Where did the laws of nature come from?

[RealityCheck01]

A no go "list of proofs"!!!

A lie, Heissonear: Transitional fossils exist.
I present no "proofs" - science is based on evidence.
Real observations show that there are multiple lines of evidence for macroevolution: 29+ Evidences for Macroevolution
This is the Physical & Life Sciences section so I am presenting the scientific evidence. If other people want to make unscientific claims then I will debunk the claims with scientific evidence.

 

[RealityCheck01]

I would have thought you got the jist of my reply was stating that I disagreed with humans and apes having a common ancestor by the fact I was saying that mutations have been shown to not be able to produce enough benefit to create new types of creatures and that there are limits to how far you can change our genomes.

So your answer to : 30 June 2016 stevevw: Do humans and chimps have a common ancestor? is No based on fantasies, stevevw !
4 July 2016 stevevw: The ignorant assertion that humans and apes do not have a common ancestor.
The fossil record says that this assertion is ignorant.
The genes of humans and apes says that this assertion is ignorant, e.g. the same ERV in the same locations in chimpanzees and humans tell us that we have a common ancestor.
29+ Evidences for Macroevolution says that this assertion is ignorant.

A scientist gains credibility through their publications not any association with "secular organizations" . But then ...
4 July 2016 stevevw: Do you believe the thousands of scientists who believe in the evidence for evolution who are "associated with the secular science organization and research position"?
4 July 2016 stevevw: If not then what makes you believe the slightly obscure (9 papers in 29 years!) Douglas Axe?

A scientist can lose credibility by going from a credible organization to not as credible organization (University of Cambridge to the Biologic Institute).
4 July 2016 stevevw:: Signing the ambiguous A Scientific Dissent From Darwinism document from the Discover Institute does not show competence from Douglas Axe - any biologist knows that modern evolutionary theory is no "Darwinism".

1. 28 June 2016 stevevw: Douglas Axe discredited his competence by associating with the Discovery Institute by being the director of the DI-funded Biologic Institute.
2. 28 June 2016 stevevw: The evidence is that Douglas Axe is not an expert on evolution - he has published 9 paper in 29 years which makes him an expert on nothing (experts publish multiple papers per year!).
3. 28 June 2016 stevevw: At least one of those papers was slightly dubious and wrongly cited by IDiots as evidence against evolution: Axe (2004) and the evolution of enzyme function

 

[stevevw]

1. Examples used to understand evolution doe not mean that evolution is dog breeding or genetic engineering as you stated, stevevw.
2. It is because that is what you states.
3. It is a myth because it is debunked by the scientific evidence that I provided you. To be more specific it is a myth that is seen from creationists.
4. Papers that do not state there is a limit to evolution are not evidence that there is a limit to evolution. Stating that they do once is a mistake, twice is an error, more times becomes a lie.
   4 July 2016 stevevw: The phrase "inhibit the rate of evolution" means that evolution goes slower (the rate of) - not that evolution stops.
5. 29+ Evidences for Macroevolution: "This hypothesis has been verified and corroborated so extensively that it is currently accepted as fact by the overwhelming majority of professional researchers in the biological and geological sciences"
   4 July 2016 stevevw: A lie about the Talk Origins site stating that the evidence for macroevolution cannot be verified.
   29+ Evidences for Macroevolution: "It must be stressed that this approach to demonstrating the scientific support for macroevolution is not a circular argument: the truth of macroevolution is not assumed a priori in this discussion. Simply put, the theory of universal common descent, combined with modern biological knowledge, is used to deduce predictions. These predictions are then compared to the real world in order see how the theory fares in light of the observable evidence."
   4 July 2016 stevevw: The ignorant assertion that the evidence for macroevolution is circular.
   4 July 2016 stevevw: Parroting the "gaps in the fossil record", "transitional fossil", "Cambrian explosion" creationist claims? Index to Creationist Claims

4 July 2016 stevevw: A fantasy about any (so far imaginary) limits to evolution being evidence against macroevolution - as far as you know the limits may be above the species level !

1. 15 June 2016 stevevw: It is a lie to state that dogs and GMO show limits to evolution. They are not examples of evolution. There seems no limit to what we can breed/engineer.
2. 21 June 2016 stevevw: The fantasy that we must be able to create new mammal species, e.g. dogs into cats, is not a limit to evolution!
3. 21 June 2016 stevevw: Now you do not need to ignorantly repeat the "most mutations are harmful" myth.
4. 23 June 2016 stevevw: Papers that do not state there is a limit to evolution are not evidence of limits to evolution.
5. 23 June 2016 stevevw: Please read and acknowledge the scientific evidence that makes the idea that microevolution does not lead to macroevolution very ignorant.
6. 23 June 2016 stevevw: The different definitions of species are not evidence of limits to evolution.
7. 23 June 2016 stevevw: Ignorance about Darwin's original work and evolution should be remedied by learning about evolution. I suggest you start with Wikipedia.
8. 23 June 2016 stevevw: None of the paper you cited state that most mutations are harmful.

 

[RealityCheck01]

Evolutionary layering and the limits to cellular perfection

Although observations from biochemistry and cell biology seemingly illustrate hundreds of examples of exquisite molecular adaptations, the fact that experimental manipulation can often result in improvements in cellular infrastructure raises the question as to what ultimately limits the level of molecular perfection achievable by natural selection. Here, it is argued that random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes. Moreover, although substantial improvements in fitness may sometimes be accomplished via the emergence of novel cellular features that improve on previously established mechanisms, such advances are expected to often be transient, with overall fitness eventually returning to the level before incorporation of the genetic novelty. As a consequence of such changes, increased molecular/cellular complexity can arise by Darwinian processes, while yielding no long-term increase in adaptation and imposing increased energetic and mutational costs.

