I agree that a eye in a totally dark world is a liability. Yet an eye has mutated to be a little less sensitive/functional remains as large an liability as the fully functional eye. The only selective advantage would be the sudden appearance of an absent eye--the hopeful monster in reverse. Yet the hopeful monster is rejected by mainstream evolutionary theory. Comments?

Since we weren't able to watch the entire process from beginning to end we are forced to conjecture. Perhaps there are some intermediary salamanders out there that they article didn't mention.

Anyway, let's say that there was a salamander with an eye that had a slight eye covering like an epicanthic fold that afforded slight protection from bumping they eye in the dark and causing injury and possible infection. Then let's say that salamanders with that covering lived 0.1% longer on average than their brethren with larger eyes. Over multiple generations that gene could be selected.

Or perhaps it happened in a larger jump due to a mutation in the DNA due to damage from natural radiation, copying error, etc. Then the lack of the eye could occur much faster.

There are probably many viable ways to de-evolve an eye. Maybe it starts by a film, like a cataract, growing over it. It provides a protective barrier and mild loss of function. Perhaps it starts by rewiring the brain, allocating valuable cranial space and processing power to other sensory faculties. Or maybe total loss of hte genes involved in eye synthesis is the nearest local maximum for fitness.

But it's presumptuous to assume it has to be one way or another. This is a common logical fallacy among evolution deniers, to just assume that since I can't think of one, no viable intermediate state can possibly exist. This is especially true since the salamanders appear to have eye sockets instead of just blank heads, so they themselves are at an intermediate state. Give it a few million more years, and they will probably lose those, and humans will lose their appendices and the skeletal framework for tails.

It COULD have happened a gazillion ways. Many ways it possibly could have happened. Therefore it did.

This is the same logical fallacy that the ID'ers are accused of--deus ex machina, except that the deus is evolution, not a deity. Evolution is an all purpose explanation for everything, except for abiogenesis, exempt from the burden of explaining as to how the whole process got started. By definition.

If all you have is a hammer, everything looks like a nail. Or as a friend is fond of saying, "When you go to a shoemaker, you get shoes."

small survival advantage makes it certain that salamander lives to reproduce? Even healthy organisms get eaten, are the victims of bad luck. And how do we know that the salamander did mate with a similarly endowed (or lack thereof) opposite sex salamander? All conjecture, but if you were building a mathematical model, you would have to factor these considerations in.

I agree about the big jump in mutation--easier to explain in a loss of a body function, just screw up the genes and it doesn't work. Much harder to make this work for the development of a new and improved organ--hence the discredit laid on the hopeful monster.

Stop-Truth-Decay: if you were building a mathematical model, you would have to factor these considerations in.

LeRoy: But there IS such a mathematical model. It is called 'population genetics'. You should Google on it sometime.

Stop-Truth-Decay: I'm not saying our hypothesis is perfect. Do you have a better one? I'm all ears.

“I agree that a eye in a totally dark world is a liability. Yet an eye has mutated to be a little less sensitive/functional remains as large an liability as the fully functional eye.

The only selective advantage would be the sudden appearance of an absent eye--the hopeful monster in reverse.” ”

>>IF there sighted versus non-scighted phenotypes exhibited idnetical fitness we could expect that we’d see a population displaying a mix of sensitive and slighty-less-sensitive eyes, just as we see a mix of blond and brunette phenotypes in the human population. They’d be equivalently fit and natural selection would act neither to conserve or oppose them.

At a later time, of course, additional genetic changes could transform lsighty-less-sensitive eyes into eyes that were not only completely insensitive abut which also did confer a fitness advantage (reduced risk of infection, for example), at which point blindness would be selected for and the frequency of alleles resulting in blindness would increase over generations.

Additionally, if the mutation resulting in the loss of sensitivity was a function of inactivation of gene expression--if the salamanders no longer expressed a gene product that conferred no change in fitness of itself--there would be a sufficient energy savings to drive selection for the salamanders that failed to express the gene

Even if the mutation caused no change in fitness the blind could become uniform throughout the population by mechanisms such as founder’s effect or genetic drift.

