Epic failure in peer review? PLOS One scientific journal cites a creator. Scientists say OMG

originally posted by: rnaa
Does anybody else see the red flag there? Hint: for the word 'authors' substitute the words 'NRA' or 'Koch Brothers' or 'Answers in Genesis' or any number of front organizations established for the purpose of pushing anti-scientific opinion and getting psuedo-science and charletanism accepted as actual science.

Should PLoS One Count as Peer Reviewd?

Clearly not a reliable place to go to find properly flushed out research. If nothing else, I'll be sure to take anything I read from this source with a grain of salt.

But..... this paper was funded by grants from two of China's most well known science foundations:
Program 973 and National Natural Science Foundation of China (NSFC)

Given that I'm not sure I buy the whole translation error story, that they meant to say nature or evolution. Especially when they referred to evolution in the same sentence they referenced "the Creator". (see above post)

And really, it's fine if the scientists who did the research came out of it believing it shows the hand of God, so to speak. But they might as well stick by that instead of coming out after and claiming that's not what was meant...

No one in their right mind believes that.

originally posted by: Cypress

originally posted by: chr0naut

originally posted by: TerryDon79

originally posted by: chr0naut

originally posted by: TerryDon79

originally posted by: chr0naut

originally posted by: TerryDon79
a reply to: chr0naut

It's not about being PC or not.

It's about coming to a conclusion based on evidence (that's what papers are).

Since there is no evidence of god then the paper is not based on any known evidence.

The authors of the paper, the peer reviewers and the editorial staff seem to have accepted that this was such evidence.

Of course, if you reject the evidence as evidence, there is obviously no evidence.

The authors of the paper are the people that wrote it.

There is NO mention of it being peer reviewed.

The editorial staff can be as few as 1 person.

There is no proof for or against a creator. Science doesn't go there as it's a subject you can't prove right or wrong.

If the paper had spoken of the intricacies of the hand's mechanics as arising from the process of evolution, would you have accepted it?

What observed science do you have of the evolutionary processes specifically giving rise to the complex mechanics of the human hand? Despite having little actual hard science, neither you nor I would nay say the role of evolutionary development. We both take that component on faith, from what we know of science, it is reasonable to do so.

But science isn't about faith.

You can go out tomorrow and test anything that is claimed to be a scientific theory. If you find something wrong with it, have proof and the results can be repeated, then you can change that theory.

Please design a test for the evolution of the mechanics of the human hand. If you or any others cannot, then you must realize that you are applying an unequal criteria to what you will 'accept'.

There are ways to study the hand and understand how it evolved. We have a fossil record as well as the ability to study yhe anatomy of other organism. Just like if I wanted to study the spinal cord I could observe how a notochord (its predecessor) operates in other lifeforms. There is already plenty of evidence from the fossil record showing a transition from being a quadraped to bipedalism, which would be the precursor due to freeing of the hands. Im sure there are several studies available to discuss the rise of himan hands.

Now one more point. Getting published is only one part of peer review process. Once the article is piblished it is open for further scrutiny. If it doesnt hold water, as is the case here, then it is shown to be inaccurate (or a poor translation in this case).

While the fossil record does show that structural change has occurred, it shows little to nothing of how it occurred or of the genetic details of the change.

Perhaps Theistic Evolution guided the change, perhaps something closer to the Modern Evolutionary Synthesis, perhaps God altered the DNA.

We don't know enough to be assured that our pet theory is "the one". The assumption that we are right, in the face of our actual ignorance, is opinion.

a reply to: PhotonEffect

But..... this paper was funded by grants from two of China's most well known science foundations:
Program 973 and National Natural Science Foundation of China (NSFC)

I did not mean to imply that this particular paper was funded by a 'benefactor' with some evil agenda. Only that the business model leaves them wide open to abuse and suspicion.

Given that I'm not sure I buy the whole translation error story, that they meant to say nature or evolution. Especially when they referred to evolution in the same sentence they referenced "the Creator". (see above post)

I don't know what to believe about this.

