Natural selection v Intelligent design

[quatona]

Yes I did read it but as I said I hadn't even got to that point. Lets just say I was trying to illicit some acknowledgement about the fine tuning argument by giving it some air time. It seems I was hitting a lot of resistance about something that has been acknowledge by many and is accepted. Now why would that be.

Well, if somebody told me "this house is fine-tuned to let the sunshine in" I would expect it to have transparent stuff all over the place - and not just an insignificantly small hole somewhere in the basement.

 

[Foxhole87]

Well, if somebody told me "this house is fine-tuned to let the sunshine in" I would expect it to have transparent stuff all over the place - and not just an insignificantly small hole somewhere in the basement.

Best of luck. I did my best to explain this but this concept, and everything that would go along with it, is something that he either won't comcede or simply can't understand.

 

[quatona]

Best of luck. I did my best to explain this but this concept, and everything that would go along with it, is something that he either won't comcede or simply can't understand.

I know - there´s not much point in trying to explain anything to him. It´s a waste of time.

The issue is actually quite simple: Unless we assume a certain outcome to be intended by a designer (or already have similar things - of which we know they are designed - to compare the thing in question to), there are no criteria available for telling intentional design from non-design. Neither rarety, unlikelihood or frequency, neither simplicity nor complexity, and - first of all - neither incredulity nor amazement.
The teleological argument is nothing but a question begging mess.

 

[quatona]

And, btw., the only design we are familiar with and can conclude from is human design. So let´s not forget that every statement of the "this looks designed" sort silently means "this looks humanly designed".
Of course, this opens the opportunity to declare something divinely designed even if it does not "look (humanly) designed". ("Who are you to tell God how to design things??").

 

[bhsmte]

Best of luck. I did my best to explain this but this concept, and everything that would go along with it, is something that he either won't comcede or simply can't understand.

This is where the denial comes in handy, to protect the belief.

 

[stevevw]

Well, if somebody told me "this house is fine-tuned to let the sunshine in" I would expect it to have transparent stuff all over the place - and not just an insignificantly small hole somewhere in the basement.

I think you are looking at it the wrong way. Its a fine tuning argument not a broad tuning argument. So we would expect the sunshine to end up specifically in that little hole and not all over the place. But if it was based on just a random process you would expect the sunshine to end up as you said all over the place. But its not and over 122 physical constants make it specifically fine tuned to happen in the first place and at this point to happen only here on earth.

Here are some of the tunings that need to be exact to for existence to happen in the way that it can produce life as we know it. Any minute change to these conditions and we wouldn't have the kind of existence needed to produce you and me.

Fine Tuning of the Physical Constants of the Universe
Parameter Max. Deviation
Ratio of Electrons protons 1:10/37
Ratio of Electromagnetic Force:Gravity 1:10/40
Expansion Rate of Universe 1:10/55
Mass Density of Universe1 1:10/59
Cosmological Constant 1:10/120
These numbers represent the maximum deviation from the accepted values, that would either prevent the universe from existing now, not having matter, or be unsuitable for any form of life. The cosmological constant deviation is an amazing in itself as it would be completely impossible to happen by a chance accident.

 

[FrumiousBandersnatch]

I said I wasn't going to do this, but what the hell...

I use type because I find it hard to understand what evolution means by species. But it would be like a species. The reason I say type is that as with say bats there are many species that still look like bats. So I say they are the same type of animal.

OK; the second bolded statement contradicts the first. Your 'type' is clearly not like a species. It seems to be whatever general shape you feel is recognisably distinct from others. Shape isn't everything.

Even evolution has several meanings for species so its a bit ambiguous.

Not really. The term generally describes distinct populations of creatures that interbreed to produce viable offspring. It's considered to be of limited scientific use because it's a bit fuzzy at the edges and only applies to creatures that reproduce sexually; but it's fine for general use, and the creatures you mainly discuss reproduce sexually. In looking at fossils, where it's harder to establish interbreeding, the distinct structural differences, and contexual information (time, place, artefacts, etc) are used.

I guess any shape that makes a different animal.

As a response to "what is the smallest difference in shape that would qualify for a 'different shape'?", can you see why that is a singularly useless answer? You went on to mention differences in various organs and structures. Please pick one or two and give one or more examples of the smallest differences that you feel evolution can't bridge. I'm trying to identify the precise point where you disagree with evolutionary theory ('micro' to 'macro'); that's why I'm asking specific questions - that you're specifically failing to answer, for example:

Is a penguin's flipper a 'different shape' from a seagull's wing, in your shape schema? Could a penguin flipper evolve from a flying wing?

Also, do you consider walruses, sea lions, seals, and manatees to be the same 'type' of animal, with the 'same shape'? If not, explain why not.

We are finding unrelated animals with large chunks of the same DNA in each. How does evolution account for this.

Wrong. All animals are related; we expect to find large chunks of common DNA.

But we still dont see that graduation now or in the past. What we see is well defined creatures that are individual and not blended. What we find are lots of gaps in the fossil records.

That's precisely what you'd expect to see from occasional, rare snapshots over long periods of time of a gradually evolving tree of life. Just as if you look through someone's photo album, you might see a rarely photographed relative as a distinct toddler, teenager, and adult. In paleontology, there have been many instances where a later fossil appeared to be a development of an earlier form, predicting a creature with features of both, in the same general area, and in the time period between the two, which has then been searched for in rock strata of appropriate age and location, and discovered.