4 July 2016 stevevw: M. Lynch (2012) has limits in one of many possible mutation–selection models for allele populations but does not state these stop macroevolution as you want.
The M. Lynch (2012) paper and its citations do not announce the evolution is dead !

 

[stevevw]

1. Examples used to understand evolution doe not mean that evolution is dog breeding or genetic engineering as you stated, stevevw.

1. I never said that dog breeding is dog breeding on its own. I said that the example of artificial breeding is used to understand evolution and Darwin used it himself. You originally said it had nothing to do with evolution which was wrong.
   

2. It is because that is what you states.

   How is this an answer, what does it mean. Are you saying just because I said it that this is why it is wrong. Or are you saying that what I said was wrong. If its to do with the second point you made about the limits of evolution then I didn't say anything. I posted evidence from science to show that there are limits and even supporters of evolution admit there are limits. You are saying there are no limits which is a fallacy based on an absolute which can easily be proven wrong even if you believe in evolution.
   

3. It is a myth because it is debunked by the scientific evidence that I provided you. To be more specific it is a myth that is seen from creationists.

   The evidence you provided from talk origin has been shown to be misleading. They provide one paper which is 17 years old and out of date. That is before the modern testing and 3 years before even ENCODE started which has revealed more evidence. You need to update your evidence and not use old outdated support which is based on old techniques which were incapable to testing properly. We have found a lot more evidence for how mutations work. The evidence I provided is current and up to date and is relevant. This paper is from 2014 showing how new testing techniques are finding more and more harmful mutations which supports what I have posted previously.

Harmful mutations can fly under the radar
Scientists have long known that the human body is a mosaic: All of our cells don't contain exactly the same genome. Every time a cell divides, genetic errors can occur, leading to variations in the DNA sequence that may proliferate and—in some cases—cause disease. Now that genetic sequencing and other technologies have made it easier to recognize mutations that occur in only a subset of cells, researchers are finding more and more harmful mutations hidden among unaffected cells.
http://science.sciencemag.org/content/345/6203/1438

1. Papers that do not state there is a limit to evolution are not evidence that there is a limit to evolution. Stating that they do once is a mistake, twice is an error, more times becomes a lie.
   4 July 2016 stevevw: The phrase "inhibit the rate of evolution" means that evolution goes slower (the rate of) - not that evolution stops.

   I could say that denying that there are no limits to evolution over and over again when even those who support evolution agree that there are limits is an obvious denial that is easily shown to be wrong. You obviously didn't read the paper as the inhibit doesn't mean slower but limits to the ability of adaptive mechanisms being able to create the type of complexity and structures we see in life. So its actually not just questioning the limits but question whether adaptive evolution through chance mutations and natural selection are responsible for creating the complex structures in organisms.
   What about the other statemnet you conveniently left out which states word for word that there are limits. That seems to indicate you are purposely leaving out certain evidence to avoid it. IE The limits to adaptation can be quantified as the magnitude of fitness load resulting from the inability of selection to promote the most advantageous alleles. As stated even the heading states that there are limits to cellular perfection.
   Evolutionary layering and the limits to cellular perfection
   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503168/

1. 29+ Evidences for Macroevolution

   : "This hypothesis has been verified and corroborated so extensively that it is currently accepted as fact by the overwhelming majority of professional researchers in the biological and geological sciences"
   4 July 2016 stevevw: A lie about the Talk Origins site stating that the evidence for macroevolution cannot be verified.
   29+ Evidences for Macroevolution: "It must be stressed that this approach to demonstrating the scientific support for macroevolution is not a circular argument: the truth of macroevolution is not assumed a priori in this discussion. Simply put, the theory of universal common descent, combined with modern biological knowledge, is used to deduce predictions. These predictions are then compared to the real world in order see how the theory fares in light of the observable evidence."

They base the evidence on macro evolution on common decent which doesn't necessarily point to macro evolution and can be the result of other processes. If a wolf is the common ancestor of all modern dogs we dont need to appeal to macro evolution to say that all modern dogs were created by macro evolution. They are variations of the pre existing genetic material that was in wolves so no new mutated creative evolution is needed that will create new types of animals. Yet it supports common ancestry. This can be the same for many creatures going right back where they had a major type of creature that has produced many variations from existing genetic material. What is seen as natural variations can be mistakenly interpreted as transitions between animals and therefore help build common ancestry.

As stated before the best way to verify this is through the genetics and molecular testing states that the tree of life for which common ancestry is built on and therefore macro evolution has many contradictions. The testing for the capabilities of mutations and natural selection being able to create macro evolution by morphing new structures to proteins has been shown to have limits and is more likely to destroy the specific structures needed to code for life. This is the best way to tell if macro evolution can work and not some observation based on interpretation of what we see and then building some concept according to that which accounts for how life was made.

