere in which molecules saturated with hydrogen atoms reduced other molecules. Now, most think that the early Earth was full of oxidants like CO2 and N2 — neutral and does not permit organic chemistry to occur. There are several theories about how life originated on earth, some more credible than others. We know that liquid water is essential in the biochemistry of living things, allowing a medium for the transport of molecules, but where might this have existed and been able to combine with other chemicals to form carbon-based life, and simple plants which would create other chemical reactions through photosynthesis?

Thermal Vents — One theory believes that life originated deep in the ocean around hydrothermal vents. The vents release hot cases from earth’s core, sometimes in excess of 600 degrees. Primitive bacteria, small worms and crabs survive in this environment today, suggesting that life may have begun here and then moved upward. Supporters of this theory believe that the organic molecules are formed in a gradient layer between the hot vent water and the ocean cold water (Van Dover, 2000).

Panspermia — Swedish chemist Svente Arrhenius developed a theory stating that life did not originate on earth, but elsewhere in the universe. Primitive cellular structures arrive through meteorite activity and since they were protected by being inside the meteorites, once they hit the earth the cells could have evolved and restructured (Hoyle and Wickramasinghe, 2000).

Frozen Ocean — Scientist Jeffery Bada of the Scripps Institution proposes that only the top 300 meters of the ocean would freeze during a thick cloud bank on the surface. The ice would shield prebiotic chemicals by preventing UV light through and allowing a safe place for life to incubate. The cooler temperatures and relative safety then encouraged organic chemical reactions (Bada and Wills, 2000),

It was essential though that primitive cells be able to develop into molecules that evolved a new strategy to use sunlight as an energy source. These cells took in sunlight, used the CO2 and H2O as raw materials produced organic molecules (carbohydrates). O2 was released as a waste product of photosynthesis, first bonding with limestone, iron and other minerals. Finally, though, once these minerals oxidized, O2 began to ooze into the atmosphere. As this O2 rose higher into the atmosphere, it changed chemically to form ozone, which was critical for development of carbon-based life b3ecause it absorbs a significant amount of ultraviolet radiation and allowed cells to colonize the ocean and eventually land. Without O2 and the resulting ozone layer, continued bombardment of the surface by intense UV light would have caused unsustainable levels of mutation in exposed cells. More than likely, without ozone, cellular structures would never have become stable enough to evolve into higher forms. Photosynthesis had another, critical impact. Oxygen was toxic; and probably much life on earth died out as its levels rose too high in what is termed the oxygen catastrophe. This occurred about 2,400 million years ago. While photosynthesis was producing oxygen both before and after this “event,” the difference was that before the catastrophe, organic matter and dissolved iron chemically captured any free oxygen. The Great Oxygenation Event (GOE) was the point when these minerals became saturated and could hold no more free O2; and the excess began accumulating in the atmosphere (Chaisson, 2005).

Thus, photosynthesis takes in CO2 and produces O2, while organic metabolism takes in O2 and respirates out CO2. Photosynthesis requires carbon dioxide and water, in the presence of sunlight, and results in oxygen and glucose. Cellular respiration requires oxygen and glucose, and forms the products of carbon dioxide, water, and ATP (energy). The mirror image of the process is likely synergism at its most basic — without one, the other would be suplerflous — but in combination they support the essence of life, and a way for the early earth to become populated with not only plants, but the precurors to animal life (Willis, 2001).


Bada and Wills. (2000). The Spark of LIfe. New York: Basic Books.

Chaisson, E. (2005, June). Early Cells. Retrieved October 2010, from Tufts University:

Fortey, R. (1999). Life:A natural history of the First Four Billion Years of Life on Earth. New York: Vintage.

Hoyle and Wickramasinghe. (2000). Astronomical Origins of Life. New York: Springer.

Palmer, D. (2003). Prehistory Past Revealed: The Four Billion Year History of Life on Earth. Los Angeles: University of California Press.

Van Dover, C. (2000). The Ecology of Deep-Sea Hydrothermal Vents. Princeton: Princeton University Press.

Willis, B. (2001, July). Photsynthesis and Cellular Respiration. Retrieved October 2010, from Worsleyschool:

Biologists have found that the majority of genetic code in higher animals appears to serve no function. These large sequences appear to be the result of mutations that led to insertions. Logically, there should be a cost to having extraneous DNA. What is this cost? Why does natural selection not act by favoring organisms without these extra sequences of nucleotides? How do you interpret the data on bacteria that tend to have small genomes and lower amounts of “Junk DNA”? Do extra copies of genes offer organisms any advantages? (hint: in your answer discuss Hox-gene complexes and their importance in the evolution of animal).

DNA is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription (Walker and Jones, 2003).