Evolution will hold up an example of transition between two animals like Archaeopteryx but its well defined and its the only one. There is nothing in between. If Archaeopteryx has fully formed wings then where are the 100 other stages getting from no wings to fully formed wings.

There are numerous examples of feathered flying or gliding avialids of various stages, many predating Archaeopteryx. Just because it was the first one found doesn't make it the only one.

From what I have read mutations are mostly a cost to fitness even the beneficial ones.

for the nth time, most mutations are neutral. There may be more adverse mutations than beneficial ones, but a beneficial mutation, by definition, increases fitness - that's what it means.

But it's a complex area - a mutation may increase fitness in some environments, and be neutral or decrease it in others; it may be adverse, neutral, or beneficial depending on whether particular other mutations are present.

Everything comes at a cost because basically you are changing what was already good. So to say that a harmful error is part of the driving force for more fitter and complex creatures seems illogical and against the evidence.

No. What is good can often be made better, and what was good once may no longer be good if circumstances have changed (e.g. the peppered moth).

If all life was microbe to begin with and a microorganisms can freely exchange genetic material wouldn't that mean that all life had access to all the genetic material and has continued to have access as it has become more complex.

HGT is common in prokaryotes, e.g. bacteria, but with increasing complexity and specialization, and the development of eukaryotic cells (with a protected nucleus) and different types of reproduction, it is rarer and less advantageous. With multi-cellular organisms and sexual reproduction, it's much less likely, as it has to affect the gametes and get past the error-checking systems that have evolved. But it does happen - viruses can insert bits of code that will hang around and spread in a population if they're not deleterious. It may even provide useful material for mutational variation in simple creatures.

Also 95% of all life is microbe anyway so if anything complex life would be a small offshoot of a bigger forest or bush of life.

And so it is. The diversity and number of microbes far exceeds macroscopic life. Estimates suggest that you have 10 times more microbial cells in and on your body than human ones. Consider yourself a support system for microbes.

I just pose the questions and challenge the general consensus of evolution. But it seems I'm not the only one.

There's nothing wrong with that - posing question and challenging the consensus drives scientific progress. But for this you need a good understanding of the subject, and you need to listen to and understand the answers to your questions. Judging from your posts, you're consistently failing to do that, probably because you appear to have a strong (faith based?) bias against it.

 

[FrumiousBandersnatch]

Actually, I don´t even see what the rarety of an event has to do with pointing to design (as in "being intentionally designed").
So, for the time being, I am assuming that all those incredibly huge (resp. small) figures are just smoke screens.

Steven Pinker, in 'How The Mind Works' (ch.3), discusses evolution and design (he distinguishes evolutionary design from intentional design), and suggests that it is some feature that provides an adaptive benefit to the organism. There's quite a good section on how replication (with variation) enables a forward-causation physical process (evolutionary design) to mimic a backward-causation or teleological process (intentional design).

 

[FrumiousBandersnatch]

Every single outcome is exactly as likely as the outcome you consider "fine tuned". EDIT: So long as you consider they are all simply "random".

How do you work that one out. ... The shapes were fine tuned to make specific fly shapes and the location on the wings were just right to make it all work.

You have - again - missed, or failed to understand, the point being made. Given an arbitrary starting point, e.g. a single blob of colour, every random variation on it in the next generation is equally likely - equally 'fine tuned'. There is no preference in the generation of the patterns. But, predators will destroy all variations that fall within their discriminatory criteria, leaving only the best-camouflaged to reproduce in the next generation - which will also present a range of random variations, all equally 'fine-tuned' (i.e not 'fine tuned' at all). Many repetitions of this process will result in a multitude of complex adaptive design patterns, from the appearance of bird droppings, to leaves, to noxious flies eating bird droppings, to eyes of various creatures, to poisonous spiders, etc.

If you can't grasp this principle, you really don't understand the basics of evolutionary theory [and the Dunning-Kruger Effect applies in spades]. Picking a striking example and trying to make a fine-tuning argument-from-incredulity around it suggests a serious lack of comprehension - or worse.

 

[FrumiousBandersnatch]

Steve, you've picked the evolution of a 'dog-like' creature (Pakicetus - a water-loving mammal) into whales as something you find inexplicable by evolution - can you pinpoint the particular stage that you find most troubling? (remember these are representative ancestral types, not necessarily direct ancestors). Is it, for example, Pakicetus to Ambulocetus? or maybe Rodhocetus to Dorudon?

Here's a diagram for reference:

 

[Loudmouth]

The best way to show that the protein picture you posted is designed or at least cannot be created by random mutations is from the tests done. Proteins have very complex 3D shapes which are necessary for that particular biological function. This is determined by the sequence of the different amino acids that make up that protein. So a mistake or a misshape in the folds will cause damage and therefore render it useless.

The shape of any cloud requires a very complex 3D shape. Does that mean every cloud is designed. We can point to tons of naturally occurring geologic formations where functions such as weather and drainage of water depends heavily on their 3D shape. And yet, they formed by natural processes.

Therefore, requiring a specific 3D shape for a specific outcome is not evidence of design.

Also, you didn't show us any tests. What are these tests?

Sequences that produce stable, functional 3D structures in proteins are very rare and hard to produce. Scientists can’t randomly create stable proteins and have to resort to reverse engineering to make artificial proteins because they are so complex. So everything about proteins is designed to the point that humans have to study that design and make computer programs to even have a chance to make them. Indeed, our supercomputers are not powerful enough to crunch the variables and locate novel 3D structures.
http://www.evolutionnews.org/2015/07/computing_the_b098101.html

That simply isn't true.