On the one hand I can easily see that poor translation could very easily give those results. Have you ever tried to read the owners manual for an Asian built car lately? I saw one not too long ago that had been translated from Chinese to German to English. The Polish translator that had inherited the mess asked a bunch of native English speaking members (including me) on a completely unrelated (but friendly) community forum for help in unmangling about a dozen pages of complete gibberish. She was a very good translator and spoke English better than a lot of native speakers, but this stuff was ridiculous.

On the other hand, PLoS policy of calling one person reading a paper a "Peer Review" obviously leaves them open to not just abuse or exploitation, but laziness. The editor probably didn't even read it.

originally posted by: rnaa
I did not mean to imply that this particular paper was funded by a 'benefactor' with some evil agenda. Only that the business model leaves them wide open to abuse and suspicion.

Totally with you.

originally posted by: rnaa
Have you ever tried to read the owners manual for an Asian built car lately? I saw one not too long ago that had been translated from Chinese to German to English.

Chinese to English, via German?

zoiks.

originally posted by: rnaa
On the other hand, PLoS policy of calling one person reading a paper a "Peer Review" obviously leaves them open to not just abuse or exploitation, but laziness. The editor probably didn't even read it.

Yeah, you're probably right.

originally posted by: chr0naut

originally posted by: Cypress

originally posted by: chr0naut

originally posted by: TerryDon79

originally posted by: chr0naut

originally posted by: TerryDon79

originally posted by: chr0naut

originally posted by: TerryDon79
a reply to: chr0naut

It's not about being PC or not.

It's about coming to a conclusion based on evidence (that's what papers are).

Since there is no evidence of god then the paper is not based on any known evidence.

The authors of the paper, the peer reviewers and the editorial staff seem to have accepted that this was such evidence.

Of course, if you reject the evidence as evidence, there is obviously no evidence.

The authors of the paper are the people that wrote it.

There is NO mention of it being peer reviewed.

The editorial staff can be as few as 1 person.

There is no proof for or against a creator. Science doesn't go there as it's a subject you can't prove right or wrong.

If the paper had spoken of the intricacies of the hand's mechanics as arising from the process of evolution, would you have accepted it?

What observed science do you have of the evolutionary processes specifically giving rise to the complex mechanics of the human hand? Despite having little actual hard science, neither you nor I would nay say the role of evolutionary development. We both take that component on faith, from what we know of science, it is reasonable to do so.

But science isn't about faith.

You can go out tomorrow and test anything that is claimed to be a scientific theory. If you find something wrong with it, have proof and the results can be repeated, then you can change that theory.

Please design a test for the evolution of the mechanics of the human hand. If you or any others cannot, then you must realize that you are applying an unequal criteria to what you will 'accept'.

There are ways to study the hand and understand how it evolved. We have a fossil record as well as the ability to study yhe anatomy of other organism. Just like if I wanted to study the spinal cord I could observe how a notochord (its predecessor) operates in other lifeforms. There is already plenty of evidence from the fossil record showing a transition from being a quadraped to bipedalism, which would be the precursor due to freeing of the hands. Im sure there are several studies available to discuss the rise of himan hands.

Now one more point. Getting published is only one part of peer review process. Once the article is piblished it is open for further scrutiny. If it doesnt hold water, as is the case here, then it is shown to be inaccurate (or a poor translation in this case).

While the fossil record does show that structural change has occurred, it shows little to nothing of how it occurred or of the genetic details of the change.

Perhaps Theistic Evolution guided the change, perhaps something closer to the Modern Evolutionary Synthesis, perhaps God altered the DNA.

We don't know enough to be assured that our pet theory is "the one". The assumption that we are right, in the face of our actual ignorance, is opinion.

