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Where did the laws of nature come from?

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Why isn't examples of dog breeding showing genetic limits....
Firstly because that question make you look like you are moving goal posts. You wrote an assertion about evolution, not breeding.

Secondly because you have still presented no evidence for "dog breeding showing genetic limits". Common sense suggests the opposite is true - there seems no limit to the extent to which we can change the genetics of dogs.

"Researchgate and science direct" do not pubish papers as you suggested in "Douglas Axe is published in other journals including the Researchgate and science direct".

Pointing out that an author is an ID proponent or that a citation shows ignorance about the source is not an ad hominem.
May 31, 2016 stevevw: You cited a paper from Douglas Axe - an ID proponent.
May 31, 2016 stevevw: You cited his paper from the defunct BIO-Complexity in-house non-peer reviewed journal published by the Biologic Institute which is staffed and funded by the Discovery Institute.

June 17, 2016 stevevw: The citation of a specific Douglas Axe paper was ignorant because it was published in a defunct, in-house, non-peer reviewed "journal" (more like a news letter!) with a dubious background.
 
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stevevw

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Firstly because that question make you look like you are moving goal posts. You wrote an assertion about evolution, not breeding.
I am not moving goal posts artificial selection and natural selection are similar and often used as comparisons. Dog breeding or in darwins case pigeon breeding was used as an example for showing natural selection over 150 years ago. So it seems I am more aware of evolution than you are in this case. But it offered problems for Darwin and his contemporaries as well in proving evolution. Sure he could make small changes with pigeons but that that was limited and came with many problems such as diseases and deformities. No one has said that there cant be changes made within a species. But they are using existing genetic info and there are limits as stated many times. Darwin and others who support evolution assumed that the process that made the small changes could result in massive changes over time. That hasn't been verified scientifically back then or today and is still based on assumption and observational evidence.

Secondly because you have still presented no evidence for "dog breeding showing genetic limits". Common sense suggests the opposite is true - there seems no limit to the extent to which we can change the genetics of dogs.
I thought you would have known about the problems with dog breeding. Many dog breeds have issues of diseases and other health problems that actually cause them to be less fit.
Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
http://www.pnas.org/content/113/1/152.abstract

"Researchgate and science direct" do not pubish papers as you suggested in "Douglas Axe is published in other journals including the Researchgate and science direct".
I never said researchgate published journals themselves if you read what I said. I said researchgate is like google scholar where you can get access to many different journals published by other sites like Plos or nature.com. You have to be registered with a Uni to join but once you have you can get many journals for free or request the author who will send it to you at no charge. that is why I like sites like researchgate. they also put many academics in touch with each other which allows collaborations.

Pointing out that an author is an ID proponent or that a citation shows ignorance about the source is not an ad hominem.
May 31, 2016 stevevw: You cited a paper from Douglas Axe - an ID proponent.
Doug Axe is also an expert in the field of evolution especially biological evolution. But you choose to focus on whatever so long as it undermines him.
After a Caltech PhD he held postdoctoral and research scientist positions at the University of Cambridge, the Cambridge Medical Research Council Centre, and the Babraham Institute in Cambridge. His work and ideas have been featured in many scientific journals, including the Journal of Molecular Biology, the Proceedings of the National Academy of Sciences, and Nature

You cited his paper from the defunct BIO-Complexity in-house non-peer reviewed journal published by the Biologic Institute which is staffed and funded by the Discovery Institute.
Well lucky he published the same papers in journals like Nature.com and the Journal of Molecular Biology as they are mainstream scientific journals. So if we use your logic in saying that because he published in Bio Complexity he must be suspect then because he published in top mainstream science journals he must also be credible. Thats what I mean by using an ad hominem. You want to use what he is associated with to discredit him and not the actual work or content of that he actually publishes.