Noncoding DNA, also known as “junk DNA” describes portions of the DNA sequence that do not appear to have any presentable use — they do not encode for proteins, etc. In fact, in a most eukaryote cells, a rather large percentage of the total genome is noncoding DNA, but this varies between species. However, it is now a misnomer to call this material “junk,” because the more sophisticated we become at biochemistry, we find that many do have subtle biological functions, including the transcriptional and translational regulation of certain protein-coding sequences. Researchers also belive that other noncoding sequences have a likely, but unconfirmed function, as an inference from high levels of inherited tratis and natural selection processes (Masters, 2005, 163-5).

Researchers know that the amount of genomic DNA varies widely between organisms, as does the proportion of coding and non-coding DNA within these genomes. For instance, 98% of the human genome does not encode for protein sequences, but may still have vestigial uses. There are also a number of exceptions that may be the result of evolutionary processes that allowed for primitive organisms to even exist in the more hostile environment of early earth. For instance, an Amoeba dubia has 200 times the amount of DNA than humans; the puffer fish has a genome only about 1/8 the size of the human genome, yet has a comparable number of genes, but 90% of those are non-coding. Further, about 80% of human nucleotide bases may be transcribed, but transcription does not necessarily imply function (Pennisi, 2007).

Further, research shows that non-coding DNA may have an important biological function. Studies in comparative genomics reveals that some regions of noncoding DNA are considered to be highly conserved — sometimes millions of years — which implies that these regions are under strong evolutionary pressure for selection of positive traits. One interesting example is that of the genomes of humans and mice, which diverged from a common ancestor about 75 million years ago. Protein-coding DNA account for only about 20% of the conserved DNA, with the remaining majority appearing in noncoding regions (Ludwig, 2002).

Further, one of the key features of biological evolution is the conservation of energy. Why would an organism carry large amounts of unnecessary molecules that require energy if there was not a reason for their existence? Noncoding DNA must influence the behavior of other coding-DNA in ways not understood, or be the result of an evolutionary necessity. Recent studies have shown that, in fact, evolution has favored those species with large amounts of noncoding DNA because some of the “junk” actually form switches that do no encode proteins, but do regulate when and where genes are expressed (Carrol, 2008).

From and evolutionary standpoint, shared sequences of apparently non-functional DNA are a major line of evidence for the idea of common descent. For instance, the Hox genes are a set of transcription factors that specify segment identity — or whether a certain segment of the embryo will form the head, heart, abdomen, etc. It is sort of a digital body patterning, but the actual function of this gene shows tendencies as being highly conserved across long evolutionary distances. This can be demonstrated by showing that a fly can function quite well with a chicken HOX protein in place of its own. This essentially proves that, despite having lost a shared ancestor over 670 million years ago, a given Hox protein in chickens and flies are so similar that they can actually take each other’s place within the overall body system. Hox is so important (conserved because it lays out the basic format of an organism) that even a single mutation in the DNA of these genes has a drastic effect on the organism, proving these genes have changed relatively little over the last several million years (Gilbert, 2000).


Carrol, S.E. (2008). Regulating Evolution. Scientific American, 298(5), 60-7.

Chaisson, E. (2005, June). Early Cells. Retrieved October 2010, from Tufts University:

Gilbert, S. (2000, July). Homeotic Selector Genes. Retrieved October 2010, from National Institute of Health:

Ludwig, M. (2002). Functional Evolution of NonCoding DNA. Current Opinion in Genetics and Development, 12(6), 634-39.

Masters, C. (2005). DNA and Your Body: What You Need to Know About Biotechnology. New South Wales: UNSW Press.

Pennisi, E. (2007). DNA Study Forces Rethink of What It Means to be a Gene. Science, 316(5831), 1556-7.

Walker and Jones. (2003). Genes and DNA. Sooke, BC: Kingfisher Press.

The Cambrian explosion is the first and only time in the fossil record that complex highly diverse organisms appear without much evidence of ancestral forms. How do you explain this? In Origin of the Species, Darwin was a little unclear as to how he envisioned changes from one species into several. In some areas he spoke of a gradual change over a long period, but in his illustration, he implied that some species remained almost constant for a long time before a radical change. The debate has continued with two views being expressed as gradualism and punctuated evolution. Which view do you think has more data and why? In your answer, please refute the view that you think has the least evidence.

Charles Darwin was a British naturalist, most well-known for his Origin of Species, published when he was 50 years old. Originally intending to train for a medical education, Darwin’s interest in nature led him to neglect medicine and sign on as staff naturalist for a five-year scientific investigation on the HMS Beagle. Between his questions on the geological age and nature of the earth, coupled with his observations of the transmutation of species, particularly during the Beagle’s visit to South America’s Gallapagos Islands, he began to develop his theory of natural selection by 1838. A collegue of his, Alfred Russel Wallace, sent Darwin a manuscript early in 1858 that described a similar exploration of the theory of evolution, causing Darwin to agree to a joiont publication of the ideas at the Linnean Society in London. Darwin, of course, had written of the theory 15 years previous, but did not publish a book-length monograph until a year after the joint release (Darwin – A Life’s Work, 2006).