"Importantly, Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 10^93 possible functional cytochrome c protein sequences, based on these genetic mutational analyses (Hampsey et al. 1986; Hampsey et al. 1988; Yockey 1992, Ch. 6, p. 254)."
http://www.talkorigins.org/faqs/comdesc/section4.html#protein_redundancy

And that's just for one protein.

Test have been done to show that random mutations cannot evolve new functions in proteins let alone create them entirely.
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

You are painting the bulls eye around the bullet hole. There is nothing requiring a specific function to arise in evolution. What you need is the chances of producing a protein with any function.

So the chances of evolution producing even a simple functional protein fold is 1 in 10(77).

That isn't true. The chances of producing a SPECIFIC function may be that high, but the chances of producing any function is much, much lower.

 

[quatona]

I think you are looking at it the wrong way. Its a fine tuning argument not a broad tuning argument. So we would expect the sunshine to end up specifically in that little hole and not all over the place. But if it was based on just a random process you would expect the sunshine to end up as you said all over the place. But its not and over 122 physical constants make it specifically fine tuned to happen in the first place and at this point to happen only here on earth.

So the universe is comparably broad tuned for life and comparably fine tuned for cancer?

Here are some of the tunings that need to be exact to for existence to happen in the way that it can produce life as we know it. Any minute change to these conditions and we wouldn't have the kind of existence needed to produce you and me.

Fine Tuning of the Physical Constants of the Universe
Parameter Max. Deviation
Ratio of Electrons protons 1:10/37
Ratio of Electromagnetic Force:Gravity 1:10/40
Expansion Rate of Universe 1:10/55
Mass Density of Universe1 1:10/59
Cosmological Constant 1:10/120

You needn´t repeat those numbers ad nauseum. They aren´t in dispute. Your conclusions are.

The cosmological constant deviation is an amazing in itself as it would be completely impossible to happen by a chance accident.

Well, no matter how large the number of possible outcomes - one of them (with equally low probability) will always be the outcome. So nothing particularly noteworthy there - unless you assume the outcome to be intended for a premise.
On another note, the dichotomy "fine-tuned/design" vs. "chance accident" makes no sense.

 

[stevevw]

I said I wasn't going to do this, but what the hell...

OK; the second bolded statement contradicts the first. Your 'type' is clearly not like a species. It seems to be whatever general shape you feel is recognisably distinct from others. Shape isn't everything.

You didn't include the last part of my statemnet on species. " Even evolution has several meanings for species so its a bit ambiguous". So its not really a contradiction if you look at how evolution interprets species. I said I use type when describing a creature that looks similar like all bats do despite evolution calling them different species. But a type of creature would be closest to what evolution calls a species. Sorry if I have a grammar problem. What do you mean that shape isn't everything.

Not really. The term generally describes distinct populations of creatures that interbreed to produce viable offspring. It's considered to be of limited scientific use because it's a bit fuzzy at the edges and only applies to creatures that reproduce sexually; but it's fine for general use, and the creatures you mainly discuss reproduce sexually. In looking at fossils, where it's harder to establish interbreeding, the distinct structural differences, and contexual information (time, place, artefacts, etc) are used.

It seems there is a problem even identifying sexually reproductive creatures into species. There can be several interpretations.
Species problem
https://en.wikipedia.org/wiki/Species_problem
I was much struck how entirely vague and arbitrary is the distinction between species and varieties
Charles Darwin, On the Origin of Species
The problem is more to do with how do you tell what is a stage for a transition between different species or types of creatures and what is normal variations between the same species. I used the skulls at Georgia as the example before. For years evolution help up all these different shaped skulls as transitionals showing the morphing shapes from ape gradually to humans. Each time a new shape was found it was quickly declared a new species that filled in the gaps for how humans evolved. Then they found a single haul of skulls which had several of the shapes together that were previously declared as different species. So now what was once considered different species was then found to be normal variation between the same species which in this case was homo erectus.

So how many times have evolution mistaken normal variation for new species and made them transitionals. How do they tell the difference when its based on observation of fossils. If you look at the major variations of dogs then you can see that there can be a lot of scope with the one species. I find it very ambiguous and something that can be easily misinterpreted and taken advantage of. It seems even Darwin was confused and unsure.

As a response to "what is the smallest difference in shape that would qualify for a 'different shape'?", can you see why that is a singularly useless answer?

Yes and this is explained above. So how can evolution be confident that all these small changes they refer to are transitional changes and not normal variations mixed up together.

You went on to mention differences in various organs and structures. Please pick one or two and give one or more examples of the smallest differences that you feel evolution can't bridge. I'm trying to identify the precise point where you disagree with evolutionary theory ('micro' to 'macro'); that's why I'm asking specific questions - that you're specifically failing to answer, for example:

I think the skulls at Georgia are a good example. Even today humans can have many of the features that evolution has used to show transitions between species. Some humans have broad foreheads, or jutting jaws and flatter foreheads. This will be especially true going back in time as populations were more isolated. How do we know that the more robust features found in the past were not just how humans looked back then because they were more isolated. Since then we have interbred more and our looks have become more blended as a single species.

The wing is another obvious one. How do we know the difference in existing wings is not normal variations of wings. The main point here is proving that a wing evolved from a limb. But it seems the only thing that is being used is fossils which show a complete wing and never one that is on the way to becoming a wing. Its either no wing or a complete wing and nothing in between. That seems to be the way for most transitions in the fossil records.

Is a penguin's flipper a 'different shape' from a seagull's wing, in your shape schema? Could a penguin flipper evolve from a flying wing?