June 17, 2016 stevevw
: The citation of a specific Douglas Axe paper was ignorant because it was published in a defunct, in-house, non-peer reviewed "journal" (more like a news letter!) with a dubious background.
But the same paper is also published in a mainstream journal thats accepted by all the scientists ie Nature.com. Plos and journal of molecular biology. They are all peer reviewed journals. The point you were trying to make was that Douglas Axe is only published in Biologic institute which is wrong. I expect you were saying this to try and undermine him as a scientists purely on the grounds that he is associated with something that is perceived as not credible. But the point with that is that this is still not a valid argument because its a false comparison. You cant assume someone is something purely on the grounds of association.[/quote]
 
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I am not moving goal posts artificial selection and natural selection are similar and often used as comparisons.
You are not using them as comparisons - you are using them as evidence. And then not actually providing any evidence. You stated: They show that there are limits to evolving organisms away from their original genetic makeup.
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.

There is another lie about "mutations are mostly negative" in that post when mutations are mostly neutral is a bit of biology that anyone who learns about evolution knows. But the post is old so maybe you can link to where you acknowledge this biology making the statement into a temporary mistake that will not be repeated.

These points are about your bad citations:
May 31, 2016 stevevw: You cited a paper from Douglas Axe - an ID proponent.
May 31, 2016 stevevw: You cited his paper from the defunct BIO-Complexity in-house non-peer reviewed journal published by the Biologic Institute which is staffed and funded by the Discovery Institute.

Now we have a bit of argument from authority and pointing out bad scholarship
* publishing valid science does not make a person incapable of supporting invalid or even deluded science.
ID is not science. A competent biologist with knowledge of evolution would not support ID. That suggests that a person is either being ignorant or denying science.
* it is not good scholarship to publish the same scientific paper in different journals.

Douglas Axe
Axe is a molecular biologist, and is as such one of relatively few people with real credentials who is affiliated with the intelligent design movement. Drawing on his knowledge of biology, Axe has authored a few relatively mundane papers, at least some of which have been published in low-tier, although genuine, journals. Although none of these papers contain – or even attempts to mount – any refutation of evolution, much less evidence for intelligent design, Axe’s work has been hailed by the Discovery Institute as evidence supporting their views. Even Axe himself has admitted that this is not the case.[2]

He has published extensively in the Biologic Institute’s house journal BIO-Complexity, but that does not count.
Does an expert in the field of evolution think Axe is an expert in the field of evolution?
Who needs an IQ test when you’ve got coalescence?
Does Axe's use of false dichotomy suggest scientific competence?
Here's Douglas Axe illustrating the false dichotomy on Evolution News & views
Does this analysis of his 2004 paper show that Axe is knowledgable about evolution?
Axe (2004) and the evolution of enzyme function
 
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stevevw

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You are not using them as comparisons - you are using them as evidence. And then not actually providing any evidence. You stated: They show that there are limits to evolving organisms away from their original genetic makeup.
15 June 2016 stevevw: It is a lie to state that dogs and GMO show limits to evolution. They are not examples of evolution.
how is it a lie and how are they not examples of evolution.
Of course there are limits. If there wasn't limits then scientists could morph as dog into a cat for example or an ape into a human or at least start the process by successfully morphing some of the new and different features needed to change one type of creature into another. But we havnt seen anything like that. The experiments with fruit flies have produced flies with extra wings, small wings, shriveled wings and changed the color of their bodies and eyes. But they have always remained flies and if there were no limits then they could have mutated another type of insect feature into them or produced a new type of feature they never had. The flies that have been changed in tests become sick and weaker and often die. Mutations are mostly errors that cause problems with what is already working well.

There is another lie about "mutations are mostly negative" in that post when mutations are mostly neutral is a bit of biology that anyone who learns about evolution knows. But the post is old so maybe you can link to where you acknowledge this biology making the statement into a temporary mistake that will not be repeated.
From what I have come to understand mutations are mostly negative to living things. How can they be anything else as they are changing what fit and functional with what all scientists call an error. What they often call neutral is a very slight negative mutation or error that doesn't have enough effect on its own. But added together they can build up and have an adverse effect. Even so called beneficial or positive mutations can affect each other and when accumulated have a negative effect through epistasis.