There is no evidence that suggests divine intervention. A mutation, which is a well documented phenomenon, easily accounts for the changes. You would need to provide quantifiable evidence of God otherwise it has no pace at the table. At this time all the evidence supports MES.

originally posted by: Cypress

originally posted by: chr0naut

originally posted by: Cypress

originally posted by: chr0naut

originally posted by: TerryDon79

originally posted by: chr0naut

originally posted by: TerryDon79

originally posted by: chr0naut

originally posted by: TerryDon79
a reply to: chr0naut

It's not about being PC or not.

It's about coming to a conclusion based on evidence (that's what papers are).

Since there is no evidence of god then the paper is not based on any known evidence.

The authors of the paper, the peer reviewers and the editorial staff seem to have accepted that this was such evidence.

Of course, if you reject the evidence as evidence, there is obviously no evidence.

The authors of the paper are the people that wrote it.

There is NO mention of it being peer reviewed.

The editorial staff can be as few as 1 person.

There is no proof for or against a creator. Science doesn't go there as it's a subject you can't prove right or wrong.

If the paper had spoken of the intricacies of the hand's mechanics as arising from the process of evolution, would you have accepted it?

What observed science do you have of the evolutionary processes specifically giving rise to the complex mechanics of the human hand? Despite having little actual hard science, neither you nor I would nay say the role of evolutionary development. We both take that component on faith, from what we know of science, it is reasonable to do so.

But science isn't about faith.

You can go out tomorrow and test anything that is claimed to be a scientific theory. If you find something wrong with it, have proof and the results can be repeated, then you can change that theory.

Please design a test for the evolution of the mechanics of the human hand. If you or any others cannot, then you must realize that you are applying an unequal criteria to what you will 'accept'.

There are ways to study the hand and understand how it evolved. We have a fossil record as well as the ability to study yhe anatomy of other organism. Just like if I wanted to study the spinal cord I could observe how a notochord (its predecessor) operates in other lifeforms. There is already plenty of evidence from the fossil record showing a transition from being a quadraped to bipedalism, which would be the precursor due to freeing of the hands. Im sure there are several studies available to discuss the rise of himan hands.

Now one more point. Getting published is only one part of peer review process. Once the article is piblished it is open for further scrutiny. If it doesnt hold water, as is the case here, then it is shown to be inaccurate (or a poor translation in this case).

While the fossil record does show that structural change has occurred, it shows little to nothing of how it occurred or of the genetic details of the change.

Perhaps Theistic Evolution guided the change, perhaps something closer to the Modern Evolutionary Synthesis, perhaps God altered the DNA.

We don't know enough to be assured that our pet theory is "the one". The assumption that we are right, in the face of our actual ignorance, is opinion.

There is no evidence that suggests divine intervention. A mutation, which is a well documented phenomenon, easily accounts for the changes. You would need to provide quantifiable evidence of God otherwise it has no pace at the table. At this time all the evidence supports MES.

Surely the speed, complexity and deep synchronicities of biological development, which cannot be explained by a reductionist theory that mandates gradualism and vast numbers of generations does indicate insufficiency in evolutionary theory.

At this time, we are seeing multiple instances of incredibly rapid trait changes in populations (on the order of a couple of generations). This may be explained by Punctuated Equilibrium or similar but not by MES.

a reply to: chr0naut

Surely the speed, complexity and deep synchronicities of biological development, which cannot be explained by a reductionist theory that mandates gradualism and vast numbers of generations does indicate insufficiency in evolutionary theory.

There is always more to learn. New data either fits in with the current model, or it needs to be explained. No theory is perfect in every way.

That said, what exactly are you referring to in the way of "speed, complexity, and deep synchronicities" that cannot currently be explained by the MES. Have there been hypotheses proposed to explain them or are scientists still scratching their collective heads looking for hypotheses? Is there work underway to test those hypotheses that have been proposed?

At this time, we are seeing multiple instances of incredibly rapid trait changes in populations (on the order of a couple of generations). This may be explained by Punctuated Equilibrium or similar but not by MES.

Punctuated Equilibrium is a recognized part of the MES.

