The Design of Life

For two hundred years, scientists have believed that the eyespots of butterflies and moths evolved to look like large eyes in order to frighten off predators. A bird might think that the bright eyespots are the eyes of a concealed cat, for example.

It sounds logical, but there is a hidden assumption: We are assuming that a predator such as a bird pays attention to the same features that we would. But does it?

Cambridge behavioral ecologist Martin Stevens and his team decided to test the longstanding assumption: They nailed paper moths to trees in Cambridgeshire, with a mealworm stuck to each one, to attract birds.

Some of the paper moths also had bright spots that looked like eyes, but others had bright spots such as bars and squares that did not look like eyes.

The researchers reasoned that if the longstanding assumption was correct, then birds such as blackbirds, and house sparrows would avoid the moths whose spots looked most like big eyes.

But that is not what happened.

Birds came to eat the "moths" at the same rate, whether their spots looked like eyes (at least to a human) or not.

However, paper moths that had lots of spots were attacked 30% less often than others. Also large spots were more effective than small ones.

The researchers concluded that the theory that eyespots evolved to look like eyes has no experimental support. Rather, the spots deter birds just by being colourful and conspicuous.

Dr. Stevens offers a suggestion as to why conspicuous spots deter predators: They suggest that the insect might be poisonous. He told New Scientist, "Predators tend to stay away from highly conspicuous prey, possibly because most conspicuous objects in nature are toxic," says Stevens. "We think this is the primary eyespot effect."

He does not rule out the idea that some eyespots evolved to look like eyes. He offers the hawkmoth caterpillar, whose eyes may look like snakes, as an example.

See also

• Butterfly "stare" doesn't intimidate birds (New Scientist, March 8, 2008)
• Insect "eyespots" don't mimic eyes, study says" by Anne Casselman (National Geographic News, February 22, 2008)
• "Zoologists Challenge Longstanding Theory That 'Eyespots' Mimic The Eyes Of Predators' Enemies" ScienceDaily (Feb. 28, 2008)

Journal reference: Conspicuousness, not eye mimicry, makes ‘‘eyespots’’ effective antipredator signals (Martin Stevens, Chloe J. Hardman, and Claire L. Stubbins) Behavioral Ecology doi:10.1093/beheco/arm162

Abstract: Many animals bear colors and patterns to reduce the risk of predation from visually hunting predators, including warning colors, camouflage, and mimicry. In addition, various species possess paired circular features often called "eyespots," which may intimidate or startle predators preventing or postponing an attack. Most explanations for how eyespots work assert that they mimic the eyes of the predators own enemies. However, recent work has indicated that spots may reduce the risk of predation based purely on how conspicuous they are to a predator's visual system. Here, we use a field technique involving artificial prey marked with stimuli of various shapes, numbers, and sizes, presented to avian predators in the field, to distinguish between the eye mimicry and conspicuousness theories. In 3 experiments, we find that the features which make effective antipredator wing markings are large size and higher numbers of spots. Stimuli with circles survived no better than those marked with other conspicuous shapes such as bars, and changing the spatial construction of the spots to increase the level of eye mimicry had no effect on the protective value of the spots. These experiments support other recent work indicating that conspicuousness, and not eye mimicry, is important in promoting avoidance behavior in predators and that eyespots on real animals need not necessarily, as most accounts claim, mimic the eyes of other animals.

Key words: antipredator, conspicuousness, eyespots, mimicry, predation, vision.

(Note: The image of a, common Buckeye found at Toronto Island, is from the Government of Canada's online listing of the butterflies of Canada. The insect is pictured with both wing faces.)

A  passage from Daniel Levitin's This Is Your Brain On Music notes the complexity of the human mind, as relates to thought and music processing, in a way that students can understand": It is difficult to appreciate the complexity of the brain because the numbers are so huge they go well beyond our everyday experience (unless you are a cosmologist). The average brain consists of one hundred billion (100,000,000,000) neurons. Suppose each neuron was one dollar, and you stood on a street corner trying to give dollars away to people as they passed by, as fast as you could hand them out- let's say one dollar per second. If you did this twenty-four hours a day, 365 days a year, without stopping, and if you had started on the day that Jesus was born, you would by the present day only have gone through about two thirds of your money. Even if you gave away hundred-dollar bills once a second, it would take you thirty-two years to pass them all out. This is a lot of neurons, but the real power and complexity of the brain (and of thought) comes through their connections. Each neuron is connected to other neurons- usually one thousand to ten thousand others. Just four neurons can be connected in sixty-three ways, or not at all, for a total of sixty-four possibilities. As the number of neurons increases, the number of possible connections grows exponentially...The number of combinations becomes so large that it is unlikely we will ever understand all the possible connections in the brain, or what they mean. The number of combinations possible- and hence the number of possible different thoughts or brain states each of us can have- exceeds the number of known particles in the entire known universe." (Levitin, pp.85-86)

Most of us, far from overestimating our brains, probably underestimate them. It's not magic, but it is reality.

Students' brains will not do everything they (or we) want, but they will do far more than they sometimes expect.