I have posted ample evidence showing that macro evolution cannot happen in previously posts and even in the last couple with the limits of evolution through adaptive processes which states non adaptive mechanisms are more likely to cause life to vary. In other words non adaptive processes are using pre existing genetic material that allows life to change to certain limits. But here is some support for the tree of life contradicting common decent and therefore macro evolution.
Phylogeny: Rewriting evolution
"I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree," he says. The technique "just changes everything about our understanding of mammal evolution".
http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885

Gene tree discordance, phylogenetic inference and the multispecies coalescent
"Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates."
http://web.stanford.edu/group/rosenberglab/papers/DegnanRosenberg2009-TREE.pdf

The universal ancestor
Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.
http://www.pnas.org/content/95/12/6854.full

The above examples show how testing the relationships of different creatures on the tree of life produce different relationships between each other genetically. It distances creatures that are suppose to be related closely and therefore transitions and links them with distant ones all of which puts common ancestry in doubt which is suppose to create links of similar features and creatures back to common ancestor.

1. 4 July 2016 stevevw

   : Parroting the "gaps in the fossil record", "transitional fossil", "Cambrian explosion" creationist claims? Index to Creationist Claims

The fossil record and Cambrian explosion problems are not just creationists claims. They are issues facing evolution period and those who want to push the issue into a creation verses evolution debate are being too blinkered. Darwin himself was concerned about the problem when he stated that there was a lack of transitional fossils. He thought that this may be sorted out as time went by but that hasn't happened. we should be seeing massive amounts of transitional and as Darwin says the blending of all life into each other. But what we see is definite separate examples of life where they dont have any connections to blending fossils and appear complex without any trace of where they came from.

This is from a text book used in education so it has nothing to do with creationism.
Most of the animal groups that are represented in the fossil record first appear, "fully formed" and identifiable as to their phylum, in the Cambrian, some 550 million years ago. These include such anatomically complex and distinctive types as trilobites, echinoderms, brachiopods, molluscs, and chordates. ... The fossil record is therefore of no help with respect to the origin and early diversification of the various animal phyla
R.S.K. Barnes, P. Calow and P.J.W. Olive, The Invertebrates: A New Synthesis, pp. 9-10 (3rd ed., Blackwell Sci. Publications, 2001).

4 July 2016 stevevw

: A fantasy about any (so far imaginary) limits to evolution being evidence against macroevolution - as far as you know the limits may be above the species level !

Well Ive supplied scientific evidence for this and the important thing is apart from all the speculative claims based on observation and personal interpretation the papers showing the testing of the ability of random chance mutations and a blind process of natural selection creating such complex and specific structures that make life from non life or simpler life is unlikely and gives evidence for non adaptive processes to account for what we see which fits the evidence better that life has the ability and always has had the ability to use existing codes to change and build life. I think I have gone beyond the level of required support for this and you ignoring this and claiming the opposite without any evidence is shown to be wrong.[/QUOTE]

 

[RealityCheck01]

This is what I replied to in the first item below.

They show that there are limits to evolving organisms away from their original genetic makeup. That mutations are mostly negative and even positive ones when working with other mutations can lead to fitness costs.

Examples of not evolution do not show limits to evolution ! Add "mutations are mostly negative" and the paragraph is a lie.
21 June 2016 stevevw: Now you do not need to ignorantly repeat the "most mutations are harmful" creationist claim myth.

The problem is that with a Gish Gallop of probably irrelevant (as your track record shows) papers is that I am left with pointing out your errors yet again. But we do have:
4 July 2016 stevevw: The fantasy that an old paper has to be invalid - are you aware how long ago Newton wrote his laws or a guy called Darwin wrote a book or 2 or the original DNA papers were published !
ETA: a little lie: Perfeito et al. 2007 is only 9 years old. The list of beneficial mutation papers goes to 2002.
4 July 2016 stevevw: A possible lie in "been shown to be misleading": What shows 21 June 2016 stevevw: Now you do not need to ignorantly repeat the "most mutations are harmful" creationist claim myth. is "misleading?"
4 July 2016 stevevw: Ignorance about the ENCODE project which was not about limits to evolution or mutations.

4 July 2016 stevevw: A misleading statement about Darwin being concerned with the lack of transitional fossils: The Quote Mine Project Or, Lies, Damned Lies and Quote Mines points out a creationist quote mine of Darwin about this.
Darwin did what he did with much of his book - raised a legitimate concern ("But, as by this theory innumerable transitional forms must have existed, why do we not find them embedded in countless numbers in the crust of the earth?") and went on to address the concern in the next sentences ("It will be more convenient to discuss this question in the chapter on the Imperfection of the Geological Record; and I will here only state that I believe the answer mainly lies in the record being incomparably less perfect than is generally supposed. The crust of the earth is a vast museum; but the natural collections have been imperfectly made, and only at long intervals of time.") and references chapter.

This is also an argument from authority - Darwin is not the only person who has ever worked on evolution. And argument from "antiquity"? - Darwin could not have known about the enormous number of fossils that would be found after his death.

