Every time a theist proposes the invalidity of evolution, they immediately follow it up by proving they don't know evolution at all. This mutantshark guy is especially dimwitted, attempting to disprove evolution through his ignorance in a thread that has already permanently refuted everything he has said or will ever say on the subject, and refuted it in the first post.

A classic example of the sheer stupidity that theists exemplify.

DNA contains the exact information for the embryo to multiply, change into different kinds of tissues and finally form various organs of the animal with precise detail. How ever its still not known how all the information is coded. When we consider cloning, there will be differences of the effect of mitocondria (major effect) and mutations(in some cases). But if you achieve monozygotic cloning with no mutational effect it will be exactly the same.

By neutral organ formations, I dont imply cancerous growth, but some thing like a new organ.
I really want to run a simulation to show you the actual effect. A mathematical iteration matching the following constraints:
1. "The majority of mutations in a multi-cellular organism's genome are neutral and do not harm the organism[1]" means at any point of time, probability of a new generation animal developing a neutral organ is much higher than that developing a useful organ.
2. "Occasional mutations are unfavorable. As a result of natural selection, unfavorable mutations will typically be eliminated from a population while favorable and neutral changes accumulate. The rate of elimination or accumulation depends on how unfavorable or favorable the mutation is". Implies natural selection eliminates unfavorable ones.
3. "rarely a mutation will be favorable." An organ developing into a fully functional one will depend on how many favorable mutations it will get.
4. The chances of an organism surviving depends on natural selection
We can argue on this after running this - not very complex mathematical simulation model (how the simulation model should be can be discussed in future posts. You can suggest your view). Is this OK?

But according to evolutionists, organs developed due to random mutations over many generations. If you say it will only result in a mess then you are disproving theory of evolution

This is just an assumption.

You are comparing the chances of survival between an animal with no neutral organs and one with only functional organs. Consider the case when all have multiple neutral organs (there is no golden reference)

I defined the concept of energy not one quantity of energy. Quantitative definition of energy is different its some thing like this "One joule of energy is the energy required to move an electric charge of one coulomb through a potential difference of one volt" Where as Energy is defined as work done in unit time.

Looks like we have the same educational background "University Degree (with Honors) in Electrical Engineering"

I believe that physics and mathematics converges at some point far below the level where current researches are taking place. And if we start deriving right from there (which may be long process) we can cover every thing including particle physics, chemistry, newtonian physics and even biological sciences. And in that case you wont have any difference between all these sciences. Whole universe and every thing in it are part of a complex mathematical equation and are balanced through mathematical equations. The only problem in studying that is that you will need to use all the processing power in the universe to uncover it and still fall short.

This is not such a difficult thing to simulate except for the fact that the simulation is going to be a mathematical one. Mutations can be simulated as random points on an XY plain with multiple successive iterations to create the effect of multiple generations. Constraint of Natural selection can be introduced by successively removing the ones that get >X% of harmful mutations.
"I am also deeply experienced in computers and software development" - I'm also experienced in computer science and software development (CPU design, OS internals and system software to be precise).

Me too

The DNA of the fertilized cell contains only a part of the information required to quide the maturation of the organism. The rest is in the other structural and chemical components of the cell, and some is in the environment it evolved in.

It would be impossible to reconstruct the whole organism if all you had was the DNA extracted from the nucleus. There is nowhere near enough information there.

No.  I realize you do not mena to imply 'cancerous growth', but a 'useless organ' is pretty much equivalent to that, or perhaps a benign tumor.

Without any function, there is no direction for the random process of mutation to go, so a series of random mutations is vastly more likely to generate a formless lump of cells than anything we could recognize as an 'organ'.

And a creature with a bunch of useless organs is going to be at least slightly less fit for reproduction than one not so encumbered, at each generation.

IOW, a useless organ is not a neutral mutation. It consumes resources for no purpose. It IS equivalent to a cancerous growth, which IS the normal effect of a mutation sufficient to cause some sort of growth of tissue, a necessary part of the formation of a new organ.

A major problem with cancer is the same as would apply to a 'useless' organ. If it grows large enough, it can seriously interfere with the proper functioning of the body, and has no positive contribute to compensate.