So heres half a dozen papers all showing that most mutations are negative or end up accumulation into a negative effect and therefore having a fitness cost. I have posted several because you seem to question ones on their own or not backed by papers from various sources. As you can see these are from a wide range of peer reviewed sources.

Harmful mutations can fly under the radar
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://www.ncbi.nlm.nih.gov/pubmed/25237080

Robustness–epistasis link shapes the fitness landscape of a randomly drifting protein
Thus, under a low selection pressure, a large fraction of mutations was initially tolerated (high robustness), but as mutations accumulated, their fitness toll increased, resulting in the observed negative epistasis

http://www.nature.com/nature/journal/v444/n7121/full/nature05385.html

Unexpectedly small effects of mutations in bacteria bring new perspectives
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


Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? (Thomas Bataillon)
Abstract……It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.
http://www.nature.com/hdy/jour.....7270a.html


Distribution of fitness effects caused by random insertion mutations in Escherichia coli
Excerpt: At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect.

http://www.ncbi.nlm.nih.gov/pubmed/9720287

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
Epistasis depended on the effects of the combined mutations—the larger the expected benefit, the more negative the epistatic effect. Epistasis thus tended to produce diminishing returns with genotype fitness,
http://www.sciencemag.org/content/332/6034/1193.abstract

: You cited a paper from Douglas Axe - an ID proponent.
May 31, 2016 stevevw: You cited his paper from the defunct BIO-Complexity in-house non-peer reviewed journal published by the Biologic Institute which is staffed and funded by the Discovery Institute.
Now we have a bit of argument from authority and pointing out bad scholarship
* publishing valid science does not make a person incapable of supporting invalid or even deluded science.
ID is not science. A competent biologist with knowledge of evolution would not support ID. That suggests that a person is either being ignorant or denying science.
Thats a ridiculous claim. many great scientists who made great discoveries including in the field of evolution and biology were supporters of ID or God. A person can have a faith in God and be a scientists as well you know. the two views can be held at the same time as they deal with different aspects of life.
* it is not good scholarship to publish the same scientific paper in different journals.
The arguments you were using to discredit someone were fallacies. Now you are the one changing the goal posts all the time. Douglas Axe published these papers in non ID journals which are all mainstream journals that are accepted by the mainstream establishment. There is no mention of ID in the papers and they deal purely with biological evolution of proteins based on scientific testing. You can get more scientific then that. If he is wrong then he is wrong based on the science and nothing to do with ID. But thats a different point. You dont even let him get that far and check his work.

You reject the work based on his association with ID. Yet mainstream science journals have accepted his work based on him being a scientists who is presenting scientific journals. His papers wouldn't have been accepted in mainstream journals if they were to do with ID. The fact that they are accepted shows that they are not associated with ID but based on scientific testing. So who is correct you who dont even allow his work to get past first base because of his association or the mainstream journals who have accepted his work based on the content of scientific testing.

Does an expert in the field of evolution think Axe is an expert in the field of evolution?
What is an expert in the field of evolution. Axe is a molecular biologist which is probably the best field in knowing about evolution. But I am not sure what is an expert in evolution. Is it a naturalist and geologists as Darwin was or a Zoologist. I think in evolution is based more on the study of molecular biology for which Douglas Axe has extensive knowledge.
Using a blog setup to bag religion is more or less the same type of discreditable site as the ones you want to claim Axe is associated with.