Maybe I'm not sure. But how do you know its not normal variation between birds. I guess it comes down to how animals are interpreted for the purpose of what is believed about how they came about in the first place. Evolution breaks all the bird type animals into species yet they all look like birds despite the differences in wings or other features. So if you look upon all birds like say dogs as being one species or type of animal then you could say all the different features of flightless wings, sizes, abilities to swim underwater ect are just variations within that type of animal. Creations sees birds as the one kind of creature that was created but with the capability of a great deal of possible variation. ie God created every winged bird according to its kind.

Also, do you consider walruses, sea lions, seals, and manatees to be the same 'type' of animal, with the 'same shape'? If not, explain why not

It would be the same as the other examples of whether this is evidence for macro evolution or just variations within a type of animal micro evolution. This is something I am not completely sure about. But some will say that all these animals could have come from one or two kinds of creatures in the beginning. Why couldn't all these creatures be a mixture of variation and other things like cross breeding and HGT that have produced these things. As we have seen with dogs there can be a lot of different shapes to the point where you may even think that they are completely different animals. I think there's a fine line between what is said to be a new species and what can be variations of the same basic animal type over time. But still there will be limitations and a dog like creature is not going to become a whale in the end.

Wrong. All animals are related; we expect to find large chunks of common DNA.
That's precisely what you'd expect to see from occasional, rare snapshots over long periods of time of a gradually evolving tree of life. Just as if you look through someone's photo album, you might see a rarely photographed relative as a distinct toddler, teenager, and adult. In paleontology, there have been many instances where a later fossil appeared to be a development of an earlier form, predicting a creature with features of both, in the same general area, and in the time period between the two, which has then been searched for in rock strata of appropriate age and location, and discovered

But what if they are finding large chunks of the same DNA between distantly related animals which is linking them closer than other animals which were suppose to be a closer relative. Doesn't this throw a spanner in the works for the predicted tree and its branching that evolution has made. As far as I understand this is happening often and is changing the way the tree of life is constructed. We should expect to see the closest matches in DNA to animals that are closest in features for the transitional links made to show the gradual morphing form one type of animal to the next in evolution.

Genetic tests on bacteria, plants and animals increasingly reveal that different species crossbreed more than originally thought, meaning that instead of genes simply being passed down individual branches of the tree of life, they are also transferred between species on different evolutionary paths. The result is a messier and more tangled "web of life".
This seems to suggest that animals cross bred more in the beginning. So there could have been a certain amount animals made after their kinds and then through some cross breeding we can get many more types of animals stemming from this. This would make a hedge or forest of life which is what we are seeing with the molecular evidence.
http://www.theguardian.com/science/2009/jan/21/charles-darwin-evolution-species-tree-life
In-congruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.
http://www.ncbi.nlm.nih.gov/pubmed/22891620
"Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record.
http://www.ncbi.nlm.nih.gov/pubmed/21930899

There are numerous examples of feathered flying or gliding avialids of various stages, many predating Archaeopteryx. Just because it was the first one found doesn't make it the only one.
for the nth time, most mutations are neutral. There may be more adverse mutations than beneficial ones, but a beneficial mutation, by definition, increases fitness - that's what it means

So if there are very very rare beneficial mutations and there are many more neutral and harmful ones how can the beneficial ones account for the vast amount of complexity and variety we see. That means for every very rare beneficial mutation we should many many millions of other mutations. That means there have to be dealt with one way or another. Evidence suggest that even neutral mutations have some cost to fitness. So we have this massive amount of slightly deleterious mutations accumulating and have an effect on things. So the evolution of fitter and more complex animals seems to be one step forward and 100 steps back. It seems like a contradictory and illogical method to account for all of life. Its like smashing a car to make it better.

But it's a complex area - a mutation may increase fitness in some environments, and be neutral or decrease it in others; it may be adverse, neutral, or beneficial depending on whether particular other mutations are present.
No. What is good can often be made better, and what was good once may no longer be good if circumstances have changed (e.g. the peppered moth)

Yes and I am not a geneticist to be able to know the finer details of how it all works. I can rely on the experts but I still can only get a decent understanding. I understand its complicated but it seems some scientists are questioning the ability of mutations and natural selection to be able to evolve new functions and the complexity we see.

HGT is common in prokaryotes, e.g. bacteria, but with increasing complexity and specialization, and the development of eukaryotic cells (with a protected nucleus) and different types of reproduction, it is rarer and less advantageous. With multi-cellular organisms and sexual reproduction, it's much less likely, as it has to affect the gametes and get past the error-checking systems that have evolved. But it does happen - viruses can insert bits of code that will hang around and spread in a population if they're not deleterious. It may even provide useful material for mutational variation in simple creatures.

Yes and it seems to have happened more than scientists thought between more complex creatures. It may have been more prevalent earlier on in history as well and it seems that hybridization was also more prevalent between animals and produced fertile off springs. As you said viruses can also transfer genetic material between complex creatures and the environment. Symbiogenesis and endosymbiotic can also account for the creation of vast genetic transfers in eukaryotes from prokaryotes. In fact it seems that all eukaryotes came about by one big HGT from prokaryotes.

Considering that 95% of all life was and is microbe and that HGT is pervasive with microorganisms then why wouldn't all of life have or had the ability to share and have access to a lot of genetic material. If all life started as bacteria life then all life was already sharing a lot of genetic material. Maybe all life has most of what it needs in its vast amounts of DNA to tap into rather than mutate into existence.