Stop-truth-decay:

It COULD have happened a gazillion ways. Many ways it possibly could have happened. Therefore it did. This is the same logical fallacy that the ID'ers are accused of--deus ex machina, except that the deus is evolution, not a deity. Evolution is an all purpose explanation for everything, except for abiogenesis, exempt from the burden of explaining as to how the whole process got started. By definition. If all you have is a hammer, everything looks like a nail. Or as a friend is fond of saying, "When you go to a shoemaker, you get shoes."

For someone with a name like "stop truth decay" and one so willing to trumpet his own logic "crap detector", you sure misread my statement. It's so off as to appear deliberate.

I never said that the possibility of intermediate forms in the loss of eyes in salamanders was proof of evolution. The proof is in the mountains of evidence in the living world. All I said was that you can't presume intermediate states don't exist, and if they do, they negate the hopeful monster problem, which is otherwise commonly known now as "irreducible complexity".

Since modern ID came up with this line of reasoning, there have been numerous supposedly irreducibly complex structures, which further research has proven to be reducible. That should be a lesson to you, that just because you or I possibly can't imagine what intermediate state might exist, doesn't mean they don't, and that when you assume, you risk making an ass of yourself.

Stop-truth-decay:

small survival advantage makes it certain that salamander lives to reproduce? Even healthy organisms get eaten, are the victims of bad luck. And how do we know that the salamander did mate with a similarly endowed (or lack thereof) opposite sex salamander? All conjecture, but if you were building a mathematical model, you would have to factor these considerations in. I agree about the big jump in mutation--easier to explain in a loss of a body function, just screw up the genes and it doesn't work. Much harder to make this work for the development of a new and improved organ--hence the discredit laid on the hopeful monster.

Like LeRoy said, there are models for this. It seems you are unware of them, but you can get a good understanding from a 1st year biology course. Or Google.

yes, there are models. Allopatric speciation, yes. Please provide me a model that takes one organism, uses known rates of mutation, known rates of selective pressure, accounts for random acts of death and violence to the fortunate gene holders, whether the genes are recessive, dominant, sex linked, accounts for migration into/out of the niche, and probably a host of other factors and plug it into a super computer, and deliver the probability of modern man, chimps and our ape progenitors diverging several million years ago. Or any other evolutionary event you would care to cite.

I've never encountered such a model--which is NOT population genetics. I do understand that the explanation for the Cambrian explosion is essentially, since we seen so many phyla in a short time, mutation rates and selection pressures must have been high to produce so many phyla--a circular argument to anyone who has an open mind.

Maybe I'm just not searching with the right parameter... post such a link. If it really existed, I think that Dawkins, et al, would be trumpeting that computer confirmed model that science has proven with a "X" per cent probability has confirmed the origin of the species. Haven't seen that yet.

was the most common topic of discussion. Not exactly the point I was making. Show me a model of: how many mutations it takes to go from no eye, to eye, what intermediate steps are necessary, reasonable rates of selection (no circular reasoning like we see in the Cambrian explosion thesis--since we see such rapid evolution, there must have been rapid mutation rate since we see such rapid evolution), how big a population it takes for the genes to become predominant, accounting for the fact that 2 animals with the fit genes don't mate all the time, the random even that the fortunate mutation could be lost because the creature was eaten by a predator (wrong place, wrong time), etc, etc. A fiendishly complex model, and subject to numerical values that could be arbitrary. That sort of model. If you want to say,we don't know enough, the numbers are too arbitrary, or some other reason--that's OK with me. But the old argument that SURELY given enough time and enough selective pressure event "X" would have happened is more a faith statement than real science. Like the million monkeys on the million typewriters for a million years producing Shakespeare. Somebody tried that, and it turns out monkeys have preferences for certain keys and would never produce any literature.