1. 15 June 2016 stevevw: It is a lie to state that dogs and GMO show limits to evolution. They are not examples of evolution. There seems no limit to what we can breed/engineer.
2. 21 June 2016 stevevw: The fantasy that we must be able to create new mammal species, e.g. dogs into cats, is not a limit to evolution!
3. 21 June 2016 stevevw: Now you do not need to ignorantly repeat the "most mutations are harmful" creationist claim myth.
4. 23 June 2016 stevevw: Papers that do not state there is a limit to evolution are not evidence of limits to evolution.
5. 23 June 2016 stevevw: Please read and acknowledge the scientific evidence that makes the idea that microevolution does not lead to macroevolution very ignorant.
6. 23 June 2016 stevevw: The different definitions of species are not evidence of limits to evolution.
7. 23 June 2016 stevevw: Ignorance about Darwin's original work and evolution should be remedied by learning about evolution. I suggest you start with Wikipedia.
8. 23 June 2016 stevevw: None of the paper you cited state that most mutations are harmful.
9. 4 July 2016 stevevw: The phrase "inhibit the rate of evolution" means that evolution goes slower (the rate of) - not that evolution stops.
10. 4 July 2016 stevevw: A lie about the Talk Origins site stating that the evidence for macroevolution cannot be verified.
11. 4 July 2016 stevevw: The ignorant assertion that the evidence for macroevolution is circular- read what you are cited.
12. 4 July 2016 stevevw: Parroting the "gaps in the fossil record", "transitional fossil", "Cambrian explosion" creationist claims?
13. 4 July 2016 stevevw: A fantasy about any (so far imaginary) limits to evolution being evidence against macroevolution - as far as you know the limits may be above the species level !
14. 4 July 2016 stevevw: The ignorant assertion that humans and apes do not have a common ancestor because the scientific evidence is that they do.

 

[RealityCheck01]

Which of the 292 citations to Estimate of the mutation rate per nucleotide in humans do you want to look at first, stevevw?

 

[stevevw]

4 July 2016 stevevw: M. Lynch (2012) has limits in one of many possible mutation–selection models for allele populations but does not state these stop macroevolution as you want.
The M. Lynch (2012) paper and its citations do not announce the evolution is dead !

So your now acknowledging that there are limits to evolution but that darwins theory is not dead. Well I guess a small acknowledgement is better then none. No one has said that there is no evolution. What we are talking about is the quality and quantity of that evolution. Darwin's theory of evolution through random chance mutations and blind natural selection isn't as creatively powerful as you think. Lynch doesn't mention the word macro evolution if thats what your trying to say he should say. But he does say that natural selection is in question and adaptive mechanisms cannot account for what we see in how life changes.

There are non adaptive forces that can mold and form life that rely on pre-existing genetic material and the ability of this being able to be drawn upon when needed. Adaptive evolution if anything works against organisms become more complex and therefore cannot account for what we see. The development processes of life (evolution-development), physical development influences the generation of variation (developmental bias), the ability of life to have some influence on how it works with environments (niche construction), how the environment directly shapes organisms traits (plasticity), populations having a say on what is selected or selected at all, genetic drift, extra-genetic inheritance other than genes being transmitted across generations, HGT, epigentics and other influences all have a say in how life can change apart from evolution through natural selection and random mutations. I have provided evidence for this in other papers which you have ignored such as http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

All of which you and some others who have rejected or ignored thinking that natural selection and random mutations are the answer to everything and the god of creation of all life. This view is outdated and almost as dogmatic as you claim creationists are. So its not a case of whether evolution exists but that evolution alone has been put on a pedal-stool and given too much creative power. According to Lynch's other paper the evidence is clear for this. I suggest you read this paper as well.

The frailty of adaptive hypotheses for the origins of organismal complexity

1. Michael Lynch*

Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive 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.

This section supports what was said about how supporters of evolution speculate about what evolution is capable of and that all of life can be explained by adaption (Darwin's theory of evolution) is perpetuated in modern literature without any evidence.

For the average person, evolution is equivalent to natural selection, and because the concept of selection is easy to grasp, a reasonable understanding of comparative biology is often taken to be a license for evolutionary speculation. It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise (6) in the popular literature.

It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement

it is difficult to reject the hypothesis that incremental expansions of eukaryotic gene complexity were largely driven by nonadaptive processes.

In contrast, unicellular lineages are expected to maintain streamlined genomes, not necessarily for metabolic reasons, but because of the exceptionally high efficiency of selection opposing the accumulation of mutationally hazardous DNA.

Most of the repatterning of the genomic real estate of eukaryotes occurred before the evolution of multicellularity.

In any event, the probability that two or three origins of multicellularity simply arose by chance within eukaryotes as opposed to prokaryotes is somewhere on the order of 1/4 to 1/2, well below the general standards of statistical validity.

Jacob (46) argues that “it is natural selection that gives direction to changes, orients chance, and slowly, progressively produces more complex structures, new organs, and new species.” The vast majority of biologists almost certainly agree with such statements. But where is the direct supportive evidence for the assumption that complexity is rooted in adaptive processes? No existing observations support such a claim, and given the massive global dominance of unicellular species over multicellular eukaryotes, both in terms of species richness and numbers of individuals, if there is an advantage of organismal complexity, one can only marvel at the inability of natural selection to promote it. Multicellular species experience reduced population sizes, reduced recombination rates, and increased deleterious mutation rates, all of which diminish the efficiency of selection (13). It may be no coincidence that such species also have substantially higher extinction rates than do unicellular taxa (47, 48).

This section even implies that much of the genetic info for structures of eukaryotes were around before or at least the same time as unicellular life and that there is a simplification of life rather than a movement towards complexity which is the opposite of evolution. Natural selection is actually a deterrent for make things more complex because it demand such refinements which are beyond its capabilities.

Many developmental genes previously thought to have originated in the vertebrate lineage, owing to their absence in arthropods and nematodes, are now known to be present in basal lineages of animals lacking mesoderm (the cnidarians), and by inference must have simply been lost from various invertebrate phyla (51). Numerous examples of morphological simplification exist in animals (e.g., limb loss in lizards and salamanders, coelom loss in nematodes, and mouth and anal loss in hydrothermal-vent worms), and a plausible, albeit controversial, case has even been made that prokaryotic cell architecture is a simplified derivative of that of eukaryotes (52).

