DNA as a programming language

The Cadet said:

Just FYI: the term you are looking for is "discrete".

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My use of "binary" was intentional, but wrong, as I thought the rungs were base-2 rather than base-4.

[serious] said:

We can actually figure that out. Say we have a plate of 1 million bacteria. We will ignore neutral mutations, and assume there are 10 time the number of bad mutations as good. So 0.1% good, 1% bad. We'll say that on average a good mutation makes a bacteria 20% more successful, and a bad mutation makes it 20% worse. Let's grow the population to 1 trillion. We'll double the baseline each generation and adjust the good and bad off of that.
Generation 1: 10,000 bad, 1,000 good, and 989,000 neutral
Generation 2: 18,000 2,200 1,978,000
Generation 3: 32,400 4,840 3,956,000
Generation 4: 58,320 10,648 7,912,000
...
Generation 12: 6,426,841 5,843,183 2,025,472,000
Generation 13: 11,568,313 12,855,002 4,050,944,000
Generation 14: 20,822,964 28,281,005 8,101,888,000
...
Generation 20: 708,235,345 3,206,497,721 518,520,832,000
Generation 21: 1,274,823,622 7,054,294,987 1,037,041,664,000
Generation 22: 2,294,682,519 15,519,448,971 2,074,083,328,000

So 13 generations for the good to overtake the bad, and by the end of our run, the good was 7 times as common as the bad.

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Lets make a point of this even simpler.

10,000 bad in the first generation.

9,900 don't make it due to a mutation that prevents the bacteria from working.

90 don't make it from competition
and of the 10 8 are out competed in the next generation.

the problem is that creationists assume all bad mutations survive, but this isn't how evolution works. Look at humans only due to our morality can many of the bad mutations that would be in the last 100 still survive, but even then they get weeded out partly because less likly to reproduce.

These mutations happen, and cause horrible problems and disfigurements and such, funny how while these mutations and bad mutations happen all the time in nature, were not seeing the world dominated by eagles with badly misshapened beaks or wings that are just nubs and such, wonder why, is there something that weeds out the severe mutations and helps weed out the less severe?

Fact mutations happen, fact even if your figures are right the world isn't dominated by bad mutations, fact there must be a reason for this. Fact it's called natural selection and evolution.

ecco said:

pshun2404

You, like many others, believe in micro evolution but not macro evolution. But you cannot see that they are one and the same. The only difference is the scale of time and the impact of environmental changes.

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I realize that pshun2404 posted this but I would like to answer as well or pose a question. Isn't micro evolution changes within a species and this is with existing genetic material ie such as with dogs. They can become bigger, faster, have different colored hair, different length or texture hair ect. Or even with bacteria that has been used an an example. Bacteria that can evolve antibiotic resistance ability is a change in existing genetics where a loss of ability or a switching off of an existing function allows it to resist antibiotics. Nothing new as far as features like evolving wings when there were none for example are occurring. Where as macro evolution is changes beyond the species where a Dino species becomes a bird or a dog like species (Pakicetus) becomes an aquatic creature.

Stevevw

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Thats me.

I certainly did not say “ the majority of mutations are not going to add anything”. I said (in part) "...some may provide a tiny bit better eyesight...Those individuals who got the "better" have a tiny bit more chance of producing offspring."

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I thought that was the case anyway. You have sort of indicated that and if you were inferring that more than a small amount of mutations can add anything that is deemed as beneficial then that goes against what evolution says. Beneficial mutations are rare according to evolution. Most mutations are either neutral or a cost to fitness. But the evidence actually points to most mutations being a cost to fitness even beneficial ones. Even though there maybe a perceived benefit it is still a change to what was already working and best for an animal.

Stevevw

Three and a half billion years is a lot of time.

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The thing is when you look into the evidence it doesn't work out. The Cambrian explosion comes over half a billion years ago with the sudden appearance of all the modern body plans. They are complex and appear without any trace of where they came from. The complexity of the Cambrian creatures is just as complex as any animals that have lived. Evidence from tests done show that it is unlikely evolution can evolve small new functions that are viable that require multiple mutations working together. Even if they did they could do it in the time permitted. Evidence shows it would take more time than the earth has been in existence.

Estimating the prevalence of protein sequences adopting functional enzyme folds.
Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.
http://www.ncbi.nlm.nih.gov/pubmed/15321723

Stevevw

Change is new stuff.

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Not in an macro evolution sense. A change in existing genetics with either switch on or off an existing function ability that is already there. Macro change will require the addition of totally new genetic ability that was never there to switch on or off or recombine. Even if it could make a tiny change as stated in the evidence this would require to many mutations that would need more time that what is available.

We've gotten off topic, but...

All religious people pick and choose how much and what parts of scripture to take literally. Using christianity as an example...

• Some take all of scripture as 100% literal, OT and NT.
• Some take parts like Genesis as allegory.
• Some completely ignore the OT and just focus on Jesus.

Wherever this line falls, it defines the level of science that an individual accepts and what parts of science to disregard. Whenever personally held religious beliefs come in conflict with science, the religious beliefs will prevail.

There are tens of thousands of scientists who consider themselves to be christians and fully accept evolution. There are thousands of christian clergy who fully accept evolution. On the other end of the spectrum are people who will never accept parts or all of evolution because it conflicts with their “line in the sand”.

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I tend to not bring in religion at all to begin with. I like to deal with the scientific evidence and am willing to look at both sides. I dont take at face value what evolution claims like some do. In that sense even those who believe in evolution can have a faith in the scientists who say that evolution is fact. Some scientists don't want to consider they are wrong and don't want to know about any contradictions that challenge what they have already decided as true.

IE when they look for fossils that already assume that anything found in a certain layer is going to be that age no matter what. They will use the layer to date fossils and use the fossils to date the layers. If a fossil is found out of place that will make it a new species rather than consider it is a contradiction to the time lines and transitional links they have made.