A fascinating article by Judith Thurman, "First Impressions: What does the world’s oldest art say about us?" (June 23, 2008) in The New Yorker explores the attempts we make to understand the artworks left by humans drawing on the walls of caves thousands of years ago. She reflects on the Chauvet paintings found in south central France. These oldest known paintings predate the Lascaux and Altamira friezes by fifteen to eighteen thousand years. The history of interpretation of older artworks has suffered from too-ready assumptions about "primitive" people, in particular that, as mud slowly morphed into mind, art would gradually become more sophisticated. For example, He had also made the Darwinian assumption that the most ancient art was the most primitive, and [i]n that respect, Chauvet was a bombshell. It is Aurignacian, and its earliest paintings are at least thirty-two thousand years old, yet they are just as sophisticated as much later compositions. What emerged with that revelation was an image of Paleolithic artists transmitting their techniques from generation to generation for twenty-five millennia with almost no innovation or revolt. A profound conservatism in art, Curtis notes, is one of the hallmarks of a “classical civilization.” For the conventions of cave painting to have endured four times as long as recorded history, the culture it served, he concludes, must have been “deeply satisfying”—and stable to a degree it is hard for modern humans to imagine. Also, curiously in the light of the notion of the "violent brute" cave man, No human conflict is recorded in cave art, although at three separate sites there are four ambiguous drawings of a creature with a man’s limbs and torso, pierced with spearlike lines. More pertinent, perhaps, is a famous vignette in the shaft at Lascaux. It depicts a rather comical stick figure with an avian beak or mask, a puny physique, and a long skinny penis. He and his erect member seem to have rigor mortis. He is flat on his back at the feet of an exquisitely realistic wounded bison, whose intestines are spilling out. The bison’s glance is turned away, but it might have an ironic smile. Could the subject be hubris? Whatever it represents, some mythic contest—and the struggle of prehistorians to interpret their subject is such a contest—has ended in a draw. Her descriptions are beautiful, A great frieze covers the back left wall: a pride of lions with Pointillist whiskers seems to be hunting a herd of bison, which appear to have stampeded a troop of rhinos, one of which looks as if it had fallen into, or is climbing out of, a cavity in the rock. As at many sites, the scratches made by a standing bear have been overlaid with a palimpsest of signs or drawings, and one has to wonder if cave art didn’t begin with a recognition that bear claws were an expressive tool for engraving a record—poignant and indelible—of a stressed creature’s passage through the dark. and I will spoil no more of them for you. A fierce controversy rages over how exactly to interpret the art and its purpose - or whether one should attempt to interpret it at all. One archaeologist defended his interpretation as follows: Clottes was hurt and outraged by the rancor of the attacks that greeted “The Shamans of Prehistory” (“psychedelic ravings,” one critic wrote), and the authors defended themselves in a subsequent edition. “You can advance a scientific hypothesis without claiming certainty,” Clottes told me one evening. “Everyone agrees that the paintings are, in some way, religious. I’m not a believer myself, and I’m certainly not a mystic. But Homo sapiens is Homo spiritualis. The ability to make tools defines us less than the need to create belief systems that influence nature. And shamanism is the most prevalent belief system of hunter-gatherers.” Influence nature, yes, but we also need to understand and interpret nature. Probably the most important thing that the cave paintings tell us about ourselves is that the mind seems to have emerged rather suddenly, not by a long series of increments, a point that Mario Beauregard and I discuss in The Spiritual Brain. Tour the caves, courtesy France's culture ministry. The image above is but one of many you can click on. Also tour Lascaux here (at Virtual visit) and view Altamira images here.

Historically, we have always assumed that an amputated finger, for example, could not be regenerated. However, medical scientists are now finding that certain cells actually have the necessary information for regeneration. The can even share this capability with other cells, tissues, and organs. The secret is coaxing them to do it, and this informative CBS report highlights significant advances: Here is the YouTube link and here's the Tube:

The scientists, it should be noted, are not creating this ability; the information was there in the cell already, but special techniques are required to enable it to be used.

In "First Detailed Map of the Human Cortex" in MIT's Technology Review, Emily Singer notes, "A new imaging technique reveals previously hidden brain structures, including the central hub" and explains, The first high-resolution map of the human cortical network reveals that the brain has its own version of Grand Central Station, a central hub that is structurally connected to many other parts of the brain. Scientists generated the map using a new type of brain imaging known as diffusion imaging. The technique maps the largely inaccessible tangle of the brain's white matter--the long, thin fibers that ferry nerve signals between cells. and we also learn, Conventional imaging techniques, such as structural magnetic resonance imaging (MRI), reveal major anatomical features of the brain. But in humans, the brain's finer architecture--the neural projections that connect its different parts--has, until recently, remained hidden. "The brain we've been looking at with conventional MRI or CT scans all these years is not the real brain," says Van Wedeen, a neuroscientist at Massachusetts General Hospital, in Boston, who was also involved in the study. "We're just seeing a shadow of its surfaces."

The notion of the "real" brain vs. "a shadow of its surfaces" is an intriguing one.

Probably, we will never find the "real" brain for the same reasons as we never find the "real" Grand Central Station or the real Canada. There is a physical reality that corresponds to Grand Central Station and one that corresponds to Canada. But usually, what we find is a series of overlapping material and immaterial things whose "reality" can only be understood as a series of generalities - the reality is not any one of the generalities nor even all of them together, nor only in specific things we can point to. Perhaps it will always be much easier to find the answers to specific questions about the brain than to find - and take in - the "real" brain.

Here’s another great animation of life inside the body and the cell, from Hybrid Medical Animations. They enter the realm of high art, achieving a combination of Truth and Beauty ... - from an unidentified endorsement The music is well suited too. I wrote to the friend who drew it to my attention,

Medical animations are quite helpful because many people still believe the “brick theory of the cell.” = that the body is built out of cells as a wall is of bricks, with the brick being less organized than the wall.

 But the cell is something between a factory and a supercomputer.

The remarkable thing is that the wretched caterpillar I found on a rosebud and threw to the wolf spider was like that. As is the spider itself.

One realizes that Darwin’s explanation for how all this came to be is not even relevant. Darwin argued that it all happened because the stronger life form survives to breed.

That, of course, is doubtless true, but it is not going to give you a supercomputer! – d.

(Note: The video starts a couple of seconds after you access the page.) Note to teachers: Teachers may wish to point out to students who have questions in this area that scientists in Darwin's and Huxley's day thought that the cell was a very simple unit that related to the body as the brick does to a wall. They thought that the question they needed to answer was, How might a structure like a wall might be built? The question we really need to answer is, how might a structure like a supercomputer be built? You will find the chapter on "specified complexity" in The Design of Life helpful in introducing students to "information" as a science concept.