The possibility of rapid changes in the expression of genes, even speciation, in few generations has been acknowledged for a long time. It is well within the parameters of the MES for some rapid turnover populations to have very significant "trait changes" in a very short time indeed (as in a couple of generations). Less likely for complete speciation in a couple of generations, but we have witnessed a new species of Galapagos Finches in a few tens of generations.

originally posted by: rnaa
a reply to: chr0naut

Surely the speed, complexity and deep synchronicities of biological development, which cannot be explained by a reductionist theory that mandates gradualism and vast numbers of generations does indicate insufficiency in evolutionary theory.

There is always more to learn. New data either fits in with the current model, or it needs to be explained. No theory is perfect in every way.

That said, what exactly are you referring to in the way of "speed, complexity, and deep synchronicities" that cannot currently be explained by the MES. Have there been hypotheses proposed to explain them or are scientists still scratching their collective heads looking for hypotheses? Is there work underway to test those hypotheses that have been proposed?

At this time, we are seeing multiple instances of incredibly rapid trait changes in populations (on the order of a couple of generations). This may be explained by Punctuated Equilibrium or similar but not by MES.

Punctuated Equilibrium is a recognized part of the MES. It has been accepted into evolution because it occurs frequently and the phyletic gradualism of the MES has very few examples.

The possibility of rapid changes in the expression of genes, even speciation, in few generations has been acknowledged for a long time. It is well within the parameters of the MES for some rapid turnover populations to have very significant "trait changes" in a very short time indeed (as in a couple of generations). Less likely for complete speciation in a couple of generations, but we have witnessed a new species of Galapagos Finches in a few tens of generations.

So, how does a mutation spread into a population in one or two generations?

How does natural selection happen in one or two generations? Surely at that rate it is better described as an extinction, the removal of all the unsuccessful phenotypes. Then who does the successful mutation breed with?

And Punctuated Equilibrium is not part of the definition of MES. It is now accepted as a part of evolution but only because examples of phyletic gradulaism required by the MES, seem to be the exception rather than the rule.

Really rapid genetic changes are more likely to be Epigenetic in nature, but how do the the Epigenetically inactive traits become selected for or encoded?

a reply to: chr0naut

So, how does a mutation spread into a population in one or two generations?

Easy.

Hit some bacteria with a potent anti-bacterial agent. It will not kill every individual bacteria - some individuals will have a mutation that allows them to survive. The surviving immune individuals are the only ones that can reproduce. They will do so and the next generation will be immune to that bacterial agent - 100% of the population. Natural selection at work and Evolution on the move at a hospital near you. Remember that the population we are talking about is your body's own private population.

Here's a specific real-world example:

Get sick with Tuberculosis in Timor Leste. Spend two days walking into the hospital at Dili. Spend two weeks in bed under constant monitoring and medical care. Get sent home with an anti-TB medication prescription and instructions to continue taking it until it runs out. Arrive home and find that your neighbor and your brother are sick from TB. Give your medicine to them, since you are no longer feeling sick. All three of you will end up with your own personal populations of Drug resistant TB.

This is not an invented scenario. IT HAPPENS ALL THE TIME ALL AROUND THE WORLD - and not just in developing countries like Timor Leste.

According to Wikipedia:

Tuberculosis is the second-most common cause of death from infectious disease (after those due to HIV/AIDS).
...
Primary resistance occurs when a person becomes infected with a resistant strain of TB. A person with fully susceptible TB may develop secondary (acquired) resistance during therapy because of inadequate treatment, not taking the prescribed regimen appropriately (lack of compliance), or using low-quality medication. Drug-resistant TB is a serious public health issue in many developing countries, as its treatment is longer and requires more expensive drugs. MDR-TB is defined as resistance to the two most effective first-line TB drugs: rifampicin and isoniazid. Extensively drug-resistant TB is also resistant to three or more of the six classes of second-line drugs. Totally drug-resistant TB is resistant to all currently used drugs. It was first observed in 2003 in Italy, but not widely reported until 2012,[89][medical citation needed] and has also been found in Iran and India. Bedaquiline is tentatively supported for use in multiple drug-resistant TB.