Stop-Truth-Decay: Please provide me a model that takes one organism, uses known rates of mutation, known rates of selective pressure, accounts for random acts of death and violence to the fortunate gene holders,

LeRoy: Please note that if "acts of death and violence" are truly random, then they would affect the unfortunate gene holders with the same probability as the fortunate gene holders. E.g., if 50% of a population of organisms possesses an advantageous allele, and the other 50% possesses a disadvantageous version of the same gene, then any truly 'random' acts of death and violence would affect both halves of the population equally...and the result would be a wash. You seem to be imagining a situation where some 'random' event wipes out all the fortunate gene holders...which is certainly possible, and then that gene variant might not arise again (or perhaps not for a long time, and by then the environment might have changed in such a way that the variant is no longer even advantageous)...BUT, if the event is truly 'random', as you are assuming, it is just as likely that it might wipe out all the unfortunate genotypes.

There would not be much point to building something into a computer model, when it is clear in advance that it would make no material difference....

I will give you a book recommendation, if you are truly curious about these subjects. The title is Evolutionary Dynamics: Exploring the Equations of Life. The author is Martin A. Nowak. Dr. Nowak is Professor of both Biology and Mathematics at Harvard University, and is the Director of the Program for Evolutionary Dynamics. I can hardly compress this book into a Fray post, so will simply give you the chapter titles, to indicate that some of the questions you are raising are indeed addressed in the book:

Chapter 1: Introduction

Chapter 2: What Evolution Is

Chapter 3: Fitness Landscapes and Sequence Spaces

Chapter 4: Evolutionary Games

Chapter 5: Prisoners of the Dilemma

Chapter 6: Finite Populations

Chapter 7: Games in Finite Populations

Chapter 8: Evolutionary Graph Theory

Chapter 9: Spatial Games

Chapter 10: HIV Infections

Chapter 11: Evolution of Virulence

Chapter 12: Evolutionary Dynamics of Cancer

Chapter 13: Language Evolution

Chapter 14: Conclusion

Not an easy book, I might add, even for a mathematician. The chapter headings do reveal that there are many very practical applications of this kind of knowledge, as well.

...a light sensitve eye-spot to the type of lensed eyes found in fish would take about 1,869 steps if we restrict morphologic changes to increments of 1% (eye, some value such as length, depth, concentration varies no more than +/- 1%, Nelson and Pelger calculated it could take 1,869 steps and roughly 350,000 generations (A Pessimistic Estimate Of The Time Required For An Eye To Evolve, D.-E. Nilsson and S. Pelger, Proceedings of the Royal Society London B, 1994, 256, pp. 53-58.)

Don Lindsay's eye page provides further details <link>

Don also indentifies intermediate steps still found functioning in living species (molluscs, planaria, nautilus's) at <link>

And finally he addresses the origin of primitive eye-spots at <link>

"But the old argument that SURELY given enough time and enough selective pressure event "X" would have happened is more a faith statement than real science."

>>But that isn't the argument evolutionary biologists are making with respect to vision--they aren't saying it could have happened, but they're pointing out how all available evidence--especially the intermediate stage that still are exhibited by many organisms--supports the conclusion that's how it did happen.

"Like the million monkeys on the million typewriters for a million years producing Shakespeare. Somebody tried that, and it turns out monkeys have preferences for certain keys and would never produce any literature."

>>A million monkeys typing isn't at all analogous to how evolution produces complex structures and generates biologically diverse population. Monkey's typing randomly at keyboards does not model two undamental elements of evolutionary change--it incorporates neither selection with respect to environment nor the inheritance of those traits selected for by subsequent generations.

If we are going to use monkeys typing randomly to approximate natural mechanisms that introduce change in a population’s genetic composition, we must add those necessary elements to our example by stating that whenever a monkey types a character in the correct location not only will subsequent attempts by that monkey begin with that character in place (allele fixing by selection) but all other monkeys typing away will begin subsequent attempts with that character alredy fixed in place (inheritance).

As time progresses and more and more characters become fixed in the 'population' of letters we'll wind up with texts more and more similar to the final complete works of Shakespeare.