British physicist David Tyler points to a recent paper by L. Vogt in the journal Cladistics which explains why attempts to construct a tree of life are generally unfalsifiable:

Putting this in more popular language, cladists have adopted a variety of rationales to justify giving weight and credence to their evolutionary trees, but these rationales do not survive critical scrutiny if the test is Popper's demarcation criterion for science.

[ ... ]

The debates within evolutionary circles are always about specifics: the broader issues are not debated because they have an axiomatic status. So, evolutionary theorists do not have the mental tools that would allow them to disprove common ancestry, or whether design inferences are warranted. Consequently, it is not unreasonable to conclude, from the perspective of empirical science, that proposed evolutionary scenarios represent not "scientific but metaphysical hypotheses".

The Vogt paper suggests that the common science criterion that a theory should be falsifiable (able to be shown to be incorrect) be abandoned where evolution is concerned.

At the Molecular and Cell Biology Learning Center, you will find a Virtual Cell Animation Collection: In addition to Virtual Cell's online game modules, animations have been developed to introduce students to new concepts. By walking through the still images and movies included for each topic, viewers can easily choose between either studying a specific step from one of the processes or taking a more immersive look at the process in it's entirety. In order to better serve all levels of educational interest, each topic is being offered with a choice between two approaches: A great way to learn about protein traffic, photosynthesis, and transcription of genes.

A recent article in Science Daily would have us believe that Richard Dawkins's "selfish gene" (that supposedly drives behaviour) really exists: Since renowned British biologist Richard Dawkins ("The God Delusion") introduced the concept of the 'selfish gene' in 1976, scientists the world over have hailed the theory as a natural extension to the work of Charles Darwin. In studying genomes, the word 'selfish' does not refer to the human-describing adjective of self-centered behavior but rather to the blind tendency of genes wanting to continue their existence into the next generation. Ironically, this 'selfish' tendency can appear anything but selfish when the gene does move ahead for selfless and even self-sacrificing reasons. Here's what researchers, Peter Oxley of the University of Sydney in Australia and University of Western Ontario (Canada) biology professor Graham Thompson actually did: They isolated a region of the honey bee genome that appears responsible for the fact that worker bees (always females) do not mate, but rather leave that task to one among their number who becomes the queen, who spends her life mating with non-working males (drones) and laying eggs. Still, "This basically provides a validation for a huge body of socio-biology," says Thompson, who adds the completion of Honey Bee Genome Project in 2006 was crucial to this discovery. Huh? This article is a classic in using just about any finding in nature to try to support a questionable, pre-existing materialist belief - in this case a belief in the "selfish gene" that is supposedly "wanting to continue its existence." People don't - according to materialist theory - have actual minds, but genes supposedly do? or something? In the real world, scientists have long inferred that a gene or group of genes is associated with the fact that most female honeybees do not mate but instead gather food and raise the eggs laid by their queen. The identification of the region in which the gene occurs does not provide support for a theory about the "selfish gene," and certainly not for the controversial field of "sociobiology," as applied to explanations of human behaviour. We can look long and hard for any such gene in human beings. As a scientist friend told me, Don’t try to make sense of this, it makes no sense at all. Even the modest discovery that they seem to have made, the gene involved in worker sterility, doesn’t seem to be nailed down. It is incredible what you can get away with if you don’t do much but provide some tenuous breath of hope for a doubtful theory associated with Darwinism. In this case, the connection is not logically there, but who cares? Sounds like good advice to me. Note: This image is from statesymbols.org - the honeybee is the agricultural symbol of the American state of Tennessee.

British biomedical researcher Angelique Corthals thinks researchers (and their supporters at the Discovery Channel) who are trying to identify the remains of Egyptian pharaohs might as well be working for CBS’s fictional Cold Case drama, rather than in the lab.

 In 2007 Corthals, a lecturer at the University of Manchester’s Centre for Biomedical Egyptology, told news media, "I think the people at the Discovery Channel went way too much 'CSI.'”

 “They think you can pick up evidence at 2 p.m. and by 6 p.m. you get results,'' added Corthals, who has helped Egypt establish the DNA lab. But US-based Discovery Channel thinks otherwise, and has put considerable funds into the enterprise.

Thanks to a $5 million laboratory provided by Discovery in 2007, the Egyptian mummy identification team led by Zahi Hawass, Egypt’s Undersecretary of the State for the Giza Monuments, has facilities that have not available to researchers in Egypt before.

According to outfitter Applied Biosystems, a Discovery partner, the new lab is the "first laboratory in Egypt dedicated to testing ancient DNA samples."

Actually, the writers of Cold Case probably wouldn’t touch a script this old: using  DNA testing to identify a 3,500 year old corpse found in the Valley of the Kings? But it’s a great way to learn about DNA - what it might and might not tell us, and why.

Is the Corpse really Thutmose I?

Researchers at the Egyptian Museum in Cairo are using DNA analysis and X-rays to identify a mummy from the Valley of the Kings at Luxor, which they think might be the famous Pharaoh Thutmose 1.

Thutmose I was a commoner who, on becoming pharaoh, distinguished himself by his building projects and military campaigns around 1500 B.C.

The search for Thutmose I began in earnest when the mummy, a male in his early thirties who was formerly identified as Thutmose, turned out to be an imposter.

How did Egyptologists know? The mummy previously on display died from an arrow wound to his chest and there is no record of Thutmose dying from such a wound. In any event, Thutmose I (approximately 1506 to 1493 BC), who was father to both Thutmose II  and the female Pharaoh, Hatshepsut, is thought to have been well past 50 when he died.

 While most events from the ancient world have not been recorded, the lives and deaths of pharaohs were recorded in considerable detail. Experts think that some unknown person was buried in Thutmose I's tomb and that the mummy of the real Thutmose I got lost a few thousand years ago, thanks to palace intrigue and rivalries.

