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Example did the brain get finished before the heart, did the eyes get finished before the feet, did the lungs get finished before the blood veseles, did the muscles get finished befoore the skeloton?

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Is there anything in the computer simulation that wasn't clear or which you find objectionable?


Like I mentioned above, why is it that we don't find rabbit fossils in the pre-cambrian?

As a side question, do you think that all the species were created at some point in the past and have remained unchanged since then? Or do you recognise that there is DNA in cells, and that it mutates, and that even in the present day new strains of bacteria and other organisms are evolving all the time? I guess my question is, do you accept the fact that evolution is occurring incessantly even today, and if so how do you reconcile that with the belief that evolutionary processes didn't occur in the past?

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Since 1802, the evolution of a structure as complex as the projecting eye by natural selection has been said to be difficult to explain.[6] Charles Darwin himself wrote, in his Origin of Species, that the evolution of the eye by natural selection at first glance seemed "absurd in the highest possible degree". However, he went on to explain that despite the difficulty in imagining it, it was perfectly feasible:

...if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.[7]

He suggested a gradation from "an optic nerve merely coated with pigment, and without any other mechanism" to "a moderately high stage of perfection", giving examples of extant intermediate grades of evolution.[7]

Darwin's suggestions were soon proven to be correct, and current research is investigating the genetic mechanisms responsible for eye development and evolution.

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Early eyes


The basic light-processing unit of the eye is the photoreceptor, a specialized cell consisting of two molecules in a membrane: the opsin, a light-sensitive protein, surrounding the chromophore, a pigment that distinguishes colors. When a photon is absorbed by the chromophore, a chemical reaction causes the photon's energy to be transduced into electrical energy and relayed to the nervous system. These photoreceptor cells form part of the retina, a thin layer of cells that relays visual information,[16] as well as the light and daylength information needed by the circadian rhythm system, to the brain.

The earliest predecessors of the eye were photoreceptor proteins that sense light, found even in unicellular organisms, called "eyespots". Eyespots can only sense ambient brightness: they can distinguish light from dark, sufficient for photoperiodism and daily synchronization of circadian rhythms. They are insufficient for vision, as they can not distinguish shapes or determine the direction light is coming from. Eyespots are found in nearly all major animal groups, and are common among unicellular organisms, including euglena. The euglena's eyespot, called a stigma, is located at its anterior end. It is a small splotch of red pigment which shades a collection of light sensitive crystals. Together with the leading flagellum, the eyespot acts as a sort of directional eye, allowing the organism to move in response to light, often toward the light to assist in photosynthesis,[17][18] and to predict day and night, the primary function of circadian rhythms.

It is likely that a key reason eyes specialize in detecting a specific, narrow range of wavelengths on the electromagnetic spectrum—the visible spectrum—is because the earliest species to develop photosensitivity were aquatic, and only two specific ranges of electromagnetic radiation can travel through water, the most significant of which[clarify] is visible light. This same light-filtering property of water also influenced the photosensitivity of plants.[19][20][21]


The multicellular eyepatch gradually depressed into a cup, which first granted the ability to discriminate brightness in directions, then in finer and finer directions as the pit deepened. While flat eyespots were ineffective at determining the direction of light, as a beam of light would activate the exact same patch of photo-sensitive cells regardless of its direction, the "cup" shape of the pit eyes allowed very limited directional differentiation by changing which cells the lights would hit depending upon its angle. Pit eyes, which had arisen by the Cambrian period, were seen in ancient snails, and are found in some invertebrates living today, such as planaria. Planaria can slightly differentiate the direction and intensity of light because of their cup-shaped, heavily-pigmented retina cells, which shield the light-sensitive cells from exposure in all directions except for the single opening for the light. However, this proto-eye is still much more useful for detecting the absence or presence of light than its direction; this gradually changes as the eye's pit deepens and the number of photoreceptive cells grows, allowing for increasingly precise visual information.[17]


During the Cambrian explosion, the development of the eye accelerated rapidly, with radical improvements in image-processing and detection of light direction.[22] As certain organisms benefited from the dramatic advantages given by full-fledged eyes, many other organisms were forced to evolve similarly advanced eyes in order to compete. As a result, the majority of major developments in eyes are thought to have occurred over the span of only a few million years. In the book In the Blink of an Eye, Andrew Parker discusses a theory that the evolution of the eye was the catalyst for the Cambrian Explosion. [23]

The "pinhole camera" eye was developed as the pit deepened into a cup, then a chamber. By reducing the size of the opening, the organism achieved true imaging, allowing for fine directional sensing and even some shape-sensing. Eyes of this nature are currently found in the nautilus. Lacking a cornea or lens, they provide poor resolution and dim imaging, but are still, for the purpose of vision, a major improvement over the early eyespots.[24]

Overgrowths of transparent cells prevented contamination and parasitic infestation. The chamber contents, now segregated, could slowly specialize into a transparent humour, for optimizations such as colour filtering, higher refractive index, blocking of ultraviolet radiation, or the ability to operate in and out of water. The layer may, in certain classes, be related to the moulting of the organism's shell or skin.