In science, evolution is one of the basic templates to understand the biology of an organism or ecological unit. It is the change in inherited traits of a population through a process called natural selection in which only the strongest traits are appropriately adapted to the environment, thus those traits from parents who live longer and are healthier are passed down to future generations. Evolution is the product of two opposing forces: variation in traits and mutation (Futuyma, Evolution). Darwin’s views convinced the scientific, and many others, that the world was not static. Instead, life is and has been continually evolving. One cannot imagine how much of a paradigm shift this was — it turned religion and philosophy around to the point that even in the 20th and 21st centuries the idea is considered so dangerous that it should be regulated in its dissemination, especially to children. Some see this explanation of life as the central organizing force that allows for complexity. Darwin’s natural selection is such a process that accounts for evolution to the point of both human minds and societies. Philosopher and cognitive scientist Daniel Dennett, in his 1995 book Darwin’s Dangerous Idea, says that:

Charles Darwin’s fundamental idea has inspired intense reactions ranging from ferocious condemnation to ecstatic allegiance, sometimes tantamount to religious zeal. Darwin’s theory has been abused and misrepresented by friend and foe alike. It has been misappropriated to lend scientific respectability to appalling political and social doctrines. It has been pilloried in caricature by opponents, some of whom would have it compete in our children’s schools with ‘creation science,’ a pathetic hodgepodge of pious pseudo-science. Almost no one is indifferent to Darwin, and no one should be (Dennett, 2005, 17-18).

That other important scholars were influenced by Darwin is undeniable. To Sigmund Freud, for instance, Darwin’s basic premise was less natural selection, which Freud did not agree wholeheartedly, but more the biological notations of the process of evolution — gradual change over time. Indeed, the premise of Freud’s work requires that there be an evolution of cognitive thinking, and certainly the development of the brain and function follows. Many of Freud’s theories, in fact, were based not just on clinical work, but on “biological and neuro-physiological assumptions of the day” (Sulloway, 1992).

Darwinism has, for some, been a major cause in the reduction of religiousituy in the 20th and 21st centuries. While it is true that Darwinism rejects all supernatual causations of change over time, he remained a Christian. His theory explains the adaptedness and diversity of the world in a materialist manner, neither empracing or requiring an outside creator. This changed scientific inquiry and thoght by removing God from the scientific equation, and making room for scientific explanation of natural phenomena. This view, called positivism, produced a powerful revolution of itself that allowed for huge leaps in physics, genetics, and medical science (Mayr, 1999).

This view certainly has not been confined to Western Europe — it is global. As the titular founder of the subject ot evolutionary biology, there is now a more secular view of life, and the processes surrounding it. More than anything else was perhaps Darwin’s set of principles that through evolution, most of life’s processes can be explained without the supernatual; that all individuals are unique (vital for education and civil rights); and that humans are indeed responsible for their own fate — whether positive or negative.. Evolutionary theory, in general, works in more than one manner. Classical evolution holds that species gradual change over time, adapting to their environment through genetic mutation and physical changes that favor those individuals who have the traits most suited for their current situation. Essentially, this means that a bird, for instance, who lives on an island that has more flowers than grains or berries will, overtime, evolve a different beak because the offspring that have longer beaks will be the ones to reproduce and pass on that trait.

Punctuated evolution (equilibrium), a theory from Stephen J. Gould and others, holds that rather than gradually, evolution gets a “kick start” with certain external or environmental changes (drastic weather, etc.). Instead of gradually over thousands of generations, then, it happens quickly (in genetic terms) over hundreds of generations. Stephen J. Gould (1941-2002), was a widely read historian of science, paleontologist, and evolutionary biologist who, in his career at the American Museum of Natural History, New York University, and Harvard, stimulated the lay person and scientist alike with a number of fascinating books about evolution and natural history. Scientifically, Gould was responsible for an addition to the Darwinian paradigm called Puntuated Equilibrium. This theory, developed with Niles Eldedge proposes that evolution is not gradual, but really the combination of long period of species stability, puntuated by dramtic instances of genetic mutation and species change. When evolution occures, it is localized in rare and rapid events that are proven by the fossil record, as well as a thorough study of natural history (Gould and Eldredge, 1972).