While that sounds strange, it is not as strange as we might at first suppose. A constant threat for ancient royal families was grave robbers. Indeed, most tombs were looted in antiquity. Families, seeking peace for their dead, were known to bury someone else in the "official" tomb. One of Thutmose I's successors is thought to have removed him from his original tomb.

While the mummy of the real Thutmose I was widely believed to be lost forever, a sharp-eyed 19th century Egyptologist, Gaston Maspero, noticed that an anonymous mummy in Egypt’s vast collection, labelled #5283, looked like the mummies of Thutmose I’s son and grandson: Thutmose II and Thutmose III. Could he in fact be Thutmose I?

However, the matter was not pursued, so the other mummy remained on display at the Egyptian Museum for decades, labelled as Thutmose I.

Dr. Hawass is convinced that Maspero is right and that the mummy previously on display at The Egyptian Museum cannot be Thutmose I.

What Can DNA Testing Tell Us?

 Dr. Hawass uses autosomal testing of nuclear DNA to identify ancient corpses. Although good nuclear DNA samples can be difficult to get from mummies, it information that cannot be found in mitochondrial DNA. In both humans and other mammals, nuclear DNA provides more genetic information than MtDNA.

We have two different types of DNA.

Nuclear DNA, found in the nucleus of the cell, consists of 46 chromosomes with three billion base pairs of DNA and approximately 25,000 genes. The mother provides an X chromosome to all her offspring. But the father may provide an X (the XX combination results in a daughter) or a Y (the XY combination results in a son).

So, the nuclear DNA, which includes an equal combination from both parents may give a fuller, more accurate, explanation. However the mitochondria or power plants of our cells, which lie outside the cell’s nucleus, each contain a copy of a loop of DNA with only about 16,569 base pairs, containing an estimated 37 genes.

Researchers believe that MtDNA is inherited mainly from the mother, not the father. But both parents contribute chromosomes to their offspring’s nuclear DNA. Therefore, nuclear DNA provides a clearer picture of both maternal and paternal inheritance than MtDNA.

The nuclear DNA of males proves even more interesting to researchers than that of females, because only males inherit the Y chromosome. Evidence suggests that the Y-chromosome may link all living human males back to a single Y-Adam (the most common recent male ancestor), whom geneticist and author Spencer Wells believes lived about 60,000 years ago.

So how do we know if the mummy is Thutmose I?

Scientists can try matching his DNA to the DNA of one of his royal relatives, such as a parent, child, or sibling, of whose identity they are pretty sure. Dr. Hawass has already performed tests on a mummy he believes is the daughter of Thutmose I, the famous female Pharaoh Hatshepsut.

On the Trail of Hatshepsut Too? In 2007, Dr. Hawass and his team performed CT scans and DNA analysis on a mummy believed to be Thutmose I’s daughter, Hateshepsut.

 The CT scan showing a broken molar in the funerary box matched a gap in her mouth. In addition, DNA test results matched DNA from Hatshepsut with her grandmother Ahmose-Nefertari, which they believe confirms her identity.

 While the team believes results of the CT scans and DNA analysis support their contention that they have found the ancient female pharaoh, others insist that the test results are inconclusive.

 The DNA analysis results have not been replicated by an independent laboratory because (a) There is no independent laboratory in Egypt; and (b) Dr. Hawass will not allow DNA testing on Egyptian mummies to be conducted by non-Egyptians and does not allow mummies to be transported to labs outside Egypt.

So while the mummy his team examined in 2007 may indeed be Hatshepsut, his results remain unconfirmed.

While Dr. Hawass says he is looking for financial support to establish another laboratory in Egypt, no one has accepted his offer. So his results have not been replicated. And without independent verification of his results, his findings cannot be published in peer reviewed journals.

How Successful Can Hawass Be In Identifying Mummies?

There is no doubt that DNA analysis has become a useful tool in identifying modern humans. Genealogy researchers and police increasingly rely on DNA test results to confirm family relationships and solve crimes.

So, it’s not surprising that viewers of The Discovery Channel are intrigued by documentaries showing Hawass and his team of Egyptian researchers unveiling the identities of ancient pharaohs.

But DNA analysis is a complicated job that may not fit into shooting schedules and may not yield clear cut results. In the first place, getting accurate DNA results from mummies is no sure thing.

Over several thousand years, nuclear DNA deteriorates, so extracting usable samples is difficult. The mummification process itself may damage and destroy nuclear DNA.

Another complicating factor for modern sleuths is contamination of samples with modern cells the specimen comes in contact during transportation or even in the laboratory. In fact, some contamination probably occurred soon after the ancient royals died - in the workshops of the embalmers.

If Dr. Hawass and his team at the Egyptian Museum prove conclusively that the ancient mummies in their care are who they are believed to be, their accomplishments outstrip the imaginations of Cold Case screenwriters.

 But, other scientists warn, that these results must be replicated by independent research teams in separate laboratories before the results can be confirmed. Peer review is also essential to giving the team’s work credibility. Otherwise, this work will remain more celebrated in the media than in the scientific community.

Further Reading:

 Douglas L. T. Rohde, On the Common Ancestors of All Living Humans

“We are All Africans under the Skin” Redcliff Interview with Dr. Spencer Wells, Redcliff.com

Mummies's DNA

HealthandDNA.com

Unravelling the Mummy Mystery on Egyptology Online

British biomedical researcher Angelique Corthals thinks researchers (and their supporters at the Discovery Channel) who are trying to identify the remains of Egyptian pharaohs might as well be working for CBS’s fictional Cold Case drama, rather than in the lab.

 In 2007 Corthals, a lecturer at the University of Manchester’s Centre for Biomedical Egyptology, told news media, "I think the people at the Discovery Channel went way too much 'CSI.'”

 “They think you can pick up evidence at 2 p.m. and by 6 p.m. you get results,'' added Corthals, who has helped Egypt establish the DNA lab. But US-based Discovery Channel thinks otherwise, and has put considerable funds into the enterprise.