A lot of the evidence is open to interpretation and it depends on what you have already decided is true. A lot of Christians accept evolution but it depends on what you mean by evolution. This is the bait and switch trick that evolution plays. They don't clarify what they mean. They can talk about examples for proof of evolution and use micro evolution examples but then apply that to macro examples without explaining how that can happen. So many Christians like myself except micro evolution where animals can change their existing genetic material to adapt to the changing environments.

But evolution takes what happens with micro evolution and give it more creative ability than has been scientifically verified. No tests have ever shown any ability for change to happen beyond existing genetic ability and the species. Anything else is speculation and assumption. A fruit fly is a fruit fly and has never shown any stage or indication of changing into a mosquito for example. It has remained a fruit fly with either extra wings or eyes which it already had. In fact the overall evidence shows that playing around with trying to change its existing genetics make it sicker and less fit.

Case in point....

Stevevw


I you look carefully at what parts of science you believe/disbelieve and what parts of scripture you believe/disbelieve, I think you will find a correlation.


I'll be out of town for a few days but I'll address your responses, if any, on Monday or Tuesday.

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I disagree. I think I am in a better position than many who have decided to only look at evolution as the answer to everything. They are the ones who have restricted their minds to be open to other possibilities. The fact is there are other possibilities besides Darwinian evolution and even the scientists who support evolution agree with this. Modern research shows that change through Darwinian adaptation means is not a major driving force for change. Other means such as HGT, epigenetics, developmental biology, genomics, population genetic theory and endosymbiosis play a bigger part.

The frailty of adaptive hypotheses for the origins of organismal complexity
The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the non adaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.
http://www.pnas.org/content/104/suppl_1/8597.full

Horizontal gene transfer: building the web of life
http://www.nature.com/nrg/journal/v16/n8/abs/nrg3962.html
Darwinian evolution in the light of genomics.
Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected.
Reticulate Evolution
Explains to non-experts how symbiosis, symbiogenesis, lateral gene transfer, hybridization and infectious heredity underlie reticulate evolution
http://www.springer.com/us/book/9783319163444

stevevw said:

I realize that pshun2404 posted this but I would like to answer as well or pose a question. Isn't micro evolution changes within a species and this is with existing genetic material ie such as with dogs. They can become bigger, faster, have different colored hair, different length or texture hair ect. Or even with bacteria that has been used an an example. Bacteria that can evolve antibiotic resistance ability is a change in existing genetics where a loss of ability or a switching off of an existing function allows it to resist antibiotics. Nothing new as far as features like evolving wings when there were none for example are occurring. Where as macro evolution is changes beyond the species where a Dino species becomes a bird or a dog like species (Pakicetus) becomes an aquatic creature.

Thats me.

I thought that was the case anyway. You have sort of indicated that and if you were inferring that more than a small amount of mutations can add anything that is deemed as beneficial then that goes against what evolution says. Beneficial mutations are rare according to evolution. Most mutations are either neutral or a cost to fitness. But the evidence actually points to most mutations being a cost to fitness even beneficial ones. Even though there maybe a perceived benefit it is still a change to what was already working and best for an animal.
The thing is when you look into the evidence it doesn't work out. The Cambrian explosion comes over half a billion years ago with the sudden appearance of all the modern body plans. They are complex and appear without any trace of where they came from. The complexity of the Cambrian creatures is just as complex as any animals that have lived. Evidence from tests done show that it is unlikely evolution can evolve small new functions that are viable that require multiple mutations working together. Even if they did they could do it in the time permitted. Evidence shows it would take more time than the earth has been in existence.

Estimating the prevalence of protein sequences adopting functional enzyme folds.
Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.
http://www.ncbi.nlm.nih.gov/pubmed/15321723

Not in an macro evolution sense. A change in existing genetics with either switch on or off an existing function ability that is already there. Macro change will require the addition of totally new genetic ability that was never there to switch on or off or recombine. Even if it could make a tiny change as stated in the evidence this would require to many mutations that would need more time that what is available.

I tend to not bring in religion at all to begin with. I like to deal with the scientific evidence and am willing to look at both sides. I dont take at face value what evolution claims like some do. In that sense even those who believe in evolution can have a faith in the scientists who say that evolution is fact. Some scientists don't want to consider they are wrong and don't want to know about any contradictions that challenge what they have already decided as true.

IE when they look for fossils that already assume that anything found in a certain layer is going to be that age no matter what. They will use the layer to date fossils and use the fossils to date the layers. If a fossil is found out of place that will make it a new species rather than consider it is a contradiction to the time lines and transitional links they have made.

A lot of the evidence is open to interpretation and it depends on what you have already decided is true. A lot of Christians accept evolution but it depends on what you mean by evolution. This is the bait and switch trick that evolution plays. They don't clarify what they mean. They can talk about examples for proof of evolution and use micro evolution examples but then apply that to macro examples without explaining how that can happen. So many Christians like myself except micro evolution where animals can change their existing genetic material to adapt to the changing environments.

But evolution takes what happens with micro evolution and give it more creative ability than has been scientifically verified. No tests have ever shown any ability for change to happen beyond existing genetic ability and the species. Anything else is speculation and assumption. A fruit fly is a fruit fly and has never shown any stage or indication of changing into a mosquito for example. It has remained a fruit fly with either extra wings or eyes which it already had. In fact the overall evidence shows that playing around with trying to change its existing genetics make it sicker and less fit.

I disagree. I think I am in a better position than many who have decided to only look at evolution as the answer to everything. They are the ones who have restricted their minds to be open to other possibilities. The fact is there are other possibilities besides Darwinian evolution and even the scientists who support evolution agree with this. Modern research shows that change through Darwinian adaptation means is not a major driving force for change. Other means such as HGT, epigenetics, developmental biology, genomics, population genetic theory and endosymbiosis play a bigger part.