Does Axe's use of false dichotomy suggest scientific competence?
Here's Douglas Axe illustrating the false dichotomy on Evolution News & views
Another blog page. At least I am presenting scientific papers for my support. I could start using blogs as well and come up with all sorts of claims. I think Larry Moran is using some false dichotomies himself. He is also assuming that Axe is saying that if evolution is false or natural processes cant explain the complexity of life then it must be from creation. I dont think he is thinking that far ahead and the tests are purely to show that natural processes cannot explain how proteins are so specific and structured that they dont have the qualities of something that can form from a naturalistic process. Its using the same logic that we use so often in design of everything else.
Does this analysis of his 2004 paper show that Axe is knowledgeable about evolution?
Axe (2004) and the evolution of enzyme function
Ok so at least your now getting past first base and looking at his work rather than trying to discredit him based on association. All scientists are subject to scrutiny for their work and that is the process of peer review. Evolution is especially scrutinized as when it comes to the detailed analysis of how the process of proteins being able to evolve there is a lot of debate and difference in opinion. When a paper is questioned the author has the right to reply and Axe has replied to those who have questioned his papers and shown they were wrong.
Correcting Four Misconceptions about my 2004 Article in JMB
http://www.biologicinstitute.org/post/19310918874/correcting-four-misconceptions-about-my-2004

As I have stated before Axe is not alone in his view. Some of the papers I have posted above are along similar lines and there are others I have previously posted which say similar things as well. So Axe is not the only one who is saying this.
 
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Loudmouth

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From what I have come to understand mutations are mostly negative to living things.

According to your logic, not a single human protein has function. Why? Because none of those proteins have beta-lactamase activity.

How do you explain that?
 
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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.
You are imagining limits are not limits to evolution, stevevw. A fact of evolution is that new species evolve. That we must magically "morph as dog into a cat is obvious a delusion - speciation in mammals takes a long time, we have no need to do so, etc. We have essentially done this in the long term e-coli experiment where we evolved a new species of bacteria.

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!

From what I have come to understand mutations are mostly negative to living things.
This ignorance about genetic is one reason I do not have to look at your irrelevant links even in totally crazy colors, stevevw :eek:!
Claim CB101:Most mutations are harmful, so the overall effect of mutations is harmful.
Most mutations are neutral. Nachman and Crowell estimate around 3 deleterious mutations out of 175 per generation in humans (2000). Of those that have significant effect, most are harmful, but the fraction which are beneficial is higher than usually though. An experiment with E. coli found that about 1 in 150 newly arising mutations and 1 in 10 functional mutations are beneficial (Perfeito et al. 2007).
21 June 2016 stevevw: Now you do not need to ignorantly repeat the "most mutations are harmful" myth.

May 31, 2016 stevevw: You cited a paper from Douglas Axe - an ID proponent.
May 31, 2016 stevevw: You cited his paper from the defunct BIO-Complexity in-house non-peer reviewed journal published by the Biologic Institute which is staffed and funded by the Discovery Institute.


You need to read what I wrote - Douglas Axe is a ID proponent (no mention of God) and so has shown incompetence by supporting a debunked ID and relying on the logical fallacy of false dichotomy. Publishing in an defunct in-house just emphasizes this.
20 June 2016 stevevw: Publishing valid science does not make a person incapable of supporting invalid or even deluded science such as ID.
20 June 2016 stevevw: It is not good scholarship to publish the same scientific paper in different journals as you assert Douglas Axe did.


All biologist are "experts" on evolution because they learn about evolution :p. A real expert in any field is one who has published many papers in that field that have in turn been cited many times and accepted by their peers as correct.
What I would expect from your assertion that Douglas Axe is an authority on evolution is a list of the many papers that he has published on evolution. What I get are unsupported assertions.

When I go to other sources I see that Douglas Axe has not published many papers on evolution and his expertise is disputed:
 
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Michael

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Nothing about the science I pointed out, e.g.

Apparently you constantly engage yourself in personal attacks regardless of the topic, and regardless of the individual that you're debating. You do not debate *topics* RC, you attack *individuals*. How sad.
 
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Denial/ignorance of science means that all you can write is irrelevant insults.

You're clearly projecting RC. :)

Where is your evidence to support
stevevw?