XDR-TB is a term sometimes used to define extensively resistant TB, and constitutes one in ten cases of MDR-TB. Cases of XDR TB have been identified in more than 90% of countries.

It happens all the time.

originally posted by: rnaa
a reply to: chr0naut

So, how does a mutation spread into a population in one or two generations?

Easy.

Hit some bacteria with a potent anti-bacterial agent. It will not kill every individual bacteria - some individuals will have a mutation that allows them to survive. The surviving immune individuals are the only ones that can reproduce. They will do so and the next generation will be immune to that bacterial agent - 100% of the population. Natural selection at work and Evolution on the move at a hospital near you. Remember that the population we are talking about is your body's own private population.

Here's a specific real-world example:

Get sick with Tuberculosis in Timor Leste. Spend two days walking into the hospital at Dili. Spend two weeks in bed under constant monitoring and medical care. Get sent home with an anti-TB medication prescription and instructions to continue taking it until it runs out. Arrive home and find that your neighbor and your brother are sick from TB. Give your medicine to them, since you are no longer feeling sick. All three of you will end up with your own personal populations of Drug resistant TB.

This is not an invented scenario. IT HAPPENS ALL THE TIME ALL AROUND THE WORLD - and not just in developing countries like Timor Leste.

According to Wikipedia:

Tuberculosis is the second-most common cause of death from infectious disease (after those due to HIV/AIDS).
...
Primary resistance occurs when a person becomes infected with a resistant strain of TB. A person with fully susceptible TB may develop secondary (acquired) resistance during therapy because of inadequate treatment, not taking the prescribed regimen appropriately (lack of compliance), or using low-quality medication. Drug-resistant TB is a serious public health issue in many developing countries, as its treatment is longer and requires more expensive drugs. MDR-TB is defined as resistance to the two most effective first-line TB drugs: rifampicin and isoniazid. Extensively drug-resistant TB is also resistant to three or more of the six classes of second-line drugs. Totally drug-resistant TB is resistant to all currently used drugs. It was first observed in 2003 in Italy, but not widely reported until 2012, and has also been found in Iran and India. Bedaquiline is tentatively supported for use in multiple drug-resistant TB.

XDR-TB is a term sometimes used to define extensively resistant TB, and constitutes one in ten cases of MDR-TB. Cases of XDR TB have been identified in more than 90% of countries.

And Punctuated Equilibrium is not part of the definition of MES. It is now accepted as a part of evolution

OK, you just completely contradicted yourself inside of two sentences. Either it is part of evolution or it isn't.

Evolution Library: Punctuated Equilibrium

The concept of punctuated equilibrium was, to some, a radical new idea when it was first proposed by Stephen Jay Gould and Niles Eldredge in 1972. Now it is widely recognized as a useful model for one kind of evolutionary change. The relative importance of punctuated and gradual patterns of evolution is a subject of debate and research.

StephenJayGould.org: Punctuated equilibrium comes of age

The intense controversies that surrounded the youth of punctuated equilibrium have helped it mature to a useful extension of evolutionary theory.

The Great Vindication Blog

For the modern biologists, they ‘constructed’ modern evolutionary synthesis (MES). Then, all new discoveries (selfish-genes, horizontal gene transfers, genetic assimilation, the Hardy–Weinberg principle, Hox genes, punctuated equilibrium, etc.) are packed into this MES.

Gradualism and Punctuated Equilibrium

The idea of punctuated equilibrium originated long after the idea of gradualism. Darwin saw evolution as being "steady, slow, and continuous". Later, scientists were studying fossils and they found that some species have their evolution almost "mapped out" in fossils. For others they found a few, very different species along the evolutionary course, but very few or no fossils of "in between" organisms. Also, when dating the fossils, scientists saw that in some species change was very slow, but in others, it must have occurred rapidly to be able to produce such change over such a short amount of time. The scientists reasoned that there had to be another way that evolution could have happened that was quicker and had fewer intermediate species, so the idea of punctuated equilibrium was formed.