No, they develop step-by-step by random mutation plus natural selection at each step (ie each generation. Without the inevitable process of 'selection', ie differential reproductive success, random mutation would indeed lead to a mess.

Again, a critter with useless organs is likely to be less successful than one not so burdened. Even if it is only slightly less successful, that is all it takes for such useless mutations to not propagate.

You are not describing Darwinian evolution, just random change.

No, it is the mechanism of evolution.

The 'golden reference' is efficiency - less useless organs means a more efficient organism, therefore likely to be a more successful one at reproducing.

An extra, useless organ IS an unlikely and harmful mutation. To be 'neutral' it would have to have some functionality to offset the resources it required - space, blood supply, etc. A useless organ is the same as a benign tumor.

Energy:

You have still just described how we quantify energy, not what it is.

Now that is 'just [a series of] assumption[s]'.

The universe is not mathematics.

Mathematics is an idealized abstract description of the workings of the Universe as we perceive them.

Genetic algorithms do NOT proceed by "removing those that get  > X% of harmful mutations". That is totally misunderstanding the whole thing, the same kind of misunderstanding you show of natural evolution itself.

It selects those which best and most efficiently perform, or come closest to performing, the target task. That is the criterion, the measure. We don't even try to identify and classify the 'mutations'. It is overall success of the algorithm, just as the measure in natural selection is overall reproductive success, not a count of useful or harmfull mutations.

'Mathematical' does not constrain anything. A series of copies of the algorithm are generated with random code variations, and run, and their outputs compared using some 'scoring' rules giving appropriate weight to how close they get to the target. The top performers are used as the starting point for generating the next set of trials.

You seem to have a somewhat distorted or peculiar view of what natural selection is and how it works. It is simply competition between variants, based on which variant survives to contribute the greatest proportion to the next generation, which requires not just survival, but mating success and numbers and viablilty of the resulting offspring. In genetic algorithms, the selection is based on different tests, and reproduction is not involved.

But it is still the basic algorithm of random small variations followed by selection of those best matching a standard of some kind, then using those selected as the starting point for the next round.

Well it seems you have more work to do getting up to speed on evolution, for a start.

So let me ask about your idea of there being latent organs just waiting for conditions to change so that they can burst out to meet new needs.

OK, so why has nobody ever noticed them before?  Seriously, uncounted thousands of surgeries are performed every day in nations around the world, all with different agendas.  No doctor has ever written a paper about those little bit of tissue that don't actually do anything.

If they exist, then they must have existed long before evolution existed on a theoretical basis right?

How about butchers?  If they are present in humans, then why not in animals as well?  Butchers would not know or care about what they don't do but they would be interested in whether they are good to eat or not.  We have been slaughtering animals for thousands of years.  Surely people would have noticed them by now?

Really, the fact is that new organs don't evolve like you think they do.  The basic layout evolved in the Cambrian and what came of that is so complete that only minor changes in shape have happened since then.

mutantshark.

 

Your obsession with reducing the process to a count of beneficial vs harmfull mutations is totally misunderstanding evolution.

It is the net effect of all the genetic variations which matters. It is not possible to even accurately assign a value to the 'benefit' or 'harm' of any specific mutation, there is just so much interaction in the complex system that is a living organism and its environment, all of which affects the impact of any genetic change. 

This failure to understand evolution was most clearly demonstrated in how you thought of 'genetic algorithms', in suggesting they would work by assessing the proportion of "harmful mutations'. That is just so wrong. Why you would think in such terms in such a context, rather than the blindingly obvious procedure of assessing how well it performed in the intended task, just stuns me. If you use an algorithm to find a strategy to maximize investment returns in business, a typical application, you assess the best ones by measuring the yield they produce in practice, not by looking at the code they generate. What is your problem??

You seem to think at a level of detail while missing the 'bigger picture', which would be consistent with your success at Math, and thinking of Physics as being closely related, and the 'ultimate theory of everything' being at an ultimate level of detail 'below' what we know now. 