Thanks to a $5 million laboratory provided by Discovery in 2007, the Egyptian mummy identification team led by Zahi Hawass, Egypt’s Undersecretary of the State for the Giza Monuments, has facilities that have not available to researchers in Egypt before.

According to outfitter Applied Biosystems, a Discovery partner, the new lab is the "first laboratory in Egypt dedicated to testing ancient DNA samples."

Actually, the writers of Cold Case probably wouldn’t touch a script this old: using  DNA testing to identify a 3,500 year old corpse found in the Valley of the Kings? But it’s a great way to learn about DNA - what it might and might not tell us, and why.

Is the Corpse really Thutmose I?

Researchers at the Egyptian Museum in Cairo are using DNA analysis and X-rays to identify a mummy from the Valley of the Kings at Luxor, which they think might be the famous Pharaoh Thutmose 1.

Thutmose I was a commoner who, on becoming pharaoh, distinguished himself by his building projects and military campaigns around 1500 B.C.

The search for Thutmose I began in earnest when the mummy, a male in his early thirties who was formerly identified as Thutmose, turned out to be an imposter.

How did Egyptologists know? The mummy previously on display died from an arrow wound to his chest and there is no record of Thutmose dying from such a wound. In any event, Thutmose I (approximately 1506 to 1493 BC), who was father to both Thutmose II  and the female Pharaoh, Hatshepsut, is thought to have been well past 50 when he died.

 While most events from the ancient world have not been recorded, the lives and deaths of pharaohs were recorded in considerable detail. Experts think that some unknown person was buried in Thutmose I's tomb and that the mummy of the real Thutmose I got lost a few thousand years ago, thanks to palace intrigue and rivalries.

While that sounds strange, it is not as strange as we might at first suppose. A constant threat for ancient royal families was grave robbers. Indeed, most tombs were looted in antiquity. Families, seeking peace for their dead, were known to bury someone else in the "official" tomb. One of Thutmose I's successors is thought to have removed him from his original tomb.

While the mummy of the real Thutmose I was widely believed to be lost forever, a sharp-eyed 19th century Egyptologist, Gaston Maspero, noticed that an anonymous mummy in Egypt’s vast collection, labelled #5283, looked like the mummies of Thutmose I’s son and grandson: Thutmose II and Thutmose III. Could he in fact be Thutmose I?

However, the matter was not pursued, so the other mummy remained on display at the Egyptian Museum for decades, labelled as Thutmose I.

Dr. Hawass is convinced that Maspero is right and that the mummy previously on display at The Egyptian Museum cannot be Thutmose I.

What Can DNA Testing Tell Us?

 Dr. Hawass uses autosomal testing of nuclear DNA to identify ancient corpses. Although good nuclear DNA samples can be difficult to get from mummies, it information that cannot be found in mitochondrial DNA. In both humans and other mammals, nuclear DNA provides more genetic information than MtDNA.

We have two different types of DNA.

Nuclear DNA, found in the nucleus of the cell, consists of 46 chromosomes with three billion base pairs of DNA and approximately 25,000 genes. The mother provides an X chromosome to all her offspring. But the father may provide an X (the XX combination results in a daughter) or a Y (the XY combination results in a son).

So, the nuclear DNA, which includes an equal combination from both parents may give a fuller, more accurate, explanation. However the mitochondria or power plants of our cells, which lie outside the cell’s nucleus, each contain a copy of a loop of DNA with only about 16,569 base pairs, containing an estimated 37 genes.

Researchers believe that MtDNA is inherited mainly from the mother, not the father. But both parents contribute chromosomes to their offspring’s nuclear DNA. Therefore, nuclear DNA provides a clearer picture of both maternal and paternal inheritance than MtDNA.

The nuclear DNA of males proves even more interesting to researchers than that of females, because only males inherit the Y chromosome. Evidence suggests that the Y-chromosome may link all living human males back to a single Y-Adam (the most common recent male ancestor), whom geneticist and author Spencer Wells believes lived about 60,000 years ago.

So how do we know if the mummy is Thutmose I?

Scientists can try matching his DNA to the DNA of one of his royal relatives, such as a parent, child, or sibling, of whose identity they are pretty sure. Dr. Hawass has already performed tests on a mummy he believes is the daughter of Thutmose I, the famous female Pharaoh Hatshepsut.

On the Trail of Hatshepsut Too? In 2007, Dr. Hawass and his team performed CT scans and DNA analysis on a mummy believed to be Thutmose I’s daughter, Hateshepsut.

 The CT scan showing a broken molar in the funerary box matched a gap in her mouth. In addition, DNA test results matched DNA from Hatshepsut with her grandmother Ahmose-Nefertari, which they believe confirms her identity.

 While the team believes results of the CT scans and DNA analysis support their contention that they have found the ancient female pharaoh, others insist that the test results are inconclusive.

 The DNA analysis results have not been replicated by an independent laboratory because (a) There is no independent laboratory in Egypt; and (b) Dr. Hawass will not allow DNA testing on Egyptian mummies to be conducted by non-Egyptians and does not allow mummies to be transported to labs outside Egypt.

So while the mummy his team examined in 2007 may indeed be Hatshepsut, his results remain unconfirmed.

While Dr. Hawass says he is looking for financial support to establish another laboratory in Egypt, no one has accepted his offer. So his results have not been replicated. And without independent verification of his results, his findings cannot be published in peer reviewed journals.

How Successful Can Hawass Be In Identifying Mummies?

There is no doubt that DNA analysis has become a useful tool in identifying modern humans. Genealogy researchers and police increasingly rely on DNA test results to confirm family relationships and solve crimes.

So, it’s not surprising that viewers of The Discovery Channel are intrigued by documentaries showing Hawass and his team of Egyptian researchers unveiling the identities of ancient pharaohs.