I wasn't trying to support his position RC, I was pointing out the unethical nature of your personal attacks and the fact that you use them on *everyone*, regardless of the topic. It's a completely unethical personality quirk of yours.
 
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I wasn't trying to support his position RC,...
Thank you for confirming that all you have is denial/ignorance of science leading to irrelevant insults.

I have relevant science and evidence, e.g.
The theory of evolution (which is not dog breeding)!
Claim CB101:Most mutations are harmful, so the overall effect of mutations is harmful.
Intelligent Design is pseudoscience with evidence against it.
Douglas Axe wrote at least one bad paper: Axe (2004) and the evolution of enzyme function
Douglas Axe uses the fallacy of false dichotomy: Here's Douglas Axe illustrating the false dichotomy on Evolution News & views
Douglas Axe expressed some ignorance about evolution: Who needs an IQ test when you’ve got coalescence?
There is no evidence presented yet that Douglas Axe has written more than few paper on ID or evolution.

Printing out an obvious lie is not an insult - it is a chance for the person to learn the truth.
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.
 
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stevevw

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If there are no limits then why do we have so many diseases caused by mutations. If most mutations affect fitness levels in the end (refer to the 6 peer reviewed papers cited in previous post) then isn't that in itself a limit to evolving fit life.
A fact of evolution is that new species evolve. That we must magically "morph as dog into a cat is obvious a delusion - speciation in mammals takes a long time, we have no need to do so, etc. We have essentially done this in the long term e-coli experiment where we evolved a new species of bacteria.
No one is disagreeing with limited evolution within the same type of organism or creature. We see this with the different type of the same animals. Just like the bacteria you talk about for example bats have 100s of species but they are still all bats. Bats have basically been that shape for millions of years and that is the same for many animals and organisms. Even Darwin questioned whether the variations of a type of creature was just natural variations within a species that happen through reproduction that is limited. Look at humans and you will see different features of size, color, shape all mating with each other causing more variations within the human species. Many taxonomists debate about what is classed as natural variation within a type of creature and what is species for which it is call

Lumpers and splitters.

There is a lot of debate and disagreement as to what a species is. What is a natural variation within a type of creature is mistaken as a new species such as with the skulls found at Georgia.
http://www.sci-news.com/othersciences/anthropology/science-dmanisi-human-skull-georgia-01474.html Several different shaped skulls that covered several different species named in the past by evolution were found together. So all those different species were then made into one species that had great variation. So there is a fine line between what is a species and what may be just the normal variation with a species. Add to that the ability of life to share genetic material through HGT and cross breeding especially in the past and you can see how much of life could have variation without Darwinian evolution. In other words there are other non adaptive processes that can cause creatures to change.

The bacteria in those experiments are still bacteria. The anti antibiotic resistance that is cited so many times is a variation with existing genetics and/or a loss of info. There are other associated fitness costs that come with that. Antibiotic resistant bacteria have been found that are millions of years old. micro organisms have a great ability to share genetic material as well.

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!
No the theory of Darwinian evolution imagines that one type of animal morphs into another with time based on assumption because they see small variations happen within a species. They assume given time that eventually this same process has produced every single creature that has ever and still does occupy the earth. It has not been proven. Lab tests and selective breeding have shown the limits for which I have posted in the above post of the fitness loss and cost to living things through mutations. A new species doesn't mean Darwinian evolution is true. It just means that micro evolution allows a creature to vary within certain limits or that life can obtain new genetic material form other processes as mentioned above.