The frailty of adaptive hypotheses for the origins of organismal complexity
The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the non adaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.
http://www.pnas.org/content/104/suppl_1/8597.full

Horizontal gene transfer: building the web of life
http://www.nature.com/nrg/journal/v16/n8/abs/nrg3962.html
Darwinian evolution in the light of genomics.
Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected.
Reticulate Evolution
Explains to non-experts how symbiosis, symbiogenesis, lateral gene transfer, hybridization and infectious heredity underlie reticulate evolution
http://www.springer.com/us/book/9783319163444

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Should be noted that for a bird to evolve from dinosaur majority of what genetic changes are done are to existing things, feathers are just like fur modified scales, wings are just bones of a arm and such in a different configuration, it's not like you go from X-Y and suddenly need 5000 brand new whole cloth genes, even the new ones are usually just copies of extisting ones allowed to mutate. This just deals with the first part may respond to rest when I get a chance.

stevevw said:

I realize that pshun2404 posted this but I would like to answer as well or pose a question. Isn't micro evolution changes within a species and this is with existing genetic material ie such as with dogs. They can become bigger, faster, have different colored hair, different length or texture hair ect. Or even with bacteria that has been used an an example. Bacteria that can evolve antibiotic resistance ability is a change in existing genetics where a loss of ability or a switching off of an existing function allows it to resist antibiotics. Nothing new as far as features like evolving wings when there were none for example are occurring. Where as macro evolution is changes beyond the species where a Dino species becomes a bird or a dog like species (Pakicetus) becomes an aquatic creature.

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What, exactly, would be the impossible step?

Taking the transition to an aquatic lifestyle as an example,
Surely being able to swim a bit better or hold your breath a bit longer would be purely in the realm of what you call micro evolution, right? Given that, what would prevent subsequent microevolutions (that's right, I made it a plural noun. deal with it) from taking a largely terrestrial creature to a largely aquatic creature? Once it's largely aquatic, what's to keep it from not bothering to go on land and becoming fully aquatic?

stevevw said:

Nothing new as far as features like evolving wings when there were none for example are occurring.

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I provided you a list of 50-odd examples of evolution producing "new information" or "new features" or whatever term you wish to use about this. Then you left the thread and didn't come back. You still haven't addressed any of that, and here you are again making the same claims.

loveofourlord said:

Should be noted that for a bird to evolve from dinosaur majority of what genetic changes are done are to existing things, feathers are just like fur modified scales, wings are just bones of a arm and such in a different configuration, it's not like you go from X-Y and suddenly need 5000 brand new whole cloth genes, even the new ones are usually just copies of extisting ones allowed to mutate. This just deals with the first part may respond to rest when I get a chance.

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I think this is a simplification of what needs to happen. It is common that people look at the obvious like scales to feathers and limbs to wings. Seeing some similarities and focusing on these as evidence that one creature can morph into the other. But when you dig a little and look at the detail of what needs to be changed it is far more complex.

Making out that something like scales evolving to feathers is logical and simple isn't the case. For starters the evidence points to feathers not being like scales. Scales are actually one uniform sheet of skin with folds in them. Feathers are more like hair follicles and have more of the proteins associated with hair than scales. So what was used as a similarity starts to become something that is more dissimilar and a proof against Dino to bird evolution.

Its not just a single step of scales or hair to feathers either. There are many steps including at the molecular level plus nerves and connections to the brain. Feathers themselves are an intricate network of design that just cant happen in one step. If it did than it points to there being some pre existing pattern and design that can produce complex features in one go. Evolution isn't suppose to have that level of design. This is the same for every change that is needed to make a Dino into a bird. There are changes in respiratory system, bone structures, nervous systems, muscles, tendons, and all the connections to the brain to tell these features what to do and how to operate.

Evolving a set of wings is useless unless you have all the structural changes of what is described as a pulley system that operate the wings. Otherwise they are just feathered limbs that have no use. The pulley system has several parts to it themselves that need to be there together to make them work and once again need to be evolved together even though there are separate parts to these systems. But evolving one little part wouldn't have any strong selection advantage so its hard to explain how this can all happen. Times this by all the small step by step complex changes that are needed through random mutations and natural selection and you begin to wonder how this could have happened.

On top of this the fossil evidence doesn't support any transitionals showing any of these small step by step changes. They only show complete sets of wings that have all the intricate details of designed wings with many components. Fossils are often contradictory to what the timeline has been claimed with more complete bird type creatures being found in earlier layers from others who were suppose to be the transitions. There have even been modern type birds found with dinos so it makes it hard to think that these birds are suppose to come from dinos who they lived with at the same time considering its suppose to take a long time to evolve.

So when you look below the claims you see that there is a lot more to it. Things that cannot be explained with random mutations. The evidence shows that random mutations dont create more complex functions that were not there in the first place. When you consider all this it isn't just about a creature changing some existing features and structures but also making new ones. Even so just to change these complex things which may involve 100s of random mutations all working together in the same direction would take more time than is available. Thats if it is continued to be selected for and each small step has any selection value. Thats if it doesnt cause the creature a cost to their fitness.

The Cadet said:

I provided you a list of 50-odd examples of evolution producing "new information" or "new features" or whatever term you wish to use about this. Then you left the thread and didn't come back. You still haven't addressed any of that, and here you are again making the same claims.

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Oh did I, sorry about that. I must have been side tracked. Ok I will go and look for the post as its only a few pages long.

PS I just looked and couldn't find anything. Can you give me a link or re-post the link. thanks.

[serious] said:

What, exactly, would be the impossible step?