The nature of cause and effect in these relationships is difficult to resolve, as all hypothetical lines of defense against introns appear to have been present in the stem eukaryote (58), raising the possibility that the colonization of nuclear genes by introns followed the origin of permissive cellular features, rather than the other way around.
Nevertheless, the idea that internal constraints played a role in cellular evolution is secure under either scenario.

And this is at the core of the debate when you say that many support evolution. Its easy to tell the story and explain the ideas of evolution. Its another thing to prove the step by step processes with scientific evidence showing how it works and came about, how mutations and natural selection (adaptive evolution) can construct those genetic pathways.

There is no evidence that gene-regulatory modules associated with complex functions arise as de novo integrated units, although some biologists seem to feel otherwise (70). Rather, like all aspects of evolution, the origins of changes in genetic pathways must be a function of descent with modification. Mutant alleles arise independently at individual loci, with features being defined by prior historical contingencies. Thus, although the idea that regulatory modules with functional significance in today's organisms can only have arisen via natural selection is seductive, it remains to be determined how the stepwise alterations necessary for the construction of genetic pathways come about.
http://www.pnas.org/content/104/suppl_1/8597.full

 

[RealityCheck01]

So your now acknowledging that there are limits to evolution

Wrong, stevevw. I am acknowledging that from my limited knowledge of biology you have cited one paper out of maybe a dozen that may show limits to evolution in "cell perfection". I see the paper has plenty of citations. I note that no biologist in the world is surprised by the results of this paper. Thus these limits seem to have no effect on evolution, e.g. the speciation that we have evidence for continues unabated for the last > 3 billion years.

Someone ignorant enough to fall for creationist claims is not competent to comment on biological papers. So my default position on all of the papers that you are citing is that your interpretations and comments are wrong. The crazy colors do not inspire confidence either ! For example this post seems to contain the ignorant demand that every "generic pathway" be described in full with every mutation that created it, etc. We do not need to know every mutation that resulted an adaption to know that evolution works - that was shown by Darwin and ~150 more years of collecting evidence.

Any one who reads about evolution knows that it is not just Darwin's theory of evolution through mutations and natural selection. We know about genes, etc. now ! The Nature commentary you link to Does evolutionary theory need a rethink? is about this point, e.g. which of the processes in the modern evolutionary synthesis should be considered fundamental.

Ditto for: "The frailty of adaptive hypotheses for the origins of organismal complexity" which is Michael Finch pointing out the known science and the bad practice on popular literature of concentrating on adaption.

Which of the 292 citations to Estimate of the mutation rate per nucleotide in humans do you want to look at first, stevevw?

Which of your 14+ errors or lies do you want to fix, stevevw?

 

[stevevw]

Wrong, stevevw. I am acknowledging that from my limited knowledge of biology you have cited one paper out of maybe a dozen that may show limits to evolution in "cell perfection". I see the paper has plenty of citations. I note that no biologist in the world is surprised by the results of this paper. Thus these limits seem to have no effect on evolution, e.g. the speciation that we have evidence for continues unabated for the last > 3 billion years.

First all the papers I have posted show limits for mutations and natural selection. I just happen to post the last one in more detail as I knew you were not reading them so that you could see the references to those limits in more detail. I can do that with all the papers if you wish but I think as you have acknowledge that this one is showing limits then one is enough to prove my point. Though you seem to try and deflect that admission by somehow no biologist in the world is surprised so therefore the limits have no effect anyway seems illogical. Either they are limits to evolution or they are not. You dont supply any evidence for these other biologists and the appeal to all the biologist in the world as evidence to back your claims is a false argument based on the fallacy of appealing to the masses. Most biologists wouldn't be surprised anyway because its an excepted understanding that there are limits to mutations. Its seems everyone acknowledges this except you.

Someone ignorant enough to fall for creationist claims is not competent to comment on biological papers. So my default position on all of the papers that you are citing is that your interpretations and comments are wrong.

Added to these false arguments now is also the fallacy of more ad hominems in claiming I'm ignorant and using creationists claims. That I,m not competent enough to make comments yet I am citing scientific support for what I am saying which states this in plain clear language. So its not me thats saying it and I havnt mentioned or linked one piece of creationists claim to anything. So it seems you are trying to attack me to attack the scientific papers and turn any evidence or reference that questions evolution into creationists claims which is a false comparison as well. Besides that in the same breath you are making all sorts of claims about these same papers without any evidence as though your word and credentials are good enough to counter everything. So its a bit hypocritical to be taking this position.

The crazy colors do not inspire confidence either ! For example this post seems to contain the ignorant demand that every "generic pathway" be described in full with every mutation that created it, etc. We do not need to know every mutation that resulted an adaption to know that evolution works - that was shown by Darwin and ~150 more years of collecting evidence.

The paper wasn't demanding anything. It was asking a question about how step wise alterations necessary for the construction of genetic pathways come about. It stated that natural selection though being a seductive idea needs to have evidence and not just make a claim. Selection sounds great and like a maths equation can be a good answer. But that in itself means little as far as how things came about and providing the evidence for it in detail. Thats where the theory breaks down as it cannot provide details and evidence of how it happened.