But DNA analysis is a complicated job that may not fit into shooting schedules and may not yield clear cut results. In the first place, getting accurate DNA results from mummies is no sure thing.

Over several thousand years, nuclear DNA deteriorates, so extracting usable samples is difficult. The mummification process itself may damage and destroy nuclear DNA.

Another complicating factor for modern sleuths is contamination of samples with modern cells the specimen comes in contact during transportation or even in the laboratory. In fact, some contamination probably occurred soon after the ancient royals died - in the workshops of the embalmers.

If Dr. Hawass and his team at the Egyptian Museum prove conclusively that the ancient mummies in their care are who they are believed to be, their accomplishments outstrip the imaginations of Cold Case screenwriters.

 But, other scientists warn, that these results must be replicated by independent research teams in separate laboratories before the results can be confirmed. Peer review is also essential to giving the team’s work credibility. Otherwise, this work will remain more celebrated in the media than in the scientific community.

Further Reading:

 Douglas L. T. Rohde, On the Common Ancestors of All Living Humans

“We are All Africans under the Skin” Redcliff Interview with Dr. Spencer Wells, Redcliff.com

Mummies's DNA

HealthandDNA.com

Unravelling the Mummy Mystery on Egyptology Online

The nautilus, assumed to be a living example of the ancestors of modern octopus and squid, lacks the brain structures of these animals, yet appears to have both short and long term memory: Training Nautilus pompilus to associate the smell of food with a blue light, the cephalopods eventually learned to respond to a flash of blue light by extending their tentacles. Then the scientists tested the cephalopods memories with a flash of light 3min, 30min, 1h, 6h, 12h and 24h after training. Amazingly, Nautilus remembered their training for up to an hour before the memory was lost, but then the memory returned 6h later, lasting up to 24h. Nautilus has both short and long term memory, just like modern cephalopods, despite lacking the same brain structures. (The Company of Biologists (2008, June 1). Living Fossils Have Long- And Short-term Memory Despite Lacking Brain Structures Of Modern Cephalopods. ScienceDaily. Retrieved June 3, 2008, from http://www.sciencedaily.com? /releases/2008/05/080531074905.htm) Modern cephalopods (octopus and squid) have complex central nervous systems and coleoid brains, but they must be doing something for the animal other than helping it remember where food is.

The nautilus, assumed to be a living example of the ancestors of modern octopus and squid, lacks the brain structures of these animals, yet appears to have both short and long term memory: Training Nautilus pompilus to associate the smell of food with a blue light, the cephalopods eventually learned to respond to a flash of blue light by extending their tentacles. Then the scientists tested the cephalopods memories with a flash of light 3min, 30min, 1h, 6h, 12h and 24h after training. Amazingly, Nautilus remembered their training for up to an hour before the memory was lost, but then the memory returned 6h later, lasting up to 24h. Nautilus has both short and long term memory, just like modern cephalopods, despite lacking the same brain structures. (The Company of Biologists (2008, June 1). Living Fossils Have Long- And Short-term Memory Despite Lacking Brain Structures Of Modern Cephalopods. ScienceDaily. Retrieved June 3, 2008, from http://www.sciencedaily.com? /releases/2008/05/080531074905.htm) Modern cephalopods (octopus and squid) have complex central nervous systems and coleoid brains, but they must be doing something for the animal other than helping it remember where food is.

Live birth is 200 million years older than previously supposed, according to a recent report of a 380 million year old fish (a placoderm) with an embryo, still attached by an umbilical cord: Until now, scientists thought creatures from these times were only able to develop their young inside eggs.

- "Fossil reveals oldest live birth" by Rebecca Morelle, BBC News (May 28, 2008)

The recently found placoderm dates from the Devonian era, called by some the Age of Fish.

Another fossil unearthed in 1986 was reexamined as a result of this find. It turned out to have three embryos inside that were considered evidence of live birth. In the past, scientists tended to assume that small fish found inside big ones had been eaten, as Carina Dennis explains in "The oldest pregnant mum" (Nature News, 28 May, 2008): The researchers identified a single embryo in a new Gogo fish genus, and three embryos in a previously described specimen. “When you find a little fish inside a big fish, you tend to think it was dinner,” Long says. But the researchers concluded that the bones were those of embryos, not ingested remains, because they were not crushed or etched by digestive acids. What nailed it, according to Long, was the identification of an umbilical structure and a putative yolk sac. Finds like this one challenge the widespread belief that live birth is a relatively recent innovation, and that egg-laying is older and perhaps more primitive.

Live birth is 200 million years older than previously supposed, according to a recent report of a 380 million year old fish (a placoderm) with an embryo, still attached by an umbilical cord: Until now, scientists thought creatures from these times were only able to develop their young inside eggs.

- "Fossil reveals oldest live birth" by Rebecca Morelle, BBC News (May 28, 2008)

The recently found placoderm dates from the Devonian era, called by some the Age of Fish.

Another fossil unearthed in 1986 was reexamined as a result of this find. It turned out to have three embryos inside that were considered evidence of live birth. In the past, scientists tended to assume that small fish found inside big ones had been eaten, as Carina Dennis explains in "The oldest pregnant mum" (Nature News, 28 May, 2008): The researchers identified a single embryo in a new Gogo fish genus, and three embryos in a previously described specimen. “When you find a little fish inside a big fish, you tend to think it was dinner,” Long says. But the researchers concluded that the bones were those of embryos, not ingested remains, because they were not crushed or etched by digestive acids. What nailed it, according to Long, was the identification of an umbilical structure and a putative yolk sac. Finds like this one challenge the widespread belief that live birth is a relatively recent innovation, and that egg-laying is older and perhaps more primitive.

Native to eastern Australia, the duckbilled platypus is regarded as a mammal. Yet it lays eggs like a bird. However, it nurses its young like a mammal, on milk.

The male platypus also has a poison spur on its hind leg, which is more characteristic of reptiles.