Taking the transition to an aquatic lifestyle as an example,
Surely being able to swim a bit better or hold your breath a bit longer would be purely in the realm of what you call micro evolution, right? Given that, what would prevent subsequent microevolutions (that's right, I made it a plural noun. deal with it) from taking a largely terrestrial creature to a largely aquatic creature? Once it's largely aquatic, what's to keep it from not bothering to go on land and becoming fully aquatic?

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As far as I understand the small micro changes such as swimming a bit better are increasing the same existing capacity that is already there. But if its a dog like creature like Pakicetus then it isnt a natural swimmer and would struggle in the water. In fact it was suppose to be a good runner so why would it want to struggle in an environment that makes it harder to live. You would think after 100 generations when its still struggling that it gives up and moves back on the land. Or at least some of the group does and they get a advantage. It seems evolution wants to explain something that seems hard to believe for the sake of making transitions.

But to then make say a creature as you say hold its breath a bit longer with lungs to gills is then evolving a feature it didn't have. Learning to hold its breath longer is building on existing ability. But making lungs into gills is morphing something different and new for which the creature wouldn't have the genetic material to make. So it not only has to struggle with swimming but it has to struggle with holding its breaths with the wrong equipment all the time.

But it isn't just about one or two changes anyway. There is entire body structure changes, muscles, nerves, respiratory systems, neuron connections to the brain to signal all the new components to work at the precise time and in conjunction with many other things at the same time. Removing legs and morphing fins, rotating the hips to accommodate a flue tail and probably 100s of other changes. Many of these changes have sub systems and components of many smaller things that make them work that also need to change.

Its easy to picture a couple of changes happening but when you begin to list the 100s and 100s it starts to get harder to explain through random mutations that normally dont make better structures and add info and make fitter creatures but are changes to something that already works fine. But I agree I can see the sense of a creature evolving to get faster when they can already run. Or grow taller when they are already growing. But that is an existing ability and not something it never had in the first place like wings or gills.

stevevw said:

Oh did I, sorry about that. I must have been side tracked. Ok I will go and look for the post as its only a few pages long.

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Lemme help you.

http://www.christianforums.com/threads/evolution-creation-on-trial.7892639/page-21#post-68239480

At which point you basically admitted that you hadn't read any of the literature on the topic, and complained that it was too much to read through. Yeah, no kidding! You're trying to bash the consensus view of a massive scientific field with no background knowledge of that field or any of its research! Science is hard, and there's no shame in not knowing everything. But there is definitely shame in pretending to know something you very clearly don't.

Or, as I put it at the time:

Right, of course. Because when you make the claim "any function or ability that is claimed to be created is from existing info and ability that is being tapped into", and I show you countless examples of scientists showing this statement to be wrong, the first thing you want to do is pore through the research with a fine-toothed comb. Why didn't you do this in the first place? It could have saved me a ton of looking if you had educated yourself on the literature beforehand. It'd be like if I stepped up to bat against the consensus viewpoint that the earth moved around the sun, and didn't know what inertia was - I'd clearly be way out of my depth, and it would rapidly become clear to me that before I discuss the issue, I need to do some more background reading. I would not just immediately spring to the next argument!

Look, this is really not that hard to understand. You made the claim that novel functions cannot arise through genetic mutation. I cited something like a hundred published papers showing that yes, actually, they can and do. I can say with extreme certainty that this is the consensus view among biologists. Among those who do this research, it is well-understood (and has been for some 40-odd years) that gene duplication and mutation can lead to new functions arising in organisms and novel genetic information. People like Meyers who claim that it is impossible clearly have not done their research.

Now will you please admit that you were wrong so we can move on to the next topic? If you can't, I don't see much of a point in continuing this discussion, or addressing your other topics. I'm quite enjoying this exchange, but if you aren't willing to admit where you are wrong (and you are very, very wrong on this point), then there's not much point going further.

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Now here we are, some months later, and you're repeating the same totally false claim. Why? I showed you that you didn't know enough about the field you were critiquing, you essentially punted on trying to understand the issue, and here you are, months later, making the exact same claims. Now please, do the gracious thing. Admit that you're wrong, and stop making the claim.

@Not_By_Chance remember what you said about these discussions always going around in circles? And remember what I said about why they always go around in circles?

stevevw said:

Ok I think I was debating with a few different people and didn't get back to you. But I did say that I needed time to read these links. I remember reading one or two and then got side tracked. For me it does take some time because I have to not only read the articles but learn them as I go as well. Though I have some basic knowledge so I am not totally ignorant. I tend to try and read and understand what I am commenting on though I am not a biologists. So its a pretty big task you ask even for a biologist having a list of 36 odd papers to go through.

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Honestly, I'm not asking you to read those 36-odd papers. I'm asking you to admit that you are critiquing a deep, complex field you have no functional understanding of or training in. As previously stated: it's like trying to critique heliocentrism without knowing what intertia is.

But still I went through some and in the first few there doesn't seem to be anything that supports what you say. It talks about changes to existing genes. Numbers 1 and 3 seem to be talking about hybridization.

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I don't think you understood either paper. Either way, they're talking about the creation of novel genetic information. Not just old stuff being turned back on, but new functions arising from a recombination of existing genes and repurposing of existing functions. You know, the way a lot of evolutionary change works. It doesn't matter if it resulted from hybridization; the end result is still novel genetic material, the thing you seem to be claiming cannot happen.

Number 4 looks like it talks about existing changes to glucose.
Multiple duplication's of yeast hexose transport genes in response to selection in a glucose-limited environment.
Selection appears to have favored changes that result in the formation of more than three chimeric genes derived from the upstream promoter of the HXT7 gene and the coding sequence of HXT6. We propose a genetic mechanism to account for these changes and speculate as to their adaptive significance in the context of gene duplication as a common response of microorganisms to nutrient limitation.