The transparent cells over the pinhole eye's aperture split into two layers, with liquid in between. The liquid originally served as a circulatory fluid for oxygen, nutrients, wastes, and immune functions, allowing greater total thickness and higher mechanical protection. In addition, multiple interfaces between solids and liquids increase optical power, allowing wider viewing angles and greater imaging resolution. Again, the division of layers may have originated with the shedding of skin; intracellular fluid may infill naturally depending on layer depth.

Note that this optical layout has not been found, nor is it expected to be found. Fossilization rarely preserves soft tissues, and even if it did, the new humour would almost certainly close as the remains desiccated, or as sediment overburden forced the layers together, making the fossilized eye resemble the previous layout.


Vertebrate lenses are composed of adapted epithelial cells which have high concentrations of the protein crystallin. The refractive index gradient which makes the lens useful is caused by the radial shift in crystallin concentration in different parts of the lens, rather than by the specific type of protein: it is not the presence of crystallin, but the relative distribution of it, that renders the lens useful.[25]

It is biologically difficult to maintain a transparent layer of cells as sizes, therefore the thicknesses, gradually increased. Deposition of transparent, but nonliving, material eased the need for nutrient supply and waste removal. In trilobites, the material was calcite; in humans, the material is crystallin. A gap between tissue layers naturally forms a biconvex shape, which is optically and mechanically ideal for substances of normal refractive index. A biconvex lens confers not only optical resolution, but aperture and low-light ability, as resolution is now decoupled from hole size—which slowly increases again, free from the circulatory constraints.

Independently, a transparent layer and a nontransparent layer may split forward from the lens: a separate cornea and iris. (These may happen before or after crystal deposition, or not at all.) Separation of the forward layer again forms a humour, the aqueous humour. This increases refractive power and again eases circulatory problems. Formation of a nontransparent ring allows more blood vessels, more circulation, and larger eye sizes. This flap around the perimeter of the lens also masks optical imperfections, which are more common at lens edges. The need to mask lens imperfections gradually increases with lens curvature and power, overall lens and eye size, and the resolution and aperture needs of the organism, driven by hunting or survival requirements. This type is now functionally identical to the eye of most vertebrates, including humans.


"Backward" Illumination of Retina

The retina may revert on itself, forming a double layer. The nerves and blood vessels can migrate to the middle, where they do not block light, or form a blind spot on the retina. This type is seen in squids, which live in the dim oceans. In cats, which hunt at night, the retina does not revert. Instead a second, reflective layer (the tapetum) forms behind the retina. Light which is not absorbed by the retina on the first pass may bounce back and be detected. As a predator, the cat simply accommodates blind spots with head and eye motion.

Color vision

The ability to see colors presents distinct selective advantages for species, such as being better able to recognize predators, food and mates. As opsin molecules were subtly fine-tuned to detect different wavelengths of light, at some point, color vision developed when photoreceptor cells developed multiple pigments.[16] As a chemical instead of mechanical adaptation, this may have occurred at any of the early stages of the eye's evolution, and the capability may have disappeared and reappeared, as organisms became predator or prey. Similarly, night and day vision emerged when receptors differentiated into rods and cones, respectively.

Focusing mechanism

Some species move the lens back and forth, some stretch the lens flatter. Another mechanism regulates focusing chemically and independently of these two, by controlling growth of the eye and maintaining focal length. Note that a focusing method is not a requirement. As photographers know, focal errors increase as f-number decreases. Thus, countless organisms with small eyes are active in direct sunlight and survive with no focus mechanism at all. As a species grows larger, or transitions to dimmer environments, a means of focusing need only appear gradually.

[edit] In creationism and intelligent design

Some creationists have claimed that only intelligent design could create a structure as as the eye, claiming that it is irreducibly complex.[26] It has even been flamboyantly described as evolutionary biologists' "greatest challenge as an example of superb 'irreducible complexity' in God's creation".[27] However, it is easily shown that the eye is not irreducibly complex, refuting this argument.[24]

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Political interpretations
Caricature from 1871 Vanity Fair

Darwin’s theories and writings, combined with Gregor Mendel’s genetics (the “modern synthesis”), form the basis of all modern biology.[133] However, Darwin’s fame and popularity led to his name being associated with ideas and movements which at times had only an indirect relation to his writings, and sometimes went directly against his express comments.

Eugenics

For more details on this topic, see Eugenics.