And now that it has been mapped, the genome of the duck-billed platypus turns out to be as mixed as the traits of the animal itself.

Said researcher Mark Batzer of Louisiana State University, "One big surprise was the patchwork nature of the genome with avian, reptilian and mammalian features".

Of particular interest was the genes for of the male's poison spur: Scientists were also eager to find out how venom production became a part of the platypus genome. When researchers began analyzing the genetic sequences responsible for venom production in the male platypus, they made a surprising finding. They discovered that venom produced by the male platypus arose from duplications in certain genes over the course of evolutionary time that had been passed on from ancestral reptile genomes. The reptilian lineage displays a similar duplication of venom genes, but that duplication appears to have occurred independently during the evolution of reptiles, giving them similar powers to produce venom.

- "Duck-Billed Platypus Genome Sequence Published", National Institutes of Health (May 7, 2008)

The platypus is one of the few survivors of a classification of mammals called monotremes, found only in Australia and New Guinea today.

It is best known for its electrosensitive bill, which it uses to locate things under water, because it keeps its eyes shut when submerged.

Native to eastern Australia, the duckbilled platypus is regarded as a mammal. Yet it lays eggs like a bird. However, it nurses its young like a mammal, on milk.

The male platypus also has a poison spur on its hind leg, which is more characteristic of reptiles.

And now that it has been mapped, the genome of the duck-billed platypus turns out to be as mixed as the traits of the animal itself.

Said researcher Mark Batzer of Louisiana State University, "One big surprise was the patchwork nature of the genome with avian, reptilian and mammalian features".

Of particular interest was the genes for of the male's poison spur: Scientists were also eager to find out how venom production became a part of the platypus genome. When researchers began analyzing the genetic sequences responsible for venom production in the male platypus, they made a surprising finding. They discovered that venom produced by the male platypus arose from duplications in certain genes over the course of evolutionary time that had been passed on from ancestral reptile genomes. The reptilian lineage displays a similar duplication of venom genes, but that duplication appears to have occurred independently during the evolution of reptiles, giving them similar powers to produce venom.

- "Duck-Billed Platypus Genome Sequence Published", National Institutes of Health (May 7, 2008)

The platypus is one of the few survivors of a classification of mammals called monotremes, found only in Australia and New Guinea today.

It is best known for its electrosensitive bill, which it uses to locate things under water, because it keeps its eyes shut when submerged.

Marine biologist Sonja Kleinlogel and quantum physicist Andrew White have found that the mantis shrimp from the Great Barrier Reef in Australia can see eleven or twelve primary colours, rather than the three that humans can see (red, yellow, and blue, and their combinations): Most animals can tell how fast the electric field in a light wave is oscillating, which is perceived as colour. (Blue light oscillates faster than green, which is faster than red). The direction of the oscillation is known as polarisation: many animals, from budgerigars to ants have some form of polarisation vision. Most life forms see this polarization of the light wave's electric field only as lighter or darker patches. But the electric field of light is not still. It can go from swinging back and forth to travelling in a circle. The sensitive mantis shrimp eye can measure four linear and two circular polarizations at once, according to the researchers, so the shrimp know both the direction and the degree of polarization of the light. Presumably, the shrimp would detect these as if they were different colours. What benefit does such a high degree of sensitivity to colour offer the shrimp? Prof. White notes, "Some of the animals they like to eat are transparent, and quite hard to see in sea-water - except they're packed full of polarising sugars - I suspect they light up like Christmas trees as far as these shrimp are concerned."

The evolution of the eye

Eye origin has long been a puzzle in evolution because a number of quite different complex systems exist. Biochemist Michael Denton of the University of Otago in New Zealand thinks that just about every conceivable means of seeing (forming an optical image) has been used by life forms:

These include the familiar camera-type of eye found in vertebrates, molluscs, and various invertebrates; the reflecting eye of the scallop pecten and the crustacean Gigantocypris, which form an image by reflection from a concave mirror onto a retina situated ast the focal point of the mirror; and the three different types of compound eye of the insects and arthropods. One type of compound eye found in diurnal insects os made up of a hexagonal array of tiny lenslets, each of which has its own photoreceptor cell that receives light only from its own lenslet. A second type (the superposition type) is found in nocturnal insects, again made up of a hexagonal array of tiny lenslets which bend the light rays so that light is focused by refraction through many le3nslets to one point in the photoreceptor layer. A third type is also a superposition eye, but in this case the light is focused by reflection from a series of tiny square mirror-lined units onto the photo-receptor layer ... Finally, there is even what appears to be a scanning eye, utilized by a small marine crustacean which scans an image formed b y a simple lens by rapidly moving a single photoreceptor back and forth across the image. (Nature's Destiny, New York: Free Press, 1998, pp. 307-8)

In addition, Denton notes, there is a "near-infinite variety" of simple eyes that do not form an image, such as the photosensitive pigments of Protozoa (one-celled life forms) and the simpler photoreceptor eyes of spiders.

What are "simple" eyes?

When biologists refer to "simple" eyes, they mean that the eye mechanism itself is simple. However, in addition to a mechanism to detect light, a visual system must have a means of transforming light signals into nervous system signals that produce information. Only if information is produced and acted on is a visual system complete. The process of transforming light into information is complex, even when the structure of the eye is simple. Biochemist Michael Behe explains the process for the human eye:

When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein's metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin.

The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water.

A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision.

If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration. Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon.

Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previously added hydrogen atoms to form 11-cis-retinal, and the cycle is complete.