Any one who reads about evolution knows that it is not just Darwin's theory of evolution through mutations and natural selection. We know about genes, etc. now ! The Nature commentary you link to Does evolutionary theory need a rethink? is about this point, e.g. which of the processes in the modern evolutionary synthesis should be considered fundamental.

Well it like the other paper from Michael Lynch "The frailty of adaptive hypotheses" are considering all the non adaptive processes that can influence and affect change in living things. These non adaptive processes dont require natural selection and random mutations and are said to be more dominant than natural selection. In fact they question the role of natural selection and that it may only play a minor role or any role at all.

Ditto for: "The frailty of adaptive hypotheses for the origins of organismal complexity" which is Michael Finch pointing out the known science and the bad practice on popular literature of concentrating on adaption.

No its actually going through the different non adaptive mechanisms and the role they play in how life changes.

Which of the 292 citations to Estimate of the mutation rate per nucleotide in humans do you want to look at first, stevevw?

Which of your 14+ errors or lies do you want to fix, stevevw?

What lies, actually in starting with the first three papers on your long list they seem to be supporting what I am saying that mutations have limits, are mostly harmful and that there are other influences (non adaptive) that cause life to change besides evolution through blind natural selection and random mutations.

The first paper is talking about the inheritance of mutations and how they can best be measured through direct sequencing analyses. No one is disputing that mutations can be inherited but it seems to be talking about the inheritance of damaging mutations which supports what I have been saying.
Estimation of the frequency of inherited germline mutations by whole exome sequencing in ethyl nitrosourea-treated and untreated gpt delta mice.
Germline mutations are heritable and may cause health disadvantages in the next generation.

These results suggest that direct sequencing analyses can be a useful tool for investigating inherited germline mutations and that the germ cells could be a good endpoint for evaluating germline mutations, which are transmitted to offspring as inherited mutations.
http://www.ncbi.nlm.nih.gov/pubmed/27350829

The second paper is once again talking about the inheritance of congenital defects but this time through epigenetic alterations which are a non adaptive (non evolutionary) influence where the conditions that a parent puts themselves through such as with diet, stress, addiction ect can have an affect on the next generation by altering the genes but not through mutations. So this supports what I was posting about non adaptive influences besides evolution that cause changes to life.
Influence of paternal preconception exposures on their offspring: through epigenetics to phenotype.

Historically, research into congenital defects has focused on maternal impacts on the fetal genome during gestation and prenatal periods. However, recent findings have sparked interest in epigenetic alterations of paternal genomes and its effects on offspring. This emergent field focuses on how environmental influences can epigenetically alter gene expression and ultimately change the phenotype and behavior of progeny. There are three primary mechanisms implicated in these changes: DNA methylation, histone modification, and miRNA expression. This paper provides a summary and subsequent review of past research, which highlights the significant impact of environmental factors on paternal germ cells during the lifetime of an individual as well as those of future generations. These findings support the existence of transgenerational epigenetic inheritance of paternal experiences. Specifically, we explore epidemiological and laboratory studies that demonstrate possible links between birth defects and paternal age, environmental factors, and alcohol consumption.
http://www.ncbi.nlm.nih.gov/pubmed/27335698

The third paper is straight forward. Its talking about cancer which cannot be more clear about the effects of mutations being harmful.
Liver carcinogenesis: from naughty chemicals to soothing fat and the surprising role of NRF2.
Currently, primary liver cancer is the second leading cause of cancer-related deaths
http://www.ncbi.nlm.nih.gov/pubmed/27207669o

So the first three papers are supporting what I have been posting. I could continue but I think the rest will just be continuing to support what has been said so far. Thats because what I am saying isn't rocket science and is common knowledge among all scientists whether they support evolution or not.

 

[KCfromNC]

No its saying in most cases when beneficial mutations are added together they incur a fitness cost.

Where does it say that?

So this is supporting what I said in that what can seem like a benefit on its own becomes a negative when mixed with other mutations and multiple mutations are needed to make anything significant in evolution.

Is your objection theoretical or has this actually been observed?

The first problem is whether there is the type of beneficial mutations that lead to increased function, complexity and fitness in the first place.

Ignoring the complexity red herring, there are. All you have to do is read your sources.

What is cited as a benefit may just be a organism tolerating slightly negative mutations or the change that has brought the perceived benefit is actually negative anyway because it is changing what was already good which will have a cost even if it is that the organism has to use more energy to deal with that change.

I guess if you play enough word games you can redefine beneficial mutations as otherwise, but I'm not really interested in that sort of creative writing exercise. I'd prefer to stick to reality.

For there to be new features and creatures beneficial mutations need to be more than very rare and need to be significant to be selected.

Citation needed.

Something around zero is not going to be often or great enough and have enough influence

And here too.

But not just that evidence says that no matter if mutations are beneficial, neutral or negative they are a cost to fitness and cannot go beyond certain limits because they are errors that are changing what is already good and working.

And here.

Seems to be a pattern in these responses. Find some abstract which can be quote mined and then go off on a tangent about what you wish the paper said. That's not particularly convincing.

 

[Loudmouth]

The problem is changing one of those small bases doesn't do anything on its own and there needs to be many added together to make a change big enough to be selected.

Where is the evidence for this claim?

Mutations added together dont build toward something that has function because its a blind process and its more likely to add up to something negative which gets selected out or makes life less fit rather than fitter.

Sorry, but your argument leads to the conclusion that there are no functional human proteins. You can't be taken seriously.

And the amount of mutations needed to do that we call cancer.

Yet another bare assertion.