This belief and fixation of random mutations and natural selection being able to create any change through adaptation has been shown to be wrong and something that traditional supporters of evolution are holding onto to. Evolution cannot address many of the things that have been observed such as how physical development influences the generation of variation (developmental bias),how the environment directly shapes organisms’ traits (plasticity); how organisms modify environments (niche construction); and how organisms transmit more than genes across generations (extra-genetic inheritance). It is now known that there are other ways for which life can change without Dawins theory.
Does evolutionary theory need a rethink?
http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

This ignorance about genetic is one reason I do not have to look at your irrelevant links even in totally crazy colors, stevevw :eek:!
Well if you never have to read the evidence then I guess your never going tio be made aware. maybe you are the one who is refusing to look at the truth.
21 June 2016 stevevw: Now you do not need to ignorantly repeat the "most mutations are harmful" myth.
Well what about the peer reviewed papers that state this that you refuse to read and acknowledge. No amount of claiming the opposite will change that fact. Besides from what I am seeing with your posts I seem to be addressing the same things and you are re-pasting the same things I am saying without using quote marks to separate them. You must have re-pasted the Doug Axe quote a few times now as below.

: You cited a paper from Douglas Axe - an ID proponent.
May 31, 2016 stevevw: You cited his paper from the defunct BIO-Complexity in-house non-peer reviewed journal published by the Biologic Institute which is staffed and funded by the Discovery Institute.
You need to read what I wrote - Douglas Axe is a ID proponent (no mention of God) and so has shown incompetence by supporting a debunked ID and relying on the logical fallacy of false dichotomy. Publishing in an defunct in-house just emphasizes this.
I did read and understand what you said. I stated that your logic is wrong and based on association and false comparisons. If you use that logic then any scientists who also believes in God ie that God created the universe and life, which is also classed on illogical thinking according to science then all those scientists should also be discredited. Yet some of the greatest scientists and discoveries come from those who believed in God and his creation. Whether that be ID or plain outright supernatural creation they still believe in God.The other false argument is that you keep referring to Doug Axe and his association with ID. He does have a scientific life as well and his papers have been published on many mainstream journals that are peer reviewed.
: Publishing valid science does not make a person incapable of supporting invalid or even deluded science such as ID.
That same logic should apply to those who have an association with ID doesn't mean that they cant be valid in their science about how proteins work. His papers on the functioning of proteins has nothing to do with ID.
20 June 2016 stevevw
: It is not good scholarship to publish the same scientific paper in different journals as you assert Douglas Axe did.
Ah all scientists do it. I can find the same paper for many journals in different journal publishers. So once again you are trying to bring up anything t discredit. For example one non religious scientist Michael Lynch has his paper for Evolutionary layering and the limits of cellular perfection in
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503168/
http://www.pubfacts.com/detail/23115338/Evolutionary-layering-and-the-limits-to-cellular-perfection
http://www.pnas.org/content/109/46/18851.abstract


All biologist are "experts" on evolution because they learn about evolution :p. A real expert in any field is one who has published many papers in that field that have in turn been cited many times and accepted by their peers as correct.
What I would expect from your assertion that Douglas Axe is an authority on evolution is a list of the many papers that he has published on evolution. What I get are unsupported assertions.
When I go to other sources I see that Douglas Axe has not published many papers on evolution and his expertise is disputed:
You have already posted this and I have posted a reply for which Doug Axe answers those claims and objections and shows how they were either wrong or misguided in their claims. The idea is to read the content rather than ignore it and then make up your mind. That is what review means. You seem to be just dismissing everything and repeating the same assertions.
That still doesn't mean that his work is wrong or he is not an expert. many great scientists were said to be wrong because they had differing ideas from the consensus. That is the idea of science. The scientists who disagree with the consensus whether they are religious or non religious will have a lot of disagreement about their work so therefore there will be little support. The other problem is that much of the accepted work in peer review and the peer review process itself has been found to be either sloppy work or wrong.
Peer review: a flawed process at the heart of science and journals
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1420798/
How science goes wrong
Too many of the findings that fill the academic ether are the result of shoddy experiments or poor analysis (see article). A rule of thumb among biotechnology venture-capitalists is that half of published research cannot be replicated.
http://www.economist.com/news/leade...it-needs-change-itself-how-science-goes-wrong
 
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