Charles Darwin described the eye as one of the "organs of extreme perfection" and considered it a problem for his theory of natural selection. Indeed, the eye gave him a "cold shudder." He thought, however, that an eye like the human eye might arise from simpler structures, like the photosensitive spot of the worm. The difficulty with his explanation is, as we have seen, that the process of vision, as well as the structure, is complex, and it is not clear that the process can be less complex. Mathematician David Berlinski phrases the problem like "this": Like vibrations passing through a spider's web, changes to any part of the eye, if they are to improve vision, must bring about changes throughout the optical system. Without a correlative increase in the size and complexity of the optic nerve, an increase in the number of photoreceptive membranes can have no effect. A change in the optic nerve must in turn induce corresponding neurological changes in the brain. If these changes come about simultaneously, it makes no sense to talk of a gradual ascent of Mount Improbable. If they do not come about simultaneously, it is not clear why they should come about at all. We know that vision got started during the Cambrian era and some have argued that it actually explains the Cambrian explosion. Whatever the merits of such a thesis, the origin of vision itself  requires explanation.

Marine biologist Sonja Kleinlogel and quantum physicist Andrew White have found that the mantis shrimp from the Great Barrier Reef in Australia can see eleven or twelve primary colours, rather than the three that humans can see (red, yellow, and blue, and their combinations): Most animals can tell how fast the electric field in a light wave is oscillating, which is perceived as colour. (Blue light oscillates faster than green, which is faster than red). The direction of the oscillation is known as polarisation: many animals, from budgerigars to ants have some form of polarisation vision. Most life forms see this polarization of the light wave's electric field only as lighter or darker patches. But the electric field of light is not still. It can go from swinging back and forth to travelling in a circle. The sensitive mantis shrimp eye can measure four linear and two circular polarizations at once, according to the researchers, so the shrimp know both the direction and the degree of polarization of the light. Presumably, the shrimp would detect these as if they were different colours. What benefit does such a high degree of sensitivity to colour offer the shrimp? Prof. White notes, "Some of the animals they like to eat are transparent, and quite hard to see in sea-water - except they're packed full of polarising sugars - I suspect they light up like Christmas trees as far as these shrimp are concerned."

The evolution of the eye

Eye origin has long been a puzzle in evolution because a number of quite different complex systems exist. Biochemist Michael Denton of the University of Otago in New Zealand thinks that just about every conceivable means of seeing (forming an optical image) has been used by life forms:

These include the familiar camera-type of eye found in vertebrates, molluscs, and various invertebrates; the reflecting eye of the scallop pecten and the crustacean Gigantocypris, which form an image by reflection from a concave mirror onto a retina situated ast the focal point of the mirror; and the three different types of compound eye of the insects and arthropods. One type of compound eye found in diurnal insects os made up of a hexagonal array of tiny lenslets, each of which has its own photoreceptor cell that receives light only from its own lenslet. A second type (the superposition type) is found in nocturnal insects, again made up of a hexagonal array of tiny lenslets which bend the light rays so that light is focused by refraction through many le3nslets to one point in the photoreceptor layer. A third type is also a superposition eye, but in this case the light is focused by reflection from a series of tiny square mirror-lined units onto the photo-receptor layer ... Finally, there is even what appears to be a scanning eye, utilized by a small marine crustacean which scans an image formed b y a simple lens by rapidly moving a single photoreceptor back and forth across the image. (Nature's Destiny, New York: Free Press, 1998, pp. 307-8)

In addition, Denton notes, there is a "near-infinite variety" of simple eyes that do not form an image, such as the photosensitive pigments of Protozoa (one-celled life forms) and the simpler photoreceptor eyes of spiders.

What are "simple" eyes?

When biologists refer to "simple" eyes, they mean that the eye mechanism itself is simple. However, in addition to a mechanism to detect light, a visual system must have a means of transforming light signals into nervous system signals that produce information. Only if information is produced and acted on is a visual system complete. The process of transforming light into information is complex, even when the structure of the eye is simple. Biochemist Michael Behe explains the process for the human eye:

When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein's metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin.

The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water.

A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision.

If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration. Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon.

Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previously added hydrogen atoms to form 11-cis-retinal, and the cycle is complete.

Charles Darwin described the eye as one of the "organs of extreme perfection" and considered it a problem for his theory of natural selection. Indeed, the eye gave him a "cold shudder." He thought, however, that an eye like the human eye might arise from simpler structures, like the photosensitive spot of the worm. The difficulty with his explanation is, as we have seen, that the process of vision, as well as the structure, is complex, and it is not clear that the process can be less complex. Mathematician David Berlinski phrases the problem like "this": Like vibrations passing through a spider's web, changes to any part of the eye, if they are to improve vision, must bring about changes throughout the optical system. Without a correlative increase in the size and complexity of the optic nerve, an increase in the number of photoreceptive membranes can have no effect. A change in the optic nerve must in turn induce corresponding neurological changes in the brain. If these changes come about simultaneously, it makes no sense to talk of a gradual ascent of Mount Improbable. If they do not come about simultaneously, it is not clear why they should come about at all. We know that vision got started during the Cambrian era and some have argued that it actually explains the Cambrian explosion. Whatever the merits of such a thesis, the origin of vision itself  requires explanation.

A research group headed by Jennifer A. Dunne of the Santa Fe Institute investigated food webs in the Cambrian era, and discovered that they are remarkably similar to food webs among species today. The many similarities between Cambrian and recent food webs point toward surprisingly strong and enduring constraints on the organization of complex feeding interactions among metazoan species. Only some assemblages of animals from the Chengjiang and Burgess Shale Cambrian era (about 540 to 525 million years ago) were well preserved enough to permit such a study. But among these they found Observed regularities reflect a systematic dependence of structure on the numbers of taxa and links in a web. Most aspects of Cambrian food-web structure are well-characterized by a simple “niche model,” which was developed for modern food webs and takes into account this scale dependence.

The few differences the researchers observed in these cases may relate to the fact that the number of phyla (basic body plans) is about the same hundreds of millions of years later, but there are many more species within some phyla today. Here are some other stories about the Cambrian era:

Cambrian explosion

The Smithsonian secretary vs. the Cambrian explosion (February 19, 2008)

Cambrian explosion ecosystems closely resemble today's (May 7, 2008) Cambrian explosion. See also big bangs in biology