I acknowledge the importance of understanding the underlying components and structure of reality, but see that it is at least as, if not more, important to grasp general principles which apply to all interactions, regardless of whether the interactions are between electrons or stars. Things like complexity theory, chaos theory, information theory, the mix of randomness and deterministic mechanisms that govern reality, the emergence of complex structures and systems from simpler ones, the whole being more than the sum of its parts, and so on. These things do not depend on the results of Physics, and Mathematics is just the indispensible tool for studying such things, but not the ultimate source of any new ideas that come out of it. The evolutionary algorithm, of the effect of random changes being repeatedly winnowed down by a non-random process of selection, is a great example of such principles.

Multiple changes will often have a different net effect from what a simple accounting process might predict, even if we could do it.

A change in one generation which has no apparent effect can prepare the ground for a subsequent mutation which would not 'work' without the earlier one.

Or a 'neutral' or 'harmful' change may be a benefit in a different environment, like longer fur will be a disadvantage, except to those individuals who move into a colder environment, maybe move up to higher altitudes or latitudes.

Are you really so convinced you have found a flaw in "evolution", that you are unable to acknowledge the possibility you have got it wrong?? 

 

 

If you dont agree to my simulation logic then tell me one that you think is right (based on Theory of evolution) so that we can simulate the development of a multicellular organism. The initial creature should be multicellular with 'no organs', developing organs gradually through mutations. Less fit versions die out based on number of unfavorable mutations it acquires and ones with more favorable mutations reproducing more as you want. We can also eliminate some percentage of ones with high number of neutral mutations.

To test evolutionary theory, you would randomly vary the genes in a group of organisms, based on the latest ideas of gene sorting and mutation rates, and model the reproductive success of the group. Since there is no clear way to predict the likely contribution of a specific gene variant until you see how the breeding success of the group is affected, your idea of assessing the genes themselves is pointless and unworkable.

What you could do is run a genetic algorithm with the target being maximum reproductive success. The test of the viability of natural selection would then be to change the rules for successful reproduction, simulating a significant change in the environment, and see how effectively the model organisms adapt.

What has been done, which is more realistic and practical, is run a program which randomly varies settings in a model which affect the appearance of some drawn object in a sufficiently complex way to roughly match the relationship between genes and physical characteristics in nature. At each generation, the user selects which variants best match some target, and we observe how quickly and effectively it converges on the target.

In either case, after achieving some measure of change, you can then look at the 'genes', and see how they have changed. You can prove nothing about the viability of evolution by natural by trying to anticipate the effect of individual changes in the DNA. Other more sophisticated simulations have continued to support evolutionary theory in general, sometimes to refine the details.

There has also been at least one now-famous evolution test based on exposing bacterial colonies to different selection pressure, such as replacing some of their normal nutrients with ones they don't normally metabolise, and seeing if they can evolve the capability to utilize them, given long enough. Which they did.

It would be hard to do the equivalent in higher organisms, since the generation time is much longer.

Your hypothesis has another problem, I just realized - it would require continuing increase in the number of genes, which doesn't happen within species. We actually have shorter genomes than many 'lower' organisms, which is a further problem for your simplistic idea.

The 'less useful' will eventually get dropped, crowded out, even without any other mechanism. Each 'new' neutral gene must replace a harmful or beneficial one. I the first case it represents a positive mutation, therefore will be selected for, so reducing the number of 'harmfuls'. In the second case, it will reduce the fitness, therefor is a negative change, therefore will be selected against, thereby reducing the number of neutrals.

 

 

"It did not take modern science to notice that the patterns on the finger-tips varied significantly from person to person, just eyes." The uniqueness of finger prints is discovered in recent history (18th century) . palm prints were used to identify people using the ridges (caused by folding and friction), but not the ones in the tip of finger. If you argue that its a metaphor, then tip of your hair should make more sense as extremities of the body.

Any way if it is the anticipation of modern scientific discoveries is my point, then I can fill a whole page with that for eg. the verse "Have We not made the earth as a bed, and the mountains as pegs? And He has set firm mountains in the earth so that it would not shake with you" is clearly a modern scientific discovery (Plate tectonics) and cannot be seen to any one with "just eyes".

But there is less decease and more health, less death and more life.. You are again looking at a small bad side of it compared to more on the bright side. Then the very idea of life in this world is "as a test", you are rewarded or not based on how good you are, in the world hereafter. Secondly I dont believe in "miracles of cure" and so on. Every thing about god is hidden and understandable only through logic you have to study the logic and check for yourself if it can be truth or falsehood.