And so it is. The diversity and number of microbes far exceeds macroscopic life. Estimates suggest that you have 10 times more microbial cells in and on your body than human ones. Consider yourself a support system for microbes.

So the tree of life would primarily be made up of microbes which would represent a forest or hedge with a lot of HGT. Then the smaller part which represents complex life would be a ting offshoot of this. So basically life is not represented by a tree of life but a forest of life with many trunks that branch out. This is more in line with design of a certain amount of main types/kinds of animals which then had the capacity to cross breed and share genetic material that created the rest of life. As the bible said go forth and multiply. But the important thing is the evidence points to there being complex life very early on as with the Cambrian explosion. To complex for a gradual evolution to have had time to evolve.

So this indicates that rather than life being mutated and naturally selected which comes from a selective and adaptive process it stems from preexisting genetic info which has always been there from an early stage and can account for the large variety and complexity in life. It can account for the incongruities because though all life has the same blue prints it didn't come from a common ancestor but many ancestors at the same time.

There's nothing wrong with that - posing question and challenging the consensus drives scientific progress. But for this you need a good understanding of the subject, and you need to listen to and understand the answers to your questions. Judging from your posts, you're consistently failing to do that, probably because you appear to have a strong (faith based?) bias against it.

Yes there is always room to learn and develop knowledge. I may have some leanings from my beliefs but who doesn't. Even evolution has some bias towards what they already assume in a lot of cases. But I try to look at both sides. I do support evolution to a certain extent and have never denied this. Anyone can see that creatures change and adapt to their environment. But there are limits and we have to establish whether this is from a self creating process of mutations or from pre existing genetic info that is tapped into, re-combined and switched on when needed.

The problem is that many scientists who are not religious are questioning the consensus of opinion. As some of the papers are saying "the more we sequence the genetic evidence the more it is contradicting the Darwinian evolution theory. It seems the evidence is pointing to other driving forces that caused creatures to change. The evidence points to non adaptive methods for change like HGT, epigenetics, symbiosis, developmental biology and genomics. These things were once seen as minor issues that needed explaining but now they are seen as the main reasons for changes in animals. All these methods minimize the role of evolution.

 

[stevevw]

So the universe is comparably broad tuned for life and comparably fine tuned for cancer?

Just because life was originally fine tuned to exist or the universe was fined tuned to end up the way it has doesn't mean that things cant deteriorate. All life is subject to entropy and things will break down and decay. Some say that with the fall of man in the garden this brought about sin and death. So the possibility of decay and sickness entered our world.

You needn´t repeat those numbers ad nauseum. They aren´t in dispute. Your conclusions are.

No not my conclusions. I am only repeating the conclusions of many scientists religious or not. The numbers point to certain conclusions that cannot be avoided. But the conclusions are only about those numbers being more than a coincident or stemming from chance or accident. They indicate some meddling or control from something to ensure that things were just right. Concluding that God or a divine agent did this is another things and something that is a belief which has no direct evidence. You could though say it can be used as indirect evidence for divine intervention or some other agent having some control over things.

Well, no matter how large the number of possible outcomes - one of them (with equally low probability) will always be the outcome. So nothing particularly noteworthy there - unless you assume the outcome to be intended for a premise.
On another note, the dichotomy "fine-tuned/design" vs. "chance accident" makes no sense.

No as I noted above it doesnt necessarily point to God. But it has the hallmarks of something beyond chance and random accident of how the universe came about and fell into just the right place for life. If it were from random chance then we should have a million different possibilities. But why one that is so precise in some cases to with a margin that is so small its like it had to be pre set to have it. Why for life as we know so that we can sit here and ask these very questions. Why not a less intelligent life, why not no life, why not life everywhere. That is why some scientists propose a multiverse hypothesis as it deals with all these questions.

 

[stevevw]

The shape of any cloud requires a very complex 3D shape. Does that mean every cloud is designed. We can point to tons of naturally occurring geologic formations where functions such as weather and drainage of water depends heavily on their 3D shape. And yet, they formed by natural processes.

A cloud is forever changing and unstable. A functional protein needs to be a certain shape and stay that way.

Therefore, requiring a specific 3D shape for a specific outcome is not evidence of design.

Why they have thousands of letters that needs to be in the right order and have the right language. Any wrong ones will render it unworkable. Out of the billions of combinations they end up with specific formations. Its like throwing up a million letters and several thousand come down to write out a Shakespearean play.

Also, you didn't show us any tests. What are these tests?

I though I posted a paper on some tests done.
http://www.ncbi.nlm.nih.gov/pubmed/15321723
The following paper seems to indicate that protein folds are from pre set forms in nature and dont stem from natural selection in the Darwinian evolution method. So this points to a design in proteins that conforms to certain construction laws like those in physics.

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

That simply isn't true.

"Importantly, Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 10^93 possible functional cytochrome c protein sequences, based on these genetic mutational analyses (Hampsey et al. 1986; Hampsey et al. 1988; Yockey 1992, Ch. 6, p. 254)."
http://www.talkorigins.org/faqs/comdesc/section4.html#protein_redundancy
And that's just for one protein.

So how are functional proteins randomly created.

You are painting the bulls eye around the bullet hole. There is nothing requiring a specific function to arise in evolution. What you need is the chances of producing a protein with any function.

It seems your examples are not function proteins and end up unstable. The point is producing stable and functional proteins. Thats part of the evidence about how evolution can make better, fitter and more complex function from random mutations. Most changes to the genetics comes at a cost to fitness because mutations are primarily an error to what is already good and functional. Even if it is said to be beneficial there can still be a cost that comes with those mutations. Because they have to change something that is already working and this is normally a loss of info and function even if it seems that there is a gain in ability.