A mutation is an error in the copying of what is already good and working.

Then explain how humans can survive with 40 million of these copying errors.

Your logic is to assume it happened so it must be true despite the dozen papers that show mutations dont deliver better and fitter life and have limits to creating more complexity.

We don't have to assume anything. We can directly observe the 40 million mutations that separate humans and chimps.

 

[Loudmouth]

Its funny how there are a few repeated examples being used all the time to prove evolution.

I am pointing to the 40 million mutations that separate humans and chimps, and you continue to ignore them.

Antibiotic resistance is ancient
http://www.nature.com/nature/journal/v477/n7365/full/nature10388.html

Here is another paper showing that even ancient bacteria 250 million years old is similar to modern bacteria. So it seems that life was very complex early in the scheme of things and has had similar abilities to today's life.
The Paradox of the “Ancient” (250 million year old) Bacterium Which Contains “Modern” Protein-Coding Genes:
“Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
http://mbe.oxfordjournals.org/...../19/9/1637

Yet another instance of creationists ignoring the most basic science. In the Lederberg plate replica experiment and the Luria-Delbruck fluctuation experiment, we see spontaneous mutations give rise to antibiotic resistance in bacteria that were previously sensitive to antibiotics. We even know which genes these mutations occur in. All you are doing is ignoring 60 years worth of science.

 

[RealityCheck01]

There are no transition fossils, not a single one out of billions of fossils discovered.

3 July 2016 Heissonear: A repeated lie that no "transition" fossils because Transitional fossils exist ![/quote]

 

[RealityCheck01]

Its funny how there are a few repeated examples being used all the time to prove evolution...

Not right, stevevw: The scientific literature contains hundreds or even thousands of examples that are evidence for evolution, e.g. the many examples of speciation, the fossil record, etc. It is this overwhelming evidence collected over the last couple of centuries that is the support for modern evolutionary theory.

The clearest, simplest examples are used to teach people who are ignorant or dubious about evolution.
Nylon-eating bacteria

Role in evolution teaching
Main article: Nylon-eating bacteria and creationism
There is scientific consensus that the capacity to synthesize nylonase most probably developed as a single-step mutation that survived because it improved the fitness of the bacteria possessing the mutation. More importantly: The enzyme involved has been produced by a mutation completely randomizing the original gene. Despite this, the new gene still had a novel, albeit weak, catalytic capacity. This is seen as a good example of how mutations easily can provide the raw material for evolution by natural selection.[6][7][8][9]

 

[RealityCheck01]

But heres the other point, they have discovered that bacteria were able to gain the ability to become antibiotic resistance thousands of years ago. So it seems they have been able to do it well before antibiotics. The chances are the ability for digesting nylon is also something that has been around for some time and is just being tapped from the preexisting genetic ability of bacteria.

Antibiotic resistance is ancient
http://www.nature.com/nature/journal/v477/n7365/full/nature10388.html

That "The chances are ..." sentence is wrong: Nylon-eating bacteria (the mutation did not exist before 1930).
You are also wrong about the paper. The paper says that the interpretation of bacteria evolving to resist antibiotics recently is incorrect because they already had resistance to natural antibiotics such as β-lactam, tetracycline and glycopeptide 30,000 years ago.
Antibiotic resistance is ancient

The discovery of antibiotics more than 70 years ago initiated a period of drug innovation and implementation in human and animal health and agriculture. These discoveries were tempered in all cases by the emergence of resistant microbes1, 2. This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the antibiotic era are highly susceptible to antibiotics3. Here we report targeted metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments and the identification of a highly diverse collection of genes encoding resistance to β-lactam, tetracycline and glycopeptide antibiotics. Structure and function studies on the complete vancomycin resistance element VanA confirmed its similarity to modern variants. These results show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.

 

[RealityCheck01]

Here is another paper showing that even ancient bacteria 250 million years old is similar to modern bacteria. So it seems that life was very complex early in the scheme of things and has had similar abilities to today's life.
The Paradox of the “Ancient” (250 million year old) Bacterium Which Contains “Modern” Protein-Coding Genes:
“Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
http://mbe.oxfordjournals.org/...../19/9/1637

This paper does not state that any 250 million old bacteria are modern.
The paper indicates that isolate 2-9-3 might be considered a strain of S. marismortui.
The paper ends by asking the question of whether the isolate could be modern and the answer is:

As it stands, our present molecular work can neither confirm nor disprove the age of isolate 2-9-3.

The context of the quote in your post is hidden so:

The isolation of microorganisms from ancient materials and the verification that they are as old as the materials from which they were isolated continue to be areas of controversy. Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels. This fact has historically been used by critics to argue that these isolates are not ancient but are modern contaminants introduced either naturally after formation of the surrounding material (for further details, see Hazen and Roeder 2001<$REFLINK> and the reply by Powers, Vreeland, and Rosenzweig 2001<$REFLINK> ) or because of flaws in the methodology of sample isolation (reviewed recently in Vreeland and Rosenzweig 2002<$REFLINK> ). Such criticism has been addressed experimentally by the development of highly rigorous protocols for sample selection, surface sterilization, and contamination detection and control procedures. Using the most scrupulous and well-documented sampling procedures and contamination-protection techniques reported to date, Vreeland, Rosenzweig, and Powers (2000)<$REFLINK> reported the isolation of a sporeforming bacterium, Bacillus strain 2-9-3, from a brine inclusion within a halite crystal recovered from the 250-Myr-old Permian Salado Formation in Carlsbad, NM.