In fact, the best argument for Gould’s theory and against gradulatism is what we know through the fossil reord regarding the Cambrian explosion. This period was characterized by a relatively rapid appearance (in geological time) of most major phyla about 530 million years ago. This was also accompanied by a huge diversifaction of organisms; animals, phytopolanton, and microbes. Prior to this period, most organisms were simple and were composed of individual cells occasionally orgnixed into patters. However stable the period was prior to this, over the next 70-80 milliosn of years the rate of evolution acceleerted by a huge order of magnitude and the diverse nature of today’s life appeared. While the fossil record may be somewhat incomplete, the evidence is compelling that there was not a “gradualist” approach to this diversification, but instead an exention and experimentaiton in species. Too, this was likely the result of changes in the environment (more O2, for instance, allowing for larger bodies), massive glacial periods that “froze” genetic diversification for a time being, the evolution of the eye within the predator/prey relationship and the increase in plankton, again contributing to a more positive chemical environment (Tobin, 2001).


Darwin – A Life’s Work. (2006, November 19). Retrieved October, 2010, from American Musem of Natural History:

Dennett, D. (2005). Darwin’s Dangerous Idea: Evolution and Me. New York: Touchstone.

Gould and Eldredge. (1972). Puntuated Equilibria: An Alternative to Phyletic Gradualism. In T. e. Schopf, Models in Paleobiolgy (pp. 82-115). San Francisco, CA: Freeman, Cooper and Company.

Mayr, E. (1999, September 23). Darwin’s Influece on Modern Thought. Retrieved October, 2010, from University of Hamburg:

Sulloway, F. (1992). Freud: Biologist of the Mind. Boston: Harvard University Press.

Tobin, A. And J. Dusheck. (2001). Asking About Life. Belmont, CA: Cenage.

There are a number of invertebrates that switch sex during their life span. What are the advantages and disadvantages of this life cycle? Why do we not see more species that can switch from sexual to asexual reproduction and why do so few possess the ability to undergo sex changes during their lifespan? What are the limits, selective advantages and selective disadvantages to sex switching?

In biology, a hermaphrodite is a plant or animal that have reproductive organs normally associated with both male and female sexes. Invertebrates, for instance, typically do not have separate sexes. Hermaphroditism is a normal condition, enabling reproduction based on the elements of the population at hand. Sequential hermaphrodites (dichogamy) occur in species in which the individual is born as one sex, but later, depending on environmental pressures, can change to the alternate sex. It is quite likely that the basic reasons for this are shaped by natural selection and the environment in order to produce the largest possible number of offspring. These events, typically surrounding juvenile development and age of sexual maturity, depend on both the physical and ecological environments of the organism with the goal being survivorship (Mueller, Guo and Ayala, 1991).

Sequential hermaphrodites fall into two major templates:

Protandry — An organism is born as a male and then changes to a female. One example of this is the reef fish called the clownfish. This fish lives in symbiosis with sea anemones. Anemones typically contain a harem of clownfish: a large female, a smaller reproductive male, and even smaller non-reproductive males. If the female dies or is removed, the reproductive male will change sex and the largest of the non-reproductive males will mature and become reproductive. Fishing pressure can change when the switch occurs, since the larger fish are usually chosen first.

Protogyny- An organism is born as a female and then changes to a male. Another reef fish, the wrasse, have an uncommon life strategy. Two male types exist, an initial phase that does not look like a male and spawns with other females but are not territorial, rather they mimic females. Terminal phase males are territorial and have bright colors. While individuals are born as either male or female, they are not born as terminal phase males. Females and initial phase males can become terminal phase males. Usually, the most dominant female or initial phase male replaces any terminal phase male when those males die or abandon the school (Barrows, 2001, 317).

Evolutionarily, there seem to be both advantages and disadvantages to this type of behavior. It is advantageous in that switching sex allows a species to ensure a greater chance of reproduction in difficult or challenging environmental times. If there are environmental pressures that cause too many males or females to exist at a given time, the ability to switch sexes allows reproduction to occur regardless of the gender disposition originally intended. In some species of crayfish, the species is self-cloning, which is another advantage if there are no sexual partners around. They are also more flexible in times of dramatic environmental change and/or catastrope and are able to ensure the preservation of their species by promoting biodiversity, exchanging genetic material in various ways. Thus, the main advantage seems to be the ability to be assured of a reproductive partner.

It is interesting to note that sex switching rarely occurs in species that actively seek mates or have a perpensity to brood care, but more common in sedentary aquatic animals that simply shed their eggs into the environment. We can conclude, then that a disadvantage to sex switching is that it disallows specizliazations for mate attraction — specific traits of maleness or femaleness that not only define the species but result in the ability to not just have thousands of offspring hoping one will survive, but a few that are nurtured to maturity (Ricklefs and Whiles, 2007)


Barrows, E. (2001). Animal Behavior Desk Reference. Boca Raton, FL: CRC Press.

Mueller, Guo and Ayala. (1991). Density Dependent natural Selction and Trade-Offs in Life History Traits. Science, 253(1), 433-35.

Ricklefs and Whiles. (2007). The Economy of Nature: Data Analysis Update. New York: Macmillan.

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