That isn't true. The chances of producing a SPECIFIC function may be that high, but the chances of producing any function is much, much lower.

So who do I trust and believe you or the experts who produced the papers.

 

[quatona]

Just because life was originally fine tuned to exist or the universe was fined tuned to end up the way it has doesn't mean that things cant deteriorate. All life is subject to entropy and things will break down and decay. Some say that with the fall of man in the garden this brought about sin and death. So the possibility of decay and sickness entered our world.

Exactly the point: Life itself could be seen as such a deterioration. What you consider designed and what you consider deterioration is completely arbitrary and does not at all follow from your claimed criteria. It follows from your preassumptions, which are basically the same as your conclusions.

 

[stevevw]

Exactly the point: Life itself could be seen as such a deterioration. What you consider designed and what you consider deterioration is completely arbitrary and does not at all follow from your claimed criteria. It follows from your preassumptions, which are basically the same as your conclusions.

I thought scientists were the ones that had some criteria as to what is designed and what is not through their research. Here is an interesting paper on design and entropy.
Information and entropy - top down or bottom up development in living systems.
This paper deals with the fundamental and challenging question of the ultimate origin of genetic information from
a thermodynamic perspective. The theory of evolution postulates that random mutations and natural selection can
increase genetic information over successive generations. It is often argued from an evolutionary perspective that
this does not violate the second law of thermodynamics because it is proposed that the entropy of a non-isolated
system could reduce due to energy input from an outside source, especially the sun when considering the earth as
a biotic system. by this it is proposed that a particular system can become organized at the expense of an increase
in entropy elsewhere. However, whilst this argument works for structures such as snowflakes that are formed by
natural forces, it does not work for genetic information because the information system is composed of machinery
which requires precise and non-spontaneous raised free energy levels – and crystals like snowflakes have zero free
energy as the phase transition occurs.

The functional machinery of biological systems such as DNA, RNA and proteins requires that precise, non-spontaneous raised free energies be formed in the molecular bonds which are maintained in a far from equilibrium state. Furthermore, biological structures contain coded instructions which, as is shown in this paper, are not defined by the matter and energy of the molecules carrying this information. Thus, the specified complexity cannot be created by natural forces even in conditions far from equilibrium. The genetic
information needed to code for complex structures like proteins actually requires information which organizes the natural forces surrounding it and not the other way around – the information is crucially not defined by the material on which it sits.

The information system locally requires the free energies of the molecular machinery to be raised in order for the information to be stored. Consequently, the fundamental laws of thermodynamics show that entropy reduction which can occur naturally in non-isolated systems is not a sufficient argument to explain the origin of either biological machinery or genetic information that is inextricably intertwined with it. This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.
https://intelligentdesignscience.fi...nformation-and-entropy-e28093-top-down-or.pdf

 

[Loudmouth]

A functional protein needs to be a certain shape and stay that way.

Where did you demonstrate that?

Why they have thousands of letters that needs to be in the right order and have the right language. Any wrong ones will render it unworkable.

That's completely untrue. Yeast cytochrome c differs from human cytochrome c by 40%, yet their function is identical. Other proteins differ by 90% or more, and they still have function. There are 6 billion human genomes that all have different letters, and they are all still functional.

I though I posted a paper on some tests done.
http://www.ncbi.nlm.nih.gov/pubmed/15321723
The following paper seems to indicate that protein folds are from pre set forms in nature and dont stem from natural selection in the Darwinian evolution method. So this points to a design in proteins that conforms to certain construction laws like those in physics.

How did they determine that? What are the methods? Also, it says that proteins follow the same laws as the rest of nature.

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

That is saying that proteins are just like rocks, water, and all other molecules.

So how are functional proteins randomly created.

By randomly changing the DNA sequence through mutation.

It seems your examples are not function proteins and end up unstable.

Where did you get that from?

Most changes to the genetics comes at a cost to fitness because mutations are primarily an error to what is already good and functional. Even if it is said to be beneficial there can still be a cost that comes with those mutations. Because they have to change something that is already working and this is normally a loss of info and function even if it seems that there is a gain in ability.

Are you saying that all of those mutations that separate humans from other species are harmful?

So who do I trust and believe you or the experts who produced the papers.

You obviously don't understand what the experts have written. They are saying that proteins are just as natural as anything else in the universe.

 

[FrumiousBandersnatch]

Maybe I'm not sure.
...
It would be the same as the other examples of whether this is evidence for macro evolution or just variations within a type of animal micro evolution. This is something I am not completely sure about.

OK, so you're unable to give any specific examples of the smallest change you feel evolution can't manage, and you don't know whether a given example might be such a change - yet you're convinced that there must be such a point...

You define a 'type' category that you prefer because 'species' is too vague, yet you're unable or unwilling to say whether specified creatures of clearly defined species belong to a single 'type'...

It all seems to break down when we get to specifics

But what if they are finding large chunks of the same DNA between distantly related animals which is linking them closer than other animals which were suppose to be a closer relative.

If the DNA indicates they're more closely related than their structure or appearance would lead you to expect, then they're more closely related. This has happened quite often since DNA sequencing became economical. Take humans, for example; although the various human races look significantly different, there is less variation in all the human genome, including all races, than is found in a single troop of chimps.