No one who knows about the history of the world thinks that 250 million years ago is "early in the scheme of things", stevevw!

• Age of the Earth: "The age of the Earth is 4.54 ± 0.05 billion years (4.54 × 109 years ± 1%).[1][2][3][4]"
• Abiogenesis: "It is thought to have occurred on Earth between 3.8 and 4.1[11] billion years ago...".
• Bacteria: "The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life.[19][20]"

 

[stevevw]

This paper does not state that any 250 million old bacteria are modern.
The paper indicates that isolate 2-9-3 might be considered a strain of S. marismortui.
The paper ends by asking the question of whether the isolate could be modern and the answer is:

Its funny when something found in ancient ground it is used to verify evolution and no questions are asked about the age and time lines matching up when it all supports evolution. But when it contradicts evolution questions are asked and it is disputed. Yes the paper states it cannot be verified whether the bacteria found in ancient material is modern or ancient yet they say it was found in ancient material. But there is a strong chance it is ancient because other discoveries show similar results. So heres some more evidence that ancient bacteria is similar to modern ones.
AMBER: THE LOOKING GLASS INTO THE PAST:
These (fossilized bacteria) cells are actually very similar to present day cyanobacteria.
http://bcb705.blogspot.com.au/2007/03/amber-looking-glass-into-past_23.html
Static evolution: is pond scum the same now as billions of years ago?
http://www.thefreelibrary.com/Static+evolution:+is+pond+scum+the+same+now+as+billions+of+years+ago?-a014909330

The context of the quote in your post is hidden so:

What context is that.

No one who knows about the history of the world thinks that 250 million years ago is "early in the scheme of things", stevevw!

The point is if ancient organisms are similar to modern then it shows that the complex codes for life have been around for a long time and life has just been an adjustment of that. The Cambrian explosion over 500 million years ago is another example of early life having modern body plans and other discoveries as shown above show that even life in the beginning had complex designs and had to have been very complex to be able to produce what we see.

In fact the evidence shows that as time has gone on complex life has become more simple rather than what evolution claims that is from simple to more complex and that life is becoming less fit rather than as evolution claims it is becoming more fit. All the opposite of evolution.

• Age of the Earth

  : "The age of the Earth is 4.54 ± 0.05 billion years (4.54 × 109 years ± 1%).[1][2][3][4]"
  [*]Abiogenesis: "It is thought to have occurred on Earth between 3.8 and 4.1[11] billion years ago...".
  [*]Bacteria: "The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life.[19][20]"

  I dont know what your point is here. Bacteria have been much the same since day 1 and they have a great ability to share genetic material.

 

[stevevw]

That "The chances are ..." sentence is wrong: Nylon-eating bacteria (the mutation did not exist before 1930).
You are also wrong about the paper. The paper says that the interpretation of bacteria evolving to resist antibiotics recently is incorrect because they already had resistance to natural antibiotics such as β-lactam, tetracycline and glycopeptide 30,000 years ago.
Antibiotic resistance is ancient

Thats the point the bacteria already had antibiotic resistance 30,000 years ago so how can it have developed resistance in modern times as evolution states which is suppose to show a new function being evolved. The point is the ability for bacteria to do this is something that may have been already available in their genetic makeups which was switched on or that the bacteria lost some info which allowed it to resist antibiotics. The same with the ability to digest nylon. Bacteria also have a great ability to share genetic info so they can rely of the billions of other bacteria to have a vast amount of genetic material that can be drawn upon which increases their genetic pool.

Scientists unlock a ‘microbial Pompeii’ – February 23, 2014
Excerpt: “…The researchers discovered that the ancient human oral microbiome already contained the basic genetic machinery for antibiotic resistance more than eight centuries before the invention of the first therapeutic antibiotics in the 1940s…”
http://phys.org/news/2014-02-s.....mpeii.html

Resistance to antibiotics is ancient
New research findings show antibiotic resistance is a natural phenomenon that predates the modern clinical antibiotic use.
Scientists were surprised at how fast bacteria developed resistance to the miracle antibiotic drugs when they were developed less than a century ago. Now scientists at McMaster University have found that resistance has been around for at least 30,000 years.
https://www.sciencedaily.com/releases/2011/08/110831155334.htm

So it seems the very few examples given for proving evolution turn out to be proving that life already has the ability to tap into a vast array of genetic material that has been there for a very long time. Perhaps to long for the slow and gradual process of evolution to have created.

 

[Loudmouth]

Its funny when something found in ancient ground it is used to verify evolution and no questions are asked about the age and time lines matching up when it all supports evolution. But when it contradicts evolution questions are asked and it is disputed.

Those bacteria do not contradict evolution.

The point is if ancient organisms are similar to modern then it shows that the complex codes for life have been around for a long time and life has just been an adjustment of that.

None of which contradicts evolution. We would expect complex codes to be around 250 million years ago if evolution is true. The first signs of bacterial life are seen over 3 billion years ago in the fossil record. This means there were over 2.5 billion years for complex codes to evolve.

The Cambrian explosion over 500 million years ago is another example of early life having modern body plans

That is 2.5 billion years after the first life emerged. Again, not a problem.

In fact the evidence shows that as time has gone on complex life has become more simple rather than what evolution claims that is from simple to more complex and that life is becoming less fit rather than as evolution claims it is becoming more fit.

Evolution doesn't say that life must go from simple to complex. It only says that life will go from less fit to more fit.