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So they're derived from existing material. So what? Just about everything in evolution is derived from existing material. It's rather rare that genes are suddenly miscopied from non-coding strings (the only kind of "de novo" gene creation that is known to exist). Evolution is not an architect, it is a tinkerer, taking the parts present and playing around with them to make new parts. Duplication and mutation is enough to create literally any novel structure. Give me enough duplications and enough mutations, and I could go from the string "01" to the contents of "Skyrim.exe". This is not really a meaningful objection to the argument.

Though I cant access some of the papers full content because you have to pay it seems from their extract that they are dealing with taking away and adding back existing genetic material. The other thing is I have read that some of these tests dont verify the results and some of the conclusions are speculated as stated in the above paper. So its hard to say at this point but as I said I am not a biologists so I am not able to know this for sure and have to rely on the experts as to what they conclude.

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Well, see, that's the thing. The "experts" here are pretty much in complete agreement. There are about as many biologists who reject evolution as there are historians who reject the existence of the holocaust. Even from the six papers you looked at, 5 of them were clearly and unambiguously talking about novel genetic information (and I have no idea how #5 made it onto that list). It's trivial to show species that develop new functions or the ability to do different things. It's trivial to show how simple mutations can lead to an increase in genetic information. These are all well-established facts that any biologist worth their salt knows. The fact that you can find some hack at Uncommon Descent or wherever else that claims that these tests are "inconclusive" does nothing to reduce the weight of the scientific evidence here.

Why should I admit I am wrong when I havnt got any solid evidence that shows this so far.

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Of course you haven't. Personally, I'd think the fact that there's an entire field of study (evo-devo) dedicated to examining the mechanisms and effects of something you think cannot happen would be pretty solid evidence of how wrong you are, but that's just me.

They go around in circles because there is disagreement. I can post just as many articles as you have showing that evolution cant evolve new functions that make functional proteins.

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And they wouldn't matter, because no matter how impossible you might think it to be, we observe it happening. But just for kicks, let's look at your articles:

Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds
http://www.sciencedirect.com/science/article/pii/S0022283604007624

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Axe has stated on numerous occasions that his work is completely misinterpreted by creationists and that he has no association with the movement. It doesn't mean what you think it means. (This is something of a common trend.)

Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2

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Bio-complexity is not a real peer-reviewed journal, but rather the in-house journal of the Discovery Institute. It is not taken seriously by any portion of biological scientists, and is nothing more than an obvious attempt by creationists to make an end-run around real peer review. As such, I have little interest in articles published there. It's a bit like publishing your paper in a Bentham Science Publishers journal - if you had anything of value to offer, you would have published it literally anywhere else.

Distribution of fitness effects caused by random insertion mutations in Escherichia coli.
http://www.ncbi.nlm.nih.gov/pubmed/9720287

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Another paper you simply did not understand. Yes, it's well-established that most mutations are deleterious. This is because in most cases, any given genetic sequence in an extant animal is likely to be at some local fitness peak, and as a result moving away from that peak will cause short- or long-term loss of fitness. But you seem to be holding this up as evidence that beneficial mutations are impossible. That's nonsense. Not only is that claim not made within the paper, the paper explicitly refutes that claim in the discussion segment, pointing out that other studies on larger scales showed positive mutations. Yes, "0 out of 10,000 mutations positive" is a neat headline. But in reality, the headline is "0 out of 10,000 mutations of a specific type in a specific species in a particular environment positive (which is exactly what we expected because we would only expect to see positive mutations about once per 100,000).

Yes, there is disagreement. But finding disagreement on an issue is trivial. There are people here who deny the existence of DNA, believe that the earth is flat, or believe that the sun rotates around the earth. And just like with those examples, evolution has one side that has all the evidence, all the peer-reviewed papers, and a massive international consensus. The other has a strong inclination to lie about existing research (here's looking at you, Casey Luskin!) and a phenomenal lack of understanding.

stevevw said:

I think this is a simplification of what needs to happen. It is common that people look at the obvious like scales to feathers and limbs to wings. Seeing some similarities and focusing on these as evidence that one creature can morph into the other. But when you dig a little and look at the detail of what needs to be changed it is far more complex.

Making out that something like scales evolving to feathers is logical and simple isn't the case. For starters the evidence points to feathers not being like scales. Scales are actually one uniform sheet of skin with folds in them. Feathers are more like hair follicles and have more of the proteins associated with hair than scales. So what was used as a similarity starts to become something that is more dissimilar and a proof against Dino to bird evolution.

Its not just a single step of scales or hair to feathers either. There are many steps including at the molecular level plus nerves and connections to the brain. Feathers themselves are an intricate network of design that just cant happen in one step. If it did than it points to there being some pre existing pattern and design that can produce complex features in one go. Evolution isn't suppose to have that level of design. This is the same for every change that is needed to make a Dino into a bird. There are changes in respiratory system, bone structures, nervous systems, muscles, tendons, and all the connections to the brain to tell these features what to do and how to operate.

Evolving a set of wings is useless unless you have all the structural changes of what is described as a pulley system that operate the wings. Otherwise they are just feathered limbs that have no use. The pulley system has several parts to it themselves that need to be there together to make them work and once again need to be evolved together even though there are separate parts to these systems. But evolving one little part wouldn't have any strong selection advantage so its hard to explain how this can all happen. Times this by all the small step by step complex changes that are needed through random mutations and natural selection and you begin to wonder how this could have happened.

On top of this the fossil evidence doesn't support any transitionals showing any of these small step by step changes. They only show complete sets of wings that have all the intricate details of designed wings with many components. Fossils are often contradictory to what the timeline has been claimed with more complete bird type creatures being found in earlier layers from others who were suppose to be the transitions. There have even been modern type birds found with dinos so it makes it hard to think that these birds are suppose to come from dinos who they lived with at the same time considering its suppose to take a long time to evolve.