Doesn't this throw a spanner in the works for the predicted tree and its branching that evolution has made. As far as I understand this is happening often and is changing the way the tree of life is constructed.

There are always adjustments being made as new data comes in. That's how science works - models are changed to better fit the evidence. The tree becomes more accurate with time.

We should expect to see the closest matches in DNA to animals that are closest in features for the transitional links made to show the gradual morphing form one type of animal to the next in evolution.

Ideally, yes. Where good quality DNA is available, it will take precedence.

Genetic tests on bacteria, plants and animals increasingly reveal that different species crossbreed more than originally thought, meaning that instead of genes simply being passed down individual branches of the tree of life, they are also transferred between species on different evolutionary paths. The result is a messier and more tangled "web of life".

It might if it was true. References for these genetic tests showing more crossbreeding?

This seems to suggest that animals cross bred more in the beginning.

No. HGT is not cross-breeding. Creatures that can cross-breed to produce viable offspring are so closely related as to be arguably the same species.

So there could have been a certain amount animals made after their kinds and then through some cross breeding we can get many more types of animals stemming from this. This would make a hedge or forest of life which is what we are seeing with the molecular evidence.

No. Even prokaryotes, where HGT is most common, have distinguishable inheritance hierarchies. Multicellular eukaryotes may have more genes from HGT than was previously thought, but they're still a relatively small contribution and can't retrospectively change the ancestral tree. It's conceivable that a gene originating from HGT could assist a speciation process, but it's unlikely, particularly in multicellular creatures, because it would be very unlikely to be expressed.

So if there are very very rare beneficial mutations and there are many more neutral and harmful ones how can the beneficial ones account for the vast amount of complexity and variety we see.

Natural selection. Mathematical modelling shows that heritable random variation with selection can produce results that surprise even the experts. For example, Dan Nilsson and Susanne Pelger made a simulation of the evolution of an eye from a flat photosensitive spot (an opaque layer, a photosensitive layer, and a clear layer of cells). They set it to select just for the best image formation. Even with pessimistic parameters, such as a 1% advantage (99% survive even without the better eye), a complex eye with a lens (like a fish's eye) developed much quicker than expected - roughly 364,000 generations, less than half-a-million years for a small marine animal. See Nilsson, D.-E. and Pelger, S. (1994). A Pessimistic Estimate of the Time Required for an Eye to Evolve. Proceedings: Biological Sciences, 256 (1345): 53-58. A simplified summary: Evolution of the Eye.

Evidence suggest that even neutral mutations have some cost to fitness.

Are you serious? 'neutral' means no overall cost or benefit to fitness.

So we have this massive amount of slightly deleterious mutations accumulating and have an effect on things. So the evolution of fitter and more complex animals seems to be one step forward and 100 steps back. It seems like a contradictory and illogical method to account for all of life. Its like smashing a car to make it better.

It might seem like that, but most mutations are neutral, the detrimental ones disappear relatively quickly, and the beneficial ones remain. Progress is slow, but cumulative. The bulk of the population at any time is well-suited to (fit for) their environment; a significant number will be slightly less fit, and a few will be slightly fitter. Hundreds of thousands of generations in populations of millions or billions can result in major changes..

... it seems that hybridization was also more prevalent between animals and produced fertile off springs.

Really? I doubt it - let's see your reference for that.

As you said viruses can also transfer genetic material between complex creatures and the environment.

Nope, I didn't say that. Viruses can insert pieces of their own genetic code. They don't transfer between complex creatures and 'the environment', whatever that means. You can't just make up sciency sounding stuff an expect it to make sense.

Symbiogenesis and endosymbiotic can also account for the creation of vast genetic transfers in eukaryotes from prokaryotes. In fact it seems that all eukaryotes came about by one big HGT from prokaryotes.

Really? please do explain how symbiogenesis and endosymbiosis can do that! And if all eukaryotes came about by 'one big HGT from prokaryotes', their genetics would be quite different from what we see. Please try to think through what you're going to say before posting.

So the tree of life would primarily be made up of microbes which would represent a forest or hedge with a lot of HGT. Then the smaller part which represents complex life would be a ting offshoot of this. So basically life is not represented by a tree of life but a forest of life with many trunks that branch out. This is more in line with design of a certain amount of main types/kinds of animals which then had the capacity to cross breed and share genetic material that created the rest of life.

HGT isn't a means of reproduction, and it isn't an effective means of sharing traits beyond single cell organisms. It's more common than was previously thought, but doesn't significantly influence the hierarchy of multicellular life; it means more care must be taken when comparing genomes, but it can also help clarify ancestral lines, as the position of an insertion is likely to be distinctive in each lineage.

...the important thing is the evidence points to there being complex life very early on as with the Cambrian explosion. To complex for a gradual evolution to have had time to evolve.

Nope, that argument from incredulity doesn't fly - simulations show such complexity can arise rapidly in the right conditions.

So this indicates that rather than life being mutated and naturally selected which comes from a selective and adaptive process it stems from preexisting genetic info which has always been there from an early stage and can account for the large variety and complexity in life. It can account for the incongruities because though all life has the same blue prints it didn't come from a common ancestor but many ancestors at the same time.

Not only is there no way that amount of information could be stored in an early prokaryote cell, but it's entirely unnecessary; all the evidence points to a selective accumulation of random changes.

I may have some leanings from my beliefs but who doesn't. Even evolution has some bias towards what they already assume in a lot of cases.

The difference is that the evolutionary model changes to fit new evidence. One clear example of a fossil in the wrong strata would upset the apple cart, but no such thing has been found; the evidence so far is unequivocal.