Following Darwin’s publication of the Origin, his cousin, Francis Galton, applied the concepts to human society, starting in 1865 with ideas to promote “hereditary improvement” which he elaborated at length in 1869.[134] In The Descent of Man Darwin agreed that Galton had demonstrated the probability that “talent” and “genius” in humans was inherited, but dismissed the social changes Galton proposed as too utopian.[135] Neither Galton nor Darwin supported government intervention and thought that, at most, heredity should be taken into consideration by people seeking potential mates.[136] In 1883, after Darwin’s death, Galton began calling his social philosophy Eugenics.[137] In the 20th century, eugenics movements gained popularity in a number of countries and became associated with reproduction control programmes such as compulsory sterilisation laws,[138] then were stigmatised after their usage in the rhetoric of Nazi Germany in its goals of genetic “purity”.[V]

Social Darwinism

For more details on this topic, see Social Darwinism.

The ideas of Thomas Malthus and Herbert Spencer which applied ideas of evolution and “survival of the fittest” to societies, nations and businesses became popular in the late 19th and early 20th century, and were used to defend various, sometimes contradictory, ideological perspectives including laissez-faire economics,[139] colonialism,[140] racism and imperialism.[140] The term “Social Darwinism” originated around the 1890s, but became popular as a derogatory term in the 1940s with Richard Hofstadter’s critique of laissez-faire conservatism.[141] The concepts predate Darwin’s publication of the Origin in 1859:[140][142] Malthus died in 1834[143] and Spencer published his books on economics in 1851 and on evolution in 1855.[144] Darwin himself insisted that social policy should not simply be guided by concepts of struggle and selection in nature,[145] and that sympathy should be extended to all races and nations.[146][VI]

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Religious views

For more details on this topic, see Charles Darwin's views on religion.

Though Charles Darwin’s family background was Nonconformist, and his father, grandfather and brother were Freethinkers,[118] at first he did not doubt the literal truth of the Bible.[119] He attended a Church of England school, then at Cambridge studied Anglican theology to become a clergyman.[120] He was convinced by William Paley’s teleological argument that design in nature proved the existence of God,[121] but during the Beagle voyage he questioned, for example, why beautiful deep-ocean creatures had been created where no one could see them, or the problem of evil of how the ichneumon wasp paralysing caterpillars as live food for its eggs could be reconciled with Paley’s vision of beneficent design.[122] He was still quite orthodox and would quote the Bible as an authority on morality, but was critical of the history in the Old Testament.[123]


When investigating transmutation of species he knew that his naturalist friends thought this a bestial heresy undermining miraculous justifications for the social order, the kind of radical argument then being used by Dissenters and atheists to attack the Church of England’s privileged position as the established church.[124] Though Darwin wrote of religion as a tribal survival strategy, he still believed that God was the ultimate lawgiver.[125] His belief dwindled, and his grief at the death of his daughter Annie in 1851 made him more certain in his scepticism.[126] He continued to help the local church with parish work, but on Sundays would go for a walk while his family attended church.[127] He now thought it better to look at pain and suffering as the result of general laws rather than direct intervention by God.[128] When asked about his religious views, he wrote that he had never been an atheist in the sense of denying the existence of a God, and that generally “an Agnostic would be the more correct description of my state of mind.”[129]

The “Lady Hope Story”, published in 1915, claimed that Darwin had reverted back to Christianity on his sickbed. The claims were refuted by Darwin’s children and have been dismissed as false by historians.[130] His daughter, Henrietta, who was at his deathbed, said that he did not convert to Christianity.[131] His last words were, in fact, directed at Emma: “Remember what a good wife you have been.”[132]

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Roving Defender of Evolution, and of Room for God

SCIENCE AND THEOLOGY Francisco J. Ayala says that belief in evolution does not necessarily rule out belief in God.

An evolutionary biologist and geneticist at the University of California, Irvine, he speaks often at universities, in churches, for social groups and elsewhere, usually in defense of the theory of evolution and against the arguments of creationism and its ideological cousin, intelligent design.

Usually he preaches to the converted. But not always.

As challenges to the teaching of evolution continue to emerge, legislators debate measures equating the teaching of creationism with academic freedom and a new movie links Darwin to evils ranging from the suppression of free speech to the Holocaust, “I get a lot of people who don’t know what to think,” Dr. Ayala said. “Or they believe in intelligent design but they want to hear.”

Dr. Ayala, a former Dominican priest, said he told his audiences not just that evolution is a well-corroborated scientific theory, but also that belief in evolution does not rule out belief in God. In fact, he said, evolution “is more consistent with belief in a personal god than intelligent design. If God has designed organisms, he has a lot to account for.”

Consider, he said, that at least 20 percent of pregnancies are known to end in spontaneous abortion. If that results from divinely inspired anatomy, Dr. Ayala said, “God is the greatest abortionist of them all.”