So when you look below the claims you see that there is a lot more to it. Things that cannot be explained with random mutations. The evidence shows that random mutations dont create more complex functions that were not there in the first place. When you consider all this it isn't just about a creature changing some existing features and structures but also making new ones. Even so just to change these complex things which may involve 100s of random mutations all working together in the same direction would take more time than is available. Thats if it is continued to be selected for and each small step has any selection value. Thats if it doesnt cause the creature a cost to their fitness.

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well one thing, we know feathers evolved on dinosaurs fairly early on, or even may predate dinosaurs as some of the earliest dinosaurs recently were discovered with them. And of course it's not one step, the earliest feathers were more like fur, and got more complicated and intricate as time went on.

And what are you talking about pully system? Dinosaurs had muscles and things already so it's just again modifications to the bone and muscles, were no talking about something brand new, it's always just modifications to that wich already exists. And wings evolved partly to help cover up nests and such, it's what we've found in the fossil record as we learn more and discover more fossils. Dinosaurs have been found using their arms/wings and feathers to protect/warm their nests just as birds, and it doesn't take much, natural and sexual selection can create many things rather easily. Remember they don't have to be used for the thing they currently do, many early dinosaurs had wing like arms before they could likly fly so there has to be a reason. One possible reason is camoflague as we found out with that one dinosaur whose feather colours we know, are very simular to modern bird colouring.

On some birds earlier then transitionals you don't understand how evolution works, this is like the old conard of, "If we evolved from monkeys why are there still monkeys." well because just because something evolved from something else doesn't mean they all go extinct, a good analogy is, "If you evolved from europeans why are there still europeans." the early bird liniedge could very easily still live on long after full birds evolved, and might want to check out your sources, we have found a ton of new dinosaurs and early bird fossils showing the transition in the last decade and a half.

Again what new features and structures may I ask you? You do realize yet again, most of whats different from bird to dinosaur is just modiciations on what already exists, hate to break this to you, especially since dinosaurs had wings/feathers and many other features thought once to be unique to birds.

pshun2404 said:

... nothing has shown the application of this in say changing creatures of one genus into creatures of an entirely different genus over time...

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Not surprising, as this doesn't happen and isn't proposed by evolutionary theory. In fact, if you were to find an example of this it would be a serious problem for evolutionary theory. That you mention it suggests you misunderstand the fundamentals of the theory.

stevevw said:

... if its a dog like creature like Pakicetus then it isnt a natural swimmer and would struggle in the water. In fact it was suppose to be a good runner so why would it want to struggle in an environment that makes it harder to live. You would think after 100 generations when its still struggling that it gives up and moves back on the land. Or at least some of the group does and they get a advantage. It seems evolution wants to explain something that seems hard to believe for the sake of making transitions.

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It needs a little thought and a little imagination. Think about current mammalian species that live around water, or spend much of their time in water, e.g. beavers, otters, hippos, seals. They don't 'struggle in the water' - they spend time around and in the water because they do better there. I'm sure you can come up with all kinds of reasons why a change in environment (plants, animals, climate, etc) might mean a land-based mammal might find life at the water margins better than on the plains or in the forests. Individuals will either adjust and adapt or die. Mutations that facilitate survival will tend to spread through the population, so it will gradually evolve to be better fitted to a watery context. If circumstances change again before significant evolution has occurred, the population might well return to the land - if they are more successful there. The population might also split, with one group continuing to be successful by or in the water, and another finding a niche back on land; they might slowly diverge into separate species, according to the selection pressures of each niche.

But to then make say a creature as you say hold its breath a bit longer with lungs to gills is then evolving a feature it didn't have. Learning to hold its breath longer is building on existing ability. But making lungs into gills is morphing something different and new for which the creature wouldn't have the genetic material to make. So it not only has to struggle with swimming but it has to struggle with holding its breaths with the wrong equipment all the time.

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Straw man. Lungs didn't morph into gills, nor did gills morph into lungs. They've always been different organs. The information is out there if you're prepared to check your facts before posting.

ChetSinger said:

I'm a programmer and I see some similarities with programming systems.

• The data is binary.
• Error-correction is possible because each kind of "bit" (rung) is made of two distinct parts.
• Genes and their switches remind me of objects and their methods.

Pretty cool, imo.

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i believe DNA could very well be thought of as some kind of compuational language.
i also believe serious effort should be made towards this concept.
here is another link that you might like:
ds9a.nl/amazing-dna/

ecco said:

Good software/hardware catches copy errors by reading the original and the copy and comparing the two.

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what happens if you don't have anything to compare to?
downloads from the internet for example?
surprisingly, there are ways to catch these types of errors too.
the most simple scheme is the CRC, or cyclical redundency check.

The Cadet said:

Honestly, I'm not asking you to read those 36-odd papers. I'm asking you to admit that you are critiquing a deep, complex field you have no functional understanding of or training in. As previously stated: it's like trying to critique heliocentrism without knowing what intertia is.

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I agree and I have always acknowledged that I am not able to understand the finer details at that level of understanding. But that doesn't disqualify me or anyone else from making comments from what we understand. You can get a commentary from those who do understand and by this you can then know what the evidence is supporting.

I don't think you understood either paper. Either way, they're talking about the creation of novel genetic information. Not just old stuff being turned back on, but new functions arising from a recombination of existing genes and repurposing of existing functions. You know, the way a lot of evolutionary change works. It doesn't matter if it resulted from hybridization; the end result is still novel genetic material, the thing you seem to be claiming cannot happen.

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If new genetic material is injected or bred into another creature then they gain new genetic material without the need for evolution through random mutations and natural selection. These methods are said to be other ways creatures get new genetic material. When I googled a couple of the papers they had a link to rationalwiki. Here it was having a go at creationism and their claim that no new function or info is created by evolution. It gave the example which was pretty easy to understand as this is a general site for the general public. It talked about something like insulin and how it can change and this was classed as new info or function. But these examples have been used before like with antibiotic resistance. This is playing around with existing genetics and the switching on or off of certain abilities within that existing gene. In fact most of the time its a loss of info to gain a new function or ability within that gene.