The problem is that many scientists who are not religious are questioning the consensus of opinion. As some of the papers are saying "the more we sequence the genetic evidence the more it is contradicting the Darwinian evolution theory. It seems the evidence is pointing to other driving forces that caused creatures to change. The evidence points to non adaptive methods for change like HGT, epigenetics, symbiosis, developmental biology and genomics. These things were once seen as minor issues that needed explaining but now they are seen as the main reasons for changes in animals. All these methods minimize the role of evolution.

References?

 

[stevevw]

Where did you demonstrate that?

That's completely untrue. Yeast cytochrome c differs from human cytochrome c by 40%, yet their function is identical. Other proteins differ by 90% or more, and they still have function. There are 6 billion human genomes that all have different letters, and they are all still functional.

It doesn't matter, each and every creature has a specific set of sequences that goes into working proteins structures. Just one small change in one amino acid and this can disrupt the entire structure and render it useless. Of course evolution will say that natural selection over long periods has defined the perfect structure needed in proteins., But this seems to defy chance considering the astronomical amount of poly peptide chains. Yet just like the fine tuning of the universe for life it seems to have all the hallmarks of design.

For a typical protein length of about 300 amino acids, more than 10/390 (20/300) different polypeptide chains could theoretically be made. This is such an enormous number that to produce just one molecule of each kind would require many more atoms than exist in the universe.

Only a very small fraction of this vast set of conceivable polypeptide chains would adopt a single, stable three-dimensional conformation—by some estimates, less than one in a billion.

Because of natural selection, not only is the amino acid sequence of a present-day protein such that a single conformation is extremely stable, but this conformation has its chemical properties finely tuned to enable the protein to perform a particular catalytic or structural function in the cell. Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of the whole molecule so severely that all function is lost.
http://www.ncbi.nlm.nih.gov/books/NBK26830/

How did they determine that? What are the methods? Also, it says that proteins follow the same laws as the rest of nature.

It seems there are some basic forms in protein folds that have been known for a long time. They take on similar structural forms like with atoms or crystals for example in which adaptation like in evolution takes on a secondary role. As the paper states "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".

This seems to back what other evidence says about life has being around from a very early stage in the history of existence and events like the Cambrian explosion lend to support to this. Very early life had complexity that is similar to what we see today. So much of the basic genetic info for building complex body parts was there very early and if not from the beginning of existence. At the very least it was there to early for evolution through random mutations and natural selection to sort through the billions and billions of possible combinations of protein sequences to find the right ones for all of the complexity and variety of life.

Considering that there are billions and billions of possible poly peptide chains that can be randomly chosen through natural selection its seems almost impossible for random mutations and natural selection to end up with the precise ones in such a short time. So having these basic protein folds already around and forming pre set building blocks for life makes sense. This is just another piece of evidence pointing to some design in nature.

That is saying that proteins are just like rocks, water, and all other molecules.

No just like physical laws have been around from a very early stage so have the genetic code for life. It has to be because the complexity of life and of physics had to be around in the beginning for everything to happen. The evidence shows that there was complexity around from the beginning that needed the same level of laws as we see today. So there wouldn't have been enough time to slowly evolve things. But rocks and water are the end result of the laws of physics. So life is the end result of the laws of the genetic code for life.

By randomly changing the DNA sequence through mutation.

And as we can see there are more possible combinations that can be randomly chosen then there are atoms in the universe. So to think that evolution could find the exact right sequences for life which is enormously complex anyway seems impossible. Thats why a pre set of existing forms/codes for life being around somehow without having to get the massive jackpot for life makes sense. This can even be related back to the fine tuning of life and the universe in that the odds of landing of the exact combination is massively high. So something had to tweak things to ensure it was spot on. Otherwise we would still be here trying to find the right combinations.

Where did you get that from?

From the paper you posted. This is just from one of the papers.
Because all of these nonfunctional iso-1-cytochromes c are produced at far below the normal level and because a representative number are labile in vitro, most of the replacements appear to be affecting stability of the protein or heme attachment.
http://www.ncbi.nlm.nih.gov/pubmed/15321723

Are you saying that all of those mutations that separate humans from other species are harmful?

You are assuming that humans have evolved from other species in the first place to even need a whole stack of beneficial mutations in the first place. If this didn't happen then we wouldn't need to go through the process of taking on all those mutations of which many would be harmful just to get a very small amount of beneficial ones which have no guarantee of doing anything significant anyway. The point is mutations are mostly harmful and we have evidence for them accumulating in us already from the small amount we have.
Diminishing returns epistasis among beneficial mutations decelerates adaptation.
http://www.ncbi.nlm.nih.gov/pubmed/21636771
Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness.
http://phys.org/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html
High genomic deleterious mutation rates in hominids
http://www.nature.com/nature/journal/v397/n6717/abs/397344a0.html

You obviously don't understand what the experts have written. They are saying that proteins are just as natural as anything else in the universe.

As far as I understand the paper is saying talking about the chances of a protein obtaining a functional fold. Not any fold but a functional one which needs to have the precise sequences in place from many many possible combinations. Thats why the odds against it were so high.

From the paper.
An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional 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),

So yes any fold can be created but its the functional folds or the folds that go towards specific functions that would contribute to fitness is what is relevant. For that the tests were to make very small substitutions as would be needed by evolution to change a function in proteins. The tests showed that the odds would be 10/77 to form a functional protein even for these small changes.
http://www.ncbi.nlm.nih.gov/pubmed/15321723