Or consider, he said, the “sadism” in parasites that live by devouring their hosts, or the mating habits of insects like female midges, tiny flies that fertilize their eggs by consuming their mates’ genitals, along with all their other parts.

For the midges, Dr. Ayala said, “it makes evolutionary sense. If you are a male and you have mated, the best thing you can do for your genes is to be eaten.” But if God or some other intelligent agent made things this way on purpose, he said, “then he is a sadist, he certainly does odd things and he is a lousy engineer.”

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A New Step In Evolution

Category: Microcosm: The Book
Posted on: June 2, 2008 9:41 PM, by Carl Zimmer

One of the most important experiments in evolution is going on right now in a laboratory in Michigan State University. A dozen flasks full of E. coli are sloshing around on a gently rocking table. The bacteria in those flasks has been evolving since 1988--for over 44,000 generations. And because they've been so carefully observed all that time, they've revealed some important lessons about how evolution works.

The experiment was launched by MSU biologist Richard Lenski. I wrote about Lenski's work last year in the New York Times, and in more detail my new book Microcosm. Lenski started off with a single microbe. It divided a few times into identical clones, from which Lenski started 12 colonies. He kept each of these 12 lines in its own flask. Each day he and his colleagues provided the bacteria with a little glucose, which was gobbled up by the afternoon. The next morning, the scientists took a small sample from each flask and put it in a new one with fresh glucose. And on and on and on, for 20 years and running.

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After 33,127 generations Lenski and his students noticed something strange in one of the colonies. The flask started to turn cloudy. This happens sometimes when contaminating bacteria slip into a flask and start feeding on a compound in the broth known as citrate. Citrate is made up of carbon, hydrogen, and oxygen; it's essentially the same as the citric acid that makes lemons tart. Our own cells produce citrate in the long chain of chemical reactions that lets us draw energy from food. Many species of bacteria can eat citrate, but in an oxygen-rich environment like Lenski's lab, E. coli can't. The problem is that the bacteria can't pull the molecule in through their membranes. In fact, their failure has long been one of the defining hallmarks of E. coli as a species.

If citrate-eating bacteria invade the flasks, however, they can feast on the abundant citrate, and their exploding population turns the flask cloudy. This has only happened rarely in Lenski's experiment, and when it does, he and his colleagues throw out the flask and start the line again from its most recently frozen ancestors.

But in one remarkable case, however, they discovered that a flask had turned cloudy without any contamination. It was E. coli chowing down on the citrate. The researchers found that when they put the bacteria in pure citrate, the microbes could thrive on it as their sole source of carbon.

In nature, there have been a few reports of E. coli that can feed on citrate. But these oddballs all acquired a ring of DNA called a plasmid from some other species of bacteria. Lenski selected a strain of E. coli for his experiments that doesn't have any plasmids, there were no other bacteria in the experiment, and the evolved bacteria remain plasmid-free. So the only explanation was that this one line of E. coli had evolved the ability to eat citrate on its own.

Blount took on the job of figuring out what happened. He first tried to figure out when it happened. He went back through the ancestral stocks to see if they included any citrate-eaters. For the first 31,000 generations, he could find none. Then, in generation 31,500, they made up 0.5% of the population. Their population rose to 19% in the next 1000 generations, but then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.

This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. The first mutation (or mutations) allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.

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Now the scientists must determine the precise genetic steps these bacteria took to evolve from glucose-eaters to citrate-eaters. In order to eat a particular molecule, E. coli needs a special channel in its membranes through which to draw it. It's possible, for example, that a channel dedicated to some other molecule mutated into a form that could also take in citrate. Later mutations could have fine-tuned it so that it could suck in citrate quickly.

If E. coli is defined as a species that can't eat citrate, does that mean that Lenski's team has witnessed the origin of a new species? The question is actually murkier than it seems, because the traditional concept of species doesn't fit bacteria very comfortably. (For the details, check out my new article on Scientific American, "What is a Species?" In nature, E. coli swaps lots of genes with other species. In just the past 15 years or so, for example, one disease-causing strain of E. coli acquired hundreds of genes not found in closely related E. coli strains. (See my recent article in Slate.) Another hallmark of E. coli is its ability to break down lactose, the sugar in milk. But several strains have lost the ability to break it down. (In fact, these strains were originally given a different name--Shigella--until scientists realized that they were just weird strains of E. coli.)

Nevertheless, Lenski and his colleagues have witnessed a significant change. And their new paper makes clear that just because the odds of such a significant change are incredibly rare doesn't mean that it can't happen. Natural selection, in fact, ensures that sometimes it does. And, finally, it demonstrates that after twenty years, Lenski's invisible dynasty still has some surprises in store.