The quote does not require the idea of being truly unique in the way we used them for ID in recent times - DNA has largely replaced fingerprints where it is available.

It merely requires it to be significantly different, in the same way that faces are, for that quote to make perfect sense in the context.

You are quoting from an Islamic account, which I have heard before, and it is a totally inaccurate description of how mountains fit into the structure of the crust. Mountains are just thicker parts of the crust, and the underlying shape is a gentle downward bulge to match the extra weight above. Nothing remotely like 'pegs' - and the guy on another forum pushing something like this argument showed some drawings, or linked to them, which showed  the idea they had in mind. Needless to say the drawings bore no resemblance to what we know by various geological techiques.

Also, mountainous areas can often be the source of earthquakes, as a fews ago in China. This is because they frequently arise at the boundaries where two techtonic plates meet, and the resultant stress as the crust is pushed and folded into mountains often results in earthquakes.

So that reference simply proves that the writers not only lacked 'advanced knowledge', they were actually quite wrong.

So for things that eyes were adequate for, they made some statements consistent with modern ideas, but not anything clearly beyond what you might conclude from basic observation.

But when it comes to something beyond what one can observe readily, the internal structure of the earth's crust, they got it completely wrong. Big surprise!

There is leas disease in countries that have benefited from the application of modern science modern science in medicine and the design of water purification and distribution systems, as well as sewage removal and treatment. That is man's work, not God's, so he cannot take the credit. He could have more clearly explained the germ theory of disease, vaccination, how to make and use antibiotics, if he were serious. Or just not filled the world with so many harmful organisms.

There are fewer deaths through man's violent actions, per capita, now that God belief has declined overall, then back when the Abrahamic religions had more control.

But, in total, there are more deaths from natural disasters, which are clearly God's responsibility if he existed, now than there used to be. What positives would you point to that you would clearly attribute to 'God'?

God is not a logical concept. A 'loving' one is even less logically justifiable. You cannot prove God through logic, especially if he is hidden. You need objective evidence that a God exists, which is impossible, since a 'God ' could manipulate the 'evidence', and even our interpretation of it, in any way he wanted to suit his unknowable ends.

The fact that to many people nowadays, the world is MORE understandable without the assumption that there is a God, is all we need to dismiss it.

They fail so often I'm beginning to wonder if they're his ideas.

Neutral mutations will progressively disappear.

They will start in one individual, and if we assume basic sexual reproduction, will be present in half his offspring, a quarter of the next generation, etc.

The only way it could avoid that happening would be if it gave some advantage to the descendants that inherited it, ie it would have to be positively beneficial, by imparting some improved chance of surviving to reproduce.

Hope that makes it clear, mutantshark, why our bodies are not littered with 'useless organs'.

I would think that to persist, they would have to be common mutations which appear with sufficient frequency to never quite get diluted out by genetic mixing through reproduction. And of course, in a finite population, there is a maximum dilution...

And you're right, to be a more accurate simulation, you would have to start with a realistic population size, probably with a randomly shuffled set of 'genes'.

I doubt mutantshark will grasp these 'subtleties', I'm sure they are not mentioned on the kind of web-sites he appears to ge his information from...

 

You're assuming that there are no variations in prey populations across these regions. There almost certainly are. I would strongly wager that the variations in venom follow variations in prey availability and susceptibility to the different kinds of toxins. Perhaps one works better on mice or other rodents, and one works better on lizards or something else that rattle snakes eat. Regional variations on rodent/lizard prey ratios would then cause regional differences in selective pressures on the toxins.

It's similar to skin pigmentation variation in humans. In areas with greater exposure to the sun (not only latitude, but also altitude and other factors), the indigenous populations have darker skin to protect against UV. In areas with less sun, the skin is paler, to allow for more production of vitamin D. A 'seemingly' neutral and consistent regional variation ends up having an underlying selective pressure after all.

AIGS, whenever you see a consistent direction in the evolution of a feature over a long period of time, you can be guaranteed that it provides some important advantage. Neutral variations are, by definition, randomly distributed, and would show a bell-shaped variation over long periods of time, not a directional variation. If leg length were neutral in horses, you would expect to see all sorts of variety in horse leg length (in the wild; obviously breeders can artificially select for shorter or longer legs). You'd have horses with little tiny legs, and horses with big long legs, and they would all do just fine in their environment. But obviously, that wasn't/isn't the case.