Simple Refutation
Perhaps the most remarkable aspect of this ID claim is that it can be refuted from first principles, without needing any specialized knowledge or evidence!
Suppose there exists a simple nucleotide sequence (called sequence A):
Sequence A: TACACACCCAAGACC
This sequence actually codes for the last five amino acids of the human insulin alpha-chain, but any other gene would suffice for this refutation. Suppose some particular mutation (mutation X) can transform sequence A into sequence B:
Sequence B: TACACACCCAAGGCC

This will change the insulin product into one that features a threonine instead of an alanine as the final amino acid of the insulin alpha chain. This will probably decrease the binding of the insulin in humans, but not enough to actually render it ineffective (pigs and cows have a threonine instead of an alanine in this position, and insulin-dependant diabetics are able to utilise porcine and bovine insulin). In any case, if a human had such a mutation, it would be almost certainly considered a loss of information by any creationist.

Suppose that this human reproduces and the child has another particular mutation (mutation Y) which transforms sequence B back into sequence A. If mutation X is one which subtracts information from a sequence, it follows that sequence A must contain more information than sequence B -- and mutation Y must, therefore, be one which adds information to a sequence. We have a mutation with a gain in information!
http://evolutionwiki.org/wiki/Evolution_of_new_information

So they're derived from existing material. So what? Just about everything in evolution is derived from existing material. It's rather rare that genes are suddenly miscopied from non-coding strings (the only kind of "de novo" gene creation that is known to exist). Evolution is not an architect, it is a tinkerer, taking the parts present and playing around with them to make new parts. Duplication and mutation is enough to create literally any novel structure. Give me enough duplication's and enough mutations, and I could go from the string "01" to the contents of "Skyrim.exe". This is not really a meaningful objection to the argument.

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Thats what is in dispute. Whether evolution can use existing genetics to make new complex living functions and features that will contribute to making new creatures for existing ones. The tests and evidence doesn't support evolution being able to mutate something from virtually nothing to a skyrim.exe. So what you are saying is that from the simple micro organisms that were suppose to start life, everything stemmed from this. The genetics of the first simple organisms has everything needed to make more complex living things. It was just a case of recombining and mixing existing genetic material somehow over and over again.

As far as I understand from what I have read its also about creating viable fit living things.Mutations can change the existing genes with copying mistakes but these are mostly harmful. Or they dont have any strong selective value. Something that may be considered beneficial and selected as such is very rare. In among that is a lot of non selected mutations and negative ones. So there should be a lot of sic, unfit and deformed creatures more than any small beneficial ones hanging around being weeded out. But what we normally see is fit well defined and formed creatures.

As I posted tests show that to even mutate a simple change in function in proteins thats fit and viable takes at least 7 mutations. To get that would take more time than is available. So its not that it may be possible its that its unbelievable to have happened. For the amount of complexity and variety that have ever existed or living now it would take an awful lot of very very rare beneficial mutations.

Well, see, that's the thing. The "experts" here are pretty much in complete agreement. There are about as many biologists who reject evolution as there are historians who reject the existence of the holocaust. Even from the six papers you looked at, 5 of them were clearly and unambiguously talking about novel genetic information (and I have no idea how #5 made it onto that list). It's trivial to show species that develop new functions or the ability to do different things. It's trivial to show how simple mutations can lead to an increase in genetic information. These are all well-established facts that any biologist worth their salt knows. The fact that you can find some hack at Uncommon Descent or wherever else that claims that these tests are "inconclusive" does nothing to reduce the weight of the scientific evidence here.

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Its not as black and white as saying that there is x amount of scientists on one side saying yes to evolution ans x amount on the other saying no. There is a lot of grey area in between where scientists are disagreeing. Many Christians support a form of evolution including myself so it also depends what you mean by evolution and thats the trickery. While evolution talks about the ability of micro evolution which has been observed and proven in tests they then use this to say that it applies to macro evolution which hasn't been observed or proven in tests.

Many scientists question evolution methods by adaptation through natural selection. They are saying that this is a minor driving force for any change. That more major driving forces are things like HGT, epigentics, developmental biology, genomics, symbiosis and endosymbiosis. So its not so black and white and you need to clarify what is evolution and what role it plays in the light of modern discoveries and evidence for what actually is the driving forces for change. Too much emphasis has been placed on Darwinian evolution and its ability to change living things and create new abilities and features.

Darwinian evolution in the light of genomics
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651812/

I will have to get back to the rest of your post. Thanks Steve.

stevevw said:

If new genetic material is injected or bred into another creature

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That's not what those studies were talking about either. Maybe one of them was, and I misunderstood, but quite a few were talking about gene duplication, which unambiguously increases the genetic information present and allows for new functions.

stevevw said:

As far as I understand from what I have read its also about creating viable fit living things.Mutations can change the existing genes with copying mistakes but these are mostly harmful. Or they dont have any strong selective value. Something that may be considered beneficial and selected as such is very rare. In among that is a lot of non selected mutations and negative ones. So there should be a lot of sic, unfit and deformed creatures more than any small beneficial ones hanging around being weeded out. But what we normally see is fit well defined and formed creatures.

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Mutations are mostly harmful, that's right. However, such harmful mutations tend to be filtered out very quickly. They aren't allowed to accumulate, as, by definition, they harm the individual's ability to survive. Neutral drift is possible because neutral mutations (the most common kind) are not filtered out, and positive development is possible because positive mutations are explicitly selected for. Not always, but often enough to have a tangible effect. This is not some big paradox; a wolf with a harmful mutation that makes it slower is far less likely to survive to pass on its genetics, so you're not going to see that mutation get passed on.

stevevw said:

There is a lot of grey area in between where scientists are disagreeing.