This last article explains both gradualism and punctuated equilibrium and why an alternative to Darwin's method was required. Science doesn't stand still and Darwin didn't have all the answers, that's why we are still doing science. There is much much more to the MES than natural selection, and there is more to evolution than gradualism.

originally posted by: RustyNailer
God is more real than you could possibly imagine. In fact, you can tell him yourself that he's not real when you stand before him during your redemption....

I sure wish the rapture would hurry up and take you types away.

a reply to: PhotonEffect

Plos One isn't Nature or Pnas. Calm down. This is a non story unless you're looking for a gotcha against science...which it's not.

originally posted by: rnaa

Hit some bacteria with a potent anti-bacterial agent. It will not kill every individual bacteria - some individuals will have a mutation that allows them to survive. The surviving immune individuals are the only ones that can reproduce. They will do so and the next generation will be immune to that bacterial agent - 100% of the population. Natural selection at work and Evolution on the move at a hospital near you.

How can you say for sure it was a genetic mutation that influenced resistance, versus say, epimutation, conjugation, transduction, or transformation ?

Remember, bacteria don't generally follow the laws of mendelian inheritance and can acquire new [and beneficial] genes laterally. In fact, it's quite well known that this mode of gene transfer can play a significant role in anti-bacterial resistance.

Too bad, HGT is not recognized by the MES as pervasive it is in prokaryotes and even eukaryotes.

originally posted by: rnaa
Science doesn't stand still and Darwin didn't have all the answers, that's why we are still doing science. There is much much more to the MES than natural selection, and there is more to evolution than gradualism.

Yes, I do believe that PE was later folded into the MES, however that was the last significant update as far as I'm aware. The theory's central tenet still rests on the foundation of Mendelian inheritance, so systems incorporating forms of HGT are a contradiction. And of course there's epigenetics., and other non-mendelian systems of inheritance.

Perhaps you can lay out the parameters of the MES as you know them to be?

If the MES has been expanded to include these other mechanisms officially within its framework, then can you provide the reference?

True, that our knowledge has progressed and expanded, but the Theory of Evolution vis a vis the MES has stood still for quite some time.

a reply to: BrokedownChevy

Noted.

And I'm as calm as they come.

Sorry, my link would not load correctly...

originally posted by: NoCorruptionAllowed

originally posted by: Phage
a reply to: NoCorruptionAllowed

After you died from the above 30k foot fall, you would then realize your mistake, but then it could be too late.

No. You might realize it just before impact but not after.

I suppose you will need to die first to find out if you are correct. I say you are wrong. I have experienced ghosts first hand, and so have many other ATS members. The spirit world exists although not many know much about it, and what people all seem to agree on that have experienced it, is that it is CREEPY.

None of that has anything to do with god. Many folks believe in the spirit realm without believing in a god/deity. Dead men tell no tales... because they're.. you know... dead.

a reply to: rnaa

originally posted by: PhotonEffect

originally posted by: rnaa

Hit some bacteria with a potent anti-bacterial agent. It will not kill every individual bacteria - some individuals will have a mutation that allows them to survive. The surviving immune individuals are the only ones that can reproduce. They will do so and the next generation will be immune to that bacterial agent - 100% of the population. Natural selection at work and Evolution on the move at a hospital near you.

How can you say for sure it was a genetic mutation that influenced resistance, versus say, epimutation, conjugation, transduction, or transformation ?

Remember, bacteria don't generally follow the laws of mendelian inheritance and can acquire new [and beneficial] genes laterally. In fact, it's quite well known that this mode of gene transfer can play a significant role in anti-bacterial resistance.

Too bad, HGT is not recognized by the MES as pervasive it is in prokaryotes and even eukaryotes.

My edit timed out, but I meant to add 2 other factors to this response that are also known to influence anti-biotic resistance – mobile genetic elements (e.g transposons) and persistence.

It actually seems less likely to be mutation driven....