I wonder, is your point here to emphasize the 'seemingly', or the 'neutral', because it is clear to me that you are identifying a non-neutral variation: "they would be better able to outrun predators and then that seemingly neutral mutation would spread across the population in general"

Truly neutral variations are, by definition, purely randomly distributed. They fall under the category of Genetic Drift. It is a significant factor in evolution (I just think your examples weren't representative of it), but it doesn't explain directional, consistent variations.

I think a bit of background is required, so we can be sure we have a simulation that takes account of work already done.

Here are several links of relevance:

http://www.talkorigins.org/indexcc/CB/CB340.html

http://www.uctv.tv/search-details.aspx?showID=16421

http://www.sciencedaily.com/releases/2011/08/110810085544.htm

http://en.wikipedia.org/wiki/Tierra_(computer_simulation)

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

I still don't see how you could predetermine what mutations are likely to be harmful or beneficial or neutral. Even there it would have to be a scale of definitely harmful to definitely beneficial, not just three states.

The ultimate test is really applied to the whole genome, including any recent changes.

Simply expose it to genuinely random mutations. Period. 

If you want, try applying different functions for generating the actual mutations from the raw random number generator.

Matching the exact shape of peg is not the intend here but the utility of one. When it says surface of earth is like a bed, it actually means a layer that floats on some thing, and its effectively true. check this - http://www.platetectonics.com/book/page_4.asp. Not that it should look like a bed - usually flat and rectangular in shape.

The usage 'pegs' really implies the effect of pegs (attaching a less stable object to a firmer object to restrict the movement of the former). In this case the tectonic plates float on the free flowing upper mantle, mountains have deeper roots that go into the lower mantle(that's harder) and acts like pegs restricting the movement of crust. As you said, it doesn't look like a peg but acts like one. In many cases, when mountains form due to the collision of plates, one side of the plate goes into the lower mantle forcing a sharper wedge like part into the lower mantle again acting like a peg.

This is true but imagine if mountains weren't there. There would have been much heavier earthquakes, more often.

God does not call this world the best place to be, He calls it a world for testing whos good and whos not. Having its share of happiness and worries. You will justify a loving God if you look at the brighter side of life. My friend recently visited Guinea, according to him the country is so poor that most of the population is deprived of even electricity and other basic stuff, but he found the people happier and more genuine than the people in developed countries. So, is it that the people are making world a bad place or God? Dont think about magical curing, publicity stunts and human Gods as part of religion, they are not, and if any religion claims that they are, then its a false religion.

 

 

This is an easy to read explanation from Dr. Lynn Fancher at the College of Dupage in IL.  Maybe not Ivy League, but the website looks to be pretty comprehensive.

http://www.cod.edu/people/faculty/fancher/genetics/Mutation.htm

 

Seems to me, a lot of what every one is talking about is not a mutation, but rather a series of mutations.  Each tiny change in the DNA adds up to venom that appears to be overkill.  Literally.

I will bet that the extreme toxicity of the venom is beneficial - or it wouldn't be selected for in that population.

 

 

Well, I remember that Deluded God posted a very long paper on the matter a couple of years ago. If memory serves, there are 64 possible codons. Thus, there are different codons that code for the same amino acid. If you look at it that way, then there must be true neutral mutations.

 

That again was not where I was going.

 

Rather, what I am trying to express is that mutations can be relatively minor and confer no survival advantage. Perhaps a change to a protein structure that does not affect the active site might be an example.

 

Yet given even a low level of reproductive isolation, a new allele can take hold in a sub group. The chiclid fish in lake Tanganyika would be an example. From one bay to the next, there is little variation but from a longer distance, the variation can be great. Fish from opposite ends of the lake are generally infertile with each other. However, even though a specific mutation may not affect reproductive success, they do add up and tend to become significant.

They eye did not start as a patch of photo-receptors. It probably started as a one or two heat-sensitive nerve ends in a useful position on the head. That is all that would be required.

A full independent organ, not an accidental copy of an existing one, or part of one, would be extremely unlikely to arise from a single mutationnidi ie in one generation. 