With selection and inheritance added Shakespeare’s plays can rapidly be generated by small numbers of random generators—monkeys, computers, whatever. In 1980s Richard Hardison of Glendale College wrote a computer program that generated phrases randomly while preserving the positions of individual letters that happened to be correctly placed, modeling how evolution selects for adaptive changes produced by mutations. On average, the program re-created the phrase TOBEORNOTTOBE in just 336 iterations, less than 90 seconds. The entire play "Hamlet" took just four and a half days to generate.

And that was a single random generator—a single monkey, as it were.

There are many competing explanations of the Cambrian explosion, but none of them involve an increase in the rate of mutation, as you seem to think. [Besides which, the Cambrian explosion presents a far more serious problem to flood geology creationists, wouldn't you think?] Below is the portion of the Wikipedia article dealing with explanations of the Cambrian explosion. I have no idea which explanation is correct, and many of them are not necessarily mutually exclusive.

Possible causes of the “explosion”

Despite the evidence that moderately complex animals (triploblastic bilaterians) existed before and possibly long before the start of the Cambrian, it seems that the pace of evolution was exceptionally fast in the early Cambrian. Possible explanations for this fall into three broad categories: environmental, developmental, and ecological changes. Any explanation must explain the timing and magnitude of the explosion. It is also possible that the "explosion" requires no special explanation.

Changes in the environment

[edit] Increase in oxygen levels

Earth’s earliest atmosphere contained no free oxygen; the oxygen that animals breathe today, both in the air and dissolved in water, is the product of billions of years of photosynthesis. As a general trend, the concentration of oxygen in the atmosphere has risen gradually over about the last 2.5 billion years.[8]

Shortage of oxygen might well have prevented the rise of large, complex animals. The amount of oxygen an animal can absorb is largely determined by the area of its oxygen-absorbing surfaces (lungs and gills in the most complex animals; the skin in less complex ones); but the amount needed is determined by its volume, which grows faster than the oxygen-absorbing area if an animal’s size increases equally in all directions. An increase in the concentration of oxygen in air or water would increase the size to which an organism could grow without its tissues becoming starved of oxygen. However, members of the Ediacara biota reached metres in length; clearly oxygen did not limit their growth.[26] Other metabolic functions may have been inhibited by lack of oxygen, for example the construction of tissue such as collagen, required for the construction of complex structures,[73] or to form molecules for the construction of a hard exoskeleton.[74]

[edit] Snowball Earths Main article: Snowball Earth

In the late Neoproterozoic (extending into the early Ediacaran period), the Earth suffered massive glaciations in which most of its surface was covered by ice. This may have caused a mass extinction, creating a genetic bottleneck; the resulting diversification may have given rise to the Ediacara biota, which appears soon after the last "Snowball Earth" episode.[75] However, the snowball episodes occurred a long time before the start of the Cambrian, and it is hard to see how so much diversity could have been caused by even a series of bottlenecks;[16] the cold periods may even have delayed the evolution of large size.[34]

[edit] Developmental Explanations

A range of theories are based on the concept that minor modifications to animals' development as they grow from embryo to adult may have been able to cause very large changes in the final adult form. The hox genes, for example, control which organs individual regions of an embryo will develop into. For instance, if a certain hox gene is expressed, a region will develop into a limb; if a different hox gene is expressed in that region (a minor change), it could develop into an eye instead (a phenotypically major change).

Such a system allows a large range of disparity to appear from a limited set of genes, but such theories linking this with the explosion struggle to explain why the origin of such a development system should by itself lead to increased diversity or disparity. Evidence of Precambrian metazoans[16] combines with molecular data[76] to show that much of the genetic architecture that could feasibly have played a role in the explosion was already well established by the Cambrian.