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Not really. Not when it comes to the basics (universal common ancestry, descent with modification, natural selection, speciation, etc.), and not among people actually working in the field.

stevevw said:

macro evolution which hasn't been observed or proven in tests

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Nonsense. The evidence for macroevolution is bountiful throughout the genomes of extant creatures, and we have observed it in a lab environment numerous times.

stevevw said:

Darwinian evolution in the light of genomics
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.

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While an interesting development, guess what effect this has on the overarching theory: very little.

The Cadet said:

That's not what those studies were talking about either. Maybe one of them was, and I misunderstood, but quite a few were talking about gene duplication, which unambiguously increases the genetic information present and allows for new functions.

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Ok well I will have to read the rest of them as well.

Mutations are mostly harmful, that's right. However, such harmful mutations tend to be filtered out very quickly. They aren't allowed to accumulate, as, by definition, they harm the individual's ability to survive. Neutral drift is possible because neutral mutations (the most common kind) are not filtered out, and positive development is possible because positive mutations are explicitly selected for. Not always, but often enough to have a tangible effect. This is not some big paradox; a wolf with a harmful mutation that makes it slower is far less likely to survive to pass on its genetics, so you're not going to see that mutation get passed on.

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I just dont think mutations, even positive ones have that much power. If a positive one is produced its only positive when everything lines up with the environment and what is needed at that time. Then things can change and what was positive in one generation may not be a couple of generation later. If a rare positive mutation gets through it can still be eliminated through circumstances. Most mutations are slight and dont have a great selective value. In fact it seems most are slight and have a negative effect and this is more dominate than anything else. So rather than be eliminated quickly small negative mutations can build up and have an effect of the entire fitness of a living thing. So how does this slight and rare occurrence which is mostly negative and a cost to fitness overall account for all the complexity and variety we have in living things.

Mutations Accelerate Each Others Damage
Robustness–epistasis link shapes the fitness landscape of a randomly drifting protein
http://www.nature.com/nature/journal/v444/n7121/full/nature05385.html
Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
http://www.sciencemag.org/content/332/6034/1190.abstract
Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
http://www.sciencemag.org/content/332/6034/1193.abstract

Then something like epigentics can put another spanner by working against what evolution does. Instead of creatures changing to suit their environments and lifestyles they are influenced to change by their lifestyles and environments. So its the other way around. This is where the more solid and predictable non adaptive forces of HGT, genomics, cross breeding and symbiosis can add genetic material that can be used for change more than evolution. In that way it is giving the creature more access to genetic material to use to become more adaptable and add variety. It seems the evidence is showing that creatures have more existing genetic material to tap into than what was though and even from an early stage in the history of life.

Not really. Not when it comes to the basics (universal common ancestry, descent with modification, natural selection, speciation, etc.), and not among people actually working in the field.

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Well its the evidence of things like the tree of life which common decent and evolution use to build their connection is being challenged. long with the other non adaptive driving forces for change it doesn't necessarily mean that everything can be traced back via one thing creating the other through evolution which is what is needed for common decent. If creatures mated more earlier on in the scheme of things which were more distantly related then they will be able to make new species without evolution with modification. It would be a sudden creation of new animals with evolution.

Nonsense

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. The evidence for macroevolution is bountiful throughout the genomes of extant creatures, and we have observed it in a lab environment numerous times

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Can you give some examples.

While an interesting development, guess what effect this has on the overarching theory: very little.

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I am not sure from what some are saying. Even the link I posted states for example that,
Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected.

Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept.

There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.

This is pointing to complexity not having a trend of gradually getting more complex from building on previous genetics. That it is more sporadic and horizontally shared. There is a very weak selective force for change and its more likely for sharing existing genetics through non adaptive and selective methods. The evidence points to there being even complex genetics very earlier on that may have been there from the beginning and then being tapped into and shared. There was a sudden appearance of complexity and the fossil records along with the tree of life not supporting what Darwinian evolution has claimed. Non adaptive forces seem to fit the evidence better what living things were like in the past and for how living things gain genetic material.

Another paper along these lines is.
The frailty of adaptive hypotheses for the origins of organismal complexity
http://www.pnas.org/content/104/suppl_1/8597.full

Many scientists are starting to question the Darwinian theory of evolution based on new evidence.
James A. Shapiro's Evolution: A View from the 21st Century proposes an important new paradigm for understanding biological evolution. Shapiro demonstrates why traditional views of evolution are inadequate to explain the latest evidence, and presents a compelling alternative.
http://shapiro.bsd.uchicago.edu/evolution21.shtml

Networks: expanding evolutionary thinking.
http://www.ncbi.nlm.nih.gov/pubmed/23764187

The Evolution Revolution - Why Thinking People are Rethinking the Theory of Evolution
This hard hitting, groundbreaking book examines the latest scientific studies and offers compelling evidence that current data neither supports the theory nor the fact of evolution. Instead, the data actually supports an entirely different theory, the Nonrandom Evolutionary Hypothesis, which, if correct, will have far-reaching consequences for humanity and revolutionize scientific research and education.
Spetner proposes what he calls the "Nonrandom Evolutionary Hypothesis" (NREH) where changes in populations occur due to nonrandom processes, as if they are preprogrammed to evolve in certain ways.
http://www.amazon.com/The-Evolution-Revolution-Thinking-Rethinking/dp/1607631555

Another paper along the same lines that is saying that genetic material especially the basic building blocks for life were always around and in fact may be natural laws in nature just like in physics.
The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law.
However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction.
http://www.ncbi.nlm.nih.gov/pubmed/12419661

Does evolutionary theory need a rethink?
The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science1, 2. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day.
http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080