Even if it did, unless it had some significant benefit to the individual in which this particular mutation occurred, it would only appear, on average, in half the offspring of that individual who survived to reproductive age. And then it would appear in a quarter of their offspring who survived to maturity. And so on.

The only way it could spread to the species would for it to have a significant survival and reproductive benefit, ie NOT NEUTRAL!!!

A mutation occurs in a single individual. It cannot spread to the whole species unless it enhances reproductive success significantly.

mutantshark, please switch on your other brain cell before replying.

 

I only respond to part of your posts as they are usually so large, and I have little time.

Briefly, no organ is neutral.  N.O.N.E.

Reason - energy requirements.  All - ALL - organisms must live by the laws of thermodynamics.  They must - absolutely must - take in enough energy to run all of their organs with enough left over for reproduction.  Extra useless organs cost the organism energy.  Energy they could be spending on having more offspring.  And thereby increasing the chances of their genes making it to future generations.

That is all evolution is about.  More babies.  Useless organs reduce the chance of increasing your number of offspring, therefore, there is no such thing as a useless/neutral organ.  All such organs will cause a reduction of offspring.  Therefore, all such organs are negative mutations, not neutral.

 

 

Once again mutant, tell me how an individual neutral mutation can spread to a whole species. 

You said at the beginning that if evolutionary theory were true, creatures should be riddled with neutral mutations.

It is true that a lot of the differences between equivalent genes in different individuals have no specific advantage, so could be legitimately labelled 'neutral'.

There may well be a lot of neutral variations, but they are not copies of a specific neutral mutation. They reflect the truth you try to build your misconceived argument on, that most mutations are 'neutral'.

So they reflect the underlying 'background' mutation rate, which will just lead to continuing randomising of the DNA sequence. If the randomising gets too serious, it will mostly lead to dysfunction, and be selected out.

To produce a new but neutral organ would require many generations, which would require something very different from this continuing random reshuffling, which is what leads to the many individual neutral variations you are referring to.

 

The most appropriate word he uses in that quote is 'imagine'. 'Cause it only works in his (uninformed) imagination....

 I would like to update the first post with even more specific examples of evolution.

Please continue to post them.  Mods feel free to move any offtopic conversation anywhere else.  This thread is only to post links or specific proofs of evolution.

If, across all individuals in a group, an average of more than two neutral mutations occur, then the number of such mutations may indeed grow.

 

But these will not be specifically related, so will not produce any species-wide characteristics that could be part of evolution.

 

It is still true that it would require that in at least one individual, the net effect of all the mutations it has inherited have a significant positive effect on survival to reproduce, for that set of mutations to have a chance of spreading, and so become a part of evolution.

 

If this was a problem in evolutionary biology I would study it. Unfortunately, it is only a problem with your strawman version of it and you haven't written your text yet.

 

It hasn't changed because it works.  If it (any pattern or adaptation) didn't work, it would change or die out.

Haven't you read my earlier posts?  The theory of evolution:

A change in the frequency of an allele (gene) in a population of organisms over time.

Just what is so problematic about this?

You might try reading Mistakes were made but not by be.  A fascinating book written by a couple of psychologists about how we all self justify.  You might be able to figure out why you are having difficulties with comprehending peer reviewed and tested science.

Neutral organs and energy:

All organisms must adhere to the laws of thermodynamics.  Neutral organs cost the organism energy.  Energy that could be used to reproduce instead.  Therefore, there are no neutral organs because there is no spare energy for them.  You did say you were an engineer and had studied physics.  Why do you seem to believe the various laws of energy consumption and conservation don't apply to biological systems?

And before we get onto to TOE violates the 2nd Law, recall that the sun and the molten core of the earth add energy to our ecological systems.  And therefore, the ecological systems are not closed.  But that does not mean that somehow we are all perpetual motion machines that have vast quantities of energy to waste on useless organs.

 

PS - I too, have an engineering degree.  My elective science was Ecology and Evolutionary Biology.  Doesn't make me an expert, but it means I have had some formal training.  And a big chunk of ecology is figuring out the tropic (energy) levels in any subsystem.  I have continued to read in evolution and ecology because I enjoy the subject.