[edit] Ecological Explanations

These focus on the interactions between different types of organism. Some of these hypotheses deal with changes in the food chain; some suggest arms races between predators and prey, and others focus on the more general mechanisms of coevolution. Such theories are well suited to explaining why there was a rapid increase in both disparity and diversity, but they must explain why the "explosion" happened when it did.[16]

[edit] End-Ediacaran mass extinction Main article: End-Ediacaran extinction

Evidence for such an extinction includes the disappearance from the fossil record of the Ediacara biota and shelly fossils such as Cloudina, and the accompanying perturbation in the δ13C record. Mass extinctions are often followed by adaptive radiations as existing clades expand to occupy the ecospace emptied by the extinction. However, once the dust had settled, overall disparity and diversity returned to the pre-extinction level in each of the Phanerozoic extinctions.[16]

[edit] Evolution of eyes Main article: Evolution of the eye

Parker has proposed that predator-prey relationships changed dramatically after eyesight evolved. Prior to that time hunting and evading were both close-range affairs – smell, vibration, and touch were the only senses used. When predators could see their prey from a distance, new defensive strategies were needed. Armor, spines, and similar defenses may also have evolved in response to vision.[77] Nevertheless many scientists doubt that vision could have caused the explosion. Eyes may well have evolved long before the start of the Cambrian.[78] It is also difficult to understand why the evolution of eyesight would have caused an explosion, since other senses such as smell and pressure detection can detect things further away than they can be seen under the sea, but the appearance of these other senses apparently did not cause an evolutionary explosion.[16]

[edit] Arms races between predators and prey

The ability to avoid or recover from predation often makes the difference between life and death, and is therefore one of the strongest components of natural selection. The pressure to adapt is stronger on the prey than on the predator: if the predator fails to win a contest, it loses its lunch; if the prey is the loser, it loses its life.[79]

But there is evidence that predation was rife long before the start of the Cambrian, for example in the increasingly spiny forms of acritarchs, the holes drilled in Cloudina shells, and traces of burrowing to avoid predators. Hence it is unlikely that the appearance of predation was the trigger for the Cambrian "explosion", although it may well have exhibited a strong influence on the body forms that the "explosion" produced.[34] Alternatively a more subtle aspect, such as the evolution of a new style of predation, may have played a role.

[edit] Increase in size and diversity of planktonic animals

Geochemical evidence strongly indicates that the total mass of plankton has been similar to modern levels since early in the Proterozoic. Before the start of the Cambrian, their corpses and droppings were too small to fall quickly towards the sea-bed, since their drag was about the same as their weight. This meant they were destroyed by scavengers or by chemical processes before they reached the sea floor.[3]

Mesozooplankton are plankton of a larger size, and early Cambrian specimens filtered microscopic plankton from the seawater. These larger organisms would have produced droppings and corpses that were large enough to fall fairly quickly. This provided a new supply of energy and nutrients to the mid-levels and bottoms of the seas, which opened up a huge range of new possible ways of life. If any of these remains sunk uneaten to the sea floor they could be buried; this would have taken some carbon out of circulation, resulting in an increase in the concentration of breathable oxygen in the seas.[3] (carbon readily combines with oxygen)

The initial herbivorous mesozooplankton were probably larvae of benthic (sea-floor) animals. A larval stage was probably an evolutionary innovation driven by the increasing level of predation at the sea-floor during the Ediacaran period.[3][80]

Metazoans have an amazing ability to increase diversity through co-evolution.[36] This means that a trait of one organism can cause another to evolve in response; a number of responses are possible, and a different species can potentially emerge for each. As a simple example, the evolution of predation may have caused one organism to develop defence while another developed motion to flee. This would cause the predator lineage to split into two species: one that was good at chasing prey, and another that was good at breaking through defences. Actual co-evolution is somewhat more subtle, but in this fashion, great diversity can arise: three quarters of living species are animals, and most of the rest have formed by co-evolution with animals.[36]

[edit] Discredited hypotheses Main article: Discredited hypotheses for the Cambrian explosion

As our understanding of the events of the Cambrian becomes clearer, data has accumulated to make some hypotheses look improbable. Causes that have been proposed but are now discounted include the evolution of herbivory, vast changes in the speed of tectonic plate movement or of the cyclic changes in the Earth's orbital motion, or the operation of different evolutionary mechanisms from those that are seen in the rest of the Phanerozoic eon.

[edit] No explanation required

The explosion may not have been a significant evolutionary event. It may represent a threshold being crossed; for example a threshold in genetic complexity that allowed a vast range of morphological forms to be employed.[verification needed][81]

[edit]